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Farkas D, Dobránszki J. Vegetal memory through the lens of transcriptomic changes - recent progress and future practical prospects for exploiting plant transcriptional memory. PLANT SIGNALING & BEHAVIOR 2024; 19:2383515. [PMID: 39077764 PMCID: PMC11290777 DOI: 10.1080/15592324.2024.2383515] [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: 06/11/2024] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 07/31/2024]
Abstract
Plant memory plays an important role in the efficient and rapid acclimation to a swiftly changing environment. In addition, since plant memory can be inherited, it is also of adaptive and evolutionary importance. The ability of a plant to store, retain, retrieve and delete information on acquired experience is based on cellular, biochemical and molecular networks in the plants. This review offers an up-to-date overview on the formation, types, checkpoints of plant memory based on our current knowledge and focusing on its transcriptional aspects, the transcriptional memory. Roles of long and small non-coding RNAs are summarized in the regulation, formation and the cooperation between the different layers of the plant memory, i.e. in the establishment of epigenetic changes associated with memory formation in plants. The RNA interference mechanisms at the RNA and DNA level and the interplays between them are also presented. Furthermore, this review gives an insight of how exploitation of plant transcriptional memory may provide new opportunities for elaborating promising cost-efficient, and effective strategies to cope with the ever-changing environmental perturbations, caused by climate change. The potentials of plant memory-based methods, such as crop priming, cross acclimatization, memory modification by miRNAs and associative use of plant memory, in the future's agriculture are also discussed.
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Affiliation(s)
- Dóra Farkas
- Centre for Agricultural Genomics and Biotechnology, Faculty of the Agricultural and Food Science and Environmental Management, University of Debrecen, Nyíregyháza, Hungary
| | - Judit Dobránszki
- Centre for Agricultural Genomics and Biotechnology, Faculty of the Agricultural and Food Science and Environmental Management, University of Debrecen, Nyíregyháza, Hungary
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2
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Guan J, Chen X, Li Z, Deng S, Wumaier A, Ma Y, Xie L, Huang S, Zhu Y, Zhuo Y. Role of N6-methyladenosine-related lncRnas in pseudoexfoliation glaucoma. Epigenetics 2024; 19:2348840. [PMID: 38716769 PMCID: PMC11086004 DOI: 10.1080/15592294.2024.2348840] [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: 12/03/2023] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
To explore the role of lncRNA m6A methylation modification in aqueous humour (AH) of patients with pseudoexfoliation glaucoma (PXG). Patients with open-angle PXG under surgery from June 2021 to December 2021 were selected. Age- and gender-matched patients with age-related cataract (ARC) were chosen as control. Patients underwent detailed ophthalmic examinations. 0.05-0.1 ml AH were extracted during surgery for MeRIP-Seq and RNA-Seq. Joint analysis was used to screen lncRNAs with differential m6A methylation modification and expression. Online software tools were used to draw lncRNA-miRNA-mRNA network (ceRNA). Expression of lncRNAs and mRNAs was confirmed using quantitative real-time PCR. A total of 4151 lncRNAs and 4386 associated m6A methylation modified peaks were identified in the PXG group. Similarly, 2490 lncRNAs and 2595 associated m6A methylation modified peaks were detected in the control. Compared to the ARC group, the PXG group had 234 hypermethylated and 402 hypomethylated m6A peaks, with statistically significant differences (| Fold Change (FC) |≥2, p < 0.05). Bioinformatic analysis revealed that these differentially methylated lncRNA enriched in extracellular matrix formation, tight adhesion, TGF- β signalling pathway, AMPK signalling pathway, and MAPK signalling pathway. Joint analysis identified 10 lncRNAs with differential m6A methylation and expression simultaneously. Among them, the expression of ENST000000485383 and ROCK1 were confirmed downregulated in the PXG group by RT-qPCR. m6A methylation modification may affect the expression of lncRNA and participate in the pathogenesis of PXG through the ceRNA network. ENST000000485383-hsa miR592-ROCK1 May be a potential target pathway for further investigation in PXG m6A methylation.
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Affiliation(s)
- Jieying Guan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, World Health Organization Collaborating Center for Eye Care and Vision, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
- Research Centre of Basic Integrative Medicine, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaohong Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, World Health Organization Collaborating Center for Eye Care and Vision, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
| | - Zhidong Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, World Health Organization Collaborating Center for Eye Care and Vision, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
| | - Shuifeng Deng
- The Department of Ophthalmology, Huizhou Hospital Affiliated to Guangzhou Medical University (Huizhou Third People’s Hospital), Huizhou, China
| | - Aizezi Wumaier
- The Affiliated Kashi Hospital, Sun Yat-sen University, Kashi, Xinjiang, China
- The First Department of Ophthalmology, The First People’s Hospital of Kashi Prefecture, Kashi, Xinjiang, China
| | - Yuncheng Ma
- The Affiliated Kashi Hospital, Sun Yat-sen University, Kashi, Xinjiang, China
- The First Department of Ophthalmology, The First People’s Hospital of Kashi Prefecture, Kashi, Xinjiang, China
| | - Lingling Xie
- The Affiliated Kashi Hospital, Sun Yat-sen University, Kashi, Xinjiang, China
- The First Department of Ophthalmology, The First People’s Hospital of Kashi Prefecture, Kashi, Xinjiang, China
| | - Shengsong Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, World Health Organization Collaborating Center for Eye Care and Vision, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
| | - Yingting Zhu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, World Health Organization Collaborating Center for Eye Care and Vision, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
| | - Yehong Zhuo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, World Health Organization Collaborating Center for Eye Care and Vision, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
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Chen S, Han J, Wu S, Guo S, Tang Y, Zheng Y, Hu L, Zhang X, Zhang P, Zhang H, Ren G, Gao S. From non-coding RNAs to histone modification: The epigenetic mechanisms in tomato fruit ripening and quality regulation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 215:109070. [PMID: 39191041 DOI: 10.1016/j.plaphy.2024.109070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/28/2024] [Accepted: 08/22/2024] [Indexed: 08/29/2024]
Abstract
Ripening is one of the most important stages of fruit development and determines the fruit quality. Various factors play a role in this process, with epigenetic mechanisms emerging as important players. Epigenetic regulation encompasses DNA methylation, histone modifications and variants, chromatin remodeling, RNA modifications, and non-coding RNAs. Over the past decade, studies using tomato as a model have made considerable progress in understanding the impact of epigenetic regulation on fleshy fruit ripening and quality. In this paper, we provide an overview of recent advancements in the epigenetic regulation of tomato fruit ripening and quality regulation, focusing on three main mechanisms: DNA/RNA modifications, non-coding RNAs, and histone modifications. Furthermore, we highlight the unresolved issues and challenges within this research field, offering perspectives for future investigations to drive agricultural innovation.
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Affiliation(s)
- Shengbo Chen
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Jiazhen Han
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Shu Wu
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Shangjing Guo
- Qingdao Agricultural University, Qingdao, 266109, China
| | - Yufei Tang
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Yujing Zheng
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Lei Hu
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Xingxing Zhang
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Peng Zhang
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | | | - Guodong Ren
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| | - Shuai Gao
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China.
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4
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Li Q, Liu Y, Li B, Zheng C, Yu B, Niu K, Qiao Y. Bioinformatics analysis of oxidative stress genes in the pathogenesis of ulcerative colitis based on a competing endogenous RNA regulatory network. PeerJ 2024; 12:e17213. [PMID: 39161963 PMCID: PMC11332386 DOI: 10.7717/peerj.17213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 03/19/2024] [Indexed: 08/21/2024] Open
Abstract
Background Ulcerative colitis (UC) is a common chronic disease associated with inflammation and oxidative stress. This study aimed to construct a long noncoding RNA (lncRNA)-microRNA (miRNA)-messenger RNA (mRNA) network based on bioinformatics analysis and to explore oxidative stress-related genes underlying the pathogenesis of UC. Methods The GSE75214, GSE48959, and GSE114603 datasets were downloaded from the Gene Expression Omnibus database. Following differentially expressed (DE) analysis, the regulatory relationships among these DERNAs were identified through miRDB, miRTarBase, and TargetScan; then, the lncRNA-miRNA-mRNA network was established. The Molecular Signatures Database (MSigDB) was used to search oxidative stress-related genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed for functional annotation and enrichment analyses. Based on the drug gene interaction database DGIdb, drugs that interact with oxidative stress-associated genes were explored. A dextran sulfate sodium (DSS)-induced UC mouse model was used for experimental validation. Results A total of 30 DE-lncRNAs, 3 DE-miRNAs, and 19 DE-mRNAs were used to construct a lncRNA-miRNA-mRNA network. By comparing these 19 DE-mRNAs with oxidative stress-related genes in MSigDB, three oxidative stress-related genes (CAV1, SLC7A11, and SLC7A5) were found in the 19 DEM sets, which were all negatively associated with miR-194. GO and KEGG analyses showed that CAV1, SLC7A11, and SLC7A5 were associated with immune inflammation and steroid hormone synthesis. In animal experiments, the results showed that dexamethasone, a well-known glucocorticoid drug, could significantly decrease the expression of CAV1, SLC7A11, and SLC7A5 as well as improve UC histology, restore antioxidant activities, inhibit inflammation, and decrease myeloperoxidase activity. Conclusion SLC7A5 was identified as a representative gene associated with glucocorticoid therapy resistance and thus may be a new therapeutic target for the treatment of UC in the clinic.
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MESH Headings
- Animals
- Humans
- Mice
- Colitis, Ulcerative/genetics
- Colitis, Ulcerative/metabolism
- Colitis, Ulcerative/chemically induced
- Computational Biology
- Databases, Genetic
- Dextran Sulfate/toxicity
- Disease Models, Animal
- Gene Expression Profiling
- Gene Regulatory Networks/drug effects
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Oxidative Stress/genetics
- Oxidative Stress/drug effects
- RNA, Competitive Endogenous/genetics
- RNA, Competitive Endogenous/metabolism
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
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Affiliation(s)
- Qifang Li
- Department of Traditional Chinese Medicine, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Yuan Liu
- College of Integrated Chinese and Western Medicine, Jining Medical University, Jining, Shandong, China
| | - Bingbing Li
- College of Integrated Chinese and Western Medicine, Jining Medical University, Jining, Shandong, China
| | - Canlei Zheng
- College of Integrated Chinese and Western Medicine, Jining Medical University, Jining, Shandong, China
| | - Bin Yu
- College of Integrated Chinese and Western Medicine, Jining Medical University, Jining, Shandong, China
| | - Kai Niu
- College of Integrated Chinese and Western Medicine, Jining Medical University, Jining, Shandong, China
| | - Yi Qiao
- School of Public Health, Jining Medical University, Jining, Shandong, China
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Abida, Eltaib L, Alhazmi BH, Alzahrani AR, Asdaq SMB, Ali A, Aldhafiri FJ, Alruwaili WT, Al-Hajeili M, Abdulkhaliq AA, Rabaan AA, Imran M. Long non-coding RNA HOTAIR: A biomarker and therapeutic target in urological tumors. Pathol Res Pract 2024; 262:155549. [PMID: 39173467 DOI: 10.1016/j.prp.2024.155549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Revised: 08/12/2024] [Accepted: 08/14/2024] [Indexed: 08/24/2024]
Abstract
Long non-coding RNAs (lncRNAs) significantly influence gene regulation across epigenetic, transcriptional, and post-transcriptional levels through their interactions with DNA, RNA, and proteins. There is growing evidence of lncRNAs' critical roles in the emergence and progression of various diseases, including urological tumors (UTs), such as cancers of the kidney, bladder, and prostate. Research increasingly links lncRNA dysregulation to diverse cellular processes like invasion, metastasis, apoptosis, and chromatin remodeling. Among these, HOTAIR stands out for its pivotal role in oncogenesis, impacting treatment resistance, cell migration, proliferation, survival, and genomic integrity. This review provides an overview of HOTAIR's functions, its identification, and its biological significance. Furthermore, it delves into HOTAIR's involvement in UTs, underlining its potential as a therapeutic target and biomarker for innovative approaches to treating these cancers.
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Affiliation(s)
- Abida
- Department of Pharmaceutical Chemistry, College of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
| | - Lina Eltaib
- Department of Pharmaceutics, College of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
| | - Bshayer Hmdan Alhazmi
- Department of Pharmacy, Northern Area Armed Forces Hospital, Hafer Al-batin 39745, Saudi Arabia
| | - Abdullah R Alzahrani
- Department of Pharmacology and Toxicology, Faculty of Medicine, Umm Al-Qura University, Al-Abidiyah, P.O. Box 13578, Makkah 21955, Saudi Arabia
| | | | - Abuzer Ali
- Department of Pharmacognosy, College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | | | - Wafaa T Alruwaili
- College of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
| | - Marwan Al-Hajeili
- Department of Medicine, King Abdulaziz University, Jeddah 23624, Saudi Arabia
| | - Altaf A Abdulkhaliq
- Department of Biochemistry, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
| | - Mohd Imran
- Department of Pharmaceutical Chemistry, College of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia; Center for Health Research, Northern Border University, Arar, Saudi Arabia.
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6
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Nie L, Wang X, Wang S, Hong Z, Wang M. Genetic insights into the complexity of premature ovarian insufficiency. Reprod Biol Endocrinol 2024; 22:94. [PMID: 39095891 PMCID: PMC11295921 DOI: 10.1186/s12958-024-01254-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 06/29/2024] [Indexed: 08/04/2024] Open
Abstract
Premature Ovarian Insufficiency (POI) is a highly heterogeneous condition characterized by ovarian dysfunction in women occurring before the age of 40, representing a significant cause of female infertility. It manifests through primary or secondary amenorrhea. While more than half of POI cases are idiopathic, genetic factors play a pivotal role in all instances with known causes, contributing to approximately 20-25% of cases. This article comprehensively reviews the genetic factors associated with POI, delineating the primary candidate genes. The discussion delves into the intricate relationship between these genes and ovarian development, elucidating the functional consequences of diverse mutations to underscore the fundamental impact of genetic effects on POI. The identified genetic factors, encompassing gene mutations and chromosomal abnormalities, are systematically classified based on whether the resulting POI is syndromic or non-syndromic. Furthermore, this paper explores the genetic interplay between mitochondrial genes, such as Required for Meiotic Nuclear Division 1 homolog Gene (RMND1), Mitochondrial Ribosomal Protein S22 Gene (MRPS22), Leucine-rich Pentapeptide Repeat Gene (LRPPRC), and non-coding RNAs, including both microRNAs and Long non-coding RNAs, with POI. The insights provided serve to consolidate and enhance our understanding of the etiology of POI, contributing to establishing a theoretical foundation for diagnosing and treating POI patients, as well as for exploring the mechanisms underlying the disease.
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Affiliation(s)
- Linhang Nie
- Center for Reproductive Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, P.R. China
- WuHan University TaiKang Medical School (School of Basic Medical Sciences), Wuhan, Hubei, P.R. China
| | - Xiaojie Wang
- Center for Reproductive Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, P.R. China
- Second Clinical Hospital of WuHan University, Wuhan, Hubei, P.R. China
| | - Songyuan Wang
- Center for Reproductive Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, P.R. China
- WuHan University TaiKang Medical School (School of Basic Medical Sciences), Wuhan, Hubei, P.R. China
| | - Zhidan Hong
- Center for Reproductive Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, P.R. China.
- Clinical Medicine Research Center of Prenatal Diagnosis and Birth Health in Hubei Province, Wuhan, Hubei, P.R. China.
- Wuhan Clinical Research Center for Reproductive Science and Birth Health, Wuhan, Hubei, P.R. China.
| | - Mei Wang
- Center for Reproductive Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, P.R. China.
- Clinical Medicine Research Center of Prenatal Diagnosis and Birth Health in Hubei Province, Wuhan, Hubei, P.R. China.
- Wuhan Clinical Research Center for Reproductive Science and Birth Health, Wuhan, Hubei, P.R. China.
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Feng K, Zhou S, Sheng Y, Lu K, Li C, Liu W, Kong H, Liu H, Mu Y, Zhang L, Zhang Q, Wang J. Disulfidptosis-Related LncRNA Signatures for Prognostic Prediction in Kidney Renal Clear Cell Carcinoma. Clin Genitourin Cancer 2024; 22:102095. [PMID: 38833825 DOI: 10.1016/j.clgc.2024.102095] [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: 02/16/2024] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 06/06/2024]
Abstract
INTRODUCTION BACKGROUND Disulfidptosis is a prevalent apoptotic mechanism, intrinsically linked to cancer prognosis. However, the specific involvement of disulfidptosis-related long non-coding RNA (DRLncRNAs) in Kidney renal clear cell carcinoma (KIRC) remains incompletely understood. This study aims to elucidate the potential prognostic significance of disulfidptosis-related LncRNAs in KIRC. MATERIALS AND METHODS Expression profiles and clinical data of KIRC patients were retrieved from the TCGA database to discern differentially expressed DRLncRNAs correlated with overall survival. Cox univariate analysis, Lasso Regression, and Cox multivariate analysis were used to construct a clinical prediction model. RESULTS Six signatures, namely FAM83C.AS1, AC136475.2, AC121338.2, AC026401.3, AC254562.3, and AC000050.2, were established to evaluate overall survival (OS) in the context of Kidney renal clear cell carcinoma (KIRC) in this study. Survival analysis and ROC curves demonstrated the strong predictive performance of the associated signature. The nomogram exhibited accurate prognostic predictions for overall patient survival, offering substantial clinical utility. Gene set enrichment analysis revealed that risk signals were enriched in various immune-related pathways. Furthermore, the risk features exhibited significant correlations with immune cells, immune function, immune cell infiltration, and immune checkpoints. CONCLUSION This study has unveiled, for the first time, six disulfdptosis-related LncRNA signatures, laying a solid foundation for enhanced and precise prognostic predictions in KIRC.
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Affiliation(s)
- Kunlun Feng
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Shanshan Zhou
- Dongying People's Hospital (Dongying Hospital of Shandong Provincial Hospital Group), Dongying, Shandong, China
| | - Yawen Sheng
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Ke Lu
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Chenghua Li
- International Office, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Wenhui Liu
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Hui Kong
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Haoxiang Liu
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Yu Mu
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Lu Zhang
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China.
| | - Qingxiang Zhang
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China.
| | - Jingwen Wang
- The second affiliated hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China.
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8
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Cui Y, Xiao Q, Zhang Q, Yang J, Liu Y, Hao W, Jiang J, Meng Q, Wei X. 1,2-bis(2,4,6-tribromophenoxy) ethane induces necroptosis via the co-competition of GAS5 and NUAK1 for miR-743a-5p in rat hepatocytes. JOURNAL OF HAZARDOUS MATERIALS 2024; 478:135375. [PMID: 39141942 DOI: 10.1016/j.jhazmat.2024.135375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 07/15/2024] [Accepted: 07/27/2024] [Indexed: 08/16/2024]
Abstract
The brominated flame retardant 1,2-bis(2,4,6-tribromophenoxy) ethane (BTBPE) widely used in manufacturing is inevitably released into the environment, resulting in the exposure of organisms to BTBPE. Therefore, it is particularly important to explore its toxic mechanism. The liver is one of the main accumulating organs of BTBPE, but the mechanism underlying BTBPE hepatotoxicity has not been thoroughly investigated. In our study, BTBPE was administered to Sprague-Dawley (SD) rats and rat hepatocytes (BRL cells) in vivo and in vitro, respectively, and HE staining, AO/EB staining, fluorescent probes, qPCR, immunofluorescence, and dual-luciferase reporter assays were performed. We investigated the mechanism of action of growth arrest-specific 5 (GAS5), miR-743a-5p, and NUAK family kinase 1 (NUAK1) in BTBPE-induced necroptosis from the perspective of competing endogenous RNAs (ceRNAs) using NUAK1 inhibitors, siRNAs, mimics, and overexpression plasmids. Our study showed that exposure to BTBPE caused necroptosis in the liver and BRL cells, accompanied by an oxidation-reduction imbalance and an inflammatory response. It is worth noting that NUAK1 is a newly discovered upstream regulatory target for necroptosis. In addition, miR-743a-5p was shown to inhibit necroptosis by targeting NUAK1 and down-regulating NUAK1. GAS5 upregulates NUAK1 expression by competitively binding to miR-743a-5p, thereby inducing necroptosis. This study demonstrated, for the first time, that the GAS5-miR-743a-5p-NUAK1 axis is involved in the regulation of necroptosis via ceRNAs. Thus, GAS5 and NUAK1 induce necroptosis by competitively binding to miR-743a-5p.
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Affiliation(s)
- Yuan Cui
- Department of Toxicology, School of Public Health, Peking University, Beijing 100191, PR China; Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, Beijing 100191, PR China
| | - Qianqian Xiao
- Department of Toxicology, School of Public Health, Peking University, Beijing 100191, PR China; Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, Beijing 100191, PR China
| | - Qiong Zhang
- Department of Toxicology, School of Public Health, Peking University, Beijing 100191, PR China; Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, Beijing 100191, PR China
| | - Jiawei Yang
- Department of Toxicology, School of Public Health, Peking University, Beijing 100191, PR China; Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, Beijing 100191, PR China
| | - Yuetong Liu
- Department of Toxicology, School of Public Health, Peking University, Beijing 100191, PR China; Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, Beijing 100191, PR China
| | - Weidong Hao
- Department of Toxicology, School of Public Health, Peking University, Beijing 100191, PR China; Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, Beijing 100191, PR China
| | - Jianjun Jiang
- Department of Toxicology, School of Public Health, Peking University, Beijing 100191, PR China; Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, Beijing 100191, PR China
| | - Qinghe Meng
- Department of Toxicology, School of Public Health, Peking University, Beijing 100191, PR China; Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, Beijing 100191, PR China
| | - Xuetao Wei
- Department of Toxicology, School of Public Health, Peking University, Beijing 100191, PR China; Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, Beijing 100191, PR China.
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9
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Wang Y, Li D, Xun J, Wu Y, Wang HL. Construction of prognostic markers for gastric cancer and comprehensive analysis of pyroptosis-related long non-coding RNAs. World J Gastrointest Surg 2024; 16:2281-2295. [PMID: 39087128 PMCID: PMC11287702 DOI: 10.4240/wjgs.v16.i7.2281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/22/2024] [Accepted: 06/14/2024] [Indexed: 07/22/2024] Open
Abstract
BACKGROUND China's most frequent malignancy is gastric cancer (GC), which has a very poor survival rate, and the survival rate for patients with advanced GC is dismal. Pyroptosis has been connected to the genesis and development of cancer. The function of pyroptosis-related long non-coding RNAs (PRLs) in GC, on the other hand, remains uncertain. AIM To explore the construction and comprehensive analysis of the prognostic characteristics of long non-coding RNA (lncRNA) related to pyroptosis in GC patients. METHODS The TCGA database provided us with 352 stomach adenocarcinoma samples, and we obtained 28 pyroptotic genes from the Reactome database. We examined the correlation between lncRNAs and pyroptosis using the Pearson correlation coefficient. Prognosis-related PRLs were identified through univariate Cox analysis. A predictive signature was constructed using stepwise Cox regression analysis, and its reliability and independence were assessed. To facilitate clinical application, a nomogram was created based on this signature. we analyzed differences in immune cell infiltration, immune function, and checkpoints between the high-risk group (HRG) and low-risk group (LRG). RESULTS Five hundred and twenty-three PRLs were screened from all lncRNAs (absolute correlation coefficient > 0.4, P < 0.05). Nine PRLs were included in the risk prediction signature that was created through stepwise Cox regression analysis. We determined the risk score for GC patients and employed the median value as the dividing line between HRG and LRG. The ability of the risk signature to predict the overall survival (OS) of GC is demonstrated by the Kaplan-Meier analysis, risk curve, receiver operating characteristic curve, and decision curve analysis curve. The risk signature was shown to be an independent prognostic factor for OS in both univariate and multivariate Cox regression analyses. HRG showed a more efficient local immune response or modulation compared to LRG, as indicated by the predicted signal pathway analysis and examination of immune cell infiltration, function, and checkpoints (P < 0.05). CONCLUSION In general, we have created a brand-new prognostic signature using PRLs, which may provide ideas for immunotherapy in patients with GC.
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Affiliation(s)
- Yu Wang
- Department of Gastrointestinal Surgery, Hospital of Integrated Chinese and Western Medicine, Tianjin University, Tianjin 300100, China
| | - Di Li
- Department of Gastrointestinal Surgery, Hospital of Integrated Chinese and Western Medicine, Tianjin University, Tianjin 300100, China
| | - Jing Xun
- Department of Gastrointestinal Surgery, Hospital of Integrated Chinese and Western Medicine, Tianjin University, Tianjin 300100, China
| | - Yu Wu
- Department of Gastrointestinal Surgery, Hospital of Integrated Chinese and Western Medicine, Tianjin University, Tianjin 300100, China
| | - Hong-Lei Wang
- Department of Gastrointestinal Surgery, Hospital of Integrated Chinese and Western Medicine, Tianjin University, Tianjin 300100, China
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10
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Rajabi D, Khanmohammadi S, Rezaei N. The role of long noncoding RNAs in amyotrophic lateral sclerosis. Rev Neurosci 2024; 35:533-547. [PMID: 38452377 DOI: 10.1515/revneuro-2023-0155] [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: 12/14/2023] [Accepted: 02/18/2024] [Indexed: 03/09/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease with a poor prognosis leading to death. The diagnosis and treatment of ALS are inherently challenging due to its complex pathomechanism. Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides involved in different cellular processes, incisively gene expression. In recent years, more studies have been conducted on lncRNA classes and interference in different disease pathologies, showing their promising contribution to diagnosing and treating neurodegenerative diseases. In this review, we discussed the role of lncRNAs like NEAT1 and C9orf72-as in ALS pathogenesis mechanisms caused by mutations in different genes, including TAR DNA-binding protein-43 (TDP-43), fused in sarcoma (FUS), superoxide dismutase type 1 (SOD1). NEAT1 is a well-established lncRNA in ALS pathogenesis; hence, we elaborate on its involvement in forming paraspeckles, stress response, inflammatory response, and apoptosis. Furthermore, antisense lncRNAs (as-lncRNAs), a key group of transcripts from the opposite strand of genes, including ZEB1-AS1 and ATXN2-AS, are discussed as newly identified components in the pathology of ALS. Ultimately, we review the current standing of using lncRNAs as biomarkers and therapeutic agents and the future vision of further studies on lncRNA applications.
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Affiliation(s)
- Darya Rajabi
- School of Medicine, Tehran University of Medical Sciences, Felestin St., Keshavarz Blvd., Tehran, 1416634793, Iran
| | - Shaghayegh Khanmohammadi
- School of Medicine, Tehran University of Medical Sciences, Felestin St., Keshavarz Blvd., Tehran, 1416634793, Iran
- Research Center for Immunodeficiencies, Children's Medical Center, No 63, Gharib Ave, Keshavarz Blv, Tehran, 1419733151, Iran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Children's Medical Center, No 63, Gharib Ave, Keshavarz Blv, Tehran, 1419733151, Iran
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical Center, No 63, Gharib Ave, Keshavarz Blv, Tehran, 1419733151, Iran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Children's Medical Center, No 63, Gharib Ave, Keshavarz Blv, Tehran, 1419733151, Iran
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Felestin St., Keshavarz Blvd., Tehran, 1416634793, Iran
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11
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Tapia A, Liu X, Malhi NK, Yuan D, Chen M, Southerland KW, Luo Y, Chen ZB. Role of long noncoding RNAs in diabetes-associated peripheral arterial disease. Cardiovasc Diabetol 2024; 23:274. [PMID: 39049097 PMCID: PMC11271017 DOI: 10.1186/s12933-024-02327-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 06/18/2024] [Indexed: 07/27/2024] Open
Abstract
Diabetes mellitus (DM) is a metabolic disease that heightens the risks of many vascular complications, including peripheral arterial disease (PAD). Various types of cells, including but not limited to endothelial cells (ECs), vascular smooth muscle cells (VSMCs), and macrophages (MΦs), play crucial roles in the pathogenesis of DM-PAD. Long non-coding RNAs (lncRNAs) are epigenetic regulators that play important roles in cellular function, and their dysregulation in DM can contribute to PAD. This review focuses on the developing field of lncRNAs and their emerging roles in linking DM and PAD. We review the studies investigating the role of lncRNAs in crucial cellular processes contributing to DM-PAD, including those in ECs, VSMCs, and MΦ. By examining the intricate molecular landscape governed by lncRNAs in these relevant cell types, we hope to shed light on the roles of lncRNAs in EC dysfunction, inflammatory responses, and vascular remodeling contributing to DM-PAD. Additionally, we provide an overview of the research approach and methodologies, from identifying disease-relevant lncRNAs to characterizing their molecular and cellular functions in the context of DM-PAD. We also discuss the potential of leveraging lncRNAs in the diagnosis and therapeutics for DM-PAD. Collectively, this review provides a summary of lncRNA-regulated cell functions contributing to DM-PAD and highlights the translational potential of leveraging lncRNA biology to tackle this increasingly prevalent and complex disease.
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Affiliation(s)
- Alonso Tapia
- Irell and Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA, 91010, USA
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA, USA
| | - Xuejing Liu
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA, USA
| | - Naseeb Kaur Malhi
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA, USA
| | - Dongqiang Yuan
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA, USA
| | - Muxi Chen
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA, USA
| | - Kevin W Southerland
- Division of Vascular and Endovascular Surgery, Department of Surgery, Duke University Medical Center, Durham, NC, 27710, USA
| | - Yingjun Luo
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA, USA
| | - Zhen Bouman Chen
- Irell and Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA, 91010, USA.
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA, USA.
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12
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Yang D, Li C, Kong Y, Pei Y, Miao B, Dai G, Ding P, Shi P, Wang Z, Pei R. Deciphering the Temporal-Spatial Interactive Heterogeneity of Long Non-Coding RNAs and RNA-Binding Proteins in Living Cells at Single-Cell Resolution. J Am Chem Soc 2024. [PMID: 39016781 DOI: 10.1021/jacs.4c05205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
The investigation of long noncoding RNAs (lncRNAs) and RNA binding proteins (RBPs) interactions in living cell holds great significance for elucidating their critical roles in a variety of biological activities, but limited techniques are available to profile the temporal-spatial dynamic heterogeneity. Here, we introduced a molecular beacon-functionalized nanoneedle array designed for spatially resolved profiling of lncRNA-RBP interactions (Nano-SpatiaLR). A nanoneedle array modified with a molecular beacon is employed to selectively isolate specific intracellular lncRNAs and their associated RBPs without affecting cell viability. The RBPs are then in situ analyzed with a fluorescent labeled antibody and colocalized with lncRNA signals to get a quantitative measurement of their dynamic interactions. Additionally, leveraging the spatial distribution and nanoscale modality of the nanoneedle array, this technique provides the spatial heterogeneity information on cellular lncRNA-RBPs interaction at single cell resolution. In this study, we tracked the temporal-spatial interactive heterogeneity dynamics of lncRNA-RBPs interaction within living cells across different biological progresses. Our findings demonstrated that the interactions between lncRNA HOTAIR and RBPs EZH2 and LSD1 undergo significant changes in response to drug treatments, particularly in tumor cells. Moreover, these interactions become more intensified as tumor cells aggregate during the proliferation process.
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Affiliation(s)
- Deyuan Yang
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory for Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Cheng Li
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory for Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Yutong Kong
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei 230026, China
- College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China
| | - Yian Pei
- CAS Key Laboratory for Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
- Duke Kunshan University Kunshan 215316, China
| | - Bing Miao
- Key Laboratory of Multifunctional Nanomaterials and Smart Systems, Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Gaole Dai
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Pi Ding
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory for Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Peng Shi
- Hong Kong Centre for Cerebro-Cardiovascular Health Engineering, Hong Kong Science Park, Shatin, Hong Kong 999077, China
- Department of Biomedical Engineering, City University of Hong Kong Kowloon, Shatin, Hong Kong 999077, China
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518000, China
| | - Zixun Wang
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory for Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Renjun Pei
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory for Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
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13
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Long F, Li X, Pan J, Ye H, Di C, Huang Y, Li J, Zhou X, Yi H, Huang Q, Si J. The role of lncRNA NEAT1 in human cancer chemoresistance. Cancer Cell Int 2024; 24:236. [PMID: 38970092 PMCID: PMC11227196 DOI: 10.1186/s12935-024-03426-x] [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: 04/03/2024] [Accepted: 07/01/2024] [Indexed: 07/07/2024] Open
Abstract
Chemotherapy is currently one of the most effective methods in clinical cancer treatment. However, chemotherapy resistance is an important reason for poor chemotherapy efficacy and prognosis, which has become an urgent problem to be solved in the field of cancer chemotherapy. Therefore, it is very important to deeply study and analyze the mechanism of cancer chemotherapy resistance and its regulatory factors. Long non-coding RNA nuclear paraspeckle assembly transcript 1 (LncRNA NEAT1) has been shown to be closely associated with chemotherapy resistance in cancer. NEAT1 induces cancer cell resistance to chemotherapeutic drugs by regulating cell apoptosis, cell cycle, drug transport and metabolism, DNA damage repair, EMT, autophagy, cancer stem cell characteristics, and metabolic reprogramming. This indicates that NEAT1 may be an important target to overcome chemotherapy resistance and is expected to be a potential biomarker to predict the effect of chemotherapy. This article summarizes the expression characteristics and clinical characteristics of NEAT1 in different cancers, and deeply discusses the regulatory role of NEAT1 in cancer chemotherapy resistance and related molecular mechanisms, aiming to clarify NEAT1 as a new target to overcome cancer chemotherapy resistance and the feasibility of chemotherapy sensitizers, with a view to providing a potential therapeutic direction for overcoming the dilemma of cancer resistance in the future.
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Affiliation(s)
- Feng Long
- School of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, China
| | - Xue Li
- School of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, China
| | - Jingyu Pan
- School of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, China
| | - Hailin Ye
- School of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, China
| | - Cuixia Di
- Department of Medical Physics, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Yong Huang
- School of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, China
| | - Jiawei Li
- School of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, China
| | - Xuan Zhou
- School of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, China
| | - Huiyi Yi
- School of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, China
| | - Qiaozhen Huang
- School of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, China
| | - Jing Si
- Department of Medical Physics, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.
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14
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Liu Y, Yuan H, Fan J, Wang H, Xie H, Wan J, Hu X, Zhou J, Liu L. The pathogenesis mechanism and potential clinical value of lncRNA in gliomas. Discov Oncol 2024; 15:266. [PMID: 38967893 PMCID: PMC11226588 DOI: 10.1007/s12672-024-01144-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 07/02/2024] [Indexed: 07/06/2024] Open
Abstract
Glioma is the most common malignant tumor in the central nervous system, and its unique pathogenesis often leads to poor treatment outcomes and prognosis. In 2021, the World Health Organization (WHO) divided gliomas into five categories based on their histological characteristics and molecular changes. Non-coding RNA is a type of RNA that does not encode proteins but can exert biological functions at the RNA level, and long non-coding RNA (lncRNA) is a type of non-coding RNA with a length exceeding 200 nt. It is controlled by various transcription factors and plays an indispensable role in the regulatory processes in various cells. Numerous studies have confirmed that the dysregulation of lncRNA is critical in the pathogenesis, progression, and malignancy of gliomas. Therefore, this article reviews the proliferation, apoptosis, invasion, migration, angiogenesis, immune regulation, glycolysis, stemness, and drug resistance changes caused by the dysregulation of lncRNA in gliomas, and summarizes their potential clinical significance in gliomas.
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Affiliation(s)
- Yuan Liu
- Department of Clinical Medicine, School of Clinical Medical, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Hui Yuan
- Department of Clinical Medicine, School of Clinical Medical, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - JingJia Fan
- Department of Clinical Medicine, School of Clinical Medical, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Han Wang
- Department of Clinical Medicine, School of Clinical Medical, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - HuiYu Xie
- Department of Clinical Medicine, School of Clinical Medical, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - JunFeng Wan
- Department of Clinical Medicine, School of Clinical Medical, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - XueYing Hu
- Department of Clinical Medicine, School of Clinical Medical, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Jie Zhou
- Dept Neurosurg, Affiliated Hosp, Southwest Med Univ, Luzhou, 646000, People's Republic of China.
| | - Liang Liu
- Dept Neurosurg, Affiliated Hosp, Southwest Med Univ, Luzhou, 646000, People's Republic of China.
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15
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Binder AK, Bremm F, Dörrie J, Schaft N. Non-Coding RNA in Tumor Cells and Tumor-Associated Myeloid Cells-Function and Therapeutic Potential. Int J Mol Sci 2024; 25:7275. [PMID: 39000381 PMCID: PMC11242727 DOI: 10.3390/ijms25137275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/19/2024] [Accepted: 06/29/2024] [Indexed: 07/16/2024] Open
Abstract
The RNA world is wide, and besides mRNA, there is a variety of other RNA types, such as non-coding (nc)RNAs, which harbor various intracellular regulatory functions. This review focuses on small interfering (si)RNA and micro (mi)RNA, which form a complex network regulating mRNA translation and, consequently, gene expression. In fact, these RNAs are critically involved in the function and phenotype of all cells in the human body, including malignant cells. In cancer, the two main targets for therapy are dysregulated cancer cells and dysfunctional immune cells. To exploit the potential of mi- or siRNA therapeutics in cancer therapy, a profound understanding of the regulatory mechanisms of RNAs and following targeted intervention is needed to re-program cancer cells and immune cell functions in vivo. The first part focuses on the function of less well-known RNAs, including siRNA and miRNA, and presents RNA-based technologies. In the second part, the therapeutic potential of these technologies in treating cancer is discussed, with particular attention on manipulating tumor-associated immune cells, especially tumor-associated myeloid cells.
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Affiliation(s)
- Amanda Katharina Binder
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (A.K.B.); (F.B.); (J.D.)
- Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg (CCC ER-EMN), 91054 Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
- Bavarian Cancer Research Center (BZKF), 91054 Erlangen, Germany
| | - Franziska Bremm
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (A.K.B.); (F.B.); (J.D.)
- Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg (CCC ER-EMN), 91054 Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
- Bavarian Cancer Research Center (BZKF), 91054 Erlangen, Germany
| | - Jan Dörrie
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (A.K.B.); (F.B.); (J.D.)
- Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg (CCC ER-EMN), 91054 Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
- Bavarian Cancer Research Center (BZKF), 91054 Erlangen, Germany
| | - Niels Schaft
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (A.K.B.); (F.B.); (J.D.)
- Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg (CCC ER-EMN), 91054 Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
- Bavarian Cancer Research Center (BZKF), 91054 Erlangen, Germany
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16
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Heydari R, Karimi P, Meyfour A. Long non-coding RNAs as pathophysiological regulators, therapeutic targets and novel extracellular vesicle biomarkers for the diagnosis of inflammatory bowel disease. Biomed Pharmacother 2024; 176:116868. [PMID: 38850647 DOI: 10.1016/j.biopha.2024.116868] [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: 04/07/2024] [Revised: 05/27/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic relapsing disease of the gastrointestinal (GI) system that includes two groups, Crohn's disease (CD) and ulcerative colitis (UC). To cope with these two classes of IBD, the investigation of pathogenic mechanisms and the discovery of new diagnostic and therapeutic approaches are crucial. Long non-coding RNAs (lncRNAs) which are non-coding RNAs with a length of longer than 200 nucleotides have indicated significant association with the pathology of IBD and strong potential to be used as accurate biomarkers in diagnosing and predicting responses to the IBD treatment. In the current review, we aim to investigate the role of lncRNAs in the pathology and development of IBD. We first describe recent advances in research on dysregulated lncRNAs in the pathogenesis of IBD from the perspective of epithelial barrier function, intestinal immunity, mitochondrial function, and intestinal autophagy. Then, we highlight the possible translational role of lncRNAs as therapeutic targets, diagnostic biomarkers, and predictors of therapeutic response in colon tissues and plasma samples. Finally, we discuss the potential of extracellular vesicles and their lncRNA cargo in the pathophysiology, diagnosis, and treatment of IBD.
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Affiliation(s)
- Raheleh Heydari
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Padideh Karimi
- CRTD/Center for Regenerative Therapies Dresden, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden 01307, Germany
| | - Anna Meyfour
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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17
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Sivagurunathan N, Rahamathulla MP, Al-Dossary H, Calivarathan L. Emerging Role of Long Noncoding RNAs in Regulating Inflammasome-Mediated Neurodegeneration in Parkinson's Disease. Mol Neurobiol 2024; 61:4619-4632. [PMID: 38105409 DOI: 10.1007/s12035-023-03809-7] [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: 09/13/2023] [Accepted: 11/14/2023] [Indexed: 12/19/2023]
Abstract
Parkinson's disease (PD) is one of the complex neurodegenerative disorders, primarily characterized by motor deficits, including bradykinesia, tremor, rigidity, and postural instability. The underlying pathophysiology involves the progressive loss of dopaminergic neurons within the substantia nigra pars compacta, leading to dopamine depletion in the basal ganglia circuitry. While motor symptoms are hallmark features of PD, emerging research highlights a wide range of non-motor symptoms, including cognitive impairments, mood disturbances, and autonomic dysfunctions. Inflammasome activation is pivotal in inducing neuroinflammation and promoting disease onset, progression, and severity of PD. Several studies have shown that long noncoding RNAs (lncRNAs) modulate inflammasomes in the pathogenesis of neurodegenerative diseases. Dysregulation of lncRNAs is linked to aberrant gene expression and cellular processes in neurodegeneration, causing the activation of inflammasomes that contribute to neuroinflammation and neurodegeneration. Inflammasomes are cytosolic proteins that form complexes upon activation, inducing inflammation and neuronal cell death. This review explores the significance of lncRNAs in regulating inflammasomes in PD, primarily focusing on specific lncRNAs such as nuclear paraspeckle assembly transcript 1 (NEATNEAT1), X-inactive specific transcript (XIST), growth arrest-specific 5 (GAS5), and HOX transcript antisense RNA (HOTAIR), which have been shown to activate or inhibit the NLRP3 inflammasome and induce the release of proinflammatory cytokines. Moreover, some lncRNAs mediate inflammasome activation through miRNA interactions. Understanding the roles of lncRNAs in inflammasome regulation provides new therapeutic targets for controlling neuroinflammation and reducing the progression of neurodegeneration. Identifying lncRNA-mediated regulatory pathways paves the way for novel therapies in the battle against these devastating neurodegenerative disorders.
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Affiliation(s)
- Narmadhaa Sivagurunathan
- Molecular Pharmacology & Toxicology Laboratory, Department of Biotechnology, School of Life Sciences, Central University of Tamil Nadu, Neelakudi Campus, Thiruvarur, 610005, India
| | - Mohamudha Parveen Rahamathulla
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj, 11942, Kingdom of Saudi Arabia
| | - Hussein Al-Dossary
- University Hospital, Prince Sattam Bin Abdulaziz University, Al-Kharj, 11942, Kingdom of Saudi Arabia
| | - Latchoumycandane Calivarathan
- Molecular Pharmacology & Toxicology Laboratory, Department of Biotechnology, School of Life Sciences, Central University of Tamil Nadu, Neelakudi Campus, Thiruvarur, 610005, India.
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18
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Kyurkchiyan SG, Stancheva G, Petkova V, Hadzhiev Y, Dobriyanova V, Popova D, Kaneva R, Popov TM. Exploration of the association between HIF3α mRNA and lncRNA MALAT1 in laryngeal squamous cell carcinoma by correlation analysis. Oncol Lett 2024; 28:292. [PMID: 38737978 PMCID: PMC11082855 DOI: 10.3892/ol.2024.14425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 03/28/2024] [Indexed: 05/14/2024] Open
Abstract
Laryngeal squamous cell carcinoma (LSCC) is a significant global health burden, for which there has been limited evidence of improved survival rates. Although the roles of hypoxia-inducible factor (HIF)1α and HIF2α have been well documented in hypoxia, the involvement of HIF3α, particularly in LSCC, has been inadequately explored. The present study aimed to investigate the correlation between HIFα subunits and the hypoxia-related long noncoding RNAs (lncRNAs) MALAT1 and HOTAIR in 63 patients diagnosed with LSCC. Total RNA was extracted from fresh-frozen laryngeal tumor and adjacent normal tissues, and was subjected to reverse transcription-quantitative PCR for target detection. Statistical analyses were conducted using SPSS software, with significance set at P<0.05. The present study is the first, to the best of our knowledge, to report a positive moderate monotonic correlation (rs=0.347) and moderately strong positive linear correlation (r=0.630) between HIF3α mRNA and lncRNA MALAT1 in LSCC. Regression analysis revealed a direct association between 39.6% of both variables. Additionally, a positive correlation was observed between lncRNAs MALAT1 and HOTAIR (rs=0.353); HIF2α mRNA and lncRNA MALAT1 (rs=0.431); HIF3α mRNA and lncRNA HOTAIR (rs=0.279); and HIF3α mRNA and HIF2α mRNA (rs=0.285). Notably, a significant negative correlation (rs=-0.341) was detected between HIF3α mRNA and HIF1α mRNA, potentially indicative of the HIF switch or negative regulation. In addition, the present study investigated the association between HIFα subunits and the clinicopathological characteristics of patients. The results revealed a notable association between HIF1α transcript levels and the location of LSCC; specifically, subglottic tumors exhibited elevated HIF1α levels compared with glottic and supraglottic LSCC. Furthermore, a significant association was identified between HIF3α transcript levels and patient age (P=0.032) and positive family history (P=0.047). In conclusion, the present findings suggested a pivotal role for HIF3α in LSCC development, potentially involving direct regulation of lncRNA MALAT1. However, further research is warranted to elucidate its precise mechanisms.
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Affiliation(s)
- Silva Garo Kyurkchiyan
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University, 1431 Sofia, Bulgaria
| | - Gergana Stancheva
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University, 1431 Sofia, Bulgaria
| | - Veronika Petkova
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University, 1431 Sofia, Bulgaria
| | - Yuliyan Hadzhiev
- Department of Ear and Nose Treatment, UMHAT ‘Tsaritsa Yoanna-ISUL’, Medical University, 1537 Sofia, Bulgaria
| | - Venera Dobriyanova
- Department of Ear and Nose Treatment, UMHAT ‘Tsaritsa Yoanna-ISUL’, Medical University, 1537 Sofia, Bulgaria
| | - Diana Popova
- Department of Ear and Nose Treatment, UMHAT ‘Tsaritsa Yoanna-ISUL’, Medical University, 1537 Sofia, Bulgaria
| | - Radka Kaneva
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University, 1431 Sofia, Bulgaria
| | - Todor Miroslavov Popov
- Department of Ear and Nose Treatment, UMHAT ‘Tsaritsa Yoanna-ISUL’, Medical University, 1537 Sofia, Bulgaria
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Huo Z, Zhu X, Peng Q, Chen C, Yang X, Huang C, Xiang Y, Tian Q, Liu J, Liu C, Zhang P. LINC08148 promotes the caveola-mediated endocytosis of Zika virus through upregulating transcription of Src. J Virol 2024; 98:e0170523. [PMID: 38742902 PMCID: PMC11237476 DOI: 10.1128/jvi.01705-23] [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: 11/07/2023] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) represent a new group of host factors involved in viral infection. Current study identified an intergenic lncRNA, LINC08148, as a proviral factor of Zika virus (ZIKV) and Dengue virus 2 (DENV2). Knockout (KO) or silencing of LINC08148 decreases the replication of ZIKV and DENV2. LINC08148 mainly acts at the endocytosis step of ZIKV but at a later stage of DENV2. RNA-seq analysis reveals that LINC08148 knockout downregulates the transcription levels of five endocytosis-related genes including AP2B1, CHMP4C, DNM1, FCHO1, and Src. Among them, loss of Src significantly decreases the uptake of ZIKV. Trans-complementation of Src in the LINC08148KO cells largely restores the caveola-mediated endocytosis of ZIKV, indicating that the proviral effect of LINC08148 is exerted through Src. Finally, LINC08148 upregulates the Src transcription through associating with its transcription factor SP1. This work establishes an essential role of LINC08148 in the ZIKV entry, underscoring a significance of lncRNAs in the viral infection. IMPORTANCE Long non-coding RNAs (lncRNAs), like proteins, participate in viral infection. However, functions of most lncRNAs remain unknown. In this study, we performed a functional screen based on microarray data and identified a new proviral lncRNA, LINC08148. Then, we uncovered that LINC08148 is involved in the caveola-mediated endocytosis of ZIKV, rather than the classical clathrin-mediated endocytosis. Mechanistically, LINC08148 upregulates the transcription of Src, an initiator of caveola-mediated endocytosis, through binding to its transcription factor SP1. This study identifies a new lncRNA involved in the ZIKV infection, suggesting lncRNAs and cellular proteins are closely linked and cooperate to regulate viral infection.
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Affiliation(s)
- Zhiting Huo
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xuanfeng Zhu
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Qinyu Peng
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Cancan Chen
- Department of Pathology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiaoyi Yang
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Changbai Huang
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yincheng Xiang
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Qingju Tian
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jingyu Liu
- Food and Cosmetics Institute, Guangzhou Customs Technology Center, Guangzhou, China
| | - Chao Liu
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Ping Zhang
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
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20
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Wang W, Liu D, Yao J, Yuan Z, Yan L, Cao B. ANXA5: A Key Regulator of Immune Cell Infiltration in Hepatocellular Carcinoma. Med Sci Monit 2024; 30:e943523. [PMID: 38824386 PMCID: PMC11155417 DOI: 10.12659/msm.943523] [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: 12/16/2023] [Accepted: 04/10/2024] [Indexed: 06/03/2024] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) poses a significant threat to human life and is the most prevalent form of liver cancer. The intricate interplay between apoptosis, a common form of programmed cell death, and its role in immune regulation stands as a crucial mechanism influencing tumor metastasis. MATERIAL AND METHODS Utilizing HCC samples from the TCGA database and 61 anoikis-related genes (ARGs) sourced from GeneCards, we analyzed the relationship between ARGs and immune cell infiltration in HCC. Subsequently, we identified long non-coding RNAs (lncRNAs) associated with ARGs, using the least absolute shrinkage and selection operator (LASSO) regression analysis to construct a robust prognostic model. The predictive capabilities of the model were then validated through examination in a single-cell dataset. RESULTS Our constructed prognostic model, derived from lncRNAs linked to ARGs, comprised 11 significant lncRNAs: NRAV, MCM3AP-AS1, OTUD6B-AS1, AC026356.1, AC009133.1, DDX11-AS1, AC108463.2, MIR4435-2HG, WARS2-AS1, LINC01094, and HCG18. The risk score assigned to HCC samples demonstrated associations with immune indicators and the infiltration of immune cells. Further, we identified Annexin A5 (ANXA5) as the pivotal gene among ARGs, with it exerting a prominent role in regulating the lncRNA gene signature. Our validation in a single-cell database elucidated the involvement of ANXA5 in immune cell infiltration, specifically in the regulation of mononuclear cells. CONCLUSIONS This study delves into the intricate correlation between ARGs and immune cell infiltration in HCC, culminating in the development of a novel prognostic model reliant on 11 ARGs-associated lncRNAs. Furthermore, our findings highlight ANXA5 as a promising target for immune regulation in HCC, offering new perspectives for immune therapy in the context of HCC.
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21
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Xie X, Sinha S. Quantitative estimates of the regulatory influence of long non-coding RNAs on global gene expression variation using TCGA breast cancer transcriptomic data. PLoS Comput Biol 2024; 20:e1012103. [PMID: 38838009 PMCID: PMC11198904 DOI: 10.1371/journal.pcbi.1012103] [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: 01/19/2023] [Revised: 06/25/2024] [Accepted: 04/24/2024] [Indexed: 06/07/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) have received attention in recent years for their regulatory roles in diverse biological contexts including cancer, yet large gaps remain in our understanding of their mechanisms and global maps of their targets. In this work, we investigated a basic unanswered question of lncRNA systems biology: to what extent can gene expression variation across individuals be attributed to lncRNA-driven regulation? To answer this, we analyzed RNA-seq data from a cohort of breast cancer patients, explaining each gene's expression variation using a small set of automatically selected lncRNA regulators. A key aspect of this analysis is that it accounts for confounding effects of transcription factors (TFs) as common regulators of a lncRNA-mRNA pair, to enrich the explained gene expression for lncRNA-mediated regulation. We found that for 16% of analyzed genes, lncRNAs can explain more than 20% of expression variation. We observed 25-50% of the putative regulator lncRNAs to be in 'cis' to, i.e., overlapping or located proximally to the target gene. This led us to quantify the global regulatory impact of such cis-located lncRNAs, which was found to be substantially greater than that of trans-located lncRNAs. Additionally, by including statistical interaction terms involving lncRNA-protein pairs as predictors in our regression models, we identified cases where a lncRNA's regulatory effect depends on the presence of a TF or RNA-binding protein. Finally, we created a high-confidence lncRNA-gene regulatory network whose edges are supported by co-expression as well as a plausible mechanism such as cis-action, protein scaffolding or competing endogenous RNAs. Our work is a first attempt to quantify the extent of gene expression control exerted globally by lncRNAs, especially those located proximally to their regulatory targets, in a specific biological (breast cancer) context. It also marks a first step towards systematic reconstruction of lncRNA regulatory networks, going beyond the current paradigm of co-expression networks, and motivates future analyses assessing the generalizability of our findings to additional biological contexts.
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Affiliation(s)
- Xiaoman Xie
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America
| | - Saurabh Sinha
- Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- H. Milton Stewart School of Industrial and Systems Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
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22
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Qin Y, Ren J, Yu H, He X, Cheng S, Chen W, Yang Z, Sun F, Wang C, Yuan S, Chen P, Wu D, Ren F, Huang A, Chen J. HOXA-AS2 Epigenetically Inhibits HBV Transcription by Recruiting the MTA1-HDAC1/2 Deacetylase Complex to cccDNA Minichromosome. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306810. [PMID: 38647380 PMCID: PMC11200093 DOI: 10.1002/advs.202306810] [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: 09/18/2023] [Revised: 03/27/2024] [Indexed: 04/25/2024]
Abstract
Persistent transcription of HBV covalently closed circular DNA (cccDNA) is critical for chronic HBV infection. Silencing cccDNA transcription through epigenetic mechanisms offers an effective strategy to control HBV. Long non-coding RNAs (lncRNAs), as important epigenetic regulators, have an unclear role in cccDNA transcription regulation. In this study, lncRNA sequencing (lncRNA seq) is conducted on five pairs of HBV-positive and HBV-negative liver tissue. Through analysis, HOXA-AS2 (HOXA cluster antisense RNA 2) is identified as a significantly upregulated lncRNA in HBV-infected livers. Further experiments demonstrate that HBV DNA polymerase (DNA pol) induces HOXA-AS2 after establishing persistent high-level HBV replication. Functional studies reveal that HOXA-AS2 physically binds to cccDNA and significantly inhibits its transcription. Mechanistically, HOXA-AS2 recruits the MTA1-HDAC1/2 deacetylase complex to cccDNA minichromosome by physically interacting with metastasis associated 1 (MTA1) subunit, resulting in reduced acetylation of histone H3 at lysine 9 (H3K9ac) and lysine 27 (H3K27ac) associated with cccDNA and subsequently suppressing cccDNA transcription. Altogether, the study reveals a mechanism to self-limit HBV replication, wherein the upregulation of lncRNA HOXA-AS2, induced by HBV DNA pol, can epigenetically suppress cccDNA transcription.
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Affiliation(s)
- YiPing Qin
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized TreatmentChongqing University Cancer HospitalChongqing400030China
| | - JiHua Ren
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - HaiBo Yu
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - Xin He
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - ShengTao Cheng
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - WeiXian Chen
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - Zhen Yang
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - FengMing Sun
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education)College of Laboratory MedicineChongqing Medical UniversityChongqing400016China
| | - ChunDuo Wang
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - SiYu Yuan
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - Peng Chen
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - DaiQing Wu
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - Fang Ren
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - AiLong Huang
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - Juan Chen
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
- State Key Laboratory of Ultrasound in Medicine and EngineeringCollege of Biomedical EngineeringChongqing Medical UniversityChongqing400016China
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Hashemi M, Mousavian Roshanzamir S, Orouei S, Daneii P, Raesi R, Zokaee H, Bikarannejad P, Salmani K, Khorrami R, Deldar Abad Paskeh M, Salimimoghadam S, Rashidi M, Hushmandi K, Taheriazam A, Entezari M. Shedding light on function of long non-coding RNAs (lncRNAs) in glioblastoma. Noncoding RNA Res 2024; 9:508-522. [PMID: 38511060 PMCID: PMC10950594 DOI: 10.1016/j.ncrna.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/29/2024] [Accepted: 02/04/2024] [Indexed: 03/22/2024] Open
Abstract
The brain tumors and especially glioblastoma, are affecting life of many people worldwide and due to their high mortality and morbidity, their treatment is of importance and has gained attention in recent years. The abnormal expression of genes is commonly observed in GBM and long non-coding RNAs (lncRNAs) have demonstrated dysregulation in this tumor. LncRNAs have length more than 200 nucleotides and they have been located in cytoplasm and nucleus. The current review focuses on the role of lncRNAs in GBM. There two types of lncRNAs in GBM including tumor-promoting and tumor-suppressor lncRNAs and overexpression of oncogenic lncRNAs increases progression of GBM. LncRNAs can regulate proliferation, cell cycle arrest and metastasis of GBM cells. Wnt, STAT3 and EZH2 are among the molecular pathways affected by lncRNAs in GBM and for regulating metastasis of GBM cells, these RNA molecules mainly affect EMT mechanism. LncRNAs are involved in drug resistance and can induce resistance of GBM cells to temozolomide chemotherapy. Furthermore, lncRNAs stimulate radio-resistance in GBM cells. LncRNAs increase PD-1 expression to mediate immune evasion. LncRNAs can be considered as diagnostic and prognostic tools in GBM and researchers have developed signature from lncRNAs in GBM.
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Affiliation(s)
- Mehrdad Hashemi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Sophie Mousavian Roshanzamir
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Sima Orouei
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Pouria Daneii
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Rasoul Raesi
- Department of Nursing, Torbat Jam Faculty of Medical Sciences, Torbat Jam, Iran
- Department of Health Services Management, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Haleh Zokaee
- Department of Oral and Maxillofacial Medicine, Dental Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Pooria Bikarannejad
- Young Researchers and Elite Club, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Kiana Salmani
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Ramin Khorrami
- Department of Food Hygiene and Quality Control, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Mahshid Deldar Abad Paskeh
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Shokooh Salimimoghadam
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Mohsen Rashidi
- Department Pharmacology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Kiavash Hushmandi
- Department of Food Hygiene and Quality Control, Division of Epidemiology & Zoonoses, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Afshin Taheriazam
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- Department of Orthopedics, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Maliheh Entezari
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
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24
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Kang Z, Zhang C, Huangfu H. Exosomal lncRNA LINC02191 Promotes Laryngeal Squamous cell Carcinoma Progression by Targeting miR-204-5p/RAB22A Axis and Regulating PI3K/Akt/mTOR Pathway. Biochem Genet 2024; 62:2117-2133. [PMID: 37863866 DOI: 10.1007/s10528-023-10541-3] [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: 06/26/2023] [Accepted: 10/01/2023] [Indexed: 10/22/2023]
Abstract
Recent research has explored the potential use of serum-derived biomarkers in cancer screening, and mounting evidence has illustrated the pivotal roles of long noncoding RNAs (lncRNAs) in regulating laryngeal squamous cell carcinoma (LSCC) progression. LINC02191 is a newly identified lncRNA and no studies have investigated its role in malignant tumors. This study aims to explore the functions and mechanisms of lncRNA LINC02191 in LSCC. LINC02191 was knocked down in LSCC cells using shRNAs for loss-of-function experiments. RT-qPCR revealed that LINC02191 was upregulated in LSCC patients' serum exosomes, tissues and cells. Western blotting and RT-qPCR were implemented for detecting molecular protein and RNA levels. Colony formation, CCK-8, wound healing and Transwell assays were employed for examining LSCC cell malignant behaviors in vitro. A tumor-bearing mouse model (n = 4/group) was established for examining LINC02191 role in vivo. The results showed that LINC02191 silencing hindered LSCC cell proliferation, invasiveness, migration as well as EMT in vitro and impeded tumorigenesis in xenograft mouse model. Luciferase reporter assay was utilized for verifying the interaction between LINC02191, miR-204-5p and RAB22A. Pearson correlation analysis was employed to evaluate their expression correlation in LSCC tissue specimens (N = 30). Mechanistically, LINC02191 upregulated RAB22A by binding to miR-204-5p, and knocking down LINC02191 inhibited PI3K/Akt/mTOR signaling transduction in LSCC cells and tumor-bearing mice. Moreover, RAB22A overexpression reversed LINC02191 depletion-triggered suppression of LSCC cell aggressiveness and inactivation of PI3K/Akt/mTOR signaling. In conclusion, LINC02191 aggravates LSCC by targeting miR-204-5p/RAB22A/PI3K/Akt/mTOR signaling pathway, which indicates that LINC02191 may serve as a promising target for LSCC treatment.
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Affiliation(s)
- Zhiwei Kang
- Department of Otolaryngology Head & Neck Surgery, Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, Shanxi Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, 030001, China
| | - Chunming Zhang
- Department of Otolaryngology Head & Neck Surgery, Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, Shanxi Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, 030001, China
| | - Hui Huangfu
- Department of Otolaryngology Head & Neck Surgery, Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, Shanxi Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, 030001, China.
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25
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Wu JD, Xu L, Chen W, Zhou Y, Zheng G, Gu W. LncRNA PCAT6 mediates UBFD1 expression via sponging miR-545-3p in breast cancer cells. Noncoding RNA Res 2024; 9:421-428. [PMID: 38511057 PMCID: PMC10950603 DOI: 10.1016/j.ncrna.2024.01.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 01/30/2024] [Indexed: 03/22/2024] Open
Abstract
Background LncRNA PCAT6 has been shown to involve in carcinogenesis of different tumors. In this study, we investigated underline mechanism by which PCAT6 promoted breast cancer cell progression. Methods RIP was used to identify lncRNAs associated with IMP1. Bioinformatics assays were used to predict potential miRNAs that interact with PCAT6 and mRNAs that are targeted by miR-545-3p. RNA-seq and RT-qPCR were used to analyze differential expression of lncRNAs and miRNA-targeted genes. Luciferase reporter and RNA pull-down assays were performed to identify the molecular interactions between PCAT6 and individual miRNAs. The role of PCAT6-mediated cell proliferation and invasion were tested by CCK-8 and transwell assays following loss-of-function and gain-of-function effects. Results We identified that PCAT6 is one of the lncRNAs that associated with IMP1. PCAT6 not only binds to IMP1, but also acts as a ceRNA to interact with multiple miRNAs, including miR-545-3p. Binding of IMP1 destabilized PCAT6, while competitive interaction with miR-545-3p allowed PCAT6 to positively regulate UBFD1 expression. Silencing UBFD1 mRNA could effectively rescue PCAT6-induced cell proliferation and invasive abilities. Conclusions Our study provided evidence that PCAT6 activates UBFD1 expression via sponging miR-545-3p to increase carcinogenesis of breast cancer cells. Based on the nature of UBFD1 as a polyubiquitin binding protein, our study suggested that ubiquitin pathway might contribute to breast cancer progression.
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Affiliation(s)
- Jun-Dong Wu
- Breast Center, Cancer Hospital of Shantou University Medical College, Shantou, Guangdong Province, 515041, China
| | - Liqun Xu
- Department of Pathophysiology, Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, Guangdong Province, 515041, China
| | - Weibin Chen
- Department of Pathophysiology, Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, Guangdong Province, 515041, China
| | - Yanchun Zhou
- Department of Pathophysiology, Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, Guangdong Province, 515041, China
| | - Guiyu Zheng
- Department of Pathophysiology, Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, Guangdong Province, 515041, China
| | - Wei Gu
- Department of Pathophysiology, Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, Guangdong Province, 515041, China
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Guo C, Zhang M, Jin X, Zhu C, Qian J, Tao M. Exploring the regulatory role of FBXL19-AS1 in triple-negative breast cancer through the miR-378a-3p/OTUB2 axis. Cell Biochem Funct 2024; 42:e4020. [PMID: 38702967 DOI: 10.1002/cbf.4020] [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: 01/12/2024] [Revised: 04/01/2024] [Accepted: 04/13/2024] [Indexed: 05/06/2024]
Abstract
The regulatory potential of long noncoding RNA (lncRNA) FBXL19-AS1 has been highlighted in various cancers, but its effect on triple-negative breast cancer (TNBC) remains unclear. Here, we aimed to elucidate the role of FBXL19-AS1 in TNBC and its underlying mechanism. RT-qPCR was employed to detect the expressions of FBXL19-AS1 and miR-378a-3p in tissues and cells. Immunohistochemical staining and western blot were utilized to detect the expression levels of proteins. Cell activities were detected using flow cytometry, CCK-8, and transwell assay. Dual-luciferase reporter and RNA immunoprecipitation (RIP) assays were deployed to investigate interactions of different molecules. Protein-protein interaction (PPI) network, gene ontology (GO), and Kyoto encyclopedia of genes and genomes (KEGG) pathways were used to analyze the downstream pathway. In vivo xenograft model was conducted to detect the effect of FBXL19-AS1 on tumor growth. FBXL19-AS1 was overexpressed in TNBC tissues and cell lines compared with counterparts. FBXL19-AS1 knockdown suppressed TNBC cell activities, whereas its overexpression exhibited the opposite effect. Mechanistically, FBXL19-AS1 was found to interact with miR-378a-3p. Further analysis revealed that miR-378a-3p exerted tumor-suppressive effects in TNBC cells. Additionally, miR-378a-3p targeted and downregulated the expression of ubiquitin aldehyde binding 2 (OTUB2), a deubiquitinase associated with TNBC progression. In vivo experiments substantiated the inhibitory effects of FBXL19-AS1 knockdown on TNBC tumorigenesis, and a miR-378a-3p inhibitor partially rescued these effects. The downstream pathway of the miR-378a-3p/OTUB2 axis was explored, revealing connections with proteins involved in modifying other proteins, removing ubiquitin molecules, and influencing signaling pathways, including the Hippo signaling pathway. Western blot analysis confirmed changes in YAP and TAZ expression levels, indicating a potential regulatory network. In summary, FBXL19-AS1 promotes exacerbation in TNBC by suppressing miR-378a-3p, leading to increased OTUB2 expression. The downstream mechanism may be related to the Hippo signaling pathway. These findings propose potential therapeutic targets for TNBC treatment.
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Affiliation(s)
- Chenxu Guo
- Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Department of Oncology, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, China
- Department of Surgical Oncology, The First Affiliated Hospital of Bengbu Medical University, Bengbu, China
| | - Mingliang Zhang
- Department of Surgical Oncology, The First Affiliated Hospital of Bengbu Medical University, Bengbu, China
| | - Xin Jin
- Department of Surgical Oncology, The First Affiliated Hospital of Bengbu Medical University, Bengbu, China
| | - Chao Zhu
- Department of Surgical Oncology, The First Affiliated Hospital of Bengbu Medical University, Bengbu, China
| | - Jun Qian
- Department of Surgical Oncology, The First Affiliated Hospital of Bengbu Medical University, Bengbu, China
| | - Min Tao
- Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Department of Oncology, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, China
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Lizano M, Carrillo-García A, De La Cruz-Hernández E, Castro-Muñoz LJ, Contreras-Paredes A. Promising predictive molecular biomarkers for cervical cancer (Review). Int J Mol Med 2024; 53:50. [PMID: 38606495 PMCID: PMC11090266 DOI: 10.3892/ijmm.2024.5374] [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: 10/10/2023] [Accepted: 03/11/2024] [Indexed: 04/13/2024] Open
Abstract
Cervical cancer (CC) constitutes a serious public health problem. Vaccination and screening programs have notably reduced the incidence of CC worldwide by >80%; however, the mortality rate in low‑income countries remains high. The staging of CC is a determining factor in therapeutic strategies: The clinical management of early stages of CC includes surgery and/or radiotherapy, whereas radiotherapy and/or concurrent chemotherapy are the recommended therapeutic strategies for locally advanced CC. The histopathological characteristics of tumors can effectively serve as prognostic markers of radiotherapy response; however, the efficacy rate of radiotherapy may significantly differ among cancer patients. Failure of radiotherapy is commonly associated with a higher risk of recurrence, persistence and metastasis; therefore, radioresistance remains the most important and unresolved clinical problem. This condition highlights the importance of precision medicine in searching for possible predictive biomarkers to timely identify patients at risk of treatment response failure and provide tailored therapeutic strategies according to genetic and epigenetic characteristics. The present review aimed to summarize the evidence that supports the role of several proteins, methylation markers and non‑coding RNAs as potential predictive biomarkers for CC.
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Affiliation(s)
- Marcela Lizano
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología, Universidad Nacional Autónoma de México, Mexico City 14080, Mexico
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Adela Carrillo-García
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología, Universidad Nacional Autónoma de México, Mexico City 14080, Mexico
| | - Erick De La Cruz-Hernández
- Laboratorio de Investigación en Enfermedades Metabólicas e Infecciosas, División Académica Multidisciplinaria de Comalcalco, Universidad Juárez Autónoma de Tabasco, Ranchería Sur Cuarta Sección, Comalcalco City, Tabasco 86650, Mexico
| | | | - Adriana Contreras-Paredes
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología, Universidad Nacional Autónoma de México, Mexico City 14080, Mexico
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Arnold CR, Mangesius J, Portnaia I, Ganswindt U, Wolff HA. Innovative therapeutic strategies to overcome radioresistance in breast cancer. Front Oncol 2024; 14:1379986. [PMID: 38873260 PMCID: PMC11169591 DOI: 10.3389/fonc.2024.1379986] [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: 01/31/2024] [Accepted: 05/10/2024] [Indexed: 06/15/2024] Open
Abstract
Despite a comparatively favorable prognosis relative to other malignancies, breast cancer continues to significantly impact women's health globally, partly due to its high incidence rate. A critical factor in treatment failure is radiation resistance - the capacity of tumor cells to withstand high doses of ionizing radiation. Advancements in understanding the cellular and molecular mechanisms underlying radioresistance, coupled with enhanced characterization of radioresistant cell clones, are paving the way for the development of novel treatment modalities that hold potential for future clinical application. In the context of combating radioresistance in breast cancer, potential targets of interest include long non-coding RNAs (lncRNAs), micro RNAs (miRNAs), and their associated signaling pathways, along with other signal transduction routes amenable to pharmacological intervention. Furthermore, technical, and methodological innovations, such as the integration of hyperthermia or nanoparticles with radiotherapy, have the potential to enhance treatment responses in patients with radioresistant breast cancer. This review endeavors to provide a comprehensive survey of the current scientific landscape, focusing on novel therapeutic advancements specifically addressing radioresistant breast cancer.
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Affiliation(s)
| | - Julian Mangesius
- Department of Radiation-Oncology, Medical University of Innsbruck, Innsbruck, Austria
| | - Iana Portnaia
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Ute Ganswindt
- Department of Radiation-Oncology, Medical University of Innsbruck, Innsbruck, Austria
| | - Hendrik Andreas Wolff
- Department of Radiology, Nuclear Medicine, and Radiotherapy, Radiology Munich, Munich, Germany
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Matboli M, Al-Amodi HS, Khaled A, Khaled R, Roushdy MMS, Ali M, Diab GI, Elnagar MF, Elmansy RA, TAhmed HH, Ahmed EME, Elzoghby DMA, M.Kamel HF, Farag MF, ELsawi HA, Farid LM, Abouelkhair MB, Habib EK, Fikry H, Saleh LA, Aboughaleb IH. Comprehensive machine learning models for predicting therapeutic targets in type 2 diabetes utilizing molecular and biochemical features in rats. Front Endocrinol (Lausanne) 2024; 15:1384984. [PMID: 38854687 PMCID: PMC11157016 DOI: 10.3389/fendo.2024.1384984] [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: 02/11/2024] [Accepted: 05/03/2024] [Indexed: 06/11/2024] Open
Abstract
Introduction With the increasing prevalence of type 2 diabetes mellitus (T2DM), there is an urgent need to discover effective therapeutic targets for this complex condition. Coding and non-coding RNAs, with traditional biochemical parameters, have shown promise as viable targets for therapy. Machine learning (ML) techniques have emerged as powerful tools for predicting drug responses. Method In this study, we developed an ML-based model to identify the most influential features for drug response in the treatment of type 2 diabetes using three medicinal plant-based drugs (Rosavin, Caffeic acid, and Isorhamnetin), and a probiotics drug (Z-biotic), at different doses. A hundred rats were randomly assigned to ten groups, including a normal group, a streptozotocin-induced diabetic group, and eight treated groups. Serum samples were collected for biochemical analysis, while liver tissues (L) and adipose tissues (A) underwent histopathological examination and molecular biomarker extraction using quantitative PCR. Utilizing five machine learning algorithms, we integrated 32 molecular features and 12 biochemical features to select the most predictive targets for each model and the combined model. Results and discussion Our results indicated that high doses of the selected drugs effectively mitigated liver inflammation, reduced insulin resistance, and improved lipid profiles and renal function biomarkers. The machine learning model identified 13 molecular features, 10 biochemical features, and 20 combined features with an accuracy of 80% and AUC (0.894, 0.93, and 0.896), respectively. This study presents an ML model that accurately identifies effective therapeutic targets implicated in the molecular pathways associated with T2DM pathogenesis.
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Affiliation(s)
- Marwa Matboli
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Hiba S. Al-Amodi
- Biochemistry Department, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Abdelrahman Khaled
- Bioinformatics Group, Center of Informatics Sciences (CIS), School of Information Technology and Computer Sciences, Nile University, Giza, Egypt
| | - Radwa Khaled
- Biotechnology/Biomolecular Chemistry Department, Faculty of Science, Cairo University, Cairo, Egypt
- Medicinal Biochemistry and Molecular Biology Department, Modern University for Technology and Information, Cairo, Egypt
| | - Marian M. S. Roushdy
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Marwa Ali
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | | | | | - Rasha A. Elmansy
- Anatomy Unit, Department of Basic Medical Sciences, College of Medicine and Medical Sciences, Qassim University, Buraydah, Saudi Arabia
- Department of Anatomy and Cell Biology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Hagir H. TAhmed
- Anatomy Unit, Department of Basic Medical Sciences, College of Medicine and Medical Sciences, AlNeelain University, Khartoum, Sudan
| | - Enshrah M. E. Ahmed
- Pathology Unit, Department of Basic Medical Sciences, College of Medicine and Medical Sciences, Gassim University, Buraydah, Saudi Arabia
| | | | - Hala F. M.Kamel
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
- Biochemistry Department, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Mohamed F. Farag
- Medical Physiology Department, Armed Forces College of Medicine, Cairo, Egypt
| | - Hind A. ELsawi
- Department of Internal Medicine, Badr University in Cairo, Badr, Egypt
| | - Laila M. Farid
- Pathology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | | | - Eman K. Habib
- Department of Anatomy and Cell Biology, Faculty of Medicine, Galala University, Attaka, Suez Governorate, Egypt
| | - Heba Fikry
- Department of Histology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Lobna A. Saleh
- Department of Clinical Pharmacology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
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Sun Y, Xu C, Luo J, Li S, Chen S, Cen Y, Xu P. Comprehensive analysis of differential long non-coding RNA and messenger RNA expression in cholelithiasis using high-throughput sequencing and bioinformatics. Front Genet 2024; 15:1375019. [PMID: 38808330 PMCID: PMC11130440 DOI: 10.3389/fgene.2024.1375019] [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: 01/23/2024] [Accepted: 04/24/2024] [Indexed: 05/30/2024] Open
Abstract
Background The etiology of gallstone disease (GSD) has not been fully elucidated. Consequently, the primary objective of this study was to scrutinize and provisionally authenticate the distinctive expression profiles of long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs) in GSD. Methods RiboNucleic Acid (RNA) sequencing was used on four paired human gallbladder samples for the purpose of this study. Differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) were identified and subjected to analysis of their biological functions. The Pearson's correlation coefficients between DElncRNAs and DEmRNAs were computed to construct a co-expression network delineating their associations. Furthermore, both cis- and trans-regulatory networks of selected lncRNAs were established and visualized. Additionally, a competing endogenous RNA (ceRNA) regulatory network was constructed. To validate the RNA-sequencing data, we performed a Quantitative Real-time Polymerase Chain Reaction (RT-qPCR) on 10 paired human gallbladder samples, assessing the expressions of the top 4 DEmRNAs and DElncRNAs in gallstone and control samples. Results A total of 934 DEmRNAs and 304DElncRNAs were successfully identified. Functional enrichment analysis indicated a predominant involvement in metabolic-related biological functions. Correlation analysis revealed a strong association between the expressions of 597 DEmRNAs and 194 DElncRNAs. Subsequently, both a cis-lncRNA-mRNA and a trans-lncRNA-Transcription Factor (TF)-mRNA regulatory network were meticulously constructed. Additionally, a ceRNA network, comprising of 24 DElncRNAs, 201 DEmRNAs, and 120 predicted miRNAs, was established. Furthermore, using RT-qPCR, we observed significant upregulation of AC004692.4, HECW1-IT1, SFRP4, and COMP, while LINC01564, SLC26A3, RP1-27K12.2, and GSTA2 exhibited marked downregulation in gallstone samples. Importantly, these findings were consistent with the sequencing. Conclusion We conducted a screening process to identify DElncRNAs and DEmRNAs in GSD. This approach contributes to a deeper understanding of the genetic factors involved in the etiology of gallstones.
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Affiliation(s)
- Yanbo Sun
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Conghui Xu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
- School of Medicine, Yunnan University, Kunming, China
| | - Jing Luo
- Department of Gastrointestinal Surgery, Qujing No. 1 People’s Hospital, Qujing, Yunnan, China
| | - Shumin Li
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Shi Chen
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yunyun Cen
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Pengyuan Xu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
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Han J, Zhu Y, Zhang J, Kapilevich L, Zhang XA. Noncoding RNAs: the crucial role of programmed cell death in osteoporosis. Front Cell Dev Biol 2024; 12:1409662. [PMID: 38799506 PMCID: PMC11116712 DOI: 10.3389/fcell.2024.1409662] [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: 03/30/2024] [Accepted: 04/26/2024] [Indexed: 05/29/2024] Open
Abstract
Osteoporosis is the most common skeletal disease characterized by an imbalance between bone resorption and bone remodeling. Osteoporosis can lead to bone loss and bone microstructural deterioration. This increases the risk of bone fragility and fracture, severely reducing patients' mobility and quality of life. However, the specific molecular mechanisms involved in the development of osteoporosis remain unclear. Increasing evidence suggests that multiple noncoding RNAs show differential expression in the osteoporosis state. Meanwhile, noncoding RNAs have been associated with an increased risk of osteoporosis and fracture. Noncoding RNAs are an important class of factors at the level of gene regulation and are mainly involved in cell proliferation, cell differentiation, and cell death. Programmed cell death is a genetically-regulated form of cell death involved in regulating the homeostasis of the internal environment. Noncoding RNA plays an important role in the programmed cell death process. The exploration of the noncoding RNA-programmed cell death axis has become an interesting area of research and has been shown to play a role in many diseases such as osteoporosis. In this review, we summarize the latest findings on the mechanism of noncoding RNA-mediated programmed cell death on bone homeostasis imbalance leading to osteoporosis. And we provide a deeper understanding of the role played by the noncoding RNA-programmed cell death axis at the gene regulatory level of osteoporosis. We hope to provide a unique opportunity to develop novel diagnostic and therapeutic approaches for osteoporosis.
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Affiliation(s)
- Juanjuan Han
- College of Exercise and Health, Shenyang Sport University, Shenyang, China
| | - Yuqing Zhu
- College of Exercise and Health, Shenyang Sport University, Shenyang, China
| | - Jiale Zhang
- College of Exercise and Health, Shenyang Sport University, Shenyang, China
| | - Leonid Kapilevich
- Faculty of Physical Education, Tomsk Stаte University, Tomsk, Russia
| | - Xin-an Zhang
- College of Exercise and Health, Shenyang Sport University, Shenyang, China
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Valverde A, Naqvi RA, Naqvi AR. Macrophage-enriched novel functional long noncoding RNAs LRRC75A-AS1 and GAPLINC regulate polarization and innate immune responses. Inflamm Res 2024; 73:771-792. [PMID: 38592458 DOI: 10.1007/s00011-024-01865-w] [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: 01/11/2024] [Revised: 01/29/2024] [Accepted: 02/21/2024] [Indexed: 04/10/2024] Open
Abstract
INTRODUCTION Macrophages (Mφs) are functionally dynamic immune cells that bridge innate and adaptive immune responses; however, the underlying epigenetic mechanisms that control Mφ plasticity and innate immune functions are not well elucidated. OBJECTIVE To identify novel functions of macrophage-enriched lncRNAs in regulating polarization and innate immune responses. METHODS Total RNA isolated from differentiating monocyte-derived M1 and M2 Mφs was profiled for lncRNAs expression using RNAseq. Impact of LRRC75A-AS1, GAPLINC and AL139099.5 knockdown was examined on macrophage differentiation, polarization markers, phagocytosis, and antigen processing by flow cytometry and florescence microscopy. Cytokine profiles were examined by multiplex bead array and cytoskeletal signaling pathway genes were quantified by PCR-based array. Gingival biopsies were collected from periodontally healthy and diseased subjects to examine lncRNAs, M1/M2 marker expression. RESULTS Transcriptome profiling of M1 and M2 Mφs identified thousands of differentially expressed known and novel lncRNAs. We characterized three Mφ-enriched lncRNAs LRRC75A-AS1, GAPLINC and AL139099.5 in polarization and innate immunity. Knockdown of LRRC75A-AS1 and GAPLINC downregulated the Mφ differentiation markers and skewed Mφ polarization by decreasing M1 markers without a significant impact on M2 markers. LRRC75A-AS1 and GAPLINC knockdown also attenuated bacterial phagocytosis, antigen processing and inflammatory cytokine secretion in Mφs, supporting their functional role in potentiating innate immune functions. Mechanistically, LRRC75A-AS1 and GAPLINC knockdown impaired Mφ migration by downregulating the expression of multiple cytoskeletal signaling pathways suggesting their critical role in regulating Mφ migration. Finally, we showed that LRRC75A-AS1 and GAPLINC were upregulated in periodontitis and their expression correlates with higher M1 markers suggesting their role in macrophage polarization in vivo. CONCLUSION Our results show that polarized Mφs acquire a unique lncRNA repertoire and identified many previously unknown lncRNA sequences. LRRC75A-AS1 and GAPLINC, which are induced in periodontitis, regulate Mφ polarization and innate immune functions supporting their critical role in inflammation.
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Affiliation(s)
- Araceli Valverde
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL, 60612, USA.
- Department of Microbiology and Immunology, College of Medicine, University of Illinois Chicago, Chicago, IL, 60612, USA.
| | - Raza Ali Naqvi
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL, 60612, USA
- Department of Microbiology and Immunology, College of Medicine, University of Illinois Chicago, Chicago, IL, 60612, USA
| | - Afsar R Naqvi
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL, 60612, USA.
- Department of Microbiology and Immunology, College of Medicine, University of Illinois Chicago, Chicago, IL, 60612, USA.
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Rey F, Esposito L, Maghraby E, Mauri A, Berardo C, Bonaventura E, Tonduti D, Carelli S, Cereda C. Role of epigenetics and alterations in RNA metabolism in leukodystrophies. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1854. [PMID: 38831585 DOI: 10.1002/wrna.1854] [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: 11/30/2023] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 06/05/2024]
Abstract
Leukodystrophies are a class of rare heterogeneous disorders which affect the white matter of the brain, ultimately leading to a disruption in brain development and a damaging effect on cognitive, motor and social-communicative development. These disorders present a great clinical heterogeneity, along with a phenotypic overlap and this could be partially due to contributions from environmental stimuli. It is in this context that there is a great need to investigate what other factors may contribute to both disease insurgence and phenotypical heterogeneity, and novel evidence are raising the attention toward the study of epigenetics and transcription mechanisms that can influence the disease phenotype beyond genetics. Modulation in the epigenetics machinery including histone modifications, DNA methylation and non-coding RNAs dysregulation, could be crucial players in the development of these disorders, and moreover an aberrant RNA maturation process has been linked to leukodystrophies. Here, we provide an overview of these mechanisms hoping to supply a closer step toward the analysis of leukodystrophies not only as genetically determined but also with an added level of complexity where epigenetic dysregulation is of key relevance. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNA RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Federica Rey
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi," Department of Biomedical and Clinical Sciences, University of Milano, Milan, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
| | - Letizia Esposito
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi," Department of Biomedical and Clinical Sciences, University of Milano, Milan, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
| | - Erika Maghraby
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
- Department of Biology and Biotechnology "L. Spallanzani" (DBB), University of Pavia, Pavia, Italy
| | - Alessia Mauri
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi," Department of Biomedical and Clinical Sciences, University of Milano, Milan, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
| | - Clarissa Berardo
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi," Department of Biomedical and Clinical Sciences, University of Milano, Milan, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
| | - Eleonora Bonaventura
- Unit of Pediatric Neurology, COALA Center for Diagnosis and Treatment of Leukodystrophies, V. Buzzi Children's Hospital, Milan, Italy
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Davide Tonduti
- Unit of Pediatric Neurology, COALA Center for Diagnosis and Treatment of Leukodystrophies, V. Buzzi Children's Hospital, Milan, Italy
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Stephana Carelli
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi," Department of Biomedical and Clinical Sciences, University of Milano, Milan, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
| | - Cristina Cereda
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
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Liu Z, Yang J, Wang N, Liu J, Geng J, Zhu J, Cong B, Sun H, Wu R. Integrative lncRNA, circRNA, and mRNA analysis reveals expression profiles of six forensic body fluids/tissue. Int J Legal Med 2024; 138:731-742. [PMID: 37994925 DOI: 10.1007/s00414-023-03131-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 11/10/2023] [Indexed: 11/24/2023]
Abstract
RNAs have attracted much attention in forensic body fluid/tissue identification (BFID) due to their tissue-specific expression characteristics. Among RNAs, long RNAs (e.g., mRNA) have a higher probability of containing more polymorphic sites that can be used to assign the specific donor of the body fluid/tissue. However, few studies have characterized their overall profiles in forensic science. In this study, we sequenced the transcriptomes of 30 samples from venous blood, menstrual blood, semen, saliva, vaginal secretion, and skin tissue, obtaining a comprehensive picture of mRNA, lncRNA, and circRNA profiles. A total of 90,305 mRNAs, 102,906 lncRNAs (including 19,549 novel lncRNAs), and 40,204 circRNAs were detected. RNA type distribution, length distribution, and expression distribution were presented according to their annotation and expression level, and many novel body fluid/tissue-specific RNA markers were identified. Furthermore, the cognate relations among the three RNAs were analyzed according to gene annotations. Finally, SNPs and InDels from RNA transcripts were genotyped, and 21,611 multi-SNP and 4,471 multi-InDel transcriptomic microhaplotypes (tMHs) were identified. These results provide a comprehensive understanding of transcriptome profiles, which could provide new avenues for tracing the origin of the body fluid/tissue and identifying an individual.
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Affiliation(s)
- Zhiyong Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, China
| | - Jingyi Yang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, China
| | - Nana Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, China
| | - Jiajun Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, China
| | - Jiaojiao Geng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, China
| | - Jianzhang Zhu
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, 510440, China
| | - Bin Cong
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Hebei Medical University, Shijiazhuang, 050017, China.
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, China.
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Hu Z, Yuan L, Yang X, Yi C, Lu J. The roles of long non-coding RNAs in ovarian cancer: from functions to therapeutic implications. Front Oncol 2024; 14:1332528. [PMID: 38725621 PMCID: PMC11079149 DOI: 10.3389/fonc.2024.1332528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/27/2024] [Indexed: 05/12/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) are multifunctional and participate in a variety of biological processes and gene regulatory networks. The deregulation of lncRNAs has been extensively implicated in diverse human diseases, especially in cancers. Overwhelming evidence demonstrates that lncRNAs are essential to the pathophysiological processes of ovarian cancer (OC), acting as regulators involved in metastasis, cell death, chemoresistance, and tumor immunity. In this review, we illustrate the expanded functions of lncRNAs in the initiation and progression of OC and elaborate on the signaling pathways in which they pitch. Additionally, the potential clinical applications of lncRNAs as biomarkers in the diagnosis and treatment of OC were emphasized, cementing the bridge of communication between clinical practice and basic research.
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Affiliation(s)
- Zhong Hu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Lijin Yuan
- Department of Obstetrics and Gynecology, Huangshi Puren Hospital, Huangshi, Hubei, China
| | - Xiu Yang
- Department of Obstetrics and Gynecology, Huangshi Central Hospital, Huangshi, Hubei, China
| | - Cunjian Yi
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Jinzhi Lu
- Department of Laboratory Medicine, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
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Long Q, Li Z, Yang W, Huang K, Du G. Necroptosis-related lncRNA-based novel signature to predict the prognosis and immune landscape in soft tissue sarcomas. J Cancer Res Clin Oncol 2024; 150:203. [PMID: 38635069 PMCID: PMC11026213 DOI: 10.1007/s00432-024-05682-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 03/04/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Necroptosis-related long noncoding RNAs (lncRNAs) play crucial roles in cancer initiation and progression. Nevertheless, the role and mechanism of necroptosis-related lncRNAs in soft tissue sarcomas (STS) is so far unknown and needs to be explored further. METHODS Clinical and genomic data were obtained from the UCSC Xena database. All STS patients' subclusters were performed by unsupervised consensus clustering method based on the prognosis-specific lncRNAs, and then assessed their survival advantage and immune infiltrates. In addition, we explored the pathways and biological processes in subclusters through gene set enrichment analysis. At last, we established the necroptosis-related lncRNA-based risk signature (NRLncSig) using the least absolute shrinkage and selection operator (LASSO) method, and explored the prediction performance and immune microenvironment of this signature in STS. RESULTS A total of 911 normal soft tissue samples and 259 STS patients were included in current study. 39 prognosis-specific necroptosis-related lncRNAs were selected. Cluster 2 had a worse survival than the cluster 1 and characterized by different immune landscape in STS. A worse outcome in the high-risk group was observed by survival analysis and indicated an immunosuppressive microenvironment. The ROC curve analyses illustrated that the NRLncSig performing competitively in prediction of prognosis for STS patients. In addition, the nomogram presents excellent performance in predicting prognosis, which may be more beneficial towards STS patients' treatment. CONCLUSIONS Our result indicated that the NRLncSig could be a good independent predictor of prognosis, and significantly connected with immune microenvironment, thereby providing new insights into the roles of necroptosis-related lncRNAs in STS.
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Affiliation(s)
- Qiuzhong Long
- Department of Bone and Joint Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Zhengtian Li
- Department of Bone and Joint Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Wenkang Yang
- Guangxi Medical University, Nanning, Guangxi, China
| | - Ke Huang
- Wuming Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China.
| | - Gang Du
- Department of Bone and Joint Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China.
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Kong N, Chi Y, Ma H, Luo D. LncRNA SNHG1 acts as a ceRNA for miR-216a-3p to regulate TMBIM6 expression in esophageal squamous cell carcinoma. J Cancer 2024; 15:3128-3139. [PMID: 38706912 PMCID: PMC11064271 DOI: 10.7150/jca.95127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/21/2024] [Indexed: 05/07/2024] Open
Abstract
Background: The long noncoding RNA small nucleolar RNA host gene 1 (SNHG1) has been demonstrated to play a crucial role in the progression of esophageal squamous cell carcinoma (ESCC). The current study aims to explore the deeper molecular mechanisms of SNHG1 in ESCC. Methods: Fifty patients with ESCC were enrolled to assess overall survival. Quantitative real-time PCR was performed to measure the levels of SNHG1, miR-216a-3p, and TMBIM6 in ESCC cells. Functional assessments of SNHG1 on ESCC cells were conducted using CCK-8 assay, flow cytometry, and Transwell assays. Western blot was conducted to detect the protein levels of TMBIM6 and proapoptotic proteins (Calpain and Caspase-12). The interaction among SNHG1, miR-216a-3p, and TMBIM6 was assessed with luciferase reporter assays. Results: Our study revealed that SNHG1 was notably increased in both clinical ESCC samples and cellular lines. Upregulation of SNHG1 in ESCC tissues was indicative of poor overall survival. Functionally, SNHG1 knockdown significantly inhibited the proliferation, migration, and invasion while promoting apoptosis in ESCC cells. Mechanistically, SNHG1 functioned as a competing endogenous RNA by sequestering miR-216a-3p to modulate TMBIM6 levels in ESCC cells. Notably, inhibiting miR-216a-3p or restoring TMBIM6 reversed the inhibitory effect induced by SNHG1 knockdown in ESCC cells. Conclusions: We demonstrate for the first time that SNHG1 may act as a competing endogenous RNA and promote ESCC progression through the miR-216a-3p/TMBIM6 axis. This highlights the potential of SNHG1 as a target for ESCC treatment.
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Affiliation(s)
- Ni Kong
- Department of Thoracic Surgery, Xinjiang Medical University Affiliated Tumor Hospital, State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi 830054, China
| | - Yuheng Chi
- Department of Thoracic Surgery, Xinjiang Medical University Affiliated Tumor Hospital, State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi 830054, China
| | - Hong Ma
- Department of Pathology, School of Basic Medical Sciences, Xinjiang Medical University, State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi, Xinjiang 830054, China
- Xinjiang Key Laboratory of Molecular Biology for Endemic Diseases, Xinjiang Medical University, Urumqi, Xinjiang 830017, China
| | - Dongbo Luo
- Department of Thoracic Surgery, Xinjiang Medical University Affiliated Tumor Hospital, State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi 830054, China
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Chang F, Liu H, Wan J, Gao Y, Wang Z, Zhang L, Feng Q. Construction and Validation of a Prognostic Risk Prediction Model for Lactate Metabolism-Related lncRNA in Endometrial Cancer. Biochem Genet 2024; 62:741-760. [PMID: 37423972 DOI: 10.1007/s10528-023-10443-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 06/29/2023] [Indexed: 07/11/2023]
Abstract
Endometrial cancer (EC) is a common group of malignant epithelial tumors that mainly occur in the female endometrium. Lactate is a key regulator of signal pathways in normal and malignant tissues. However, there is still no research on lactate metabolism-related lncRNA in EC. Here, we intended to establish a prognostic risk model for EC based on lactate metabolism-related lncRNA to forecast the prognosis of EC patients. First, we found that 38 lactate metabolism-associated lncRNAs were significantly overall survival through univariate Cox regression analysis. Using minimum absolute contraction and selection operator (LASSO) regression analysis and multivariate Cox regression analysis, six lactate metabolism-related lncRNAs were established as independent predictor in EC patients and were used to establish a prognostic risk signature. We next used multifactorial COX regression analysis and receiver operating characteristic (ROC) curve analysis to confirm that risk score was an independent prognostic factor of overall patient survival. The survival time of patients with EC in different high-risk populations was obviously related to clinicopathological factors. In addition, lactate metabolism-related lncRNA in high-risk population participated in multiple aspects of EC malignant progress through Gene Set Enrichment Analysis, Genomes pathway and Kyoto Encyclopedia of Genes and Gene Ontology. And risk scores were strongly associated with tumor mutation burden, immunotherapy response and microsatellite instability. Finally, we chose a lncRNA SRP14-AS1 to validate the model we have constructed. Interestingly, we observed that the expression degree of SRP14-AS1 was lower in tumor tissues of EC patients than in normal tissues, which was consistent with our findings in the TCGA database. In conclusion, our study constructed a prognostic risk model through lactate metabolism-related lncRNA and validated the model, confirming that the model can be used to predict the prognosis of EC patients and providing a molecular analysis of potential prognostic lncRNA for EC.
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Affiliation(s)
- Fenghua Chang
- Department of Obstetrics and Gynecology, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Hongyang Liu
- Department of Obstetrics and Gynecology, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Junhu Wan
- Department of Clinical Laboratory, Key Clinical Laboratory of Henan Province, First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Ya Gao
- Department of Obstetrics and Gynecology, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Zhiting Wang
- Department of Obstetrics and Gynecology, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Lindong Zhang
- Department of Obstetrics and Gynecology, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Quanling Feng
- Department of Obstetrics and Gynecology, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
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Li P, Ding H, Han S, Ding S, Yang Y. Long noncoding RNA LINC00858 aggravates the progression of esophageal squamous cell carcinoma via regulating the miR-425-5p/ABL2 axis. Heliyon 2024; 10:e27337. [PMID: 38496838 PMCID: PMC10944188 DOI: 10.1016/j.heliyon.2024.e27337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/19/2024] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is one of the most fatal cancers with high morbidity and mortality, which severely affects people's lives. Long intergenic non-protein coding RNA 858 (LINC00858) was confirmed to promote the progression of colorectal cancer and lung cancer. However, the role of lncRNA LINC00858 is still unknown in ESCC. Herein, the main purpose of research was to explore LINC00858 function and its impact on ESCC cell biological behaviors. RT-qPCR was used to test the expression of LINC00858, miR-425-5p and ABL proto-oncogene 2 (ABL2) in ESCC cells. Functional experiments such as EdU assay, CCK-8 assay, transwell assay and Western blot assay were conducted to investigate the biological behaviors of ESCC cells. Luciferase reporter assay and RIP assay were implemented to determine the binding situation among RNAs. LINC00858 expression was abnormally high in ESCC cells and down-regulation of LINC00858 could restrain the proliferation, invasion, migration and EMT process of ESCC cells. Furthermore, miR-425-5p was proved to be sponged by LINC00858 and was down-regulated in ESCC cells. Besides, we discovered that miR-425-5p could target ABL2. Moreover, knockdown of ABL2 reversed the promoting function of miR-425-5p inhibitor on ESCC progression. LINC00858 aggravated ESCC progression via regulating the miR-425-5p/ABL2 axis.
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Affiliation(s)
- Pengfei Li
- Department of Gastroenterology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, 450003, China
| | - Hui Ding
- Department of Gastroenterology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, 450003, China
| | - Shuangyin Han
- Department of Gastroenterology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, 450003, China
| | - Songze Ding
- Department of Gastroenterology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, 450003, China
| | - Yuxiu Yang
- Department of Gastroenterology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, 450003, China
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Hosseinzadeh S, Hasanpur K. Whole genome discovery of regulatory genes responsible for the response of chicken to heat stress. Sci Rep 2024; 14:6544. [PMID: 38503864 PMCID: PMC10951342 DOI: 10.1038/s41598-024-56757-0] [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: 11/11/2023] [Accepted: 03/11/2024] [Indexed: 03/21/2024] Open
Abstract
Long noncoding RNAs (lncRNAs) are functional bridges connecting the genome with phenotypes by interacting with DNA, mRNA, and proteins. Using publically available acute heat stress (AHS)-related RNA-seq data, we discovered novel lncRNAs and tested their association with AHS along with ~ 8800 known lncRNAs and ~ 28,000 mRNA transcripts. Our pipeline discovered a total of 145 potentially novel-lncRNAs. One of them (Fishcomb_p-value = 0.06) along with another novel transcript (annotated as protein-coding; Fishcomb_p-value = 0.03) were identified as significantly associated with AHS. We found five known-lncRNAs and 134 mRNAs transcripts that were significantly associated with AHS. Four novel lncRNAs interact cis-regulated with 12 mRNA transcripts and are targeted by 11 miRNAs. Also six meta-lncRNAs associate with 134 meta-mRNAs through trans-acting co-expression, each targeted by 15 and 216 miRNAs, respectively. Three of the known-lncRNAs significantly co-expressed with almost 97 of the significant mRNAs (Pearson correlation p-value < 0.05). We report the mentioned three known-lncRNAs (ENSGALT00000099876, ENSGALT00000107573, and ENSGALT00000106323) as the most, significantly regulatory elements of AHS in chicken. It can be concluded that in order to alleviate the adverse effects of AHS on chicken, the manipulation of the three regulatory lncRNAs could lead to a more desirable result than the manipulation of the most significant mRNAs.
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Affiliation(s)
- Sevda Hosseinzadeh
- Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Karim Hasanpur
- Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran.
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41
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Wu Z, Jiang S, Chen Y. Non-coding RNA and Drug resistance in cholangiocarcinoma. Noncoding RNA Res 2024; 9:194-202. [PMID: 38125756 PMCID: PMC10730441 DOI: 10.1016/j.ncrna.2023.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 12/23/2023] Open
Abstract
Cholangiocarcinoma is a highly aggressive cancer with a dismal prognosis and limited resectability. Chemotherapy has demonstrated tremendous benefits for patients with advanced and inoperable cancer, but drug resistance poses a significant obstacle. Despite recent progress in cancer therapy, the mechanisms driving drug resistance are multifaceted and not completely comprehended. Non-coding RNA refers to RNA molecules that are endogenous and do not code for proteins. Particularly microRNAs, long non-coding RNAs, circular RNAs, are widely acknowledged to be involved in cancer initiation, proliferation, and metastasis. Recently, evidences suggests that abnormal expression of non-coding RNAs contributes to resistance to different type of cancer therapies in cholangiocarcinoma. This occurs via the rewiring of signaling pathways including the reduction of anticancer drugs, apoptosis, interaction between cholangiocarcinoma and tumor-infiltrating immune cells, and cancer stemness. Thus, our review aims to demonstrate the potential of targeting non-coding RNA to override drug resistance and summarize the molecular mechanisms of how non-coding RNA contributes to drug resistance in cholangiocarcinoma.
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Affiliation(s)
- Zhaowei Wu
- Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Medical College Street, Yuzhong District, 404100, Chongqing, China
| | - Shiming Jiang
- Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Medical College Street, Yuzhong District, 404100, Chongqing, China
| | - Yong Chen
- Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Medical College Street, Yuzhong District, 404100, Chongqing, China
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42
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Cao W, Yang L, Zhuang M, Lv H, Wang Y, Zhang Y, Ji J. Plant non-coding RNAs: The new frontier for the regulation of plant development and adaptation to stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 208:108435. [PMID: 38402798 DOI: 10.1016/j.plaphy.2024.108435] [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: 08/31/2023] [Revised: 02/07/2024] [Accepted: 02/11/2024] [Indexed: 02/27/2024]
Abstract
Most plant transcriptomes constitute functional non-coding RNAs (ncRNAs) that lack the ability to encode proteins. In recent years, more research has demonstrated that ncRNAs play important regulatory roles in almost all plant biological processes by modulating gene expression. Thus, it is important to study the biogenesis and function of ncRNAs, particularly in plant growth and development and stress tolerance. In this review, we systematically explore the process of formation and regulatory mechanisms of ncRNAs, particularly those of microRNAs (miRNAs), small interfering RNAs (siRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs). Additionally, we provide a comprehensive overview of the recent advancements in ncRNAs research, including their regulation of plant growth and development (seed germination, root growth, leaf morphogenesis, floral development, and fruit and seed development) and responses to abiotic and biotic stress (drought, heat, cold, salinity, pathogens and insects). We also discuss research challenges and provide recommendations to advance the understanding of the roles of ncRNAs in agronomic applications.
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Affiliation(s)
- Wenxue Cao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing 100081, China
| | - Limei Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing 100081, China
| | - Mu Zhuang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing 100081, China
| | - Honghao Lv
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing 100081, China
| | - Yong Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing 100081, China
| | - Yangyong Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing 100081, China.
| | - Jialei Ji
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing 100081, China.
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Olajide JS, Qu Z, Yang S, Yang B, Xu X, Wang J, Cai J. Eimeria falciformis extracellular vesicles differentially express host cell lncRNAs. J Eukaryot Microbiol 2024; 71:e13009. [PMID: 38073253 DOI: 10.1111/jeu.13009] [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: 08/29/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 03/10/2024]
Abstract
Long noncoding RNAs (lncRNAs) are regulatory transcripts during protozoan infections in the host intestinal epithelial cells (IECs). Apicomplexan Eimeria falciformis sporozoite extracellular vesicles (EVs) contain virulence factors that modulate host IECs pro-inflammatory genes and immune responses. In this study, E. falciformis sporozoites were made to interact with inactivated host cells, and the parasite EVs were separated from total secretome by ultracentrifugation and purified on density gradient medium. Dose-dependent bio-activity of E. falciformis EVs was investigated by RNA sequencing, functional annotation and quantitative PCR. It was found that E. falciformis EVs induced mRNA, circRNA, and lncRNA expressions in mouse IECs. Of 38, 217 lncRNAs assembled, 157 and 152 were upwardly and downwardly expressed respectively. Differentially expressed lncRNAs were associated with cytokines, pyroptosis, and immune signaling pathways including FoxO, NF-κB, MAPK, and TGF-β. In essence, E. falciformis EVs altered host cell RNA expressions during the interaction with host IECs. Also, differentially expressed lncRNAs are potential diagnostic transcripts during Eimeria infections.
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Affiliation(s)
- Joshua S Olajide
- State Key Laboratory of Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Centre for Distance Learning, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Zigang Qu
- State Key Laboratory of Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Shunli Yang
- State Key Laboratory of Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Bin Yang
- State Key Laboratory of Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xiao Xu
- State Key Laboratory of Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jing Wang
- State Key Laboratory of Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jianping Cai
- State Key Laboratory of Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
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To KKW, Huang Z, Zhang H, Ashby CR, Fu L. Utilizing non-coding RNA-mediated regulation of ATP binding cassette (ABC) transporters to overcome multidrug resistance to cancer chemotherapy. Drug Resist Updat 2024; 73:101058. [PMID: 38277757 DOI: 10.1016/j.drup.2024.101058] [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: 11/06/2023] [Revised: 12/27/2023] [Accepted: 01/16/2024] [Indexed: 01/28/2024]
Abstract
Multidrug resistance (MDR) is one of the primary factors that produces treatment failure in patients receiving cancer chemotherapy. MDR is a complex multifactorial phenomenon, characterized by a decrease or abrogation of the efficacy of a wide spectrum of anticancer drugs that are structurally and mechanistically distinct. The overexpression of the ATP-binding cassette (ABC) transporters, notably ABCG2 and ABCB1, are one of the primary mediators of MDR in cancer cells, which promotes the efflux of certain chemotherapeutic drugs from cancer cells, thereby decreasing or abolishing their therapeutic efficacy. A number of studies have suggested that non-coding RNAs (ncRNAs), particularly microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), play a pivotal role in mediating the upregulation of ABC transporters in certain MDR cancer cells. This review will provide updated information about the induction of ABC transporters due to the aberrant regulation of ncRNAs in cancer cells. We will also discuss the measurement and biological profile of circulating ncRNAs in various body fluids as potential biomarkers for predicting the response of cancer patients to chemotherapy. Sequence variations, such as alternative polyadenylation of mRNA and single nucleotide polymorphism (SNPs) at miRNA target sites, which may indicate the interaction of miRNA-mediated gene regulation with genetic variations to modulate the MDR phenotype, will be reviewed. Finally, we will highlight novel strategies that could be used to modulate ncRNAs and circumvent ABC transporter-mediated MDR.
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Affiliation(s)
- Kenneth K W To
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region.
| | - Zoufang Huang
- Department of Hematology, The First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Hang Zhang
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region
| | - Charles R Ashby
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY 11439, United States
| | - Liwu Fu
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Sun Yat-sen University Cancer Center, Guangzhou 510060, China.
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Cao Q, Wang H, Zhu J, Qi C, Huang H, Chu X. lncRNA CYTOR promotes lung adenocarcinoma gemcitabine resistance and epithelial-mesenchymal transition by sponging miR-125a-5p and upregulating ANLN and RRM2. Acta Biochim Biophys Sin (Shanghai) 2024; 56:210-222. [PMID: 38273783 PMCID: PMC10984860 DOI: 10.3724/abbs.2023287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 09/15/2023] [Indexed: 01/27/2024] Open
Abstract
Lung adenocarcinoma (LUAD) is one of the most aggressive types of lung cancer. The prognosis of LUAD patients remains poor, and the overall efficacy of gemcitabine-based chemotherapy is still unsatisfactory. Long noncoding RNAs (lncRNAs) play important roles in several cancer types by interacting with multiple proteins, RNA, and DNA. However, the relationship between lncRNA dysregulation and gemcitabine resistance in LUAD has not been fully elucidated. In this study, lncRNA CYTOR expression and its association with the prognosis of LUAD patients are assessed by quantitative RT-PCR and Kaplan-Meier survival analysis. In vitro and in vivo functional studies are conducted to evaluate the biological functions of CYTOR in LUAD. The underlying mechanism regarding the tumor-promoting effects of CYTOR is explored using RNA immunoprecipitation, biotin-labelled RNA pulldown, luciferase reporter assays, and western blot analysis. We identify that CYTOR is an oncogenic lncRNA and is apparently upregulated in LUAD by analysing TCGA-LUAD data. High CYTOR expression is a poor prognostic factor for LUAD. Functional studies reveal that CYTOR confers LUAD cells with stronger resistance to gemcitabine treatment and upregulates the expression levels of epithelial-mesenchymal transition (EMT)-related proteins. Mechanically, CYTOR acts as a competitive endogenous RNA (ceRNA) to absorb miR-125a-5p, weakens the antitumor function of miR-125a-5p, and ultimately upregulates ANLN and RRM2 expressions. Taken together, this study explains the mechanism of lncRNA in the gemcitabine resistance of LUAD and formulates a theoretical framework for the in depth study of LUAD.
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Affiliation(s)
- Qijun Cao
- Department of Medical OncologyJinling Hospitalthe First School of Clinical MedicineSouthern Medical UniversityNanjing210016China
- Department of Medical OncologyCixi Hospital Affiliated to Wenzhou Medical UniversityNingbo315300China
| | - Haixia Wang
- Department of Cardiovascular MedicineCixi Hospital Affiliated to Wenzhou Medical UniversityNingbo315300China
| | - Jialong Zhu
- Department of Medical OncologyJinling Hospitalthe First School of Clinical MedicineSouthern Medical UniversityNanjing210016China
| | - Chen Qi
- Department of Cardiothoracic SurgeryJinling HospitalMedical School of Nanjing UniversityNanjing210093China
| | - Hairong Huang
- Department of Cardiothoracic SurgeryJinling HospitalMedical School of Nanjing UniversityNanjing210093China
| | - Xiaoyuan Chu
- Department of Medical OncologyJinling Hospitalthe First School of Clinical MedicineSouthern Medical UniversityNanjing210016China
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Khanaliha K, Sadri Nahand J, Khatami A, Mirzaei H, Chavoshpour S, Taghizadieh M, Karimzadeh M, Donyavi T, Bokharaei‐Salim F. Analyzing the expression pattern of the noncoding RNAs (HOTAIR, PVT-1, XIST, H19, and miRNA-34a) in PBMC samples of patients with COVID-19, according to the disease severity in Iran during 2022-2023: A cross-sectional study. Health Sci Rep 2024; 7:e1861. [PMID: 38332929 PMCID: PMC10850438 DOI: 10.1002/hsr2.1861] [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: 08/10/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 02/10/2024] Open
Abstract
Background and aims MicroRNAs (miRNAs) and long noncoding RNAs (lncRNAs) are well-known types of noncoding RNAs (ncRNAs), which have been known as the key regulators of gene expression. They can play critical roles in viral infection by regulating the host immune response and interacting with genes in the viral genome. In this regard, ncRNAs can be employed as biomarkers for viral diseases. The current study aimed to evaluate peripheral blood mononuclear cell (PBMC) ncRNAs (lncRNAs-homeobox C antisense intergenic RNA [HOTAIR], -H19, X-inactive-specific transcript [XIST], plasmacytoma variant translocation 1 [PVT-1], and miR-34a) as diagnostic biomarkers to differentiate severe COVID-19 cases from mild ones. Methods Candidate ncRNAs were selected according to previous studies and assessed by real-time polymerase chain reaction in the PBMC samples of patients with severe coronavirus disease 2019 (COVID-19) (n = 40), healthy subjects (n = 40), and mild COVID-19 cases (n = 40). Furthermore, the diagnostic value of the selected ncRNAs was assessed by analyzing the receiver-operating characteristic (ROC). Results The results demonstrated that the expression pattern of the selected ncRNAs was significantly different between the studied groups. The levels of HOTAIR, XIST, and miR-34a were remarkably overexpressed in the severe COVID-19 group in comparison with the mild COVID-19 group, and in return, the PVT-1 levels were lower than in the mild COVID-19 group. Interestingly, the XIST expression level in men with severe COVID-19 was higher compared to women with mild COVID-19. ROC results suggested that HOTAIR and PVT-1 could serve as useful biomarkers for screening mild COVID-19 from severe COVID-19. Conclusions Overall, different expression patterns of the selected ncRNAs and ROC curve results revealed that these factors can contribute to COVID-19 pathogenicity and can be considered diagnostic markers of COVID-19 severe outcomes.
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Affiliation(s)
- Khadijeh Khanaliha
- Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious DiseasesIran University of Medical SciencesTehranIran
| | - Javid Sadri Nahand
- Infectious and Tropical Diseases Research CenterTabriz University of Medical SciencesTabrizIran
| | - AliReza Khatami
- Department of VirologyIran University of Medical SciencesTehranIran
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic DiseasesKashan University of Medical SciencesKashanIran
| | - Sara Chavoshpour
- Department of VirologyTehran University of Medical SciencesTehranIran
| | - Mohammad Taghizadieh
- Department of Pathology, Faculty of MedicineTabriz University of Medical SciencesTabrizIran
| | - Mohammad Karimzadeh
- Core Research Facilities (CRF)Isfahan University of Medical ScienceIsfahanIran
| | - Tahereh Donyavi
- Department of Medical Biotechnology, Faculty of Allied MedicineIran University of Medical SciencesTehranIran
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Xu C, Xu P, Zhang J, He S, Hua T, Huang A. Research progress and perspectives of noncoding RNAs in adrenocortical carcinoma: A review. Medicine (Baltimore) 2024; 103:e36908. [PMID: 38277554 PMCID: PMC10817030 DOI: 10.1097/md.0000000000036908] [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: 10/04/2023] [Accepted: 12/18/2023] [Indexed: 01/28/2024] Open
Abstract
Adrenocortical carcinoma (ACC) is a rare and highly aggressive endocrine malignancy. Although surgery can cure localized disease, but the majority of patients experience recurrence of ACC. The 5-year survival rate of patients with metastatic ACC is <15%, and the prognosis is poor. Therefore, it is urgent to explore the potential diagnostic markers and therapeutic targets for ACC. Recently, it has been proved that non-coding RNA (ncRNAs) is widely involved in pathological and physiological processes, including tumorigenesis and development. Aberrantly expressed ncRNAs have been found to be involved in the pathogenesis of ACC. Here, we summarized the expression patterns and the molecular mechanism of the involvement of microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) in ACC development. To explore the clinical value of ncRNAs as noninvasive biomarkers of ACC, we also displayed the relationship between the expression level of ncRNAs and the diagnosis and prognosis of patients with ACC.
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Affiliation(s)
- Changfen Xu
- Department of Gynecology and Obstetrics, Hangzhou Lin’an TCM Hospital, Lin’an District, Hangzhou, China
| | - Peiyao Xu
- Department of Gynecology and Obstetrics, Hangzhou Lin’an TCM Hospital, Lin’an District, Hangzhou, China
| | - Jiaqi Zhang
- Department of Gynecology and Obstetrics, Hangzhou Lin’an TCM Hospital, Lin’an District, Hangzhou, China
| | - Sheng He
- Department of Gynecology and Obstetrics, Hangzhou Lin’an TCM Hospital, Lin’an District, Hangzhou, China
| | - Tingting Hua
- Department of Gynecology and Obstetrics, Hangzhou Lin’an TCM Hospital, Lin’an District, Hangzhou, China
| | - Aiwu Huang
- Department of Gynecology and Obstetrics, Hangzhou Lin’an TCM Hospital, Lin’an District, Hangzhou, China
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48
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Ahmadi M, Morshedzadeh F, Ghaderian SMH, Mousavi P, Habibipour L, Peymani M, Abbaszadegan MR, Ghafouri-Fard S. Carcinogenic roles of MAFG-AS1 in human cancers. Clin Transl Oncol 2024; 26:52-68. [PMID: 37351806 DOI: 10.1007/s12094-023-03246-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 06/02/2023] [Indexed: 06/24/2023]
Abstract
The MAF bZIP transcription factor G-antisense RNA 1 (MAFG-AS1) is located on chromosome 17. MAFG-AS1 was upregulated in 15 human cancers. MAFG-AS1 not only suppresses 16 miRNAs but also directly impacts 22 protein-coding genes' expression. Notably, abnormal MAFG-AS1 expression is connected to clinicopathological characteristics and a worse prognosis in a variety of cancers. Moreover, MAFG-AS1 takes its part in the tumorigenesis and progression of various human malignancies by suppressing apoptosis and promoting proliferation, migration, invasion, aerobic glycolysis, ferroptosis, angiogenesis, EMT, and metastasis. Besides, it can predict treatment effectiveness in ER + breast cancer, urothelial bladder carcinoma, and liver cancer by functioning as a trigger of resistance to tamoxifen, sorafenib, and cisplatin. This study systematically presents the functions of MAFG-AS1 in various cancers, as well as the findings of bioinformatics analyses of the MAFG-AS1, which should give clear advice for future research.
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Affiliation(s)
- Mohsen Ahmadi
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Firouzeh Morshedzadeh
- Department of Genetics, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Pegah Mousavi
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran.
| | - Leila Habibipour
- Department of Biotechnology, Institute of Science and High Technology and Environmental Science, Graduate University of Advanced Technology, Kerman, Iran
| | - Maryam Peymani
- Department of Genetics, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Mohammad Reza Abbaszadegan
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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49
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Xie D, Han Y, Zhang W, Wu J, An B, Huang S, Sun F. Long Non-Coding RNA H19 Leads to Upregulation of γ-Globin Gene Expression during Erythroid Differentiation. Hemoglobin 2024; 48:4-14. [PMID: 38419555 DOI: 10.1080/03630269.2023.2284950] [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: 06/21/2023] [Accepted: 11/13/2023] [Indexed: 03/02/2024]
Abstract
Long noncoding RNAs (lncRNAs) are important because they are involved in a variety of life activities and have many downstream targets. Moreover, there is also increasing evidence that some lncRNAs play important roles in the expression and regulation of γ-globin genes. In our previous study, we analyzed genetic material from nucleated red blood cells (NRBCs) extracted from premature and full-term umbilical cord blood samples. Through RNA sequencing (RNA-Seq) analysis, lncRNA H19 emerged as a differentially expressed transcript between the two blood types. While this discovery provided insight into H19, previous studies had not investigated its effect on the γ-globin gene. Therefore, the focus of our study was to explore the impact of H19 on the γ-globin gene. In this study, we discovered that overexpressing H19 led to a decrease in HBG mRNA levels during erythroid differentiation in K562 cells. Conversely, in CD34+ hematopoietic stem cells and human umbilical cord blood-derived erythroid progenitor (HUDEP-2) cells, HBG expression increased. Additionally, we observed that H19 was primarily located in the nucleus of K562 cells, while in HUDEP-2 cells, H19 was present predominantly in the cytoplasm. These findings suggest a significant upregulation of HBG due to H19 overexpression. Notably, cytoplasmic localization in HUDEP-2 cells hints at its potential role as a competing endogenous RNA (ceRNA), regulating γ-globin expression by targeting microRNA/mRNA interactions.
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Affiliation(s)
- Dan Xie
- Medical College, Guizhou University, Guiyang, China
| | - Yuanyuan Han
- Department of laboratory medicine, Guangzhou Second Provincial General Hospotal, Guangzhou, China
| | - Wenyi Zhang
- Medical College, Guizhou University, Guiyang, China
| | - Jiangfen Wu
- Medical College, Guizhou University, Guiyang, China
| | - Banquan An
- Discipline Inspection and Supervision Office, Guizhou Provincial People's Hospital, Guiyang, Guizhou, China
| | - Shengwen Huang
- Medical College, Guizhou University, Guiyang, China
- Prenatal Diagnostic Center, Guizhou Provincial People's Hospital, Guiyang, Guizhou, China
| | - Fa Sun
- Medical College, Guizhou University, Guiyang, China
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50
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Wang Y, Zhu W, Ma R, Tian Y, Chen X, Gao P. PIN1P1 is activated by CREB1 and promotes gastric cancer progression via interacting with YBX1 and upregulating PIN1. J Cell Mol Med 2024; 28:e18022. [PMID: 37929660 PMCID: PMC10805483 DOI: 10.1111/jcmm.18022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 10/05/2023] [Accepted: 10/22/2023] [Indexed: 11/07/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) play critical roles in the carcinogenesis and progression of cancers. However, the role and mechanism of the pseudogene lncRNA PIN1P1 in gastric carcinoma remain unclear. The expression and effects of lncRNA PIN1P1 in gastric cancer were investigated. The transcriptional regulation of CREB1 on PIN1P1 was determined by ChIP and luciferase assays. The mechanistic model of PIN1P1 in gastric cancer was further explored by RNA pull-down, RIP and western blot analysis. PIN1P1 was overexpressed in gastric cancer tissues, and upregulated PIN1P1 predicted poor prognosis in patients. CREB1 was directly combined with the promoter region of PIN1P1 to promote the transcription of PIN1P1. CREB1-mediated enhanced proliferation, migration and invasion could be partially reversed by downregulation of PIN1P1. Overexpressed PIN1P1 promoted the proliferation, migration and invasion of gastric cancer cells, whereas decreased PIN1P1 showed the opposite effects. PIN1P1 directly interacted with YBX1 and promoted YBX1 protein expression, leading to upregulation of PIN1, in which E2F1 may be involved. Silencing of YBX1 during PIN1P1 overexpression could partially rescue PIN1 upregulation. PIN1, the parental gene of PIN1P1, was elevated in gastric cancer tissues, and its upregulation was correlated with poor patient outcomes. PIN1 facilitated gastric cancer cell proliferation, migration and invasion. To sum up, CREB1-activated PIN1P1 could promote gastric cancer progression through YBX1 and upregulating PIN1, suggesting that it is a potential target for gastric cancer.
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Affiliation(s)
- Ya‐Wen Wang
- Department of PathologyQilu Hospital of Shandong UniversityJinanShandongChina
- Key Laboratory for Experimental Teratology of Ministry of Education, Department of Pathology, School of Basic Medical SciencesShandong UniversityJinanShandongChina
| | - Wen‐Jie Zhu
- Department of PathologyQilu Hospital of Shandong UniversityJinanShandongChina
- Key Laboratory for Experimental Teratology of Ministry of Education, Department of Pathology, School of Basic Medical SciencesShandong UniversityJinanShandongChina
| | - Ran‐Ran Ma
- Department of PathologyQilu Hospital of Shandong UniversityJinanShandongChina
- Key Laboratory for Experimental Teratology of Ministry of Education, Department of Pathology, School of Basic Medical SciencesShandong UniversityJinanShandongChina
| | - Ya‐Ru Tian
- Department of Radiation Oncology, Shandong Cancer Hospital and InstituteShandong First Medical University and Shandong Academy of Medical ScienceJinanShandongChina
| | - Xu Chen
- Department of PathologyQilu Hospital of Shandong UniversityJinanShandongChina
- Key Laboratory for Experimental Teratology of Ministry of Education, Department of Pathology, School of Basic Medical SciencesShandong UniversityJinanShandongChina
| | - Peng Gao
- Department of PathologyQilu Hospital of Shandong UniversityJinanShandongChina
- Key Laboratory for Experimental Teratology of Ministry of Education, Department of Pathology, School of Basic Medical SciencesShandong UniversityJinanShandongChina
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