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Hillson LVS, McCulloch AK, Edwards J, Dunne PD, O'Cathail SM, Roxburgh CS. Radiation-induced changes in gene expression in rectal cancer specimens. Clin Transl Oncol 2024; 26:1419-1428. [PMID: 38243085 PMCID: PMC11108951 DOI: 10.1007/s12094-023-03361-9] [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: 10/03/2023] [Accepted: 11/26/2023] [Indexed: 01/21/2024]
Abstract
PURPOSE The standard-of-care for locally advanced rectal cancer is radiotherapy-based neoadjuvant therapy followed by surgical resection. This article reviews the evidence of molecular changes at the transcriptome level induced through radiotherapy in rectal cancer. METHODS The PubMed search "(radiation OR radiotherapy) cancer (transcriptome OR "gene expression") rectal" was used. The studies taken forward utilised gene-expression data on both pre-treatment and post-treatment rectal adenocarcinoma biospecimens from patients treated with RT-based neoadjuvant strategies. RESULTS Twelve publications met the review criteria. There was variation in approaches in terms of design, patient population, cohort size, timing of the post-radiotherapy sampling and method of measuring gene expression. Most of the post-treatment biospecimen retrievals were at resection. The literature indicates a broad upregulation of immune activity through radiotherapy using gene-expression data. CONCLUSION Future studies would benefit from standardised prospective approaches to sampling to enable the inclusion of timepoints relevant to the tumour and immune response.
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Affiliation(s)
- Lily Victoria Sarah Hillson
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow, G61 1QH, UK.
| | - Ashley Kathryn McCulloch
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow, G61 1QH, UK
| | - Joanne Edwards
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow, G61 1QH, UK
| | - Philip David Dunne
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - Sean Michael O'Cathail
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow, G61 1QH, UK
| | - Campbell Stuart Roxburgh
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow, G61 1QH, UK
- Academic Unit of Surgery, Glasgow Royal Infirmary, Glasgow, UK
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Huang KCY, Chiang SF, Chang HY, Hong WZ, Chen JY, Lee PC, Liang JA, Ke TW, Peng SL, Shiau AC, Chen TW, Yang PC, Chen WTL, Chao KSC. Colorectal cancer-specific IFNβ delivery overcomes dysfunctional dsRNA-mediated type I interferon signaling to increase the abscopal effect of radiotherapy. J Immunother Cancer 2024; 12:e008515. [PMID: 38749537 PMCID: PMC11097864 DOI: 10.1136/jitc-2023-008515] [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] [Accepted: 04/19/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Cancer-intrinsic type I interferon (IFN-I) production triggered by radiotherapy (RT) is mainly dependent on cytosolic double-stranded DNA (dsDNA)-mediated cGAS/STING signaling and increases cancer immunogenicity and enhances the antitumor immune response to increase therapeutic efficacy. However, cGAS/STING deficiency in colorectal cancer (CRC) may suppress the RT-induced antitumor immunity. Therefore, we aimed to evaluate the importance of the dsRNA-mediated antitumor immune response induced by RT in patients with CRC. METHODS Cytosolic dsRNA level and its sensors were evaluated via cell-based assays (co-culture assay, confocal microscopy, pharmacological inhibition and immunofluorescent staining) and in vivo experiments. Biopsies and surgical tissues from patients with CRC who received preoperative chemoradiotherapy (neoCRT) were collected for multiplex cytokine assays, immunohistochemical analysis and SNP genotyping. We also generated a cancer-specific adenovirus-associated virus (AAV)-IFNβ1 construct to evaluate its therapeutic efficacy in combination with RT, and the immune profiles were analyzed by flow cytometry and RNA-seq. RESULTS Our studies revealed that RT stimulates the autonomous release of dsRNA from cancer cells to activate TLR3-mediated IFN-I signatures to facilitate antitumor immune responses. Patients harboring a dysfunctional TLR3 variant had reduced serum levels of IFN-I-related cytokines and intratumoral CD8+ immune cells and shorter disease-free survival following neoCRT treatment. The engineered cancer-targeted construct AAV-IFNβ1 significantly improved the response to RT, leading to systematic eradication of distant tumors and prolonged survival in defective TLR3 preclinical models. CONCLUSION Our results support that increasing cancer-intrinsic IFNβ1 expression is an immunotherapeutic strategy that enhances the RT-induced antitumor immune response in locally patients with advanced CRC with dysfunctional TLR3.
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Affiliation(s)
- Kevin Chih-Yang Huang
- Department of Biomedical Imaging and Radiological Science, China Medical University, Taichung, Taiwan
- Translation Research Core, China Medical University Hospital, Taichung, Taiwan
- Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung, Taiwan
| | - Shu-Fen Chiang
- Lab of Precision Medicine, Feng-Yuan Hospital Ministry of Health and Welfare, Taichung, Taiwan
| | - Hsin-Yu Chang
- Translation Research Core, China Medical University Hospital, Taichung, Taiwan
- Proton Cancer, China Medical University Hospital, Taichung, Taiwan
| | - Wei-Ze Hong
- Proton Cancer, China Medical University Hospital, Taichung, Taiwan
| | - Jhen-Yu Chen
- Department of Biomedical Imaging and Radiological Science, China Medical University, Taichung, Taiwan
- Translation Research Core, China Medical University Hospital, Taichung, Taiwan
- Proton Cancer, China Medical University Hospital, Taichung, Taiwan
| | - Pei-Chih Lee
- Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung, Taiwan
- Graduate Institute of Biomedical Science, China Medical University, Taichung, Taiwan
| | - Ji-An Liang
- Department of Radiation Oncology, China Medical University Hospital, Taichung, Taiwan
- School of Medicine, China Medical University, Taichung, Taiwan
| | - Tao-Wei Ke
- Department of Colorectal Cancer, China Medical University Hospital, Taichung, Taiwan
- School of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Shin-Lei Peng
- Department of Biomedical Imaging and Radiological Science, China Medical University, Taichung, Taiwan
| | - An-Cheng Shiau
- Department of Biomedical Imaging and Radiological Science, China Medical University, Taichung, Taiwan
- Proton Cancer, China Medical University Hospital, Taichung, Taiwan
- Department of Radiation Oncology, China Medical University Hospital, Taichung, Taiwan
| | - Tsung-Wei Chen
- Department of Pathology, Asia University, Taichung, Taiwan
| | - Pei-Chen Yang
- Proton Cancer, China Medical University Hospital, Taichung, Taiwan
| | - William Tzu-Liang Chen
- School of Medicine, China Medical University, Taichung, Taiwan
- Department of Colorectal Cancer, China Medical University Hospital, Taichung, Taiwan
- Department of Colorectal Surgery, China Medical University HsinChu Hospital, China Medical University Hospital, HsinChu, Taiwan
| | - K S Clifford Chao
- Proton Cancer, China Medical University Hospital, Taichung, Taiwan
- Department of Radiation Oncology, China Medical University Hospital, Taichung, Taiwan
- School of Medicine, China Medical University, Taichung, Taiwan
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Azizan S, Cheng KJ, Mejia Mohamed EH, Ibrahim K, Faruqu FN, Vellasamy KM, Khong TL, Syafruddin SE, Ibrahim ZA. Insights into the molecular mechanisms and signalling pathways of epithelial to mesenchymal transition (EMT) in colorectal cancer: A systematic review and bioinformatic analysis of gene expression. Gene 2024; 896:148057. [PMID: 38043836 DOI: 10.1016/j.gene.2023.148057] [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: 06/15/2023] [Revised: 11/19/2023] [Accepted: 11/29/2023] [Indexed: 12/05/2023]
Abstract
Colorectal cancer (CRC) is ranked as the second leading cause of mortality worldwide, mainly due to metastasis. Epithelial to mesenchymal transition (EMT) is a complex cellular process that drives CRC metastasis, regulated by changes in EMT-associated gene expression. However, while numerous genes have been identified as EMT regulators through various in vivo and in vitro studies, little is known about the genes that are differentially expressed in CRC tumour tissue and their signalling pathway in regulating EMT. Using an integration of systematic search and bioinformatic analysis, gene expression profiles of CRC tumour tissues were compared to non-tumour adjacent tissues to identify differentially expressed genes (DEGs), followed by performing systematic review on common identified DEGs. Fifty-eight common DEGs were identified from the analysis of 82 tumour tissue samples obtained from four gene expression datasets (NCBI GEO). These DEGS were then systematically searched for their roles in modulating EMT in CRC based on previously published studies. Following this, 10 common DEGs (CXCL1, CXCL8, MMP1, MMP3, MMP7, TACSTD2, VIP, HPGD, ABCG2, CLCA4) were included in this study and subsequently subjected to further bioinformatic analysis. Their roles and functions in modulating EMT in CRC were discussed in this review. This study enhances our understanding of the molecular mechanisms underlying EMT and uncovers potential candidate genes and pathways that could be targeted in CRC.
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Affiliation(s)
- Suha Azizan
- Department of Pharmacology, Faculty of Medicine, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kim Jun Cheng
- Department of Pharmacology, Faculty of Medicine, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | | | - Kamariah Ibrahim
- Department of Biomedical Science, Faculty of Medicine, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Farid Nazer Faruqu
- Department of Pharmacology, Faculty of Medicine, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kumutha Malar Vellasamy
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Tak Loon Khong
- Department of Surgery, Faculty of Medicine, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Saiful Effendi Syafruddin
- UKM Medical Molecular Biology Institute (UMBI), UKM Medical Centre, 56000 Cheras, Kuala Lumpur, Malaysia
| | - Zaridatul Aini Ibrahim
- Department of Pharmacology, Faculty of Medicine, Universiti Malaya, 50603 Kuala Lumpur, Malaysia.
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Lu Y, Peng R, Dong L, Xia K, Wu R, Xu S, Wang J. Multiomics dynamic learning enables personalized diagnosis and prognosis for pancancer and cancer subtypes. Brief Bioinform 2023; 24:bbad378. [PMID: 37889117 PMCID: PMC10605059 DOI: 10.1093/bib/bbad378] [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: 07/07/2023] [Revised: 09/26/2023] [Accepted: 09/30/2023] [Indexed: 10/28/2023] Open
Abstract
Artificial intelligence (AI) approaches in cancer analysis typically utilize a 'one-size-fits-all' methodology characterizing average patient responses. This manner neglects the diverse conditions in the pancancer and cancer subtypes of individual patients, resulting in suboptimal outcomes in diagnosis and treatment. To overcome this limitation, we shift from a blanket application of statistics to a focus on the explicit recognition of patient-specific abnormalities. Our objective is to use multiomics data to empower clinicians with personalized molecular descriptions that allow for customized diagnosis and interventions. Here, we propose a highly trustworthy multiomics learning (HTML) framework that employs multiomics self-adaptive dynamic learning to process each sample with data-dependent architectures and computational flows, ensuring personalized and trustworthy patient-centering of cancer diagnosis and prognosis. Extensive testing on a 33-type pancancer dataset and 12 cancer subtype datasets underscored the superior performance of HTML compared with static-architecture-based methods. Our findings also highlighting the potential of HTML in elucidating complex biological pathogenesis and paving the way for improved patient-specific care in cancer treatment.
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Affiliation(s)
- Yuxing Lu
- Department of Big Data and Biomedical AI, College of Future Technology, Peking University, Beijing, China
| | - Rui Peng
- Department of Big Data and Biomedical AI, College of Future Technology, Peking University, Beijing, China
| | - Lingkai Dong
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Kun Xia
- Department of Big Data and Biomedical AI, College of Future Technology, Peking University, Beijing, China
| | - Renjie Wu
- School of Life Sciences, Peking University, Beijing, China
| | - Shuai Xu
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Jinzhuo Wang
- Department of Big Data and Biomedical AI, College of Future Technology, Peking University, Beijing, China
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Hosseini-Abgir A, Naghizadeh MM, Igder S, Miladpour B. Insilco prediction of the role of the FriZZled5 gene in colorectal cancer. Cancer Treat Res Commun 2023; 36:100751. [PMID: 37595345 DOI: 10.1016/j.ctarc.2023.100751] [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: 03/19/2023] [Revised: 07/27/2023] [Accepted: 08/14/2023] [Indexed: 08/20/2023]
Abstract
INTRODUCTION In this study, we aimed to elucidate the crosstalk between the Wnt/β-catenin signaling pathway and colorectal cancer (CRC) associated with inflammatory bowel disease (IBD) using a bioinformatics analysis of putative common biomarkers and a systems biology approach. MATERIALS AND METHODS The following criteria were used to search the GEO and ArrayExpress databases for terms related to CRC and IBD: 1. The dataset containing the transcriptomic data, and 2. Untreated samples by medications or drugs. A total of 42 datasets were selected for additional analysis. The GEO2R identified the differentially expressed genes. The genes involved in the Wnt signaling pathway were extracted from the KEGG database. Enrichment analysis and miRNA target prediction were conducted through the ToppGene online tool. RESULTS In CRC datasets, there were 1168 up- and 998 down-regulated probes, whereas, in IBD datasets, there were 256 up- and 200 down-regulated probes. There were 65 upregulated and 57 downregulated genes shared by CRC and IBD. According to KEGG, there were 166 genes in the Wnt pathway. FriZZled5 (FZD5) was a down-regulated gene in both CRC and IBD, as determined by the intersection of CRC- and IBD-related DEGs with the Wnt pathway. It was also demonstrated that miR-191, miR-885-5p, miR-378a-3p, and miR-396-3p affect the FriZZled5 gene expression. CONCLUSION It is possible that increased expression of miR-191 and miR-885-5p, or decreased expression of miR-378a -3p and miR396-3, in IBD and CRC results in decreased expression of the FZD5 gene. Based on the function of this gene, FZD5 may be a potential therapeutic target in IBD that progresses to CRC.
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Affiliation(s)
| | | | - Somayeh Igder
- Department of Clinical Biochemistry, Faculty of Medicine, Ahvaz Jundishapur University of Medical Science, Ahvaz, Iran
| | - Behnoosh Miladpour
- Department of Clinical Biochemistry, Fasa University of Medical Sciences, Fasa, Iran.
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Afshar S, Leili T, Amini P, Dinu I. Introducing novel key genes and transcription factors associated with rectal cancer response to chemoradiation through co-expression network analysis. Heliyon 2023; 9:e18869. [PMID: 37636389 PMCID: PMC10447927 DOI: 10.1016/j.heliyon.2023.e18869] [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: 04/03/2023] [Revised: 07/16/2023] [Accepted: 08/01/2023] [Indexed: 08/29/2023] Open
Abstract
Preoperative radiochemotherapy is a promising therapeutic method for locally advanced rectal cancer patients. However, the response of colorectal cancer (CRC) patients to preoperative radiotherapy varies widely. In this study, we aimed to identify novel biomarkers that could predict the response of colorectal tumors to treatment using a systems biology approach. We applied the Weighted Gene Co-Expression Network Analysis to construct co-expression networks and evaluated the correlation of these networks with radiation using the module-trait relationship. We then identified hub genes and related transcription factors in the selected co-expression module. Our analysis of seven constructed modules revealed that one module, which contained 113 nodes and 6066 edges, had the strongest correlation with radiation effects on CRC (correlation = 0.85; p-value = 6e-7). By analyzing the selected module with the CytoHubba plugin, we identified four hub genes, including ZEB2, JAM2, NDN, and PPAP2A. We also identified seven important transcription factors, including KLF4, SUZ12, TCF4, NANOG, POU5F1, SOX2, and SMARCA4, which may play essential roles in regulating the four hub genes. In summary, our findings suggest that ZEB2, JAM2, NDN, and PPAP2A, along with the seven transcription factors related to these hub genes, may be associated with the response of colorectal tumors to chemoradiotherapy.
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Affiliation(s)
- Saeid Afshar
- Cancer Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Tapak Leili
- Department of Biostatistics, School of Public Health and Modeling of Noncommunicable Diseases Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Payam Amini
- School of Medicine, Keele University, Keele, Staffordshire, ST5 5BG, UK
| | - Irina Dinu
- School of Public Health, University of Alberta, Edmonton, AB, Canada
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Liu Y, Azizian NG, Sullivan DK, Li Y. mTOR inhibition attenuates chemosensitivity through the induction of chemotherapy resistant persisters. Nat Commun 2022; 13:7047. [PMID: 36396656 PMCID: PMC9671908 DOI: 10.1038/s41467-022-34890-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 11/10/2022] [Indexed: 11/18/2022] Open
Abstract
Chemotherapy can eradicate a majority of cancer cells. However, a small population of tumor cells often survives drug treatments through genetic and/or non-genetic mechanisms, leading to tumor recurrence. Here we report a reversible chemoresistance phenotype regulated by the mTOR pathway. Through a genome-wide CRISPR knockout library screen in pancreatic cancer cells treated with chemotherapeutic agents, we have identified the mTOR pathway as a prominent determinant of chemosensitivity. Pharmacological suppression of mTOR activity in cancer cells from diverse tissue origins leads to the persistence of a reversibly resistant population, which is otherwise eliminated by chemotherapeutic agents. Conversely, activation of the mTOR pathway increases chemosensitivity in vitro and in vivo and predicts better survival among various human cancers. Persister cells display a senescence phenotype. Inhibition of mTOR does not induce cellular senescence per se, but rather promotes the survival of senescent cells through regulation of autophagy and G2/M cell cycle arrest, as revealed by a small-molecule chemical library screen. Thus, mTOR plays a causal yet paradoxical role in regulating chemotherapeutic response; inhibition of the mTOR pathway, while suppressing tumor expansion, facilitates the development of a reversible drug-tolerant senescence state.
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Affiliation(s)
- Yuanhui Liu
- grid.63368.380000 0004 0445 0041Center for Immunotherapy Research, Houston Methodist Research Institute, Houston, TX 77030 USA ,grid.5386.8000000041936877XDepartment of Medicine, Weill Cornell Medical College, New York, NY 10065 USA
| | - Nancy G. Azizian
- grid.63368.380000 0004 0445 0041Center for Immunotherapy Research, Houston Methodist Research Institute, Houston, TX 77030 USA ,grid.5386.8000000041936877XDepartment of Medicine, Weill Cornell Medical College, New York, NY 10065 USA
| | - Delaney K. Sullivan
- grid.19006.3e0000 0000 9632 6718UCLA-Caltech Medical Scientist Training Program, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095 USA
| | - Yulin Li
- grid.63368.380000 0004 0445 0041Center for Immunotherapy Research, Houston Methodist Research Institute, Houston, TX 77030 USA ,grid.5386.8000000041936877XDepartment of Medicine, Weill Cornell Medical College, New York, NY 10065 USA
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A novel focal adhesion-related risk model predicts prognosis of bladder cancer —— a bioinformatic study based on TCGA and GEO database. BMC Cancer 2022; 22:1158. [PMID: 36357874 PMCID: PMC9647995 DOI: 10.1186/s12885-022-10264-5] [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: 04/22/2022] [Accepted: 11/01/2022] [Indexed: 11/11/2022] Open
Abstract
Background Bladder cancer (BLCA) is the ninth most common cancer globally, as well as the fourth most common cancer in men, with an incidence of 7%. However, few effective prognostic biomarkers or models of BLCA are available at present. Methods The prognostic genes of BLCA were screened from one cohort of The Cancer Genome Atlas (TCGA) database through univariate Cox regression analysis and functionally annotated by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. The intersecting genes of the BLCA gene set and focal adhesion-related gene were obtained and subjected to the least absolute shrinkage and selection operator regression (LASSO) to construct a prognostic model. Gene set enrichment analysis (GSEA) of high- and low-risk patients was performed to explore further the biological process related to focal adhesion genes. Univariate and multivariate Cox analysis, receiver operating characteristic (ROC) curve analysis, and Kaplan–Meier survival analysis (KM) were used to evaluate the prognostic model. DNA methylation analysis was presented to explore the relationship between prognosis and gene methylation. Furthermore, immune cell infiltration was assessed by CIBERSORT, ESTIMATE, and TIMER. The model was verified in an external GSE32894 cohort of the Gene Expression Omnibus (GEO) database, and the Prognoscan database presented further validation of genes. The HPA database validated the related protein level, and functional experiments verified significant risk factors in the model. Results VCL, COL6A1, RAC3, PDGFD, JUN, LAMA2, and ITGB6 were used to construct a prognostic model in the TCGA-BLCA cohort and validated in the GSE32894 cohort. The 7-gene model successfully stratified the patients into both cohorts’ high- and low-risk groups. The higher risk score was associated with a worse prognosis. Conclusions The 7-gene prognostic model can classify BLCA patients into high- and low-risk groups based on the risk score and predict the overall survival, which may aid clinical decision-making. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-10264-5.
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Nishiga Y, Drainas AP, Baron M, Bhattacharya D, Barkal AA, Ahrari Y, Mancusi R, Ross JB, Takahashi N, Thomas A, Diehn M, Weissman IL, Graves EE, Sage J. Radiotherapy in combination with CD47 blockade elicits a macrophage-mediated abscopal effect. NATURE CANCER 2022; 3:1351-1366. [PMID: 36411318 PMCID: PMC9701141 DOI: 10.1038/s43018-022-00456-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 10/04/2022] [Indexed: 11/22/2022]
Abstract
Radiation therapy is a mainstay of cancer treatment but does not always lead to complete tumor regression. Here we combine radiotherapy with blockade of the 'don't-eat-me' cell-surface molecule CD47 in small cell lung cancer (SCLC), a highly metastatic form of lung cancer. CD47 blockade potently enhances the local antitumor effects of radiotherapy in preclinical models of SCLC. Notably, CD47 blockade also stimulates off-target 'abscopal' effects inhibiting non-irradiated SCLC tumors in mice receiving radiation. These abscopal effects are independent of T cells but require macrophages that migrate into non-irradiated tumor sites in response to inflammatory signals produced by radiation and are locally activated by CD47 blockade to phagocytose cancer cells. Similar abscopal antitumor effects were observed in other cancer models treated with radiation and CD47 blockade. The systemic activation of antitumor macrophages following radiotherapy and CD47 blockade may be particularly important in patients with cancer who suffer from metastatic disease.
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Affiliation(s)
- Yoko Nishiga
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Alexandros P Drainas
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Maya Baron
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Debadrita Bhattacharya
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Amira A Barkal
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Yasaman Ahrari
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Rebecca Mancusi
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Jason B Ross
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Nobuyuki Takahashi
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
- Department of Medical Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Anish Thomas
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Irving L Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Edward E Graves
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA.
| | - Julien Sage
- Department of Pediatrics, Stanford University, Stanford, CA, USA.
- Department of Genetics, Stanford University, Stanford, CA, USA.
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10
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Wen S, Xu X, Kong J, Luo L, Yue P, Cao W, Zhang Y, Liu M, Fan Y, Chen J, Ma M, Tao L, Peng Y, Wang F, Dong Y, Li B, Luo S, Zhou G, Chen T, Li L, Liu A, Bao F. Comprehensive analyses of transcriptomes induced by Lyme spirochete infection to CNS model system. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 103:105349. [PMID: 35964914 DOI: 10.1016/j.meegid.2022.105349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 06/12/2022] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Lyme disease is a zoonotic disease caused by infection with Borrelia burgdorferi (Bb), the involvement of the nervous system in Lyme disease is usually referred to as Lyme neuroborreliosis (LNB). LNB has diverse clinical manifestations, most commonly including meningitis, Bell's palsy, and encephalitis. However, the molecular pathogenesis of neuroborreliosis is still poorly understood. Comprehensive transcriptomic analysis following Bb infection could provide new insights into the pathogenesis of LNB and may identify novel biomarkers or therapeutic targets for LNB diagnosis and treatment. METHODS In the present study, we pooled transcriptomic dataset of Macaca mulatta (rhesus) from our laboratory and the human astrocyte dataset GSE85143 from the Gene Expression Omnibus database to screen common differentially expressed genes (DEGs) in the Bb infection group and the control group. Functional and enrichment analyses were applied for the DEGs. Protein-Protein Interaction network, and hub genes were identified using the Search Tool for the Retrieval of Interaction Genes database and the CytoHubba plugin. Finally, mRNA expression of hub genes was validated in vitro and ex vivo from Bb infected models and normal controls by quantitative reverse transcription PCR (qRT-PCR). RESULTS A total of 80 upregulated DEGs and 32 downregulated DEGs were identified. Among them, 11 hub genes were selected. The pathway enrichment analyses on 11 hub genes revealed that the PI3K-Akt signaling pathway was significantly enriched. The mRNA levels of ANGPT1, TLR6, SREBF1, LDLR, TNC, and ITGA2 in U251 cells and/or rhesus brain explants by exposure to Bb were validated by qRT-PCR. CONCLUSION Our study suggested that TLR6, ANGPT1, LDLR, SREBF1, TNC, and ITGA may be candidate mammal biomarkers for LNB, and the TLR6/PI3K-Akt signaling pathway may play an important role in LNB pathogenesis.
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Affiliation(s)
- Shiyuan Wen
- Department of Microbiology and Immunology, Kunming Medical University, Kunming 650500, China; Department of Intensive Care Unit, First People's Hospital of Yunnan Province, Kunming 650500, China
| | - Xin Xu
- Department of Microbiology and Immunology, Kunming Medical University, Kunming 650500, China
| | - Jing Kong
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming 650500, China
| | - Lisha Luo
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming 650500, China
| | - Peng Yue
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming 650500, China
| | - Wenjing Cao
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming 650500, China
| | - Yu Zhang
- Department of Microbiology and Immunology, Kunming Medical University, Kunming 650500, China
| | - Meixiao Liu
- Department of Microbiology and Immunology, Kunming Medical University, Kunming 650500, China
| | - Yuxin Fan
- Department of Microbiology and Immunology, Kunming Medical University, Kunming 650500, China
| | - Jingjing Chen
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming 650500, China
| | - Mingbiao Ma
- Department of Microbiology and Immunology, Kunming Medical University, Kunming 650500, China; Yunnan Province Key Laboratory of Children's Major Diseases Research, The Affiliated Children's Hospital of Kunming, Kunming Medical University, Kunming 650030, China
| | - Lvyan Tao
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming 650500, China; Yunnan Province Key Laboratory of Children's Major Diseases Research, The Affiliated Children's Hospital of Kunming, Kunming Medical University, Kunming 650030, China
| | - Yun Peng
- Department of Microbiology and Immunology, Kunming Medical University, Kunming 650500, China
| | - Feng Wang
- Department of Microbiology and Immunology, Kunming Medical University, Kunming 650500, China
| | - Yan Dong
- Department of Microbiology and Immunology, Kunming Medical University, Kunming 650500, China
| | - Bingxue Li
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming 650500, China
| | - Suyi Luo
- Department of Microbiology and Immunology, Kunming Medical University, Kunming 650500, China
| | - Guozhong Zhou
- Department of Microbiology and Immunology, Kunming Medical University, Kunming 650500, China
| | - Taigui Chen
- Department of Microbiology and Immunology, Kunming Medical University, Kunming 650500, China
| | - Lianbao Li
- Department of Microbiology and Immunology, Kunming Medical University, Kunming 650500, China
| | - Aihua Liu
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming 650500, China; Yunnan Province Key Laboratory of Children's Major Diseases Research, The Affiliated Children's Hospital of Kunming, Kunming Medical University, Kunming 650030, China; The Institute for Tropical Medicine, Kunming Medical University, Kunming 650500, China; Yunnan Demonstration Base of International Science and Technology Cooperation for Tropical Diseases, Kunming 650500, China.
| | - Fukai Bao
- Department of Microbiology and Immunology, Kunming Medical University, Kunming 650500, China; Yunnan Province Key Laboratory of Children's Major Diseases Research, The Affiliated Children's Hospital of Kunming, Kunming Medical University, Kunming 650030, China; The Institute for Tropical Medicine, Kunming Medical University, Kunming 650500, China; Yunnan Demonstration Base of International Science and Technology Cooperation for Tropical Diseases, Kunming 650500, China.
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11
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Huang J, Zhou M, Zhang H, Fang Y, Chen G, Wen J, Liu L. Characterization of the mechanism of Scutellaria baicalensis on reversing radio-resistance in colorectal cancer. Transl Oncol 2022; 24:101488. [PMID: 35872478 PMCID: PMC9307497 DOI: 10.1016/j.tranon.2022.101488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/30/2022] [Accepted: 07/09/2022] [Indexed: 12/09/2022] Open
Abstract
Scutellaria baicalensis (SB) has been shown to improve the therapeutic effects of colorectal cancer (CRC) and perform well for reversing radio-resistance in different cancers. However, its potential function and mechanism related to radio-resistance in CRC has not been explored. A radio-resistant human CRC cell line (HCT116R) was applied. A network pharmacological analysis was performed to reveal the potential mechanism of SB for reversing radio-resistance in CRC, and computational pathological analysis was applied to indicate the clinicopathological significance of the key targets. Then, our hypothesis was further verified by molecular docking. The network pharmacology analysis showed that wogonin is the key compound of SB for reversing the radio-resistance of CRC. A Kyoto Encyclopedia of Genes and Genomes analysis showed that the genes for SB that reverse radio-resistance in CRC are mainly involved in steroid hormone biosynthesis. An enrichment analysis pointed out that Sulfotransferase family 2B member 1 (SULT2B1) is a potentially vital gene. SULT2B1 was demonstrated as being highly expressed in CRC and upregulated in radio-resistant rectal tissues or cell lines. A CCK-8 and clone formation test showed that the viability and clone formation ability of HCT116R were significantly decreased by wogonin combined with radiotherapy, compared to radiotherapy alone. By contrast, flow cytometry revealed that the apoptosis of HCT116R was significantly increased when wogonin treatment combined with radiotherapy, compared with radiotherapy alone. Molecular docking verification indicated that SULT2B1 and wogonin have a good binding ability. Taken together, SULT2B1 may be the potential drug target in treating radio-resistant CRC. Wogonin may be the core compound of SB for reversing radio-resistance in CRC by targeting SULT2B1.
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Affiliation(s)
- Jinmei Huang
- Department of Drug Toxicology, College of Pharmacy of Guangxi Medical University, Nanning 530021, PR China.
| | - Ming Zhou
- Department of Pharmacy, Wuhan Pulmonary Hospital, Wuhan, PR China.
| | - Huan Zhang
- Department of Pharmacy, Wuhan Pulmonary Hospital, Wuhan, PR China.
| | - Yeying Fang
- Department of Radiotherapy, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, PR China.
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, PR China.
| | - Jiaying Wen
- Department of Radiotherapy, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, PR China.
| | - LiMin Liu
- Department of Drug Toxicology, College of Pharmacy of Guangxi Medical University, Nanning 530021, PR China.
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12
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Metformin suppresses the growth of colorectal cancer by targeting INHBA to inhibit TGF-β/PI3K/AKT signaling transduction. Cell Death Dis 2022; 13:202. [PMID: 35236827 PMCID: PMC8891354 DOI: 10.1038/s41419-022-04649-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 02/08/2022] [Accepted: 02/16/2022] [Indexed: 01/01/2023]
Abstract
Multiple evidence shows that metformin serves as a potential agent for Colorectal Cancer (CRC) treatment, while its molecular mechanisms still require detailed investigation. Here, we revealed that metformin specifically suppressed the proliferation of CRC cells by causing G1/S arrest, and INHBA is a potential target for metformin to play an anti-proliferation effect in CRC. We verified the oncogene role of INHBA by knocking down and overexpressing INHBA in CRC cells. Silencing INHBA abrogated the cell growth, while overexpression INHBA promotes the proliferation of CRC cells. As an oncogene, INHBA was aberrant overexpression in CRC tissues and closely related to the poor prognosis of CRC patients. In mechanism, INHBA is an important ligand of TGF-β signaling and metformin blocked the activation of TGF-β signaling by targeting INHBA, and then down-regulated the activity of PI3K/Akt pathway, leading to the reduction of cyclinD1 and cell cycle arrest. Together, these findings indicate that metformin down-regulates the expression of INHBA, then attenuating TGF-β/PI3K/Akt signaling transduction, thus inhibiting the proliferation of CRC. Our study elucidated a novel molecular mechanism for the anti-proliferation effect of metformin, providing a theoretical basis for the application of metformin in CRC therapy.
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13
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Roblek M, Bicher J, van Gogh M, György A, Seeböck R, Szulc B, Damme M, Olczak M, Borsig L, Siekhaus DE. The Solute Carrier MFSD1 Decreases the Activation Status of β1 Integrin and Thus Tumor Metastasis. Front Oncol 2022; 12:777634. [PMID: 35211397 PMCID: PMC8861502 DOI: 10.3389/fonc.2022.777634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/13/2022] [Indexed: 11/17/2022] Open
Abstract
Solute carriers are increasingly recognized as participating in a plethora of pathologies, including cancer. We describe here the involvement of the orphan solute carrier Major Facilitator Superfamily Domain-containing protein 1 (MFSD1) in the regulation of tumor cell migration. Loss of MFSD1 enabled higher levels of metastasis in experimental and spontaneous metastasis mouse models. We identified an increased migratory potential in MFSD1−/− tumor cells which was mediated by increased focal adhesion turnover, reduced stability of mature inactive β1 integrin, and the resulting increased integrin activation index. We show that MFSD1 promoted recycling to the cell surface of endocytosed inactive β1 integrin and thereby protected β1 integrin from proteolytic degradation; this led to dampening of the integrin activation index. Furthermore, downregulation of MFSD1 expression was observed during the early steps of tumorigenesis, and higher MFSD1 expression levels correlate with a better cancer patient prognosis. In sum, we describe a requirement for endolysosomal MFSD1 in efficient β1 integrin recycling to suppress tumor cell dissemination.
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Affiliation(s)
- Marko Roblek
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Julia Bicher
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Merel van Gogh
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Attila György
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Rita Seeböck
- Institute of Clinical Pathology, University Hospital St. Polten, St. Polten, Austria
| | - Bozena Szulc
- Laboratory of Biochemistry, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Markus Damme
- Institute of Biochemistry, University of Kiel, Kiel, Germany
| | - Mariusz Olczak
- Laboratory of Biochemistry, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Lubor Borsig
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Daria E Siekhaus
- Institute of Science and Technology Austria, Klosterneuburg, Austria
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14
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Katsuta E, Sawant Dessai A, Ebos JML, Yan L, Ouchi T, Takabe K. H2AX mRNA expression reflects DNA repair, cell proliferation, metastasis, and worse survival in breast cancer. Am J Cancer Res 2022; 12:793-804. [PMID: 35261802 PMCID: PMC8900000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023] Open
Abstract
The phosphorylated histone variant, γ-H2AX, is known to play a key role in DNA damage repair. However, the clinical significance of H2AX mRNA expression in breast cancer remains unclear. Utilizing a bioinformatical approach, a total of 3594 breast cancer patients with clinical and transcriptomic data were investigated. Bioinformatical analysis showed that high expression of H2AX is associated with worse disease-free, disease-specific, and overall survival consistently in two independent cohorts. High H2AX expressing tumors were associated with upregulated DNA repair gene sets. Although H2AX was not predictive of chemotherapy response, it was significantly downregulated after effective chemotherapy or radio-chemotherapy. Notably, tumors with high H2AX expression were enriched for DNA replication and MYC targets gene sets, and associated with increased MKI67 expression, suggesting alterations in cell proliferation machinery. H2AX knockdown cells showed decreased cell proliferation as compared to the control cells. Finally, H2AX mRNA expression was higher in the metastatic clones as compared to the parental cells and in the metastatic tumors as compared to the primary tumors in patients, with higher H2AX mRNA expression found in advanced stage cancer patients. In conclusion, high H2AX mRNA expression is associated with increased DNA repair, cell proliferation, metastasis, and worse survival in breast cancer patients.
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Affiliation(s)
- Eriko Katsuta
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, NY, USA
| | - Abhisha Sawant Dessai
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer CenterBuffalo, NY, USA
| | - John ML Ebos
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer CenterBuffalo, NY, USA
| | - Li Yan
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer CenterBuffalo, NY, USA
| | - Toru Ouchi
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer CenterBuffalo, NY, USA
| | - Kazuaki Takabe
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, NY, USA
- Department of Surgery, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, The State University of New YorkBuffalo, NY, USA
- Department of Breast Surgery and Oncology, Tokyo Medical UniversityTokyo, Japan
- Department of Surgery, Yokohama City UniversityYokohama, Japan
- Department of Surgery, Niigata University Graduate School of Medical and Dental SciencesNiigata, Japan
- Department of Breast Surgery, Fukushima Medical UniversityFukushima, Japan
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15
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Asghari Alashti F, Goliaei B, Minuchehr Z. Analyzing large scale gene expression data in colorectal cancer reveals important clues; CLCA1 and SELENBP1 downregulated in CRC not in normal and not in adenoma. Am J Cancer Res 2022; 12:371-380. [PMID: 35141024 PMCID: PMC8822279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/26/2021] [Indexed: 06/14/2023] Open
Abstract
Early detection of colorectal cancer (CRC) increases the chances of survival and reduces the therapeutic problems and costs of treatment. Since molecular biomarkers can help us diagnose colorectal cancer early, we need to identify novel gene for predicting the early stages of tumorigenesis. Here, we integrated five independent CRC gene expression datasets derived from expression profiling by array comparing CRC with normal samples in: GSE21510, GSE4107, GSE25071, GSE15781 dataset, and GSE8671 dataset, including 64 samples from 32 patients comparing 32 colonic normal mucosa with 32 colorectal adenoma. To detect genes that expressed differentially in experimental circumstances of these datasets, we used web tool of GEO2R to compare groups of samples in the GEO data series. Furthermore, we constructed the protein-protein interactions network by STRING database for mostly downregulated genes and the expression of their members in PPI network were studied into five datasets separately. Also, the level of expression of selected biomarker genes in different stages of CRC compared to normal was studied. Our data revealed 17 common downregulated genes (average fold change (FC) in five tests ≥6) in CRC in comparison with normal (Test 1 to Test 4) and in adenoma compared with normal (Test 5). Studying of gene expression of PPI network members of these downregulated genes led to identifying of CLCA1, SELENBP1, CWC25, ACOT11, GUCY2C and ALDH1A1 as suppressor genes and PTGS2, PROCR, MOCS3 and NFS1 as oncogenes which respectively downregulated and upregulated in CRC. Since decreasing of gene expression was seen in CRC comparing with normal and due to no different expression seen for these 10 genes in adenoma, they, especially CLCA1 and SELENBP1, could be considered as biomarkers for early detection of CRC. Before using these signature genes in the clinic; however, further validations are required.
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Affiliation(s)
- Fariborz Asghari Alashti
- Institute of Biochemistry and Biophysics (IBB), University of TehranTehran, Iran
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Department of Laboratory Medicine and Pathobiology, University of TorontoOntario, Canada
| | - Bahram Goliaei
- Institute of Biochemistry and Biophysics (IBB), University of TehranTehran, Iran
| | - Zarrin Minuchehr
- National Institute of Genetic Engineering and Biotechnology (NIGEB)Tehran, Iran
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16
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Fernandes MT, Yassuda V, Bragança J, Link W, Ferreira BI, De Sousa-Coelho AL. Tribbles Gene Expression Profiles in Colorectal Cancer. GASTROINTESTINAL DISORDERS 2021; 3:218-236. [DOI: https:/doi.org/10.3390/gidisord3040021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/01/2023] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer and the second leading cause of death due to cancer in the world. Therefore, the identification of novel druggable targets is urgently needed. Tribbles proteins belong to a pseudokinase family, previously recognized in CRC as oncogenes and potential therapeutic targets. Here, we analyzed the expression of TRIB1, TRIB2, and TRIB3 simultaneously in 33 data sets from CRC based on available GEO profiles. We show that all three Tribbles genes are overrepresented in CRC cell lines and primary tumors, though depending on specific features of the CRC samples. Higher expression of TRIB2 in the tumor microenvironment and TRIB3 overexpression in an early stage of CRC development, unveil a potential and unexplored role for these proteins in the context of CRC. Differential Tribbles expression was also explored in diverse cellular experimental conditions where either genetic or pharmacological approaches were used, providing novel hints for future research. This comprehensive bioinformatic analysis provides new insights into Tribbles gene expression and transcript regulation in CRC.
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17
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Tribbles Gene Expression Profiles in Colorectal Cancer. GASTROINTESTINAL DISORDERS 2021. [DOI: 10.3390/gidisord3040021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer and the second leading cause of death due to cancer in the world. Therefore, the identification of novel druggable targets is urgently needed. Tribbles proteins belong to a pseudokinase family, previously recognized in CRC as oncogenes and potential therapeutic targets. Here, we analyzed the expression of TRIB1, TRIB2, and TRIB3 simultaneously in 33 data sets from CRC based on available GEO profiles. We show that all three Tribbles genes are overrepresented in CRC cell lines and primary tumors, though depending on specific features of the CRC samples. Higher expression of TRIB2 in the tumor microenvironment and TRIB3 overexpression in an early stage of CRC development, unveil a potential and unexplored role for these proteins in the context of CRC. Differential Tribbles expression was also explored in diverse cellular experimental conditions where either genetic or pharmacological approaches were used, providing novel hints for future research. This comprehensive bioinformatic analysis provides new insights into Tribbles gene expression and transcript regulation in CRC.
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18
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Kim S, Joo M, Yeo MK, Cho MJ, Kim JS, Jo EK, Kim JM. Small heterodimer partner as a predictor of neoadjuvant radiochemotherapy response and survival in patients with rectal cancer: A preliminary study. Oncol Lett 2021; 22:708. [PMID: 34457063 PMCID: PMC8358587 DOI: 10.3892/ol.2021.12969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/16/2021] [Indexed: 11/06/2022] Open
Abstract
Small heterodimer partner (SHP) plays an essential role in the regulation of innate immune and inflammatory responses. The aim of the present study was to identify whether SHP levels are associated with cancer immunology and treatment outcomes in rectal cancer. SHP expression was analyzed via gene set enrichment analysis and the OncoLnc database. In addition, immunohistochemistry and reverse transcription-quantitative PCR analyses were performed on the tissues of patients with locally advanced rectal cancer, and the associations of SHP expression with the clinicopathological and hematological features or treatment response to preoperative radiochemotherapy (pRCT) were analyzed retrospectively. Furthermore, the present study investigated whether SHP expression correlated with immune infiltration levels and immune checkpoint molecules in rectal cancer. The results revealed that low SHP mRNA expression was significantly associated with an inflammatory response and poor prognosis. The nuclear expression of SHP was associated with clinical N stage, neutrophil count, lymphocyte count, neutrophil-lymphocyte ratio and complete pathologic response following pRCT. The low nuclear expression of SHP was associated with poor overall and distant metastasis-free survival (DMFS). In multivariate analysis, the low nuclear expression of SHP was identified as a significant independent prognostic factor for DMFS and a marginally significant prognostic factor for overall survival in rectal cancer. Furthermore, patients with low SHP expression exhibited higher neutrophil and CD8+ T cell infiltration levels and higher PD-L1 expression in rectal adenocarcinoma. These results indicate that SHP may act as an anti-inflammatory mediator via the regulation of systemic and local immune responses in rectal cancer. Moreover, SHP might be useful a potential marker or therapeutic target in rectal cancer.
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Affiliation(s)
- Sup Kim
- Department of Radiation Oncology, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea
| | - Mina Joo
- Department of Pathology and Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea
| | - Min-Kyung Yeo
- Department of Pathology and Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea
| | - Moon-June Cho
- Department of Radiation Oncology, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea
| | - Jun-Sang Kim
- Department of Radiation Oncology, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea
| | - Eun-Kyeong Jo
- Department of Microbiology and Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea.,Infection Control Convergence Research Center, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea
| | - Jin-Man Kim
- Department of Pathology and Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea.,Infection Control Convergence Research Center, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea
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19
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Seo I, Lee HW, Byun SJ, Park JY, Min H, Lee SH, Lee JS, Kim S, Bae SU. Neoadjuvant chemoradiation alters biomarkers of anticancer immunotherapy responses in locally advanced rectal cancer. J Immunother Cancer 2021; 9:jitc-2020-001610. [PMID: 33692216 PMCID: PMC7949478 DOI: 10.1136/jitc-2020-001610] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Neoadjuvant chemoradiation therapy (CRT) is a widely used preoperative treatment strategy for locally advanced rectal cancer (LARC). However, a few studies have evaluated the molecular changes caused by neoadjuvant CRT in these cancer tissues. Here, we aimed to investigate changes in immunotherapy-related immunogenic effects in response to preoperative CRT in LARC. METHODS We analyzed 60 pairs of human LARC tissues before and after irradiation from three independent LARC cohorts, including a LARC patient RNA sequencing (RNA-seq) dataset from our cohort and GSE15781 and GSE94104 datasets. RESULTS Gene ontology analysis showed that preoperative CRT significantly enriched the immune response in LARC tissues. Moreover, gene set enrichment analysis revealed six significantly enriched Kyoto Encyclopedia of Genes and Genomes pathways associated with downregulated genes, including mismatch repair (MMR) genes, in LARC tissues after CRT in all three cohorts. Radiation also induced apoptosis and downregulated various MMR system-related genes in three colorectal cancer cells. One patient with LARC showed a change in microsatellite instability (MSI) status after CRT, as demonstrated by the loss of MMR protein and PCR for MSI. Moreover, CRT significantly increased tumor mutational burden in LARC tissues. CIBERSORT analysis revealed that the proportions of M2 macrophages and CD8 T cells were significantly increased after CRT in both the RNA-seq dataset and GSE94104. Notably, preoperative CRT increased various immune biomarker scores, such as the interferon-γ signature, the cytolytic activity and the immune signature. CONCLUSIONS Taken together, our findings demonstrated that neoadjuvant CRT modulated the immune-related characteristics of LARC, suggesting that neoadjuvant CRT may enhance the responsiveness of LARC to immunotherapy.
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Affiliation(s)
- Incheol Seo
- Department of Microbiology, Dongguk University College of Medicine, Gyeongju, Gyeongsangbuk-do, Korea (the Republic of)
| | - Hye Won Lee
- Department of Pathology, Keimyung University Dongsan Medical Center, Daegu, Korea (the Republic of).,Institute for Cancer Research, Keimyung University, Daegu, Korea (the Republic of)
| | - Sang Jun Byun
- Department of Radiation Oncology, Keimyung University School of Medicine, Daegu, Korea (the Republic of)
| | - Jee Young Park
- Department of Pathology, Keimyung University Dongsan Medical Center, Daegu, Korea (the Republic of).,Department of Immunology, Keimyung University School of Medicine, Daegu, Korea (the Republic of)
| | - Hyeonji Min
- Department of Immunology, Keimyung University School of Medicine, Daegu, Korea (the Republic of)
| | - Sung Hwan Lee
- Department of Surgery, CHA University - Bundang Campus, Seongnam, Gyeonggi-do, Korea (the Republic of).,Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ju-Seog Lee
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Shin Kim
- Department of Immunology, Keimyung University School of Medicine, Daegu, Korea (the Republic of) .,Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,Institute of Medical Science & Institute for Cancer Research, Keimyung University, Daegu, Korea (the Republic of)
| | - Sung Uk Bae
- Institute of Medical Science & Institute for Cancer Research, Keimyung University, Daegu, Korea (the Republic of) .,Department of Surgery, Keimyung University Dongsan Medical Center, Daegu, Korea (the Republic of)
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20
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Gao L, Wu X, Zhang L, Dai Y, Zhu Z, Zhi Y, Wang K. REG4 is a Potential Biomarker for Radiochemotherapy Sensitivity in Colorectal Cancer. Onco Targets Ther 2021; 14:1605-1611. [PMID: 33688207 PMCID: PMC7936684 DOI: 10.2147/ott.s296031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 02/03/2021] [Indexed: 12/24/2022] Open
Abstract
Purpose Colorectal cancer (CRC) is one of the most common types of malignancies, and radiochemotherapy (RCT) followed by surgery is the recommended approach for CRC treatment. However, some cases do not respond to first-line conventional chemotherapy or even progress further after treatment. Moreover, there is a risk of severe side effects, such as radiodermatitis. Therefore, identifying predictors for RCT sensitivity is an essential step toward predicting and eventually overcoming resistance. Materials and Methods We used integrative bioinformatics analysis and experimental validation to show that regenerating family member 4 (REG4) may be a potential biomarker for RCT sensitivity in CRC. Results REG4, whose expression is upregulated in some CRC tissues and downregulated in RCT-sensitive CRC cells, was identified as a potential genetic marker for RCT sensitivity in CRC. Immunohistochemistry-based tissue microarray of human CRC was used to experimentally validate REG4 data obtained from the bioinformatics analysis. Conclusion Collectively, these results indicate that REG4 may be a potential biomarker for RCT sensitivity in CRC.
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Affiliation(s)
- Lei Gao
- Department of Thoracic Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, Anhui, 230001, People's Republic of China
| | - Xingjun Wu
- Department of Oncology, Jiangsu Taizhou NO. 2 People Hospital, Jiangsu, People's Republic of China
| | - Libo Zhang
- Department of Hepatological Surgery, General Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, People's Republic of China
| | - Yang Dai
- Department of Transplantation, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Zhe Zhu
- Department of Hepatological Surgery, General Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, People's Republic of China
| | - Yunqing Zhi
- Department of Transplantation, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Department of Gynecology, Shanghai Changning Maternity and Infant Health Hospital, Shanghai, People's Republic of China
| | - Kaijing Wang
- Department of Hepatological Surgery, General Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, People's Republic of China
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21
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Elevation in viral entry genes and innate immunity compromise underlying increased infectivity and severity of COVID-19 in cancer patients. Sci Rep 2021; 11:4533. [PMID: 33633121 PMCID: PMC7907391 DOI: 10.1038/s41598-021-83366-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/03/2020] [Indexed: 12/30/2022] Open
Abstract
Multiple studies have reported a doubling in risk of Coronavirus Disease-2019 (COVID-19) among cancer patients. Here, we examine the potential biological rationale behind this recurrent epidemiological observation. By leveraging large-scale genome-wide transcriptional data of normal and malignant tissues from adults and children, we found evidence of increased expression of SARS-CoV-2 viral entry genes in the cancer state, particularly in respiratory, gastrointestinal, and genitourinary tract tissues, with decreased expression in pediatric vs. adult samples. Additionally, by interrogating the temporal effects of radiotherapy on human peripheral blood mononuclear and mucosal cells, we observed important treatment-related alterations in host innate immunity, specifically type I interferon responses. Overall, cancers enhance expression of critical viral entry genes, and innate viral defenses can be dysregulated transiently during radiation treatments. These factors may contribute to the observed increased susceptibility to SARS-CoV-2 entry and severity of COVID-19 in cancer patients.
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22
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Xu Z, Li Y, Cui Y, Guo Y. Identifications of Candidate Genes Significantly Associated With Rectal Cancer by Integrated Bioinformatics Analysis. Technol Cancer Res Treat 2020; 19:1533033820973270. [PMID: 33327880 PMCID: PMC7750891 DOI: 10.1177/1533033820973270] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
INTRODUCTION Rectal cancer ranks as the eighth in cancer-related morbidity and the tenth in the cancer-related mortality. A few studies have explored several biomarkers for colorectal cancer. However, there is still a great need for us to excavate novel biomarkers with effective and efficient diagnostic and prognostic values to discover the etiology and pathogenesis of rectal cancer separately. Therefore, we aimed to identify more novel candidate genes that were significantly associated with rectal cancer through integrated bioinformatics analysis. METHODS We analyzed the gene expression profiles of GSE15781 and GSE20842 from Gene Expression Omnibus database to identify differentially expressed genes between normal rectal tissue and rectal cancer tissue. RESULTS We searched for core genes, carried out survival analysis and analyzed the expressions of core genes. We found that 142 genes were significantly upregulated, and 229 genes were significantly downregulated in all 3 independent studies. In KEGG analysis, the upregulated genes were significantly enriched in cytokine-cytokine receptor interaction, IL-17 signaling pathway, cell cycle, etc. The downregulated genes were primarily enriched in nitrogen metabolism, mineral absorption and pentose and glucuronate interconversions. Inhibin subunit beta B (INHBB) expressed markedly higher in rectal cancer tissues compared with normal tissues, and claudins (CLDN) 23 expressed significantly lower in rectal cancer tissues. CONCLUSION In conclusion, we discovered that INHBB could provide a great significant diagnostic and prognostic values for rectal cancer.
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Affiliation(s)
- Zhili Xu
- The First Clinical Medical College, Zhejiang Chinese Medical University, Zhejiang, China.,The First Affiliated Hospital of Zhejiang Chinese Medical University, Zhejiang, China
| | - Yan Li
- The First Clinical Medical College, Zhejiang Chinese Medical University, Zhejiang, China.,The First Affiliated Hospital of Zhejiang Chinese Medical University, Zhejiang, China
| | - Yiyi Cui
- The Third Affiliated Hospital of Zhejiang Chinese Medical University, Zhejiang, China
| | - Yong Guo
- The First Clinical Medical College, Zhejiang Chinese Medical University, Zhejiang, China.,The First Affiliated Hospital of Zhejiang Chinese Medical University, Zhejiang, China
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23
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Hou X, Hou N, Fu J, He X, Xiong H, Xie W, Jia G, Zuo X, Qin X, Pang M. Identification of Key mRNAs and Pathways in Colorectal Cancer. Nutr Cancer 2020; 73:1040-1046. [PMID: 32586129 DOI: 10.1080/01635581.2020.1783328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Colorectal cancer (CRC) is the third most cancer-related death worldwide. This work aimed to identify potential hub genes and dysregulated pathways in the CRC by bioinformatics analysis. Three gene expression datasets were collected from GEO datasets, including tumor sample (N = 242) and adjacent nontumor tissue sample (N = 59). RankProd was used to discover the differential expressed genes between tumor and adjacent nontumor tissues for datasets generated by different laboratories. The gene set enrichment analysis conducted on the DE genes, followed by the protein-protein interaction (PPI) network. In total, 2,007 significant differential expression (DE) genes between tumor and adjacent nontumor tissues, include 1,090 upregulated genes and 917 downregulated genes in the tumor. The DE mRNAs are involved in cancer-related pathways. We comprehensively identified the CRC-related key mRNAs. Our data demonstrated combined different resources of transcriptomes will promote the understanding of the molecular mechanisms underlying CRC development and may be useful in discovering candidate molecular biomarkers for diagnosing, prognosis, and treating of CRC.
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Affiliation(s)
- Xiaolin Hou
- Department of Internal Medicine; Hospital of University of Electronic Science and Technology of China & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Nengyi Hou
- Department of Gastrointestinal Surgery; Hospital of University of Electronic Science and Technology of China & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Junwen Fu
- Department of Gastrointestinal Surgery; Hospital of University of Electronic Science and Technology of China & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Xuelai He
- Department of Gastrointestinal Surgery; Hospital of University of Electronic Science and Technology of China & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Haibo Xiong
- Department of Gastrointestinal Surgery; Hospital of University of Electronic Science and Technology of China & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Wei Xie
- Department of Gastrointestinal Surgery; Hospital of University of Electronic Science and Technology of China & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Guiqing Jia
- Department of Gastrointestinal Surgery; Hospital of University of Electronic Science and Technology of China & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Xiaofei Zuo
- Department of Gastrointestinal Surgery; Hospital of University of Electronic Science and Technology of China & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Xianpeng Qin
- Department of Gastrointestinal Surgery; Hospital of University of Electronic Science and Technology of China & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Minghui Pang
- Department of Gastrointestinal Surgery; Hospital of University of Electronic Science and Technology of China & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
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24
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Identification and Verification of Core Genes in Colorectal Cancer. BIOMED RESEARCH INTERNATIONAL 2020; 2020:8082697. [PMID: 32462020 PMCID: PMC7232680 DOI: 10.1155/2020/8082697] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 03/25/2020] [Accepted: 04/18/2020] [Indexed: 02/06/2023]
Abstract
Colorectal cancer, a malignant neoplasm that occurs in the colorectal mucosa, is one of the most common types of gastrointestinal cancer. Colorectal cancer has been studied extensively, but the molecular mechanisms of this malignancy have not been characterized. This study identified and verified core genes associated with colorectal cancer using integrated bioinformatics analysis. Three gene expression profiles (GSE15781, GSE110223, and GSE110224) were downloaded from the Gene Expression Omnibus (GEO) databases. A total of 87 common differentially expressed genes (DEGs) among GSE15781, GSE110223, and GSE110224 were identified, including 19 upregulated genes and 68 downregulated genes. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis was performed for common DEGs using clusterProfiler. These common DEGs were significantly involved in cancer-associated functions and signaling pathways. Then, we constructed protein-protein interaction networks of these common DEGs using Cytoscape software, which resulted in the identification of the following 10 core genes: SST, PYY, CXCL1, CXCL8, CXCL3, ZG16, AQP8, CLCA4, MS4A12, and GUCA2A. Analysis using qRT-PCR has shown that SST, CXCL8, and MS4A12 were significant differentially expressed between colorectal cancer tissues and normal colorectal tissues (P < 0.05). Gene Expression Profiling Interactive Analysis (GEPIA) overall survival (OS) has shown that low expressions of AQP8, ZG16, CXCL3, and CXCL8 may predict poor survival outcome in colorectal cancer. In conclusion, the core genes identified in this study contributed to the understanding of the molecular mechanisms involved in colorectal cancer development and may be targets for early diagnosis, prevention, and treatment of colorectal cancer.
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25
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Zhu S, He M, Liu Z, Qin Z, Wang Z, Duan L. Shared genetic susceptibilities for irritable bowel syndrome and depressive disorder in Chinese patients uncovered by pooled whole-exome sequencing. J Adv Res 2020; 23:113-121. [PMID: 32099673 PMCID: PMC7029050 DOI: 10.1016/j.jare.2020.01.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 12/25/2019] [Accepted: 01/28/2020] [Indexed: 02/07/2023] Open
Abstract
Irritable bowel syndrome (IBS) is the most prevalent functional gastrointestinal disorder presenting a high comorbidity with depressive disorder (DD). Many studies have confirmed that these two disease share the similar pathophysiological process, but evidence of the genetic risks is limited. This study aimed to analyze the genetic susceptibilities for IBS and DD in Chinese patients. Pooled whole-exome sequencing (pooled-WES) was performed to identify the candidate variants in the group of diarrhea predominant IBS (IBS-D) patients, DD patients, and healthy controls (HC). Then, targeted sequencing was used to validate the candidate variants in three additional cohorts of IBS-D, DD, and HC. Four variants associated with both IBS-D and DD were identified through pooled-WES, and three of them were validated in targeted sequencing. SYT8 rs3741231 G allele and SSPO rs12536873 TT genotype were associated with both IBS-D and DD. The genes of these variants are important in neurogenesis and neurotransmission. In addition, we found COL6A1 rs13051496, a unique risk variation for IBS-D. It increased the IBS-D risk and had a positive correlation with the scores of abdominal bloating and dissatisfaction of bowel habits. Through the results of this study, it provides a genetic basis for the high comorbidity of IBS-D and DD.
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Affiliation(s)
- Shiwei Zhu
- Department of Gastroenterology, Peking University Third Hospital, No. 49 North Garden Rd., Haidian District, Beijing 100191, China
| | - Meibo He
- Department of Gastroenterology, Peking University Third Hospital, No. 49 North Garden Rd., Haidian District, Beijing 100191, China
| | - Zuojing Liu
- Department of Gastroenterology, Peking University Third Hospital, No. 49 North Garden Rd., Haidian District, Beijing 100191, China
| | - Zelian Qin
- Department of Plastic Surgery, Peking University Third Hospital, No.49 North Garden Rd., Haidian District, Beijing 100191, China
| | - Zhiren Wang
- Department of Science & Technology, Peking University HuiLongGuan Clinical Medical School, Beijing HuiLongGuan Hospital, Huilongguan Town, Changping District, Beijing 100096, China
| | - Liping Duan
- Department of Gastroenterology, Peking University Third Hospital, No. 49 North Garden Rd., Haidian District, Beijing 100191, China
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26
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Liu X, Liu X, Qiao T, Chen W. Identification of crucial genes and pathways associated with colorectal cancer by bioinformatics analysis. Oncol Lett 2020; 19:1881-1889. [PMID: 32194683 PMCID: PMC7039150 DOI: 10.3892/ol.2020.11278] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 10/22/2019] [Indexed: 12/18/2022] Open
Abstract
Colorectal cancer (CRC) is a prevalent malignant tumour type arising from the colon and rectum. The present study aimed to explore the molecular mechanisms of the development and progression of CRC. Initially, differentially expressed genes (DEGs) between CRC tissues and corresponding non-cancerous tissues were obtained by analysing the GSE15781 microarray dataset. The Database for Annotation, Visualization and Integrated Discovery was then utilized for functional and pathway enrichment analysis of the DEGs. Subsequently, a protein-protein interaction (PPI) network was created using the Search Tool for the Retrieval of Interacting Genes and Proteins database and visualized by Cytoscape software. Furthermore, CytoNCA, a Cytoscape plugin, was used for centrality analysis of the PPI network to identify crucial genes. Finally, UALCAN was employed to validate the expression of the crucial genes and to estimate their effect on the survival of patients with colon cancer by Kaplan-Meier curves and log-rank tests. A total of 1,085 DEGs, including 496 upregulated and 589 downregulated genes, were screened out. The DEGs identified were enriched in various pathways, including ‘metabolic pathway’, ‘cell cycle’, ‘DNA replication’, ‘nitrogen metabolism’, ‘p53 signalling’ and ‘fatty acid degradation’. PPI network analysis suggested that interleukin-6, MYC, NOTCH1, inhibin subunit βA (INHBA), CDK1, cyclin (CCN)B1 and CCNA2 were crucial genes, and their expression levels were markedly upregulated. Survival analysis suggested that upregulated INHBA significantly decreased the survival probability of patients with CRC. Conversely, upregulation of CCNB1 and CCNA2 expression levels were associated with increased survival probabalities. The identified DEGs, particularly the crucial genes, may enhance the current understanding of the genesis and progression of CRC, and certain genes, including INHBA, CCNB1 and CCNA2, may be candidate diagnostic and prognostic markers, as well as targets for the treatment of CRC.
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Affiliation(s)
- Xiaoqun Liu
- Center for Tumor Diagnosis and Therapy, Jinshan Hospital, Fudan University, Shanghai 201508, P.R. China
| | - Xiangdong Liu
- Department of Ophthalmology, Jinshan Hospital, Fudan University, Shanghai 201508, P.R. China
| | - Tiankui Qiao
- Center for Tumor Diagnosis and Therapy, Jinshan Hospital, Fudan University, Shanghai 201508, P.R. China
| | - Wei Chen
- Center for Tumor Diagnosis and Therapy, Jinshan Hospital, Fudan University, Shanghai 201508, P.R. China
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27
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Jeon HY, Ham SW, Kim JK, Jin X, Lee SY, Shin YJ, Choi CY, Sa JK, Kim SH, Chun T, Jin X, Nam DH, Kim H. Ly6G + inflammatory cells enable the conversion of cancer cells to cancer stem cells in an irradiated glioblastoma model. Cell Death Differ 2019; 26:2139-2156. [PMID: 30804471 PMCID: PMC6748155 DOI: 10.1038/s41418-019-0282-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 01/07/2019] [Accepted: 01/09/2019] [Indexed: 02/08/2023] Open
Abstract
Most glioblastomas frequently recur at sites of radiotherapy, but it is unclear if changes in the tumor microenvironment due to radiotherapy influence glioblastoma recurrence. Here, we demonstrate that radiation-induced senescent glioblastoma cells exhibit a senescence-associated secretory phenotype that functions through NFκB signaling to influence changes in the tumor microenvironment, such as recruitment of Ly6G+ inflammatory cells and vessel formation. In particular, Ly6G+ cells promote conversion of glioblastoma cells to glioblastoma stem cells (GSCs) through the NOS2-NO-ID4 regulatory axis. Specific inhibition of NFκB signaling in irradiated glioma cells using the IκBα super repressor prevents changes in the tumor microenvironment and dedifferentiation of glioblastoma cells. Treatment with Ly6G-neutralizing antibodies also reduces the number of GSCs and prolongs survival in tumor-bearing mice after radiotherapy. Clinically, a positive correlation exists between Ly6G+ cells and the NOS2-NO-ID4 regulatory axis in patients diagnosed with recurrent glioblastoma. Together, our results illustrate important roles for Ly6G+ inflammatory cells recruited by radiation-induced SASP in cancer cell dedifferentiation and tumor recurrence.
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Affiliation(s)
- Hee-Young Jeon
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea.,Institute of Animal Molecular Biotechnology, Korea University, Seoul, Republic of Korea
| | - Seok Won Ham
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea.,Institute of Animal Molecular Biotechnology, Korea University, Seoul, Republic of Korea
| | - Jun-Kyum Kim
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea.,Institute of Animal Molecular Biotechnology, Korea University, Seoul, Republic of Korea
| | - Xiong Jin
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea.,Institute of Animal Molecular Biotechnology, Korea University, Seoul, Republic of Korea
| | - Seon Yong Lee
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Yong Jae Shin
- Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.,Institute for Refractory Cancer Research, Research Institute for Future Medicine, Samsung Medical Center, Seoul, Republic of Korea
| | - Chang-Yong Choi
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea.,Institute of Animal Molecular Biotechnology, Korea University, Seoul, Republic of Korea
| | - Jason K Sa
- Institute for Refractory Cancer Research, Research Institute for Future Medicine, Samsung Medical Center, Seoul, Republic of Korea
| | - Se Hoon Kim
- Department of Pathology, College of Medicine, Yonsei University, Seoul, Republic of Korea
| | - Taehoon Chun
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea.,Institute of Animal Molecular Biotechnology, Korea University, Seoul, Republic of Korea
| | - Xun Jin
- Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,Institute of Translational Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Do-Hyun Nam
- Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.,Institute for Refractory Cancer Research, Research Institute for Future Medicine, Samsung Medical Center, Seoul, Republic of Korea.,Department of Health Science & Technology, Samsung Advanced Institute for Health Science & Technology, Sungkyunkwan University, Seoul, Republic of Korea
| | - Hyunggee Kim
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea. .,Institute of Animal Molecular Biotechnology, Korea University, Seoul, Republic of Korea. .,Department of Medical Engineering, College of Medicine, Korea University, Seoul, Republic of Korea.
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28
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Han B, Feng D, Yu X, Liu Y, Yang M, Luo F, Zhou L, Liu F. MicroRNA-144 mediates chronic inflammation and tumorigenesis in colorectal cancer progression via regulating C-X-C motif chemokine ligand 11. Exp Ther Med 2018; 16:1935-1943. [PMID: 30186421 PMCID: PMC6122338 DOI: 10.3892/etm.2018.6389] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 06/01/2018] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common malignancies worldwide. The aim of the present study was to investigate the expression of microRNA-144 (miR-144) and C-X-C motif chemokine ligand 11 (CXCL11) in CRC and their association. Data from Gene Expression Omnibus (GEO) DataSets were analyzed to obtain the expression profile of CXCL11 in CRC. Subsequently, serum samples were collected from 65 subjects, including 39 patients with CRC and 26 controls; CRC and adjacent normal tissues were collected from all 39 CRC patients and the expression of CXCL11 was measured in these specimens. After searching for the potential regulator of CXCL11 through bioinformatics analysis, the levels of miR-144 in the clinical specimens were also detected. Finally, the regulatory association between miR-144 and CXCL11 was certified via the dual-luciferase reporter assay. Microarray data and bioinformatics analysis demonstrated that CXCL11 was significantly upregulated in CRC tissues and miR-144 was a potential regulator of CXCL11. In line with this finding, the expression of CXCL11 was significantly increased in the serum and tumor samples of patients with CRC, while that of miR-144 was downregulated. Dual-luciferase reporter assay revealed that miR-144 directly targets the 3′-untranslated region of CXCL11 mRNA to regulate its expression. These results demonstrated that enhanced CXCL11 expression in patients with CRC was associated with reduced miR-144 expression. The results of the present study may indicate a novel regulatory role of miR-144 in CRC through CXCL11 downregulation.
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Affiliation(s)
- Bin Han
- Department of Pharmacy, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China.,Department of Pharmacology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Dan Feng
- Department of Pharmacy, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China
| | - Xin Yu
- Health Service Center of Southeast Community, Nanchong, Sichuan 637000, P.R. China
| | - Yuanqi Liu
- Department of Pharmacology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Ming Yang
- Department of Pharmacy, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China
| | - Fei Luo
- Department of Pharmacy, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China
| | - Liming Zhou
- Department of Pharmacology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Fu Liu
- Department of Pharmacy, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China
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29
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Over-activation of AKT signaling leading to 5-Fluorouracil resistance in SNU-C5/5-FU cells. Oncotarget 2018; 9:19911-19928. [PMID: 29731993 PMCID: PMC5929436 DOI: 10.18632/oncotarget.24952] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 03/13/2018] [Indexed: 12/13/2022] Open
Abstract
Here, we investigated whether over-activation of AKT pathway is important in the resistance to 5-fluorouracil (5-FU) in SNU-C5/5-FU cells, 5-FU-resistant human colon cancer cells. When compared to wild type SNU-C5 cells (WT), SNU-C5/5-FU cells showed over-activation of PI3K/AKT pathway, like increased phosphorylation of AKT, mTOR, and GSK-3β, nuclear localization of β-catenin, and decreased E-cadherin. Moreover, E-cadherin level was down-regulated in recurrent colon cancer tissues compared to primary colon cancer tissues. Gene silencing of AKT1 or treatment of LY294002 (PI3 kinase inhibitor) increased E-cadherin, whereas decreased phospho-GSK-3β. LY294002 also reduced protein level of β-catenin with no influence on mRNA level. PTEN level was higher in SNU-C5/WT than SNU-C5/5-FU cells, whereas the loss of PETN in SNU-C5/WT cells induced characteristics of SNU-C5/5-FU cells. In SNU-C5/5-FU cells, NF-κB signaling was activated, along with the overexpression of COX-2 and stabilization of survivin. However, increased COX-2 contributed to the stabilization of survivin, which directly interacts with cytoplasmic procaspase-3, while the inhibition of AKT reduced this cascade. We finally confirmed that combination treatment with 5-FU and LY294002 or Vioxx could induce apoptosis in SNU-C5/5-FU cells. These data suggest that inhibition of AKT activation may overcome 5-FU-resistance in SNU-C5/5-FU cells. These findings provide evidence that over-activation of AKT is crucial for the acquisition of resistance to anticancer drugs and AKT pathway could be a therapeutic target for cancer treatment.
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30
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Aghdam R, Baghfalaki T, Khosravi P, Saberi Ansari E. The Ability of Different Imputation Methods to Preserve the Significant Genes and Pathways in Cancer. GENOMICS, PROTEOMICS & BIOINFORMATICS 2017; 15:396-404. [PMID: 29247873 PMCID: PMC5828654 DOI: 10.1016/j.gpb.2017.08.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Revised: 07/18/2017] [Accepted: 08/08/2017] [Indexed: 11/23/2022]
Abstract
Deciphering important genes and pathways from incomplete gene expression data could facilitate a better understanding of cancer. Different imputation methods can be applied to estimate the missing values. In our study, we evaluated various imputation methods for their performance in preserving significant genes and pathways. In the first step, 5% genes are considered in random for two types of ignorable and non-ignorable missingness mechanisms with various missing rates. Next, 10 well-known imputation methods were applied to the complete datasets. The significance analysis of microarrays (SAM) method was applied to detect the significant genes in rectal and lung cancers to showcase the utility of imputation approaches in preserving significant genes. To determine the impact of different imputation methods on the identification of important genes, the chi-squared test was used to compare the proportions of overlaps between significant genes detected from original data and those detected from the imputed datasets. Additionally, the significant genes are tested for their enrichment in important pathways, using the ConsensusPathDB. Our results showed that almost all the significant genes and pathways of the original dataset can be detected in all imputed datasets, indicating that there is no significant difference in the performance of various imputation methods tested. The source code and selected datasets are available on http://profiles.bs.ipm.ir/softwares/imputation_methods/.
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Affiliation(s)
- Rosa Aghdam
- School of Biological Science, Institute for Research in Fundamental Sciences (IPM), Tehran 19395-5746, Iran.
| | - Taban Baghfalaki
- Department of Statistics, Faculty of Mathematical Sciences, Tarbiat Modares University, Tehran 14115-111, Iran
| | - Pegah Khosravi
- School of Biological Science, Institute for Research in Fundamental Sciences (IPM), Tehran 19395-5746, Iran; Department of Physiology and Biophysics, Institute for Computational Biomedicine and Institute for Precision Medicine, Weill Cornell Medical College, New York, NY 10021, USA
| | - Elnaz Saberi Ansari
- School of Biological Science, Institute for Research in Fundamental Sciences (IPM), Tehran 19395-5746, Iran; Institut Cochin, Inserm U1016, CNRS UMR 8104, Universit Paris Descartes UMR-S1016, F-75014 Paris, France.
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31
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E-Cadherin–Mediated Cell Contact Controls the Epidermal Damage Response in Radiation Dermatitis. J Invest Dermatol 2017; 137:1731-1739. [DOI: 10.1016/j.jid.2017.03.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 03/23/2017] [Accepted: 03/30/2017] [Indexed: 11/23/2022]
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32
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Gomez-Millan J, Queipo MI, del Mar Delgado M, Perez-Villa L, Roman A, De la Portilla F, Torres E, De Luque V, Bayo E, Medina JA. The impact of body mass index and nuclear β-catenin on survival in locally advanced rectal cancer treated with preoperative radiochemotherapy. J Surg Oncol 2017; 115:301-306. [DOI: 10.1002/jso.24494] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 10/23/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Jaime Gomez-Millan
- Department of Radiation Oncology; University Hospital Virgen de la Victoria; Málaga Spain
| | - Maria Isabel Queipo
- Department of Endocrinology; Biomedical Research Institute (IBIMA); Málaga Spain
| | - Maria del Mar Delgado
- Department of Radiation Oncology; University Hospital Juan Ramón Jiménez; Huelva Spain
| | - Lidia Perez-Villa
- Department of Pathology; University Hospital Virgen de la Victoria; Málaga Spain
| | - Alicia Roman
- Department of Radiation Oncology; University Hospital Virgen de la Victoria; Málaga Spain
| | - Fernando De la Portilla
- Department of Surgery; Colorectal Surgery; University Hospital Virgen del Rocío; Seville Spain
| | - Esperanza Torres
- Department of Medical Oncology; University Hospital Virgen de la Victoria; Málaga Spain
| | - Vanessa De Luque
- Department of Medical Oncology; University Hospital Virgen de la Victoria; Málaga Spain
| | - Eloisa Bayo
- Department of Radiation Oncology; University Hospital Juan Ramón Jiménez; Huelva Spain
| | - Jose Antonio Medina
- Department of Radiation Oncology; University Hospital Virgen de la Victoria; Málaga Spain
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33
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Lee M, Chen GT, Puttock E, Wang K, Edwards RA, Waterman ML, Lowengrub J. Mathematical modeling links Wnt signaling to emergent patterns of metabolism in colon cancer. Mol Syst Biol 2017; 13:912. [PMID: 28183841 PMCID: PMC5327728 DOI: 10.15252/msb.20167386] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 01/05/2017] [Accepted: 01/12/2017] [Indexed: 12/14/2022] Open
Abstract
Cell-intrinsic metabolic reprogramming is a hallmark of cancer that provides anabolic support to cell proliferation. How reprogramming influences tumor heterogeneity or drug sensitivities is not well understood. Here, we report a self-organizing spatial pattern of glycolysis in xenograft colon tumors where pyruvate dehydrogenase kinase (PDK1), a negative regulator of oxidative phosphorylation, is highly active in clusters of cells arranged in a spotted array. To understand this pattern, we developed a reaction-diffusion model that incorporates Wnt signaling, a pathway known to upregulate PDK1 and Warburg metabolism. Partial interference with Wnt alters the size and intensity of the spotted pattern in tumors and in the model. The model predicts that Wnt inhibition should trigger an increase in proteins that enhance the range of Wnt ligand diffusion. Not only was this prediction validated in xenograft tumors but similar patterns also emerge in radiochemotherapy-treated colorectal cancer. The model also predicts that inhibitors that target glycolysis or Wnt signaling in combination should synergize and be more effective than each treatment individually. We validated this prediction in 3D colon tumor spheroids.
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Affiliation(s)
- Mary Lee
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA
| | - George T Chen
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA, USA
| | - Eric Puttock
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA
| | - Kehui Wang
- Department of Pathology, School of Medicine, University of California, Irvine, Irvine, CA, USA
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, USA
| | - Robert A Edwards
- Department of Pathology, School of Medicine, University of California, Irvine, Irvine, CA, USA
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, USA
| | - Marian L Waterman
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA, USA
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA
| | - John Lowengrub
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, USA
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Discriminating cancer-related and cancer-unrelated chemoradiation-response genes for locally advanced rectal cancers. Sci Rep 2016; 6:36935. [PMID: 27845363 PMCID: PMC5109405 DOI: 10.1038/srep36935] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 10/24/2016] [Indexed: 02/07/2023] Open
Abstract
For patients with locally advanced rectal cancer (LARC) treated with preoperation chemoradiation (pCRT), identifying differentially expressed (DE) genes between non-responders and responders is a common approach for investigating mechanisms of chemoradiation resistance. However, some of such DE genes might be irrelevant to cancer itself but simply reflect the pharmacokinetic differences of the normal tissues. In this study, we adopted the RankComp algorithm to identify DE genes for each of LARC sample compared with its own normal state. Then, we identified genes with significantly different deregulation frequencies between the non-responders and responders, defined as cancer-related pCRT-response genes. Pathway enrichment and protein-protein interaction analyses showed that these genes specifically and intensively interacted with currently known effective genes of pCRT, involving in DNA replication, cell cycle and DNA repair. In contrast, after excluding the cancer-related pCRT-response genes, the other DE genes between non-responders and responders were enriched in many pathways of drug and protein metabolisms and transports, and interacted with both the known effective genes and pharmacokinetic genes. Hence, these two types of DE genes should be distinguished for investigating mechanisms of pCRT response in LARCs.
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Eke I, Makinde AY, Aryankalayil MJ, Ahmed MM, Coleman CN. Comprehensive molecular tumor profiling in radiation oncology: How it could be used for precision medicine. Cancer Lett 2016; 382:118-126. [PMID: 26828133 DOI: 10.1016/j.canlet.2016.01.041] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 01/21/2016] [Accepted: 01/26/2016] [Indexed: 12/16/2022]
Abstract
New technologies enabling the analysis of various molecules, including DNA, RNA, proteins and small metabolites, can aid in understanding the complex molecular processes in cancer cells. In particular, for the use of novel targeted therapeutics, elucidation of the mechanisms leading to cell death or survival is crucial to eliminate tumor resistance and optimize therapeutic efficacy. While some techniques, such as genomic analysis for identifying specific gene mutations or epigenetic testing of promoter methylation, are already in clinical use, other "omics-based" assays are still evolving. Here, we provide an overview of the current status of molecular profiling methods, including promising research strategies, as well as possible challenges, and their emerging role in radiation oncology.
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Affiliation(s)
- Iris Eke
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Adeola Y Makinde
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Molykutty J Aryankalayil
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mansoor M Ahmed
- Radiation Research Program, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA
| | - C Norman Coleman
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Radiation Research Program, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA
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Palma P, Cano C, Conde-Muiño R, Comino A, Bueno P, Ferrón JA, Cuadros M. Expression profiling of rectal tumors defines response to neoadjuvant treatment related genes. PLoS One 2014; 9:e112189. [PMID: 25380052 PMCID: PMC4224421 DOI: 10.1371/journal.pone.0112189] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 10/13/2014] [Indexed: 01/23/2023] Open
Abstract
To date, no effective method exists that predicts the response to preoperative chemoradiation (CRT) in locally advanced rectal cancer (LARC). Nevertheless, identification of patients who have a higher likelihood of responding to preoperative CRT could be crucial in decreasing treatment morbidity and avoiding expensive and time-consuming treatments. The aim of this study was to identify signatures or molecular markers related to response to pre-operative CRT in LARC. We analyzed the gene expression profiles of 26 pre-treatment biopsies of LARC (10 responders and 16 non-responders) without metastasis using Human WG CodeLink microarray platform. Two hundred and fifty seven genes were differentially over-expressed in the responder patient subgroup. Ingenuity Pathway Analysis revealed a significant ratio of differentially expressed genes related to cancer, cellular growth and proliferation pathways, and c-Myc network. We demonstrated that high Gng4, c-Myc, Pola1, and Rrm1 mRNA expression levels was a significant prognostic factor for response to treatment in LARC patients (p<0.05). Using this gene set, we were able to establish a new model for predicting the response to CRT in rectal cancer with a sensitivity of 60% and 100% specificity. Our results reflect the value of gene expression profiling to gain insight about the molecular pathways involved in the response to treatment of LARC patients. These findings could be clinically relevant and support the use of mRNA levels when aiming to identify patients who respond to CRT therapy.
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Affiliation(s)
- Pablo Palma
- Division of Colon & Rectal Surgery, Virgen de las Nieves Hospital (HUVN), Granada, Spain
| | - Carlos Cano
- Department of Computer Science and Artificial Intelligence, University of Granada, Granada, Spain
| | - Raquel Conde-Muiño
- Division of Colon & Rectal Surgery, Virgen de las Nieves Hospital (HUVN), Granada, Spain
| | - Ana Comino
- Department of Surgical Research, Virgen de las Nieves Hospital (HUVN), Granada, Spain
| | - Pablo Bueno
- Department of Surgical Research, Virgen de las Nieves Hospital (HUVN), Granada, Spain
| | - J. Antonio Ferrón
- Division of Colon & Rectal Surgery, Virgen de las Nieves Hospital (HUVN), Granada, Spain
- Department of Surgical Research, Virgen de las Nieves Hospital (HUVN), Granada, Spain
| | - Marta Cuadros
- Department of Biochemistry and Molecular Biology III e Immunology, University of Granada, Granada, Spain
- GENYO, Centre for Genomics and Oncological Research: Pfizer/University of de Granada/Junta de Andalucía, Granada, Spain
- * E-mail:
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Akiyoshi T, Kobunai T, Watanabe T. Predicting the response to preoperative radiation or chemoradiation by a microarray analysis of the gene expression profiles in rectal cancer. Surg Today 2012; 42:713-9. [PMID: 22706722 DOI: 10.1007/s00595-012-0223-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Accepted: 10/19/2011] [Indexed: 12/25/2022]
Abstract
Preoperative radiotherapy or chemoradiotherapy (CRT) has become a standard treatment for patients with locally advanced rectal cancer. However, there is a wide spectrum of responses to preoperative CRT, ranging from none to complete. There has been intense interest in the identification of molecular biomarkers to predict the response to preoperative CRT, in order to spare potentially non-responsive patients from unnecessary treatment. However, no specific molecular biomarkers have yet been definitively proven to be predictive of the response to CRT. Instead of focusing on specific factors, microarray-based gene expression profiling technology enables the simultaneous analysis of large numbers of genes, and might therefore have immense potential for predicting the response to preoperative CRT. We herein review published studies using a microarray-based analysis to identify gene expression profiles associated with the response of rectal cancer to radiation or CRT. Although some studies have reported gene expression signatures capable of high predictive accuracy, the compositions of these signatures have differed considerably, with little gene overlap. However, considering the promising data regarding gene profiling in breast cancer, the microarray analysis could still have potential to improve the management of locally advanced rectal cancer. Increasing the number of patients analyzed for more accurate prediction and the extensive validation of predictive classifiers in prospective clinical trials are necessary before such profiling can be incorporated into future clinical practice.
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Affiliation(s)
- Takashi Akiyoshi
- Gastroenterological Center, Department of Gastroenterological Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
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Abstract
The topoisomerase I (Top 1) poison irinotecan is an important component of the modern treatment of colorectal cancer. By stabilising Top 1-DNA complexes, irinotecan generates Top 1-linked DNA single-strand breaks that can evolve into double-strand breaks and ultimately cause cell death. However, cancer cells may overcome cell killing by releasing the stalled topoisomerase from DNA termini, thereby reducing the efficacy of Top 1 poisons in clinics. Thus, understanding the DNA repair mechanisms involved in the repair of Top 1-mediated DNA damage provides a useful tool to identify potential biomarkers that predict response to this class of chemotherapy. Furthermore, targeting these pathways could enhance the therapeutic benefits of Top 1 poisons. In this review, we describe the cellular mechanisms and consequences of targeting Top 1 activity in cells. We summarise preclinical data and discuss the potential clinical utility of small-molecule inhibitors of the key proteins.
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Lafferty-Whyte K, Bilsland A, Cairney CJ, Hanley L, Jamieson NB, Zaffaroni N, Oien KA, Burns S, Roffey J, Boyd SM, Keith WN. Scoring of senescence signalling in multiple human tumour gene expression datasets, identification of a correlation between senescence score and drug toxicity in the NCI60 panel and a pro-inflammatory signature correlating with survival advantage in peritoneal mesothelioma. BMC Genomics 2010; 11:532. [PMID: 20920304 PMCID: PMC3091681 DOI: 10.1186/1471-2164-11-532] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Accepted: 10/01/2010] [Indexed: 11/10/2022] Open
Abstract
Background Cellular senescence is a major barrier to tumour progression, though its role in pathogenesis of cancer and other diseases is poorly understood in vivo. Improved understanding of the degree to which latent senescence signalling persists in tumours might identify intervention strategies to provoke "accelerated senescence" responses as a therapeutic outcome. Senescence involves convergence of multiple pathways and requires ongoing dynamic signalling throughout its establishment and maintenance. Recent discovery of several new markers allows for an expression profiling approach to study specific senescence phenotypes in relevant tissue samples. We adopted a "senescence scoring" methodology based on expression profiles of multiple senescence markers to examine the degree to which signals of damage-associated or secretory senescence persist in various human tumours. Results We first show that scoring captures differential induction of damage or inflammatory pathways in a series of public datasets involving radiotherapy of colon adenocarcinoma, chemotherapy of breast cancer cells, replicative senescence of mesenchymal stem cells, and progression of melanoma. We extended these results to investigate correlations between senescence score and growth inhibition in response to ~1500 compounds in the NCI60 panel. Scoring of our own mesenchymal tumour dataset highlighted differential expression of secretory signalling pathways between distinct subgroups of MPNST, liposarcomas and peritoneal mesothelioma. Furthermore, a pro-inflammatory signature yielded by hierarchical clustering of secretory markers showed prognostic significance in mesothelioma. Conclusions We find that "senescence scoring" accurately reports senescence signalling in a variety of situations where senescence would be expected to occur and highlights differential expression of damage associated and secretory senescence pathways in a context-dependent manner.
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Affiliation(s)
- Kyle Lafferty-Whyte
- Centre for Oncology and Applied Pharmacology, University of Glasgow, Cancer Research UK Beatson Laboratories, Garscube Estate, Switchback Road, Bearsden, Glasgow G611BD, UK
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Snipstad K, Fenton CG, Kjaeve J, Cui G, Anderssen E, Paulssen RH. New specific molecular targets for radio-chemotherapy of rectal cancer. Mol Oncol 2009; 4:52-64. [PMID: 19969511 DOI: 10.1016/j.molonc.2009.11.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2009] [Revised: 11/10/2009] [Accepted: 11/13/2009] [Indexed: 01/03/2023] Open
Abstract
Patients with locally advanced rectal cancer often receive preoperative radio-chemotherapy (RCT). The mechanisms of tumour response to radiotherapy are not understood. The aim of this study was to identify the effects of RCT on gene expression in rectal tumour and normal rectal tissue. For that purpose tissue samples from 21 patients with resectable adenocarcinomas were collected for use in whole genome-microarray based gene expression analysis. A factorial experimental design allowed us to determine the effect of RCT on tumour tissue alone by removing the effect of radiation on normal tissue. This resulted in 1327 differentially expressed genes in tumour tissue with p<0.05. In addition to known markers for radio-chemotherapy, a Gene Set Enrichment Analysis (GSEA) showed a significant enrichment in gene sets associated with cell adhesion and leukocyte transendothelial migration. The profound change of cell adhesion molecule expression in rectal tumour tissue could either increase the risk of metastasis, or decrease the tumour's invasive potential.
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Affiliation(s)
- Kristin Snipstad
- Laboratory of Molecular Medical Research, Institute of Clinical Medicine, University of Tromsø, N-9037 Tromsø, Norway
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