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Li R, Liu X, Huang X, Zhang D, Chen Z, Zhang J, Bai R, Zhang S, Zhao H, Xu Z, Zeng L, Zhuang L, Wen S, Wu S, Li M, Zuo Z, Lin J, Lin D, Zheng J. Single-cell transcriptomic analysis deciphers heterogenous cancer stem-like cells in colorectal cancer and their organ-specific metastasis. Gut 2024; 73:470-484. [PMID: 38050068 PMCID: PMC10894846 DOI: 10.1136/gutjnl-2023-330243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 11/13/2023] [Indexed: 12/06/2023]
Abstract
OBJECTIVE Metastasis is the major cause of cancer death. However, what types of heterogenous cancer cells in primary tumour and how they metastasise to the target organs remain largely undiscovered. DESIGN We performed single-cell RNA sequencing and spatial transcriptomic analysis in primary colorectal cancer (CRC) and metastases in the liver (lCRC) or ovary (oCRC). We also conducted immunofluorescence staining and functional experiments to examine the mechanism. RESULTS Integrative analyses of epithelial cells reveal a stem-like cell cluster with high protein tyrosine phosphatase receptor type O (PTPRO) and achaete scute-like 2 (ASCL2) expression as the metastatic culprit. This cell cluster comprising distinct subpopulations shows distinct liver or ovary metastatic preference. Population 1 (P1) cells with high delta-like ligand 4 (DLL4) and MAF bZIP transcription factor A (MAFA) expression are enriched in primary CRC and oCRC, thus may be associated with ovarian metastasis. P3 cells having a similar expression pattern as cholangiocytes are found mainly in primary CRC and lCRC, presuming to be likely the culprits that specifically metastasise to the liver. Stem-like cells interacted with cancer-associated fibroblasts and endothelial cells via the DLL4-NOTCH signalling pathway to metastasise from primary CRC to the ovary. In the oCRC microenvironment, myofibroblasts provide cancer cells with glutamine and perform a metabolic reprogramming, which may be essential for cancer cells to localise and develop in the ovary. CONCLUSION We uncover a mechanism for organ-specific CRC metastasis.
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Affiliation(s)
- Rui Li
- State Key Laboratory of Oncology in South China and Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xuefei Liu
- State Key Laboratory of Oncology in South China and Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, China
- Shenzhen Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen, China
| | - Xudong Huang
- State Key Laboratory of Oncology in South China and Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Di Zhang
- Department of General Surgery (Colorectal Surgery), Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ziming Chen
- State Key Laboratory of Oncology in South China and Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jialiang Zhang
- State Key Laboratory of Oncology in South China and Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ruihong Bai
- State Key Laboratory of Oncology in South China and Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Shaoping Zhang
- State Key Laboratory of Oncology in South China and Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Hongzhe Zhao
- State Key Laboratory of Oncology in South China and Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zilan Xu
- State Key Laboratory of Oncology in South China and Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Lingxing Zeng
- State Key Laboratory of Oncology in South China and Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Lisha Zhuang
- State Key Laboratory of Oncology in South China and Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Shujuan Wen
- State Key Laboratory of Oncology in South China and Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Shaojia Wu
- State Key Laboratory of Oncology in South China and Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Mei Li
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zhixiang Zuo
- State Key Laboratory of Oncology in South China and Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Junzhong Lin
- Department of Colorectal Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Dongxin Lin
- State Key Laboratory of Oncology in South China and Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Jian Zheng
- State Key Laboratory of Oncology in South China and Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
- Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
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Zhang D, Ni QQ, Liang QY, He LL, Qiu BW, Zhang LJ, Mou TY, Le CC, Huang Y, Li TT, Wang SY, Ding YQ, Jiao HL, Ye YP. ASCL2 induces an immune excluded microenvironment by activating cancer-associated fibroblasts in microsatellite stable colorectal cancer. Oncogene 2023; 42:2841-2853. [PMID: 37591954 PMCID: PMC10504082 DOI: 10.1038/s41388-023-02806-3] [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: 11/17/2022] [Revised: 07/28/2023] [Accepted: 08/03/2023] [Indexed: 08/19/2023]
Abstract
Proficient mismatch repair or microsatellite stable (pMMR/MSS) colorectal cancers (CRCs) are vastly outnumbered by deficient mismatch repair or microsatellite instability-high (dMMR/MSI-H) tumors and lack a response to immune checkpoint inhibitors (ICIs). In this study, we reported two distinct expression patterns of ASCL2 in pMMR/MSS and dMMR/MSI-H CRCs. ASCL2 is overexpressed in pMMR/MSS CRCs and maintains a stemness phenotype, accompanied by a lower density of tumor-infiltrating lymphocytes (TILs) than those in dMMR/MSI CRCs. In addition, coadministration of anti-PD-L1 antibodies facilitated T cell infiltration and provoked strong antitumor immunity and tumor regression in the MC38/shASCL2 mouse CRC model. Furthermore, overexpression of ASCL2 was associated with increased TGFB levels, which stimulate local Cancer-associated fibroblasts (CAFs) activation, inducing an immune-excluded microenvironment. Consistently, mice with deletion of Ascl2 specifically in the intestine (Villin-Cre+, Ascl2 flox/flox, named Ascl2 CKO) revealed fewer activated CAFs and higher proportions of infiltrating CD8+ T cells; We further intercrossed Ascl2 CKO with ApcMin/+ model suggesting that Ascl2-deficient expression in intestinal represented an immune infiltrating environment associated with a good prognosis. Together, our findings indicated ASCL2 induces an immune excluded microenvironment by activating CAFs through transcriptionally activating TGFB, and targeting ASCL2 combined with ICIs could present a therapeutic opportunity for MSS CRCs.
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Affiliation(s)
- Dan Zhang
- Department of Pathology, School of Basic Medical Sciences and Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Qi-Qi Ni
- Department of Pathology, School of Basic Medical Sciences and Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Qiao-Yan Liang
- Department of Pathology, School of Basic Medical Sciences and Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Li-Ling He
- Department of Pathology, School of Basic Medical Sciences and Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Bo-Wen Qiu
- Department of Pathology, School of Basic Medical Sciences and Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Ling-Jie Zhang
- Department of Pathology, School of Basic Medical Sciences and Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Ting-Yu Mou
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Chen-Chen Le
- Department of Pathology, School of Basic Medical Sciences and Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Yuan Huang
- Department of Pathology, School of Basic Medical Sciences and Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Ting-Ting Li
- Department of Pathology, School of Basic Medical Sciences and Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Shu-Yang Wang
- Department of Pathology, School of Basic Medical Sciences and Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Yan-Qing Ding
- Department of Pathology, School of Basic Medical Sciences and Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China.
| | - Hong-Li Jiao
- Department of Pathology, School of Basic Medical Sciences and Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China.
| | - Ya-Ping Ye
- Department of Pathology, School of Basic Medical Sciences and Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China.
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Zheng J, Huang J, Xia J, Zhou W, Dai L, Lin S, Gao L, Zou C. Transcription factor E2F8 is a therapeutic target in the basal-like subtype of breast cancer. Front Oncol 2023; 13:1038787. [PMID: 36814821 PMCID: PMC9939474 DOI: 10.3389/fonc.2023.1038787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/17/2023] [Indexed: 02/09/2023] Open
Abstract
Introduction Tumorigenesis in breast cancers usually accompanied by the dysregulation of transcription factors (TFs). Abnormal amplification of TFs leads aberrant expression of its downstream target genes. However, breast cancers are heterogeneous disease with different subtypes that have distinguished clinical behaviours, and the identification of prognostic TFs may enable to provide diagnosis and treatment of breast cancer based on subtypes, especially in Basal-like breast cancer. Methods The RNA-sequencing was performed to screen differential TFs in breast cancer subtypes. The GEPIA dataset analysis was used to analyze the genes expression in invasive breast carcinoma. The expression of MYBL2, HOXC13, and E2F8 was verified by qRT-PCR assay in breast cancers. The depiction analysis of co-expressed proteins was revealed using the STRING datasets. The cellular infiltration level analysis by the TISIDB and TIMER databases. The transwell assay was performed to analyze cellular migration and invasion. CCK-8 assay was used to evaluate cellular drug susceptibility for docetaxel treatment. Predicted targeted drugs in breast cancers by GSCA Lite database online. Results Kaplan-Meier plotter suggested that high expression of both E2F8 and MYBL2 in Basal-like subtype had a poor relapse-free survival. Functional enrichment results identified that apoptosis, cell cycle, and hormone ER pathway were represented the crucial regulation pathways by both E2F8 and MYBL2. In the meantime, database analysis indicated that high expression of E2F8 responded to chemotherapy, while those patients of high expression of MYBL2 responded to endocrinotherapy, and a positive correlation between the expression of E2F8 and PD-L1/CTLA4. Our cell line experiments confirmed the importance of E2F8 and MYBL2 in proliferation and chemotherapy sensitivity, possibly, the relationship with PD-L1. Additionally, we also observed that the up-regulation of E2F8 was accompanied with higher enrichments of CD4+ T cells and CD8+ T cells in breast cancers. Conclusion Taken together, our findings elucidated a prospective target in Basal-like breast cancer, providing underlying molecular biomarkers for the development of breast cancer treatment.
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Affiliation(s)
- Jing Zheng
- Department of Ultrasound, The Second Clinical Medical College, Jinan University (Shenzhen People’s Hospital), The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Jingyi Huang
- Department of Clinical Medical Research Center, The First Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Jinquan Xia
- Department of Clinical Medical Research Center, The Second Clinical Medical College, Jinan University (Shenzhen People’s Hospital), The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Wenbin Zhou
- Department of Thyroid and Breast Surgery, Department of General Surgery, The Second Clinical Medical College, Jinan University (Shenzhen People’s Hospital), The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Lingyun Dai
- Department of Clinical Medical Research Center, The Second Clinical Medical College, Jinan University (Shenzhen People’s Hospital), The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Sihang Lin
- Department of Thyroid and Breast Surgery, Department of General Surgery, The Second Clinical Medical College, Jinan University (Shenzhen People’s Hospital), The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Lin Gao
- Department of Clinical Medical Research Center, The Second Clinical Medical College, Jinan University (Shenzhen People’s Hospital), The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, China,*Correspondence: Lin Gao, ; Chang Zou,
| | - Chang Zou
- Department of Clinical Medical Research Center, The Second Clinical Medical College, Jinan University (Shenzhen People’s Hospital), The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, China,Shenzhen Public Service Platform on Tumor Precision Medicine and Molecular Diagnosis, Shenzhen, Guangdong, China,School of Life and Health Sciences, The Chinese University of Kong Hong, Shenzhen, Guangdong, China,*Correspondence: Lin Gao, ; Chang Zou,
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Zheng E, Cai Z, Li W, Ni C, Fang Q. Achaete-scute complex-like 2 regulated inflammatory mechanism through Toll-like receptor 4 activating in stomach adenocarcinoma. World J Surg Oncol 2022; 20:266. [PMID: 36008864 PMCID: PMC9404661 DOI: 10.1186/s12957-022-02722-y] [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: 01/25/2022] [Accepted: 08/02/2022] [Indexed: 11/18/2022] Open
Abstract
Background To investigate the role of achaete-scute complex-like 2 (ASCL2) in stomach adenocarcinoma (STAD), we analyze whether ASCL2 suppression could retard cancer development and further observe the relevance between ASCL2 and inflammation via Toll-like receptor 4 (TLR4) activation in STAD, both in vitro and in vivo. Methods Proliferation, development, inflammation, and apoptosis in STAD are observed using sh-ASCL2 lentivirus via TLR4 activation in vitro and in vivo. The relationship between ASCL2 and inflammation is analyzed. Western blotting of ASCL2 with the target protein of immune-associated cells is performed. The prognosis of STAD and associated ASCL2 mutation are analyzed. Results The ASCL2 level in STAD tumor tissues is increased, compared to normal tissues, and brings a worse prognosis. The ASCL2 shows a negative correlation with inflammation, and TLR4 reveals a positive correlation with gastric cancer. ASCL2 expression is high in MGC803 cells. Sh-ASCL2 could reduce STAD development by decreasing proliferation, tumor volume, and biomarker levels and increasing apoptosis in vitro and in vivo. The inflammatory role of ASCL2 is regulated through TLR4 activation. ASCL2 levels may be related to CNTNAP3, CLIP1, C9orf84, ARIH2, and IL1R2 mutations; positively correlated with M2 macrophage and T follicular helper cell levels; negatively correlated with neutrophil, dendritic cell, monocyte, CD8 T cell, and M1 macrophage levels; and involved in STAD prognosis. Conclusions The ASCL2 may adjust inflammation in STAD through TLR4 activation and may be associated with related immune cells. ASCL2 is possibly an upstream target factor of the TLR4 signaling pathway.
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Affiliation(s)
- Enqi Zheng
- Department of General Surgery, The First People's Hospital of Wenling, No.333 south Chuan-an road, Chengxi street, Wenling, 317500, Zhejinag Province, People's Republic of China
| | - Zhun Cai
- Department of General Surgery, The First People's Hospital of Wenling, No.333 south Chuan-an road, Chengxi street, Wenling, 317500, Zhejinag Province, People's Republic of China
| | - Wangyong Li
- Department of General Surgery, The First People's Hospital of Wenling, No.333 south Chuan-an road, Chengxi street, Wenling, 317500, Zhejinag Province, People's Republic of China
| | - Chuandou Ni
- Department of General Surgery, The First People's Hospital of Wenling, No.333 south Chuan-an road, Chengxi street, Wenling, 317500, Zhejinag Province, People's Republic of China
| | - Qian Fang
- Department of General Surgery, The First People's Hospital of Wenling, No.333 south Chuan-an road, Chengxi street, Wenling, 317500, Zhejinag Province, People's Republic of China.
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Wu L, Sun S, Qu F, Liu X, Sun M, Pan Y, Zheng Y, Su G. ASCL2 Affects the Efficacy of Immunotherapy in Colon Adenocarcinoma Based on Single-Cell RNA Sequencing Analysis. Front Immunol 2022; 13:829640. [PMID: 35774798 PMCID: PMC9237783 DOI: 10.3389/fimmu.2022.829640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
Colon adenocarcinoma (COAD) is one of the leading causes of cancer-associated deaths worldwide. Patients with microsatellite instability-high (MSI-H) tumors were shown to highly benefit from immune checkpoint inhibitors (ICIs) than patients with microsatellite stable (MSS) tumors. Furthermore, the infiltration of immune cells and the expression of cancer stem cells (CSCs) in COAD were associated with the anti-tumor immune response. However, the potential mechanisms showing the relationship between microsatellite instability and CSCs or tumor-infiltrating immune cells (TIICs) have not been elucidated. Accumulating evidence reveals that achaete-scute family bHLH transcription factor 2 (ASCL2) plays a crucial role in the initiation and progression of COAD and drug resistance. However, the specific biological functions of ASCL2 in COAD remain unknown. In this study, we performed weighted gene co-expression network analysis (WGCNA) between MSS and MSI-H subsets of COAD. The results revealed that ASCL2 was a potential key candidate in COAD. Subsequently, the single-cell RNA-seq revealed that ASCL2 was positively associated with CSCs. Further, ASCL2 was shown to indirectly affect tumor immune cell infiltration by negatively regulating the expression of DUSP4. Finally, we inferred that the immunotherapy-sensitive role of ASCL2/DUSP4 axis on COAD is partly attributed to the activation of WNT/β-catenin pathway. In conclusion, this study revealed that ASCL2 was positively correlated to CSCs and tumor immune infiltration in COAD. Therefore, ASCL2 is a promising predictor of clinical responsiveness to anti-PD-1/PD-L1 therapy in COAD.
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Affiliation(s)
- Lei Wu
- Research Center of Translational Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Research Center of Translational Medicine, Jinan Central Hospital, Shandong University, Jinan, China
- Department of Oncology, Central Hospital Affiliated to Shandong First Medical University, Zhuhai, China
| | - Shengnan Sun
- Research Center of Translational Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Research Center of Translational Medicine, Jinan Central Hospital, Shandong University, Jinan, China
| | - Fei Qu
- Department of Pathology, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Xiuxiu Liu
- Research Center of Translational Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Research Center of Translational Medicine, Jinan Central Hospital, Shandong University, Jinan, China
| | - Meili Sun
- Department of Oncology, Central Hospital Affiliated to Shandong First Medical University, Zhuhai, China
| | - Ying Pan
- Department of Oncology, Zhuhai People’s Hospital (Zhuhai Hospital Affiliated With Jinan University), Zhuhai, China
| | - Yan Zheng
- Research Center of Translational Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- *Correspondence: Yan Zheng, ; Guohai Su,
| | - Guohai Su
- Research Center of Translational Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Research Center of Translational Medicine, Jinan Central Hospital, Shandong University, Jinan, China
- *Correspondence: Yan Zheng, ; Guohai Su,
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Li YR, Meng K, Yang G, Liu BH, Li CQ, Zhang JY, Zhang XM. Diagnostic genes and immune infiltration analysis of colorectal cancer determined by LASSO and SVM machine learning methods: a bioinformatics analysis. J Gastrointest Oncol 2022; 13:1188-1203. [PMID: 35837194 PMCID: PMC9274036 DOI: 10.21037/jgo-22-536] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 06/16/2022] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND Genetic factors account for approximately 35% of colorectal cancer risk. The specificity and sensitivity of previous diagnostic biomarkers for colorectal cancer could not meet the need of clinical application. The expanding scale and inherent complexity of biological data have encouraged a growing use of machine learning to build informative and predictive models of the underlying biological processes. The aim of this study is to identify diagnostic genes of colorectal cancer by using machine learning methods. METHODS The GSE41328 and GSE106582 data sets were downloaded from the Gene Expression Omnibus (GEO) database. The gene expression differences between colon cancer and normal tissues were analyzed. The key colorectal cancer genes were screened and validated by Least Absolute Shrinkage and Selection Operator (LASSO) and Support Vector Machine (SVM) regression. Immune cell infiltration and the correlation with the key genes in patients with colon cancer were further analyzed by CIBERSORT. RESULTS Eleven key genes were identified as biomarkers for colon cancer, namely ASCL2, BEST4, CFD, DPEPCFD, FOXQ1, TRIB3, KLF4, MMP7, MMP11, PYY, and PDK4. The mean area under the receiver operating characteristic (ROC) curve (AUC) of all 11 genes for colon cancer diagnosis were 0.94 with a range of 0.91-0.97. In the validation set, the expression of the 11 key genes was significantly different between colon cancer and normal subjects (P<0.05) and the mean AUCs were 0.82 with a range of 0.70-0.88. Immune cell infiltration analyses demonstrated that the relative quantity of plasma cells, T cells, B cells, NK cells, MO, M1, Dendritic cells resting, Mast cells resting, Mast cells activated, and Neutrophils in the tumor group were significantly different to the normal group. CONCLUSIONS ASCL2, BEST4, CFD, DPEPCFD, FOXQ1, TRIB3, KLF4, MMP7, MMP11, PYY, and PDK4 were identified as the key genes for colon cancer diagnosis. These genes are expected to become novel diagnostic markers and targets of new pharmacotherapies for colorectal cancer.
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Affiliation(s)
- Yan-Rong Li
- Department of Gastroenterology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Ke Meng
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Guang Yang
- Department of Laboratory, The Red Cross (SEN GONG GENERAL) Hospital of Heilongjiang, Heilongjiang, China
| | - Bao-Hai Liu
- Department of Gastroenterology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Chu-Qiao Li
- Department of Gastroenterology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Jia-Yuan Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Xiao-Mei Zhang
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
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Zhang W, Kong L, Zhu H, Sun D, Han Q, Yan B, Cui Z, Zhang W, Zhang S, Kang X, Dai G, Qian N, Yan W. Retinoic Acid-Induced 2 (RAI2) Is a Novel Antagonist of Wnt/β-Catenin Signaling Pathway and Potential Biomarker of Chemosensitivity in Colorectal Cancer. Front Oncol 2022; 12:805290. [PMID: 35299743 PMCID: PMC8922473 DOI: 10.3389/fonc.2022.805290] [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: 10/30/2021] [Accepted: 02/04/2022] [Indexed: 11/24/2022] Open
Abstract
Objective Aberrant activation of Wnt/β-catenin signaling contributes to the maintenance of cancer stem cells and chemoresistance in colorectal cancer (CRC). Retinoic acid-induced 2 (RAI2) was proved to be a tumor suppressor in CRC in our previous report. In this study, the role of RAI2 in Wnt/β-catenin signaling was further investigated. Methods As a transcriptional co-regulator, C-terminal Binding Protein 2 (CtBP2) was reported to be involved in Wnt signaling in multiple and complex ways. The correlation of RAI2 and CtBP2 in CRC was analyzed by TCGA dataset, and the interaction between RAI2 and CtBP2 was explored by co-immunoprecipitation (Co-IP) in CRC cells. The effect of RAI2 on the activity of Wnt signaling and the location of β-catenin was detected by Dual-Luciferase reporter assay and Immunofluorescence respectively. Western blotting analysis was performed to detect the expression of target genes involved in Wnt signaling. Sphere formation assay was employed to detect the effect of RAI2 on stem cell like properties. Cell viability assay was used to detect the chemosensitivity of cells before and after transfection of RAI2. Results The interaction between RAI2 and CtBP2 was confirmed by Co-IP in CRC cells. Besides, the negative correlation of RAI2 and CtBP2 in CRC was found by analyzing the TCGA dataset. Re-expression of RAI2 in human colon cancer cells (HCT116 and LoVo) suppressed the fluorescent activity of Wnt signaling, increased the phosphorylation and inhibited nuclear translocation of β-catenin, with down-regulation of target genes like c-Myc, CyclinD1, ASCL2, and LGR5. In contrast, the mutated RAI2, which can’t interact with CtBP2, has no above effects. We observed low expression of RAI2 in 33.89% (101/298) of CRC patients, which was significantly associated with reduced phosphorylation of β-catenin (r=0.8866, P<0.0001), poor 5-year relapse-free survival (RFS) (P = 0.0029) and overall survival (OS) (P = 0.0102). Restoration of RAI2 in HCT116 and LoVo cells inhibited stem cell-like properties of CRC cells and increased chemosensitivity of these cells to oxaliplatin and fluorouracil. Conclusion Low expression of RAI2 can serve as an independent poor prognostic marker. RAI2 inhibits Wnt signaling by interacting with or down-regulating CtBP2, resulting in repression of stem cell-like properties and increased chemosensitivity of CRC cells.
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Affiliation(s)
- Weitao Zhang
- Department of Oncology, The First Medical Center, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China.,Cancer Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Lu Kong
- Department of Oncology, The First Medical Center, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China.,Medical Department, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Hongbin Zhu
- Department of Gastroenterology and Hepatology, Chinese People's Liberation Army (PLA) NO.983 Hospital, Tianjin, China
| | - Decong Sun
- Department of Oncology, The First Medical Center, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Quanli Han
- Department of Oncology, The First Medical Center, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Bin Yan
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Zhi Cui
- Department of Oncology, The First Medical Center, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Weiwei Zhang
- Department of Oncology, The First Medical Center, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Shurong Zhang
- Cancer Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Xindan Kang
- Department of Oncology, The First Medical Center, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Guanghai Dai
- Department of Oncology, The First Medical Center, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Niansong Qian
- Department of Oncology, The First Medical Center, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Wenji Yan
- Department of Oncology, The First Medical Center, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
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