Integrated analysis of RNA-sequencing data and clinical data for the molecular insights and applicability of immunotherapy in the Korean colorectal cancer patients |
Jinseon Yoo 1,*,# (Research worker), Jong Lyul Lee 2,# (Medical Doctor), Hyeran Shim 4,# (Graduate Student), Jong-Hwan Kim 1 (Research worker), Jongbum Jeon 1 (Research worker), Jisu Kim 1 (Research worker), Chan Wook Kim 2 (Medical Doctor), Seok-Byung Lim 2 (Medical Doctor), In Ja Park 2 (Medical Doctor), Yong Sik Yoon 2 (Medical Doctor), Hoang Bao Khanh Chu 4 (Graduate Student), Jisun Kang 4 (Graduate Student), Sheehyun Cho 4 (Graduate Student), Hong Seok Lee4 (Research Professor), Young-Joon Kim 4,5 (Professor) |
1Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea, 2Department of Surgery, Division of Colon and Rectal Surgery, University of Ulsan College of Medicine and Asan Medical Center, Seoul, Republic of Korea, 3Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea, 4Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea, 5LepiDyne Co., Ltd., Seoul 04779, Korea, 6Department of Functional Genomics, University of Science and Technology (UST), Daejeon 34113, Korea |
Abstract
Colorectal cancer (CRC) is a major health concern and understanding its molecular characteristics is crucial for improving its diagnosis and treatment. Here, we present a comprehensive analysis utilizing RNA-sequencing (RNA-seq) data and clinical information from Korean patients with CRC. Differential gene expression analysis identified significant changes in gene expression between tumor and normal tissues. Gene Set Enrichment Analysis (GSEA) revealed dysregulated pathways associated with tumor progression. Furthermore, using CMScaller, we successfully stratified CRC tissues into distinct molecular subtypes. Upon reviewing the public consensus molecular subtype (CMS) signature, it was confirmed that it shares similar biological characteristics with the existing CRC. Additionally, biological characteristics of the group that could not be classified using CMScaller were found to resemble those of CMS2. Finally, distinguishing characteristics were observed between the tumor and normal groups when analyzed from an immunological perspective. Patients with CRC were checked for immunotherapy responsiveness, and those who clinically responded to immunotherapy were identified. Survival analysis confirmed that certain microsatellite stable (MSS) samples were responsive to immunotherapy and showed a relatively better prognosis. Furthermore, analysis of various immune cell types to identify genes involved in the response to immunotherapy revealed that RORC, NOS2, and KLRK1 are potential candidate genes. Our findings provide valuable insights into the molecular landscape of CRC in the Korean population and underscore the potential for integrating RNA-seq data with clinical information to improve cancer research and patient care. Immunotherapy was found to be effective in Korean patients with CRC.
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Abstract, Accepted Manuscript [Submitted on November 18, 2024, Accepted on March 8, 2025] |
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