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Yang J, Zhao Y, Yuan R, Wang Y, Wang S, Chang Z, Zhao W. Identifying individualized prognostic signature and unraveling the molecular mechanism of recurrence in early-onset colorectal cancer. Eur J Med Res 2023; 28:533. [PMID: 37986009 PMCID: PMC10658991 DOI: 10.1186/s40001-023-01491-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 10/31/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND The incidence and mortality of early-onset colorectal cancer (EOCRC; < 50 years old) is increasing worldwide, with a high recurrence rate. The inherent heterogeneity of EOCRC makes its treatment challenging. Hence, to further understand the biology and reveal the molecular mechanisms of EOCRC, a recurrence risk signature is needed to guide clinical management. METHODS Based on the relative expression orderings (REOs) of genes in each sample, a prognostic signature was developed and validated utilizing multiple independent datasets. The underlying molecular mechanisms between distinct prognostic groups were explored via integrative analysis of multi-omics data. RESULTS The prognostic signature consisting of 6 gene pairs (6-GPS) could predict the recurrence risk for EOCRC at the individual level. High-risk EOCRC classified by 6-GPS showed a poor prognosis but a good response to adjuvant chemotherapy. Moreover, high-risk EOCRC was characterized by epithelial-mesenchymal transition (EMT) and enriched angiogenesis, and had higher mutation burden, immune cell infiltration, and PD-1/PD-L1 expression. Furthermore, we identified four genes associated with relapse-free survival in EOCRC, including SERPINE1, PECAM1, CDH1, and ANXA1. They were consistently differentially expressed at the transcriptome and proteome levels between high-risk and low-risk EOCRCs. They were also involved in regulating cancer progression and immune microenvironment in EOCRC. Notably, the expression of SERPINE1 and ANXA1 positively correlated with M2-like macrophage infiltration. CONCLUSION Our results indicate that 6-GPS can robustly predict the recurrence risk of EOCRC, and that SERPINE1, PECAM1, CDH1, and ANXA1 may serve as potential therapeutic targets. This study provides valuable information for the precision treatment of EOCRC.
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Affiliation(s)
- Jia Yang
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Yuting Zhao
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Rongqiang Yuan
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Yongtong Wang
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Shiyi Wang
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Zhiqiang Chang
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China.
| | - Wenyuan Zhao
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China.
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Dias Carvalho P, Martins F, Mendonça S, Ribeiro A, Machado AL, Carvalho J, Oliveira MJ, Velho S. Mutant KRAS modulates colorectal cancer cells invasive response to fibroblast‐secreted factors through the HGF/C‐MET axis. Int J Cancer 2022; 151:1810-1823. [DOI: 10.1002/ijc.34225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 07/07/2022] [Accepted: 07/19/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Patrícia Dias Carvalho
- i3S ‐ Instituto de Investigação e Inovação em Saúde, Universidade do Porto Portugal
- IPATIMUP – Instituto de Patologia e Imunologia Molecular da Universidade do Porto Porto Portugal
- ICBAS ‐ Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto Porto Portugal
| | - Flávia Martins
- i3S ‐ Instituto de Investigação e Inovação em Saúde, Universidade do Porto Portugal
- IPATIMUP – Instituto de Patologia e Imunologia Molecular da Universidade do Porto Porto Portugal
- Department of Pathology FMUP – Faculty of Medicine of the University of Porto Porto Portugal
| | - Susana Mendonça
- i3S ‐ Instituto de Investigação e Inovação em Saúde, Universidade do Porto Portugal
- IPATIMUP – Instituto de Patologia e Imunologia Molecular da Universidade do Porto Porto Portugal
- Department of Pathology FMUP – Faculty of Medicine of the University of Porto Porto Portugal
| | - Andreia Ribeiro
- i3S ‐ Instituto de Investigação e Inovação em Saúde, Universidade do Porto Portugal
- IPATIMUP – Instituto de Patologia e Imunologia Molecular da Universidade do Porto Porto Portugal
| | - Ana Luísa Machado
- i3S ‐ Instituto de Investigação e Inovação em Saúde, Universidade do Porto Portugal
- IPATIMUP – Instituto de Patologia e Imunologia Molecular da Universidade do Porto Porto Portugal
- Department of Pathology FMUP – Faculty of Medicine of the University of Porto Porto Portugal
- Ciências Químicas e das Biomoléculas, Centro de Investigação em Saúde e Ambiente, Escola Superior de Saúde do Porto, Instituto Politécnico do Porto Porto Portugal
| | - Joana Carvalho
- i3S ‐ Instituto de Investigação e Inovação em Saúde, Universidade do Porto Portugal
- IPATIMUP – Instituto de Patologia e Imunologia Molecular da Universidade do Porto Porto Portugal
| | - Maria José Oliveira
- i3S ‐ Instituto de Investigação e Inovação em Saúde, Universidade do Porto Portugal
- INEB – Institute of Biomedical Engineering, University of Porto Porto Portugal
| | - Sérgia Velho
- i3S ‐ Instituto de Investigação e Inovação em Saúde, Universidade do Porto Portugal
- IPATIMUP – Instituto de Patologia e Imunologia Molecular da Universidade do Porto Porto Portugal
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Song K, Liu C, Zhang J, Yao Y, Xiao H, Yuan R, Li K, Yang J, Zhao W, Zhang Y. Integrated multi-omics analysis reveals miR-20a as a regulator for metabolic colorectal cancer. Heliyon 2022; 8:e09068. [PMID: 35284668 PMCID: PMC8914124 DOI: 10.1016/j.heliyon.2022.e09068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/21/2021] [Accepted: 03/03/2022] [Indexed: 11/28/2022] Open
Abstract
Single-driver molecular events specific to the metabolic colorectal cancer (CRC) have not been clearly elucidated. Herein, we identified 12 functional miRNAs linked to activated metabolism by integrating multi-omics features in metabolic CRC. These miRNAs exhibited significantly enriched CRC driver miRNAs, significant impacts on CRC cell growth and significantly correlated metabolites. Importantly, miR-20a is minimally expressed in normal colorectal tissues but highly expressed in metabolic CRC, suggesting the potential therapeutic target. Bioinformatics analyses further revealed miR-20a as the most powerful determinant that regulates a cascade of dysregulated events, including Wnt signaling pathway, core enzymes involved in FA metabolism program and triacylglycerol abundances. In vitro assays demonstrated that elevated miR-20a up-regulated FA synthesis enzymes via Wnt/β-catenin signaling, and finally promoted proliferative and migration of metabolic CRC cells. Overall, our study revealed that miR-20a promoted progression of metabolic CRC by regulating FA metabolism and served as a potential target for preventing tumor metastasis.
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Affiliation(s)
- Kai Song
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, Guangdong, 519000, China
| | - Chao Liu
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, 150086, China
| | - Jiashuai Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Yang Yao
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, 150086, China
| | - Huiting Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Rongqiang Yuan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Keru Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Jia Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Wenyuan Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
- Corresponding author.
| | - Yanqiao Zhang
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, 150086, China
- Corresponding author.
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Song K, Cai H, Zheng H, Yang J, Jin L, Xiao H, Zhang J, Zhao Z, Li X, Zhao W, Li X. Multilevel prioritization of gene regulators associated with consensus molecular subtypes of colorectal cancer. Brief Bioinform 2021; 22:6225088. [PMID: 33855351 DOI: 10.1093/bib/bbab077] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 12/31/2022] Open
Abstract
Consensus molecular subtypes (CMSs) are emerging as critical factor for prognosis and treatment of colorectal cancer. Gene regulators, including chromatin regulator, RNA-binding protein and transcriptional factor, are critical modulators of cancer hallmark, yet little is known regarding the underlying functional mechanism in CMSs. Herein, we identified a core set of 235 functional gene regulators (FGRs) by integrating genome, epigenome, transcriptome and interactome of CMSs. FGRs exhibited significant multi-omics alterations and impacts on cell lines growth, as well as significantly enriched cancer driver genes and pathways. Moreover, common FGRs played different roles in the context of CMSs. In accordance with the immune characteristics of CMSs, we found that the anti-tumor immune pathways were mainly activated by FGRs (e.g. STAT1 and CREBBP) in CMS1, while inhibited by FGRs in CMS2-4. FGRs mediated aberrant expression of ligands, which bind to receptor on immune cells, and modulated tumor immune microenvironment of subtypes. Intriguingly, systematic exploration of datasets using genomic and transcriptome co-similarity reveals the coordinated manner in FGRs act in CMSs to orchestrate their pathways and patients' prognosis. Expression signatures of the FGRs revealed an optimized CMS classifier, which demonstrated 88% concordance with the gold-standard classifier, but avoiding the influence of sample composition. Overall, our integrative analysis identified FGRs to regulate core tumorigenic processes/pathways across CMSs.
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Affiliation(s)
- Kai Song
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Hao Cai
- Medical Big Data and Bioinformatics Research Center, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Hailong Zheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Jing Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Liangliang Jin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Huiting Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Jiashuai Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Zhangxiang Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | | | | | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
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Qiu C, Xie S, Cheng N, Lin Q, Shen G, Xiang Z, Huang T, Zhang X, Duan J, Wei L, Zheng Z. Case Report: Cetuximab in Combination With Chemotherapy for the Treatment of Multifocal Hepatic Metastases From Colorectal Cancer Guided by Genetic Tests. Front Oncol 2021; 11:612171. [PMID: 33889542 PMCID: PMC8056263 DOI: 10.3389/fonc.2021.612171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/16/2021] [Indexed: 12/22/2022] Open
Abstract
Hepatic metastases were reported in up to 70% of colorectal cancer patients, among which multifocal hepatic metastasis represents one of the complications that lead to poor prognosis. The majority of the patients carrying multifocal hepatic metastases required pharmaceutical treatments to reduce the tumor size prior to surgical resection. However, the clinical responses to pharmaceutical agents were difficult to predict due to the heterogeneous nature of the multifocal tumors. Here, we report a case with multifocal hepatic metastases from colorectal cancer that was resistant to the primary chemotherapy and Bevacizumab plus chemotherapy, but responded to the combined therapy of Cetuximab and FOLFOX. Genetic tests had revealed that the tumor was highly metastatic due to the mutations of the WNT signaling pathway, and the metastatic tumors might be sensitive to Cetuximab. Consistent with the molecular characterizations, the metastatic tumors continue to emerge after chemotherapy, and rapidly relapsed in great numbers after liver resection. However, the combined therapy of Cetuximab and FOLFOX guided by the genetic tests significantly reduced the size and number of metastatic tumors. To conclude, deciphering the mutation profiles of multifocal metastatic tumors may guide the determination of treatment tactics, which may benefit the patients with non-resectable advanced carcinoma.
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Affiliation(s)
- Chunhui Qiu
- Department of Hepatic Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Sidong Xie
- Department of Radiology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Na Cheng
- Department of Pathology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Qu Lin
- Department of Medical Oncology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Guanzhu Shen
- Department of Radiation Oncology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zhanwang Xiang
- Department of Intenational Radiology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Tanxiao Huang
- Department of Oncology, HaploX Biotechnology, Shenzhen, China
| | - Xiaoni Zhang
- Department of Oncology, HaploX Biotechnology, Shenzhen, China
| | - Jingxian Duan
- Department of Oncology, HaploX Biotechnology, Shenzhen, China
| | - Li Wei
- Department of Medical Oncology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zongheng Zheng
- Department of Gastrointestinal Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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