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Zheng H, Li Q, Yang K. A circadian rhythm-related lncRNA signature correlates with prognosis and tumor immune microenvironment in head and neck squamous cell carcinoma. Discov Oncol 2024; 15:308. [PMID: 39052123 PMCID: PMC11272767 DOI: 10.1007/s12672-024-01181-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024] Open
Abstract
OBJECTIVE To investigate circadian rhythm-associated long non-coding RNA (lncRNA) signatures in predicting prognosis, metabolism, and immune infiltration in Head and Neck Squamous Cell Carcinoma (HNSC). METHODS HNSC samples were collected from the TCGA database. A signature was constructed using Cox regression and Least Absolute Shrinkage and Selection Operator (LASSO) methods. The immune cell infiltration was analyzed using CIBERSORT, ssGSEA, and MCPcounter. The RT-qPCR was used to detect the expression of signature lncRNAs. RESULTS A signature comprising 8 lncRNAs was constructed. The constructed signature demonstrated good prognostic prediction capability for HNSC. A nomogram encompassing risk score accurately predicted the long-term OS probability of HNSC. The infiltration levels of T cell, B cell and Macrophages were significantly higher in the high-risk group than in the low-risk group. Cluster analysis showed that the signature lncRNAs could classify the HNSC samples into two clusters. The RT-qPCR suggested that the expression of lncRNAs in signature was consistent with the data in TCGA. CONCLUSION The circadian rhythm-associated lncRNA signature has potential as a prognostic indicator for HNSC. It exhibits associations with metabolism, immune microenvironment, and drug sensitivity, thereby providing valuable insights for informing the treatment of HNSC.
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Affiliation(s)
- Hongyu Zheng
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Chongqing Medical University, No.1, Youyi Road, Yuzhong District, Chongqing, 400016, China
| | - Qiuyue Li
- Department of Emergency Medicine, The Second Hospital of Tianjin Medical University, No.23, Pingjiang Road, Hexi District, Tianjin, 300211, China
| | - Kai Yang
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Chongqing Medical University, No.1, Youyi Road, Yuzhong District, Chongqing, 400016, China.
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2
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Tian H, Tang L, Yang Z, Xiang Y, Min Q, Yin M, You H, Xiao Z, Shen J. Current understanding of functional peptides encoded by lncRNA in cancer. Cancer Cell Int 2024; 24:252. [PMID: 39030557 PMCID: PMC11265036 DOI: 10.1186/s12935-024-03446-7] [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: 10/20/2023] [Accepted: 07/09/2024] [Indexed: 07/21/2024] Open
Abstract
Dysregulated gene expression and imbalance of transcriptional regulation are typical features of cancer. RNA always plays a key role in these processes. Human transcripts contain many RNAs without long open reading frames (ORF, > 100 aa) and that are more than 200 bp in length. They are usually regarded as long non-coding RNA (lncRNA) which play an important role in cancer regulation, including chromatin remodeling, transcriptional regulation, translational regulation and as miRNA sponges. With the advancement of ribosome profiling and sequencing technologies, increasing research evidence revealed that some ORFs in lncRNA can also encode peptides and participate in the regulation of multiple organ tumors, which undoubtedly opens a new chapter in the field of lncRNA and oncology research. In this review, we discuss the biological function of lncRNA in tumors, the current methods to evaluate their coding potential and the role of functional small peptides encoded by lncRNA in cancers. Investigating the small peptides encoded by lncRNA and understanding the regulatory mechanisms of these functional peptides may contribute to a deeper understanding of cancer and the development of new targeted anticancer therapies.
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Affiliation(s)
- Hua Tian
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy and Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
- School of Nursing, Chongqing College of Humanities, Science & Technology, Chongqing, China
| | - Lu Tang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy and Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Zihan Yang
- Department of Pathology, The Affiliated Hospital of Southwest Medical University, Luzhou, China, 646000
| | - Yanxi Xiang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy and Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Qi Min
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy and Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Mengshuang Yin
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy and Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Huili You
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy and Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Zhangang Xiao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China.
- Cell Therapy and Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China.
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China.
- Gulin Traditional Chinese Medicine Hospital, Luzhou, China.
- Department of Pharmacology, School of Pharmacy, Sichuan College of Traditional Chinese Medicine, Mianyang, China.
| | - Jing Shen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China.
- Cell Therapy and Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China.
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China.
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3
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Zhang J, Wu L, Wang C, Xie X, Han Y. Research Progress of Long Non-Coding RNA in Tumor Drug Resistance: A New Paradigm. Drug Des Devel Ther 2024; 18:1385-1398. [PMID: 38689609 PMCID: PMC11060174 DOI: 10.2147/dddt.s448707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 03/25/2024] [Indexed: 05/02/2024] Open
Abstract
In the past few decades, chemotherapy has been one of the most effective cancer treatment options. Drug resistance is currently one of the greatest obstacles to effective cancer treatment. Even though drug resistance mechanisms have been extensively investigated, they have not been fully elucidated. Recent genome-wide investigations have revealed the existence of a substantial quantity of long non-coding RNAs (lncRNAs) transcribed from the human genome, which actively participate in numerous biological processes, such as transcription, splicing, epigenetics, the cell cycle, cell differentiation, development, pluripotency, immune microenvironment. The abnormal expression of lncRNA is considered a contributing factor to the drug resistance. Furthermore, drug resistance may be influenced by genetic and epigenetic variations, as well as individual differences in patient treatment response, attributable to polymorphisms in metabolic enzyme genes. This review focuses on the mechanism of lncRNAs resistance to target drugs in the study of tumors with high mortality, aiming to establish a theoretical foundation for targeted therapy.
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Affiliation(s)
- Jing Zhang
- Laboratory of Tissue Engineering, Faculty of Life Science, Northwest University, Xi’an, Shaanxi, People’s Republic of China
| | - Le Wu
- Laboratory of Tissue Engineering, Faculty of Life Science, Northwest University, Xi’an, Shaanxi, People’s Republic of China
| | - Chenchen Wang
- Department of Critical Care Medicine, the 940th Hospital of Joint Logistics Support Force of PLA, Lanzhou, Gansu, People’s Republic of China
| | - Xin Xie
- Laboratory of Tissue Engineering, Faculty of Life Science, Northwest University, Xi’an, Shaanxi, People’s Republic of China
| | - Yuying Han
- Laboratory of Tissue Engineering, Faculty of Life Science, Northwest University, Xi’an, Shaanxi, People’s Republic of China
- Department of Critical Care Medicine, the 940th Hospital of Joint Logistics Support Force of PLA, Lanzhou, Gansu, People’s Republic of China
- Science and Education Department, Xi’an No. 5 Hospital, Xi’an, Shaanxi, People’s Republic of China
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Carpenter S, O'Neill LAJ. From periphery to center stage: 50 years of advancements in innate immunity. Cell 2024; 187:2030-2051. [PMID: 38670064 PMCID: PMC11060700 DOI: 10.1016/j.cell.2024.03.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/24/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024]
Abstract
Over the past 50 years in the field of immunology, something of a Copernican revolution has happened. For a long time, immunologists were mainly concerned with what is termed adaptive immunity, which involves the exquisitely specific activities of lymphocytes. But the other arm of immunity, so-called "innate immunity," had been neglected. To celebrate Cell's 50th anniversary, we have put together a review of the processes and components of innate immunity and trace the seminal contributions leading to the modern state of this field. Innate immunity has joined adaptive immunity in the center of interest for all those who study the body's defenses, as well as homeostasis and pathology. We are now entering the era where therapeutic targeting of innate immune receptors and downstream signals hold substantial promise for infectious and inflammatory diseases and cancer.
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Affiliation(s)
- Susan Carpenter
- University of California Santa Cruz, 1156 High St., Santa Cruz, CA 95064, USA.
| | - Luke A J O'Neill
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland.
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Fitzgerald KA, Shmuel-Galia L. Lnc-ing RNA to intestinal homeostasis and inflammation. Trends Immunol 2024; 45:127-137. [PMID: 38220553 DOI: 10.1016/j.it.2023.12.005] [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: 11/28/2023] [Revised: 12/14/2023] [Accepted: 12/21/2023] [Indexed: 01/16/2024]
Abstract
Long noncoding RNAs (lncRNAs) play important roles in numerous biological processes, including the immune system. Initial research in this area focused on cell-based studies, but recent advances underscore the profound significance of lncRNAs at the organismal level, providing invaluable insights into their roles in inflammatory diseases. In this rapidly evolving field, lncRNAs have been described with pivotal roles in the intestinal tract where they regulate intestinal homeostasis and inflammation by influencing processes such as immune cell development, inflammatory signaling pathways, epithelial barrier function, and cellular metabolism. Understanding the regulation and function of lncRNAs in this tissue may position lncRNAs not only as potential disease biomarkers but also as promising targets for therapeutic intervention in inflammatory bowel disease and related diseases.
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Affiliation(s)
- Katherine A Fitzgerald
- Program in Innate Immunity, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
| | - Liraz Shmuel-Galia
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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6
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Ji L, Liang S, Cheng Y, Gao R, Yan W, Pang F, Zhang F. Identification of a novel necroptosis-related LncRNA signature for prognostic prediction and immune response in oral squamous cell carcinoma. Cancer Biomark 2024; 40:319-342. [PMID: 39213052 PMCID: PMC11380221 DOI: 10.3233/cbm-230407] [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] [Indexed: 09/04/2024]
Abstract
BACKGROUND Necroptosis is a caspase-independent regulated necrotic cell death modality that elicits strong adaptive immune responses, and has the potential to activate antitumor immunity. Long non-coding RNAs (lncRNAs) have critical effects on oral squamous cell carcinoma (OSCC), which are closely associated with the prognosis and immune regulation of OSCC patients. OBJECTIVE This study aimed to identify a novel necroptosis-related lncRNAs signature to predict the prognosis and immune response of OSCC patients and provide patients with anti-tumor drug selection through bioinformatics analysis and in vitro experiments. METHODS A series of analyses, including differential lncRNA screening, survival analysis, Cox regression analysis, ROC analysis, nomogram prediction, enrichment analysis, tumor-infiltrating immune cells, drug sensitivity analysis, and consensus cluster analysis, were performed to determine and validate the prognostic value of necroptosis-associated lncRNAs signature in OSCC. And real-time quantitative polymerase chain reaction (RT-qPCR) was used to determine the expression levels of these lncRNAs. RESULTS This signature including 5 lncRNAs (AC099850.3, StarD4-AS1, AC011978.1, LINC01503, CDKN2A-DT) in OSCC associated with necroptosis were established and verified by bioinformatics. Further, ROC, K-M, univariate/multivariate Cox regression, and nomogram analysis were used to evaluate the model's features for OSCC prognosis. Using multiple bioinformatics techniques, the levels of tumor-infiltrating immune cells, immune checkpoints and semi-inhibitory concentrations showed significant differences across risk subtypes. By consensus cluster analysis, there were significant differences between clusters in survival, immune checkpoint expression, clinicopathological correlation, and tumor immunity. RT-qPCR showed that AC099850.3, AC011978.1, LINC01503 were up-regulated, STARD4-AS1 and CDKN2A-DT were down-regulated in OSCC cell lines compared with human normal oral keratinoid cell line. CONCLUSION We established 5-NRLs markers, which is useful for assessing OSCC immune response and prognosis, recommending personalized antitumor drugs. The expression level of 5-NRLs in OSCC was identified in vitro, and the results preliminarily verified this model. And this study would generate new insights for future experimental research.
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Affiliation(s)
- Lanting Ji
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi, China
| | - Shuang Liang
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi, China
| | | | - Ruifang Gao
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi, China
| | - Wenpeng Yan
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi, China
| | - Fang Pang
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi, China
| | - Fang Zhang
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi, China
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7
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Calanca N, Francisco ALN, Bizinelli D, Kuasne H, Barros Filho MC, Flores BCT, Pinto CAL, Rainho CA, Soares MBP, Marchi FA, Kowalski LP, Rogatto SR. DNA methylation-based depiction of the immune microenvironment and immune-associated long non-coding RNAs in oral cavity squamous cell carcinomas. Biomed Pharmacother 2023; 167:115559. [PMID: 37742611 DOI: 10.1016/j.biopha.2023.115559] [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: 06/15/2023] [Revised: 09/18/2023] [Accepted: 09/19/2023] [Indexed: 09/26/2023] Open
Abstract
Oral cavity squamous cell carcinoma (OSCC) is a complex and dynamic disease characterized by clinicopathological and molecular heterogeneity. Spatial and temporal heterogeneity of cell subpopulations has been associated with cancer progression and implicated in the prognosis and therapy response. Emerging evidence indicates that aberrant epigenetic profiles in OSCC may foster an immunosuppressive tumor microenvironment by modulating the expression of immune-related long non-coding RNAs (lncRNAs). DNA methylation analysis was performed in 46 matched OSCC and normal adjacent tissue samples using a genome-wide platform (Infinium HumanMethylation450 BeadChip). Reference-based computational deconvolution (MethylCIBERSORT) was applied to infer the immune cell composition of the bulk samples. The expression levels of genes encoding immune markers and differentially methylated lncRNAs were investigated using The Cancer Genome Atlas dataset. OSCC specimens presented distinct immune cell composition, including the enrichment of monocyte lineage cells, natural killer cells, cytotoxic T-lymphocytes, regulatory T-lymphocytes, and neutrophils. In contrast, B-lymphocytes, effector T-lymphocytes, and fibroblasts were diminished in tumor samples. The hypomethylation of three immune-associated lncRNAs (MEG3, MIR155HG, and WFDC21P) at individual CpG sites was confirmed by bisulfite-pyrosequencing. Also, the upregulation of a set of immune markers (FOXP3, GZMB, IL10, IL2RA, TGFB, IFNG, TDO2, IDO1, and HIF1A) was detected. The immune cell composition, immune markers alteration, and dysregulation of immune-associated lncRNAs reinforce the impact of the immune microenvironment in OSCC. These concurrent factors contribute to tumor heterogeneity, suggesting that epi-immunotherapy could be an efficient alternative to treat OSCC.
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Affiliation(s)
- Naiade Calanca
- Department of Clinical Genetics, University Hospital of Southern Denmark-Vejle, Institute of Regional Health Research, University of Southern Denmark, Odense 5000, Denmark; Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, SP, Brazil
| | - Ana Lucia Noronha Francisco
- Department of Head and Neck Surgery and Otorhinolaryngology, A.C.Camargo Cancer Center, São Paulo 01509-001, SP, Brazil
| | - Daniela Bizinelli
- International Research Center (CIPE), A.C.Camargo Cancer Center, São Paulo 01508-010, SP, Brazil
| | - Hellen Kuasne
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal H3A1A3, QC, Canada
| | | | - Bianca Campos Troncarelli Flores
- Department of Clinical Genetics, University Hospital of Southern Denmark-Vejle, Institute of Regional Health Research, University of Southern Denmark, Odense 5000, Denmark
| | | | - Claudia Aparecida Rainho
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, SP, Brazil
| | - Milena Botelho Pereira Soares
- Health Technology Institute, SENAI CIMATEC, Salvador 41650-010, BA, Brazil; Gonçalo Moniz Institute, FIOCRUZ, Salvador 40296-710, BA, Brazil
| | - Fabio Albuquerque Marchi
- Department of Head and Neck Surgery, University of São Paulo Medical School, São Paulo 05402-000, SP, Brazil
| | - Luiz Paulo Kowalski
- Department of Head and Neck Surgery and Otorhinolaryngology, A.C.Camargo Cancer Center, São Paulo 01509-001, SP, Brazil; Department of Head and Neck Surgery, University of São Paulo Medical School, São Paulo 05402-000, SP, Brazil
| | - Silvia Regina Rogatto
- Department of Clinical Genetics, University Hospital of Southern Denmark-Vejle, Institute of Regional Health Research, University of Southern Denmark, Odense 5000, Denmark.
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Zhang J, Liu L, Wei X, Zhao C, Li S, Li J, Le TD. Pan-cancer characterization of ncRNA synergistic competition uncovers potential carcinogenic biomarkers. PLoS Comput Biol 2023; 19:e1011308. [PMID: 37812646 PMCID: PMC10586676 DOI: 10.1371/journal.pcbi.1011308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/19/2023] [Accepted: 09/25/2023] [Indexed: 10/11/2023] Open
Abstract
Non-coding RNAs (ncRNAs) act as important modulators of gene expression and they have been confirmed to play critical roles in the physiology and development of malignant tumors. Understanding the synergism of multiple ncRNAs in competing endogenous RNA (ceRNA) regulation can provide important insights into the mechanisms of malignant tumors caused by ncRNA regulation. In this work, we present a framework, SCOM, for identifying ncRNA synergistic competition. We systematically construct the landscape of ncRNA synergistic competition across 31 malignant tumors, and reveal that malignant tumors tend to share hub ncRNAs rather than the ncRNA interactions involved in the synergistic competition. In addition, the synergistic competition ncRNAs (i.e. ncRNAs involved in the synergistic competition) are likely to be involved in drug resistance, contribute to distinguishing molecular subtypes of malignant tumors, and participate in immune regulation. Furthermore, SCOM can help to infer ncRNA synergistic competition across malignant tumors and uncover potential diagnostic and prognostic biomarkers of malignant tumors. Altogether, the SCOM framework (https://github.com/zhangjunpeng411/SCOM/) and the resulting web-based database SCOMdb (https://comblab.cn/SCOMdb/) serve as a useful resource for exploring ncRNA regulation and to accelerate the identification of carcinogenic biomarkers.
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Affiliation(s)
- Junpeng Zhang
- School of Engineering, Dali University, Dali, Yunnan, People’s Republic of China
| | - Lin Liu
- UniSA STEM, University of South Australia, Mawson Lakes, South Australia, Australia
| | - Xuemei Wei
- School of Engineering, Dali University, Dali, Yunnan, People’s Republic of China
| | - Chunwen Zhao
- School of Engineering, Dali University, Dali, Yunnan, People’s Republic of China
| | - Sijing Li
- School of Engineering, Dali University, Dali, Yunnan, People’s Republic of China
| | - Jiuyong Li
- UniSA STEM, University of South Australia, Mawson Lakes, South Australia, Australia
| | - Thuc Duy Le
- UniSA STEM, University of South Australia, Mawson Lakes, South Australia, Australia
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Shakhpazyan NK, Mikhaleva LM, Bedzhanyan AL, Sadykhov NK, Midiber KY, Konyukova AK, Kontorschikov AS, Maslenkina KS, Orekhov AN. Long Non-Coding RNAs in Colorectal Cancer: Navigating the Intersections of Immunity, Intercellular Communication, and Therapeutic Potential. Biomedicines 2023; 11:2411. [PMID: 37760852 PMCID: PMC10525929 DOI: 10.3390/biomedicines11092411] [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: 07/12/2023] [Revised: 08/18/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
This comprehensive review elucidates the intricate roles of long non-coding RNAs (lncRNAs) within the colorectal cancer (CRC) microenvironment, intersecting the domains of immunity, intercellular communication, and therapeutic potential. lncRNAs, which are significantly involved in the pathogenesis of CRC, immune evasion, and the treatment response to CRC, have crucial implications in inflammation and serve as promising candidates for novel therapeutic strategies and biomarkers. This review scrutinizes the interaction of lncRNAs with the Consensus Molecular Subtypes (CMSs) of CRC, their complex interplay with the tumor stroma affecting immunity and inflammation, and their conveyance via extracellular vesicles, particularly exosomes. Furthermore, we delve into the intricate relationship between lncRNAs and other non-coding RNAs, including microRNAs and circular RNAs, in mediating cell-to-cell communication within the CRC microenvironment. Lastly, we propose potential strategies to manipulate lncRNAs to enhance anti-tumor immunity, thereby underlining the significance of lncRNAs in devising innovative therapeutic interventions in CRC.
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Affiliation(s)
- Nikolay K. Shakhpazyan
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Liudmila M. Mikhaleva
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Arcady L. Bedzhanyan
- Department of Abdominal Surgery and Oncology II (Coloproctology and Uro-Gynecology), Petrovsky National Research Center of Surgery, 119435 Moscow, Russia;
| | - Nikolay K. Sadykhov
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Konstantin Y. Midiber
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Alexandra K. Konyukova
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Andrey S. Kontorschikov
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Ksenia S. Maslenkina
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Alexander N. Orekhov
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia
- Institute for Atherosclerosis Research, 121096 Moscow, Russia
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10
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Miao R, Yao Z, Hu B, Jin T, Zhu D, Shi Y, Gong Y, Shao S, Shao C. A novel long non-coding RNA XLOC_004787, is associated with migration and promotes cancer cell proliferation by downregulating mir-203a-3p in gastric cancer. BMC Gastroenterol 2023; 23:280. [PMID: 37573302 PMCID: PMC10422700 DOI: 10.1186/s12876-023-02912-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 08/02/2023] [Indexed: 08/14/2023] Open
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) have been identified as important regulatory factors implicated in a wide array of diseases, including various forms of cancer. However, the roles of most lncRNAs in the progression of gastric cancer (GC) remain largely unexplored. This study investigates the biological function and underlying mechanism of a novel lncRNA, XLOC_004787 in GC. METHODS The location of XLOC_004787 in GES-1 cells and HGC-27 cells were detected by fluorescence in situ hybridization (FISH) assay. The expression levels of XLOC_004787 were assessed using quantitative real-time fluorescence PCR (qRT-PCR) in various cell lines, including GES-1, MGC-803, MKN-45, BGC-823, SGC-7901, and HGC-27 cells. Functional assays such as Transwell migration, cell counting kit-8 (CCK-8), and colony formation experiments were employed to analyze the effects of XLOC_004787 and miR-203a-3p on cell migration and proliferation. Protein levels associated with GC in these cell lines were examined by Western blotting. The intracellular localization of β-catenin and P-Smad2/3 was assessed using immunofluorescence (IF) assay. Additionally, the interaction between XLOC_004787 and miR-203a-3p was investigated using a dual luciferase assay. RESULTS XLOC_004787 was localized at both the cytoplasm and nucleus of GES-1 cells and HGC-27 cells. Compared to normal tissues and GES-1 cells, XLOC_004787 expression was significantly upregulated in GC tissues and cells, with the highest and lowest expression observed in SGC-7901 and HGC-27 cells, respectively. Furthermore, a reduced expression of XLOC_004787 was seen to inhibit migration and proliferation in SGC-7901 cells. Western blotting analysis revealed that a decrease in XLOC_004787 expression correspondingly decreased the expression of N-cadherin, mmp2, mmp9, Snail, Vimentin, β-catenin, C-myc, Cyclin D1, and TGF-β, while concurrently increasing E-cadherin expression. This was also associated with diminished expression of P-Smad2/3 in relation to Smad2/3, and reduced P-Gsk3β expression in comparison to Gsk3β. Additionally, the nuclear entry of P-Smad2/3 and β-catenin was reduced by lower XLOC_004787 expression. Amplifying XLOC_004787 expression via pcDNA_XLOC_004787 suggested a potential for cancer promotion. Notably, XLOC_004787 was found to negatively regulate mir-203a-3p expression, with potential binding sites identified between the two. Higher mir-203a-3p expression was observed to decrease migration and proliferation, and enhance E-cadherin expression. Conversely, suppression of mir-203a-3p expression suggested a potential promotion of proliferation and migration in GC cells. CONCLUSIONS These results suggest that XLOC_004787, found to be upregulated in GC tissues, potentially promotes proliferation and migration in GC cells. This occurs through the activation of TGF-β and Wnt/β-catenin signaling pathways and the expression of EMT-related proteins. Additionally, XLOC_004787 may influence cell migration and proliferation by modulating the signaling pathway via the adsorption and inhibition of mir-203a-3p.
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Affiliation(s)
- Renjie Miao
- Department of Clinical Laboratory, Affiliated Third Hospital of Zhenjiang to Jiangsu University, Zhenjiang, 212001, Jiangsu, China
| | - Zhendong Yao
- Department of Gastroenterology, The Affiliated Yixing Hospital of Jiangsu University, Yixing, 214200, Jiangsu, China
| | - Bingheng Hu
- The Affiliated Hospital of Jiangsu University, Yizheng Road, Zhenjiang, 212013, Jiangsu, China
| | - Tao Jin
- Department of Gastroenterology, The Affiliated Yixing Hospital of Jiangsu University, Yixing, 214200, Jiangsu, China
| | - Donglai Zhu
- Department of Clinical Laboratory, Affiliated Third Hospital of Zhenjiang to Jiangsu University, Zhenjiang, 212001, Jiangsu, China
| | - Yun Shi
- Department of Oncology, The Second Affiliated Hospital of Soochow University, Suzhou 215000, Jiangsu, China
| | - Yuhua Gong
- Department of Clinical Laboratory, Affiliated Third Hospital of Zhenjiang to Jiangsu University, Zhenjiang, 212001, Jiangsu, China
| | - Shihe Shao
- Department of Clinical Laboratory, Affiliated Third Hospital of Zhenjiang to Jiangsu University, Zhenjiang, 212001, Jiangsu, China
| | - Chen Shao
- The Affiliated Hospital of Jiangsu University, Yizheng Road, Zhenjiang, 212013, Jiangsu, China.
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Huang LA, Lin C, Yang L. Plumbing mysterious RNAs in "dark genome" for the conquest of human diseases. Mol Ther 2023; 31:1577-1595. [PMID: 37165619 PMCID: PMC10278048 DOI: 10.1016/j.ymthe.2023.05.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/11/2023] [Accepted: 05/05/2023] [Indexed: 05/12/2023] Open
Abstract
Next-generation sequencing has revealed that less than 2% of transcribed genes are translated into proteins, with a large portion transcribed into noncoding RNAs (ncRNAs). Among these, long noncoding RNAs (lncRNAs) represent the largest group and are pervasively transcribed throughout the genome. Dysfunctions in lncRNAs have been found in various diseases, highlighting their potential as therapeutic, diagnostic, and prognostic targets. However, challenges, such as unknown molecular mechanisms and nonspecific immune responses, and issues of drug specificity and delivery present obstacles in translating lncRNAs into clinical applications. In this review, we summarize recent publications that have explored lncRNA functions in human diseases. We also discuss challenges and future directions for developing lncRNA treatments, aiming to bridge the gap between functional studies and clinical potential and inspire further exploration in the field.
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Affiliation(s)
- Lisa A Huang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chunru Lin
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Liuqing Yang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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12
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Erber J, Herndler-Brandstetter D. Regulation of T cell differentiation and function by long noncoding RNAs in homeostasis and cancer. Front Immunol 2023; 14:1181499. [PMID: 37346034 PMCID: PMC10281531 DOI: 10.3389/fimmu.2023.1181499] [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: 03/07/2023] [Accepted: 05/02/2023] [Indexed: 06/23/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) increase in genomes of complex organisms and represent the largest group of RNA genes transcribed in mammalian cells. Previously considered only transcriptional noise, lncRNAs comprise a heterogeneous class of transcripts that are emerging as critical regulators of T cell-mediated immunity. Here we summarize the lncRNA expression landscape of different T cell subsets and highlight recent advances in the role of lncRNAs in regulating T cell differentiation, function and exhaustion during homeostasis and cancer. We discuss the different molecular mechanisms of lncRNAs and highlight lncRNAs that can serve as novel targets to modulate T cell function or to improve the response to cancer immunotherapies by modulating the immunosuppressive tumor microenvironment.
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13
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Ktena YP, Dionysiou M, Gondek LP, Cooke KR. The impact of epigenetic modifications on allogeneic hematopoietic stem cell transplantation. Front Immunol 2023; 14:1188853. [PMID: 37325668 PMCID: PMC10264773 DOI: 10.3389/fimmu.2023.1188853] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/18/2023] [Indexed: 06/17/2023] Open
Abstract
The field of epigenetics studies the complex processes that regulate gene expression without altering the DNA sequence itself. It is well established that epigenetic modifications are crucial to cellular homeostasis and differentiation and play a vital role in hematopoiesis and immunity. Epigenetic marks can be mitotically and/or meiotically heritable upon cell division, forming the basis of cellular memory, and have the potential to be reversed between cellular fate transitions. Hence, over the past decade, there has been increasing interest in the role that epigenetic modifications may have on the outcomes of allogeneic hematopoietic transplantation and growing enthusiasm in the therapeutic potential these pathways may hold. In this brief review, we provide a basic overview of the types of epigenetic modifications and their biological functions, summarizing the current literature with a focus on hematopoiesis and immunity specifically in the context of allogeneic hematopoietic stem cell transplantation.
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Affiliation(s)
- Yiouli P. Ktena
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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14
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Decoding Roles of Exosomal lncRNAs in Tumor-Immune Regulation and Therapeutic Potential. Cancers (Basel) 2022; 15:cancers15010286. [PMID: 36612282 PMCID: PMC9818565 DOI: 10.3390/cancers15010286] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/12/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023] Open
Abstract
Exosomes are nanovesicles secreted into biofluids by various cell types and have been implicated in different physiological and pathological processes. Interestingly, a plethora of studies emphasized the mediating role of exosomes in the bidirectional communication between donor and recipient cells. Among the various cargoes of exosomes, long non-coding RNAs (lncRNAs) have been identified as crucial regulators between cancer cells and immune cells in the tumor microenvironment (TME) that can interfere with innate and adaptive immune responses to affect the therapeutic efficiency. Recently, a few major studies have focused on the exosomal lncRNA-mediated interaction between cancer cells and immune cells infiltrated into TME. Nevertheless, a dearth of studies pertains to the immune regulating role of exosomal lncRNAs in cancer and is still in the early stages. Comprehensive mechanisms of exosomal lncRNAs in tumor immunity are not well understood. Herein, we provide an overview of the immunomodulatory function of exosomal lncRNAs in cancer and treatment resistance. In addition, we also summarize the potential therapeutic strategies toward exosomal lncRNAs in TME.
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15
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Huang Q, You Q, Zhu N, Wu Z, Xiang Z, Wu K, Ren J, Gui Y. Prognostic prediction of head and neck squamous cell carcinoma: Construction of cuproptosis-related long non-coding RNA signature. J Clin Lab Anal 2022; 36:e24723. [PMID: 36189780 PMCID: PMC9701877 DOI: 10.1002/jcla.24723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Recently, a new type of programmed cell death, cuproptosis, has been identified to play important role in the progression of tumors. We constructed a cuproptosis-related long non-coding RNA (lncRNA) signature to predict the prognostic significance for head and neck squamous cell carcinoma (HNSCC). METHODS The risk model was developed based on differentially expressed lncRNAs associated with cuproptosis. Principal component analysis was used to assess the validity. The Kaplan-Meier curves were analyzed to compare the overall survival (OS), disease-specific survival (DSS), and progression-free survival (PFS) values. The multivariate and univariate Cox regression analyses were used to evaluate the prognostic efficiency. Furthermore, the functional enrichment, immune cell infiltration, tumor mutation burden (TMB), and sensitivity toward chemotherapy were also explored. RESULTS Six cuproptosis-related lncRNAs (AL109936.2, CDKN2A-DT, AC090587.1, KLF3-AS1, AL133395.1, and LINC01063) were identified to construct the independent prognostic predictor for HNSCC. The area under the curve and C-index values obtained using the risk model were higher than the values corresponding to the clinical factors. Analysis of Kaplan-Meier curves indicated that the OS, PFS, and DSS time recorded for the patients in the low-risk group were higher than the corresponding values recorded for the patients belonging to the high-risk group. By functional enrichment analysis, we observed that differentially expressed genes were enriched in the immune response and tumor-associated pathways. The patients characterized by a low-risk score exhibited better immune cell infiltration than the patients belonging to the other group. We also observed that the sensitivity of the individuals belonging to the low-risk group to chemotherapeutic agents (cisplatin, docetaxel, and paclitaxel) was higher than the sensitivity of those in the other group. CONCLUSIONS A cuproptosis-related lncRNA-based signature that functioned as an independent prognosis predictor for HNSCC patients was constructed. The chemosensitivity of individual patients can be potentially predicted using this signature.
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Affiliation(s)
- Qi Huang
- Department of Otorhinolaryngology Head and Neck SurgeryNingbo Medical Center Lihuili HospitalNingboChina,Department of Otorhinolaryngology Head and Neck SurgeryLihuili Hospital affiliated to Ningbo UniversityNingboChina
| | - Quanjie You
- Department of Otorhinolaryngology Head and Neck SurgeryNingbo Medical Center Lihuili HospitalNingboChina,Department of Otorhinolaryngology Head and Neck SurgeryLihuili Hospital affiliated to Ningbo UniversityNingboChina
| | - Ning Zhu
- Department of OtolaryngologySecond Hospital of Ninghai CountyNingboChina
| | - Zhenhua Wu
- Department of Otorhinolaryngology Head and Neck SurgeryNingbo Medical Center Lihuili HospitalNingboChina,Department of Otorhinolaryngology Head and Neck SurgeryLihuili Hospital affiliated to Ningbo UniversityNingboChina
| | - Zhenfei Xiang
- Department of Radiation OncologyLihuili Hospital affiliated to Ningbo UniversityNingboChina
| | - Kaiyuan Wu
- Department of Otorhinolaryngology Head and Neck SurgeryNingbo Medical Center Lihuili HospitalNingboChina,Department of Otorhinolaryngology Head and Neck SurgeryLihuili Hospital affiliated to Ningbo UniversityNingboChina
| | - Jianjun Ren
- Department of Otorhinolaryngology Head and Neck SurgeryNingbo Medical Center Lihuili HospitalNingboChina,Department of Otorhinolaryngology Head and Neck SurgeryLihuili Hospital affiliated to Ningbo UniversityNingboChina
| | - Yihua Gui
- Department of Otorhinolaryngology Head and Neck SurgeryNingbo Medical Center Lihuili HospitalNingboChina,Department of Otorhinolaryngology Head and Neck SurgeryLihuili Hospital affiliated to Ningbo UniversityNingboChina
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Liu YJ, Wang H, Zhong HJ, Chong CM, Yang GJ. Editorial: Epigenetics of the immune component of inflammation. Front Immunol 2022; 13:1000836. [PMID: 36072580 PMCID: PMC9443511 DOI: 10.3389/fimmu.2022.1000836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Yan-Jun Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Aquacultral Biotechnology Ministry of Education, Ningbo University, Ningbo, China
| | - Haitao Wang
- Thoracic Surgery Branch, Center for Cancer Research, NCI, NIH, Bethesda, MA, United States
- *Correspondence: Guan-Jun Yang, ; Haitao Wang, ; Cheong-Meng Chong, ; Hai-Jing Zhong,
| | - Hai-Jing Zhong
- College of Pharmacy, Jinan University, Guangzhou, China
- *Correspondence: Guan-Jun Yang, ; Haitao Wang, ; Cheong-Meng Chong, ; Hai-Jing Zhong,
| | - Cheong-Meng Chong
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, Macao SAR, China
- *Correspondence: Guan-Jun Yang, ; Haitao Wang, ; Cheong-Meng Chong, ; Hai-Jing Zhong,
| | - Guan-Jun Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Aquacultral Biotechnology Ministry of Education, Ningbo University, Ningbo, China
- *Correspondence: Guan-Jun Yang, ; Haitao Wang, ; Cheong-Meng Chong, ; Hai-Jing Zhong,
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