Long non-coding RNA AC087388.1 as a novel biomarker in colorectal cancer

Mohammad Amin Kerachian,Mohammad Reza Abbaszadegan,Arash Poursheikhani

doi:10.1186/s12885-022-09282-0

Mohammad Amin Kerachian, Mohammad Reza Abbaszadegan + Show 1 more

Open Access

https://doi.org/10.1186/s12885-022-09282-0

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Abstract

BackgroundSeveral investigations have reported diverse roles of long non-coding RNA (lncRNA) in biological processes, tumor development, and progression of colorectal cancer (CRC). In this study, we investigated the lncRNA AC087388.1 tumorigenic role in CRC cells.MethodsThe CRC tissues were collected at the Reza Radiotherapy and Oncology Center, Mashhad, Iran. The human SW-48 and HT-29 CRC cell lines were obtained from the national cell bank of Iran. The cells were cultured according to ATCC (the American Type Culture Collection) recommendations. Quantitative real-time PCR was applied to assess the RNA expression. ShRNA transfection was done to downregulate the target gene. MTT and apoptosis assays were conducted to evaluate cell proliferation and viability, respectively. Colony formation assay, wound healing assay, and invasion assay were applied to determine growth, motility, and invasion of the cells, respectively. ENCORI online tool was used as downstream enrichment analysis.ResultsForty CRC patients were encompassed in this study. The results demonstrated that the lncRNA SLC16A1-AS1, AC087388.1, and ELFN1-AS1 were significantly overexpressed in the CRC tissues in comparison to their normal counterpart margins. All the lncRNAs have shown significant Area Under Curve (AUC) values in the patients. Downregulation of lncRNA AC087388.1 remarkably decreased the cell proliferation and viability of the CRC cells. In addition, the data demonstrated that the downregulation of lncRNA AC087388.1 significantly suppressed cell growth and colony formation capability in the cells. Also, downregulation of lncRNA AC087388.1 attenuated motility and invasion of CRC cells, and significantly decreased the expression of invasion genes. In-silico functional enrichment analysis indicated that the lncRNA AC087388.1 has contributed to crucial signaling pathways in tumorigenesis such as the p53 and Wnt signaling pathways, apoptosis, and cell cycle.ConclusionsAltogether, we showed that lncRNA AC087388.1 has an oncogenic role in tumorigenesis of CRC, and it can be considered as a novel diagnostic and prognostic biomarker in CRC.

Highlights

Several investigations have reported diverse roles of long non-coding RNA in biological processes, tumor development, and progression of colorectal cancer (CRC)
We demonstrated that 2995 mRNAs, 205 long non-coding RNA (lncRNA), and 345 miRNAs were differentially expressed in CRC
Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathway were conducted and we demonstrated that the main number of the differentially expressed genes were enriched in important pathways in CRC

Summary

Introduction

Several investigations have reported diverse roles of long non-coding RNA (lncRNA) in biological processes, tumor development, and progression of colorectal cancer (CRC). We investigated the lncRNA AC087388.1 tumorigenic role in CRC cells. The gold standard method for screening CRC patients is colonoscopy which combines diagnosis, and treatment, but it is an invasive approach. There are other screening methods such as guaiac fecal occult blood test (gFOBT), and fecal immunochemical test (FIT) which have a lack of Poursheikhani et al BMC Cancer (2022) 22:196 sensitivity and specificity [6]. Despite improving the CRC treatment approaches such as surgical resection, radiation, and chemotherapy, the 5-year survival rate of the patients is disappointing (less than 30%) [9, 10].

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