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Yu CY, Xiang S, Huang Z, Johnson TS, Zhan X, Han Z, Abu Zaid M, Huang K. Gene Co-expression Network and Copy Number Variation Analyses Identify Transcription Factors Associated With Multiple Myeloma Progression. Front Genet 2019; 10:468. [PMID: 31156714 PMCID: PMC6533571 DOI: 10.3389/fgene.2019.00468] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 05/01/2019] [Indexed: 11/29/2022] Open
Abstract
Multiple myeloma (MM) has two clinical precursor stages of disease: monoclonal gammopathy of undetermined significance (MGUS) and smoldering multiple myeloma (SMM). However, the mechanism of progression is not well understood. Because gene co-expression network analysis is a well-known method for discovering new gene functions and regulatory relationships, we utilized this framework to conduct differential co-expression analysis to identify interesting transcription factors (TFs) in two publicly available datasets. We then used copy number variation (CNV) data from a third public dataset to validate these TFs. First, we identified co-expressed gene modules in two publicly available datasets each containing three conditions: normal, MGUS, and SMM. These modules were assessed for condition-specific gene expression, and then enrichment analysis was conducted on condition-specific modules to identify their biological function and upstream TFs. TFs were assessed for differential gene expression between normal and MM precursors, then validated with CNV analysis to identify candidate genes. Functional enrichment analysis reaffirmed known functional categories in MM pathology, the main one relating to immune function. Enrichment analysis revealed a handful of differentially expressed TFs between normal and either MGUS or SMM in gene expression and/or CNV. Overall, we identified four genes of interest (MAX, TCF4, ZNF148, and ZNF281) that aid in our understanding of MM initiation and progression.
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Affiliation(s)
- Christina Y Yu
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, United States.,Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Shunian Xiang
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, IN, United States.,National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, China
| | - Zhi Huang
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States.,School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, United States
| | - Travis S Johnson
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, United States.,Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Xiaohui Zhan
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States.,National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, China
| | - Zhi Han
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States.,Regenstrief Institute, Indianapolis, IN, United States
| | - Mohammad Abu Zaid
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Kun Huang
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States.,Regenstrief Institute, Indianapolis, IN, United States
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Storti P, Agnelli L, Palma BD, Todoerti K, Marchica V, Accardi F, Sammarelli G, Deluca F, Toscani D, Costa F, Vicario E, Todaro G, Martella E, Neri A, Giuliani N. The transcriptomic profile of CD138 + cells from patients with early progression from smoldering to active multiple myeloma remains substantially unchanged. Haematologica 2019; 104:e465-e469. [PMID: 30846495 DOI: 10.3324/haematol.2018.209999] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Affiliation(s)
- Paola Storti
- Department of Medicine and Surgery, University of Parma, Parma .,CORELAB Azienda Ospedaliero-Universitaria di Parma, Parma
| | - Luca Agnelli
- Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan.,Department of Oncology and Hemato-oncology, University of Milan, Milan
| | - Benedetta Dalla Palma
- Department of Medicine and Surgery, University of Parma, Parma.,Hematological Unit Azienda Ospedaliero-Universitaria di Parma, Parma
| | - Katia Todoerti
- Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan.,Department of Oncology and Hemato-oncology, University of Milan, Milan
| | - Valentina Marchica
- Department of Medicine and Surgery, University of Parma, Parma.,CORELAB Azienda Ospedaliero-Universitaria di Parma, Parma
| | - Fabrizio Accardi
- Department of Medicine and Surgery, University of Parma, Parma.,Hematological Unit Azienda Ospedaliero-Universitaria di Parma, Parma
| | | | - Federica Deluca
- Department of Medicine and Surgery, University of Parma, Parma
| | - Denise Toscani
- Department of Medicine and Surgery, University of Parma, Parma
| | - Federica Costa
- Department of Medicine and Surgery, University of Parma, Parma
| | | | | | - Eugenia Martella
- Pathology, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Antonino Neri
- Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan.,Department of Oncology and Hemato-oncology, University of Milan, Milan
| | - Nicola Giuliani
- Department of Medicine and Surgery, University of Parma, Parma .,CORELAB Azienda Ospedaliero-Universitaria di Parma, Parma.,Hematological Unit Azienda Ospedaliero-Universitaria di Parma, Parma
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