1
|
Zhao X, Li X, Miao Z. Identification and validation of regulatory T cell-associated gene signatures to predict colon adenocarcinoma prognosis. Int Immunopharmacol 2024; 132:112034. [PMID: 38588631 DOI: 10.1016/j.intimp.2024.112034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 03/17/2024] [Accepted: 04/05/2024] [Indexed: 04/10/2024]
Abstract
Colon adenocarcinoma (COAD) is a common cause of cancer-related death. Due to the difficulty in early diagnosis and drug resistance, conventional treatments are difficult to be effective. Some studies have found that the functional recovery of T cells in the tumor microenvironment, especially regulatory T cells (Tregs), plays an important role in the progression of cancer. This study used the TCGA data set, clinical information and RNA-seq data of COAD patients to construct a Tregs-related risk score (TRS) through methods such as WGCNA, single-factor Cox, multi-factor Cox and random survival forest (RSF). Moreover, we also used the TCGA test set and internal validation set to verify the predictive ability of TRS, and used functional enrichment analysis and somatic mutation analysis to mine genes related to TRS, such as like thrombin/trypsin receptor 2 (F2RL2), inhibin subunit beta B (INHBB) and melanoma antigen family A12 (MAGEA12). Moreover, this study confirmed the expression of these prognostic genes using scRNA-seq data. We also performed qPCR analysis of various genes in normal and cancerous colon cancer cell lines to verify that these genes indeed play a role in CODA patients. We also constructed a mouse CODA model to study and evaluate the impact of key genes such as MAGEA12 on tumor growth in mice. This study explores the important role of Treg cells in the prognosis of COAD and discovers some potential biomarkers for the occurrence and development of COAD, which provides some new ideas for the treatment of COAD.
Collapse
Affiliation(s)
- Xiaomeng Zhao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, PR China
| | - Xuanwen Li
- Department of Nutritional, Tianjin Beichen Hospital of Chinese Medicine, Tianjin, PR China
| | - Zhi Miao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, PR China.
| |
Collapse
|
2
|
Feng X, He S, Chen Y, Zhang L. Deubiquitinase BRCC3 promotes the migration, invasion and EMT progression of colon adenocarcinoma by stabilizing MET expression. Genes Genomics 2024; 46:637-646. [PMID: 38470543 DOI: 10.1007/s13258-024-01508-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 02/24/2024] [Indexed: 03/14/2024]
Abstract
BACKGROUND Breast cancer type 1 susceptibility protein/breast cancer type 2 susceptibility protein-containing complex subunit 3 (BRCC3), a deubiquitinase (DUBs), is overexpressed in various cancers. However, the underlying biological roles of BRCC3 in adenocarcinoma colon (COAD) have yet to be decrypted. OBJECTIVE In this work, we explored the potential biological function of BRCC3 in the natural process of COAD cells. METHODS The expression levels of BRCC3 in COAD tissues and cell lines were investigated via quantitative real time polymerase chain reaction and western blotting analyses. Meanwhile, short hairpin RNAs targeting BRCC3 (sh-BRCC3) or mesenchymal-epithelial transition factor (MET) (sh-MET) were used to investigate the biological function, including proliferation, apoptosis, migration, invasion, and epithelial-mesenchymal transition (EMT) progression in COAD cells. Furthermore, the expression levels of EMT-related biomarkers were detected with western blotting analysis. Furthermore, we also performed Co-IP assay to identify the correlation between BRCC3 and MET. RESULTS BRCC3 expression was increased in COAD tissues and cell lines. ShRNA-mediated downmodulation of BRCC3 in COAD cell lines induced EMT progression. BRCC3 knockdown resulted in decreased migration as well as invasion and increased apoptosis of SW480 and Lovo cells. Besides, MET was regulated by BRCC3 and involved in the migration, invasion, and EMT in SW480 and Lovo cells. Finally, we uncovered that the overexpressed MET reversed the effects of BRCC3 knockdown in COAD cell development. CONCLUSIONS BRCC3 acted as a critical factor in the development of COAD by deubiquitinating and stabilizing MET, which might provide an emerging biomarker for the therapeutic and diagnosis strategy of COAD.
Collapse
Affiliation(s)
- Xiu Feng
- Department of Oncology, Nantong First People's Hospital and Affiliated Hospital 2 of Nantong University, No.666 Shengli Road, Chongchuan District, Nantong, 226000, Jiangsu, China
| | - Shengnan He
- Department of Oncology, Nantong First People's Hospital and Affiliated Hospital 2 of Nantong University, No.666 Shengli Road, Chongchuan District, Nantong, 226000, Jiangsu, China
| | - Ying Chen
- Department of Oncology, Nantong First People's Hospital and Affiliated Hospital 2 of Nantong University, No.666 Shengli Road, Chongchuan District, Nantong, 226000, Jiangsu, China.
| | - Liang Zhang
- Department of Oncology, Nantong First People's Hospital and Affiliated Hospital 2 of Nantong University, No.666 Shengli Road, Chongchuan District, Nantong, 226000, Jiangsu, China.
| |
Collapse
|
3
|
Chen J, Wang Z, Zhu Q, Ren S, Xu Y, Wang G, Zhou L. Comprehensive analysis and experimental verification of the mechanism of action of T cell-mediated tumor-killing related genes in Colon adenocarcinoma. Transl Oncol 2024; 43:101918. [PMID: 38412662 PMCID: PMC10907202 DOI: 10.1016/j.tranon.2024.101918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 02/07/2024] [Accepted: 02/17/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is a prevalent malignancy of the digestive tract. A new prognostic scoring model for colon adenocarcinoma (COAD) is developed in this study based on the genes involved in tumor cell-mediated killing of T cells (GSTTKs), accurately stratifying COAD patients, thus improving the current status of personalized treatment. METHOD The GEO and TCGA databases served as the sources of the data for the COAD cohort. This study identified GSTTKs-related genes in COAD through single-factor Cox analysis. These genes were used to categorize COAD patients into several subtypes via unsupervised clustering analysis. The biological pathways and tumor microenvironments of different subgroups were compared. We performed intersection analysis between different subtypes to obtain intersection genes. Single-factor Cox regression analysis and Lasso-Cox analysis were conducted to establish clinical prognostic models. Two methods are used to assess the accuracy of model predictions: ROC and Kaplan-Meier analysis. Next, the prediction model was further validated in the validation cohort. Differential immune cell infiltration between various risk categories was identified via single sample gene set enrichment analysis (ssGSEA). The COAD model's gene expression was validated via single-cell data analysis and experiments. RESULT We established two distinct GSTTKs-related subtypes. Biological processes and immune cell tumor invasion differed significantly between various subtypes. Clinical prognostic models were created using five GSTTKs-related genes. The model's risk score independently served as a prognostic factor. COAD patients were classified as low- or high-risk depending on their risk scores. Patients in the low-risk category recorded a greater chance of surviving. The outcomes from the validation cohort match those from the training set. Risk scores and several tumor-infiltrating immune cells were strongly correlated, according to ssGSEA. Single-cell data illustrated that the model's genes were linked to several immune cells. The experimental results demonstrated a significant increase in the expression of HOXC6 in colon cancer tissue. CONCLUSION Our research findings established a new gene signature for COAD. This gene signature helps to accurately stratify the risk of COAD patients and improve the current status of individualized care.
Collapse
Affiliation(s)
- Jing Chen
- Department of Medical Laboratory, Clinical Medical College, Yangzhou University, Northern Jiangsu People's Hospital, Yangzhou, Jiangsu, 225009, China
| | - Zhengfang Wang
- Department of Medical Laboratory, Clinical Medical College, Yangzhou University, Northern Jiangsu People's Hospital, Yangzhou, Jiangsu, 225009, China
| | - Qin Zhu
- Department of Trauma Hand Surgery, Dalian Third People's Hospital, Dalian 116000, China
| | - Shiqi Ren
- Department of Hand Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| | - Yanhua Xu
- Department of Medical Laboratory, Clinical Medical College, Yangzhou University, Northern Jiangsu People's Hospital, Yangzhou, Jiangsu, 225009, China
| | - Guangzhou Wang
- Department of Medical Laboratory, Clinical Medical College, Yangzhou University, Northern Jiangsu People's Hospital, Yangzhou, Jiangsu, 225009, China.
| | - Lin Zhou
- Department of Medical Laboratory, Clinical Medical College, Yangzhou University, Northern Jiangsu People's Hospital, Yangzhou, Jiangsu, 225009, China.
| |
Collapse
|
4
|
Hao L, Lu W, Wu J, Chen Y, Xu D, Wang P. Construction and verification of a histone deacetylases-related prognostic signature model for colon cancer. Sci Rep 2024; 14:8983. [PMID: 38637684 PMCID: PMC11026370 DOI: 10.1038/s41598-024-59724-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 04/15/2024] [Indexed: 04/20/2024] Open
Abstract
Histone deacetylases (HDACs) contribute significantly to the initiation, progression, and prognosis of colorectal adenocarcinoma (COAD). Additionally, HDACs regulate the tumor microenvironment, immune escape, and tumor stem cells, and are closely linked to COAD prognosis. We developed a prognostic model for COAD that incorporates HDACs to evaluate their specific roles. The COAD dataset containing clinical and mutation data was collected using the TCGA and GEO databases to obtain genes associated with HDAC. LASSO analysis and univariate and multivariate Cox regression analysis were used to determine the presence of prognostic genes. Multivariate Cox analysis was also used to determine risk scores for HDAC-related features. Furthermore, genomic alterations, immune infiltration, and drug response were compared between high- and low-risk groups. Cellular experiments validated the potential regulatory role of BRD3 on COAD proliferation, migration, and apoptosis. The median risk scores, calculated based on the characteristics, demonstrated a more significant prognostic improvement in patients in the low-risk group. Furthermore, HDAC-related features were identified as important independent prognostic factors for patients with COAD. Additionally, genomic mutation status, immune infiltration, and function, as well as response to immunotherapy and chemotherapy, were found to be associated with risk scores. Subgroup analyses indicate that anti-PD-1 therapy may be beneficial for patients in the low-risk group. Additionally, a decrease in risk score was associated with a decrease in immune infiltration. Finally, HCT116 and HT29 cells exhibited inhibition of BRD3 gene proliferation and migration, as well as promotion of apoptosis. In patients with COAD, HDAC-related characteristics may be useful in predicting survival and selecting treatment.
Collapse
Affiliation(s)
- Lei Hao
- Thyroid Hernia Surgery, The First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, 510405, People's Republic of China
| | - Weiqi Lu
- Thyroid Hernia Surgery, The First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, 510405, People's Republic of China
| | - Jianyu Wu
- Thyroid Hernia Surgery, The First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, 510405, People's Republic of China
| | - Yuzhong Chen
- Thyroid Hernia Surgery, The First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, 510405, People's Republic of China
| | - Dongni Xu
- Department of Anesthesiology, Sun Yat-Sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, People's Republic of China.
| | - Peizong Wang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, People's Republic of China.
| |
Collapse
|
5
|
Cheng S, Li M, Li C, Dai Y, Zhuo J, Wang J, Qian J, Hao Z. JAML inhibits colorectal carcinogenesis by modulating the tumor immune microenvironment. In Vitro Cell Dev Biol Anim 2024:10.1007/s11626-024-00881-8. [PMID: 38625487 DOI: 10.1007/s11626-024-00881-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 02/09/2024] [Indexed: 04/17/2024]
Abstract
It is necessary to explore new targets for the treatment of colon adenocarcinoma (COAD) according to the tumor microenvironment. The expression levels of JAML and CXADR were analyzed by bioinformatics analysis and validation of clinical samples. JAML over-expression CD8+ T cell line was constructed, and the proliferation activity was detected by MTT. The production of inflammatory factors was detected by ELISA. The expression of immune checkpoint PD-1 and TIM-3 was detected by Western blot. The apoptosis level was detected by flow cytometry and apoptosis markers. The AOM/DSS mouse model of colorectal cancer was constructed. The expression levels of JAML, CXADR and PD-1 were detected by PCR and Western blot, and the proportion of CD8+ T cells and exhausted T cells were detected by flow cytometry. The expression levels of JAML and CXADR were significantly decreased in colon cancer tissues. Overexpression of JAML can promote the proliferation of T cells, secrete a variety of inflammatory factors. Overexpression of CXADR can reduce the proliferation of colorectal cancer cells, promote apoptosis, and down-regulate the migration and invasion ability of tumor cells. Both JAML agonists and PD-L1 inhibitors can effectively treat colorectal cancer, and the combined use of JAML agonists and PD-L1 inhibitors can enhance the effect. JAML can promote the proliferation and toxicity of CD8+ T cells and down-regulate the expression of immune checkpoints in colon cancer. CXADR can inhibit the proliferation of cancer cells and promote the apoptosis. JAML agonist can effectively treat colorectal cancer by regulating CD8+ T cells.
Collapse
Affiliation(s)
- Shiliang Cheng
- Department of Clinical Laboratory, Shandong Provincial Third Hospital, Shandong University, 250031, Jinan, People's Republic of China.
| | - Meng Li
- Department of Clinical Laboratory, Shandong Provincial Third Hospital, Shandong University, 250031, Jinan, People's Republic of China
| | - Chunguang Li
- Emergency Medicine Department, Shandong Provincial Third Hospital, Shandong University, Jinan, People's Republic of China
| | - Yonggang Dai
- Department of Clinical Laboratory, Shandong Provincial Third Hospital, Shandong University, 250031, Jinan, People's Republic of China
| | - Jinhua Zhuo
- Department of Clinical Laboratory, Shandong Provincial Third Hospital, Shandong University, 250031, Jinan, People's Republic of China
| | - Jue Wang
- Department of Clinical Laboratory, Shandong Provincial Third Hospital, Shandong University, 250031, Jinan, People's Republic of China
| | - Jingrong Qian
- Department of Clinical Laboratory, Shandong Provincial Third Hospital, Shandong University, 250031, Jinan, People's Republic of China
| | - Zhihao Hao
- Department of Clinical Laboratory, Shandong Provincial Third Hospital, Shandong University, 250031, Jinan, People's Republic of China
| |
Collapse
|
6
|
Gama JM, Oliveira RC, Fonseca R, Cipriano MA, Casanova J. Extraskeletal myxoid chondrosarcoma metastasis to a Meckel's diverticulum adenocarcinoma. Rev Esp Patol 2024; 57:141-145. [PMID: 38599736 DOI: 10.1016/j.patol.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 04/12/2024]
Abstract
Extraskeletal myxoid chondrosarcoma is a rare soft tissue tumour with a high local and distant metastasis rate and limited response to chemotherapy. Meckel's diverticulum is the most frequent congenital anomaly, and it is associated with a considerable risk of malignant transformation. In this case report, we describe a 50-year-old female patient with a history of extraskeletal myxoid chondrosarcoma of the lower limb and metastasis to the forearm who went to the emergency department with abdominal pain. The investigations revealed a caecal volvulus. A lesion in the middle third of the ileum was incidentally discovered and removed during surgery. Pathology examination revealed a Meckel's diverticulum adenocarcinoma, with metastasis of extraskeletal myxoid chondrosarcoma. Resection was complete; however, the patient had diffuse metastatic pulmonary disease and died eight months later due to disease progression. This mechanism of tumour-to-tumour metastasis is described in other locations, but, regarding the Meckel's diverticulum, this is a unique situation, previously unreported in the literature.
Collapse
Affiliation(s)
- João Martins Gama
- Centro Hospitalar e Universitário de Coimbra, Pathology Department, Coimbra, Portugal; Doctoral Programme in Molecular Pathology and Genetics, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Porto, Portugal.
| | - Rui Caetano Oliveira
- Centro Hospitalar e Universitário de Coimbra, Pathology Department, Coimbra, Portugal; University of Coimbra, Faculty of Medicine, Coimbra Institute for Clinical and Biomedical Research Area of Environment Genetics and Oncobiology, Coimbra, Portugal
| | - Rúben Fonseca
- Centro Hospitalar e Universitário de Coimbra, Pathology Department, Coimbra, Portugal
| | | | - José Casanova
- University of Coimbra, Faculty of Medicine, Coimbra Institute for Clinical and Biomedical Research Area of Environment Genetics and Oncobiology, Coimbra, Portugal; Orthopedics Department, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal; Faculdade de Medicina da Universidade de Coimbra, Coimbra, Portugal
| |
Collapse
|
7
|
Bai H, Yan DS, Chen YL, Li QZ, Qi YC. Potential biomarkers: The hypomethylation of cg18949415 and cg22193385 sites in colon adenocarcinoma. Comput Biol Med 2024; 169:107884. [PMID: 38154158 DOI: 10.1016/j.compbiomed.2023.107884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/20/2023] [Accepted: 12/18/2023] [Indexed: 12/30/2023]
Abstract
Overall cancer hypomethylation had been identified in the past, but it is not clear exactly which hypomethylation site is the more important for the occurrence of cancer. To identify key hypomethylation sites, we studied the effect of hypomethylation in twelve regions on gene expression in colon adenocarcinoma (COAD). The key DNA methylation sites of cg18949415, cg22193385 and important genes of C6orf223, KRT7 were found by constructing a prognostic model, survival analysis and random combination prediction a series of in-depth systematic calculations and analyses, and the results were validated by GEO database, immune microenvironment, drug and functional enrichment analysis. Based on the expression values of C6orf223, KRT7 genes and the DNA methylation values of cg18949415, cg22193385 sites, the least diversity increment algorithm were used to predict COAD and normal sample. The 100 % reliability and 97.12 % correctness of predicting tumor samples were obtained in jackknife test. Moreover, we found that C6orf223 gene, cg18949415 site play a more important role than KRT7 gene, cg22193385 site in COAD. In addition, we investigate the impact of key methylation sites on three-dimensional chromatin structure. Our results will be help for experimental studies and may be an epigenetic biomarker for COAD.
Collapse
Affiliation(s)
- Hui Bai
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China.
| | - Dong-Sheng Yan
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China.
| | - Ying-Li Chen
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China; The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010070, China.
| | - Qian-Zhong Li
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China; The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010070, China.
| | - Ye-Chen Qi
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China.
| |
Collapse
|
8
|
Zhang Z, Jiang X, Li K, Qiao S, Li M, Mei Y, Ding L, Lv Q, Ding Y, Zhao Y, Lv G, Tan G, Yang H, Li G, Gao X, Liu M. KLF7 promotes colon adenocarcinoma progression through the PDGFB signaling pathway. Int J Biol Sci 2024; 20:387-402. [PMID: 38164176 PMCID: PMC10750276 DOI: 10.7150/ijbs.86385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 11/06/2023] [Indexed: 01/03/2024] Open
Abstract
Colon adenocarcinoma (COAD) is the most common malignancy of the digestive tract, which is characterized by a dismal prognosis. No effective treatment has been established presently, thus there is an urgent need to understand the mechanisms driving COAD progression in order to develop effective therapeutic approaches and enhance clinical outcomes. In this study, we found that KLF7 is overexpressed in COAD tissues and correlated with clinicopathological features of COAD. Both gain-of-function and loss-of-function experiments have unequivocally demonstrated that overexpression of KLF7 promotes the growth and metastasis of COAD in vitro and in vivo, while KLF7 knockdown attenuated these effects. Mechanistically, our findings reveal that KLF7 can specifically bind to the promoter region of PDGFB (TGGGTGGAG), thus promoting the transcription of PDGFB and increasing its secretion. Subsequently, secreted PDGFB facilitates the progression of COAD by activating MAPK/ERK, PI3K/AKT, and JAK/STAT3 signaling pathways through PDGFRβ. Additionally, we found that sunitinib can block PDGFB signaling and inhibit COAD progression, offering a promising therapeutic strategy for COAD treatment.
Collapse
Affiliation(s)
- Zhicheng Zhang
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin,150001, China
- Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Xiaochen Jiang
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, 150001, China
- Editorial Board of Harbin Medical University, Harbin Medical University, Harbin 150001, China
| | - Kai Li
- School of Medicine and Health, Harbin Institute of Technology, Harbin, 150001, China
| | - Shupei Qiao
- Heilongjiang Key Laboratory of Children Development and Genetic Research, Harbin Medical University, Harbin,150001, China
| | - Mengmeng Li
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - Yu Mei
- Drug Engineering and Technology Research Center, Harbin University of Commerce, Harbin, 150001, China
| | - Lixian Ding
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin,150001, China
- Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Qiang Lv
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin,150001, China
- Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Yike Ding
- St John's College William Nicholls Drive, Old St Mellons, Cardiff, CF35YX, United Kingdom
| | - Yunhan Zhao
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, 150001, China
| | - Guixiang Lv
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, 150001, China
| | - Gang Tan
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin,150001, China
- Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Huanjie Yang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - Guodong Li
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin,150001, China
- Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Xu Gao
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, 150001, China
| | - Ming Liu
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin,150001, China
- Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| |
Collapse
|
9
|
Yang Z, Wu H, Dai D, Yuan Y, Shao X. ZNF692 Promotes the Progression of Colon Adenocarcinoma by Regulating HSF4 Expression. Iran J Public Health 2023; 52:2601-2610. [PMID: 38435777 PMCID: PMC10903307 DOI: 10.18502/ijph.v52i12.14321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 07/18/2023] [Indexed: 03/05/2024]
Abstract
Background Colon adenocarcinoma (COAD) is one of the most common cancer happened in gastrointestinal tract, with the overall incidence rate of 4%-5% among human beings. Like most malignancies, we uncovered the exact mechanisms of the pathogenesis of colorectal cancer yet. Therefore, there is an urgent need to explore the molecules that can be used as diagnostic maker at early stage. In addition, we also need to define the essential factors that related to the prognosis and treatment of the colon carcinoma. Methods The study was conducted at the Third Affiliated Hospital of Qiqihar Medical University, Qiqihar, China in September 2020. The R language was used to identify the differentially expressed genes. We performed receiver operating characteristic curve analysis to determine the diagnostic markers for COAD. The machine learning strategy was used to assess the effectiveness of genes in the diagnosis of COAD. The molecular mechanism and prognostic value of genes were explored by bioinformatics analysis and molecular experiments. Results The expression level of heat shock factor 4 (HSF4) was significantly elevated in COAD patients (P=1.89×10-29), according to The Cancer Genome Atlas (TCGA) database. Additionally, survival analysis showed the higher expression level of the HSF4 was correlated with the poor prognosis in COAD. Conclusion The HSF4 was the target gene of zinc finger protein 692(ZNF692). HSF4 might promote the progression of COAD through the apoptosis pathway. It was diagnostic and prognosis maker of COAD. Furthermore, the upstream gene of HSF4, ZNF692, promotes the progression of colorectal cancer by regulating HSF4 expression.
Collapse
Affiliation(s)
- Zhengpeng Yang
- Department of General Surgery, the Third Affiliated Hospital of Qiqihar Medical University, Qiqihar 161002, China
| | - Hao Wu
- Department of General Surgery, the Third Affiliated Hospital of Qiqihar Medical University, Qiqihar 161002, China
| | - Defu Dai
- Department of General Surgery, the Third Affiliated Hospital of Qiqihar Medical University, Qiqihar 161002, China
| | - Yufeng Yuan
- Department of General Surgery, the Third Affiliated Hospital of Qiqihar Medical University, Qiqihar 161002, China
| | - Xueqian Shao
- Department of General Surgery, the Third Affiliated Hospital of Qiqihar Medical University, Qiqihar 161002, China
| |
Collapse
|
10
|
Ye N, Wang Y, Jiang P, Jiang H, Ding W, Zhang Z, Xi C. Hypoxia-induced the upregulation of NDUFA4L2 promoted colon adenocarcinoma progression through ROS-mediated PI3K/AKT pathway. Cytotechnology 2023; 75:461-472. [PMID: 37841958 PMCID: PMC10575837 DOI: 10.1007/s10616-023-00590-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 08/18/2023] [Indexed: 10/17/2023] Open
Abstract
The NADH dehydrogenase (ubiquinone) 1 alpha subcomplex 4-like 2 (NDUFA4L2) gene has been reported to be upregulated in colorectal cancer (CRC) and is associated with worse prognosis. However, the specific function and underlying mechanism of NDUFA4L2 in colon adenocarcinoma (COAD) under hypoxia has never been investigated. Our study discovered that hypoxia promoted the viability, metastasis, and epithelial-mesenchymal transition (EMT) of COAD cells. Besides, hypoxia-induced HIF-1α upregulated the expression of NDUFA4L2 which served as an oncogene and an independent diagnostic and prognostic marker in COAD. Under hypoxic environment, NDUFA4L2 mediated the viability, metastasis, and epithelial-EMT of COAD cells. Additionally, the ROS-dependent PI3K/Akt signaling was activated by NDUFA4L2 in COAD in hypoxia and NDUFA4L2 facilitated the malignant behaviors of hypoxia-treated COAD cells by elevating ROS production. Collectively, abundant NDUFA4L2 expression induced by HIF-1α under hypoxia promoted the development of COAD through activation of the PI3K/AKT signaling in a ROS-dependent manner, indicating NDUFA4L2 as a promising target in COAD diagnosis and treatment.
Collapse
Affiliation(s)
- Nianyuan Ye
- Department of Oncology, Wujin People Hospital Affiliated with Jiangsu University, and Wujin Clinical College of Xuzhou Medical University, No.2 Yongning North Road, Tianning District, Changzhou, 213000 Jiangsu China
| | - Yibo Wang
- Department of Oncology, Wujin People Hospital Affiliated with Jiangsu University, and Wujin Clinical College of Xuzhou Medical University, No.2 Yongning North Road, Tianning District, Changzhou, 213000 Jiangsu China
| | - Peng Jiang
- Department of Oncology, Wujin People Hospital Affiliated with Jiangsu University, and Wujin Clinical College of Xuzhou Medical University, No.2 Yongning North Road, Tianning District, Changzhou, 213000 Jiangsu China
| | - Huaji Jiang
- Department of Oncology, Wujin People Hospital Affiliated with Jiangsu University, and Wujin Clinical College of Xuzhou Medical University, No.2 Yongning North Road, Tianning District, Changzhou, 213000 Jiangsu China
| | - Wei Ding
- Department of Oncology, Wujin People Hospital Affiliated with Jiangsu University, and Wujin Clinical College of Xuzhou Medical University, No.2 Yongning North Road, Tianning District, Changzhou, 213000 Jiangsu China
| | - Zheng Zhang
- Department of Oncology, Wujin People Hospital Affiliated with Jiangsu University, and Wujin Clinical College of Xuzhou Medical University, No.2 Yongning North Road, Tianning District, Changzhou, 213000 Jiangsu China
| | - Cheng Xi
- Department of Oncology, Wujin People Hospital Affiliated with Jiangsu University, and Wujin Clinical College of Xuzhou Medical University, No.2 Yongning North Road, Tianning District, Changzhou, 213000 Jiangsu China
| |
Collapse
|
11
|
Chen D, Zhang B, Kang K, Li L, Liao Y, Qing S, Di Y. Development of a prognostic model for personalized prediction of colon adenocarcinoma (COAD) patient outcomes using methylation-driven genes. J Appl Genet 2023; 64:713-721. [PMID: 37589877 DOI: 10.1007/s13353-023-00778-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/22/2023] [Accepted: 08/03/2023] [Indexed: 08/18/2023]
Abstract
The objective of this study was to identify methylation-driven genes and explore their prognostic value in colon adenocarcinoma (COAD). The Cancer Genome Atlas (TCGA) database was used to acquire collated COAD transcriptome gene expression matrix (containing 59,427 transcripts), transcriptome gene methylation level matrix (containing 29,602 methylated modified genes), which included 517 samples containing 41 samples of normal tissue (NT) & 476 samples of COAD, and patient clinical information files (including patient survival time, survival status, age, gender and tumor stage, etc.), for all COAD samples. A total of 9807 differentially expressed genes (DEGs) were obtained by DEG analysis of the COAD transcriptional expression matrix, of which 5874 were up-regulated and 3933 were down-regulated. And 46 methylation-driven DEGs (MD-DEGs) in COAD were obtained by DEG analysis, differential analysis of gene methylation levels, and correlation analysis between them. Next, three prognostic associated MD-DEGs (PMD-DEGs) (IDUA, ZBTB18 and C5orf38) were identified by Cox regression analysis, and a prognostic model composed of the three PMD-DEGs was constructed by least absolute shrinkage and selection operator (LASSO) regression analysis and cross-validation analysis. In addition, survival analysis, the receiver operating characteristics (ROC) curve analysis and independent prognostic analysis were used to evaluate and verify that the prognostic model we constructed could accurately and independently predict the prognosis of COAD patients. Finally, we constructed a nomogram based on the prognosis model to accurately and personalized predict the survival prognosis of COAD patients. In conclusion, we identified the methylation driver gene of COAD and constructed a prognostic model and nomogram to personalized predict the prognosis of patients, which opened a new prospect for accurate diagnosis and treatment in clinical practice.
Collapse
Affiliation(s)
- Di Chen
- Gastroenterology Department, Beijing Aerospace General Hospital, Beijing, China
| | - Bo Zhang
- Gastroenterology Department, Beijing Aerospace General Hospital, Beijing, China
| | - Kui Kang
- Gastroenterology Department, Beijing Aerospace General Hospital, Beijing, China
| | - LiKun Li
- Gastroenterology Department, Beijing Aerospace General Hospital, Beijing, China
| | - Yuan Liao
- Gastroenterology Department, Beijing Aerospace General Hospital, Beijing, China
| | - Sheng Qing
- Gastroenterology Department, Beijing Aerospace General Hospital, Beijing, China
| | - YaNan Di
- Gastroenterology Department, Beijing Aerospace General Hospital, Beijing, China.
| |
Collapse
|
12
|
Wu J, Lu X, Yu J, Li P, Yu X. LINC02253 promote the malignant phenotype of Colon adenocarcinoma cells by up-regulating WWP1-mediated SMAD3 ubiquitination. Mol Cell Probes 2023; 72:101928. [PMID: 37597669 DOI: 10.1016/j.mcp.2023.101928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 08/16/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023]
Abstract
OBJECTIVES Colon adenocarcinoma (COAD) represents a type of common malignant tumor originating in the digestive tract. Long non-coding RNAs (lncRNAs) have been identified to engage in regulating the initiation and development of COAD. LncRNA LINC02253 has been reported abnormal expressed in COAD, but the underlying mechanism has not been discussed so far. This study aimed to determine the role and the molecular biology mechanism of LINC02253 in COAD progression and unearthed its specific molecular mechanism. MATERIALS AND RESULTS RT-qPCR and Western blot assays were conducted to detect gene expression. Function assays were performed to evaluate the effect of gene expression on COAD cell phenotype. Mechanism analyses were done to verify the association among genes after bioinformatics analysis. The obtained data revealed that LINC02253 demonstrated a high expression in COAD tissues and cells. This gene served as an oncogene, permitting to stimulate proliferation and suppress apoptosis of COAD cells. Mechanically, it was found that LINC02253 recruited FUS to stabilize WWP1 mRNA and WWP1 could mediate SMAD3 ubiquitination, thereby promoting the malignant phenotype formation of COAD cells. CONCLUSIONS LINC02253 was uncovered to exert an oncogenic role, enhancing the proliferation of COAD cells and repressing the cell apoptosis by recruiting FUS and encouraging WWP1-mediated SMAD3 ubiquitination.
Collapse
Affiliation(s)
- Jinfeng Wu
- Department of Gastroenterology, Shenzhen Luohu People's Hospital, Shenzhen, 518001, Guangdong, China
| | - Xianhong Lu
- Department of Gastroenterology, Shenzhen Luohu People's Hospital, Shenzhen, 518001, Guangdong, China
| | - Jinzhong Yu
- Department of Gastroenterology, Shuguang Hospital Affiliated to Shanghai University of Chinese Medicine, Shanghai, 200120, China
| | - Pan Li
- Institute of Ultrasound Imaging Engineering, Chongqing Medical University, Chongqing, 400000, China
| | - Xiqiu Yu
- Department of Gastroenterology, Shenzhen Luohu People's Hospital, Shenzhen, 518001, Guangdong, China.
| |
Collapse
|
13
|
Pilon A, Avecilla F, Rácz B, Gátszegi GT, Spengler G, Robalo MP, Enyedy ÉA, Garcia MH, Valente A. Iron(II)-cyclopentadienyl compounds are cytotoxic against colon adenocarcinoma cell lines: Ethylenebis(diphenylphosphane) vs. triphenylphosphane. J Inorg Biochem 2023; 249:112386. [PMID: 37827090 DOI: 10.1016/j.jinorgbio.2023.112386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/13/2023] [Accepted: 09/23/2023] [Indexed: 10/14/2023]
Abstract
Structure-activity studies aiming to understand the role of each coligand in the formulation of new metallodrugs is an important subject. In that frame, six new compounds with general formula [Fe(η5-C5H5)(dppe)(L)][CF3SO3] with L = benzonitriles (1-4) or carbon monoxide (5) and compound [Fe(η5-C5H5)(CO)(PPh3)2][CF3SO3] (6) were synthesized and compared with three other previously reported compounds [Fe(η5-C5H5)(CO)(L)(PPh3)][CF3SO3]. We were particularly interested in assessing the effect of dppe vs. (PPh3 + CO) for this set of compounds. For that, all compounds were tested against two human colon adenocarcinoma cell lines, Colo205 and the refractile Colo320 (expressing ABCB1, an efflux pump causing multidrug resistance), showing IC50 values in the micromolar range. The presence of dppe in the compound's coordination sphere over (PPh3 + CO) allows for more redox stable compounds showing higher cytotoxicity and selectivity, with improved cytotoxicity towards resistant cells that is not related to the inhibition of ABCB1. Further studies with GSH and H2O2 for selected compounds indicated that their antioxidant ability is not probably the main responsible for their cytotoxicity.
Collapse
Affiliation(s)
- Adhan Pilon
- Centro de Química Estrutural, Institute of Molecular Sciences and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Fernando Avecilla
- Universidade da Coruña, Grupo NanoToxGen, Centro Interdisciplinar de Química y Biología (CICA), Departamento de Química, Facultade de Ciencias, Campus de A Coruña, 15071 A Coruña, Spain
| | - Bálint Rácz
- Department of Medical Microbiology, Albert Szent-Györgyi Medical School, University of Szeged, Semmelweis utca 6, H-6725 Szeged, Hungary
| | - Gerda T Gátszegi
- Department of Medical Microbiology, Albert Szent-Györgyi Medical School, University of Szeged, Semmelweis utca 6, H-6725 Szeged, Hungary; MTA-SZTE Lendület Functional Metal Complexes Research Group, Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720 Szeged, Hungary
| | - Gabriella Spengler
- Department of Medical Microbiology, Albert Szent-Györgyi Medical School, University of Szeged, Semmelweis utca 6, H-6725 Szeged, Hungary
| | - M Paula Robalo
- Centro de Química Estrutural, Institute of Molecular Sciences, Av. Rovisco Pais, 1049-001 Lisboa, Portugal; Departamento de Engenharia Química, Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, Av. Conselheiro Emídio Navarro, 1, 1959-007 Lisboa, Portugal
| | - Éva A Enyedy
- MTA-SZTE Lendület Functional Metal Complexes Research Group, Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720 Szeged, Hungary
| | - M Helena Garcia
- Centro de Química Estrutural, Institute of Molecular Sciences and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Andreia Valente
- Centro de Química Estrutural, Institute of Molecular Sciences and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal.
| |
Collapse
|
14
|
Huang H, Lu L, Li Y, Chen X, Li M, Yang M, Huang X. Development of a 5-mRNAsi-related gene signature to predict the prognosis of colon adenocarcinoma. PeerJ 2023; 11:e16477. [PMID: 38025763 PMCID: PMC10680455 DOI: 10.7717/peerj.16477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023] Open
Abstract
Aim To create a prognosis model based on mRNA-based stem index (mRNAsi) for evaluating the prognostic outcomes of colon adenocarcinoma (COAD). Background Generation of heterogeneous COAD cells could be promoted by the self-renewal and differentiation potential of cancer stem cells (CSCs). Biomarkers contributing to the development of COAD stem cells remained to be discovered. Objective To develop and validate an mRNAsi-based risk model for estimating the prognostic outcomes of patients suffering from COAD. Methods Samples were collected from Rectal Adenocarcinoma (TCGA-READ) PanCancer Atlas datasets, The Cancer Genome Atlas Colon Adenocarcinoma (TCGA-COAD), and the GSE87211 dataset. MRNAsi was calculated by one-class logistic regression (OCLR) algorithm. Under the criterion of correlation greater than 0.4, genes related to mRNAsi were screened and clustered. Meanwhile, differentially expressed genes (DEGs) between molecular subtypes were identified to establish a risk model. According to the median risk score value for immunotherapy and results from immune cell infiltration and clinicopathological analyses, clusters and patients were divided into high-RiskScore and low-RiskScore groups. Cell apoptosis and viability were detected by flow cytometer and Cell Counting Kit-8 (CCK-8) assay, respectively. Results A negative correlation between mRNAsi and clinical stages was observed. Three clusters of patients (C1, C2, and C3) were defined based on a total of 165 survival-related mRNAsi genes. Specifically, C1 patients had greater immune cell infiltration and a poorer prognosis. A 5-mRNAsi-gene signature (HEYL, FSTL3, FABP4, ADAM8, and EBF4) served as a prediction index for COAD prognosis. High-RiskScore patients had a poorer prognosis and higher level of immune cell infiltration. In addition, the five genes in the signature all showed a high expression in COAD cells. Knocking down HEYL promoted COAD cell apoptosis and inhibited viability. Conclusion Our mRNAsi risk model could better predict the prognosis of COAD patients.
Collapse
Affiliation(s)
- Haifu Huang
- Department of Hematology and Oncology, Shenzhen Hospital of Guangzhou University of Traditional Chinese Medicine, Shenzhen, China
| | - Lin Lu
- Department of Hematology and Oncology, Shenzhen Hospital of Guangzhou University of Traditional Chinese Medicine, Shenzhen, China
| | - Yaoxuan Li
- Department of Hematology and Oncology, Shenzhen Hospital of Guangzhou University of Traditional Chinese Medicine, Shenzhen, China
| | - Xiumei Chen
- Department of Hematology and Oncology, Shenzhen Hospital of Guangzhou University of Traditional Chinese Medicine, Shenzhen, China
| | - Meng Li
- Department of Hematology and Oncology, Shenzhen Hospital of Guangzhou University of Traditional Chinese Medicine, Shenzhen, China
| | - Meiling Yang
- Department of Hematology and Oncology, Shenzhen Hospital of Guangzhou University of Traditional Chinese Medicine, Shenzhen, China
| | - Xuewu Huang
- Tumor Center, The First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, China
| |
Collapse
|
15
|
Huang W, Hu Y, Zhang X, Xu Y, Sun Z, Ding P, Qian X, Ali A, Chen Z. Integrated multiplex network based approach reveled CC and CXC chemokines associated key biomarkers in colon adenocarcinoma patients. Am J Cancer Res 2023; 13:5531-5548. [PMID: 38058831 PMCID: PMC10695786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/15/2023] [Indexed: 12/08/2023] Open
Abstract
Colon adenocarcinoma (COAD) is a prevalent and aggressive form of cancer that necessitates the identification of robust biomarkers for early diagnosis and treatment. Therefore, this project was launched to identify a few key biomarkers from CC and CXC chemokine families for the accurate detection of COAD. Hub gene identification was performed using CytoHubba analysis. Clinical samples from COAD patients and normal individuals were collected and subjected to appropriate methods for DNA and RNA extraction. The expression levels of hub genes were analyzed using reverse transcription-quantitative polymerase chain reaction (RT-qPCR), while promoter methylation analysis was conducted using targeted bisulfite sequencing (bisulfite-seq). Additionally, The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets were utilized to validate the findings based on clinical samples. CXCL10 (C-X-C motif chemokine ligand 10), CXCL12 (C-X-C motif chemokine ligand 12), CXCL16 (C-X-C motif chemokine ligand 16), and CCL25 (CC motif chemokine ligand 25) were denoted as the key hubs among CC and CXC chemokine families. Through RT-qPCR analysis, it was found that CXCL10, CXCL12, and CXCL16 were significantly up-regulated, while CCL25 was down-regulated in COAD patients compared to healthy controls. Later on, these findings were also validated using TCGA and GEO datasets consisting of COAD and normal control samples. Furthermore, we investigated the promoter methylation status of these chemokine genes in COAD patients. Our results revealed significant dysregulation of promoter methylation, suggesting an epigenetic mechanism underlying the altered expression of CXCL10, CXCL12, CXCL16, and CCL25 in COAD. In addition to this, various additional aspects of the CCL25, CXCL10, CXCL12, and CXCL16 have also been uncovered in COAD during the present study. This study highlights the dysregulation of CXCL10, CXCL12, CXCL16, and CCL25 chemokine members in COAD patients, emphasizing their significance as potential biomarkers and therapeutic targets in the management of this deadly disease. However, further investigations are warranted to elucidate the underlying molecular mechanisms and evaluate the clinical utility of these findings.
Collapse
Affiliation(s)
- Wei Huang
- Department of Oncology, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese MedicineNanjing, Jiangsu, China
- Department of Oncology, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese MedicineNanjing, Jiangsu, China
| | - Yanyan Hu
- Jiangsu Provincial Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese MedicineNanjing, Jiangsu, China
| | - Xiaotao Zhang
- Jiangsu Provincial Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese MedicineNanjing, Jiangsu, China
| | - Yan Xu
- Nanjing Hospital Affiliated to Nanjing University of Chinese MedicineNanjing, Jiangsu, China
| | - Zhiling Sun
- Jiangsu Provincial Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese MedicineNanjing, Jiangsu, China
| | - Pingan Ding
- The Third Department of Surgery, The Fourth Hospital of Hebei Medical UniversityShijiazhuang, Hebei, China
| | - Xiaoping Qian
- Department of Oncology, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese MedicineNanjing, Jiangsu, China
- Department of Oncology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical SchoolNanjing, Jiangsu, China
| | - Akbar Ali
- Nishtar Medial CollegeMultan, Punjab, Pakistan
| | - Zilu Chen
- Center for Molecular Imaging and Nuclear Medicine, School of Radiological & Interdisciplinary Sciences (RAD-X), Soochow UniversitySuzhou, Jiangsu, China
| |
Collapse
|
16
|
Li X, Lei J, Shi Y, Peng Z, Gong M, Shu X. Developing a RiskS-core Model based on Angiogenesis-related lncRNAs for Colon Adenocarcinoma Prognostic Prediction. Curr Med Chem 2023; 31:CMC-EPUB-136102. [PMID: 37961859 DOI: 10.2174/0109298673277243231108071620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/25/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023]
Abstract
AIM We screened key angiogenesis-related lncRNAs based on colon adenocarcinoma (COAD) to construct a RiskS-core model for predicting COAD prognosis and help reveal the pathogenesis of the COAD as well as optimize clinical treatment. BACKGROUND Regulatory roles of lncRNAs in tumor progression and prognosis have been confirmed, but few studies have probed into the role of angiogenesis-related lncRNAs in COAD. OBJECTIVE To identify key angiogenesis-related lncRNAs and build a RiskS-core model to predict the survival probability of COAD patients and help optimize clinical treatment. METHODS Sample data were collected from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database. The HALLMARK pathway score in the samples was calculated using the single sample gene set enrichment analysis (ssGSEA) method. LncRNAs associated with angiogenesis were filtered by an integrated pipeline algorithm. LncRNA-based subtypes were classified by ConsensusClusterPlus and then compared with other established subtypes. A RiskS-core model was created based on univariate Cox, least absolute shrinkage and selection operator (LASSO) regression and stepwise regression analysis. The Kaplan-Meier curve was drawn by applying R package survival. The time-dependent ROC curves were drawn by the timeROC package. Finally, immunotherapy benefits and drug sensitivity were analyzed using tumor immune dysfunction and exclusion (TIDE) software and pRRophetic package. RESULTS Pathway analysis showed that the angiogenesis pathway was a risk factor affecting the prognosis of COAD patients. A total of 66 lncRNAs associated with angiogenesis were screened, and three molecular subtypes (S1, S2, S3) were obtained. The prognosis of S1 and S2 was better than that of S3. Compared with the existing subtypes, the S3 subtype was significantly different from the other two subtypes. Immunoassay showed that immune cell scores of the S2 subtype were lower than those of the S1 and S3 subtypes, which also had the highest TIDE scores. We recruited 8 key lncRNAs to develop a RiskS-core model. The high RiskS-core group with inferior survival and higher TIDE scores was predicted to benefit limitedly from immunotherapy, but it may be more sensitive to chemotherapeutics. A nomogram designed by RiskS-core signature and other clinicopathological characteristics shed light on rational predictive power for COAD treatment. CONCLUSION We constructed a RiskS-core model based on angiogenesis-related lncRNAs, which could serve as potential prognostic predictors for COAD patients and may offer clues for the intervention of anti-angiogenic application. Our results may help evaluate the prognosis of COAD and provide better treatment strategies.
Collapse
Affiliation(s)
- Xianguo Li
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430014, China
| | - Junping Lei
- Department of General surgery, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, 441021, China
| | - Yongping Shi
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430014, China
| | - Zuojie Peng
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430014, China
| | - Minmin Gong
- Department of General surgery, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, 441021, China
| | - Xiaogang Shu
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430014, China
| |
Collapse
|
17
|
Chen X, Yang M, Tu J, Yuan X. Integrated bioinformatics and validation reveal SOX12 as potential biomarker in colon adenocarcinoma based on an immune infiltration-related ceRNA network. J Cancer Res Clin Oncol 2023; 149:15737-15762. [PMID: 37668799 DOI: 10.1007/s00432-023-05316-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 08/17/2023] [Indexed: 09/06/2023]
Abstract
PURPOSE The primary objective of this study was to construct competing endogenous RNA (ceRNA) networks and evaluate the prognostic significance of tumor-infiltrating immune cells (TIICs) and key biomarkers within the ceRNA networks in colon adenocarcinoma (COAD) patients. METHODS Comprehensive bioinformatics tools were used to screen differentially expressed genes (DEGs), miRNAs (DEMs), and lncRNAs (DELs) related to COAD, leading to the creation of ceRNA networks. The CIBERSORT technique was employed to assess the significance of TIICs in COAD, and an immune-related prognosis prediction model was subsequently developed. Co-expression analyses were conducted to determine the relationship between key genes in ceRNA networks and immunologically significant TIICs. The study also utilized 5 GEO datasets and web-based databases to externally validate the findings. RESULTS The study revealed a statistically significant relationship between key hub genes and immune cells, as determined through co-expression analysis. Two hub regulators (SOX12 and H19) demonstrated significant prognostic value in the ceRNA-related prognostic model, and their elevated expression levels were verified across multiple CRC cell lines. Additionally, the knockdown of SOX12 led to a suppression of proliferation, migration, and invasion in colon cancer cells. CONCLUSION Through the construction of ceRNA networks and evaluation of TIICs, the study successfully established two risk score models and nomograms. These models serve as valuable tools for understanding the molecular processes and predicting the prognosis of COAD patients. Further validation of hub regulators SOX12 and H19 substantiates their potential role as key biomarkers in COAD.
Collapse
Affiliation(s)
- Xinyi Chen
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jie Fang Road 1095, Wuhan, Hubei, China
| | - Mu Yang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jie Fang Road 1095, Wuhan, Hubei, China
| | - Jingyao Tu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jie Fang Road 1095, Wuhan, Hubei, China.
| | - Xianglin Yuan
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jie Fang Road 1095, Wuhan, Hubei, China.
| |
Collapse
|
18
|
Wang Y, Jia Z, Wang Q, Zhu Z. Amino acids and risk of colon adenocarcinoma: a Mendelian randomization study. BMC Cancer 2023; 23:1041. [PMID: 37898769 PMCID: PMC10612249 DOI: 10.1186/s12885-023-11514-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/11/2023] [Indexed: 10/30/2023] Open
Abstract
BACKGROUND The existence of amino acid metabolic reprogramming in tumor cells is well established. However, the potential correlation between blood amino acids and the risk of colon adenocarcinoma remains largely unexplored. METHODS We utilized Mendelian randomization (MR) analysis to examine the association between 20 amino acids in the blood and the risk of colon adenocarcinoma. Additionally, reverse MR analysis was employed to identify the presence of reverse causality. A two-step MR analysis was conducted to ascertain the potential mediating effect. Lastly, the alanine detection data from colon adenocarcinoma patients in our hospital were utilized to investigate the differences in alanine levels among healthy individuals and patients with colon cancer, as well as among patients with different stages and locations of colon cancer. Furthermore, a Kaplan-Meier curve was employed to examine the correlation between alanine and overall survival, followed by the implementation of COX univariate analysis. RESULTS The results of our study indicate that there is an inverse correlation between alanine and the risk of colon adenocarcinoma. Additionally, we found no significant evidence to support a causal relationship between colon adenocarcinoma and alanine. Furthermore, our analysis revealed that alanine aminotransferase (ALT) and blood glucose do not act as mediators in this causal pathway. Moreover, individuals diagnosed with colon adenocarcinoma exhibited a significant decrease in alanine levels, particularly in cases of stage IV colon adenocarcinoma with distant metastasis. Additionally, elevated alanine levels were associated with improved overall survival rates among colon adenocarcinoma patients. CONCLUSIONS The results of this study indicate that alanine exhibits protective characteristics against the onset of colon adenocarcinoma and may play a role in promoting a more favorable disease prognosis. Consequently, dietary interventions aimed at increasing alanine intake may serve as a potential strategy for the prevention and treatment of colon adenocarcinoma.
Collapse
Affiliation(s)
- Yuanyuan Wang
- Cancer Clinical Research Ward, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, 121000, China
| | - Zhihan Jia
- Department of Oncology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, 121000, China
| | - Qingjun Wang
- Cancer Clinical Research Ward, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, 121000, China
| | - Zhitu Zhu
- Liaoning Provincial Key Laboratory of Clinical Oncology Metabonomics, Institute of Clinical Bioinformatics, Cancer Center of Jinzhou Medical University, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, 121000, China.
| |
Collapse
|
19
|
Hu J, Wu Y, Dong X, Zeng Y, Wang Y. The Diagnostic and Prognostic Value of Neurotransmitter Receptor-Related Genes in Colon Adenocarcinoma. Mol Biotechnol 2023:10.1007/s12033-023-00910-z. [PMID: 37833465 DOI: 10.1007/s12033-023-00910-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 09/18/2023] [Indexed: 10/15/2023]
Abstract
Colorectal cancer (CRC) is a malignant tumor with high morbidity and mortality in the world. This study aimed to find receptor-related genes (NRGs) with diagnostic and prognostic value in colon adenocarcinoma (COAD). The Cancer Genome Atlas (TCGA) and the Human Protein Atlas database databases were applied to find differential expression NRGs between COAD and normal colonic tissues. Subsequently, Cox regression analysis and minimum absolute contraction and selection operator algorithm were used to construct a prognosis nomogram based on TCGA and Gene Expression Omnibus databases. Expression levels of 35 NRGs were significant differences in COAD and normal colonic tissues. ROC curves showed that 24 NRGs had high diagnostic accuracy (AUC > 0.850) in COAD. Risk score was constructed based on 10 NRGs for the first time. Cox regression analysis revealed risk score was an independent risk factor and a higher risk score predicts a later TNM stage. Finally, a prognostic nomogram containing risk score and clinical features was established. Calibration curves and C-index suggested the powerful predictable value of the model. This study identified the NRGs with diagnostic value and prognostic value, providing a direction for treatment of COAD patients.
Collapse
Affiliation(s)
- Jia Hu
- Department of Gastroenterology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China
- Research Center of Digestive Disease, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China
| | - Yun Wu
- National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Xiaoping Dong
- National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Yong Zeng
- National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Yongjun Wang
- Department of Gastroenterology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China.
- Research Center of Digestive Disease, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China.
| |
Collapse
|
20
|
Xue W, Qiu K, Dong B, Guo D, Fu J, Zhu C, Niu Z. Disulfidptosis-associated long non-coding RNA signature predicts the prognosis, tumor microenvironment, and immunotherapy and chemotherapy options in colon adenocarcinoma. Cancer Cell Int 2023; 23:218. [PMID: 37759294 PMCID: PMC10523716 DOI: 10.1186/s12935-023-03065-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Disulfidptosis is independent of apoptosis, ferroptosis, and cuproptosis and is associated with cancer progression, treatment response, and prognosis. However, the predictive potential of disulfidptosis-associated lncRNAs in colon adenocarcinoma (COAD) and their features in the tumor immune microenvironment (TIME) require further elucidation. METHODS RNA transcriptome, clinical information, and mutation data of COAD samples were obtained from the TCGA database. The risk model was first constructed by co-expression analysis of disulfidptosis genes and lncRNAs, and prognostic lncRNAs were screened using Cox regression, followed by least absolute shrinkage and selection operator analysis. Enrichment analyses were performed to explore the underlying biological functions and signaling of model-associated differentially expressed genes (MADEGs). Moreover, TIME of MADEGs was analyzed to assess the immunotherapy. Finally, the expression levels of the lncRNAs were verified by taking specimens of patients with COAD from the Affiliated Hospital of Qingdao University. RESULTS We constructed a prognosis-related risk model based on four disulfidptosis-associated lncRNAs (ZEB1-AS1, SNHG16, SATB2-AS1, and ALMS1-IT1). By analyzing the survival of patients in the whole, training, and test groups, we found that patients with COAD in the low-risk group had better overall survival than those in the high-risk group. Validation of the model via Cox analysis and clinical indicators demonstrated that the model had a decent potential for predicting the prognosis of patients with COAD. Enrichment analyses revealed that the MADEGs were related to disulfidptosis-associated biological functions and cancer pathways. Furthermore, patients with COAD in the high-risk group had more positive responses to immune checkpoint inhibitors (ICIs) than those in the low-risk group, as confirmed by TIME analysis. ZEB1-AS1, SNHG16, and ALMS1-IT1 were expressed at higher levels in tumor samples than those in the corresponding paracancerous samples (p < 0.05), whereas SATB2-AS1 was upregulated in the paracancerous samples (p < 0.05). CONCLUSIONS This signature may guide prognosis, molecular mechanisms, and treatment strategies, including ICIs and chemotherapy, in patients with COAD.
Collapse
Affiliation(s)
- Weijie Xue
- Kumamoto University Graduate School of Medical Sciences, Kumamoto, Japan
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Qingdao University, No.16 Jiangsu Road, Qingdao, 266003, China
| | - Kang Qiu
- Department of Hepatobiliary and Pancreatic Surgery, The Affiliated Hospital of Qingdao University, No. 16 Jiangsu Road, Qingdao, 266003, China
| | - Bingzi Dong
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Qingdao University, 16 Jiangsu Road, Qingdao, 266003, China
| | - Dong Guo
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Qingdao University, No.16 Jiangsu Road, Qingdao, 266003, China
| | - Junhua Fu
- Department of Operation Room, The Affiliated Hospital of Qingdao University, No.16 Jiangsu Road, Qingdao, 266003, China
| | - Chengzhan Zhu
- Department of Hepatobiliary and Pancreatic Surgery, The Affiliated Hospital of Qingdao University, No. 16 Jiangsu Road, Qingdao, 266003, China.
| | - Zhaojian Niu
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Qingdao University, No.16 Jiangsu Road, Qingdao, 266003, China.
| |
Collapse
|
21
|
Xie Q, Wang J, Peng X. Dysregulated Forkhead Box (FOX) Genes Association with Survival Prognosis, Anti-tumor Immunity, and Key Targeting Drugs in Colon Adenocarcinoma. Arch Iran Med 2023; 26:510-528. [PMID: 38310407 PMCID: PMC10862056 DOI: 10.34172/aim.2023.77] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 07/03/2023] [Indexed: 02/05/2024]
Abstract
BACKGROUND Several studies have revealed that the aberrant expressions of forkhead box (FOX) genes are associated with carcinogenesis. However, the crucial biological functions of the FOX gene in colon adenocarcinoma (COAD) remain unknown. METHODS The TCGA-COAD dataset (n=328) was utilized for determining the deregulated FOX genes and their association with functional enrichment, protein-protein interaction (PPI), survival prognosis, anti-tumor immunity, cancer-associated pathways, and biological processes in COAD. In addition, we used GSE166427 (GPL13667) as a validation cohort (n=196). Molecular docking studies were applied to perform the drug interactions. RESULTS The FOX genes are deregulated in the COAD (Log2 FC>0.50, P<0.05), and the PPI network of FOX members is substantially related to the enrichment of cancerous signaling, immune responses, and cellular development (FDR<0.05). A worse prognosis for overall survival in COAD individuals is connected with the subgroup of FOX transcripts (P≤0.05). FOXD4, FOXH1, and FOXS1 were identified as predictive variables in the univariate and multivariate Cox regression models (P≤0.05). FOXH1 and FOXS1 are substantially linked to the deregulated immunity in COAD (R>0.20, P<0.01). Furthermore, FOXS1 expression regulates cancer-associated pathways and biological processes (P<0.05). Moreover, FOXD4, FOXH1, and FOXS1 are genetically altered and showed diagnostic efficacy in COAD. We revealed that FOXD4, FOXH1, and FOXS1 are consistently deregulated in GSE166427 (P<0.05). Finally, molecular docking revealed that FOXH1 interacted with various drugs, including belinostat, entinostat, and panobinostat. CONCLUSION The FOX genes have a strong correlation with the poor prognosis for survival, tumor immunity, cancer-associated pathways, and biochemical processes that cause the pathogenesis of COAD.
Collapse
Affiliation(s)
- Qian Xie
- International Medical Center/Ward of General Practice, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Jie Wang
- Department of Pharmacy, First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, China
| | - Xingchen Peng
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610000, China
| |
Collapse
|
22
|
Ji J, Liu S, Liang Y, Zheng G. Comprehensive analysis of m6A regulators and relationship with tumor microenvironment, immunotherapy strategies in colorectal adenocarcinoma. BMC Genom Data 2023; 24:44. [PMID: 37568073 PMCID: PMC10422724 DOI: 10.1186/s12863-023-01149-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 08/08/2023] [Indexed: 08/13/2023] Open
Abstract
BACKGROUND The N6-methyladenosine (m6A) RNA modification is the most prevalent and abundant type found in eukaryotic cells. It plays a crucial role in the initiation and progression of cancers. In this study, we aimed to comprehensively investigate the landscape of m6A regulators and their association with tumor microenvironment (TME), immunotherapeutic strategies in colon adenocarcinoma (COAD). RESULTS The differential expression, mutation, CNV frequency and prognostic value of 27 m6A regulators were systematically analyzed in COAD. Patients were classified into two clusters based on m6A regulators through consistent clustering analysis, with cluster A showing significant survival benefits. Most of the m6A regulators were negatively correlated with immune cells, except for WTAP, IGF2BP3, FTO, ALKBH5, which showed a positive correlation. We developed an m6A scoring system to calculate the m6Ascore for each patient. Patients with a high-m6Ascore had a better outcome, with the AUC of 0.775. An independent cohort of 416 COAD patients acquired from GSE38832 database was used to validate the prognosis prediction ability of m6Ascore. Moreover, the m6Ascore was negatively correlated with infiltration of anti-tumor immune cells. Additionally, patients with a high-m6Ascore responded better to anti-PD1 and anti-CTLA4 therapies, and those with MSI-H had a higher m6Ascore. Finally, we investigated the value of m6Ascore in predicting the response of patients to 15 commonly used drugs. CONCLUSIONS We comprehensively analyzed m6A regulators in COAD, including RNA expression, CNV changes, mutations and their correlation with TME. Our results showed that the m6A scoring system had significant predictive power for the prognosis of COAD patients, potentially leading to new personalized immunotherapy strategies.
Collapse
Affiliation(s)
- Jian Ji
- Department of Clinical Laboratory, Shandong Province, Qilu Hospital of Shandong University, Jinan, 250012, People's Republic of China
| | - Shichao Liu
- Department of Clinical Laboratory, Shandong Province, Qilu Hospital of Shandong University, Jinan, 250012, People's Republic of China
- Department of Clinical Laboratory, Shandong Province, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250014, People's Republic of China
| | - Yongyuan Liang
- Department of Clinical Laboratory, Shandong Province, Qilu Hospital of Shandong University, Jinan, 250012, People's Republic of China
- Department of Clinical Laboratory, Shandong Province, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250014, People's Republic of China
| | - Guixi Zheng
- Department of Clinical Laboratory, Shandong Province, Qilu Hospital of Shandong University, Jinan, 250012, People's Republic of China.
| |
Collapse
|
23
|
Zhou L, Zhang Y, Xu Y, Jiang T, Tang L. Identification of a novel prognostic signature composed of 3 cuproptosis-related transcription factors in colon adenocarcinoma. Genes Genomics 2023; 45:1047-1061. [PMID: 37318704 DOI: 10.1007/s13258-023-01406-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/17/2023] [Indexed: 06/16/2023]
Abstract
BACKGROUND Since the mechanism of cuproptosis was recently revealed, many molecules related to this pathway have been widely concerned and exploited to have prognostic potential. However, it is still unknown whether the transcription factors related to cuproptosis could be competent as tumor biomarkers of colon adenocarcinoma (COAD). OBJECTIVE To analyze the prognostic potential of cuproptosis-related transcription factors in COAD, and validate the representative molecule. METHODS Transcriptome data and patients' clinical parameters were obtained from the TCGA and GEO database. 19 cuproptosis genes were identified through literature consulting. Cuproptosis-related transcription factors were screened by COX regression analyses. Multivariate Cox regression was applied to construct the signature. Prognostic effects were evaluated by Kaplan Meier survival analyses and ROC analyses. KEGG, GO, and ssGSEA analyses were performed for function prediction. 48 COAD tissues were collected for immunohistochemistry stain to observe the expression level and prognostic value of E2F3. qRT-PCR was performed to detect mRNA expression levels, while cell viability assay was applied to detect the response of COAD cells to elesclomol treatment. RESULTS A novel signature based on 3 prognostic transcription factors related to cuproptosis was successfully established and verified. Patients in the low-risk group tended to have better overall survival and lower immune phenotype scores than those in the high-risk group. Meanwhile, we also constructed a nomogram based on this signature and predict 10 candidate compounds targeting this signature. As an essential member of this signature, E2F3 was confirmed to be overexpressed in COAD tissues and was associated with poor prognosis of COAD patients. Importantly, CuCl2 and cuproptosis inducer elesclomol treatment could increase the expression of E2F3 in COAD cell while the overexpression of E2F3 significantly enhanced the resistance of COAD cells to elesclomol treatment. CONCLUSION Our research has identified a new prognostic biomarker and provides some innovative insights into the diagnosis and therapy of patients with COAD.
Collapse
Affiliation(s)
- Lei Zhou
- The Graduate School, Dalian Medical University, Dalian, Liaoning, China
- Department of General Surgery, Yancheng Third People's Hospital, The Clinical Teaching Hospital of Jiangsu Vocational College of Medicine, Yancheng, Jiangsu, China
| | - Yuwan Zhang
- School of Management, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yixin Xu
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, Jiangsu, China
| | - Tao Jiang
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, Jiangsu, China.
| | - Liming Tang
- The Graduate School, Dalian Medical University, Dalian, Liaoning, China.
- Department of General Surgery, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, No. 68 Gehu Middle Road, Changzhou, 213164, Jiangsu, China.
| |
Collapse
|
24
|
Mao J, Shen J, Lu X, Cai Y, Tao R, Deng Y, Zhang Y, Wu Y, Chen W. MCM5 is an oncogene of colon adenocarcinoma and promotes progression through cell cycle control. Acta Histochem 2023; 125:152072. [PMID: 37385108 DOI: 10.1016/j.acthis.2023.152072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 06/22/2023] [Accepted: 06/23/2023] [Indexed: 07/01/2023]
Abstract
Many patients with colon adenocarcinoma (COAD) are diagnosed at an advanced stage, and the molecular mechanism of COAD progression is intricate and controversial. Therefore, there is an urgent need to identify more novel prognosis biomarkers for COAD and elucidate the molecular mechanism of this disease. The present study aimed to screen out key genes correlated with COAD prognosis. In this study, a key module was identified and four hub genes (MCM5 (encoding minichromosome maintenance complex component 5), NOLC1 (encoding nucleolar and coiled-body phosphoprotein 1), MYC (encoding MYC proto-oncogene, BHLH transcription factor), and CDK4 (encoding cyclin dependent kinase 4)) were selected that correlated with COAD prognosis, based on the GSE9348 dataset in Gene Expression Omnibus database. Gene ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated that MCM5 correlated with the cell cycle. Furthermore, MCM5 expression was upregulated in tumor tissues of patients with COAD compared with that in adjacent tissues, based on various databases, including The Cancer Genome Atlas, the Clinical Proteomic Tumor Analysis Consortium database, and the Human Protein Atlas database. Small interfering RNA-mediated knockdown of MCM5 inhibited the cell cycle and migration of colorectal cancer cells in vitro. And western blotting results indicated that factors correlated with cell cycle (CDK2/6, Cyclin D3, P21) were downregulated after knockdown of MCM5 in vitro. Besides, downregulation of MCM5 was demonstrated to inhibit lung metastasis of COAD in nude mice model. In conclusion, MCM5 is an oncogene of COAD that promotes COAD progression via cell cycle control.
Collapse
Affiliation(s)
- Jiayan Mao
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310051, China; Cancer Institute of Integrated Traditional Chinese and Western Medicine, Key Laboratory of Cancer Prevention and Therapy Combining Traditional Chinese and Western Medicine of Zhejiang Province, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang 310012, China
| | - Jian Shen
- Cancer Institute of Integrated Traditional Chinese and Western Medicine, Key Laboratory of Cancer Prevention and Therapy Combining Traditional Chinese and Western Medicine of Zhejiang Province, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang 310012, China; School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xuemei Lu
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310051, China; Cancer Institute of Integrated Traditional Chinese and Western Medicine, Key Laboratory of Cancer Prevention and Therapy Combining Traditional Chinese and Western Medicine of Zhejiang Province, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang 310012, China
| | - Ying Cai
- Cancer Institute of Integrated Traditional Chinese and Western Medicine, Key Laboratory of Cancer Prevention and Therapy Combining Traditional Chinese and Western Medicine of Zhejiang Province, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang 310012, China
| | - Rujia Tao
- Cancer Institute of Integrated Traditional Chinese and Western Medicine, Key Laboratory of Cancer Prevention and Therapy Combining Traditional Chinese and Western Medicine of Zhejiang Province, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang 310012, China
| | - Yuqin Deng
- Cancer Institute of Integrated Traditional Chinese and Western Medicine, Key Laboratory of Cancer Prevention and Therapy Combining Traditional Chinese and Western Medicine of Zhejiang Province, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang 310012, China
| | - Yuanting Zhang
- Cancer Institute of Integrated Traditional Chinese and Western Medicine, Key Laboratory of Cancer Prevention and Therapy Combining Traditional Chinese and Western Medicine of Zhejiang Province, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang 310012, China
| | - Yuan Wu
- Department of Respiratory Medicine, The Fourth Affiliated Hospital, College of Medicine, Zhejiang University, Yiwu, Zhejiang 322000, China.
| | - Wei Chen
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310051, China; Cancer Institute of Integrated Traditional Chinese and Western Medicine, Key Laboratory of Cancer Prevention and Therapy Combining Traditional Chinese and Western Medicine of Zhejiang Province, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang 310012, China.
| |
Collapse
|
25
|
Zhang D, Zhao Y, Wang S, Wang X, Sun Y. A Prognostic Model of Angiogenesis and Neutrophil Extracellular Traps Related Genes Manipulating Tumor Microenvironment in Colon Cancer. J Cancer 2023; 14:2109-2127. [PMID: 37497410 PMCID: PMC10367930 DOI: 10.7150/jca.85778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 06/26/2023] [Indexed: 07/28/2023] Open
Abstract
Colon adenocarcinoma (COAD) is one of the most common carcinomas worldwide. The main causes of cancer-related mortality of COAD are metastases. The fundamental processes for how angiogenesis and neutrophil extracellular traps (NETs) contributing to tumor progression and metastasis are still uncertain. In our study, The Cancer Genome Atlas (TCGA)-COAD dataset (train set) and GSE17536 (test set) were analyzed. Angiogenesis potential index (API) and NETs potential index (NPI) based on angiogenesis and NETs-related genes were respectively built using bioinformatic methods and machine learning algorithms. Subjects were split into groups with low API/NPI or high API/NPI. Survival analysis showed the high API and high NPI patients with the worst survival compared with the others. Between the high API/NPI group and the other groups, differentially expressed genes (DEGs) were found. A four-gene signature (TIMP1, FSL3, CALB2, and FABP4) was included in a risk model based on least absolute shrinkage and selection operator (LASSO) analysis. Additionally, the model displayed a significant association with many immune microenvironment characteristics. Finally, we verified the clinical significance of CALB2 expression and its role to promote the invasion and migration of colon cancer cells in vitro.
Collapse
Affiliation(s)
- Dongsheng Zhang
- Department of Colorectal Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Colorectal Institute of Nanjing Medical University, Nanjing, China
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Yan Zhao
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Shirui Wang
- Department of Colorectal Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Colorectal Institute of Nanjing Medical University, Nanjing, China
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Xiaowei Wang
- Department of Colorectal Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Yueming Sun
- Department of Colorectal Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Colorectal Institute of Nanjing Medical University, Nanjing, China
| |
Collapse
|
26
|
Parsazad E, Esrafili F, Yazdani B, Ghafarzadeh S, Razmavar N, Sirous H. Integrative bioinformatics analysis of ACS enzymes as candidate prognostic and diagnostic biomarkers in colon adenocarcinoma. Res Pharm Sci 2023; 18:413-429. [PMID: 37614614 PMCID: PMC10443664 DOI: 10.4103/1735-5362.378088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/17/2023] [Accepted: 05/06/2023] [Indexed: 08/25/2023] Open
Abstract
Background and purpose Acyl-CoA synthetase (ACS) enzymes play an important role in the activation of fatty acids. While many studies have found correlations between the expression levels of ACS enzymes with the progression, growth, and survival of cancer cells, their role and expression patterns in colon adenocarcinoma are still greatly unknown and demand further investigation. Experimental approach The expression data of colon adenocarcinoma samples were downloaded from the Cancer Genome Atlas (TCGA) database. Normalization and differential expression analysis were performed to identify differentially expressed genes (DEGs). Gene set enrichment analysis was applied to identify top enriched genes from ACS enzymes in cancer samples. Gene ontology and protein-protein interaction analyses were performed for the prediction of molecular functions and interactions. Survival analysis and receiver operating characteristic test (ROC) were performed to find potential prognostic and diagnostic biomarkers. Findings/Results ACSL6 and ACSM5 genes demonstrated more significant differential expression and LogFC value compared to other ACS enzymes and also achieved the highest enrichment scores. Gene ontology analysis predicted the involvement of top DEGs in fatty acids metabolism, while protein-protein interaction network analysis presented strong interactions between ACSLs, ACSSs, ACSMs, and ACSBG enzymes with each other. Survival analysis suggested ACSM3 and ACSM5 as potential prognostic biomarkers, while the ROC test predicted stronger diagnostic potential for ACSM5, ACSS2, and ACSF2 genes. Conclusion and implications Our findings revealed the expression patterns, prognostic, and diagnostic biomarker potential of ACS enzymes in colon adenocarcinoma. ACSM3, ACSM5, ACSS2, and ACSF2 genes are suggested as possible prognostic and diagnostic biomarkers.
Collapse
Affiliation(s)
- Ehsan Parsazad
- Department of Bioscience and Biotechnology, Malek Ashtar University, Tehran, I.R. Iran
- Medvac Biopharma Company, Alborz Province, I.R. Iran
| | - Farina Esrafili
- Department of Genetics, Zanjan Branch, Islamic Azad University, Zanjan, I.R. Iran
| | - Behnaz Yazdani
- Department of Tissue Engineering, Najafabad Branch, Islamic Azad University, Najafabad, I.R. Iran
| | - Saghi Ghafarzadeh
- Department of Royan Institute, University of Science and Culture, Tehran, I.R. Iran
| | - Namdar Razmavar
- Department of Biology, University of Guilan, Rasht, I.R. Iran
| | - Hajar Sirous
- Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| |
Collapse
|
27
|
Chao G, Zhang L. Correlation analysis of PBX family with immune invasion and drug sensitivity in colon adenocarcinoma. Heliyon 2023; 9:e17220. [PMID: 37360109 PMCID: PMC10285256 DOI: 10.1016/j.heliyon.2023.e17220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 06/08/2023] [Accepted: 06/10/2023] [Indexed: 06/28/2023] Open
Abstract
Objedtive Pre-B cell leukemia (PBX) has been found to be associated with cancer, but poorly studied with colon adenocarcinoma (COAD). In this study, the correlation between PBX family and COAD pathogenesis and immune cytokine infiltration was further explored by analyzing online tumor databases, in order to find new biomarkers for the diagnosis of COAD. Methods The online database was used to analyze gene differential expression, methylation level, gene mutation rate, immune infiltration difference, drug sensitivity, and so on. Results PBX1 and PBX3 decreased in COAD. PBX2 and PBX4 increased. The expression of PBX1 and PBX2 in different clinical stages was different. PBX4 was valuable for the prognosis of COAD. PBX family has correlation between COAD and immune infiltration. PBX2 was correlated with different pathological stages. PBX3 had the highest gene mutation rate, followed by PBX1, PBX2 and PBX4. PBX1, PBX2 and PBX4 were correlated with the sensitivity of multiple drugs. Conclusion The PBX family is differentially expressed in COAD and has a genetic mutation, and its protein network is closely related to the HOX family and is associated with immune infiltration of COAD.
Collapse
|
28
|
Pilon A, Avecilla F, Mohai M, Enyedy ÉA, Rácz B, Spengler G, Garcia MH, Valente A. First iron(II) organometallic compound acting as ABCB1 inhibitor. Eur J Med Chem 2023; 256:115466. [PMID: 37187089 DOI: 10.1016/j.ejmech.2023.115466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/03/2023] [Accepted: 05/05/2023] [Indexed: 05/17/2023]
Abstract
Five new iron (II) complexes bearing imidazole-based (Imi-R) ligands with the general formula [Fe(η5-C5H5)(CO)(PPh3)(Imi-R)][CF3SO3] were synthesized and fully characterized by several spectroscopic and analytical techniques. All compounds crystallize in centrosymmetric space groups in a typical "piano stool" distribution. Given the growing importance of finding alternatives to overcome different forms of multidrug resistance, all compounds were tested against cancer cell lines with different ABCB1 efflux pump expression, namely, the doxorubicin-sensitive (Colo205) and doxorubicin-resistant (Colo320) human colon adenocarcinoma cell lines. Compound 3 bearing 1-benzylimidazole was the most active in both cell lines with IC50 values of 1.26 ± 0.11 and 2.21 ± 0.26 μM, respectively, being also slightly selective against the cancer cells (vs. MRC5 normal human embryonic fibroblast cell lines). This compound, together with compound 2 bearing 1H-1,3-benzodiazole, were found to display very potent ABCB1 inhibitory effect. Compound 3 also showed the ability to induce cell apoptosis. Iron cellular accumulation studies by ICP-MS and ICP-OES methods revealed that the compounds' cytotoxicity is not related to the extent of iron accumulation. Yet, it is worth mentioning that, from the compounds tested, 3 was the only one where iron accumulation was greater in the resistant cell line than in the sensitive one, validating the possible role of ABCB1 inhibition in its mechanism of action.
Collapse
Affiliation(s)
- Adhan Pilon
- Centro de Química Estrutural, Institute of Molecular Sciences and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Fernando Avecilla
- Universidade da Coruña, Grupo NanoToxGen, Centro Interdisciplinar de Química y Biología (CICA), Departamento de Química, Facultade de Ciencias, Campus de A Coruña, 15071, A Coruña, Spain
| | - Miklós Mohai
- Research Centre for Natural Sciences, Institute of Materials and Environmental Chemistry, Magyar tudósok körútja 2, H-1117, Budapest, Hungary
| | - Éva A Enyedy
- MTA-SZTE Lendület Functional Metal Complexes Research Group, Department of Inorganic and Analytical Chemistry, Interdisciplinary Excellence Centre, University of Szeged, Dóm tér 7, H-6720, Szeged, Hungary
| | - Bálint Rácz
- Department of Medical Microbiology, Albert Szent-Györgyi Medical School, University of Szeged, Semmelweis utca 6, H-6725, Szeged, Hungary
| | - Gabriella Spengler
- Department of Medical Microbiology, Albert Szent-Györgyi Medical School, University of Szeged, Semmelweis utca 6, H-6725, Szeged, Hungary
| | - M Helena Garcia
- Centro de Química Estrutural, Institute of Molecular Sciences and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Andreia Valente
- Centro de Química Estrutural, Institute of Molecular Sciences and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.
| |
Collapse
|
29
|
Khalil HKM, Hammam OA, Anis SE, Elashry MAEH, El-Yasergy DF. Comparative Study of DNA ploidy and BRAF Immunohistochemistry between Colonic Adenocarcinoma and Inflammatory Colonic Lesions. Asian Pac J Cancer Prev 2023; 24:1389-1400. [PMID: 37116163 DOI: 10.31557/apjcp.2023.24.4.1389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Indexed: 04/30/2023] Open
Abstract
OBJECTIVES To evaluate DNA ploidy and S-phase fraction (SPF) in non-Lynch colonic adenocarcinoma, ulcerative colitis (UC), Crohn disease (CD) which are known as risk factors, and colitis. We correlated ploidy and SPF with tumor grading, staging and BRAF expression. METHODS All studied adenocarcinomas have intact mismatch repair genes as proved by immunohistochemistry. All were assessed for ploidy by automated image-based DNA cytometry and histograms were drawn. Immunostaining by anti-BRAF V600E was performed. Diagnostic laparoscopy (DL) was done as a preliminary step for staging GI cancers. RESULTS there is significant difference in DNA ploidy between groups; 77.5% and 17.5% of aneuploid cases are adenocarcinoma and UC. Groups are compared in terms of 2C, 4C, above 4C DNA content and SPF and significant difference is principally found between adenocarcinoma group and others. In adenocarcinomas, DNA ploidy is significantly correlated with tumor staging and grading. Regarding BRAF expression, there is significant difference between groups; all adenocarcinomas, 83.33% of UC were positive, while all cases of colitis, bilharzial colitis, CD were negative. There is significant relation between BRAF and SPF among all diploid cases including adenocarcinoma, and among non-neoplastic diploid cases. There is direct significant relation between BRAF intensity and adenocarcinoma staging. There is no significant difference between BRAF and ploidy among UC cases, although 75% of aneuploid UC are positive. DL helps in GI cancer staging. Routine laparoscopy before laparotomy, especially in cancers which have equivocal operability helps to avoid unnecessary laparotomies. CONCLUSION Based on significant difference in ploidy between adenocarcinoma and UC and between SPF and ploidy, assessment of ploidy by DNA cytometry for UC and other colitis could therefore predict impending malignant transformation before development of colonic dysplasia. Also measuring SPF in adenocarcinoma helps to select patients who could greatly benefit from chemotherapy. DL has vital role in staging GI cancers.
Collapse
Affiliation(s)
| | - Olfat Ali Hammam
- Department of Pathology, Theodor Bilharz Research Institute, Giza, Egypt
| | - Shady Elia Anis
- Department of Pathology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | | | | |
Collapse
|
30
|
Liu S, Zhang S, Liu Y, Yang X, Zheng G. Comprehensive analysis of cuproptosis-related long noncoding RNA for predicting prognostic and diagnostic value and immune landscape in colorectal adenocarcinoma. Hum Genomics 2023; 17:22. [PMID: 36915193 PMCID: PMC10009981 DOI: 10.1186/s40246-023-00469-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 03/04/2023] [Indexed: 03/16/2023] Open
Abstract
BACKGROUND Cuproptosis, as a copper-induced mitochondrial cell death, has attracted extensive attention recently, especially in cancer. Although some key regulatory genes have been identified in cuproptosis, the related lncRNAs have not been further studied. Exploring the prognostic and diagnostic value of cuproptosis-related lncRNAs (CRLs) in colon adenocarcinoma and providing guidance for individualized immunotherapy for patients are of great significance. RESULTS A total of 2003 lncRNAs were correlated with cuproptosis genes and considered as CRLs. We screened 33 survival-associated CRLs and established a prognostic signature base on 7 CRLs in the training group. The patients in the low-risk group had better outcomes in both training group (P < 0.001) and test group (P = 0.016). More exciting, our model showed good prognosis prediction in both stage I-II (P = 0.020) and stage III-IV (P = 0.001). The nomogram model could further improve the accuracy of prognosis prediction. Interestingly, glucose-related metabolic pathways, which were closely related to cuproptosis, were enriched in the low-risk group. Meanwhile, the immune infiltration scores were lower in the high-risk group. The high-risk group was more sensitive to OSI.906 and ABT.888, while low-risk group was more sensitive to Sorafenib. Three lncRNAs, FALEC, AC083967.1 and AC010997.4, were highly expressed in serum of COAD patients, and the AUC was 0.772, 0.726 and 0.714, respectively, indicating their valuable diagnostic value. CONCLUSIONS Our research constructed a prognostic signature based on 7 CRLs and found three promising diagnostic markers for COAD patients. Our results provided a reference to the personalized immunotherapy strategies.
Collapse
Affiliation(s)
- Shichao Liu
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China.,Department of Clinical Laboratory, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong Province, People's Republic of China
| | - Shoucai Zhang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China.,Department of Clinical Laboratory, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong Province, People's Republic of China
| | - Yingjie Liu
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China.,Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan, China
| | - XiaoRong Yang
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, China
| | - Guixi Zheng
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China. .,Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan, China.
| |
Collapse
|
31
|
Lin YS, Chiang SF, Chen CY, Hong WZ, Chen TW, Chen WTL, Ke TW, Yang PC, Liang JA, Shiau AC, Chao KSC, Huang KCY. Targeting CD73 increases therapeutic response to immunogenic chemotherapy by promoting dendritic cell maturation. Cancer Immunol Immunother 2023:10.1007/s00262-023-03416-4. [PMID: 36881132 DOI: 10.1007/s00262-023-03416-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 02/22/2023] [Indexed: 03/08/2023]
Abstract
The CD39-CD73-adenosinergic pathway converts adenosine triphosphate (ATP) to adenosine for inhibiting anti-tumor immune responses. Therefore, targeting CD73 to reinvigorate anti-tumor immunity is considered the novel cancer immunotherapy to eradicate tumor cells. To fully understand the critical role of CD39/CD73 in colon adenocarcinoma (COAD), this study aims to comprehensive investigate the prognostic significance of CD39 and CD73 in stage I-IV COAD. Our data demonstrated that CD73 staining strongly marked malignant epithelial cells and CD39 was highly expressed in stromal cells. Attractively, tumor CD73 expression was significantly associated with tumor stage and the risk of distant metastasis, which suggested CD73 was as an independent factor for colon adenocarcinoma patients in univariate COX analysis [HR = 1.465, 95%CI = 1.084-1.978, p = 0.013]; however, high stromal CD39 in COAD patients was more likely to have favorable survival outcome [HR = 1.458, p = 1.103-1.927, p = 0.008]. Notably, high CD73 expression in COAD patients showed poor response to adjuvant chemotherapy and high risk of distant metastasis. High CD73 expression was inversely associated with less infiltration of CD45+ and CD8+ immune cells. However, administration with anti-CD73 antibodies significantly increased the response to oxaliplatin (OXP). Blockade of CD73 signaling synergistically enhanced OXP-induced ATP release, which is a marker of immunogenic cell death (ICD), promotes dendritic cell maturation and immune cell infiltration. Moreover, the risk of colorectal cancer lung metastasis was also decreased. Taken together, the present study revealed tumor CD73 expression inhibited the recruitment of immune cells and correlated with a poor prognosis in COAD patients, especially patients received adjuvant chemotherapy. Targeting CD73 to markedly increased the therapeutic response to chemotherapy and inhibited lung metastasis. Therefore, tumor CD73 may be an independent prognostic factor as well as the potential of therapeutic target for immunotherapy to benefit colon adenocarcinoma patients.
Collapse
Affiliation(s)
- Yun-Shan Lin
- Department of Pathology, China Medical University Hospital, China Medical University, Taichung, 40402, Taiwan, ROC
| | - Shu-Fen Chiang
- Lab of Precision Medicine, Feng-Yuan Hospital, Ministry of Health and Welfare, Taichung, 42055, Taiwan, ROC
| | - Chia-Yi Chen
- Proton Therapy and Science Center, China Medical University Hospital, China Medical University, Taichung, 40402, Taiwan, ROC
| | - Wei-Ze Hong
- Proton Therapy and Science Center, China Medical University Hospital, China Medical University, Taichung, 40402, Taiwan, ROC
| | - Tsung-Wei Chen
- Graduate Institute of Biomedical Science, China Medical University, Taichung, 40402, Taiwan, ROC
- Department of Pathology, Asia University Hospital, Asia University, Taichung, 41354, Taiwan, ROC
| | - William Tzu-Liang Chen
- Department of Colorectal Surgery, China Medical University HsinChu Hospital, China Medical University, HsinChu, 302, Taiwan, ROC
- Department of Colorectal Surgery, China Medical University Hospital, China Medical University, Taichung, 40402, Taiwan, ROC
- Department of Surgery, School of Medicine, China Medical University, Taichung, 40402, Taiwan, ROC
| | - Tao-Wei Ke
- Department of Colorectal Surgery, China Medical University Hospital, China Medical University, Taichung, 40402, Taiwan, ROC
- School of Chinese Medicine, China Medical University, Taichung, 40402, Taiwan, ROC
| | - Pei-Chen Yang
- Proton Therapy and Science Center, China Medical University Hospital, China Medical University, Taichung, 40402, Taiwan, ROC
| | - Ji-An Liang
- Department of Radiation Oncology, China Medical University Hospital, China Medical University, Taichung, Taiwan, ROC
- Department of Radiotherapy, School of Medicine, China Medical University Hospital, China Medical University, Taichung, 40402, Taiwan, ROC
| | - An-Cheng Shiau
- Proton Therapy and Science Center, China Medical University Hospital, China Medical University, Taichung, 40402, Taiwan, ROC
- Department of Biomedical Imaging and Radiological Science, China Medical University, Taichung, 40402, Taiwan, ROC
| | - K S Clifford Chao
- Proton Therapy and Science Center, China Medical University Hospital, China Medical University, Taichung, 40402, Taiwan, ROC.
- Graduate Institute of Biomedical Science, China Medical University, Taichung, 40402, Taiwan, ROC.
- Department of Radiation Oncology, China Medical University Hospital, China Medical University, Taichung, Taiwan, ROC.
- Department of Radiotherapy, School of Medicine, China Medical University Hospital, China Medical University, Taichung, 40402, Taiwan, ROC.
| | - Kevin Chih-Yang Huang
- Department of Biomedical Imaging and Radiological Science, China Medical University, Taichung, 40402, Taiwan, ROC.
- Translation Research Core, China Medical University Hospital, China Medical University, Taichung, 40402, Taiwan, ROC.
| |
Collapse
|
32
|
Yang HD, Jin XX, Gu BB, Yu-Zhang, Li D, Yan LL. ARL9 is upregulated and serves as a biomarker for a poor prognosis in colon adenocarcinoma. BMC Gastroenterol 2023; 23:48. [PMID: 36823542 PMCID: PMC9951453 DOI: 10.1186/s12876-023-02677-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/13/2023] [Indexed: 02/25/2023] Open
Abstract
BACKGROUND ARL9 is a newly identified member of the ARF family, and the clinical significance of ARL9 in colon adenocarcinoma is unknown. In this study, we aimed to explore the expression of ARL9 mRNA in colon adenocarcinoma, and its effect on the prognosis of patients with colon adenocarcinoma. METHODS We investigated the differential expression of ARL9 between colon adenocarcinoma tissue and adjacent tissues through a bioinformatics analysis using The Cancer Genome Atlas (TCGA) database. The correlation between clinical characteristics and the mRNA expression level of ARL9 were analyzed. A survival analysis and a Cox regression analysis were used to determine the prognostic significance of ARL9. Finally, we conducted a gene set enrichment analysis (GSEA) to explore the ARL9 signaling pathways involved in the development of colon adenocarcinoma. The effect of the expression of ARL9 on the proliferation and migration of colon adenocarcinoma was analyzed by the CCK8 method and a cell scratch test, respectively. RESULTS The mRNA expression of ARL9 in colon adenocarcinoma tissues was higher in comparison to the level in normal adjacent tissues (P < 0.05). The mRNA expression of ARL9 was not related to sex, tumor stage, T stage, N stage, M stage, but to age. The 5-year survival rate of colon adenocarcinoma patients with high ARL9 mRNA expression levels was significantly lower than that of patients with low ARL9 mRNA expression levels (P < 0.05). Age and the high mRNA expression of ARL9 were independent risk factors for a poor prognosis in patients with colon adenocarcinoma. The GSEA suggested that ARL9 may be able to upregulate cell adhesion, extracellular matrix receptor interactions, tumor-associated pathways, and downregulate the citrate cycle and tricarboxylic acid cycle pathway, which are involved in the development of colon adenocarcinoma. After knocking down ARL9, the proliferation and migration abilities of colon adenocarcinoma cells were decreased (P < 0.01). CONCLUSION The mRNA expression of ARL9 is upregulated in colon adenocarcinoma, and higher mRNA expression levels are associated with a poor prognosis. Knocking down ARL9 can reduce the proliferation and migration of colon adenocarcinoma cells. ARL9 mRNA can be used as a prognostic biomarker in patients with colon adenocarcinoma.
Collapse
Affiliation(s)
- Hai-deng Yang
- Key Laboratory of Minimally Invasive Techniques and Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Linhai, China ,grid.469636.8Department of Gastroenterology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| | - Xiu-xiu Jin
- Key Laboratory of Minimally Invasive Techniques and Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Linhai, China ,grid.469636.8Department of Gastroenterology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| | - Bin-bin Gu
- Key Laboratory of Minimally Invasive Techniques and Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Linhai, China ,grid.469636.8Department of Gastroenterology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| | - Yu-Zhang
- Key Laboratory of Minimally Invasive Techniques and Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Linhai, China ,grid.469636.8Department of Gastroenterology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| | - Dan Li
- grid.469636.8Endoscopy Center, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| | - Ling-ling Yan
- Key Laboratory of Minimally Invasive Techniques and Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Linhai, China ,grid.469636.8Department of Gastroenterology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| |
Collapse
|
33
|
Jiang H, Cheng X, Liang Y, Wang Y, Li Y, Li Y. Aberrant expression of WNK lysine deficient protein kinase 1 is associated with poor prognosis of colon adenocarcinoma. Ir J Med Sci 2023; 192:57-64. [PMID: 35138567 DOI: 10.1007/s11845-021-02916-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 12/30/2021] [Indexed: 02/04/2023]
Abstract
BACKGROUNDS WNK1 (WNK lysine deficient protein kinase 1) is a kind of protein kinase and participates in angiogenesis, having a potent tumor promoting role. WNK1 is ubiquitously expressed, and its upregulated expression has been reported in several tumor types. AIMS Here, we aimed to investigate the correlation between WNK1 expression and colon adenocarcinoma (COAD) progression. METHODS In the current study, WNK1 expression was evaluated by immunohistochemically in adjacent normal colonic mucosae and primary adenocarcinomas. The effect of WNK1 on overall survival (OS) and its associations with the clinicopathological parameters were analyzed in a retrospective cohort of COAD patients (n = 185). The tumor-related effects of WNK1 in COAD were further tested via cellular and mice experiments. RESULTS According to our cohort, higher WNK1 expression was significantly associated with unfavorable prognostic factors, such as high pT stage, pN stage, as well as shorter OS. Moreover, WNK1 exhibited tumor promoting role in COAD cancer cell lines as well as in nude mice. Silencing WNK1 can significantly inhibit the proliferation of COAD both in vitro and in vivo. CONCLUSIONS In all, WNK1 acts as a tumor promoter and may be used as a COAD prognostic biomarker.
Collapse
Affiliation(s)
- Huiyuan Jiang
- Department of Colorectal & Anal Surgery, Affiliated Tumor Hospital of Shanxi Medical University, Taiyuan, China
| | - Xin Cheng
- Department of Gynecology, First Affiliated Hospital of Shanxi Medical University, Taiyuan, China
| | - Yanjie Liang
- Department of Laboratory Medicine, Affiliated Tumor Hospital of Shanxi Medical University, Taiyuan, China
| | - Yan Wang
- Department of Aetiology, Affiliated Tumor Hospital of Shanxi Medical University, Taiyuan, China
| | - Yiqun Li
- Department of Colorectal & Anal Surgery, Affiliated People's Hospital of Shanxi Medical University, 29 Shuangtasi Street, Taiyuan, 030012, China
| | - Yaoping Li
- Department of Colorectal & Anal Surgery, Affiliated People's Hospital of Shanxi Medical University, 29 Shuangtasi Street, Taiyuan, 030012, China.
| |
Collapse
|
34
|
Li S, Wang Y, Xuan Z, Zhang Y, Miao Z. High expression of homeobox B2 predicts poor survival of colon adenocarcinoma by enhancing tumor proliferation and invasion. Ir J Med Sci 2023; 192:89-97. [PMID: 35320486 DOI: 10.1007/s11845-022-02964-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 12/27/2021] [Indexed: 02/04/2023]
Abstract
OBJECTIVE Homeobox B2 (HOXB2) is known to be correlated with the development and prognosis of various cancers. However, its role in colon cancer remains unclear. AIMS In this study, we explored the prognostic value of HOXB2 in colon adenocarcinoma (COAD). METHODS A total of 264 colon adenocarcinoma cases were retrospectively enrolled to evaluate HOXB2 expression and clinical significance. Chi-square test was applied to identify relationship between clinical features and HOXB2 expression. The effect of HOXB2 expression and clinical features on the survival of COAD patients was evaluated using Kaplan-Meier and Cox regression analyses. Cellular assays and mice models were conducted to validate the tumor-related role of HOXB2 in COAD. RESULTS Higher expression of HOXB2 in COAD tissues was significantly associated with tumor size, invasion depth, and lymph node metastasis (all P < 0.05). Univariate and multivariate analyses showed that high expression of HOXB2 was significantly correlated with a poor overall survival. In vitro cellular assays combined with knockdown strategies demonstrated that HOXB2 can promote tumor proliferation and invasion of COAD, which was further confirmed by in vivo xenograft experiments. CONCLUSIONS HOXB2 may be a valuable biomarker and potential therapeutic target for the treatment of COAD.
Collapse
Affiliation(s)
- Shengjie Li
- Department of Gastroenterology Surgery, Dalian Municipal Central Hospital, Liaoning, 116033, China
| | - Yujie Wang
- Department of Gastroenterology Surgery, Dalian Municipal Central Hospital, Liaoning, 116033, China
| | - Zhiqiang Xuan
- Department of Gastroenterology Surgery, Dalian Municipal Central Hospital, Liaoning, 116033, China
| | - Yue Zhang
- Department of Gastroenterology Surgery, Dalian Municipal Central Hospital, Liaoning, 116033, China
| | - Zhongxing Miao
- Department of Gastroenterology Surgery, Dalian Municipal Central Hospital, Liaoning, 116033, China.
| |
Collapse
|
35
|
Liang L, Liu L, Mai S, Chen Y. A novel machine learning model based on ubiquitin-related gene pairs and clinical features to predict prognosis and treatment effect in colon adenocarcinoma. Eur J Med Res 2023; 28:41. [PMID: 36681855 PMCID: PMC9863211 DOI: 10.1186/s40001-023-00993-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 01/04/2023] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Ubiquitin and ubiquitin-like (UB/UBL) conjugations are essential post-translational modifications that contribute to cancer onset and advancement. In colon adenocarcinoma (COAD), nonetheless, the biological role, as well as the clinical value of ubiquitin-related genes (URGs), is unclear. The current study sought to design and verify a ubiquitin-related gene pairs (URGPs)-related prognostic signature for predicting COAD prognoses. METHODS Using univariate, least absolute shrinkage and selection operator (LASSO), and multivariate Cox regression, URGP's predictive signature was discovered. Signatures differentiated high-risk and low-risk patients. ROC and Kaplan-Meier assessed URGPs' signature. Gene set enrichment analysis (GSEA) examined biological nomogram enrichment. Chemotherapy and tumor immune microenvironment were also studied. RESULTS The predictive signature used six URGPs. High-risk patients had a worse prognosis than low-risk patients, according to Kaplan-Meier. After adjusting for other clinical characteristics, the URGPs signature could reliably predict COAD patients. In the low-risk group, we found higher amounts of invading CD4 memory-activated T cells, follicular helper T cells, macrophages, and resting dendritic cells. Moreover, low-risk group had higher immune checkpoint-related gene expression and chemosensitivity. CONCLUSION Our research developed a nomogram and a URGPs prognostic signature to predict COAD prognosis, which may aid in patient risk stratification and offer an effective evaluation method of individualized treatment in clinical settings.
Collapse
Affiliation(s)
- Liping Liang
- grid.284723.80000 0000 8877 7471Department of Gastroenterology, State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515 China
| | - Le Liu
- grid.284723.80000 0000 8877 7471Department of Gastroenterology, Integrated Clinical Microecology Center, Shenzhen Hospital, Southern Medical University, 1333 New Lake Road, Shenzhen, 518100 China
| | - Shijie Mai
- grid.284723.80000 0000 8877 7471Department of Thoracic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515 China
| | - Ye Chen
- grid.284723.80000 0000 8877 7471Department of Gastroenterology, State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515 China ,grid.284723.80000 0000 8877 7471Department of Gastroenterology, Integrated Clinical Microecology Center, Shenzhen Hospital, Southern Medical University, 1333 New Lake Road, Shenzhen, 518100 China
| |
Collapse
|
36
|
Zhu Y, Zhao Z, Thandar M, Cheng J, Chi P, Huang S. Expression patterns and prognostic value of key regulators associated with m7G RNA modification based on all gene expression in colon adenocarcinoma. BMC Gastroenterol 2023; 23:22. [PMID: 36681801 PMCID: PMC9867544 DOI: 10.1186/s12876-023-02657-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 01/18/2023] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND N7-methylguanosine (m7G) is present in a wide variety of organisms and has important roles. m7G has been reported to be involved in multiple biological processes, and recent studies have reported that changes in RNA modifications result in tumor cellular transformation and cancer, such as colon adenocarcinoma, lung cancer, and intrahepatic cholangiocarcinoma. However, little is known about the function of the m7G in colon adenocarcinoma. METHODS We established two clusters based on the expression of all genes associated with m7G to explore the expression pattern of 31 key regulatory factors of m7G RNA and assess the prognostic value of regulatory factors. Wilcoxon test and differential box line plots were applied for bioinformatics analysis. Receiver Operating and Kaplan‒Meier curves were utilized to evaluate the prognostic value. Finally, four genes' expression in the colon cancer cell line was confirmed by qRT-PCR. RESULTS From The Cancer Genome Atlas database, we found that the expression levels of 25 out of the 31 key N7-methylguanosine RNA modification regulators were significantly different in colon adenocarcinoma. According to 25 methylation regulators' expression, we identified two subgroups by consensus clustering, in which the prognosis was worse in Group 2 than in Group 1 and was significantly correlated with age. Cluster 2 was significantly enriched in tumor-associated pathways, and immune cells were highly infiltrated in Cluster 1 but weakly infiltrated in Cluster 2. Further results indicated that this risk profile may serve as a standalone predictive factor for colon adenocarcinoma, and the four genetic risk profiles' prognostic relatedness was successfully verified through Gene Expression Omnibus dataset. At last, A nomogram for prognosis was created according to age, sex, histological grading, clinicopathological staging, and hazard score to accurately predict patient prognosis in colon adenocarcinoma. We successfully validated the differential expression of four genes using qRT-PCR. CONCLUSIONS In the present study, we revealed the important contribution of key regulators associated with m7G RNA modifications based on all gene expression in colon adenocarcinoma and developed a signature of risk that serves as a promising prognostic marker for patients with colon adenocarcinoma.
Collapse
Affiliation(s)
- Yuanchang Zhu
- grid.411176.40000 0004 1758 0478Department of Colorectal Surgery, Fujian Medical University Union Hospital, No. 29, Xinquan Road, Gulou District, Fuzhou City, Fujian Province China
| | - Zeyi Zhao
- grid.411176.40000 0004 1758 0478Department of Colorectal Surgery, Fujian Medical University Union Hospital, No. 29, Xinquan Road, Gulou District, Fuzhou City, Fujian Province China
| | - Mya Thandar
- grid.411176.40000 0004 1758 0478Department of Colorectal Surgery, Fujian Medical University Union Hospital, No. 29, Xinquan Road, Gulou District, Fuzhou City, Fujian Province China
| | - Junhao Cheng
- grid.411176.40000 0004 1758 0478Department of Colorectal Surgery, Fujian Medical University Union Hospital, No. 29, Xinquan Road, Gulou District, Fuzhou City, Fujian Province China
| | - Pan Chi
- grid.411176.40000 0004 1758 0478Department of Colorectal Surgery, Fujian Medical University Union Hospital, No. 29, Xinquan Road, Gulou District, Fuzhou City, Fujian Province China ,grid.411176.40000 0004 1758 0478Training Center of Minimally Invasive Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian China
| | - Shenghui Huang
- grid.411176.40000 0004 1758 0478Department of Colorectal Surgery, Fujian Medical University Union Hospital, No. 29, Xinquan Road, Gulou District, Fuzhou City, Fujian Province China ,grid.411176.40000 0004 1758 0478Training Center of Minimally Invasive Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian China
| |
Collapse
|
37
|
Jia X, Zhang T, Lv X, Du H, Sun Y, Guan Y. Identification of the six-hormone secretion-related gene signature as a prognostic biomarker for colon adenocarcinoma. Cancer Biomark 2023; 38:523-535. [PMID: 38143338 DOI: 10.3233/cbm-230126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2023]
Abstract
BACKGROUND Colon adenocarcinoma (COAD) is a globally prevalent cancer, with hormone secretion playing a crucial role in its progression. Despite this, there is limited understanding of the impact of hormone secretion on COAD prognosis. This study aimed to establish a prognostic signature based on hormone secretion-related genes and to elucidate the potential functional mechanisms of these genes in COAD. METHODS Using data from The Cancer Genome Atlas COAD cohort (TCGA-COAD), six hormone secretion-related genes were identified (CYP19A1, FOXD1, GRP, INHBB, SPP1, and UCN). These genes were used to develop a Hormone secretion score (HSS), which was then evaluated using the Kaplan-Meier curve and multivariable Cox analysis. The HSS model was further validated with external GEO cohorts (GSE41258, GSE39582, and GSE87211). Functional enrichment analyses were performed, and the CIBERSORT and TIDE algorithms were used to assess tumor infiltration. RESULTS The study developed a prognostic signature, dividing patients into HSS-high and HSS-low groups. The HSS-high group showed a notably worse prognosis within the TCGA-COAD dataset and in three independent datasets: GSE41258, GSE39582, and GSE87211. Moreover, the HSS-high group predicted a shorter overall survival rate in patients maintaining microsatellite stability (MSS). The functional analysis associated HSS-high with the hypoxic, epithelial-mesenchymal transition (EMT), and TGF-β signaling pathways and correlated with distant and lymph node metastases. The tumor immune microenvironment analysis revealed an elevated CIBERSORT score in the HSS-high group, suggesting an association with tumor metastasis. Further, the HSS-high group showed a higher TIDE score, indicating that patients with high HSS scores are less likely to benefit from Immune Checkpoint Inhibitor (ICI) therapy. CONCLUSIONS This study demonstrated the prognostic significance of a HSS signature based on six hormone secretion-related genes in COAD. The findings suggest that this gene signature may serve as a reliable biomarker for predicting survival outcomes in COAD patients.
Collapse
Affiliation(s)
- Xiongjie Jia
- Department of Gastrointestinal Surgery, Affiliated Hospital of Hebei University, Baoding, Heibei, China
- Department of Gastrointestinal Surgery, Affiliated Hospital of Hebei University, Baoding, Heibei, China
| | - Tao Zhang
- Department of Gastrointestinal Surgery, Affiliated Hospital of Hebei University, Baoding, Heibei, China
- Department of Gastrointestinal Surgery, Affiliated Hospital of Hebei University, Baoding, Heibei, China
| | - Xinze Lv
- Burning Rock Biotech, Guangzhou, Guangdong, China
| | - Haiwei Du
- Burning Rock Biotech, Guangzhou, Guangdong, China
| | - Yongkun Sun
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yin Guan
- Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| |
Collapse
|
38
|
Ji F, Yao Z, Liu C, Fu S, Ren B, Liu Y, Ma L, Wei J, Sun D. A novel lnc-LAMC2-1:1 SNP promotes colon adenocarcinoma progression by targeting miR-216a-3p/HMGB3. Heliyon 2022; 8:e12342. [PMID: 36582685 PMCID: PMC9792752 DOI: 10.1016/j.heliyon.2022.e12342] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 09/01/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) was associated with altering the secondary structure of long non-coding RNA (lncRNA). Increasing reports showed that lnc-LAMC2-1:1 SNP played an important role in cancer development and invasion. This study is to elucidate the molecular function of lnc-LAMC2-1:1 SNP rs2147578 promoting tumor progression in colon adenocarcinoma (COAD). In this study, we found that the lnc-LAMC2-1:1 SNP rs2147578 was upregulated in COAD cell lines. Furthermore, lnc-LAMC2-1:1 SNP rs2147578 promoted colon cancer migration, invasion, and proliferation. Interestingly, lnc-LAMC2-1:1 SNP rs2147578 positively regulated HMGB3 expression via miR-216a-3p in colon cancer cells. Functional enrichment analysis showed that targeting genes of miR-216a-3p were enriched in regulating the pluripotency of stem cells, MAPK signaling pathway, TNF signaling pathway, neurotrophin signaling pathway, relaxin signaling pathway, and FoxO signaling pathway. Tumor Immune Estimation Resource (TIMER) database revealed that there was a significantly positive correlation between HMGB3 expression and the infiltration of CD8+ T cells, B cells, neutrophils, macrophages, and CD4+ T cells. Finally, HMGB3 overexpression was validated in external data. In conclusions, lnc-LAMC2-1:1 SNP rs2147578 was involved in promoting COAD progression by targeting miR-216a-3p/HMGB3, and this study will provide a novel molecular target for COAD.
Collapse
Affiliation(s)
- Fulong Ji
- Department of Pediatric Surgery, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Zhiwei Yao
- Department of Pediatric Surgery, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Chunxiang Liu
- Department of Pediatric Surgery, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Siqi Fu
- Department of Pediatric Surgery, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Bingbing Ren
- Department of Pediatric Surgery, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Yong Liu
- Department of Pediatric Surgery, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Lushun Ma
- Department of Pediatric Surgery, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Jianming Wei
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, 300052, China,Corresponding author.
| | - Daqing Sun
- Department of Pediatric Surgery, Tianjin Medical University General Hospital, Tianjin, 300052, China,Corresponding author.
| |
Collapse
|
39
|
Yin GL, Zhu JB, Fu CL, Ding RL, Zhang JM, Lin Q. Metachronous isolated penile metastasis from sigmoid colon adenocarcinoma: A case report. World J Clin Cases 2022; 10:11658-11664. [PMID: 36387791 PMCID: PMC9649525 DOI: 10.12998/wjcc.v10.i31.11658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/24/2022] [Accepted: 10/17/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Sigmoid colon adenocarcinoma has a high incidence among gastrointestinal tumors, and it very rarely metastasizes to the penis. The literature reports that the prognosis after penile metastasis is generally poor, with a median survival of about 9 mo. Metachronous isolated metastasis to the penis originating from sigmoid colon adenocarcinoma has not been reported so far. Here, we report a case of sigmoid colon adenocarcinoma with isolated penile metastasis occurring 2 years after surgery. The mass was pathologically confirmed as metastatic adenocarcinoma, and oral chemotherapy with capecitabine was given after surgery. The tumor did not recur during the 2-year follow-up period.
CASE SUMMARY A 79-year-old man presented to the urology department with "a mass located at the root of the penis since 1 mo". Enhanced computed tomography (CT) examination suggested a 12 mm × 10 mm × 9 mm nodule at the root of the right penile corpus cavernosum. Cranial, pulmonary, and abdominal CT; and bone scan did not show any tumorigenic lesions. The carcinoembryonic antigen (CEA) level was slightly elevated (6.01 ng/mL, reference value 0-5 ng/mL). The patient had undergone laparoscopic radical sigmoidectomy for sigmoid colon cancer 2 years ago. The postoperative pathology showed moderately differentiated adenocarcinoma of the sigmoid colon, and the stage was PT2N0M0. The penile mass was removed under general anesthesia. The postoperative pathology showed adenocarcinoma, and immunohistochemistry showed CDX2(+), CK20(+), and Villin(+). Based on the medical history, he was diagnosed with penile metastasis from sigmoid colon adenocarcinoma. The CEA level returned to normal (3.34 ng/mL) 4 d after surgery. Oral chemotherapy with capecitabine was given subsequently, and tumor recurrence was not found during the 2-year follow-up period.
CONCLUSION To our knowledge, this is a rare case of metachronous isolated penile metastasis from sigmoid colon adenocarcinoma. The penis is a potential site of metastasis of colon adenocarcinoma, and the possibility of metastasis should be considered in patients with a history of colon cancer who present with a penile mass. Solitary penile metastasis can be removed surgically, in combination with chemotherapy, and it may have good long-term outcomes.
Collapse
Affiliation(s)
- Guo-Lin Yin
- Department of Urology, Taizhou First People's Hospital, Taizhou 318020, Zhejiang Province, China
| | - Jiang-Bo Zhu
- Department of Urology, Taizhou First People's Hospital, Taizhou 318020, Zhejiang Province, China
| | - Cheng-Lin Fu
- Department of Pathology, Taizhou First People's Hospital, Taizhou 318020, Zhejiang Province, China
| | - Ru-Liang Ding
- Department of Anorectology, Taizhou First People's Hospital, Taizhou 318020, Zhejiang Province, China
| | - Jun-Miao Zhang
- Department of Urology, Taizhou First People's Hospital, Taizhou 318020, Zhejiang Province, China
| | - Qian Lin
- Department of Urology, Taizhou First People's Hospital, Taizhou 318020, Zhejiang Province, China
| |
Collapse
|
40
|
Hao Z, Liang P, He C, Sha S, Yang Z, Liu Y, Shi J, Zhu Z, Chang Q. Prognostic risk assessment model and drug sensitivity analysis of colon adenocarcinoma (COAD) based on immune-related lncRNA pairs. BMC Bioinformatics 2022; 23:435. [PMID: 36258178 PMCID: PMC9579580 DOI: 10.1186/s12859-022-04969-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 09/30/2022] [Indexed: 11/10/2022] Open
Abstract
PURPOSE The aim of this study was to identify and screen long non-coding RNA (lncRNA) associated with immune genes in colon cancer, construct immune-related lncRNA pairs, establish a prognostic risk assessment model for colon adenocarcinoma (COAD), and explore prognostic factors and drug sensitivity. METHOD Our method was based on data from The Cancer Genome Atlas (TCGA). To begin, we obtained all pertinent demographic and clinical information on 385 patients with COAD. All lncRNAs significantly related to immune genes and with differential expression were identified to construct immune lncRNA pairs. Subsequently, least absolute shrinkage and selection operator and Cox models were used to screen out prognostic-related immune lncRNAs for the establishment of a prognostic risk scoring formula. Finally, We analysed the functional differences between subgroups and screened the drugs, and establish an individual prediction nomogram model. RESULTS Our final analysis confirmed eight lncRNA pairs to construct prognostic risk assessment model. Results showed that the high-risk and low-risk groups had significant differences (training (n = 249): p < 0.001, validation (n = 114): p = 0.022). The prognostic model was certified as an independent prognosis model. Compared with the common clinicopathological indicators, the prognostic model had better predictive efficiency (area under the curve (AUC) = 0.805). Finally, We have analysed highly differentiated cellular pathways such as mucosal immune response, identified 9 differential immune cells, 10 sensitive drugs, and establish an individual prediction nomogram model (C-index = 0.820). CONCLUSION Our study verified that the eight lncRNA pairs mentioned can be used as biomarkers to predict the prognosis of COAD patients. Identified cells, drugs may have an positive effect on colon cancer prognosis.
Collapse
Affiliation(s)
- Zezhou Hao
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China.,Clinical Research Center, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences, Shanghai, 201800, China
| | - Pengchen Liang
- School of Microelectronics, Shanghai University, Shanghai, 201800, China
| | - Changyu He
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200020, China
| | - Shuang Sha
- Clinical Research Center, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences, Shanghai, 201800, China
| | - Ziyuan Yang
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Yixin Liu
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Junfeng Shi
- Department of Prosthodontics, Shanghai Engineering Research Center of Advanced Dental Technology and Materials, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai, 200011, China
| | - Zhenggang Zhu
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200020, China.
| | - Qing Chang
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China. .,Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200020, China.
| |
Collapse
|
41
|
Lu J, Annunziata F, Sirvinskas D, Omrani O, Li H, Rasa SMM, Krepelova A, Adam L, Neri F. Establishment and evaluation of module-based immune-associated gene signature to predict overall survival in patients of colon adenocarcinoma. J Biomed Sci 2022; 29:81. [PMID: 36229806 PMCID: PMC9563160 DOI: 10.1186/s12929-022-00867-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/04/2022] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Patients with colon adenocarcinoma (COAD) exhibit significant heterogeneity in overall survival. The current tumor-node-metastasis staging system is insufficient to provide a precise prediction for prognosis. Identification and evaluation of new risk models by using big cancer data may provide a good way to identify prognosis-related signature. METHODS We integrated different datasets and applied bioinformatic and statistical methods to construct a robust immune-associated risk model for COAD prognosis. Furthermore, a nomogram was constructed based on the gene signature and clinicopathological features to improve risk stratification and quantify risk assessment for individual patients. RESULTS The immune-associated risk model discriminated high-risk patients in our investigated and validated cohorts. Survival analyses demonstrated that our gene signature served as an independent risk factor for overall survival and the nomogram exhibited high accuracy. Functional analysis interpreted the correlation between our risk model and its role in prognosis by classifying groups with different immune activities. Remarkably, patients in the low-risk group showed higher immune activity, while those in the high-risk group displayed a lower immune activity. CONCLUSIONS Our study provides a novel tool that may contribute to the optimization of risk stratification for survival and personalized management of COAD.
Collapse
Affiliation(s)
- Jing Lu
- grid.418245.e0000 0000 9999 5706Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Jena, Germany
| | - Francesco Annunziata
- grid.418245.e0000 0000 9999 5706Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Jena, Germany
| | - Dovydas Sirvinskas
- grid.418245.e0000 0000 9999 5706Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Jena, Germany
| | - Omid Omrani
- grid.418245.e0000 0000 9999 5706Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Jena, Germany
| | - Huahui Li
- grid.418245.e0000 0000 9999 5706Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Jena, Germany
| | - Seyed Mohammad Mahdi Rasa
- grid.418245.e0000 0000 9999 5706Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Jena, Germany
| | - Anna Krepelova
- grid.418245.e0000 0000 9999 5706Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Jena, Germany
| | - Lisa Adam
- grid.418245.e0000 0000 9999 5706Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Jena, Germany
| | - Francesco Neri
- grid.418245.e0000 0000 9999 5706Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Jena, Germany ,grid.7605.40000 0001 2336 6580Present Address: Life Sciences and Systems Biology Department, University of Torino, MBC, via Nizza 52, 10126 Turin, Italy
| |
Collapse
|
42
|
Zhou R, Gao Z, Ju Y. Novel six-gene prognostic signature based on colon adenocarcinoma immune-related genes. BMC Bioinformatics 2022; 23:418. [PMID: 36221049 PMCID: PMC9552517 DOI: 10.1186/s12859-022-04909-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/23/2022] [Indexed: 12/05/2022] Open
Abstract
Background Colon adenocarcinoma (COAD) is one of the most common gastrointestinal tumors worldwide, and immunotherapy is one of the most promising treatments for it. Identifying immune genes involved in the development and maintenance of cancer is key to the use of tumor immunotherapy. This study aimed to determine the prognostic value of immune genes in patients with COAD and to establish an immune-related gene signature. Differentially expressed genes, immune-related genes (DEIGs), and transcription factors (DETFs) were screened using the following databases: Cistrome, The Cancer Genome Atlas (TCGA), the Immunology Database and Analysis Portal, and InnateDB. We constructed a network showing the regulation of DEIGs by DETFs. Using weighted gene co-expression network analysis, we prepared 5 co-expressed gene modules; 6 hub genes (CD1A, CD1B, FGF9, GRP, SERPINE1, and F2RL2) obtained using univariate and multivariate regression analysis were used to construct a risk model. Patients from TCGA database were divided into high- and low-risk groups based on whether their risk score was greater or less than the mean; the public dataset GSE40967, which contains gene expression profiles of 566 colon cancer patients, was used for validation. Results Survival analysis, somatic gene mutations, and tumor-infiltrating immune cells differed significantly between the high- and low-risk groups. Conclusions This immune-related gene signature could play an important role in guiding treatment, making prognoses, and potentially developing future clinical applications. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04909-2.
Collapse
Affiliation(s)
- Rui Zhou
- Surgical Department of Gastrointestinal Surgery, Shunde Hospital of Southern Medical University, No. 1 Jiazi Road, Shunde District, Foshan, 528399, Guangdong, China
| | - Zhuowei Gao
- Medical Department of Traditional Chinese Medicine, Shunde Hospital of Guangzhou University of Traditional Chinese Medicine, No. 12, Jinsha Avenue, Shunde District, Foshan, 510006, Guangdong, China
| | - Yongle Ju
- Surgical Department of Gastrointestinal Surgery, Shunde Hospital of Southern Medical University, No. 1 Jiazi Road, Shunde District, Foshan, 528399, Guangdong, China.
| |
Collapse
|
43
|
Chen Y, Tian Z, Hou H, Gai W. The noncoding RNAs regulating pyroptosis in colon adenocarcinoma were derived from the construction of a ceRNA network and used to develop a prognostic model. BMC Med Genomics 2022; 15:201. [PMID: 36127676 PMCID: PMC9490888 DOI: 10.1186/s12920-022-01359-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/16/2022] [Indexed: 11/27/2022] Open
Abstract
Background Noncoding RNAs (ncRNAs), pyroptosis and tumours are all hot topics in current research, but there are very limited studies on pyroptosis and its regulated ncRNAs in colon adenocarcinoma (COAD). Methods The COAD transcription profile dataset from TCGA was used for differential expression analysis. Pyroptosis-related genes (PRGs), the top 200 long noncoding RNAs (lncRNAs) and circular RNA (circRNAs) were selected from the results to construct an endogenous competitive RNA (ceRNA) network. Moreover, the expression of the ceRNAs was used for consensus cluster analysis of COAD and developing a risk model after combining clinical follow-up data by the least absolute shrinkage and selection operator method. The stability and independent prognostic ability of the risk model were evaluated. Finally, gene set enrichment analysis (GSEA) and immune score comparisons between the high-risk and low-risk groups were performed. Results There were 87 PRGs with significant differences, among which casp3/8, NLRP1/3, and IL-1α/1β were at the core of the interactions. The ceRNA network consisted of 58 lncRNAs, 6 circRNAs, 25 PRGs, and 55 microRNAs. We speculated that KCNQ1OT1-miRNAs-SQSTM1 and HSA_CIRC_0001495-miRNAs-PTEN have great potential and value in the pyroptosis mechanism of COAD. Nine RNAs were involved in the risk score, which had excellent independent prognostic ability. Survival analyses were significant between the high-risk (HR) and low-risk (LR) groups (training cohort: P < 0.001; test cohort: P = 0.037). GSEA was mainly enriched in tumour proliferation and metastasis related pathways, while differences in immune activity showed a bipolar distribution between the HR and LR groups. Conclusions The overall mechanism of pyroptosis in COAD was revealed. CeRNAs most closely related to the pyroptosis mechanism of COAD were selected and used to develop a prognostic model. The results may present new regulatory sites and potential targets for COAD pyroptosis mechanisms. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01359-w.
Collapse
Affiliation(s)
- Yanfeng Chen
- Department of Gastroenterology, TengZhou Central People's Hospital, Tengzhou, Shandong, China
| | - Zongbiao Tian
- Department of Gastroenterology, TengZhou Central People's Hospital, Tengzhou, Shandong, China
| | - Hebin Hou
- Department of Gastroenterology, TengZhou Central People's Hospital, Tengzhou, Shandong, China
| | - Wei Gai
- Department of Gastroenterology, TengZhou Central People's Hospital, Tengzhou, Shandong, China.
| |
Collapse
|
44
|
Bai H, Li QZ, Qi YC, Zhai YY, Jin W. The prediction of tumor and normal tissues based on the DNA methylation values of ten key sites. Biochim Biophys Acta Gene Regul Mech 2022; 1865:194841. [PMID: 35798200 DOI: 10.1016/j.bbagrm.2022.194841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 05/28/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
Abnormal DNA methylation can alter the gene expression to promote or inhibit tumorigenesis in colon adenocarcinoma (COAD). However, the finding important genes and key sites of abnormal DNA methylation which result in the occurrence of COAD is still an eventful task. Here, we studied the effects of DNA methylation in the 12 types of genomic features on the changes of gene expression in COAD, the 10 important COAD-related genes and the key abnormal DNA methylation sites were identified. The effects of important genes on the prognosis were verified by survival analysis. Moreover, it was shown that the important genes were participated in cancer pathways and were hub genes in a co-expression network. Based on the DNA methylation levels in the ten sites, the least diversity increment algorithm for predicting tumor tissues and normal tissues in seventeen cancer types are proposed. The better results are obtained in jackknife test. For example, the predictive accuracies are 94.17 %, 91.28 %, 89.04 % and 88.89 %, respectively, for COAD, rectum adenocarcinoma, pancreatic adenocarcinoma and cholangiocarcinoma. Finally, by computing enrichment score of infiltrating immunocytes and the activity of immune pathways, we found that the genes are highly correlated with immune microenvironment.
Collapse
Affiliation(s)
- Hui Bai
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Qian-Zhong Li
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China; The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot 010070, China.
| | - Ye-Chen Qi
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Yuan-Yuan Zhai
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Wen Jin
- Inner Mongolia key laboratory of gene regulation of the metabolic disease, Department of Clinical Medical Research Center, Inner Mongolia People's Hospital, Hohhot 010010, China
| |
Collapse
|
45
|
Wu S, Gong Y, Chen J, Zhao X, Qing H, Dong Y, Li S, Li J, Wang Z. Identification of fatty acid metabolism-related lncRNAs in the prognosis and immune microenvironment of colon adenocarcinoma. Biol Direct 2022; 17:19. [PMID: 35902970 DOI: 10.1186/s13062-022-00332-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/23/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Cancer metabolism is largely altered compared to normal cells. This study aims to explore critical metabolism pathways in colon adenocarcinoma (COAD), and reveal the possible mechanism of their role in cancer progression. METHODS Expression data and sequencing data of COAD samples were obtained from The Cancer Genome Atlas and Gene Expression Omnibus databases. The expression profiles between tumor and normal samples were compared to identify differential metabolism pathways through single sample gene set enrichment analysis. RESULTS Fatty acid synthesis was identified as a key metabolism pathway in COAD. Based on fatty acid-related lncRNAs, two molecular subtypes (C1 and C2) were defined. C2 subtype with worse prognosis had higher immune infiltration and higher expression of immune checkpoints. Five transcription factors (TFs) including FOS, JUN, HIF1A, STAT3 and STAT2 were highly expressed in C2 subtype. Five fatty acid-related lncRNAs were identified to be biomarkers for predicting COAD prognosis. Finally, further experients showed that knockdown of lncRNA PAXIP1-AS1 decreased the triglyceride content and the fatty acid synthase and acetyl-CoA carboxylase 1 expressions, which suggested that lncRNA PAXIP1-AS1 plays an important role in fatty acid metabolism of COAD. CONCLUSIONS This study demonstrated that fatty acid synthesis was greatly altered in COAD. Fatty acid-related lncRNAs were speculated to be involved in cancer progression through associating with TFs. The five screened TFs may serve as new drug targets for treating COAD.
Collapse
|
46
|
Munro MJ, Wickremesekera SK, Tan ST, Peng L. Proteomic analysis of low- and high-grade human colon adenocarcinoma tissues and tissue-derived primary cell lines reveals unique biological functions of tumours and new protein biomarker candidates. Clin Proteomics 2022; 19:27. [PMID: 35842572 PMCID: PMC9287856 DOI: 10.1186/s12014-022-09364-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/22/2022] [Indexed: 11/10/2022] Open
Abstract
Background Colon cancer is the third most common cancer and second highest cause of cancer deaths worldwide. The aim of the study was to find new biomarkers for diagnosis, prognosis and therapeutic drug targets for this disease. Methods Four low-grade and four high-grade human colon adenocarcinoma tumours with patient-matched normal colon tissues were analysed. Additionally, tissue-derived primary cell lines were established from each tumour tissue. The cell lines were validated using DNA sequencing to confirm that they are a suitable in vitro model for colon adenocarcinoma based on conserved gene mutations. Label-free quantitation proteomics was performed to compare the proteomes of colon adenocarcinoma samples to normal colon samples, and of colon adenocarcinoma tissues to tissue-derived cell lines to find significantly differentially abundant proteins. The functions enriched within the differentially expressed proteins were assessed using STRING. Proteomics data was validated by Western blotting. Results A total of 4767 proteins were identified across all tissues, and 4711 across primary tissue-derived cell lines. Of these, 3302 proteins were detected in both the tissues and the cell lines. On average, primary cell lines shared about 70% of proteins with their parent tissue, and they retained mutations to key colon adenocarcinoma-related genes and did not diverge far genetically from their parent tissues. Colon adenocarcinoma tissues displayed upregulation of RNA processing, steroid biosynthesis and detoxification, and downregulation of cytoskeletal organisation and loss of normal muscle function. Tissue-derived cell lines exhibited increased interferon-gamma signalling and aberrant ferroptosis. Overall, 318 proteins were significantly up-regulated and 362 proteins significantly down-regulated by comparisons of high-grade with low-grade tumours and low-grade tumour with normal colon tissues from both sample types. Conclusions The differences exhibited between tissues and cell lines highlight the additional information that can be obtained from patient-derived primary cell lines. DNA sequencing and proteomics confirmed that these cell lines can be considered suitable in vitro models of the parent tumours. Various potential biomarkers for colon adenocarcinoma initiation and progression and drug targets were identified and discussed, including seven novel markers: ACSL4, ANK2, AMER3, EXOSC1, EXOSC6, GCLM, and TFRC. Supplementary Information The online version contains supplementary material available at 10.1186/s12014-022-09364-y.
Collapse
Affiliation(s)
- Matthew J Munro
- School of Biological Sciences and Centre for Biodiscovery, Victoria University of Wellington, Wellington, 6140, New Zealand.,Gillies McIndoe Research Institute, Newtown, PO Box 7184, Wellington, 6242, New Zealand
| | - Susrutha K Wickremesekera
- Gillies McIndoe Research Institute, Newtown, PO Box 7184, Wellington, 6242, New Zealand.,Upper Gastrointestinal, Hepatobiliary & Pancreatic Section, Department of General Surgery, Wellington Regional Hospital, Wellington, 6021, New Zealand
| | - Swee T Tan
- Gillies McIndoe Research Institute, Newtown, PO Box 7184, Wellington, 6242, New Zealand. .,Wellington Regional Plastic, Maxillofacial & Burns Unit, Hutt Hospital, Lower Hutt, 5040, New Zealand. .,Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, Melbourne, VIC, 3050, Australia.
| | - Lifeng Peng
- School of Biological Sciences and Centre for Biodiscovery, Victoria University of Wellington, Wellington, 6140, New Zealand.
| |
Collapse
|
47
|
Mou W, Zhu L, Yang T, Lin A, Lyu Q, Guo L, Liu Z, Cheng Q, Zhang J, Luo P. Relationship between ATOH1 and tumor microenvironment in colon adenocarcinoma patients with different microsatellite instability status. Cancer Cell Int 2022; 22:229. [PMID: 35836254 PMCID: PMC9281179 DOI: 10.1186/s12935-022-02651-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 07/05/2022] [Indexed: 11/19/2022] Open
Abstract
Background Colon adenocarcinoma (COAD) is one of the major varieties of malignant tumors threatening human health today. Immune checkpoint inhibitors (ICIs) have recently begun to emerge as an effective option for the treatment of COAD patients, but not all patients can benefit from ICI treatment. Previous studies have suggested that ICIs boast significant clinical effects on patients with microsatellite instability-high (MSI-H), while conversely patients with microsatellite-stable/microsatellite instability-low (MSS/MSI-L) have shown limited response. Methods We used ATAC-seq, RNA-seq, and mutation data from The Cancer Genome Atlas Colon adenocarcinoma (TCGA-COAD) cohort to perform multi-omics differential analysis on COAD samples with different MSI statuses, then further screened genes by additionally combining these results with survival analysis. We analyzed the effects of the screened genes on the tumor microenvironment and immunogenicity of COAD patients, and subsequently determined their influence on the efficacy of ICIs in COAD patients using a series of predictive indexes. Results Twelve genes were screened in the TCGA-COAD cohort, and after the combined survival analysis, we identified ATOH1 as having significant effects. ATOH1 is characterized by high chromatin accessibility, high expression, and high mutation in COAD patients in the MSI-H group. COAD patients with high ATOH1 expression are associated with a better prognosis, unique immune microenvironment, and higher efficacy in ICI treatment. Enrichment analysis showed that COAD patients with high ATOH1 expression displayed significant upregulation in their humoral immunity and other related pathways. Conclusions We speculate that ATOH1 may influence the efficacy of ICIs therapy in patients with COAD by affecting the immune microenvironment and immunogenicity of the tumor. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-022-02651-6.
Collapse
Affiliation(s)
- Weiming Mou
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China.,The First Clinical Medical School, Southern Medical University, 1023 Shatai South Road, Guangzhou, 510515, Guangdong, China
| | - Lingxuan Zhu
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China.,The First Clinical Medical School, Southern Medical University, 1023 Shatai South Road, Guangzhou, 510515, Guangdong, China
| | - Tao Yang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China.,The First Clinical Medical School, Southern Medical University, 1023 Shatai South Road, Guangzhou, 510515, Guangdong, China
| | - Anqi Lin
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China
| | - Qiong Lyu
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China
| | - Linlang Guo
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, Guangdong, China
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China.
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China.
| |
Collapse
|
48
|
Li Z, Chen J, Zhu D, Wang X, Chen J, Zhang Y, Lian Q, Gu B. Identification of prognostic stemness biomarkers in colon adenocarcinoma drug resistance. BMC Genom Data 2022; 23:51. [PMID: 35794546 PMCID: PMC9261069 DOI: 10.1186/s12863-022-01063-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 06/06/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Colon adenocarcinoma (COAD) is one of the leading causes of death worldwide. Cancer stem cells (CSCs) are vital for COAD chemoresistance and recurrence, however little is known about stem cell-related biomarkers in drug resistance and COAD prognosis prediction. METHODS To uncover the roles of CSC in COAD tumorigenesis, chemoresistance, and prognosis, we retrieved COAD patients' RNAseq data from TCGA (The Cancer Genome Atlas). We further performed analysis of differentially expressed genes (DEGs) and mRNA expression-based stemness index (mRNAsi) to identify stemness-related COAD biomarkers. We then evaluated the roles of mRNAsi in tumorigenesis, clinical-stage, overall survival (OS), and chemoresistance. Afterward, we used identified prognostic stemness-related genes (PSRGs) to construct a prediction model. After constructing the prediction model, we used elastic Net regression and area under the curve (AUC) to explore the prediction value of PSRGs based on risk scores and the receiver operator characteristic (ROC) curve. To elucidate the underlying interconnected systems, we examined relationships between the levels of TFs, PSRGs, and 50 cancer hallmarks by a Pearson correlation analysis. RESULTS Twelve thousand one hundred eight DEGs were identified by comparing 456 primary COADs and 41 normal solid tissue samples. Furthermore, we identified 4351 clinical stage-related DEGs, 16,516 stemness-associated DEGs, and 54 chemoresistance-related DEGs from cancer stages: mRNAsi, and COAD chemoresistance. Compared to normal tissue samples, mRNAsi in COAD patients were marked on an elevation and involved in prognosis (p = 0.027), stemness-related DEGs based on chemoresistance (OR = 3.28, p ≤ 0.001) and AJCC clinical stage relating (OR = 4.02, p ≤ 0.001) to COAD patients. The prediction model of prognosis were constructed using the 6 PSRGs with high accuracy (AUC: 0.659). The model identified universal correlation between NRIP2 and FDFT1 (key PRSGs), and some cancer related transcription factors (TFs) and trademarks of cancer gene were in the regulatory network. CONCLUSION We found that mRNAsi is a reliable predictive biomarker of tumorigenesis and COAD prognosis. Our established prediction model of COAD chemoresistance, which includes the six PSRGs, is effective, as the model provides promising therapeutic targets in the COAD.
Collapse
Affiliation(s)
- Ziyue Li
- Cord Blood Bank, Guangzhou Institute of Eugenics and Perinatology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510000, China
| | - Jierong Chen
- Division of Laboratory Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan 2nd Rd, Yuexiu District, Guangzhou, Guangdong, 510000, P. R. China
| | - Dandan Zhu
- Division of Laboratory Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan 2nd Rd, Yuexiu District, Guangzhou, Guangdong, 510000, P. R. China
| | - Xiaoxiao Wang
- Division of Laboratory Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan 2nd Rd, Yuexiu District, Guangzhou, Guangdong, 510000, P. R. China
| | - Jace Chen
- Laboratory Schools, the University of Chicago, Chicago, IL, USA
| | - Yu Zhang
- Division of Laboratory Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan 2nd Rd, Yuexiu District, Guangzhou, Guangdong, 510000, P. R. China
| | - Qizhou Lian
- Cord Blood Bank, Guangzhou Institute of Eugenics and Perinatology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510000, China.
| | - Bing Gu
- Division of Laboratory Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan 2nd Rd, Yuexiu District, Guangzhou, Guangdong, 510000, P. R. China.
| |
Collapse
|
49
|
Romano C, Di Gregorio S, Pennisi MS, Tirrò E, Broggi G, Caltabiano R, Manzella L, Ruggieri M, Vigneri P, Di Cataldo A. Multiple primary malignances managed with surgical excision: a case report with next generation sequencing analysis. Mol Biol Rep 2022; 49:9059-9064. [PMID: 35715605 DOI: 10.1007/s11033-022-07630-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Multiple primary malignancies (MPM) are defined as tumors originating in the same individual without any correlation between them. In addition to morphological and immunohistochemical analyses, sensitive DNA sequencing methods such as next generation sequencing (NGS) may help to discriminate the common or different genetic alterations driving each malignancy, to better diagnose these uncommon cases. METHODS AND RESULTS Here we report the case of a man who developed a poorly differentiated gastric adenocarcinoma invading the pancreas followed, two years later, by a colorectal cancer involving also the kidney and the diaphragm. Despite the advanced stage of both diseases, adjuvant chemotherapy was successful. While the second tumor was initially interpreted as a relapse of his stomach cancer, NGS-based mutation profiling of the two carcinomas revealed two distinct malignances, independently developing in different times and indicative of metachronous MPM. Indeed, sequencing of cancer-associated genes identified somatic mutations only in the first gastric cancer, besides germline variants on three different genes (PDGFRA, APC and TP53). However, analysis of both somatic and germline mutations with bio-informatics prediction tools failed to find a correlation between these variants and the unexpectedly good prognosis of both cancers. CONCLUSIONS In summary, NGS analysis contributed to defined different molecular profiles for two tumors developed in the span of two years, thus allowing diagnosing the case as MPN. However, NGS was unable to establish a direct correlation between the identified alterations and cancer development.
Collapse
Affiliation(s)
- Chiara Romano
- Department of Clinical and Experimental Medicine, University of Catania, 95123, Catania, Italy. .,Center of Experimental Oncology and Hematology, A.O.U. Policlinico "G. Rodolico - San Marco", 95123, Catania, Italy.
| | - Sandra Di Gregorio
- Department of Clinical and Experimental Medicine, University of Catania, 95123, Catania, Italy.,Center of Experimental Oncology and Hematology, A.O.U. Policlinico "G. Rodolico - San Marco", 95123, Catania, Italy
| | - Maria Stella Pennisi
- Department of Clinical and Experimental Medicine, University of Catania, 95123, Catania, Italy.,Center of Experimental Oncology and Hematology, A.O.U. Policlinico "G. Rodolico - San Marco", 95123, Catania, Italy
| | - Elena Tirrò
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico "G. Rodolico - San Marco", 95123, Catania, Italy.,Department of Surgical, Oncological and Stomatological Sciences, University of Palermo, 90127, Palermo, Italy
| | - Giuseppe Broggi
- Department of Medical, Surgical Sciences and Advanced Technologies "G.F. Ingrassia", Section of Anatomic Pathology, University of Catania, 95123, Catania, Italy
| | - Rosario Caltabiano
- Department of Medical, Surgical Sciences and Advanced Technologies "G.F. Ingrassia", Section of Anatomic Pathology, University of Catania, 95123, Catania, Italy
| | - Livia Manzella
- Department of Clinical and Experimental Medicine, University of Catania, 95123, Catania, Italy.,Center of Experimental Oncology and Hematology, A.O.U. Policlinico "G. Rodolico - San Marco", 95123, Catania, Italy
| | - Martino Ruggieri
- Unit of Rare Diseases of the Nervous System in Childhood, Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry, University of Catania, 95123, Catania, Italy
| | - Paolo Vigneri
- Department of Clinical and Experimental Medicine, University of Catania, 95123, Catania, Italy.,Center of Experimental Oncology and Hematology, A.O.U. Policlinico "G. Rodolico - San Marco", 95123, Catania, Italy
| | - Antonio Di Cataldo
- Department of General Surgery and Medical-Surgical Specialties, University of Catania, 95123, Catania, Italy
| |
Collapse
|
50
|
Liu T, Li H, Du G, Ma J, Shen J, Zhao H, Luo F, Li H. Comprehensive analysis of m 6A regulator-based methylation modification patterns characterized by distinct immune profiles in colon adenocarcinomas. Gene 2022; 821:146250. [PMID: 35151825 DOI: 10.1016/j.gene.2022.146250] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/05/2022] [Accepted: 01/21/2022] [Indexed: 01/02/2023]
Abstract
Mounting evidences have indicated that RNA N6-methyladenosine (m6A) modification played important roles in tumor formation and growth. However, it is rarely reported that m6A modifications are involved in the immune regulation and tumor microenvironment (TME) formation. In this study, we aimed to investigate the correlation between m6A modifications and TME regulation of colon adenocarcinoma (COAD) by bioinformatic analysis. NMF algorithm was applied to carry out consensus molecular subtype analysis on 36 selected m6A regulators regarding methylation modification, to identify m6A modification patterns and characteristics of m6A related genes in colon adenocarcinoma (COAD). Further, the relative infiltration levels of different immune cell subsets were quantified by ssGSEA and CIBERSORT algorithms, and a m6Sig scoring scheme was constructed to predict the prognosis and evaluate the response to immunotherapy in the patients with COAD. Among 579 COAD samples, we identified three different m6A modification patterns which were related to different biological pathways and clinical outcomes. Then, a scoring scheme termed "m6Sig score" was developed based on m6A-related characteristic genes, and was utilized to score patients with COAD into groups. We found that COAD patients with lower m6Sig scores exhibited prolonged survival and potentiated immune infiltration, which were associated with higher tumor mutation load, lower PD-L1 expression, and higher mutation rates of SMG (such as TTN and KRAS). Moreover, analysis regarding evaluation of immune response revealed that the patients with lower m6Sig scores had higher Immunophenoscore. Collectively, our study provided in depth insight into the interactions between m6A modification and regulation of TME. In addition, the quantitative evaluation of m6A modification patterns in our results may have implications in further immunotherapy for individual COAD patients.
Collapse
|