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Gallardo-Dodd CJ, Kutter C. The regulatory landscape of interacting RNA and protein pools in cellular homeostasis and cancer. Hum Genomics 2024; 18:109. [PMID: 39334294 PMCID: PMC11437681 DOI: 10.1186/s40246-024-00678-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 09/22/2024] [Indexed: 09/30/2024] Open
Abstract
Biological systems encompass intricate networks governed by RNA-protein interactions that play pivotal roles in cellular functions. RNA and proteins constituting 1.1% and 18% of the mammalian cell weight, respectively, orchestrate vital processes from genome organization to translation. To date, disentangling the functional fraction of the human genome has presented a major challenge, particularly for noncoding regions, yet recent discoveries have started to unveil a host of regulatory functions for noncoding RNAs (ncRNAs). While ncRNAs exist at different sizes, structures, degrees of evolutionary conservation and abundances within the cell, they partake in diverse roles either alone or in combination. However, certain ncRNA subtypes, including those that have been described or remain to be discovered, are poorly characterized given their heterogeneous nature. RNA activity is in most cases coordinated through interactions with RNA-binding proteins (RBPs). Extensive efforts are being made to accurately reconstruct RNA-RBP regulatory networks, which have provided unprecedented insight into cellular physiology and human disease. In this review, we provide a comprehensive view of RNAs and RBPs, focusing on how their interactions generate functional signals in living cells, particularly in the context of post-transcriptional regulatory processes and cancer.
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Affiliation(s)
- Carlos J Gallardo-Dodd
- Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden
| | - Claudia Kutter
- Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden.
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2
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Majer AD, Hua X, Katona BW. Menin in Cancer. Genes (Basel) 2024; 15:1231. [PMID: 39336822 PMCID: PMC11431421 DOI: 10.3390/genes15091231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2024] [Revised: 09/13/2024] [Accepted: 09/14/2024] [Indexed: 09/30/2024] Open
Abstract
The protein menin is encoded by the MEN1 gene and primarily serves as a nuclear scaffold protein, regulating gene expression through its interaction with and regulation of chromatin modifiers and transcription factors. While the scope of menin's functions continues to expand, one area of growing investigation is the role of menin in cancer. Menin is increasingly recognized for its dual function as either a tumor suppressor or a tumor promoter in a highly tumor-dependent and context-specific manner. While menin serves as a suppressor of neuroendocrine tumor growth, as seen in the cancer risk syndrome multiple endocrine neoplasia type 1 (MEN1) syndrome caused by pathogenic germline variants in MEN1, recent data demonstrate that menin also suppresses cholangiocarcinoma, pancreatic ductal adenocarcinoma, gastric adenocarcinoma, lung adenocarcinoma, and melanoma. On the other hand, menin can also serve as a tumor promoter in leukemia, colorectal cancer, ovarian and endometrial cancers, Ewing sarcoma, and gliomas. Moreover, menin can either suppress or promote tumorigenesis in the breast and prostate depending on hormone receptor status and may also have mixed roles in hepatocellular carcinoma. Here, we review the rapidly expanding literature on the role and function of menin across a broad array of different cancer types, outlining tumor-specific differences in menin's function and mechanism of action, as well as identifying its therapeutic potential and highlighting areas for future investigation.
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Affiliation(s)
- Ariana D Majer
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xianxin Hua
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bryson W Katona
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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3
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Shao M, Tian M, Chen K, Jiang H, Zhang S, Li Z, Shen Y, Chen F, Shen B, Cao C, Gu N. Leveraging Random Effects in Cistrome-Wide Association Studies for Decoding the Genetic Determinants of Prostate Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400815. [PMID: 39099406 PMCID: PMC11423091 DOI: 10.1002/advs.202400815] [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: 01/23/2024] [Revised: 07/09/2024] [Indexed: 08/06/2024]
Abstract
Cistrome-wide association studies (CWAS) are pivotal for identifying genetic determinants of diseases by correlating genetically regulated cistrome states with phenotypes. Traditional CWAS typically develops a model based on cistrome and genotype data to associate predicted cistrome states with phenotypes. The random effect cistrome-wide association study (RECWAS), reevaluates the necessity of cistrome state prediction in CWAS. RECWAS utilizes either a linear model or marginal effect for initial feature selection, followed by kernel-based feature aggregation for association testing is introduced. Through simulations and analysis of prostate cancer data, a thorough evaluation of CWAS and RECWAS is conducted. The results suggest that RECWAS offers improved power compared to traditional CWAS, identifying additional genomic regions associated with prostate cancer. CWAS identified 102 significant regions, while RECWAS found 50 additional significant regions compared to CWAS, many of which are validated. Validation encompassed a range of biological evidence, including risk signals from the GWAS catalog, susceptibility genes from the DisGeNET database, and enhancer-domain scores. RECWAS consistently demonstrated improved performance over traditional CWAS in identifying genomic regions associated with prostate cancer. These findings demonstrate the benefits of incorporating kernel methods into CWAS and provide new insights for genetic discovery in complex diseases.
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Affiliation(s)
- Mengting Shao
- Key Laboratory for Bio‐Electromagnetic Environment and Advanced Medical TheranosticsSchool of Biomedical Engineering and InformaticsNanjing Medical UniversityNanjing211166P. R. China
| | - Min Tian
- Key Laboratory for Bio‐Electromagnetic Environment and Advanced Medical TheranosticsSchool of Biomedical Engineering and InformaticsNanjing Medical UniversityNanjing211166P. R. China
| | - Kaiyang Chen
- Key Laboratory for Bio‐Electromagnetic Environment and Advanced Medical TheranosticsSchool of Biomedical Engineering and InformaticsNanjing Medical UniversityNanjing211166P. R. China
| | - Hangjin Jiang
- Center for Data ScienceZhejiang UniversityHangzhou310058P. R. China
| | - Shuting Zhang
- Key Laboratory for Bio‐Electromagnetic Environment and Advanced Medical TheranosticsSchool of Biomedical Engineering and InformaticsNanjing Medical UniversityNanjing211166P. R. China
| | - Zhenghui Li
- Key Laboratory for Bio‐Electromagnetic Environment and Advanced Medical TheranosticsSchool of Biomedical Engineering and InformaticsNanjing Medical UniversityNanjing211166P. R. China
| | - Yan Shen
- Key Laboratory for Bio‐Electromagnetic Environment and Advanced Medical TheranosticsSchool of Biomedical Engineering and InformaticsNanjing Medical UniversityNanjing211166P. R. China
| | - Feng Chen
- Key Laboratory for Bio‐Electromagnetic Environment and Advanced Medical TheranosticsSchool of Biomedical Engineering and InformaticsNanjing Medical UniversityNanjing211166P. R. China
| | - Baixin Shen
- Department of UrologyThe Second Affiliated Hospital of Nanjing Medical UniversityNanjing210011P. R. China
| | - Chen Cao
- Key Laboratory for Bio‐Electromagnetic Environment and Advanced Medical TheranosticsSchool of Biomedical Engineering and InformaticsNanjing Medical UniversityNanjing211166P. R. China
- Department of UrologyThe Second Affiliated Hospital of Nanjing Medical UniversityNanjing210011P. R. China
| | - Ning Gu
- Key Laboratory for Bio‐Electromagnetic Environment and Advanced Medical TheranosticsSchool of Biomedical Engineering and InformaticsNanjing Medical UniversityNanjing211166P. R. China
- Nanjing Key Laboratory for Cardiovascular Information and Health Engineering MedicineInstitute of Clinical MedicineNanjing Drum Tower HospitalMedical SchoolNanjing UniversityNanjing210093P. R. China
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Qiu J, Lai C, Yuan Z, Hu J, Wu J, Liu C, Xu K. Utilizing Liquid-liquid phase separation-related lncRNAs to predict the prognosis and treatment response of PCa. Discov Oncol 2024; 15:352. [PMID: 39150479 PMCID: PMC11329450 DOI: 10.1007/s12672-024-01226-3] [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: 03/04/2024] [Accepted: 08/07/2024] [Indexed: 08/17/2024] Open
Abstract
BACKGROUND Studies have indicated a close association between genes linked to liquid-liquid phase separation (LLPS) and the progression of prostate cancer (PCa). However, the interplay among long non-coding RNAs (lncRNAs) linked to LLPS in PCa remains elusive. Therefore, we constructed a prediction model based on LLPS-related LncRNA in PCa to explore its relationship with the prognosis and drug treatment of PCa. METHODS We obtained clinical and sequencing data from TCGA and LLPS genes from the Phase Separation Protein Database. By analyzing the differential expression of LLPS-related genes and lncRNAs in prostate cancer, and using Poisson correlation, we identified LLPS-related lncRNAs. Prognostic LLPS-lncRNAs were found through prognostic correlation analysis and included in a Cox model to compute regression coefficients. Patients were scored and divided into high- and low-risk groups. Independent prognostic factors were integrated into a prognostic nomogram with risk and Gleason scores. We also conducted drug sensitivity analyses, GSEA, and validated the impact of key lncRNAs through functional experiments. RESULTS Our study identified five LLPS-associated lncRNAs that are of prognostic importance. And found notable disparities in biochemical recurrence rates and survival outcomes between these risk groups, with the low-risk cohort exhibiting superior prognostic indicators. Moreover, our prediction nomogram demonstrated robust predictive accuracy and significant clinical utility. Furthermore, our model exhibited promising capabilities in forecasting patient sensitivity to various conventional therapeutic drugs, thereby highlighting its potential in personalized treatment strategies. GSEA showed that these lncRNAs may influence PCa prognosis and sensitivity to therapeutic agents by affecting pathways such as cell cycle. Knockdown of AC009812.4 could inhibit the ability of PCa cells to proliferate, migrate and invade, and compare to paracancerous tissue, AC009812.4 in PCa tissue has significantly higher expression. CONCLUSION Our research uncovers the prognostic significance of lncRNAs associated with LLPS in PCa and established a model exhibiting excellent predictive accuracy for prognosis. Those lncRNAs may influence progress of PCa as well as sensitivity to therapy drugs through pathways such as cell cycle.
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Affiliation(s)
- Jiangping Qiu
- Shenshan Medical Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, No.1 Zhanqian Heng'er Road, Dongchong Town, Shanwei City, 516621, Guangdong, China
| | - Cong Lai
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, No.107 Yanjiang West Road, Guangzhou, 510000, Guangdong, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510000, Guangdong, China
| | - Zhihan Yuan
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, No.107 Yanjiang West Road, Guangzhou, 510000, Guangdong, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510000, Guangdong, China
| | - Jintao Hu
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, No.107 Yanjiang West Road, Guangzhou, 510000, Guangdong, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510000, Guangdong, China
| | - Jiang Wu
- Shenshan Medical Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, No.1 Zhanqian Heng'er Road, Dongchong Town, Shanwei City, 516621, Guangdong, China.
| | - Cheng Liu
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, No.107 Yanjiang West Road, Guangzhou, 510000, Guangdong, China.
- Guangdong Provincial Clinical Research Center for Urological Diseases, Guangzhou, 510000, Guangdong, China.
| | - Kewei Xu
- Shenshan Medical Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, No.1 Zhanqian Heng'er Road, Dongchong Town, Shanwei City, 516621, Guangdong, China.
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, No.107 Yanjiang West Road, Guangzhou, 510000, Guangdong, China.
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510000, Guangdong, China.
- Guangdong Provincial Clinical Research Center for Urological Diseases, Guangzhou, 510000, Guangdong, China.
- Sun Yat-Sen University School of Medicine, Sun Yat-Sen University, Shenzhen, 518000, Guangdong, China.
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Lei Z, Zhu Z, Yao Z, Dai X, Dong Y, Chen B, Wang S, Wang S, Bentum-Ennin L, Jin L, Gu H, Hu W. Reciprocal interactions between lncRNAs and MYC in colorectal cancer: partners in crime. Cell Death Dis 2024; 15:539. [PMID: 39075086 PMCID: PMC11286766 DOI: 10.1038/s41419-024-06918-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: 02/22/2024] [Revised: 07/11/2024] [Accepted: 07/17/2024] [Indexed: 07/31/2024]
Abstract
Proto-oncogenic MYC is frequently dysregulated in colorectal cancer (CRC). In the past decades, long noncoding RNAs (lncRNAs) have emerged as important regulators in cancers, acting as scaffolds, molecular decoys, post-transcriptional regulators, and others. Interestingly, lncRNAs are able to control MYC expression both at transcriptional and post-transcriptional levels. It is suggested that the reciprocal interaction of MYC and lncRNAs often occurs in CRC. MYC can affect the cell fate by promoting or inhibiting the transcription of some lncRNAs. At the same time, some lncRNAs can also affect MYC expression or transcriptional activity, and in turn decide the cell fate. In this review we summarized the current knowledge about the MYC and lncRNA axis, focusing on its mutual regulation, roles in CRC, and proposed potential therapeutic prospects for CRC treatment.
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Affiliation(s)
- Zhen Lei
- Translational Research Institute, People's Hospital of Zhengzhou University, Academy of Medical Science, Henan International Joint Laboratory of Non-coding RNA and Metabolism in Cancer, Tianjian Laboratory of Advanced Biomedical Sciences, State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, 450003, China
| | - Zhipu Zhu
- Translational Research Institute, People's Hospital of Zhengzhou University, Academy of Medical Science, Henan International Joint Laboratory of Non-coding RNA and Metabolism in Cancer, Tianjian Laboratory of Advanced Biomedical Sciences, State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, 450003, China
| | - Zhihui Yao
- Translational Research Institute, People's Hospital of Zhengzhou University, Academy of Medical Science, Henan International Joint Laboratory of Non-coding RNA and Metabolism in Cancer, Tianjian Laboratory of Advanced Biomedical Sciences, State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, 450003, China
| | - Xiangyu Dai
- Translational Research Institute, People's Hospital of Zhengzhou University, Academy of Medical Science, Henan International Joint Laboratory of Non-coding RNA and Metabolism in Cancer, Tianjian Laboratory of Advanced Biomedical Sciences, State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, 450003, China
| | - Yi Dong
- Translational Research Institute, People's Hospital of Zhengzhou University, Academy of Medical Science, Henan International Joint Laboratory of Non-coding RNA and Metabolism in Cancer, Tianjian Laboratory of Advanced Biomedical Sciences, State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, 450003, China
| | - Bing Chen
- Translational Research Institute, People's Hospital of Zhengzhou University, Academy of Medical Science, Henan International Joint Laboratory of Non-coding RNA and Metabolism in Cancer, Tianjian Laboratory of Advanced Biomedical Sciences, State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, 450003, China
| | - Songyu Wang
- Translational Research Institute, People's Hospital of Zhengzhou University, Academy of Medical Science, Henan International Joint Laboratory of Non-coding RNA and Metabolism in Cancer, Tianjian Laboratory of Advanced Biomedical Sciences, State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, 450003, China
| | - Siyue Wang
- Translational Research Institute, People's Hospital of Zhengzhou University, Academy of Medical Science, Henan International Joint Laboratory of Non-coding RNA and Metabolism in Cancer, Tianjian Laboratory of Advanced Biomedical Sciences, State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, 450003, China
| | - Lutterodt Bentum-Ennin
- Department of Immunology, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230027, China
| | - Lei Jin
- Translational Research Institute, People's Hospital of Zhengzhou University, Academy of Medical Science, Henan International Joint Laboratory of Non-coding RNA and Metabolism in Cancer, Tianjian Laboratory of Advanced Biomedical Sciences, State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, 450003, China.
| | - Hao Gu
- Department of Immunology, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230027, China.
| | - Wanglai Hu
- Translational Research Institute, People's Hospital of Zhengzhou University, Academy of Medical Science, Henan International Joint Laboratory of Non-coding RNA and Metabolism in Cancer, Tianjian Laboratory of Advanced Biomedical Sciences, State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, 450003, China.
- Department of Immunology, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230027, China.
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Zhu K, Jones MG, Luebeck J, Bu X, Yi H, Hung KL, Wong ITL, Zhang S, Mischel PS, Chang HY, Bafna V. CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.15.580594. [PMID: 38405779 PMCID: PMC10888815 DOI: 10.1101/2024.02.15.580594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Extrachromosomal DNA (ecDNA) is a central mechanism for focal oncogene amplification in cancer, occurring in approximately 15% of early stage cancers and 30% of late-stage cancers. EcDNAs drive tumor formation, evolution, and drug resistance by dynamically modulating oncogene copy-number and rewiring gene-regulatory networks. Elucidating the genomic architecture of ecDNA amplifications is critical for understanding tumor pathology and developing more effective therapies. Paired-end short-read (Illumina) sequencing and mapping have been utilized to represent ecDNA amplifications using a breakpoint graph, where the inferred architecture of ecDNA is encoded as a cycle in the graph. Traversals of breakpoint graph have been used to successfully predict ecDNA presence in cancer samples. However, short-read technologies are intrinsically limited in the identification of breakpoints, phasing together of complex rearrangements and internal duplications, and deconvolution of cell-to-cell heterogeneity of ecDNA structures. Long-read technologies, such as from Oxford Nanopore Technologies, have the potential to improve inference as the longer reads are better at mapping structural variants and are more likely to span rearranged or duplicated regions. Here, we propose CoRAL (Complete Reconstruction of Amplifications with Long reads), for reconstructing ecDNA architectures using long-read data. CoRAL reconstructs likely cyclic architectures using quadratic programming that simultaneously optimizes parsimony of reconstruction, explained copy number, and consistency of long-read mapping. CoRAL substantially improves reconstructions in extensive simulations and 9 datasets from previously-characterized cell-lines as compared to previous short-read-based tools. As long-read usage becomes wide-spread, we anticipate that CoRAL will be a valuable tool for profiling the landscape and evolution of focal amplifications in tumors.
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Affiliation(s)
- Kaiyuan Zhu
- Department of Computer Science & Engineering, UC San Diego, La Jolla, CA, USA
- These authors contributed equally to this work
| | - Matthew G. Jones
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- These authors contributed equally to this work
| | - Jens Luebeck
- Department of Computer Science & Engineering, UC San Diego, La Jolla, CA, USA
| | - Xinxin Bu
- Bioinformatics Undergraduate Program, School of Biological Sciences, UC San Diego, La Jolla, CA, USA
| | - Hyerim Yi
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - King L. Hung
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Ivy Tsz-Lo Wong
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan Chemistry, Engineering, and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA, USA
| | - Shu Zhang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Paul S. Mischel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan Chemistry, Engineering, and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA, USA
| | - Howard Y. Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Vineet Bafna
- Department of Computer Science & Engineering, UC San Diego, La Jolla, CA, USA
- Halicioglu Data Science Institute, UC San Diego, La Jolla, CA, USA
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7
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Ke Z, Hu X, Liu Y, Shen D, Khan MI, Xiao J. Updated review on analysis of long non-coding RNAs as emerging diagnostic and therapeutic targets in prostate cancers. Crit Rev Oncol Hematol 2024; 196:104275. [PMID: 38302050 DOI: 10.1016/j.critrevonc.2024.104275] [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: 10/08/2023] [Revised: 01/22/2024] [Accepted: 01/26/2024] [Indexed: 02/03/2024] Open
Abstract
Despite advancements, prostate cancers (PCa) pose a significant global health challenge due to delayed diagnosis and therapeutic resistance. This review delves into the complex landscape of prostate cancer, with a focus on long-noncoding RNAs (lncRNAs). Also explores the influence of aberrant lncRNAs expression in progressive PCa stages, impacting traits like proliferation, invasion, metastasis and therapeutic resistance. The study elucidates how lncRNAs modulate crucial molecular effectors, including transcription factors and microRNAs, affecting signaling pathways such as androgen receptor signaling. Besides, this manuscript sheds light on novel concepts and mechanisms driving PCa progression through lncRNAs, providing a critical analysis of their impact on the disease's diverse characteristics. Besides, it discusses the potential of lncRNAs as diagnostics and therapeutic targets in PCa. Collectively, this work highlights state of art mechanistic comprehension and rigorous scientific approaches to advance our understanding of PCa and depict innovations in this evolving field of research.
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Affiliation(s)
- Zongpan Ke
- Department of Urology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, No. 17 Lujiang Road, Luyang District, Hefei 230001, China; Wannan Medical College, No. 22 Wenchangxi Road, Yijiang District, Wuhu 241000, China
| | - Xuechun Hu
- Department of Urology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, No. 17 Lujiang Road, Luyang District, Hefei 230001, China
| | - Yixun Liu
- Department of Urology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, No. 17 Lujiang Road, Luyang District, Hefei 230001, China
| | - Deyun Shen
- Department of Urology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, No. 17 Lujiang Road, Luyang District, Hefei 230001, China.
| | - Muhammad Imran Khan
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, 230026 China.
| | - Jun Xiao
- Department of Urology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, No. 17 Lujiang Road, Luyang District, Hefei 230001, China.
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Davodabadi F, Mirinejad S, Malik S, Dhasmana A, Ulucan-Karnak F, Sargazi S, Sargazi S, Fathi-Karkan S, Rahdar A. Nanotherapeutic approaches for delivery of long non-coding RNAs: an updated review with emphasis on cancer. NANOSCALE 2024; 16:3881-3914. [PMID: 38353296 DOI: 10.1039/d3nr05656b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
The long noncoding RNAs (lncRNAs) comprise a wide range of RNA species whose length exceeds 200 nucleotides, which regulate the expression of genes and cellular functions in a wide range of organisms. Several diseases, including malignancy, have been associated with lncRNA dysregulation. Due to their functions in cancer development and progression, lncRNAs have emerged as promising biomarkers and therapeutic targets in cancer diagnosis and treatment. Several studies have investigated the anti-cancer properties of lncRNAs; however, only a few lncRNAs have been found to exhibit tumor suppressor properties. Furthermore, their length and poor stability make them difficult to synthesize. Thus, to overcome the instability of lncRNAs, poor specificity, and their off-target effects, researchers have constructed nanocarriers that encapsulate lncRNAs. Recently, translational medicine research has focused on delivering lncRNAs into tumor cells, including cancer cells, through nano-drug delivery systems in vivo. The developed nanocarriers can protect, target, and release lncRNAs under controlled conditions without appreciable adverse effects. To deliver lncRNAs to cancer cells, various nanocarriers, such as exosomes, microbubbles, polymer nanoparticles, 1,2-dioleyl-3-trimethylammoniumpropane chloride nanocarriers, and virus-like particles, have been successfully developed. Despite this, every nanocarrier has its own advantages and disadvantages when it comes to delivering nucleic acids effectively and safely. This article examines the current status of nanocarriers for lncRNA delivery in cancer therapy, focusing on their potential to enhance cancer treatment.
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Affiliation(s)
- Fatemeh Davodabadi
- Department of Biology, Faculty of Basic Science, Payame Noor University, Tehran, Iran.
| | - Shekoufeh Mirinejad
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran.
| | - Sumira Malik
- Amity Institute of Biotechnology, Amity University Jharkhand, Ranchi-834002, India.
| | - Archna Dhasmana
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun, Uttarakhand, 248140, India.
| | - Fulden Ulucan-Karnak
- Department of Medical Biochemistry, Institute of Health Sciences, Ege University, İzmir 35100, Turkey.
| | - Sara Sargazi
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran.
| | - Saman Sargazi
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran.
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Sonia Fathi-Karkan
- Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, 94531-55166, Iran
- Department of Advanced Sciences and Technologies in Medicine, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd 9414974877, Iran.
| | - Abbas Rahdar
- Department of Physics, University of Zabol, Zabol, P. O. Box. 98613-35856, Iran.
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Sadi Khosroshahi N, Koulaeizadeh S, Abdi A, Akbarzadeh S, Hashemi Aghdam SM, Rajabi A, Safaralizadeh R. Upregulation of Long Noncoding RNA PCAT1 in Iranian Patients with Colorectal Cancer and Its Performance as a Potential Diagnostic Biomarker. Genet Test Mol Biomarkers 2024; 28:65-69. [PMID: 38416663 DOI: 10.1089/gtmb.2023.0676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2024] Open
Abstract
Background: Long noncoding RNAs (lncRNAs) as critical molecules play an essential role in the development of cancers. In colorectal cancer (CRC), various lncRNAs are related to cell proliferation, apoptosis, migration, and invasion. LncRNA prostate cancer-associated transcript 1 (PCAT-1), as an oncogenic factor, is a diagnostic biomarker that regulates cell proliferation, migration, invasion, and apoptosis. Methods: This study evaluated the relationship between PCAT-1, CRC occurrence, and pathological features of Iranian patients. The studied samples included 100 colorectal tumor tissues and 100 adjacent healthy tissues of Iranian CRC patients. RNAs were extracted from cancerous and noncancerous tissues to synthesize complementary DNA. The expression level of PCAT-1 was assessed using the real-time PCR method, and the data analysis was assessed using SPSS software. Results: In this study, expression level of PCAT-1 in tumor tissue was significantly increased in Iranian patients, and pathological studies of the patients had no significant relationship with the PCAT-1 expression profile. Conclusion: Our results suggested that the high expression of PCAT-1 resulted in the occurrence of colorectal tumor tissues in Iranian patients, which can be considered a diagnostic biomarker in CRC.
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Affiliation(s)
- Negin Sadi Khosroshahi
- Department of Biology, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Shabnam Koulaeizadeh
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Adel Abdi
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Sama Akbarzadeh
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | | | - Ali Rajabi
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Reza Safaralizadeh
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
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Mahato RK, Bhattacharya S, Khullar N, Sidhu IS, Reddy PH, Bhatti GK, Bhatti JS. Targeting long non-coding RNAs in cancer therapy using CRISPR-Cas9 technology: A novel paradigm for precision oncology. J Biotechnol 2024; 379:98-119. [PMID: 38065367 DOI: 10.1016/j.jbiotec.2023.12.003] [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: 09/08/2023] [Revised: 11/30/2023] [Accepted: 12/03/2023] [Indexed: 12/25/2023]
Abstract
Cancer is the second leading cause of death worldwide, despite recent advances in its identification and management. To improve cancer patient diagnosis and care, it is necessary to identify new biomarkers and molecular targets. In recent years, long non-coding RNAs (lncRNAs) have surfaced as important contributors to various cellular activities, with growing proof indicating their substantial role in the genesis, development, and spread of cancer. Their unique expression profiles within specific tissues and their wide-ranging functionalities make lncRNAs excellent candidates for potential therapeutic intervention in cancer management. They are implicated in multiple hallmarks of cancer, such as uncontrolled proliferation, angiogenesis, and immune evasion. This review article explores the innovative application of CRISPR-Cas9 technology in targeting lncRNAs as a cancer therapeutic strategy. The CRISPR-Cas9 system has been widely applied in functional genomics, gene therapy, and cancer research, offering a versatile platform for lncRNA targeting. CRISPR-Cas9-mediated targeting of lncRNAs can be achieved through CRISPR interference, activation or the complete knockout of lncRNA loci. Combining CRISPR-Cas9 technology with high-throughput functional genomics makes it possible to identify lncRNAs critical for the survival of specific cancer subtypes, opening the door for tailored treatments and personalised cancer therapies. CRISPR-Cas9-mediated lncRNA targeting with other cutting-edge cancer therapies, such as immunotherapy and targeted molecular therapeutics can be used to overcome the drug resistance in cancer. The synergy of lncRNA research and CRISPR-Cas9 technology presents immense potential for individualized cancer treatment, offering renewed hope in the battle against this disease.
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Affiliation(s)
- Rahul Kumar Mahato
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Srinjan Bhattacharya
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Naina Khullar
- Department of Zoology, Mata Gujri College, Fatehgarh Sahib, Punjab, India
| | - Inderpal Singh Sidhu
- Department of Zoology, Sri Guru Gobind Singh College, Sector 26, Chandigarh, India
| | - P Hemachandra Reddy
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Department of Pharmacology & Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Departments of Neurology, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Public Health Department of Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Department of Speech, Language and Hearing Sciences, School Health Professions, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Gurjit Kaur Bhatti
- Department of Medical Lab Technology, University Institute of Applied Health Sciences, Chandigarh University, Mohali, India.
| | - Jasvinder Singh Bhatti
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India.
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11
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Rebbeck T, Janivara R, Chen W, Hazra U, Baichoo S, Agalliu I, Kachambwa P, Simonti C, Brown L, Tambe S, Kim M, Harlemon M, Jalloh M, Muzondiwa D, Naidoo D, Ajayi O, Snyper N, Niang L, Diop H, Ndoye M, Mensah J, Darkwa-Abrahams A, Biritwum R, Adjei A, Adebiyi A, Shittu O, Ogunbiyi O, Adebayo S, Nwegbu M, Ajibola H, Oluwole O, Jamda M, Pentz A, Haiman C, Spies P, Van der Merwe A, Cook M, Chanock SJ, Berndt SI, Watya S, Lubwama A, Muchengeti M, Doherty S, Smyth N, Lounsbury D, Fortier B, Rohan T, Jacobson J, Neugut A, Hsing A, Gusev A, Aisuodionoe-Shadrach O, Joffe M, Adusei B, Gueye S, Fernandez P, McBride J, Andrews C, Petersen L, Lachance J. Heterogeneous genetic architectures and evolutionary genomics of prostate cancer in Sub-Saharan Africa. RESEARCH SQUARE 2023:rs.3.rs-3378303. [PMID: 37886553 PMCID: PMC10602179 DOI: 10.21203/rs.3.rs-3378303/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Men of African descent have the highest prostate cancer (CaP) incidence and mortality rates, yet the genetic basis of CaP in African men has been understudied. We used genomic data from 3,963 CaP cases and 3,509 controls recruited in Ghana, Nigeria, Senegal, South Africa, and Uganda, to infer ancestry-specific genetic architectures and fine-mapped disease associations. Fifteen independent associations at 8q24.21, 6q22.1, and 11q13.3 reached genome-wide significance, including four novel associations. Intriguingly, multiple lead SNPs are private alleles, a pattern arising from recent mutations and the out-of-Africa bottleneck. These African-specific alleles contribute to haplotypes with odds ratios above 2.4. We found that the genetic architecture of CaP differs across Africa, with effect size differences contributing more to this heterogeneity than allele frequency differences. Population genetic analyses reveal that African CaP associations are largely governed by neutral evolution. Collectively, our findings emphasize the utility of conducting genetic studies that use diverse populations.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Maxwell Nwegbu
- University of Abuja Teaching Hospital and Cancer Science Center
| | - Hafees Ajibola
- University of Abuja Teaching Hospital and Cancer Science Center
| | - Olabode Oluwole
- University of Abuja and University of Abuja Teaching Hospital
| | - Mustapha Jamda
- University of Abuja Teaching Hospital and Cancer Science Center
| | | | | | | | | | | | | | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda
| | | | | | - Mazvita Muchengeti
- National Institute for Communicable Diseases a Division of the National Health Laboratory Service
| | | | | | | | | | | | | | | | - Ann Hsing
- Stanford University School of Medicine
| | | | | | | | | | | | | | - Jo McBride
- Centre for Proteomic and Genomic Research
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12
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Feng D, Li L, Shi X, Zhu W, Wang J, Wu R, Li D, Wei W, Han P. Identification of senescence-related lncRNA prognostic index correlating with prognosis and radiosensitivity in prostate cancer patients. Aging (Albany NY) 2023; 15:9358-9376. [PMID: 37742230 PMCID: PMC10564441 DOI: 10.18632/aging.204888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 06/22/2023] [Indexed: 09/26/2023]
Abstract
BACKGROUND An increasing number of studies are shown how crucial a role cellular senescence plays in tumor development. In this study, we developed a senescence-related lncRNA prognostic index (SRLPI) to forecast radiosensitivity and the probability of biochemical recurrence (BCR) in patients with prostate cancer (PCa). METHODS PCa cohorts in TCGA and GEO databases were downloaded. Senescence-and prognosis-related lncRNA with differential expression in tumor and normal samples were identified and used to establish the SRLPI score. Mutation landscape, function pathway, tumor stemness and heterogeneity and tumor immune microenvironment were also analyzed. We performed the analysis using R 3.6.3 and the appropriate tools. RESULTS A SRLPI score was constructed based on SNHG1 and MIAT in the TCGA cohort. Our classification of PCa patients into high- and low-risk groups was based on the median SRLPI score. When compared to the low-SRLPI group, the high-SRLPI group was more vulnerable to BCR (HR: 3.33). In terms of BCR-free survival and metastasis-free survival, the GSE116918 showed similar findings. Surprisingly, the SRLPI score demonstrated a high level of radiosensitivity for diagnosis (AUC: 0.98). Age, Gleason score, T stage, N stage, positive lymph nodes, and residual tumor were all significantly greater in patients with high SRLPI scores. Furthermore, this score was significantly related to markers of senescence. Protein secretion and androgen response were found to be substantially enriched in the low-SRLPI group, whereas E2F targets were found to be strongly enriched in the high-SRLPI group for pathway analysis. For the tumor microenvironment assessment, B cells, CD8+ T cells, immune score and TIDE score were positively related to SRLPI score while endothelial level was negatively associated with SRLPI score with statistical significance. CONCLUSIONS We developed a SRLPI score that was related to prognosis and radiosensitivity and might be helpful in clinical practice.
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Affiliation(s)
- Dechao Feng
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Li Li
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xu Shi
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Weizhen Zhu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jie Wang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ruicheng Wu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Dengxiong Li
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Wuran Wei
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ping Han
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu 610041, China
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13
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Logotheti S, Papadaki E, Zolota V, Logothetis C, Vrahatis AG, Soundararajan R, Tzelepi V. Lineage Plasticity and Stemness Phenotypes in Prostate Cancer: Harnessing the Power of Integrated "Omics" Approaches to Explore Measurable Metrics. Cancers (Basel) 2023; 15:4357. [PMID: 37686633 PMCID: PMC10486655 DOI: 10.3390/cancers15174357] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/21/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Prostate cancer (PCa), the most frequent and second most lethal cancer type in men in developed countries, is a highly heterogeneous disease. PCa heterogeneity, therapy resistance, stemness, and lethal progression have been attributed to lineage plasticity, which refers to the ability of neoplastic cells to undergo phenotypic changes under microenvironmental pressures by switching between developmental cell states. What remains to be elucidated is how to identify measurements of lineage plasticity, how to implement them to inform preclinical and clinical research, and, further, how to classify patients and inform therapeutic strategies in the clinic. Recent research has highlighted the crucial role of next-generation sequencing technologies in identifying potential biomarkers associated with lineage plasticity. Here, we review the genomic, transcriptomic, and epigenetic events that have been described in PCa and highlight those with significance for lineage plasticity. We further focus on their relevance in PCa research and their benefits in PCa patient classification. Finally, we explore ways in which bioinformatic analyses can be used to determine lineage plasticity based on large omics analyses and algorithms that can shed light on upstream and downstream events. Most importantly, an integrated multiomics approach may soon allow for the identification of a lineage plasticity signature, which would revolutionize the molecular classification of PCa patients.
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Affiliation(s)
- Souzana Logotheti
- Department of Pathology, University of Patras, 26504 Patras, Greece; (S.L.); (E.P.); (V.Z.)
| | - Eugenia Papadaki
- Department of Pathology, University of Patras, 26504 Patras, Greece; (S.L.); (E.P.); (V.Z.)
- Department of Informatics, Ionian University, 49100 Corfu, Greece;
| | - Vasiliki Zolota
- Department of Pathology, University of Patras, 26504 Patras, Greece; (S.L.); (E.P.); (V.Z.)
| | - Christopher Logothetis
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | | | - Rama Soundararajan
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Vasiliki Tzelepi
- Department of Pathology, University of Patras, 26504 Patras, Greece; (S.L.); (E.P.); (V.Z.)
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14
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Veys C, Boulouard F, Benmoussa A, Jammes M, Brotin E, Rédini F, Poulain L, Gruchy N, Denoyelle C, Legendre F, Galera P. MiR-4270 acts as a tumor suppressor by directly targeting Bcl-xL in human osteosarcoma cells. Front Oncol 2023; 13:1220459. [PMID: 37719019 PMCID: PMC10501397 DOI: 10.3389/fonc.2023.1220459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/03/2023] [Indexed: 09/19/2023] Open
Abstract
Chondrosarcomas and osteosarcomas are malignant bone tumors with a poor prognosis when unresectable or metastasized. Moreover, radiotherapy and chemotherapy could be ineffective. MiRNAs represent an alternative therapeutic approach. Based on high-throughput functional screening, we identified four miRNAs with a potential antiproliferative effect on SW1353 chondrosarcoma cells. Individual functional validations were then performed in SW1353 cells, as well as in three osteosarcoma cell lines. The antiproliferative and cytotoxic effects of miRNAs were evaluated in comparison with a positive control, miR-342-5p. The cytotoxic effect of four selected miRNAs was not confirmed on SW1353 cells, but we unambiguously revealed that miR-4270 had a potent cytotoxic effect on HOS and MG-63 osteosarcoma cell lines, but not on SaOS-2 cell line. Furthermore, like miR-342-5p, miR-4270 induced apoptosis in these two cell lines. In addition, we provided the first report of Bcl-xL as a direct target of miR-4270. MiR-4270 also decreased the expression of the anti-apoptotic protein Mcl-1, and increased the expression of the pro-apoptotic protein Bak. Our findings demonstrated that miR-4270 has tumor suppressive activity in osteosarcoma cells, particularly through Bcl-xL downregulation.
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Affiliation(s)
- Clément Veys
- Normandie Univ., UNICAEN, BIOTARGEN, Caen, France
| | - Flavie Boulouard
- Normandie Univ., UNICAEN, BIOTARGEN, Caen, France
- Department of Genetics, Normandy Center for Genomic and Personalized Medicine, Caen University Hospital, Caen, France
| | - Abderrahim Benmoussa
- Normandie Univ., UNICAEN, BIOTARGEN, Caen, France
- Research Center of the UHC Sainte-Justine and Department of Nutrition, Université de Montréal, Montréal, QC, Canada
| | - Manon Jammes
- Normandie Univ., UNICAEN, BIOTARGEN, Caen, France
| | - Emilie Brotin
- Normandie Univ., UNICAEN, Federative Structure Normandie Oncology, US Platon, ImpedanCELL Platform, Caen, France
- Normandie Univ., UNICAEN, INSERM U1086 ANTICIPE, Biology and Innovative Therapeutics for Ovarian Cancer (BioTICLA), Caen, France
- UNICANCER, Comprehensive Cancer Center F. Baclesse, Caen, France
| | - Françoise Rédini
- UMR 1238 Phy-Os “Bone Sarcomas and Remodeling of Calcified Tissues”, INSERM, Nantes University, Nantes, France
| | - Laurent Poulain
- Normandie Univ., UNICAEN, INSERM U1086 ANTICIPE, Biology and Innovative Therapeutics for Ovarian Cancer (BioTICLA), Caen, France
- UNICANCER, Comprehensive Cancer Center F. Baclesse, Caen, France
| | - Nicolas Gruchy
- Normandie Univ., UNICAEN, BIOTARGEN, Caen, France
- Department of Genetics, Normandy Center for Genomic and Personalized Medicine, Caen University Hospital, Caen, France
| | - Christophe Denoyelle
- Normandie Univ., UNICAEN, Federative Structure Normandie Oncology, US Platon, ImpedanCELL Platform, Caen, France
- Normandie Univ., UNICAEN, INSERM U1086 ANTICIPE, Biology and Innovative Therapeutics for Ovarian Cancer (BioTICLA), Caen, France
- UNICANCER, Comprehensive Cancer Center F. Baclesse, Caen, France
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15
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Akhgari H, Shokri N, Dehghanzadeh P, Tayefeh-Gholami S, Rajabi A, Safaralizadeh R. Expression pattern of PCAT1, PCAT2, and PCAT5 lncRNAs and their value as diagnostic biomarkers in patients with gastric cancer. Pathol Res Pract 2023; 248:154654. [PMID: 37392552 DOI: 10.1016/j.prp.2023.154654] [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: 05/18/2023] [Revised: 06/04/2023] [Accepted: 06/25/2023] [Indexed: 07/03/2023]
Abstract
BACKGROUND Gastric cancer (GC), is a complex multifactorial neoplasm with a high mortality and prevalence rate all over the world. Hence, it is necessary to identify the multiple pathways that are previously unknown and are involved in its initiation and progression. Recently, it has become clear that long non-coding RNAs (lncRNAs) play a crucial role in the onset and spread of cancer. The current study assessed the lncRNAs PCAT1, PCAT2, and PCAT5 expression in primary gastric tumors and adjacent noncancerous tissues. METHODS 90 pairs of GC and adjacent noncancerous tissue samples were obtained. Total RNA was extracted, then cDNA was synthesized. Using quantitative reverse transcriptase PCR (qRT-PCR), PCAT1, PCAT2, and PCAT5 expression levels were evaluated. Using the SPSS statistical package, the correlation between clinicopathological characteristics and the expression of PCAT1, PCAT2, and PCAT5 was investigated. The diagnostic value of PCAT1, PCAT2, and PCAT5 in GC was assessed using the receiver operating characteristic (ROC) curve analysis. RESULTS Compared to surrounding non-cancerous tissues, PCAT1, PCAT2, and PCAT5 were all significantly overexpressed in tumoral tissues (P = 0.001, P = 0.019, and P = 0.0001, respectively). PCAT5 expression was significantly associated with gender (P = 0.020), according to our research. The ROC curve's findings indicated that PCAT1, PCAT2, and PCAT5 may each function as poor diagnostic biomarkers, with respective AUC values of 64 %, 60 %, and 68 %, specificity values of 68 %, 60 %, and 76 %, and sensitivity values of 55 %, 72 %, and 52 %. CONCLUSION Our research suggested that PCAT1, PCAT2, and PCAT5 may be engaged in promoting and developing GC cells as a novel oncogene because of the increased expression of PCAT1, PCAT2 and PCAT5 in tumor tissues of GC patients. Additionally, PCAT1, PCAT2, and PCAT5 can be thought of as poor diagnostic biomarkers for GC case detection.
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Affiliation(s)
- Hossein Akhgari
- Departmant of Animal Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran
| | - Neda Shokri
- Departmant of Animal Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran
| | - Parisa Dehghanzadeh
- Departmant of Animal Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran
| | - Samaneh Tayefeh-Gholami
- Departmant of Animal Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran
| | - Ali Rajabi
- Departmant of Animal Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran
| | - Reza Safaralizadeh
- Departmant of Animal Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran.
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16
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Chuang YT, Shiau JP, Tang JY, Farooqi AA, Chang FR, Tsai YH, Yen CY, Chang HW. Connection of Cancer Exosomal LncRNAs, Sponging miRNAs, and Exosomal Processing and Their Potential Modulation by Natural Products. Cancers (Basel) 2023; 15:cancers15082215. [PMID: 37190145 DOI: 10.3390/cancers15082215] [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: 03/20/2023] [Revised: 04/06/2023] [Accepted: 04/07/2023] [Indexed: 05/17/2023] Open
Abstract
Cancerous exosomes contain diverse biomolecules that regulate cancer progression. Modulating exosome biogenesis with clinical drugs has become an effective strategy for cancer therapy. Suppressing exosomal processing (assembly and secretion) may block exosomal function to reduce the proliferation of cancer cells. However, the information on natural products that modulate cancer exosomes lacks systemic organization, particularly for exosomal long noncoding RNAs (lncRNAs). There is a gap in the connection between exosomal lncRNAs and exosomal processing. This review introduces the database (LncTarD) to explore the potential of exosomal lncRNAs and their sponging miRNAs. The names of sponging miRNAs were transferred to the database (miRDB) for the target prediction of exosomal processing genes. Moreover, the impacts of lncRNAs, sponging miRNAs, and exosomal processing on the tumor microenvironment (TME) and natural-product-modulating anticancer effects were then retrieved and organized. This review sheds light on the functions of exosomal lncRNAs, sponging miRNAs, and exosomal processing in anticancer processes. It also provides future directions for the application of natural products when regulating cancerous exosomal lncRNAs.
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Affiliation(s)
- Ya-Ting Chuang
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Jun-Ping Shiau
- Division of Breast Oncology and Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Jen-Yang Tang
- School of Post-Baccalaureate Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Radiation Oncology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Ammad Ahmad Farooqi
- Institute of Biomedical and Genetic Engineering (IBGE), Islamabad 54000, Pakistan
| | - Fang-Rong Chang
- Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Yi-Hong Tsai
- Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Ching-Yu Yen
- School of Dentistry, Taipei Medical University, Taipei 11031, Taiwan
- Department of Oral and Maxillofacial Surgery, Chi-Mei Medical Center, Tainan 71004, Taiwan
| | - Hsueh-Wei Chang
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Biomedical Science and Environmental Biology, College of Life Science, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Center for Cancer Research, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
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17
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Taheri M, Badrlou E, Hussen BM, Kashi AH, Ghafouri-Fard S, Baniahmad A. Importance of long non-coding RNAs in the pathogenesis, diagnosis, and treatment of prostate cancer. Front Oncol 2023; 13:1123101. [PMID: 37025585 PMCID: PMC10070735 DOI: 10.3389/fonc.2023.1123101] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/07/2023] [Indexed: 04/08/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are regulatory transcripts with essential roles in the pathogenesis of almost all types of cancers, including prostate cancer. They can act as either oncogenic lncRNAs or tumor suppressor ones in prostate cancer. Small nucleolar RNA host genes are among the mostly assessed oncogenic lncRNAs in this cancer. PCA3 is an example of oncogenic lncRNAs that has been approved as a diagnostic marker in prostate cancer. A number of well-known oncogenic lncRNAs in other cancers such as DANCR, MALAT1, CCAT1, PVT1, TUG1 and NEAT1 have also been shown to act as oncogenes in prostate cancer. On the other hand, LINC00893, LINC01679, MIR22HG, RP1-59D14.5, MAGI2-AS3, NXTAR, FGF14-AS2 and ADAMTS9-AS1 are among lncRNAs that act as tumor suppressors in prostate cancer. LncRNAs can contribute to the pathogenesis of prostate cancer via modulation of androgen receptor (AR) signaling, ubiquitin-proteasome degradation process of AR or other important signaling pathways. The current review summarizes the role of lncRNAs in the evolution of prostate cancer with an especial focus on their importance in design of novel biomarker panels and therapeutic targets.
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Affiliation(s)
- Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Elham Badrlou
- Men’s Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bashdar Mahmud Hussen
- Department of Clinical Analysis, College of Pharmacy, Hawler Medical University, Erbil, Kurdistan, Iraq
| | - Amir Hossein Kashi
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Aria Baniahmad
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
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18
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Winkle M, Tayari MM, Kok K, Duns G, Grot N, Kazimierska M, Seitz A, de Jong D, Koerts J, Diepstra A, Dzikiewicz-Krawczyk A, Steidl C, Kluiver J, van den Berg A. The lncRNA KTN1-AS1 co-regulates a variety of Myc-target genes and enhances proliferation of Burkitt lymphoma cells. Hum Mol Genet 2022; 31:4193-4206. [PMID: 35866590 DOI: 10.1093/hmg/ddac159] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/22/2022] [Accepted: 07/07/2022] [Indexed: 01/21/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are involved in many normal and oncogenic pathways through a diverse repertoire of transcriptional and posttranscriptional regulatory mechanisms. LncRNAs that are under tight regulation of well-known oncogenic transcription factors such as c-Myc (Myc) are likely to be functionally involved in their disease-promoting mechanisms. Myc is a major driver of many subsets of B cell lymphoma and to date remains an undruggable target. We identified three Myc-induced and four Myc-repressed lncRNAs by use of multiple in vitro models of Myc-driven Burkitt lymphoma and detailed analysis of Myc binding profiles. We show that the top Myc-induced lncRNA KTN1-AS1 is strongly upregulated in different types of B cell lymphoma compared with their normal counterparts. We used CRISPR-mediated genome editing to confirm that the direct induction of KTN1-AS1 by Myc is dependent on the presence of a Myc E-box-binding motif. Knockdown of KTN1-AS1 revealed a strong negative effect on the growth of three BL cell lines. Global gene expression analysis upon KTN1-AS1 depletion shows a strong enrichment of key genes in the cholesterol biosynthesis pathway as well as co-regulation of many Myc-target genes, including a moderate negative effect on the levels of Myc itself. Our study suggests a critical role for KTN1-AS1 in supporting BL cell growth by mediating co-regulation of a variety of Myc-target genes and co-activating key genes involved in cholesterol biosynthesis. Therefore, KTN1-AS1 may represent a putative novel therapeutic target in lymphoma.
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Affiliation(s)
- Melanie Winkle
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands.,Department of Translational Molecular Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mina M Tayari
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands.,Department of Human Genetics, University of Miami, Sylvester Comprehensive Cancer Center, Miami, FL, USA
| | - Klaas Kok
- Department of Genetics, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands
| | - Gerben Duns
- Department of Lymphoid Cancer Research, BC Cancer Center, Vancouver, BC, Canada
| | - Natalia Grot
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Marta Kazimierska
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Annika Seitz
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands
| | - Debora de Jong
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands
| | - Jasper Koerts
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands
| | - Arjan Diepstra
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands
| | | | - Christian Steidl
- Department of Lymphoid Cancer Research, BC Cancer Center, Vancouver, BC, Canada
| | - Joost Kluiver
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands
| | - Anke van den Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands
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19
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Huseynova G, Özgür E, Bilgiç Gazioğlu S, Esin Yörüker E, Gezer U. Androgen Receptor Blockade Using Enzalutamide Suppresses Long Non-Coding RNA ARLNC1 in Prostate Cancer Cells. CELL JOURNAL 2022; 24:774-778. [PMID: 36527350 PMCID: PMC9790070 DOI: 10.22074/cellj.2022.557563.1076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 07/19/2022] [Indexed: 01/05/2023]
Abstract
Prostate cancer (PCa) is a common malignant disease with high mortality rates that develops and progresses in an androgen-dependent way. In recent years, RNA sequencing enabled identification of many PCa-related long noncoding RNAs including androgen receptor-regulated long non-coding RNA 1 (ARLNC1) and prostate cancer-associated transcript 1 (PCAT1). In the present study, our goal was to illuminate expression changes of ARLNC1 and PCAT1 in the context of androgen stimulation or androgen receptor (AR) blockade with respect to AR expression status. In this experimental study, LNCaP cells and higher AR-expressing LNCaP-AR++ cells were used as cell models. Cells were treated with dihydrotestosterone (DHT) as an androgen stimulator and/or enzalutamide as an AR inhibitor. Cell viability was assessed using annexin V and propidium iodide (PI) staining in flow cytometry. Androgen stimulation prompted baseline ARLNC1 levels by 53.5-fold in the LNCaP cells (P=0.01) and by 25-fold in the LNCAP-AR+ cells (P=0.18). AR inhibition by enzalutamide reduced baseline ARLNC1 in LNCaP-AR++ cells by 2-fold (P=0.01), but to a lesser extent in LNCaP cells. Co-treatment of cells with DHT and enzalutamide led to a remarkable decrease in the DHT effect on ARLNC1 expression. No specific effect of androgen stimulation or AR blockade on PCAT1 expression was detected. Our results revealed that the extent of induction of ARLNC1 by androgen is modulated by receptor expression status. In addition, we determined that AR blockade, via enzalutamide, effectively suppresses ARLNC1 both at baseline and after induction by DHT.
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Affiliation(s)
- Günel Huseynova
- Institute of Health Sciences, Istanbul University, Istanbul, Turkey
| | - Emre Özgür
- Department of Basic Oncology, Istanbul University Oncology Institute, Istanbul, Turkey
| | - Sema Bilgiç Gazioğlu
- Department of Immunology, Istanbul University Aziz Sancar Institute of Experimental 7 Medicine, Istanbul, Turkey
| | - Ebru Esin Yörüker
- Department of Basic Oncology, Istanbul University Oncology Institute, Istanbul, Turkey
| | - Ugur Gezer
- Department of Basic Oncology, Istanbul University Oncology Institute, Istanbul, Turkey,Department of Basic OncologyIstanbul University Oncology InstituteIstanbulTurkey
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20
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Ke H, Ren Z, Qi J, Chen S, Tseng GC, Ye Z, Ma T. High-dimension to high-dimension screening for detecting genome-wide epigenetic and noncoding RNA regulators of gene expression. Bioinformatics 2022; 38:4078-4087. [PMID: 35856716 PMCID: PMC9438953 DOI: 10.1093/bioinformatics/btac518] [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: 02/03/2022] [Revised: 06/29/2022] [Accepted: 07/19/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION The advancement of high-throughput technology characterizes a wide variety of epigenetic modifications and noncoding RNAs across the genome involved in disease pathogenesis via regulating gene expression. The high dimensionality of both epigenetic/noncoding RNA and gene expression data make it challenging to identify the important regulators of genes. Conducting univariate test for each possible regulator-gene pair is subject to serious multiple comparison burden, and direct application of regularization methods to select regulator-gene pairs is computationally infeasible. Applying fast screening to reduce dimension first before regularization is more efficient and stable than applying regularization methods alone. RESULTS We propose a novel screening method based on robust partial correlation to detect epigenetic and noncoding RNA regulators of gene expression over the whole genome, a problem that includes both high-dimensional predictors and high-dimensional responses. Compared to existing screening methods, our method is conceptually innovative that it reduces the dimension of both predictor and response, and screens at both node (regulators or genes) and edge (regulator-gene pairs) levels. We develop data-driven procedures to determine the conditional sets and the optimal screening threshold, and implement a fast iterative algorithm. Simulations and applications to long noncoding RNA and microRNA regulation in Kidney cancer and DNA methylation regulation in Glioblastoma Multiforme illustrate the validity and advantage of our method. AVAILABILITY AND IMPLEMENTATION The R package, related source codes and real datasets used in this article are provided at https://github.com/kehongjie/rPCor. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Hongjie Ke
- Department of Epidemiology and Biostatistics, University of Maryland, College Park, MD 20742, USA
| | - Zhao Ren
- Department of Statistics, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Jianfei Qi
- Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, MD 21201, USA
| | - Shuo Chen
- Department of Epidemiology & Public Health, University of Maryland, Baltimore, MD 21201, USA
| | - George C Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Zhenyao Ye
- Department of Epidemiology & Public Health, University of Maryland, Baltimore, MD 21201, USA
| | - Tianzhou Ma
- Department of Epidemiology and Biostatistics, University of Maryland, College Park, MD 20742, USA
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21
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Li N, Zeng A, Wang Q, Chen M, Zhu S, Song L. Regulatory function of DNA methylation mediated lncRNAs in gastric cancer. Cancer Cell Int 2022; 22:227. [PMID: 35810299 PMCID: PMC9270757 DOI: 10.1186/s12935-022-02648-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/28/2022] [Indexed: 12/31/2022] Open
Abstract
As one of the most common malignancies worldwide, gastric cancer contributes to cancer death with a high mortality rate partly responsible for its out-of-control progression as well as limited diagnosis. DNA methylation, one of the epigenetic events, plays an essential role in the carcinogenesis of many cancers, including gastric cancer. Long non-coding RNAs have emerged as the significant factors in the cancer progression functioned as the oncogene genes, the suppressor genes and regulators of signaling pathways over the decade. Intriguingly, increasing reports, recently, have claimed that abnormal DNA methylation regulates the expression of lncRNAs as tumor suppressor genes in gastric cancer and lncRNAs as regulators could exert the critical influence on tumor progression through acting on DNA methylation of other cancer-related genes. In this review, we summarized the DNA methylation-associated lncRNAs in gastric cancer which play a large impact on tumor progression, such as proliferation, invasion, metastasis and so on. Furthermore, the underlying molecular mechanism and signaling pathway might be developed as key points of gastric cancer range from diagnosis to prognosis and treatment in the future.
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Affiliation(s)
- Nan Li
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, People's Republic of China
| | - Anqi Zeng
- Institute of Translational Pharmacology and Clinical Application, Sichuan Academy of Chinese Medical Science, Chengdu, Sichuan, 610041, People's Republic of China
| | - Qian Wang
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, People's Republic of China
| | - Maohua Chen
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, People's Republic of China
| | - Shaomi Zhu
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, People's Republic of China.
| | - Linjiang Song
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, People's Republic of China.
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22
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An C, Wang I, Li X, Xia R, Deng F. Long non-coding RNA in prostate cancer. AMERICAN JOURNAL OF CLINICAL AND EXPERIMENTAL UROLOGY 2022; 10:170-179. [PMID: 35874287 PMCID: PMC9301060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/15/2022] [Indexed: 06/15/2023]
Abstract
Prostate cancer is the most frequently diagnosed cancer in males and its development and progression remains an important area of study. Recently, long non-coding RNAs (lncRNAs) have been evidenced as key players in cancer pathogenesis. Specifically, dysregulation of long non-coding RNA (lncRNA) expression has shown to affect tumor proliferation and metastasis, acting as either tumor suppressors or oncogenes. However, its specific mechanisms and functions in prostate cancer remain unclear. This review provides an overview of currently available information on prostate cancer-related lncRNAs, including GAS5, GAS-007, MEG3, PCA3, PCAT14, PCAT1, PVT1, UCA1, SChLAP1, MALAT1, HOTAIR, and NEAT1. Notable tumor growth inhibitors include GAS5 and MEG3. GAS5 is evidenced to interfere with the AKT/MTOR signaling pathway through targeting microRNA mir-103. MEG3, however, is proposed to inhibit the cycle, sponge miR-9-5p, and induce gene silencing. PCAT1, PVT1, and UCA1 are important tumor growth promoters. PCAT1 is indicated to be a transcriptional repressor, a mir-145-5P sponge, and a P13K/AKT pathway activator. Studies suggest that PVT1 acts via microRNA targeting and regulating proliferating cell nuclear antigen. UCA1 may sponge miR-204 and miR-331-3p as well as regulate myosin VI. Thorough understanding of these lncRNAs may elucidate new aspects of prostate cancer pathology and serve a pivotal role in developing novel diagnostic and prognostic techniques.
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Affiliation(s)
- Christine An
- Institute of Human Nutrition, Columbia UniversityNew York, NY, USA
| | - Ian Wang
- State University of New York, Hofstra UniversityHempstead, NY, USA
| | - Xin Li
- Department of Molecular Pathobiology, New York University College of DentistryNY, USA
| | - Rong Xia
- Department of Pathology and Urology, New York University School of MedicineNY, USA
| | - Fangming Deng
- Department of Pathology and Urology, New York University School of MedicineNY, USA
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23
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Long non-coding RNAs involved in different steps of cancer metastasis. Clin Transl Oncol 2022; 24:997-1013. [PMID: 35119654 DOI: 10.1007/s12094-021-02761-z] [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: 10/18/2021] [Accepted: 12/14/2021] [Indexed: 11/09/2022]
Abstract
Non-proteincoding transcripts bearing 200 base pairs known as long non-coding RNAs (lncRNAs) play a role in a variety of molecular mechanisms, including cell differentiation, apoptosis and metastasis. Previous studies have suggested that frequently dysregulated lncRNAs play a crucial role in various aspects of cancer metastasis. Metastasis is the main leading cause of death in cancer. The role of lncRNAs in different stages of metastasis is the subject of this review. Based on in vitro and in vivo investigations on metastasis, we categorized lncRNAs into distinct stages of metastasis including angiogenesis, invasion, intravasation, survival in circulation, and extravasation. The involvement of lncRNAs in angiogenesis and invasion has been extensively studied. Here, we comprehensively discuss the role and functions of these lncRNAs with a particular focus on the molecular mechanisms.
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24
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Yin X, Lin H, Lin L, Miao L, He J, Zhuo Z. LncRNAs and CircRNAs in cancer. MedComm (Beijing) 2022; 3:e141. [PMID: 35592755 PMCID: PMC9099016 DOI: 10.1002/mco2.141] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 12/24/2022] Open
Affiliation(s)
- Xin Yin
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center Guangzhou Medical University Guangzhou Guangdong China
- College of Pharmacy Jinan University Guangzhou Guangdong China
| | - Huiran Lin
- Faculty of Medicine Macau University of Science and Technology Macau China
| | - Lei Lin
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center Guangzhou Medical University Guangzhou Guangdong China
| | - Lei Miao
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center Guangzhou Medical University Guangzhou Guangdong China
| | - Jing He
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center Guangzhou Medical University Guangzhou Guangdong China
| | - Zhenjian Zhuo
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center Guangzhou Medical University Guangzhou Guangdong China
- Laboratory Animal Center, School of Chemical Biology and Biotechnology Peking University Shenzhen Graduate School Shenzhen China
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25
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The promising role of new molecular biomarkers in prostate cancer: from coding and non-coding genes to artificial intelligence approaches. Prostate Cancer Prostatic Dis 2022; 25:431-443. [PMID: 35422101 PMCID: PMC9385485 DOI: 10.1038/s41391-022-00537-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/24/2022] [Accepted: 03/30/2022] [Indexed: 12/15/2022]
Abstract
Background Risk stratification or progression in prostate cancer is performed with the support of clinical-pathological data such as the sum of the Gleason score and serum levels PSA. For several decades, methods aimed at the early detection of prostate cancer have included the determination of PSA serum levels. The aim of this systematic review is to provide an overview about recent advances in the discovery of new molecular biomarkers through transcriptomics, genomics and artificial intelligence that are expected to improve clinical management of the prostate cancer patient. Methods An exhaustive search was conducted by Pubmed, Google Scholar and Connected Papers using keywords relating to the genetics, genomics and artificial intelligence in prostate cancer, it includes “biomarkers”, “non-coding RNAs”, “lncRNAs”, “microRNAs”, “repetitive sequence”, “prognosis”, “prediction”, “whole-genome sequencing”, “RNA-Seq”, “transcriptome”, “machine learning”, and “deep learning”. Results New advances, including the search for changes in novel biomarkers such as mRNAs, microRNAs, lncRNAs, and repetitive sequences, are expected to contribute to an earlier and accurate diagnosis for each patient in the context of precision medicine, thus improving the prognosis and quality of life of patients. We analyze several aspects that are relevant for prostate cancer including its new molecular markers associated with diagnosis, prognosis, and prediction to therapy and how bioinformatic approaches such as machine learning and deep learning can contribute to clinic. Furthermore, we also include current techniques that will allow an earlier diagnosis, such as Spatial Transcriptomics, Exome Sequencing, and Whole-Genome Sequencing. Conclusion Transcriptomic and genomic analysis have contributed to generate knowledge in the field of prostate carcinogenesis, new information about coding and non-coding genes as biomarkers has emerged. Synergies created by the implementation of artificial intelligence to analyze and understand sequencing data have allowed the development of clinical strategies that facilitate decision-making and improve personalized management in prostate cancer.
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26
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Gao Y, Zhang N, Zeng Z, Wu Q, Jiang X, Li S, Sun W, Zhang J, Li Y, Li J, He F, Huang Z, Zhang J, Gong Y, Xie C. LncRNA PCAT1 activates SOX2 and suppresses radioimmune responses via regulating cGAS/STING signalling in non-small cell lung cancer. Clin Transl Med 2022; 12:e792. [PMID: 35415876 PMCID: PMC9005924 DOI: 10.1002/ctm2.792] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 03/10/2022] [Accepted: 03/14/2022] [Indexed: 01/03/2023] Open
Abstract
Background The expression of long non‐coding RNA (lncRNA) prostate cancer‐associated ncRNA transcripts 1 (PCAT1) is increased in non‐small cell lung cancer (NSCLC). It stimulates tumour growth and metastasis, but its role in the radioimmune responses remain unknown. We aimed to explore the impacts of PCAT1 on tumorigenesis and radioimmune responses and the underlying molecular mechanisms in NSCLC. Methods Comprehensive bioinformatics analysis was performed to identify immunosuppressive lncRNAs involved with tumour invasion in NSCLC. The expression levels of PCAT1 were analysed by in situ hybridisation in 55 paired NSCLC tissues and adjacent normal tissues. Both loss‐ and gain‐of‐function assays were performed to examine the effects of PCAT1 and SOX2 on NSCLC cell behaviours in vivo and in vitro. Bioinformatic analyses, chromatin isolation by RNA purification (ChIRP) and dual‐luciferase reporter assays were applied to validate the regulatory effects of PCAT1 on SOX2 expression. Chromatin immunoprecipitation, luciferase and rescue assays were utilised to identify the relationship between SOX2 and the cGAS/stimulator of interferon genes (STING) signalling. Results PCAT1 was immunosuppressive and related with NSCLC invasion. Increased PCAT1 was negatively correlated with immune cell infiltration in NSCLC. PCAT1 knockdown restrained proliferation, increased apoptosis, and repressed cell metastasis in vivo and in vitro. PCAT1 activated SOX2 that accelerated tumorigenesis and immunosuppression. SOX2 promoted tumour growth through inhibiting cytotoxic T‐cell immunity. Moreover, SOX2 restrained cGAS transcription and hampered downstream type I interferon (IFN)‐induced immune responses. Inhibition of PCAT1/SOX2 in collaboration with radiation further inhibited tumour growth, and initiated the cGAS/STING signalling pathway, which enhanced the immune responses of radiotherapy in NSCLC. Conclusions PCAT1/SOX2 axis promoted tumorigenesis and immunosuppression through inhibition of cGAS/STING signalling‐mediated T‐cell activation. Inhibition of PCAT1 and SOX2 synergised with radiotherapy to activate the immune response and could serve as potential therapeutic targets.
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Affiliation(s)
- Yanping Gao
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Nannan Zhang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zihang Zeng
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Qiuji Wu
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xueping Jiang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Shuying Li
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Wenjie Sun
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jianguo Zhang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yangyi Li
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jiali Li
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Fajian He
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhengrong Huang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.,Tumor Precision Diagnosis and Treatment Technology and Translational Medicine, Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jinfang Zhang
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, China
| | - Yan Gong
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.,Tumor Precision Diagnosis and Treatment Technology and Translational Medicine, Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Conghua Xie
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China.,Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China
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27
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Giridharan M, Rupani V, Banerjee S. Signaling Pathways and Targeted Therapies for Stem Cells in Prostate Cancer. ACS Pharmacol Transl Sci 2022; 5:193-206. [PMID: 35434534 PMCID: PMC9003388 DOI: 10.1021/acsptsci.2c00019] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Indexed: 12/30/2022]
Abstract
Prostate cancer (PCa) is one of the most frequently occurring cancers among men, and the current statistics show that it is the second leading cause of cancer-related deaths among men. Over the years, research in PCa treatment and therapies has made many advances. Despite these efforts, the standardized therapies such as radiation, chemotherapy, hormonal therapy and surgery are not considered completely effective in treating advanced and metastatic PCa. In most situations, fast-dividing tumor cells are targeted, leaving behind relatively slowly dividing, chemoresistant cells known as cancer stem cells. Therefore, following the seemingly successful treatments, the lingering quiescent cancer stem cells are able to renew themselves, undergo differentiation into mature tumor cells, and sufficiently reinitiate the disease, leading to cancer relapse. Thus, prostate cancer stem cells (PCSCs) have been reported to play a vital role in controlling the dynamics of tumorigenesis, progression, and resistance to therapies in PCa. However, the complete knowledge on the mechanisms regulating the stemness of PCSCs is still unclear. Thus, studying the stemness of PCSCs will allow for the development of more effective cancer therapies due to the durable response, resulting in a reduction in recurrences of cancer. In this Review, we will specifically describe the molecular mechanisms responsible for regulating the stemness of PCSCs. Furthermore, current developments in stem cell-specific therapeutic approaches along with future prospects will also be discussed.
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Affiliation(s)
- Madhuvanthi Giridharan
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore-632104, Tamil Nadu, India
| | - Vasu Rupani
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore-632104, Tamil Nadu, India
| | - Satarupa Banerjee
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore-632104, Tamil Nadu, India
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28
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Abdi E, Latifi-Navid S. LncRNA polymorphisms and urologic cancer risk. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2022; 63:190-203. [PMID: 35178782 DOI: 10.1002/em.22472] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 01/11/2022] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
Urologic cancers involve nearly one-quarter of all cancers and include the prostate, bladder, and kidney cancers. Long non-coding RNAs (LncRNAs) are expressed in a tissue-specific manner and affect cell proliferation, apoptosis, and differentiation. LncRNAs expression is misregulated in urologic cancers, as their aberrant expression may make them capable of being utilized in the diagnosis, prognosis, and treatment of cancers. LncRNAs polymorphisms can affect their structure, expression, and function by interfering with the associated target mRNAs. As a result, lncRNA polymorphisms may be linked to the mechanism driving cancer susceptibility. Therefore, SNPs in lncRNAs may be a beneficial biomarker for early diagnosis and prognosis of cancers, as they affect lncRNA role in tumorigenesis and cancer progression. Moreover, the genetic heredity of lncRNA SNPs affects the personal therapeutic response to drugs. In this study, the lncRNAs polymorphism is summarized in relation to urologic cancers. It is proposed that lncRNA-related polymorphisms, as an individual or combined genotypes, can predict urologic cancer risk, even clinical and prognostic outcomes. However, large-scale population-based prospective studies and comprehensive meta-analyses should be conducted to validate and use these lncRNAs SNPs as the indicators of urologic cancers. Future research should examine the function of these SNPs to explain their associations with urologic cancers.
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Affiliation(s)
- Esmat Abdi
- Department of Biology, Faculty of Sciences, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Saeid Latifi-Navid
- Department of Biology, Faculty of Sciences, University of Mohaghegh Ardabili, Ardabil, Iran
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29
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Zhu YS, Zhu J. Molecular and cellular functions of long non-coding RNAs in prostate and breast cancer. Adv Clin Chem 2022; 106:91-179. [PMID: 35152976 DOI: 10.1016/bs.acc.2021.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Long noncoding RNAs (lncRNAs) are defined as noncoding RNA transcripts with a length greater than 200 nucleotides. Research over the last decade has made great strides in our understanding of lncRNAs, especially in the biology of their role in cancer. In this article, we will briefly discuss the biogenesis and characteristics of lncRNAs, then review their molecular and cellular functions in cancer by using prostate and breast cancer as examples. LncRNAs are abundant, diverse, and evolutionarily, less conserved than protein-coding genes. They are often expressed in a tumor and cell-specific manner. As a key epigenetic factor, lncRNAs can use a wide variety of molecular mechanisms to regulate gene expression at each step of the genetic information flow pathway. LncRNAs display widespread effects on cell behavior, tumor growth, and metastasis. They act intracellularly and extracellularly in an autocrine, paracrine and endocrine fashion. Increased understanding of lncRNA's role in cancer has facilitated the development of novel biomarkers for cancer diagnosis, led to greater understanding of cancer prognosis, enabled better prediction of therapeutic responses, and promoted identification of potential targets for cancer therapy.
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Affiliation(s)
- Yuan-Shan Zhu
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Clinical and Translational Science Center, Weill Cornell Medicine, New York, NY, United States.
| | - Jifeng Zhu
- Clinical and Translational Science Center, Weill Cornell Medicine, New York, NY, United States
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30
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Han W, Liu M, Han D, Toure AA, Li M, Besschetnova A, Wang Z, Patalano S, Macoska JA, Lam HM, Corey E, He HH, Gao S, Balk SP, Cai C. Exploiting the tumor-suppressive activity of the androgen receptor by CDK4/6 inhibition in castration-resistant prostate cancer. Mol Ther 2022; 30:1628-1644. [PMID: 35121110 PMCID: PMC9077383 DOI: 10.1016/j.ymthe.2022.01.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 12/15/2021] [Accepted: 01/28/2022] [Indexed: 10/19/2022] Open
Abstract
The androgen receptor (AR) plays a pivotal role in driving prostate cancer (PCa) development. However, when stimulated by high levels of androgens, AR can also function as a tumor suppressor in PCa cells. While the high-dose testosterone (high-T) treatment is currently being tested in clinical trials of castration-resistant prostate cancer (CRPC), there is still a pressing need to fully understand the underlying mechanism and thus develop treatment strategies to exploit this tumor-suppressive activity of AR. In this study, we demonstrate that retinoblastoma (Rb) family proteins play a central role in maintaining the global chromatin binding and transcriptional repression program of AR and that Rb inactivation desensitizes CRPC to the high-dose testosterone treatment in vitro and in vivo. Using a series of patient-derived xenograft (PDX) CRPC models, we further show that the efficacy of high-T treatment can be fully exploited by a CDK4/6 inhibitor, which strengthens the chromatin binding of the Rb-E2F repressor complex by blocking the hyperphosphorylation of Rb proteins. Overall, our study provides strong mechanistic and preclinical evidence on further developing clinical trials to combine high-T with CDK4/6 inhibitors in treating CRPC.
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Peng Y, Liu H, Liu J, Long J. Post-translational modifications on mitochondrial metabolic enzymes in cancer. Free Radic Biol Med 2022; 179:11-23. [PMID: 34929314 DOI: 10.1016/j.freeradbiomed.2021.12.264] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 11/26/2021] [Accepted: 12/15/2021] [Indexed: 12/22/2022]
Abstract
Mitochondrion is the powerhouse of the cell. The research of nearly a century has expanded our understanding of mitochondrion, far beyond the view that mitochondrion is an important energy generator of cells. During the initiation, growth and survival of tumor cells, significant mitochondrial metabolic changes have taken place in the important enzymes of respiratory chain and tricarboxylic acid cycle, mitochondrial biogenesis and dynamics, oxidative stress regulation and molecular signaling. Therefore, mitochondrial metabolic proteins are the key mediators of tumorigenesis. Post-translational modification is the molecular switch that regulates protein function. Understanding how these mitochondria-related post-translational modification function during tumorigenesis will bring new ideas for the next generation of cancer treatment.
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Affiliation(s)
- Yunhua Peng
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Huadong Liu
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China.
| | - Jiankang Liu
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China; University of Health and Rehabilitation Sciences, Qingdao, 266071, China
| | - Jiangang Long
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China.
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32
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Crosstalk between Long Non Coding RNAs, microRNAs and DNA Damage Repair in Prostate Cancer: New Therapeutic Opportunities? Cancers (Basel) 2022; 14:cancers14030755. [PMID: 35159022 PMCID: PMC8834032 DOI: 10.3390/cancers14030755] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Non-coding RNAs are a type of genetic material that doesn’t make protein, but performs diverse regulatory functions. In prostate cancer, most treatments target proteins, and resistance to such therapies is common, leading to disease progression. Targeting non-coding RNAs may provide alterative treatment options and potentially overcome drug resistance. Major types of non-coding RNAs include tiny ‘microRNAs’ and much longer ‘long non-coding RNAs’. Scientific studies have shown that these form a major part of the human genome, and play key roles in altering gene activity and determining the fate of cells. Importantly, in cancer, their activity is altered. Recent evidence suggests that microRNAs and long non-coding RNAs play important roles in controlling response to DNA damage. In this review, we explore how different types of non-coding RNA interact to control cell DNA damage responses, and how this knowledge may be used to design better prostate cancer treatments and tests. Abstract It is increasingly appreciated that transcripts derived from non-coding parts of the human genome, such as long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), are key regulators of biological processes both in normal physiology and disease. Their dysregulation during tumourigenesis has attracted significant interest in their exploitation as novel cancer therapeutics. Prostate cancer (PCa), as one of the most diagnosed malignancies and a leading cause of cancer-related death in men, continues to pose a major public health problem. In particular, survival of men with metastatic disease is very poor. Defects in DNA damage response (DDR) pathways culminate in genomic instability in PCa, which is associated with aggressive disease and poor patient outcome. Treatment options for metastatic PCa remain limited. Thus, researchers are increasingly targeting ncRNAs and DDR pathways to develop new biomarkers and therapeutics for PCa. Increasing evidence points to a widespread and biologically-relevant regulatory network of interactions between lncRNAs and miRNAs, with implications for major biological and pathological processes. This review summarises the current state of knowledge surrounding the roles of the lncRNA:miRNA interactions in PCa DDR, and their emerging potential as predictive and diagnostic biomarkers. We also discuss their therapeutic promise for the clinical management of PCa.
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Long Noncoding RNA Mediated Regulation in Human Embryogenesis, Pluripotency, and Reproduction. Stem Cells Int 2022; 2022:8051717. [PMID: 35103065 PMCID: PMC8800634 DOI: 10.1155/2022/8051717] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/27/2021] [Indexed: 12/12/2022] Open
Abstract
Long noncoding RNAs (lncRNAs), a class of noncoding RNAs with more than 200 bp in length, are produced by pervasive transcription in mammalian genomes and regulate gene expression through various action mechanisms. Accumulating data indicate that lncRNAs mediate essential biological functions in human development, including early embryogenesis, induction of pluripotency, and germ cell development. Comprehensive analysis of sequencing data highlights that lncRNAs are expressed in a stage-specific and human/primate-specific pattern during early human development. They contribute to cell fate determination through interacting with almost all classes of cellular biomolecules, including proteins, DNA, mRNAs, and microRNAs. Furthermore, the expression of a few of lncRNAs is highly associated with the pathogenesis and progression of many reproductive diseases, suggesting that they could serve as candidate biomarkers for diagnosis or novel targets for treatment. Here, we review research on lncRNAs and their roles in embryogenesis, pluripotency, and reproduction. We aim to identify the underlying molecular mechanisms essential for human development and provide novel insight into the causes and treatments of human reproductive diseases.
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Long Non-Coding RNAs at the Chromosomal Risk Loci Identified by Prostate and Breast Cancer GWAS. Genes (Basel) 2021; 12:genes12122028. [PMID: 34946977 PMCID: PMC8701176 DOI: 10.3390/genes12122028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 12/20/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are emerging as key players in a variety of cellular processes. Deregulation of the lncRNAs has been implicated in prostate and breast cancers. Recently, germline genetic variations associated with cancer risk have been correlated with lncRNA expression and/or function. In addition, single nucleotide polymorphisms (SNPs) at well-characterized cancer-associated lncRNAs have been analyzed for their association with cancer risk. These SNPs may occur within the lncRNA transcripts or spanning regions that may alter the structure, function, and expression of these lncRNA molecules and contribute to cancer progression and may have potential as therapeutic targets for cancer treatment. Additionally, some of these lncRNA have a tissue-specific expression profile, suggesting them as biomarkers for specific cancers. In this review, we highlight some of the cancer risk-associated SNPs that modulated lncRNAs with a potential role in prostate and breast cancers and speculate on how these lncRNAs may contribute to cancer development.
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Luo Y, Vlaeminck-Guillem V, Teinturier R, Abou Ziki R, Bertolino P, Le Romancer M, Zhang CX. The scaffold protein menin is essential for activating the MYC locus and MYC-mediated androgen receptor transcription in androgen receptor-dependent prostate cancer cells. Cancer Commun (Lond) 2021; 41:1427-1430. [PMID: 34850609 PMCID: PMC8696212 DOI: 10.1002/cac2.12217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 08/18/2021] [Accepted: 09/07/2021] [Indexed: 12/20/2022] Open
Affiliation(s)
- Yakun Luo
- Department of Tumor Escape, Resistance and Immunity, Université Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, 69008, France
| | - Virginie Vlaeminck-Guillem
- Department of Tumor Escape, Resistance and Immunity, Université Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, 69008, France.,Centre de Biologie Sud, Hôpital Lyon Sud, Hospices Civils de Lyon, Pierre-Bénite, 69310, France
| | - Romain Teinturier
- Department of Tumor Escape, Resistance and Immunity, Université Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, 69008, France
| | - Razan Abou Ziki
- Department of Tumor Escape, Resistance and Immunity, Université Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, 69008, France
| | - Philippe Bertolino
- Department of Tumor Escape, Resistance and Immunity, Université Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, 69008, France
| | - Muriel Le Romancer
- Department of Tumor Escape, Resistance and Immunity, Université Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, 69008, France
| | - Chang Xian Zhang
- Department of Tumor Escape, Resistance and Immunity, Université Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, 69008, France
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Liu D, Yin H, Wang Y, Cao Y, Yin J, Zhang J, Yin H, Zhao X. Development of a highly sensitive digital PCR assay to quantify long non-coding RNA MYU in urine samples which exhibited great potential as an alternative diagnostic biomarker for prostate cancer. Transl Androl Urol 2021; 10:3815-3825. [PMID: 34804824 PMCID: PMC8575588 DOI: 10.21037/tau-21-820] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/21/2021] [Indexed: 12/31/2022] Open
Abstract
Background The diagnostic methods of prostate cancer (PCa) present major drawbacks in that serum prostate specific antigen (PSA) testing lacks specificity for PCa and prostate needle biopsy is a painful and highly invasive procedure for patients. Thus, new alternative screening methods which are specific and non-invasive both in the early detection and in the clinical definitive diagnosis of PCa are in urgent need. Long non-coding RNA MYU has been shown to promote PCa cell proliferation and migration, and is significantly upregulated both at the cellular and tumor tissue level. Therefore, long non-coding RNA MYU may be a new potential diagnostic biomarker for PCa. Methods In the present study, we successfully developed a highly sensitive digital PCR assay to detect long non-coding RNA in clinical urine samples. dPCR was carried out using Qx200 ddPCR EvaGreen Supermix (Bio-Rad) according to the manufacturer’s instructions. Results Our results indicated that the digital PCR assay showed better linearity, repeatability, and reproducibility when compared with real-time quantitative PCR. In addition, we identified the normalized MYU level and used the digital PCR assay to measure it in 100 clinical urine samples. Our study showed that the normalized MYU level is a promising diagnostic biomarker for predicting and evaluating the malignancy of PCa. Conclusions Our findings presented a non-invasive liquid biopsy method to detect an alternative diagnostic parameter which can assist the diagnosis of PCa in clinical practice.
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Affiliation(s)
- Di Liu
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China.,JiHua Laboratory, Foshan, China
| | - Huming Yin
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yong Wang
- College of Biomedical Engineering, University of Science and Technology of China, Hefei, China
| | - Yang Cao
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jian Yin
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China.,JiHua Laboratory, Foshan, China
| | - Jianping Zhang
- Department of Tuberculosis, The Affiliated Infectious Diseases Hospital of Soochow University, Suzhou, China
| | - Huancai Yin
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China.,JiHua Laboratory, Foshan, China
| | - Xiaojun Zhao
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
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ceRNAs in Cancer: Mechanism and Functions in a Comprehensive Regulatory Network. JOURNAL OF ONCOLOGY 2021; 2021:4279039. [PMID: 34659409 PMCID: PMC8516523 DOI: 10.1155/2021/4279039] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 12/15/2022]
Abstract
Noncoding RNAs have been shown with powerful ability in post-transcriptional regulation, enabling intertwined RNA crosstalk and global molecular interaction in a large amount of dysfunctional conditions including cancer. Competing endogenous RNAs (ceRNAs) are those competitively binding with shared microRNAs (miRNAs), freeing their counterparts from miRNA-induced degradation, thus actively influencing and connecting with each other. Constantly updated analytical approaches boost outstanding advancement achieved in this burgeoning hotspot in multilayered intracellular communication, providing new insights into pathogenesis and clinical treatment. Here, we summarize the mechanisms and correlated factors under this RNA interplay and deregulated transcription profile in neoplasm and tumor progression, underscoring the great significance of ceRNAs for diagnostic values, monitoring biomarkers, and prognosis evaluation in cancer.
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38
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Dovey ZS, Nair SS, Chakravarty D, Tewari AK. Racial disparity in prostate cancer in the African American population with actionable ideas and novel immunotherapies. Cancer Rep (Hoboken) 2021; 4:e1340. [PMID: 33599076 PMCID: PMC8551995 DOI: 10.1002/cnr2.1340] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 11/22/2020] [Accepted: 12/02/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND African Americans (AAs) in the United States are known to have a higher incidence and mortality for Prostate Cancer (PCa). The drivers of this epidemiological disparity are multifactorial, including socioeconomic factors leading to lifestyle and dietary issues, healthcare access problems, and potentially tumor biology. RECENT FINDINGS Although recent evidence suggests once access is equal, AA men have equal outcomes to Caucasian American (CA) men, differences in PCa incidence remain, and there is much to do to reverse disparities in mortality across the USA. A deeper understanding of these issues, both at the clinical and molecular level, can facilitate improved outcomes in the AA population. This review first discusses PCa oncogenesis in the context of its diverse hallmarks before benchmarking key molecular and genomic differences for PCa in AA men that have emerged in the recent literature. Studies have emphasized the importance of tumor microenvironment that contributes to both the unequal cancer burden and differences in clinical outcome between the races. Management of comorbidities like obesity, hypertension, and diabetes will provide an essential means of reducing prostate cancer incidence in AA men. Although requiring further AA specific research, several new treatment strategies such as immune checkpoint inhibitors used in combination PARP inhibitors and other emerging vaccines, including Sipuleucel-T, have demonstrated some proven efficacy. CONCLUSION Genomic profiling to integrate clinical and genomic data for diagnosis, prognosis, and treatment will allow physicians to plan a "Precision Medicine" approach to AA men. There is a pressing need for further research for risk stratification, which may allow early identification of AA men with higher risk disease based on their unique clinical, genomic, and immunological profiles, which can then be mapped to appropriate clinical trials. Treatment options are outlined, with a concise description of recent work in AA specific populations, detailing several targeted therapies, including immunotherapy. Also, a summary of current clinical trials involving AA men is presented, and it is important that policies are adopted to ensure that AA men are actively recruited. Although it is encouraging that many of these explore the lifestyle and educational initiatives and therapeutic interventions, there is much still work to be done to reduce incidence and mortality in AA men and equalize current racial disparities.
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Affiliation(s)
- Zachary S. Dovey
- The Department of UrologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Sujit S. Nair
- The Department of UrologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Dimple Chakravarty
- The Department of UrologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Ashutosh K. Tewari
- The Department of UrologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
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The Role of Non-Coding RNAs in the Regulation of the Proto-Oncogene MYC in Different Types of Cancer. Biomedicines 2021; 9:biomedicines9080921. [PMID: 34440124 PMCID: PMC8389562 DOI: 10.3390/biomedicines9080921] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 07/25/2021] [Accepted: 07/28/2021] [Indexed: 01/17/2023] Open
Abstract
Alterations in the expression level of the MYC gene are often found in the cells of various malignant tumors. Overexpressed MYC has been shown to stimulate the main processes of oncogenesis: uncontrolled growth, unlimited cell divisions, avoidance of apoptosis and immune response, changes in cellular metabolism, genomic instability, metastasis, and angiogenesis. Thus, controlling the expression of MYC is considered as an approach for targeted cancer treatment. Since c-Myc is also a crucial regulator of many cellular processes in healthy cells, it is necessary to find ways for selective regulation of MYC expression in tumor cells. Many recent studies have demonstrated that non-coding RNAs play an important role in the regulation of the transcription and translation of this gene and some RNAs directly interact with the c-Myc protein, affecting its stability. In this review, we summarize current data on the regulation of MYC by various non-coding RNAs that can potentially be targeted in specific tumor types.
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40
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Kang B, Qiu C, Zhang Y. The Effect of lncRNA SNHG3 Overexpression on Lung Adenocarcinoma by Regulating the Expression of miR-890. JOURNAL OF HEALTHCARE ENGINEERING 2021; 2021:1643788. [PMID: 34306585 PMCID: PMC8285187 DOI: 10.1155/2021/1643788] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/25/2021] [Indexed: 12/17/2022]
Abstract
The lncRNA small nucleolar host gene 3 (SNHG3) was discovered to play an important role in the occurrence and development of lung adenocarcinoma (LUAD). However, the underlying molecular mechanism of SNHG3 in LUAD remains unclear. In the present study, SNHG3 expression levels in LUAD tissues and cell lines were analyzed using reverse transcription-quantitative PCR. The effects of SNHG3 on the proliferation, apoptosis, migration, and invasion of LUAD cells were determined using Cell Counting Kit-8, colony formation, flow cytometry, wound healing, and Transwell chamber assays, respectively. The specific underlying mechanism of SNHG3 in LUAD was investigated using bioinformatics analysis and a dual luciferase reporter assay. The results revealed that SNHG3 expression levels were downregulated in LUAD tissues and cell lines. Functionally, SNHG3 overexpression suppressed the proliferation, migration, and invasion of LUAD cells, while promoting apoptosis. Mechanistically, microRNA- (miR-) 890 was identified as a potential target of SNHG3, and its expression was negatively regulated by SNHG3. Notably, SNHG3 was found to promote LUAD progression by targeting miR-890. In conclusion, the findings of the present study revealed that lncRNA SNHG3 promoted the occurrence and progression of LUAD by regulating miR-890 expression.
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Affiliation(s)
- Baojie Kang
- Department of Respiratory, Weifang Yidu Central Hospital, Weifang City, Shandong, China
| | - Caihong Qiu
- Department of Respiratory, Weifang Yidu Central Hospital, Weifang City, Shandong, China
| | - Ying Zhang
- Department of ICU, Zibo Central Hospital, Zibo City, Shandong, China
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41
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Ahadi A. Functional roles of lncRNAs in the pathogenesis and progression of cancer. Genes Dis 2021; 8:424-437. [PMID: 34179307 PMCID: PMC8209321 DOI: 10.1016/j.gendis.2020.04.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/02/2020] [Accepted: 04/13/2020] [Indexed: 12/18/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) act as regulators of gene expression and pivotal transcriptional regulators in cancer cells via diverse mechanisms. lncRNAs involves a variety of pathological and biological activities, such as apoptosis, cell proliferation, metastasis, and invasion. By using microarray and RNA sequencing, it was identified that dysregulation of lncRNAs affects the tumorigenesis process. Taken together, these lncRNAs are putative biomarker and therapeutic target in human malignancies. In this review, I discuss the latest finding regarding the dysregulation of some important lncRNAs and their diverse mechanisms of these lncRNAs in the pathogenesis and progression of certain cancers; also, I summarize the possible roles of lncRNAs in clinical application for diagnosis and prognosis of cancer.
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Affiliation(s)
- Alireza Ahadi
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, 198396-3113, Iran
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Current Trends in Prevalence and Role of Long Noncoding RNA and Gene Fusion in Prostate Cancer: An Overview. ANNALS OF THE NATIONAL ACADEMY OF MEDICAL SCIENCES (INDIA) 2021. [DOI: 10.1055/s-0041-1729780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Abstract
Objectives The aim of this study is to analyze the current scenario in the diagnostic modalities for prostate cancer.
Materials and Methods We searched PubMed, Google Scholar, and ResearchGate for relevant data. Articles published in the last 10 years were taken into consideration. The role of long noncoding RNA and gene fusion products in the context of prostate cancer was reviewed, which included their roles in diagnosis, prognosis, and assessment of response to therapy.
Results Several long noncoding RNAs (lncRNA) have been isolated and have been shown to be useful in diagnosing and prognosticating prostate cancer. We have also looked into the role of TMPRSS2:ERG gene fusion in prostate carcinoma diagnosis. These molecular parameters have been looked into due to the fact that the current parameters in use such as prostate-specific antigen have several drawbacks that limit their potential.
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43
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Yang Y, Liu KY, Liu Q, Cao Q. Androgen Receptor-Related Non-coding RNAs in Prostate Cancer. Front Cell Dev Biol 2021; 9:660853. [PMID: 33869227 PMCID: PMC8049439 DOI: 10.3389/fcell.2021.660853] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/12/2021] [Indexed: 12/20/2022] Open
Abstract
Prostate cancer (PCa) is the second leading cause of cancer-related death among men in the United States. Androgen receptor (AR) signaling is the dominant oncogenic pathway in PCa and the main strategy of PCa treatment is to control the AR activity. A large number of patients acquire resistance to Androgen deprivation therapy (ADT) due to AR aberrant activation, resulting in castration-resistant prostate cancer (CRPC). Understanding the molecular mechanisms underlying AR signaling in the PCa is critical to identify new therapeutic targets for PCa patients. The recent advances in high-throughput RNA sequencing (RNA-seq) techniques identified an increasing number of non-coding RNAs (ncRNAs) that play critical roles through various mechanisms in different diseases. Some ncRNAs have shown great potentials as biomarkers and therapeutic targets. Many ncRNAs have been investigated to regulate PCa through direct association with AR. In this review, we aim to comprehensively summarize recent findings of the functional roles and molecular mechanisms of AR-related ncRNAs as AR regulators or targets in the progression of PCa.
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Affiliation(s)
- Yongyong Yang
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States.,Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Kilia Y Liu
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States.,Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Qi Liu
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States.,Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Qi Cao
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States.,Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
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Giles KA, Gould CM, Achinger-Kawecka J, Page SG, Kafer GR, Rogers S, Luu PL, Cesare AJ, Clark SJ, Taberlay PC. BRG1 knockdown inhibits proliferation through multiple cellular pathways in prostate cancer. Clin Epigenetics 2021; 13:37. [PMID: 33596994 PMCID: PMC7888175 DOI: 10.1186/s13148-021-01023-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 02/04/2021] [Indexed: 12/13/2022] Open
Abstract
Background BRG1 (encoded by SMARCA4) is a catalytic component of the SWI/SNF chromatin remodelling complex, with key roles in modulating DNA accessibility. Dysregulation of BRG1 is observed, but functionally uncharacterised, in a wide range of malignancies. We have probed the functions of BRG1 on a background of prostate cancer to investigate how BRG1 controls gene expression programmes and cancer cell behaviour. Results Our investigation of SMARCA4 revealed that BRG1 is over-expressed in the majority of the 486 tumours from The Cancer Genome Atlas prostate cohort, as well as in a complementary panel of 21 prostate cell lines. Next, we utilised a temporal model of BRG1 depletion to investigate the molecular effects on global transcription programmes. Depleting BRG1 had no impact on alternative splicing and conferred only modest effect on global expression. However, of the transcriptional changes that occurred, most manifested as down-regulated expression. Deeper examination found the common thread linking down-regulated genes was involvement in proliferation, including several known to increase prostate cancer proliferation (KLK2, PCAT1 and VAV3). Interestingly, the promoters of genes driving proliferation were bound by BRG1 as well as the transcription factors, AR and FOXA1. We also noted that BRG1 depletion repressed genes involved in cell cycle progression and DNA replication, but intriguingly, these pathways operated independently of AR and FOXA1. In agreement with transcriptional changes, depleting BRG1 conferred G1 arrest. Conclusions Our data have revealed that BRG1 promotes cell cycle progression and DNA replication, consistent with the increased cell proliferation associated with oncogenesis. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01023-7.
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Affiliation(s)
- Katherine A Giles
- Epigenetics Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,Genome Integrity Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia.,Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, TAS, Hobart, 7000, Australia
| | - Cathryn M Gould
- Epigenetics Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Joanna Achinger-Kawecka
- Epigenetics Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2000, Australia
| | - Scott G Page
- Genome Integrity Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | - Georgia R Kafer
- Genome Integrity Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | - Samuel Rogers
- Genome Integrity Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | - Phuc-Loi Luu
- Epigenetics Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2000, Australia
| | - Anthony J Cesare
- Genome Integrity Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | - Susan J Clark
- Epigenetics Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2000, Australia
| | - Phillippa C Taberlay
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, TAS, Hobart, 7000, Australia.
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45
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Wilson C, Kanhere A. 8q24.21 Locus: A Paradigm to Link Non-Coding RNAs, Genome Polymorphisms and Cancer. Int J Mol Sci 2021; 22:1094. [PMID: 33499210 PMCID: PMC7865353 DOI: 10.3390/ijms22031094] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/15/2021] [Accepted: 01/20/2021] [Indexed: 01/17/2023] Open
Abstract
The majority of the human genome is comprised of non-protein-coding genes, but the relevance of non-coding RNAs in complex diseases has yet to be fully elucidated. One class of non-coding RNAs is long non-coding RNAs or lncRNAs, many of which have been identified to play a range of roles in transcription and translation. While the clinical importance of the majority of lncRNAs have yet to be identified, it is puzzling that a large number of disease-associated genetic variations are seen in lncRNA genes. The 8q24.21 locus is rich in lncRNAs and very few protein-coding genes are located in this region. Interestingly, the 8q24.21 region is also a hot spot for genetic variants associated with an increased risk of cancer. Research focusing on the lncRNAs in this area of the genome has indicated clinical relevance of lncRNAs in different cancers. In this review, we summarise the lncRNAs in the 8q24.21 region with respect to their role in cancer and discuss the potential impact of cancer-associated genetic polymorphisms on the function of lncRNAs in initiation and progression of cancer.
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Affiliation(s)
| | - Aditi Kanhere
- Department of Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 3BX, UK;
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46
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Zhu P, He F, Hou Y, Tu G, Li Q, Jin T, Zeng H, Qin Y, Wan X, Qiao Y, Qiu Y, Teng Y, Liu M. A novel hypoxic long noncoding RNA KB-1980E6.3 maintains breast cancer stem cell stemness via interacting with IGF2BP1 to facilitate c-Myc mRNA stability. Oncogene 2021; 40:1609-1627. [PMID: 33469161 PMCID: PMC7932928 DOI: 10.1038/s41388-020-01638-9] [Citation(s) in RCA: 140] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 11/13/2020] [Accepted: 12/18/2020] [Indexed: 01/13/2023]
Abstract
The hostile hypoxic microenvironment takes primary responsibility for the rapid expansion of breast cancer tumors. However, the underlying mechanism is not fully understood. Here, using RNA sequencing (RNA-seq) analysis, we identified a hypoxia-induced long noncoding RNA (lncRNA) KB-1980E6.3, which is aberrantly upregulated in clinical breast cancer tissues and closely correlated with poor prognosis of breast cancer patients. The enhanced lncRNA KB-1980E6.3 facilitates breast cancer stem cells (BCSCs) self-renewal and tumorigenesis under hypoxic microenvironment both in vitro and in vivo. Mechanistically, lncRNA KB-1980E6.3 recruited insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) to form a lncRNA KB-1980E6.3/IGF2BP1/c-Myc signaling axis that retained the stability of c-Myc mRNA through increasing binding of IGF2BP1 with m6A-modified c-Myc coding region instability determinant (CRD) mRNA. In conclusion, we confirm that lncRNA KB-1980E6.3 maintains the stemness of BCSCs through lncRNA KB-1980E6.3/IGF2BP1/c-Myc axis and suggest that disrupting this axis might provide a new therapeutic target for refractory hypoxic tumors.
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Affiliation(s)
- Pengpeng Zhu
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Fang He
- Department of pharmacy, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Yixuan Hou
- Experimental Teaching Center of Basic Medicine Science, Chongqing Medical University, Chongqing, 400016, China
| | - Gang Tu
- Department of Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Qiao Li
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Ting Jin
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Huan Zeng
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Yilu Qin
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Xueying Wan
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Yina Qiao
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Yuxiang Qiu
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Yong Teng
- Department of Oral Biology and Dx Sciences, Dental College of Georgia; Georgia Cancer Center, Augusta University, Augusta, GA, 30907, USA
| | - Manran Liu
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China.
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47
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Liu SY, Zhao ZY, Qiao Z, Li SM, Zhang WN. LncRNA PCAT1 Interacts with DKC1 to Regulate Proliferation, Invasion and Apoptosis in NSCLC Cells via the VEGF/AKT/Bcl2/Caspase9 Pathway. Cell Transplant 2021; 30:963689720986071. [PMID: 33461333 PMCID: PMC7818005 DOI: 10.1177/0963689720986071] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are increasingly recognized as indispensable
components of the regulatory network in the progression of various cancers,
including nonsmall cell lung cancer (NSCLC). The lncRNA prostate cancer
associated transcript 1 (PCAT1) has been involved in tumorigenesis of multiple
malignant solid tumors, but it is largely unknown that what is the role of
lncRNA-PCAT1 and how it functions in the progression of lung cancer. Herein, we
observed that lncRNA PCAT1 expression was upregulated in both human NSCLC
tissues and cell lines, which was determined by qualitative polymerase chain
reaction analysis. Then, gain-and loss-of-function manipulations were performed
in A549 cells by transfection with a specific short interfering RNA against
PCAT1 or a pcDNA-PCAT1 expression vector. The results showed that PCAT1 not only
promoted NSCLC cell proliferation and invasion but also inhibited cell
apoptosis. Bioinformatics and expression correlation analyses revealed that
there was a potential interaction between PCAT1 and the dyskerin pseudouridine
synthase 1 (DKC1) protein, an RNA-binding protein. Then, RNA pull-down assays
with biotinylated probes and transcripts both confirmed that PCAT1 directly
bounds with DKC1 that could also promote NSCLC cell proliferation and invasion
and inhibit cell apoptosis. Moreover, the effects of PCAT1 and DKC1 on NSCLC
functions are synergistic. Furthermore, PCAT1 and DKC1 activated the vascular
endothelial growth factor (VEGF)/protein kinase B (AKT)/Bcl-2/caspase9 pathway
in NSCLC cells, and inhibition of epidermal growth factor receptor, AKT, or
Bcl-2 could eliminate the effect of PCAT1/DKC1 co-overexpression on NSCLC cell
behaviors. In conclusion, lncRNA PCAT1 interacts with DKC1 to regulate
proliferation, invasion, and apoptosis in NSCLC cells via the
VEGF/AKT/Bcl-2/caspase9 pathway.
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Affiliation(s)
- Shi-Yuan Liu
- Department of Thoracic Surgery, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, P. R. China
| | - Zhi-Yu Zhao
- Department of Cardiac Surgery, the First Hospital of Lanzhou University, Lanzhou, Gansu Province, P. R. China
| | - Zhe Qiao
- Department of Thoracic Surgery, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, P. R. China
| | - Shao-Min Li
- Department of Thoracic Surgery, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, P. R. China
| | - Wei-Ning Zhang
- Department of Surgical Chest and Oncology, the Hospital of Xidian Group, Xi'an, Shaanxi Province, P. R. China
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48
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Taniue K, Akimitsu N. The Functions and Unique Features of LncRNAs in Cancer Development and Tumorigenesis. Int J Mol Sci 2021; 22:E632. [PMID: 33435206 PMCID: PMC7826647 DOI: 10.3390/ijms22020632] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 01/05/2021] [Accepted: 01/07/2021] [Indexed: 12/19/2022] Open
Abstract
Over the past decades, research on cancer biology has focused on the involvement of protein-coding genes in cancer development. Long noncoding RNAs (lncRNAs), which are transcripts longer than 200 nucleotides that lack protein-coding potential, are an important class of RNA molecules that are involved in a variety of biological functions. Although the functions of a majority of lncRNAs have yet to be clarified, some lncRNAs have been shown to be associated with human diseases such as cancer. LncRNAs have been shown to contribute to many important cancer phenotypes through their interactions with other cellular macromolecules including DNA, protein and RNA. Here we describe the literature regarding the biogenesis and features of lncRNAs. We also present an overview of the current knowledge regarding the roles of lncRNAs in cancer from the view of various aspects of cellular homeostasis, including proliferation, survival, migration and genomic stability. Furthermore, we discuss the methodologies used to identify the function of lncRNAs in cancer development and tumorigenesis. Better understanding of the molecular mechanisms involving lncRNA functions in cancer is critical for the development of diagnostic and therapeutic strategies against tumorigenesis.
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Affiliation(s)
- Kenzui Taniue
- Isotope Science Center, The University of Tokyo, 2-11-16, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Cancer Genomics and Precision Medicine, Division of Gastroenterology and Hematology-Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa 078-8510, Hokkaido, Japan
| | - Nobuyoshi Akimitsu
- Isotope Science Center, The University of Tokyo, 2-11-16, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
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49
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Tezerjani MD, Kalantar SM. Unraveling the dark matter, long non-coding RNAs, in male reproductive diseases: A narrative review. Int J Reprod Biomed 2020; 18:921-934. [PMID: 33349800 PMCID: PMC7749978 DOI: 10.18502/ijrm.v13i11.7959] [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: 12/02/2019] [Revised: 05/10/2020] [Accepted: 06/28/2020] [Indexed: 12/09/2022] Open
Abstract
Recent advances in human transcriptome have revealed the fundamental and functional roles of long non-coding RNA in the susceptibility to diverse diseases and pathological conditions. They participate in wide range of biological processes such as the modulating of chromatin structure, transcription, translation, and post-translation modification. In addition, based on their unique expression profiles and their association with clinical abnormalities such as those of related to male reproductive diseases, they can be used to develop therapeutic methods and biomarkers for screening of the diseases. In this study, we will review the identified lncRNAs and their molecular functions in the pathogenesis of male reproductive diseases such as prostate cancer, benign prostatic hyperplasia, prostatitis, testicular cancer, varicocele, and sperm abnormalities.
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Affiliation(s)
- Masoud Dehghan Tezerjani
- Abortion Research Centre, Yazd Reproductive Sciences Institute, Shahid Sadoughi University of Medical Science, Yazd, Iran
| | - Seyed Mehdi Kalantar
- Abortion Research Centre, Yazd Reproductive Sciences Institute, Shahid Sadoughi University of Medical Science, Yazd, Iran.,Department of Genetics, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
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50
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Gao N, Li Y, Li J, Gao Z, Yang Z, Li Y, Liu H, Fan T. Long Non-Coding RNAs: The Regulatory Mechanisms, Research Strategies, and Future Directions in Cancers. Front Oncol 2020; 10:598817. [PMID: 33392092 PMCID: PMC7775490 DOI: 10.3389/fonc.2020.598817] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 11/18/2020] [Indexed: 12/12/2022] Open
Abstract
The development and application of whole genome sequencing technology has greatly broadened our horizons on the capabilities of long non-coding RNAs (lncRNAs). LncRNAs are more than 200 nucleotides in length and lack protein-coding potential. Increasing evidence indicates that lncRNAs exert an irreplaceable role in tumor initiation, progression, as well as metastasis, and are novel molecular biomarkers for diagnosis and prognosis of cancer patients. Furthermore, lncRNAs and the pathways they influence might represent promising therapeutic targets for a number of tumors. Here, we discuss the recent advances in understanding of the specific regulatory mechanisms of lncRNAs. We focused on the signal, decoy, guide, and scaffold functions of lncRNAs at the epigenetic, transcription, and post-transcription levels in cancer cells. Additionally, we summarize the research strategies used to investigate the roles of lncRNAs in tumors, including lncRNAs screening, lncRNAs characteristic analyses, functional studies, and molecular mechanisms of lncRNAs. This review will provide a short but comprehensive description of the lncRNA functions in tumor development and progression, thus accelerating the clinical implementation of lncRNAs as tumor biomarkers and therapeutic targets.
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Affiliation(s)
- Na Gao
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
| | - Yueheng Li
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
| | - Jing Li
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
| | - Zhengfan Gao
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
| | - Zhenzhen Yang
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
- Translational Medicine Research Center, People’s Hospital of Zhengzhou, Zhengzhou, China
| | - Yong Li
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
- Faculty of Medicine, St George and Sutherland Clinical School, St George Hospital, The University of New South Wales (UNSW) Sydney, Kensington, NSW, Australia
| | - Hongtao Liu
- Laboratory for Cell Biology, College of Life Sciences of Zhengzhou University, Zhengzhou, China
| | - Tianli Fan
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
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