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Long Noncoding RNAs in Colorectal Adenocarcinoma; an in silico Analysis

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Pathology & Oncology Research

Abstract

Long noncoding RNAs (lncRNAs) are lengthy noncoding transcripts which are involved in critical signaling pathways including cell cycle and apoptosis so it is not surprising to see their altered expression in human tumors. Colorectal adenocarcinoma is one the most frequent malignancies worldwide. The role of lncRNAs in colorectal adenocarcinoma is not well understood. To study the significance of lncRNAs in colorectal adenocarcinoma, we retrieved 189 approved lncRNAs from HGNC. The genes were imported into the cBioPortal database for transcriptomic analyses. We queried all the samples from TCGA provisional colorectal adenocarcinoma with RNA-seq v2 data in our study and considered RNA dysregulation with Z-score: ±2. The lncRNA which was altered in most of the patients were considered as “significant lncRNA” for further analyses. We considered the association of candidate lncRNAs with clinicopathologic parameters of samples including tumor disease anatomic site, neoplasm histologic types, tumor stage and survival. We also compute the specificity of the significant lncRNAs expression in colorectal adenocarcinoma comparing with other human cancers in cancer portal. Our analysis showed that lncRNAs SNHG6, PVT1 and ZFAS1 allocated the maximum alteration among the colorectal cases. The expression of SNHG6 and ZFAS1 was more in rectal adenocarcinoma than the colon carcinoma while the PVT1 showed the same expression levels in both tissues. However, we found that upregulation of PVT1 has been reduced the overall survival in patients. Altogether these data showed SNHG6, PVT1 and ZFAS1, are promising candidates for experimental research on colorectal adenocarcinoma to discover novel biomarker for this prevalent cancer.

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Acknowledgements

This study was accepted at Ahvaz Jundishapur University of Medical Sciences. The authors were attributed to the manuscript as follow; HA: data collection and manuscript preparation, AS: data collection and analysis, MTB: literature review, data collection and analysis, manuscript editing, MH: manuscript preparation and revision, YTB: statistical analysis and English editing, JMA: manuscript revision.

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Authors and Affiliations

  1. Department of Biotechnology, Ahvaz Branch, Islamic Azad University, Ahvaz, Iran

    Hossein Ansari

  2. Department of Molecular Genetics, Faculty of Biosciences, Tarbiat Modares University, Tehran, Iran

    Arman Shahrisa

  3. Department of Environmental Health Engineering, School of Public Health, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran

    Yaser Tahmasebi Birgani

  4. Environmental Technologies Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran

    Yaser Tahmasebi Birgani

  5. Department of Medical Genetics, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran

    Maryam Tahmasebi Birgani & Javad Mohammadi Asl

  6. Cellular and Molecular Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran

    Maryam Tahmasebi Birgani

  7. Department of Genetics, Faculty of Sciences, Shahid Chmaran University of Ahvaz, Ahvaz, Iran

    Mohammadreza Hajjari

  8. Noor Medical Genetics, Ahvaz, Khuzestan, Iran

    Javad Mohammadi Asl

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  1. Hossein Ansari
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Correspondence to Arman Shahrisa or Maryam Tahmasebi Birgani.

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It is an in silico analysis on recorded raw data on cancer bioportals.

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Ansari, H., Shahrisa, A., Birgani, Y.T. et al. Long Noncoding RNAs in Colorectal Adenocarcinoma; an in silico Analysis. Pathol. Oncol. Res. 25, 1387–1394 (2019). https://doi.org/10.1007/s12253-018-0428-2

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  • DOI: https://doi.org/10.1007/s12253-018-0428-2

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