Title: Development of a RNA-Seq based prognostic signature for colon cancer

Authors: Bjarne Bartlett; Yong Zhu; Mark Menor; Vedbar S. Khadka; Jicai Zhang; Jie Zheng; Bin Jiang; Youping Deng

Addresses: Bioinformatics Core, Department of Complementary and Integrative Medicine, University of Hawaii, 651 Ilalo Street, Honolulu, Hawaii, 96813, USA; Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI, 96822, USA ' National Medical Centre of Colorectal Disease, The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210022, China ' Bioinformatics Core, Department of Complementary and Integrative Medicine, University of Hawaii, 651 Ilalo Street, Honolulu, Hawaii, 96813, USA ' Bioinformatics Core, Department of Complementary and Integrative Medicine, University of Hawaii, 651 Ilalo Street, Honolulu, Hawaii, 96813, USA ' Department of Laboratory Medicine, Shiyan Taihe Hospital, College of Biomedical Engineering, Hubei University of Medicine, Shiyan, Hubei, 442000, China ' Department of Pathology, Jinmen First Hospital, Jinmen, Hubei, 448000, China ' National Medical Centre of Colorectal Disease, The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210022, China ' Bioinformatics Core, Department of Complementary and Integrative Medicine, University of Hawaii, 651 Ilalo Street, Honolulu, Hawaii, 96813, USA; Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI, 96822, USA

Abstract: RNA-Seq data has recently been used to successfully develop prognostic signatures to predict cancer patients who will have a worse prognosis. We designed a study to ascertain whether a prognostic model, based on RNA-Seq data, would have clinical utility for predicting survival in patients with colon adenocarcinomas (COAD). Of particular interest are early stage COAD patients, for whom the benefits of adjuvant therapy are unclear. High-risk patients predicted by our 5-gene, RNA-Seq signature had significantly shorter survival in both the training (p = 0.00) and test (p = 0.003) cohorts. Here we present an RNA-Seq prognostic signature that can identify high-risk COAD patients with shorter survival. This signature would have clinical utility as part of an RNA-Seq screening program, particularly for identifying early stage COAD patients who could be recommended adjuvant therapy after resection based on the results of this prognostic signature.

Keywords: lncRNA; colon cancer; RNA-Seq; cancer prognosis; cancer diagnosis.

DOI: 10.1504/IJCBDD.2020.113872

International Journal of Computational Biology and Drug Design, 2020 Vol.13 No.5/6, pp.488 - 503

Received: 21 Feb 2020
Accepted: 23 Sep 2020
Published online: 31 Mar 2021 *

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