Core signaling pathways in ovarian cancer stem cell revealed by integrative analysis of multi-marker genomics data

RESEARCH ARTICLE Core signaling pathways in ovarian cancer stem cell revealed by integrative analysis of multi-marker genomics data Tianyu Zhang1,2, Jielin Xu1, Siyuan Deng1, Fengqi Zhou1, Jin Li1, Liwei Zhang2, Lang Li1, Qi-En Wang3, Fuhai Li1* a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 OPEN ACCESS Citation: Zhang T, Xu J, Deng S, Zhou F, Li J, Zhang L, et al. (2018) Core signaling pathways in ovarian cancer stem cell revealed by integrative analysis of multi-marker genomics data. PLoS ONE 13(5): e0196351. https://doi.org/10.1371/journal. pone.0196351 Editor: Gianpaolo Papaccio, Università degli Studi della Campania, ITALY Received: March 19, 2018 Accepted: April 11, 2018 Published: May 3, 2018 Copyright: © 2018 Zhang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: Part of the data underlying this study are accessible using the following accession numbers: GSE33874 and GSE82304, in the NCBI GEO database. The TFTarget interactions, derived from TRANSFAC database, are third party data and are available using the following link: https://genome.cshlp.org/ content/24/11/1869/suppl/DC1. The authors did not have special access privileges. 1 Department of BioMedical Informatics (BMI), The Ohio State University, Columbus, Ohio, United States of America, 2 School of Mathematical Sciences, Dalian University of Technology, Dalian, China, 3 Department of Radiology, The Ohio State University, Columbus, Ohio, United States of America * Abstract Tumor recurrence occurs in more than 70% of ovarian cancer patients, and the majority eventually becomes refractory to treatments. Ovarian Cancer Stem Cells (OCSCs) are believed to be responsible for the tumor relapse and drug resistance. Therefore, eliminating ovarian CSCs is important to improve the prognosis of ovarian cancer patients. However, there is a lack of effective drugs to eliminate OCSCs because the core signaling pathways regulating OCSCs remain unclear. Also it is often hard for biologists to identify a few testable targets and infer driver signaling pathways regulating CSCs from a large number of differentially expression genes in an unbiased manner. In this study, we propose a straightforward and integrative analysis to identify potential core signaling pathways of OCSCs by integrating transcriptome data of OCSCs isolated based on two distinctive markers, ALDH and side population, with regulatory network (Transcription Factor (TF) and Target Interactome) and signaling pathways. We first identify the common activated TFs in two OCSC populations integrating the gene expression and TF-target Interactome; and then uncover up-stream signaling cascades regulating the activated TFs. In specific, 22 activated TFs are identified. Through literature search validation, 15 of them have been reported in association with cancer stem cells. Additionally, 10 TFs are found in the KEGG signaling pathways, and their upstream signaling cascades are extracted, which also provide potential treatment targets. Moreover, 40 FDA approved drugs are identified to target on the up-stream signaling cascades, and 15 of them have been reported in literatures in cancer stem cell treatment. In conclusion, the proposed approach can uncover the activated up-stream signaling, activated TFs and up-regulated target genes that constitute the potential core signaling pathways of ovarian CSC. Also drugs and drug combinations targeting on the core signaling pathways might be able to eliminate OCSCs. The proposed approach can also be applied for identifying potential activated signaling pathways of other types of cancers. Funding: This work is supported in part by the startup fund from Department of Biomedical PLOS ONE | https://doi.org/10.1371/journal.pone.0196351 May 3, 2018 1 / 14 Signaling pathways of ovarian cancer stem cell Informatics, Translational Data Analytics, The Ohio State University to FL. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing interests: The authors have declared that no competing interests exist. Introduction Over 90% of ovarian cancers are epithelial in origin, and epithelial ovarian cancer, especially the most aggressive subtype high-grade serous ovarian cancer (HGSOC), accounts for the majority of ovarian cancer deaths [1, 2]. Most tumors are initially responsive to the conventional chemotherapy, and the patients enter into clinical remission after initial treatment. However, tumor recurrence occurs in more than 70% of patients despite treatment, and the majority eventually becomes refractory to treatments [3]. Recent research evidences show that tumor is a mixture of heterogeneous populations of cells with different levels of malignity. A subpopulation of tumor cells characterized by the capacity of self-renewing, differentiation, and tumor-initiating are called cancer stem cells (CSCs) or tumor initiating cells (TICs) [4]. CSCs play important roles in tumor initiation, progression, metastasis, recurrence and drug resistance [4–7]. Thus, elimination of CSCs is important to overcome drug resistance to improve the prognosis of cancer patients. The knowledge about CSCs is limited, and one major challenge is that it is difficult to identify and isolate CSCs with few biomarkers because CSCs are heterogeneous and could exist a specific hierarchy [8–10]. Ovarian cancer stem cells (OCSCs) have been successfully identified and isolated based on their expression of distinctive cell surface markers CD44, CD117, MyD88, and CD133 [11, 12], as well as the activity of ALDH [13]. These CSCs harbor enhanced tumorigenicity and chemoresistance [14]) and are thought to drive the universal recurrence of ovarian cancer, as well as responsible for the development of therapeutic resistance [15]. Though studies with these markers show evidence in support of OCSCs [16], there is still a lack of effective drugs to differentiate and eliminate them [17]. Though common signaling pathways, e.g., WNT, NOTCH, SHH, JAK/STAT, have been associated with all types of CSCs [18, 19], the core signaling mechanism regulating Ovarian CSCs remain unclear. The differential gene expression analysis often fails to identify genes regulate CSCs because it is difficult to identify a few testable targets from a large number of differentially expressed genes mixed with many passenger genes. Additionally, important proteins regulating CSCs might be missed because either the fold change is small or the gene expression data is not available. Therefore, it is necessary to integrate multi-datasets with prior knowledge, e.g., regulatory network and signaling pathways, to increase the possibility of identifying the true CSC driver genes in the systems biology pe (...truncated)