1
|
Xiang G, Guo Y, Bumcrot D, Sigova A. JMnorm: a novel joint multi-feature normalization method for integrative and comparative epigenomics. Nucleic Acids Res 2024; 52:e11. [PMID: 38055833 PMCID: PMC10810286 DOI: 10.1093/nar/gkad1146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/25/2023] [Accepted: 11/14/2023] [Indexed: 12/08/2023] Open
Abstract
Combinatorial patterns of epigenetic features reflect transcriptional states and functions of genomic regions. While many epigenetic features have correlated relationships, most existing data normalization approaches analyze each feature independently. Such strategies may distort relationships between functionally correlated epigenetic features and hinder biological interpretation. We present a novel approach named JMnorm that simultaneously normalizes multiple epigenetic features across cell types, species, and experimental conditions by leveraging information from partially correlated epigenetic features. We demonstrate that JMnorm-normalized data can better preserve cross-epigenetic-feature correlations across different cell types and enhance consistency between biological replicates than data normalized by other methods. Additionally, we show that JMnorm-normalized data can consistently improve the performance of various downstream analyses, which include candidate cis-regulatory element clustering, cross-cell-type gene expression prediction, detection of transcription factor binding and changes upon perturbations. These findings suggest that JMnorm effectively minimizes technical noise while preserving true biologically significant relationships between epigenetic datasets. We anticipate that JMnorm will enhance integrative and comparative epigenomics.
Collapse
Affiliation(s)
- Guanjue Xiang
- CAMP4 Therapeutics Corp., One Kendall Square, Building 1400 West, Cambridge, MA 02139, USA
| | - Yuchun Guo
- CAMP4 Therapeutics Corp., One Kendall Square, Building 1400 West, Cambridge, MA 02139, USA
| | - David Bumcrot
- CAMP4 Therapeutics Corp., One Kendall Square, Building 1400 West, Cambridge, MA 02139, USA
| | - Alla Sigova
- CAMP4 Therapeutics Corp., One Kendall Square, Building 1400 West, Cambridge, MA 02139, USA
| |
Collapse
|
2
|
Giannos P, Prokopidis K, Raleigh SM, Kelaiditi E, Hill M. Altered mitochondrial microenvironment at the spotlight of musculoskeletal aging and Alzheimer's disease. Sci Rep 2022; 12:11290. [PMID: 35788655 PMCID: PMC9253146 DOI: 10.1038/s41598-022-15578-9] [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: 03/25/2022] [Accepted: 06/27/2022] [Indexed: 11/23/2022] Open
Abstract
Emerging evidence has linked Alzheimer's disease (AD) onset with musculoskeletal aging via a muscle-brain crosstalk mediated by dysregulation of the mitochondrial microenvironment. This study investigated gene expression profiles from skeletal muscle tissues of older healthy adults to identify potential gene biomarkers whose dysregulated expression and protein interactome were involved in AD. Screening of the literature resulted in 12 relevant microarray datasets (GSE25941, GSE28392, GSE28422, GSE47881, GSE47969, GSE59880) in musculoskeletal aging and (GSE4757, GSE5281, GSE16759, GSE28146, GSE48350, GSE84422) in AD. Retrieved differentially expressed genes (DEGs) were used to construct two unique protein-protein interaction networks and clustering gene modules were identified. Overlapping module DEGs in the musculoskeletal aging and AD networks were ranked based on 11 topological algorithms and the five highest-ranked ones were considered as hub genes. The analysis revealed that the dysregulated expression of the mitochondrial microenvironment genes, NDUFAB1, UQCRC1, UQCRFS1, NDUFS3, and MRPL15, overlapped between both musculoskeletal aging and AD networks. Thus, these genes may have a potential role as markers of AD occurrence in musculoskeletal aging. Human studies are warranted to evaluate the functional role and prognostic value of these genes in aging populations with sarcopenia and AD.
Collapse
Affiliation(s)
- Panagiotis Giannos
- Society of Meta-research and Biomedical Innovation, London, UK. .,Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, South Kensington, London, SW7 2AZ, UK.
| | - Konstantinos Prokopidis
- Society of Meta-research and Biomedical Innovation, London, UK.,Department of Musculoskeletal Biology, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK
| | - Stuart M Raleigh
- Cardiovascular and Lifestyle Medicine Research Group, Centre for Sport, Exercise and Life Sciences, Coventry University, Coventry, UK
| | - Eirini Kelaiditi
- Faculty of Sport, Allied Health and Performance Science, St Mary's University Twickenham, Twickenham, UK
| | - Mathew Hill
- Centre for Sport, Exercise and Life Sciences, School of Life Sciences, Coventry University, Coventry, UK
| |
Collapse
|
3
|
Giannos P, Triantafyllidis KK, Giannos G, Kechagias KS. SPP1 in infliximab resistant ulcerative colitis and associated colorectal cancer: an analysis of differentially expressed genes. Eur J Gastroenterol Hepatol 2022; 34:598-606. [PMID: 35102110 DOI: 10.1097/meg.0000000000002349] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
OBJECTIVE Infliximab, a tumour necrosis factor-α (TNFα) antagonist, has advanced the management of ulcerative colitis. Although efficacious, considerable percentage of patients are resistant to treatment. Accumulative inflammatory burden in long-term ulcerative colitis patients refractory to therapy increases the risk of developing colorectal cancer (CRC). Our study investigated anti-TNFα-naïve patients with active ulcerative colitis to identify gene biomarkers whose dysregulated expression correlated with resistance to infliximab (IFX) treatment and poor prognosis in CRC. METHODS Differentially expressed genes (DEGs) from two studies (GSE73661 and GSE14580) with colonic mucosal samples were retrieved. Noninflammatory bowel disease controls were compared with those with active ulcerative colitis that either responded or were resistant to IFX before treatment. DEGs from ulcerative colitis samples resistant to IFX were used to construct a protein-protein interaction network, and clustering gene modules were identified. Module DEGs that overlapped with ulcerative colitis samples responsive to IFX were analysed, based on topological closeness and radiality. Hub genes were obtained, and their correlation with CRC progression was evaluated. Their expression in CRC tissues and their tumour microenvironment immune status was estimated. RESULTS Three clusters composed of 582 DEGs from ulcerative colitis samples resistant to IFX were retrieved. Comparative analysis identified 305 overlapping DEGs with ulcerative colitis samples responsive to IFX. Topological analysis revealed a hub gene - SPP1 - whose overexpression in CRC tissues and patients correlated with increased infiltration of immune signatures and poor prognosis. CONCLUSION SPP1 may serve as potential gene biomarker and predictor of resistance to IFX therapy in ulcerative colitis and CRC development.
Collapse
Affiliation(s)
- Panagiotis Giannos
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London
- Society of Meta-research and Biomedical Innovation, London
| | | | - Georgios Giannos
- Second Department of Surgery, Evaggelismos Hospital, Athens
- Department of Medicine, University of Crete Medical School, Heraklion, Crete, Greece
| | - Konstantinos S Kechagias
- Society of Meta-research and Biomedical Innovation, London
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London
- Department of Obstetrics and Gynaecology, Chelsea and Westminster Hospital National Health Service (NHS) Foundation Trust, London, UK
| |
Collapse
|
4
|
Giannos P, Prokopidis K. Gene Expression Profiles of the Aging Rat Hippocampus Imply Altered Immunoglobulin Dynamics. Front Neurosci 2022; 16:915907. [PMID: 35692421 PMCID: PMC9174800 DOI: 10.3389/fnins.2022.915907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/03/2022] [Indexed: 11/13/2022] Open
Abstract
Aging is a process that leads to the deterioration in physiological functioning of the brain. Prior research has proposed that hippocampal aging is accompanied by genetic alterations in neural, synaptic, and immune functions. Nevertheless, interactome-based interrogations of gene alterations in hippocampal aging, remain scarce. Our study integrated gene expression profiles of the hippocampus from young and aged rats and functionally classified network-mapped genes based on their interactome. Hippocampal differentially expressed genes (DEGs) between young (5-8 months) and aged (21-26 months) male rats (Rattus norvegicus) were retrieved from five publicly available datasets (GSE14505, GSE20219, GSE14723, GSE14724, and GSE14725; 38 young and 29 aged samples). Encoded hippocampal proteins of age-related DEGs and their interactome were predicted. Clustered network DEGs were identified and the highest-ranked was functionally annotated. A single cluster of 19 age-related hippocampal DEGs was revealed, which was linked with immune response (biological process, P = 1.71E-17), immunoglobulin G binding (molecular function, P = 1.92E-08), and intrinsic component of plasma membrane (cellular component, P = 1.25E-06). Our findings revealed dysregulated hippocampal immunoglobulin dynamics in the aging rat brain. Whether a consequence of neurovascular perturbations and dysregulated blood-brain barrier permeability, the role of hippocampal immunoregulation in the pathobiology of aging warrants further investigation.
Collapse
Affiliation(s)
- Panagiotis Giannos
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
- Society of Meta-Research and Biomedical Innovation, London, United Kingdom
| | - Konstantinos Prokopidis
- Society of Meta-Research and Biomedical Innovation, London, United Kingdom
- Department of Musculoskeletal Biology, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
| |
Collapse
|
5
|
Giannos P, Kechagias KS, Bowden S, Tabassum N, Paraskevaidi M, Kyrgiou M. PCNA in Cervical Intraepithelial Neoplasia and Cervical Cancer: An Interaction Network Analysis of Differentially Expressed Genes. Front Oncol 2021; 11:779042. [PMID: 34900731 PMCID: PMC8661029 DOI: 10.3389/fonc.2021.779042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 10/28/2021] [Indexed: 11/30/2022] Open
Abstract
The investigation of differentially expressed genes (DEGs) and their interactome could provide valuable insights for the development of markers to optimize cervical intraepithelial neoplasia (CIN) screening and treatment. This study investigated patients with cervical disease to identify gene markers whose dysregulated expression and protein interaction interface were linked with CIN and cervical cancer (CC). Literature search of microarray datasets containing cervical epithelial samples was conducted in Gene Expression Omnibus and Pubmed/Medline from inception until March 2021. Retrieved DEGs were used to construct two protein-protein interaction (PPI) networks. Module DEGs that overlapped between CIN and CC samples, were ranked based on 11 topological algorithms. The highest-ranked hub gene was retrieved and its correlation with prognosis, tissue expression and tumor purity in patients with CC, was evaluated. Screening of the literature yielded 9 microarray datasets (GSE7803, GSE27678, GSE63514, GSE6791, GSE9750, GSE29570, GSE39001, GSE63678, GSE67522). Two PPI networks from CIN and CC samples were constructed and consisted of 1704 and 3748 DEGs along 21393 and 79828 interactions, respectively. Two gene clusters were retrieved in the CIN network and three in the CC network. Multi-algorithmic topological analysis revealed PCNA as the highest ranked hub gene between the two networks, both in terms of expression and interactions. Further analysis revealed that while PCNA was overexpressed in CC tissues, it was correlated with favorable prognosis (log-rank P=0.022, HR=0.58) and tumor purity (P=9.86 × 10-4, partial rho=0.197) in CC patients. This study identified that cervical PCNA exhibited multi-algorithmic topological significance among DEGs from CIN and CC samples. Overall, PCNA may serve as a potential gene marker of CIN progression. Experimental validation is necessary to examine its value in patients with cervical disease.
Collapse
Affiliation(s)
- Panagiotis Giannos
- Society of Meta-Research and Biomedical Innovation, Cancer Research Working Group, London, United Kingdom.,Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | - Konstantinos S Kechagias
- Society of Meta-Research and Biomedical Innovation, Cancer Research Working Group, London, United Kingdom.,Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom.,Department of Obstetrics and Gynaecology, Chelsea and Westminster Hospital National Health Service (NHS) Foundation Trust, London, United Kingdom
| | - Sarah Bowden
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom.,Institute of Reproductive and Developmental Biology, Imperial College London, London, United Kingdom
| | - Neha Tabassum
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | - Maria Paraskevaidi
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom.,Institute of Reproductive and Developmental Biology, Imperial College London, London, United Kingdom
| | - Maria Kyrgiou
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom.,Institute of Reproductive and Developmental Biology, Imperial College London, London, United Kingdom.,Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, United Kingdom.,West London Gynaecological Cancer Centre, Imperial College Healthcare National Health Service (NHS) Trust, London, United Kingdom
| |
Collapse
|
6
|
Joseph K, Kirsch M, Johnston M, Münkel C, Stieglitz T, Haas CA, Hofmann UG. Transcriptional characterization of the glial response due to chronic neural implantation of flexible microprobes. Biomaterials 2021; 279:121230. [PMID: 34736153 DOI: 10.1016/j.biomaterials.2021.121230] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 10/20/2021] [Accepted: 10/24/2021] [Indexed: 01/13/2023]
Abstract
Long term implantation of (micro-)probes into neural tissue causes unique and disruptive responses. In this study, we investigate the transcriptional trajectory of glial cells responding to chronic implantation of 380 μm flexible micro-probes for up to 18 weeks. Transcriptomic analysis shows a rapid activation of microglial cells and a strong reactive astrocytic polarization, both of which are lost over the chronic of the implant duration. Animals that were implanted for 18 weeks show a transcriptional profile similar to non-implanted controls, with increased expression of genes associated with wound healing and angiogenesis, which raises hope of a normalization of the neuropil to the pre-injury state when using flexible probes. Nevertheless, our data shows that a subset of genes upregulated after 18 weeks belong to the family of immediate early genes, which indicates that structural and functional remodeling is not complete at this time point. Our results confirm and extend previous work on the molecular changes resulting from the presence of neural probes and provide a rational basis for developing interventional strategies to control them.
Collapse
Affiliation(s)
- Kevin Joseph
- Neuroelectronic Systems, Department of Neurosurgery, Medical Center, University of Freiburg, Germany; Department of Neurosurgery, Medical Center University of Freiburg, Germany; Faculty of Medicine, University of Freiburg, Germany; BrainLinks-BrainTools, University of Freiburg, Germany.
| | - Matthias Kirsch
- BrainLinks-BrainTools, University of Freiburg, Germany; Department of Neuroanatomy, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Midori Johnston
- Faculty of Medicine, University of Freiburg, Germany; BrainLinks-BrainTools, University of Freiburg, Germany; Experimental Epilepsy Research, Dept. of Neurosurgery, Medical Center- University of Freiburg, Germany
| | - Christian Münkel
- Neuroelectronic Systems, Department of Neurosurgery, Medical Center, University of Freiburg, Germany; Department of Neurosurgery, Medical Center University of Freiburg, Germany; Faculty of Medicine, University of Freiburg, Germany
| | - Thomas Stieglitz
- BrainLinks-BrainTools, University of Freiburg, Germany; Laboratory for Biomedical Microtechnology, Department of Microsystems Engineering-IMTEK, Faculty of Engineering, University of Freiburg, Germany
| | - Carola A Haas
- Faculty of Medicine, University of Freiburg, Germany; Experimental Epilepsy Research, Dept. of Neurosurgery, Medical Center- University of Freiburg, Germany
| | - Ulrich G Hofmann
- Neuroelectronic Systems, Department of Neurosurgery, Medical Center, University of Freiburg, Germany; Department of Neurosurgery, Medical Center University of Freiburg, Germany; Faculty of Medicine, University of Freiburg, Germany; BrainLinks-BrainTools, University of Freiburg, Germany
| |
Collapse
|
7
|
Systematic comparison and assessment of RNA-seq procedures for gene expression quantitative analysis. Sci Rep 2020; 10:19737. [PMID: 33184454 PMCID: PMC7665074 DOI: 10.1038/s41598-020-76881-x] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 11/03/2020] [Indexed: 01/16/2023] Open
Abstract
RNA-seq is currently considered the most powerful, robust and adaptable technique for measuring gene expression and transcription activation at genome-wide level. As the analysis of RNA-seq data is complex, it has prompted a large amount of research on algorithms and methods. This has resulted in a substantial increase in the number of options available at each step of the analysis. Consequently, there is no clear consensus about the most appropriate algorithms and pipelines that should be used to analyse RNA-seq data. In the present study, 192 pipelines using alternative methods were applied to 18 samples from two human cell lines and the performance of the results was evaluated. Raw gene expression signal was quantified by non-parametric statistics to measure precision and accuracy. Differential gene expression performance was estimated by testing 17 differential expression methods. The procedures were validated by qRT-PCR in the same samples. This study weighs up the advantages and disadvantages of the tested algorithms and pipelines providing a comprehensive guide to the different methods and procedures applied to the analysis of RNA-seq data, both for the quantification of the raw expression signal and for the differential gene expression.
Collapse
|
8
|
Xiang G, Keller CA, Giardine B, An L, Li Q, Zhang Y, Hardison RC. S3norm: simultaneous normalization of sequencing depth and signal-to-noise ratio in epigenomic data. Nucleic Acids Res 2020; 48:e43. [PMID: 32086521 PMCID: PMC7192629 DOI: 10.1093/nar/gkaa105] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 01/20/2020] [Accepted: 02/10/2020] [Indexed: 12/12/2022] Open
Abstract
Quantitative comparison of epigenomic data across multiple cell types or experimental conditions is a promising way to understand the biological functions of epigenetic modifications. However, differences in sequencing depth and signal-to-noise ratios in the data from different experiments can hinder our ability to identify real biological variation from raw epigenomic data. Proper normalization is required prior to data analysis to gain meaningful insights. Most existing methods for data normalization standardize signals by rescaling either background regions or peak regions, assuming that the same scale factor is applicable to both background and peak regions. While such methods adjust for differences in sequencing depths, they do not address differences in the signal-to-noise ratios across different experiments. We developed a new data normalization method, called S3norm, that normalizes the sequencing depths and signal-to-noise ratios across different data sets simultaneously by a monotonic nonlinear transformation. We show empirically that the epigenomic data normalized by our method, compared to existing methods, can better capture real biological variation, such as impact on gene expression regulation.
Collapse
Affiliation(s)
- Guanjue Xiang
- The Bioinformatics and Genomics program, Center for Computational Biology and Bioinformatics, Huck Institutes of the Life Sciences, Wartik Laboratory, The Pennsylvania State University, University Park, PA 16802, USA
| | - Cheryl A Keller
- Dept. of Biochemistry and Molecular Biology, The Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, USA
| | - Belinda Giardine
- Dept. of Biochemistry and Molecular Biology, The Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, USA
| | - Lin An
- The Bioinformatics and Genomics program, Center for Computational Biology and Bioinformatics, Huck Institutes of the Life Sciences, Wartik Laboratory, The Pennsylvania State University, University Park, PA 16802, USA
| | - Qunhua Li
- Dept. of Statistics, The Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, USA
| | - Yu Zhang
- Dept. of Statistics, The Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, USA
| | - Ross C Hardison
- Dept. of Biochemistry and Molecular Biology, The Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, USA
| |
Collapse
|
9
|
Borisov N, Shabalina I, Tkachev V, Sorokin M, Garazha A, Pulin A, Eremin II, Buzdin A. Shambhala: a platform-agnostic data harmonizer for gene expression data. BMC Bioinformatics 2019; 20:66. [PMID: 30727942 PMCID: PMC6366102 DOI: 10.1186/s12859-019-2641-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 01/18/2019] [Indexed: 11/10/2022] Open
Abstract
Background Harmonization techniques make different gene expression profiles and their sets compatible and ready for comparisons. Here we present a new bioinformatic tool termed Shambhala for harmonization of multiple human gene expression datasets obtained using different experimental methods and platforms of microarray hybridization and RNA sequencing. Results Unlike previously published methods enabling good quality data harmonization for only two datasets, Shambhala allows conversion of multiple datasets into the universal form suitable for further comparisons. Shambhala harmonization is based on the calibration of gene expression profiles using the auxiliary standardization dataset. Each profile is transformed to make it similar to the output of microarray hybridization platform Affymetrix Human Gene. This platform was chosen because it has the biggest number of human gene expression profiles deposited in public databases. We evaluated Shambhala ability to retain biologically important features after harmonization. The same four biological samples taken in multiple replicates were profiled independently using three and four different experimental platforms, respectively, then Shambhala-harmonized and investigated by hierarchical clustering. Conclusion Our results showed that unlike other frequently used methods: quantile normalization and DESeq/DESeq2 normalization, Shambhala harmonization was the only method supporting sample-specific and platform-independent biologically meaningful clustering for the data obtained from multiple experimental platforms. Electronic supplementary material The online version of this article (10.1186/s12859-019-2641-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Nicolas Borisov
- I.M. Sechenov First Moscow State Medical University, Sechenov University, Moscow, 119991, Russia. .,Department of bioinformatics and molecular networks, OmicsWay Corporation, Walnut, CA, USA.
| | - Irina Shabalina
- Faculty of Mathematics and Information Technologies, Petrozavodsk State University, Anokhina str., 20, Petrozavodsk, 185910, Russia
| | - Victor Tkachev
- Department of bioinformatics and molecular networks, OmicsWay Corporation, Walnut, CA, USA
| | - Maxim Sorokin
- I.M. Sechenov First Moscow State Medical University, Sechenov University, Moscow, 119991, Russia.,Department of bioinformatics and molecular networks, OmicsWay Corporation, Walnut, CA, USA.,Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Andrew Garazha
- Department of bioinformatics and molecular networks, OmicsWay Corporation, Walnut, CA, USA.,Laboratory of Bioinformatics, Oncology and Immunology, D. Rogachyov Federal Research Center of Pediatric Hematology, Moscow, 117198, Russia
| | - Andrey Pulin
- Laboratory for Cell Biology and Developmental Pathology, Federal State Institution "Institute of General Pathology and Pathophysiology", FSBSI "IGPP", Moscow, Russia
| | - Ilya I Eremin
- Department for Regenerative Medicine, JSC Generium, Moscow, Russia
| | - Anton Buzdin
- I.M. Sechenov First Moscow State Medical University, Sechenov University, Moscow, 119991, Russia.,Department of bioinformatics and molecular networks, OmicsWay Corporation, Walnut, CA, USA.,Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| |
Collapse
|
10
|
Expression analysis of RNA sequencing data from human neural and glial cell lines depends on technical replication and normalization methods. BMC Bioinformatics 2018; 19:412. [PMID: 30453873 PMCID: PMC6245503 DOI: 10.1186/s12859-018-2382-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background The potential for astrocyte participation in central nervous system recovery is highlighted by in vitro experiments demonstrating their capacity to transdifferentiate into neurons. Understanding astrocyte plasticity could be advanced by comparing astrocytes with stem cells. RNA sequencing (RNA-seq) is ideal for comparing differences across cell types. However, this novel multi-stage process has the potential to introduce unwanted technical variation at several points in the experimental workflow. Quantitative understanding of the contribution of experimental parameters to technical variation would facilitate the design of robust RNA-Seq experiments. Results RNA-Seq was used to achieve biological and technical objectives. The biological aspect compared gene expression between normal human fetal-derived astrocytes and human neural stem cells cultured in identical conditions. When differential expression threshold criteria of |log2fold change| > 2 were applied to the data, no significant differences were observed. The technical component quantified variation arising from particular steps in the research pathway, and compared the ability of different normalization methods to reduce unwanted variance. To facilitate this objective, a liberal false discovery rate of 10% and a |log2fold change| > 0.5 were implemented for the differential expression threshold. Data were normalized with RPKM, TMM, and UQS methods using JMP Genomics. The contributions of key replicable experimental parameters (cell lot; library preparation; flow cell) to variance in the data were evaluated using principal variance component analysis. Our analysis showed that, although the variance for every parameter is strongly influenced by the normalization method, the largest contributor to technical variance was library preparation. The ability to detect differentially expressed genes was also affected by normalization; differences were only detected in non-normalized and TMM-normalized data. Conclusions The similarity in gene expression between astrocytes and neural stem cells supports the potential for astrocytic transdifferentiation into neurons, and emphasizes the need to evaluate the therapeutic potential of astrocytes for central nervous system damage. The choice of normalization method influences the contributions to experimental variance as well as the outcomes of differential expression analysis. However irrespective of normalization method, our findings illustrate that library preparation contributed the largest component of technical variance. Electronic supplementary material The online version of this article (10.1186/s12859-018-2382-0) contains supplementary material, which is available to authorized users.
Collapse
|