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Xu H, Li W, Xue K, Zhang H, Li H, Yu H, Hu L, Gu Y, Li H, Sun X, Liu Q, Wang D. ADAR1-regulated miR-142-3p/RIG-I axis suppresses antitumor immunity in nasopharyngeal carcinoma. Noncoding RNA Res 2025; 10:116-129. [PMID: 39351449 PMCID: PMC11439846 DOI: 10.1016/j.ncrna.2024.08.003] [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: 06/24/2024] [Revised: 08/04/2024] [Accepted: 08/14/2024] [Indexed: 10/04/2024] Open
Abstract
Following the initial treatment of nasopharyngeal carcinoma (NPC), tumor progression often portends an adverse prognosis for these patients. MicroRNAs (miRNAs) have emerged as critical regulators of tumor immunity, yet their intricate mechanisms in NPC remain elusive. Through comprehensive miRNA sequencing, tumor tissue microarrays and tissue samples analysis, we identified miR-142-3p as a significantly upregulated miRNA that is strongly associated with poor prognosis in recurrent NPC patients. To elucidate the underlying molecular mechanism, we employed RNA sequencing, coupled with cellular and tissue assays, to identify the downstream targets and associated signaling pathways of miR-142-3p. Our findings revealed two potential targets, CFL2 and WASL, which are directly targeted by miR-142-3p. Functionally, overexpressing CFL2 or WASL significantly reversed the malignant phenotypes induced by miR-142-3p both in vitro and in vivo. Furthermore, signaling pathway analysis revealed that miR-142-3p repressed the RIG-I-mediated immune defense response in NPC by inhibiting the nuclear translocation of IRF3, IRF7 and p65. Moreover, we discovered that ADAR1 physically interacted with Dicer and promoted the formation of mature miR-142-3p in a dose-dependent manner. Collectively, ADAR1-mediated miR-142-3p processing promotes tumor progression and suppresses antitumor immunity, indicating that miR-142-3p may serve as a promising prognostic biomarker and therapeutic target for NPC patients.
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Affiliation(s)
- Haoyuan Xu
- Department of Otolaryngology-Head and Neck Surgery, Affiliated Eye Ear Nose and Throat Hospital, Fudan University, Shanghai, 200031, China
| | - Wanpeng Li
- Department of Otolaryngology-Head and Neck Surgery, Affiliated Eye Ear Nose and Throat Hospital, Fudan University, Shanghai, 200031, China
| | - Kai Xue
- Department of Otolaryngology-Head and Neck Surgery, Affiliated Eye Ear Nose and Throat Hospital, Fudan University, Shanghai, 200031, China
| | - Huankang Zhang
- Department of Otolaryngology-Head and Neck Surgery, Affiliated Eye Ear Nose and Throat Hospital, Fudan University, Shanghai, 200031, China
| | - Han Li
- Department of Otolaryngology-Head and Neck Surgery, Affiliated Eye Ear Nose and Throat Hospital, Fudan University, Shanghai, 200031, China
| | - Haoran Yu
- Department of Otorhinolaryngology-Head and Neck Surgery, Affiliated Zhongshan Hospital, Fudan University, Shanghai, 200030, China
| | - Li Hu
- Department of Otolaryngology-Head and Neck Surgery, Affiliated Eye Ear Nose and Throat Hospital, Fudan University, Shanghai, 200031, China
| | - Yurong Gu
- Department of Otolaryngology-Head and Neck Surgery, Affiliated Eye Ear Nose and Throat Hospital, Fudan University, Shanghai, 200031, China
| | - Houyong Li
- Department of Otolaryngology-Head and Neck Surgery, Affiliated Eye Ear Nose and Throat Hospital, Fudan University, Shanghai, 200031, China
| | - Xicai Sun
- Department of Otolaryngology-Head and Neck Surgery, Affiliated Eye Ear Nose and Throat Hospital, Fudan University, Shanghai, 200031, China
| | - Quan Liu
- Department of Otolaryngology-Head and Neck Surgery, Affiliated Eye Ear Nose and Throat Hospital, Fudan University, Shanghai, 200031, China
| | - Dehui Wang
- Department of Otolaryngology-Head and Neck Surgery, Affiliated Eye Ear Nose and Throat Hospital, Fudan University, Shanghai, 200031, China
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Hu F, Qiu Z. Spotlight on the function and trends on extrachromosomal circular DNA (eccDNA): A bibliometric analysis from 2008 - 2023. Exp Cell Res 2025; 444:114318. [PMID: 39547353 DOI: 10.1016/j.yexcr.2024.114318] [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: 07/22/2024] [Revised: 09/28/2024] [Accepted: 10/31/2024] [Indexed: 11/17/2024]
Abstract
Extrachromosomal circular DNA (eccDNA),a type of circular DNA that has a nucleosomal structure, is widely distributed in eukaryotic chromosomes and has been found to modulate genome instability and plasticity, playing a role in regulating gene expression and genome evolution. To comprehensively outline the stages of eccDNA research development, including author collaborations, research topics and hotspots, and their temporal evolution trends, we conducted a bibliometric analysis of 242 publications related to eccDNA research published from 2008 to 2023 in the Web of Science Core Collection. The bibliometric analysis was performed using CiteSpace, the R package Bibliometrix, and VOSviewer. The USA, the University of California system, and Turner Km were found to be the most influential nation, organization, and author in this field, respectively. The exploration of Characterization and Diagnosis, Heterochromatin,Circ-Seq and Cancer Drug Resistance on eccDNA are the most concerned hotspots. EccDNA research has become a rapidly growing hotspot, receiving extensive attention from scholars in recent years. This study is the first to investigate the development and current challenges of eccDNA research through bibliometric analysis.The research on eccDNA has advanced from disorder to more intricate molecular functions. At present, the rapid growth of eccDNA studies in cancer has not been accompanied by an intuitive analysis of its evolutionary patterns. This review provides an overview of eccDNA's biological characteristics and functions, with a focus on its role in cancer research.
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Affiliation(s)
- Fan Hu
- Zhuhai Jingyuan Biomedical Technology Co., LTD, Zhuhai, Guangdong, 519000, People's Republic of China.
| | - Zhengqi Qiu
- Faculty of Medicine, Macau University of Science and Technology, Est. Seak Pai Van Praia Park, Rés-Do-Chão R, Coloane, Macao, 999078, People's Republic of China
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Lin Z, Dai F, Li B, Zhao Y, Wang C. Integrating Circle-Seq with transcriptomics reveals genome-wide characterization of extrachromosomal circular DNA for dilated cardiomyopathy. Biol Direct 2024; 19:125. [PMID: 39614284 DOI: 10.1186/s13062-024-00556-0] [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: 09/17/2024] [Accepted: 10/28/2024] [Indexed: 12/01/2024] Open
Abstract
BACKGROUND Extrachromosomal circular DNAs (eccDNAs) are commonly found in various tumors and play a critical role in promoting oncogenesis. However, little is known about the characteristics and nature of eccDNAs in human heart failure. The aim of this study was to comprehensively analyze eccDNAs in human heart failure caused by dilated cardiomyopathy (DCM) and explore their potential functions. METHODS Circle-Seq and RNA-Seq were performed in cardiac tissue samples obtained from patients with DCM and healthy controls to identify eccDNAs and corresponding genes. Inward PCR, outward PCR and Sanger sequencing were conducted to validate the circular structure of eccDNAs. Bioinformatics was employed to probe the transcriptional activity of eccDNAs and their potential roles in the development of DCM. Ligase assisted minicircle accumulation strategy was used to synthesize a 500 bp circular DNA with a random sequence. RESULTS EccDNAs originated from all chromosomes, with the majority being less than 1 kb in size and about half containing genes or gene fragments. They were derived from specific repeat elements and primarily mapped to 5'UTR, 3'UTR, and CpG islands. Gene-rich chromosomes 17 and 19 exhibited higher eccDNA enrichment. Sequence motifs flanking eccDNA junction sites displayed frequent nucleotide repeats. The circular structure of eccDNAs were confirmed. Integration of Circle-Seq and RNA-Seq data identified that large eccDNAs can be directly transcribed in non-dividing cardiomyocytes, indicating their potential roles in gene expression. Small circular DNA elicited a stronger cytokine response than linear DNA with the same sequence. CONCLUSIONS Our work provided a detailed profiling of eccDNAs in both healthy and DCM hearts and demonstrated the potential functions of both large and small eccDNAs. These findings enhance the comprehension of the role of eccDNAs in cardiac pathophysiology and establish a theoretical foundation for future investigations on eccDNAs in DCM.
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Affiliation(s)
- Zhenhao Lin
- Department of Cardiology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200001, China
| | - Fangjie Dai
- Department of Cardiology, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Bo Li
- Department of Radiology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
- Key Laboratory of Anesthesiology, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yongchao Zhao
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563099, China.
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai, 200030, China.
| | - Changqian Wang
- Department of Cardiology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200001, China.
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Ming Y, Gong Y, Fu X, Ouyang X, Peng Y, Pu W. Small-molecule-based targeted therapy in liver cancer. Mol Ther 2024; 32:3260-3287. [PMID: 39113358 PMCID: PMC11489561 DOI: 10.1016/j.ymthe.2024.08.001] [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: 11/22/2023] [Revised: 03/13/2024] [Accepted: 08/02/2024] [Indexed: 08/23/2024] Open
Abstract
Liver cancer is one of the most prevalent malignant tumors worldwide. According to the Barcelona Clinic Liver Cancer staging criteria, clinical guidelines provide tutorials to clinical management of liver cancer at their individual stages. However, most patients diagnosed with liver cancer are at advanced stage; therefore, many researchers conduct investigations on targeted therapy, aiming to improve the overall survival of these patients. To date, small-molecule-based targeted therapies are highly recommended (first line: sorafenib and lenvatinib; second line: regorafenib and cabozantinib) by current the clinical guidelines of the American Society of Clinical Oncology, European Society for Medical Oncology, and National Comprehensive Cancer Network. Herein, we summarize the small-molecule-based targeted therapies in liver cancer, including the approved and preclinical therapies as well as the therapies under clinical trials, and introduce their history of discovery, clinical trials, indications, and molecular mechanisms. For drug resistance, the revealed mechanisms of action and the combination therapies are also discussed. In fact, the known small-molecule-based therapies still have limited clinical benefits to liver cancer patients. Therefore, we analyze the current status and give our ideas for the urgent issues and future directions in this field, suggesting clues for novel techniques in liver cancer treatment.
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Affiliation(s)
- Yue Ming
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Yanqiu Gong
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xuewen Fu
- Jinhua Huanke Environmental Technology Co., Ltd., Jinhua 321000, China
| | - Xinyu Ouyang
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China; West China School of Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yong Peng
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China; Frontier Medical Center, Tianfu Jincheng Laboratory, Chengdu 610212, China.
| | - Wenchen Pu
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China; West China School of Medicine, West China Hospital, Sichuan University, Chengdu 610041, China.
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Yu M, Yu H, Wang H, Xu X, Sun Z, Chen W, Yu M, Liu C, Jiang M, Zhang X. Tumor‑associated macrophages activated in the tumor environment of hepatocellular carcinoma: Characterization and treatment (Review). Int J Oncol 2024; 65:100. [PMID: 39239752 PMCID: PMC11387121 DOI: 10.3892/ijo.2024.5688] [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: 05/09/2024] [Accepted: 08/08/2024] [Indexed: 09/07/2024] Open
Abstract
Hepatocellular carcinoma (HCC) tissue is rich in dendritic cells, T cells, B cells, macrophages, natural killer cells and cellular stroma. Together they form the tumor microenvironment (TME), which is also rich in numerous cytokines. Tumor‑associated macrophages (TAMs) are involved in the regulation of tumor development. TAMs in HCC receive stimuli in different directions, polarize in different directions and release different cytokines to regulate the development of HCC. TAMs are mostly divided into two cell phenotypes: M1 and M2. M1 TAMs secrete pro‑inflammatory mediators, and M2 TAMs secrete a variety of anti‑inflammatory and pro‑tumorigenic substances. The TAM polarization in HCC tumors is M2. Both direct and indirect methods for TAMs to regulate the development of HCC are discussed. TAMs indirectly support HCC development by promoting peripheral angiogenesis and regulating the immune microenvironment of the TME. In terms of the direct regulation between TAMs and HCC cells, the present review mainly focuses on the molecular mechanism. TAMs are involved in both the proliferation and apoptosis of HCC cells to regulate the quantitative changes of HCC, and stimulate the related invasive migratory ability and cell stemness of HCC cells. The present review aims to identify immunotherapeutic options based on the mechanisms of TAMs in the TME of HCC.
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Affiliation(s)
- Mingkai Yu
- School of Clinical Medicine and Basic Medical Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, Shandong 250000, P.R. China
| | - Haixia Yu
- Pharmacy College, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, Shandong 250000, P.R. China
| | - Hongmei Wang
- Department of Pharmacology, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Xiaoya Xu
- School of Clinical Medicine and Basic Medical Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, Shandong 250000, P.R. China
| | - Zhaoqing Sun
- School of Clinical Medicine and Basic Medical Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, Shandong 250000, P.R. China
| | - Wenshuai Chen
- School of Clinical Medicine and Basic Medical Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, Shandong 250000, P.R. China
| | - Miaomiao Yu
- School of Clinical Medicine and Basic Medical Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, Shandong 250000, P.R. China
| | - Chunhua Liu
- Department of Physiology and Neurobiology, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, Shandong 250000, P.R. China
| | - Mingchun Jiang
- Department of Physiology and Neurobiology, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, Shandong 250000, P.R. China
| | - Xiaowei Zhang
- Department of Gastroenterology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong 271000, P.R. China
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Peng Y, Tao H, Wang G, Wu M, Xu T, Wen C, Zheng X, Dai Y. Exploring the Role of Extrachromosomal Circular DNA in Human Diseases. Cytogenet Genome Res 2024:1-13. [PMID: 39348807 DOI: 10.1159/000541563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Accepted: 09/19/2024] [Indexed: 10/02/2024] Open
Abstract
BACKGROUND Extrachromosomal circular DNA (eccDNA) has emerged as a central focus in molecular biology, with various types being found across species through advanced techniques, including high-throughput sequencing. This dynamic molecule exerts a significant influence on aging and immune function and plays pivotal roles in autoimmune diseases, type 2 diabetes mellitus, cancer, and genetic disorders. SUMMARY This comprehensive review investigates the classification, characteristics, formation processes, and multifaceted functions of eccDNA, providing an in-depth exploration of its mechanisms in diverse diseases. KEY MESSAGES The goal of this review was to establish a robust theoretical foundation for a more comprehensive understanding of eccDNA, offering valuable insights for the development of clinical diagnostics and innovative therapeutic strategies in the context of related diseases.
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Affiliation(s)
- Yali Peng
- School of Medicine, Anhui University of Science and Technology, Huainan, China
| | - Huihui Tao
- School of Medicine, Anhui University of Science and Technology, Huainan, China
- Key Laboratory of Industrial Dust Deep Reduction and Occupational Health and Safety of Anhui Higher Education Institutes, Huainan, China
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Huainan, China
| | - Guoying Wang
- School of Medicine, Anhui University of Science and Technology, Huainan, China
| | - Mengyao Wu
- School of Medicine, Anhui University of Science and Technology, Huainan, China
| | - Tinatin Xu
- School of Medicine, Anhui University of Science and Technology, Huainan, China
| | - Chunmei Wen
- School of Medicine, Anhui University of Science and Technology, Huainan, China
| | - Xuejia Zheng
- The First Hospital of Anhui University of Science and Technology, Huainan, China
| | - Yong Dai
- School of Medicine, Anhui University of Science and Technology, Huainan, China
- Key Laboratory of Industrial Dust Deep Reduction and Occupational Health and Safety of Anhui Higher Education Institutes, Huainan, China
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Huainan, China
- The First Hospital of Anhui University of Science and Technology, Huainan, China
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He Q, Su Q, Wei C, Zhang P, Liu W, Chen J, Su X, Zhuang W. Extrachromosomal circular DNAs in prostate adenocarcinoma: global characterizations and a novel prediction model. Front Pharmacol 2024; 15:1464145. [PMID: 39355773 PMCID: PMC11442297 DOI: 10.3389/fphar.2024.1464145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2024] [Accepted: 08/19/2024] [Indexed: 10/03/2024] Open
Abstract
Background The role of focal amplifications and extrachromosomal circular DNA (eccDNA) is still uncertain in prostate adenocarcinoma (PRAD). Here, we first mapped the global characterizations of eccDNA and then investigate the characterization of eccDNA-amplified key differentially expressed encoded genes (eKDEGs) in the progression, immune response and immunotherapy of PRAD. Methods Circular_seq was used in conjunction with the TCGA-PRAD transcriptome dataset to sequence, annotate, and filter for eccDNA-amplified differentially expressed coding genes (eDEGs) in PRAD and para-cancerous normal prostate tissues. Afterwards, risk models were created and eKDEGs linked to the PRAD prognosis were identified using Cox and Lasso regression analysis. The immune microenvironment of the risk model was quantified using a variety of immunological algorithms, which also identified its characteristics with regard to immunotherapy, immune response, and immune infiltration. Results In this research, there was no significant difference in the size, type, and chromosomal distribution of eccDNA in PRAD and para-cancerous normal prostate tissues. However, 4,290 differentially expressed eccDNAs were identified and 1,981 coding genes were amplified. Following that, 499 eDEGs were tested in conjunction with the transcriptome dataset from TCGA-PRAD. By using Cox and Lasso regression techniques, ZNF330 and PITPNM3 were identified as eKDEGs of PRAD, and a new PRAD risk model was conducted based on this. Survival analysis showed that the high-risk group of this model was associated with poor prognosis and validated in external data. Immune infiltration analysis showed that the model risks affected immune cell infiltration in PRAD, not only mediating changes in immune cell function, but also correlating with immunophenotyping. Furthermore, the high-risk group was negatively associated with anti-CTLA-4/anti-PD-1 response and mutational burden. In addition, Tumor Immune Dysfunction and Exclusion analyses showed that high-risk group was more prone to immune escape. Drug sensitivity analyses identified 10 drugs, which were instructive for PRAD treatment. Conclusion ZNF330 and PITPNM are the eKDEGs for PRAD, which can be used as potential new prognostic markers. The two-factor combined risk model can effectively assess the survival and prognosis of PRAD patients, but also can predict the different responses of immunotherapy to PRAD patients, which may provide new ideas for PRAD immunotherapy.
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Affiliation(s)
- Qingliu He
- Department of Urology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Qingfu Su
- Department of Urology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Chengcheng Wei
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Pu Zhang
- Department of Urology, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Weihui Liu
- Department of Urology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Junyi Chen
- Department of Urology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Xiaoping Su
- Department of Urology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
- Department of Nursing, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Wei Zhuang
- Department of Urology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
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Yuan XQ, Zhou N, Song SJ, Xie YX, Chen SQ, Yang TF, Peng X, Zhang CY, Zhu YH, Peng L. Decoding the genomic enigma: Approaches to studying extrachromosomal circular DNA. Heliyon 2024; 10:e36659. [PMID: 39263178 PMCID: PMC11388731 DOI: 10.1016/j.heliyon.2024.e36659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 08/19/2024] [Accepted: 08/20/2024] [Indexed: 09/13/2024] Open
Abstract
Extrachromosomal circular DNA (eccDNA), a pervasive yet enigmatic component of the eukaryotic genome, exists autonomously from its chromosomal counterparts. Ubiquitous in eukaryotes, eccDNA plays a critical role in the orchestration of cellular processes and the etiology of diseases, particularly cancers. However, the full scope of its influence on health and disease remains elusive, presenting a rich vein of research yet to be mined. Unraveling the complexities of eccDNA necessitates a distillation of methodologies - from biogenesis to functional analysis - a landscape we overview in this study with precision and clarity. Here, we systematically outline cutting-edge methodologies from high-throughput sequencing and bioinformatics to experimental validations, showcasing the intricate world of eccDNAs. We combed through a treasure trove of auxiliary research resources and analytical tools. Moreover, we chart a course for future inquiry, illuminating the horizon with potential groundbreaking strategies for designing eccDNA research projects and pioneering new methodological frontiers.
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Affiliation(s)
- Xiao-Qing Yuan
- Guangdong Provincial Key Laboratory of Cancer Pathogenesis and Precision Diagnosis and Treatment, Shenshan Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Shanwei, 516621, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Nan Zhou
- The Affiliated Brain Hospital, Guangzhou Medical University, Guangzhou, 510370, China
| | - Shi-Jian Song
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Yi-Xia Xie
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Shui-Qin Chen
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Teng-Fei Yang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Xian Peng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
- Puai Medical College, Shaoyang University, Shaoyang, 422100, China
| | - Chao-Yang Zhang
- Research Unit Analytical Pathology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, 85764, Germany
| | - Ying-Hua Zhu
- Department of Genetic Medicine, Dongguan Children's Hospital Affiliated to Guangdong Medical University, Dongguan, 523325, China
| | - Li Peng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
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Wang Y, Li N, Qu L, Zhang M, Li Z, Li X, Cai D. Hemoglobin nanoclusters-mediated regulation of KPNA4 in hypoxic tumor microenvironment enhances photodynamic therapy in hepatocellular carcinoma. J Nanobiotechnology 2024; 22:473. [PMID: 39135024 PMCID: PMC11318167 DOI: 10.1186/s12951-024-02717-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 07/09/2024] [Indexed: 08/16/2024] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a highly malignant tumor known for its hypoxic environment, which contributes to resistance against the anticancer drug Sorafenib (SF). Addressing SF resistance in HCC requires innovative strategies to improve tumor oxygenation and effectively deliver therapeutics. RESULTS In our study, we explored the role of KPNA4 in mediating hypoxia-induced SF resistance in HCC. We developed hemoglobin nanoclusters (Hb-NCs) capable of carrying oxygen, loaded with indocyanine green (ICG) and SF, named HPRG@SF. In vitro, HPRG@SF targeted HCC cells, alleviated hypoxia, suppressed KPNA4 expression, and enhanced the cytotoxicity of PDT against hypoxic, SF-resistant HCC cells. In vivo experiments supported these findings, showing that HPRG@SF effectively improved the oxygenation within the tumor microenvironment and countered SF resistance through combined photodynamic therapy (PDT). CONCLUSION The combination of Hb-NCs with ICG and SF, forming HPRG@SF, presents a potent strategy to overcome drug resistance in hepatocellular carcinoma by improving hypoxia and employing PDT. This approach not only targets the hypoxic conditions that underlie resistance but also provides a synergistic anticancer effect, highlighting its potential for clinical applications in treating resistant HCC.
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Affiliation(s)
- Yiliang Wang
- Department of Anesthesiology, The First Hospital of China Medical University, No. 155, Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, China
| | - Nu Li
- Department of breast surgery, The First Hospital of China Medical University, Shenyang, 110001, Liaoning Province, China
| | - Letian Qu
- Department of Geriatrics, The First Hospital of China Medical University, Shenyang, 110001, Liaoning Province, China
| | - Mu Zhang
- Department of Geriatrics, The First Hospital of China Medical University, Shenyang, 110001, Liaoning Province, China
| | - Zhuo Li
- The Fourth People's Hospital of Shenyang, 110002, Liaoning Province, China
| | - Xiang Li
- Department of Neurosurgery, The First Hospital of China Medical University, No. 155, Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, China.
| | - Dasheng Cai
- Department of Anesthesiology, The First Hospital of China Medical University, No. 155, Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, China.
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Li Z, Kim W, Utturkar S, Yan B, Lanman NA, Elzey BD, Kazemian M, Yeo Y, Andrisani O. DDX5 deficiency drives non-canonical NF-κB activation and NRF2 expression, influencing sorafenib response and hepatocellular carcinoma progression. Cell Death Dis 2024; 15:583. [PMID: 39122708 PMCID: PMC11315975 DOI: 10.1038/s41419-024-06977-z] [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: 04/03/2024] [Revised: 08/01/2024] [Accepted: 08/05/2024] [Indexed: 08/12/2024]
Abstract
In advanced hepatocellular carcinoma (HCC), RNA helicase DDX5 regulates the Wnt/β-catenin-ferroptosis axis, influencing the efficacy of the multi-tyrosine kinase inhibitor (mTKI) sorafenib. DDX5 inhibits Wnt/β-catenin signaling, preventing sorafenib-induced ferroptosis escape. Sorafenib/mTKIs reduce DDX5 expression, correlating with poor patient survival post-sorafenib treatment. Notably, DDX5-knockout in HCC cells activates Wnt/β-catenin signaling persistently. Herein, we investigate the mechanistic impact of Wnt/β-catenin activation resulting from DDX5 downregulation in the progression and treatment of HCC. RNAseq analyses identified shared genes repressed by DDX5 and upregulated by sorafenib, including Wnt signaling genes, NF-κB-inducing kinase (NIK) essential for non-canonical NF-κB (p52/RelB) activation, and cytoprotective transcription factor NRF2. We demonstrate, Wnt/β-catenin activation induced NIK transcription, leading to non-canonical NF-κB activation, which subsequently mediated NRF2 transcription. Additionally, DDX5 deficiency extended NRF2 protein half-life by inactivating KEAP1 through p62/SQSTM1 stabilization. In a preclinical HCC mouse model, NRF2 knockdown or DDX5 overexpression restricted tumor growth upon sorafenib treatment, via induction of ferroptosis. Importantly, DDX5-knockout HCC cells exhibited elevated expression of Wnt signaling genes, NIK, p52/RelB, and NRF2-regulated genes, regardless of sorafenib treatment. Transcriptomic analyses of HCCs from TCGA and the Stelic Animal Model (STAM) of non-alcoholic steatohepatitis revealed elevated expression of these interconnected pathways in the context of DDX5 downregulation. In conclusion, DDX5 deficiency triggers Wnt/β-catenin signaling, promoting p52/RelB and NRF2 activation, thereby enabling ferroptosis evasion upon sorafenib treatment. Similarly, independent of sorafenib, DDX5 deficiency in liver tumors enhances activation and gene expression of these interconnected pathways, underscoring the clinical relevance of DDX5 deficiency in HCC progression and therapeutic response.
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Affiliation(s)
- Zhili Li
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN, USA
- Purdue Institute for Cancer Research, West Lafayette, IN, USA
| | - Woojun Kim
- Purdue Institute for Cancer Research, West Lafayette, IN, USA
- Department of Industrial and Physical Pharmacy, Purdue University, West Lafayette, IN, USA
| | - Sagar Utturkar
- Purdue Institute for Cancer Research, West Lafayette, IN, USA
| | - Bingyu Yan
- Purdue Institute for Cancer Research, West Lafayette, IN, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Nadia Atallah Lanman
- Purdue Institute for Cancer Research, West Lafayette, IN, USA
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, USA
| | - Bennett D Elzey
- Purdue Institute for Cancer Research, West Lafayette, IN, USA
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, USA
| | - Majid Kazemian
- Purdue Institute for Cancer Research, West Lafayette, IN, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | - Yoon Yeo
- Purdue Institute for Cancer Research, West Lafayette, IN, USA
- Department of Industrial and Physical Pharmacy, Purdue University, West Lafayette, IN, USA
| | - Ourania Andrisani
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN, USA.
- Purdue Institute for Cancer Research, West Lafayette, IN, USA.
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11
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Liu L, Li YN, Zhang A, Yin Y, Yue Z, Pei L, Xia CS, Wang D, Jia M, Wang H, Cao LL. Clinical potential of serum prostaglandin A2 as a novel diagnostic biomarker for hepatocellular cancer. Clin Chim Acta 2024; 561:119814. [PMID: 38879063 DOI: 10.1016/j.cca.2024.119814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/18/2024] [Accepted: 06/12/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND Hepatocellular cancer (HCC) is one of the most harmful tumors to human health. Currently, there is still a lack of highly sensitive and specific HCC biomarkers in clinical practice. In this study, we aimed to explore the diagnostic performance of prostaglandin A2 (PGA2) for the early detection of HCC. METHODS Untargeted metabolomic analyses on normal control (NC) and HCC participants in the discovery cohort were performed, and PGA2 was identified to be dysregulated in HCC. A liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for detecting serum PGA2 was established and applied to validate the dysregulation of PGA2 in another independent validation cohort. Receiver operating characteristic (ROC), decision curve analysis (DCA) and some other statistical analyses were performed to evaluate the diagnostic performance of PGA2 for HCC. RESULTS At first, PGA2 was found to be dysregulated in HCC in untargeted metabolomic analyses. Then a precise quantitative LC-MS/MS method for PGA2 has been established and has passed rigorous method validation. Targeted PGA2 analyses confirmed that serum PGA2 was decreased in HCC compared to normal-risk NC and high-risk cirrhosis group. Subsequently, PGA2 was identified as a novel biomarker for the diagnosis of HCC, with an area under the ROC curve (AUC) of 0.911 for differentiating HCC from the combined NC + cirrhosis groups. In addition, PGA2 exhibited high performance for differentiating small-size (AUC = 0.924), early-stage (AUC = 0.917) and AFP (-) HCC (AUC = 0.909) from the control groups. The combination of PGA2 and AFP might be useful in the surveillance of risk population for HCC and early diagnosis of HCC. CONCLUSION This study establishes that PGA2 might be a novel diagnostic biomarker for HCC.
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Affiliation(s)
- Li Liu
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China; Department of Clinical Laboratory, Beihua University Affiliated Hospital, Jilin 132011, China
| | - Yi-Ning Li
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China
| | - Aimin Zhang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China
| | - Yue Yin
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China
| | - Zhihong Yue
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China
| | - Lin Pei
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China
| | - Chang-Sheng Xia
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China
| | - Dong Wang
- SCIEX Analytical Instrument Trading Co., Shanghai 200335, China
| | - Mei Jia
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China
| | - Lin-Lin Cao
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China.
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12
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Zhou M, Lv W, Han P, Sun K, Hao Z, Gao L, Xu Y, Xu Z, Shao S, Ma S, Guo Q, Zhang H, Liu K, Yang F, Yuan Z, Wu G, Yu C, Luo Y, Yao Z, Zhao J. Plasma extrachromosomal circular DNA as a potential diagnostic biomarker for nodular thyroid disease. Clin Transl Med 2024; 14:e1740. [PMID: 39031834 PMCID: PMC11189768 DOI: 10.1002/ctm2.1740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 07/22/2024] Open
Affiliation(s)
- Meng Zhou
- Key Laboratory of Endocrine Glucose & Lipids Metabolism and Brain Aging, Ministry of Education, Department of EndocrinologyShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanShandongChina
- Shandong Engineering Laboratory of Prevention and Control for Endocrine and Metabolic DiseasesJinanShandongChina
- Shandong Institute of Endocrine and Metabolic DiseaseJinanShandongChina
| | - Wei Lv
- College of Life Sciences, University of Chinese Academy of ScienceBeijingChina
| | - Peng Han
- Lars Bolund Institute of Regenerative Medicine, HIM‐BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of SciencesHangzhouZhejiangChina
| | - Kai Sun
- College of Artificial Intelligence and Big Data for Medical Sciences, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
- Shandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanShandongChina
- Central Hospital Affiliated to Shandong First Medical UniversityJinanShandongChina
| | - Ziqian Hao
- College of Artificial Intelligence and Big Data for Medical Sciences, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Ling Gao
- Key Laboratory of Endocrine Glucose & Lipids Metabolism and Brain Aging, Ministry of Education, Department of EndocrinologyShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanShandongChina
- Shandong Engineering Laboratory of Prevention and Control for Endocrine and Metabolic DiseasesJinanShandongChina
- Shandong Institute of Endocrine and Metabolic DiseaseJinanShandongChina
| | - Yunyun Xu
- Key Laboratory of Endocrine Glucose & Lipids Metabolism and Brain Aging, Ministry of Education, Department of EndocrinologyShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanShandongChina
- Shandong Engineering Laboratory of Prevention and Control for Endocrine and Metabolic DiseasesJinanShandongChina
- Shandong Institute of Endocrine and Metabolic DiseaseJinanShandongChina
| | - Zhe Xu
- College of Life Sciences, University of Chinese Academy of ScienceBeijingChina
| | - Shanshan Shao
- Key Laboratory of Endocrine Glucose & Lipids Metabolism and Brain Aging, Ministry of Education, Department of EndocrinologyShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanShandongChina
- Shandong Engineering Laboratory of Prevention and Control for Endocrine and Metabolic DiseasesJinanShandongChina
- Shandong Institute of Endocrine and Metabolic DiseaseJinanShandongChina
| | - Shizhan Ma
- Key Laboratory of Endocrine Glucose & Lipids Metabolism and Brain Aging, Ministry of Education, Department of EndocrinologyShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanShandongChina
- Shandong Engineering Laboratory of Prevention and Control for Endocrine and Metabolic DiseasesJinanShandongChina
- Shandong Institute of Endocrine and Metabolic DiseaseJinanShandongChina
| | - Qingling Guo
- Key Laboratory of Endocrine Glucose & Lipids Metabolism and Brain Aging, Ministry of Education, Department of EndocrinologyShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanShandongChina
- Shandong Engineering Laboratory of Prevention and Control for Endocrine and Metabolic DiseasesJinanShandongChina
- Shandong Institute of Endocrine and Metabolic DiseaseJinanShandongChina
| | - Haiqing Zhang
- Key Laboratory of Endocrine Glucose & Lipids Metabolism and Brain Aging, Ministry of Education, Department of EndocrinologyShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanShandongChina
- Shandong Engineering Laboratory of Prevention and Control for Endocrine and Metabolic DiseasesJinanShandongChina
- Shandong Institute of Endocrine and Metabolic DiseaseJinanShandongChina
| | - Ke Liu
- Department of Bio‐statistics School of Public HealthCheeloo College of Medicine, Shandong UniversityJinanShandongChina
| | - Fan Yang
- Department of Bio‐statistics School of Public HealthCheeloo College of Medicine, Shandong UniversityJinanShandongChina
| | - Zhongshang Yuan
- Department of Bio‐statistics School of Public HealthCheeloo College of Medicine, Shandong UniversityJinanShandongChina
| | - Guojun Wu
- Department of Breast and Thyroid SurgeryShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanShandongChina
| | - Changbin Yu
- College of Artificial Intelligence and Big Data for Medical Sciences, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Yonglun Luo
- Lars Bolund Institute of Regenerative Medicine, HIM‐BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of SciencesHangzhouZhejiangChina
| | - Zhenyu Yao
- Key Laboratory of Endocrine Glucose & Lipids Metabolism and Brain Aging, Ministry of Education, Department of EndocrinologyShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanShandongChina
- Shandong Engineering Laboratory of Prevention and Control for Endocrine and Metabolic DiseasesJinanShandongChina
- Shandong Institute of Endocrine and Metabolic DiseaseJinanShandongChina
| | - Jiajun Zhao
- Key Laboratory of Endocrine Glucose & Lipids Metabolism and Brain Aging, Ministry of Education, Department of EndocrinologyShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanShandongChina
- Shandong Engineering Laboratory of Prevention and Control for Endocrine and Metabolic DiseasesJinanShandongChina
- Shandong Institute of Endocrine and Metabolic DiseaseJinanShandongChina
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13
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Zhang Y, Chen S, Tian Y, Fu X. Host factors of SARS-CoV-2 in infection, pathogenesis, and long-term effects. Front Cell Infect Microbiol 2024; 14:1407261. [PMID: 38846354 PMCID: PMC11155306 DOI: 10.3389/fcimb.2024.1407261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 05/08/2024] [Indexed: 06/09/2024] Open
Abstract
SARS-CoV-2 is the causative virus of the devastating COVID-19 pandemic that results in an unparalleled global health and economic crisis. Despite unprecedented scientific efforts and therapeutic interventions, the fight against COVID-19 continues as the rapid emergence of different SARS-CoV-2 variants of concern and the increasing challenge of long COVID-19, raising a vast demand to understand the pathomechanisms of COVID-19 and its long-term sequelae and develop therapeutic strategies beyond the virus per se. Notably, in addition to the virus itself, the replication cycle of SARS-CoV-2 and clinical severity of COVID-19 is also governed by host factors. In this review, we therefore comprehensively overview the replication cycle and pathogenesis of SARS-CoV-2 from the perspective of host factors and host-virus interactions. We sequentially outline the pathological implications of molecular interactions between host factors and SARS-CoV-2 in multi-organ and multi-system long COVID-19, and summarize current therapeutic strategies and agents targeting host factors for treating these diseases. This knowledge would be key for the identification of new pathophysiological aspects and mechanisms, and the development of actionable therapeutic targets and strategies for tackling COVID-19 and its sequelae.
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Affiliation(s)
| | | | - Yan Tian
- Department of Endocrinology and Metabolism, Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Medical School, West China Hospital and Cancer Center, Sichuan University and Collaborative Innovation Center of Biotherapy, Sichuan, Chengdu, China
| | - Xianghui Fu
- Department of Endocrinology and Metabolism, Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Medical School, West China Hospital and Cancer Center, Sichuan University and Collaborative Innovation Center of Biotherapy, Sichuan, Chengdu, China
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14
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Liang Y, Li C, Hou X, Lin Y, Cheng J. MicroRNA-875-5p inhibits the growth and metastasis of cervical cancer cells by promoting autophagy and apoptosis and inhibiting the epithelial-mesenchymal transition. Front Oncol 2024; 14:1361721. [PMID: 38800376 PMCID: PMC11116804 DOI: 10.3389/fonc.2024.1361721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 04/22/2024] [Indexed: 05/29/2024] Open
Abstract
Introduction MicroRNA-875-5p (miR-875-5p) is a cancer-related microRNA. It has been demonstrated that miR-875-5p participates in the development of various types of cancer such as hepatocellular carcinoma, gastric carcinoma, prostate and bladder cancer. Previous research suggested that miR-875 is implicated in the development of cervical cancer cells. However, the exact role and function of miR-875-5p in cervical cancer remain unexplored. It is important to examine the role and function of miR-875-5p and the associated signaling pathway, as the findings may have diagnostic and therapeutic significance. Thus, in this study, we investigated the effect of miR-875-5p on the growth and metastasis of cervical cancer cells and the possible underlying mechanisms. Methods Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was used to detect the expression of miR-875-5p in cervical cancer cells and normal cervical epithelium. After overexpression or co-expression of miR-875-5p in cells, the changes in cell function were analyzed. Western blot was used to detect the expression changes of epithelial-mesenchymal transition (EMT) -related proteins and autophagy-related proteins. Results Functional studies demonstrated that miR-875-5p overexpression significantly inhibited the proliferation, migration, invasion, and EMT, and promotes apoptosis and autophagy of cervical cancer cells., while miR-875-5p knockdown promoted the proliferation, migration, invasion, and EMT, and inhibited apoptosis and autophagy cervical cancer cells. Furthermore, Western blot results showed that overexpression of miR-875-5p downregulated the expressions of N-cadherin, Snail, Vimentin and microtubule-associated protein 1 light chain 3B I (LC3B I). Conversely, miR-875-5p upregulated the expression of E-cadherin. Conclusion In conclusion, our findings suggest that miR-875-5p functions as a tumor inhibitor suppressing the growth and metastasis of cervical cancer. Overexpression of miR-875-5p inhibits malignant behavior and promotes autophagy and apoptosis in cervical cancer cells. These findings advance our understanding of the role and function of miR-875-5p in cervical cancer and could facilitate the development of early genetic markers or biomarkers and therapeutic targets for cervical cancer.
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Affiliation(s)
- Yingxiu Liang
- Reproductive Center, Department of Obstetrics and Gynecology, The Second Affiliated Hospital and the Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
| | - Chunyang Li
- Department of Biochemistry, School of Basic Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xiaohong Hou
- Reproductive Center, Department of Obstetrics and Gynecology, The Second Affiliated Hospital and the Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yiguang Lin
- School of Pharmaceutical Science, Guangdong Pharmaceutical University, Guangzhou, China
- Department of Traditional Chinese Medicine (TCM), Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
- Research & Development Division, Guangzhou Anjie Biomedical Technology Co. Ltd, Guangzhou, China
| | - Jing Cheng
- Reproductive Center, Department of Obstetrics and Gynecology, The Second Affiliated Hospital and the Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
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15
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Zhou L, Tang W, Ye B, Zou L. Characterization, biogenesis model, and current bioinformatics of human extrachromosomal circular DNA. Front Genet 2024; 15:1385150. [PMID: 38746056 PMCID: PMC11092383 DOI: 10.3389/fgene.2024.1385150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 04/12/2024] [Indexed: 05/16/2024] Open
Abstract
Human extrachromosomal circular DNA, or eccDNA, has been the topic of extensive investigation in the last decade due to its prominent regulatory role in the development of disorders including cancer. With the rapid advancement of experimental, sequencing and computational technology, millions of eccDNA records are now accessible. Unfortunately, the literature and databases only provide snippets of this information, preventing us from fully understanding eccDNAs. Researchers frequently struggle with the process of selecting algorithms and tools to examine eccDNAs of interest. To explain the underlying formation mechanisms of the five basic classes of eccDNAs, we categorized their characteristics and functions and summarized eight biogenesis theories. Most significantly, we created a clear procedure to help in the selection of suitable techniques and tools and thoroughly examined the most recent experimental and bioinformatics methodologies and data resources for identifying, measuring and analyzing eccDNA sequences. In conclusion, we highlighted the current obstacles and prospective paths for eccDNA research, specifically discussing their probable uses in molecular diagnostics and clinical prediction, with an emphasis on the potential contribution of novel computational strategies.
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Affiliation(s)
- Lina Zhou
- School of Medicine, Chongqing University, Department of Clinical Data Research, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing University, Chongqing, China
| | - Wenyi Tang
- School of Medicine, Chongqing University, Department of Clinical Data Research, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing University, Chongqing, China
| | - Bo Ye
- School of Medicine, Chongqing University, Department of Clinical Data Research, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing University, Chongqing, China
| | - Lingyun Zou
- School of Medicine, Chongqing University, Department of Clinical Data Research, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing University, Chongqing, China
- School of Medicine, Jinan University, Guangzhou, Guangdong, China
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16
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Zhang C, Du Q, Zhou X, Qu T, Liu Y, Ma K, Shen Z, Wang Q, Zhang Z, Zhang R. Differential expression and analysis of extrachromosomal circular DNAs as serum biomarkers in pulmonary arterial hypertension. Respir Res 2024; 25:181. [PMID: 38664836 PMCID: PMC11046951 DOI: 10.1186/s12931-024-02808-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 04/06/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Extrachromosomal circular DNAs (eccDNAs) have been reported to play a key role in the occurrence and development of various diseases. However, the characterization and role of eccDNAs in pulmonary arterial hypertension (PAH) remain unclear. METHODS In the discovery cohort, we first explored eccDNA expression profiles by Circle-sequencing analysis. The candidate eccDNAs were validated by routine polymerase chain reaction (PCR), TOPO-TA cloning and Sanger sequencing. In the validation cohort, 30 patients with PAH and 10 healthy controls were recruited for qPCR amplification to detect the candidate eccDNAs. Datas at the baseline were collected, including clinical background, biochemical variables, echocardiography and hemodynamic factors. Receiver operating characteristic curve was used to investigate the diagnostic effect of the eccDNA. RESULTS We identified a total of 21,741 eccDNAs in plasma samples of 3 IPAH patients and 3 individuals in good health, and the expression frequency, GC content, length distribution, and genome distribution of the eccDNAs were thoroughly characterized and analyzed. In the validation cohort, 687 eccDNAs were differentially expressed in patients with IPAH compared with healthy controls (screening threshold: |FC|≥2 and P < 0.05). Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the specific eccDNAs in IPAH were significantly enriched in calcium channel activity, the mitogen-activated protein kinase pathway, and the wnt signaling pathway. Verification queue found that the expression of eccDNA-chr2:131208878-131,424,362 in PAH was considerably higher than that in healthy controls and exhibited a high level of accuracy in predicting PAH with a sensitivity of 86.67% and a specificity of 90%. Furthermore, correlation analysis disclosed a significant association between serum eccDNA-chr2:131208878-131,424,362 and mean pulmonary artery pressure (mPAP) (r = 0.396, P = 0.03), 6 min walking distance (6MWD) (r = -0.399, P = 0.029), N-terminal pro-B-type natriuretic peptide (NT-proBNP) (r = 0.685, P < 0.001) and cardiac index (CI) (r = - 0.419, P = 0.021). CONCLUSIONS This is the first study to identify and characterize eccDNAs in patients with PAH. We revealed that serum eccDNA-chr2:131208878-131,424,362 is significantly overexpressed and can be used in the diagnosis of PAH, indicating its potential as a novel non-invasive biomarker.
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Affiliation(s)
- Chun Zhang
- Department of Respiratory Medicine, Zhongda Hospital of Southeast University, Dingjiaqiao 87, Nanjing City, Jiangsu Province, 210000, People's Republic of China
| | - Qiang Du
- Department of Respiratory Medicine, Zhongda Hospital of Southeast University, Dingjiaqiao 87, Nanjing City, Jiangsu Province, 210000, People's Republic of China
| | - Xiao Zhou
- Department of Respiratory Medicine, Zhongda Hospital of Southeast University, Dingjiaqiao 87, Nanjing City, Jiangsu Province, 210000, People's Republic of China
| | - Tianyu Qu
- Department of Respiratory Medicine, Zhongda Hospital of Southeast University, Dingjiaqiao 87, Nanjing City, Jiangsu Province, 210000, People's Republic of China
| | - Yingying Liu
- Department of Respiratory Medicine, Zhongda Hospital of Southeast University, Dingjiaqiao 87, Nanjing City, Jiangsu Province, 210000, People's Republic of China
| | - Kai Ma
- Department of Respiratory Medicine, Zhongda Hospital of Southeast University, Dingjiaqiao 87, Nanjing City, Jiangsu Province, 210000, People's Republic of China
| | - Ziling Shen
- Department of Respiratory Medicine, Zhongda Hospital of Southeast University, Dingjiaqiao 87, Nanjing City, Jiangsu Province, 210000, People's Republic of China
| | - Qun Wang
- Department of Respiratory Medicine, Zhongda Hospital of Southeast University, Dingjiaqiao 87, Nanjing City, Jiangsu Province, 210000, People's Republic of China
| | - Zaikui Zhang
- Center of Pathology and Clinical Laboratory, Sir Run Run Hospital, Nanjing Medical University, Nanjing, 210000, People's Republic of China
| | - Ruifeng Zhang
- Department of Respiratory Medicine, Zhongda Hospital of Southeast University, Dingjiaqiao 87, Nanjing City, Jiangsu Province, 210000, People's Republic of China.
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17
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Cao R, Tian H, Tian Y, Fu X. A Hierarchical Mechanotransduction System: From Macro to Micro. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2302327. [PMID: 38145330 PMCID: PMC10953595 DOI: 10.1002/advs.202302327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 10/27/2023] [Indexed: 12/26/2023]
Abstract
Mechanotransduction is a strictly regulated process whereby mechanical stimuli, including mechanical forces and properties, are sensed and translated into biochemical signals. Increasing data demonstrate that mechanotransduction is crucial for regulating macroscopic and microscopic dynamics and functionalities. However, the actions and mechanisms of mechanotransduction across multiple hierarchies, from molecules, subcellular structures, cells, tissues/organs, to the whole-body level, have not been yet comprehensively documented. Herein, the biological roles and operational mechanisms of mechanotransduction from macro to micro are revisited, with a focus on the orchestrations across diverse hierarchies. The implications, applications, and challenges of mechanotransduction in human diseases are also summarized and discussed. Together, this knowledge from a hierarchical perspective has the potential to refresh insights into mechanotransduction regulation and disease pathogenesis and therapy, and ultimately revolutionize the prevention, diagnosis, and treatment of human diseases.
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Affiliation(s)
- Rong Cao
- Department of Endocrinology and MetabolismCenter for Diabetes Metabolism ResearchState Key Laboratory of Biotherapy and Cancer CenterWest China Medical SchoolWest China HospitalSichuan University and Collaborative Innovation CenterChengduSichuan610041China
| | - Huimin Tian
- Department of Endocrinology and MetabolismCenter for Diabetes Metabolism ResearchState Key Laboratory of Biotherapy and Cancer CenterWest China Medical SchoolWest China HospitalSichuan University and Collaborative Innovation CenterChengduSichuan610041China
| | - Yan Tian
- Department of Endocrinology and MetabolismCenter for Diabetes Metabolism ResearchState Key Laboratory of Biotherapy and Cancer CenterWest China Medical SchoolWest China HospitalSichuan University and Collaborative Innovation CenterChengduSichuan610041China
| | - Xianghui Fu
- Department of Endocrinology and MetabolismCenter for Diabetes Metabolism ResearchState Key Laboratory of Biotherapy and Cancer CenterWest China Medical SchoolWest China HospitalSichuan University and Collaborative Innovation CenterChengduSichuan610041China
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18
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Tavabie OD, Salehi S, Aluvihare VR. The challenges and potential of microRNA-based therapy for patients with liver failure syndromes and hepatocellular carcinoma. Expert Opin Ther Targets 2024; 28:179-191. [PMID: 38487923 DOI: 10.1080/14728222.2024.2331598] [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: 12/21/2023] [Accepted: 03/13/2024] [Indexed: 03/20/2024]
Abstract
INTRODUCTION Morbidity and mortality from liver disease continues to rise worldwide. There are currently limited curative treatments for patients with liver failure syndromes, encompassing acute liver failure and decompensated cirrhosis states, outside of transplantation. Whilst there have been improvements in therapeutic options for patients with hepatocellular carcinoma (HCC), there remain challenges necessitating novel therapeutic agents. microRNA have long been seen as potential therapeutic targets but there has been limited clinical translation. AREAS COVERED We will discuss the limitations of conventional non-transplant management of patients with liver failure syndromes and HCC. We will provide an overview of microRNA and the challenges in developing and delivering microRNA-based therapeutic agents. We will finally provide an overview of microRNA-based therapeutic agents which have progressed to clinical trials. EXPERT OPINION microRNA have great potential to be developed into therapeutic agents due to their association with critical biological processes which govern health and disease. Utilizing microRNA sponges to target multiple microRNA associated with specific biological processes may improve their therapeutic efficacy. However, there needs to be significant improvements in delivery systems to ensure the safe delivery of microRNA to target sites and minimize systemic distribution. This currently significantly impacts the clinical translation of microRNA-based therapeutic agents.
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Affiliation(s)
| | - Siamak Salehi
- Institute of Liver Studies, King's College Hospital, London, UK
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Kong X, Wan SJ, Chen TB, Jiang L, Xing YJ, Bai YP, Hua Q, Yao XM, Zhao YL, Zhang HM, Wang DG, Su Q, Lv K. Increased serum extrachromosomal circular DNA SORBS1 circle level is associated with insulin resistance in patients with newly diagnosed type 2 diabetes mellitus. Cell Mol Biol Lett 2024; 29:12. [PMID: 38212723 PMCID: PMC10785328 DOI: 10.1186/s11658-023-00530-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 12/21/2023] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND Extrachromosomal circular DNAs (eccDNAs) exist in human blood and somatic cells, and are essential for oncogene plasticity and drug resistance. However, the presence and impact of eccDNAs in type 2 diabetes mellitus (T2DM) remains inadequately understood. METHODS We purified and sequenced the serum eccDNAs obtained from newly diagnosed T2DM patients and normal control (NC) subjects using Circle-sequencing. We validated the level of a novel circulating eccDNA named sorbin and SH3-domain- containing-1circle97206791-97208025 (SORBS1circle) in 106 newly diagnosed T2DM patients. The relationship between eccDNA SORBS1circle and clinical data was analyzed. Furthermore, we explored the source and expression level of eccDNA SORBS1circle in the high glucose and palmitate (HG/PA)-induced hepatocyte (HepG2 cell) insulin resistance model. RESULTS A total of 22,543 and 19,195 eccDNAs were found in serum samples obtained from newly diagnosed T2DM patients and NC subjects, respectively. The T2DM patients had a greater distribution of eccDNA on chromosomes 1, 14, 16, 17, 18, 19, 20 and X. Additionally, 598 serum eccDNAs were found to be upregulated, while 856 eccDNAs were downregulated in T2DM patients compared with NC subjects. KEGG analysis demonstrated that the genes carried by eccDNAs were mainly associated with insulin resistance. Moreover, it was validated that the eccDNA SORBS1circle was significantly increased in serum of newly diagnosed T2DM patients (106 T2DM patients vs. 40 NC subjects). The serum eccDNA SORBS1circle content was positively correlated with the levels of glycosylated hemoglobin A1C (HbA1C) and homeostasis model assessment of insulin resistance (HOMA-IR) in T2DM patients. Intracellular eccDNA SORBS1circle expression was significantly enhanced in the high glucose and palmitate (HG/PA)-induced hepatocyte (HepG2 cell) insulin resistance model. Moreover, the upregulation of eccDNA SORBS1circle in the HG/PA-treated HepG2 cells was dependent on generation of apoptotic DNA fragmentation. CONCLUSIONS These results provide a preliminary understanding of the circulating eccDNA patterns at the early stage of T2DM and suggest that eccDNA SORBS1circle may be involved in the development of insulin resistance.
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Affiliation(s)
- Xiang Kong
- Anhui Provincial Key Laboratory of Non-Coding RNA Basic and Clinical Transformation, Wannan Medical College, Wuhu, 241002, China
- Geriatric Endocrinology Unit, Department of Gerontology, The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital, Wuhu, 241001, China
- Central Laboratory of Yijishan Hospital, Wuhu, 241001, China
| | - Shu-Jun Wan
- Anhui Provincial Key Laboratory of Non-Coding RNA Basic and Clinical Transformation, Wannan Medical College, Wuhu, 241002, China
- Central Laboratory of Yijishan Hospital, Wuhu, 241001, China
| | - Tian-Bing Chen
- Anhui Provincial Key Laboratory of Non-Coding RNA Basic and Clinical Transformation, Wannan Medical College, Wuhu, 241002, China
- Central Laboratory of Yijishan Hospital, Wuhu, 241001, China
| | - Lan Jiang
- Anhui Provincial Key Laboratory of Non-Coding RNA Basic and Clinical Transformation, Wannan Medical College, Wuhu, 241002, China
- Central Laboratory of Yijishan Hospital, Wuhu, 241001, China
| | - Yu-Jie Xing
- Anhui Provincial Key Laboratory of Non-Coding RNA Basic and Clinical Transformation, Wannan Medical College, Wuhu, 241002, China
- Geriatric Endocrinology Unit, Department of Gerontology, The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital, Wuhu, 241001, China
| | - Ya-Ping Bai
- Anhui Provincial Key Laboratory of Non-Coding RNA Basic and Clinical Transformation, Wannan Medical College, Wuhu, 241002, China
| | - Qiang Hua
- Department of Endocrinology, The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital, Wuhu, 241001, China
| | - Xin-Ming Yao
- Department of Endocrinology, The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital, Wuhu, 241001, China
| | - Yong-Li Zhao
- Department of Endocrinology, The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital, Wuhu, 241001, China
| | - Hong-Mei Zhang
- Department of Endocrinology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China
| | - De-Guo Wang
- Geriatric Endocrinology Unit, Department of Gerontology, The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital, Wuhu, 241001, China.
| | - Qing Su
- Department of Endocrinology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China.
| | - Kun Lv
- Anhui Provincial Key Laboratory of Non-Coding RNA Basic and Clinical Transformation, Wannan Medical College, Wuhu, 241002, China.
- Central Laboratory of Yijishan Hospital, Wuhu, 241001, China.
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Zhao X, Zhao H, Liu Y, Guo Z. Methods, bioinformatics tools and databases in ecDNA research: An overview. Comput Biol Med 2023; 167:107680. [PMID: 37976817 DOI: 10.1016/j.compbiomed.2023.107680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/25/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023]
Abstract
Extrachromosomal DNA (ecDNA), derived from chromosomes, is a cancer-specific circular DNA molecule. EcDNA drives tumor initiation and progression, which is associated with poor clinical outcomes and drug resistance in a wide range of cancers. Although ecDNA was first discovered in 1965, tremendous technological revolutions in recent years have provided crucial new insights into its key biological functions and regulatory mechanisms. Here, we provide a thorough overview of the methods, bioinformatics tools, and database resources used in ecDNA research, mainly focusing on their performance, strengths, and limitations. This study can provide important reference for selecting the most appropriate method in ecDNA research. Furthermore, we offer suggestions for the current bioinformatics analysis of ecDNA and provide an outlook to the future research.
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Affiliation(s)
- Xinyu Zhao
- School of Life Sciences and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Huan Zhao
- Key Laboratory of Marine Bio-resource Restoration and Habitat Reparation, Dalian Ocean University, Dalian, 116023, China
| | - Yupeng Liu
- School of Life Sciences and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Zhiyun Guo
- School of Life Sciences and Engineering, Southwest Jiaotong University, Chengdu, 610031, China.
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21
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Li Z, Caron de Fromentel C, Kim W, Wang WH, Sun J, Yan B, Utturkar S, Lanman NA, Elzey BD, Yeo Y, Zhang H, Kazemian M, Levrero M, Andrisani O. RNA helicase DDX5 modulates sorafenib sensitivity in hepatocellular carcinoma via the Wnt/β-catenin-ferroptosis axis. Cell Death Dis 2023; 14:786. [PMID: 38036507 PMCID: PMC10689482 DOI: 10.1038/s41419-023-06302-0] [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: 06/19/2023] [Revised: 10/25/2023] [Accepted: 11/13/2023] [Indexed: 12/02/2023]
Abstract
Reduced expression of the RNA helicase DDX5 associated with increased hepatocellular carcinoma (HCC) tumor grade and poor patient survival following treatment with sorafenib. While immunotherapy is the first-line treatment for HCC, sorafenib and other multi-tyrosine kinase inhibitors (mTKIs) are widely used when immunotherapy is contra-indicated or fails. Herein, we elucidate the role of DDX5 in sensitizing HCC to sorafenib, offering new therapeutic strategies. Treatment of various human HCC cell lines with sorafenib/mTKIs downregulated DDX5 in vitro and in preclinical HCC models. Conversely, DDX5 overexpression reduced the viability of sorafenib-treated cells via ferroptosis, suggesting a role for DDX5 in sorafenib sensitivity. RNAseq of wild-type vs. DDX5-knockdown cells treated with or without sorafenib identified a set of common genes repressed by DDX5 and upregulated by sorafenib. This set significantly overlaps with Wnt signaling genes, including Disheveled-1 (DVL1), an indispensable Wnt activator and prognostic indicator of poor survival for sorafenib-treated patients. DDX5-knockout (DDX5KO) HCC cells exhibited DVL1 induction, Wnt/β-catenin pathway activation, and ferroptosis upon inhibition of canonical Wnt signaling. Consistently, xenograft HCC tumors exhibited reduced growth by inhibition of Wnt/β-catenin signaling via induction of ferroptosis. Significantly, overexpression of DDX5 in HCC xenografts repressed DVL1 expression and increased ferroptosis, resulting in reduced tumor growth by sorafenib. We conclude that DDX5 downregulation by sorafenib mediates adaptive resistance by activating Wnt/β-catenin signaling, leading to ferroptosis escape. Conversely, overexpression of DDX5 in vivo enhances the anti-tumor efficacy of sorafenib by suppressing Wnt/β-catenin activation and induction of ferroptosis. Thus, DDX5 overexpression in combination with mTKIs is a promising therapeutic strategy for HCC.
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Affiliation(s)
- Zhili Li
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN, USA
- Purdue Institute for Cancer Research, West Lafayette, IN, USA
| | - Claude Caron de Fromentel
- Cancer Research Center of Lyon (CRCL) - INSERM U1052, CNRS5286, University Lyon, Université Claude Bernard Lyon 1, F69000, Lyon, France
| | - Woojun Kim
- Purdue Institute for Cancer Research, West Lafayette, IN, USA
- Department of Industrial and Physical Pharmacy, Purdue University, West Lafayette, IN, USA
| | - Wen-Hung Wang
- Purdue Institute for Cancer Research, West Lafayette, IN, USA
| | - Jiazeng Sun
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN, USA
- Purdue Institute for Cancer Research, West Lafayette, IN, USA
| | - Bingyu Yan
- Purdue Institute for Cancer Research, West Lafayette, IN, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Sagar Utturkar
- Purdue Institute for Cancer Research, West Lafayette, IN, USA
| | - Nadia Atallah Lanman
- Purdue Institute for Cancer Research, West Lafayette, IN, USA
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, USA
| | - Bennett D Elzey
- Purdue Institute for Cancer Research, West Lafayette, IN, USA
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, USA
| | - Yoon Yeo
- Purdue Institute for Cancer Research, West Lafayette, IN, USA
- Department of Industrial and Physical Pharmacy, Purdue University, West Lafayette, IN, USA
| | - Hao Zhang
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Majid Kazemian
- Purdue Institute for Cancer Research, West Lafayette, IN, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA
| | - Massimo Levrero
- Cancer Research Center of Lyon (CRCL) - INSERM U1052, CNRS5286, University Lyon, Université Claude Bernard Lyon 1, F69000, Lyon, France.
- Hospices Civils de Lyon, Service d'Hépatologie et Gastroentérologie, Groupement Hospitalier Lyon Nord, Lyon, France.
| | - Ourania Andrisani
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN, USA.
- Purdue Institute for Cancer Research, West Lafayette, IN, USA.
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Ren S, Wu D, Shen X, Wu Q, Li C, Xiong H, Xiong Z, Gong R, Liu Z, Wang W, Chen J. Deciphering the role of extrachromosomal circular DNA in adipose stem cells from old and young donors. Stem Cell Res Ther 2023; 14:341. [PMID: 38017497 PMCID: PMC10683086 DOI: 10.1186/s13287-023-03575-2] [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: 06/27/2023] [Accepted: 11/16/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND The functional impairment of adipose stem cells (ASCs) during aging limits their clinical transformation. Studies have shown that extrachromosomal circular DNAs (eccDNAs) are associated with tumor progression and cell aging, but the roles of eccDNAs in ASCs remain unknown. METHOD We conducted Circle sequencing (Circle-seq) to identify eccDNAs in ASCs isolated from young and old donors. The differentially expressed eccDNAs were calculated, annotated and validated via polymerase chain reaction. RESULTS Thousands of eccDNAs were identified and comprehensively characterized. Most of them were GC-rich, < 1000 base pairs in size, and were enriched on chromosome 19 and 17 with a high density of Alu elements and genes, 2 kb upstream/downstream of genes and satellites. In total, 3025 eccDNAs were differentially expressed among the two ASC groups. Conjoint analysis of the Circle-seq results and previous RNA-seq results revealed that 73 eccDNAs and 55 genes exhibited the same differential expression between the two groups. KEGG and GO analyses revealed that genes encoding differentially expressed eccDNAs were enriched for cell adhesion, cellular senescence and TGF-β receptor signaling pathway. We also found that aged ASCs exhibited loss of eccDNAs, including CAMK2G (chr10: 75577899-75578176), TRABD2B (chr1: 48305638-48307008) and TRABD2B (chr1: 48305425-48307091). CONCLUSION In this study, we elucidated the first eccDNA profile relating to ASCs and demonstrated that three eccDNAs are lost in aged ASCs, which may be potential biomarkers of stem cell aging and valuable targets for stem cell rejuvenation.
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Affiliation(s)
- Sen Ren
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Du Wu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Xiaoyong Shen
- Hospital of Stomatology Wuhan University, Wuhan, 430079, China
| | - Qian Wu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Chengcheng Li
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Hewei Xiong
- Department of Emergency Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Zhongwei Xiong
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Rui Gong
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Zheng Liu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
| | - Wei Wang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
| | - Jincao Chen
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
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Ye J, Huang P, Ma K, Zhao Z, Hua T, Zai W, Chen J, Fu X. Genome-Wide Extrachromosomal Circular DNA Profiling of Paired Hepatocellular Carcinoma and Adjacent Liver Tissues. Cancers (Basel) 2023; 15:5309. [PMID: 38001569 PMCID: PMC10670553 DOI: 10.3390/cancers15225309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/27/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
Hepatocellular carcinoma (HCC) develops through multiple mechanisms. While recent studies have shown the presence of extrachromosomal circular DNA (eccDNA) in most cancer types, the eccDNA expression pattern and its association with HCC remain obscure. We aimed to investigate this problem. The genome-wide eccDNA profiles of eight paired HCC and adjacent non-tumor tissue samples were comprehensively elucidated based on Circle-seq, and they were further cross-analyzed with the RNA sequencing data to determine the association between eccDNA expression and transcriptome dysregulation. A total of 60,423 unique eccDNA types were identified. Most of the detected eccDNAs were smaller than 1 kb, with a length up to 182,363 bp and a mean sizes of 674 bp (non-tumor) and 813 bp (tumor), showing a greater association with gene-rich rather than with gene-poor regions. Although there was no statistical difference in length and chromosome distribution, the eccDNA patterns between HCC and adjacent non-tumor tissues showed significant differences at both the chromosomal and single gene levels. Five of the eight HCC tissues showed significantly higher amounts of chromosome 22-derived eccDNA expression compared to the non-tumor tissue. Furthermore, two genes, SLC16A3 and BAIAP2L2, with a higher transcription level in tumor tissues, were related to eccDNAs exclusively detected in three HCC samples and were negatively associated with survival rates in HCC cohorts from public databases. These results indicate the existence and massive heterogeneity of eccDNAs in HCC and adjacent liver tissues, and suggest their potential association with dysregulated gene expression.
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Affiliation(s)
- Jianyu Ye
- Key Laboratory of Medical Molecular Virology (MOE & NHC), Research Unit of Cure of Chronic Hepatitis B Virus Infection (CAMS), School of Basic Medical Sciences, Shanghai Medical College Fudan University, Shanghai 200032, China; (J.Y.); (K.M.); (Z.Z.); (T.H.); (W.Z.)
| | - Peixin Huang
- Liver Cancer Institute, Fudan University, Shanghai 200032, China;
- Department of Hepatic Oncology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Kewei Ma
- Key Laboratory of Medical Molecular Virology (MOE & NHC), Research Unit of Cure of Chronic Hepatitis B Virus Infection (CAMS), School of Basic Medical Sciences, Shanghai Medical College Fudan University, Shanghai 200032, China; (J.Y.); (K.M.); (Z.Z.); (T.H.); (W.Z.)
| | - Zixin Zhao
- Key Laboratory of Medical Molecular Virology (MOE & NHC), Research Unit of Cure of Chronic Hepatitis B Virus Infection (CAMS), School of Basic Medical Sciences, Shanghai Medical College Fudan University, Shanghai 200032, China; (J.Y.); (K.M.); (Z.Z.); (T.H.); (W.Z.)
| | - Ting Hua
- Key Laboratory of Medical Molecular Virology (MOE & NHC), Research Unit of Cure of Chronic Hepatitis B Virus Infection (CAMS), School of Basic Medical Sciences, Shanghai Medical College Fudan University, Shanghai 200032, China; (J.Y.); (K.M.); (Z.Z.); (T.H.); (W.Z.)
| | - Wenjing Zai
- Key Laboratory of Medical Molecular Virology (MOE & NHC), Research Unit of Cure of Chronic Hepatitis B Virus Infection (CAMS), School of Basic Medical Sciences, Shanghai Medical College Fudan University, Shanghai 200032, China; (J.Y.); (K.M.); (Z.Z.); (T.H.); (W.Z.)
| | - Jieliang Chen
- Key Laboratory of Medical Molecular Virology (MOE & NHC), Research Unit of Cure of Chronic Hepatitis B Virus Infection (CAMS), School of Basic Medical Sciences, Shanghai Medical College Fudan University, Shanghai 200032, China; (J.Y.); (K.M.); (Z.Z.); (T.H.); (W.Z.)
| | - Xiutao Fu
- Liver Cancer Institute, Fudan University, Shanghai 200032, China;
- Department of Liver Surgery and Transplantation, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Shanghai 200032, China
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Wu S, Tao T, Zhang L, Zhu X, Zhou X. Extrachromosomal DNA (ecDNA): Unveiling its role in cancer progression and implications for early detection. Heliyon 2023; 9:e21327. [PMID: 38027570 PMCID: PMC10643110 DOI: 10.1016/j.heliyon.2023.e21327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 10/16/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023] Open
Abstract
Extrachromosomal DNA (ecDNA) is a special class of circular DNA in eukaryotes, which is independent of conventional chromosomes. These circular molecules play important roles in biology, especially in cancer biology. The emergence of sequencing technologies such as CCDA-seq and Amplicon Architect has led to a progressive unraveling of the mystery of ecDNA. Consequently, insights into its function and potential applications have begun to surface. Among these studies, the most noteworthy research pertains to cancer-related investigations into ecDNA. Numerous studies have underscored the significance of ecDNA in the pathogenesis of cancer and its role in accelerating cancer evolution. This review provides an overview of the source, structure, and function of ecDNA, while compiling recent advancements in ecDNA in the field of cancer. Nonetheless, further research is imperative to determine its effectiveness and specificity as a biomarker for early cancer detection.
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Affiliation(s)
- Shuhong Wu
- Department of Immunology, School of Medicine, Nantong University, Nantong, China
- Computational Systems Biology Lab (CSBL), The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, China
| | - Tao Tao
- Department of Gastroenterology, Zibo Central Hospital, Zibo, China
| | - Lin Zhang
- Computational Systems Biology Lab (CSBL), The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, China
| | - Xiao Zhu
- Computational Systems Biology Lab (CSBL), The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, China
- Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou Medical College, Hangzhou, China
| | - Xiaorong Zhou
- Department of Immunology, School of Medicine, Nantong University, Nantong, China
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Rao G, Peng X, Tian Y, Fu X, Zhang Y. Circular RNAs in hepatocellular carcinoma: biogenesis, function, and pathology. Front Genet 2023; 14:1106665. [PMID: 37485335 PMCID: PMC10361733 DOI: 10.3389/fgene.2023.1106665] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 06/16/2023] [Indexed: 07/25/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common causes of cancer-related death worldwide. Both genetic and environmental factors through a multitude of underlying molecular mechanisms participate in the pathogenesis of HCC. Recently, numerous studies have shown that circular RNAs (circRNAs), an emerging class of non-coding RNAs characterized by the presence of covalent bonds linking 3' and 5' ends, play an important role in the initiation and progression of cancers, including HCC. In this review, we outline the current status of the field of circRNAs, with an emphasis on the functions and mechanisms of circRNAs in HCC and its microenvironment. We also summarize and discuss recent advances of circRNAs as biomarkers and therapeutic targets. These efforts are anticipated to throw new insights into future perspectives about circRNAs in basic, translational and clinical research, eventually advancing the diagnosis, prevention and treatment of HCC.
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Affiliation(s)
- Guocheng Rao
- Department of Endocrinology and Metabolism, Cancer Center West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Endocrinology and Metabolism, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Xi Peng
- Department of Endocrinology and Metabolism, Cancer Center West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Endocrinology and Metabolism, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Yan Tian
- Department of Endocrinology and Metabolism, Cancer Center West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xianghui Fu
- Department of Endocrinology and Metabolism, Cancer Center West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Endocrinology and Metabolism, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Yuwei Zhang
- Department of Endocrinology and Metabolism, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
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