1
|
Golozar M, Motlagh AV, Mahdevar M, Peymani M, InanlooRahatloo K, Ghaedi K. TBX15 and SDHB expression changes in colorectal cancer serve as potential prognostic biomarkers. Exp Mol Pathol 2024; 136:104890. [PMID: 38378070 DOI: 10.1016/j.yexmp.2024.104890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 01/07/2024] [Accepted: 02/16/2024] [Indexed: 02/22/2024]
Abstract
Alterations in the expression of certain genes could be associated with both patient mortality rates and drug resistance. This study aimed to identify genes in colorectal cancer (CRC) that potentially serve as hub genes influencing patient survival rates. RNA-Seq data were downloaded from the cancer genome atlas database, and differential expression analysis was performed between tumors and healthy controls. Through the utilization of univariate and multivariate Cox regression analyses, in combination with the MCODE clustering module, the genes whose expression changes were related to survival rate and the hub genes related to them were identified. The mortality risk model was computed using the hub genes. CRC samples and the RT-qPCR method were utilized to confirm the outcomes. PharmacoGx data were employed to link the expression of potential genes to medication resistance and sensitivity. The results revealed the discovery of seven hub genes, which emerged as independent prognostic markers. These included HOXC6, HOXC13, HOXC8, and TBX15, which were associated with poor prognosis and overexpression, as well as SDHB, COX5A, and UQCRC1, linked to favorable prognosis and downregulation. Applying the risk model developed with the mentioned genes revealed a markedly higher incidence of deceased patients in the high-risk group compared to the low-risk group. RT-qPCR results indicated a decrease in SDHB expression and an elevation in TBX15 levels in cancer samples relative to adjacent healthy tissue. Also, PharmacoGx data indicated that the expression level of SDHB was correlated with drug sensitivity to Crizotinib and Dovitinib. Our findings highlight the potential association between alterations in the expression of genes such as HOXC6, HOXC13, HOXC8, TBX15, SDHB, COX5A, and UQCRC1 and increased mortality rates in CRC patients. As revealed by the PPI network, these genes exhibited the most connections with other genes linked to survival.
Collapse
Affiliation(s)
- Melika Golozar
- Kish International Campus, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Ali Valipour Motlagh
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan 8165131378, Iran
| | - Mohammad Mahdevar
- Genius Gene, Genetics and Biotechnology Company, Tehran, Iran; Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Kolsoum InanlooRahatloo
- Kish International Campus, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| |
Collapse
|
2
|
Zhou X, Qian Y, Ling C, He Z, Shi P, Gao Y, Sui X. An integrated framework for prognosis prediction and drug response modeling in colorectal liver metastasis drug discovery. J Transl Med 2024; 22:321. [PMID: 38555418 PMCID: PMC10981831 DOI: 10.1186/s12967-024-05127-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 03/23/2024] [Indexed: 04/02/2024] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is the third most prevalent cancer globally, and liver metastasis (CRLM) is the primary cause of death. Hence, it is essential to discover novel prognostic biomarkers and therapeutic drugs for CRLM. METHODS This study developed two liver metastasis-associated prognostic signatures based on differentially expressed genes (DEGs) in CRLM. Additionally, we employed an interpretable deep learning model utilizing drug sensitivity databases to identify potential therapeutic drugs for high-risk CRLM patients. Subsequently, in vitro and in vivo experiments were performed to verify the efficacy of these compounds. RESULTS These two prognostic models exhibited superior performance compared to previously reported ones. Obatoclax, a BCL-2 inhibitor, showed significant differential responses between high and low risk groups classified by prognostic models, and demonstrated remarkable effectiveness in both Transwell assay and CT26 colorectal liver metastasis mouse model. CONCLUSIONS This study highlights the significance of developing specialized prognostication approaches and investigating effective therapeutic drugs for patients with CRLM. The application of a deep learning drug response model provides a new drug discovery strategy for translational medicine in precision oncology.
Collapse
Affiliation(s)
- Xiuman Zhou
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong Province, 518107, China
| | - Yuzhen Qian
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Chen Ling
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong Province, 518107, China
| | - Zhuoying He
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong Province, 518107, China
| | - Peishang Shi
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Yanfeng Gao
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong Province, 518107, China.
| | - Xinghua Sui
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong Province, 518107, China.
| |
Collapse
|
3
|
Man Y, Xin D, Ji Y, Liu Y, Kou L, Jiang L. Identification and validation of a novel six-gene signature based on mucinous adenocarcinoma-related gene molecular typing in colorectal cancer. Discov Oncol 2024; 15:63. [PMID: 38443703 PMCID: PMC10914658 DOI: 10.1007/s12672-024-00916-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 02/28/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND AND OBJECTIVES Colorectal mucinous adenocarcinoma (MAC) is a particular pathological type that has yet to be thoroughly studied. This study aims to investigate the characteristics of colorectal MAC-related genes in colorectal cancer (CRC), explore the role of MAC-related genes in accurately classifying CRC, and further construct a prognostic signature. METHODS CRC samples were collected from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). MAC-related differentially expressed genes (DEGs) were analyzed in TCGA samples. Based on colorectal MAC-related genes, TCGA CRC samples were molecularly typed by the non-negative matrix factorization (NMF). According to the molecular subtype characteristics, the RiskScore signature was constructed through univariate Cox, the least absolute shrinkage and selection operator (LASSO), and multivariate Cox regression analyses. Clinical significance in CRC of the RiskScore signature was analyzed. A nomogram was further built based on the RiskScore signature. RESULTS From the colorectal MAC-related genes, three distinct molecular subtypes were identified. A RiskScore signature composed of six CRC subtype-related genes (CALB1, MMP1, HOXC6, ZIC2, SFTA2, and HYAL1) was constructed. Patients with high-RiskScores had the worse prognoses. RiskScores led to differences in gene mutation characteristics, antitumor drug sensitivity, and tumor microenvironment of CRC. A nomogram based on the signature was developed to predict the one-, three-, and five-year survival of CRC patients. CONCLUSION MAC-related genes were able to classify CRC. A RiskScore signature based on the colorectal MAC-related molecular subtype was constructed, which had important clinical significance for guiding the accurate stratification of CRC patients.
Collapse
Affiliation(s)
- Yuxin Man
- Department of Medical Oncology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Dao Xin
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yang Ji
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yang Liu
- Department of Medical Oncology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Lingna Kou
- Department of Medical Oncology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Lingxi Jiang
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, China.
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China.
| |
Collapse
|
4
|
Wang Q, Shen K, Fei B, Wei M, Xie Z. Nomogram for predicting occurrence and prognosis of liver metastasis in elderly colorectal cancer patients: a population-based study. Front Oncol 2024; 13:1295650. [PMID: 38239646 PMCID: PMC10794770 DOI: 10.3389/fonc.2023.1295650] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/05/2023] [Indexed: 01/22/2024] Open
Abstract
Introduction This study aimed to explore independent risk and prognostic factors in elderly patients with colorectal cancer liver metastasis (ECRLM) and generate nomograms for predicting the occurrence and overall survival (OS) rates of such patients. Method Elderly colorectal cancer patients (ECRC) from 2010 to 2015 in the Surveillance, Epidemiology, and End Results (SEER) database were included in this study. External validation relied on Chinese patients from the China-Japan Union Hospital of Jilin University. Univariate and multivariate logistic regression analyses were employed to identify liver metastasis (LM) risk variables, which were used to create a nomogram to estimate LM probabilities in patients with ECRC. Univariate and multivariable Cox analyses were performed to identify prognostic variables and further derive nomograms that could predict the OS of patients with ERCLM. Differences in lifespan were assessed using the Kaplan-Meier analysis. Finally, the quality of the nomograms was verified using decision curve analysis (DCA), calibration curves, and receiver operating characteristic curves (ROC). Result In the SEER cohort, 32,330 patients were selected, of those, 3,012 (9.32%) were diagnosed with LM. A total of 188 ECRLM cases from a Chinese medical center were assigned for external validation. LM occurrence can be affected by 13 factors, including age at diagnosis, marital status, race, bone metastases, lung metastases, CEA level, tumor size, Grade, histology, primary site, T stage, N stage and sex. Furthermore, in ECRLM patients, 10 variables, including age at diagnosis, CEA level, tumor size, lung metastasis, bone metastasis, chemotherapy, surgery, N stage, grade, and race, have been shown to be independent prognostic predictors. The results from both internal and external validation revealed a high level of accuracy in predicting outcomes, as well as significant clinical utility, for the two nomograms. Conclusion We created two nomograms to predict the occurrence and prognosis of LM in patients with ECRC, which would contribute significantly to the improvement in disease detection accuracy and the formulation of personalized cures for that particular demographic.
Collapse
Affiliation(s)
| | | | | | | | - Zhongshi Xie
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| |
Collapse
|
5
|
Wang Q, Shen K, Fei B, Luo H, Li R, Wang Z, Wei M, Xie Z. A predictive model for early death in elderly colorectal cancer patients: a population-based study. Front Oncol 2023; 13:1278137. [PMID: 38173840 PMCID: PMC10764026 DOI: 10.3389/fonc.2023.1278137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024] Open
Abstract
Purpose The purpose of this study is to determine what variables contribute to the early death of elderly colorectal cancer patients (ECRC) and to generate predictive nomograms for this population. Methods This retrospective cohort analysis included elderly individuals (≥75 years old) diagnosed with colorectal cancer (CRC) from 2010-2015 in the Surveillance, Epidemiology, and End Result databases (SEER) databases. The external validation was conducted using a sample of the Chinese population obtained from the China-Japan Union Hospital of Jilin University. Logistic regression analyses were used to ascertain variables associated with early death and to develop nomograms. The nomograms were internally and externally validated with the help of the receiver operating characteristic curve (ROC), calibration curve, and decision curve analysis (DCA). Results The SEER cohort consisted of 28,111 individuals, while the Chinese cohort contained 315 cases. Logistic regression analyses shown that race, marital status, tumor size, Grade, T stage, N stage, M stage, brain metastasis, liver metastasis, bone metastasis, surgery, chemotherapy, and radiotherapy were independent prognostic factors for all-cause and cancer-specific early death in ECRC patients; The variable of sex was only related to an increased risk of all-cause early death, whereas the factor of insurance status was solely associated with an increased risk of cancer-specific early death. Subsequently, two nomograms were devised to estimate the likelihood of all-cause and cancer-specific early death among individuals with ECRC. The nomograms exhibited robust predictive accuracy for predicting early death of ECRC patients, as evidenced by both internal and external validation. Conclusion We developed two easy-to-use nomograms to predicting the likelihood of early death in ECRC patients, which would contribute significantly to the improvement of clinical decision-making and the formulation of personalized treatment approaches for this particular population.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Zhongshi Xie
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| |
Collapse
|
6
|
Hajebi Khaniki S, Shokoohi F, Esmaily H, Kerachian MA. Analyzing aberrant DNA methylation in colorectal cancer uncovered intangible heterogeneity of gene effects in the survival time of patients. Sci Rep 2023; 13:22104. [PMID: 38092774 PMCID: PMC10719305 DOI: 10.1038/s41598-023-47377-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 11/13/2023] [Indexed: 12/17/2023] Open
Abstract
Colorectal cancer (CRC) involves epigenetic alterations. Irregular gene-methylation alteration causes and advances CRC tumor growth. Detecting differentially methylated genes (DMGs) in CRC and patient survival time paves the way to early cancer detection and prognosis. However, CRC data including survival times are heterogeneous. Almost all studies tend to ignore the heterogeneity of DMG effects on survival. To this end, we utilized a sparse estimation method in the finite mixture of accelerated failure time (AFT) regression models to capture such heterogeneity. We analyzed a dataset of CRC and normal colon tissues and identified 3406 DMGs. Analysis of overlapped DMGs with several Gene Expression Omnibus datasets led to 917 hypo- and 654 hyper-methylated DMGs. CRC pathways were revealed via gene ontology enrichment. Hub genes were selected based on Protein-Protein-Interaction network including SEMA7A, GATA4, LHX2, SOST, and CTLA4, regulating the Wnt signaling pathway. The relationship between identified DMGs/hub genes and patient survival time uncovered a two-component mixture of AFT regression model. The genes NMNAT2, ZFP42, NPAS2, MYLK3, NUDT13, KIRREL3, and FKBP6 and hub genes SOST, NFATC1, and TLE4 were associated with survival time in the most aggressive form of the disease that can serve as potential diagnostic targets for early CRC detection.
Collapse
Affiliation(s)
- Saeedeh Hajebi Khaniki
- Department of Biostatistics, School of Health, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Mathematical Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Farhad Shokoohi
- Department of Mathematical Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
| | - Habibollah Esmaily
- Department of Biostatistics, School of Health, Mashhad University of Medical Sciences, Mashhad, Iran
- Social Determinants of Health Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | | |
Collapse
|
7
|
Chen T, Chu Y, Xu H, Dai H, Zhou Y, Du H, Zhu W. Kinesin superfamily member KIFC2 as an independent prognostic biomarker of colon adenocarcinoma associated with poor immune response. Medicine (Baltimore) 2023; 102:e35491. [PMID: 37904433 PMCID: PMC10615560 DOI: 10.1097/md.0000000000035491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 09/13/2023] [Indexed: 11/01/2023] Open
Abstract
Clinical outcomes of colon adenocarcinoma (COAD) exhibit heterogeneity among different patients, highlighting the need for novel prognostic biomarkers. Kinesin superfamily members have been shown to play a crucial role in tumors and can predict cancer diagnosis and prognosis. However, the role of kinesin family member C2 (KIFC2) in tumors, particularly its prognostic value in COAD, remains poorly understood. Our bioinformatics analysis of the cancer genome atlas and GEO databases revealed significantly higher expression of KIFC2 in COAD, correlating with a worse prognosis in the cancer genome atlas-COAD and GSE17536 cohorts. Additionally, differentially expressed genes in COAD were enriched in immune-related pathways, and patients with higher KIFC2 expression showed fewer activated CD4 + T cells. These findings suggest KIFC2 as a potential prognostic biomarker for COAD, warranting further validation in clinical studies.
Collapse
Affiliation(s)
- Tao Chen
- Department of Gastrointestinal Surgery, The Affiliated Changzhou No.2 People’s Hospital with Nanjing Medical University, Changzhou, Jiangsu, China
| | - Yunqian Chu
- Cancer Center, The Affiliated Changzhou No. 2 People’s Hospital with Nanjing Medical University, Changzhou, Jiangsu, China
| | - Haiyuan Xu
- Department of Medical Oncology, Kunshan First People’s Hospital Affiliated to Jiangsu University, Kunshan, Jiangsu, China
| | - Hanjue Dai
- Cancer Center, The Affiliated Changzhou No. 2 People’s Hospital with Nanjing Medical University, Changzhou, Jiangsu, China
| | - Yuxi Zhou
- Burning Rock Biotech, Guangzhou, China
| | - Haiwei Du
- Burning Rock Biotech, Guangzhou, China
| | - Wenyu Zhu
- Cancer Center, The Affiliated Changzhou No. 2 People’s Hospital with Nanjing Medical University, Changzhou, Jiangsu, China
| |
Collapse
|
8
|
Mobeen SA, Saxena P, Jain AK, Deval R, Riazunnisa K, Pradhan D. Integrated bioinformatics approach to unwind key genes and pathways involved in colorectal cancer. J Cancer Res Ther 2023; 19:1766-1774. [PMID: 38376276 DOI: 10.4103/jcrt.jcrt_620_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 12/13/2021] [Indexed: 02/21/2024]
Abstract
BACKGROUND Colorectal cancer (CRC) is the fifth leading cause of death in India. Until now, the exact pathogenesis concerning CRC signaling pathways is largely unknown; however, the diseased condition is believed to deteriorate with lifestyle, aging, and inherited genetic disorders. Hence, the identification of hub genes and therapeutic targets is of great importance for disease monitoring. OBJECTIVE Identification of hub genes and targets for identification of candidate hub genes for CRC diagnosis and monitoring. MATERIALS AND METHODS The present study applied gene expression analysis by integrating two profile datasets (GSE20916 and GSE33113) from NCBI-GEO database to elucidate the potential key candidate genes and pathways in CRC. Differentially expressed genes (DEGs) between CRC (195 CRC tissues) and healthy control (46 normal mucosal tissue) were sorted using GEO2R tool. Further, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis were performed using Cluster Profiler in Rv. 3.6.1. Moreover, protein-protein interactions (PPI), module detection, and hub gene identification were accomplished and visualized through the Search Tool for the Retrieval of Interacting Genes, Molecular Complex Detection (MCODE) plug-in of Cytoscape v3.8.0. Further hub genes were imported into ToppGene webserver for pathway analysis and prognostic expression analysis was conducted using Gene Expression Profiling Interactive Analysis webserver. RESULTS A total of 2221 DEGs, including 1286 up-regulated and 935down-regulated genes mainly enriched in signaling pathways of NOD-like receptor, FoxO, AMPK signalling and leishmaniasis. Three key modules were detected from PPI network using MCODE. Besides, top 20 high prioritized hub genes were selected. Further, prognostic expression analysis revealed ten of the hub genes, namely IL1B, CD44, Glyceraldehyde-3-phosphate dehydrogenase (GAPDH, MMP9, CREB1, STAT1, vascular endothelial growth factor (VEGFA), CDC5 L, Ataxia-telangiectasia mutated (ATM + and CDH1 to be differently expressed in normal and cancer patients. CONCLUSION The present study proposed five novel therapeutic targets, i.e., ATM, GAPDH, CREB1, VEGFA, and CDH1 genes that might provide new insights into molecular oncogenesis of CRC.
Collapse
Affiliation(s)
- Syeda Anjum Mobeen
- Department of Biotechnology and Bioinformatics, Yogi Vemana University, Andhra Pradesh, India
| | - Pallavi Saxena
- Biomedical Informatics Centre, Indian Council of Medical Research, National Institute of Pathology, New Delhi, India
- Department of Biotechnology, Invertis University, Bareilly, Uttar Pradesh, India
| | - Arun Kumar Jain
- Biomedical Informatics Centre, Indian Council of Medical Research, National Institute of Pathology, New Delhi, India
| | - Ravi Deval
- Department of Biotechnology, Invertis University, Bareilly, Uttar Pradesh, India
| | - Khateef Riazunnisa
- Department of Biotechnology and Bioinformatics, Yogi Vemana University, Andhra Pradesh, India
| | | |
Collapse
|
9
|
Chen J, Wu S, Peng Y, Zhao Y, Dong Y, Ran F, Geng H, Zhang K, Li J, Huang S, Wang Z. Constructing a cancer stem cell related prognostic model for predicting immune landscape and drug sensitivity in colorectal cancer. Front Pharmacol 2023; 14:1200017. [PMID: 37377935 PMCID: PMC10292801 DOI: 10.3389/fphar.2023.1200017] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
Background: Colorectal cancer (CRC) ranks the second malignancy with high incidence and mortality worldwide. Cancer stem cells (CSCs) function critically in cancer progression and metastasis via the interplay with immune cells in tumor microenvironment. This study aimed to identify important CSC marker genes and parsed the role of these marker genes in CRC. Materials and methods: CRC samples' single-cell RNA sequencing data and bulk transcriptome data were utilized. Seurat R package annotated CSCs and identified CSC marker genes. Consensus clustering subtyped CRC samples based on CSC marker genes. Immune microenvironment, pathway and oxidative stress analysis was performed using ESTIMATE, MCP-counter analysis and ssGSEA analysis. A prognostic model was established by Lasso and stepAIC. Sensitivity to chemotherapeutic drugs was determined by the biochemical half maximal inhibitory concentration with pRRophetic R package. Results: We identified a total of 29 CSC marker genes related to disease-specific survival (DSS). Two clusters (CSC1 and CSC2) were determined, and CSC2 showed shorter DSS, a larger proportion of late-stage samples, and higher oxidative stress response. Two clusters exhibited differential activation of biological pathways associated with immune response and oncogenic signaling. Drug sensitivity analysis showed that 44 chemotherapy drugs were more sensitive to CSC2 that those in CSC1. We constructed a seven-gene prognostic model (DRD4, DPP7, UCN, INHBA, SFTA2, SYNPO2, and NXPH4) that was effectively to distinguish high-risk and low-risk patients. 14 chemotherapy drugs were more sensitive to high-risk group and 13 chemotherapy drugs were more sensitive to low-risk group. Combination of higher oxidative stress and risk score indicated dismal prognosis. Conclusion: The CSC marker genes we identified may help to further decipher the role of CSCs in CRC development and progression. The seven-gene prognostic model could serve as an indicator for predicting the response to immunotherapy and chemotherapy as well as prognosis of CRC patients.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Jianjun Li
- *Correspondence: Jianjun Li, ; Shuo Huang, ; Zhe Wang,
| | - Shuo Huang
- *Correspondence: Jianjun Li, ; Shuo Huang, ; Zhe Wang,
| | - Zhe Wang
- *Correspondence: Jianjun Li, ; Shuo Huang, ; Zhe Wang,
| |
Collapse
|
10
|
Korbecki J, Bosiacki M, Barczak K, Łagocka R, Chlubek D, Baranowska-Bosiacka I. The Clinical Significance and Role of CXCL1 Chemokine in Gastrointestinal Cancers. Cells 2023; 12:1406. [PMID: 37408240 DOI: 10.3390/cells12101406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/09/2023] [Accepted: 05/15/2023] [Indexed: 07/07/2023] Open
Abstract
One area of cancer research is the interaction between cancer cells and immune cells, in which chemokines play a vital role. Despite this, a comprehensive summary of the involvement of C-X-C motif ligand 1 (CXCL1) chemokine (also known as growth-regulated gene-α (GRO-α), melanoma growth-stimulatory activity (MGSA)) in cancer processes is lacking. To address this gap, this review provides a detailed analysis of CXCL1's role in gastrointestinal cancers, including head and neck cancer, esophageal cancer, gastric cancer, liver cancer (hepatocellular carcinoma (HCC)), cholangiocarcinoma, pancreatic cancer (pancreatic ductal adenocarcinoma), and colorectal cancer (colon cancer and rectal cancer). This paper presents the impact of CXCL1 on various molecular cancer processes, such as cancer cell proliferation, migration, and invasion, lymph node metastasis, angiogenesis, recruitment to the tumor microenvironment, and its effect on immune system cells, such as tumor-associated neutrophils (TAN), regulatory T (Treg) cells, myeloid-derived suppressor cells (MDSCs), and macrophages. Furthermore, this review discusses the association of CXCL1 with clinical aspects of gastrointestinal cancers, including its correlation with tumor size, cancer grade, tumor-node-metastasis (TNM) stage, and patient prognosis. This paper concludes by exploring CXCL1's potential as a therapeutic target in anticancer therapy.
Collapse
Affiliation(s)
- Jan Korbecki
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University in Szczecin, Powstańców Wlkp. 72, 70-111 Szczecin, Poland
- Department of Anatomy and Histology, Collegium Medicum, University of Zielona Góra, Zyty 28 St., 65-046 Zielona Góra, Poland
| | - Mateusz Bosiacki
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University in Szczecin, Powstańców Wlkp. 72, 70-111 Szczecin, Poland
- Department of Functional Diagnostics and Physical Medicine, Faculty of Health Sciences, Pomeranian Medical University in Szczecin, Żołnierska 54 Str., 71-210 Szczecin, Poland
| | - Katarzyna Barczak
- Department of Conservative Dentistry and Endodontics, Pomeranian Medical University, Powstańców Wlkp. 72, 70-111 Szczecin, Poland
| | - Ryta Łagocka
- Department of Conservative Dentistry and Endodontics, Pomeranian Medical University, Powstańców Wlkp. 72, 70-111 Szczecin, Poland
| | - Dariusz Chlubek
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University in Szczecin, Powstańców Wlkp. 72, 70-111 Szczecin, Poland
| | - Irena Baranowska-Bosiacka
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University in Szczecin, Powstańców Wlkp. 72, 70-111 Szczecin, Poland
| |
Collapse
|
11
|
A novel DNA methylation signature to improve survival prediction of progression-free survival for testicular germ cell tumors. Sci Rep 2023; 13:3759. [PMID: 36882567 PMCID: PMC9992461 DOI: 10.1038/s41598-023-30957-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/03/2023] [Indexed: 03/09/2023] Open
Abstract
This study aimed to develop a nomogram for predicting the progression-free survival (PFS) of testicular germ cell tumors (TGCT) patients based on DNA methylation signature and clinicopathological characteristics. The DNA methylation profiles, transcriptome data, and clinical information of TGCT patients were obtained from the Cancer Genome Atlas (TCGA) database. Univariate Cox, lasso Cox, and stepwise multivariate Cox regression were applied to identify a prognostic CpG sites-derived risk signature. Differential expression analysis, functional enrichment analysis, immunoinfiltration analysis, chemotherapy sensitivity analysis, and clinical feature correlation analysis were performed to elucidate the differences among risk groups. A prognostic nomogram integrating CpG sites-derived risk signature and clinicopathological features was further established and evaluated likewise. A risk score model based on 7 CpG sites was developed and found to exhibit significant differences among different survival, staging, radiotherapy, and chemotherapy subgroups. There were 1452 differentially expressed genes between the high- and low-risk groups, with 666 being higher expressed and 786 being lower expressed. Genes highly expressed were significantly enriched in immune-related biological processes and related to T-cell differentiation pathways; meanwhile, down-regulated genes were significantly enriched in extracellular matrix tissue organization-related biological processes and involved in multiple signaling pathways such as PI3K-AKT. As compared with the low-risk group, patients in the high-risk group had decreased lymphocyte infiltration (including T-cell and B-cell) and increased macrophage infiltration (M2 macrophages). They also showed decreased sensitivity to etoposide and bleomycin chemotherapy. Three clusters were obtained by consensus clustering analysis based on the 7 CpG sites and showed distinct prognostic features, and the risk scores in each cluster were significantly different. Multivariate Cox regression analysis found that the risk scores, age, chemotherapy, and staging were independent prognostic factors of PFS of TGCT, and the results were used to formulate a nomogram model that was validated to have a C-index of 0.812. Decision curve analysis showed that the nomogram model was superior to other strategies in the prediction of PFS of TGCT. In this study, we successfully established CpG sites-derived risk signature, which might serve as a useful tool in the prediction of PFS, immunoinfiltration, and chemotherapy sensitivity for TGCT patients.
Collapse
|
12
|
Zafari N, Bathaei P, Velayati M, Khojasteh-Leylakoohi F, Khazaei M, Fiuji H, Nassiri M, Hassanian SM, Ferns GA, Nazari E, Avan A. Integrated analysis of multi-omics data for the discovery of biomarkers and therapeutic targets for colorectal cancer. Comput Biol Med 2023; 155:106639. [PMID: 36805214 DOI: 10.1016/j.compbiomed.2023.106639] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/14/2023] [Accepted: 02/05/2023] [Indexed: 02/12/2023]
Abstract
The considerable burden of colorectal cancer and the rising trend in young adults emphasize the necessity of understanding its underlying mechanisms, providing new diagnostic and prognostic markers, and improving therapeutic approaches. Precision medicine is a new trend all over the world and identification of novel biomarkers and therapeutic targets is a step forward towards this trend. In this context, multi-omics data and integrated analysis are being investigated to develop personalized medicine in the management of colorectal cancer. Given the large amount of data from multi-omics approach, data integration and analysis is a great challenge. In this Review, we summarize how statistical and machine learning techniques are applied to analyze multi-omics data and how it contributes to the discovery of useful diagnostic and prognostic biomarkers and therapeutic targets. Moreover, we discuss the importance of these biomarkers and therapeutic targets in the clinical management of colorectal cancer in the future. Taken together, integrated analysis of multi-omics data has great potential for finding novel diagnostic and prognostic biomarkers and therapeutic targets, however, there are still challenges to overcome in future studies.
Collapse
Affiliation(s)
- Nima Zafari
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Parsa Bathaei
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahla Velayati
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Khojasteh-Leylakoohi
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Majid Khazaei
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hamid Fiuji
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammadreza Nassiri
- Recombinant Proteins Research Group, The Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Seyed Mahdi Hassanian
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Gordon A Ferns
- Brighton & Sussex Medical School, Division of Medical Education, Falmer, Brighton, Sussex, BN1 9PH, UK
| | - Elham Nazari
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Amir Avan
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
| |
Collapse
|
13
|
Ershov P, Poyarkov S, Konstantinova Y, Veselovsky E, Makarova A. Transcriptomic Signatures in Colorectal Cancer Progression. Curr Mol Med 2023; 23:239-249. [PMID: 35490318 DOI: 10.2174/1566524022666220427102048] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/05/2021] [Accepted: 03/09/2022] [Indexed: 02/08/2023]
Abstract
AIMS Due to a large number of identified hub-genes encoding key molecular regulators, which are involved in signal transduction and metabolic pathways in cancers, it is relevant to systemize and update these findings. BACKGROUND Colorectal cancer (CRC) is the third leading cause of cancer death in the world, with high metastatic potential. Elucidating the pathogenic mechanisms and selection of novel biomarkers in CRC is of great clinical significance. OBJECTIVE This analytical review aims at the systematization of bioinformatics and experimental identification of hub-genes associated with CRC for a more consolidated understanding of common features in networks and pathways in CRC progression as well as hub-genes selection. RESULTS In total, 301 hub-genes were derived from 40 articles. The "core" consisted of 28 hub-genes (CCNB1, LPAR1, BGN, CXCL3, COL1A2, UBE2C, NMU, COL1A1, CXCL2, CXCL11, CDK1, TOP2A, AURKA, SST, CXCL5, MMP3, CCND1, TIMP1, CXCL8, CXCL1, CXCL12, MYC, CCNA2, GCG, GUCA2A, PAICS, PYY and THBS2) mentioned in not less than three articles and having clinical significance in cancerassociated pathways. Of them, there were two discrete clusters enriched in chemokine signaling and cell cycle regulatory genes. High expression levels of BGN and TIMP1 and low expression levels of CCNB1, CXCL3, CXCL2, CXCL2 and PAICS were associated with unfavorable overall survival of patients with CRC. Differently expressed genes such as LPAR1, SST, CXCL12, GUCA2A, and PYY were shown as down regulated, whereas BGN, CXCL3, UBE2C, NMU, CXCL11, CDK1, TOP2A, AURKA, MMP3, CCND1, CXCL1, MYC, CCNA2, PAICS were up regulated genes in CRC. It was also found that MMP3, THBS2, TIMP1 and CXCL12 genes were associated with metastatic CRC. Network analysis in ONCO.IO showed that upstream master regulators RELA, STAT3, SOX2, FOXM1, SMAD3 and NF-kB were connected with "core" hub-genes. Conclusión: Results obtained are of useful fundamental information on revealing the mechanism of pathogenicity, cellular target selection for optimization of therapeutic interventions, as well as transcriptomics prognostic and predictive biomarkers development.
Collapse
Affiliation(s)
- Pavel Ershov
- Department of Analysis and Forecasting of Medical and Biological Health Risks, Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - Stanislav Poyarkov
- Department of Analysis and Forecasting of Medical and Biological Health Risks, Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - Yulia Konstantinova
- Oncology Department, Federal Research and Clinical Center of Specialized Kinds of Medical Care and Medical Technology of the Federal Medical Biological Agency, Moscow, Russia
| | - Egor Veselovsky
- Department of Analysis and Forecasting of Medical and Biological Health Risks, Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - Anna Makarova
- Department of Analysis and Forecasting of Medical and Biological Health Risks, Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| |
Collapse
|
14
|
Li T, Yu Q, Liu T, Yang W, Chen W, Jin A, Wang H, Ding L, Zhang C, Pan B, Wang B, Guo W. Development of 14-gene signature prognostic model based on metastasis for colorectal cancer. J Clin Lab Anal 2022; 37:e24800. [PMID: 36524971 PMCID: PMC9833974 DOI: 10.1002/jcla.24800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 01/27/2022] [Accepted: 10/31/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Metastasis is the main cause of death of colorectal tumors, in our study a prognosis model was built by analyzing the differentially expressed genes between metastatic and non-metastatic colorectal cancer (CRC). We used this feature to predict CRC patient prognosis and explore the causes of colorectal tumor metastasis by characterizing the immune status alteration. METHODS CRC patient data were obtained from TCGA and GEO databases. We constructed a risk prognostic model by using Cox regression and the least absolute shrinkage and selection operator (LASSO) based on CRC metastasis-related genes. We also obtained a nomogram to predict the prognosis of CRC patients. Finally, we explored the underlying mechanism of these metastasis-related genes and CRC prognosis using immune infiltration analysis and experimental verification. RESULTS According to our prognostic model, in TCGA, the area under the curve (AUC) values of the training and test sets were 0.72 and 0.76, respectively, and 0.68 for the GEO external data set. This suggested that the treatment and prognosis of patients could be effectively determined. At the same time, we found that the B and T cells in both tissues and peripheral blood of high MR-risk score patients were mostly in immune static or inactivated states compared with those of low MR-risk score patients. CONCLUSIONS MR-risk score has a direct correlation with CRC patient prognosis. It is useful for predicting the prognosis and patient immune status for these patients.
Collapse
Affiliation(s)
- Tong Li
- Department of Laboratory MedicineZhongshan Hospital, Fudan UniversityShanghaiChina
| | - Qian Yu
- Department of Laboratory MedicineZhongshan Hospital, Fudan UniversityShanghaiChina
- Department of Laboratory Medicine, Wusong Branch, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Te Liu
- Department of Laboratory MedicineZhongshan Hospital, Fudan UniversityShanghaiChina
- Shanghai Geriatric Institute of Chinese MedicineShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Wenjing Yang
- Department of Laboratory MedicineZhongshan Hospital, Fudan UniversityShanghaiChina
| | - Wei Chen
- Department of Laboratory MedicineZhongshan Hospital, Fudan UniversityShanghaiChina
| | - Anli Jin
- Department of Laboratory MedicineZhongshan Hospital, Fudan UniversityShanghaiChina
| | - Hao Wang
- Department of Laboratory MedicineZhongshan Hospital, Fudan UniversityShanghaiChina
| | - Lin Ding
- Department of Laboratory MedicineZhongshan Hospital, Fudan UniversityShanghaiChina
| | - Chunyan Zhang
- Department of Laboratory MedicineZhongshan Hospital, Fudan UniversityShanghaiChina
- Department of Laboratory Medicine, Xiamen BranchZhongshan Hospital, Fudan UniversityXiamenChina
| | - Baishen Pan
- Department of Laboratory MedicineZhongshan Hospital, Fudan UniversityShanghaiChina
| | - Beili Wang
- Department of Laboratory MedicineZhongshan Hospital, Fudan UniversityShanghaiChina
- Department of Laboratory Medicine, Xiamen BranchZhongshan Hospital, Fudan UniversityXiamenChina
| | - Wei Guo
- Department of Laboratory MedicineZhongshan Hospital, Fudan UniversityShanghaiChina
- Department of Laboratory Medicine, Wusong Branch, Zhongshan HospitalFudan UniversityShanghaiChina
- Department of Laboratory Medicine, Xiamen BranchZhongshan Hospital, Fudan UniversityXiamenChina
- Cancer Center, Shanghai Zhongshan HospitalFudan UniversityShanghaiChina
| |
Collapse
|
15
|
Przygodzka P, Soboska K, Sochacka E, Pacholczyk M, Braun M, Kassassir H, Papiewska-Pająk I, Kielbik M, Boncela J. Neuromedin U secreted by colorectal cancer cells promotes a tumour-supporting microenvironment. Cell Commun Signal 2022; 20:193. [PMID: 36482448 PMCID: PMC9733105 DOI: 10.1186/s12964-022-01003-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 11/04/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Neuromedin U (NMU) was identified as one of the hub genes closely related to colorectal cancer (CRC) progression and was recently shown to be a motility inducer in CRC cells. Its autocrine signalling through specific receptors increases cancer cell migration and invasiveness. Because of insufficient knowledge concerning NMU accessibility and action in the tumour microenvironment, its role in CRC remains poorly understood and its potential as a therapeutic target is still difficult to define. METHODS NMU expression in CRC tissue was detected by IHC. Data from The Cancer Genome Atlas were used to analyse gene expression in CRC. mRNA and protein expression was detected by real-time PCR, immunoblotting or immunofluorescence staining and analysed using confocal microscopy or flow cytometry. Proteome Profiler was used to detect changes in the profiles of cytokines released by cells constituting tumour microenvironment after NMU treatment. NMU receptor activity was monitored by detecting ERK1/2 activation. Transwell cell migration, wound healing assay and microtube formation assay were used to evaluate the effects of NMU on the migration of cancer cells, human macrophages and endothelial cells. RESULTS Our current study showed increased NMU levels in human CRC when compared to normal adjacent tissue. We detected a correlation between high NMUR1 expression and shorter overall survival of patients with CRC. We identified NMUR1 expression on macrophages, endothelial cells, platelets, and NMUR1 presence in platelet microparticles. We confirmed ERK1/2 activation by treatment of macrophages and endothelial cells with NMU, which induced pro-metastatic phenotypes of analysed cells and changed their secretome. Finally, we showed that NMU-stimulated macrophages increased the migratory potential of CRC cells. CONCLUSIONS We propose that NMU is involved in the modulation and promotion of the pro-metastatic tumour microenvironment in CRC through the activation of cancer cells and other tumour niche cells, macrophages and endothelial cells. Video abstract.
Collapse
Affiliation(s)
- Patrycja Przygodzka
- grid.413454.30000 0001 1958 0162Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232 Lodz, Poland
| | - Kamila Soboska
- grid.413454.30000 0001 1958 0162Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232 Lodz, Poland ,grid.10789.370000 0000 9730 2769Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
| | - Ewelina Sochacka
- grid.413454.30000 0001 1958 0162Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232 Lodz, Poland ,grid.10789.370000 0000 9730 2769Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
| | - Marcin Pacholczyk
- grid.6979.10000 0001 2335 3149Department of Systems Biology and Engineering, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland
| | - Marcin Braun
- grid.8267.b0000 0001 2165 3025Department of Pathology, Medical University of Lodz, Pomorska 251, 92-213 Lodz, Poland
| | - Hassan Kassassir
- grid.413454.30000 0001 1958 0162Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232 Lodz, Poland
| | - Izabela Papiewska-Pająk
- grid.413454.30000 0001 1958 0162Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232 Lodz, Poland
| | - Michal Kielbik
- grid.413454.30000 0001 1958 0162Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232 Lodz, Poland
| | - Joanna Boncela
- grid.413454.30000 0001 1958 0162Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232 Lodz, Poland
| |
Collapse
|
16
|
Dobre M, Trandafir B, Milanesi E, Salvi A, Bucuroiu I, Vasilescu C, Niculae AM, Herlea V, Hinescu ME, Constantinescu G. Molecular profile of the NF-κB signalling pathway in human colorectal cancer. J Cell Mol Med 2022; 26:5966-5975. [PMID: 36433652 PMCID: PMC9753446 DOI: 10.1111/jcmm.17545] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 07/06/2022] [Accepted: 07/23/2022] [Indexed: 11/27/2022] Open
Abstract
The development and progression of colorectal cancer (CRC) have been associated with inflammation processes that involve the overactivation of the NF-κB signalling pathway. The characterization of the NF-κB expression profile in CRC is an important topic since the suppression of NF-κB represents a potential therapeutic approach. In this study, we assessed the expression levels of 84 NF-κB-related genes in paired tumoral (T) and peritumoral (PT) tissues from 18 CRC patients and 18 normal colonic mucosae, and the expression levels of three miRNAs targeting the most dysregulated genes revealed by the case-control analysis. Comparing the gene expression profile of T and controls, 60 genes were dysregulated. The comparison of T and PT revealed 17 dysregulated genes in the tumoral tissues, with IL1B, CXCL8, IL1A, and CSF2 being the most upregulated. Notably, through a bioinformatics analysis, the differential gene expression of 11 out of the 17 genes was validated on a larger cohort of 308 CRC patients compared with 41 controls. Moreover, a decrease in the levels of RELA, NOD1, CASP8, BCL2L1, ELK1, and IKBKB was identified in poorly differentiated tumours compared to moderately differentiated tumours. The analysis of the three miRNAs targeting IL1B, CXCL8, IL1A, and CSF2 showed that miR-182-5p was upregulated in T compared with PT, whereas miR-10b-5p was downregulated in T compared with PT and control tissues. Our results may contribute to the design of new experimental therapeutic strategies based on endogenous molecules, such as miRNAs, to target the genetic key players of the NF- κB pathway.
Collapse
Affiliation(s)
- Maria Dobre
- Victor Babes National Institute of PathologyBucharestRomania
| | - Bogdan Trandafir
- Faculty of MedicineCarol Davila University of Medicine and PharmacyBucharestRomania,Fundeni Clinical InstituteBucharestRomania
| | - Elena Milanesi
- Victor Babes National Institute of PathologyBucharestRomania
| | - Alessandro Salvi
- Division of Biology and Genetics, Department of Molecular and Translational MedicineUniversity of BresciaBresciaItaly
| | - Ioana Alina Bucuroiu
- Faculty of MedicineCarol Davila University of Medicine and PharmacyBucharestRomania
| | - Catalin Vasilescu
- Faculty of MedicineCarol Davila University of Medicine and PharmacyBucharestRomania,Fundeni Clinical InstituteBucharestRomania
| | - Andrei Marian Niculae
- Victor Babes National Institute of PathologyBucharestRomania,Faculty of MedicineCarol Davila University of Medicine and PharmacyBucharestRomania
| | | | - Mihail Eugen Hinescu
- Victor Babes National Institute of PathologyBucharestRomania,Faculty of MedicineCarol Davila University of Medicine and PharmacyBucharestRomania
| | - Gabriel Constantinescu
- Faculty of MedicineCarol Davila University of Medicine and PharmacyBucharestRomania,Clinical Emergency Hospital BucharestBucharestRomania
| |
Collapse
|
17
|
Fang ZX, Li CL, Wu Z, Hou YY, Wu HT, Liu J. Comprehensive analysis of the potential role and prognostic value of sine oculis homeobox homolog family in colorectal cancer. World J Gastrointest Oncol 2022; 14:2138-2156. [PMID: 36438701 PMCID: PMC9694273 DOI: 10.4251/wjgo.v14.i11.2138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/30/2022] [Accepted: 10/31/2022] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Several genes, important for development, are reduced or silenced in adulthood, and their abnormal expression has been related to the occurrence and development of malignant tumors. Human sine oculis homeobox homolog (SIX) proteins belong to the homeobox family and play important roles in the development of different organs. Importantly, SIXs are predicted to have chromatin-binding and DNA-binding transcription factor activity with reported roles in cancers. However, a comprehensive analysis of SIXs in colorectal cancers (CRCs) has not been performed.
AIM To explore the expression pattern of six SIX proteins in CRCs and their relationship with the clinicopathological parameters of CRC patients as well as investigate the potential utilization of SIXs as novel prognostic indicators in CRCs.
METHODS The expression level of SIXs in normal tissues of different organs and related cancerous tissues was analyzed in the Human Protein Atlas. Kaplan-Meier Plotter and GEPIA2 were used to analyze the prognostic values of SIXs. To analyze the potential signaling pathways with SIX family involvement, LinkedOmics was used to perform Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses of SIX4-related genes. Subsequently, immunohistochemical experiments were performed on CRC tissues and adjacent normal tissues, and we examined the SIX4 expression level in 87 pairs of patients with tissue microarray. The relationship between SIX4 and clinicopathological parameters in CRC patients was tested using the χ2 test and Fisher’s exact probability to verify the results of the database analysis.
RESULTS The RNA levels of SIX1-4 and SIX6 were relatively low in normal human tissues, while SIX5 was highly expressed at both the RNA and protein levels. However, the protein level of SIX4 was found to be elevated in various malignancies. In CRC tissues, SIX1, SIX2 and SIX4 were elevated in cancer tissues compared with adjacent normal tissue. Among all SIXs, a high level of SIX4 was found to be associated with poor overall and disease-free survival in patients with CRC. For different clinicopathological parameters, increased SIX4 expression was positively correlated with advanced CRC. The top 50 SIX4-related genes were involved with oxidative phosphorylation and the respiratory chain signaling pathways.
CONCLUSION The current results provided a comprehensive analysis of the expression and prognostic values of SIX family members in CRC. Among different SIXs, SIX4 plays an oncogenic role in CRC to promote the development of malignancy. In CRC, SIX4 mRNA and protein expression is higher than that in normal tissues and associated with shorter CRC patient survival, suggesting that SIX4 may be a potential therapeutic target for treatment of CRC patients.
Collapse
Affiliation(s)
- Ze-Xuan Fang
- Guangdong Provincial Key Laboratory for Diagnosis and Treatment of Breast Cancer, Cancer Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Chun-Lan Li
- Guangdong Provincial Key Laboratory for Diagnosis and Treatment of Breast Cancer, Cancer Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Zheng Wu
- Guangdong Provincial Key Laboratory for Diagnosis and Treatment of Breast Cancer, Cancer Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Yan-Yu Hou
- Guangdong Provincial Key Laboratory for Diagnosis and Treatment of Breast Cancer, Cancer Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Hua-Tao Wu
- Department of General Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Jing Liu
- Guangdong Provincial Key Laboratory for Diagnosis and Treatment of Breast Cancer, Cancer Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
| |
Collapse
|
18
|
Chen D, Ye Z, Lew Z, Luo S, Yu Z, Lin Y. Expression of NMU, PPBP and GNG4 in colon cancer and their influences on prognosis. Transl Cancer Res 2022; 11:3572-3583. [PMID: 36388046 PMCID: PMC9641087 DOI: 10.21037/tcr-22-1377] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 08/17/2022] [Indexed: 01/24/2023]
Abstract
BACKGROUND This study aims to identify the core genes that influence the prognosis of colon cancer (CC) and analyze their relationships with clinical characteristics. METHODS The gene expression profiles were downloaded from The Cancer Genome Atlas (TCGA) database. Differentially expressed genes (DEGs) were identified. The top ten core genes were selected by bioinformatics tools and screened through the Oncomine database. The expression of core genes in CC tissues and cells was validated by immunohistochemistry, immunoblotting and quantitative real-time polymerase chain reaction. Spearman correlation was used to analyze the relationship between different parameters. Overall survival was assessed by the Kaplan-Meier method. The area under the curve (AUC) and the receiver operating curve (ROC) were applied to assess the accuracy of genes for predicting prognosis. RESULTS There were 1,665 DEGs that were identified from TCGA database. Bioinformatics analysis found that GNGT1, NMU, PPBP, AGT, and GNG4 were differentially expressed in CC tissue. Overexpression of NMU, PPBP, AGT, and GNG4 in CC was associated with shortened survival time (P<0.05). In the validation studies, the high expression levels of NMU, PPBP and GNG4 in CC cells and tissues were confirmed compared to the control groups (P<0.05) and were adverse prognostic biomarkers (P<0.01). The combination prognostic model of the three core genes predicted the 1-, 3-, and 5-year survival of CC with AUCs of 0.868, 0.635 and 0.770, respectively. CONCLUSIONS High levels of NMU, PPBP, and GNG4 were associated with poor prognosis in CC. The combination prognostic model of these three genes could be a new option.
Collapse
Affiliation(s)
- Danyu Chen
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China;,Department of Gastroenterology and Hepatology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhen Ye
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China;,Department of Gastroenterology and Hepatology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhenxian Lew
- Department of Surgery, Guangzhou Concord Cancer Center, Guangzhou, China
| | - Simin Luo
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China;,Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhong Yu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China;,Department of Gastroenterology and Hepatology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ying Lin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China;,Department of Gastroenterology and Hepatology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| |
Collapse
|
19
|
Li N, Zhai Z, Chen Y, Li X. Transcriptomic and immunologic implications of the epithelial–mesenchymal transition model reveal a novel role of SFTA2 in prognosis of non-small-cell lung carcinoma. Front Genet 2022; 13:911801. [PMID: 36092941 PMCID: PMC9458971 DOI: 10.3389/fgene.2022.911801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 07/21/2022] [Indexed: 12/12/2022] Open
Abstract
Non-small-cell lung cancer (NSCLC) is the second most common cancer worldwide, and most deaths are associated with epithelial–mesenchymal transition (EMT). Therefore, this study aimed to explore the role of EMT-related transcriptomic profiles in NSCLC and the effect of EMT-based signatures on clinical diagnosis, prognosis, and treatment responses for patients with NSCLC. After integrating the transcriptomics and clinicopathological data, we first constructed EMT clusters (C1 and C2) using machine learning algorithms, found the significant relationship between EMT clusters and survival outcomes, and then explored the impact of EMT clusters on the tumor heterogeneity, drug efficiency, and immune microenvironment of NSCLC. Prominently, differential-enriched tumor-infiltrated lymphocytes were found between EMT clusters, especially the macrophages and monocyte. Next, we identified the most significantly down-regulated gene SFTA2 in the EMT clusters C2 with poor prognosis. Using RT-qPCR and RNA-seq data from the public database, we found prominently elevated SFTA2 expression in NSCLC tissues compared with normal lung tissues, and the tumor suppressor role of SFTA2 in 82 Chinese patients with NSCLC. After Cox regression and survival analysis, we demonstrated that higher SFTA2 expression in tumor samples significantly predicts favorable prognosis of NSCLC based on multiple independent cohorts. In addition, the prognostic value of SFTA2 expression differs for patients with lung adenocarcinoma and squamous cell carcinoma. In conclusion, this study demonstrated that the EMT process is involved in the malignant progression and the constructed EMT clusters exerted significant predictive drug resistance and prognostic value for NSCLC patients. In addition, we first identified the high tumoral expression of SFTA2 correlated with better prognosis and could serve as a predictive biomarker for outcomes and treatment response of NSCLC patients.
Collapse
Affiliation(s)
- Na Li
- Department of Respiratory Medicine, The First Hospital of Jiaxing (the Affiliated Hospital of Jiaxing University), Zhejiang, China
| | - Zhanqiang Zhai
- Department of Thoracic Disease Center, Zhejiang Rongjun Hospital, Zhejiang, China
| | - Yuanbiao Chen
- Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- *Correspondence: Yuanbiao Chen, ; Xiaofeng Li,
| | - Xiaofeng Li
- Department of Thoracic Disease Center, Zhejiang Rongjun Hospital, Zhejiang, China
- *Correspondence: Yuanbiao Chen, ; Xiaofeng Li,
| |
Collapse
|
20
|
Damian L, Login CC, Solomon C, Belizna C, Encica S, Urian L, Jurcut C, Stancu B, Vulturar R. Inclusion Body Myositis and Neoplasia: A Narrative Review. Int J Mol Sci 2022; 23:ijms23137358. [PMID: 35806366 PMCID: PMC9266341 DOI: 10.3390/ijms23137358] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 06/28/2022] [Accepted: 06/28/2022] [Indexed: 02/04/2023] Open
Abstract
Inclusion body myositis (IBM) is an acquired, late-onset inflammatory myopathy, with both inflammatory and degenerative pathogenesis. Although idiopathic inflammatory myopathies may be associated with malignancies, IBM is generally not considered paraneoplastic. Many studies of malignancy in inflammatory myopathies did not include IBM patients. Indeed, IBM is often diagnosed only after around 5 years from onset, while paraneoplastic myositis is generally defined as the co-occurrence of malignancy and myopathy within 1 to 3 years of each other. Nevertheless, a significant association with large granular lymphocyte leukemia has been recently described in IBM, and there are reports of cancer-associated IBM. We review the pathogenic mechanisms supposed to be involved in IBM and outline the common mechanisms in IBM and malignancy, as well as the therapeutic perspectives. The terminally differentiated, CD8+ highly cytotoxic T cells expressing NK features are central in the pathogenesis of IBM and, paradoxically, play a role in some cancers as well. Interferon gamma plays a central role, mostly during the early stages of the disease. The secondary mitochondrial dysfunction, the autophagy and cell cycle dysregulation, and the crosstalk between metabolic and mitogenic pathways could be shared by IBM and cancer. There are intermingled subcellular mechanisms in IBM and neoplasia, and probably their co-existence is underestimated. The link between IBM and cancers deserves further interest, in order to search for efficient therapies in IBM and to improve muscle function, life quality, and survival in both diseases.
Collapse
Affiliation(s)
- Laura Damian
- Centre for Rare Autoimmune and Autoinflammatory Diseases (ERN-ReCONNET), Department of Rheumatology, Emergency Clinical County Hospital Cluj, 400347 Cluj-Napoca, Romania;
- CMI Reumatologie Dr. Damian, 6-8 Petru Maior St., 400002 Cluj-Napoca, Romania
| | - Cristian Cezar Login
- Department of Physiology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania
- Correspondence:
| | - Carolina Solomon
- Radiology Department, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania;
- Radiology Department, Emergency Clinical County Hospital Cluj, 400006 Cluj-Napoca, Romania
| | - Cristina Belizna
- UMR CNRS 6015—INSERM U1083, University of Angers, 49100 Angers, France;
- Internal Medicine Department Clinique de l’Anjou, Angers and Vascular and Coagulation Department, University Hospital Angers, 49100 Angers, France
| | - Svetlana Encica
- Department of Pathology, “Niculae Stancioiu” Heart Institute Cluj-Napoca, 19-21 Calea Moților St., 400001 Cluj-Napoca, Romania;
| | - Laura Urian
- Department of Hematology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400004 Cluj-Napoca, Romania;
- Department of Hematology, Ion Chiricuta Clinical Cancer Center, 400014 Cluj-Napoca, Romania
| | - Ciprian Jurcut
- Department of Internal Medicine, “Carol Davila” Central Military Emergency University Hospital, Calea Plevnei No 134, 010825 Bucharest, Romania;
| | - Bogdan Stancu
- 2nd Surgical Department, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania;
| | - Romana Vulturar
- Department of Molecular Sciences, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania;
- Cognitive Neuroscience Laboratory, University “Babes-Bolyai” Cluj-Napoca, 400294 Cluj-Napoca, Romania
| |
Collapse
|
21
|
Liu Y, Chen L, Meng X, Ye S, Ma L. Identification of Hub Genes in Colorectal Adenocarcinoma by Integrated Bioinformatics. Front Cell Dev Biol 2022; 10:897568. [PMID: 35693937 PMCID: PMC9184445 DOI: 10.3389/fcell.2022.897568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/20/2022] [Indexed: 11/13/2022] Open
Abstract
An improved understanding of the molecular mechanism of colorectal adenocarcinoma is necessary to predict the prognosis and develop new target gene therapy strategies. This study aims to identify hub genes associated with colorectal adenocarcinoma and further analyze their prognostic significance. In this study, The Cancer Genome Atlas (TCGA) COAD-READ database and the gene expression profiles of GSE25070 from the Gene Expression Omnibus were collected to explore the differentially expressed genes between colorectal adenocarcinoma and normal tissues. The weighted gene co-expression network analysis (WGCNA) and differential expression analysis identified 82 differentially co-expressed genes in the collected datasets. Enrichment analysis was applied to explore the regulated signaling pathway in colorectal adenocarcinoma. In addition, 10 hub genes were identified in the protein–protein interaction (PPI) network by using the cytoHubba plug-in of Cytoscape, where five genes were further proven to be significantly related to the survival rate. Compared with normal tissues, the expressions of the five genes were both downregulated in the GSE110224 dataset. Subsequently, the expression of the five hub genes was confirmed by the Human Protein Atlas database. Finally, we used Cox regression analysis to identify genes associated with prognosis, and a 3-gene signature (CLCA1–CLCA4–GUCA2A) was constructed to predict the prognosis of patients with colorectal cancer. In conclusion, our study revealed that the five hub genes and CLCA1–CLCA4–GUCA2A signature are highly correlated with the development of colorectal adenocarcinoma and can serve as promising prognosis factors to predict the overall survival rate of patients.
Collapse
Affiliation(s)
- Yang Liu
- Endoscopy Center, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Lanlan Chen
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Changchun, China
| | - Xiangbo Meng
- Endoscopy Center, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Shujun Ye
- Endoscopy Center, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Lianjun Ma
- Endoscopy Center, China-Japan Union Hospital of Jilin University, Changchun, China
- *Correspondence: Lianjun Ma,
| |
Collapse
|
22
|
Prognostic Lnc-S100B-2 Affects Cell Apoptosis and Microenvironment of Colorectal Cancer through MLLT10 Signaling. JOURNAL OF ONCOLOGY 2022; 2022:3565118. [PMID: 35126515 PMCID: PMC8808143 DOI: 10.1155/2022/3565118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 12/24/2021] [Accepted: 12/29/2021] [Indexed: 11/19/2022]
Abstract
Long noncoding RNA (LncRNA) is closely associated with the development of colorectal cancer (CRC). The chip data and clinical information of GSE104364 and GSE151021 were downloaded by GEOquery. Limma and Kaplan–Meier analysis were performed. Lnc-S100B-2 was obtained, and high expression of Lnc-S100B-2 was predicted to be associated with a lower survival rate. Online software was adopted to predict downstream regulatory genes, and miR-331-3p and Mixed Lineage Leukemia Translocated to 10 (MLLT10) were screened and verified. After silencing Lnc-S100B-2 and MLLT10, the proliferative activity of CRC cells decreased, and the apoptosis rate increased. At the gene and protein levels, the expressions of PCNA, Ki67, and Bcl-2 were decreased in the sh-Lnc-S100B-2 group, sh-MLLT10 group, and sh-Lnc-S100B-2 + sh-MLLT10 group, while the expressions of cleaved caspase 3, caspase 9, and Bax were increased. In vivo, the volume and mass of the tumor decreased in the sh-Lnc-S100B-2 + sh-MLLT10 group. Proliferation and apoptosis-related index (PCNA, Ki67, cleaved caspase 3, caspase 9, Bax, and Bcl-2) expression level was also altered. Meanwhile, the infiltration of immune cells (CD3 (-), CD16 (+), and CD11b (+) cells) decreased. The expressions of epithelial-mesenchymal transformation (EMT) related indicators (E-cadherin, N-cadherin, Vimentin, β-catenin, Snail, and Slug) were changed. E-cadherin and β-catenin were increased in the sh-Lnc-S100B-2 + sh-MLLT10 group, while N-cadherin, vimentin, snail, and slug were decreased. In conclusion, our study found that the expression of Lnc-S100B-2 was dysregulated in CRC. Lnc-S100B-2 could affect cell apoptosis and the microenvironment of CRC through regulating MLLT10.
Collapse
|
23
|
Li Y, Li Y, Xia Z, Zhang D, Chen X, Wang X, Liao J, Yi W, Chen J. Identification of a novel immune signature for optimizing prognosis and treatment prediction in colorectal cancer. Aging (Albany NY) 2021; 13:25518-25549. [PMID: 34898475 PMCID: PMC8714135 DOI: 10.18632/aging.203771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/22/2021] [Indexed: 04/11/2023]
Abstract
BACKGROUND Globally, colorectal cancer (CRC) is one of the most lethal malignant diseases. However, the currently approved therapeutic options for CRC failed to acquire satisfactory treatment efficacy. Tailoring therapeutic strategies for CRC individuals can provide new insights into personalized prediction approaches and thus maximize clinical benefits. METHODS In this study, a multi-step process was used to construct an immune-related genes (IRGs) based signature leveraging the expression profiles and clinical characteristics of CRC from the Gene Expression Omnibus (GEO) database and the Cancer Genome Atlas (TCGA) database. An integrated immunogenomic analysis was performed to determine the association between IRGs with prognostic significance and cancer genotypes in the tumor immune microenvironment (TIME). Moreover, we performed a comprehensive in silico therapeutics screening to identify agents with subclass-specific efficacy. RESULTS The established signature was shown to be a promising biomarker for evaluating clinical outcomes in CRC. The immune risk score as calculated by this classifier was significantly correlated with over-riding malignant phenotypes and immunophenotypes. Further analyses demonstrated that CRCs with low immune risk scores achieved better therapeutic benefits from immunotherapy, while AZD4547, Cytochalasin B and S-crizotinib might have potential therapeutic implications in the immune risk score-high CRCs. CONCLUSIONS Overall, this IRGs-based signature not only afforded a useful tool for determining the prognosis and evaluating the TIME features of CRCs, but also shed new light on tailoring CRCs with precise treatment.
Collapse
Affiliation(s)
- Yan Li
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Yiyi Li
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Zijin Xia
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Dun Zhang
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Xiaomei Chen
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Xinyu Wang
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Jing Liao
- The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Wei Yi
- Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Jun Chen
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Guangdong Engineering and Technology Research Center for Disease-Model Animals, Laboratory Animal Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control of the Ministry of Education, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Precision Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
| |
Collapse
|
24
|
Novel diagnostic and prognostic biomarkers of colorectal cancer: Capable to overcome the heterogeneity-specific barrier and valid for global applications. PLoS One 2021; 16:e0256020. [PMID: 34473751 PMCID: PMC8412268 DOI: 10.1371/journal.pone.0256020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 07/28/2021] [Indexed: 02/05/2023] Open
Abstract
Introduction The heterogeneity-specific nature of the available colorectal cancer (CRC) biomarkers is significantly contributing to the cancer-associated high mortality rate worldwide. Hence, this study was initiated to investigate a system of novel CRC biomarkers that could commonly be employed to the CRC patients and helpful to overcome the heterogenetic-specific barrier. Methods Initially, CRC-related hub genes were extracted through PubMed based literature mining. A protein-protein interaction (PPI) network of the extracted hub genes was constructed and analyzed to identify few more closely CRC-related hub genes (real hub genes). Later, a comprehensive bioinformatics approach was applied to uncover the diagnostic and prognostic role of the identified real hub genes in CRC patients of various clinicopathological features. Results Out of 210 collected hub genes, in total 6 genes (CXCL12, CXCL8, AGT, GNB1, GNG4, and CXCL1) were identified as the real hub genes. We further revealed that all the six real hub genes were significantly dysregulated in colon adenocarcinoma (COAD) patients of various clinicopathological features including different races, cancer stages, genders, age groups, and body weights. Additionally, the dysregulation of real hub genes has shown different abnormal correlations with many other parameters including promoter methylation, overall survival (OS), genetic alterations and copy number variations (CNVs), and CD8+T immune cells level. Finally, we identified a potential miRNA and various chemotherapeutic drugs via miRNA, and real hub genes drug interaction network that could be used in the treatment of CRC by regulating the expression of real hub genes. Conclusion In conclusion, we have identified six real hub genes as potential biomarkers of CRC patients that could help to overcome the heterogenetic-specific barrier across different clinicopathological features.
Collapse
|
25
|
Patil AR, Leung MY, Roy S. Identification of Hub Genes in Different Stages of Colorectal Cancer through an Integrated Bioinformatics Approach. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:5564. [PMID: 34070979 PMCID: PMC8197092 DOI: 10.3390/ijerph18115564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 11/16/2022]
Abstract
Colorectal cancer (CRC) is the third most common cancer that contributes to cancer-related morbidity. However, the differential expression of genes in different phases of CRC is largely unknown. Moreover, very little is known about the role of stress-survival pathways in CRC. We sought to discover the hub genes and identify their roles in several key pathways, including oxidative stress and apoptosis in the different stages of CRC. To identify the hub genes that may be involved in the different stages of CRC, gene expression datasets were obtained from the gene expression omnibus (GEO) database. The differentially expressed genes (DEGs) common among the different datasets for each group were obtained using the robust rank aggregation method. Then, gene enrichment analysis was carried out with Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases. Finally, the protein-protein interaction networks were constructed using the Cytoscape software. We identified 40 hub genes and performed enrichment analysis for each group. We also used the Oncomine database to identify the DEGs related to stress-survival and apoptosis pathways involved in different stages of CRC. In conclusion, the hub genes were found to be enriched in several key pathways, including the cell cycle and p53 signaling pathway. Some of the hub genes were also reported in the stress-survival and apoptosis pathways. The hub DEGs revealed from our study may be used as biomarkers and may explain CRC development and progression mechanisms.
Collapse
Affiliation(s)
- Abhijeet R. Patil
- Computational Science Program, The University of Texas at El Paso, El Paso, TX 79968, USA; (A.R.P.); (M.-Y.L.)
| | - Ming-Ying Leung
- Computational Science Program, The University of Texas at El Paso, El Paso, TX 79968, USA; (A.R.P.); (M.-Y.L.)
- Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968, USA
- Department of Mathematical Sciences, The University of Texas at El Paso, El Paso, TX 79968, USA
| | - Sourav Roy
- Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968, USA
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX 79968, USA
| |
Collapse
|
26
|
Li E, Yang X, Du Y, Wang G, Chan DW, Wu D, Xu P, Ni P, Xu D, Hu Y. CXCL8 Associated Dendritic Cell Activation Marker Expression and Recruitment as Indicators of Favorable Outcomes in Colorectal Cancer. Front Immunol 2021; 12:667177. [PMID: 34025668 PMCID: PMC8138166 DOI: 10.3389/fimmu.2021.667177] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/21/2021] [Indexed: 12/14/2022] Open
Abstract
Accumulating evidence suggests that tumor-infiltrating immune cells (TICs) in the tumor microenvironment (TME) serve as promising therapeutic targets. CXCL8 (IL-8) may also be a potential therapeutic target in cancer. CXCL8 is a potent chemotactic factor for neutrophils, myeloid-derived suppressor cells (MDSCs) and monocytes, which are considered immunosuppressive components in cancer-bearing hosts. Here, we identified the TME-related gene CXCL8 in a high-ImmuneScore population that contributed to better survival in colorectal cancer (CRC) patients from The Cancer Genome Atlas (TCGA) database. An integrated gene profile and functional analysis of TIC proportions revealed that the dendritic cell (DC) activation markers CD80, CD83, and CD86 were positively correlated with CXCL8 expression, suggesting that CXCL8 may be functional as antitumor immune response status in the TME. The gene signature was further validated in independent GSE14333 and GSE38832 cohorts from the Gene Expression Omnibus (GEO). To test the differential contributions of immune and tumor components to progression, three CRC cell lines, CT26, MC38 and HCT116, were used. In vitro results suggested no significant growth or survival changes following treatment with an inhibitor of the CXCL8 receptor (CXCR1/2) such as reparixin or danirixin. In vivo treatment with danirixin (antagonists of CXCR2) promoted tumor progression in animal models established with CT26 cells. CXCR2 antagonism may function via an immune component, with CXCR2 antagonist treatment in mice resulting in reduced activated DCs and correlating with decreased Interferon gamma (IFN-γ) or Granzyme B expressed CD8+ T cells. Furthermore, CXCL8 induced DC migration in transwell migration assays. Taken together, our data suggested that targeting the CXCL8-CXCR2 axis might impede DC activation or recruitment, and this axis could be considered a favorable factor rather than a target for critical antitumor effects on CRC.
Collapse
Affiliation(s)
- Enhao Li
- Faculty of Medical Laboratory Science, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaobao Yang
- Faculty of Medical Laboratory Science, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yuzhang Du
- Faculty of Medical Laboratory Science, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Guanzheng Wang
- Faculty of Medical Laboratory Science, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - David W Chan
- Department of Obstetrics & Gynaecology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Di Wu
- Faculty of Medical Laboratory Science, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Peiqing Xu
- Faculty of Medical Laboratory Science, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Peihua Ni
- Faculty of Medical Laboratory Science, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Dakang Xu
- Faculty of Medical Laboratory Science, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yiqun Hu
- Faculty of Medical Laboratory Science, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
27
|
Liang X, Peng J, Chen D, Tang L, Liu A, Fu Z, Shi L, Wang K, Shao C. Identification of novel hub genes and lncRNAs related to the prognosis and progression of pancreatic cancer by microarray and integrated bioinformatics analysis. Gland Surg 2021; 10:1104-1117. [PMID: 33842254 PMCID: PMC8033078 DOI: 10.21037/gs-21-151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/22/2021] [Indexed: 11/06/2022]
Abstract
BACKGROUND Pancreatic cancer (PC) is one of the most invasive and metastatic neoplasms among the fatal malignancies of the digestive system. Abnormal expression of genes and long non-coding RNAs (lncRNAs) are reportedly linked to multiple cancers. However, the lncRNA-mRNA expression profiles and their molecular mechanisms in PC progression are poorly known. This study aimed to map the hub genes and lncRNAs which might play core roles in the development of PC. METHODS This study used microarray expression analysis to screen for both differentially expressed genes (DEGs) and differentially expressed lncRNAs (DElncRNAs) between PC and matched adjacent non-tumor (AN) tissues. In order to clarify the functional classification of DEGs, we conducted GO and KEGG pathway enrichment analyses via the Enrichr database. LncRNA-mRNA co-expressed networks were also constructed to explore the probable core regulating DEGs and DElncRNAs. Subsequently, the hub genes and lncRNAs were validated via the ONCOMINE and GEPIA databases and the co-expressed networks. RESULTS By analyzing an mRNA-lncRNA microarray, we identified 943 mRNAs and 1,138 lncRNAs differentially expressed in PC tumors compared with the matched AN tissues. GO analysis confirmed that both up-regulated and down-regulated DEGs were enriched in multiple terms. The KEGG pathways enrichment analyses revealed that DEGs were mostly enriched in the focal adhesion and glutathione metabolism pathways, amongst others. Co-expressed networks were established to reveal the differential interactions between DEGs and DElncRNAs, and to indicate the core regulatory factors located at the core nodes of the co-expressed networks. The expression levels of potential core-regulating DEGs were validated by the GEPIA and ONCOMINE databases, and the relationship between overall survival and tumor stage and the potential core-regulating DEGs was analyzed using the GEPIA database. As a result, five genes and sixteen lncRNAs were finally considered as the hub transcripts in PC. CONCLUSIONS This study identified DEGs and DElncRNAs between PC tumors and matched AN tissues, and these transcripts were connected with malignant phenotypes in PC through different BPs and signaling pathways. Furthermore, five hub genes and sixteen lncRNAs were identified, which are expected to represent candidate diagnostic biomarkers or potential therapeutic targets for PC.
Collapse
Affiliation(s)
- Xing Liang
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Junfeng Peng
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Danlei Chen
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Liang Tang
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Anan Liu
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Zhiping Fu
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Ligang Shi
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Keqi Wang
- Department of Gastroenterology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Chenghao Shao
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| |
Collapse
|
28
|
Zhang X, Zhao H, Shi X, Jia X, Yang Y. Identification and validation of an immune-related gene signature predictive of overall survival in colon cancer. Aging (Albany NY) 2020; 12:26095-26120. [PMID: 33401247 PMCID: PMC7803520 DOI: 10.18632/aging.202317] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/10/2020] [Indexed: 02/07/2023]
Abstract
The heterogeneity and complexity of tumor-immune microenvironments lead to diverse immunotherapy effects among colon cancer patients. It is crucial to identify immune microenvironment-related biomarkers and construct prognostic risk models. In this study, the immune and stromal scores of 415 cases from TCGA were calculated using the ESTIMATE algorithm. AXIN2, CCL22, CLEC10A, CRIP2, RUNX3, and TRPM5 were screened and established a prognostic immune-related gene (IRG) signature using by univariate, LASSO, and multivariate Cox regression models. The predicted performance of IRG signature was external validated by GSE39582 (n=519). Stratified survival analysis showed IRG signature was an effective predictor of survival in patients with different clinical characteristics. The protein expression level of six genes was validated by immunohistochemistry analysis. Difference analysis indicated the mutation rate, immune cell of resting NK cells and regulatory T cells infiltration and four immune checkpoints of PD-1, PD-L1, LAG3 and VSIR expression levels in the high-risk group were significantly higher than those in the low-risk group. A nomogram incorporating the gene signatures and clinical factors was demonstrated had a good accuracy (1-, 3-, and 5-year AUC= 0.799, 0.791, 0.738). Our study identified a novel IRG signature, which may provide some references for the clinical precision immunotherapy of patients.
Collapse
Affiliation(s)
- Xuening Zhang
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Hao Zhao
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Xuezhong Shi
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Xiaocan Jia
- Zhengzhou University Library, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Yongli Yang
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou 450001, Henan, China
| |
Collapse
|