1
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Raith J, Bachmann M, Gonther S, Stülb H, Aghdassi AA, Pham CTN, Mühl H. Targeting cathepsin C ameliorates murine acetaminophen-induced liver injury. Theranostics 2024; 14:3029-3042. [PMID: 38855187 PMCID: PMC11155399 DOI: 10.7150/thno.96092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 04/27/2024] [Indexed: 06/11/2024] Open
Abstract
Acetaminophen (APAP) overdosing is a major cause of acute liver failure worldwide and an established model for drug-induced acute liver injury (ALI). While studying gene expression during murine APAP-induced ALI by 3'mRNA sequencing (massive analysis of cDNA ends, MACE), we observed splenic mRNA accumulation encoding for the neutrophil serine proteases cathepsin G, neutrophil elastase, and proteinase-3 - all are hierarchically activated by cathepsin C (CtsC). This, along with increased serum levels of these proteases in diseased mice, concurs with the established phenomenon of myeloid cell mobilization during APAP intoxication. Objective: In order to functionally characterize CtsC in murine APAP-induced ALI, effects of its genetic or pharmacological inhibition were investigated. Methods and Results: We report on substantially reduced APAP toxicity in CtsC deficient mice. Alleviation of disease was likewise observed by treating mice with the CtsC inhibitor AZD7986, both in short-term prophylactic and therapeutic protocols. This latter observation indicates a mode of action beyond inhibition of granule-associated serine proteases. Protection in CtsC knockout or AZD7986-treated wildtype mice was unrelated to APAP metabolization but, as revealed by MACE, realtime PCR, or ELISA, associated with impaired expression of inflammatory genes with proven pathogenic roles in ALI. Genes consistently downregulated in protocols tested herein included cxcl2, mmp9, and angpt2. Moreover, ptpn22, a positive regulator of the toll-like receptor/interferon-axis, was reduced by targeting CtsC. Conclusions: This work suggests CtsC as promising therapeutic target for the treatment of ALI, among others paradigmatic APAP-induced ALI. Being also currently evaluated in phase III clinical trials for bronchiectasis, successful application of AZD7986 in experimental APAP intoxication emphasizes the translational potential of this latter therapeutic approach.
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Affiliation(s)
- Jessica Raith
- pharmazentrum frankfurt/ZAFES, Institute of General Pharmacology and Toxicology, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Malte Bachmann
- pharmazentrum frankfurt/ZAFES, Institute of General Pharmacology and Toxicology, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Sina Gonther
- pharmazentrum frankfurt/ZAFES, Institute of General Pharmacology and Toxicology, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Hendrik Stülb
- pharmazentrum frankfurt/ZAFES, Institute of General Pharmacology and Toxicology, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Ali A. Aghdassi
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | - Christine T. N. Pham
- John Cochran VA Medical Center, Saint Louis, MO, USA; Department of Medicine, Division of Rheumatology and the Department of Surgery, Section of Vascular Surgery, Washington University School of Medicine, Saint Louis, MO, USA
| | - Heiko Mühl
- pharmazentrum frankfurt/ZAFES, Institute of General Pharmacology and Toxicology, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
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2
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Chen Q, Guo X, Wang H, Sun S, Jiang H, Zhang P, Shang E, Zhang R, Cao Z, Niu Q, Zhang C, Liu Y, Shi L, Yu Y, Hou W, Zheng Y. Plasma-Free Blood as a Potential Alternative to Whole Blood for Transcriptomic Analysis. PHENOMICS (CHAM, SWITZERLAND) 2024; 4:109-124. [PMID: 38884056 PMCID: PMC11169349 DOI: 10.1007/s43657-023-00121-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/29/2023] [Accepted: 07/13/2023] [Indexed: 06/18/2024]
Abstract
RNA sequencing (RNAseq) technology has become increasingly important in precision medicine and clinical diagnostics, and emerged as a powerful tool for identifying protein-coding genes, performing differential gene analysis, and inferring immune cell composition. Human peripheral blood samples are widely used for RNAseq, providing valuable insights into individual biomolecular information. Blood samples can be classified as whole blood (WB), plasma, serum, and remaining sediment samples, including plasma-free blood (PFB) and serum-free blood (SFB) samples that are generally considered less useful byproducts during the processes of plasma and serum separation, respectively. However, the feasibility of using PFB and SFB samples for transcriptome analysis remains unclear. In this study, we aimed to assess the suitability of employing PFB or SFB samples as an alternative RNA source in transcriptomic analysis. We performed a comparative analysis of WB, PFB, and SFB samples for different applications. Our results revealed that PFB samples exhibit greater similarity to WB samples than SFB samples in terms of protein-coding gene expression patterns, detection of differentially expressed genes, and immunological characterizations, suggesting that PFB can serve as a viable alternative to WB for transcriptomic analysis. Our study contributes to the optimization of blood sample utilization and the advancement of precision medicine research. Supplementary Information The online version contains supplementary material available at 10.1007/s43657-023-00121-1.
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Affiliation(s)
- Qingwang Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Xiaorou Guo
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Haiyan Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Shanyue Sun
- Shandong Provincial Hospital, Shandong First Medical University, Jinan, 250021 China
| | - He Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Peipei Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Erfei Shang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Ruolan Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Zehui Cao
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Quanne Niu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Chao Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Yaqing Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
- The International Human Phenome Institutes, Shanghai, 200438 China
| | - Ying Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Wanwan Hou
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Yuanting Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
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3
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Sheerin D, Lakay F, Esmail H, Kinnear C, Sansom B, Glanzmann B, Wilkinson RJ, Ritchie ME, Coussens AK. Identification and control for the effects of bioinformatic globin depletion on human RNA-seq differential expression analysis. Sci Rep 2023; 13:1859. [PMID: 36725870 PMCID: PMC9892020 DOI: 10.1038/s41598-023-28218-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/16/2023] [Indexed: 02/03/2023] Open
Abstract
When profiling blood samples by RNA-sequencing (RNA-seq), RNA from haemoglobin (Hgb) can account for up to 70% of the transcriptome. Due to considerations of sequencing depth and power to detect biological variation, Hgb RNA is typically depleted prior to sequencing by hybridisation-based methods; an alternative approach is to deplete reads arising from Hgb RNA bioinformatically. In the present study, we compared the impact of these two approaches on the outcome of differential gene expression analysis performed using RNA-seq data from 58 human tuberculosis (TB) patient or contact whole blood samples-29 globin kit-depleted and 29 matched non-depleted-a subset of which were taken at TB diagnosis and at six months post-TB treatment from the same patient. Bioinformatic depletion of Hgb genes from the non-depleted samples (bioinformatic-depleted) substantially reduced library sizes (median = 57.24%) and fewer long non-coding, micro, small nuclear and small nucleolar RNAs were captured in these libraries. Profiling published TB gene signatures across all samples revealed inferior correlation between kit-depleted and bioinformatic-depleted pairs when the proportion of reads mapping to Hgb genes was higher in the non-depleted sample, particularly at the TB diagnosis time point. A set of putative "globin-fingerprint" genes were identified by directly comparing kit-depleted and bioinformatic-depleted samples at each timepoint. Two TB treatment response signatures were also shown to have decreased differential performance when comparing samples at TB diagnosis to six months post-TB treatment when profiled on the bioinformatic-depleted samples compared with their kit-depleted counterparts. These results demonstrate that failure to deplete Hgb RNA prior to sequencing has a negative impact on the sensitivity to detect disease-relevant gene expression changes even when bioinformatic removal is performed.
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Affiliation(s)
- Dylan Sheerin
- Infectious Diseases and Immune Defence Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.
| | - Francisco Lakay
- Wellcome Centre for Infectious Diseases Research in Africa and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, Western Cape, South Africa
- Vuka Research Clinic, University of Cape Town, Department of Medicine, 8 Mzala Street, Khayelitsha, Cape Town, Western Cape, South Africa
| | - Hanif Esmail
- Wellcome Centre for Infectious Diseases Research in Africa and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, Western Cape, South Africa
- MRC Clinical Trials Unit at University College London, Institute of Clinical Trials and Methodology, London, WC1V 6LJ, UK
- Institute for Global Health, University College London, London, WC1E 6JB, UK
| | - Craig Kinnear
- South African Medical Research Council Genomics Centre, Francie Van Zijl Drive, Parow Valley, Cape Town, Western Cape, South Africa
| | - Bianca Sansom
- South African Medical Research Council Genomics Centre, Francie Van Zijl Drive, Parow Valley, Cape Town, Western Cape, South Africa
| | - Brigitte Glanzmann
- South African Medical Research Council Genomics Centre, Francie Van Zijl Drive, Parow Valley, Cape Town, Western Cape, South Africa
| | - Robert J Wilkinson
- Wellcome Centre for Infectious Diseases Research in Africa and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, Western Cape, South Africa
- Francis Crick Institute, London, NW1 1AT, UK
- Imperial College London, SW7 2AZ, London, UK
| | - Matthew E Ritchie
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Anna K Coussens
- Infectious Diseases and Immune Defence Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.
- Wellcome Centre for Infectious Diseases Research in Africa and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, Western Cape, South Africa.
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4
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Qi D, Geng Y, Cardenas J, Gu J, Yi SS, Huang JH, Fonkem E, Wu E. Transcriptomic analyses of patient peripheral blood with hemoglobin depletion reveal glioblastoma biomarkers. NPJ Genom Med 2023; 8:2. [PMID: 36697401 PMCID: PMC9877004 DOI: 10.1038/s41525-022-00348-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 12/21/2022] [Indexed: 01/26/2023] Open
Abstract
Peripheral blood is gaining prominence as a noninvasive alternative to tissue biopsy to develop biomarkers for glioblastoma (GBM); however, widely utilized blood-based biomarkers in clinical settings have not yet been identified due to the lack of a robust detection approach. Here, we describe the application of globin reduction in RNA sequencing of whole blood (i.e., WBGR) and perform transcriptomic analysis to identify GBM-associated transcriptomic changes. By using WBGR, we improved the detection sensitivity of informatic reads and identified differential gene expression in GBM blood. By analyzing tumor tissues, we identified transcriptomic traits of GBM blood. Further functional enrichment analyses retained the most changed genes in GBM. Subsequent validation elicited a 10-gene panel covering mRNA, long noncoding RNA, and microRNA (i.e., GBM-Dx panel) that has translational potential to aid in the early detection or clinical management of GBM. Here, we report an integrated approach, WBGR, with comprehensive analytic capacity for blood-based marker identification.
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Affiliation(s)
- Dan Qi
- Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX, 76508, USA
| | - Yiqun Geng
- Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX, 76508, USA
- Laboratory of Molecular Pathology, Shantou University Medical College, 515041, Shantou, China
| | - Jacob Cardenas
- Baylor Scott & White Research Institute, Dallas, TX, 75204, USA
| | - Jinghua Gu
- Baylor Scott & White Research Institute, Dallas, TX, 75204, USA
| | - S Stephen Yi
- Institute for Cellular and Molecular Biology (ICMB), College of Natural Sciences, The University of Texas at Austin, Austin, TX, 78712, USA
- Oden Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, Austin, TX, 78712, USA
- Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
- Department of Oncology, LIVESTRONG Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Jason H Huang
- Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX, 76508, USA.
- Texas A & M University School of Medicine, Temple, TX, 76508, USA.
| | - Ekokobe Fonkem
- Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX, 76508, USA.
- Texas A & M University School of Medicine, Temple, TX, 76508, USA.
| | - Erxi Wu
- Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX, 76508, USA.
- Department of Oncology, LIVESTRONG Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, 78712, USA.
- Texas A & M University School of Medicine, Temple, TX, 76508, USA.
- Texas A & M University School of Pharmacy, College Station, TX, 77843, USA.
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5
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Chen LN, Jing T, Lin ZB, Song W, Du WH, Fan XY, Li C, Li S, Xie FY, Ou XH, Huang L, Ma JY. Metabolomic and transcriptomic responses of mouse testis to the dextran sulfate sodium induced colitis. Reprod Toxicol 2022; 108:35-42. [PMID: 35093514 DOI: 10.1016/j.reprotox.2022.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 01/11/2022] [Accepted: 01/22/2022] [Indexed: 11/23/2022]
Abstract
Inflammatory bowel diseases (IBDs), including Crohn's disease (CD) and ulcerative colitis, are widespread in developed countries and gradually increasing in developing countries. Evidences showed that man with CD has a decrease of serum testosterone, but how IBD take effects on testicular testosterone synthesis is not well elucidated. To investigate the effects of IBD on testis, we analyzed testicular metabolome and transcriptome data of the dextran sulfate sodium (DSS) induced IBD mice. As a result, metabolomic data showed that DSS indeed induced androgen decrease in mouse testis. Correspondingly, androgen synthesis associated genes, especially Lhcgr, were down-regulated in DSS testis. From the metabolomic data, we found vitamin intake associated metabolites vitamin B2 and pyridoxamine were significantly decreased, whereas fatty acid metabolism associated molecules N-lauroylglycine and N-decanoylglycine were increased in DSS testis. In addition, we found 8-hydroxy-deoxyguanosine, a DNA oxidative damage marker, and 8-oxoguanine, a molecule responsible for DNA damage repair, were also changed in DSS testis. Simultaneously, our data also showed that DSS up-regulated the expression of meiosis initiation associated gene Stra8 and oxygen transport associated genes in testis. In summary, these results depicted the complex effects of colitis on testis. These metabolites and transcripts changed in DSS testis could be used as potential targets for IBD treatment or symptom relieve.
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Affiliation(s)
- Lei-Ning Chen
- Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China; Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - Tao Jing
- Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China; Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - Zi-Bin Lin
- Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China; Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - Wei Song
- Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China; College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Wen-Hao Du
- Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China; Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - Xiao-Yan Fan
- Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China; Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - Chao Li
- Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China; State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Sen Li
- Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China; Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - Feng-Yun Xie
- Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China; Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - Xiang-Hong Ou
- Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China; Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China; Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510320, China
| | - Lin Huang
- Clinical Research Institute, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, China.
| | - Jun-Yu Ma
- Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China; Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China.
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6
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Xing Y, Yang X, Chen H, Zhu S, Xu J, Chen Y, Zeng J, Chen F, Johnson MR, Jiang H, Wang WJ. The effect of cell isolation methods on the human transcriptome profiling and microbial transcripts of peripheral blood. Mol Biol Rep 2021; 48:3059-3068. [PMID: 33929647 PMCID: PMC8085658 DOI: 10.1007/s11033-021-06382-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 04/24/2021] [Indexed: 11/25/2022]
Abstract
The expression of human and microbial genes serves as biomarkers for disease and health. Blood RNA is an important biological resource for precision medicine and translational medicine. However, few studies have assessed the human transcriptome profiles and microbial communities composition and diversity of peripheral blood from different cell isolation methods, which could affect the reproducibility of researches. We collected peripheral blood from three healthy donors and processed it immediately. We used RNA sequencing to investigate the effect of three leukocyte isolation methods including buffy coat (BC) extraction, red blood cell (RBC) lysis and peripheral blood mononuclear cell (PBMC) isolation with the comparison with whole blood (WB), through analyzing the sensitivity of gene detection, the whole transcriptome profiling and microbial composition and diversity. Our data showed that BC extraction with high globin mRNA mapping rate had similar transcriptome profiles with WB, while RBC lysis and PBMC isolation depleted RBCs effectively. With the efficient depletion of RBC and distinct compositions of leukocyte subsets, RNA-seq of RBC lysis and PBMC isolation uniquely detected genes from specific cell types, like granulocytes and NK cells. In addition, we observed that the microbial composition and diversity were more affected by individuals than isolation methods. Our results showed that blood cell isolations could largely influence the sensitivity of detection of human genes and transcriptome profile.
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Affiliation(s)
- Yanru Xing
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Xi Yang
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Haixiao Chen
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Sujun Zhu
- Obstetrics Department, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong Province, China
| | - Jinjin Xu
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Yuan Chen
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Juan Zeng
- Obstetrics Department, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong Province, China
| | - Fang Chen
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Mark Richard Johnson
- Academic Obstetric Department, Imperial College London, Chelsea & Westminster Hospital campus, London, UK
| | - Hui Jiang
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- Guangdong Enterprise Key Laboratory of Human Disease Genomics, Shenzhen, China
| | - Wen-Jing Wang
- BGI-Shenzhen, Shenzhen, 518083, China.
- China National GeneBank, BGI-Shenzhen, Shenzhen, China.
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7
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Jang JS, Berg B, Holicky E, Eckloff B, Mutawe M, Carrasquillo MM, Ertekin-Taner N, Cuninngham JM. Comparative evaluation for the globin gene depletion methods for mRNA sequencing using the whole blood-derived total RNAs. BMC Genomics 2020; 21:890. [PMID: 33308163 PMCID: PMC7733259 DOI: 10.1186/s12864-020-07304-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 12/06/2020] [Indexed: 01/12/2023] Open
Abstract
Background There are challenges in generating mRNA-Seq data from whole-blood derived RNA as globin gene and rRNA are frequent contaminants. Given the abundance of erythrocytes in whole blood, globin genes comprise some 80% or more of the total RNA. Therefore, depletion of globin gene RNA and rRNA are critical steps required to have adequate coverage of reads mapping to the reference transcripts and thus reduce the total cost of sequencing. In this study, we directly compared the performance of probe hybridization (GLOBINClear Kit and Globin-Zero Gold rRNA Removal Kit) and RNAse-H enzymatic depletion (NEBNext® Globin & rRNA Depletion Kit and Ribo-Zero Plus rRNA Depletion Kit) methods from 1 μg of whole blood-derived RNA on mRNA-Seq profiling. All RNA samples were treated with DNaseI for additional cleanup before the depletion step and were processed for poly-A selection for library generation. Results Probe hybridization revealed a better overall performance than the RNAse-H enzymatic depletion method, detecting a higher number of genes and transcripts without 3′ region bias. After depletion, samples treated with probe hybridization showed globin genes at 0.5% (±0.6%) of the total mapped reads; the RNAse-H enzymatic depletion had 3.2% (±3.8%). Probe hybridization showed more junction reads and transcripts compared with RNAse-H enzymatic depletion and also had a higher correlation (R > 0.9) than RNAse-H enzymatic depletion (R > 0.85). Conclusion In this study, our results showed that 1 μg of high-quality RNA from whole blood could be routinely used for transcriptional profiling analysis studies with globin gene and rRNA depletion pre-processing. We also demonstrated that the probe hybridization depletion method is better suited to mRNA sequencing analysis with minimal effect on RNA quality during depletion procedures.
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Affiliation(s)
- Jin Sung Jang
- Medical Genome Facility, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA. .,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
| | - Brianna Berg
- Medical Genome Facility, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Eileen Holicky
- Medical Genome Facility, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Bruce Eckloff
- Medical Genome Facility, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Mark Mutawe
- Medical Genome Facility, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.,Department of Neurology, Mayo Clinic, Jacksonville, FL, USA
| | - Julie M Cuninngham
- Medical Genome Facility, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA. .,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
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8
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Zhao S, Ye Z, Stanton R. Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols. RNA (NEW YORK, N.Y.) 2020; 26:903-909. [PMID: 32284352 PMCID: PMC7373998 DOI: 10.1261/rna.074922.120] [Citation(s) in RCA: 191] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
In recent years, RNA-sequencing (RNA-seq) has emerged as a powerful technology for transcriptome profiling. For a given gene, the number of mapped reads is not only dependent on its expression level and gene length, but also the sequencing depth. To normalize these dependencies, RPKM (reads per kilobase of transcript per million reads mapped) and TPM (transcripts per million) are used to measure gene or transcript expression levels. A common misconception is that RPKM and TPM values are already normalized, and thus should be comparable across samples or RNA-seq projects. However, RPKM and TPM represent the relative abundance of a transcript among a population of sequenced transcripts, and therefore depend on the composition of the RNA population in a sample. Quite often, it is reasonable to assume that total RNA concentration and distributions are very close across compared samples. Nevertheless, the sequenced RNA repertoires may differ significantly under different experimental conditions and/or across sequencing protocols; thus, the proportion of gene expression is not directly comparable in such cases. In this review, we illustrate typical scenarios in which RPKM and TPM are misused, unintentionally, and hope to raise scientists' awareness of this issue when comparing them across samples or different sequencing protocols.
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Affiliation(s)
- Shanrong Zhao
- Integrative Biology Center of Excellence, Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, USA
| | - Zhan Ye
- Early Clinical Development, Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, USA
| | - Robert Stanton
- Integrative Biology Center of Excellence, Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, USA
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9
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Singh KP, Dhruva A, Flowers E, Paul SM, Hammer MJ, Wright F, Cartwright F, Conley YP, Melisko M, Levine JD, Miaskowski C, Kober KM. Alterations in Patterns of Gene Expression and Perturbed Pathways in the Gut-Brain Axis Are Associated With Chemotherapy-Induced Nausea. J Pain Symptom Manage 2020; 59:1248-1259.e5. [PMID: 31923555 PMCID: PMC7239734 DOI: 10.1016/j.jpainsymman.2019.12.352] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 12/10/2019] [Accepted: 12/11/2019] [Indexed: 12/12/2022]
Abstract
CONTEXT Despite current advances in antiemetic treatments, approximately 50% of oncology patients experience chemotherapy-induced nausea (CIN). OBJECTIVES The purpose of this study was to evaluate for differentially expressed genes and perturbed pathways associated with the gut-brain axis (GBA) across two independent samples of oncology patients who did and did not experience CIN. METHODS Oncology patients (n = 735) completed study questionnaires in the week before their second or third cycle of chemotherapy. CIN occurrence was assessed using the Memorial Symptom Assessment Scale. Gene expression analyses were performed in two independent samples using ribonucleic acid sequencing (Sample 1, n = 357) and microarray (Sample 2, n = 352) methodologies. Fisher's combined probability method was used to determine genes that were differentially expressed and pathways that were perturbed between the two nausea groups across both samples. RESULTS CIN was reported by 63.6% of the patients in Sample 1 and 48.9% of the patients in Sample 2. Across the two samples, 703 genes were differentially expressed, and 37 pathways were found to be perturbed between the two CIN groups. We identified nine perturbed pathways that are involved in mechanisms associated with alterations in the GBA (i.e., mucosal inflammation, disruption of gut microbiome). CONCLUSION Persistent CIN remains a significant clinical problem. Our study is the first to identify novel GBA-related pathways associated with the occurrence of CIN. Our findings warrant confirmation and suggest directions for future clinical studies to decrease CIN occurrence.
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Affiliation(s)
- Komal P Singh
- School of Nursing, University of California, San Francisco, San Francisco, California, USA
| | - Anand Dhruva
- School of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Elena Flowers
- School of Nursing, University of California, San Francisco, San Francisco, California, USA
| | - Steven M Paul
- School of Nursing, University of California, San Francisco, San Francisco, California, USA
| | - Marilyn J Hammer
- The Phyllis F. Cantor Center for Research in Nursing and Patient Care Services, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Fay Wright
- Rory Meyers College of Nursing, New York University, New York, New York, USA
| | - Frances Cartwright
- Department of Nursing, Mount Sinai Medical Center, New York, New York, USA
| | - Yvette P Conley
- School of Nursing, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Michelle Melisko
- School of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Jon D Levine
- School of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Christine Miaskowski
- School of Nursing, University of California, San Francisco, San Francisco, California, USA
| | - Kord M Kober
- School of Nursing, University of California, San Francisco, San Francisco, California, USA.
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10
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Tindale LC, Thiessen N, Leach S, Brooks-Wilson AR. Allele-Specific Transcript Abundance: A Pilot Study in Healthy Centenarians. J Gerontol A Biol Sci Med Sci 2020; 75:1068-1072. [PMID: 31504207 PMCID: PMC7243586 DOI: 10.1093/gerona/glz188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Indexed: 11/13/2022] Open
Abstract
The genetic basis of healthy aging and longevity remains largely unexplained. One hypothesis as to why long-lived individuals do not appear to have a lower number of common-complex disease variants, is that despite carrying risk variants, they express disease-linked alleles at a lower level than the wild-type alleles. Allele-specific abundance (ASA) is the different transcript abundance of the two haplotypes of a diploid individual. We sequenced the transcriptomes of four healthy centenarians and four mid-life controls. CIBERSORT was used to estimate blood cell fractions: neutrophils were the most abundant source of RNA, followed by CD8+ T cells, resting NK cells, and monocytes. ASA variants were more common in noncoding than coding regions. Centenarians and controls had a comparable distribution of ASA variants by predicted effect, and we did not observe an overall bias in expression toward major or minor alleles. Immune pathways were most highly represented among the gene set that showed ASA. Although we found evidence of ASA in disease-associated genes and transcription factors, we did not observe any differences in the pattern of expression between centenarians and controls in this small pilot study.
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Affiliation(s)
- Lauren C Tindale
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada.,Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, Canada
| | - Nina Thiessen
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
| | - Stephen Leach
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
| | - Angela R Brooks-Wilson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada.,Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, Canada
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11
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Harrington CA, Fei SS, Minnier J, Carbone L, Searles R, Davis BA, Ogle K, Planck SR, Rosenbaum JT, Choi D. RNA-Seq of human whole blood: Evaluation of globin RNA depletion on Ribo-Zero library method. Sci Rep 2020; 10:6271. [PMID: 32286338 PMCID: PMC7156519 DOI: 10.1038/s41598-020-62801-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 03/18/2020] [Indexed: 11/11/2022] Open
Abstract
Peripheral blood is a highly accessible biofluid providing a rich source of information about human physiology and health status. However, for studies of the blood transcriptome with RNA sequencing (RNA-Seq) techniques, high levels of hemoglobin mRNAs (hgbRNA) present in blood can occupy valuable sequencing space, impacting detection and quantification of non-hgbRNAs. In this study, we evaluated two methods for preparing ribosomal RNA (rRNA)-depleted sequencing libraries for RNA-Seq of whole blood, one of which is also designed to deplete hgbRNAs. Two experiments were performed: one evaluating library performance across 6 human blood samples and the other examining library reproducibility and performance in a two-subject subset. We find that addition of hgbRNA depletion to the rRNA-depletion protocol for library preparation from blood RNA effectively reduces highly abundant hgbRNA reads; however, it does not result in a statistically significant increase in differentially expressed genes in our patient-control study. Bioinformatic removal of globin gene counts in non-hgbRNA depleted libraries provides improvement in overall performance of these libraries. We conclude that use of a standard ribosomal RNA depletion method for library preparation coupled with bioinformatic removal of globin gene counts is sufficient for reproducible and sensitive measurement of both coding and noncoding RNAs in the blood transcriptome.
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Affiliation(s)
- Christina A Harrington
- Integrated Genomics Laboratory, Oregon Health & Science University, Portland, Oregon, USA. .,Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, Oregon, USA.
| | - Suzanne S Fei
- Bioinformatics & Biostatistics Core, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Jessica Minnier
- Integrated Genomics Laboratory, Oregon Health & Science University, Portland, Oregon, USA.,OHSU-PSU School of Public Health, Oregon Health & Science University, Portland, Oregon, USA
| | - Lucia Carbone
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, Oregon, USA.,Bioinformatics & Biostatistics Core, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA.,Knight Cardiovascular Institute, Oregon Health & Science University Portland, Oregon, USA.,3181 Sam Jackson Park Rd, Oregon Health & Science University, Portland, Oregon, United States
| | - Robert Searles
- Integrated Genomics Laboratory, Oregon Health & Science University, Portland, Oregon, USA.,3181 Sam Jackson Park Rd, Oregon Health & Science University, Portland, Oregon, United States
| | - Brett A Davis
- Bioinformatics & Biostatistics Core, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA.,Knight Cardiovascular Institute, Oregon Health & Science University Portland, Oregon, USA
| | - Kimberly Ogle
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Stephen R Planck
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, USA.,Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
| | - James T Rosenbaum
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, USA.,Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA.,Legacy Devers Eye Institute, Legacy Health System, Portland, Oregon, USA
| | - Dongseok Choi
- OHSU-PSU School of Public Health, Oregon Health & Science University, Portland, Oregon, USA.,Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, USA.,Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA.,Graduate School of Dentistry, Kyung Hee University, Seoul, Korea
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12
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A benchmark of hemoglobin blocking during library preparation for mRNA-Sequencing of human blood samples. Sci Rep 2020; 10:5630. [PMID: 32221409 PMCID: PMC7101437 DOI: 10.1038/s41598-020-62637-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 03/17/2020] [Indexed: 01/03/2023] Open
Abstract
RNA-Sequencing (RNA-Seq) of peripheral blood can be a valuable source of information for investigating the status and mechanism of diseases. However, blood contains 50–80% unwanted hemoglobin (Hb) transcripts. Lexogen’s QuantSeq mRNA-Seq-Kit for Illumina RNA-Seq features a ‘Globin Block’ (GB) module that depletes Hb cDNAs during library preparation. Here, we aimed to assess GB’s effectiveness and checked for technical biases attributable to GB. Using whole blood total RNA samples of 91 healthy individuals, we sequenced 91 pairs of GB and non-blocked samples (noGB) on Illumina HiSeq2500 and 8 pairs of GB/noGB technical replicates on HiSeq4000. GB reduced the fraction of Hb transcripts from 43% (s.d. 14%) to 8.0% (s.d. 4.3%). From GB samples we detected 1,397 more expressed genes at approximately 11 million reads per RNA-isolate. Enrichment and differential expression analyses did not reveal significant differences for GB and noGB samples with respect to molecular function. In contrast to results from studies that have examined the performance of GB during RNA isolation, we were able to assign GB to corresponding noGB samples (from multiple sequencing runs on HiSeq2500) with at least 89.8% accuracy from the complete correlation matrix of all GB/GB, noGB/noGB and GB/noGB pairs. However, the use of different sequencers (HiSeq2500 vs HiSeq4000) impaired assignment of technical replicates, whereas assignment of GB to corresponding noGB samples worked perfectly when sequencing on one lane on HiSeq4000. Lexogen’s GB RNA-Seq module is a valuable addition during mRNA-Seq library preparation which works even with low amounts of input total RNA (50 ng per sample). GB facilitated the detection of low abundant transcripts and yielded more non-hemoglobin reads, while preserving biological information. We observed that differences in sequencing run and platform have a far greater effect on technical variation than the use of GB.
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13
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Lim KS, Dong Q, Moll P, Vitkovska J, Wiktorin G, Bannister S, Daujotyte D, Tuggle CK, Lunney JK, Plastow GS, Dekkers JCM. The effects of a globin blocker on the resolution of 3'mRNA sequencing data in porcine blood. BMC Genomics 2019; 20:741. [PMID: 31615396 PMCID: PMC6794815 DOI: 10.1186/s12864-019-6122-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 09/20/2019] [Indexed: 12/27/2022] Open
Abstract
Background Gene expression profiling in blood is a potential source of biomarkers to evaluate or predict phenotypic differences between pigs but is expensive and inefficient because of the high abundance of globin mRNA in porcine blood. These limitations can be overcome by the use of QuantSeq 3’mRNA sequencing (QuantSeq) combined with a method to deplete or block the processing of globin mRNA prior to or during library construction. Here, we validated the effectiveness of QuantSeq using a novel specific globin blocker (GB) that is included in the library preparation step of QuantSeq. Results In data set 1, four concentrations of the GB were applied to RNA samples from two pigs. The GB significantly reduced the proportion of globin reads compared to non-GB (NGB) samples (P = 0.005) and increased the number of detectable non-globin genes. The highest evaluated concentration (C1) of the GB resulted in the largest reduction of globin reads compared to the NGB (from 56.4 to 10.1%). The second highest concentration C2, which showed very similar globin depletion rates (12%) as C1 but a better correlation of the expression of non-globin genes between NGB and GB (r = 0.98), allowed the expression of an additional 1295 non-globin genes to be detected, although 40 genes that were detected in the NGB sample (at a low level) were not present in the GB library. Concentration C2 was applied in the rest of the study. In data set 2, the distribution of the percentage of globin reads for NGB (n = 184) and GB (n = 189) samples clearly showed the effects of the GB on reducing globin reads, in particular for HBB, similar to results from data set 1. Data set 3 (n = 84) revealed that the proportion of globin reads that remained in GB samples was significantly and positively correlated with the reticulocyte count in the original blood sample (P < 0.001). Conclusions The effect of the GB on reducing the proportion of globin reads in porcine blood QuantSeq was demonstrated in three data sets. In addition to increasing the efficiency of sequencing non-globin mRNA, the GB for QuantSeq has an advantage that it does not require an additional step prior to or during library creation. Therefore, the GB is a useful tool in the quantification of whole gene expression profiles in porcine blood.
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Affiliation(s)
- Kyu-Sang Lim
- Department of Animal Science, Iowa State University, Ames, 50011, Iowa, USA
| | - Qian Dong
- Department of Animal Science, Iowa State University, Ames, 50011, Iowa, USA
| | - Pamela Moll
- Lexogen GmbH, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Jana Vitkovska
- Lexogen GmbH, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Gregor Wiktorin
- Lexogen GmbH, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | | | - Dalia Daujotyte
- Lexogen GmbH, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | | | | | | | - Jack C M Dekkers
- Department of Animal Science, Iowa State University, Ames, 50011, Iowa, USA.
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14
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Byrne A, Supple MA, Volden R, Laidre KL, Shapiro B, Vollmers C. Depletion of Hemoglobin Transcripts and Long-Read Sequencing Improves the Transcriptome Annotation of the Polar Bear ( Ursus maritimus). Front Genet 2019; 10:643. [PMID: 31379921 PMCID: PMC6658610 DOI: 10.3389/fgene.2019.00643] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 06/18/2019] [Indexed: 11/26/2022] Open
Abstract
Transcriptome studies evaluating whole blood and tissues are often confounded by overrepresentation of highly abundant transcripts. These abundant transcripts are problematic, as they compete with and prevent the detection of rare RNA transcripts, obscuring their biological importance. This issue is more pronounced when using long-read sequencing technologies for isoform-level transcriptome analysis, as they have relatively lower throughput compared to short-read sequencers. As a result, long-read based transcriptome analysis is prohibitively expensive for non-model organisms. While there are off-the-shelf kits available for select model organisms capable of depleting highly abundant transcripts for alpha (HBA) and beta (HBB) hemoglobin, they are unsuitable for non-model organisms. To address this, we have adapted the recent CRISPR/Cas9-based depletion method (depletion of abundant sequences by hybridization) for long-read full-length cDNA sequencing approaches that we call Long-DASH. Using a recombinant Cas9 protein with appropriate guide RNAs, full-length hemoglobin transcripts can be depleted in vitro prior to performing any short- and long-read sequencing library preparations. Using this method, we sequenced depleted full-length cDNA in parallel using both our Oxford Nanopore Technology (ONT) based R2C2 long-read approach, as well as the Illumina short-read based Smart-seq2 approach. To showcase this, we have applied our methods to create an isoform-level transcriptome from whole blood samples derived from three polar bears (Ursus maritimus). Using Long-DASH, we succeeded in depleting hemoglobin transcripts and generated deep Smart-seq2 Illumina datasets and 3.8 million R2C2 full-length cDNA consensus reads. Applying Long-DASH with our isoform identification pipeline, Mandalorion, we discovered ∼6,000 high-confidence isoforms and a number of novel genes. This indicates that there is a high diversity of gene isoforms within U. maritimus not yet reported. This reproducible and straightforward approach has not only improved the polar bear transcriptome annotations but will serve as the foundation for future efforts to investigate transcriptional dynamics within the 19 polar bear subpopulations around the Arctic.
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Affiliation(s)
- Ashley Byrne
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Cruz, CA, United States
- Genomics Institute, University of California, Santa Cruz, CA, United States
| | - Megan A. Supple
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States
| | - Roger Volden
- Genomics Institute, University of California, Santa Cruz, CA, United States
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Kristin L. Laidre
- Polar Science Center, Applied Physics Laboratory, University of Washington, Seattle, WA, United States
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Christopher Vollmers
- Genomics Institute, University of California, Santa Cruz, CA, United States
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
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15
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Brodhagen J, Weikard R, Thom U, Heimes A, Günther J, Hadlich F, Zerbe H, Petzl W, Meyerholz MM, Hoedemaker M, Schuberth HJ, Engelmann S, Kühn C. Development and evaluation of a milk protein transcript depletion method for differential transcriptome analysis in mammary gland tissue. BMC Genomics 2019; 20:400. [PMID: 31117949 PMCID: PMC6530097 DOI: 10.1186/s12864-019-5781-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 05/07/2019] [Indexed: 11/30/2022] Open
Abstract
Background In the mammary gland transcriptome of lactating dairy cows genes encoding milk proteins are highly abundant, which can impair the detection of lowly expressed transcripts and can bias the outcome in global transcriptome analyses. Therefore, the aim of this study was to develop and evaluate a method to deplete extremely highly expressed transcripts in mRNA from lactating mammary gland tissue. Results Selective RNA depletion was performed by hybridization of antisense oligonucleotides targeting genes encoding the caseins (CSN1S1, CSN1S2, CSN2 and CSN3) and whey proteins (LALBA and PAEP) within total RNA followed by RNase H-mediated elimination of the respective transcripts. The effect of the RNA depletion procedure was monitored by RNA sequencing analysis comparing depleted and non-depleted RNA samples from Escherichia coli (E. coli) challenged and non-challenged udder tissue of lactating cows in a proof of principle experiment. Using RNase H-mediated RNA depletion, the ratio of highly abundant milk protein gene transcripts was reduced in all depleted samples by an average of more than 50% compared to the non-depleted samples. Furthermore, the sensitivity for discovering transcripts with marginal expression levels and transcripts not yet annotated was improved. Finally, the sensitivity to detect significantly differentially expressed transcripts between non-challenged and challenged udder tissue was increased without leading to an inadvertent bias in the pathogen challenge-associated biological signaling pathway patterns. Conclusions The implementation of selective RNase H-mediated RNA depletion of milk protein gene transcripts from the mammary gland transcriptome of lactating cows will be highly beneficial to establish comprehensive transcript catalogues of the tissue that better reflects its transcriptome complexity. Electronic supplementary material The online version of this article (10.1186/s12864-019-5781-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Johanna Brodhagen
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, 18196, Dummerstorf, Germany
| | - Rosemarie Weikard
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, 18196, Dummerstorf, Germany
| | - Ulrike Thom
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, 18196, Dummerstorf, Germany
| | - Annika Heimes
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, 18196, Dummerstorf, Germany
| | - Juliane Günther
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, 18196, Dummerstorf, Germany
| | - Frieder Hadlich
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, 18196, Dummerstorf, Germany
| | - Holm Zerbe
- Clinic for Ruminants with Ambulatory and Herd Health Services, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, 85764, Oberschleissheim, Germany
| | - Wolfgang Petzl
- Clinic for Ruminants with Ambulatory and Herd Health Services, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, 85764, Oberschleissheim, Germany
| | - Marie M Meyerholz
- Clinic for Ruminants with Ambulatory and Herd Health Services, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, 85764, Oberschleissheim, Germany
| | - Martina Hoedemaker
- Clinic for Cattle, University of Veterinary Medicine, Foundation, 30173, Hannover, Germany
| | - Hans-Joachim Schuberth
- Immunology Unit, University of Veterinary Medicine, Foundation, 30559, Hannover, Germany
| | - Susanne Engelmann
- Institute for Microbiology, Technical University Braunschweig, 38106, Braunschweig, Germany.,Microbial Proteomics, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Christa Kühn
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, 18196, Dummerstorf, Germany. .,Agricultural and Environmental Faculty, University Rostock, 18059, Rostock, Germany.
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16
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Kober KM, Olshen A, Conley YP, Schumacher M, Topp K, Smoot B, Mazor M, Chesney M, Hammer M, Paul SM, Levine JD, Miaskowski C. Expression of mitochondrial dysfunction-related genes and pathways in paclitaxel-induced peripheral neuropathy in breast cancer survivors. Mol Pain 2018; 14:1744806918816462. [PMID: 30426838 PMCID: PMC6293373 DOI: 10.1177/1744806918816462] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Background Paclitaxel is one of the most commonly used drugs to treat breast cancer. Its
major dose-limiting toxicity is paclitaxel-induced peripheral neuropathy
(PIPN). PIPN persists into survivorship and has a negative impact on
patient’s mood, functional status, and quality of life. No interventions are
available to treat PIPN. A critical barrier to the development of
efficacious interventions is the lack of understanding of the mechanisms
that underlie PIPN. Mitochondrial dysfunction has been evaluated in
preclinical studies as a hypothesized mechanism for PIPN, but clinical data
to support this hypothesis are limited. The purpose of this pilot study was
to evaluate for differential gene expression and perturbed pathways between
breast cancer survivors with and without PIPN. Methods Gene expression in peripheral blood was assayed using RNA-seq. Differentially
expressed genes (DEG) and pathways associated with mitochondrial dysfunction
were identified between survivors who received paclitaxel and did (n = 25)
and did not (n = 25) develop PIPN. Results Breast cancer survivors with PIPN were significantly older; more likely to be
unemployed; reported lower alcohol use; had a higher body mass index and
poorer functional status; and had a higher number of lower extremity sites
with loss of light touch, cold, and pain sensations and higher vibration
thresholds. No between-group differences were found in the cumulative dose
of paclitaxel received or in the percentage of patients who had a dose
reduction or delay due to PIPN. Five DEGs and nine perturbed pathways were
associated with mitochondrial dysfunction related to oxidative stress, iron
homeostasis, mitochondrial fission, apoptosis, and autophagy. Conclusions This study is the first to provide molecular evidence that a number of
mitochondrial dysfunction mechanisms identified in preclinical models of
various types of neuropathic pain including chemotherapy-induced peripheral
neuropathy are found in breast cancer survivors with persistent PIPN and
suggest genes for validation and as potential therapeutic targets.
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Affiliation(s)
- Kord M Kober
- 1 School of Nursing, University of California, San Francisco, San Francisco, CA, USA
| | - Adam Olshen
- 2 School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Yvettte P Conley
- 3 School of Nursing, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mark Schumacher
- 2 School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Kimberly Topp
- 2 School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Betty Smoot
- 2 School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Melissa Mazor
- 1 School of Nursing, University of California, San Francisco, San Francisco, CA, USA
| | - Margaret Chesney
- 2 School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Marilyn Hammer
- 4 Department of Nursing, Mount Sinai Medical Center, New York, NY, USA
| | - Steven M Paul
- 1 School of Nursing, University of California, San Francisco, San Francisco, CA, USA
| | - Jon D Levine
- 2 School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Christine Miaskowski
- 1 School of Nursing, University of California, San Francisco, San Francisco, CA, USA
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17
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Correia CN, McLoughlin KE, Nalpas NC, Magee DA, Browne JA, Rue-Albrecht K, Gordon SV, MacHugh DE. RNA Sequencing (RNA-Seq) Reveals Extremely Low Levels of Reticulocyte-Derived Globin Gene Transcripts in Peripheral Blood From Horses ( Equus caballus) and Cattle ( Bos taurus). Front Genet 2018; 9:278. [PMID: 30154823 PMCID: PMC6102425 DOI: 10.3389/fgene.2018.00278] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/09/2018] [Indexed: 12/15/2022] Open
Abstract
RNA-seq has emerged as an important technology for measuring gene expression in peripheral blood samples collected from humans and other vertebrate species. In particular, transcriptomics analyses of whole blood can be used to study immunobiology and develop novel biomarkers of infectious disease. However, an obstacle to these methods in many mammalian species is the presence of reticulocyte-derived globin mRNAs in large quantities, which can complicate RNA-seq library sequencing and impede detection of other mRNA transcripts. A range of supplementary procedures for targeted depletion of globin transcripts have, therefore, been developed to alleviate this problem. Here, we use comparative analyses of RNA-seq data sets generated from human, porcine, equine, and bovine peripheral blood to systematically assess the impact of globin mRNA on routine transcriptome profiling of whole blood in cattle and horses. The results of these analyses demonstrate that total RNA isolated from equine and bovine peripheral blood contains very low levels of globin mRNA transcripts, thereby negating the need for globin depletion and greatly simplifying blood-based transcriptomic studies in these two domestic species.
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Affiliation(s)
- Carolina N Correia
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences University College Dublin, Dublin, Ireland
| | - Kirsten E McLoughlin
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences University College Dublin, Dublin, Ireland
| | - Nicolas C Nalpas
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences University College Dublin, Dublin, Ireland
| | - David A Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences University College Dublin, Dublin, Ireland
| | - John A Browne
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences University College Dublin, Dublin, Ireland
| | - Kevin Rue-Albrecht
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences University College Dublin, Dublin, Ireland
| | - Stephen V Gordon
- UCD School of Veterinary Medicine, UCD College of Health and Agricultural Sciences University College Dublin, Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research University College Dublin, Dublin, Ireland
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences University College Dublin, Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research University College Dublin, Dublin, Ireland
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Evaluation of two main RNA-seq approaches for gene quantification in clinical RNA sequencing: polyA+ selection versus rRNA depletion. Sci Rep 2018; 8:4781. [PMID: 29556074 PMCID: PMC5859127 DOI: 10.1038/s41598-018-23226-4] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 03/07/2018] [Indexed: 12/17/2022] Open
Abstract
To allow efficient transcript/gene detection, highly abundant ribosomal RNAs (rRNA) are generally removed from total RNA either by positive polyA+ selection or by rRNA depletion (negative selection) before sequencing. Comparisons between the two methods have been carried out by various groups, but the assessments have relied largely on non-clinical samples. In this study, we evaluated these two RNA sequencing approaches using human blood and colon tissue samples. Our analyses showed that rRNA depletion captured more unique transcriptome features, whereas polyA+ selection outperformed rRNA depletion with higher exonic coverage and better accuracy of gene quantification. For blood- and colon-derived RNAs, we found that 220% and 50% more reads, respectively, would have to be sequenced to achieve the same level of exonic coverage in the rRNA depletion method compared with the polyA+ selection method. Therefore, in most cases we strongly recommend polyA+ selection over rRNA depletion for gene quantification in clinical RNA sequencing. Our evaluation revealed that a small number of lncRNAs and small RNAs made up a large fraction of the reads in the rRNA depletion RNA sequencing data. Thus, we recommend that these RNAs are specifically depleted to improve the sequencing depth of the remaining RNAs.
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Salinas-Santander M, Trevino V, De la Rosa-Moreno E, Verduzco-Garza B, Sánchez-Domínguez CN, Cantú-Salinas C, Ocampo-Garza J, Lagos-Rodríguez A, Ocampo-Candiani J, Ortiz-López R. CAPN3, DCT, MLANA and TYRP1 are overexpressed in skin of vitiligo vulgaris Mexican patients. Exp Ther Med 2018; 15:2804-2811. [PMID: 29456684 PMCID: PMC5795480 DOI: 10.3892/etm.2018.5764] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 01/05/2018] [Indexed: 12/18/2022] Open
Abstract
Vitiligo is a disorder causing skin depigmentation, in which several factors have been proposed for its pathogenesis: Environmental, genetic and biological aspects of melanocytes, even those of the surrounding keratinocytes. However, the lack of understanding of the mechanisms has complicated the task of predicting the development and progression. The present study used microarray analysis to characterize the transcriptional profile of skin from Vitiligo Vulgaris (VV) patients and the identified transcripts were validated using targeted high-throughput RNA sequencing in a broader set of patients. For microarrays, mRNA was taken from 20 skin biopsies of 10 patients with VV (pigmented and depigmented skin biopsy of each), and 5 biopsies of healthy subjects matched for age and sex were used as a control. A signature was identified that contains the expression pattern of 722 genes between depigmented vitiligo skin vs. healthy control, 1,108 between the pigmented skin of vitiligo vs. healthy controls and 1,927 between pigmented skin, depigmented vitiligo and healthy controls (P<0.05; false discovery rate, <0.1). When comparing the pigmented and depigmented skin of patients with vitiligo, which reflects the real difference between both skin types, 5 differentially expressed genes were identified and further validated in 45 additional VV patients by RNA sequencing. This analysis showed significantly higher RNA levels of calpain-3, dopachrome tautomerase, melan-A and tyrosinase-related protein-1 genes. The data revealed that the pigmented skin of vitiligo is already affected at the level of gene expression and that the main differences between pigmented and non-pigmented skin are explained by the expression of genes associated with pigment metabolism.
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Affiliation(s)
- Mauricio Salinas-Santander
- Departamento de Bioquímica y Medicina Molecular, Universidad Autónoma de Nuevo León, Facultad de Medicina, Monterrey, Nuevo León 64460, México.,Departamento de Investigación, Facultad de Medicina Unidad Saltillo, Universidad Autónoma de Coahuila, Saltillo, Coahuila 25000, México
| | - Víctor Trevino
- Grupo de Investigación en Bioinformática, Escuela de Medicina, Tecnológico de Monterrey, Monterrey, Nuevo León 64849, México
| | - Eduardo De la Rosa-Moreno
- Centro de Investigación y Desarrollo en Ciencias de la Salud, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León 64460, México
| | - Bárbara Verduzco-Garza
- Centro de Investigación y Desarrollo en Ciencias de la Salud, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León 64460, México
| | - Celia N Sánchez-Domínguez
- Departamento de Bioquímica y Medicina Molecular, Universidad Autónoma de Nuevo León, Facultad de Medicina, Monterrey, Nuevo León 64460, México
| | - Cristina Cantú-Salinas
- Servicio de Dermatología, Universidad Autónoma de Nuevo León, Hospital Universitario Dr. José Eleuterio González, Facultad de Medicina, Monterrey, Nuevo León 64460, México
| | - Jorge Ocampo-Garza
- Servicio de Dermatología, Universidad Autónoma de Nuevo León, Hospital Universitario Dr. José Eleuterio González, Facultad de Medicina, Monterrey, Nuevo León 64460, México
| | - Armando Lagos-Rodríguez
- Servicio de Dermatología, Universidad Autónoma de Nuevo León, Hospital Universitario Dr. José Eleuterio González, Facultad de Medicina, Monterrey, Nuevo León 64460, México
| | - Jorge Ocampo-Candiani
- Servicio de Dermatología, Universidad Autónoma de Nuevo León, Hospital Universitario Dr. José Eleuterio González, Facultad de Medicina, Monterrey, Nuevo León 64460, México
| | - Rocio Ortiz-López
- Centro de Investigación y Desarrollo en Ciencias de la Salud, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León 64460, México.,Escuela de Medicina, Tecnológico de Monterrey, Monterrey, Nuevo León 64849, México
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20
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Fiori LM, Lin R, Ju C, Belzeaux R, Turecki G. Using Epigenetic Tools to Investigate Antidepressant Response. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 158:255-272. [DOI: 10.1016/bs.pmbts.2018.04.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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21
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Massolt ET, Meima ME, Swagemakers SMA, Leeuwenburgh S, van den Hout-van Vroonhoven MCGM, Brigante G, Kam BLR, van der Spek PJ, van IJcken WFJ, Visser TJ, Peeters RP, Visser WE. Thyroid State Regulates Gene Expression in Human Whole Blood. J Clin Endocrinol Metab 2018; 103:169-178. [PMID: 29069456 DOI: 10.1210/jc.2017-01144] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 10/16/2017] [Indexed: 02/03/2023]
Abstract
CONTEXT Despite the well-recognized clinical features resulting from insufficient or excessive thyroid hormone (TH) levels in humans, it is largely unknown which genes are regulated by TH in human tissues. OBJECTIVE To study the effect of TH on human gene expression profiles in whole blood, mainly consisting of T3 receptor (TR) α-expressing cells. METHODS We performed next-generation RNA sequencing on whole blood samples from eight athyroid patients (four females) on and after 4 weeks off levothyroxine replacement. Gene expression changes were analyzed through paired differential expression analysis and confirmed in a validation cohort. Weighted gene coexpression network analysis (WGCNA) was applied to identify thyroid state-related networks. RESULTS We detected 486 differentially expressed genes (fold-change >1.5; multiple testing corrected P value < 0.05), of which 76% were positively and 24% were negatively regulated. Gene ontology (GO) enrichment analysis revealed that three biological processes were significantly overrepresented, of which the process translational elongation showed the highest fold enrichment (7.3-fold, P = 1.8 × 10-6). WGCNA analysis independently identified various gene clusters that correlated with thyroid state. Further GO analysis suggested that thyroid state affects platelet function. CONCLUSIONS Changes in thyroid state regulate numerous genes in human whole blood, predominantly TRα-expressing leukocytes. In addition, TH may regulate gene transcripts in platelets.
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Affiliation(s)
- Elske T Massolt
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
- Academic Center for Thyroid Diseases, Erasmus MC, Rotterdam, the Netherlands
| | - Marcel E Meima
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
- Academic Center for Thyroid Diseases, Erasmus MC, Rotterdam, the Netherlands
| | | | - Selmar Leeuwenburgh
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
- Academic Center for Thyroid Diseases, Erasmus MC, Rotterdam, the Netherlands
| | | | - Giulia Brigante
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
- Academic Center for Thyroid Diseases, Erasmus MC, Rotterdam, the Netherlands
- Unit of Endocrinology, Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Boen L R Kam
- Department of Nuclear Medicine, Erasmus MC, Rotterdam, the Netherlands
| | | | | | - Theo J Visser
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
- Academic Center for Thyroid Diseases, Erasmus MC, Rotterdam, the Netherlands
| | - Robin P Peeters
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
- Academic Center for Thyroid Diseases, Erasmus MC, Rotterdam, the Netherlands
| | - W Edward Visser
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
- Academic Center for Thyroid Diseases, Erasmus MC, Rotterdam, the Netherlands
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22
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Bybjerg-Grauholm J, Hagen CM, Khoo SK, Johannesen ML, Hansen CS, Bækvad-Hansen M, Christiansen M, Hougaard DM, Hollegaard MV. RNA sequencing of archived neonatal dried blood spots. Mol Genet Metab Rep 2016; 10:33-37. [PMID: 28053876 PMCID: PMC5198792 DOI: 10.1016/j.ymgmr.2016.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 12/16/2016] [Accepted: 12/16/2016] [Indexed: 01/25/2023] Open
Abstract
Neonatal dried blood spots (DBS) are routinely collected on standard Guthrie cards for all-comprising national newborn screening programs for inborn errors of metabolism, hypothyroidism and other diseases. In Denmark, the Guthrie cards are stored at − 20 °C in the Danish Neonatal Screening Biobank and each sample is linked to elaborate social and medical registries. This provides a unique biospecimen repository to enable large population research at a perinatal level. Here, we demonstrate the feasibility to obtain gene expression data from DBS using next-generation RNA sequencing (RNA-seq). RNA-seq was performed on five males and five females. Sequencing results have an average of > 30 million reads per sample. 26,799 annotated features can be identified with 64% features detectable without fragments per kilobase of transcript per million mapped reads (FPKM) cutoff; number of detectable features dropped to 18% when FPKM ≥ 1. Sex can be discriminated using blood-based sex-specific gene set identified by the Genotype-Tissue Expression consortium. Here, we demonstrate the feasibility to acquire biologically-relevant gene expression from DBS using RNA-seq which provide a new avenue to investigate perinatal diseases in a high throughput manner.
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Affiliation(s)
- Jonas Bybjerg-Grauholm
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Christian Munch Hagen
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Sok Kean Khoo
- Department of Cell and Molecular Biology, Grand Valley State University, Grand Rapids, MI 49503, USA
| | - Maria Louise Johannesen
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Christine Søholm Hansen
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Marie Bækvad-Hansen
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Michael Christiansen
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; Department of Biomedicine, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - David Michael Hougaard
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Mads V Hollegaard
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
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23
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Morey JS, Neely MG, Lunardi D, Anderson PE, Schwacke LH, Campbell M, Van Dolah FM. RNA-Seq analysis of seasonal and individual variation in blood transcriptomes of healthy managed bottlenose dolphins. BMC Genomics 2016; 17:720. [PMID: 27608714 PMCID: PMC5016863 DOI: 10.1186/s12864-016-3020-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Accepted: 08/16/2016] [Indexed: 11/30/2022] Open
Abstract
Background The blood transcriptome can reflect both systemic exposures and pathological changes in other organs of the body because immune cells recirculate through the blood, lymphoid tissues, and affected sites. In human and veterinary medicine, blood transcriptome analysis has been used successfully to identify markers of disease or pathological conditions, but can be confounded by large seasonal changes in expression. In comparison, the use of transcriptomic based analyses in wildlife has been limited. Here we report a longitudinal study of four managed bottlenose dolphins located in Waikoloa, Hawaii, serially sampled (approximately monthly) over the course of 1 year to establish baseline information on the content and variation of the dolphin blood transcriptome. Results Illumina based RNA-seq analyses were carried out using both the Ensembl dolphin genome and a de novo blood transcriptome as guides. Overall, the blood transcriptome encompassed a wide array of cellular functions and processes and was relatively stable within and between animals over the course of 1 year. Principal components analysis revealed moderate clustering by sex associated with the variation among global gene expression profiles (PC1, 22 % of variance). Limited seasonal change was observed, with < 2.5 % of genes differentially expressed between winter and summer months (FDR < 0.05). Among the differentially expressed genes, cosinor analysis identified seasonal rhythmicity for the observed changes in blood gene expression, consistent with studies in humans. While the proportion of seasonally variant genes in these dolphins is much smaller than that reported in humans, the majority of those identified in dolphins were also shown to vary with season in humans. Gene co-expression network analysis identified several gene modules with significant correlation to age, sex, or hematological parameters. Conclusions This longitudinal analysis of healthy managed dolphins establishes a preliminary baseline for blood transcriptome analysis in this species. Correlations with hematological parameters, distinct from muted seasonal effects, suggest that the otherwise relatively stable blood transcriptome may be a useful indicator of health and exposure. A robust database of gene expression in free-ranging and managed dolphins across seasons with known adverse health conditions or contaminant exposures will be needed to establish predictive gene expression profiles suitable for biomonitoring. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3020-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jeanine S Morey
- National Centers for Coastal Ocean Sciences, National Ocean Service, NOAA, 331 Fort Johnson Rd, Charleston, SC, 29412, USA.
| | - Marion G Neely
- National Centers for Coastal Ocean Sciences, National Ocean Service, NOAA, 331 Fort Johnson Rd, Charleston, SC, 29412, USA
| | - Denise Lunardi
- Department of Life Sciences and Biotechnology, University of Ferrara, via L. Borsari 46, 44121, Ferrara, Italy
| | - Paul E Anderson
- Department of Computer Science, College of Charleston, Charleston, SC, 29424, USA
| | - Lori H Schwacke
- National Centers for Coastal Ocean Sciences, National Ocean Service, NOAA, 331 Fort Johnson Rd, Charleston, SC, 29412, USA
| | | | - Frances M Van Dolah
- National Centers for Coastal Ocean Sciences, National Ocean Service, NOAA, 331 Fort Johnson Rd, Charleston, SC, 29412, USA. .,Present Address: Graduate Program in Marine Biology, University of Charleston, Charleston, SC, 29412, USA.
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24
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Comparison of blood RNA isolation methods from samples stabilized in Tempus tubes and stored at a large human biobank. BMC Res Notes 2016; 9:430. [PMID: 27587079 PMCID: PMC5009671 DOI: 10.1186/s13104-016-2224-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 08/15/2016] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND More than 50,000 adult and cord blood samples were collected in Tempus tubes and stored at the Norwegian Institute of Public Health Biobank for future use. In this study, we systematically evaluated and compared five blood-RNA isolation protocols: three blood-RNA isolation protocols optimized for simultaneous isolation of all blood-RNA species (MagMAX RNA Isolation Kit, both manual and semi-automated protocols; and Norgen Preserved Blood RNA kit I); and two protocols optimized for large RNAs only (Tempus Spin RNA, and Tempus 6-port isolation kit). We estimated the following parameters: RNA quality, RNA yield, processing time, cost per sample, and RNA transcript stability of six selected mRNAs and 13 miRNAs using real-time qPCR. FINDINGS Whole blood samples from adults (n = 59 tubes) and umbilical cord blood (n = 18 tubes) samples collected in Tempus tubes were analyzed. High-quality blood-RNAs with average RIN-values above seven were extracted using all five RNA isolation protocols. The transcript levels of the six selected genes showed minimal variation between the five protocols. Unexplained differences within the transcript levels of the 13 miRNA were observed; however, the 13 miRNAs had similar expression direction and they were within the same order of magnitude. Some differences in the RNA processing time and cost were noted. CONCLUSIONS Sufficient amounts of high-quality RNA were obtained using all five protocols, and the Tempus blood RNA system therefore seems not to be dependent on one specific RNA isolation method.
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25
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Krjutškov K, Koel M, Roost AM, Katayama S, Einarsdottir E, Jouhilahti EM, Söderhäll C, Jaakma Ü, Plaas M, Vesterlund L, Lohi H, Salumets A, Kere J. Globin mRNA reduction for whole-blood transcriptome sequencing. Sci Rep 2016; 6:31584. [PMID: 27515369 PMCID: PMC4981843 DOI: 10.1038/srep31584] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 07/26/2016] [Indexed: 12/15/2022] Open
Abstract
The transcriptome analysis of whole-blood RNA by sequencing holds promise for the identification and tracking of biomarkers; however, the high globin mRNA (gmRNA) content of erythrocytes hampers whole-blood and buffy coat analyses. We introduce a novel gmRNA locking assay (GlobinLock, GL) as a robust and simple gmRNA reduction tool to preserve RNA quality, save time and cost. GL consists of a pair of gmRNA-specific oligonucleotides in RNA initial denaturation buffer that is effective immediately after RNA denaturation and adds only ten minutes of incubation to the whole cDNA synthesis procedure when compared to non-blood RNA analysis. We show that GL is fully effective not only for human samples but also for mouse and rat, and so far incompletely studied cow, dog and zebrafish.
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Affiliation(s)
- Kaarel Krjutškov
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Competence Centre on Health Technologies, Tartu, Estonia.,Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Mariann Koel
- Competence Centre on Health Technologies, Tartu, Estonia.,Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | | | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Elisabet Einarsdottir
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Eeva-Mari Jouhilahti
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Cilla Söderhäll
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Ülle Jaakma
- Competence Centre on Health Technologies, Tartu, Estonia.,Department of Reproductive Biology, Estonian University of Life Sciences, Tartu, Estonia
| | - Mario Plaas
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Liselotte Vesterlund
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Hannes Lohi
- Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Andres Salumets
- Competence Centre on Health Technologies, Tartu, Estonia.,Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia.,Department of Obstetrics and Gynaecology, University of Tartu, Tartu, Estonia.,Department of Obstetrics and Gynecology, Helsinki University Hospital, Helsinki, Finland
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland
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Sixteen kiwi (Apteryx spp) transcriptomes provide a wealth of genetic markers and insight into sex chromosome evolution in birds. BMC Genomics 2016; 17:410. [PMID: 27230888 PMCID: PMC4882810 DOI: 10.1186/s12864-016-2714-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 05/07/2016] [Indexed: 01/08/2023] Open
Abstract
Background Kiwi represent the most basal extant avian lineage (paleognaths) and exhibit biological attributes that are unusual or extreme among living birds, such as large egg size, strong olfaction, nocturnality, flightlessness and long lifespan. Despite intense interest in their evolution and their threatened status, genomic resources for kiwi were virtually non-existent until the recent publication of a single genome. Here we present the most comprehensive kiwi transcriptomes to date, obtained via Illumina sequencing of whole blood and de novo assembly of mRNA sequences of eight individuals from each of the two rarest kiwi species, little spotted kiwi (LSK; Apteryx owenii) and rowi (A. rowi). Results Sequences obtained were orthologous with a wide diversity of functional genes despite the sequencing of a single tissue type. Individual and composite assemblies contain more than 7900 unique protein coding transcripts in each of LSK and rowi that show strong homology with chicken (Gallus gallus), including those associated with growth, development, disease resistance, reproduction and behavior. The assemblies also contain 66,909 SNPs that distinguish between LSK and rowi, 12,384 SNPs among LSK (associated with 3088 genes), and 29,313 SNPs among rowi (associated with 4953 genes). We found 3084 transcripts differentially expressed between LSK and rowi and 150 transcripts differentially expressed between the sexes. Of the latter, 83 could be mapped to chicken chromosomes with 95% syntenic with chromosome Z. Conclusions Our study has simultaneously sequenced multiple species, sexes, and individual kiwi at thousands of genes, and thus represents a significant leap forward in genomic resources available for kiwi. The expression pattern we observed among chromosome Z related genes in kiwi is similar to that observed in ostriches and emu, suggesting a common and ancestral pattern of sex chromosome homomorphy, recombination, and gene dosage among living paleognaths. The transcriptome assemblies described here will provide a rich resource for polymorphic marker development and studies of adaptation of these highly unusual and endangered birds. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2714-2) contains supplementary material, which is available to authorized users.
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27
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Solano-Aguilar G, Molokin A, Botelho C, Fiorino AM, Vinyard B, Li R, Chen C, Urban J, Dawson H, Andreyeva I, Haverkamp M, Hibberd PL. Transcriptomic Profile of Whole Blood Cells from Elderly Subjects Fed Probiotic Bacteria Lactobacillus rhamnosus GG ATCC 53103 (LGG) in a Phase I Open Label Study. PLoS One 2016; 11:e0147426. [PMID: 26859761 PMCID: PMC4747532 DOI: 10.1371/journal.pone.0147426] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 12/31/2015] [Indexed: 02/07/2023] Open
Abstract
We examined gene expression of whole blood cells (WBC) from 11 healthy elderly volunteers participating on a Phase I open label study before and after oral treatment with Lactobacillus rhamnosus GG-ATCC 53103 (LGG)) using RNA-sequencing (RNA-Seq). Elderly patients (65–80 yrs) completed a clinical assessment for health status and had blood drawn for cellular RNA extraction at study admission (Baseline), after 28 days of daily LGG treatment (Day 28) and at the end of the study (Day 56) after LGG treatment had been suspended for 28 days. Treatment compliance was verified by measuring LGG-DNA copy levels detected in host fecal samples. Normalized gene expression levels in WBC RNA were analyzed using a paired design built within three analysis platforms (edgeR, DESeq2 and TSPM) commonly used for gene count data analysis. From the 25,990 transcripts detected, 95 differentially expressed genes (DEGs) were detected in common by all analysis platforms with a nominal significant difference in gene expression at Day 28 following LGG treatment (FDR<0.1; 77 decreased and 18 increased). With a more stringent significance threshold (FDR<0.05), only two genes (FCER2 and LY86), were down-regulated more than 1.5 fold and met the criteria for differential expression across two analysis platforms. The remaining 93 genes were only detected at this threshold level with DESeq2 platform. Data analysis for biological interpretation of DEGs with an absolute fold change of 1.5 revealed down-regulation of overlapping genes involved with Cellular movement, Cell to cell signaling interactions, Immune cell trafficking and Inflammatory response. These data provide evidence for LGG-induced transcriptional modulation in healthy elderly volunteers because pre-treatment transcription levels were restored at 28 days after LGG treatment was stopped. To gain insight into the signaling pathways affected in response to LGG treatment, DEG were mapped using biological pathways and genomic data mining packages to indicate significant biological relevance. Trial Registration: ClinicalTrials.gov NCT01274598
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Affiliation(s)
- Gloria Solano-Aguilar
- Diet, Genomics, and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America
- * E-mail:
| | - Aleksey Molokin
- Diet, Genomics, and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America
| | - Christine Botelho
- Division of Global Health, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Anne-Maria Fiorino
- Division of Global Health, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Bryan Vinyard
- Statistics Group, Northeast Area, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America
| | - Robert Li
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America
| | - Celine Chen
- Diet, Genomics, and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America
| | - Joseph Urban
- Diet, Genomics, and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America
| | - Harry Dawson
- Diet, Genomics, and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America
| | - Irina Andreyeva
- Division of Global Health, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Miriam Haverkamp
- Division of Global Health, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Patricia L. Hibberd
- Division of Global Health, Massachusetts General Hospital, Boston, Massachusetts, United States of America
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Mastrokolias A, Pool R, Mina E, Hettne KM, van Duijn E, van der Mast RC, van Ommen G, ‘t Hoen PAC, Prehn C, Adamski J, van Roon-Mom W. Integration of targeted metabolomics and transcriptomics identifies deregulation of phosphatidylcholine metabolism in Huntington's disease peripheral blood samples. Metabolomics 2016; 12:137. [PMID: 27524956 PMCID: PMC4963448 DOI: 10.1007/s11306-016-1084-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 07/19/2016] [Indexed: 01/22/2023]
Abstract
INTRODUCTION Metabolic changes have been frequently associated with Huntington's disease (HD). At the same time peripheral blood represents a minimally invasive sampling avenue with little distress to Huntington's disease patients especially when brain or other tissue samples are difficult to collect. OBJECTIVES We investigated the levels of 163 metabolites in HD patient and control serum samples in order to identify disease related changes. Additionally, we integrated the metabolomics data with our previously published next generation sequencing-based gene expression data from the same patients in order to interconnect the metabolomics changes with transcriptional alterations. METHODS This analysis was performed using targeted metabolomics and flow injection electrospray ionization tandem mass spectrometry in 133 serum samples from 97 Huntington's disease patients (29 pre-symptomatic and 68 symptomatic) and 36 controls. RESULTS By comparing HD mutation carriers with controls we identified 3 metabolites significantly changed in HD (serine and threonine and one phosphatidylcholine-PC ae C36:0) and an additional 8 phosphatidylcholines (PC aa C38:6, PC aa C36:0, PC ae C38:0, PC aa C38:0, PC ae C38:6, PC ae C42:0, PC aa C36:5 and PC ae C36:0) that exhibited a significant association with disease severity. Using workflow based exploitation of pathway databases and by integrating our metabolomics data with our gene expression data from the same patients we identified 4 deregulated phosphatidylcholine metabolism related genes (ALDH1B1, MBOAT1, MTRR and PLB1) that showed significant association with the changes in metabolite concentrations. CONCLUSION Our results support the notion that phosphatidylcholine metabolism is deregulated in HD blood and that these metabolite alterations are associated with specific gene expression changes.
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Affiliation(s)
- Anastasios Mastrokolias
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Rene Pool
- Department of Biological Psychology, Faculty of Psychology and Education, VU University Amsterdam, Amsterdam, The Netherlands
- The EMGO + Institute for Health and Care Research, VU University Medical Center, Amsterdam, The Netherlands
| | - Eleni Mina
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Kristina M. Hettne
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Erik van Duijn
- Department of Psychiatry, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
- Center for Mental Health Care Delfland, Jorisweg 2, Delft, The Netherlands
| | - Roos C. van der Mast
- Department of Psychiatry, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - GertJan van Ommen
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Peter A. C. ‘t Hoen
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Cornelia Prehn
- Helmholtz Zentrum, München, German Research Center for Environmental Health, Institute of Experimental Genetics, Genome Analysis Center, Neuherberg, Germany
| | - Jerzy Adamski
- Helmholtz Zentrum, München, German Research Center for Environmental Health, Institute of Experimental Genetics, Genome Analysis Center, Neuherberg, Germany
- German Center for Diabetes Research, Neuherberg, Germany
- Lehrstuhl für Experimentelle Genetik, Technische Universität München, Freising-Weihenstephan, Germany
| | - Willeke van Roon-Mom
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
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Pilarsky C, Nanduri LK, Roy J. Gene Expression Analysis in the Age of Mass Sequencing: An Introduction. Methods Mol Biol 2015; 1381:67-73. [PMID: 26667455 DOI: 10.1007/978-1-4939-3204-7_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] [Indexed: 02/17/2023]
Abstract
During the last years the technology used for gene expression analysis has changed dramatically. The old mainstay, DNA microarray, has served its due course and will soon be replaced by next-generation sequencing (NGS), the Swiss army knife of modern high-throughput nucleic acid-based analysis. Therefore preparation technologies have to adapt to suit the emerging NGS technology platform. Moreover, interpretation of the results is still time consuming and employs the use of high-end computers usually not found in molecular biology laboratories. Alternatively, cloud computing might solve this problem. Nevertheless, these new challenges have to be embraced for gene expression analysis in general.
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Affiliation(s)
- Christian Pilarsky
- Department of Surgery, TU Dresden, Fetscherstr. 74, Dresden, 01307, Germany.
| | | | - Janine Roy
- Biotechnology Center, Technische Universität Dresden, Tatzberg 47-49, Dresden, 01307, Germany
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Leung RKK, Wu YK. Circulating microbial RNA and health. Sci Rep 2015; 5:16814. [PMID: 26576508 PMCID: PMC4649493 DOI: 10.1038/srep16814] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 10/15/2015] [Indexed: 12/22/2022] Open
Abstract
Measurement of health indicators in the blood is a commonly performed diagnostic procedure. Two blood studies one involving extended observations on the health of an individual by integrative Personal Omics Profiling (iPOP), and the other tracking the impact of Left Ventricular Assist Device (LVAD) placement on nine heart failure patients were examined for the association of change in health status with change in microbial RNA species. Decrease in RNA expression ratios of human to bacteria and viruses accompanying deteriorated conditions was evident in both studies. Despite large between-subject variations in bacterial composition before LVAD implantation among all the patients, on day 180 after the implantation they manifested apparent between-subject bacterial similarity. In the iPOP study three periods, namely, pre-respiratory syncytial virus (RSV) infection with normal blood glucose level, RSV infection with normal blood glucose level, and post-RSV infection with high blood glucose level could be defined. The upsurge of Enterobacteria phage PhiX 174 sensu lato and Escherichia coli gene expression, in which membrane transporters, membrane receptors for environment signalling, carbohydrate catabolic genes and carbohydrate-active enzymes were enriched only throughout the second period, which suggests a potentially overlooked microbial response to or modulation of the host blood glucose level.
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Affiliation(s)
- Ross Ka-Kit Leung
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Shatin, NT, Hong Kong, The People's Republic of China.,Division of Genomics and Bioinformatics, CUHK-BGI Innovation Institute of Trans-omics, The Chinese University of Hong Kong Shatin, N.T., Hong Kong, The People's Republic of China
| | - Ying-Kit Wu
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Shatin, NT, Hong Kong, The People's Republic of China.,Division of Genomics and Bioinformatics, CUHK-BGI Innovation Institute of Trans-omics, The Chinese University of Hong Kong Shatin, N.T., Hong Kong, The People's Republic of China
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31
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Calkoen FGJ, Vervat C, Eising E, Vijfhuizen LS, 't Hoen PBAC, van den Heuvel-Eibrink MM, Egeler RM, van Tol MJD, Ball LM. Gene-expression and in vitro function of mesenchymal stromal cells are affected in juvenile myelomonocytic leukemia. Haematologica 2015; 100:1434-41. [PMID: 26294732 DOI: 10.3324/haematol.2015.126938] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 08/17/2015] [Indexed: 12/29/2022] Open
Abstract
An aberrant interaction between hematopoietic stem cells and mesenchymal stromal cells has been linked to disease and shown to contribute to the pathophysiology of hematologic malignancies in murine models. Juvenile myelomonocytic leukemia is an aggressive malignant disease affecting young infants. Here we investigated the impact of juvenile myelomonocytic leukemia on mesenchymal stromal cells. Mesenchymal stromal cells were expanded from bone marrow samples of patients at diagnosis (n=9) and after hematopoietic stem cell transplantation (n=7; from 5 patients) and from healthy children (n=10). Cells were characterized by phenotyping, differentiation, gene expression analysis (of controls and samples obtained at diagnosis) and in vitro functional studies assessing immunomodulation and hematopoietic support. Mesenchymal stromal cells from patients did not differ from controls in differentiation capacity nor did they differ in their capacity to support in vitro hematopoiesis. Deep-SAGE sequencing revealed differential mRNA expression in patient-derived samples, including genes encoding proteins involved in immunomodulation and cell-cell interaction. Selected gene expression normalized during remission after successful hematopoietic stem cell transplantation. Whereas natural killer cell activation and peripheral blood mononuclear cell proliferation were not differentially affected, the suppressive effect on monocyte to dendritic cell differentiation was increased by mesenchymal stromal cells obtained at diagnosis, but not at time of remission. This study shows that active juvenile myelomonocytic leukemia affects the immune response-related gene expression and function of mesenchymal stromal cells. In contrast, the differential gene expression of hematopoiesis-related genes could not be supported by functional data. Decreased immune surveillance might contribute to the therapy resistance and progression in juvenile myelomonocytic leukemia.
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Affiliation(s)
- Friso G J Calkoen
- Department of Pediatrics, Immunology, Hematology/Oncology and Hematopoietic Stem Cell Transplantation, Leiden University Medical Center, the Netherlands
| | - Carly Vervat
- Department of Pediatrics, Immunology, Hematology/Oncology and Hematopoietic Stem Cell Transplantation, Leiden University Medical Center, the Netherlands
| | - Else Eising
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Lisanne S Vijfhuizen
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Marry M van den Heuvel-Eibrink
- Dutch Childhood Oncology Group (DCOG), The Hague, the Netherlands Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - R Maarten Egeler
- Department of Pediatrics, Immunology, Hematology/Oncology and Hematopoietic Stem Cell Transplantation, Leiden University Medical Center, the Netherlands Department of Hematology/Oncology and Hematopoietic Stem Cell Transplantation, Hospital for Sick Children, University of Toronto, ON, Canada
| | - Maarten J D van Tol
- Department of Pediatrics, Immunology, Hematology/Oncology and Hematopoietic Stem Cell Transplantation, Leiden University Medical Center, the Netherlands
| | - Lynne M Ball
- Department of Pediatrics, Immunology, Hematology/Oncology and Hematopoietic Stem Cell Transplantation, Leiden University Medical Center, the Netherlands
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Huang Z, Gallot A, Lao NT, Puechmaille SJ, Foley NM, Jebb D, Bekaert M, Teeling EC. A nonlethal sampling method to obtain, generate and assemble whole blood transcriptomes from small, wild mammals. Mol Ecol Resour 2015; 16:150-62. [PMID: 26186236 DOI: 10.1111/1755-0998.12447] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 07/08/2015] [Accepted: 07/13/2015] [Indexed: 12/01/2022]
Abstract
The acquisition of tissue samples from wild populations is a constant challenge in conservation biology, especially for endangered species and protected species where nonlethal sampling is the only option. Whole blood has been suggested as a nonlethal sample type that contains a high percentage of bodywide and genomewide transcripts and therefore can be used to assess the transcriptional status of an individual, and to infer a high percentage of the genome. However, only limited quantities of blood can be nonlethally sampled from small species and it is not known if enough genetic material is contained in only a few drops of blood, which represents the upper limit of sample collection for some small species. In this study, we developed a nonlethal sampling method, the laboratory protocols and a bioinformatic pipeline to sequence and assemble the whole blood transcriptome, using Illumina RNA-Seq, from wild greater mouse-eared bats (Myotis myotis). For optimal results, both ribosomal and globin RNAs must be removed before library construction. Treatment of DNase is recommended but not required enabling the use of smaller amounts of starting RNA. A large proportion of protein-coding genes (61%) in the genome were expressed in the blood transcriptome, comparable to brain (65%), kidney (63%) and liver (58%) transcriptomes, and up to 99% of the mitogenome (excluding D-loop) was recovered in the RNA-Seq data. In conclusion, this nonlethal blood sampling method provides an opportunity for a genomewide transcriptomic study of small, endangered or critically protected species, without sacrificing any individuals.
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Affiliation(s)
- Zixia Huang
- UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Aurore Gallot
- UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.,Laboratoire de Biométrie et Biologie Évolutive, UMR 5558, Centre National de la Recherche Scientifique, Université Lyon 1, Lyon, France
| | - Nga T Lao
- UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.,Molecular Biology Laboratory, National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Sébastien J Puechmaille
- UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.,Applied Zoology and Nature Conservation, Greifswald University, J.-S.-Bach-Str. 11/12, 17489, Greifswald, Germany
| | - Nicole M Foley
- UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - David Jebb
- UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Michaël Bekaert
- NSilico Lifescience Limited, Melbourn Building, CIT Campus, Bishopstown, Co., Cork, Ireland
| | - Emma C Teeling
- UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
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Bowyer JF, Tranter KM, Hanig JP, Crabtree NM, Schleimer RP, George NI. Evaluating the Stability of RNA-Seq Transcriptome Profiles and Drug-Induced Immune-Related Expression Changes in Whole Blood. PLoS One 2015; 10:e0133315. [PMID: 26177368 PMCID: PMC4503719 DOI: 10.1371/journal.pone.0133315] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 06/24/2015] [Indexed: 12/01/2022] Open
Abstract
Methods were developed to evaluate the stability of rat whole blood expression obtained from RNA sequencing (RNA-seq) and assess changes in whole blood transcriptome profiles in experiments replicated over time. Expression was measured in globin-depleted RNA extracted from the whole blood of Sprague-Dawley rats, given either saline (control) or neurotoxic doses of amphetamine (AMPH). The experiment was repeated four times (paired control and AMPH groups) over a 2-year span. The transcriptome of the control and AMPH-treated groups was evaluated on: 1) transcript levels for ribosomal protein subunits; 2) relative expression of immune-related genes; 3) stability of the control transcriptome over 2 years; and 4) stability of the effects of AMPH on immune-related genes over 2 years. All, except one, of the 70 genes that encode the 80s ribosome had levels that ranked in the top 5% of all mean expression levels. Deviations in sequencing performance led to significant changes in the ribosomal transcripts. The overall expression profile of immune-related genes and genes specific to monocytes, T-cells or B-cells were well represented and consistent within treatment groups. There were no differences between the levels of ribosomal transcripts in time-matched control and AMPH groups but significant differences in the expression of immune-related genes between control and AMPH groups. AMPH significantly increased expression of some genes related to monocytes but down-regulated those specific to T-cells. These changes were partially due to changes in the two types of leukocytes present in blood, which indicate an activation of the innate immune system by AMPH. Thus, the stability of RNA-seq whole blood transcriptome can be verified by assessing ribosomal protein subunits and immune-related gene expression. Such stability enables the pooling of samples from replicate experiments to carry out differential expression analysis with acceptable power.
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Affiliation(s)
- John F. Bowyer
- Division of Neurotoxicology, National Center for Toxicological Research, United States Food and Drug Administration, Jefferson, Arkansas, United States of America
- * E-mail:
| | - Karen M. Tranter
- Division of Neurotoxicology, National Center for Toxicological Research, United States Food and Drug Administration, Jefferson, Arkansas, United States of America
| | - Joseph P. Hanig
- Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Nathaniel M. Crabtree
- Division of Neurotoxicology, National Center for Toxicological Research, United States Food and Drug Administration, Jefferson, Arkansas, United States of America
| | - Robert P. Schleimer
- Division of Allergy and Immunology, Northwestern Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Nysia I. George
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, United States Food and Drug Administration, Jefferson, Arkansas, United States of America
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Stabilization of cellular RNA in blood during storage at room temperature: a comparison of cell-free RNA BCT(®) with K3EDTA tubes. Mol Diagn Ther 2015; 18:647-53. [PMID: 25178583 PMCID: PMC4245490 DOI: 10.1007/s40291-014-0118-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background Messenger RNA (mRNA) expression levels in blood cells are important in disease diagnosis, prognosis and biomarker discovery research. Accurate measurements of intracellular mRNA levels in blood cells depend upon several pre-analytical factors, including delays in RNA extraction from blood after phlebotomy. Dramatic changes in mRNA expression levels caused by delays in blood sample processing may render such samples unsuitable for gene expression analysis. Objectives This study was conducted to evaluate a blood collection tube, cell-free RNA-BCT® (RNA-BCT), for its ability to stabilize mRNA expression level in blood cells post-phlebotomy using indicator mRNAs in reverse transcription quantitative real-time PCR (RT-qPCR) assays. Methods Blood samples from presumed healthy donors were drawn into both RNA-BCT and K3EDTA tubes and maintained at room temperature (18–22 °C). The samples were processed to obtain white blood cells (WBCs) at days 0, 1, 2 and 3. Total cellular RNA was extracted from WBCs and mRNA concentrations were quantified by RT-qPCR for glyceraldehyde-3-phosphate dehydrogenase (GAPDH), c-fos, and p53 transcripts. Results While blood cells isolated from K3EDTA tubes showed significant changes in cellular mRNA concentrations for GAPDH, c-fos, and p53, these mRNAs concentrations were stable in blood drawn into RNA-BCT. Conclusion The reagent in the RNA-BCT device stabilizes cellular mRNA concentrations for GAPDH, c-fos and p53 for at least three days at room temperature.
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Huntington's disease biomarker progression profile identified by transcriptome sequencing in peripheral blood. Eur J Hum Genet 2015; 23:1349-56. [PMID: 25626709 PMCID: PMC4592077 DOI: 10.1038/ejhg.2014.281] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 11/04/2014] [Accepted: 11/26/2014] [Indexed: 12/28/2022] Open
Abstract
With several therapeutic approaches in development for Huntington's disease, there is a need for easily accessible biomarkers to monitor disease progression and therapy response. We performed next-generation sequencing-based transcriptome analysis of total RNA from peripheral blood of 91 mutation carriers (27 presymptomatic and, 64 symptomatic) and 33 controls. Transcriptome analysis by DeepSAGE identified 167 genes significantly associated with clinical total motor score in Huntington's disease patients. Relative to previous studies, this yielded novel genes and confirmed previously identified genes, such as H2AFY, an overlap in results that has proven difficult in the past. Pathway analysis showed enrichment of genes of the immune system and target genes of miRNAs, which are downregulated in Huntington's disease models. Using a highly parallelized microfluidics array chip (Fluidigm), we validated 12 of the top 20 significant genes in our discovery cohort and 7 in a second independent cohort. The five genes (PROK2, ZNF238, AQP9, CYSTM1 and ANXA3) that were validated independently in both cohorts present a candidate biomarker panel for stage determination and therapeutic readout in Huntington's disease. Finally we suggest a first empiric formula predicting total motor score from the expression levels of our biomarker panel. Our data support the view that peripheral blood is a useful source to identify biomarkers for Huntington's disease and monitor disease progression in future clinical trials.
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Calkoen FGJ, Vervat C, van Pel M, de Haas V, Vijfhuizen LS, Eising E, Kroes WGM, 't Hoen PAC, van den Heuvel-Eibrink MM, Egeler RM, van Tol MJD, Ball LM. Despite differential gene expression profiles pediatric MDS derived mesenchymal stromal cells display functionality in vitro. Stem Cell Res 2015; 14:198-210. [PMID: 25679997 DOI: 10.1016/j.scr.2015.01.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 12/03/2014] [Accepted: 01/19/2015] [Indexed: 12/21/2022] Open
Abstract
Pediatric myelodysplastic syndrome (MDS) is a heterogeneous disease covering a spectrum ranging from aplasia (RCC) to myeloproliferation (RAEB(t)). In adult-type MDS there is increasing evidence for abnormal function of the bone-marrow microenvironment. Here, we extensively studied the mesenchymal stromal cells (MSCs) derived from children with MDS. MSCs were expanded from the bone-marrow of 17 MDS patients (RCC: n=10 and advanced MDS: n=7) and pediatric controls (n=10). No differences were observed with respect to phenotype, differentiation capacity, immunomodulatory capacity or hematopoietic support. mRNA expression analysis by Deep-SAGE revealed increased IL-6 expression in RCC- and RAEB(t)-MDS. RCC-MDS MSC expressed increased levels of DKK3, a protein associated with decreased apoptosis. RAEB(t)-MDS revealed increased CRLF1 and decreased DAPK1 expressions. This pattern has been associated with transformation in hematopoietic malignancies. Genes reported to be differentially expressed in adult MDS-MSC did not differ between MSC of pediatric MDS and controls. An altered mRNA expression profile, associated with cell survival and malignant transformation, of MSC derived from children with MDS strengthens the hypothesis that the micro-environment is of importance in this disease. Our data support the understanding that pediatric and adult MDS are two different diseases. Further evaluation of the pathways involved might reveal additional therapy targets.
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Affiliation(s)
- F G J Calkoen
- Department of Pediatrics, Section Immunology, Hematology/Oncology and Hematopoietic Stem Cell Transplantation, Leiden University Medical Center, Leiden, The Netherlands.
| | - C Vervat
- Department of Pediatrics, Section Immunology, Hematology/Oncology and Hematopoietic Stem Cell Transplantation, Leiden University Medical Center, Leiden, The Netherlands
| | - M van Pel
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - V de Haas
- Dutch Childhood Oncology Group (DCOG), The Hague, The Netherlands
| | - L S Vijfhuizen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - E Eising
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - W G M Kroes
- Laboratory for Diagnostic Genome Analysis, Leiden University Medical Center, Leiden, The Netherlands
| | - P A C 't Hoen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - M M van den Heuvel-Eibrink
- Dutch Childhood Oncology Group (DCOG), The Hague, The Netherlands; Department of Pediatric Oncology/Hematology, Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - R M Egeler
- Department of Pediatrics, Section Immunology, Hematology/Oncology and Hematopoietic Stem Cell Transplantation, Leiden University Medical Center, Leiden, The Netherlands; Department of Hematology/Oncology and Hematopoietic Stem Cell Transplantation, Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - M J D van Tol
- Department of Pediatrics, Section Immunology, Hematology/Oncology and Hematopoietic Stem Cell Transplantation, Leiden University Medical Center, Leiden, The Netherlands
| | - L M Ball
- Department of Pediatrics, Section Immunology, Hematology/Oncology and Hematopoietic Stem Cell Transplantation, Leiden University Medical Center, Leiden, The Netherlands
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Sellin Jeffries MK, Kiss AJ, Smith AW, Oris JT. A comparison of commercially-available automated and manual extraction kits for the isolation of total RNA from small tissue samples. BMC Biotechnol 2014; 14:94. [PMID: 25394494 PMCID: PMC4239376 DOI: 10.1186/s12896-014-0094-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 10/22/2014] [Indexed: 11/25/2022] Open
Abstract
Background This study compared the performance of five commercially available kits in extracting total RNA from small eukaryotic tissue samples (<15 mg). Total RNA was isolated from fathead minnow (Pimephales promelas) tissues (spleen, blood, kidney, embryo, and larvae) using the Qiagen RNeasy® Plus Mini, Qiagen RNeasy® Plus Universal, Promega Maxwell® 16 LEV simplyRNA, Ambion MagMAX™-96 and Promega SimplyRNA HT kits. Kit performance was evaluated via measures of RNA quantity (e.g., total RNA amount) and quality (e.g., ratio of absorbance at 260 and 280 nm, RNA integrity number (RIN), presence of gDNA). Results With the exception of embryos, each kit generally extracted ≥5 μg of total RNA from each sample. With regard to RNA quality, the RINs of RNA samples isolated via the Plus Mini and Maxwell® 16 kits were consistently higher than those of samples extracted via the remaining three kits and for all tissues, these kits produced intact RNA with average RIN values ≥7. The Plus Universal and SimplyRNA HT kits produced moderately degraded (RIN values <7, but ≥5), while the RNA recovered via the MagMAX™ kit tended to exhibit a high degree of degradation (RIN values <5). Conclusions Each kit was generally capable of extracting the amount of RNA required for most downstream gene expression applications suggesting that RNA yield is unlikely to be a limiting factor for any of the kits evaluated. However, differences in the quality of RNA extracted via each of the kits indicate that these kits may differ in their ability to yield RNA acceptable for some applications. Overall, the findings of this study demonstrate that there are practical differences between commercially available RNA extraction kits that should be taken into account when selecting extraction methods to be used for isolating RNA designated for gene expression analysis. Electronic supplementary material The online version of this article (doi:10.1186/s12896-014-0094-8) contains supplementary material, which is available to authorized users.
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Choi I, Bao H, Kommadath A, Hosseini A, Sun X, Meng Y, Stothard P, Plastow GS, Tuggle CK, Reecy JM, Fritz-Waters E, Abrams SM, Lunney JK, Guan LL. Increasing gene discovery and coverage using RNA-seq of globin RNA reduced porcine blood samples. BMC Genomics 2014; 15:954. [PMID: 25374277 PMCID: PMC4230834 DOI: 10.1186/1471-2164-15-954] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 10/16/2014] [Indexed: 11/21/2022] Open
Abstract
Background Transcriptome analysis of porcine whole blood has several applications, which include deciphering genetic mechanisms for host responses to viral infection and vaccination. The abundance of alpha- and beta-globin transcripts in blood, however, impedes the ability to cost-effectively detect transcripts of low abundance. Although protocols exist for reduction of globin transcripts from human and mouse/rat blood, preliminary work demonstrated these are not useful for porcine blood Globin Reduction (GR). Our objectives were to develop a porcine specific GR protocol and to evaluate the GR effects on gene discovery and sequence read coverage in RNA-sequencing (RNA-seq) experiments. Results A GR protocol for porcine blood samples was developed using RNase H with antisense oligonucleotides specifically targeting porcine hemoglobin alpha (HBA) and beta (HBB) mRNAs. Whole blood samples (n = 12) collected in Tempus tubes were used for evaluating the efficacy and effects of GR on RNA-seq. The HBA and HBB mRNA transcripts comprised an average of 46.1% of the mapped reads in pre-GR samples, but those reads reduced to an average of 8.9% in post-GR samples. Differential gene expression analysis showed that the expression level of 11,046 genes were increased, whereas 34 genes, excluding HBA and HBB, showed decreased expression after GR (FDR <0.05). An additional 815 genes were detected only in post-GR samples. Conclusions Our porcine specific GR primers and protocol minimize the number of reads of globin transcripts in whole blood samples and provides increased coverage as well as accuracy and reproducibility of transcriptome analysis. Increased detection of low abundance mRNAs will ensure that studies relying on transcriptome analyses do not miss information that may be vital to the success of the study. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-954) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Joan K Lunney
- Animal Parasitic Diseases Laboratory, ARS, USDA, Beltsville, MD, USA.
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Duale N, Lipkin WI, Briese T, Aarem J, Rønningen KS, Aas KK, Magnus P, Harbak K, Susser E, Brunborg G. Long-term storage of blood RNA collected in RNA stabilizing Tempus tubes in a large biobank--evaluation of RNA quality and stability. BMC Res Notes 2014; 7:633. [PMID: 25214016 PMCID: PMC4168124 DOI: 10.1186/1756-0500-7-633] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 09/04/2014] [Indexed: 11/30/2022] Open
Abstract
Background Establishing methods for secure long term storage of RNA is critical to realizing the promise of biobanks in biomedical research. Here, we describe the results of yearly analyses of the same set of umbilical cord and adult whole blood RNA collected in Tempus Blood RNA tubes and stored at -80°C, over a period of up to six years. We systematically investigated the effects of long-term storage of samples (75 Tempus tubes form three adult donors and 30 Tempus tubes from three cord blood donors) on the RNA quality and transcript stability of six selected genes (CDKN1A, FOS, IL1B, IL8, MYC and TP53). This is the first systematic study of both cord and adult blood samples stored for many years. Findings The RNA purity and integrity, expressed as RIN-values, were stable up to six years of storage, and there were no storage-related deleterious effects on RNA purity. There were limited intra- and inter-individual variations in RNA yields; however, no consistent trend of decreasing RNA yield was observed with the duration of storage. Some long-term storage effects were found on the relative transcript levels of the six genes when compared to the year 0 samples. However, these changes were within ± 2–fold for both types of blood samples, except for two genes. Our results show that storage of these samples for up to six years did not have significant effects on the RNA quality and transcript stability of the six genes. Conclusions Blood RNA is stable in Tempus tubes stored at -80°C over a period of six years. Intact and good-quality RNA suitable for transcript profiling analyses in epidemiological studies was obtained from blood samples stored in Tempus tubes. This suggests that blood samples collected in large biobanks–such as the Mother and Child (MoBa) Cohort at Norwegian Institute of Public Health (NIPH) and frozen in suitable collection tubes for total RNA stabilization, can be used for quantitative studies after at least six years of storage. Electronic supplementary material The online version of this article (doi:10.1186/1756-0500-7-633) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nur Duale
- The Norwegian Institute of Public Health, PO Box 4404, Nydalen, NO-0403, Oslo, Norway.
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Abstract
Pancreatic cancer is one of the worst prognostic cancers because of the late diagnosis and the absence of effective treatment. Within all subtypes of this disease, ductal adenocarcinoma has the shortest survival time. In recent years, global genomics profiling allowed the identification of hundreds of genes that are perturbed in pancreatic cancer. The integration of different omics sources in the study of pancreatic cancer has revealed several molecular mechanisms, indicating the complex history of its development. However, validation of these genes as biomarkers for early diagnosis, prognosis or treatment efficacy is still incomplete but should lead to new approaches for the treatment of the disease in the future.
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Affiliation(s)
- Christian Pilarsky
- Department of Vascular-, Thoracic and Visceral Surgery, University Hospital Dresden, Technische Universit?t Dresden, Fetscherstr. 74, Dresden 01307, Germany.
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Archer SK, Shirokikh NE, Preiss T. Selective and flexible depletion of problematic sequences from RNA-seq libraries at the cDNA stage. BMC Genomics 2014; 15:401. [PMID: 24886553 PMCID: PMC4045971 DOI: 10.1186/1471-2164-15-401] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 05/16/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A major hurdle to transcriptome profiling by deep-sequencing technologies is that abundant transcripts, such as rRNAs, can overwhelm the libraries, severely reducing transcriptome-wide coverage. Methods for depletion of such unwanted sequences typically require treatment of RNA samples prior to library preparation, are costly and not suited to unusual species and applications. Here we describe Probe-Directed Degradation (PDD), an approach that employs hybridisation to DNA oligonucleotides at the single-stranded cDNA library stage and digestion with Duplex-Specific Nuclease (DSN). RESULTS Targeting Saccharomyces cerevisiae rRNA sequences in Illumina HiSeq libraries generated by the split adapter method we show that PDD results in efficient removal of rRNA. The probes generate extended zones of depletion as a function of library insert size and the requirements for DSN cleavage. Using intact total RNA as starting material, probes can be spaced at the minimum anticipated library size minus 20 nucleotides to achieve continuous depletion. No off-target bias is detectable when comparing PDD-treated with untreated libraries. We further provide a bioinformatics tool to design suitable PDD probe sets. CONCLUSION We find that PDD is a rapid procedure that results in effective and specific depletion of unwanted sequences from deep-sequencing libraries. Because PDD acts at the cDNA stage, handling of fragile RNA samples can be minimised and it should further be feasible to remediate existing libraries. Importantly, PDD preserves the original RNA fragment boundaries as is required for nucleotide-resolution footprinting or base-cleavage studies. Finally, as PDD utilises unmodified DNA oligonucleotides it can provide a low-cost option for large-scale projects, or be flexibly customised to suit different depletion targets, sample types and organisms.
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Affiliation(s)
| | | | - Thomas Preiss
- Genome Biology Department, The John Curtin School of Medical Research (JCSMR), The Australian National University, Acton, Canberra, Australian Capital Territory, Australia.
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Shin H, Shannon CP, Fishbane N, Ruan J, Zhou M, Balshaw R, Wilson-McManus JE, Ng RT, McManus BM, Tebbutt SJ. Variation in RNA-Seq transcriptome profiles of peripheral whole blood from healthy individuals with and without globin depletion. PLoS One 2014; 9:e91041. [PMID: 24608128 PMCID: PMC3946641 DOI: 10.1371/journal.pone.0091041] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 02/08/2014] [Indexed: 12/21/2022] Open
Abstract
Background The molecular profile of circulating blood can reflect physiological and pathological events occurring in other tissues and organs of the body and delivers a comprehensive view of the status of the immune system. Blood has been useful in studying the pathobiology of many diseases. It is accessible and easily collected making it ideally suited to the development of diagnostic biomarker tests. The blood transcriptome has a high complement of globin RNA that could potentially saturate next-generation sequencing platforms, masking lower abundance transcripts. Methods to deplete globin mRNA are available, but their effect has not been comprehensively studied in peripheral whole blood RNA-Seq data. In this study we aimed to assess technical variability associated with globin depletion in addition to assessing general technical variability in RNA-Seq from whole blood derived samples. Results We compared technical and biological replicates having undergone globin depletion or not and found that the experimental globin depletion protocol employed removed approximately 80% of globin transcripts, improved the correlation of technical replicates, allowed for reliable detection of thousands of additional transcripts and generally increased transcript abundance measures. Differential expression analysis revealed thousands of genes significantly up-regulated as a result of globin depletion. In addition, globin depletion resulted in the down-regulation of genes involved in both iron and zinc metal ion bonding. Conclusions Globin depletion appears to meaningfully improve the quality of peripheral whole blood RNA-Seq data, and may improve our ability to detect true biological variation. Some concerns remain, however. Key amongst them the significant reduction in RNA yields following globin depletion. More generally, our investigation of technical and biological variation with and without globin depletion finds that high-throughput sequencing by RNA-Seq is highly reproducible within a large dynamic range of detection and provides an accurate estimation of RNA concentration in peripheral whole blood. High-throughput sequencing is thus a promising technology for whole blood transcriptomics and biomarker discovery.
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Affiliation(s)
- Heesun Shin
- NCE CECR PROOF Centre of Excellence, Vancouver, British Columbia, Canada
- UBC Department of Medicine (Division of Respiratory Medicine), University of British Columbia, Vancouver, British Columbia, Canada
- UBC James Hogg Research Centre & Institute for HEART + LUNG Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Casey P. Shannon
- NCE CECR PROOF Centre of Excellence, Vancouver, British Columbia, Canada
| | - Nick Fishbane
- NCE CECR PROOF Centre of Excellence, Vancouver, British Columbia, Canada
- UBC Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jian Ruan
- NCE CECR PROOF Centre of Excellence, Vancouver, British Columbia, Canada
- UBC James Hogg Research Centre & Institute for HEART + LUNG Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mi Zhou
- NCE CECR PROOF Centre of Excellence, Vancouver, British Columbia, Canada
| | - Robert Balshaw
- NCE CECR PROOF Centre of Excellence, Vancouver, British Columbia, Canada
- UBC Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Raymond T. Ng
- NCE CECR PROOF Centre of Excellence, Vancouver, British Columbia, Canada
- UBC Department of Computer Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bruce M. McManus
- NCE CECR PROOF Centre of Excellence, Vancouver, British Columbia, Canada
- UBC Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- UBC James Hogg Research Centre & Institute for HEART + LUNG Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Scott J. Tebbutt
- NCE CECR PROOF Centre of Excellence, Vancouver, British Columbia, Canada
- UBC Department of Medicine (Division of Respiratory Medicine), University of British Columbia, Vancouver, British Columbia, Canada
- UBC James Hogg Research Centre & Institute for HEART + LUNG Health, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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Head SR, Mondala T, Gelbart T, Ordoukhanian P, Chappel R, Hernandez G, Salomon DR. RNA purification and expression analysis using microarrays and RNA deep sequencing. Methods Mol Biol 2014; 1034:385-403. [PMID: 23775753 DOI: 10.1007/978-1-62703-493-7_25] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Transcriptome analysis or global gene expression profiling is a powerful tool for discovery as well as -understanding biological mechanisms in health and disease. We present in this chapter a description of methods used to isolate mRNA from cells and tissues that has been optimized for preservation of RNA quality using clinical materials and implemented successfully in several large, multicenter studies by the authors. In addition, two methods, gene expression microarrays and RNAseq, are described for mRNA profiling of cells and tissues from clinical or laboratory sources.
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Affiliation(s)
- Steven R Head
- Microarray and Next Generation Sequencing Core Facility, The Scripps Research Institute, La Jolla, CA, USA
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Demasius W, Weikard R, Hadlich F, Müller KE, Kühn C. Monitoring the immune response to vaccination with an inactivated vaccine associated to bovine neonatal pancytopenia by deep sequencing transcriptome analysis in cattle. Vet Res 2013; 44:93. [PMID: 24099437 PMCID: PMC3851820 DOI: 10.1186/1297-9716-44-93] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 09/24/2013] [Indexed: 11/18/2022] Open
Abstract
Bovine neonatal pancytopenia (BNP) is a new fatal, alloimmune/alloantibody mediated disease of new-born calves induced by ingestion of colostrum from cows, which had been vaccinated with a specific vaccine against the Bovine Virus Diarrhoea Virus (BVDV). The hypothesis of pathogenic MHC class I molecules in the vaccine had been put up, but no formal proof of specific causal MHC class I alleles has been provided yet. However, the unique features of the vaccine obviously result in extremely high specific antibody titres in the vaccinated animals, but apparently also in further molecules inducing BNP. Thus, a comprehensive picture of the immune response to the vaccine is essential. Applying the novel approach of next generation RNA sequencing (RNAseq), our study provides a new holistic, comprehensive analysis of the blood transcriptome regulation after vaccination with the specific BVDV vaccine. Our RNAseq approach identified a novel cytokine-like gene in the bovine genome that is highly upregulated after vaccination. This gene has never been described before in any other species and might be specific to ruminant immune response. Furthermore, our data revealed a very coordinated immune response to double-stranded (ds) RNA or a dsRNA analogue after vaccination with the inactivated single-stranded (ss) RNA vaccine. This would suggest either a substantial contamination of the vaccine with dsRNA from host cells after virus culture or a dsRNA analogue applied to the vaccine. The first option would highlight the potential risks associated with virus culture on homologous cells during vaccine production; the latter option would emphasise the potential risks associated with immune stimulating adjuvants used in vaccine production.
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Affiliation(s)
- Wiebke Demasius
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany.
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45
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Bao H, Kommadath A, Sun X, Meng Y, Arantes AS, Plastow GS, Guan LL, Stothard P. Expansion of ruminant-specific microRNAs shapes target gene expression divergence between ruminant and non-ruminant species. BMC Genomics 2013; 14:609. [PMID: 24020371 PMCID: PMC3847189 DOI: 10.1186/1471-2164-14-609] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 09/06/2013] [Indexed: 12/20/2022] Open
Abstract
Background Understanding how species-specific microRNAs (miRNAs) contribute to species-specific phenotypes is a central topic in biology. This study aimed to elucidate the role of ruminant-specific miRNAs in shaping mRNA expression divergence between ruminant and non-ruminant species. Results We analyzed miRNA and mRNA transcriptomes generated by Illumina sequencing from whole blood samples of cattle and a closely related non-ruminant species, pig. We found evidence of expansion of cattle-specific miRNAs by analyzing miRNA conservation among 57 vertebrate species. The emergence of cattle-specific miRNAs was accompanied by accelerated sequence evolution at their target sites. Further, the target genes of cattle-specific miRNAs show markedly reduced expression compared to their pig and human orthologues. We found that target genes with conserved or non-conserved target sites of cattle-specific miRNAs exhibit reduced expression. One of the significantly enriched KEGG pathway terms for the target genes of the cattle-specific miRNAs is the insulin signalling pathway, raising the possibility that some of these miRNAs may modulate insulin resistance in ruminants. Conclusions We provide evidence of rapid miRNA-mediated regulatory evolution in the ruminant lineage. Cattle-specific miRNAs play an important role in shaping gene expression divergence between ruminant and non-ruminant species, by influencing the expression of targets genes through both conserved and cattle-specific target sites.
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Affiliation(s)
- Hua Bao
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada.
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Gupta R, Dewan I, Bharti R, Bhattacharya A. Differential Expression Analysis for RNA-Seq Data. ISRN BIOINFORMATICS 2012; 2012:817508. [PMID: 25937942 PMCID: PMC4393055 DOI: 10.5402/2012/817508] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Accepted: 08/09/2012] [Indexed: 02/05/2023]
Abstract
RNA-Seq is increasingly being used for gene expression profiling. In this approach, next-generation sequencing (NGS) platforms are used for sequencing. Due to highly parallel nature, millions of reads are generated in a short time and at low cost. Therefore analysis of the data is a major challenge and development of statistical and computational methods is essential for drawing meaningful conclusions from this huge data. In here, we assessed three different types of normalization (transcript parts per million, trimmed mean of M values, quantile normalization) and evaluated if normalized data reduces technical variability across replicates. In addition, we also proposed two novel methods for detecting differentially expressed genes between two biological conditions: (i) likelihood ratio method, and (ii) Bayesian method. Our proposed methods for finding differentially expressed genes were tested on three real datasets. Our methods performed at least as well as, and often better than, the existing methods for analysis of differential expression.
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Affiliation(s)
- Rashi Gupta
- School of Computational and Integrative Sciences, JNU, New Delhi 110067, India ; CorrZ Technosolutions Pvt. Ltd., Noida 201304, India
| | - Isha Dewan
- Indian Statistical Institute, New Delhi 110016, India
| | - Richa Bharti
- School of Computational and Integrative Sciences, JNU, New Delhi 110067, India
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