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Gao X, Tang M, Tian S, Li J, Wei S, Hua S, Liu W. ncRNAs-mediated TIMELESS overexpression in lung adenocarcinoma correlates with reduced tumor immune cell infiltration and poor prognosis. PLoS One 2024; 19:e0296829. [PMID: 38261568 PMCID: PMC10805305 DOI: 10.1371/journal.pone.0296829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 10/24/2023] [Indexed: 01/25/2024] Open
Abstract
Lung adenocarcinoma (LUAD) has a poor prognosis. Circadian genes such as TIMELESS have been associated with several pathologies, including cancer. The expression of TIMELESS and the relationship between TIMELESS, infiltration of tumors and prognosis in LUAD requires further investigation. In this study, we investigated the expression of TIMELESS and its association with survival across several types of human cancer using data from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression Program. Noncoding RNAs (ncRNAs) regulating overexpression of TIMELESS in lung adenocarcinoma (LUAD) were explored with expression, correlation, and survival analyses. Immune cell infiltration and biomarkers were analyzed between different TIMELESS expression levels. The relationship between TIMELESS expression and immunophenoscores, which were used to predict response to immunotherapy, was evaluated. TIMELESS was identified as a potential oncogene in LUAD. NcRNA analysis showed MIR4435-2HG/hsa-miR-1-3p may interact with TIMELESS in a competitive endogenous RNA network in LUAD tumor tissues. Most immune cells were significantly decreased in TCGA LUAD tumor tissues with high TIMELESS expression except for CD4+T cells and Th2 cells. TIMELESS expression in LUAD tumor tissues was significantly negatively correlated with neutrophil biomarkers, dendritic cell biomarkers (HLA-DPB1, HLA-DQB1, HLA-DRA, HLA-DPA1, CD1C) and an immunophenoscore that predicted outcomes associated with the use of immune checkpoint inhibitors. These findings imply that ncRNAs-mediated TIMELESS overexpression in LUAD tumor tissues correlated with poor prognosis, reduced immune cell infiltration in the tumor microenvironment, and poor response to immune checkpoint inhibitors.
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Affiliation(s)
- Xinliang Gao
- Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, Jilin Province, PR China
| | - Mingbo Tang
- Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, Jilin Province, PR China
| | - Suyan Tian
- Division of Clinical Research, The First Hospital of Jilin University, Changchun, Jilin Province, PR China
| | - Jialin Li
- Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, Jilin Province, PR China
| | - Shixiong Wei
- Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, Jilin Province, PR China
| | - Shucheng Hua
- Department of Respiratory Medicine, Center for Pathogen Biology and Infectious Diseases, Changchun, Jilin Province, PR China
| | - Wei Liu
- Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, Jilin Province, PR China
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2
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Vipat S, Moiseeva TN. The TIMELESS Roles in Genome Stability and Beyond. J Mol Biol 2024; 436:168206. [PMID: 37481157 DOI: 10.1016/j.jmb.2023.168206] [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: 05/01/2023] [Revised: 06/20/2023] [Accepted: 07/12/2023] [Indexed: 07/24/2023]
Abstract
TIMELESS protein (TIM) protects replication forks from stalling at difficult-to-replicate regions and plays an important role in DNA damage response, including checkpoint signaling, protection of stalled replication forks and DNA repair. Loss of TIM causes severe replication stress, while its overexpression is common in various types of cancer, providing protection from DNA damage and resistance to chemotherapy. Although TIM has mostly been studied for its part in replication stress response, its additional roles in supporting genome stability and a wide variety of other cellular pathways are gradually coming to light. This review discusses the diverse functions of TIM and its orthologs in healthy and cancer cells, open questions, and potential future directions.
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Affiliation(s)
- Sameera Vipat
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn 12618, Estonia
| | - Tatiana N Moiseeva
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn 12618, Estonia.
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Shi D, Fang G, Chen Q, Li J, Ruan X, Lian X. Six-hour time-restricted feeding inhibits lung cancer progression and reshapes circadian metabolism. BMC Med 2023; 21:417. [PMID: 37924048 PMCID: PMC10625271 DOI: 10.1186/s12916-023-03131-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 10/25/2023] [Indexed: 11/06/2023] Open
Abstract
BACKGROUND Accumulating evidence has suggested an oncogenic effect of diurnal disruption on cancer progression. To test whether targeting circadian rhythm by dietary strategy suppressed lung cancer progression, we adopted 6-h time-restricted feeding (TRF) paradigm to elucidate whether and how TRF impacts lung cancer progression. METHODS This study used multiple lung cancer cell lines, two xenograft mouse models, and a chemical-treated mouse lung cancer model. Stable TIM-knockdown and TIM-overexpressing A549 cells were constructed. Cancer behaviors in vitro were determined by colony formation, EdU proliferation, wound healing, transwell migration, flow cytometer, and CCK8 assays. Immunofluorescence, pathology examinations, and targeted metabolomics were also used in tumor cells and tissues. mCherry-GFP-LC3 plasmid was used to detect autophagic flux. RESULTS We found for the first time that compared to normal ad libitum feeding, 6-h TRF inhibited lung cancer progression and reprogrammed the rhythms of metabolites or genes involved in glycolysis and the circadian rhythm in tumors. After TRF intervention, only timeless (TIM) gene among five lung cancer-associated clock genes was found to consistently align rhythm of tumor cells to that of tumor tissues. Further, we demonstrated that the anti-tumor effect upon TRF was partially mediated by the rhythmic downregulation of the TIM and the subsequent activation of autophagy. Combining TRF with TIM inhibition further enhanced the anti-tumor effect, comparable to treatment efficacy of chemotherapy in xenograft model. CONCLUSIONS Six-hour TRF inhibits lung cancer progression and reshapes circadian metabolism, which is partially mediated by the rhythmic downregulation of the TIM and the subsequent upregulation of autophagy.
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Affiliation(s)
- Dan Shi
- Center for Lipid Research, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, P.R. China.
- Department of Nutrition and Food Hygiene, School of Public Health, Chongqing Medical University, Chongqing, 400016, P.R. China.
- Research Center for Environment and Population Health, School of Public Health, Chongqing Medical University, Chongqing, 400016, P. R. China.
- Nutrition Innovation Platform-Sichuan and Chongqing, School of Public Health, Chongqing Medical University, Chongqing, China.
| | - Gaofeng Fang
- Center for Lipid Research, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, P.R. China
- Department of Nutrition and Food Hygiene, School of Public Health, Chongqing Medical University, Chongqing, 400016, P.R. China
| | - Qianyao Chen
- Center for Lipid Research, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, P.R. China
- Department of Nutrition and Food Hygiene, School of Public Health, Chongqing Medical University, Chongqing, 400016, P.R. China
| | - Jianling Li
- Center for Lipid Research, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, P.R. China
- Department of Nutrition and Food Hygiene, School of Public Health, Chongqing Medical University, Chongqing, 400016, P.R. China
| | - Xiongzhong Ruan
- Center for Lipid Research, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, P.R. China.
| | - Xuemei Lian
- Center for Lipid Research, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, P.R. China.
- Department of Nutrition and Food Hygiene, School of Public Health, Chongqing Medical University, Chongqing, 400016, P.R. China.
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Li F, Zhao C, Diao Y, Wang Z, Peng J, Yang N, Qiu C, Kong B, Li Y. MEX3A promotes the malignant progression of ovarian cancer by regulating intron retention in TIMELESS. Cell Death Dis 2022; 13:553. [PMID: 35715407 PMCID: PMC9205863 DOI: 10.1038/s41419-022-05000-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 05/31/2022] [Accepted: 06/07/2022] [Indexed: 01/21/2023]
Abstract
The latest research shows that RNA-binding proteins (RBPs) could serve as novel potential targets for cancer therapy. We used bioinformatics analysis to screen and identify the key RBPs in ovarian cancer, from which we found that Mex-3 RNA Binding Family Member A (MEX3A) was intimately associated with the clinical prognosis of ovarian cancer. Nevertheless, little is known about its biological roles in ovarian cancer. In this case, we observed that MEX3A was highly overexpressed in fresh-frozen ovarian cancer tissues. MEX3A knockdown suppressed the development and invasion of ovarian cancer cells, while MEX3A overexpression promoted the proliferation and invasion of ovarian cancer cells. Mechanistically, TIMELESS was the critical downstream target gene of MEX3A, as demonstrated through alternative splicing event analysis based on RNA-seq. MEX3A knockdown resulted in retention of intron twenty-three of TIMELESS mRNA and decreased TIMELESS mRNA owing to stimulation of nonsense-mediated RNA decay (NMD). Additionally, we found that TIMELESS overexpression with MEX3A knockdown partially restored the proliferation ability of ovarian cancer cells. The results of this paper demonstrated that the MEX3A/TIMELESS signaling pathway was a key regulator of ovarian cancer, and MEX3A was a novel possible treatment target for ovarian cancer patients.
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Affiliation(s)
- Fangfang Li
- grid.452402.50000 0004 1808 3430Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, Shandong 250012 China ,grid.452240.50000 0004 8342 6962Department of Obstetrics and Gynaecology, Binzhou Medical University Hospital, Binzhou, 256600 Shangdong China
| | - Chen Zhao
- grid.452402.50000 0004 1808 3430Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, Shandong 250012 China
| | - Yuchao Diao
- grid.412521.10000 0004 1769 1119Department of Obstetrics and Gynaecology, The Affiliated Hospital of Qingdao University, Qingdao, 266000 Shangdong China
| | - Zixiang Wang
- grid.27255.370000 0004 1761 1174Medical Integration and Practice Center, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012 China
| | - Jiali Peng
- grid.452402.50000 0004 1808 3430Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, Shandong 250012 China
| | - Ning Yang
- grid.452402.50000 0004 1808 3430Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, Shandong 250012 China
| | - Chunping Qiu
- grid.452402.50000 0004 1808 3430Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, Shandong 250012 China
| | - Beihua Kong
- grid.452402.50000 0004 1808 3430Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, Shandong 250012 China
| | - Yingwei Li
- grid.452402.50000 0004 1808 3430Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, Shandong 250012 China ,grid.27255.370000 0004 1761 1174Medical Integration and Practice Center, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012 China
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Colangelo T, Carbone A, Mazzarelli F, Cuttano R, Dama E, Nittoli T, Albanesi J, Barisciano G, Forte N, Palumbo O, Graziano P, di Masi A, Colantuoni V, Sabatino L, Bianchi F, Mazzoccoli G. Loss of circadian gene Timeless induces EMT and tumor progression in colorectal cancer via Zeb1-dependent mechanism. Cell Death Differ 2022; 29:1552-1568. [PMID: 35034102 PMCID: PMC9345857 DOI: 10.1038/s41418-022-00935-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 01/05/2022] [Accepted: 01/07/2022] [Indexed: 12/13/2022] Open
Abstract
The circadian gene Timeless (TIM) provides a molecular bridge between circadian and cell cycle/DNA replication regulatory systems and has been recently involved in human cancer development and progression. However, its functional role in colorectal cancer (CRC), the third leading cause of cancer-related deaths worldwide, has not been fully clarified yet. Here, the analysis of two independent CRC patient cohorts (total 1159 samples) reveals that loss of TIM expression is an unfavorable prognostic factor significantly correlated with advanced tumor stage, metastatic spreading, and microsatellite stability status. Genome-wide expression profiling, in vitro and in vivo experiments, revealed that TIM knockdown induces the activation of the epithelial-to-mesenchymal transition (EMT) program. Accordingly, the analysis of a large set of human samples showed that TIM expression inversely correlated with a previously established gene signature of canonical EMT markers (EMT score), and its ectopic silencing promotes migration, invasion, and acquisition of stem-like phenotype in CRC cells. Mechanistically, we found that loss of TIM expression unleashes ZEB1 expression that in turn drives the EMT program and enhances the aggressive behavior of CRC cells. Besides, the deranged TIM-ZEB1 axis sets off the accumulation of DNA damage and delays DNA damage recovery. Furthermore, we show that the aggressive and genetically unstable 'CMS4 colorectal cancer molecular subtype' is characterized by a lower expression of TIM and that patients with the combination of low-TIM/high-ZEB1 expression have a poorer outcome. In conclusion, our results as a whole suggest the engagement of an unedited TIM-ZEB1 axis in key pathological processes driving malignant phenotype acquisition in colorectal carcinogenesis. Thus, TIM-ZEB1 expression profiling could provide a robust prognostic biomarker in CRC patients, supporting targeted therapeutic strategies with better treatment selection and patients' outcomes.
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Affiliation(s)
- Tommaso Colangelo
- Fondazione IRCCS Casa Sollievo della Sofferenza, Cancer Biomarkers Unit, Viale Padre Pio 7, 71013, San Giovanni Rotondo, (FG), Italy
| | - Annalucia Carbone
- Fondazione IRCCS Casa Sollievo della Sofferenza, Department of Medical Sciences, Division of Internal Medicine and Chronobiology Laboratory, Viale Cappuccini snc, 71013, San Giovanni Rotondo, (FG), Italy
| | - Francesco Mazzarelli
- Fondazione IRCCS Casa Sollievo della Sofferenza, Cancer Biomarkers Unit, Viale Padre Pio 7, 71013, San Giovanni Rotondo, (FG), Italy
| | - Roberto Cuttano
- Fondazione IRCCS Casa Sollievo della Sofferenza, Cancer Biomarkers Unit, Viale Padre Pio 7, 71013, San Giovanni Rotondo, (FG), Italy
| | - Elisa Dama
- Fondazione IRCCS Casa Sollievo della Sofferenza, Cancer Biomarkers Unit, Viale Padre Pio 7, 71013, San Giovanni Rotondo, (FG), Italy
| | - Teresa Nittoli
- Fondazione IRCCS Casa Sollievo della Sofferenza, Cancer Biomarkers Unit, Viale Padre Pio 7, 71013, San Giovanni Rotondo, (FG), Italy
| | - Jacopo Albanesi
- Department of Sciences, Roma Tre University, Viale G. Marconi, 446, 00154, Rome, (RM), Italy
| | - Giovannina Barisciano
- Department of Sciences and Technologies, University of Sannio, Via Traiano, 3, 82100, Benevento, (BN), Italy
| | - Nicola Forte
- UOC- Patologia Clinica-Settore Anatomia Patologica, Ospedale Fatebenefratelli, Viale Principe di Napoli, 14/A, 82100, Benevento, (BN), Italy
| | - Orazio Palumbo
- Fondazione IRCCS Casa Sollievo della Sofferenza, Division of Medical Genetics, Viale Padre Pio, 7d, 71013, San Giovanni Rotondo, (FG), Italy
| | - Paolo Graziano
- Pathology Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, Viale Cappuccini snc, 71013, San Giovanni Rotondo, (FG), Italy
| | - Alessandra di Masi
- Department of Sciences, Roma Tre University, Viale G. Marconi, 446, 00154, Rome, (RM), Italy
| | - Vittorio Colantuoni
- Department of Sciences and Technologies, University of Sannio, Via Traiano, 3, 82100, Benevento, (BN), Italy
| | - Lina Sabatino
- Department of Sciences and Technologies, University of Sannio, Via Traiano, 3, 82100, Benevento, (BN), Italy
| | - Fabrizio Bianchi
- Fondazione IRCCS Casa Sollievo della Sofferenza, Cancer Biomarkers Unit, Viale Padre Pio 7, 71013, San Giovanni Rotondo, (FG), Italy.
| | - Gianluigi Mazzoccoli
- Fondazione IRCCS Casa Sollievo della Sofferenza, Department of Medical Sciences, Division of Internal Medicine and Chronobiology Laboratory, Viale Cappuccini snc, 71013, San Giovanni Rotondo, (FG), Italy.
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Xing X, Gu F, Hua L, Cui X, Li D, Wu Z, Zhang R. TIMELESS Promotes Tumor Progression by Enhancing Macrophages Recruitment in Ovarian Cancer. Front Oncol 2021; 11:732058. [PMID: 34490127 PMCID: PMC8417241 DOI: 10.3389/fonc.2021.732058] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 07/29/2021] [Indexed: 01/11/2023] Open
Abstract
Objective Ovarian cancer (OV) is the most fatal and frequent type of gynecological malignancy worldwide. TIMELESS (TIM), as a circadian clock gene, has been found to be highly expressed and predictive of poor prognosis in various cancers. However, the function of TIM in OV is not known. This study was designed to investigate the biological functions and underlying mechanisms of TIM during OV progression. Methods Cell viability assay, cell migration assay, immunohistochemistry staining, qPCR analyses, and tumor xenograft model were used to identify the functions of TIM in OV. Bioinformatics analyses, including GEPIA, cBioPortal, GeneMANIA, and TIMER, were used to analyze the gene expression, genetic alteration, and immune cell infiltration of TIM in OV. Results TIM is highly expressed in OV patients. TIM knockdown inhibited OV cell proliferation, migration, and invasion both in vitro and in vivo. Genetic alteration of TIM was identified in patients with OV. TIM co-expression network indicates that TIM had a wide effect on the immune cell infiltration and activation in OV. Further analysis and experimental verification revealed that TIM was positively correlated with macrophages infiltration in OV. Conclusions Our study unveiled a novel function of highly expressed TIM associated with immune cell especially macrophages infiltration in OV. TIM may serve as a potential prognostic biomarker and immunotherapy target for OV patients.
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Affiliation(s)
- Xin Xing
- Department of Obstetrics and Gynecology, Fengxian Hospital Affiliated to the Southern Medical University, Shanghai, China
| | - Fei Gu
- Department of Obstetrics and Gynecology, Fengxian Hospital Affiliated to the Southern Medical University, Shanghai, China
| | - Lanyu Hua
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Xiaoxiao Cui
- Department of Obstetrics and Gynecology, Fengxian Hospital Affiliated to the Southern Medical University, Shanghai, China
| | - Dongxue Li
- Shanghai Cancer Institute, Shanghai, China
| | - Zhiyong Wu
- Gynecology Department, Shanghai Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Rong Zhang
- Department of Obstetrics and Gynecology, Fengxian Hospital Affiliated to the Southern Medical University, Shanghai, China.,The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
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