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Yu M, Huo D, Yu K, Zhou K, Xu F, Meng Q, Cai Y, Chen X. Crosstalk of different cell-death patterns predicts prognosis and drug sensitivity in glioma. Comput Biol Med 2024; 175:108532. [PMID: 38703547 DOI: 10.1016/j.compbiomed.2024.108532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/17/2024] [Accepted: 04/28/2024] [Indexed: 05/06/2024]
Abstract
BACKGROUND Glioma is a malignant brain tumor originating from glial cells, and there still a challenge to accurately predict the prognosis. Programmed cell death (PCD) plays a key role in tumorigenesis and immune response. However, the crosstalk and potential role of various PCDs in prognosis and tumor microenvironment remains unknown. Therefore, we comprehensively discussed the relationship between different models of PCD and the prognosis of glioma and provided new ideas for the optimal targeted therapy of glioma. MATERIALS AND METHODS We compared and analyzed the role of 14 PCD patterns on the prognosis from different levels. We constructed the cell death risk score (CDRS) index and conducted a comprehensive analysis of CDRS and TME characteristics, clinical characteristics, and drug response. RESULTS Effects of different PCDs at the genomic, functional, and immune microenvironment levels were discussed. CDRS index containing 6 gene signatures and a nomogram were established. High CDRS is associated with a worse prognosis. Through transcriptome and single-cell data, we found that patients with high CDRS showed stronger immunosuppressive characteristics. Moreover, the high-CDRS group was resistant to the traditional glioma chemotherapy drug Vincristine, but more sensitive to the Temozolomide and the clinical experimental drug Bortezomib. In addition, we identified 19 key potential therapeutic targets during malignant differentiation of tumor cells. CONCLUSION Overall, we provide the first systematic description of the role of 14 PCDs in glioma. A new CDRS model was built to predict the prognosis and to provide a new idea for the targeted therapy of glioma.
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Affiliation(s)
- Meini Yu
- Department of pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, 150081, Harbin, Heilongjiang, China
| | - Diwei Huo
- Fourth Affiliated Hospital of Harbin Medical University, China
| | - Kexin Yu
- Department of pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, 150081, Harbin, Heilongjiang, China
| | - Kun Zhou
- Department of pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, 150081, Harbin, Heilongjiang, China
| | - Fei Xu
- Department of pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, 150081, Harbin, Heilongjiang, China
| | - Qingkang Meng
- Department of pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, 150081, Harbin, Heilongjiang, China
| | - Yiyang Cai
- Department of pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, 150081, Harbin, Heilongjiang, China
| | - Xiujie Chen
- Department of pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, 150081, Harbin, Heilongjiang, China.
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Chen Z, Lin W, Cai Q, Kweon SS, Shu XO, Tanikawa C, Jia WH, Wang Y, Su X, Yuan Y, Wen W, Kim J, Shin A, Jee SH, Matsuo K, Kim DH, Wang N, Ping J, Shin MH, Ren Z, Oh JH, Oze I, Ahn YO, Jung KJ, Gao YT, Pan ZZ, Kamatani Y, Han W, Long J, Matsuda K, Zheng W, Guo X. A large-scale microRNA transcriptome-wide association study identifies two susceptibility microRNAs, miR-1307-5p and miR-192-3p, for colorectal cancer risk. Hum Mol Genet 2024; 33:333-341. [PMID: 37903058 PMCID: PMC10840382 DOI: 10.1093/hmg/ddad185] [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: 08/03/2022] [Revised: 07/20/2023] [Accepted: 10/24/2023] [Indexed: 11/01/2023] Open
Abstract
Transcriptome-wide association studies (TWAS) have identified many putative susceptibility genes for colorectal cancer (CRC) risk. However, susceptibility miRNAs, critical dysregulators of gene expression, remain unexplored. We genotyped DNA samples from 313 CRC East Asian patients and performed small RNA sequencing in their normal colon tissues distant from tumors to build genetic models for predicting miRNA expression. We applied these models and data from genome-wide association studies (GWAS) including 23 942 cases and 217 267 controls of East Asian ancestry to investigate associations of predicted miRNA expression with CRC risk. Perturbation experiments separately by promoting and inhibiting miRNAs expressions and further in vitro assays in both SW480 and HCT116 cells were conducted. At a Bonferroni-corrected threshold of P < 4.5 × 10-4, we identified two putative susceptibility miRNAs, miR-1307-5p and miR-192-3p, located in regions more than 500 kb away from any GWAS-identified risk variants in CRC. We observed that a high predicted expression of miR-1307-5p was associated with increased CRC risk, while a low predicted expression of miR-192-3p was associated with increased CRC risk. Our experimental results further provide strong evidence of their susceptible roles by showing that miR-1307-5p and miR-192-3p play a regulatory role, respectively, in promoting and inhibiting CRC cell proliferation, migration, and invasion, which was consistently observed in both SW480 and HCT116 cells. Our study provides additional insights into the biological mechanisms underlying CRC development.
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Affiliation(s)
- Zhishan Chen
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, 2525 West End Ave, Nashville, TN 37203, United States
| | - Weiqiang Lin
- International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, No. N1, Shangcheng Avenue, Yiwu, 322000 China
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, 2525 West End Ave, Nashville, TN 37203, United States
| | - Sun-Seog Kweon
- Department of Preventive Medicine, Chonnam National University Medical School, 160, Baekseo-ro, Dong-gu, Gwangju 61469, South Korea
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, 2525 West End Ave, Nashville, TN 37203, United States
| | - Chizu Tanikawa
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, University of Tokyo, 4 Chome-6-1 Shirokanedai, Minato City, Tokyo 108-8639, Japan
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-sen University, No. 651 Dongfeng Road East, Guangzhou 510060, China
| | - Ying Wang
- International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, No. N1, Shangcheng Avenue, Yiwu, 322000 China
| | - Xinwan Su
- The Kidney Disease Center, the First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd, Hangzhou, 310003 China
| | - Yuan Yuan
- The Kidney Disease Center, the First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd, Hangzhou, 310003 China
| | - Wanqing Wen
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, 2525 West End Ave, Nashville, TN 37203, United States
| | - Jeongseon Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang-si, 10408, Gyeonggi-do, South Korea
| | - Aesun Shin
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul National University Cancer Research Institute, 03 Daehak-ro, Jongno-gu, 03080, Seoul, Korea
| | - Sun Ha Jee
- Department of Epidemiology and Health Promotion, Graduate School of Public Health, Yonsei University, 50-1, Yonsei-Ro, Seodaemun-gu, Seoul 03722, South Korea
| | - Keitaro Matsuo
- Division of Molecular and Clinical Epidemiology, Aichi Cancer Center Research Institute, 1-1 Kanokoden, Chikusa-ku Nagoya 464-8681, Japan
- Department of Epidemiology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Dong-Hyun Kim
- Department of Social and Preventive Medicine, Hallym University College of Medicine, Okcheon-dong, Chuncheon, 200-702 South Korea
| | - Nan Wang
- Department of General Surgery, Tangdu Hospital, the Air Force Medical University, 569 Xinsi Road, Xi'an, Shaanxi, 710038 China
| | - Jie Ping
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, 2525 West End Ave, Nashville, TN 37203, United States
| | - Min-Ho Shin
- Department of Preventive Medicine, Chonnam National University Medical School, 160, Baekseo-ro, Dong-gu, Gwangju 61469, South Korea
| | - Zefang Ren
- School of Public Health, Sun Yat-sen University, No. 74 Zhongshan Road 2, Yuexiu, Guangzhou, Guangdong 510080 China
| | - Jae Hwan Oh
- Center for Colorectal Cancer, National Cancer Center Hospital, National Cancer Center, 323, Ilsan-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do,10408, South Korea
| | - Isao Oze
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, 1-1 Kanokoden, Chikusa-ku Nagoya 464-8681, Japan
| | - Yoon-Ok Ahn
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul National University Cancer Research Institute, 03 Daehak-ro, Jongno-gu, 03080, Seoul, Korea
| | - Keum Ji Jung
- Department of Epidemiology and Health Promotion, Graduate School of Public Health, Yonsei University, 50-1, Yonsei-Ro, Seodaemun-gu, Seoul 03722, South Korea
| | - Yu-Tang Gao
- State Key Laboratory of Oncogene and Related Genes & Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 227 South Chongqing Road, Shanghai, China
| | - Zhi-Zhong Pan
- State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-sen University, No. 651 Dongfeng Road East, Guangzhou 510060, China
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- Kyoto-McGill International Collaborative School in Genomic Medicine, Kyoto University Graduate School of Medicine, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Weidong Han
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Zhejiang University College of Medicine, Xiasha Road, Hangzhou, 310018 China
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, 2525 West End Ave, Nashville, TN 37203, United States
| | - Koichi Matsuda
- Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba-ken 277-8562, Japan
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, 2525 West End Ave, Nashville, TN 37203, United States
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, 2525 West End Ave, Nashville, TN 37203, United States
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, 2525 West End Ave, Nashville, TN 37203, United States
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Liu J, Zhang F, Wang J, Wang Y. MicroRNA‑mediated regulation in lung adenocarcinoma: Signaling pathways and potential therapeutic implications (Review). Oncol Rep 2023; 50:211. [PMID: 37859595 PMCID: PMC10603552 DOI: 10.3892/or.2023.8648] [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: 08/16/2023] [Accepted: 10/10/2023] [Indexed: 10/21/2023] Open
Abstract
Lung adenocarcinoma (LUAD) poses a significant global health burden owing to its high incidence rate and unfavorable prognosis, driven by frequent recurrence and drug resistance. Understanding the biological mechanisms underlying LUAD is imperative to developing advanced therapeutic strategies. Recent research has highlighted the role of dysregulated microRNAs (miRNAs) in LUAD progression through diverse signaling pathways, including the Wnt and AKT pathways. Of particular interest is the novel pathological mechanism involving the interaction between competing endogenous RNAs (ceRNAs) and miRNAs. This review critically analyzed the impact of aberrant miRNA expression on LUAD development, shedding light on the associated signaling pathways. It also highlighted the emerging significance of ceRNA‑miRNA interactions in LUAD pathogenesis. Elucidating the intricate regulatory networks involving miRNAs and ceRNAs presents a promising avenue for the development of potential therapeutic interventions and diagnostic biomarkers in LUAD. Further research in this area is essential to advance precision medicine approaches and improve patient outcomes.
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Affiliation(s)
- Jiye Liu
- Department of Family Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110000, P.R. China
- Department of Rehabilitation Medicine, Huludao Central Hospital, Huludao, Liaoning 125000, P.R. China
| | - Fei Zhang
- Department of Family Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110000, P.R. China
| | - Jiahe Wang
- Department of Family Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110000, P.R. China
| | - Yibing Wang
- Department of Urology Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110000, P.R. China
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Wang W, Wang S, Wang M, Ma Y, Hu W, Wu B, Li C, Zhang D. Effects of TRAF3 on the proliferation and migration of lung adenocarcinoma depend partly on pyroptosis. BMC Cancer 2023; 23:942. [PMID: 37798663 PMCID: PMC10557279 DOI: 10.1186/s12885-023-11468-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 10/02/2023] [Indexed: 10/07/2023] Open
Abstract
BACKGROUND Tumor necrosis factor receptor-associated factor 3 (TRAF3) has specific regulatory effects on a wide range of diseases, including tumors. However, the effect and mechanism of TRAF3 on lung adenocarcinoma (LUAD) are still unknown. The aim of the present study was to make clear the role and potential mechanism of TRAF3 in LUAD. METHODS TIMER2.0 database and western blot were applied to detect the expression of TRAF3 in lung adenocarcinoma tissue. Kaplan-Meier Plotter database was utilized to explore the effect of TRAF3 on the clinical prognosis of lung adenocarcinoma patients. Specific siRNA was used to inhibit the expression of TRAF3 in LUAD cells (A549 and H1299). CCK-8 and EdU assays were performed for assessing LUAD cells proliferation. Wound healing assay and transwell assay were performed for determining cells migration. CCK-8 assay was used to assess the response of the LUAD cells to paclitaxel. TIMER2.0 bioinformatics and western blot were employed to detect the effects of TRAF3 on pyroptosis in LUAD. RESULTS TRAF3 was highly expressed in lung adenocarcinoma tissues and cell lines. Patients with TRAF3 hyperexpression had a good prognosis compared to those with lower expression. TRAF3 inhibition notably induced proliferation and migration of LUAD cells. Inhibition of TRAF3 also weakened the sensitivity of LUAD cells to paclitaxel. Moreover, bioinformatics results showed that TRAF3 was positively correlated with the expression of pyroptosis-related genes in LUAD. Western blot assays showed that TRAF3 inhibition visibly decreased the expression of apoptosis-associated speck-like protein (ASC), cleaved caspase-1 and matured- IL-1β. CONCLUSIONS Inhibition of TRAF3 promotes the proliferation and migration of LUAD cells, and reduces the sensitivity of LUAD cells to paclitaxel. The effects of TRAF3 on LUAD cells were mediated in part by caspase-1-dependent pyroptosis.
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Affiliation(s)
- Wangjia Wang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, 325000, China
- Department of Rheumatism and Immunology, Shangyu People's Hospital, Shaoxing, 312300, China
| | - Shiqi Wang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, 325000, China
| | - Min Wang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, 325000, China
| | - Yamei Ma
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, 325000, China
| | - Wanting Hu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, 325000, China
| | - Binsha Wu
- Department of Plastic Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, 325000, China
| | - Chichi Li
- Department of Plastic Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, 325000, China.
| | - Dan Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, 325000, China.
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Predicting Microenvironment in CXCR4- and FAP-Positive Solid Tumors-A Pan-Cancer Machine Learning Workflow for Theranostic Target Structures. Cancers (Basel) 2023; 15:cancers15020392. [PMID: 36672341 PMCID: PMC9856808 DOI: 10.3390/cancers15020392] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
(1) Background: C-X-C Motif Chemokine Receptor 4 (CXCR4) and Fibroblast Activation Protein Alpha (FAP) are promising theranostic targets. However, it is unclear whether CXCR4 and FAP positivity mark distinct microenvironments, especially in solid tumors. (2) Methods: Using Random Forest (RF) analysis, we searched for entity-independent mRNA and microRNA signatures related to CXCR4 and FAP overexpression in our pan-cancer cohort from The Cancer Genome Atlas (TCGA) database-representing n = 9242 specimens from 29 tumor entities. CXCR4- and FAP-positive samples were assessed via StringDB cluster analysis, EnrichR, Metascape, and Gene Set Enrichment Analysis (GSEA). Findings were validated via correlation analyses in n = 1541 tumor samples. TIMER2.0 analyzed the association of CXCR4 / FAP expression and infiltration levels of immune-related cells. (3) Results: We identified entity-independent CXCR4 and FAP gene signatures representative for the majority of solid cancers. While CXCR4 positivity marked an immune-related microenvironment, FAP overexpression highlighted an angiogenesis-associated niche. TIMER2.0 analysis confirmed characteristic infiltration levels of CD8+ cells for CXCR4-positive tumors and endothelial cells for FAP-positive tumors. (4) Conclusions: CXCR4- and FAP-directed PET imaging could provide a non-invasive decision aid for entity-agnostic treatment of microenvironment in solid malignancies. Moreover, this machine learning workflow can easily be transferred towards other theranostic targets.
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Ye R, Lu X, Liu J, Duan Q, Xiao J, Duan X, Yue Z, Liu F. CircSOD2 Contributes to Tumor Progression, Immune Evasion and Anti-PD-1 Resistance in Hepatocellular Carcinoma by Targeting miR-497-5p/ANXA11 Axis. Biochem Genet 2022; 61:597-614. [PMID: 36008700 DOI: 10.1007/s10528-022-10273-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 06/22/2022] [Indexed: 11/25/2022]
Abstract
Circular RNAs (circRNAs) can function as functional molecules in hepatocellular carcinoma (HCC). Herein, circRNA superoxide dismutase 2 (circSOD2) was researched in HCC progression and immune system. The real-time polymerase chain reaction (qRT-PCR) was used for quantification of circSOD2, microRNA-497-5p (miR-497-5p) and Annexin A11 (ANXA11). Cell assays were performed by 3-(4, 5-dimethylthiazol-2-y1)-2, 5-diphenyl tetrazolium bromide (MTT) and colony formation assays for proliferation, flow cytometry for apoptosis and cell cycle, wound healing assay for migration and transwell assay for migration/invasion. ANXA11 and metastatic protein levels were measured by western blot. Dual-luciferase reporter and RNA immunoprecipitation (RIP) assays were performed to analyze target binding. CD8+ T cell immunity was assessed by Immunohistochemistry (IHC) assay, and the effect of circSOD2 on programmed cell death 1 (PD-1) immune checkpoint inhibitors (anti-PD-1) therapy was evaluated by mice xenograft assay. CircSOD2 was upregulated in HCC tissues and cells. Knockdown of circSOD2 resulted in HCC cell growth inhibition, apoptosis promotion, cell cycle arrest and metastasis suppression. Mechanically, circSOD2 promoted HCC development by acting as a miR-497-5p sponge and miR-497-5p played a tumor-inhibitory role in HCC cells by targeting ANXA11. Moreover, circSOD2 induced upregulation of ANXA11 expression by interacting with miR-497-5p. Also, the promoting effects of circSOD2 on immune evasion and anti-PD-1 resistance were related to miR-497-5p/ANXA11 axis. This study elucidated the pivotal function of circSOD2 in HCC progression and immunosuppression by mediating miR-497-6p/ANXA11 axis. CircSOD2/miR-497-5p/ANXA11 axis was a novel view of circRNA research in HCC.
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Affiliation(s)
- Rong Ye
- Department of General Surgery 3, The First Affiliated Hospital of Gannan Medical University, No. 128 Jinling Road, Jingkai District, Ganzhou, 341000, China
| | - Xingyu Lu
- Outpatient department, Ganzhou City Third People's Hospital, Ganzhou, 341001, China
| | - Jianping Liu
- Department of General Surgery 3, The First Affiliated Hospital of Gannan Medical University, No. 128 Jinling Road, Jingkai District, Ganzhou, 341000, China
| | - Qing Duan
- Department of General Surgery 3, The First Affiliated Hospital of Gannan Medical University, No. 128 Jinling Road, Jingkai District, Ganzhou, 341000, China
| | - Junqi Xiao
- Department of General Surgery 3, The First Affiliated Hospital of Gannan Medical University, No. 128 Jinling Road, Jingkai District, Ganzhou, 341000, China
| | - Xunhong Duan
- Department of General Surgery 3, The First Affiliated Hospital of Gannan Medical University, No. 128 Jinling Road, Jingkai District, Ganzhou, 341000, China
| | - Zhibiao Yue
- Department of General Surgery 3, The First Affiliated Hospital of Gannan Medical University, No. 128 Jinling Road, Jingkai District, Ganzhou, 341000, China.
| | - Fengen Liu
- Department of General Surgery 3, The First Affiliated Hospital of Gannan Medical University, No. 128 Jinling Road, Jingkai District, Ganzhou, 341000, China.
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Cai Q, Duan J, Ding L. Prognostic model of immune-related genes for patients with hepatocellular carcinoma. Front Surg 2022; 9:819491. [PMID: 35937592 PMCID: PMC9349350 DOI: 10.3389/fsurg.2022.819491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 06/30/2022] [Indexed: 11/30/2022] Open
Abstract
Background Immune-related genes (IRGs) are closely connected to the occurrence and development of tumors. Their influence on the prognosis of patients with HCC, however, remains unclear. Methods From the TCGA database, we integrated 365 liver cancer tissues and 50 normal tissues to identify differential immune genes related to prognosis. Multivariate COX analysis was used to establish a new prognostic index on account of IRGs, whereby risk score = (Expression level of HSPA4*0.022) + (Expression level of PSMD14*0.042) + (Expression level of RBP2*0.019) + (Expression level of MAPT*0.197) + (Expression level of TRAF3*0.146) + (Expression level of NDRG1*(0.006) + (Expression level of NRAS*0.027) + (Expression level of IL17D*0.075). Results The risk score was clearly correlated with an unfavorable survival rate and with clinical characteristics. By integrating the immune-related risk score model with clinical features, a nomogram was constructed to predict the survival rate of HCC patients (1-, 3- and 5-year AUC of 0.721, 0.747 and 0.781, respectively). Conclusion We have established a valuable prognostic risk score for HCC patients that may be a better predictor of survival than the present method. With the risk score's strong predictive value for immune cells and functions, it may provide clinical guidance for the diagnosis and prognosis of different immunophenotypes, and provide multiple therapeutic targets for the treatment of HCC patients based on subtype-specific immune molecules.
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Affiliation(s)
- Qun Cai
- Department of Infectious Diseases and Liver Diseases, Ningbo Medical Center Lihuili Hospital, Affiliated Lihuili Hospital of Ningbo University, Ningbo, China
- Correspondence: Qun Cai
| | - Jinnan Duan
- Department of Infectious Diseases, Shaoxing People's Hospital, Shaoxing, China
| | - Liang Ding
- Department of Infectious Diseases, Shaoxing People's Hospital, Shaoxing, China
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Bahado-Singh R, Vlachos KT, Aydas B, Gordevicius J, Radhakrishna U, Vishweswaraiah S. Precision Oncology: Artificial Intelligence and DNA Methylation Analysis of Circulating Cell-Free DNA for Lung Cancer Detection. Front Oncol 2022; 12:790645. [PMID: 35600397 PMCID: PMC9114890 DOI: 10.3389/fonc.2022.790645] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 04/04/2022] [Indexed: 12/12/2022] Open
Abstract
Background Lung cancer (LC) is a leading cause of cancer-deaths globally. Its lethality is due in large part to the paucity of accurate screening markers. Precision Medicine includes the use of omics technology and novel analytic approaches for biomarker development. We combined Artificial Intelligence (AI) and DNA methylation analysis of circulating cell-free tumor DNA (ctDNA), to identify putative biomarkers for and to elucidate the pathogenesis of LC. Methods Illumina Infinium MethylationEPIC BeadChip array analysis was used to measure cytosine (CpG) methylation changes across the genome in LC. Six different AI platforms including support vector machine (SVM) and Deep Learning (DL) were used to identify CpG biomarkers and for LC detection. Training set and validation sets were generated, and 10-fold cross validation performed. Gene enrichment analysis using g:profiler and GREAT enrichment was used to elucidate the LC pathogenesis. Results Using a stringent GWAS significance threshold, p-value <5x10-8, we identified 4389 CpGs (cytosine methylation loci) in coding genes and 1812 CpGs in non-protein coding DNA regions that were differentially methylated in LC. SVM and three other AI platforms achieved an AUC=1.00; 95% CI (0.90-1.00) for LC detection. DL achieved an AUC=1.00; 95% CI (0.95-1.00) and 100% sensitivity and specificity. High diagnostic accuracies were achieved with only intragenic or only intergenic CpG loci. Gene enrichment analysis found dysregulation of molecular pathways involved in the development of small cell and non-small cell LC. Conclusion Using AI and DNA methylation analysis of ctDNA, high LC detection rates were achieved. Further, many of the genes that were epigenetically altered are known to be involved in the biology of neoplasms in general and lung cancer in particular.
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Affiliation(s)
- Ray Bahado-Singh
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, United States
| | - Kyriacos T Vlachos
- Department of Biomedical Sciences, Wayne State School of Medicine, Basic Medical Sciences, Detroit, MI, United States
| | - Buket Aydas
- Department of Healthcare Analytics, Meridian Health Plans, Detroit, MI, United States
| | | | - Uppala Radhakrishna
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, United States
| | - Sangeetha Vishweswaraiah
- Department of Obstetrics and Gynecology, Beaumont Research Institute, Royal Oak, MI, United States
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Jiang H, Jiang Q, He Y, Li X, Xu Y, Liu X. XBP1s promotes the development of lung adenocarcinoma via the p‑JNK MAPK pathway. Int J Mol Med 2022; 49:34. [PMID: 35059734 PMCID: PMC8815418 DOI: 10.3892/ijmm.2022.5089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/16/2021] [Indexed: 11/12/2022] Open
Abstract
Spliced X-box binding protein 1 (XBP1s) has been reported to participate in the pathogenesis of numerous types of cancer; however, whether XBP1s plays a role in lung cancer remains to be elucidated. In the present study, bioinformatics analysis was performed to determine the mRNA expression level of XBP1 in lung cancer and adjacent normal tissues. Gene Ontology terms, pathway enrichment and Pearson's correlation analysis were performed to investigate the possible mechanism involved. Western blot and reverse transcription-quantitative PCR were performed to quantify the protein and mRNA expression level of target proteins, respectively. Small interfering RNA or overexpression plasmid were used to knockdown or overexpress the expression level of XBP1s. EdU staining, colony formation, Cell Counting Kit-8, Transwell and wound healing assays, and flow cytometry were performed to detect the proliferation, colony forming ability, cell viability, migration and invasion ability, and the apoptosis rate. The results showed that the mRNA and protein expression level of XBP1 was higher in tumor tissues compared with that in adjacent normal tissues using data from the TIMER2.0, ONCOMINE and UALCAN online databases. In addition, the mRNA expression level of XBP1 was also associated with clinical features, including age, smoking habit, individual cancer stage and nodal metastasis status. In the in vitro experiments, the mRNA and protein expression level of XBP1s was increased in the A549 cell line compared with that in the human bronchial epithelial (HBE), H1299, PC9 and H460 cell lines. Hypoxia further increased the protein expression level of XBP1s in the A549 cell line. Knockdown of XBP1s expression in the A549 cell line resulted in decreased proliferation, colony formation, cell viability, migration and invasion, and increased apoptosis. By contrast, overexpressing XBP1s in the HBE cell line led to the opposite results. To investigate the mechanism involved, proteins associated with XBP1 were analyzed using the LinkedOmics database. Pathway enrichment revealed the MAPK pathway to be the possible XBP1 downstream target. Furthermore, Pearson's correlation and western blot analyses verified that phosphorylated (p)-JNK rather than p-ERK or p-p38 was the downstream effector of XBP1s. Phosphorylation of JNK was decreased when XBP1s expression was knocked down in the A549 cell line under normoxic and hypoxic conditions. Inhibiting p-JNK with SP600125 reversed the increased prosurvival effects caused by XBP1s overexpression. The results from the present study suggest that XBP1s/p-JNK function as a prosurvival factors in the A549 cell line and could be a potential target for the treatment of lung adenocarcinoma.
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Affiliation(s)
- Hongxia Jiang
- Department of Pulmonary and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Qianqian Jiang
- Department of Pulmonary and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Yuanzhou He
- Department of Pulmonary and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Xiaochen Li
- Department of Pulmonary and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Yongjian Xu
- Department of Pulmonary and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Xiansheng Liu
- Department of Pulmonary and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
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10
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Høye E, Fromm B, Böttger PHM, Domanska D, Torgunrud A, Lund-Andersen C, Abrahamsen TW, Fretland Å, Dagenborg VJ, Lorenz S, Edwin B, Hovig E, Flatmark K. A comprehensive framework for analysis of microRNA sequencing data in metastatic colorectal cancer. NAR Cancer 2022; 4:zcab051. [PMID: 35047825 PMCID: PMC8759566 DOI: 10.1093/narcan/zcab051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 11/24/2021] [Accepted: 12/15/2021] [Indexed: 11/29/2022] Open
Abstract
Although microRNAs (miRNAs) contribute to all hallmarks of cancer, miRNA dysregulation in metastasis remains poorly understood. The aim of this work was to reliably identify miRNAs associated with metastatic progression of colorectal cancer (CRC) using novel and previously published next-generation sequencing (NGS) datasets generated from 268 samples of primary (pCRC) and metastatic CRC (mCRC; liver, lung and peritoneal metastases) and tumor adjacent tissues. Differential expression analysis was performed using a meticulous bioinformatics pipeline, including only bona fide miRNAs, and utilizing miRNA-tailored quality control and processing. Five miRNAs were identified as up-regulated at multiple metastatic sites Mir-210_3p, Mir-191_5p, Mir-8-P1b_3p [mir-141–3p], Mir-1307_5p and Mir-155_5p. Several have previously been implicated in metastasis through involvement in epithelial-to-mesenchymal transition and hypoxia, while other identified miRNAs represent novel findings. The use of a publicly available pipeline facilitates reproducibility and allows new datasets to be added as they become available. The set of miRNAs identified here provides a reliable starting-point for further research into the role of miRNAs in metastatic progression.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Kjersti Flatmark
- To whom correspondence should be addressed. Tel: +47 22 78 18 63;
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11
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MiR-1307: A comprehensive review of its role in various cancer. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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12
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Xie S, Jiang X, Qin R, Song S, Lu Y, Wang L, Chen Y, Lu D. miR-1307 promotes hepatocarcinogenesis by CALR-OSTC-endoplasmic reticulum protein folding pathway. iScience 2021; 24:103271. [PMID: 34761190 PMCID: PMC8567365 DOI: 10.1016/j.isci.2021.103271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/27/2021] [Accepted: 10/12/2021] [Indexed: 12/20/2022] Open
Abstract
miR-1307 is highly expressed in liver cancer and inhibits methyltransferase protein8. Thereby, miR-1307 inhibits the expression of KDM3A and KDM3B and increases the methylation modification of histone H3 lysine 9, which enhances the expression of endoplasmic-reticulum-related gene CALR. Of note, miR-1307 weakens the binding ability of OSTC to CDK2, CDK4, CyclinD1, and cyclinE and enhances the binding ability of CALR to CDK2, CDK4, CyclinD1, and cyclinE, decreasing of p21WAF1/CIP1, GADD45, pRB, and p18, and decreasing of ppRB. Furthermore, miR-1307 increases the activity of H-Ras, PKM2, and PLK1. Strikingly, miR-1307 reduces the binding ability of OSTC to ATG4 and enhances the binding ability of CALR to ATG4. Therefore, miR-1307 reduces the occurrence of autophagy based on ATG4-LC3-ATG3-ATG7-ATG5-ATG16L1-ATG12-ATG9- Beclin1. In particular, miR-1307 enhances the expression of PAK2, PLK1, PRKAR2A, MYBL1, and Trim44 and inhibits the expression of Sash1 and Smad5 via autophagy. Our observations suggest that miR-1307 promotes hepatocarcinogenesis by CALR-OSTC-endoplasmic reticulum protein folding pathway.
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Affiliation(s)
- Sijie Xie
- Shanghai Putuo People's Hospital, School of Life Science and Technology, Tongji University, 200092 Shanghai, China
| | - Xiaoxue Jiang
- Shanghai Putuo People's Hospital, School of Life Science and Technology, Tongji University, 200092 Shanghai, China
| | - Rushi Qin
- Shanghai Putuo People's Hospital, School of Life Science and Technology, Tongji University, 200092 Shanghai, China
| | - Shuting Song
- Shanghai Putuo People's Hospital, School of Life Science and Technology, Tongji University, 200092 Shanghai, China
| | - Yanan Lu
- Shanghai Putuo People's Hospital, School of Life Science and Technology, Tongji University, 200092 Shanghai, China
| | - Liyan Wang
- Shanghai Putuo People's Hospital, School of Life Science and Technology, Tongji University, 200092 Shanghai, China
| | - Yingjie Chen
- Shanghai Putuo People's Hospital, School of Life Science and Technology, Tongji University, 200092 Shanghai, China
| | - Dongdong Lu
- Shanghai Putuo People's Hospital, School of Life Science and Technology, Tongji University, 200092 Shanghai, China
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13
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Chen B, Zheng S, Jiang F. miR-1293 acts as a tumor promotor in lung adenocarcinoma via targeting phosphoglucomutase 5. PeerJ 2021; 9:e12140. [PMID: 34616611 PMCID: PMC8450003 DOI: 10.7717/peerj.12140] [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: 05/27/2021] [Accepted: 08/19/2021] [Indexed: 12/27/2022] Open
Abstract
Background Lung adenocarcinoma (LUAD) is the most common histologic subtype of lung cancer. Studies have found that miR-1293 is related to the survival of LUAD patients. Unfortunately, its role in LUAD remains not fully clarified. Methods miR-1293 expression and its association with LUAD patients’ clinical characteristics were analyzed in TCGA database. Also, miR-1293 expression was detected in LUAD cell lines. Cell viability, migration, invasion and expression of MMP2 and MMP9 were measured in LUAD cells following transfection with miR-1293 mimic or antagomir. Phosphoglucomutase (PGM) 5 was identified to be negatively related to miR-1293 in LUAD patients in TCGA database, and their association was predicated by Targetscan software. Hence, we further verified the relationship between miR-1293 and PGM5. Additionally, the effect and mechanism of miR-1293 were validated in a xenograft mouse model. Results We found miR-1293 expression was elevated, but PGM5 was decreased, in LUAD patients and cell lines. Higher miR-1293 expression was positively related to LUAD patients’ pathologic stage and poor overall survival. miR-1293 mimic significantly promoted, whereas miR-1293 antagomir suppressed the viability, migration, invasion, and expression of MMP2 and MMP9 in LUAD cells. PGM5 was a target of miR-1293. Overexpression of PGM5 abrogated the effects of miR-1293 on the malignant phenotypes of LUAD cells. Administration of miR-1293 antagomir reduced tumor volume and staining of Ki-67 and MMP9, but elevated PGM5 expression in vivo. Conclusions miR-1293 promoted the proliferation, migration and invasion of LUAD cells via targeting PGM5, which indicated that miR-1293 might serve as a potential therapeutic target for LUAD patients.
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Affiliation(s)
- Bing Chen
- Department of Thoracic Surgery, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital, Nanjing, China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China
| | - Shiya Zheng
- Department of Oncology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Feng Jiang
- Department of Thoracic Surgery, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital, Nanjing, China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China
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14
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Fan Y, Hao J, Cen X, Song K, Yang C, Xiao S, Cheng S. Downregulation of miR-487a-3p suppresses the progression of non-small cell lung cancer via targeting Smad7. Drug Dev Res 2021; 83:564. [PMID: 34523739 DOI: 10.1002/ddr.21876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Non-small cell lung cancer (NSCLC) is the most prevalent type of lung cancer; however, the treatment efficacy of advanced NSCLC remains poor. MicroRNAs (miRNAs) are closely associated with the pathogenesis of lung cancer, while the detailed function of miR-487a-3p in NSCLC remains unclear. Bioinformatic analysis was performed to identify differentially expressed miRNAs (DEmiRNAs) between NSCLC and normal tissues. The effects of miR-487a-3p antagomir on the proliferation and invasion of NSCLC cells were explored with CCK-8 and Transwell assays. A total of 48 overlapping miRNAs were identified, including 9 commonly downregulated and 39 commonly upregulated miRNAs. MiR-487a-3p was found to be associated with poor survival rate of patients with NSCLC. MiR-487a-3p level was notably upregulated in NSCLC cells compared with that in human bronchial epithelial cells. Downregulation of miR-487a-3p inhibited the proliferation of NCI-H1299 and A549 cells via inducing apoptosis. In addition, miR-487a-3p antagomir significantly decreased the migration and invasion ability of NCI-H1299 cells. The results of the dual-luciferase reporter assay and western blotting indicated that miR-487a-3p antagomir exerted antitumor effects via targeting Smad7. The findings of the present study revealed that downregulation of miR-487a-3p suppressed the progression of NSCLC via inhibiting the Smads pathway, and it may serve as a novel promising target for the treatment of NSCLC.
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Affiliation(s)
- Youqiang Fan
- Department of Thoracic Surgery, Ningbo Zhenhai People's Hospital, Ningbo, Zhejiang, China
| | - Jingduo Hao
- Department of Oncology, Ningbo Zhenhai People's Hospital, Ningbo, Zhejiang, China
| | - Xueying Cen
- Department of Oncology, Ningbo Zhenhai People's Hospital, Ningbo, Zhejiang, China
| | - Kun Song
- Department of Oncology, Ningbo Zhenhai People's Hospital, Ningbo, Zhejiang, China
| | - Chunbo Yang
- Department of Thoracic Surgery, Ningbo Zhenhai People's Hospital, Ningbo, Zhejiang, China
| | - Shengwen Xiao
- Department of Thoracic Surgery, Ningbo Zhenhai People's Hospital, Ningbo, Zhejiang, China
| | - Siming Cheng
- Department of Thoracic Surgery, Ningbo Zhenhai People's Hospital, Ningbo, Zhejiang, China
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15
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Ghafouri-Fard S, Abak A, Fattahi F, Hussen BM, Bahroudi Z, Shoorei H, Taheri M. The interaction between miRNAs/lncRNAs and nuclear factor-κB (NF-κB) in human disorders. Biomed Pharmacother 2021; 138:111519. [PMID: 33756159 DOI: 10.1016/j.biopha.2021.111519] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/27/2021] [Accepted: 03/14/2021] [Indexed: 12/13/2022] Open
Abstract
Nuclear factor-κB (NF-κB) represents a group of inducible transcription factors (TFs) regulating the expression of a great variety of genes implicated in diverse processes, particularly modulation of immune system responses. This TF has functional interactions with non-coding RNAs, constructing a complicated network through which NF-κB, miRNAs, and lncRNAs coordinately regulate gene expression at different facets. This type of interaction is involved in the pathophysiology of several human disorders including both neoplastic disorders and non-neoplastic conditions. MALAT1 and NKILA are among lncRNAs whose interactions with NF-κB have been vastly assessed in different conditions including cancer and inflammatory conditions. In addition, miR-146a/b has functional interactions with this TF in different contexts. Although miRNAs have mutual interactions with NF-κB, the regulatory role of miRNAs on this TF has been more clarified. The aim of the current review is to explore the function of NF-κB-related miRNAs and lncRNAs in these two types of human disorders.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Afete Abak
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Faranak Fattahi
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Bashdar M Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq
| | - Zahra Bahroudi
- Department of Anatomical Sciences, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamed Shoorei
- Department of Anatomical Sciences, Faculty of Medicine, Birjand University of Medical Sciences, Birjand, Iran
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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16
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Lin HC, Li J, Cheng DD, Zhang X, Yu T, Zhao FY, Geng Q, Zhu MX, Kong HW, Li H, Yao M. Nuclear export protein CSE1L interacts with P65 and promotes NSCLC growth via NF-κB/MAPK pathway. MOLECULAR THERAPY-ONCOLYTICS 2021; 21:23-36. [PMID: 33869740 PMCID: PMC8039531 DOI: 10.1016/j.omto.2021.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/06/2021] [Indexed: 12/24/2022]
Abstract
Non-small cell lung cancer (NSCLC) is characterized with high morbidity and mortality, mainly due to frequent recurrence and metastasis. However, the underlying molecular mechanisms of NSCLC tumorigenesis are largely unclear. Through data mining in the ONCOMINE and Gene Expression Omnibus (GEO) databases, the expression of CSE1L (chromosome segregation like 1 protein/CAS), an exportin, was identified to be significantly upregulated in NSCLC and positively associated with poor prognosis of patients. By use of in vitro and in vivo gain- and loss-of-function experiments, we found that CSE1L can promote NSCLC cell proliferation while inhibiting cell apoptosis. Through immunoprecipitation and mass spectrometry experiments, we demonstrated that CSE1L interacted with RELA (named as P65) and affected its location in the nucleus. Moreover, we found that one of the mechanisms by which CSE1L promotes proliferation and inhibits apoptosis is through activating the nuclear factor-κB (NF-κB)/mitogen-activated protein kinase (MAPK) signaling pathway. In summary, our findings indicated an oncogenic role of CSE1L in NSCLC tumorigenesis.
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Affiliation(s)
- H C Lin
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China
| | - J Li
- Department of Oncology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - D D Cheng
- Department of Orthopedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - X Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China
| | - T Yu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China
| | - F Y Zhao
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China
| | - Q Geng
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China
| | - M X Zhu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China
| | - H W Kong
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China
| | - H Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China
| | - M Yao
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China
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17
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Wang W, Zhao Z, Xu C, Li C, Ding C, Chen J, Chen T, Zhao J. LncRNA FAM83A-AS1 promotes lung adenocarcinoma progression by enhancing the pre-mRNA stability of FAM83A. Thorac Cancer 2021; 12:1495-1502. [PMID: 33687144 PMCID: PMC8107032 DOI: 10.1111/1759-7714.13928] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 02/06/2023] Open
Abstract
Background Lung cancer is the leading cause of cancer deaths worldwide. Long non‐coding RNAs (lncRNAs) affect a series of cellular biological processes, including oncogene function promotion. In this study, we explored the functions and mechanisms of FAM83A antisense RNA 1 (FAM83A‐AS1) in non‐small cell lung cancer (NSCLC) progression. Methods The expression of FAM83A‐AS1and FAM83A mRNA was analyzed using the Cancer Genome Atlas (TCGA) data. Proliferation, migration, invasion and Western blotting were measured after treatment with overexpressed or knockdown FAM83A‐AS1. To determine the relationship between FAM83A‐AS1 and FAM83A, RNase protection assay (RPA), amanitin treatment, RNA pulldown assay and RNA immunoprecipitation (RIP) assay were performed. Results High expression of FAM83A‐AS1 in lung adenocarcinoma (LUAD) was closely associated with low overall survival (OS) and progression‐free survival (PFS). Functionally, high FAM83A‐AS1 expression increased LUAD cell proliferation and metastasis, indicating that FAM83A‐AS1 exerted its oncogenic functions. Furthermore, FAM83A‐AS1 promoted NSCLC progression via ERK signaling pathways. Mechanistically, FAM83A‐AS1 post‐transcriptionally increased FAM83A expression by enhancing pre‐mRNA stability. FAM83A‐AS1 enhanced FAM83A mRNA stability not only by forming an RNA duplex but also by binding to FBL. Conclusions We determined that FAM83A‐AS1 increased FAM83A expression by enhancing FAM83A pre‐mRNA stability and promoted the tumorigenesis of LUAD.
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Affiliation(s)
- Wenyi Wang
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Medical College of Soochow University, Suzhou, China
| | - Zhunlin Zhao
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Medical College of Soochow University, Suzhou, China
| | - Chun Xu
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Medical College of Soochow University, Suzhou, China
| | - Chang Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Medical College of Soochow University, Suzhou, China
| | - Cheng Ding
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Medical College of Soochow University, Suzhou, China
| | - Jun Chen
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Medical College of Soochow University, Suzhou, China
| | - Tengfei Chen
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Medical College of Soochow University, Suzhou, China
| | - Jun Zhao
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Medical College of Soochow University, Suzhou, China
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18
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Stempor PA, Avni D, Leibowitz R, Sidi Y, Stępień M, Dzieciątkowski T, Dobosz P. Comprehensive Analysis of Correlations in the Expression of miRNA Genes and Immune Checkpoint Genes in Bladder Cancer Cells. Int J Mol Sci 2021; 22:2553. [PMID: 33806327 PMCID: PMC7961343 DOI: 10.3390/ijms22052553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/21/2021] [Accepted: 02/23/2021] [Indexed: 12/13/2022] Open
Abstract
Personalised medicine is the future and hope for many patients, including those with cancers. Early detection, as well as rapid, well-selected treatment, are key factors leading to a good prognosis. MicroRNA mediated gene regulation is a promising area of development for new diagnostic and therapeutic methods, crucial for better prospects for patients. Bladder cancer is a frequent neoplasm, with high lethality and lacking modern, advanced therapeutic modalities, such as immunotherapy. MicroRNAs are involved in bladder cancer pathogenesis, proliferation, control and response to treatment, which we summarise in this perspective in response to lack of recent review publications in this field. We further performed a correlation-based analysis of microRNA and gene expression data in bladder cancer (BLCA) TCGA dataset. We identified 27 microRNAs hits with opposite expression profiles to genes involved in immune response in bladder cancer, and 24 microRNAs hits with similar expression profiles. We discuss previous studies linking the functions of these microRNAs to bladder cancer and assess if they are good candidates for personalised medicine therapeutics and diagnostics. The discussed functions include regulation of gene expression, interplay with transcription factors, response to treatment, apoptosis, cell proliferation and angiogenesis, initiation and development of cancer, genome instability and tumour-associated inflammatory reaction.
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Affiliation(s)
- Przemysław A. Stempor
- SmartImmune Ltd, Accelerate Cambridge, University of Cambridge Judge Business School, Cambridge CB4 1EE, UK;
| | - Dror Avni
- Laboratory of Molecular Cell Biology, Center for Cancer Research and Department of Medicine C, Sheba Medical Center, Tel Hashome 52621, Israel;
| | - Raya Leibowitz
- Oncology Institute, Shamir Medical Center, Be’er Yaakov, Tel Hashome 52621, Israel;
- Faculty of Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv-Yafo 6997801, Israel;
| | - Yechezkel Sidi
- Faculty of Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv-Yafo 6997801, Israel;
| | - Maria Stępień
- Faculty of Medicine, Medical University of Lublin, 20-059 Lublin, Poland;
| | | | - Paula Dobosz
- Department of Hematology, Transplantationand Internal Medicine, Medical University of Warsaw, 02-097 Warsaw, Poland
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Ahmad S, Manzoor S, Siddiqui S, Mariappan N, Zafar I, Ahmad A, Ahmad A. Epigenetic underpinnings of inflammation: Connecting the dots between pulmonary diseases, lung cancer and COVID-19. Semin Cancer Biol 2021; 83:384-398. [PMID: 33484868 PMCID: PMC8046427 DOI: 10.1016/j.semcancer.2021.01.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/08/2020] [Accepted: 01/07/2021] [Indexed: 12/11/2022]
Abstract
Inflammation is an essential component of several respiratory diseases, such as chronic obstructive pulmonary disease (COPD), asthma and acute respiratory distress syndrome (ARDS). It is central to lung cancer, the leading cancer in terms of associated mortality that has affected millions of individuals worldwide. Inflammation and pulmonary manifestations are also the major causes of COVID-19 related deaths. Acute hyperinflammation plays an important role in the COVID-19 disease progression and severity, and development of protective immunity against the virus is greatly sought. Further, the severity of COVID-19 is greatly enhanced in lung cancer patients, probably due to the genes such as ACE2, TMPRSS2, PAI-1 and furin that are commonly involved in cancer progression as well as SAR-CoV-2 infection. The importance of inflammation in pulmonary manifestations, cancer and COVID-19 calls for a closer look at the underlying processes, particularly the associated increase in IL-6 and other cytokines, the dysregulation of immune cells and the coagulation pathway. Towards this end, several reports have identified epigenetic regulation of inflammation at different levels. Expression of several key inflammation-related cytokines, chemokines and other genes is affected by methylation and acetylation while non-coding RNAs, including microRNAs as well as long non-coding RNAs, also affect the overall inflammatory responses. Select miRNAs can regulate inflammation in COVID-19 infection, lung cancer as well as other inflammatory lung diseases, and can serve as epigenetic links that can be therapeutically targeted. Furthermore, epigenetic changes also mediate the environmental factors-induced inflammation. Therefore, a better understanding of epigenetic regulation of inflammation can potentially help develop novel strategies to prevent, diagnose and treat chronic pulmonary diseases, lung cancer and COVID-19.
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Affiliation(s)
- Shama Ahmad
- Division of Molecular and Translational Biomedicine, Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Shajer Manzoor
- Division of Molecular and Translational Biomedicine, Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Simmone Siddiqui
- Division of Molecular and Translational Biomedicine, Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nithya Mariappan
- Division of Molecular and Translational Biomedicine, Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Iram Zafar
- Division of Molecular and Translational Biomedicine, Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Aamir Ahmad
- Division of Molecular and Translational Biomedicine, Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Aftab Ahmad
- Division of Molecular and Translational Biomedicine, Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
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The role of microRNA-338-3p in cancer: growth, invasion, chemoresistance, and mediators. Life Sci 2021; 268:119005. [PMID: 33421526 DOI: 10.1016/j.lfs.2020.119005] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/25/2020] [Accepted: 12/29/2020] [Indexed: 12/14/2022]
Abstract
Cancer still remains as one of the leading causes of death worldwide. Metastasis and proliferation are abnormally increased in cancer cells that subsequently, mediate resistance of cancer cells to different therapies such as radio-, chemo- and immune-therapy. MicroRNAs (miRNAs) are endogenous short non-coding RNAs that can regulate expression of target genes at post-transcriptional level and capable of interaction with mRNA-coding genes. Vital biological mechanisms including apoptosis, migration and differentiation are modulated by these small molecules. MiRNAs are key players in regulating cancer proliferation and metastasis as well as cancer therapy response. MiRNAs can function as both tumor-suppressing and tumor-promoting factors. In the present review, regulatory impact of miRNA-338-3p on cancer growth and migration is discussed. This new emerging miRNA can regulate response of cancer cells to chemotherapy and radiotherapy. It seems that miRNA-338-3p has dual role in cancer chemotherapy, acting as tumor-promoting or tumor-suppressor factor. Experiments reveal anti-tumor activity of miRNA-338-3p in cancer. Hence, increasing miRNA-338-3p expression is of importance in effective cancer therapy. Long non-coding RNAs, circular RNAs and hypoxia are potential upstream mediators of miRNA-338-3p in cancer. Anti-tumor agents including baicalin and arbutin can promote expression of miRNA-338-3p in suppressing cancer progression. These topics are discussed to shed some light on function of miRNA-338-3p in cancer cells.
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