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Huang P, Wen F, Li Y, Li Q. The tale of SOX2: Focusing on lncRNA regulation in cancer progression and therapy. Life Sci 2024; 344:122576. [PMID: 38492918 DOI: 10.1016/j.lfs.2024.122576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/06/2024] [Accepted: 03/13/2024] [Indexed: 03/18/2024]
Abstract
Long non-coding RNAs (lncRNAs) have emerged as influential contributors to diverse cellular processes, which regulate gene function and expression via multiple mechanistic pathways. Therefore, it is essential to exploit the structures and interactions of lncRNAs to comprehend their mechanistic functions within cells. A growing body of evidence has revealed that deregulated lncRNAs are involved in multiple regulations of malignant events including cell proliferation, growth, invasion, and metabolism. SRY-related high mobility group box (SOX)2, a well-recognized member of the SOX family, is commonly overexpressed in various types of cancer, contributing to tumor progression and maintenance of stemness. Emerging studies have shown that lncRNAs interact with SOX2 to remarkably contribute to carcinogenesis and disease states. This review elaborates on the crosstalk between the intricate and complicated functions of lncRNAs and SOX2 in the context of malignant diseases. We elucidate distinct molecular mechanisms that contribute to the onset/advancement of cancer, indicating that lncRNAs/SOX2 axes hold immense promise for potential therapeutic targets. Furthermore, we delve into the modalities of emerging feasible treatment options for targeting lncRNAs, highlighting the limitations of such therapies and providing novel insights into further ameliorations of targeted strategies of lncRNAs to promote the clinical implications. Translating current discoveries into clinical applications could ultimately boost improved survival and prognosis of cancer patients.
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Affiliation(s)
- Peng Huang
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Feng Wen
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - YiShan Li
- Thoracic Oncology Ward, Cancer Center, West China Hospital, Sichuan University, West China School of Nursing, Chengdu, Sichuan 610041, China
| | - Qiu Li
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
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2
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Zhou C, Balmer L, Song M, Wu K, Wang W, Wang H. CircPVT1 promotes migration and invasion by regulating miR-490-5p/HAVCR2 axis in osteosarcoma cells. J Cell Mol Med 2024; 28:e18269. [PMID: 38568056 PMCID: PMC10989635 DOI: 10.1111/jcmm.18269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 03/04/2024] [Accepted: 03/13/2024] [Indexed: 04/05/2024] Open
Abstract
Circular RNAs (circRNAs) play an important role in the progression of osteosarcoma. However, the precise function of circPVT1 in osteosarcoma remains elusive. This study aims to explore the molecular mechanism underlying the involvement of circPVT1 in osteosarcoma cells. We quantified circPVT1 expression using qRT-PCR in both control and osteosarcoma cell lines. To investigate the roles of circPVT1, miR-490-5p and HAVCR2 in vitro, we separately conducted overexpression and inhibition experiments for circPVT1, miR-490-5p and HAVCR2 in HOS and U2OS cells. Cell migration was assessed through wound healing and transwell migration assays, and invasion was measured via the Matrigel invasion assay. To elucidate the regulatory mechanism of circPVT1 in osteosarcoma, a comprehensive approach was employed, including fluorescence in situ hybridization, qRT-PCR, Western blot, bioinformatics, dual-luciferase reporter assay and rescue assay. CircPVT1 expression in osteosarcoma cell lines surpassed that in control cells. The depletion of circPVT1 resulted in a notable reduction in the in vitro migration and invasion of osteosarcoma cells. Mechanism experiments revealed that circPVT1 functioned as a miR-490-5p sequester, and directly targeted HAVCR2. Overexpression of miR-490-5p led to a significant attenuation of migration and invasion of osteosarcoma cells, whereas HAVCR2 overexpression had the opposite effect, promoting these abilities. Additionally, circPVT1 upregulated HAVCR2 expression via sequestering miR-490-5p, thereby orchestrating the migration and invasion in osteosarcoma cells. CircPVT1 orchestrates osteosarcoma migration and invasion by regulating the miR-490-5p/HAVCR2 axis, underscoring its potential as a promising therapeutic target for osteosarcoma.
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Affiliation(s)
- Chunbin Zhou
- Department of OrthopaedicsFirst Affiliated Hospital of Shantou University Medical CollegeShantouGuangdongChina
- Center for Precision Health, School of Medical and Health ScienceEdith Cowan UniversityPerthWestern AustraliaAustralia
| | - Lois Balmer
- Center for Precision Health, School of Medical and Health ScienceEdith Cowan UniversityPerthWestern AustraliaAustralia
| | - Manshu Song
- Center for Precision Health, School of Medical and Health ScienceEdith Cowan UniversityPerthWestern AustraliaAustralia
| | - Kezhou Wu
- Department of OrthopaedicsFirst Affiliated Hospital of Shantou University Medical CollegeShantouGuangdongChina
| | - Wei Wang
- Center for Precision Health, School of Medical and Health ScienceEdith Cowan UniversityPerthWestern AustraliaAustralia
- First Affiliated Hospital of Shantou University Medical CollegeShantouGuangdongChina
| | - Hu Wang
- Department of OrthopaedicsFirst Affiliated Hospital of Shantou University Medical CollegeShantouGuangdongChina
- Minimally Invasive Spine CenterFirst Affiliated Hospital of Shantou University Medical CollegeShantouGuangdongChina
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3
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Almalki WH, Almujri SS. The dual roles of circRNAs in Wnt/β-Catenin signaling and cancer progression. Pathol Res Pract 2024; 255:155132. [PMID: 38335783 DOI: 10.1016/j.prp.2024.155132] [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: 12/06/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 02/12/2024]
Abstract
Cancer, a complex pathophysiological condition, arises from the abnormal proliferation and survival of cells due to genetic mutations. Dysregulation of cell cycle control, apoptosis, and genomic stability contribute to uncontrolled growth and metastasis. Tumor heterogeneity, microenvironmental influences, and immune evasion further complicate cancer dynamics. The intricate interplay between circular RNAs (circRNAs) and the Wnt/β-Catenin signalling pathway has emerged as a pivotal axis in the landscape of cancer biology. The Wnt/β-Catenin pathway, a critical regulator of cell fate and proliferation, is frequently dysregulated in various cancers. CircRNAs, a class of non-coding RNAs with closed-loop structures, have garnered increasing attention for their diverse regulatory functions. This review systematically explores the intricate crosstalk between circRNAs and the Wnt/β-Catenin pathway, shedding light on their collective impact on cancer initiation and progression. The review explores the diverse mechanisms through which circRNAs modulate the Wnt/β-Catenin pathway, including sponging microRNAs, interacting with RNA-binding proteins, and influencing the expression of key components in the pathway. Furthermore, the review highlights specific circRNAs implicated in various cancer types, elucidating their roles as either oncogenic or tumour-suppressive players in the context of Wnt/β-Catenin signaling. The intricate regulatory networks formed by circRNAs in conjunction with the Wnt/β-Catenin pathway are discussed, providing insights into potential therapeutic targets and diagnostic biomarkers. This comprehensive review delves into the multifaceted roles of circRNAs in orchestrating tumorigenesis through their regulatory influence on the Wnt/β-Catenin pathway.
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Affiliation(s)
- Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia.
| | - Salem Salman Almujri
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha 61421, Aseer, Saudi Arabia
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Zhao X, van den Berg A, Winkle M, Koerts J, Seitz A, de Jong D, Rutgers B, van der Sluis T, Bakker E, Kluiver J. Proliferation-promoting roles of linear and circular PVT1 are independent of their ability to bind miRNAs in B-cell lymphoma. Int J Biol Macromol 2023; 253:126744. [PMID: 37689284 DOI: 10.1016/j.ijbiomac.2023.126744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/01/2023] [Accepted: 08/27/2023] [Indexed: 09/11/2023]
Abstract
Plasmacytoma Variant Translocation 1 (PVT1) is a long non-coding RNA located at 8q24.21 immediately downstream of MYC. Both the linear and circular PVT1 transcripts contribute to cancer pathogenesis by binding microRNAs. However, little is known about their roles in B-cell lymphoma. Here we studied their expression patterns, role in growth, and ability to bind miRNAs in B-cell lymphoma. Linear PVT1 transcripts were downregulated in B-cell cell lymphoma lines compared to germinal center B cells, while circPVT1 levels were increased. Two Hodgkin lymphoma cell lines had a homozygous deletion including the 5' region of the PVT1 locus, resulting in a complete lack of circPVT1 and 5' linear PVT1 transcripts. Inhibition of both linear and circular PVT1 decreased growth of Burkitt lymphoma, while the effects on Hodgkin lymphoma and diffuse large B cell lymphoma were less pronounced. Overexpression of circPVT1 promoted growth of B-cell lymphoma lacking or having low endogenous circPVT1 levels. Contrary to other types of cancer, linear and circular PVT1 transcripts did not interact with miRNAs in B-cell lymphoma. Overall, we showed an opposite expression pattern of linear and circular PVT1 in B-cell lymphoma. Their effect on growth was independent of their ability to bind miRNAs.
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Affiliation(s)
- Xing Zhao
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Anke van den Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands.
| | - Melanie Winkle
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Jasper Koerts
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Annika Seitz
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Debora de Jong
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Bea Rutgers
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Tineke van der Sluis
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Emke Bakker
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Joost Kluiver
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands.
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Ghetti M, Vannini I, Bochicchio MT, Azzali I, Ledda L, Marconi G, Melloni M, Fabbri F, Rondoni M, Chicchi R, Angeli D, Ghelli Luserna di Rorà A, Giannini B, Zacheo I, Biguzzi R, Lanza F, Martinelli G, Simonetti G. Uncovering the expression of circPVT1 in the extracellular vesicles of acute myeloid leukemia patients. Biomed Pharmacother 2023; 165:115235. [PMID: 37536029 DOI: 10.1016/j.biopha.2023.115235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/19/2023] [Accepted: 07/25/2023] [Indexed: 08/05/2023] Open
Abstract
Extracellular vesicles (EVs) act as molecular mediators in the tumor microenvironment, by shuttling information contained within malignant cells and functioning as regulators of the immune system. Circular (circ)RNAs are characterized by a closed loop-like structure that makes them more stable in the extracellular milieu and suitable to be packaged inside EVs. circPVT1 (hsa_circ_0001821) showed an oncogenic role in several cancer types and immunosuppressive properties in myeloid and lymphoid cell subsets. In this study, we characterized EVs from acute myeloid leukemia (AML) patients in terms of size, concentrations, surface markers and circPVT1 cargo. We showed that circPVT1 is overexpressed by primary blast cells from newly-diagnosed AML patients compared with hematopoietic stem-progenitor cells and is released as cell-free RNA in the plasma. We isolated EVs from the plasma of AML patients and healthy subjects by size exclusion chromatography and characterized them by nanoparticle tracking analysis. EVs from patients' plasma are larger compared with those from healthy subjects and their surface profile is characterized by higher levels of the leukemic cell markers CD133, CD105, CD49e and other immune-related epitopes, with differences according to AML molecular profile. Moreover, digital PCR analysis revealed that circPVT1 is more abundant inside EVs from the plasma of AML patients compared with healthy subjects. Our findings provide new insights on the features and content of AML EVs and suggest a role of circPVT1 in the crosstalk between AML cells and the tumor microenvironment.
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Affiliation(s)
- Martina Ghetti
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Ivan Vannini
- Pathology Unit, Morgagni-Pierantoni Hospital, AUSL Romagna, Forlì, Italy
| | - Maria Teresa Bochicchio
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Irene Azzali
- Unit of Biostatistics and Clinical Trials, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Lorenzo Ledda
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Giovanni Marconi
- Hematology Unit, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Mattia Melloni
- Laboratory of Biomarkers, Biomolecular Targets and Personalized Medicine in Oncology, Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Francesco Fabbri
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Michela Rondoni
- Hematology Unit & Romagna Transplant Network, Ravenna Hospital, Ravenna, Italy
| | - Roberta Chicchi
- Laboratorio Unico AUSL della Romagna, U.O. Medicina Trasfusionale di Forlì-Cesena e Officina Trasfusionale della Romagna, Pievesestina di Cesena, Italy
| | - Davide Angeli
- Unit of Biostatistics and Clinical Trials, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Andrea Ghelli Luserna di Rorà
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy; Fondazione Pisana per la Scienza ONLUS, San Giuliano Terme, Italy
| | - Barbara Giannini
- Laboratorio Unico AUSL della Romagna, U.O. Genetica Medica, Pievesestina di Cesena, Italy
| | - Irene Zacheo
- Hematology Unit, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Rino Biguzzi
- Laboratorio Unico AUSL della Romagna, U.O. Medicina Trasfusionale di Forlì-Cesena e Officina Trasfusionale della Romagna, Pievesestina di Cesena, Italy
| | - Francesco Lanza
- Hematology Unit & Romagna Transplant Network, Ravenna Hospital, Ravenna, Italy
| | - Giovanni Martinelli
- Scientific Directorate, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Giorgia Simonetti
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy.
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Han W, Shi CT, Chen H, Zhou Q, Ding W, Chen F, Liang ZW, Teng YJ, Shao QX, Dong XQ. Role of LncRNA MIR99AHG in breast cancer: Bioinformatic analysis and preliminary verification. Heliyon 2023; 9:e19805. [PMID: 37809464 PMCID: PMC10559167 DOI: 10.1016/j.heliyon.2023.e19805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 08/27/2023] [Accepted: 09/01/2023] [Indexed: 10/10/2023] Open
Abstract
Objective This research was aimed to preliminarily explore the clinical roles and potential molecular mechanisms of MIR99AHG and its significant transcripts in breast cancer (BRCA). Methods Public databases were utilized to analyze the expression and prognostic roles of MIR99AHG and its transcripts. Relationships between MIR99AHG expression and immune cells infiltration were analyzed in Xiantao platform. In addition, co-expressed genes and interacting proteins of MIR99AHG were predicted. CancerSEA analyzed its relationship with functional states. Next, CNV status, DNA methylation, interacting transcription factors (TFs) and ceRNA network were analyzed to explore its possible mechanisms. Then, RNA ISH and FISH assays were used to detect its expression and location in BRCA tissues and cell lines, respectively. Finally, qRT-PCR was utilized to investigate MIR99AHG expression in cell lines. Results Compared with the corresponding normal tissues, MIR99AHG expression levels were lower in all BRCA subtypes, and luminal B's was the lowest one. And MIR99AHG expression was negatively related to the tumor stage. In addition, 4 transcripts (ENST00000619222.4, ENST00000418813.6, ENST00000602901.5 and ENST00000453910.5) of MIR99AHG showed significant differences in the expression. Databases also suggested that the high MIR99AHG expression levels indicated good prognosis, especially in patients without lymph node metastasis. Xiantao found that MIR99AHG was positively related to 17 immune cells and negatively linked with 2 immune cells. CancerSEA analysis showed no relationships between MIR99AHG and functional states. From GEPIA and BCIP databases, 19 co-expressed genes were highly related to these four significant transcripts of MIR99AHG. StarBase, RNAct and HDOCK showed that several tumor-associated proteins, including U2AF65, hnRNPC, AEBP2, CHIC1 and so on, might interact with MIR99AHG. Genetically, BRCA had a higher proportion of MIR99AHG CNV loss than CNV gain, and the high level of DNA methylation indicated a good prognosis. Furthermore, 19 TFs were predicted to combine with the promoter of MIR99AHG. Then, we screened out 10 miRNAs potentially interacting with the significant transcripts of MIR99AHG, and five were significantly increased in breast tumors compared to normal tissues, including miR-194-5p, miR-320 b and so on, which could combine 14 mRNAs. Through ISH and FISH assays, we verified that MIR99AHG was down-regulated in BRCA samples and cell lines in comparison to non-tumor tissues and mammary epithelial cell line (MCF10A), and MIR99AHG was located both in cytoplasm and nucleus. qRT-PCR assay also showed the lower expression of MIR99AHG in breast cancer cells than that in MCF10A. Conclusion These results indicate that MIR99AHG can be a favorable prognostic indicator for BRCA. ENST00000619222.4, ENST00000418813.6, ENST00000602901.5 and ENST00000453910.5 are significant transcripts and their down-regulation may play crucial roles in the progression of BRCA.
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Affiliation(s)
- Wei Han
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, PR China
- Department of General Surgery, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, Jiangsu, 215300, PR China
| | - Chun-tao Shi
- Department of General Surgery, Wuxi Xishan People's Hospital, Wuxi, Jiangsu, 214000, PR China
| | - Hua Chen
- Department of General Surgery, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, Jiangsu, 215300, PR China
| | - Qin Zhou
- Department of General Surgery, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, Jiangsu, 215300, PR China
| | - Wei Ding
- Ultrasonic Department, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, Jiangsu, 215300, PR China
| | - Fang Chen
- Department of Pathology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, Jiangsu, 215300, PR China
| | - Zhi-wei Liang
- Central Laboratory, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, Jiangsu, 215300, PR China
| | - Ya-jie Teng
- Central Laboratory, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, Jiangsu, 215300, PR China
| | - Qi-xiang Shao
- Department of Immunology, Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, PR China
| | - Xiao-qiang Dong
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, PR China
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Zeng C, Chujo T, Hirose T, Hamada M. Landscape of semi-extractable RNAs across five human cell lines. Nucleic Acids Res 2023; 51:7820-7831. [PMID: 37463833 PMCID: PMC10450185 DOI: 10.1093/nar/gkad567] [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: 10/03/2022] [Revised: 05/23/2023] [Accepted: 06/21/2023] [Indexed: 07/20/2023] Open
Abstract
Phase-separated membraneless organelles often contain RNAs that exhibit unusual semi-extractability using the conventional RNA extraction method, and can be efficiently retrieved by needle shearing or heating during RNA extraction. Semi-extractable RNAs are promising resources for understanding RNA-centric phase separation. However, limited assessments have been performed to systematically identify and characterize semi-extractable RNAs. In this study, 1074 semi-extractable RNAs, including ASAP1, DANT2, EXT1, FTX, IGF1R, LIMS1, NEAT1, PHF21A, PVT1, SCMH1, STRG.3024.1, TBL1X, TCF7L2, TVP23C-CDRT4, UBE2E2, ZCCHC7, ZFAND3 and ZSWIM6, which exhibited consistent semi-extractability were identified across five human cell lines. By integrating publicly available datasets, we found that semi-extractable RNAs tend to be distributed in the nuclear compartments but are dissociated from the chromatin. Long and repeat-containing semi-extractable RNAs act as hubs to provide global RNA-RNA interactions. Semi-extractable RNAs were divided into four groups based on their k-mer content. The NEAT1 group preferred to interact with paraspeckle proteins, such as FUS and NONO, implying that RNAs in this group are potential candidates of architectural RNAs that constitute nuclear bodies.
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Affiliation(s)
- Chao Zeng
- Faculty of Science and Engineering, Waseda University, Tokyo 1698555, Japan
| | - Takeshi Chujo
- Faculty of Life Sciences, Kumamoto University, Kumamoto 8608556, Japan
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Suita 5650871, Japan
- Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita 5650871, Japan
| | - Michiaki Hamada
- Faculty of Science and Engineering, Waseda University, Tokyo 1698555, Japan
- AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo 1698555, Japan
- Graduate School of Medicine, Nippon Medical School, Tokyo 1138602, Japan
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Palcau AC, Brandi R, Mehterov NH, Botti C, Blandino G, Pulito C. Exploiting Long Non-Coding RNAs and Circular RNAs as Pharmacological Targets in Triple-Negative Breast Cancer Treatment. Cancers (Basel) 2023; 15:4181. [PMID: 37627209 PMCID: PMC10453179 DOI: 10.3390/cancers15164181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/13/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Breast cancer is one of the most frequent causes of cancer death among women worldwide. In particular, triple-negative breast cancer (TNBC) represents the most aggressive breast cancer subtype because it is characterized by the absence of molecular targets, thus making it an orphan type of malignancy. The discovery of new molecular druggable targets is mandatory to improve treatment success. In that context, non-coding RNAs represent an opportunity for modulation of cancer. They are RNA molecules with apparently no protein coding potential, which have been already demonstrated to play pivotal roles within cells, being involved in different processes, such as proliferation, cell cycle regulation, apoptosis, migration, and diseases, including cancer. Accordingly, they could be used as targets for future TNBC personalized therapy. Moreover, the peculiar characteristics of non-coding RNAs make them reliable biomarkers to monitor cancer treatment, thus, to monitor recurrence or chemoresistance, which are the most challenging aspects in TNBC. In the present review, we focused on the oncogenic or oncosuppressor role of long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) mostly involved in TNBC, highlighting their mode of action and depicting their potential role as a biomarker and/or as targets of new non-coding RNA-based therapeutics.
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Affiliation(s)
- Alina Catalina Palcau
- Translational Oncology Research Unit, Department of Research, Advanced Diagnostic and Technological Innovation, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy; (A.C.P.); (R.B.); (G.B.)
| | - Renata Brandi
- Translational Oncology Research Unit, Department of Research, Advanced Diagnostic and Technological Innovation, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy; (A.C.P.); (R.B.); (G.B.)
| | - Nikolay Hristov Mehterov
- Department of Medical Biology, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria;
- Research Institute, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria
| | - Claudio Botti
- Breast Surgery Unit, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy;
| | - Giovanni Blandino
- Translational Oncology Research Unit, Department of Research, Advanced Diagnostic and Technological Innovation, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy; (A.C.P.); (R.B.); (G.B.)
| | - Claudio Pulito
- Translational Oncology Research Unit, Department of Research, Advanced Diagnostic and Technological Innovation, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy; (A.C.P.); (R.B.); (G.B.)
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9
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Baljon KJ, Ramaiah P, Saleh EAM, Al-Dolaimy F, Al-Dami FH, Gandla K, Alkhafaji AT, Abbas AHR, Alsaalamy AH, Bisht YS. LncRNA PVT1: as a therapeutic target for breast cancer. Pathol Res Pract 2023; 248:154675. [PMID: 37531833 DOI: 10.1016/j.prp.2023.154675] [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: 06/21/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 08/04/2023]
Abstract
A significant number of women are identified with breast cancer (BC) every year, making it among the most prevalent malignancies and one of the leading causes of mortality globally. Despite significant progress in understanding BC pathogenesis and treatment options, there is still a need to identify new therapeutic targets and develop more effective treatments. LncRNAs have been discovered as biomarkers and a promising target for various cancers, including BC. PVT1 is a particular one of these lncRNAs, and research has indicated that it has a significant impact on the appearance and progression of BC.PVT1 is an attractive therapeutic target for BC due to its role in promoting cancer cell growth, metastasis and invasion. In addition to its potential as a treatment strategy, PVT1 may also have diagnostic value in BC. In this article, we will discuss targeting PVT1 as a treatment strategy for BC.
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Affiliation(s)
| | | | - Ebraheem Abdu Musad Saleh
- Department of Chemistry,College of Arts and Science, Prince Sattam Bin Abdulaziz University, Wadi Al-Dawasir 11991, Saudi Arabia.
| | | | - Farqad Hassan Al-Dami
- Department of Medical Laboratory Techniques, Altoosi University College, Najaf, Iraq
| | - Kumaraswamy Gandla
- Department of Pharmaceutical Analysis, Chaitanya Deemed to be University, Hanamkonda, India.
| | | | - Ahmed Hussien R Abbas
- College of technical engineering, the Islamic University, Najaf, Iraq; College of technical engineering, the Islamic University of Al Diwaniyah, Iraq; College of technical engineering, the Islamic University of Babylon, Iraq
| | - Ali Hashiem Alsaalamy
- College of technical engineering, Imam Ja'afar Al-Sadiq University, Al-Muthanna 66002, Iraq
| | - Yashwant Singh Bisht
- Uttaranchal Institute of Technology, Uttaranchal University, Dehradun 248007, India
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10
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Arshadi A, Tolomeo D, Venuto S, Storlazzi CT. Advancements in Focal Amplification Detection in Tumor/Liquid Biopsies and Emerging Clinical Applications. Genes (Basel) 2023; 14:1304. [PMID: 37372484 PMCID: PMC10298061 DOI: 10.3390/genes14061304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Focal amplifications (FAs) are crucial in cancer research due to their significant diagnostic, prognostic, and therapeutic implications. FAs manifest in various forms, such as episomes, double minute chromosomes, and homogeneously staining regions, arising through different mechanisms and mainly contributing to cancer cell heterogeneity, the leading cause of drug resistance in therapy. Numerous wet-lab, mainly FISH, PCR-based assays, next-generation sequencing, and bioinformatics approaches have been set up to detect FAs, unravel the internal structure of amplicons, assess their chromatin compaction status, and investigate the transcriptional landscape associated with their occurrence in cancer cells. Most of them are tailored for tumor samples, even at the single-cell level. Conversely, very limited approaches have been set up to detect FAs in liquid biopsies. This evidence suggests the need to improve these non-invasive investigations for early tumor detection, monitoring disease progression, and evaluating treatment response. Despite the potential therapeutic implications of FAs, such as, for example, the use of HER2-specific compounds for patients with ERBB2 amplification, challenges remain, including developing selective and effective FA-targeting agents and understanding the molecular mechanisms underlying FA maintenance and replication. This review details a state-of-the-art of FA investigation, with a particular focus on liquid biopsies and single-cell approaches in tumor samples, emphasizing their potential to revolutionize the future diagnosis, prognosis, and treatment of cancer patients.
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Affiliation(s)
| | | | | | - Clelia Tiziana Storlazzi
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, 70125 Bari, Italy; (A.A.); (D.T.); (S.V.)
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11
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Liu S, Shi G, Pan Z, Cheng W, Xu L, Lin X, Lin Y, Zhang L, Ji G, Lv X, Wang D. Integrated Bioinformatics Analysis for the Identification of Key lncRNAs, mRNAs, and Potential Drugs in Clear Cell Renal Cell Carcinomas. Int J Gen Med 2023; 16:2063-2080. [PMID: 37275334 PMCID: PMC10238222 DOI: 10.2147/ijgm.s409711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/18/2023] [Indexed: 06/07/2023] Open
Abstract
Purpose The overall survival of clear cell renal cell carcinoma (ccRCC) is poor. Markers for early detection and progression could improve disease outcomes. This study aims to reveal the potential pathogenesis of ccRCC by integrative bioinformatics analysis and to further develop new therapeutic strategies. Patients and Methods RNA-seq data of 530 ccRCC cases in TCGA were downloaded, and a comprehensive analysis was carried out using bioinformatics tools. Another 14 tissue samples were included to verify the expression of selected lncRNAs by qRT-PCR. DGIdb database was used to screen out potential drugs, and molecular docking was used to explore the interaction and mechanism between candidate drugs and targets. Results A total of 58 differentially expressed lncRNAs (DElncRNAs) and 660 differentially expressed mRNAs (DEmRNAs) were identified in ccRCC. LINC02038, FAM242C, LINC01762, and PVT1 were identified as the optimal diagnostic lncRNAs, of which PVT1 was significantly correlated with the survival rate of ccRCC. GO analysis of cell components showed that DEmRNAs co-expressed with 4 DElncRNAs were mainly distributed in the extracellular area and the plasma membrane, involved in the transport of metal ions, the transport of proteins across membranes, and the binding of immunoglobulins. Immune infiltration analysis showed that MDSC was the most correlated immune cells with PVT1 and key mRNA SIGLEC8. Validation analysis showed that GABRD, SIGLEC8 and CDKN2A were significantly overexpressed, while ESRRB, ELF5 and UMOD were significantly down-regulated, which was consistent with the expression in our analysis. Furthermore, 84 potential drugs were screened by 6 key mRNAs, of which ABEMACICLIB and RIBOCICLIB were selected for molecular docking with CDKN2A, with stable binding affinity. Conclusion In summary, 4 key lncRNAs and key mRNAs of ccRCC were identified by integrative bioinformatics analysis. Potential drugs were screened for the treatment of ccRCC, providing a new perspective for disease diagnosis and treatment.
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Affiliation(s)
- Sheng Liu
- Department of Urinary Surgery, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, Zhejiang Province, People’s Republic of China
| | - Guanyun Shi
- Department of Urinary Surgery, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, Zhejiang Province, People’s Republic of China
| | - Zhengbo Pan
- Department of Urinary Surgery, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, Zhejiang Province, People’s Republic of China
| | - Weisong Cheng
- Department of Urinary Surgery, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, Zhejiang Province, People’s Republic of China
| | - Linfei Xu
- Department of Urinary Surgery, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, Zhejiang Province, People’s Republic of China
| | - Xingzhang Lin
- Department of Urinary Surgery, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, Zhejiang Province, People’s Republic of China
| | - Yongfeng Lin
- Department of Urinary Surgery, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, Zhejiang Province, People’s Republic of China
| | - Liming Zhang
- Department of Urinary Surgery, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, Zhejiang Province, People’s Republic of China
| | - Guanghua Ji
- Department of Urinary Surgery, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, Zhejiang Province, People’s Republic of China
| | - Xin Lv
- Department of Urinary Surgery, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, Zhejiang Province, People’s Republic of China
| | - Dongguo Wang
- Department of Central Laboratory, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, Zhejiang Province, People’s Republic of China
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12
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Chen Y, Ma F, Zhang Z, Guo Y, Shen H, Chen H. LncRNA-PVT1 was identified as a key regulator for TMZ resistance and STAT-related pathway in glioma. BMC Cancer 2023; 23:455. [PMID: 37202742 PMCID: PMC10197392 DOI: 10.1186/s12885-023-10937-9] [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: 12/18/2022] [Accepted: 05/09/2023] [Indexed: 05/20/2023] Open
Abstract
BACKGROUND PVT1, a previously uncharacterized lncRNA, was identified as a critical regulator involved in multiple functions in tumor, including cell proliferation, cell motility, angiogenesis and so on. However, the clinical significance and underlying mechanism of PVT1 was not be fully explored in glioma. METHODS In this study, 1210 glioma samples with transcriptome data from three independent databases (CGGA RNA-seq, TCGA RNA-seq and GSE16011 cohorts) were enrolled in this study. Clinical information and genomic profiles containing somatic mutations and DNA copy numbers were collected from TCGA cohort. The R software was performed for statistical calculations and graphics. Furthermore, we validated the function of PVT1 in vitro. RESULTS The results indicated that higher PVT1 expression was associated with aggressive progression of glioma. Cases with higher PVT1 expression always accompanied by PTEN and EGFR alteration. In addition, functional analyses and western blot results suggested that PVT1 inhibited the sensitivity of TMZ chemotherapy via JAK/STAT signaling. Meanwhile, knockdown of PVT1 increased the sensitivity of TZM chemotherapy in vitro. Finally, high PVT1 expression was associated with reduced survival time and may serve as a strong prognostic indicator for gliomas. CONCLUSIONS This study demonstrated that PVT1 expression strongly correlated with tumor progression and chemo-resistance. PVT1 may become a potential biomarker for the diagnosis and treatment in glioma.
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Affiliation(s)
- Yusheng Chen
- Department of Neurosurgery, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, No.7 WeiWu Street, 450003, Zhengzhou, Zhengzhou, China
| | - Fengjin Ma
- Department of Intensive Care Unit, The Third People's Hospital of Zhengzhou, Zhengzhou, China
| | - Zhe Zhang
- Department of Neurosurgery, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, No.7 WeiWu Street, 450003, Zhengzhou, Zhengzhou, China
| | - Yang Guo
- Department of Neurosurgery, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, No.7 WeiWu Street, 450003, Zhengzhou, Zhengzhou, China
| | - Hanwei Shen
- Department of Neurosurgery, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, No.7 WeiWu Street, 450003, Zhengzhou, Zhengzhou, China
| | - Hang Chen
- Department of Neurosurgery, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, No.7 WeiWu Street, 450003, Zhengzhou, Zhengzhou, China.
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13
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Xie S, Choudhari S, Wu CL, Abramson K, Corcoran D, Gregory SG, Thimmapuram J, Guilak F, Little D. Aging and obesity prime the methylome and transcriptome of adipose stem cells for disease and dysfunction. FASEB J 2023; 37:e22785. [PMID: 36794668 PMCID: PMC10561192 DOI: 10.1096/fj.202201413r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/20/2022] [Accepted: 01/09/2023] [Indexed: 02/17/2023]
Abstract
The epigenome of stem cells occupies a critical interface between genes and environment, serving to regulate expression through modification by intrinsic and extrinsic factors. We hypothesized that aging and obesity, which represent major risk factors for a variety of diseases, synergistically modify the epigenome of adult adipose stem cells (ASCs). Using integrated RNA- and targeted bisulfite-sequencing in murine ASCs from lean and obese mice at 5- and 12-months of age, we identified global DNA hypomethylation with either aging or obesity, and a synergistic effect of aging combined with obesity. The transcriptome of ASCs in lean mice was relatively stable to the effects of age, but this was not true in obese mice. Functional pathway analyses identified a subset of genes with critical roles in progenitors and in diseases of obesity and aging. Specifically, Mapt, Nr3c2, App, and Ctnnb1 emerged as potential hypomethylated upstream regulators in both aging and obesity (AL vs. YL and AO vs. YO), and App, Ctnnb1, Hipk2, Id2, and Tp53 exhibited additional effects of aging in obese animals. Furthermore, Foxo3 and Ccnd1 were potential hypermethylated upstream regulators of healthy aging (AL vs. YL), and of the effects of obesity in young animals (YO vs. YL), suggesting that these factors could play a role in accelerated aging with obesity. Finally, we identified candidate driver genes that appeared recurrently in all analyses and comparisons undertaken. Further mechanistic studies are needed to validate the roles of these genes capable of priming ASCs for dysfunction in aging- and obesity-associated pathologies.
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Affiliation(s)
- Shaojun Xie
- Bioinformatics Core, Purdue University, 1022 Young Hall, 155 S. Grant Street, West Lafayette, IN 47907
| | - Sulbha Choudhari
- Bioinformatics Core, Purdue University, 1022 Young Hall, 155 S. Grant Street, West Lafayette, IN 47907
- Advanced Biomedical Computational Science, Bioinformatics and Computational Science, Frederick National Laboratory for Cancer Research, 8560 Progress Drive, Frederick, MD 2170
| | - Chia-Lung Wu
- Department of Orthopaedics and Rehabilitation, Center for Musculoskeletal Research, University of Rochester, Rochester, NY, 14611
| | - Karen Abramson
- Duke Molecular Physiology Institute, 300 North Duke Street, Durham, NC 27701
| | - David Corcoran
- Genomic Analysis and Bioinformatics Shared Resource, Duke Center for Genomic and Computational Biology, 101 Science Drive, Duke University Medical Center Box 3382, Durham, NC 27708
- Lineberger Bioinformatics Core, 5200 Marsico Hall, University of North Carolina-Chapel Hill, Chapel Hill, NC 27516
| | - Simon G. Gregory
- Duke Molecular Physiology Institute, 300 North Duke Street, Durham, NC 27701
- Department of Neurology, Duke University School of Medicine, 311 Research Drive, Durham, NC 27710
| | - Jyothi Thimmapuram
- Bioinformatics Core, Purdue University, 1022 Young Hall, 155 S. Grant Street, West Lafayette, IN 47907
| | - Farshid Guilak
- Department of Orthopaedic Surgery, Washington University in St. Louis, 4515 McKinley Ave., St. Louis, MO 63110
- Shriners Hospitals for Children – St. Louis, 4400 Clayton Ave, St. Louis Missouri 63110
| | - Dianne Little
- Departments of Basic Medical Sciences and Biomedical Engineering, Purdue University, 2186 Lynn Hall, 625 Harrison St, West Lafayette, IN 47907-2026
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14
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Fontemaggi G. Non-coding RNA regulatory networks in post-transcriptional regulation of VEGFA in cancer. IUBMB Life 2023; 75:30-39. [PMID: 35467790 PMCID: PMC10084289 DOI: 10.1002/iub.2620] [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: 02/15/2022] [Accepted: 04/10/2022] [Indexed: 12/29/2022]
Abstract
The switch from the normal quiescent vasculature to angiogenesis in tumors is induced by a variety of growth factors, released from cancer and stromal cells upon oxygen and nutrients deprivation. Vascular endothelial growth factor A (VEGF-A) is a potent-secreted mitogen and the only growth factor specific to endothelial cells that is observed almost ubiquitously at sites of angiogenesis. Expression of VEGF-A in cancer cells is controlled through transcriptional and post-transcriptional mechanisms. Post-transcriptional regulation of VEGF-A occurs at multiple levels, through the control of splicing, mRNA stability and translation rate, enabling a fine-tuned expression and release of VEGF-A. Mounting evidence is highlighting the important role played by microRNAs (miRNAs) in the control of VEGF-A mRNA stability and translation in cancer. Moreover, non-coding RNAs, as long non-coding RNAs and circular RNAs, are emerging as crucial modulators of VEGF-A-targeting miRNAs, with consequent ability to modulate VEGF-A expression. This review discusses the recent progress on the ncRNA-related networks controlling VEGF-A expression in cancer cells and provides insights into the complexity of VEGF-A post-transcriptional regulation.
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Affiliation(s)
- Giulia Fontemaggi
- Oncogenomic and Epigenetic Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
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15
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Tolomeo D, Traversa D, Venuto S, Ebbesen KK, García Rodríguez JL, Tamma G, Ranieri M, Simonetti G, Ghetti M, Paganelli M, Visci G, Liso A, Kok K, Muscarella LA, Fabrizio FP, Frassanito MA, Lamanuzzi A, Saltarella I, Solimando AG, Fatica A, Ianniello Z, Marsano RM, Palazzo A, Azzariti A, Longo V, Tommasi S, Galetta D, Catino A, Zito A, Mazza T, Napoli A, Martinelli G, Kjems J, Kristensen LS, Vacca A, Storlazzi CT. circPVT1 and PVT1/AKT3 show a role in cell proliferation, apoptosis, and tumor subtype-definition in small cell lung cancer. Genes Chromosomes Cancer 2022; 62:377-391. [PMID: 36562080 DOI: 10.1002/gcc.23121] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/06/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Small cell lung cancer (SCLC) is treated as a homogeneous disease, although the expression of NEUROD1, ASCL1, POU2F3, and YAP1 identifies distinct molecular subtypes. The MYC oncogene, amplified in SCLC, was recently shown to act as a lineage-specific factor to associate subtypes with histological classes. Indeed, MYC-driven SCLCs show a distinct metabolic profile and drug sensitivity. To disentangle their molecular features, we focused on the co-amplified PVT1, frequently overexpressed and originating circular (circRNA) and chimeric RNAs. We analyzed hsa_circ_0001821 (circPVT1) and PVT1/AKT3 (chimPVT1) as examples of such transcripts, respectively, to unveil their tumorigenic contribution to SCLC. In detail, circPVT1 activated a pro-proliferative and anti-apoptotic program when over-expressed in lung cells, and knockdown of chimPVT1 induced a decrease in cell growth and an increase of apoptosis in SCLC in vitro. Moreover, the investigated PVT1 transcripts underlined a functional connection between MYC and YAP1/POU2F3, suggesting that they contribute to the transcriptional landscape associated with MYC amplification. In conclusion, we have uncovered a functional role of circular and chimeric PVT1 transcripts in SCLC; these entities may prove useful as novel biomarkers in MYC-amplified tumors.
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Affiliation(s)
- Doron Tolomeo
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
| | - Debora Traversa
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
| | - Santina Venuto
- Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy
| | - Karoline K Ebbesen
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus, Denmark
| | | | - Grazia Tamma
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
| | - Marianna Ranieri
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
| | - Giorgia Simonetti
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola (FC), Italy
| | - Martina Ghetti
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola (FC), Italy
| | - Matteo Paganelli
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola (FC), Italy
| | - Grazia Visci
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
| | - Arcangelo Liso
- Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy
| | - Klaas Kok
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Lucia Anna Muscarella
- Laboratory of Oncology, Fondazione IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Federico Pio Fabrizio
- Laboratory of Oncology, Fondazione IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Maria Antonia Frassanito
- Department of Precision and Regenerative Medicine and Ionian Area - (DiMePRe-J), School of Medicine, Aldo Moro University of Bari, Bari, Italy
| | - Aurelia Lamanuzzi
- Department of Precision and Regenerative Medicine and Ionian Area - (DiMePRe-J), School of Medicine, Aldo Moro University of Bari, Bari, Italy
| | - Ilaria Saltarella
- Department of Precision and Regenerative Medicine and Ionian Area - (DiMePRe-J), School of Medicine, Aldo Moro University of Bari, Bari, Italy
| | - Antonio Giovanni Solimando
- Department of Precision and Regenerative Medicine and Ionian Area - (DiMePRe-J), School of Medicine, Aldo Moro University of Bari, Bari, Italy
| | - Alessandro Fatica
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Zaira Ianniello
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | | | - Antonio Palazzo
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
| | - Amalia Azzariti
- Laboratory of Experimental Pharmacology, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Vito Longo
- Medical Thoracic Oncology Unit, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Stefania Tommasi
- Molecular Diagnostics and Pharmacogenetics Unit, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Domenico Galetta
- Medical Thoracic Oncology Unit, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Annamaria Catino
- Medical Thoracic Oncology Unit, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Alfredo Zito
- Pathology Unit, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Tommaso Mazza
- Bioinformatics Unit, Fondazione IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Alessandro Napoli
- Bioinformatics Unit, Fondazione IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Giovanni Martinelli
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola (FC), Italy
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus, Denmark
| | | | - Angelo Vacca
- Department of Precision and Regenerative Medicine and Ionian Area - (DiMePRe-J), School of Medicine, Aldo Moro University of Bari, Bari, Italy
| | - Clelia Tiziana Storlazzi
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
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16
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Khanbabaei H, Ebrahimi S, García-Rodríguez JL, Ghasemi Z, Pourghadamyari H, Mohammadi M, Kristensen LS. Non-coding RNAs and epithelial mesenchymal transition in cancer: molecular mechanisms and clinical implications. J Exp Clin Cancer Res 2022; 41:278. [PMID: 36114510 PMCID: PMC9479306 DOI: 10.1186/s13046-022-02488-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 09/06/2022] [Indexed: 11/30/2022] Open
Abstract
Epithelial-mesenchymal transition (EMT) is a fundamental process for embryonic development during which epithelial cells acquire mesenchymal characteristics, and the underlying mechanisms confer malignant features to carcinoma cells such as dissemination throughout the organism and resistance to anticancer treatments. During the past decades, an entire class of molecules, called non-coding RNA (ncRNA), has been characterized as a key regulator of almost every cellular process, including EMT. Like protein-coding genes, ncRNAs can be deregulated in cancer, acting as oncogenes or tumor suppressors. The various forms of ncRNAs, including microRNAs, PIWI-interacting RNAs, small nucleolar RNAs, transfer RNA-derived RNA fragments, long non-coding RNAs, and circular RNAs can orchestrate the complex regulatory networks of EMT at multiple levels. Understanding the molecular mechanism underlying ncRNAs in EMT can provide fundamental insights into cancer metastasis and may lead to novel therapeutic approaches. In this review, we describe recent advances in the understanding of ncRNAs in EMT and provide an overview of recent ncRNA applications in the clinic.
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17
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Guo L, Jia L, Luo L, Xu X, Xiang Y, Ren Y, Ren D, Shen L, Liang T. Critical Roles of Circular RNA in Tumor Metastasis via Acting as a Sponge of miRNA/isomiR. Int J Mol Sci 2022; 23:ijms23137024. [PMID: 35806027 PMCID: PMC9267010 DOI: 10.3390/ijms23137024] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/20/2022] [Accepted: 06/23/2022] [Indexed: 02/06/2023] Open
Abstract
Circular RNAs (circRNAs), a class of new endogenous non-coding RNAs (ncRNAs), are closely related to the carcinogenic process and play a critical role in tumor metastasis. CircRNAs can lay the foundation for tumor metastasis via promoting tumor angiogenesis, make tumor cells gain the ability of migration and invasion by regulating epithelial-mesenchymal transition (EMT), interact with immune cells, cytokines, chemokines, and other non-cellular components in the tumor microenvironment, damage the normal immune function or escape the immunosuppressive network, and further promote cell survival and metastasis. Herein, based on the characteristics and biological functions of circRNA, we elaborated on the effect of circRNA via circRNA-associated competing endogenous RNA (ceRNA) network by acting as miRNA/isomiR sponges on tumor angiogenesis, cancer cell migration and invasion, and interaction with the tumor microenvironment (TME), then explored the potential interactions across different RNAs, and finally discussed the potential clinical value and application as a promising biomarker. These results provide a theoretical basis for the further application of metastasis-related circRNAs in cancer treatment. In summary, we briefly summarize the diverse roles of a circRNA-associated ceRNA network in cancer metastasis and the potential clinical application, especially the interaction of circRNA and miRNA/isomiR, which may complicate the RNA regulatory network and which will contribute to a novel insight into circRNA in the future.
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Affiliation(s)
- Li Guo
- Smart Health Big Data Analysis and Location Services Engineering Laboratory of Jiangsu Province, Department of Bioinformatics, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (L.G.); (Y.X.); (Y.R.); (D.R.)
| | - Lin Jia
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (L.J.); (L.L.); (X.X.); (L.S.)
| | - Lulu Luo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (L.J.); (L.L.); (X.X.); (L.S.)
| | - Xinru Xu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (L.J.); (L.L.); (X.X.); (L.S.)
| | - Yangyang Xiang
- Smart Health Big Data Analysis and Location Services Engineering Laboratory of Jiangsu Province, Department of Bioinformatics, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (L.G.); (Y.X.); (Y.R.); (D.R.)
| | - Yujie Ren
- Smart Health Big Data Analysis and Location Services Engineering Laboratory of Jiangsu Province, Department of Bioinformatics, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (L.G.); (Y.X.); (Y.R.); (D.R.)
| | - Dekang Ren
- Smart Health Big Data Analysis and Location Services Engineering Laboratory of Jiangsu Province, Department of Bioinformatics, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (L.G.); (Y.X.); (Y.R.); (D.R.)
| | - Lulu Shen
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (L.J.); (L.L.); (X.X.); (L.S.)
| | - Tingming Liang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (L.J.); (L.L.); (X.X.); (L.S.)
- Correspondence:
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18
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Long Non-Coding RNAs Might Regulate Phenotypic Switch of Vascular Smooth Muscle Cells Acting as ceRNA: Implications for In-Stent Restenosis. Int J Mol Sci 2022; 23:ijms23063074. [PMID: 35328496 PMCID: PMC8952224 DOI: 10.3390/ijms23063074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/07/2022] [Accepted: 03/09/2022] [Indexed: 02/01/2023] Open
Abstract
Coronary in-stent restenosis is a late complication of angioplasty. It is a multifactorial process that involves vascular smooth muscle cells (VSMCs), endothelial cells, and inflammatory and genetic factors. In this study, the transcriptomic landscape of VSMCs’ phenotypic switch process was assessed under stimuli resembling stent injury. Co-cultured contractile VSMCs and endothelial cells were exposed to a bare metal stent and platelet-derived growth factor (PDGF-BB) 20 ng/mL. Migratory capacity (wound healing assay), proliferative capacity, and cell cycle analysis of the VSMCs were performed. RNAseq analysis of contractile vs. proliferative VSMCs was performed. Gene differential expression (DE), identification of new long non-coding RNA candidates (lncRNAs), gene ontology (GO), and pathway enrichment (KEGG) were analyzed. A competing endogenous RNA network was constructed, and significant lncRNA–miRNA–mRNA axes were selected. VSMCs exposed to “stent injury” conditions showed morphologic changes, with proliferative and migratory capacities progressing from G0-G1 cell cycle phase to S and G2-M. RNAseq analysis showed DE of 1099, 509 and 64 differentially expressed mRNAs, lncRNAs, and miRNAs, respectively. GO analysis of DE genes showed significant enrichment in collagen and extracellular matrix organization, regulation of smooth muscle cell proliferation, and collagen biosynthetic process. The main upregulated nodes in the lncRNA-mediated ceRNA network were PVT1 and HIF1-AS2, with downregulation of ACTA2-AS1 and MIR663AHG. The PVT1 ceRNA axis appears to be an attractive target for in-stent restenosis diagnosis and treatment.
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Zeng L, Yuan S, Zhou P, Gong J, Kong X, Wu M. Circular RNA Pvt1 oncogene (CircPVT1) promotes the progression of papillary thyroid carcinoma by activating the Wnt/β-catenin signaling pathway and modulating the ratio of microRNA-195 (miR-195) to vascular endothelial growth factor A (VEGFA) expression. Bioengineered 2021; 12:11795-11810. [PMID: 34927541 PMCID: PMC8810178 DOI: 10.1080/21655979.2021.2008639] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Circular RNAs (circRNAs) have been reported to be involved in the progression of papillary thyroid carcinoma (PTC). However, the role of circular RNA Pvt1 oncogene (circPVT1) in PTC has rarely been reported. In this study, we aimed to investigate the function and mechanism of circPVT1 in PTC. The expression level of circPVT1, miR-195 and VEGFA were determined by reverse transcription‑quantitative PCR (RT‑qPCR). Fisher's exact test was used to analyze the correlation between circPVT1 expression and PTC clinical features. Cell Counting Kit-8 (CCK-8) and 5-Ethynyl-2'-deoxyuridine (EdU) staining assay and transwell assay were conducted to evaluate the cell proliferation, migration and invasion ability. Dual-luciferase reporter and Western blot assay were conducted for evaluating the correlation between miR-195 and circPVT1 or VEGFA. The results of RT-PCR showed that the expression level of circPVT1 was significantly upregulated in PTC tissues and cell lines. After downregulating circPVT1 expression in PTC cells, the abilities of cell proliferation, migration, and invasion were obviously suppressed, and the Wnt/β-catenin signaling pathway was also repressed. Besides, miR-195 could both bind to PVT1 and VEGFA, while PVT1 could promote the expression of VEGFA by binding to miR-195. Downregulation of VEGFA expression in PTC cells revealed weakened cell proliferation, migration, and invasion capacities, and restrained Wnt/β-catenin signaling pathway. Therefore, we demonstrated that circPVT1 could promote VEGFA expression by sponging miR-195. CircPVT1 could serve as a molecule sponge for miR-195 and mediate the ceRNA network to promote the expression of VEGFA, thus contributed to the malignant progression of PTC.
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Affiliation(s)
- Linwen Zeng
- Department of Surgery, Tinglin Hospital of Jinshan District, Shanghai, China
| | - Shaofeng Yuan
- Department of Surgery, Tinglin Hospital of Jinshan District, Shanghai, China
| | - Pengfei Zhou
- Department of Surgery, Tinglin Hospital of Jinshan District, Shanghai, China
| | - Jianming Gong
- Department of Surgery, Tinglin Hospital of Jinshan District, Shanghai, China
| | - Xiangdong Kong
- Department of Surgery, Tinglin Hospital of Jinshan District, Shanghai, China
| | - Ming Wu
- Department of Surgery, Tinglin Hospital of Jinshan District, Shanghai, China
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Németh K, Calin GA. Standardisation of protocols can be crucial in long non-coding RNA research. Br J Cancer 2021; 126:833-834. [PMID: 34912071 DOI: 10.1038/s41416-021-01656-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/13/2021] [Accepted: 11/23/2021] [Indexed: 11/09/2022] Open
Abstract
In this issue, Traversa et al. [1] reviewed our current knowledge about the role of circular and linear forms of PVT1 non-coding RNA in cancer and human diseases. They highlighted the technical challenges of these studies and raised a potential bias in the publications, which require more attention from researchers.
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Affiliation(s)
- Kinga Németh
- Department of Translational Molecular Pathology, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - George A Calin
- Department of Translational Molecular Pathology, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA. .,Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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