TGM2, HMGA2, FXYD3, and LGALS4 genes as biomarkers in acquired oxaliplatin resistance of human colorectal cancer: A systems biology approach
Tayebeh Cheraghi-shavi, Razieh Jalal, Zarrin Minuchehr
Abstract
Acquired resistance to oxaliplatin is considered as the primary reason for failure in colorectal cancer (CRC) therapy. Identifying the underlying resistance mechanisms may improve CRC treatment. The present study aims to identify the key genes involved in acquired oxaliplatin-resistant in CRC by confirming the oxaliplatin resistance index (OX-RI). To this aim, two public microarray datasets regarding oxaliplatin-resistant CRC cells with different OX-RI, GSE42387, and GSE76092 were downloaded from GEO database to identify differentially expressed genes (DEGs). The results indicated that the OX-RI affects the gene expression pattern significantly. Then, 54 common DEGs in both datasets including 18 up- and 36 down-regulated genes were identified. Protein-protein interaction (PPI) analysis revealed 13 up- (MAGEA6, TGM2, MAGEA4, SCHIP1, ECI2, CD33, AKAP12, MAGEA12, CALD1, WFDC2, VSNL1, HMGA2, and MAGEA2B) and 12 down-regulated (PDZK1IP1, FXYD3, ALDH2, CEACAM6, QPRT, GRB10, TM4SF4, LGALS4, ALDH3A1, USH1C, KCNE3, and CA12) hub genes. In the next step, two novel up-regulated hub genes including ECI2 and SCHIP1 were identified to be related to oxaliplatin resistance. Functional enrichment and pathway analysis indicated that metabolic pathways, proliferation, and epithelial-mesenchymal transition may play dominant roles in CRC progression and oxaliplatin resistance.
Introduction
Colorectal cancer (CRC) is regarded as the third most commonly diagnosed cancer and the second leading reason for cancer-related mortality worldwide with 1.9 million new cases and 0.9 million deaths during 2020 [1,2]. The CRC treatment strategies include surgery, radiation therapy, chemotherapy, targeted therapy, immunotherapy, and their combination depending on the stage of cancer [3]. Today, cytotoxic chemotherapy is considered as the backbone of CRC treatment [4]. The conventional chemotherapy of CRC contains 5-fluorouracil (5FU) alone or in combination with leucovorin (LV), irinotecan (FOLFIRI), or oxaliplatin (FOLFOX) which are accompanied by the epidermal growth factor receptor (EGFR)- or vascular endothelial growth factor (VEGF)-targeted monoclonal antibodies [5,6]. Chemotherapy, radiotherapy, and targeted therapies only provide a limited overall survival increase, despite advanced screening and treatment in CRC. Resistance to therapy such as chemotherapy and radiotherapy is regarded as the major reason for cancer recurrence and low survival rate. Thus, evaluating the expression levels of critical genes and detecting molecular pathways play a critical role in overcoming the chemoresistance and radioresistance of CRC [7,8].
Materials and methods
Bibliographic search and data source
A primary study was conducted applying the GEO database (https://www.ncbi.nlm.nih.gov/geo/) [30] up to April 2023 using the search term [("Colorectal Neoplasms") and ("resistance" or "resistant") and "sensitivity"], which was limited to Homo sapiens in order to achieve microarray expression data of chemoresistant CRC cells. The gene expression datasets were selected utilizing acquired oxaliplatin resistance in the same CRC cell lines, mRNA expression profile, and datasets with biological replicates.
Results
Selecting datasets and identifying DEGs
Fig 1 shows the detailed process of literature retrieval. Totally, 741 records were identified through GEO database screening, and six microarray datasets were recognized based on the criteria indicated in the materials and methods section. There are two datasets which compared three replicates of gene expression profiles of oxaliplatin-resistant and susceptible CRC cells, and their GEO accession numbers included GSE42387 and GSE76092.
Discussion
Acquired resistance to chemotherapeutic drugs decreased effectiveness and overall survival, and is considered as the leading reason for death, despite advances in the medical treatment of CRC [45]. Identifying novel hub genes involved in CRC cells resistant to platinum-based agents improves survival rates and avoids cancer recurrence [46]. Thus, the extracted DEGs of oxaliplatin-resistant HT-29 cells from the two datasets of GSE42387 and GSE76092 were analyzed in two different methods to identify the key genes involved in the molecular mechanisms of oxaliplatin-resistance, as well as those related to the RI of CRC cells to oxaliplatin. In addition, two sub-lines resistant to oxaliplatin including HCT116/OX-R4.3 and HCT116/OX-R10 cells were established. The mRNA expression level of FXYD3, LGALS4, USH1C, ECI2, TGM2, and HMGA2 genes which are involved in EMT, drug resistance, and cancer progression were measured in HCT116/OX-R4.3 and HCT116/OX-R10 cells by qRT-PCR.
Conclusion
The present study identified a number of hub genes related to the molecular mechanism of oxaliplatin resistance by comprehensive bioinformatics analysis, which may help determine potential gene therapy targets for oxaliplatin-resistant CRC cells. Based on the results, OX-RI value affects the gene expression pattern significantly. Therefore, different levels of drug resistance should be studied to achieve a reliable result. The present data propose the involvement of different pathways and processes, as well as metabolism alterations to facilitate metastasis and oxaliplatin resistance. The results indicated the down-regulation of LGALS4, FXYD3, and ECI2 and the up-regulation of TGM2 and HMGA2 in HCT116/OX-R10 cells with high OX-RI value. The above-mentioned genes via EMT induction and apoptosis reduction can resist CRC cells to oxaliplatin. Combined targeting therapy strategies involving multiple genes and pathways may achieve better therapeutic responses. This study focused on bioinformatics and the qRT-PCR results only in two acquired oxaliplatin-resistant HCT116 sub-lines with different OX-RI values.
Citation: Cheraghi-shavi T, Jalal R, Minuchehr Z (2023) TGM2, HMGA2, FXYD3, and LGALS4 genes as biomarkers in acquired oxaliplatin resistance of human colorectal cancer: A systems biology approach. PLoS ONE 18(8): e0289535. https://doi.org/10.1371/journal.pone.0289535
Editor: Lay-Hong Chuah, Monash University Malaysia, MALAYSIA
Received: November 8, 2022; Accepted: July 20, 2023; Published: August 3, 2023
Copyright: © 2023 Cheraghi-shavi 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: All relevant data are within the paper and its Supporting Information files.
Funding: This project was supported by Ferdowsi University of Mashhad, grant number 3/48932. The funders 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.
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0289535#abstract0
