1
|
Qin J, Hu S, Lou J, Xu M, Gao R, Xiao Q, Chen Y, Ding M, Pan Y, Wang S. Selumetinib overcomes ITGA2-induced 5-fluorouracil resistance in colorectal cancer. Int Immunopharmacol 2024; 137:112487. [PMID: 38889513 DOI: 10.1016/j.intimp.2024.112487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/24/2024] [Accepted: 06/12/2024] [Indexed: 06/20/2024]
Abstract
BACKGROUND Colorectal cancer (CRC) is the third most malignant tumor in the world. 5-fluorouracil (5‑FU) -based chemotherapy is the first-line chemotherapy scheme for CRC, whereas acquired drug resistance poses a huge obstacle to curing CRC patients and the mechanism is still obscure. Therefore, identification of genes associated with 5‑FU chemotherapy and seeking second-line treatment are necessary means to improve survival and prognosis of patients with CRC. METHODS The Cancer Therapeutics Response Portal (CTRP) database and Genomics of Drug Sensitivity in Cancer (GDSC) database were used to identify CRC-related genes and potential second-line therapies for 5-FU-resistant CRC. The single-cell RNA sequencing data for CRC tissues were obtained from a GEO dataset. The relationship between ITGA2 and 5-FU-resistant was investigated in vitro and in vivo models. RESULTS ACOX1 and ITGA2 were identified as risk biomarkers associated with 5-FU-resistance. We developed a risk signature, consisting of ACOX1 and ITGA2, that was able to distinguish well between 5-FU-resistance and 5-FU-sensitive. The single-cell sequencing data showed that ITGA2 was mainly enriched in malignant cells. ITGA2 was negatively correlated with IC50 values of most small molecule inhibitors, of which selumetinib had the highest negative correlation. Finally, knocking down ITGA2 can make 5-FU-resistant CRC cells sensitive to 5-FU and combining with selumetinib can improve the therapeutic effect of 5-FU resistant cells. CONCLUSION In summary, our findings demonstrated the critical role of ITGA2 in enhancing chemotherapy resistance in CRC cells and suggested that selumetinib can restore the sensitivity of chemotherapy-resistant CRC cells to 5-FU by inhibiting ITGA2 expression.
Collapse
Affiliation(s)
- Jian Qin
- School of Medicine, Southeast University, Nanjing, Jiangsu, China; General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Shangshang Hu
- School of Medicine, Southeast University, Nanjing, Jiangsu, China; General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jinwei Lou
- School of Basic Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Mu Xu
- Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Rui Gao
- School of Basic Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Qianni Xiao
- School of Basic Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Yuhan Chen
- School of Basic Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Muzi Ding
- School of Basic Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Yuqin Pan
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China; School of Basic Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China; Jiangsu Collaborative Innovation Center on Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Shukui Wang
- School of Medicine, Southeast University, Nanjing, Jiangsu, China; General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China; School of Basic Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China; Jiangsu Collaborative Innovation Center on Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, China.
| |
Collapse
|
2
|
Zhu W, Wu C, Liu Z, Zhao S, Cheng X, Huang J. SULF1 regulates malignant progression of colorectal cancer by modulating ARSH via FAK/PI3K/AKT/mTOR signaling. Cancer Cell Int 2024; 24:201. [PMID: 38844922 PMCID: PMC11157809 DOI: 10.1186/s12935-024-03383-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 05/25/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND Colorectal cancer (CRC) has the third highest incidence and second mortality rate of malignant tumors globally, highlighting the urgency to explore the mechanisms underlying CRC progression for refined treatment of this patient population. METHODS R Studio was used for data sorting and analysis. Cell apoptosis and cell cycle detection were performed by flow cytometry. Quantitative real-time PCR (qRT-PCR) was used to explore mRNA expression levels. Western blotting was used to explore protein expression levels. CCK8, EdU, and colony formation assays were performed to explore the proliferation capacity of CRC cells. Transwell invasion and migration assays, along with the wound healing assay, were used to explore the invasive and migratory abilities of CRC cells. Subcutaneous Xenograft Assay was utilized to evaluate the tumorigenic capacity of CRC cells in vivo. RESULTS SULF1 was highly expressed in CRC samples and cell lines. The knockdown of SULF1 inhibited the proliferation, invasion, and migration of CRC and increased the rate of cell apoptosis. Meanwhile, we demonstrated that SULF1 could negatively regulate ARSH through the FAK/PI3K/AKT/mTOR pathway. CONCLUSION We demonstrated that SULF1 could promote CRC progression by regulating ARSH. The SULF1/ARSH/FAK/PI3K/AKT/mTOR signaling pathway represents a promising target for the treatment of this patient population. Colorectal cancer (CRC) has the third highest incidence and second mortality rate of malignant tumors globally. Sulfatase 1 (SULF1) belongs to the sulfatase family, The function of SULF1 in CRC remains elusive. Our study demonstrated that the knockdown of SULF1 could inhibit the proliferation, invasion, and migration of CRC. Meanwhile, our findings indicated that SULF1 could interact with Arylsulfatase Family Member H (ARSH) to regulate the proliferation, invasion, and migration of CRC via the FAK/PI3K/AKT/mTOR signaling pathway. Taken together, our findings suggest that SULF1 might be a new therapeutic target in CRC.
Collapse
Affiliation(s)
- Wenjie Zhu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi Province, China
- Jiangxi Province Key Laboratory of Molecular Medicine, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi Province, China
| | - Changlei Wu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi Province, China
- Jiangxi Province Key Laboratory of Molecular Medicine, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi Province, China
| | - Zitao Liu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi Province, China
- Jiangxi Province Key Laboratory of Molecular Medicine, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi Province, China
| | - Shimin Zhao
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi Province, China
- Jiangxi Province Key Laboratory of Molecular Medicine, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi Province, China
| | - Xiufeng Cheng
- Department of Critical Care Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi Province, China
| | - Jun Huang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi Province, China.
| |
Collapse
|
3
|
Hu S, Xiao Q, Gao R, Qin J, Nie J, Chen Y, Lou J, Ding M, Pan Y, Wang S. Identification of BGN positive fibroblasts as a driving factor for colorectal cancer and development of its related prognostic model combined with machine learning. BMC Cancer 2024; 24:516. [PMID: 38654221 PMCID: PMC11041013 DOI: 10.1186/s12885-024-12251-4] [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: 12/29/2023] [Accepted: 04/11/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Numerous studies have indicated that cancer-associated fibroblasts (CAFs) play a crucial role in the progression of colorectal cancer (CRC). However, there are still many unknowns regarding the exact role of CAF subtypes in CRC. METHODS The data for this study were obtained from bulk, single-cell, and spatial transcriptomic sequencing data. Bioinformatics analysis, in vitro experiments, and machine learning methods were employed to investigate the functional characteristics of CAF subtypes and construct prognostic models. RESULTS Our study demonstrates that Biglycan (BGN) positive cancer-associated fibroblasts (BGN + Fib) serve as a driver in colorectal cancer (CRC). The proportion of BGN + Fib increases gradually with the progression of CRC, and high infiltration of BGN + Fib is associated with poor prognosis in terms of overall survival (OS) and recurrence-free survival (RFS) in CRC. Downregulation of BGN expression in cancer-associated fibroblasts (CAFs) significantly reduces migration and proliferation of CRC cells. Among 101 combinations of 10 machine learning algorithms, the StepCox[both] + plsRcox combination was utilized to develop a BGN + Fib derived risk signature (BGNFRS). BGNFRS was identified as an independent adverse prognostic factor for CRC OS and RFS, outperforming 92 previously published risk signatures. A Nomogram model constructed based on BGNFRS and clinical-pathological features proved to be a valuable tool for predicting CRC prognosis. CONCLUSION In summary, our study identified BGN + Fib as drivers of CRC, and the derived BGNFRS was effective in predicting the OS and RFS of CRC patients.
Collapse
Affiliation(s)
- Shangshang Hu
- School of Medicine, Southeast University, 210009, Nanjing, Jiangsu, China
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, No. 68, Changle Road, 210006, Nanjing, Jiangsu, China
| | - Qianni Xiao
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, 211122, Nanjing, Jiangsu, China
| | - Rui Gao
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, 211122, Nanjing, Jiangsu, China
| | - Jian Qin
- School of Medicine, Southeast University, 210009, Nanjing, Jiangsu, China
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, No. 68, Changle Road, 210006, Nanjing, Jiangsu, China
| | - Junjie Nie
- School of Medicine, Southeast University, 210009, Nanjing, Jiangsu, China
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, No. 68, Changle Road, 210006, Nanjing, Jiangsu, China
| | - Yuhan Chen
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, 211122, Nanjing, Jiangsu, China
| | - Jinwei Lou
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, 211122, Nanjing, Jiangsu, China
| | - Muzi Ding
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, 211122, Nanjing, Jiangsu, China
| | - Yuqin Pan
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, No. 68, Changle Road, 210006, Nanjing, Jiangsu, China.
- Jiangsu Collaborative Innovation Center on Cancer Personalized Medicine, Nanjing Medical University, 211100, Nanjing, Jiangsu, China.
| | - Shukui Wang
- School of Medicine, Southeast University, 210009, Nanjing, Jiangsu, China.
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, No. 68, Changle Road, 210006, Nanjing, Jiangsu, China.
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, 211122, Nanjing, Jiangsu, China.
- Jiangsu Collaborative Innovation Center on Cancer Personalized Medicine, Nanjing Medical University, 211100, Nanjing, Jiangsu, China.
| |
Collapse
|
4
|
Ma Y, Fang F, Liao K, Zhang J, Wei C, Liao Y, Zhao B, Fang Y, Chen Y, Zhang X, Tang D. Identification and validation of the clinical prediction model and biomarkers based on chromatin regulators in colon cancer by integrated analysis of bulk- and single-cell RNA sequencing data. Transl Cancer Res 2024; 13:1290-1313. [PMID: 38617504 PMCID: PMC11009811 DOI: 10.21037/tcr-23-1886] [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: 10/12/2023] [Accepted: 02/08/2024] [Indexed: 04/16/2024]
Abstract
Background Chromatin regulators (CRs) are implicated in the development of cancer, but a comprehensive investigation of their role in colon adenocarcinoma (COAD) is inadequate. The purpose of this study is to find CRs that can provide recommendations for clinical diagnosis and treatment, and to explore the reasons why they serve as critical CRs. Methods We obtained data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Weighted Gene Co-Expression Network Analysis (WGCNA) screened tumor-associated CRs. LASSO-Cox regression was used to construct the model and to screen key CRs together with support vector machine (SVM), the univariate Cox regression. We used single-cell data to explore the expression of CRs in cells and their communication. Immune infiltration, immune checkpoints, mutation, methylation, and drug sensitivity analyses were performed. Gene expression was verified by quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR). Pan-cancer analysis was used to explore the importance of hub CRs. Results We finally obtained 32 tumor-associated CRs. The prognostic model was constructed based on RCOR2, PPARGC1A, PKM, RAC3, PHF19, MYBBP1A, ORC1, and EYA2 by the LASSO-Cox regression. Single-cell data revealed that the model was immune-related. Combined with immune infiltration analysis, immune checkpoint analysis, and tumor immune dysfunction and exclusion (TIDE) analysis, the low-score risk group had more immune cell infiltration and better immune response. Mutation and methylation analysis showed that multiple CRs may be mutated and methylated in colon cancer. Drug sensitivity analysis revealed that the low-risk group may be more sensitive to several drugs and PKM was associated with multiple drugs. Combined with machine learning, PKM is perhaps the most critical gene in CRs. Pan-cancer analysis showed that PKM plays a role in the prognosis of cancers. Conclusions We developed a prognostic model for COAD based on CRs. Increased expression of the core gene PKM is linked with a poor prognosis in several malignancies.
Collapse
Affiliation(s)
- Yichao Ma
- Clinical Medical College, Yangzhou University, Yangzhou, China
- Department of General Surgery, Institute of General Surgery, Northern Jiangsu People’s Hospital, Clinical Medical College, Yangzhou University, Yangzhou, China
| | - Fang Fang
- Department of General Surgery, Institute of General Surgery, Northern Jiangsu People’s Hospital, Clinical Medical College, Yangzhou University, Yangzhou, China
| | - Kai Liao
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Jingqiu Zhang
- Department of General Surgery, Institute of General Surgery, Northern Jiangsu People’s Hospital, Clinical Medical College, Yangzhou University, Yangzhou, China
| | - Chen Wei
- Clinical Medical College, Yangzhou University, Yangzhou, China
- Department of General Surgery, Institute of General Surgery, Northern Jiangsu People’s Hospital, Clinical Medical College, Yangzhou University, Yangzhou, China
| | - Yiqun Liao
- Department of Clinical Medical college, Dalian Medical University, Dalian, China
| | - Bin Zhao
- Department of Clinical Medical college, Dalian Medical University, Dalian, China
| | - Yongkun Fang
- Department of Clinical Medical college, Dalian Medical University, Dalian, China
| | - Yuji Chen
- Clinical Medical College, Yangzhou University, Yangzhou, China
- Department of General Surgery, Institute of General Surgery, Northern Jiangsu People’s Hospital, Clinical Medical College, Yangzhou University, Yangzhou, China
| | - Xinyue Zhang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Dong Tang
- Clinical Medical College, Yangzhou University, Yangzhou, China
- Department of General Surgery, Institute of General Surgery, Northern Jiangsu People’s Hospital, Clinical Medical College, Yangzhou University, Yangzhou, China
| |
Collapse
|
5
|
Zhang Z, Liu S, Wang Z, Wang S, Jiang L, Wang X, Li J, Shen L. Influential upregulation of KCNE4: Propelling cancer associated fibroblasts-driven colorectal cancer progression. Cancer Cell Int 2024; 24:103. [PMID: 38462626 PMCID: PMC10926681 DOI: 10.1186/s12935-024-03274-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 02/15/2024] [Indexed: 03/12/2024] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is a malignancy of remarkable heterogeneity and heightened morbidity. Cancer associated fibroblasts (CAFs) are abundant in CRC tissues and are essential for CRC growth. Here, we aimed to develop a CAF-related classifier for predicting the prognosis of CRC and identify critical pro-tumorigenic genes in CAFs. METHOD The mRNA expression and clinical information of CRC samples were sourced from two comprehensive databases, The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). Using a weighted gene co-expression network analysis (WGCNA) approach, CAF-related genes were identified and a CAF risk signature was developed through the application of univariate analysis and the least absolute shrinkage and selection operator (LASSO) Cox regression model. EdU cell proliferation assay, and transwell assay were performed to detect the oncogenic role of KCNE4 in CAFs. RESULTS We constructed a prognostic CAF model consisting of two genes (SFRP2 and KCNE4). CRC patients were classified into low- and high-CAF-risk groups using the median CAF risk score, and patients in the high-CAF-risk group had worse prognosis. Meanwhile, a higher risk score for CAFs was associated with greater stromal and CAF infiltrations, as well as higher expression of CAF markers. Furthermore, TIDE analysis indicated that patients with a high CAF risk score are less responsive to immunotherapy. Our further experiments had confirmed the strong correlation between KCNE4 and the malignant phenotypes of CAFs. Moreover, we had shown that KCNE4 could actively promote tumor-promoting phenotypes in CAFs, indicating its critical role in cancer progression. CONCLUSION The two-gene prognostic CAF signature was constructed and could be reliable for predicting prognosis for CRC patients. Moreover, KCNE4 may be a promising strategy for the development of novel anti-cancer therapeutics specifically directed against CAFs.
Collapse
Affiliation(s)
- Zizhen Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China.
| | - Shengde Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Zhenghang Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Shuo Wang
- Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Lei Jiang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Xicheng Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Jian Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China.
| | - Lin Shen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China.
| |
Collapse
|
6
|
Ma Y, Wang Z, Sun J, Tang J, Zhou J, Dong M. Investigating the Diagnostic and Therapeutic Potential of SREBF2-Related Lipid Metabolism Genes in Colon Cancer. Onco Targets Ther 2023; 16:1027-1042. [PMID: 38107762 PMCID: PMC10723182 DOI: 10.2147/ott.s428150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 11/08/2023] [Indexed: 12/19/2023] Open
Abstract
Purpose Colon cancer is one of the leading causes of death worldwide, and screening of effective molecular markers for the diagnosis is prioritised for prevention and treatment. This study aimed to investigate the diagnostic and predictive potential of genes related to the lipid metabolism pathway, regulated by a protein called sterol-regulatory element-binding transcription Factor 2 (SREBF2), for colon cancer and patient outcomes. Methods We used machine-learning algorithms to identify key genes associated with SREBF2 in colon cancer based on a public database. A nomogram was created to assess the diagnostic value of these genes and validated in the Cancer Genome Atlas. We also analysed the relationship between these genes and the immune microenvironment of colon tumours, as well as the correlation between gene expression and clinicopathological characteristics and prognosis in the China Medical University (CMU) clinical cohort. Results Three genes, 7-dehydrocholesterol reductase (DHCR7), hydroxysteroid 11-beta dehydrogenase 2 (HSD11B2), and Ral guanine nucleotide dissociation stimulator-like 1 (RGL1), were identified as hub genes related to SREBF2 and colon cancer. Using the TCGA dataset, receiver operating characteristic curve analysis showed the area under the curve values of 0.943, 0.976, and 0.868 for DHCR7, HSD11B2, and RGL1, respectively. In the CMU cohort, SREBF2 and DHCR7 expression levels were correlated with TNM stage and tumour invasion depth (P < 0.05), and high DHCR7 expression was related to poor prognosis of colon cancer (P < 0.05). Furthermore, DHCR7 gene expression was positively correlated with the abundance of M0 and M1 macrophages and inversely correlated with the abundance of M2 macrophages, suggesting that the immune microenvironment may play a role in colon cancer surveillance. There was a correlation between SREBF2 and DHCR7 expression across cancers in the TCGA database. Conclusion This study highlights the potential of DHCR7 as a diagnostic marker and therapeutic target for colon cancer.
Collapse
Affiliation(s)
- Yuteng Ma
- Department of Gastrointestinal Surgery, First Hospital of China Medical University, Shenyang, 110001, People’s Republic of China
| | - Zhe Wang
- Department of Pathology, Shengjing Hospital of China Medical University, Shenyang, 110001, People’s Republic of China
| | - Jian Sun
- Department of Gastrointestinal Surgery, First Hospital of China Medical University, Shenyang, 110001, People’s Republic of China
| | - Jingtong Tang
- Department of Gastrointestinal Surgery, First Hospital of China Medical University, Shenyang, 110001, People’s Republic of China
| | - Jianping Zhou
- Department of Gastrointestinal Surgery, First Hospital of China Medical University, Shenyang, 110001, People’s Republic of China
| | - Ming Dong
- Department of Gastrointestinal Surgery, First Hospital of China Medical University, Shenyang, 110001, People’s Republic of China
| |
Collapse
|
7
|
Wang XJ, Liu Y, Ke B, Zhang L, Liang H. RNA-binding protein CPSF6 regulates IBSP to affect pyroptosis in gastric cancer. World J Gastrointest Oncol 2023; 15:1531-1543. [PMID: 37746647 PMCID: PMC10514719 DOI: 10.4251/wjgo.v15.i9.1531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 07/31/2023] [Accepted: 08/18/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND Extensive evidence has illustrated the promotive role of integrin binding sialoprotein (IBSP) in the progression of multiple cancers. However, little is known about the functions of IBSP in gastric cancer (GC) progression. AIM To investigate the mechanism underlying the regulatory effects of IBSP in GC progression, and the relationship between IBSP and cleavage and polyadenylation factor 6 (CPSF6) in this process. METHODS The mRNA and protein expression of relevant genes were assessed through real-time quantitative polymerase chain reaction and Western blot, respectively. Cell viability was evaluated by Cell Counting Kit-8 assay. Cell invasion and migration were evaluated by Transwell assay. Pyroptosis was measured by flow cytometry. The binding between CPSF6 and IBSP was confirmed by luciferase reporter and RNA immunoprecipitation (RIP) assays. RESULTS IBSP exhibited higher expression in GC tissues and cell lines than in normal tissues and cell lines. IBSP knockdown suppressed cell proliferation, migration, and invasion but facilitated pyroptosis. In the exploration of the regulatory mechanism of IBSP, potential RNA binding proteins for IBSP were screened with catRAPID omics v2.0. The RNA-binding protein CPSF6 was selected due to its higher expression in stomach adenocarcinoma. Luciferase reporter and RIP assays revealed that CPSF6 binds to the 3'-untranslated region of IBSP and regulates its expression. Knockdown of CPSF6 inhibited cell proliferation, migration, and invasion but boosted pyroptosis. Through rescue assays, it was uncovered that the retarded GC progression mediated by CPSF6 knockdown was reversed by IBSP overexpression. CONCLUSION Our study highlighted the vital role of the CPSF6/IBSP axis in GC, suggesting that IBSP might be an effective bio-target for GC treatment.
Collapse
Affiliation(s)
- Xue-Jun Wang
- Department of Gastric Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, Tianjin 300060, China
| | - Yong Liu
- Department of Gastric Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, Tianjin 300060, China
| | - Bin Ke
- Department of Gastric Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, Tianjin 300060, China
| | - Li Zhang
- Department of Gastric Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, Tianjin 300060, China
| | - Han Liang
- Department of Gastric Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, Tianjin 300060, China
| |
Collapse
|
8
|
Chen W, Wang Y, Gu H, Zhang Y, Chen C, Yu T, Chen T. Molecular characteristics, clinical significance, and immune landscape of extracellular matrix remodeling-associated genes in colorectal cancer. Front Oncol 2023; 13:1109181. [PMID: 37621680 PMCID: PMC10446763 DOI: 10.3389/fonc.2023.1109181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 07/24/2023] [Indexed: 08/26/2023] Open
Abstract
Background Extracellular matrix (ECM) remodeling is one of the hallmark events in cancer and has been shown to be closely related to tumor immunity. Immunotherapy has evolved as an important tool to treat various cancers and improve patient prognosis. The positive response to immunotherapy relies on the unique interaction between cancer and the tumor microenvironment (TME). However, the relationship between ECM remodeling and clinical outcomes, immune cell infiltration, and immunotherapy in colorectal cancer (CRC) remains unknown. Methods We systematically evaluated 69 ECM remodeling-associated genes (EAGs) and comprehensively identified interactions between ECM remodeling and prognosis and the immune microenvironment in CRC patients. The EAG_score was used to quantify the subtype of ECM remodeling in patients. We then assessed their value in predicting prognosis and responding to treatment in CRC. Results After elaborating the molecular characteristics of ECM remodeling-related genes in CRC patients, a model consisting of two ECM remodeling-related genes (MEIS2, SLC2A3) was developed for predicting the prognosis of CRC patients, Receiver Operating Characteristic (ROC) and Kaplan-Meier (K-M) analysis verified its reliable predictive ability. Furthermore, we created a highly reliable nomogram to enhance the clinical feasibility of the EAG_score. Significantly differences in TME and immune function, such as macrophages and CD8+ T cells, were observed between high- and low-risk CRC patients. In addition, drug sensitivity is also strongly related to EAG_score. Conclusion Overall, we developed a prognostic model associated with ECM remodeling, provided meaningful clinical implications for immunotherapy, and facilitated individualized treatment for CRC patients. Further studies are needed to reveal the underlying mechanisms of ECM remodeling in CRC.
Collapse
Affiliation(s)
- Wenlong Chen
- Department of Colorectal Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yiwen Wang
- Department of Colorectal Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Haitao Gu
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi Zhang
- Department of Colorectal Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Cong Chen
- Department of Neurology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Tingting Yu
- Department of Medical Genetics, School of Basic Medical Science, Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing, China
| | - Tao Chen
- Department of Colorectal Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| |
Collapse
|
9
|
Iyer AS, Shaik MR, Raufman JP, Xie G. The Roles of Zinc Finger Proteins in Colorectal Cancer. Int J Mol Sci 2023; 24:10249. [PMID: 37373394 DOI: 10.3390/ijms241210249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Despite colorectal cancer remaining a leading worldwide cause of cancer-related death, there remains a paucity of effective treatments for advanced disease. The molecular mechanisms underlying the development of colorectal cancer include altered cell signaling and cell cycle regulation that may result from epigenetic modifications of gene expression and function. Acting as important transcriptional regulators of normal biological processes, zinc finger proteins also play key roles in regulating the cellular mechanisms underlying colorectal neoplasia. These actions impact cell differentiation and proliferation, epithelial-mesenchymal transition, apoptosis, homeostasis, senescence, and maintenance of stemness. With the goal of highlighting promising points of therapeutic intervention, we review the oncogenic and tumor suppressor roles of zinc finger proteins with respect to colorectal cancer tumorigenesis and progression.
Collapse
Affiliation(s)
- Aishwarya S Iyer
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Mohammed Rifat Shaik
- Department of Medicine, University of Maryland Medical Center Midtown Campus, Baltimore, MD 21201, USA
| | - Jean-Pierre Raufman
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- VA Maryland Healthcare System, Baltimore, MD 21201, USA
- Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Guofeng Xie
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- VA Maryland Healthcare System, Baltimore, MD 21201, USA
- Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| |
Collapse
|
10
|
Liang C, Ji D, Qin F, Chen G. CAF signature predicts the prognosis of colorectal cancer patients: A retrospective study based on bulk RNA sequencing and single-cell RNA sequencing data. Medicine (Baltimore) 2023; 102:e33149. [PMID: 36897717 PMCID: PMC9997814 DOI: 10.1097/md.0000000000033149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/10/2023] [Indexed: 03/11/2023] Open
Abstract
The incidence rate and mortality rate of colorectal cancer (CRC) ranks third and second globally. Cancer-associated fibroblasts (CAFs) are the major constituent of the stromal cells in the tumor microenvironment (TME) and are closely associated with patients' prognoses. Our study intended to establish a prognostic model for CRC using hallmark genes of CAFs. The expression values of genes and clinicopathological characteristics of patients were enrolled from the cancer genome atlas database as well as the gene expression omnibus database. The single-cell RNA sequencing data were collected and analyzed in the deeply integrated human single-cell omics database and cancer single-cell expression map databases. The ESTIMATE algorithm was applied to access the infiltration levels of immune and stromal cells. The prognostic genes were selected by the Cox regression analysis and the prognostic signature was constructed by the least absolute shrinkage and selection operator algorithm. gene set enrichment analysis was used to explore the enriched gene sets. In this study, based on bulk RNA sequencing and single-cell RNA sequencing data, and we found that more CAFs were infiltrated in the tumor microenvironment and consisted of 3 subtypes. Then we constructed a prognostic signature for CRC using hallmark genes of CAFs and proved that this signature exhibited high values to predict the overall survival of CRC patients in independent training and validating cohorts. Besides, function enrichment analysis revealed that our prognostic model was significantly associated with immune regulation. Further analysis showed that the infiltrated levels of tumor-suppressing immune cells and the expression of higher immune checkpoint genes in CRC tissues were higher in patients with high-risk scores. Furthermore, immunohistochemistry analysis exhibited that these genes in our prognostic signature were markedly upregulated in CRC tissues. We first constructed a signature based on CAFs hallmark genes to predict the survival of CRC patients and further revealed that the tumor-suppressing microenvironment and dysregulated immune checkpoint genes in CRC tissues were partly responsible for the poor prognosis of patients.
Collapse
Affiliation(s)
- Chen Liang
- Department of Pathology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Dongze Ji
- Department of Pathology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Feng Qin
- Department of Pathology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| |
Collapse
|
11
|
Scott P, Wang S, Onyeaghala G, Pankratz N, Starr T, Prizment AE. Lower Expression of CFTR Is Associated with Higher Mortality in a Meta-Analysis of Individuals with Colorectal Cancer. Cancers (Basel) 2023; 15:989. [PMID: 36765944 PMCID: PMC9913301 DOI: 10.3390/cancers15030989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/25/2023] [Accepted: 01/30/2023] [Indexed: 02/08/2023] Open
Abstract
Individuals with cystic fibrosis (CF), caused by biallelic germline mutations in the cystic fibrosis transmembrane conductance regulator (CFTR), have higher risk and earlier onset of colorectal cancer (CRC). A subset of CRC patients in the non-CF population expresses low levels of tumoral CFTR mRNA which may also cause decreased CFTR activity. To determine the consequences of reduced CFTR expression in this population, we investigated association of tumoral CFTR expression with overall and disease-specific mortality in CRC patients. CFTR mRNA expression, clinical factors and survival data from 1177 CRC patients reported in the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus studies GSE39582 and GSE17538 were included. Log-transformed and z-normalized [mean = 0, standard deviation (SD) = 1] CFTR expression values were modeled as quartiles or dichotomized at the median. Univariate and multivariable Cox proportional hazards regression models were used to estimate hazard ratios (HR) and 95% confidence intervals (CI) for overall and disease-specific mortality in individual studies and meta-analyses. Analyses of each of the three individual datasets showed a robust association of decreased CFTR expression with increased mortality. In meta-analyses adjusted for stage at diagnosis, age and sex, CFTR expression was inversely associated with risk of overall death [pooled HR (95% CI): 0.70 (0.57-0.86)] and disease-specific death [pooled HR (95% CI): 0.68 (0.47-0.99)]. Associations did not differ by stage at diagnosis, age, or sex. Meta-analysis of overall death stratified by microsatellite instable (MSI) versus microsatellite stable (MSS) status indicated potential interaction between MSI/MSS status and CFTR expression, (p-interaction: 0.06). The findings from these three datasets support the hypothesis that low CFTR expression is associated with increased CRC mortality.
Collapse
Affiliation(s)
- Patricia Scott
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA
| | - Shuo Wang
- Division of Epidemiology and Community Health, University of Minnesota School of Public Health, Minneapolis, MN 55455, USA
| | - Guillaume Onyeaghala
- Division of Epidemiology and Community Health, University of Minnesota School of Public Health, Minneapolis, MN 55455, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Timothy Starr
- Department of Obstetrics, Gynecology and Women’s Health, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Anna E. Prizment
- Division of Hematology, Oncology and Transplantation, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| |
Collapse
|
12
|
Identification of prognostic immune-related lncRNA signature predicting the overall survival for colorectal cancer. Sci Rep 2023; 13:1333. [PMID: 36693898 PMCID: PMC9873726 DOI: 10.1038/s41598-023-28305-9] [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: 08/13/2022] [Accepted: 01/17/2023] [Indexed: 01/25/2023] Open
Abstract
Long non-coding RNA (lncRNA) is an important regulator of gene expression and serves a fundamental role in immune regulation. The present study aimed to develop a novel immune-related lncRNA signature to assess the prognosis of patients with colorectal cancer (CRC). Transcriptome data and clinical information of patients with CRC were downloaded from The Cancer Genome Atlas (TCGA) and UCSC Xena platforms. Immune-related mRNAs were extracted from the Molecular Signatures Database (MSigDB), and the immune-related lncRNAs were identified based on correlation analysis. Then, univariate, Lasso and multivariate Cox regression were applied to construct an immune-related lncRNA signature, and CRC patients were divided into high- and low-risk groups according to the median risk score. Finally, we evaluated the signature from the perspectives of clinical outcome, clinicopathological parameters, tumor-infiltrating immune cells (TIICs), immune status, tumor mutation burden (TMB) and immunotherapy responsiveness. In total, 272 immune-related lncRNAs were identified, five of which were applied to construct an immune-related lncRNA signature. The signature divided patients with CRC into low- and high-risk groups, the prognosis of patients in the high-risk group were significantly poorer than those in low-risk group, and the results were further confirmed in external validation cohort. Furthermore, the high-risk group showed aggressive clinicopathological characteristics, specific TIIC and immune function status, and low sensitivity to immunotherapy. The immune-related lncRNA signature could be exploited as a promising biomarker for predicting the prognosis and immune status of patients with CRC.
Collapse
|
13
|
Shen X, Zuo X, Liang L, Wang L, Luo B. Integrating machine learning and single-cell trajectories to analyze T-cell exhaustion to predict prognosis and immunotherapy in colon cancer patients. Front Immunol 2023; 14:1162843. [PMID: 37207222 PMCID: PMC10191250 DOI: 10.3389/fimmu.2023.1162843] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 04/13/2023] [Indexed: 05/21/2023] Open
Abstract
Introduction The incidence of colon adenocarcinoma (COAD) has recently increased, and patients with advanced COAD have a poor prognosis due to treatment resistance. Combining conventional treatment with targeted therapy and immunotherapy has shown unexpectedly positive results in improving the prognosis of patients with COAD. More study is needed to determine the prognosis for patients with COAD and establish the appropriate course of treatment. Methods This study aimed to explore the trajectory of T-cell exhaustion in COAD to predict the overall survival and treatment outcome of COAD patients. Clinical data were derived from the TCGA-COAD cohort through "UCSC", as well as the whole genome data. Prognostic genes driving T-cell trajectory differentiation were identified on the basis of single-cell trajectories and univariate Cox regression. Subsequently, T-cell exhaustion score (TES) was created by iterative LASSO regression. The potential biological logic associated with TES was explored through functional analysis, immune microenvironment assessment, immunotherapy response prediction, and in vitro experiments. Results Data showed that patients with significant TES had fewer favorable outcomes. Expression, proliferation, and invasion of COAD cells treated with TXK siRNA were also examined by cellular experiments. Both univariate and multivariate Cox regression indicated that TES was an independent prognostic factor in patients with COAD; in addition, subgroup analysis supported this finding. Functional assay revealed that immune response and cytotoxicity pathways are associated with TES, as the subgroup with low TES has an active immune microenvironment. Furthermore, patients with low TES responded better to chemotherapy and immunotherapy. Conclusion In this study, we systematically explored the T-cell exhaustion trajectory in COAD and developed a TES model to assess prognosis and provide guidelines for the treatment decision. This discovery gave rise to a fresh concept for novel therapeutic procedures for the clinical treatment of COAD.
Collapse
Affiliation(s)
- Xiaogang Shen
- Department of Gastrointestinal Surgery, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
| | - Xiaofei Zuo
- Department of Gastrointestinal Surgery, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
| | - Liang Liang
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
- Cancer Center, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Lin Wang
- Department of Gastrointestinal Surgery, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
- *Correspondence: Bin Luo, ; Lin Wang,
| | - Bin Luo
- Department of Gastrointestinal Surgery, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
- *Correspondence: Bin Luo, ; Lin Wang,
| |
Collapse
|
14
|
Ping G, Tian Y, Zhou Z. Constructing a Tregs-associated signature to predict the prognosis of colorectal cancer patients: A STROBE-compliant retrospective study. Medicine (Baltimore) 2022; 101:e31382. [PMID: 36451426 PMCID: PMC9704903 DOI: 10.1097/md.0000000000031382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Colorectal cancer (CRC) ranks as the second leading cause of cancer-related mortality worldwide. Regulatory T cells (Tregs) are a key constituent of immune cells in the tumor microenvironment (TME) and are significantly associated with patient outcomes. Our study aimed to construct a Treg-associated signature to predict the prognosis of CRC patients. The genes' expression values and patients' clinicopathological features were downloaded from TCGA and gene expression omnibus (GEO) databases. The single-cell RNA (scRNA) sequencing data of CRC were analyzed through the Deeply Integrated human Single-Cell Omics database. WGCNA analysis was used to select Tregs-associated genes (TrAGs). The infiltrated levels of immune and stromal cells were accessed through the ESTIMATE algorithm. Cox regression analysis and the LASSO algorithm were implemented to construct prognostic models. Gene set enrichment analysis (GSEA) was performed to annotate enriched gene sets. Based on scRNA sequencing data, our study uncovered that more Tregs were significantly enriched in the TME of CRC. Then we identified 123 differentially expressed TrAGs which mainly participated in immune regulation. Given that CRC patients were reclassified into 2 subgroups with distinct overall survival based on 26 differentially expressed TrAGs with prognostic values, we subsequently constructed a signature for CRC. After training and validating in independent cohorts, we proved that this prognostic model can be well applied to predict the prognosis of CRC patients. Further analysis exhibited that more tumor-suppressing immune cells and higher immune checkpoint genes were enriched in CRC patients with high-risk scores. Moreover, immunohistochemistry analysis validated that the genes in the prognostic model were significantly elevated in CRC tissues. We were the first to construct a prognostic signature for CRC based on TrAGs and further revealed that the poor prognosis of patients was mainly attributed to the tumor-suppressing microenvironment and upregulated immune checkpoint genes in tumor tissues.
Collapse
Affiliation(s)
- Guoqiang Ping
- Department of Pathology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yichen Tian
- Department of Pathology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Ziqiang Zhou
- Department of Pathology, Zibo Central Hospital, Zibo, Shandong, China
- *Correspondence: Ziqiang Zhou, Department of Pathology, Zibo Central Hospital, No. 54 Gongqingtuanxi Road, Zhangdian District, Zibo 255020, China (e-mail: )
| |
Collapse
|
15
|
Chen PB, Fiaux PC, Zhang K, Li B, Kubo N, Jiang S, Hu R, Rooholfada E, Wu S, Wang M, Wang W, McVicker G, Mischel PS, Ren B. Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation. Cell Rep 2022; 41:111630. [PMID: 36351387 PMCID: PMC9687083 DOI: 10.1016/j.celrep.2022.111630] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 07/21/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022] Open
Abstract
A scarcity of functionally validated enhancers in the human genome presents a significant hurdle to understanding how these cis-regulatory elements contribute to human diseases. We carry out highly multiplexed CRISPR-based perturbation and sequencing to identify enhancers required for cell proliferation and fitness in 10 human cancer cell lines. Our results suggest that the cell fitness enhancers, unlike their target genes, display high cell-type specificity of chromatin features. They typically adopt a modular structure, comprised of activating elements enriched for motifs of oncogenic transcription factors, surrounded by repressive elements enriched for motifs recognized by transcription factors with tumor suppressor functions. We further identify cell fitness enhancers that are selectively accessible in clinical tumor samples, and the levels of chromatin accessibility are associated with patient survival. These results reveal functional enhancers across multiple cancer cell lines, characterize their context-dependent chromatin organization, and yield insights into altered transcription programs in cancer cells.
Collapse
Affiliation(s)
- Poshen B Chen
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA; Genome Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), Singapore 138672, Singapore
| | - Patrick C Fiaux
- Bioinformatics and System Biology Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - Kai Zhang
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Bin Li
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Naoki Kubo
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Shan Jiang
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Rong Hu
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Emma Rooholfada
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Sihan Wu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
| | - Mengchi Wang
- Bioinformatics and System Biology Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - Wei Wang
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA; Bioinformatics and System Biology Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - Graham McVicker
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Paul S Mischel
- Department of Pathology, Stanford Medicine, Stanford University, Stanford, CA 94305, USA; ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Bing Ren
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California at San Diego, La Jolla, CA 92093, USA; Institute of Genome Medicine, UCSD School of Medicine, La Jolla, CA 92093, USA; Ludwig Institute for Cancer Research, San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
16
|
Liu X, Qin J, Nie J, Sun H, Pan Y, Wang S. Reclassifying TNM stage I/II colorectal cancer into two subgroups with different overall survival, tumor microenvironment, and response to immune checkpoint blockade treatment. Front Genet 2022; 13:948920. [PMID: 36212126 PMCID: PMC9532767 DOI: 10.3389/fgene.2022.948920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
Background: The traditional TNM staging system is often insufficient to differentiate the survival discrepancies of colorectal cancer (CRC) patients at TNM stage I/II. Our study aimed to reclassify stage I/II CRC patients into several subgroups with different prognoses and explore their suitable therapeutic methods. Methods: Single-cell RNA (scRNA) sequencing data, bulk RNA sequencing data, and clinicopathological information of CRC patients were enrolled from the TCGA and GEO databases. The tumor microenvironment of CRC tissues was accessed by the ESTIMATE algorithm. The prognostic genes were identified by Cox regression analysis. GO and KEGG analyses were conducted in the DAVID database. GSEA analysis was performed for annotation of the correlated gene sets. Results: We successfully reclassified stage I/II CRC patients into two subgroups and discovered that patients in cluster-2 underwent worse overall survival than those in cluster-1. GSEA analysis showed that immune-associated gene sets were positively enriched in cluster-2. Besides, the differentially expressed genes (DEGs) between cluster-1 and cluster-2 patients also participated in immune-related biological processes and signaling pathways. Moreover, we found that more immune cells infiltrated the microenvironment of cluster-2 patients compared to that of cluster-1 patients, such as Tregs and tumor-associated macrophages. ScRNA sequencing analysis uncovered that most of the enriched immune-associated signaling in cluster-2 patients was mainly attributed to these upregulated immune cells whose infiltration levels were also high in CRC tissues rather than in normal tissues. In addition, we demonstrated that the expression of immune checkpoint genes was significantly higher in cluster-2 patients compared to cluster-1 patients. ScRNA sequencing analysis revealed that the infiltrated CD8+T cells in CRC were naïve T cells and can be activated into effector T cells after immune checkpoint blockade (ICB) treatment. Conclusion: TNM stage I/II CRC patients can be divided into two subgroups, which have different overall survival rates, tumor microenvironment, and response to ICB therapy.
Collapse
Affiliation(s)
- Xiangxiang Liu
- School of Medicine, Southeast University, Nanjing, Jiangsu, China
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jian Qin
- School of Medicine, Southeast University, Nanjing, Jiangsu, China
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Junjie Nie
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Huiling Sun
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yuqin Pan
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
- *Correspondence: Yuqin Pan, ; Shukui Wang,
| | - Shukui Wang
- School of Medicine, Southeast University, Nanjing, Jiangsu, China
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
- *Correspondence: Yuqin Pan, ; Shukui Wang,
| |
Collapse
|
17
|
Hu C, Cai D, Zhong ME, Fan D, Li CH, Lv MY, Huang ZP, Wang W, Wu XJ, Gao F. Predicting prognosis and immunotherapy response among colorectal cancer patients based on a tumor immune microenvironment-related lncRNA signature. Front Genet 2022; 13:993714. [PMID: 36159987 PMCID: PMC9489948 DOI: 10.3389/fgene.2022.993714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/15/2022] [Indexed: 11/23/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) remodel the tumor immune microenvironment (TIME) by regulating the functions of tumor-infiltrating immune cells. It remains uncertain the way that TIME-related lncRNAs (TRLs) influence the prognosis and immunotherapy response of colorectal cancer (CRC). Aiming at providing survival and immunotherapy response predictions, a CRC TIME-related lncRNA signature (TRLs signature) was developed and the related potential regulatory mechanisms were explored with a comprehensive analysis on gene expression profiles from 97 immune cell lines, 61 CRC cell lines and 1807 CRC patients. Stratifying CRC patients with the TRLs signature, prolonged survival was observed in the low-risk group, while the patients in the high-risk group had significantly higher pro-tumor immune cells infiltration and higher immunotherapy response rate. Through the complex TRLs-mRNA regulation network, immunoregulation pathways and immunotherapy response pathways were found to be differently activated between the groups. In conclusion, the CRC TRLs signature is capable of making prognosis and immunotherapy response predictions, which may find application in stratifying patients for immunotherapy in the bedside.
Collapse
Affiliation(s)
- Chuling Hu
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Institute of Gastroenterology, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Du Cai
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Institute of Gastroenterology, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Min-Er Zhong
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Institute of Gastroenterology, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Dejun Fan
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Institute of Gastroenterology, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Gastrointestinal Endoscopy, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Cheng-Hang Li
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Institute of Gastroenterology, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Min-Yi Lv
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Institute of Gastroenterology, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ze-Ping Huang
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Institute of Gastroenterology, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wei Wang
- Department of Pathology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xiao-Jian Wu
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Institute of Gastroenterology, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Xiao-Jian Wu, ; Feng Gao,
| | - Feng Gao
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Institute of Gastroenterology, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Xiao-Jian Wu, ; Feng Gao,
| |
Collapse
|
18
|
Khaliq AM, Erdogan C, Kurt Z, Turgut SS, Grunvald MW, Rand T, Khare S, Borgia JA, Hayden DM, Pappas SG, Govekar HR, Kam AE, Reiser J, Turaga K, Radovich M, Zang Y, Qiu Y, Liu Y, Fishel ML, Turk A, Gupta V, Al-Sabti R, Subramanian J, Kuzel TM, Sadanandam A, Waldron L, Hussain A, Saleem M, El-Rayes B, Salahudeen AA, Masood A. Refining colorectal cancer classification and clinical stratification through a single-cell atlas. Genome Biol 2022; 23:113. [PMID: 35538548 PMCID: PMC9092724 DOI: 10.1186/s13059-022-02677-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 04/21/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) consensus molecular subtypes (CMS) have different immunological, stromal cell, and clinicopathological characteristics. Single-cell characterization of CMS subtype tumor microenvironments is required to elucidate mechanisms of tumor and stroma cell contributions to pathogenesis which may advance subtype-specific therapeutic development. We interrogate racially diverse human CRC samples and analyze multiple independent external cohorts for a total of 487,829 single cells enabling high-resolution depiction of the cellular diversity and heterogeneity within the tumor and microenvironmental cells. RESULTS Tumor cells recapitulate individual CMS subgroups yet exhibit significant intratumoral CMS heterogeneity. Both CMS1 microsatellite instability (MSI-H) CRCs and microsatellite stable (MSS) CRC demonstrate similar pathway activations at the tumor epithelial level. However, CD8+ cytotoxic T cell phenotype infiltration in MSI-H CRCs may explain why these tumors respond to immune checkpoint inhibitors. Cellular transcriptomic profiles in CRC exist in a tumor immune stromal continuum in contrast to discrete subtypes proposed by studies utilizing bulk transcriptomics. We note a dichotomy in tumor microenvironments across CMS subgroups exists by which patients with high cancer-associated fibroblasts (CAFs) and C1Q+TAM content exhibit poor outcomes, providing a higher level of personalization and precision than would distinct subtypes. Additionally, we discover CAF subtypes known to be associated with immunotherapy resistance. CONCLUSIONS Distinct CAFs and C1Q+ TAMs are sufficient to explain CMS predictive ability and a simpler signature based on these cellular phenotypes could stratify CRC patient prognosis with greater precision. Therapeutically targeting specific CAF subtypes and C1Q + TAMs may promote immunotherapy responses in CRC patients.
Collapse
Affiliation(s)
- Ateeq M Khaliq
- Indiana University School of Medicine, Indianapolis, IN, USA
| | - Cihat Erdogan
- Isparta University of Applied Sciences, Isparta, Turkey
| | - Zeyneb Kurt
- Northumbria University, Newcastle Upon Tyne, UK
| | | | | | - Tim Rand
- Tempus Labs, Inc., Chicago, IL, USA
| | | | | | | | - Sam G Pappas
- Rush University Medical Center, Chicago, IL, USA
| | | | - Audrey E Kam
- Rush University Medical Center, Chicago, IL, USA
| | | | | | - Milan Radovich
- Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yong Zang
- Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yingjie Qiu
- Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yunlong Liu
- Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Anita Turk
- Indiana University School of Medicine, Indianapolis, IN, USA
| | - Vineet Gupta
- Rush University Medical Center, Chicago, IL, USA
| | - Ram Al-Sabti
- Rush University Medical Center, Chicago, IL, USA
| | | | | | | | - Levi Waldron
- CUNY Graduate School of Public Health and Health Policy, New York, NY, USA
| | - Arif Hussain
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA
| | | | - Bassel El-Rayes
- University of Alabama, O'Neil Comprehensive Cancer Institute, Birmingham, AL, USA
| | | | - Ashiq Masood
- Indiana University School of Medicine, Indianapolis, IN, USA.
| |
Collapse
|
19
|
Du J, Tao Q, Liu Y, Huang Z, Jin H, Lin W, Huang X, Zeng J, Zhao Y, Liu L, Xu Q, Han X, Chen L, Chen XL, Wen Y. Assessment of the targeted effect of Sijunzi decoction on the colorectal cancer microenvironment via the ESTIMATE algorithm. PLoS One 2022; 17:e0264720. [PMID: 35303006 PMCID: PMC8932555 DOI: 10.1371/journal.pone.0264720] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 02/15/2022] [Indexed: 11/18/2022] Open
Abstract
Objective Sijunzi decoction (SJZD) was used to treat patients with colorectal cancer (CRC) as an adjuvant method. The aim of the study was to investigate the therapeutic targets and pathways of SJZD towards the tumor microenvironment of CRC via network pharmacology and the ESTIMATE algorithm. Methods The ESTIMATE algorithm was used to calculate immune and stromal scores to predict the level of infiltrating immune and stromal cells. The active targets of SJZD were searched in the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) and UniProt database. The core targets were obtained by matching the differentially expressed genes in CRC tissues and the targets of SJZD. Then, GO, KEGG and validation in TCGA were carried out. Results According to the ESTIMATE algorithm and survival analysis, the median survival time of the low stromal score group was significantly higher than that of the high stromal score group (P = 0.018), while the patients showed no significant difference of OS between different immune groups (P = 0.19). A total of 929 genes were upregulated and 115 genes were downregulated between the stromal score groups (|logFC| > 2, adjusted P < 0.05); 357 genes were upregulated and 472 genes were downregulated between the immune score groups. The component-target network included 139 active components and 52 related targets. The core targets were HSPB1, SPP1, IGFBP3, and TGFB1, which were significantly associated with poor prognosis in TCGA validation. GO terms included the response to hypoxia, the extracellular space, protein binding and the TNF signaling pathway. Immunoreaction was the main enriched pathway identified by KEGG analysis. Conclusion The core genes (HSPB1, SPP1, IGFBP3 and TGFB1) affected CRC development and prognosis by regulating hypoxia, protein binding and epithelial-mesenchymal transition in the extracellular matrix.
Collapse
Affiliation(s)
- Jiaxin Du
- School of Basic Medical Science, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Quyuan Tao
- School of Basic Medical Science, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ying Liu
- School of Basic Medical Science, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhanming Huang
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - He Jin
- School of Basic Medical Science, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wenjia Lin
- School of Basic Medical Science, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xinying Huang
- School of Basic Medical Science, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jingyan Zeng
- Shenzhen Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yongchang Zhao
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lingyu Liu
- School of Basic Medical Science, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qian Xu
- School of Basic Medical Science, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xue Han
- School of Basic Medical Science, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lixia Chen
- School of Basic Medical Science, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xin-lin Chen
- School of Basic Medical Science, Guangzhou University of Chinese Medicine, Guangzhou, China
- * E-mail: (XC); (YW)
| | - Yi Wen
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
- * E-mail: (XC); (YW)
| |
Collapse
|
20
|
Wu Q, Huang Q, Jiang Y, Sun F, Liang B, Wang J, Hu X, Sun M, Ma Z, Shi Y, Liang Y, Tan Y, Zeng D, Yao F, Xu X, Yao Z, Li S, Rong X, Huang N, Sun L, Liao W, Shi M. Remodeling Chondroitin-6-Sulfate-Mediated Immune Exclusion Enhances Anti-PD-1 Response in Colorectal Cancer with Microsatellite Stability. Cancer Immunol Res 2022; 10:182-199. [PMID: 34933913 PMCID: PMC9414301 DOI: 10.1158/2326-6066.cir-21-0124] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 09/30/2021] [Accepted: 12/17/2021] [Indexed: 01/07/2023]
Abstract
Metastatic microsatellite-stable (MSS) colorectal cancer rarely responds to immune checkpoint inhibitors (ICI). Metabolism heterogeneity in the tumor microenvironment (TME) presents obstacles to antitumor immune response. Combining transcriptome (The Cancer Genome Atlas MSS colorectal cancer, n = 383) and digital pathology (n = 96) analysis, we demonstrated a stroma metabolism-immune excluded subtype with poor prognosis in MSS colorectal cancer, which could be attributed to interaction between chondroitin-6-sulfate (C-6-S) metabolites and M2 macrophages, forming the "exclusion barrier" in the invasive margin. Furthermore, C-6-S derived from cancer-associated fibroblasts promoted co-nuclear translocation of pSTAT3 and GLI1, activating the JAK/STAT3 and Hedgehog pathways. In vivo experiments with C-6-S-targeted strategies decreased M2 macrophages and reprogrammed the immunosuppressive TME, leading to enhanced response to anti-PD-1 in MSS colorectal cancer. Therefore, C-6-S-induced immune exclusion represents an "immunometabolic checkpoint" that can be exploited for the application of combination strategies in MSS colorectal cancer ICI treatment.
Collapse
Affiliation(s)
- Qijing Wu
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Qiong Huang
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Yu Jiang
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Fei Sun
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Bishan Liang
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Jiao Wang
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Xingbin Hu
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Mengting Sun
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Zhenfeng Ma
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Yulu Shi
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Yanxiao Liang
- Department of Pathology, Guangzhou First People's Hospital, Guangzhou, Guangdong, P.R. China
| | - Yujing Tan
- Department of Radiation Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Dongqiang Zeng
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Fangzhen Yao
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Xin Xu
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Zhiqi Yao
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Shaowei Li
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Xiaoxiang Rong
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Na Huang
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Li Sun
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Wangjun Liao
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Min Shi
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R. China.,Corresponding Author: Min Shi, Department of Oncology, Nanfang Hospital, Guangzhou, Guangdong 510515, P.R. China. E-mail:
| |
Collapse
|
21
|
Curcumin as an Epigenetic Therapeutic Agent in Myelodysplastic Syndromes (MDS). Int J Mol Sci 2021; 23:ijms23010411. [PMID: 35008835 PMCID: PMC8745143 DOI: 10.3390/ijms23010411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 12/19/2022] Open
Abstract
Growth Factor Independence 1 (GFI1) is a transcription factor with an important role in the regulation of development of myeloid and lymphoid cell lineages and was implicated in the development of myelodysplastic syndrome (MDS) and acute myeloid leukaemia (AML). Reduced expression of GFI1 or presence of the GFI1-36N (serine replaced with asparagine) variant leads to epigenetic changes in human and murine AML blasts and accelerated the development of leukaemia in a murine model of human MDS and AML. We and other groups previously showed that the GFI1-36N allele or reduced expression of GFI1 in human AML blasts is associated with an inferior prognosis. Using GFI1-36S, -36N -KD, NUP98-HOXD13-tg mice and curcumin (a natural histone acetyltransferase inhibitor (HATi)), we now demonstrate that expansion of GFI1-36N or –KD, NUP98-HODXD13 leukaemic cells can be delayed. Curcumin treatment significantly reduced AML progression in GFI1-36N or -KD mice and prolonged AML-free survival. Of note, curcumin treatment had no effect in GFI1-36S, NUP98-HODXD13 expressing mice. On a molecular level, curcumin treatment negatively affected open chromatin structure in the GFI1-36N or -KD haematopoietic cells but not GFI1-36S cells. Taken together, our study thus identified a therapeutic role for curcumin treatment in the treatment of AML patients (homo or heterozygous for GFI1-36N or reduced GFI1 expression) and possibly improved therapy outcome.
Collapse
|
22
|
Ma W, Chen Y, Xiong W, Li W, Xu Z, Wang Y, Wei Z, Mou T, Wu Z, Cheng M, Zou Y, Zhu Y, Zhou W, Liu F, Geng Y. STOML2 interacts with PHB through activating MAPK signaling pathway to promote colorectal Cancer proliferation. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:359. [PMID: 34781982 PMCID: PMC8591804 DOI: 10.1186/s13046-021-02116-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 09/24/2021] [Indexed: 12/30/2022]
Abstract
BACKGROUND Highly expressed STOML2 has been reported in a variety of cancers, yet few have detailed its function and regulatory mechanism. This research aims to reveal regulatory mechanism of STOML2 and to provide evidence for clinical therapeutics, via exploration of its role in colorectal cancer, and identification of its interacting protein. METHODS Expression level of STOML2 in normal colon and CRC tissue from biobank in Nanfang Hospital was detected by pathologic methods. The malignant proliferation of CRC induced by STOML2 was validated via gain-of-function and loss-of-function experiments, with novel techniques applied, such as organoid culture, orthotopic model and endoscopy monitoring. Yeast two-hybrid assay screened interacting proteins of STOML2, followed by bioinformatics analysis to predict biological function and signaling pathway of candidate proteins. Target protein with most functional similarity to STOML2 was validated with co-immunoprecipitation, and immunofluorescence were conducted to co-localize STOML2 and PHB. Pathway regulated by STOML2 was detected with immunoblotting, and subsequent experimental therapy was conducted with RAF inhibitor Sorafenib. RESULTS STOML2 was significantly overexpressed in colorectal cancer and its elevation was associated with unfavorable prognosis. Knockdown of STOML2 suppressed proliferation of colorectal cancer, thus attenuated subcutaneous and orthotopic tumor growth, while overexpressed STOML2 promoted proliferation in cell lines and organoids. A list of 13 interacting proteins was screened out by yeast two-hybrid assay. DTYMK and PHB were identified to be most similar to STOML2 according to bioinformatics in terms of biological process and signaling pathways; however, co-immunoprecipitation confirmed interaction between STOML2 and PHB, rather than DTYMK, despite its highest rank in previous analysis. Co-localization between STOML2 and PHB was confirmed in cell lines and tissue level. Furthermore, knockdown of STOML2 downregulated phosphorylation of RAF1, MEK1/2, and ERK1/2 on the MAPK signaling pathway, indicating common pathway activated by STOML2 and PHB in colorectal cancer proliferation. CONCLUSIONS This study demonstrated that in colorectal cancer, STOML2 expression is elevated and interacts with PHB through activating MAPK signaling pathway, to promote proliferation both in vitro and in vivo. In addition, combination of screening assay and bioinformatics marks great significance in methodology to explore regulatory mechanism of protein of interest.
Collapse
Affiliation(s)
- Wenhui Ma
- Department of Gastrointestinal Surgery, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), No. 1 Jiazi Road, Lunjiao, Shunde District, Foshan City, 528308, Guangdong Province, China.,Departments of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, Guangdong, China.,Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Yuehong Chen
- Department of Gastrointestinal Surgery, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), No. 1 Jiazi Road, Lunjiao, Shunde District, Foshan City, 528308, Guangdong Province, China.,Departments of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, Guangdong, China.,Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Wenjun Xiong
- Departments of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Guangzhou, China.,Department of Gastrointestinal Surgery, Guangdong Provincial Hospital of Chinese Medicine, the Second Affiliated Hospital of Guangzhou University of Chinese, Guangzhou, Guangdong, China
| | - Wenyi Li
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, Guangdong, China.,Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Zhuoluo Xu
- Departments of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, Guangdong, China.,Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Ying Wang
- Departments of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Zhigang Wei
- Departments of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Guangzhou, China
| | - Tingyu Mou
- Departments of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Guangzhou, China
| | - Zhaokun Wu
- Departments of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, Guangdong, China.,Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Mingzhen Cheng
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, Guangdong, China.,Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Yini Zou
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, Guangdong, China.,Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Yu Zhu
- Departments of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Guangzhou, China
| | - Weijie Zhou
- Department of Gastrointestinal Surgery, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), No. 1 Jiazi Road, Lunjiao, Shunde District, Foshan City, 528308, Guangdong Province, China. .,Departments of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China. .,Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Guangzhou, China. .,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, Guangdong, China. .,Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China.
| | - Feng Liu
- Departments of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China. .,Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Guangzhou, China. .,Department of Colorectal and Anal Surgery, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, 510180, Guangdong, China.
| | - Yan Geng
- Department of Gastrointestinal Surgery, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), No. 1 Jiazi Road, Lunjiao, Shunde District, Foshan City, 528308, Guangdong Province, China.
| |
Collapse
|
23
|
Shi J, Bao M, Wang W, Wu X, Li Y, Zhao C, Liu W. Integrated Profiling Identifies PLOD3 as a Potential Prognostic and Immunotherapy Relevant Biomarker in Colorectal Cancer. Front Immunol 2021; 12:722807. [PMID: 34646265 PMCID: PMC8503557 DOI: 10.3389/fimmu.2021.722807] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 09/08/2021] [Indexed: 12/12/2022] Open
Abstract
Procollagen-Lysine,2-Oxoglutarate 5-Dioxygenase 3 (PLOD3) is related to a variety of human diseases. However, its function in Colorectal cancer (CRC) remains uncertain. PLOD3 expression was analyzed using The Cancer Genome Atlas (TCGA) pan-cancer data. DAVID was used for enrichment analysis of PLOD3-related genes. The correlation between PLOD3 expression and immune cell infiltration was evaluated. Four expression profile datasets (GSE17536, GSE39582, GSE74602, and GSE113513) from Gene Expression Omnibus, and two proteomic datasets were used as validation cohorts for assessing the diagnostic and prognostic value of PLOD3 in CRC. What's more, we performed immunohistochemistry (IHC) staining for PLOD3 in 160 paired CRC specimens and corresponding adjacent non-tumor tissues. PLOD3 was highly expressed in many tumors including CRC. PLOD3 was upregulated in advanced stage CRCs, and high PLOD3 expression was associated with poor survival. High PLOD3 expression was associated with low levels of B cells, CD4+ T cells, M1 macrophages, CD8+ T cells, and multiple immunerelated characteristics. In addition, the high PLOD3 expression group had a higher TIDE score and a lower tumor mutation burden and microsatellite instability, indicating that patients with high PLOD3 expression may be resistant to immunotherapy. Additional datasets and IHC analysis were used to validate the diagnostic and prognostic value of PLOD3 at the mRNA and protein levels in CRC. Patients with non-response to immunotherapy showed increased PLOD3 expression in an immunotherapy treated dataset. PLOD3 is a potential biomarker for CRC diagnosis and prognosis prediction. CRCs with high PLOD3 expression may be resistant to immune checkpoint therapy.
Collapse
Affiliation(s)
- Junhong Shi
- Department of Laboratory Medicine and Central Laboratory, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Meiyu Bao
- Department of Central Laboratory, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
| | - Weifeng Wang
- Department of Central Laboratory, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
| | - Xuan Wu
- Department of Laboratory Medicine and Central Laboratory, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yueying Li
- Department of Laboratory Medicine and Central Laboratory, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Changdong Zhao
- Department of Gastroenterology, Second People's Hospital of Lianyungang City, Lianyungang, China
| | - Weiwei Liu
- Department of Laboratory Medicine and Central Laboratory, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Laboratory Medicine, Shanghai Skin Disease Hospital, Tongji University School of Medicine, Shanghai, China
| |
Collapse
|
24
|
Zheng C, Tan Z. A novel identified pyroptosis-related prognostic signature of colorectal cancer. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2021; 18:8783-8796. [PMID: 34814322 DOI: 10.3934/mbe.2021433] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Colorectal cancer (CRC), one of the most common malignancies worldwide, leads to abundant cancer-related mortalities annually. Pyroptosis, a new kind of programmed cell death, plays a critical role in immune response and tumor progression. Our study aimed to identify a prognostic signature for CRC based on pyroptosis-related genes (PRGs). The difference in PRGs between CRC tissues and normal tissues deposited in the TCGA database was calculated by "limma" R package. The tumor microenvironment (TME) of CRC cases was accessed by the ESTIMATE algorithm. The prognostic PRGs were identified using Cox regression analysis. A least absolute shrinkage and selector operation (LASSO) algorithm was used to calculate the risk scores and construct a clinical predictive model of CRC. Gene Set Enrichment Analysis (GSEA) was performed for understanding the function annotation of the signature in the tumor microenvironment. We found that most PRGs were significantly dysregulated in CRC. Through the LASSO method, three key PRGs were selected to calculate the risk scores and construct the prognostic model for CRC. The risk score was an independent indicator of patient's prognosis. In addition, we classified the CRC patients into two clusters based on risk scores and discovered that CRC patients in cluster 2 underwent worse overall survival and owned higher expression levels of immune checkpoint genes in tumor tissues. In conclusion, our study identified a PRG-related prognostic signature for CRC, according to which we classified the CRC patients into two clusters with distinct prognosis and immunotherapy potential.
Collapse
Affiliation(s)
- Chen Zheng
- First Department of General Surgery, Xi'an Central Hospital, Xi'an, Shaanxi Province, China
| | - Zhaobang Tan
- Department of digestive surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| |
Collapse
|
25
|
Gu Y, Tang S, Wang Z, Cai L, Lian H, Shen Y, Zhou Y. A pan-cancer analysis of the prognostic and immunological role of β-actin (ACTB) in human cancers. Bioengineered 2021; 12:6166-6185. [PMID: 34486492 PMCID: PMC8806805 DOI: 10.1080/21655979.2021.1973220] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Beta-actin (ACTB), a highly conserved cytoskeleton structural protein, has been regarded as a common housekeep gene and used as a reference gene for years. However, accumulating evidence indicates that ACTB is abnormally expressed in multiple cancers and hence changes the cytoskeleton to affect the invasiveness and metastasis of tumors. This study aimed to investigate the function and clinical significance of ACTB in pan-cancer. The role of ACTB for prognosis and immune regulation across 33 tumors was explored based on the datasets of gene expression omnibus and the cancer genome atlas. Differential expression of ACTB was found between cancer and adjacent normal tissues, and significant associations was found between ACTB expression and prognosis of tumor patients. In most cancers, ACTB expression was associated with immune cells infiltration, immune checkpoints and other immune modulators. Relevance between ACTB and metastasis and invasion was identified in various types of cancers by CancerSEA. Moreover, focal adhesion and actin regulation-associated pathways were included in the functional mechanisms of ACTB. The expression of ACTB was verified by quantitative real-time polymerase chain reaction. Knockdown of ACTB inhibited head and neck squamous carcinoma cell migration and invasion by NF-κB and Wnt/β-catenin pathways. Our first pan-cancer study of ACTB offers insight into the prognostic and immunological roles of ACTB across different tumors, indicating ACTB may be a potential biomarker for poor prognosis and immune infiltration in cancers, and the role of ACTB as a reference gene in cancers was challenged.
Collapse
Affiliation(s)
- Yuxi Gu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Shouyi Tang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Zhen Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Luyao Cai
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Haosen Lian
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yingqiang Shen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yu Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| |
Collapse
|
26
|
Español A, Salem A, Sanchez Y, Sales ME. Breast cancer: Muscarinic receptors as new targets for tumor therapy. World J Clin Oncol 2021; 12:404-428. [PMID: 34189066 PMCID: PMC8223712 DOI: 10.5306/wjco.v12.i6.404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/26/2021] [Accepted: 06/02/2021] [Indexed: 02/06/2023] Open
Abstract
The development of breast cancer is a complex process that involves the participation of different factors. Several authors have demonstrated the overexpression of muscarinic acetylcholine receptors (mAChRs) in different tumor tissues and their role in the modulation of tumor biology, positioning them as therapeutic targets in cancer. The conventional treatment for breast cancer involves surgery, radiotherapy, and/or chemotherapy. The latter presents disadvantages such as limited specificity, the appearance of resistance to treatment and other side effects. To prevent these side effects, several schedules of drug administration, like metronomic therapy, have been developed. Metronomic therapy is a type of chemotherapy in which one or more drugs are administered at low concentrations repetitively. Recently, two chemotherapeutic agents usually used to treat breast cancer have been considered able to activate mAChRs. The combination of low concentrations of these chemotherapeutic agents with muscarinic agonists could be a useful option to be applied in breast cancer treatment, since this combination not only reduces tumor cell survival without affecting normal cells, but also decreases pathological neo-angiogenesis, the expression of drug extrusion proteins and the cancer stem cell fraction. In this review, we focus on the previous evidences that have positioned mAChRs as relevant therapeutic targets in breast cancer and analyze the effects of administering muscarinic agonists in combination with conventional chemotherapeutic agents in a metronomic schedule.
Collapse
Affiliation(s)
- Alejandro Español
- Laboratory of Immunopharmacology and Tumor Biology, CEFYBO CONICET University of Buenos Aires, Buenos Aires C1121ABG, Argentina
| | - Agustina Salem
- Laboratory of Immunopharmacology and Tumor Biology, CEFYBO CONICET University of Buenos Aires, Buenos Aires C1121ABG, Argentina
| | - Yamila Sanchez
- Laboratory of Immunopharmacology and Tumor Biology, CEFYBO CONICET University of Buenos Aires, Buenos Aires C1121ABG, Argentina
| | - María Elena Sales
- Laboratory of Immunopharmacology and Tumor Biology, CEFYBO CONICET University of Buenos Aires, Buenos Aires C1121ABG, Argentina
| |
Collapse
|
27
|
Gao H, Liang J, Duan J, Chen L, Li H, Zhen T, Zhang F, Dong Y, Shi H, Han A. A Prognosis Marker SLC2A3 Correlates With EMT and Immune Signature in Colorectal Cancer. Front Oncol 2021; 11:638099. [PMID: 34211835 PMCID: PMC8240412 DOI: 10.3389/fonc.2021.638099] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 05/27/2021] [Indexed: 12/26/2022] Open
Abstract
SLC2A3 is a membrane transporter that belongs to the solute carrier family, whose function includes transmembrane transport and glucose transmembrane transport activity. To clarify the expression and role of SLC2A3 in colorectal cancer (CRC), we analyzed the TCGA and GEO databases and found that SLC2A3 mRNA levels were significantly higher in CRC tissues than that in adjacent non-tumor tissues. Furthermore, high expression of SLC2A3 predicted poor overall survival and disease free survival for CRC patients. For validation, we collected 174 CRC samples and found that SLC2A3 expression was higher in CRC tissues than that in adjacent non-tumor colorectal mucosa tissues by immunohistochemistry staining. Further study showed that high expression of SLC2A3 was enriched in epithelial–mesenchymal transition (EMT) classical pathway, interferon-γ pathway by GSEA analysis enrichment, indicating that SLC2A3 may play a key role in the progression of CRC through EMT and immune response, which also has been validated by the global gene expression profiling of human CRC cell lines. The expression of SLC2A3 was positively correlated with CD4 and CD8+T cells by using TIMER and EPIC algorithm, respectively. SLC2A3 knockdown suppressed migration and inhibited the expression of Vimentin and MMP9 in CRC cell line SW480 and RKO. Meanwhile, PD-L1 expression was also significantly attenuated in SW480 and RKO cells transfected with SLC2A3 siRNA. The result suggests that SLC2A3 may be involved in the immune response of CRC by regulating PD-L1 immune checkpoint. In our series, SLC2A3 and PD-L1 positive expression was 74% (128/174) and 22% (39/174) of CRC, respectively. SLC2A3 expression was significantly associated with perineural invasion in CRC patients. In conclusion, SLC2A3 may play an important role in progression of CRC by regulating EMT and PD-L1 mediated immune responses.
Collapse
Affiliation(s)
- Huabin Gao
- Department of Pathology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Jiangtao Liang
- Department of Pathology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Jing Duan
- Department of Pathology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Lin Chen
- Department of Pathology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Hui Li
- Department of Pathology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Tiantian Zhen
- Department of Pathology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Fenfen Zhang
- Department of Pathology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yu Dong
- Department of Pathology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Huijuan Shi
- Department of Pathology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Anjia Han
- Department of Pathology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| |
Collapse
|
28
|
Ye W, Luo C, Liu F, Liu Z, Chen F. CD96 Correlates With Immune Infiltration and Impacts Patient Prognosis: A Pan-Cancer Analysis. Front Oncol 2021; 11:634617. [PMID: 33680972 PMCID: PMC7935557 DOI: 10.3389/fonc.2021.634617] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 01/05/2021] [Indexed: 01/08/2023] Open
Abstract
Background Immunotherapy has significantly improved patient outcomes, but encountered obstacles recently. CD96, a novel immune checkpoint expressed on T cells and natural killer (NK) cells, is essential for regulating immune functions. However, how CD96 correlating with immune infiltration and patient prognosis in pan-cancer remains unclear. Methods HPA, TCGA, GEO, GTEx, Oncomine, TIMER2.0, PrognoScan, Linkedomics, Metascape, and GEPIA2 databases were used to analyze CD96 in cancers. Visualization of data was mostly achieved by R language, version 4.0.2. Results In general, CD96 was differentially expressed between most cancer and adjacent normal tissues. CD96 significantly impacted the prognosis of diverse cancers. Especially, high CD96 expression was associated with poorer overall survival (OS) and disease-specific survival (DSS) in the TCGA lower grade glioma (LGG) cohort (OS, HR = 2.18, 95% CI = 1.79–2.66, P < 0.001). The opposite association was significantly observed in skin cutaneous melanoma (SKCM) cohort (OS, HR = 0.96, 95% CI = 0.94–0.98, P < 0.001). Notably, SKCM samples demonstrated the highest CD96 mutation frequency among all cancer types. Furthermore, in most cancers, CD96 expression level was significantly correlated with expression levels of recognized immune checkpoints and abundance of multiple immune infiltrates including CD8+ T cells, dendric cells (DCs), macrophages, monocytes, NK cells, neutrophils, regulatory T cells (Tregs), and follicular helper T cells (Tfh). CD96 was identified as a risk factor, protective factor, and irrelevant variable in LGG, SKCM and adrenocortical carcinoma (ACC), respectively. CD96 related genes were involved in negative regulation of leukocyte in LGG, however, involved in multiple positive immune processes in SKCM. Furthermore, CD96 was significantly associated with particular immune marker subsets. Importantly, it strongly correlated with markers of type 1 helper T cell (Th1) in SKCM, but not in LGG or ACC either. Conclusions CD96 participates in diverse immune responses, governs immune cell infiltration, and impacts malignant properties of various cancer types, thus standing as a potential biomarker for determining patient prognosis and immune infiltration in multiple cancers, especially in glioma and melanoma.
Collapse
Affiliation(s)
- Wenrui Ye
- Department of Neurosurgery, Xiangya Hospital, Central South University (CSU), Changsha, China.,Clinical Medicine Eight-year Program, Xiangya Medical School of Central South University, Changsha, China
| | - Cong Luo
- Clinical Medicine Eight-year Program, Xiangya Medical School of Central South University, Changsha, China.,Department of Urology, Xiangya Hospital, Central South University (CSU), Changsha, China
| | - Fangkun Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University (CSU), Changsha, China
| | - Zhixiong Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University (CSU), Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University (CSU), Changsha, China
| | - Fenghua Chen
- Department of Neurosurgery, Xiangya Hospital, Central South University (CSU), Changsha, China
| |
Collapse
|
29
|
Lu L, Li S, Zhang Y, Luo Z, Chen Y, Ma J, Chen P, Wang W, Pu J, Wang J. GFI1-Mediated Upregulation of LINC00675 as a ceRNA Restrains Hepatocellular Carcinoma Metastasis by Sponging miR-942-5p. Front Oncol 2021; 10:607593. [PMID: 33489916 PMCID: PMC7820889 DOI: 10.3389/fonc.2020.607593] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 11/11/2020] [Indexed: 01/18/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a common malignant liver tumor worldwide. Tumor recurrence and metastasis contribute to the bad clinical outcome of HCC patients. Substantial studies have displayed lncRNAs modulate various tumorigenic processes of many cancers. Our current work was aimed to investigate the function of LINC00675 in HCC and to recognize the potential interactions between lncRNAs and microRNAs. GFI1 can exhibit a significant role in the progression of human malignant tumors. Firstly, GFI1 was identified using real-time PCR in HCC tissues and cells. In this work, we indicated GFI1 was remarkably reduced in HCC tissues and cells. Meanwhile, GFI1 specifically interacted with the promoter of LINC00675. Up-regulation of LINC00675 obviously repressed the migration and invasion capacity of SMCC-7721 and QGY-7703 cells in vitro. Moreover, decrease of LINC00675 competitively bound to miR-942-5p that contributed to the miRNA-mediated degradation of GFI1, thus facilitated HCC metastasis. The ceRNA function of LINC00675 in HCC cells was assessed and confirmed using RNA immunoprecipitation assay and RNA pull-down assays in our work. Additionally, we proved overexpression of miR-942-5p promoted HCC progression, which was reversed by the up-regulation of GFI1. In summary, LINC00675 might act as a prognostic marker for HCC, which can inhibit HCC development via regulating miR-942-5p and GFI1.
Collapse
Affiliation(s)
- Libai Lu
- Department of Hepatobiliary Surgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Shubo Li
- Department of Biochemistry and Molecular Biology, Youjiang Medical University for Nationalities, Baise, China
| | - Ying Zhang
- Library of Youjiang Medical University for Nationalities, Baise, China
| | - Zongjiang Luo
- Department of Hepatobiliary Surgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Yichen Chen
- Department of Hepatobiliary Surgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Jiasheng Ma
- Department of Hepatobiliary Surgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Pengyu Chen
- Department of Hepatobiliary Surgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Wei Wang
- Department of Hepatobiliary Surgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Jian Pu
- Department of Hepatobiliary Surgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Jianchu Wang
- Department of Hepatobiliary Surgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| |
Collapse
|
30
|
Zhang Y, Zhang J, Mao L, Li X. Long noncoding RNA HCG11 inhibited growth and invasion in cervical cancer by sponging miR-942-5p and targeting GFI1. Cancer Med 2020; 9:7062-7071. [PMID: 32794340 PMCID: PMC7541137 DOI: 10.1002/cam4.3203] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/12/2020] [Accepted: 05/13/2020] [Indexed: 12/11/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) act as essential regulators in cancer tumorigenesis. Our study aimed to explore the underlying mechanism of lncRNA human leukocyte antigen complex group 11 (HCG11) in cervical cancer (CC) progression. Long noncoding RNA HCG11 was downregulated in CC. Functional assays demonstrated that lncRNA HCG11 inhibited CC cell proliferation and invasion. Then, we confirmed that lncRNA HCG11 could directly bind to miR-942-5p. Moreover, inhibition of miR-942-5p suppressed the growth and invasion of CC cells, and growth factor-independent transcription repressor 1 (GFI1) gene was the target gene of miR-942-5p. Long noncoding RNA HCG11 increased the expression of GFI1 and suppressed cell proliferation and invasion by acting as a miR-942-5p sponge. Finally, the overexpression of lncRNA HCG11 suppressed the proliferation and metastasis of CC cells in vivo.
Collapse
Affiliation(s)
- Yan Zhang
- Department of Obstetrics and GynecologyRenmin Hospital of Wuhan UniversityWuhanChina
| | - Jun Zhang
- Department of Obstetrics and GynecologyRenmin Hospital of Wuhan UniversityWuhanChina
| | - Lin Mao
- Department of Obstetrics and GynecologyRenmin Hospital of Wuhan UniversityWuhanChina
| | - Xing Li
- Department of Obstetrics and GynecologyRenmin Hospital of Wuhan UniversityWuhanChina
| |
Collapse
|
31
|
Ashour N, Angulo JC, González-Corpas A, Orea MJ, Lobo MVT, Colomer R, Colás B, Esteller M, Ropero S. Epigenetic Regulation of Gfi1 in Endocrine-Related Cancers: a Role Regulating Tumor Growth. Int J Mol Sci 2020; 21:ijms21134687. [PMID: 32630147 PMCID: PMC7370116 DOI: 10.3390/ijms21134687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 06/25/2020] [Accepted: 06/29/2020] [Indexed: 02/06/2023] Open
Abstract
Prostate and breast cancer constitute the most common cancers among men and women worldwide. The aging population is one of the main risk factors for prostate and breast cancer development and accumulating studies link aging with epigenetic changes. Growth factor independence-1 (Gfi1) is a transcriptional repressor with an important role in human malignancies, including leukemia, colorectal carcinoma, and lung cancer, but its role in prostate and breast cancer is unknown. We have found that Gfi1 epigenetic silencing is a common event in prostate and breast cancer. Gfi1 re-expression in prostate and breast cancer cell lines displaying Gfi1 epigenetic silencing decreases cell proliferation, reduced colony formation density, and tumor growth in nude mice xenografts. In addition, we found that Gfi1 repress alpha 1-anti-trypsin (AAT) and alpha 1-anti-chymotrypsin (ACT) expression, two genes with important functions in cancer development, suggesting that Gfi1 silencing promotes tumor growth by increasing AAT and ACT expression in our system. Finally, Gfi1 epigenetic silencing could be a promising biomarker for prostate cancer progression because it is associated with shorter disease-free survival. In conclusion, our findings strongly indicate that Gfi1 epigenetic silencing in prostate and breast cancer could be a crucial step in the development of these two-well characterized endocrine related tumors.
Collapse
Affiliation(s)
- Nadia Ashour
- Departamento de Biología de Sistemas, Unidad Docente de Bioquímica y Biología Molecular, Universidad de Alcalá, Alcalá de Henares, 28054 Madrid, Spain; (N.A.); (A.G.-C.); (M.J.O.); (B.C.)
| | - Javier C. Angulo
- Servicio de Urología, Hospital Universitario de Getafe, Fundación para la Investigación Biomédica del Hospital Universitario de Getafe, Universidad Europea de Madrid, Getafe, 28905 Madrid, Spain;
| | - Ana González-Corpas
- Departamento de Biología de Sistemas, Unidad Docente de Bioquímica y Biología Molecular, Universidad de Alcalá, Alcalá de Henares, 28054 Madrid, Spain; (N.A.); (A.G.-C.); (M.J.O.); (B.C.)
| | - María J. Orea
- Departamento de Biología de Sistemas, Unidad Docente de Bioquímica y Biología Molecular, Universidad de Alcalá, Alcalá de Henares, 28054 Madrid, Spain; (N.A.); (A.G.-C.); (M.J.O.); (B.C.)
| | - María V. T. Lobo
- Departamento de Biomedicina y Biotecnología, Universidad de Alcalá; Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), 28054 Madrid, Spain;
| | - Ramón Colomer
- Medical Oncology Department, Instituto De Investigación Sanitaria La Princesa, HU La Princesa, 28029 Madrid, Spain;
- Department of Medicine, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Begoña Colás
- Departamento de Biología de Sistemas, Unidad Docente de Bioquímica y Biología Molecular, Universidad de Alcalá, Alcalá de Henares, 28054 Madrid, Spain; (N.A.); (A.G.-C.); (M.J.O.); (B.C.)
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Catalonia, Spain;
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), 28040 Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), 08028 Barcelona, Catalonia, Spain
| | - Santiago Ropero
- Departamento de Biología de Sistemas, Unidad Docente de Bioquímica y Biología Molecular, Universidad de Alcalá, Alcalá de Henares, 28054 Madrid, Spain; (N.A.); (A.G.-C.); (M.J.O.); (B.C.)
- Correspondence:
| |
Collapse
|
32
|
Wang YR, Meng LB, Su F, Qiu Y, Shi JH, Xu X, Luo QF. Insights regarding novel biomarkers and the pathogenesis of primary colorectal carcinoma based on bioinformatic analysis. Comput Biol Chem 2020; 85:107229. [PMID: 32058945 DOI: 10.1016/j.compbiolchem.2020.107229] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/29/2020] [Accepted: 02/02/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Biomarkers are important in the study of tumor processes for early detection and precise treatment. The biomarkers that have been previously detected are not useful for clinical application for primary colorectal carcinoma (PCRC). The aim of this study was to explore clinically valuable biomarkers of PCRC based on integrated bioinformatic analysis. MATERIAL AND METHODS Gene expression data were acquired from the GSE41258 dataset, and the differentially expressed genes were determined between PCRC and normal colorectal samples. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were implemented via Gene Set Enrichment Analysis. A protein-protein interaction (PPI) network was constructed. The significant modules and hub genes were screened and identified in the PPI network. RESULTS A total of 202 DEGs were identified, including 58 upregulated and 144 downregulated genes in PCRC samples compared to those in normal colorectal samples. Enrichment analysis demonstrated that the gene sets enriched in PCRC were significantly related to bicarbonate transport, regulation of sodium ion transport, potassium ion homeostasis, regulation of telomere maintenance, and other processes. A total of 10 hub genes was identified by cytoHubba: PYY, CXCL3, CXCL11, CXCL8, CXCL12, CCL20, MMP3, P2RY14, NPY1R, and CXCL1. CONCLUSION The hub genes, such as NPY1R, P2RY14, and CXCL12, and the electrolyte disequilibrium resulting from the differential expression of genes, especially bicarbonate imbalance, may provide novel insights and evidence for the future diagnosis and targeted therapy of PCRC.
Collapse
Affiliation(s)
- Yi-Ran Wang
- Department of Gastroenterology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China.
| | - Ling-Bing Meng
- Department of Neurology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China.
| | - Fei Su
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China.
| | - Yong Qiu
- Department of Anesthesia, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China.
| | - Ji-Hua Shi
- Department of Gastroenterology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China.
| | - Xue Xu
- Department of Gastroenterology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China.
| | - Qing-Feng Luo
- Department of Gastroenterology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China.
| |
Collapse
|