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Desmurget C, Perilleux A, Souquet J, Borth N, Douet J. Molecular biomarkers identification and applications in CHO bioprocessing. J Biotechnol 2024; 392:11-24. [PMID: 38852681 DOI: 10.1016/j.jbiotec.2024.06.005] [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: 12/18/2023] [Revised: 05/23/2024] [Accepted: 06/04/2024] [Indexed: 06/11/2024]
Abstract
Biomarkers are valuable tools in clinical research where they allow to predict susceptibility to diseases, or response to specific treatments. Likewise, biomarkers can be extremely useful in the biomanufacturing of therapeutic proteins. Indeed, constraints such as short timelines and the need to find hyper-productive cells could benefit from a data-driven approach during cell line and process development. Many companies still rely on large screening capacities to develop productive cell lines, but as they reach a limit of production, there is a need to go from empirical to rationale procedures. Similarly, during bioprocessing runs, substrate consumption and metabolism wastes are commonly monitored. None of them possess the ability to predict the culture behavior in the bioreactor. Big data driven approaches are being adapted to the study of industrial mammalian cell lines, enabled by the publication of Chinese hamster and CHO genome assemblies which allowed the use of next-generation sequencing with these cells, as well as continuous proteome and metabolome annotation. However, if these different -omics technologies contributed to the characterization of CHO cells, there is a significant effort remaining to apply this knowledge to biomanufacturing methods. The correlation of a complex phenotype such as high productivity or rapid growth to the presence or expression level of a specific biomarker could save time and effort in the screening of manufacturing cell lines or culture conditions. In this review we will first discuss the different biological molecules that can be identified and quantified in cells, their detection techniques, and associated challenges. We will then review how these markers are used during the different steps of cell line and bioprocess development, and the inherent limitations of this strategy.
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Affiliation(s)
- Caroline Desmurget
- Merck Biotech Development Center, Ares Trading SA (an affiliate of Merck KGaA, Darmstadt, Germany), Fenil-sur-Corsier, Switzerland
| | - Arnaud Perilleux
- Merck Biotech Development Center, Ares Trading SA (an affiliate of Merck KGaA, Darmstadt, Germany), Fenil-sur-Corsier, Switzerland
| | - Jonathan Souquet
- Merck Biotech Development Center, Ares Trading SA (an affiliate of Merck KGaA, Darmstadt, Germany), Fenil-sur-Corsier, Switzerland
| | - Nicole Borth
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Julien Douet
- Merck Biotech Development Center, Ares Trading SA (an affiliate of Merck KGaA, Darmstadt, Germany), Fenil-sur-Corsier, Switzerland.
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2
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Zhang Y, Xie J. Targeting non-coding RNAs as a promising biomarker in peritoneal metastasis: Background, mechanism, and therapeutic approach. Biomed Pharmacother 2024; 179:117294. [PMID: 39226726 DOI: 10.1016/j.biopha.2024.117294] [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: 06/09/2024] [Revised: 08/08/2024] [Accepted: 08/09/2024] [Indexed: 09/05/2024] Open
Abstract
Peritoneal metastasis (PM) pathophysiology is complex and not fully understood. PM, originating from gastrointestinal (GI) cancer, is a condition that significantly worsens patient prognosis due to its complex nature and limited treatment options. The non-coding RNAs (ncRNAs) have been shown to play pivotal roles in cancer biology, influencing tumorigenesis, progression, metastasis, and therapeutic resistance. Increasing evidence has demonstrated the regulatory functions of different classes of ncRNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) in PM. Identifying biomarkers for early detection of PM is a crucial step towards improving patient outcomes, and how ncRNA profiles correlate with survival rates, response to therapy, and recurrence risks have raised much attention in recent years. Additionally, exploring innovative therapeutic approaches utilizing ncRNAs, such as targeted therapy and gene silencing, may offer new horizons in treating this dire condition. Recent advances in systemic treatments and the development of novel loco-regional therapies have opened doors to multimodal treatment approaches. Radical surgeries combined with hyperthermic intraperitoneal chemotherapy (HIPEC) have shown promising results, leading to extended patient survival. Current research is focused on the molecular characterization of PM, which is crucial for early detection and developing future therapeutic strategies. By summarizing the latest findings, this study underscores the transformative potential of ncRNAs in enhancing the diagnosis, prognosis, and treatment of PM in GI cancer, paving the way for more personalized and effective clinical strategies.
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Affiliation(s)
- Yiping Zhang
- School of Life Sciences, Fudan University, Shanghai 200438, China; Wanchuanhui (Shanghai) Medical Technology Co., Ltd, Shanghai 201501, China.
| | - Jun Xie
- School of Life Sciences, Fudan University, Shanghai 200438, China; Wanchuanhui (Shanghai) Medical Technology Co., Ltd, Shanghai 201501, China.
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Peng X, Li S, Zeng A, Song L. Regulatory function of glycolysis-related lncRNAs in tumor progression: Mechanism, facts, and perspectives. Biochem Pharmacol 2024; 229:116511. [PMID: 39222714 DOI: 10.1016/j.bcp.2024.116511] [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: 05/27/2024] [Revised: 08/22/2024] [Accepted: 08/29/2024] [Indexed: 09/04/2024]
Abstract
Altered metabolism is a hallmark of cancer, and reprogramming of energy metabolism, known as the "Warburg effect", has long been associated with cancer. Cancer cells use the process of glycolysis to quickly manufacture energy from glucose, pyruvic acid, and lactate, which in turn accelerates the growth of cancer and glycolysis becomes a key target for anti-cancer therapies. Recent groundbreaking discoveries regarding long noncoding RNAs (lncRNAs) have opened a new chapter in the mechanism of cancer occurrence. It is widely recognized that lncRNAs regulate energy metabolism through glycolysis in cancer cells. LncRNAs have been demonstrated to engage in several cancer processes such as proliferation, apoptosis, migration, invasion, and chemoresistance, whereas glycolysis is enhanced or inhibited by the dysregulation of lncRNAs. As a result, cancer survival and development are influenced by different signaling pathways. In this review, we summarize the roles of lncRNAs in a variety of cancers and describe the mechanisms underlying their role in glycolysis. Additionally, the predictive potential of glycolysis and lncRNAs in cancer therapy is discussed.
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Affiliation(s)
- Xinyi Peng
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan Province 611137, PR China
| | - Shuhao Li
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan Province 611137, PR China
| | - Anqi Zeng
- Translational Chinese Medicine Key Laboratory of Sichuan Province, Sichuan Academy of Chinese Medicine Sciences, Sichuan Institute for Translational Chinese Medicine, Chengdu, Sichuan 610041, P.R. China.
| | - Linjiang Song
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan Province 611137, PR China.
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Lu J, Ma H, Wang Q, Song Z, Wang J. Chemotherapy-mediated lncRNA-induced immune cell plasticity in cancer immunopathogenesis. Int Immunopharmacol 2024; 141:112967. [PMID: 39181018 DOI: 10.1016/j.intimp.2024.112967] [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: 07/02/2024] [Revised: 08/05/2024] [Accepted: 08/15/2024] [Indexed: 08/27/2024]
Abstract
Tumor cells engage with the immune system in a complex manner, utilizing evasion and adaptability mechanisms. The development of cancer and resistance to treatment relies on the ability of immune cells to adjust their phenotype and function in response to cues from the tumor microenvironment, known as immunological cell plasticity. This study delves into the role of long non-coding RNAs (lncRNAs) in enhancing immune cell flexibility in cancer, focusing on their regulatory actions in the tumor microenvironment and potential therapeutic implications. Through a comprehensive review of existing literature, the study analyzes the impact of lncRNAs on macrophages, T-cells, and MDSCs, as well as the influence of cytokines and growth factors like TNF, IL-6, HGF, and TGFβ on immunological cell plasticity and tumor immunoediting. LncRNAs exert a strong influence on immune cell plasticity through mechanisms such as transcriptional regulation, post-transcriptional modifications, and chromatin remodeling. These RNA molecules intricately modulate gene expression networks, acting as scaffolding, decoys, guides, and sponges. Moreover, both direct cell-cell interactions and soluble chemicals in the tumor microenvironment contribute to enhancing immune cell activation and survival. Understanding the influence of lncRNAs on immune cell flexibility sheds light on the biological pathways of immune evasion and cancer progression. Targeting long non-coding RNAs holds promise for amplifying anti-tumor immunity and overcoming drug resistance in cancer treatment. However, further research is necessary to determine the therapeutic potential of manipulating lncRNAs in the tumor microenvironment.
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Affiliation(s)
- Jingyuan Lu
- Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430030, China.
| | - Haowei Ma
- Department of Mechanical and Aerospace Engineering, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Qian Wang
- Division of Hematology and Solid Tumor Oncology, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Zhiheng Song
- Plasma Applied Physics Lab, C&J Nyheim Plasma Institute, Drexel University, 200 Federal St, Suite 500, Camden, NJ 08103.
| | - Jinli Wang
- School of Medicine, Department of Epidemiology and Biochemistry and Molecular & Cellular Biology, Georgetown University, 3700 O ST NW, Washington, DC 20057.
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Luo Q, Shen F, Zhao S, Dong L, Wei J, Hu H, Huang Q, Wang Q, Yang P, Liang W, Li W, He F, Cao J. LINC00460/miR-186-3p/MYC feedback loop facilitates colorectal cancer immune escape by enhancing CD47 and PD-L1 expressions. J Exp Clin Cancer Res 2024; 43:225. [PMID: 39135122 PMCID: PMC11321182 DOI: 10.1186/s13046-024-03145-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 07/29/2024] [Indexed: 08/15/2024] Open
Abstract
BACKGROUND Long non-coding RNAs (LncRNAs) have been implicated as critical regulators of cancer tumorigenesis and progression. However, their functions and molecular mechanisms in colorectal cancer (CRC) still remain to be further elucidated. METHODS LINC00460 was identified by differential analysis between human CRC and normal tissues and verified by in situ hybridization (ISH) and qRT-PCR. We investigated the biological functions of LINC00460 in CRC by in vitro and in vivo experiments. We predicted the mechanism and downstream functional molecules of LINC00460 by bioinformatics analysis, and confirmed them by dual luciferase reporter gene assay, RNA immunoprecipitation (RIP), RNA pull-down, etc. RESULTS: LINC00460 was found to be significantly overexpressed in CRC and associated with poor prognosis. Overexpression of LINC00460 promoted CRC cell immune escape and remodeled a suppressive tumor immune microenvironment, thereby promoting CRC proliferation and metastasis. Mechanistic studies showed that LINC00460 served as a molecular sponge for miR-186-3p, and then promoted the expressions of MYC, CD47 and PD-L1 to facilitate CRC cell immune escape. We also demonstrated that MYC upregulated LINC00460 expression at the transcriptional level and formed a positive feedback loop. CONCLUSIONS The LINC00460/miR-186-3p/MYC feedback loop promotes CRC cell immune escape and subsequently facilitates CRC proliferation and metastasis. Our findings provide novel insight into LINC00460 as a CRC immune regulator, and provide a potential therapeutic target for CRC patients.
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Affiliation(s)
- Qingqing Luo
- Department of Gastroenterology and Hepatology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
- Guangzhou Key Laboratory of Digestive Diseases, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
| | - Fei Shen
- Department of General Surgery, The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong, 510630, China
- Department of Thyroid surgery, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
| | - Sheng Zhao
- Department of Nephrology, The Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
| | - Lan Dong
- Guangzhou Key Laboratory of Digestive Diseases, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
- Guangzhou Digestive Disease Center, Department of Gastrointestinal Surgery, The Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
| | - Jianchang Wei
- Guangzhou Key Laboratory of Digestive Diseases, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
- Guangzhou Digestive Disease Center, Department of Gastrointestinal Surgery, The Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
| | - He Hu
- Guangzhou Key Laboratory of Digestive Diseases, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
- Guangzhou Digestive Disease Center, Department of Gastrointestinal Surgery, The Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
| | - Qing Huang
- Guangzhou Key Laboratory of Digestive Diseases, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
- Guangzhou Digestive Disease Center, Department of Gastrointestinal Surgery, The Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
| | - Qiang Wang
- Guangzhou Key Laboratory of Digestive Diseases, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
- Guangzhou Digestive Disease Center, Department of Gastrointestinal Surgery, The Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
| | - Ping Yang
- Guangzhou Key Laboratory of Digestive Diseases, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
- Guangzhou Digestive Disease Center, Department of Gastrointestinal Surgery, The Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
| | - Wenlong Liang
- Guangzhou Key Laboratory of Digestive Diseases, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
- Guangzhou Digestive Disease Center, Department of Gastrointestinal Surgery, The Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
| | - Wanglin Li
- Guangzhou Key Laboratory of Digestive Diseases, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
- Guangzhou Digestive Disease Center, Department of Gastrointestinal Surgery, The Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
| | - Feng He
- Department of Nephrology, The Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China.
| | - Jie Cao
- Guangzhou Key Laboratory of Digestive Diseases, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China.
- Guangzhou Digestive Disease Center, Department of Gastrointestinal Surgery, The Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China.
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Liu M, Du Y, Gao D. Licochalcone A: a review of its pharmacology activities and molecular mechanisms. Front Pharmacol 2024; 15:1453426. [PMID: 39188947 PMCID: PMC11345200 DOI: 10.3389/fphar.2024.1453426] [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: 06/23/2024] [Accepted: 08/02/2024] [Indexed: 08/28/2024] Open
Abstract
Licorice, derived from the root of Glycyrrhiza uralensis Fisch, is a key Traditional Chinese Medicine known for its detoxifying, spleen-nourishing, and qi-replenishing properties. Licochalcone A (Lico A), a significant component of licorice, has garnered interest due to its molecular versatility and receptor-binding affinity. This review explores the specific roles of Lico A in various diseases, providing new insights into its characteristics and guiding the rational use of licorice. Comprehensive literature searches using terms such as "licorice application" and "pharmacological activity of Lico A" were conducted across databases including CNKI, PubMed, and Google Scholar to gather relevant studies on Lico A's pharmacological activities and mechanisms. Lico A, a representative chalcone in licorice, targets specific mechanisms in anti-cancer and anti-inflammatory activities. It also plays a role in post-transcriptional regulation. This review delineates the similarities and differences in the anti-cancer and anti-inflammatory mechanisms of Lico A, concluding that its effects on non-coding RNA through post-transcriptional mechanisms deserve further exploration.
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Affiliation(s)
- Meihua Liu
- Research Center of Emotional Diseases, Shenyang Anning Hospital, Shenyang, China
- Shenyang Key Laboratory for Causes and Drug Discovery of Chronic, Shenyang, China
| | - Yang Du
- The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Dejiang Gao
- Research Center of Emotional Diseases, Shenyang Anning Hospital, Shenyang, China
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Li S, Guo Y, Yi L, Chen Y. The role of LncRNA TUG1 in DNA damage and malignant transformation induced by Helicobacter pylori and N-methyl-N'-nitro-N-nitrosoguanidine on human esophageal epithelial cells. Food Chem Toxicol 2024; 192:114928. [PMID: 39142553 DOI: 10.1016/j.fct.2024.114928] [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: 05/07/2024] [Revised: 07/11/2024] [Accepted: 08/09/2024] [Indexed: 08/16/2024]
Abstract
N-Methyl-N'-nitro-N-nitrosoguanidine (MNNG) and Helicobacter pylori might synergistically promote the malignant transformation of human esophageal epithelial cells (HEECs) through inducing DNA double-strand breaks (DSBs) and inhibition of PAXX protein expression. The long noncoding RNA (lncRNA) TUG1 is associated with multiple cancers, and its overexpression can promote cancer by interfering with the functions of oncogenes. LncRNA TUG1 is also associated with DNA methyltransferase 1 (DNMT1) and the epithelial signaling pathway of H. pylori infection. To explore the role of LncRNA TUG1 in the malignant transformation of HEECs induced by H.pylori + MNNG, a stable strain of HEECs with LncRNA TUG1 knockdown (LncRNA TUG1-KD) was constructed using RNA interference technology with lentivirus as a vector. Set up negative controls LncRNA TUG1-NC (null carrier lentivirus was selected to transfect HEECs) and block controls (normal HEECs without exposure). H. pylori + MNNG were added to the LncRNA TUG1-KD and LncRNA TUG1-NC groups for 6 h and then passaged until their malignant transformation. From each group, cells in the early, intermediate, and late stages of malignant transformation were used for the alkaline comet assay and determination of protein expression, including γ-H2AX and PAXX, by western blotting assay to assess DNA damage and repair processes. Clone formation assay in soft agar and nude mouse xenograft model was used to assess malignancy. This study suggests that H. pylori + MNNG promotes the malignant transformation of HEECs by inducing DNA DSBs and inhibiting PAXX expression, and this effect may be alleviated by LncRNA TUG1 knockdown. It elucidates the pathogenesis of EC from the perspective of the combined effect of epigenetic and environmental carcinogens, offering new insights for the comprehensive prevention and treatment of EC.
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Affiliation(s)
- Siyao Li
- Medical College, Jiaxing University, Jiaxing, 314000, China; Hangzhou Xiaoshan District Center for Disease Control and Prevention, Hangzhou, 310000, China
| | - Yusong Guo
- Medical College, Jiaxing University, Jiaxing, 314000, China
| | - Lei Yi
- Medical College, Jiaxing University, Jiaxing, 314000, China
| | - Yan Chen
- Medical College, Jiaxing University, Jiaxing, 314000, China.
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Xiao L, Chen J, He X, Zhang X, Luo W. Whole-transcriptome sequencing revealed the ceRNA regulatory network during the proliferation and differentiation of goose myoblast. Poult Sci 2024; 103:104173. [PMID: 39153268 DOI: 10.1016/j.psj.2024.104173] [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: 05/26/2024] [Revised: 07/13/2024] [Accepted: 07/31/2024] [Indexed: 08/19/2024] Open
Abstract
The Shitou goose, the largest meat-type goose breed, is an ideal model for offering insights into enhancing meat production efficiency through understanding its genetic regulation of muscle development. Here, through whole-transcriptomic analysis of embryonic leg muscles, we identified 847 differentially expressed genes (DEG), 244 differentially expressed lncRNAs (DEL), 37 differentially expressed circRNAs (DEC), and 84 differentially expressed miRNAs (DEM). Gene ontology (GO) analysis highlighted the significant enrichment of differentially expressed RNAs in muscle structure development, actin filament-based processes, and the actin cytoskeleton pathway. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified pathways associated with the FoxO signaling pathway, AMPK signaling pathway, Wnt signaling pathway and calcium signaling pathway. Furthermore, we utilized Miranda, TargetScan, and miRDB to identify regulatory networks that involve interactions between lncRNA-mRNA, circRNA-mRNA, miRNA-mRNA, lncRNA-miRNA-mRNA, and circRNA-miRNA-mRNA, which regulated the growth and development of skeletal muscle. Notably, differentially expressed genes within the ceRNA network were most significantly enriched in the regulation of actin cytoskeletal organization. Additionally, a lncRNA/circRNA-miRNA-mRNA ceRNA network related to muscle growth and development was constructed based on protein-protein interaction (PPI) analysis and hub genes selection using Cytoscape. This further elucidated the regulatory roles of noncoding RNAs (ncRNA) in the formation of muscle fibers in Shitou goose. In summary, this study provides a valuable transcriptional regulatory network for goose muscle development laying the groundwork for further exploration of the molecular regulatory mechanisms underlying the excellent meat production performance of Shitou goose.
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Affiliation(s)
- Liangchao Xiao
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| | - Jiahui Chen
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| | - Xueying He
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| | - Xiquan Zhang
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| | - Wen Luo
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China.
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Shen X, Yan H, Hu M, Zhou H, Wang J, Gao R, Liu Q, Wang X, Liu Y. The potential regulatory role of the non-coding RNAs in regulating the exogenous estrogen-induced feminization in Takifugu rubripes gonad. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2024; 273:107022. [PMID: 39032423 DOI: 10.1016/j.aquatox.2024.107022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 07/06/2024] [Accepted: 07/08/2024] [Indexed: 07/23/2024]
Abstract
Estrogen plays a pivotal role in the early stage of sex differentiation in teleost. However, the underlying mechanisms of estrogen-induced feminization process are still needed for further clarification. Here, the comparative analysis of whole-transcriptome RNA sequencing was conducted between 17beta-Estradiol induced feminized XY (E-XY) gonads and control gonads (C) in Takifugu rubripes. A total of 57 miRNAs, 65 lncRNAs, and 4 circRNAs were found to be expressed at lower levels in control-XY (C-XY) than that in control-XX (C-XX), and were up-regulated in XY during E2-induced feminization process. The expression levels of 24 miRNAs, and 55 lncRNAs were higher in C-XY than that in C-XX, and were down-regulated in E2-treated XY. Furthermore, a correlation analysis was performed between miRNA-seq and mRNA-seq data. In C-XX/C-XY, 114 differential expression (DE) miRNAs were predicted to target to 904 differential expression genes (DEGs), while in C-XY/E-XY, 226 DEmiRNAs were predicted to target to 2,048 DEGs. In C-XX/C-XY, and C-XY/E-XY, KEGG pathway enrichment analysis showed that those targeted genes were mainly enriched in MAPK signaling, calcium signaling, steroid hormone biosynthesis and ovarian steroidogenesis pathway. Additionally, the competitive endogenous RNA (ceRNA) regulatory network was constructed by 24 miRNAs, 21 lncRNAs, 4 circRNAs and 5 key sex-related genes. These findings suggested that the expression of critical genes in sex differentiation were altered in E2-treated XY T. rubripes may via the lncRNA-miRNA-mRNA regulation network to facilitate the differentiation and maintenance of ovaries. Our results provide a new insight into the comprehensive understanding of the effects of estrogen signaling pathways on sex differentiation in teleost gonads.
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Affiliation(s)
- Xufang Shen
- College of Biosystems Engineering and Food Science, Zhejiang University, 310058, China; Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian Ocean University, Dalian, Liaoning 116023, China
| | - Hongwei Yan
- Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian Ocean University, Dalian, Liaoning 116023, China; College of Fisheries and Life Science, Dalian Ocean University, Dalian, Liaoning 116023, China; The Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, 116023, China.
| | - Mingtao Hu
- Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian Ocean University, Dalian, Liaoning 116023, China; College of Fisheries and Life Science, Dalian Ocean University, Dalian, Liaoning 116023, China; The Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, 116023, China
| | - Huiting Zhou
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, Liaoning 116023, China; The Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, 116023, China
| | - Jia Wang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, Liaoning 116023, China; The Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, 116023, China
| | - Rui Gao
- Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian Ocean University, Dalian, Liaoning 116023, China; The Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, 116023, China
| | - Qi Liu
- Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian Ocean University, Dalian, Liaoning 116023, China; The Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, 116023, China; College of Marine Science and Environment Engineering, Dalian Ocean University, Dalian, Liaoning 116023, China
| | - Xiuli Wang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, Liaoning 116023, China; The Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, 116023, China
| | - Ying Liu
- College of Biosystems Engineering and Food Science, Zhejiang University, 310058, China; Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian Ocean University, Dalian, Liaoning 116023, China
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Hassan M, Shahzadi S, Yasir M, Chun W, Kloczkowski A. Therapeutic Implication of miRNAs as an Active Regulatory Player in the Management of Pain: A Review. Genes (Basel) 2024; 15:1003. [PMID: 39202362 PMCID: PMC11353898 DOI: 10.3390/genes15081003] [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: 11/30/2023] [Revised: 07/15/2024] [Accepted: 07/26/2024] [Indexed: 09/03/2024] Open
Abstract
Chronic pain is frequently associated with neuropathy, inflammation, or the malfunctioning of nerves. Chronic pain is associated with a significant burden of morbidity due to opioid use, associated with addiction and tolerance, and disability. MicroRNAs (miRs) are emerging therapeutic targets to treat chronic pain through the regulation of genes associated with inflammation, neuronal excitability, survival, or de-differentiation. In this review, we discuss the possible involvement of miRs in pain-related molecular pathways. miRs are known to regulate high-conviction pain genes, supporting their potential as therapeutic targets.
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Affiliation(s)
- Mubashir Hassan
- The Steve and Cindy Rasmussen Institute for Genomic Medicine at Nationwide Children’s Hospital, Columbus, OH 43205, USA; (S.S.); (A.K.)
| | - Saba Shahzadi
- The Steve and Cindy Rasmussen Institute for Genomic Medicine at Nationwide Children’s Hospital, Columbus, OH 43205, USA; (S.S.); (A.K.)
| | - Muhammad Yasir
- Department of Pharmacology, College of Medicine, Kangwon National University, Chuncheon 24341, Republic of Korea; (M.Y.); (W.C.)
| | - Wanjoo Chun
- Department of Pharmacology, College of Medicine, Kangwon National University, Chuncheon 24341, Republic of Korea; (M.Y.); (W.C.)
| | - Andrzej Kloczkowski
- The Steve and Cindy Rasmussen Institute for Genomic Medicine at Nationwide Children’s Hospital, Columbus, OH 43205, USA; (S.S.); (A.K.)
- Department of Pediatrics, The Ohio State University School of Medicine, Columbus, OH 43205, USA
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA
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11
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Youness RA, Hassan HA, Abaza T, Hady AA, El Magdoub HM, Ali M, Vogel J, Thiersch M, Gassmann M, Hamdy NM, Aboouf MA. A Comprehensive Insight and In Silico Analysis of CircRNAs in Hepatocellular Carcinoma: A Step toward ncRNA-Based Precision Medicine. Cells 2024; 13:1245. [PMID: 39120276 PMCID: PMC11312109 DOI: 10.3390/cells13151245] [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: 05/22/2024] [Revised: 07/11/2024] [Accepted: 07/22/2024] [Indexed: 08/10/2024] Open
Abstract
Circular RNAs (circRNAs) are cardinal players in numerous physiological and pathological processes. CircRNAs play dual roles as tumor suppressors and oncogenes in different oncological contexts, including hepatocellular carcinoma (HCC). Their roles significantly impact the disease at all stages, including initiation, development, progression, invasion, and metastasis, in addition to the response to treatment. In this review, we discuss the biogenesis and regulatory functional roles of circRNAs, as well as circRNA-protein-mRNA ternary complex formation, elucidating the intricate pathways tuned by circRNAs to modulate gene expression and cellular processes through a comprehensive literature search, in silico search, and bioinformatics analysis. With a particular focus on the interplay between circRNAs, epigenetics, and HCC pathology, the article sets the stage for further exploration of circRNAs as novel investigational theranostic agents in the dynamic realm of HCC.
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Affiliation(s)
- Rana A. Youness
- Molecular Genetics Research Team (MGRT), Molecular Biology and Biochemistry Department, Faculty of Biotechnology, German International University (GIU), Cairo 11835, Egypt; (R.A.Y.); (H.A.H.); (T.A.)
| | - Hossam A. Hassan
- Molecular Genetics Research Team (MGRT), Molecular Biology and Biochemistry Department, Faculty of Biotechnology, German International University (GIU), Cairo 11835, Egypt; (R.A.Y.); (H.A.H.); (T.A.)
| | - Tasneem Abaza
- Molecular Genetics Research Team (MGRT), Molecular Biology and Biochemistry Department, Faculty of Biotechnology, German International University (GIU), Cairo 11835, Egypt; (R.A.Y.); (H.A.H.); (T.A.)
- Biotechnology Program, Institute of Basic and Applied Sciences (BAS), Egypt-Japan University of Science and Technology (E-JUST), New Borg El-Arab City 21934, Egypt
| | - Ahmed A. Hady
- Clinical Oncology Department, Faculty of Medicine, Mansoura University, Mansoura 35511, Egypt;
| | - Hekmat M. El Magdoub
- Biochemistry Department, Faculty of Pharmacy, Misr International University, Cairo 19648, Egypt;
| | - Mohamed Ali
- Department of Obstetrics and Gynecology, University of Chicago, Chicago, IL 60637, USA;
- Clinical Pharmacy Department, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt
| | - Johannes Vogel
- Zurich Center for Integrative Human Physiology and Institute of V. Physiology, University of Zurich, 8057 Zurich, Switzerland; (J.V.); (M.T.); (M.G.)
| | - Markus Thiersch
- Zurich Center for Integrative Human Physiology and Institute of V. Physiology, University of Zurich, 8057 Zurich, Switzerland; (J.V.); (M.T.); (M.G.)
| | - Max Gassmann
- Zurich Center for Integrative Human Physiology and Institute of V. Physiology, University of Zurich, 8057 Zurich, Switzerland; (J.V.); (M.T.); (M.G.)
| | - Nadia M. Hamdy
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, Abassia, Cairo 11566, Egypt
| | - Mostafa A. Aboouf
- Zurich Center for Integrative Human Physiology and Institute of V. Physiology, University of Zurich, 8057 Zurich, Switzerland; (J.V.); (M.T.); (M.G.)
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, Abassia, Cairo 11566, Egypt
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12
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Shi L, Han X, Liu F, Long J, Jin Y, Chen S, Duan G, Yang H. Review on Long Non-Coding RNAs as Biomarkers and Potentially Therapeutic Targets for Bacterial Infections. Curr Issues Mol Biol 2024; 46:7558-7576. [PMID: 39057090 PMCID: PMC11276060 DOI: 10.3390/cimb46070449] [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: 06/19/2024] [Revised: 07/13/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
The confrontation between humans and bacteria is ongoing, with strategies for combating bacterial infections continually evolving. With the advancement of RNA sequencing technology, non-coding RNAs (ncRNAs) associated with bacterial infections have garnered significant attention. Recently, long ncRNAs (lncRNAs) have been identified as regulators of sterile inflammatory responses and cellular defense against live bacterial pathogens. They are involved in regulating host antimicrobial immunity in both the nucleus and cytoplasm. Increasing evidence indicates that lncRNAs are critical for the intricate interactions between host and pathogen during bacterial infections. This paper emphatically elaborates on the potential applications of lncRNAs in clinical hallmarks, cellular damage, immunity, virulence, and drug resistance in bacterial infections in greater detail. Additionally, we discuss the challenges and limitations of studying lncRNAs in the context of bacterial infections and highlight clear directions for this promising field.
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Affiliation(s)
| | | | | | | | | | | | | | - Haiyan Yang
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China; (L.S.); (X.H.); (F.L.); (J.L.); (Y.J.); (S.C.); (G.D.)
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13
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Alonso-García M, Gutiérrez-Gil B, Pelayo R, Fonseca PAS, Marina H, Arranz JJ, Suárez-Vega A. A meta-analysis approach for annotation and identification of lncRNAs controlling perirenal fat deposition in suckling lambs. Anim Biotechnol 2024; 35:2374328. [PMID: 39003576 DOI: 10.1080/10495398.2024.2374328] [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: 07/15/2024]
Abstract
Long non-coding RNAs (lncRNAs) are being studied in farm animals due to their association with traits of economic interest, such as fat deposition. Based on the analysis of perirenal fat transcriptomes, this research explored the relevance of these regulatory elements to fat deposition in suckling lambs. To that end, meta-analysis techniques have been implemented to efficiently characterize and detect differentially expressed transcripts from two different RNA-seq datasets, one including samples of two sheep breeds that differ in fat deposition features, Churra and Assaf (n = 14), and one generated from Assaf suckling lambs with different fat deposition levels (n = 8). The joint analysis of the 22 perirenal fat RNA-seq samples with the FEELnc software allowed the detection of 3953 novel lncRNAs. After the meta-analysis, 251 differentially expressed genes were identified, 21 of which were novel lncRNAs. Additionally, a co-expression analysis revealed that, in suckling lambs, lncRNAs may play a role in controlling angiogenesis and thermogenesis, processes highlighted in relation to high and low fat deposition levels, respectively. Overall, while providing information that could be applied for the improvement of suckling lamb carcass traits, this study offers insights into the biology of perirenal fat deposition regulation in mammals.
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Affiliation(s)
- María Alonso-García
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - Beatriz Gutiérrez-Gil
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - Rocío Pelayo
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - Pablo A S Fonseca
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - Héctor Marina
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - Juan José Arranz
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - Aroa Suárez-Vega
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, León, Spain
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Campos FG, Ibelli AMG, Cantão ME, Oliveira HC, Peixoto JO, Ledur MC, Guimarães SEF. Long Non-Coding RNAs Differentially Expressed in Swine Fetuses. Animals (Basel) 2024; 14:1897. [PMID: 38998009 PMCID: PMC11240794 DOI: 10.3390/ani14131897] [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: 04/07/2024] [Revised: 06/24/2024] [Accepted: 06/24/2024] [Indexed: 07/14/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) are non-coding transcripts involved in various biological processes. The Y chromosome is known for determining the male sex in mammals. LncRNAs on the Y chromosome may play important regulatory roles. However, knowledge about their action mechanisms is still limited, especially during early fetal development. Therefore, we conducted this exploratory study aiming to identify, characterize, and investigate the differential expression of lncRNAs between male and female swine fetuses at 35 days of gestation. RNA-Seq libraries from 10 fetuses were prepared and sequenced using the Illumina platform. After sequencing, a data quality control was performed using Trimmomatic, alignment with HISAT2, and transcript assembly with StringTie. The differentially expressed lncRNAs were identified using the limma package of the R software (4.3.1). A total of 871 potentially novel lncRNAs were identified and characterized. Considering differential expression, eight lncRNAs were upregulated in male fetuses. One was mapped onto SSC12 and seven were located on the Y chromosome; among them, one lncRNA is potentially novel. These lncRNAs are involved in diverse functions, including the regulation of gene expression and the modulation of chromosomal structure. These discoveries enable future studies on lncRNAs in the fetal stage in pigs.
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Affiliation(s)
- Francelly G Campos
- Laboratory of Animal Biotecnology, Department of Animal Science, Universidade Federal de Viçosa, Viçosa 36570-000, MG, Brazil
| | - Adriana M G Ibelli
- Embrapa Suínos e Aves, Concordia 89715-899, SC, Brazil
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Estadual do Centro Oeste, Guarapuava 85040-167, PR, Brazil
| | | | - Haniel C Oliveira
- Laboratory of Animal Biotecnology, Department of Animal Science, Universidade Federal de Viçosa, Viçosa 36570-000, MG, Brazil
| | - Jane O Peixoto
- Embrapa Suínos e Aves, Concordia 89715-899, SC, Brazil
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Estadual do Centro Oeste, Guarapuava 85040-167, PR, Brazil
| | - Mônica C Ledur
- Embrapa Suínos e Aves, Concordia 89715-899, SC, Brazil
- Programa de Pós-Graduação em Zootecnia, Universidade do Estado de Santa Catarina, UDESC-Oeste, Chapecó 89815-630, SC, Brazil
| | - Simone E F Guimarães
- Laboratory of Animal Biotecnology, Department of Animal Science, Universidade Federal de Viçosa, Viçosa 36570-000, MG, Brazil
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15
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Zhu M, Yuan Z, Wen C, Wei X. DEX Inhibits H/R-induced Cardiomyocyte Ferroptosis by the miR-141-3p/lncRNA TUG1 Axis. Thorac Cardiovasc Surg 2024. [PMID: 38889747 DOI: 10.1055/s-0044-1787691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
BACKGROUND Ferroptosis is emerging as a critical pathway in ischemia/reperfusion (I/R) injury, contributing to compromised cardiac function and predisposing individuals to sepsis and myocardial failure. The study investigates the underlying mechanism of dexmedetomidine (DEX) in hypoxia/reoxygenation (H/R)-induced ferroptosis in cardiomyocytes, aiming to identify novel targets for myocardial I/R injury treatment. METHODS H9C2 cells were subjected to H/R and treated with varying concentrations of DEX. Additionally, H9C2 cells were transfected with miR-141-3p inhibitor followed by H/R treatment. Levels of miR-141-3p, long noncoding RNA (lncRNA) taurine upregulated 1 (TUG1), Fe2+, glutathione (GSH), and malondialdehyde were assessed. Reactive oxygen species (ROS) generation was measured via fluorescent labeling. Expression of ferroptosis-related proteins glutathione peroxidase 4 (GPX4) and acyl-CoA synthetase long-chain family member 4 (ACSL4) was determined using Western blot. The interaction between miR-141-3p and lncRNA TUG1 was evaluated through RNA pull-down assay and dual-luciferase reporter gene assays. The stability of lncRNA TUG1 was assessed using actinomycin D. RESULTS DEX ameliorated H/R-induced cardiomyocyte injury and elevated miR-141-3p expression in cardiomyocytes. DEX treatment increased cell viability, Fe2+, and ROS levels while decreasing ACSL4 protein expression. Furthermore, DEX upregulated GSH and GPX4 protein levels. miR-141-3p targeted lncRNA TUG1, reducing its stability and overall expression. Inhibition of miR-141-3p or overexpression of lncRNA TUG1 partially reversed the inhibitory effect of DEX on H/R-induced ferroptosis in cardiomyocytes. CONCLUSION DEX mitigated H/R-induced ferroptosis in cardiomyocytes by upregulating miR-141-3p expression and downregulating lncRNA TUG1 expression, unveiling a potential therapeutic strategy for myocardial I/R injury.
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Affiliation(s)
- Mei Zhu
- Department of Anesthesiology, Taizhou People's Hospital Affiliated to Nanjing Medical University, Taizhou, People's Republic of China
| | - Zhiguo Yuan
- Department of Anesthesiology, Taizhou People's Hospital Affiliated to Nanjing Medical University, Taizhou, People's Republic of China
| | - Chuanyun Wen
- Department of Anesthesiology, Taizhou People's Hospital Affiliated to Nanjing Medical University, Taizhou, People's Republic of China
| | - Xiaojia Wei
- Department of Anesthesiology, Taizhou People's Hospital Affiliated to Nanjing Medical University, Taizhou, People's Republic of China
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16
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Li HM, Wang LJ, Wang YP, Li XM, Pan HF. Differences in the expression of long noncoding RNAs in peripheral blood mononuclear cells indicate potential biomarkers for rheumatoid arthritis. Int Immunopharmacol 2024; 134:112218. [PMID: 38733828 DOI: 10.1016/j.intimp.2024.112218] [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: 02/01/2024] [Revised: 04/12/2024] [Accepted: 05/05/2024] [Indexed: 05/13/2024]
Abstract
OBJECTIVE Long noncoding RNAs (lncRNAs) play an increasingly important role in various autoimmune diseases. We aimed to characterize the expression profiles of lncRNAs in peripheral blood mononuclear cells (PBMCs) from RA patients and to assess the potential of these lncRNAs as RA biomarkers. METHODS Whole-transcriptome sequencing was used to establish a lncRNA expression profile. A total of 155 RA patients, 145 healthy controls, 59 systemic lupus erythematosus (SLE) patients and 59 primary Sjögren's syndrome (pSS) patients were recruited for this study. Four candidate lncRNAs (linc00152, lnc-ADM-1, ITSN1-2, and lnc-FTH1-7) were validated via qRT-PCR in independent samples, and their expression, association with RA clinical features and value as RA biomarkers were evaluated. RESULTS Linc00152 and lnc-ADM-1 exhibited upregulated expression (p = 0.001, p = 0.014, respectively), while ITSN1-2 and lnc-FTH1-7 exhibited downregulated expression (both p < 0.001, respectively) in RA patients compared to controls. Lnc-ADM-1 and lnc-FTH1-7 expression correlated positively with the C4 level (p = 0.016 and p = 0.012, respectively). ITSN1-2 levels were negatively associated with CRP levels (p = 0.024). Linc00152, lnc-ADM-1, ITSN1-2, and lnc-FTH1-7 showed potential as RA biomarkers, with the four-lncRNA panel distinguishing RA patients from controls, SLE patients, or pSS patients (AUC = 0.886, 0.746, and 0.749, respectively). CONCLUSION The altered expression of linc00152, lnc-ADM-1, ITSN1-2 and lnc-FTH1-7 in RA patients suggested that these genes may serve as potential biomarkers for RA and could be involved in its pathogenesis.
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Affiliation(s)
- Hong-Miao Li
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Li-Jun Wang
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Yi-Ping Wang
- Westmead Institute for Medical Research, University of Sydney, Westmead, 2145 NSW, Australia
| | - Xiao-Mei Li
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
| | - Hai-Feng Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.
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17
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Mohammad T, Zolotovskaia MA, Suntsova MV, Buzdin AA. Cancer fusion transcripts with human non-coding RNAs. Front Oncol 2024; 14:1415801. [PMID: 38919532 PMCID: PMC11196610 DOI: 10.3389/fonc.2024.1415801] [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: 04/11/2024] [Accepted: 05/27/2024] [Indexed: 06/27/2024] Open
Abstract
Cancer chimeric, or fusion, transcripts are thought to most frequently appear due to chromosomal aberrations that combine moieties of unrelated normal genes. When being expressed, this results in chimeric RNAs having upstream and downstream parts relatively to the breakpoint position for the 5'- and 3'-fusion components, respectively. As many other types of cancer mutations, fusion genes can be of either driver or passenger type. The driver fusions may have pivotal roles in malignisation by regulating survival, growth, and proliferation of tumor cells, whereas the passenger fusions most likely have no specific function in cancer. The majority of research on fusion gene formation events is concentrated on identifying fusion proteins through chimeric transcripts. However, contemporary studies evidence that fusion events involving non-coding RNA (ncRNA) genes may also have strong oncogenic potential. In this review we highlight most frequent classes of ncRNAs fusions and summarize current understanding of their functional roles. In many cases, cancer ncRNA fusion can result in altered concentration of the non-coding RNA itself, or it can promote protein expression from the protein-coding fusion moiety. Differential splicing, in turn, can enrich the repertoire of cancer chimeric transcripts, e.g. as observed for the fusions of circular RNAs and long non-coding RNAs. These and other ncRNA fusions are being increasingly recognized as cancer biomarkers and even potential therapeutic targets. Finally, we discuss the use of ncRNA fusion genes in the context of cancer detection and therapy.
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Affiliation(s)
- Tharaa Mohammad
- Laboratory for Translational and Genomic Bioinformatics, Moscow Center for Advanced Studies, Moscow, Russia
- Department of Molecular Genetic Technologies, Laboratory of Bioinformatics, Endocrinology Research Center, Moscow, Russia
| | - Marianna A. Zolotovskaia
- Laboratory for Translational and Genomic Bioinformatics, Moscow Center for Advanced Studies, Moscow, Russia
- Department of Molecular Genetic Technologies, Laboratory of Bioinformatics, Endocrinology Research Center, Moscow, Russia
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | | | - Anton A. Buzdin
- Laboratory for Translational and Genomic Bioinformatics, Moscow Center for Advanced Studies, Moscow, Russia
- Department of Molecular Genetic Technologies, Laboratory of Bioinformatics, Endocrinology Research Center, Moscow, Russia
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
- PathoBiology Group, European Organization for Research and Treatment of Cancer (EORTC), Brussels, Belgium
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
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18
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Danga AK, Kour S, Kumari A, Rath PC. Cell-type specific and differential expression of LINC-RSAS long noncoding RNA declines in the testes during ageing of the rat. Biogerontology 2024; 25:543-566. [PMID: 38353919 DOI: 10.1007/s10522-023-10088-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 12/15/2023] [Indexed: 03/26/2024]
Abstract
Long noncoding RNAs (lncRNAs) have emerged as major regulators of gene expression, chromatin structure, epigenetic changes, post-transcriptional processing of RNAs, translation of mRNAs into proteins as well as contributing to the process of ageing. Ageing is a universal, slow, progressive change in almost all physiological processes of organisms after attaining reproductive maturity and often associated with age-related diseases. Mammalian testes contain various cell-types, vast reservoir of transcriptome complexity, produce haploid male gametes for reproduction and testosterone for development and maintenance of male sexual characters as well as contribute genetic variation to the species. We report age-related decline in expression and cellular localization of Long intergenic noncoding repeat-rich sense-antisense (LINC-RSAS) RNA in the testes and its major cell-types such as primary spermatocytes, Leydig cells and Sertoli cells during ageing of the rat. LINC-RSAS expression in testes increased from immature (4-weeks) to adult (16- and 44-weeks) and declined from adult (44-weeks) to nearly-old (70-weeks) rats. Genomic DNA methylation in the testes showed a similar pattern. Cell-type specific higher expression of LINC-RSAS was observed in primary spermatocytes (pachytene cells), Leydig cells and Sertoli cells of testes of adult rats. Over-expression of LINC-RSAS in cultured human cell lines revealed its possible role in cell-cycle control and apoptosis. We propose that LINC-RSAS expression is involved in molecular physiology of primary spermatocytes, Leydig cells and Sertoli cells of adult testes and its decline is associated with diminishing function of testes during ageing of the rat.
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Affiliation(s)
- Ajay Kumar Danga
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Sukhleen Kour
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, 15224, USA
| | - Anita Kumari
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Pramod C Rath
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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Shi L, Luo B, Deng L, Zhang Q, Li Y, Sun D, Zhang H, Zhuang L. The lncRNA TRG-AS1 promotes the growth of colorectal cancer cells through the regulation of P2RY10/GNA13. Scand J Gastroenterol 2024; 59:710-721. [PMID: 38357893 DOI: 10.1080/00365521.2024.2318363] [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: 11/10/2023] [Accepted: 02/09/2024] [Indexed: 02/16/2024]
Abstract
BACKGROUND The lncRNA TRG-AS1 and its co-expressed gene P2RY10 are important for colorectal cancer (CRC) occurrence and development. The purpose of our research was to explore the roles of TRG-AS1 and P2RY10 in CRC progression. METHODS The abundance of TRG-AS1 and P2RY10 in CRC cell lines (HT-29 and LoVo) and normal colon cells FHC was determined and difference between CRC cells and normal cells was compared. LoVo cells were transfected with si-TRG-AS1 and si-P2RY10 constructs. Subsequently, the viability, colony formation, and migration of the transfected cells were analyzed using cell counting kit-8, clonogenicity, and scratch-wound/Transwell® assays, respectively. Cells overexpressing GNA13 were used to further explore the relationship between TRG-AS1 and P2RY10 along with their downstream functions. Finally, nude mice were injected with different transfected cell types to observe tumor formation in vivo. RESULTS TRG-AS1 and P2RY10 were significantly upregulated in HT-29 and LoVo compared to FHC cells. TRG-AS1 knockdown and P2RY10 silencing suppressed the viability, colony formation, and migration of LoVo cells. TRG-AS1 knockdown downregulated the expression of P2RY10, GNA12, and GNA13, while P2RY10 silencing downregulated the expression of TRG-AS1, GNA12, and GNA13. Additionally, GNA13 overexpression reversed the cell growth and gene expression changes in LoVo cells induced by TRG-AS1 knockdown or P2RY10 silencing. In vivo experiments revealed that CRC tumor growth was suppressed by TRG-AS1 knockdown and P2RY10 silencing. CONCLUSIONS TRG-AS1 knockdown repressed the growth of HT-29 and LoVo by regulating P2RY10 and GNA13 expression.
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Affiliation(s)
- Longqing Shi
- The First People's Hospital of Changzhou, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Baoyang Luo
- The First People's Hospital of Changzhou, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Linghui Deng
- Department of Oncology, Wujin Affiliated Hospital of Jiangsu University and The Wujin Clinical College of Xuzhou Medical University, Changzhou, Jiangsu, China
- Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Qi Zhang
- Department of Oncology, Wujin Affiliated Hospital of Jiangsu University and The Wujin Clinical College of Xuzhou Medical University, Changzhou, Jiangsu, China
| | - Yuanjiu Li
- The First People's Hospital of Changzhou, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Donglin Sun
- The First People's Hospital of Changzhou, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Hua Zhang
- Department of Oncology, Wujin Affiliated Hospital of Jiangsu University and The Wujin Clinical College of Xuzhou Medical University, Changzhou, Jiangsu, China
| | - Lin Zhuang
- The First People's Hospital of Changzhou, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
- Department of General Surgery, Wujin Affiliated Hospital of Jiangsu University and The Wujin Clinical College of Xuzhou Medical University, Changzhou, Jiangsu, China
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20
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Rai A, Bhagchandani T, Tandon R. Transcriptional landscape of long non-coding RNAs (lncRNAs) and its implication in viral diseases. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195023. [PMID: 38513793 DOI: 10.1016/j.bbagrm.2024.195023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 02/26/2024] [Accepted: 03/13/2024] [Indexed: 03/23/2024]
Abstract
Long non-coding RNAs (lncRNAs) are RNA transcripts of size >200 bp that do not translate into proteins. Emerging data revealed that viral infection results in systemic changes in the host at transcriptional level. These include alterations in the lncRNA expression levels and triggering of antiviral immune response involving several effector molecules and diverse signalling pathways. Thus, lncRNAs have emerged as an essential mediatory element at distinct phases of the virus infection cycle. The complete eradication of the viral disease requires more precise and novel approach, thus manipulation of the lncRNAs could be one of them. This review shed light upon the existing knowledge of lncRNAs wherein the implication of differentially expressed lncRNAs in blood-borne, air-borne, and vector-borne viral diseases and its promising therapeutic applications under clinical settings has been discussed. It further enhances our understanding of the complex interplay at host-pathogen interface with respect to lncRNA expression and function.
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Affiliation(s)
- Ankita Rai
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Tannu Bhagchandani
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Ravi Tandon
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.
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Kerro Dego O, Vidlund J. Staphylococcal mastitis in dairy cows. Front Vet Sci 2024; 11:1356259. [PMID: 38863450 PMCID: PMC11165426 DOI: 10.3389/fvets.2024.1356259] [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: 01/17/2024] [Accepted: 05/06/2024] [Indexed: 06/13/2024] Open
Abstract
Bovine mastitis is one of the most common diseases of dairy cattle. Even though different infectious microorganisms and mechanical injury can cause mastitis, bacteria are the most common cause of mastitis in dairy cows. Staphylococci, streptococci, and coliforms are the most frequently diagnosed etiological agents of mastitis in dairy cows. Staphylococci that cause mastitis are broadly divided into Staphylococcus aureus and non-aureus staphylococci (NAS). NAS is mainly comprised of coagulase-negative Staphylococcus species (CNS) and some coagulase-positive and coagulase-variable staphylococci. Current staphylococcal mastitis control measures are ineffective, and dependence on antimicrobial drugs is not sustainable because of the low cure rate with antimicrobial treatment and the development of resistance. Non-antimicrobial effective and sustainable control tools are critically needed. This review describes the current status of S. aureus and NAS mastitis in dairy cows and flags areas of knowledge gaps.
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Affiliation(s)
- Oudessa Kerro Dego
- Department of Animal Science, University of Tennessee, Knoxville, TN, United States
| | - Jessica Vidlund
- Department of Animal Science, University of Tennessee, Knoxville, TN, United States
- East Tennessee AgResearch and Education Center-Little River Animal and Environmental Unit, University of Tennessee, Walland, TN, United States
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22
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Khan MM, Kirabo A. Long Noncoding RNA MALAT1: Salt-Sensitive Hypertension. Int J Mol Sci 2024; 25:5507. [PMID: 38791545 PMCID: PMC11122212 DOI: 10.3390/ijms25105507] [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: 03/14/2024] [Revised: 05/06/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Hypertension stands as the leading global cause of mortality, affecting one billion individuals and serving as a crucial risk indicator for cardiovascular morbidity and mortality. Elevated salt intake triggers inflammation and hypertension by activating antigen-presenting cells (APCs). We found that one of the primary reasons behind this pro-inflammatory response is the epithelial sodium channel (ENaC), responsible for transporting sodium ions into APCs and the activation of NADPH oxidase, leading to increased oxidative stress. Oxidative stress increases lipid peroxidation and the formation of pro-inflammatory isolevuglandins (IsoLG). Long noncoding RNAs (lncRNAs) play a crucial role in regulating gene expression, and MALAT1, broadly expressed across cell types, including blood vessels and inflammatory cells, is also associated with inflammation regulation. In hypertension, the decreased transcriptional activity of nuclear factor erythroid 2-related factor 2 (Nrf2 or Nfe2l2) correlates with heightened oxidative stress in APCs and impaired control of various antioxidant genes. Kelch-like ECH-associated protein 1 (Keap1), an intracellular inhibitor of Nrf2, exhibits elevated levels of hypertension. Sodium, through an increase in Sp1 transcription factor binding at its promoter, upregulates MALAT1 expression. Silencing MALAT1 inhibits sodium-induced Keap1 upregulation, facilitating the nuclear translocation of Nrf2 and subsequent antioxidant gene transcription. Thus, MALAT1, acting via the Keap1-Nrf2 pathway, modulates antioxidant defense in hypertension. This review explores the potential role of the lncRNA MALAT1 in controlling the Keap1-Nrf2-antioxidant defense pathway in salt-induced hypertension. The inhibition of MALAT1 holds therapeutic potential for the progression of salt-induced hypertension and cardiovascular disease (CVD).
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Affiliation(s)
- Mohd Mabood Khan
- Department of Medicine, Preston Research Building, Vanderbilt University Medical Centre, Nashville, TN 37232, USA
| | - Annet Kirabo
- Department of Medicine, Preston Research Building, Vanderbilt University Medical Centre, Nashville, TN 37232, USA
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Ren Y, Fu S, Dong W, Chen J, Xue H, Bu W. The ncRNA-mediated regulatory networks of defensins and lysozymes in Riptortus pedestris: involvement in response to gut bacterial disturbances. Front Microbiol 2024; 15:1386345. [PMID: 38827147 PMCID: PMC11140134 DOI: 10.3389/fmicb.2024.1386345] [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: 02/15/2024] [Accepted: 04/23/2024] [Indexed: 06/04/2024] Open
Abstract
Insects depend on humoral immunity against intruders through the secretion of antimicrobial peptides (AMPs) and immune effectors via NF-κB transcription factors, and their fitness is improved by gut bacterial microbiota. Although there are growing numbers of reports on noncoding RNAs (ncRNAs) involving in immune responses against pathogens, comprehensive studies of ncRNA-AMP regulatory networks in Riptortus pedestris, which is one of the widely distributed pests in East Asia, are still not well understood under feeding environmental changes. The objective of this study employed the whole-transcriptome sequencing (WTS) to systematically identify the lncRNAs (long noncoding RNA) and circRNAs (circular RNA) and to obtain their differential expression from the R. pedestris gut under different feeding conditions. Functional annotation indicated that they were mainly enriched in various biological processes with the GO and KEGG databases, especially in immune signaling pathways. Five defensin (four novel members) and eleven lysozyme (nine novel members) family genes were identified and characterized from WTS data, and meanwhile, phylogenetic analysis confirmed their classification. Subsequently, the miRNA-mRNA interaction network of above two AMPs and lncRNA-involved ceRNA (competing endogenous RNA) regulatory network of one lysozyme were predicted and built based on bioinformatic prediction and calculation, and the expression patterns of differentially expressed (DE) defensins, and DE lysozymes and related DE ncRNAs were estimated and selected among all the comparison groups. Finally, to integrate the analyses of WTS and previous 16S rRNA amplicon sequencing, we conducted the Pearson correlation analysis to reveal the significantly positive or negative correlation between above DE AMPs and ncRNAs, as well as most changes in the gut bacterial microbiota at the genus level of R. pedestris. Taken together, the present observations provide great insights into the ncRNA regulatory networks of AMPs in response to rearing environmental changes in insects and uncover new potential strategies for pest control in the future.
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Affiliation(s)
- Yipeng Ren
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Siying Fu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Wenhao Dong
- Tianjin Key Laboratory of Food and Biotechnology, School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Juhong Chen
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Huaijun Xue
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
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24
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Li X, Hou Z, Meng S, Jia Q, Xing S, Wang Z, Chen M, Xu H, Li M, Cai H. LncRNA BlncAD1 Modulates Bovine Adipogenesis by Binding to MYH10, PI3K/Akt Signaling Pathway, and miR-27a-5p/CDK6 Axis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:11094-11110. [PMID: 38661523 DOI: 10.1021/acs.jafc.4c00165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Research on adipogenesis will help to improve the meat quality of livestock. Long noncoding RNAs (lncRNAs) are involved in mammalian adipogenesis as epigenetic modulators. In this study, we analyzed lncRNA expression during bovine adipogenesis and detected 195 differentially expressed lncRNAs, including lncRNA BlncAD1, which was significantly upregulated in mature bovine adipocytes. Gain- and loss-of-function experiments confirmed that BlncAD1 promoted the proliferation, apoptosis, and differentiation of bovine preadipocytes. RNA pull-down revealed that the nonmuscle myosin 10 (MYH10) is a potential binding protein of BlncAD1. Then, we elucidated that loss of BlncAD1 caused increased ubiquitination of MYH10, which confirmed that BlncAD1 regulates adipogenesis by enhancing the stability of the MYH10 protein. Western blotting was used to demonstrate that BlncAD1 activated the PI3K/Akt signaling pathway. Bioinformatic analysis and dual-luciferase reporter assays indicated that BlncAD1 competitively absorbed miR-27a-5p. The overexpression and interference of miR-27a-5p in bovine preadipocytes displayed that miR-27a-5p inhibited proliferation, apoptosis, and differentiation. Further results suggested that miR-27a-5p targeted the CDK6 gene and that BlncAD1 controlled the proliferation of bovine preadipocytes by modulating the miR-27a-5p/CDK6 axis. This study revealed the complex mechanisms of BlncAD1 underlying bovine adipogenesis for the first time, which would provide useful information for genetics and breeding improvement of Chinese beef cattle.
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Affiliation(s)
- Xin Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Zhongyi Hou
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Shengbo Meng
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Qihui Jia
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Shanshan Xing
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Zhitong Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Mengjuan Chen
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Huifen Xu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Ming Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Hanfang Cai
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
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25
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Liao J, Chen R, Lin B, Deng R, Liang Y, Zeng J, Ma S, Qiu X. Cross-Talk between the TGF-β and Cell Adhesion Signaling Pathways in Cancer. Int J Med Sci 2024; 21:1307-1320. [PMID: 38818471 PMCID: PMC11134594 DOI: 10.7150/ijms.96274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 04/30/2024] [Indexed: 06/01/2024] Open
Abstract
Transforming growth factor-β (TGF-β) is strongly associated with the cell adhesion signaling pathway in cell differentiation, migration, etc. Mechanistically, TGF-β is secreted in an inactive form and localizes to the extracellular matrix (ECM) via the latent TGF-β binding protein (LTBP). However, it is the release of mature TGF-β that is essential for the activation of the TGF-β signaling pathway. This progress requires specific integrins (one of the main groups of cell adhesion molecules (CAMs)) to recognize and activate the dormant TGF-β. In addition, TGF-β regulates cell adhesion ability through modulating CAMs expression. The aberrant activation of the TGF-β signaling pathway, caused by abnormal expression of key regulatory molecules (such as Smad proteins, certain transcription factors, and non-coding RNAs), promotes tumor invasive and metastasis ability via epithelial-mesenchymal transition (EMT) during the late stages of tumorigenesis. In this paper, we summarize the crosstalk between TGF-β and cell adhesion signaling pathway in cancer and its underlying molecular mechanisms.
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Affiliation(s)
- Jiahao Liao
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, Guangdong, 523808, China
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan, Guangdong, 523808, China
| | - Rentang Chen
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, Guangdong, 523808, China
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan, Guangdong, 523808, China
| | - Bihua Lin
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, Guangdong, 523808, China
| | - Runhua Deng
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, Guangdong, 523808, China
| | - Yanfang Liang
- Department of Pathology, Binhaiwan Central Hospital of Dongguan, Dongguan, Guangdong, 523905, China
| | - Jincheng Zeng
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, Guangdong, 523808, China
| | - Sha Ma
- School of Biomedical Engineering, Guangdong Medical University, Dongguan, Guangdong, 523808, China
| | - Xianxiu Qiu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, Guangdong, 523808, China
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26
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Wang Y, Liu J, Yao Q, Wang Y, Liu Z, Zhang L. LncRNA SNHG6 Promotes Wilms' Tumor Progression Through Regulating miR-429/FRS2 Axis. Cancer Biother Radiopharm 2024; 39:264-275. [PMID: 33481659 DOI: 10.1089/cbr.2020.3705] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Background: Long noncoding RNA (lncRNA) small nucleolar RNA host gene 6 (SNHG6) has been reported to be an oncogene in a variety of cancers. However, the role of SNHG6 and its associated mechanisms in Wilms' tumor progression remain largely unknown. Methods: The expression of SNHG6, microRNA-429 (miR-429), and FGF receptor substrates 2 (FRS2) messenger RNA (mRNA) was detected by quantitative real-time polymerase chain reaction. Cell proliferation was analyzed through 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and plate colony assay. The apoptosis was assessed by flow cytometry. Cell glycolytic metabolism was analyzed through detecting the lactate dehydrogenase activity, glucose uptake, lactate production, and ATP level. The target relationship between miR-429 and SNHG6 or FRS2 was predicted by miRcode or Starbase and then validated by dual-luciferase reporter assay and RNA pull-down assay. Murine xenograft model was established to validate the function of SNHG6 in vivo. Results: The level of SNHG6 was elevated in Wilms' tumor tissues and cells, and SNHG6 played an oncogenic role to promote the proliferation and glycolysis and restrain the apoptosis of Wilms' tumor cells. MiR-429 was identified as a target of SNHG6, and miR-429 interference partly reversed the inhibitory effects induced by SNHG6 silencing on the malignant behaviors of Wilms' tumor cells. FRS2 mRNA bound to miR-429 in Wilms' tumor cells. SNHG6 upregulated the expression of FRS2 through acting as a sponge of miR-429. MiR-429-induced influences in Wilms' tumor cells were largely counteracted by the overexpression of FRS2. SNHG6 silencing suppressed the Wilms' tumor growth through miR-429/FRS2 axis in vivo. Conclusion: SNHG6 accelerated Wilms' tumor progression through regulating miR-429/FRS2 signaling in vitro and in vivo.
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Affiliation(s)
- Yingjie Wang
- Department of Pediatrics, The Second Hospital of Dalian Medical University, Dalian, China
| | - Junli Liu
- Department of Pediatrics, The Second Hospital of Dalian Medical University, Dalian, China
| | - Qiying Yao
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Yuchuan Wang
- Department of Pediatrics, The Second Hospital of Dalian Medical University, Dalian, China
| | - Zhengjuan Liu
- Department of Pediatrics, The Second Hospital of Dalian Medical University, Dalian, China
| | - Li Zhang
- Department of Pediatrics, The Second Hospital of Dalian Medical University, Dalian, China
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Fan Q, Bao X, Zhao H, Li S. LncRNA MRPL39 inhibits cell proliferation and migration by regulating miR-130/TSC1 axis in non-small cell lung cancer. 3 Biotech 2024; 14:125. [PMID: 38577417 PMCID: PMC10987421 DOI: 10.1007/s13205-024-03975-y] [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: 12/22/2023] [Accepted: 03/08/2024] [Indexed: 04/06/2024] Open
Abstract
Currently, the effect of miR-130 on non-small cell lung cancer (NSCLC) remains controversial. In this study, the expression of miR-130 and lncRNA MRPL39 in tumor and non-tumor tissues of NSCLC patients was examined using real-time PCR (RT-PCR) and correlated with the prognosis of NSCLC. The phenotypic effects of miR-130 and MRPL39 on proliferation and migration of NSCLC cell line A549 cells were assessed through CCK-8 and Transwell assays with miR-130 mimic and MRPL39 (mitochondrial ribosomal protein L39) overexpressed plasmid transfection. StarBase/TargetScan analysis and dual-luciferase reporter gene assays were conducted to investigate the relationship between MRPL39, miR-130, and Tuberculosis sclerosis 1 (TSC1). MiR-130 was overexpressed, and MRPL39 was downregulated in NSCLC tissues and cells. Inhibition of miR-130 expression and overexpression of MRPL39 resulted in the inhibition of the viability and migration of A549 cells. MRPL39 is a potential upstream regulatory long non-coding RNA of miR-130, and its expression is negatively regulated by miR-130. TSC1 was identified as a target of miR-130, suppressing the antitumor effects of FGD5-AS1 silencing on GBM cells. After overexpression of MRPL39, the mRNA and protein levels of TSC1 in A549 cells significantly increased. However, after transfection with miR-130 mimic, the up-regulation of mRNA and protein was inhibited, leading to the suppression of cell proliferation and migration.
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Affiliation(s)
- Qinghao Fan
- Cardiothoracic Surgery, Jinhua People’s Hospital, Jinhua, 321000 China
| | - Xianrong Bao
- Cardiothoracic Surgery, Jinhua People’s Hospital, Jinhua, 321000 China
| | - Han Zhao
- Cardiothoracic Surgery, Jinhua People’s Hospital, Jinhua, 321000 China
| | - Sichen Li
- Cardiothoracic Surgery, Jinhua People’s Hospital, Jinhua, 321000 China
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28
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Ciftci YC, Vatansever İE, Akgül B. Unraveling the intriguing interplay: Exploring the role of lncRNAs in caspase-independent cell death. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1862. [PMID: 38837618 DOI: 10.1002/wrna.1862] [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: 11/05/2023] [Revised: 05/12/2024] [Accepted: 05/13/2024] [Indexed: 06/07/2024]
Abstract
Cell death plays a crucial role in various physiological and pathological processes. Until recently, programmed cell death was mainly attributed to caspase-dependent apoptosis. However, emerging evidence suggests that caspase-independent cell death (CICD) mechanisms also contribute significantly to cellular demise. We and others have reported and functionally characterized numerous long noncoding RNAs (lncRNAs) that modulate caspase-dependent apoptotic pathways potentially in a pathway-dependent manner. However, the interplay between lncRNAs and CICD pathways has not been comprehensively documented. One major reason for this is that most CICD pathways have been recently discovered with some being partially characterized at the molecular level. In this review, we discuss the emerging evidence that implicates specific lncRNAs in the regulation and execution of CICD. We summarize the diverse mechanisms through which lncRNAs modulate different forms of CICD, including ferroptosis, necroptosis, cuproptosis, and others. Furthermore, we highlight the intricate regulatory networks involving lncRNAs, protein-coding genes, and signaling pathways that orchestrate CICD in health and disease. Understanding the molecular mechanisms and functional implications of lncRNAs in CICD may unravel novel therapeutic targets and diagnostic tools for various diseases, paving the way for innovative strategies in disease management and personalized medicine. This article is categorized under: RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Yusuf Cem Ciftci
- Noncoding RNA Laboratory, Department of Molecular Biology and Genetics, Izmir Institute of Technology, Izmir, Gülbahçeköyü, Urla, Turkey
| | - İpek Erdoğan Vatansever
- Noncoding RNA Laboratory, Department of Molecular Biology and Genetics, Izmir Institute of Technology, Izmir, Gülbahçeköyü, Urla, Turkey
| | - Bünyamin Akgül
- Noncoding RNA Laboratory, Department of Molecular Biology and Genetics, Izmir Institute of Technology, Izmir, Gülbahçeköyü, Urla, Turkey
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29
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Shadkam R, Saadat P, Azadmehr A, Chehrazi M, Daraei A. Key Non-coding Variants in Three Neuroapoptosis and Neuroinflammation-Related LncRNAs Are Protectively Associated with Susceptibility to Parkinson's Disease and Some of Its Clinical Features. Mol Neurobiol 2024; 61:2854-2865. [PMID: 37946005 DOI: 10.1007/s12035-023-03708-x] [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: 08/30/2023] [Accepted: 10/10/2023] [Indexed: 11/12/2023]
Abstract
Research findings show that genetic susceptibility to sporadic Parkinson's disease (PD), a common neurodegenerative disorder, is determined through gene variation of loci involved in its development and pathogenesis. A growing body of strong evidence has revealed that dysfunction of long non-coding RNAs (lncRNAs) plays key roles in the pathogenesis and progression of PD through impairing neuronal signaling pathways, but little is known about the relationship between their variants and PD susceptibility. In this research, we intended to study the relationship between functional SNPs rs12826786C>T, rs3200401C>T, and rs6931097G>A in the key lncRNAs stimulating neuroapoptosis and neuroinflammation in PD, including HOTAIR, MALAT1, and lincRNA-P21, respectively, with susceptibility to PD as well as its clinical symptoms.The population of this study consisted of 240 individuals, including 120 controls and 120 cases, and the sample taken from them was peripheral blood. Genotyping of the target SNPs was done using PCR-RFLP. We found that the healthy individuals carry more T allele of MALAT1-rs3200401C>T compared to the patients (P= 0.019). Furthermore, it was observed that in the dominant genetic model, subjects with genotypes carrying the T allele have a lower risk of PD (OR= 0.530; CI= 0.296-0.950; P= 0.033). Regarding the lincRNA-P21-rs6931097G>A, we observed a significant protective relationship between its GA (OR= 0.144; CI= 0.030-0.680; P= 0.014) and AA (OR= 0.195; CI= 00.047-0.799; P= 0.023) genotypes with the manifestation of tremor and bradykinesia symptoms, respectively. Furthermore, the findings indicated that the minor TT genotype of HOTAIR-rs12826786C>T was significantly associated with a reduced risk of bradykinesia symptoms (OR= 0.147; CI= 0.039-0.555; P= 0.005). Collectively, these findings suggest that MALAT1-rs3200401C>T may be an important lncRNA SNP against the development of PD, while the other two SNPs show protective effects on the clinical manifestations of PD in a way that lincRNA-P21-rs6931097G>A has a protective effect against the occurrence of tremor and bradykinesia symptoms in PD patients, and HOTAIR -rs12826786C>T indicates a protective effect against the display of bradykinesia feature. Therefore, they can have valuable potential as biomarkers for clinical evaluations of this disease.
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Affiliation(s)
- Roshanak Shadkam
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
- Department of Medical Genetics, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Payam Saadat
- Mobility Impairment Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Abbas Azadmehr
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Mohammad Chehrazi
- Department of Biostatistics and Epidemiology, School of Public Health, Babol University of Medical Sciences, Babol, Iran
| | - Abdolreza Daraei
- Department of Medical Genetics, School of Medicine, Babol University of Medical Sciences, Babol, Iran.
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran.
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Dos Reis RS, Wagner MCE, McKenna S, Ayyavoo V. Neuroinflammation driven by human immunodeficiency virus-1 (HIV-1) directs the expression of long noncoding RNA RP11-677M14.2 resulting in dysregulation of neurogranin in vivo and in vitro. J Neuroinflammation 2024; 21:107. [PMID: 38659061 PMCID: PMC11043047 DOI: 10.1186/s12974-024-03102-x] [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: 12/27/2023] [Accepted: 04/15/2024] [Indexed: 04/26/2024] Open
Abstract
Neuroinflammation and synaptodendritic damage represent the pathological hallmarks of HIV-1 associated cognitive disorders (HAND). The post-synaptic protein neurogranin (Nrgn) is significantly reduced in the frontal cortex of postmortem brains from people with HIV (PWH) and it is associated with inflammatory factors released by infected microglia/macrophages. However, the mechanism involved in synaptic loss have yet to be elucidated. In this study, we characterized a newly identified long non-coding RNA (lncRNA) transcript (RP11-677M14.2), which is antisense to the NRGN locus and is highly expressed in the frontal cortex of HIV-1 individuals. Further analysis indicates an inverse correlation between the expression of RP11-677M14.2 RNA and Nrgn mRNA. Additionally, the Nrgn-lncRNA axis is dysregulated in neurons exposed to HIV-1 infected microglia conditioned medium enriched with IL-1β. Moreover, in vitro overexpression of this lncRNA impacts Nrgn expression at both mRNA and protein levels. Finally, we modeled the Nrgn-lncRNA dysregulation within an HIV-1-induced inflammatory environment using brain organoids, thereby corroborating our in vivo and in vitro findings. Together, our study implicates a plausible role for lncRNA RP11-677M14.2 in modulating Nrgn expression that might serve as the mechanistic link between Nrgn loss and cognitive dysfunction in HAND, thus shedding new light on the mechanisms underlying synaptodendritic damage.
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Affiliation(s)
- Roberta S Dos Reis
- Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, 2117 Pitt Public Health, 130 DeSoto Street, Pittsburgh, PA, 15260, USA
| | - Marc C E Wagner
- Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, 2117 Pitt Public Health, 130 DeSoto Street, Pittsburgh, PA, 15260, USA
| | - Savannah McKenna
- Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, 2117 Pitt Public Health, 130 DeSoto Street, Pittsburgh, PA, 15260, USA
| | - Velpandi Ayyavoo
- Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, 2117 Pitt Public Health, 130 DeSoto Street, Pittsburgh, PA, 15260, USA.
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Du Y, Guan X, Zhu Y, Jin S, Liu J. LncRNA in periodontal tissue-derived cells on osteogenic differentiation in the periodontitis field. Oral Dis 2024. [PMID: 38655682 DOI: 10.1111/odi.14970] [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: 07/14/2023] [Revised: 02/06/2024] [Accepted: 04/09/2024] [Indexed: 04/26/2024]
Abstract
OBJECTIVE Periodontitis can lead to the destruction of periodontal tissues and potentially tooth loss. Numerous periodontal tissue-derived cells display osteogenic differentiation potential. The presence of differentially expressed long non-coding RNAs (lncRNAs) in these cells indicate their ability to regulate the process of osteogenic differentiation. We aim to elucidate the various lncRNA-mediated regulatory mechanisms in the osteogenic differentiation of periodontal tissue-derived cells in the field of periodontitis at epigenetic modification, transcriptional, and post-transcriptional levels. SUBJECTS AND METHODS We systematically searched the PubMed, Web of Science, and ScienceDirect databases to identify relevant literature in the field of periodontitis discussing the role of lncRNAs in regulating osteogenic differentiation of periodontal tissue-derived cells. The identified literature was subsequently summarized for comprehensive review. RESULTS In this review, we have comprehensively summarized the regulatory mechanisms of lncRNAs in the osteogenic differentiation of periodontal tissue-derived cells in the field of periodontitis and discussed how these lncRNAs provide novel perspectives for understanding the pathogenesis and progression of periodontitis. CONCLUSION These results indicate the pivotal role of lncRNAs as regulators in the osteogenic differentiation of periodontal tissue-derived cells, providing a solid basis for future investigations on the role of lncRNAs in the periodontitis field.
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Affiliation(s)
- Yuanhang Du
- School of Stomatology, Zunyi Medical University, Zunyi, China
| | - Xiaoyan Guan
- Department of Orthodontics, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, China
| | - Yinci Zhu
- School of Stomatology, Zunyi Medical University, Zunyi, China
| | - Suhan Jin
- Department of Orthodontics, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, China
| | - Jianguo Liu
- School of Stomatology, Zunyi Medical University, Zunyi, China
- Special Key Laboratory of Oral Diseases Research, Higher Education Institution, Zunyi, China
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Huang C, Aghaei-Zarch SM. From molecular pathogenesis to therapy: Unraveling non-coding RNAs/DNMT3A axis in human cancers. Biochem Pharmacol 2024; 222:116107. [PMID: 38438051 DOI: 10.1016/j.bcp.2024.116107] [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: 11/23/2023] [Revised: 02/03/2024] [Accepted: 03/01/2024] [Indexed: 03/06/2024]
Abstract
Cancer is a comprehensive classification encompassing more than 100 forms of malignancies that manifest in diverse tissues within the human body. Recent studies have provided evidence that aberrant epigenetic modifications are pivotal indicators of cancer. Epigenetics encapsulates DNA methyltransferases as a crucial class of modifiers. DNMTs, including DNMT3A, assume central roles in DNA methylation processes that orchestrate normal biological functions, such as gene transcription, predominantly in mammals. Typically, deviations in DNMT3A function engender distortions in factors that drive tumor growth and progression, thereby exacerbating the malignant phenotype of tumors. Consequently, such abnormalities pose significant challenges in cancer therapy because they impede treatment efficacy. Non-coding RNAs (ncRNAs) represent a group of RNA molecules that cannot encode functional proteins. Recent investigation attests to the crucial significance of regulatory ncRNAs in epigenetic regulation. Notably, recent reports have illuminated the complex interplay between ncRNA expression and epigenetic regulatory machinery, including DNMT3A, particularly in cancer. Recent findings have demonstrated that miRNAs, namely miR-770-5p, miR-101, and miR-145 exhibit the capability to target DNMT3A directly, and their aberration is implicated in diverse cellular abnormalities that predispose to cancer development. This review aims to articulate the interplay between DNMT3A and the ncRNAs, focusing on its impact on the development and progression of cancer, cancer therapy resistance, cancer stem cells, and prognosis. Importantly, the emergence of such reports that suggest a connection between DNMT3A and ncRNAs in several cancers indicates that this connecting axis offers a valuable target with significant therapeutic potential that might be exploited for cancer management.
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Affiliation(s)
- Chunjie Huang
- School of Medicine, Nantong University, Nantong 226001, China
| | - Seyed Mohsen Aghaei-Zarch
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Yu B, Cai Z, Liu J, Zhang T, Feng X, Wang C, Li J, Gu Y, Zhang J. Identification of key differentially methylated genes in regulating muscle development and intramuscular fat deposition in chickens. Int J Biol Macromol 2024; 264:130737. [PMID: 38460642 DOI: 10.1016/j.ijbiomac.2024.130737] [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: 12/20/2023] [Revised: 02/26/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024]
Abstract
Muscle development and intramuscular fat (IMF) deposition are intricate physiological processes characterized by multiple gene expressions and interactions. In this research, the phenotypic variations in the breast muscle of Jingyuan chickens were examined at three different time points: 42, 126, and 180 days old. Differential expression analysis and weighted gene co-expression network analysis (WGCNA) were performed to identify differentially methylated genes (DMGs) responsible for regulating muscle development and IMF deposition. The findings indicate a significant increase in breast muscle weight (BMW), myofiber diameter, and cross-sectional area, as well as IMF content, in correlation with the progressive number of growing days in Jingyuan chickens. The findings also revealed that 380 hypo-methylated and 253 hyper-methylated DMGs were identified between the three groups of breast muscle. Module gene and DMG association analysis identified m6A methylation-mediated multiple DMGs associated with muscle development and fat metabolism. In vitro cell modeling analysis reveals stage-specific differences in the expression of CUBN, MEGF10, BOP1, and BMPR2 during the differentiation of myoblasts and intramuscular preadipocytes. Cycloleucine treatment significantly inhibited the expression levels of CUBN, BOP1, and BMPR2, and promoted the expression of MEGF10. These results suggest that m6A methylation-mediated CUBN, MEGF10, BOP1, and BMPR2 can serve as potential candidate genes for regulating muscle development and IMF deposition, and provide an important theoretical basis for further investigation of the functional mechanism of m6A modification involved in adipogenesis.
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Affiliation(s)
- Baojun Yu
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Zhengyun Cai
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Jiamin Liu
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Tong Zhang
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Xiaofang Feng
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Chuanchuan Wang
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Jiwei Li
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Yaling Gu
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Juan Zhang
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China.
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34
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Jasim SA, Al-Hawary SIS, Kaur I, Ahmad I, Hjazi A, Petkov I, Ali SHJ, Redhee AH, Shuhata Alubiady MH, Al-Ani AM. Critical role of exosome, exosomal non-coding RNAs and non-coding RNAs in head and neck cancer angiogenesis. Pathol Res Pract 2024; 256:155238. [PMID: 38493725 DOI: 10.1016/j.prp.2024.155238] [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: 01/25/2024] [Revised: 02/13/2024] [Accepted: 03/02/2024] [Indexed: 03/19/2024]
Abstract
Head and neck cancer (HNC) refers to the epithelial malignancies of the upper aerodigestive tract. HNCs have a constant yet slow-growing rate with an unsatisfactory overall survival rate globally. The development of new blood vessels from existing blood conduits is regarded as angiogenesis, which is implicated in the growth, progression, and metastasis of cancer. Aberrant angiogenesis is a known contributor to human cancer progression. Representing a promising therapeutic target, the blockade of angiogenesis aids in the reduction of the tumor cells oxygen and nutrient supplies. Despite the promise, the association of existing anti-angiogenic approaches with severe side effects, elevated cancer regrowth rates, and limited survival advantages is incontrovertible. Exosomes appear to have an essential contribution to the support of vascular proliferation, the regulation of tumor growth, tumor invasion, and metastasis, as they are a key mediator of information transfer between cells. In the exocrine region, various types of noncoding RNAs (ncRNAs) identified to be enriched and stable and contribute to the occurrence and progression of cancer. Mounting evidence suggest that exosome-derived ncRNAs are implicated in tumor angiogenesis. In this review, the characteristics of angiogenesis, particularly in HNC, and the impact of ncRNAs on HNC angiogenesis will be outlined. Besides, we aim to provide an insight on the regulatory role of exosomes and exosome-derived ncRNAs in angiogenesis in different types of HNC.
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Affiliation(s)
| | | | - Irwanjot Kaur
- Department of Biotechnology and Genetics, Jain (Deemed-to-be) University, Bengaluru, Karnataka 560069, India; Department of Allied Healthcare and Sciences, Vivekananda Global University, Jaipur, Rajasthan 303012, India
| | - Irfan Ahmad
- Department of Clinical Laboratory Sciences, College of Applied Medical Science, King Khalid University, Abha, Saudi Arabia
| | - Ahmed Hjazi
- Department of Medical Laboratory, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia.
| | - Iliya Petkov
- Medical University - Sofia, Department of Neurology, Sofia, Bulgaria
| | - Saad Hayif Jasim Ali
- Department of medical laboratory, College of Health and Medical Technololgy, Al-Ayen University, Thi-Qar, Iraq
| | - Ahmed Huseen Redhee
- Medical laboratory technique college, the Islamic University, Najaf, Iraq; Medical laboratory technique college, the Islamic University of Al Diwaniyah, Al Diwaniyah, Iraq; Medical laboratory technique college, the Islamic University of Babylon, Babylon, Iraq
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Cong L, Zhao Q, Sun H, Zhou Z, Hu Y, Li C, Hao M, Cong X. A novel long non-coding RNA SLNCR1 promotes proliferation, migration, and invasion of melanoma via transcriptionally regulating SOX5. Cell Death Discov 2024; 10:160. [PMID: 38561355 PMCID: PMC10984963 DOI: 10.1038/s41420-024-01922-7] [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: 07/06/2023] [Revised: 03/13/2024] [Accepted: 03/19/2024] [Indexed: 04/04/2024] Open
Abstract
Steroid receptor RNA activator (SRA)-like non-coding RNA (SLNCR1) has been implicated in various tumorigenic processes, but the precise regulatory role in melanoma progression remains uncertain. We performed a comprehensive analysis to investigate the prognostic value of SLNCR1 expression in patients with melanoma by TCGA database and melanoma tissue samples via the Kaplan-Meier method. Subsequently, we conducted qRT-PCR and Fluorescence in Situ Hybridization (FISH) assays to identify SLNCR1 expression levels and localization in tissues and cells, respectively. Loss-of-function assays utilizing shRNAs vectors were used to investigate the potential impact of SLNCR1. Our data showed that SLNCR1 is significantly up-regulated in human malignant melanoma tissues and cell lines and functions as an oncogene. Silencing of SLNCR1 suppressed melanoma cell proliferation, migration, invasion, and inhibited tumorigenesis in a mouse xenograft model. Additionally, we employed bioinformatic predictive analysis, combined with dual-luciferase reporter analysis and functional rescue assays, to elucidate the mechanistic target of the SLNCR1/SOX5 axis in melanoma. Mechanistically, we discovered that SLNCR1 promotes EMT of human melanoma by targeting SOX5, as downregulation of SLNCR1 expression leads to a decrease in SOX5 protein levels and inhibits melanoma tumorigenesis. Our research offers promising insights for more precise diagnosis and treatment of human melanoma.
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Affiliation(s)
- Lele Cong
- Department of Dermatology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Qing Zhao
- Department of Neurology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Hongyan Sun
- Department of Biobank, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Zilong Zhou
- Department of Biobank, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Yue Hu
- Department of Biobank, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Chunyi Li
- Institute of Antler Science and Product Technology, Changchun Sci-Tech University, Changchun, China
| | - Miao Hao
- Scientific Research Center, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China.
| | - Xianling Cong
- Department of Biobank, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China.
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36
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Zhang W, Li Q, Zhang Y, Wang Z, Yuan S, Zhang X, Zhao M, Zhuang W, Li B. Multiple myeloma with high expression of SLC7A11 is sensitive to erastin-induced ferroptosis. Apoptosis 2024; 29:412-423. [PMID: 38001343 DOI: 10.1007/s10495-023-01909-2] [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] [Accepted: 10/22/2023] [Indexed: 11/26/2023]
Abstract
Ferroptosis, a nonapoptotic form of cell death marked by iron-dependent peroxidation of phospholipids, is associated with the occurrence and progression of tumors. Erastin, a selective inhibitor of the cystine/glutamate transporter system Xc-, can induce the ferroptosis of cancer cells. Multiple myeloma (MM) has been reported to be insensitive to erastin-induced ferroptosis. However, we found the erastin sensitivity of different MM cells varied widely. Specifically, SLC7A11 abundance determined the sensitivity of MM cells to erastin-induced ferroptosis. MM cells expressing a high SLC7A11 level were more sensitive to erastin-induced ferroptosis than cells expressing a low level of SLC7A11. Moreover, the expression of SLC7A11 gradually increased with the progression of plasma cell dyscrasias. Survival analysis indicated that high levels of SLC7A11 predicted a poor prognosis for MM patients. Knocking down SLC7A11 expression significantly inhibited the proliferation of MM cells and induced ferroptotic cell death. Additionally, we revealed that the long noncoding RNA (lncRNA) SLC7A11-AS1 was a critical regulatory factor of SLC7A11 expression. SLC7A11-AS1 overexpression diminished SLC7A11 levels, leading to the ferroptosis of MM cells. In summary, our data show that heterogeneous SLC7A11 expression affects MM cell sensitivity to ferroptosis, providing a theoretical basis for improving the clinical treatment of MM.
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Affiliation(s)
- Weimin Zhang
- Department of Hematology, The Second Affiliated Hospital of Soochow University, San Xiang Road 1055, Suzhou, 215006, China
| | - Qi Li
- Department of Hematology, The Second Affiliated Hospital of Soochow University, San Xiang Road 1055, Suzhou, 215006, China
| | - Yuchen Zhang
- Department of Hematology, The Second Affiliated Hospital of Soochow University, San Xiang Road 1055, Suzhou, 215006, China
| | - Zhiming Wang
- Department of Cell Biology, School of Biology & Basic Medical Sciences, Suzhou Medical College of Soochow University, Ren Ai Road 199, Suzhou, 215123, China
| | - Shushu Yuan
- Department of Hematology, The Second Affiliated Hospital of Soochow University, San Xiang Road 1055, Suzhou, 215006, China
| | - Xinyun Zhang
- Department of Hematology, The Second Affiliated Hospital of Soochow University, San Xiang Road 1055, Suzhou, 215006, China
| | - Meifang Zhao
- Department of Hematology, The Second Affiliated Hospital of Soochow University, San Xiang Road 1055, Suzhou, 215006, China
| | - Wenzhuo Zhuang
- Department of Cell Biology, School of Biology & Basic Medical Sciences, Suzhou Medical College of Soochow University, Ren Ai Road 199, Suzhou, 215123, China.
| | - Bingzong Li
- Department of Hematology, The Second Affiliated Hospital of Soochow University, San Xiang Road 1055, Suzhou, 215006, China.
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37
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Wang T, Chen Y, Liu Z, Zhou J, Li N, Shan Y, He Y. Long noncoding RNA Glis2 regulates podocyte mitochondrial dysfunction and apoptosis in diabetic nephropathy via sponging miR-328-5p. J Cell Mol Med 2024; 28:e18204. [PMID: 38506068 PMCID: PMC10951868 DOI: 10.1111/jcmm.18204] [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: 08/12/2023] [Revised: 01/13/2024] [Accepted: 02/20/2024] [Indexed: 03/21/2024] Open
Abstract
Podocyte apoptosis exerts a crucial role in the pathogenesis of DN. Recently, long noncoding RNAs (lncRNAs) have been gradually identified to be functional in a variety of different mechanisms associated with podocyte apoptosis. This study aimed to investigate whether lncRNA Glis2 could regulate podocyte apoptosis in DN and uncover the underlying mechanism. The apoptosis rate was detected by flow cytometry. Mitochondrial membrane potential (ΔΨM) was measured using JC-1 staining. Mitochondrial morphology was detected by MitoTracker Deep Red staining. Then, the histopathological and ultrastructure changes of renal tissues in diabetic mice were observed using periodic acid-Schiff (PAS) staining and transmission electron microscopy. We found that lncRNA Glis2 was significantly downregulated in high-glucose cultured podocytes and renal tissues of db/db mice. LncRNA Glis2 overexpression was found to alleviate podocyte mitochondrial dysfunction and apoptosis. The direct interaction between lncRNA Glis2 and miR-328-5p was confirmed by dual luciferase reporter assay. Furthermore, lncRNA Glis2 overexpression alleviated podocyte apoptosis in diabetic mice. Taken together, this study demonstrated that lncRNA Glis2, acting as a competing endogenous RNA (ceRNA) of miRNA-328-5p, regulated Sirt1-mediated mitochondrial dysfunction and podocyte apoptosis in DN.
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Affiliation(s)
- Ting Wang
- Department of EndocrinologySecond Hospital of Hebei Medical UniversityShijiazhuangHebeiP.R. China
| | - Yanxia Chen
- Department of EndocrinologySecond Hospital of Hebei Medical UniversityShijiazhuangHebeiP.R. China
| | - Zhihong Liu
- Department of EndocrinologySecond Hospital of Hebei Medical UniversityShijiazhuangHebeiP.R. China
| | - Jing Zhou
- Department of EndocrinologySecond Hospital of Hebei Medical UniversityShijiazhuangHebeiP.R. China
| | - Na Li
- Department of EndocrinologySecond Hospital of Hebei Medical UniversityShijiazhuangHebeiP.R. China
| | - Yue Shan
- Department of EndocrinologySecond Hospital of Hebei Medical UniversityShijiazhuangHebeiP.R. China
| | - Yinxi He
- Department of Orthopaedic TraumaThe Third Hospital of ShijiazhuangShijiazhuangHebeiP.R. China
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Yang Z, Zhou J, Su N, Zhang Z, Chen J, Liu P, Ling P. Insights into the defensive roles of lncRNAs during Mycoplasma pneumoniae infection. Front Microbiol 2024; 15:1330660. [PMID: 38585701 PMCID: PMC10995346 DOI: 10.3389/fmicb.2024.1330660] [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: 11/21/2023] [Accepted: 02/27/2024] [Indexed: 04/09/2024] Open
Abstract
Mycoplasma pneumoniae causes respiratory tract infections, affecting both children and adults, with varying degrees of severity ranging from mild to life-threatening. In recent years, a new class of regulatory RNAs called long non-coding RNAs (lncRNAs) has been discovered to play crucial roles in regulating gene expression in the host. Research on lncRNAs has greatly expanded our understanding of cellular functions involving RNAs, and it has significantly increased the range of functions of lncRNAs. In lung cancer, transcripts associated with lncRNAs have been identified as regulators of airway and lung inflammation in a process involving protein complexes. An excessive immune response and antibacterial immunity are closely linked to the pathogenesis of M. pneumoniae. The relationship between lncRNAs and M. pneumoniae infection largely involves lncRNAs that participate in antibacterial immunity. This comprehensive review aimed to examine the dysregulation of lncRNAs during M. pneumoniae infection, highlighting the latest advancements in our understanding of the biological functions and molecular mechanisms of lncRNAs in the context of M. pneumoniae infection and indicating avenues for investigating lncRNAs-related therapeutic targets.
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Affiliation(s)
- Zhujun Yang
- Department of Critical Care Medicine, The Central Hospital of Shaoyang City and Affiliated Shaoyang Hospital, Hengyang Medical College, University of South China, Shaoyang, China
- Institute of Pathogenic Biology, Basic Medical School, Hengyang Medical School, University of South China, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hengyang, China
| | - Junjun Zhou
- Department of Critical Care Medicine, The Central Hospital of Shaoyang City and Affiliated Shaoyang Hospital, Hengyang Medical College, University of South China, Shaoyang, China
- Institute of Pathogenic Biology, Basic Medical School, Hengyang Medical School, University of South China, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hengyang, China
| | - Nana Su
- Department of Critical Care Medicine, The Central Hospital of Shaoyang City and Affiliated Shaoyang Hospital, Hengyang Medical College, University of South China, Shaoyang, China
- Institute of Pathogenic Biology, Basic Medical School, Hengyang Medical School, University of South China, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hengyang, China
| | - Zifan Zhang
- Department of Critical Care Medicine, The Central Hospital of Shaoyang City and Affiliated Shaoyang Hospital, Hengyang Medical College, University of South China, Shaoyang, China
- Institute of Pathogenic Biology, Basic Medical School, Hengyang Medical School, University of South China, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hengyang, China
| | - Jiaxin Chen
- Department of Critical Care Medicine, The Central Hospital of Shaoyang City and Affiliated Shaoyang Hospital, Hengyang Medical College, University of South China, Shaoyang, China
- Institute of Pathogenic Biology, Basic Medical School, Hengyang Medical School, University of South China, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hengyang, China
| | - Peng Liu
- Department of Critical Care Medicine, The Central Hospital of Shaoyang City and Affiliated Shaoyang Hospital, Hengyang Medical College, University of South China, Shaoyang, China
- Institute of Pathogenic Biology, Basic Medical School, Hengyang Medical School, University of South China, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hengyang, China
| | - Peng Ling
- Department of Critical Care Medicine, The Central Hospital of Shaoyang City and Affiliated Shaoyang Hospital, Hengyang Medical College, University of South China, Shaoyang, China
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Taheri M, Shirvani-Farsani Z, Harsij A, Fathi M, Khalilian S, Ghafouri-Fard S, Baniahmad A. A review on the role of KCNQ1OT1 lncRNA in human disorders. Pathol Res Pract 2024; 255:155188. [PMID: 38330620 DOI: 10.1016/j.prp.2024.155188] [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: 01/02/2024] [Revised: 01/28/2024] [Accepted: 01/31/2024] [Indexed: 02/10/2024]
Abstract
KCNQ1OT1 is an lncRNA located within KCNQ1 gene on chromosome 11p15.5. This lncRNAs participates in the pathogenesis of a diversity of cancers as well as non-cancerous conditions. In most types of cancers, KCNQ1OT1 is regarded as an oncogene. In a wide array of cancers, high level of KCNQ1OT1 is associated with lower overall survival time. This lncRNA has been found to adsorb a variety of miRNAs, namely miR-15a, miR-211-5p, hsa-miR-107, miR-145, miR-34a, miR-204-5p, miR-129-5p, miR-372-3p, miR-491-5p, miR-153, miR-185-5p, miR-124-3p, miR-211-5p, miR-149, miR-148a-3p, miR-140-5p, miR-125b-5p, miR-9, miR-329-3p, miR-760, miR-296-5p, miR-3666 and miR-129-5p, thus regulating the downstream targets of these miRNAs. In this manuscript, our attention is on this lncRNA and its biomolecular roles in human cancers and other disorders. KCNQ1OT1 plays significant roles in the tumorigenesis and may function as a prospective target for cancer therapy.
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Affiliation(s)
- Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Zeinab Shirvani-Farsani
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Atefeh Harsij
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohadeseh Fathi
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sheyda Khalilian
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Aria Baniahmad
- Institute of Human Genetics, Jena University Hospital, Jena, Germany.
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Wang M, Yan M, Tan L, Zhao X, Liu G, Zhang Z, Zhang J, Gao H, Qin W. Non-coding RNAs: targets for Chinese herbal medicine in treating myocardial fibrosis. Front Pharmacol 2024; 15:1337623. [PMID: 38476331 PMCID: PMC10928947 DOI: 10.3389/fphar.2024.1337623] [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: 11/13/2023] [Accepted: 02/07/2024] [Indexed: 03/14/2024] Open
Abstract
Cardiovascular diseases have become the leading cause of death in urban and rural areas. Myocardial fibrosis is a common pathological manifestation at the adaptive and repair stage of cardiovascular diseases, easily predisposing to cardiac death. Non-coding RNAs (ncRNAs), RNA molecules with no coding potential, can regulate gene expression in the occurrence and development of myocardial fibrosis. Recent studies have suggested that Chinese herbal medicine can relieve myocardial fibrosis through targeting various ncRNAs, mainly including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs). Thus, ncRNAs are novel drug targets for Chinese herbal medicine. Herein, we summarized the current understanding of ncRNAs in the pathogenesis of myocardial fibrosis, and highlighted the contribution of ncRNAs to the therapeutic effect of Chinese herbal medicine on myocardial fibrosis. Further, we discussed the future directions regarding the potential applications of ncRNA-based drug screening platform to screen drugs for myocardial fibrosis.
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Affiliation(s)
- Minghui Wang
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
- School of Pharmacy, Jining Medical University, Rizhao, Shandong, China
| | - Maocai Yan
- School of Pharmacy, Jining Medical University, Rizhao, Shandong, China
| | - Liqiang Tan
- Department of Nasopharyngeal Carcinoma, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
| | - Xiaona Zhao
- School of Pharmacy, Jining Medical University, Rizhao, Shandong, China
- School of Pharmacy, Weifang Medical University, Weifang, Shandong, China
| | - Guoqing Liu
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
- School of Pharmacy, Jining Medical University, Rizhao, Shandong, China
| | - Zejin Zhang
- School of Pharmacy, Jining Medical University, Rizhao, Shandong, China
- School of Pharmacy, Binzhou Medical University, Yantai, Shandong, China
| | - Jing Zhang
- School of Pharmacy, Jining Medical University, Rizhao, Shandong, China
| | - Honggang Gao
- School of Pharmacy, Jining Medical University, Rizhao, Shandong, China
| | - Wei Qin
- School of Pharmacy, Jining Medical University, Rizhao, Shandong, China
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41
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Qattan A. Genomic Alterations Affecting Competitive Endogenous RNAs (ceRNAs) and Regulatory Networks (ceRNETs) with Clinical Implications in Triple-Negative Breast Cancer (TNBC). Int J Mol Sci 2024; 25:2624. [PMID: 38473871 DOI: 10.3390/ijms25052624] [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: 01/16/2024] [Revised: 02/18/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
The concept of competitive endogenous RNA regulation has brought on a change in the way we think about transcriptional regulation by miRNA-mRNA interactions. Rather than the relatively simple idea of miRNAs negatively regulating mRNA transcripts, mRNAs and other non-coding RNAs can regulate miRNAs and, therefore, broad networks of gene products through competitive interactions. While this concept is not new, its significant roles in and implications on cancer have just recently come to light. The field is now ripe for the extrapolation of technologies with a substantial clinical impact on cancer. With the majority of the genome consisting of non-coding regions encoding regulatory RNAs, genomic alterations in cancer have considerable effects on these networks that have been previously unappreciated. Triple-negative breast cancer (TNBC) is characterized by high mutational burden, genomic instability and heterogeneity, making this aggressive breast cancer subtype particularly relevant to these changes. In the past few years, much has been learned about the roles of competitive endogenous RNA network regulation in tumorigenesis, disease progression and drug response in triple-negative breast cancer. In this review, we present a comprehensive view of the new knowledge and future perspectives on competitive endogenous RNA networks affected by genomic alterations in triple-negative breast cancer. An overview of the competitive endogenous RNA (ceRNA) hypothesis and its bearing on cellular function and disease is provided, followed by a thorough review of the literature surrounding key competitive endogenous RNAs in triple-negative breast cancer, the genomic alterations affecting them, key disease-relevant molecular and functional pathways regulated by them and the clinical implications and significance of their dysregulation. New knowledge of the roles of these regulatory mechanisms and the current acceleration of research in the field promises to generate insights into the diagnosis, classification and treatment of triple-negative breast cancer through the elucidation of new molecular mechanisms, therapeutic targets and biomarkers.
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Affiliation(s)
- Amal Qattan
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
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Maurya SK, Rehman AU, Zaidi MAA, Khan P, Gautam SK, Santamaria-Barria JA, Siddiqui JA, Batra SK, Nasser MW. Epigenetic alterations fuel brain metastasis via regulating inflammatory cascade. Semin Cell Dev Biol 2024; 154:261-274. [PMID: 36379848 PMCID: PMC10198579 DOI: 10.1016/j.semcdb.2022.11.001] [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: 09/09/2022] [Revised: 10/28/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022]
Abstract
Brain metastasis (BrM) is a major threat to the survival of melanoma, breast, and lung cancer patients. Circulating tumor cells (CTCs) cross the blood-brain barrier (BBB) and sustain in the brain microenvironment. Genetic mutations and epigenetic modifications have been found to be critical in controlling key aspects of cancer metastasis. Metastasizing cells confront inflammation and gradually adapt in the unique brain microenvironment. Currently, it is one of the major areas that has gained momentum. Researchers are interested in the factors that modulate neuroinflammation during BrM. We review here various epigenetic factors and mechanisms modulating neuroinflammation and how this helps CTCs to adapt and survive in the brain microenvironment. Since epigenetic changes could be modulated by targeting enzymes such as histone/DNA methyltransferase, deacetylases, acetyltransferases, and demethylases, we also summarize our current understanding of potential drugs targeting various aspects of epigenetic regulation in BrM.
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Affiliation(s)
- Shailendra Kumar Maurya
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68108, USA
| | - Asad Ur Rehman
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68108, USA
| | - Mohd Ali Abbas Zaidi
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68108, USA
| | - Parvez Khan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68108, USA
| | - Shailendra K Gautam
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68108, USA
| | | | - Jawed Akhtar Siddiqui
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68108, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68108, USA
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68108, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68108, USA; Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Mohd Wasim Nasser
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68108, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68108, USA.
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Sun H, Cao X, Sumayya, Ma Y, Li H, Han W, Qu L. Genome-wide transcriptional profiling and functional analysis of long noncoding RNAs and mRNAs in chicken macrophages associated with the infection of avian pathogenic E. coli. BMC Vet Res 2024; 20:49. [PMID: 38326918 PMCID: PMC10848384 DOI: 10.1186/s12917-024-03890-7] [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: 08/10/2023] [Accepted: 01/18/2024] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND Avian pathogenic E. coli (APEC) can cause localized or systemic infections, collectively known as avian colibacillosis, resulting in huge economic losses to poultry industry globally per year. In addition, increasing evidence indicates that long non-coding RNAs (lncRNAs) play a critical role in regulating host inflammation in response to bacterial infection. However, the role of lncRNAs in the host response to APEC infection remains unclear. RESULTS Here, we found 816 differentially expressed (DE) lncRNAs and 1,798 DE mRNAs in APEC infected chicken macrophages by RNAseq. The identified DE lncRNA-mRNAs were involved in Toll like receptor signaling pathway, VEGF signaling pathway, fatty acid metabolism, phosphatidylinositol signaling system, and other types of O-glycan biosynthesis. Furthermore, we found the novel lncRNA TCONS_00007391 as an important immune regulator in APEC infection was able to regulate the inflammatory response by directly targeting CD86. CONCLUSION These findings provided a better understanding of host response to APEC infection and also offered the potential drug targets for therapy development against APEC infection.
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Affiliation(s)
- Hongyan Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
| | - Xinqi Cao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Sumayya
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Yuyi Ma
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Huan Li
- School of Biological and Chemical Engineering, Yangzhou Polytechnic College, Yangzhou, 225009, China
| | - Wei Han
- The Poultry Research Institute of Chinese Academy of Agricultural Sciences, Yangzhou, 225009, China
| | - Lujiang Qu
- College of Animal Science and Technology, China Agricultural University, Beijing, 100091, China
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Dai Y, Gao X, Zhang S, Li F, Zhang H, Li G, Sun R, Zhang S, Hou X. Exploring the Regulatory Dynamics of BrFLC-Associated lncRNA in Modulating the Flowering Response of Chinese Cabbage. Int J Mol Sci 2024; 25:1924. [PMID: 38339202 PMCID: PMC10856242 DOI: 10.3390/ijms25031924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 01/28/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024] Open
Abstract
Vernalization plays a crucial role in the flowering and yield of Chinese cabbage, a process intricately influenced by long non-coding RNAs (lncRNAs). Our research focused on lncFLC1, lncFLC2a, and lncFLC2b, which emerged as key players in this process. These lncRNAs exhibited an inverse expression pattern to the flowering repressor genes FLOWERING LOCUS C 1 (BrFLC1) and FLOWERING LOCUS C 2 (BrFLC2) during vernalization, suggesting a complex regulatory mechanism. Notably, their expression in the shoot apex and leaves was confirmed through in fluorescent in situ hybridization (FISH). Furthermore, when these lncRNAs were overexpressed in Arabidopsis, a noticeable acceleration in flowering was observed, unveiling functional similarities to Arabidopsis's COLD ASSISTED INTRONIC NONCODING RNA (COOLAIR). This resemblance suggests a potentially conserved regulatory mechanism across species. This study not only enhances our understanding of lncRNAs in flowering regulation, but also opens up new possibilities for their application in agricultural practices.
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Affiliation(s)
- Yun Dai
- National Key Laboratory of Crop Genetics & Germplasm Innovation and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China;
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.G.); (S.Z.); (F.L.); (H.Z.); (G.L.); (R.S.)
| | - Xinyu Gao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.G.); (S.Z.); (F.L.); (H.Z.); (G.L.); (R.S.)
| | - Shifan Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.G.); (S.Z.); (F.L.); (H.Z.); (G.L.); (R.S.)
| | - Fei Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.G.); (S.Z.); (F.L.); (H.Z.); (G.L.); (R.S.)
| | - Hui Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.G.); (S.Z.); (F.L.); (H.Z.); (G.L.); (R.S.)
| | - Guoliang Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.G.); (S.Z.); (F.L.); (H.Z.); (G.L.); (R.S.)
| | - Rifei Sun
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.G.); (S.Z.); (F.L.); (H.Z.); (G.L.); (R.S.)
| | - Shujiang Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.G.); (S.Z.); (F.L.); (H.Z.); (G.L.); (R.S.)
| | - Xilin Hou
- National Key Laboratory of Crop Genetics & Germplasm Innovation and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China;
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Yang R, Fu Y, Li C, Chen Y, He A, Jiang X, Ma J, Zhang T. Profiling of Long Non-Coding RNAs in Auricular Cartilage of Patients with Isolated Microtia. Genet Test Mol Biomarkers 2024; 28:50-58. [PMID: 38416666 DOI: 10.1089/gtmb.2023.0360] [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: 03/01/2024] Open
Abstract
Introduction: Microtia is the second most common maxillofacial birth defect worldwide. However, the involvement of long non-coding RNAs (lncRNAs) in isolated microtia is not well understood. This study aimed at identifying lncRNAs that regulate the expression of genes associated with isolated microtia. Methods: We used our microarray data to analyze the expression pattern of lncRNA in the auricular cartilage tissues from 10 patients diagnosed with isolated microtia, alongside 15 control subjects. Five lncRNAs were chosen for validation using real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Results: We identified 4651 differentially expressed lncRNAs in the auricular cartilage from patients with isolated microtia. By Gene Ontology/Kyoto Encyclopedia of Genes and Genomes pathway (GO/KEGG) analysis, we identified 27 differentially expressed genes enriched in pathways associated with microtia. In addition, we predicted 9 differentially expressed genes as potential cis-acting targets of 12 differentially expressed lncRNAs. Our findings by qRT-PCR demonstrate significantly elevated expression levels of ZFAS1 and DAB1-AS1, whereas ADIRF-AS1, HOTAIRM1, and EPB41L4A-AS1 exhibited significantly reduced expression levels in the auricular cartilage tissues of patients with isolated microtia. Conclusions: Our study sheds light on the potential involvement of lncRNAs in microtia and provides a basis for further investigation into their functional roles and underlying mechanisms.
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Affiliation(s)
- Run Yang
- Department of Facial Plastic and Reconstructive Surgery, ENT Institute, Eye & ENT Hospital of Fudan University, Shanghai, China
| | - Yaoyao Fu
- Department of Facial Plastic and Reconstructive Surgery, ENT Institute, Eye & ENT Hospital of Fudan University, Shanghai, China
| | - Chenlong Li
- Department of Facial Plastic and Reconstructive Surgery, ENT Institute, Eye & ENT Hospital of Fudan University, Shanghai, China
| | - Yin Chen
- Department of Facial Plastic and Reconstructive Surgery, ENT Institute, Eye & ENT Hospital of Fudan University, Shanghai, China
| | - Aijuan He
- Department of Facial Plastic and Reconstructive Surgery, ENT Institute, Eye & ENT Hospital of Fudan University, Shanghai, China
| | - Xin Jiang
- Medical Laboratory of Nantong Zhongke, Department of Bioinformatics, Nantong, Jiangsu, China
| | - Jing Ma
- Department of Facial Plastic and Reconstructive Surgery, ENT Institute, Eye & ENT Hospital of Fudan University, Shanghai, China
| | - Tianyu Zhang
- Department of Facial Plastic and Reconstructive Surgery, ENT Institute, Eye & ENT Hospital of Fudan University, Shanghai, China
- NHC Key Laboratory of Hearing Medicine, Fudan University, Shanghai, China
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Dadras N, Hasanpur K, Razeghi J, Kianianmomeni A. Different transcription of novel, functional long non-coding RNA genes by UV-B in green algae, Volvox carteri. Int Microbiol 2024; 27:213-225. [PMID: 37264144 DOI: 10.1007/s10123-023-00378-6] [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: 02/04/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 06/03/2023]
Abstract
Long non-coding RNAs (lncRNAs) are identified as important regulatory molecules related to diverse biological processes. In recent years, benefiting from the rapid development of high-throughput sequencing technology, RNA-seq, and analysis methods, more lncRNAs have been identified and discovered in various plant and algal species. However, so far, only limited studies related to algal lncRNAs are available. Volvox carteri f. nagariensis is the best multicellular model organism to study in developmental and evolutionary biology; therefore, studying and increasing information about this species is important. This study identified lncRNAs in the multicellular green algae Volvox carteri and 1457 lncRNAs were reported, using RNA-seq data and with the help of bioinformatics tools and software. This study investigated the effect of low-dose UV-B radiation on changes in the expression profile of lncRNAs in gonidial and somatic cells. The differential expression of lncRNAs was analyzed between the treatment (UV-B) and the control (WL) groups in gonidial and somatic cells. A total of 37 and 26 lncRNAs with significant differential expression in gonidial and somatic cells, respectively, were reported. Co-expression analysis between the lncRNAs and their neighbor protein-coding genes (in the interval of ± 10 Kb) was accomplished. In gonidial cells, 184 genes with a positive correlation and 13 genes with a negative correlation (greater than 0.95), and in somatic cells, 174 genes with a positive correlation, and 18 genes with a negative correlation were detected. Functional analysis of neighboring coding genes was also performed based on gene ontology. The results of the current work may help gain deeper insight into the regulation of gene expression in the studied model organism, Volvox carteri.
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Affiliation(s)
- Negin Dadras
- Department of Plant, Cellular and Molecular Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Karim Hasanpur
- Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran.
| | - Jafar Razeghi
- Department of Plant, Cellular and Molecular Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran.
| | - Arash Kianianmomeni
- Department of Cellular and Developmental Biology of Plants, Faculty of Natural Sciences, University of Bielefeld, Bielefeld, Germany
- CNSAC MedShop GmbH, Heinrich-Schneidmadl-Str. 15, 3100, St. Pölten, Austria
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Wang Y, Wang P, Wang Q, Chen S, Wang X, Zhong X, Hu W, Thorne RF, Han S, Wu M, Zhang L. The long noncoding RNA HNF1A-AS1 with dual functions in the regulation of cytochrome P450 3A4. Biochem Pharmacol 2024; 220:116016. [PMID: 38176619 DOI: 10.1016/j.bcp.2023.116016] [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: 10/25/2023] [Revised: 12/21/2023] [Accepted: 12/28/2023] [Indexed: 01/06/2024]
Abstract
Cytochrome P450 3A4 (CYP3A4) is the most important and abundant drug-metabolizing enzyme in the human liver. Inter-individual differences in the expression and activity of CYP3A4 affect clinical and precision medicine. Increasing evidence indicates that long noncoding RNAs (lncRNAs) play crucial roles in the regulation of CYP3A4 expression. Here, we showed that lncRNA hepatocyte nuclear factor 1 alpha-antisense 1 (HNF1A-AS1) exerted dual functions in regulating CYP3A4 expression in Huh7 and HepG2 cells. Mechanistically, HNF1A-AS1 served as an RNA scaffold to interact with both protein arginine methyltransferase 1 and pregnane X receptor (PXR), thereby facilitating their protein interactions and resulting in the transactivation of PXR and transcriptional alteration of CYP3A4 via histone modifications. Furthermore, HNF1A-AS1 bound to the HNF1A protein, a liver-specific transcription factor, thereby blocking its interaction with the E3 ubiquitin ligase tripartite motif containing 25, ultimately preventing HNF1A ubiquitination and protein degradation, further regulating the expression of CYP3A4. In summary, these results reveal the novel functions of HNF1A-AS1 as the transcriptional and post-translational regulator of CYP3A4; thus, HNF1A-AS1 may serve as a new indicator for establishing or predicting individual differences in CYP3A4 expression.
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Affiliation(s)
- Yiting Wang
- Department of Pharmacology, School of Basic Medical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, 450001 Zhengzhou, China; Department of Clinical Pharmacology, School of Medicine, Henan University of Chinese Medicine, 450046 Zhengzhou, China
| | - Pei Wang
- Department of Pharmacology, School of Basic Medical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, 450001 Zhengzhou, China
| | - Qi Wang
- Department of Pharmacology, School of Basic Medical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, 450001 Zhengzhou, China
| | - Shitong Chen
- Department of Pharmacology, School of Basic Medical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, 450001 Zhengzhou, China
| | - Xiaofei Wang
- Department of Pharmacology, School of Basic Medical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, 450001 Zhengzhou, China
| | - Xiaobo Zhong
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, 06269 Storrs, CT, USA
| | - Wanglai Hu
- Translational Research Institute, Zhengzhou University People's Hospital, Academy of Medical Science, Zhengzhou University, 450003 Zhengzhou, China
| | - Rick F Thorne
- Translational Research Institute, Zhengzhou University People's Hospital, Academy of Medical Science, Zhengzhou University, 450003 Zhengzhou, China
| | - Shengna Han
- Department of Pharmacology, School of Basic Medical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, 450001 Zhengzhou, China.
| | - Mian Wu
- Translational Research Institute, Zhengzhou University People's Hospital, Academy of Medical Science, Zhengzhou University, 450003 Zhengzhou, China.
| | - Lirong Zhang
- Department of Pharmacology, School of Basic Medical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, 450001 Zhengzhou, China.
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Wang J, Jia Q, Jiang S, Lu W, Ning H. POU6F1 promotes ferroptosis by increasing lncRNA-CASC2 transcription to regulate SOCS2/SLC7A11 signaling in gastric cancer. Cell Biol Toxicol 2024; 40:3. [PMID: 38267746 PMCID: PMC10808632 DOI: 10.1007/s10565-024-09843-y] [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: 08/18/2023] [Accepted: 11/22/2023] [Indexed: 01/26/2024]
Abstract
OBJECTIVE This study investigated the effect and mechanism of POU6F1 and lncRNA-CASC2 on ferroptosis of gastric cancer (GC) cells. METHODS GC cells treated with erastin and RSL3 were detected for ferroptosis, reactive oxygen species (ROS) level, and cell viability. The expression levels of POU6F1, lncRNA-CASC2, SOCS2, and ferroptosis-related molecules (GPX4 and SLC7A11) were also measured. The regulations among POU6F1, lncRNA-CASC2, FMR1, SOCS2, and SLC7A11 were determined. Subcutaneous tumor models were established, in which the expressions of Ki-67, SOCS2, and GPX4 were detected by immunohistochemistry. RESULTS GC patients with decreased expressions of POU6F1 and lncRNA-CASC2 had lower survival rate. Overexpression of POU6F1 or lncRNA-CASC2 decreased cell proliferation and GSH levels in GC cells, in addition to increasing total iron, Fe2+, MDA, and ROS levels. POU6F1 directly binds to the lncRNA-CASC2 promoter to promote its transcription. LncRNA-CASC2 can target FMR1 and increase SOCS2 mRNA stability to promote SLC7A11 ubiquitination degradation and activate ferroptosis signaling. Knockdown of SOCS2 inhibited the ferroptosis sensitivity of GC cells and reversed the effects of POU6F1 and lncRNA-CASC2 overexpression on ferroptosis in GC cells. CONCLUSION Transcription factor POU6F1 binds directly to the lncRNA-CASC2 promoter to promote its expression, while upregulated lncRNA-CASC2 increases SOCS2 stability and expression by targeting FMR1, thereby inhibiting SLC7A11 signaling to promote ferroptosis in GC cells and inhibit GC progression.
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Affiliation(s)
- Jingyun Wang
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, No.1 Jianshe East Road, Erqi District, Zhengzhou, Henan, 450000, People's Republic of China
| | - Qiaoyu Jia
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, No.1 Jianshe East Road, Erqi District, Zhengzhou, Henan, 450000, People's Republic of China
| | - Shuqin Jiang
- Department of Child Development and Behavior, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450000, People's Republic of China
| | - Wenquan Lu
- Department of Gastroenterology, The Second Affiliated Hospital of Zhengzhou University, No.2 JingBa Road, Jinshui District, Zhengzhou, Henan, 450014, People's Republic of China
| | - Hanbing Ning
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, No.1 Jianshe East Road, Erqi District, Zhengzhou, Henan, 450000, People's Republic of China.
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Yu X, Qian F, Zhang X, Zhu Y, He G, Yang J, Wu X, Zhou Y, Shen L, Shi X, Zhang H, Liu X. Promotion effect of FOXCUT as a microRNA sponge for miR-24-3p on progression in triple-negative breast cancer through the p38 MAPK signaling pathway. Chin Med J (Engl) 2024; 137:105-114. [PMID: 38178324 PMCID: PMC10766298 DOI: 10.1097/cm9.0000000000002700] [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: 12/12/2022] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) is a type of highly invasive breast cancer with a poor prognosis. According to new research, long noncoding RNAs (lncRNAs) play a significant role in the progression of cancer. Although the role of lncRNAs in breast cancer has been well reported, few studies have focused on TNBC. This study aimed to explore the biological function and clinical significance of forkhead box C1 promoter upstream transcript (FOXCUT) in triple-negative breast cancer. METHODS Based on a bioinformatic analysis of the cancer genome atlas (TCGA) database, we detected that the lncRNA FOXCUT was overexpressed in TNBC tissues, which was further validated in an external cohort of tissues from the General Surgery Department of the First Affiliated Hospital of Nanjing Medical University. The functions of FOXCUT in proliferation, migration, and invasion were detected in vitro or in vivo. Luciferase assays and RNA immunoprecipitation (RIP) were performed to reveal that FOXCUT acted as a competitive endogenous RNA (ceRNA) for the microRNA miR-24-3p and consequently inhibited the degradation of p38. RESULTS lncRNA FOXCUT was markedly highly expressed in breast cancer, which was associated with poor prognosis in some cases. Knockdown of FOXCUT significantly inhibited cancer growth and metastasis in vitro or in vivo. Mechanistically, FOXCUT competitively bounded to miR-24-3p to prevent the degradation of p38, which might act as an oncogene in breast cancer. CONCLUSION Collectively, this research revealed a novel FOXCUT/miR-24-3p/p38 axis that affected breast cancer progression and suggested that the lncRNA FOXCUT could be a diagnostic marker and therapeutic target for breast cancer.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Xiao'an Liu
- Department of Breast Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
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Reis RSD, Wagner MCE, McKenna S, Ayyavoo V. Neuroinflammation driven by Human Immunodeficiency Virus-1 (HIV-1) directs the expression of long noncoding RNA RP11-677M14.2 resulting in dysregulation of Neurogranin in vivo and in vitro. RESEARCH SQUARE 2024:rs.3.rs-3810214. [PMID: 38260270 PMCID: PMC10802713 DOI: 10.21203/rs.3.rs-3810214/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Neuroinflammation and synaptodendritic damage represent the pathological hallmarks of HIV-1 associated cognitive disorders (HAND). The post-synaptic protein neurogranin (Nrgn) is significantly reduced in the frontal cortex of postmortem brains from people with HIV (PWH) and it is associated with inflammatory factors released by infected microglia/macrophages. However, the mechanism involved in synaptic loss have yet to be elucidated. In this study, we characterized a newly identified long non-coding RNA (lncRNA) transcript (RP11-677M14.2), which is antisense to the NRGN locus and is highly expressed in the frontal cortex of HIV-1 individuals. Further analysis indicates an inverse correlation between the expression of RP11-677M14.2 RNA and Nrgn mRNA. Additionally, the Nrgn-lncRNA axis is dysregulated in neurons exposed to HIV-1 infected microglia conditioned medium enriched with IL-1b. Moreover, in vitro overexpression of this lncRNA impact Nrgn expression at both mRNA and protein levels. Finally, we modeled the Nrgn-lncRNA dysregulation within an HIV-1-induced neuroinflammatory environment using brain organoids, thereby corroborating our in vivo and in vitro findings. Together, our study implicates a plausible role for lncRNA RP11-677M14.2 in modulating Nrgn expression that might serve as the mechanistic link between Nrgn loss and cognitive dysfunction in HAND, thus shedding new light on the mechanisms underlying synaptodendritic damage.
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