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Tashakori N, Kolour SSP, Ghafouri K, Ahmed SI, Kahrizi MS, Gerami R, Altafi M, Nazari A. Critical role of the long non-coding RNAs (lncRNAs) in radiotherapy (RT)-resistance of gastrointestinal (GI) cancer: Is there a way to defeat this resistance? Pathol Res Pract 2024; 258:155289. [PMID: 38703607 DOI: 10.1016/j.prp.2024.155289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/29/2024] [Accepted: 03/31/2024] [Indexed: 05/06/2024]
Abstract
Radiotherapy (RT) is a frequently used treatment for cervical cancer, effectively decreasing the likelihood of the disease returning in the same area and extending the lifespan of individuals with cervical cancer. Nevertheless, the primary reason for treatment failure in cancer patients is the cancer cells' resistance to radiation therapy (RT). Long non-coding RNAs (LncRNAs) are a subset of RNA molecules that do not code for proteins and are longer than 200 nucleotides. They have a significant impact on the regulation of gastrointestinal (GI) cancers biological processes. Recent research has shown that lncRNAs have a significant impact in controlling the responsiveness of GI cancer to radiation. This review provides a concise overview of the composition and operation of lncRNAs as well as the intricate molecular process behind radiosensitivity in GI cancer. Additionally, it compiles a comprehensive list of lncRNAs that are linked to radiosensitivity in such cancers. Furthermore, it delves into the potential practical implementation of these lncRNAs in modulating radiosensitivity in GI cancer.
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Affiliation(s)
- Nafiseh Tashakori
- Department of Internal Medicine, Faculty of Medicine, Tehran branch, Islamic Azad University, Tehran, Iran
| | | | - Kimia Ghafouri
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Sarah Ibrahem Ahmed
- Department of Anesthesia Techniques, Al-Noor University College, Nineveh, Iraq
| | | | - Reza Gerami
- Department of Radiology, Faculty of Medicine, AJA University of Medical Science, Tehran, Iran
| | - Mana Altafi
- Department of Radiology, Faculty of Biological Science and Technology, Shiraz Pardis Branch, Islamic Azad University, Shiraz, Iran.
| | - Afsaneh Nazari
- Department of Genetics, Faculty of Basic Sciences, Islamic Azad University, Zanjan Branch, Zanjan, Iran.
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Han L, Wang Z, Li C, Fan M, Wang Y, Sun G, Dai G. Functional identification and prediction of lncRNAs in esophageal cancer. Comput Biol Med 2023; 165:107205. [PMID: 37611425 DOI: 10.1016/j.compbiomed.2023.107205] [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: 04/26/2023] [Revised: 05/29/2023] [Accepted: 06/25/2023] [Indexed: 08/25/2023]
Abstract
Esophageal cancer is a highly lethal malignancy with poor prognosis, and the identification of molecular biomarkers is crucial for improving diagnosis and treatment. Long non-coding RNAs (lncRNAs) have been shown to play important roles in the development and progression of esophageal cancer. However, due to the time cost of biological experiments, only a small number of lncRNAs related to esophageal cancer have been discovered. Currently, computational methods have emerged as powerful tools for identifying and characterizing lncRNAs, as well as predicting their potential functions. Therefore, this article proposes a transformer-based method for identifying esophageal cancer-related lncRNAs. Experimental results show that the AUC and AUPR of this method are superior to other comparison methods, with an AUC of 0.87 and an AUPR of 0.83, and the identified lncRNA targets are closely associated with esophageal cancer. We focus on the role of esophageal cancer-related lncRNAs in the immune microenvironment, and fully explore the functions of the target genes regulated by lncRNAs. Enrichment analysis shows that the predicted target genes are related to multiple pathways involved in the occurrence, development, and prognosis of esophageal cancer. This not only demonstrates the effectiveness of the method but also indicates the accuracy of the prediction results.
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Affiliation(s)
- Lu Han
- Department of Oncology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China; Medical School of Chinese PLA, Beijing, China
| | - Zhikuan Wang
- Department of Oncology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Congyong Li
- Medical School of Chinese PLA, Beijing, China; Sixth Health Care Department, The Second Medical Center of PLA General Hospital, Beijing, China
| | - Mengjiao Fan
- Department of Oncology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China; Medical School of Chinese PLA, Beijing, China
| | - Yanrong Wang
- Department of Oncology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China; Medical School of Chinese PLA, Beijing, China
| | - Gang Sun
- Department of Gastroenterology and Hepatology, The First Medical Center of Chinese PLA General Hospital, Beijing, China.
| | - Guanghai Dai
- Department of Oncology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China.
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Xu K, Guo H, Xia A, Wang Z, Wang S, Wang Q. Non-coding RNAs in radiotherapy resistance: Roles and therapeutic implications in gastrointestinal cancer. Biomed Pharmacother 2023; 161:114485. [PMID: 36917887 DOI: 10.1016/j.biopha.2023.114485] [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: 01/03/2023] [Revised: 02/19/2023] [Accepted: 03/07/2023] [Indexed: 03/14/2023] Open
Abstract
Radiotherapy has become an indispensable and conventional means for patients with advanced solid tumors including gastrointestinal cancer. However, innate or acquired radiotherapy resistance remains a significant challenge and greatly limits the therapeutic effect, which results in cancer relapse and poor prognosis. Therefore, it is an urgent need to identify novel biomarkers and therapeutic targets for clarify the biological characteristics and mechanism of radiotherapy resistance. Recently, lots of studies have revealed that non-coding RNAs (ncRNAs) are the potential indicators and regulators of radiotherapy resistance via the mediation of various targets/pathways in different cancers. These findings may serve as a potential therapeutic strategy to overcome radiotherapy resistance. In this review, we will shed light on the recent findings regarding the functions and regulatory mechanisms of ncRNAs following radiotherapy, and comprehensively discuss their potential as biomarkers and therapeutic targets in radiotherapy resistance of gastrointestinal cancer.
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Affiliation(s)
- Kaiyue Xu
- Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210000, China; Department of Radiation Oncology, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing University Medical School, Suzhou 215000, China
| | - Huimin Guo
- Department of Gastroenterology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210000, China
| | - Anliang Xia
- Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210000, China
| | - Zhangding Wang
- Department of Gastroenterology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210000, China.
| | - Shouyu Wang
- Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210000, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University Medical School, Nanjing 210093, China.
| | - Qiang Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230000, China; Medical Transformation Research Institute, The First Affiliated Hospital of Anhui Medical University, Hefei 230000, China.
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Noncoding RNAs in esophageal cancer: A glimpse into implications for therapy resistance. Pharmacol Res 2023; 188:106678. [PMID: 36709789 DOI: 10.1016/j.phrs.2023.106678] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 01/09/2023] [Accepted: 01/25/2023] [Indexed: 01/27/2023]
Abstract
Esophageal cancer (EC) is one of the most common malignancies of the digestive system and has a high morbidity and mortality worldwide. Chemotherapy in combination with radiotherapy is one of the most important treatment modalities for EC. Chemoradiotherapy is currently acknowledged worldwide as being the standard treatment for locally advanced or unresectable disease. Unfortunately, due to the existence of therapy resistance, a number of EC patients fail to benefit from drug or irradiation treatment, which ultimately leads to poor outcomes. Considerable efforts have been made to explore the mechanisms underlying the therapy resistance of EC. Notably, noncoding RNAs (ncRNAs), including microRNAs (miRNAs), long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs), are current research areas for the modulation of therapy responses and may serve as new targets to overcome treatment resistance in EC. Herein, we summarized the mechanisms by which ncRNAs are involved in drug and radiation resistance in EC and highlighted their role in promoting or repressing treatment resistance. Additionally, we discussed the clinical relevance of ncRNAs, which may serve as potential therapeutic targets and predictive biomarkers for EC.
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Zhu C, Jiang J, Feng G, Fan S. The exciting encounter between lncRNAs and radiosensitivity in IR-induced DNA damage events. Mol Biol Rep 2023; 50:1829-1843. [PMID: 36507968 DOI: 10.1007/s11033-022-07966-1] [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: 01/08/2022] [Accepted: 09/22/2022] [Indexed: 12/14/2022]
Abstract
Radiation therapy is a commonly used tool in cancer management due to its ability to destroy malignant tumors. Mechanically, the efficacy of radiotherapy mainly depends on the inherent radiosensitivity of cancer cells and surrounding normal tissues, which mostly accounts for molecular dynamics associated with radiation-induced DNA damage. However, the relationship between radiosensitivity and DNA damage mechanism deserves to be further probed. As the well-established RNA regulators or effectors, long noncoding RNAs (lncRNAs) dominate vital roles in modulating ionizing radiation response by targeting crucial molecular pathways, including DNA damage repair. Recently, emerging evidence has constantly confirmed that overexpression or inhibition of lncRNAs can greatly influence the sensitivity of radiotherapy for many kinds of cancers, by driving a diverse array of DNA damage-associated signaling cascades. In conclusion, this review critically summarizes the recent progress in the molecular mechanism of IR-responsive lncRNAs in the context of radiation-induced DNA damage. The different response of lncRNAs when IR exposure. IR exposure can trigger the changes in expression pattern and subcellular localization of lncRNAs that influences the different radiology processes.
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Affiliation(s)
- Changchun Zhu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, 238 Baidi Road, 300192, Tianjin, PR China
| | - Jin Jiang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, 238 Baidi Road, 300192, Tianjin, PR China
| | - Guoxing Feng
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, 238 Baidi Road, 300192, Tianjin, PR China.
| | - Saijun Fan
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, 238 Baidi Road, 300192, Tianjin, PR China.
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Zheng J, Chen X, Huang B, Li J. A novel immune-related radioresistant lncRNAs signature based model for risk stratification and prognosis prediction in esophageal squamous cell carcinoma. Front Genet 2022; 13:921902. [PMID: 36147506 PMCID: PMC9485730 DOI: 10.3389/fgene.2022.921902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 07/25/2022] [Indexed: 12/16/2022] Open
Abstract
Background and purpose: Radioresistance remains a major reason of radiotherapeutic failure in esophageal squamous cell carcinoma (ESCC). Our study is to screen the immune-related long non-coding RNA (ir-lncRNAs) of radiation-resistant ESCC (rr-ESCC) via Gene Expression Omnibus (GEO) database and to construct a prognostic risk model. Methods: Microarray data (GSE45670) related to radioresistance of ESCC was downloaded from GEO. Based on pathologic responses after chemoradiotherapy, patients were divided into a non-responder (17 samples) and responder group (11 samples), and the difference in expression profiles of ir-lncRNAs were compared therein. Ir-lncRNA pairs were constructed for the differentially expressed lncRNAs as prognostic variables, and the microarray dataset (GSE53625) was downloaded from GEO to verify the effect of ir-lncRNA pairs on the long-term survival of ESCC. After modelling, patients are divided into high- and low-risk groups according to prognostic risk scores, and the outcomes were compared within groups based on the COX proportional hazards model. The different expression of ir-lncRNAs were validated using ECA 109 and ECA 109R cell lines via RT-qPCR. Results: 26 ir-lncRNA genes were screened in the GSE45670 dataset with differential expression, and 180 ir-lncRNA pairs were constructed. After matching with ir-lncRNA pairs constructed by GSE53625, six ir-lncRNA pairs had a significant impact on the prognosis of ESCC from univariate analysis model, of which three ir-lncRNA pairs were significantly associated with prognosis in multivariate COX analysis. These three lncRNA pairs were used as prognostic indicators to construct a prognostic risk model, and the predicted risk scores were calculated. With a median value of 2.371, the patients were divided into two groups. The overall survival (OS) in the high-risk group was significantly worse than that in the low-risk group (p < 0.001). The 1-, 2-, and 3-year prediction performance of this risk-model was 0.666, 0.702, and 0.686, respectively. In the validation setting, three ir-lncRNAs were significantly up-regulated, while two ir-lncRNAs were obviouly down-regulated in the responder group. Conclusion: Ir-lncRNAs may be involved in the biological regulation of radioresistance in patients with ESCC; and the prognostic risk-model, established by three ir-lncRNAs pairs has important clinical value in predicting the prognosis of patients with rr-ESCC.
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Affiliation(s)
- Jianqing Zheng
- Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian, China
- Department of Radiation Oncology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China
- The Graduate School of Fujian Medical University, Fuzhou, Fujian, China
| | - Xiaohui Chen
- Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian, China
- The Graduate School of Fujian Medical University, Fuzhou, Fujian, China
- Department of Thoracic Surgery, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian, China
| | - Bifen Huang
- Department of Obstetrics and Gynecology, Quanzhou Medical College People’s Hospital Affiliated, Fuzhou, Fujian, China
| | - Jiancheng Li
- Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian, China
- The Graduate School of Fujian Medical University, Fuzhou, Fujian, China
- Department of Radiation Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian, China
- *Correspondence: Jiancheng Li,
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Wang M, Xia H, Yan Q, Liu W, Liu M, Wang X. Identification of Pyroptosis-Related Gene Signatures and Construction of the Risk Model to Predict BCR in Prostate Cancer. Front Mol Biosci 2022; 9:850758. [PMID: 35813821 PMCID: PMC9259891 DOI: 10.3389/fmolb.2022.850758] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 04/25/2022] [Indexed: 12/27/2022] Open
Abstract
Prostate cancer is one of the most common malignant tumors in men. Pyroptosis is related to tumor immune infiltration and tumor microenvironment (TME) and has been confirmed to be related to the progression of a variety of tumors. However, the relationship between prostate cancer and pyroptosis, as well as TME and tumor immune infiltration, has not been discussed yet. We obtained and combined the RNA-seq data of prostate cancer from TCGA and GEO databases, analyzed the differential expression of pyroptosis-related genes (PRGs), and divided them into two groups according to the PRG expression level. The relationship between pyroptosis subtypes and the TME of prostate cancer was further verified, and the differential expression genes (DEGs) in the two subtypes were identified. The relationship between the DEGs and clinicopathology was explored and KEGG and GO enrichment analysis was conducted; it was found that most DEGs were enriched in immune-related pathways. Then, we randomly divided datasets into training and testing sets, performed the LASSO and multicox progression analysis, selected eight genes as prognostic signatures and used the eight genes, calculated the risk score, and then separated the entire cohort into high- and low-risk groups. The prognosis between two groups and the 1-, 3-, and 5-year ROC curves of biochemical relapse (BCR) were verified in training, testing, and the entire cohort, respectively. The TME, CSC index, mutation, and drug susceptibility were also discussed.
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Affiliation(s)
- Miaomiao Wang
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Haoran Xia
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Qiuxia Yan
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Peking University Fifth School of Clinical Medicine, Beijing, China
| | - Wen Liu
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Ming Liu
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Xuan Wang
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- *Correspondence: Xuan Wang,
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Lin P, Xing W, Ren Q, Wang Q, Yan J, Mao G. LncRNAs as Theragnostic Biomarkers for Predicting Radioresistance in Cancer: A Systematic Review and Meta-Analysis. Front Oncol 2022; 12:767750. [PMID: 35692742 PMCID: PMC9176206 DOI: 10.3389/fonc.2022.767750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 04/21/2022] [Indexed: 11/23/2022] Open
Abstract
Background Radioresistance is the major obstacle after cancer radiotherapy. The dysregulation of long non-coding RNAs (lncRNAs) was closely related the radioresistance response. This meta-analysis was aimed to interpret the relationship between lncRNAs and radiotherapy responses in different cancers. Method The studies were selected from databases including PubMed, ISI Web of Science, Embase, Google Scholar, PMC, and CNKI (China National Knowledge Infrastructure). The publication time was limited to before March 20, 2021. The hazard ratios (HRs) and 95% confidence interval were calculated with random-effects models. Subgroup analyses, sensitivity analyses, and publication bias were also conducted. Result Twenty-seven lncRNAs in 14 cancer types were investigated, in which 23 lncRNAs were upregulated and four lncRNAs were downregulated. Dysregulation of these lncRNAs were found to be related to radioresistance response. The pooled HR and 95% confidence interval for the combined up-regulated lncRNAs was 1.73 (95% CI=1.50-2.00; P< 0.01) and down-regulated lncRNAs was 2.09 (95% CI= 1.60-2.72; P< 0.01). The HR values of the subgroup analysis for glioma (HR= 2.22, 95% CI= 1.79-2.74; p< 0.01), non-small cell lung cancer (HR=1.48, 95% CI=1.18-1.85; P<0.01), nasopharyngeal carcinoma (HR=4.26; 95% CI= 1.58-11.46; P< 0.01), and breast cancer (HR=1.29; 95% CI= 1.08-1.54; P< 0.01) were obtained. Moreover, the expression of lncRNAs was significantly related to overall survival of patients no matter if the sample size was >50 or not. In addition, the HR values of the subgroup analysis for lncRNA H19 (HR=2.68; 95% CI= 1.92-3.74; P <0.01), lncRNA FAM201A (HR=2.15; 95% CI= 1.15-3.99; P <0.01), and lncRNA HOTAIR (HR=1.22; 95% CI= 0.98-1.54; P =0.08) were also obtained. Conclusion LncRNAs can induce cancer radioresistance by regulating cell death-related signaling pathways. Results indicated that lncRNAs, especially lncRNA H19, FAM201A, and HOTAIR, could be considered as a predictive theragnostic biomarker to evaluate radiotherapy response.
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Affiliation(s)
- Ping Lin
- Department of Geriatrics, The Third People’s Hospital of Hangzhou, Hangzhou, China
| | - Wenmin Xing
- Zhejiang Provincial Key Laboratory of Geriatrics, Department of Geriatrics, Zhejiang Hospital, Hangzhou, China
| | - Qian Ren
- Department of Geriatrics, The Third People’s Hospital of Hangzhou, Hangzhou, China
| | - Qin Wang
- Department of Geriatrics, The Third People’s Hospital of Hangzhou, Hangzhou, China
| | - Jing Yan
- Zhejiang Provincial Key Laboratory of Geriatrics, Department of Geriatrics, Zhejiang Hospital, Hangzhou, China
- *Correspondence: Genxiang Mao, ; Jing Yan,
| | - Genxiang Mao
- Zhejiang Provincial Key Laboratory of Geriatrics, Department of Geriatrics, Zhejiang Hospital, Hangzhou, China
- *Correspondence: Genxiang Mao, ; Jing Yan,
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