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Chen J, Apizi A, Wang L, Wu G, Zhu Z, Yao H, Chen G, Shi X, Shi B, Tai Q, Shen C, Zhou G, Wu L, He S. TCGA database analysis of the tumor mutation burden and its clinical significance in colon cancer. J Gastrointest Oncol 2021; 12:2244-2259. [PMID: 34790389 DOI: 10.21037/jgo-21-661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/22/2021] [Indexed: 12/12/2022] Open
Abstract
Background Colon cancer is one of the most common malignant tumors, with high rates of incidence and death. The tumor mutational burden (TMB), which is characterized by microsatellite instability, has been becoming a powerful predictor which can show tumor behavior and response to immunotherapy. Methods In this study, we analyzed 437 mutation data of colon cancer samples obtained from The Cancer Genome Atlas (TCGA) and divided patients into low- and high-TMB groups according to the TMB value. Then we identified differentially-expressed genes (DEGs), conducted immune cell infiltration and survival analyses between groups. Results The higher TMB of the patients with colon cancer predicts a poorer prognosis. Functional analysis was performed to assess the prognostic value of the top 30 core genes. The CIBER-SORT algorithm was used to investigate the correlation between the immune cells and TMB subtypes. An immune prognosis model was constructed to screen out immune genes related to prognosis, and the tumor immunity assessment resource (TIMER) was then used to determine the correlation between gene expression and the abundance of tumor-infiltrating immune cell subsets in colon cancer. We observed that APC, TP53, TTN, KRAS, MUC16, SYNE1, PIK3CA have higher somatic mutations. DEGs enrichment analysis showed that they are involved in the regulation of neuroactive ligand-receptor interaction, the Cyclic adenosine monophosphate (cAMP) signaling pathway, the calcium signaling pathway, and pantothenate and Coenzyme A (CoA) biosynthesis. The difference in the abundance of various white blood cell subtypes showed that Cluster of Differentiation 8 (CD8) T cells (P=0.008), activated CD4 memory T cells (P=0.019), M1 macrophages (P=0.002), follicular helper T cells (P=0.034), activated Natural killer (NK cell) cells (P=0.017) increased remarkably, while M0 macrophages significantly reduced (P=0.025). The two immune model genes showed that secretin (SCT) was negatively correlated with survival, while Guanylate cyclase activator 2A (GUCA2A) was positively correlated. Conclusions This study conducted a systematically comprehensive analysis of the prediction and clinical significance of TMB in colon cancer in identification, monitoring, and prognosis of colon cancer, and providing reference information for immunotherapy.
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Affiliation(s)
- Junjie Chen
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Anwaier Apizi
- Department of Gastrointestinal Tumors, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Lin Wang
- Department of Gastrointestinal Tumors, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Guanting Wu
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zheng Zhu
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Huihui Yao
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Guoliang Chen
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xinyu Shi
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Bo Shi
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Qingliang Tai
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Chenglong Shen
- Department of Gastrointestinal Surgery, Changshu No. 2 Hospital, Changshu, China
| | - Guoqiang Zhou
- Department of Gastrointestinal Surgery, Changshu No. 2 Hospital, Changshu, China
| | - Lingzhi Wu
- Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Songbing He
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
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Zhao H, Su W, Sun Y, Wu Z. WBSCR22 Competes with Long Non-coding RNA Linc00346 for miR-509-5p Binding Site to Regulate Cancer Stem Cell Phenotypes of Colorectal Cancer. Biochem Genet 2020; 58:384-398. [PMID: 32008219 DOI: 10.1007/s10528-020-09949-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 01/23/2020] [Indexed: 12/18/2022]
Abstract
Various Long non-coding RNAs (lncRNAs) and MicroRNAs (miRNAs) have been demonstrated to be involved in colorectal cancer stem cells (CSCs). WBSCR22 is a key gene we previously found that functions in colorectal cancer (CRC). This paper aims to investigate the effects of WBSCR22 and its corresponding miRNA and lncRNA in CRC. The expression of WBSCR22 was detected by Western blot and qRT-PCR analysis. Tumor sphere formation assays, CCK-8 analysis, and Transwell assays were applied to examine the colorectal cancer stem cell properties. Luciferase assay and biotin RNA pulldown assay were used to detect the interaction between miR-509-5p and WBSCR22/Linc00346. WBSCR22 is highly expressed in CRC and correlates with poor prognosis. Knockdown of WBSCR22 decreased the sphere-forming capacities, cell proliferation, and invasion abilities. WBSCR22 was negatively regulated by miR-509-5p. Linc00346 promoted the expression of WBSCR22 by adsorbing miR-509-5p. The Linc00346/miR-509-5p/WBSCR22 signal axis regulated the characteristics of colon cancer stem cells. Linc00346 regulated the expression of WBSCR22 by binding to miR-509-5p, thereby monitoring the characteristics of colorectal cancer stem cells. Thus, WBSCR22, Linc00346, and miR-509-5p might be utilized as potential targets for clinical diagnosis and treatment of CRC.
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Affiliation(s)
- Haiyan Zhao
- Department of Oncology, the Affiliated Hospital of Inner Mongolia Medical University, Huimin District, North Street, Hohhot, 010050, Inner Mongolia, China.
| | - Wuyun Su
- Department of Oncology, the Affiliated Hospital of Inner Mongolia Medical University, Huimin District, North Street, Hohhot, 010050, Inner Mongolia, China
| | - Yushu Sun
- Department of Oncology, Inner Mongolia Autonomous Region Cancer Hospital, Hottot, 010020, China
| | - Zhongjun Wu
- Hepatobiliay Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 646000, Sichuan, China
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