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Damiescu R, Efferth T, Dawood M. Dysregulation of different modes of programmed cell death by epigenetic modifications and their role in cancer. Cancer Lett 2024; 584:216623. [PMID: 38246223 DOI: 10.1016/j.canlet.2024.216623] [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: 11/03/2023] [Revised: 12/19/2023] [Accepted: 01/07/2024] [Indexed: 01/23/2024]
Abstract
Modifications of epigenetic factors affect our lives and can give important information regarding one's state of health. In cancer, epigenetic modifications play a crucial role, as they influence various programmed cell death types. The purpose of this review is to investigate how epigenetic modifications, such as DNA methylation, histone modifications, and non-coding RNAs, influence various cell death processes in suppressing or promoting cancer development. Autophagy and apoptosis are the most investigated programmed cell death modes, as based on the tumor stage these cell death types can either promote or prevent cancer evolution. Therefore, our discussion focuses on how epigenetic modifications affect autophagy and apoptosis, as well as their diagnostic and therapeutical potential in combination with available chemotherapeutics. Additionally, we summarize the available data regarding the role of epigenetic modifications on other programmed cell death modes, such as ferroptosis, necroptosis, and parthanatos in cancer and discuss current advancements.
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Affiliation(s)
- R Damiescu
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, Mainz, Germany
| | - T Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, Mainz, Germany
| | - M Dawood
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, Mainz, Germany.
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2
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Therapeutic Strategies and Oncological Outcome of Peritoneal Metastases from Lung Cancer: A Systematic Review and Pooled Analysis. Curr Oncol 2023; 30:2928-2941. [PMID: 36975437 PMCID: PMC10047709 DOI: 10.3390/curroncol30030224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/21/2023] [Accepted: 02/24/2023] [Indexed: 03/05/2023] Open
Abstract
The peritoneum is an unusual site of metastases from lung cancer, and optimal management at the moment remains unclear and mostly based on palliative strategies. Therefore, the aim of the study was to investigate demographic characteristics, management and overall survival of patients with peritoneal metastases from lung cancer (PCLC). A PRISMA-compliant systematic review and pooled analysis was performed searching all English studies published until December 2022. PROSPERO, CRD42022349362. Inclusion criteria were original articles including patients with peritoneal carcinomatosis from lung cancer, specifying at least one outcome of interest. Exclusion criteria were being unable to retrieve patient data from articles, and the same patient series included in different studies. Among 1746 studies imported for screening, twenty-one were included (2783 patients). Mean overall survival was between 0.5 and 5 months after peritoneal carcinomatosis diagnosis and 9 and 21 months from lung cancer diagnosis. In total, 27% of patients underwent first-line or palliative chemotherapy and 7% of them surgery. Management differs significantly among published studies. The literature on PCLC is scarce. Its incidence is low but appears to be substantially rising and is likely to be an underestimation. Prognosis is very poor and therapeutic strategies have been limited and used in a minority of patients. Subcategories of PCLC patients may have an improved prognosis and may benefit from an aggressive oncological approach, including cytoreductive surgery. Further investigation would be needed in this regard.
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Mao Y, Cai F, Jiang T, Zhu X. Identification Invasion-Related Long Non-Coding RNAs in Lung Adenocarcinoma and Analysis of Competitive Endogenous RNA Regulatory Networks. Int J Gen Med 2023; 16:1817-1831. [PMID: 37213476 PMCID: PMC10198273 DOI: 10.2147/ijgm.s407266] [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: 02/18/2023] [Accepted: 05/01/2023] [Indexed: 05/23/2023] Open
Abstract
Background Cell invasion plays a vital role in cancer development and progression. Aberrant expression of long non-coding RNAs (lncRNAs) is also critical in carcinogenesis. However, the prognostic value of invasion-related lncRNAs in lung adenocarcinoma (LUAD) remains unknown. Methods Differentially expressed mRNAs (DEmRNAs), lncRNAs (DElncRNAs), and microRNAs (DEmiRNAs) were between LUAD and control samples. Pearson correlation analyses were performed to screen for invasion-related DElncRNAs (DEIRLs). Univariate and multivariate Cox regression algorithms were applied to identify key genes and construct the risk score model, which was evaluated using receiver operating characteristic (ROC) curves. Gene set enrichment analysis (GSEA) was used to explore the underlying pathways of the risk model. Moreover, an invasion-related competitive endogenous RNA (ceRNA) regulatory network was constructed. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was performed to detect the expression of prognostic lncRNAs in the LUAD and control samples. Results A total of 45 DElncRNAs were identified as DEIRLs. RP3-525N10.2, LINC00857, EP300-AS1, PDZRN3-AS1, and RP5-1102E8.3 were potential prognostic lncRNAs, the expression of which was verified by RT-qPCR in LUAD samples. Both the risk score model and nomogram used the prognostic lncRNAs. ROC curves showed the risk score model had moderate accuracy and the nomogram had high accuracy in predicting patient prognosis. GSEA results indicated that the risk score model was associated with many biological processes and pathways relevant to cell proliferation. A ceRNA regulatory network was constructed in which PDZRN3-miR-96-5p-CPEB1, EP300-AS1-miR-93-5p-CORO2B, and RP3-525N10.2-miR-130a-5p-GHR may be key invasion-related regulatory pathways in LUAD. Conclusion Our study identified five novel invasion-related prognostic lncRNAs (RP3-525N10.2, LINC00857, EP300-AS1, PDZRN3-AS1, and RP5-1102E8.3) and established an accurate model for predicting the prognosis of patients with LUAD. These findings enrich our understanding of the relationships between cell invasion, lncRNAs, and LUAD and may provide novel treatment directions.
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Affiliation(s)
- Yuze Mao
- Department of Cardio-Thoracic Surgery, First Affiliated Hospital of Jiamusi University, Jiamusi, Heilongjiang, 154000, People’s Republic of China
| | - Fangyu Cai
- Department of Thoracic Surgery, Beidahuang Industry Group General Hospital, Harbin, Heilongjiang, 150088, People’s Republic of China
| | - Tengjiao Jiang
- Department of Cardio-Thoracic Surgery, First Affiliated Hospital of Jiamusi University, Jiamusi, Heilongjiang, 154000, People’s Republic of China
| | - Xiaofeng Zhu
- Department of Cardio-Thoracic Surgery, First Affiliated Hospital of Jiamusi University, Jiamusi, Heilongjiang, 154000, People’s Republic of China
- Correspondence: Xiaofeng Zhu, Department of Cardio-Thoracic Surgery, First Affiliated Hospital of Jiamusi University, Jiamusi, Heilongjiang, 154000, People’s Republic of China, Tel +86-13845456700, Email
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Jiang A, Liu N, Wang J, Zheng X, Ren M, Zhang W, Yao Y. The role of PD-1/PD-L1 axis in idiopathic pulmonary fibrosis: Friend or foe? Front Immunol 2022; 13:1022228. [PMID: 36544757 PMCID: PMC9760949 DOI: 10.3389/fimmu.2022.1022228] [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: 08/22/2022] [Accepted: 11/16/2022] [Indexed: 12/08/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a devastating interstitial lung disease with a bleak prognosis. Mounting evidence suggests that IPF shares bio-molecular similarities with lung cancer. Given the deep understanding of the programmed cell death-1 (PD-1)/programmed death-ligand 1 (PD-L1) pathway in cancer immunity and the successful application of immune checkpoint inhibitors (ICIs) in lung cancer, recent studies have noticed the role of the PD-1/PD-L1 axis in IPF. However, the conclusions are ambiguous, and the latent mechanisms remain unclear. In this review, we will summarize the role of the PD-1/PD-L1 axis in IPF based on current murine models and clinical studies. We found that the PD-1/PD-L1 pathway plays a more predominant profibrotic role than its immunomodulatory role in IPF by interacting with multiple cell types and pathways. Most preclinical studies also indicated that blockade of the PD-1/PD-L1 pathway could attenuate the severity of pulmonary fibrosis in mice models. This review will bring significant insights into understanding the role of the PD-1/PD-L1 pathway in IPF and identifying new therapeutic targets.
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Affiliation(s)
- Aimin Jiang
- Department of Medical Oncology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Na Liu
- Department of Medical Oncology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Jingjing Wang
- Department of Medical Oncology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Xiaoqiang Zheng
- Department of Medical Oncology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China,Institute for Stem Cell & Regenerative Medicine, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Mengdi Ren
- Department of Medical Oncology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Wei Zhang
- Military Physical Education Teaching and Research Section of Air Force Medical Service Training Base, Air Force Medical University, Xi’an, China,*Correspondence: Yu Yao, ; Wei Zhang,
| | - Yu Yao
- Department of Medical Oncology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China,*Correspondence: Yu Yao, ; Wei Zhang,
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Autophagy-Related Gene Signature Highlights Metabolic and Immunogenic Status of Malignant Cells in Non-Small Cell Lung Cancer Adenocarcinoma. Cancers (Basel) 2022; 14:cancers14143462. [PMID: 35884522 PMCID: PMC9317787 DOI: 10.3390/cancers14143462] [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: 07/11/2022] [Accepted: 07/14/2022] [Indexed: 11/23/2022] Open
Abstract
Simple Summary The role of autophagy in lung cancers is still controversial, mainly because the visualization of autophagy levels in patients remains challenging. One interesting approach consists of studying autophagy at the transcriptomic level. In this line, many transcriptomics analyses performed on autophagy genes focused on the discovery of new biomarkers to predict the efficiency of antitumor therapies. However, the majority of these studies were based on global transcriptomic analysis of the whole tumor microenvironment, and few investigations have been performed on malignant cells themselves. The goal of this study was not to determine another new predictive signature based on autophagy-related genes. Instead, we investigated the expression of autophagy genes to understand the involvement of this process in lung cancer homeostasis. Specifically, we discovered a new autophagy signature that correlates with the metabolic and immunogenic status of malignant cells, supporting the relationship between autophagy and tumor growth in lung cancer patients. Abstract Autophagy is a self-degradative mechanism involved in many biological processes, including cell death, survival, proliferation or migration. In tumors, autophagy plays an important role in tumorigenesis as well as cancer progression and resistance to therapies. Usually, a high level of autophagy in malignant cells has been associated with tumor progression and poor prognostic for patients. However, the investigation of autophagy levels in patients remains difficult, especially because quantification of autophagy proteins is challenging in the tumor microenvironment. In this study, we analyzed the expression of autophagy genes in non-small cell lung (NSCLC) cancer patients using public datasets and revealed an autophagy gene signature for proliferative and immune-checkpoint-expressed malignant cells in lung adenocarcinoma (LUAD). Analysis of autophagy-related gene expression profiles in tumor and adjacent tissues revealed differential signatures, namely signature A (23 genes) and signature B (12 genes). Signature B correlated with a bad prognosis and poor overall and disease-specific survival. Univariate and multivariate analyses revealed that this signature was an independent factor for prognosis. Moreover, patients with high expression of signature B exhibited more genes related to proliferation and fewer genes related to immune cells or immune response. The analysis of datasets from sorted fresh tumor cells or single cells revealed that signature B is predominantly represented in malignant cells, with poor expression in pan-immune population or in fibroblast or endothelial cells. Interestingly, autophagy was increased in malignant cells exhibiting high levels of signature B, which correlated with an elevated expression of genes involved in cell proliferation and immune checkpoint signaling. Taken together, our analysis reveals a novel autophagy-based signature to define the metabolic and immunogenic status of malignant cells in LUAD.
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Luo XJ, He MM, Liu J, Zheng JB, Wu QN, Chen YX, Meng Q, Luo KJ, Chen DL, Xu RH, Zeng ZL, Liu ZX, Luo HY. LncRNA TMPO-AS1 promotes esophageal squamous cell carcinoma progression by forming biomolecular condensates with FUS and p300 to regulate TMPO transcription. Exp Mol Med 2022; 54:834-847. [PMID: 35760875 PMCID: PMC9243820 DOI: 10.1038/s12276-022-00791-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/20/2022] [Accepted: 03/28/2022] [Indexed: 12/24/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is one of the most life- and health-threatening malignant diseases worldwide, especially in China. Long noncoding RNAs (lncRNAs) have emerged as important regulators of tumorigenesis and tumor progression. However, the roles and mechanisms of lncRNAs in ESCC require further exploration. Here, in combination with a small interfering RNA (siRNA) library targeting specific lncRNAs, we performed MTS and Transwell assays to screen functional lncRNAs that were overexpressed in ESCC. TMPO-AS1 expression was significantly upregulated in ESCC tumor samples, with higher TMPO-AS1 expression positively correlated with shorter overall survival times. In vitro and in vivo functional experiments revealed that TMPO-AS1 promotes the proliferation and metastasis of ESCC cells. Mechanistically, TMPO-AS1 bound to fused in sarcoma (FUS) and recruited p300 to the TMPO promoter, forming biomolecular condensates in situ to activate TMPO transcription in cis by increasing the acetylation of histone H3 lysine 27 (H3K27ac). Targeting TMPO-AS1 led to impaired ESCC tumor growth in a patient-derived xenograft (PDX) model. We found that TMPO-AS1 is required for cell proliferation and metastasis in ESCC by promoting the expression of TMPO, and both TMPO-AS1 and TMPO might be potential biomarkers and therapeutic targets in ESCC. The role of a regulatory RNA in promoting esophageal squamous cell carcinoma (ESCC) has been clarified, revealing molecular details that might help in cancer diagnosis and treatment. Xiao-Jing Luo and colleagues at Sun Yat-sen University in China found that overproduction of an RNA molecule called thymopoietin-antisense RNA 1 (TMPO-AS1) in ESCC tissue samples from cancer patients was associated with shorter survival times. Overproduction of this RNA promoted proliferation and spread (metastasis) of the cancer cells. Research on details of the molecular mechanisms involved showed that the RNA ultimately activated the gene that codes for the protein hormone thymopoietin, which has previously been linked with various cancers. The authors suggest that TMPO-AS1 and thymopoietin could serve as diagnostic biomarkers of cancer and become targets for anti-cancer drugs.
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Affiliation(s)
- Xiao-Jing Luo
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, People's Republic of China.,Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, 510060, People's Republic of China
| | - Ming-Ming He
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, People's Republic of China
| | - Jia Liu
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, People's Republic of China
| | - Jia-Bo Zheng
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, People's Republic of China
| | - Qi-Nian Wu
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, People's Republic of China.,Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Yan-Xing Chen
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, People's Republic of China
| | - Qi Meng
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, People's Republic of China
| | - Kong-Jia Luo
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, People's Republic of China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Dong-Liang Chen
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, People's Republic of China
| | - Rui-Hua Xu
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, People's Republic of China.,Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, 510060, People's Republic of China
| | - Zhao-Lei Zeng
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, People's Republic of China.
| | - Ze-Xian Liu
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, People's Republic of China.
| | - Hui-Yan Luo
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, People's Republic of China. .,Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, 510060, People's Republic of China.
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Tian J, Fu C, Zeng X, Fan X, Wu Y. An Independent Prognostic Model Based on Ten Autophagy-Related Long Noncoding RNAs in Pancreatic Cancer Patients. Genet Res (Camb) 2022; 2022:3895396. [PMID: 35645615 PMCID: PMC9124146 DOI: 10.1155/2022/3895396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 04/27/2022] [Indexed: 11/17/2022] Open
Abstract
Purpose Pancreatic cancer (PC) is a common, highly lethal cancer with a low survival rate. Autophagy is involved in the occurrence and progression of PC. This study aims to explore the feasibility of using an autophagy-related long noncoding RNA (lncRNA) signature for assessing PC patient survival. Methods We obtained RNA sequencing and clinical data of patients from the TCGA website. Autophagy genes were obtained from the Human Autophagy Database. The prognostic model, generated through univariate and multivariate Cox regression analyses, included 10 autophagy-related lncRNAs. Receiver operating characteristic (ROC) curves and forest plots were generated for univariate and multivariate Cox regression analyses, to examine the predictive feasibility of the risk model. Gene set enrichment analysis (GSEA) was used to screen enriched gene sets. Results Twenty-eight autophagy-related lncRNAs were filtered out through univariate Cox regression analysis (P < 0.001). Ten autophagy-related lncRNAs, including 4 poor prognosis factors and 6 beneficial prognosis factors, were further screened via multivariate Cox regression analysis. The AUC value of the ROC curve was 0.815. GSEA results demonstrated that cancer-related gene sets were significantly enriched. Conclusion A signature based on ten autophagy-related lncRNAs was identified. This signature could be potentially used for evaluating clinical prognosis and might be used for targeted therapy against PC.
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Affiliation(s)
- Jiahui Tian
- Department of Laboratory, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan 410005, China
- Department of Medicine, Hunan Normal University, Changsha, Hunan 410005, China
| | - Chunyan Fu
- Department of Medicine, Hunan Normal University, Changsha, Hunan 410005, China
| | - Xuan Zeng
- Department of Medicine, Hunan Normal University, Changsha, Hunan 410005, China
| | - Xiaoxiao Fan
- Department of Laboratory, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan 410005, China
| | - Yi Wu
- Department of Laboratory, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan 410005, China
- Department of Medicine, Hunan Normal University, Changsha, Hunan 410005, China
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Guo W, Du K, Luo S, Hu D. Recent Advances of Autophagy in Non-Small Cell Lung Cancer: From Basic Mechanisms to Clinical Application. Front Oncol 2022; 12:861959. [PMID: 35600411 PMCID: PMC9115384 DOI: 10.3389/fonc.2022.861959] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/04/2022] [Indexed: 12/27/2022] Open
Abstract
Lung cancer is characterized by the most common oncological disease and leading cause of cancer death worldwide, of which a group of subtypes known as non-small cell lung cancer (NSCLC) accounts for approximately 85%. In the past few decades, important progression in the therapies of NSCLC has enhanced our understanding of the biology and progression mechanisms of tumor. The application of immunotherapy and small molecule tyrosine kinase inhibitors has brought significant clinical benefits in certain patients. However, early metastasis and the emergence of resistance to antitumor therapy have resulted in the relatively low overall cure and survival rates for NSCLC. Autophagy is a conserved process that allows cells to recycle unused or damaged organelles and cellular components. It has been reported to be related to the progression of NSCLC and resistance to targeted therapy and cytotoxic chemotherapy. Therefore, autophagy is considered as a potential therapeutic target for NSCLC. Mounting results have been reported about the combination of tyrosine kinase inhibitors and inhibitors of autophagy in models of NSCLC. This review aims to provide a comprehensive review on the roles of autophagy in NSCLC, focusing on related clinical data of agents that regulate autophagy in NSCLC. Furthermore, this study will provide a theoretical basis for further improvement of autophagy-based cancer therapy.
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Affiliation(s)
- Weina Guo
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Keye Du
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shanshan Luo
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Desheng Hu
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Biological Targeted Therapy, The Ministry of Education, Wuhan, China
- Department of immunology, Hubei Clinical Research Center of Cancer Immunotherapy, Wuhan, China
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Li X, Dai Z, Wu X, Zhang N, Zhang H, Wang Z, Zhang X, Liang X, Luo P, Zhang J, Liu Z, Zhou Y, Cheng Q, Chang R. The Comprehensive Analysis Identified an Autophagy Signature for the Prognosis and the Immunotherapy Efficiency Prediction in Lung Adenocarcinoma. Front Immunol 2022; 13:749241. [PMID: 35529878 PMCID: PMC9072793 DOI: 10.3389/fimmu.2022.749241] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 03/09/2022] [Indexed: 12/30/2022] Open
Abstract
Background Lung adenocarcinoma (LUAD) is a fatal malignancy in the world. Growing evidence demonstrated that autophagy-related genes regulated the immune cell infiltration and correlated with the prognosis of LUAD. However, the autophagy-based signature that can predict the prognosis and the efficiency of checkpoint immunotherapy in LUAD patients is yet to be discovered. Methods We used conventional autophagy-related genes to screen candidates for signature construction in TCGA cohort and 9 GEO datasets (tumor samples, n=2181; normal samples, n=419). An autophagy-based signature was constructed, its correlation with the prognosis and the immune infiltration of LUAD patients was explored. The prognostic value of the autophagy-based signature was validated in an independent cohort with 70 LUAD patients. Single-cell sequencing data was used to further characterize the various immunological patterns in tumors with different signature levels. Moreover, the predictive value of autophagy-based signature in PD-1 immunotherapy was explored in the IMvigor210 dataset. At last, the protective role of DRAM1 in LUAD was validated by in vitro experiments. Results After screening autophagy-related gene candidates, a signature composed by CCR2, ITGB1, and DRAM1 was established with the ATscore in each sample. Further analyses showed that the ATscore was significantly associated with immune cell infiltration and low ATscore indicated poor prognosis. Meanwhile, the prognostic value of ATscore was validated in our independent LUAD cohort. GSEA analyses and single-cell sequencing analyses revealed that ATscore was associated with the immunological status of LUAD tumors, and ATscore could predict the efficacy of PD-1 immunotherapy. Moreover, in vitro experiments demonstrated that the inhibition of DRAM1 suppressed the proliferation and migration capacity of LUAD cells. Conclusion Our study identified a new autophagy-based signature that can predict the prognosis of LUAD patients, and this ATscore has potential applicative value in the checkpoint therapy efficiency prediction.
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Affiliation(s)
- Xizhe Li
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, China
- Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, China
| | - Ziyu Dai
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Xianning Wu
- Department of Thoracic Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Nan Zhang
- One-third Lab, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hao Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Zeyu Wang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Xun Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Xisong Liang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yanwu Zhou
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, China
- Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Ruimin Chang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, China
- Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Changsha, China
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Li Y, Sun X. An Effective Hypoxia-Related Long Non-Coding RNA Assessment Model for Prognosis of Lung Adenocarcinoma. Front Genet 2022; 13:768971. [PMID: 35368654 PMCID: PMC8966506 DOI: 10.3389/fgene.2022.768971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 02/03/2022] [Indexed: 12/23/2022] Open
Abstract
Background: Lung adenocarcinoma (LUAD) represents one of the highest incidence rates worldwide. Hypoxia is a significant biomarker associated with poor prognosis of LUAD. However, there are no definitive markers of hypoxia-related long non-coding RNAs (lncRNAs) in LUAD. Methods: From The Cancer Genome Atlas (TCGA) and the Molecular Signatures Database (MSigDB), we acquired the expression of hypoxia-related lncRNAs and corresponding clinical information of LUAD patients. The hypoxia-related prognostic model was constructed by univariable COX regression analysis, least absolute shrinkage and selection operator (LASSO), and multivariable Cox regression analysis. To assess the performance of the model, the Kaplan–Meier (KM) survival and receiver operating characteristic (ROC) curve analyses were performed. Results: We found seven lncRNAs, AC022613.1, AC026355.1, GSEC, LINC00941, NKILA, HSPC324, and MYO16-AS1, as biomarkers of the potential hypoxia-related prognostic signature. In the low-risk group, patients had a better overall survival (OS). In addition, the results of ROC analysis indicated that the risk score predicted LUAD prognosis exactly. Furthermore, combining the expression of lncRNAs with clinical features, two predictive nomograms were constructed, which could accurately predict OS and had high clinical application value. Conclusion: In summary, the seven-lncRNA prognostic signature related to hypoxia might be useful in predicting clinical outcomes and provided new molecular targets for the research of LUAD patients.
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Affiliation(s)
- Yuanshuai Li
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, China
| | - Xiaofang Sun
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, China
- *Correspondence: Xiaofang Sun,
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Jiang A, Wang J, Liu N, Zheng X, Li Y, Ma Y, Zheng H, Chen X, Fan C, Zhang R, Fu X, Yao Y. Integration of Single-Cell RNA Sequencing and Bulk RNA Sequencing Data to Establish and Validate a Prognostic Model for Patients With Lung Adenocarcinoma. Front Genet 2022; 13:833797. [PMID: 35154287 PMCID: PMC8829512 DOI: 10.3389/fgene.2022.833797] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 01/14/2022] [Indexed: 12/27/2022] Open
Abstract
Background: Lung adenocarcinoma (LUAD) remains a lethal disease worldwide, with numerous studies exploring its potential prognostic markers using traditional RNA sequencing (RNA-seq) data. However, it cannot detect the exact cellular and molecular changes in tumor cells. This study aimed to construct a prognostic model for LUAD using single-cell RNA-seq (scRNA-seq) and traditional RNA-seq data. Methods: Bulk RNA-seq data were downloaded from The Cancer Genome Atlas (TCGA) database. LUAD scRNA-seq data were acquired from Gene Expression Omnibus (GEO) database. The uniform manifold approximation and projection (UMAP) was used for dimensionality reduction and cluster identification. Weighted Gene Correlation Network Analysis (WGCNA) was utilized to identify key modules and differentially expressed genes (DEGs). The non-negative Matrix Factorization (NMF) algorithm was used to identify different subtypes based on DEGs. The Cox regression analysis was used to develop the prognostic model. The characteristics of mutation landscape, immune status, and immune checkpoint inhibitors (ICIs) related genes between different risk groups were also investigated. Results: scRNA-seq data of four samples were integrated to identify 13 clusters and 9cell types. After applying differential analysis, NK cells, bladder epithelial cells, and bronchial epithelial cells were identified as significant cell types. Overall, 329 DEGs were selected for prognostic model construction through differential analysis and WGCNA. Besides, NMF identified two clusters based on DEGs in the TCGA cohort, with distinct prognosis and immune characteristics being observed. We developed a prognostic model based on the expression levels of six DEGs. A higher risk score was significantly correlated with poor survival outcomes but was associated with a more frequent TP53 mutation rate, higher tumor mutation burden (TMB), and up-regulation of PD-L1. Two independent external validation cohorts were also adopted to verify our results, with consistent results observed in them. Conclusion: This study constructed and validated a prognostic model for LUAD by integrating 10× scRNA-seq and bulk RNA-seq data. Besides, we observed two distinct subtypes in this population, with different prognosis and immune characteristics.
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Affiliation(s)
- Aimin Jiang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jingjing Wang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Na Liu
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiaoqiang Zheng
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yimeng Li
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yuyan Ma
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Haoran Zheng
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xue Chen
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Chaoxin Fan
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Rui Zhang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiao Fu
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yu Yao
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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Over Fifty Years of Life, Death, and Cannibalism: A Historical Recollection of Apoptosis and Autophagy. Int J Mol Sci 2021; 22:ijms222212466. [PMID: 34830349 PMCID: PMC8618802 DOI: 10.3390/ijms222212466] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 01/18/2023] Open
Abstract
Research in biomedical sciences has changed dramatically over the past fifty years. There is no doubt that the discovery of apoptosis and autophagy as two highly synchronized and regulated mechanisms in cellular homeostasis are among the most important discoveries in these decades. Along with the advancement in molecular biology, identifying the genetic players in apoptosis and autophagy has shed light on our understanding of their function in physiological and pathological conditions. In this review, we first describe the history of key discoveries in apoptosis with a molecular insight and continue with apoptosis pathways and their regulation. We touch upon the role of apoptosis in human health and its malfunction in several diseases. We discuss the path to the morphological and molecular discovery of autophagy. Moreover, we dive deep into the precise regulation of autophagy and recent findings from basic research to clinical applications of autophagy modulation in human health and illnesses and the available therapies for many diseases caused by impaired autophagy. We conclude with the exciting crosstalk between apoptosis and autophagy, from the early discoveries to recent findings.
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Zhao J, Lin X, Zhuang J, He F. Relationships of N6-Methyladenosine-Related Long Non-Coding RNAs With Tumor Immune Microenvironment and Clinical Prognosis in Lung Adenocarcinoma. Front Genet 2021; 12:714697. [PMID: 34777460 PMCID: PMC8585518 DOI: 10.3389/fgene.2021.714697] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/24/2021] [Indexed: 12/25/2022] Open
Abstract
Background: Lung adenocarcinoma (LUAD) is the major subtype of lung cancer and is associated with very high mortality. Emerging studies have shown that N6-methyladenosine (m6A)-related long non-coding (lnc) RNAs play crucial roles in tumor prognosis and the tumor immune microenvironment (TME). We aimed to explore the expression patterns of different m6A-related lncRNAs concerning patient prognosis and construct an m6A-related lncRNA prognostic model for LUAD. Methods: The prognostic value of m6A-related lncRNAs was investigated in LUAD samples from The Cancer Genome Atlas (TCGA). Potential prognostic m6A-related lncRNAs were selected by Pearson's correlation and univariate Cox regression analysis. Patients were divided into clusters using principal component analysis and the m6A-related lncRNA prognostic signature was calculated using least absolute shrinkage and selection operator (LASSO) Cox regression analysis. Results: Based on 91 prognostic m6A-related lncRNAs, we identified two m6A-related-lncRNA pattern clusters with different overall survival (OS) and different TMEs. We subsequently verified our findings multidimensionally by constructing a 13 m6A-related lncRNA prognostic signature (m6A-LPS) to calculate the risk score, which was robust in different subgroups. The receiver operating characteristic (ROC) curves and concordance index demonstrated that m6A-LPS harbored a promising ability to predict OS in TCGA data set and independent GSE11969 cohort. The risk score was also related to OS, TME, and clinical stage, and the risk score calculated by our model was also identified as independent prognostic predictive factors for LUAD patients after adjustment for age, smoking, gender, and stage. Enrichment analysis indicated that malignancy and drug resistance-associated pathways were more common in cluster2 (LUAD-unfavorable m6A-LPS). Furthermore, the results indicated that the signaling pathway enriched by the target gene of 13 m6A-related lncRNAs may be associated with metastasis and progression of cancer according to current studies. Conclusion: The current results indicated that different m6A-related-lncRNA patterns could affect OS and TME in patients with LUAD, and the prognostic signature based on 13 m6A-related lncRNAs may help to predict the prognosis in LUAD patients.
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Affiliation(s)
- Jianhui Zhao
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Xi Lin
- Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Jinman Zhuang
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Fei He
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou, China.,Fujian Provincial Key Laboratory of Tumor Microbiology, Fujian Digital Tumor Data Research Center, Fujian Medical University, Fuzhou, China
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