1
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Nickerson JA, Momen-Heravi F. Long non-coding RNAs: roles in cellular stress responses and epigenetic mechanisms regulating chromatin. Nucleus 2024; 15:2350180. [PMID: 38773934 PMCID: PMC11123517 DOI: 10.1080/19491034.2024.2350180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/22/2024] [Indexed: 05/24/2024] Open
Abstract
Most of the genome is transcribed into RNA but only 2% of the sequence codes for proteins. Non-coding RNA transcripts include a very large number of long noncoding RNAs (lncRNAs). A growing number of identified lncRNAs operate in cellular stress responses, for example in response to hypoxia, genotoxic stress, and oxidative stress. Additionally, lncRNA plays important roles in epigenetic mechanisms operating at chromatin and in maintaining chromatin architecture. Here, we address three lncRNA topics that have had significant recent advances. The first is an emerging role for many lncRNAs in cellular stress responses. The second is the development of high throughput screening assays to develop causal relationships between lncRNAs across the genome with cellular functions. Finally, we turn to recent advances in understanding the role of lncRNAs in regulating chromatin architecture and epigenetics, advances that build on some of the earliest work linking RNA to chromatin architecture.
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Affiliation(s)
- Jeffrey A Nickerson
- Division of Genes & Development, Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Fatemeh Momen-Heravi
- College of Dental Medicine, Columbia University Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
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2
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Abida, Eltaib L, Alhazmi BH, Alzahrani AR, Asdaq SMB, Ali A, Aldhafiri FJ, Alruwaili WT, Al-Hajeili M, Abdulkhaliq AA, Rabaan AA, Imran M. Long non-coding RNA HOTAIR: A biomarker and therapeutic target in urological tumors. Pathol Res Pract 2024; 262:155549. [PMID: 39173467 DOI: 10.1016/j.prp.2024.155549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Revised: 08/12/2024] [Accepted: 08/14/2024] [Indexed: 08/24/2024]
Abstract
Long non-coding RNAs (lncRNAs) significantly influence gene regulation across epigenetic, transcriptional, and post-transcriptional levels through their interactions with DNA, RNA, and proteins. There is growing evidence of lncRNAs' critical roles in the emergence and progression of various diseases, including urological tumors (UTs), such as cancers of the kidney, bladder, and prostate. Research increasingly links lncRNA dysregulation to diverse cellular processes like invasion, metastasis, apoptosis, and chromatin remodeling. Among these, HOTAIR stands out for its pivotal role in oncogenesis, impacting treatment resistance, cell migration, proliferation, survival, and genomic integrity. This review provides an overview of HOTAIR's functions, its identification, and its biological significance. Furthermore, it delves into HOTAIR's involvement in UTs, underlining its potential as a therapeutic target and biomarker for innovative approaches to treating these cancers.
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Affiliation(s)
- Abida
- Department of Pharmaceutical Chemistry, College of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
| | - Lina Eltaib
- Department of Pharmaceutics, College of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
| | - Bshayer Hmdan Alhazmi
- Department of Pharmacy, Northern Area Armed Forces Hospital, Hafer Al-batin 39745, Saudi Arabia
| | - Abdullah R Alzahrani
- Department of Pharmacology and Toxicology, Faculty of Medicine, Umm Al-Qura University, Al-Abidiyah, P.O. Box 13578, Makkah 21955, Saudi Arabia
| | | | - Abuzer Ali
- Department of Pharmacognosy, College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | | | - Wafaa T Alruwaili
- College of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
| | - Marwan Al-Hajeili
- Department of Medicine, King Abdulaziz University, Jeddah 23624, Saudi Arabia
| | - Altaf A Abdulkhaliq
- Department of Biochemistry, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
| | - Mohd Imran
- Department of Pharmaceutical Chemistry, College of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia; Center for Health Research, Northern Border University, Arar, Saudi Arabia.
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3
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Trujano-Camacho S, Cantú-de León D, Pérez-Yepez E, Contreras-Romero C, Coronel-Hernandez J, Millan-Catalan O, Rodríguez-Dorantes M, López-Camarillo C, Gutiérrez-Ruiz C, Jacobo-Herrera N, Pérez-Plasencia C. HOTAIR Promotes the Hyperactivation of PI3K/Akt and Wnt/β-Catenin Signaling Pathways via PTEN Hypermethylation in Cervical Cancer. Cells 2024; 13:1484. [PMID: 39273054 PMCID: PMC11394386 DOI: 10.3390/cells13171484] [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: 08/01/2024] [Revised: 08/27/2024] [Accepted: 08/29/2024] [Indexed: 09/15/2024] Open
Abstract
The mechanisms underlying the sustained activation of the PI3K/AKT and Wnt/β-catenin pathways mediated by HOTAIR in cervical cancer (CC) have not been extensively described. To address this knowledge gap in the literature, we explored the interactions between these pathways by driving HOTAIR expression levels in HeLa cells. Our findings reveal that HOTAIR is a key regulator in sustaining the activation of both signaling pathways. Specifically, altering HOTAIR expression-either by knockdown or overexpression-significantly influenced the transcriptional activity of the PI3K/AKT and Wnt/β-catenin pathways. Additionally, we discovered that HIF1α directly induces HOTAIR transcription, which in turn leads to the epigenetic silencing of the PTEN promoter via DNMT1. This process leads to the sustained activation of both pathways, highlighting a novel regulatory axis involving HOTAIR and HIF1α in cervical cancer. Our results suggest a new model in which HOTAIR sustains reciprocal activation of the PI3K/AKT and Wnt/β-catenin pathways through the HOTAIR/HIF1α axis, thereby contributing to the oncogenic phenotype of cervical cancer.
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Affiliation(s)
- Samuel Trujano-Camacho
- Experimental Biology PhD Program, DCBS, Universidad Autónoma Metropolitana-Iztapalapa, Mexico City 09340, Mexico
- Laboratorio de Genómica, Instituto Nacional de Cancerología, Av. San Fernando 22, Belisario Domínguez Secc 16, Tlalpan, Ciudad de México 14080, Mexico
| | - David Cantú-de León
- Laboratorio de Genómica, Instituto Nacional de Cancerología, Av. San Fernando 22, Belisario Domínguez Secc 16, Tlalpan, Ciudad de México 14080, Mexico
| | - Eloy Pérez-Yepez
- Laboratorio de Genómica, Instituto Nacional de Cancerología, Av. San Fernando 22, Belisario Domínguez Secc 16, Tlalpan, Ciudad de México 14080, Mexico
| | - Carlos Contreras-Romero
- Laboratorio de Genómica, Instituto Nacional de Cancerología, Av. San Fernando 22, Belisario Domínguez Secc 16, Tlalpan, Ciudad de México 14080, Mexico
| | - Jossimar Coronel-Hernandez
- Laboratorio de Genómica, Instituto Nacional de Cancerología, Av. San Fernando 22, Belisario Domínguez Secc 16, Tlalpan, Ciudad de México 14080, Mexico
| | - Oliver Millan-Catalan
- Laboratorio de Genómica, Instituto Nacional de Cancerología, Av. San Fernando 22, Belisario Domínguez Secc 16, Tlalpan, Ciudad de México 14080, Mexico
| | | | - Cesar López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Ciudad de México 03100, Mexico
| | - Concepción Gutiérrez-Ruiz
- Laboratory of Experimental Medicine, Translational Medicine Unit, Instituto de Investigaciones Biomédicas, UNAM/Instituto Nacional de Cardiología Ignacio Chávez, Tlalpan, Mexico City 14080, Mexico
- Department of Health Sciences, Universidad Autónoma Metropolitana-Iztapalapa, Mexico City 09340, Mexico
| | - Nadia Jacobo-Herrera
- Unidad de Bioquímica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubiran, Av. Vasco de Quiroga 15, Col. Belisario Domínguez Sección XVI, Tlalpan, Ciudad de México 14080, Mexico
| | - Carlos Pérez-Plasencia
- Laboratorio de Genómica, Instituto Nacional de Cancerología, Av. San Fernando 22, Belisario Domínguez Secc 16, Tlalpan, Ciudad de México 14080, Mexico
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México (UNAM), Tlalnepantla 54090, Mexico
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4
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Chen W, Pan Z, Feng Z, Wang X, Zhu S. Deciphering the code: the pivotal role of lncRNAs in advancing TNBC therapy. Front Oncol 2024; 14:1450980. [PMID: 39286016 PMCID: PMC11402698 DOI: 10.3389/fonc.2024.1450980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Accepted: 08/05/2024] [Indexed: 09/19/2024] Open
Abstract
Triple-negative breast cancer (TNBC) represents the most formidable subtype of breast cancer, characterized by a notable dearth in targeted therapeutic options. Deciphering the underlying molecular mechanisms of TNBC is pivotal for improving patient outcomes. Recent scientific advancements have spotlighted long non-coding RNAs (lncRNAs) as key players in the genesis, progression, and metastasis of cancers. This review delineates the significant influence of lncRNAs on the advancement, detection, and neoadjuvant chemotherapy efficacy in TNBC, detailing the diverse expression patterns of aberrant lncRNAs. The paper explores the specific mechanisms by which lncRNAs regulate gene expression in both the nucleus and cytoplasm, with a special focus on their involvement in TNBC's post-transcriptional landscape. Thorough investigations into TNBC-associated lncRNAs not only forge new avenues for early diagnosis and potent treatment strategies but also highlight these molecules as promising therapeutic targets, heralding an era of personalized and precision medicine in TNBC management.
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Affiliation(s)
- Weiping Chen
- Department of Respiratory, The Affiliated Qingyuan Hospital (Qingyuan People's Hospital), Guangzhou Medical University, Qingyuan, China
| | - Zhiyong Pan
- Department of Radiotherapy, The Affiliated Qingyuan Hospital (Qingyuan People's Hospital), Guangzhou Medical University, Qingyuan, China
| | - Zhengfu Feng
- Department of Radiotherapy, The Affiliated Qingyuan Hospital (Qingyuan People's Hospital), Guangzhou Medical University, Qingyuan, China
| | - Xin Wang
- Department of Radiotherapy, The Affiliated Qingyuan Hospital (Qingyuan People's Hospital), Guangzhou Medical University, Qingyuan, China
| | - Song Zhu
- Department of Radiotherapy, The Affiliated Qingyuan Hospital (Qingyuan People's Hospital), Guangzhou Medical University, Qingyuan, China
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5
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Coan M, Haefliger S, Ounzain S, Johnson R. Targeting and engineering long non-coding RNAs for cancer therapy. Nat Rev Genet 2024; 25:578-595. [PMID: 38424237 DOI: 10.1038/s41576-024-00693-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2024] [Indexed: 03/02/2024]
Abstract
RNA therapeutics (RNATx) aim to treat diseases, including cancer, by targeting or employing RNA molecules for therapeutic purposes. Amongst the most promising targets are long non-coding RNAs (lncRNAs), which regulate oncogenic molecular networks in a cell type-restricted manner. lncRNAs are distinct from protein-coding genes in important ways that increase their therapeutic potential yet also present hurdles to conventional clinical development. Advances in genome editing, oligonucleotide chemistry, multi-omics and RNA engineering are paving the way for efficient and cost-effective lncRNA-focused drug discovery pipelines. In this Review, we present the emerging field of lncRNA therapeutics for oncology, with emphasis on the unique strengths and challenges of lncRNAs within the broader RNATx framework. We outline the necessary steps for lncRNA therapeutics to deliver effective, durable, tolerable and personalized treatments for cancer.
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Affiliation(s)
- Michela Coan
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Dublin, Ireland
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Simon Haefliger
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | | | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland.
- Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Dublin, Ireland.
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
- Department for BioMedical Research, University of Bern, Bern, Switzerland.
- FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, Dublin, Ireland.
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6
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Allen S, O'Reilly D, Miller R, Sapp E, Summers A, Paquette J, Echeverria Moreno D, Bramato B, McHugh N, Yamada K, Aronin N, DiFiglia M, Khvorova A. mRNA Nuclear Clustering Leads to a Difference in Mutant Huntingtin mRNA and Protein Silencing by siRNAs In Vivo. Nucleic Acid Ther 2024; 34:164-172. [PMID: 39023561 PMCID: PMC11387003 DOI: 10.1089/nat.2024.0027] [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] [Indexed: 07/20/2024] Open
Abstract
Huntington's disease (HD) is an autosomal dominant neurodegenerative disease caused by CAG repeat expansion in the first exon of the huntingtin gene (HTT). Oligonucleotide therapeutics, such as short interfering RNA (siRNA), reduce levels of huntingtin mRNA and protein in vivo and are considered a viable therapeutic strategy. However, the extent to which they silence huntingtin mRNA in the nucleus is not established. We synthesized siRNA cross-reactive to mouse (wild-type) Htt and human (mutant) HTT in a divalent scaffold and delivered to two mouse models of HD. In both models, divalent siRNA sustained lowering of wild-type Htt, but not mutant HTT mRNA expression in striatum and cortex. Near-complete silencing of both mutant HTT protein and wild-type HTT protein was observed in both models. Subsequent fluorescent in situ hybridization analysis shows that divalent siRNA acts predominantly on cytoplasmic mutant HTT transcripts, leaving clustered mutant HTT transcripts in the nucleus largely intact in treated HD mouse brains. The observed differences between mRNA and protein levels, exaggerated in the case of extended repeats, might apply to other repeat-associated neurological disorders.
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Affiliation(s)
- Sarah Allen
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Daniel O'Reilly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Rachael Miller
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Ellen Sapp
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Ashley Summers
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Joseph Paquette
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Dimas Echeverria Moreno
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Brianna Bramato
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Nicholas McHugh
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Ken Yamada
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Neil Aronin
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Marian DiFiglia
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
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7
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Hou G, Alissa M, Alsuwat MA, Ali Alarjany HM, Alzahrani KJ, Althobaiti FM, Mujalli HM, Alotaiby MM, Al-Doaiss AA, Anthony S. The art of healing hearts: Mastering advanced RNA therapeutic techniques to shape the evolution of cardiovascular medicine in biomedical science. Curr Probl Cardiol 2024; 49:102627. [PMID: 38723793 DOI: 10.1016/j.cpcardiol.2024.102627] [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: 05/06/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024]
Abstract
Cardiovascular diseases (CVDs) are the leading cause of death worldwide and are associated with increasing financial health burden that requires research into novel therapeutic approaches. Since the early 2000s, the availability of next-generation sequencing techniques such as microRNAs, circular RNAs, and long non-coding RNAs have been proven as potential therapeutic targets for treating various CVDs. Therapeutics based on RNAs have become a viable option for addressing the intricate molecular pathways that underlie the pathophysiology of CVDs. We provide an in-depth analysis of the state of RNA therapies in the context of CVDs, emphasizing various approaches that target the various stages of the basic dogma of molecular biology to effect temporary or long-term changes. In this review, we summarize recent methodologies used to screen for novel coding and non-coding RNA candidates with diagnostic and treatment possibilities in cardiovascular diseases. These methods include single-cell sequencing techniques, functional RNA screening, and next-generation sequencing.Lastly, we highlighted the potential of using oligonucleotide-based chemical products such as modified RNA and RNA mimics/inhibitors for the treatment of CVDs. Moreover, there will be an increasing number of potential RNA diagnostic and therapeutic for CVDs that will progress to expand for years to come.
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Affiliation(s)
- Guoliang Hou
- Department of Cardiology, Tengzhou Central People's Hospital, Shandong 277599, China
| | - Mohammed Alissa
- Department of Medical Laboratory, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia.
| | - Meshari A Alsuwat
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21974, Saudi Arabia
| | | | - Khalid J Alzahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21974, Saudi Arabia
| | - Fahad M Althobaiti
- Department of Nursing Leadership and Education, Nursing College, Taif University, Taif 21974, Saudi Arabia
| | | | - Monearah M Alotaiby
- Department of Laboratory, King Faisal Medical Complex, Ministry of Health, Taif 26514, Saudi Arabia
| | - Amin A Al-Doaiss
- Biology Department, College of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Stefan Anthony
- Liaoning Provincial Key Laboratory of Cerebral Diseases, Department of Physiology, Dalian Medical University Liaoning Provence China, China.
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8
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Song J, Xie D, Wei X, Liu B, Yao F, Ye W. A cuproptosis-related lncRNAs signature predicts prognosis and reveals pivotal interactions between immune cells in colon cancer. Heliyon 2024; 10:e34586. [PMID: 39114018 PMCID: PMC11305305 DOI: 10.1016/j.heliyon.2024.e34586] [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: 09/17/2023] [Revised: 07/11/2024] [Accepted: 07/11/2024] [Indexed: 08/10/2024] Open
Abstract
Copper-mediated cell death presents distinct pathways from established apoptosis processes, suggesting alternative therapeutic approaches for colon cancer. Our research aims to develop a predictive framework utilizing long-noncoding RNAs (lncRNAs) related to cuproptosis to predict colon cancer outcomes while examining immune interactions and intercellular signaling. We obtained colon cancer-related human mRNA expression profiles and clinical information from the Cancer Genome Atlas repository. To isolate lncRNAs involved in cuproptosis, we applied Cox proportional hazards modeling alongside the least absolute shrinkage and selection operator technique. We elucidated the underlying mechanisms by examining the tumor mutational burden, the extent of immune cell penetration, and intercellular communication dynamics. Based on the model, drugs were predicted and validated with cytological experiments. A 13 lncRNA-cuproptosis-associated risk model was constructed. Two colon cancer cell lines were used to validate the predicted representative mRNAs with high correlation coefficients with copper-induced cell death. Survival enhancement in the low-risk cohort was evidenced by the trends in Kaplan-Meier survival estimates. Analysis of immune cell infiltration suggested that survival was induced by the increased infiltration of naïve CD4+ T cells and a reduction of M2 macrophages within the low-risk faction. Decreased infiltration of naïve B cells, resting NK cells, and M0 macrophages was significantly associated with better overall survival. Combined single-cell analysis suggested that CCL5-ACKR1, CCL2-ACKR1, and CCL5-CCR1 pathways play key roles in mediating intercellular dialogues among immune constituents within the neoplastic microhabitat. We identified three drugs with a high sensitivity in the high-risk group. In summary, this discovery establishes the possibility of using 13 cuproptosis-associated lncRNAs as a risk model to assess the prognosis, unravel the immune mechanisms and cell communication, and improve treatment options, which may provide a new idea for treating colon cancer.
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Affiliation(s)
- Jingru Song
- Department of Gastroenterology, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, 310007, Zhejiang, China
| | - Dong Xie
- Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Xia Wei
- Department of Gastroenterology, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, 310007, Zhejiang, China
| | - Binbin Liu
- Department of Gastroenterology, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, 310007, Zhejiang, China
| | - Fang Yao
- Department of Gastroenterology, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, 310007, Zhejiang, China
| | - Wei Ye
- Department of Gastroenterology, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, 310007, Zhejiang, China
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9
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Zhang S, Wang S, Lu F, Bie L, Luo Y, Sun J, Zhang Y, Wang Y, Zhang Y, Lyu QR. LncRNAway: a web-based sgRNA design tool for precise and effective suppression of long noncoding RNAs. Nucleic Acids Res 2024; 52:W95-W101. [PMID: 38738626 PMCID: PMC11223879 DOI: 10.1093/nar/gkae383] [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: 03/12/2024] [Revised: 04/17/2024] [Accepted: 04/29/2024] [Indexed: 05/14/2024] Open
Abstract
Thousands of long noncoding RNAs (lncRNAs) have been annotated via high-throughput RNA sequencing, yet only a small fraction have been functionally investigated. Genomic knockout is the mainstream strategy for studying the biological function of protein-coding genes and lncRNAs, whereas the complexity of the lncRNA locus, especially the natural antisense lncRNAs (NAT-lncRNAs), presents great challenges. Knocking out lncRNAs often results in unintended disruptions of neighboring protein-coding genes and small RNAs, leading to ambiguity in observing phenotypes and interpreting biological function. To address this issue, we launched LncRNAway, a user-friendly web tool based on the BESST (branchpoint to 3' splicing site targeting) method, to design sgRNAs for lncRNA knockout. LncRNAway not only provides specific and effective lncRNA knockout guidelines but also integrates genotyping primers and quantitative PCR primers designing, thereby streamlining experimental procedures of lncRNA function study. LncRNAway is freely available at https://www.lncrnaway.com.
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Affiliation(s)
- Shikuan Zhang
- Medical Research Center, Chongqing General Hospital, Chongqing University, Chongqing 401147, China
| | - Songmao Wang
- China State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
- The Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
| | - Fang Lu
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China
| | - Lingzi Bie
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China
| | - Yongjiang Luo
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China
| | - Jiahe Sun
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China
| | - Yang Zhang
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China
| | - Yi Wang
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China
| | - Yaou Zhang
- China State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
- The Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
| | - Qing Rex Lyu
- Medical Research Center, Chongqing General Hospital, Chongqing University, Chongqing 401147, China
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10
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Jin X, Huang CX, Tian Y. The multifaceted perspectives on the regulation of lncRNAs in hepatocellular carcinoma ferroptosis: from bench-to-bedside. Clin Exp Med 2024; 24:146. [PMID: 38960924 PMCID: PMC11222271 DOI: 10.1007/s10238-024-01418-9] [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: 05/18/2024] [Accepted: 06/24/2024] [Indexed: 07/05/2024]
Abstract
Despite being characterized by high malignancy, high morbidity, and low survival rates, the underlying mechanism of hepatocellular carcinoma (HCC) has not been fully elucidated. Ferroptosis, a non-apoptotic form of regulated cell death, possesses distinct morphological, biochemical, and genetic characteristics compared to other types of cell death. Dysregulated actions within the molecular network that regulates ferroptosis have been identified as significant contributors to the progression of HCC. Long non-coding RNAs (lncRNAs) have emerged as influential contributors to diverse cellular processes, regulating gene function and expression through multiple mechanistic pathways. An increasing body of evidence indicates that deregulated lncRNAs are implicated in regulating malignant events such as cell proliferation, growth, invasion, and metabolism by influencing ferroptosis in HCC. Therefore, elucidating the inherent role of ferroptosis and the modulatory functions of lncRNAs on ferroptosis in HCC might promote the development of novel therapeutic interventions for this disease. This review provides a succinct overview of the roles of ferroptosis and ferroptosis-related lncRNAs in HCC progression and treatment, aiming to drive the development of promising therapeutic targets and biomarkers for HCC patients.
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Affiliation(s)
- Xin Jin
- Department of Gastroenterology and Hepatology, Fengdu People's Hospital, Fengdu County, Chongqing, 408200, China
| | - Chun Xia Huang
- Department of Gastroenterology and Hepatology, Fengdu People's Hospital, Fengdu County, Chongqing, 408200, China
| | - Yue Tian
- Department of Gastroenterology and Hepatology, Fengdu People's Hospital, Fengdu County, Chongqing, 408200, China.
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11
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Li K, Li M, Luo Y, Zou D, Li Y, Mang X, Zhang Z, Li P, Lu Y, Miao S, Song W. Adeno-associated-virus-mediated delivery of CRISPR-CasRx induces efficient RNA knockdown in the mouse testis. Theranostics 2024; 14:3827-3842. [PMID: 38994027 PMCID: PMC11234267 DOI: 10.7150/thno.95633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 06/03/2024] [Indexed: 07/13/2024] Open
Abstract
Rationale: In male mammals, many developmental-stage-specific RNA transcripts (both coding and noncoding) are preferentially or exclusively expressed in the testis, where they play important roles in spermatogenesis and male fertility. However, a reliable platform for efficiently depleting various types of RNA transcripts to study their biological functions during spermatogenesis in vivo has not been developed. Methods: We used an adeno-associated virus serotype nine (AAV9)-mediated CRISPR-CasRx system to knock down the expression of exogenous and endogenous RNA transcripts in the testis. Virus particles were injected into the seminiferous tubules via the efferent duct. Using an autophagy inhibitor, 3-methyladenine (3-MA), we optimized the AAV9 transduction efficiency in germ cells in vivo. Results: AAV9-mediated delivery of CRISPR-CasRx effectively and specifically induces RNA transcripts (both coding and noncoding) knockdown in the testis in vivo. In addition, we showed that the co-microinjection of AAV9 and 3-MA into the seminiferous tubules enabled long-term transgene expression in the testis. Finally, we found that a promoter of Sycp1 gene induced CRISPR-CasRx-mediated RNA transcript knockdown in a germ-cell-type-specific manner. Conclusion: Our results demonstrate the efficacy and versatility of the AAV9-mediated CRISPR-CasRx system as a flexible knockdown platform for studying gene function during spermatogenesis in vivo. This approach may advance the development of RNA-targeting therapies for conditions affecting reproductive health.
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Affiliation(s)
- Kai Li
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Mengzhen Li
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Yanyun Luo
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Dingfeng Zou
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Yahui Li
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Xinyu Mang
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Zexuan Zhang
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Pengyu Li
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Yan Lu
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Shiying Miao
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Wei Song
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
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12
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Arnold CR, Mangesius J, Portnaia I, Ganswindt U, Wolff HA. Innovative therapeutic strategies to overcome radioresistance in breast cancer. Front Oncol 2024; 14:1379986. [PMID: 38873260 PMCID: PMC11169591 DOI: 10.3389/fonc.2024.1379986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/10/2024] [Indexed: 06/15/2024] Open
Abstract
Despite a comparatively favorable prognosis relative to other malignancies, breast cancer continues to significantly impact women's health globally, partly due to its high incidence rate. A critical factor in treatment failure is radiation resistance - the capacity of tumor cells to withstand high doses of ionizing radiation. Advancements in understanding the cellular and molecular mechanisms underlying radioresistance, coupled with enhanced characterization of radioresistant cell clones, are paving the way for the development of novel treatment modalities that hold potential for future clinical application. In the context of combating radioresistance in breast cancer, potential targets of interest include long non-coding RNAs (lncRNAs), micro RNAs (miRNAs), and their associated signaling pathways, along with other signal transduction routes amenable to pharmacological intervention. Furthermore, technical, and methodological innovations, such as the integration of hyperthermia or nanoparticles with radiotherapy, have the potential to enhance treatment responses in patients with radioresistant breast cancer. This review endeavors to provide a comprehensive survey of the current scientific landscape, focusing on novel therapeutic advancements specifically addressing radioresistant breast cancer.
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Affiliation(s)
| | - Julian Mangesius
- Department of Radiation-Oncology, Medical University of Innsbruck, Innsbruck, Austria
| | - Iana Portnaia
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Ute Ganswindt
- Department of Radiation-Oncology, Medical University of Innsbruck, Innsbruck, Austria
| | - Hendrik Andreas Wolff
- Department of Radiology, Nuclear Medicine, and Radiotherapy, Radiology Munich, Munich, Germany
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13
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Vercouillie N, Ren Z, Terras E, Lammens T. Long Non-Coding RNAs in Neuroblastoma: Pathogenesis, Biomarkers and Therapeutic Targets. Int J Mol Sci 2024; 25:5690. [PMID: 38891878 PMCID: PMC11171840 DOI: 10.3390/ijms25115690] [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: 04/18/2024] [Revised: 05/18/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024] Open
Abstract
Neuroblastoma is the most common malignant extracranial solid tumor of childhood. Recent studies involving the application of advanced high-throughput "omics" techniques have revealed numerous genomic alterations, including aberrant coding-gene transcript levels and dysfunctional pathways, that drive the onset, growth, progression, and treatment resistance of neuroblastoma. Research conducted in the past decade has shown that long non-coding RNAs, once thought to be transcriptomic noise, play key roles in cancer development. With the recent and continuing increase in the amount of evidence for the underlying roles of long non-coding RNAs in neuroblastoma, the potential clinical implications of these RNAs cannot be ignored. In this review, we discuss their biological mechanisms of action in the context of the central driving mechanisms of neuroblastoma, focusing on potential contributions to the diagnosis, prognosis, and treatment of this disease. We also aim to provide a clear, integrated picture of future research opportunities.
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Affiliation(s)
- Niels Vercouillie
- Department of Internal Medicine and Pediatrics, Ghent University, 9000 Ghent, Belgium; (N.V.); (Z.R.); (E.T.)
| | - Zhiyao Ren
- Department of Internal Medicine and Pediatrics, Ghent University, 9000 Ghent, Belgium; (N.V.); (Z.R.); (E.T.)
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, 9000 Ghent, Belgium
- Cancer Research Institute Ghent, 9000 Ghent, Belgium
| | - Eva Terras
- Department of Internal Medicine and Pediatrics, Ghent University, 9000 Ghent, Belgium; (N.V.); (Z.R.); (E.T.)
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, 9000 Ghent, Belgium
- Cancer Research Institute Ghent, 9000 Ghent, Belgium
| | - Tim Lammens
- Department of Internal Medicine and Pediatrics, Ghent University, 9000 Ghent, Belgium; (N.V.); (Z.R.); (E.T.)
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, 9000 Ghent, Belgium
- Cancer Research Institute Ghent, 9000 Ghent, Belgium
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14
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Brown SD, Klimi E, Bakker WAM, Beqqali A, Baker AH. Non-coding RNAs to treat vascular smooth muscle cell dysfunction. Br J Pharmacol 2024. [PMID: 38773733 DOI: 10.1111/bph.16409] [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: 11/17/2023] [Revised: 02/19/2024] [Accepted: 03/14/2024] [Indexed: 05/24/2024] Open
Abstract
Vascular smooth muscle cell (vSMC) dysfunction is a critical contributor to cardiovascular diseases, including atherosclerosis, restenosis and vein graft failure. Recent advances have unveiled a fascinating range of non-coding RNAs (ncRNAs) that play a pivotal role in regulating vSMC function. This review aims to provide an in-depth analysis of the mechanisms underlying vSMC dysfunction and the therapeutic potential of various ncRNAs in mitigating this dysfunction, either preventing or reversing it. We explore the intricate interplay of microRNAs, long-non-coding RNAs and circular RNAs, shedding light on their roles in regulating key signalling pathways associated with vSMC dysfunction. We also discuss the prospects and challenges associated with developing ncRNA-based therapies for this prevalent type of cardiovascular pathology.
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Affiliation(s)
- Simon D Brown
- BHF Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Eftychia Klimi
- BHF Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | | | - Abdelaziz Beqqali
- BHF Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Andrew H Baker
- BHF Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Centre, Maastricht, The Netherlands
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15
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Scuderi C, Di Bella V, Privitera AP, Giustolisi FM, Barresi V, Condorelli DF. Gain-Type Aneuploidies Influence the Burden of Selective Long Non-Coding Transcripts in Colorectal Cancer. Int J Mol Sci 2024; 25:5538. [PMID: 38791575 PMCID: PMC11122260 DOI: 10.3390/ijms25105538] [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: 02/29/2024] [Revised: 05/10/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Chromosomal instability is a hallmark of colorectal carcinogenesis and produces an accumulation of different forms of aneuploidies or broad copy number aberrations. Colorectal cancer is characterized by gain-type broad copy number aberrations, specifically in Chr20, Chr8q, Chr13 and Chr7, but their roles and mechanisms in cancer progression are not fully understood. It has been suggested that broad copy number gains might contribute to tumor development through the so-called caricature transcriptomic effect. We intend to investigate the impact of broad copy number gains on long non-coding RNAs' expression in colorectal cancer, given their well-known role in oncogenesis. The influence of such chromosomal aberrations on lncRNAs' transcriptome profile was investigated by SNP and transcriptome arrays in our series of colorectal cancer samples and cell lines. The correlation between aneuploidies and transcriptomic profiles led us to obtain a class of Over-UpT lncRNAs, which are transcripts upregulated in CRC and further overexpressed in colon tumors bearing specific chromosomal aberrations. The identified lncRNAs can contribute to a wide interaction network to establish the cancer driving effect of gain-type aneuploidies.
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Affiliation(s)
| | | | | | | | - Vincenza Barresi
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (C.S.); (V.D.B.); (A.P.P.); (F.M.G.); (D.F.C.)
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16
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Tian Y, Zhang M, Liu LX, Wang ZC, Liu B, Huang Y, Wang X, Ling YZ, Wang F, Feng X, Tu Y. Exploring non-coding RNA mechanisms in hepatocellular carcinoma: implications for therapy and prognosis. Front Immunol 2024; 15:1400744. [PMID: 38799446 PMCID: PMC11116607 DOI: 10.3389/fimmu.2024.1400744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 04/03/2024] [Indexed: 05/29/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is a significant contributor to cancer-related deaths in the world. The development and progression of HCC are closely correlated with the abnormal regulation of non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs). Important biological pathways in cancer biology, such as cell proliferation, death, and metastasis, are impacted by these ncRNAs, which modulate gene expression. The abnormal expression of non-coding RNAs in HCC raises the possibility that they could be applied as new biomarkers for diagnosis, prognosis, and treatment targets. Furthermore, by controlling the expression of cancer-related genes, miRNAs can function as either tumor suppressors or oncogenes. On the other hand, lncRNAs play a role in the advancement of cancer by interacting with other molecules within the cell, which, in turn, affects processes such as chromatin remodeling, transcription, and post-transcriptional processes. The importance of ncRNA-driven regulatory systems in HCC is being highlighted by current research, which sheds light on tumor behavior and therapy response. This research highlights the great potential of ncRNAs to improve patient outcomes in this difficult disease landscape by augmenting the present methods of HCC care through the use of precision medicine approaches.
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Affiliation(s)
- Yu Tian
- Research Center, The Huizhou Central People’s Hospital, Guangdong Medical University, Huizhou, Guangdong, China
- School of Public Health, Benedictine University, Lisle, IL, United States
| | - Meng Zhang
- Department of Hepatobiliary Surgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Li-xia Liu
- Department of Ultrasound, Hebei Key Laboratory of Precise Imaging of Inflammation Related Tumors, Affiliated Hospital of Hebei University, Baoding, Hebei, China
| | - Zi-chao Wang
- Department of Ultrasound, Hebei Key Laboratory of Precise Imaging of Inflammation Related Tumors, Affiliated Hospital of Hebei University, Baoding, Hebei, China
| | - Bin Liu
- Central Laboratory, Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, Affiliated Hospital of Hebei University, Baoding, Hebei, China
| | - Youcai Huang
- Research Center, The Huizhou Central People’s Hospital, Guangdong Medical University, Huizhou, Guangdong, China
| | - Xiaoling Wang
- Research Center, The Huizhou Central People’s Hospital, Guangdong Medical University, Huizhou, Guangdong, China
| | - Yun-zhi Ling
- Research Center, The Huizhou Central People’s Hospital, Guangdong Medical University, Huizhou, Guangdong, China
| | - Furong Wang
- Department of Pathology, The Huizhou Central People’s Hospital, Guangdong Medical University, Huizhou, Guangdong, China
| | - Xiaoqiang Feng
- Center of Stem Cell and Regenerative Medicine, Gaozhou People’s Hospital, Gaozhou, Guangdong, China
| | - Yanyang Tu
- Research Center, The Huizhou Central People’s Hospital, Guangdong Medical University, Huizhou, Guangdong, China
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17
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Thapa R, Marmo K, Ma L, Torry DS, Bany BM. The Long Non-Coding RNA Gene AC027288.3 Plays a Role in Human Endometrial Stromal Fibroblast Decidualization. Cells 2024; 13:778. [PMID: 38727314 PMCID: PMC11083667 DOI: 10.3390/cells13090778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
During the secretory phase of the menstrual cycle, endometrial fibroblast cells begin to change into large epithelial-like cells called decidual cells in a process called decidualization. This differentiation continues more broadly in the endometrium and forms the decidual tissue during early pregnancy. The cells undergoing decidualization as well as the resulting decidual cells, support successful implantation and placentation during early pregnancy. This study was carried out to identify new potentially important long non-coding RNA (lncRNA) genes that may play a role in human endometrial stromal fibroblast cells (hESF) undergoing decidualization in vitro, and several were found. The expression of nine was further characterized. One of these, AC027288.3, showed a dramatic increase in the expression of hESF cells undergoing decidualization. When AC027288.3 expression was targeted, the ability of the cells to undergo decidualization as determined by the expression of decidualization marker protein-coding genes was significantly altered. The most affected markers of decidualization whose expression was significantly reduced were FOXO1, FZD4, and INHBA. Therefore, AC027288.3 may be a major upstream regulator of the WNT-FOXO1 pathway and activin-SMAD3 pathways previously shown as critical for hESF decidualization. Finally, we explored possible regulators of AC027288.3 expression during human ESF decidualization. Expression was regulated by cAMP and progesterone. Our results suggest that AC027288.3 plays a role in hESF decidualization and identifies several other lncRNA genes that may also play a role.
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Affiliation(s)
- Rupak Thapa
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA; (R.T.)
| | - Kevin Marmo
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA; (R.T.)
| | - Liang Ma
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Donald S. Torry
- Department of Medical Microbiology, Immunology and Cell Biology, Southern Illinois University School of Medicine, Springfield, IL 62702, USA
| | - Brent M. Bany
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA; (R.T.)
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18
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Allen S, O'Reilly D, Miller R, Sapp E, Summers A, Paquette J, Moreno DE, Bramato B, McHugh N, Yamada K, Aronin N, DiFiglia M, Khvorova A. mRNA nuclear clustering leads to a difference in mutant huntingtin mRNA and protein silencing by siRNAs in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.24.590997. [PMID: 38774633 PMCID: PMC11106801 DOI: 10.1101/2024.04.24.590997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/24/2024]
Abstract
Huntington's disease (HD) is an autosomal dominant neurodegenerative disease caused by CAG repeat expansion in the first exon of the huntingtin gene (HTT). Oligonucleotide therapeutics, such as short interfering RNA (siRNA), reduce levels of huntingtin mRNA and protein in vivo and are considered a viable therapeutic strategy. However, the extent to which they silence HTT mRNA in the nucleus is not established. We synthesized siRNA cross-reactive to mouse (wild-type) Htt and human (mutant) HTT in a di-valent scaffold and delivered to two mouse models of HD. In both models, di-valent siRNA sustained lowering of wild-type Htt, but not mutant HTT mRNA expression in striatum and cortex. Near-complete silencing of both mutant HTT protein and wild-type Htt protein was observed in both models. Subsequent fluorescent in situ hybridization (FISH) analysis shows that di-valent siRNA acts predominantly on cytoplasmic mutant HTT transcripts, leaving clustered mutant HTT transcripts in the nucleus largely intact in treated HD mouse brains. The observed differences between mRNA and protein levels, exaggerated in the case of extended repeats, might apply to other repeat-associated neurological disorders.
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19
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Sakurai K, Ito H. Multifaced roles of the long non-coding RNA DRAIC in cancer progression. Life Sci 2024; 343:122544. [PMID: 38458555 DOI: 10.1016/j.lfs.2024.122544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/15/2024] [Accepted: 03/04/2024] [Indexed: 03/10/2024]
Abstract
Long non-coding RNAs (lncRNA) are functional RNAs, with over 200 nucleotides in length and lacking protein-coding potential. Studies have indicated that lncRNAs are important gene regulators under physiological conditions. Aberrant lncRNA expression is associated with the initiation and progression of various diseases, including cancers. High-throughput transcriptome analyses have revealed thousands of lncRNAs as putative tumor suppressors or promoters in various cancers, but the detailed molecular mechanisms of each lncRNA remain unclear. Downregulated RNA In Cancer, inhibitor of cell invasion and migration (DRAIC) (also known as LOC145837 and RP11-279F6.1) is a lncRNA that inhibits or promotes cancer progression with several modes of action. DRAIC was originally identified as a tumor-suppressive lncRNA in prostate adenocarcinoma. Subsequent studies also revealed that it has an anti-tumor role in glioblastoma, triple-negative breast cancer, and stomach adenocarcinoma. However, DRAIC exhibits oncogenic functions in other malignancies, such as lung adenocarcinoma and esophageal carcinoma, indicating its highly context-dependent effects on cancer progression and clinical outcomes. DRAIC and its associated pathways regulate various biological processes, including proliferation, invasion, metastasis, autophagy, and neuroendocrine function. This review introduces the multifaceted roles of DRAIC, particularly in cancer progression, and discusses its biological significance and clinical implications.
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Affiliation(s)
- Kouhei Sakurai
- Department of Joint Research Laboratory of Clinical Medicine, School of Medicine, Fujita Health University, Toyoake, Aichi, 470-1192, Japan.
| | - Hiroyasu Ito
- Department of Joint Research Laboratory of Clinical Medicine, School of Medicine, Fujita Health University, Toyoake, Aichi, 470-1192, Japan
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20
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Montero JJ, Trozzo R, Sugden M, Öllinger R, Belka A, Zhigalova E, Waetzig P, Engleitner T, Schmidt-Supprian M, Saur D, Rad R. Genome-scale pan-cancer interrogation of lncRNA dependencies using CasRx. Nat Methods 2024; 21:584-596. [PMID: 38409225 PMCID: PMC11009108 DOI: 10.1038/s41592-024-02190-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 01/19/2024] [Indexed: 02/28/2024]
Abstract
Although long noncoding RNAs (lncRNAs) dominate the transcriptome, their functions are largely unexplored. The extensive overlap of lncRNAs with coding and regulatory sequences restricts their systematic interrogation by DNA-directed perturbation. Here we developed genome-scale lncRNA transcriptome screening using Cas13d/CasRx. We show that RNA targeting overcomes limitations inherent to other screening methods, thereby considerably expanding the explorable space of the lncRNAome. By evolving the screening system toward pan-cancer applicability, it supports molecular and phenotypic data integration to contextualize screening hits or infer lncRNA function. We thereby addressed challenges posed by the enormous transcriptome size and tissue specificity through a size-reduced multiplexed gRNA library termed Albarossa, targeting 24,171 lncRNA genes. Its rational design incorporates target prioritization based on expression, evolutionary conservation and tissue specificity, thereby reconciling high discovery power and pan-cancer representation with scalable experimental throughput. Applied across entities, the screening platform identified numerous context-specific and common essential lncRNAs. Our work sets the stage for systematic exploration of lncRNA biology in health and disease.
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Affiliation(s)
- Juan J Montero
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany.
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany.
| | - Riccardo Trozzo
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Maya Sugden
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Rupert Öllinger
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Alexander Belka
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Ekaterina Zhigalova
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Paul Waetzig
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Thomas Engleitner
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Marc Schmidt-Supprian
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Experimental Hematology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Dieter Saur
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technische Universität München, Munich, Germany
- Institute for Experimental Cancer Therapy, School of Medicine, Technische Universität München, Munich, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany.
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany.
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
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21
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Chia SPS, Pang JKS, Soh BS. Current RNA strategies in treating cardiovascular diseases. Mol Ther 2024; 32:580-608. [PMID: 38291757 PMCID: PMC10928165 DOI: 10.1016/j.ymthe.2024.01.028] [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: 09/14/2023] [Revised: 12/22/2023] [Accepted: 01/23/2024] [Indexed: 02/01/2024] Open
Abstract
Cardiovascular disease (CVD) continues to impose a significant global health burden, necessitating the exploration of innovative treatment strategies. Ribonucleic acid (RNA)-based therapeutics have emerged as a promising avenue to address the complex molecular mechanisms underlying CVD pathogenesis. We present a comprehensive review of the current state of RNA therapeutics in the context of CVD, focusing on the diverse modalities that bring about transient or permanent modifications by targeting the different stages of the molecular biology central dogma. Considering the immense potential of RNA therapeutics, we have identified common gene targets that could serve as potential interventions for prevalent Mendelian CVD caused by single gene mutations, as well as acquired CVDs developed over time due to various factors. These gene targets offer opportunities to develop RNA-based treatments tailored to specific genetic and molecular pathways, presenting a novel and precise approach to address the complex pathogenesis of both types of cardiovascular conditions. Additionally, we discuss the challenges and opportunities associated with delivery strategies to achieve targeted delivery of RNA therapeutics to the cardiovascular system. This review highlights the immense potential of RNA-based interventions as a novel and precise approach to combat CVD, paving the way for future advancements in cardiovascular therapeutics.
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Affiliation(s)
- Shirley Pei Shan Chia
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A∗STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore; Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore
| | - Jeremy Kah Sheng Pang
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A∗STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Boon-Seng Soh
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A∗STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore; Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore.
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22
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Feichtenschlager V, Chen L, Zheng YJ, Ho W, Sanlorenzo M, Vujic I, Fewings E, Lee A, Chen C, Callanan C, Lin K, Qu T, Hohlova D, Vujic M, Hwang Y, Lai K, Chen S, Nguyen T, Muñoz DP, Kohwi Y, Posch C, Daud A, Rappersberger K, Kohwi-Shigematsu T, Coppé JP, Ortiz-Urda S. The therapeutically actionable long non-coding RNA 'T-RECS' is essential to cancer cells' survival in NRAS/MAPK-driven melanoma. Mol Cancer 2024; 23:40. [PMID: 38383439 PMCID: PMC10882889 DOI: 10.1186/s12943-024-01955-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 02/05/2024] [Indexed: 02/23/2024] Open
Abstract
Finding effective therapeutic targets to treat NRAS-mutated melanoma remains a challenge. Long non-coding RNAs (lncRNAs) recently emerged as essential regulators of tumorigenesis. Using a discovery approach combining experimental models and unbiased computational analysis complemented by validation in patient biospecimens, we identified a nuclear-enriched lncRNA (AC004540.4) that is upregulated in NRAS/MAPK-dependent melanoma, and that we named T-RECS. Considering potential innovative treatment strategies, we designed antisense oligonucleotides (ASOs) to target T-RECS. T-RECS ASOs reduced the growth of melanoma cells and induced apoptotic cell death, while having minimal impact on normal primary melanocytes. Mechanistically, treatment with T-RECS ASOs downregulated the activity of pro-survival kinases and reduced the protein stability of hnRNPA2/B1, a pro-oncogenic regulator of MAPK signaling. Using patient- and cell line- derived tumor xenograft mouse models, we demonstrated that systemic treatment with T-RECS ASOs significantly suppressed the growth of melanoma tumors, with no noticeable toxicity. ASO-mediated T-RECS inhibition represents a promising RNA-targeting approach to improve the outcome of MAPK pathway-activated melanoma.
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Affiliation(s)
- Valentin Feichtenschlager
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA.
- Department of Dermatology, Academic Teaching Hospital, Clinic Landstrasse Vienna, Medical University Vienna, Vienna, Austria.
| | - Linan Chen
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
| | - Yixuan James Zheng
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
- School of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Wilson Ho
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
| | - Martina Sanlorenzo
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
| | - Igor Vujic
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
- Department of Dermatology, Academic Teaching Hospital, Clinic Landstrasse Vienna, Medical University Vienna, Vienna, Austria
- Faculty of Medicine, Sigmund Freud Private University, Vienna, Austria
| | - Eleanor Fewings
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
| | - Albert Lee
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
| | - Christopher Chen
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
| | - Ciara Callanan
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
| | - Kevin Lin
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
| | - Tiange Qu
- Department of Orofacial Science, Health Science West, University of California San Francisco School of Dentistry, San Francisco, CA, USA
| | - Dasha Hohlova
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
- Department of Biology, University of San Francisco, San Francisco, CA, USA
| | - Marin Vujic
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
- Department of Dermatology, Academic Teaching Hospital, Clinic Landstrasse Vienna, Medical University Vienna, Vienna, Austria
| | - Yeonjoo Hwang
- Department of Hematology-Oncology, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Kevin Lai
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
| | - Stephanie Chen
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
| | - Thuan Nguyen
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
| | - Denise P Muñoz
- Department of Hematology-Oncology, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Yoshinori Kohwi
- Department of Orofacial Science, Health Science West, University of California San Francisco School of Dentistry, San Francisco, CA, USA
| | - Christian Posch
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
- Department of Dermatology, Academic Teaching Hospital, Clinic Landstrasse Vienna, Medical University Vienna, Vienna, Austria
- Faculty of Medicine, Sigmund Freud Private University, Vienna, Austria
- Department of Dermatology and Allergy, School of Medicine, German Cancer Consortium (DKTK), Technical University of Munich, Munich, Germany
| | - Adil Daud
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
| | - Klemens Rappersberger
- Department of Dermatology, Academic Teaching Hospital, Clinic Landstrasse Vienna, Medical University Vienna, Vienna, Austria
| | - Terumi Kohwi-Shigematsu
- Department of Orofacial Science, Health Science West, University of California San Francisco School of Dentistry, San Francisco, CA, USA
| | - Jean-Philippe Coppé
- Department of Radiation Oncology, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Susana Ortiz-Urda
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
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23
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Islam SS, Al-Tweigeri T, Al-Harbi L, Ujjahan S, Al-Mozaini M, Tulbah A, Aboussekhra A. Long noncoding RNA DLEU2 and ROR1 pathway induces epithelial-to-mesenchymal transition and cancer stem cells in breast cancer. Cell Death Discov 2024; 10:61. [PMID: 38296962 PMCID: PMC10830457 DOI: 10.1038/s41420-024-01829-3] [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: 04/18/2023] [Revised: 01/15/2024] [Accepted: 01/19/2024] [Indexed: 02/02/2024] Open
Abstract
Breast cancer (BC) patient who receives chemotherapy for an extended length of time may experience profound repercussions in terms of metastases and clinical outcomes due to the involvement of the epithelial-to-mesenchymal transition (EMT) mechanism and enriched cancer stem cells (CSCs). BC cells that express high levels of lncRNA deleted in lymphocytic leukemia-2 (lncRNA DLEU2) and type I tyrosine kinase-like orphan receptor ROR1 (ROR1) may play roles in the enhanced ability of the activation EMT and CSC induction. Here we find that lncRNA DLEU2 and ROR1 are specifically upregulated in tumor tissues compared to their normal counterparts in TCGA, PubMed GEO datasets, and samples from archived breast cancer tumor tissues. Following chemotherapy, lncRNA DLEU2 and ROR1 were enhanced in BC tumor cells, coupled with the expression of CSCs, EMT-related genes, and BMI1. Mechanistically, ROR1 and lncRNA DLEU2 overexpression led to enhanced tumor cell proliferation, inhibition of apoptosis, cell-cycle dysregulation, chemoresistance, as well as BC cell's abilities to invade, migrate, develop spheroids. These findings imply that the role of lncRNA DLEU2 and ROR1 in BC therapeutic failure is largely attributed to EMT, which is intricately linked to enriched CSCs. In conclusion, our findings indicate that a lncRNA DLEU2 and ROR1-based regulatory loop governs EMT and CSC self-renewal, implying that targeting this regulatory pathway may improve patients' responses to chemotherapy and survival.
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Affiliation(s)
- Syed S Islam
- Department of Molecular Oncology, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia.
- School of Medicine, Al-Faisal University, Riyadh, Saudi Arabia.
| | - Taher Al-Tweigeri
- Breast Cancer Unit, Oncology Centre, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Layla Al-Harbi
- Department of Infection and Immunity, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Shafat Ujjahan
- Department of Medical Oncology and Radiotherapy, Park View Hospital, Chattagram, Bangladesh
| | - Maha Al-Mozaini
- Department of Infection and Immunity, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Asma Tulbah
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Abdelilah Aboussekhra
- Department of Molecular Oncology, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
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24
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Hofman CR, Corey DR. Targeting RNA with synthetic oligonucleotides: Clinical success invites new challenges. Cell Chem Biol 2024; 31:125-138. [PMID: 37804835 PMCID: PMC10841528 DOI: 10.1016/j.chembiol.2023.09.005] [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: 07/05/2023] [Revised: 08/27/2023] [Accepted: 09/15/2023] [Indexed: 10/09/2023]
Abstract
Synthetic antisense oligonucleotides (ASOs) and duplex RNAs (dsRNAs) are an increasingly successful strategy for drug development. After a slow start, the pace of success has accelerated since the approval of Spinraza (nusinersen) in 2016 with several drug approvals. These accomplishments have been achieved even though oligonucleotides are large, negatively charged, and have little resemblance to traditional small-molecule drugs-a remarkable achievement of basic and applied science. The goal of this review is to summarize the foundation underlying recent progress and describe ongoing research programs that may increase the scope and impact of oligonucleotide therapeutics.
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Affiliation(s)
- Cristina R Hofman
- The Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - David R Corey
- The Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA.
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25
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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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26
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Malakar P, Shukla S, Mondal M, Kar RK, Siddiqui JA. The nexus of long noncoding RNAs, splicing factors, alternative splicing and their modulations. RNA Biol 2024; 21:1-20. [PMID: 38017665 PMCID: PMC10761143 DOI: 10.1080/15476286.2023.2286099] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2023] [Indexed: 11/30/2023] Open
Abstract
The process of alternative splicing (AS) is widely deregulated in a variety of cancers. Splicing is dependent upon splicing factors. Recently, several long noncoding RNAs (lncRNAs) have been shown to regulate AS by directly/indirectly interacting with splicing factors. This review focuses on the regulation of AS by lncRNAs through their interaction with splicing factors. AS mis-regulation caused by either mutation in splicing factors or deregulated expression of splicing factors and lncRNAs has been shown to be involved in cancer development and progression, making aberrant splicing, splicing factors and lncRNA suitable targets for cancer therapy. This review also addresses some of the current approaches used to target AS, splicing factors and lncRNAs. Finally, we discuss research challenges, some of the unanswered questions in the field and provide recommendations to advance understanding of the nexus of lncRNAs, AS and splicing factors in cancer.
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Affiliation(s)
- Pushkar Malakar
- Department of Biomedical Science and Technology, School of Biological Sciences, Ramakrishna Mission Vivekananda Educational Research Institute (RKMVERI), Kolkata, India
| | - Sudhanshu Shukla
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, Karnataka, India
| | - Meghna Mondal
- Department of Biomedical Science and Technology, School of Biological Sciences, Ramakrishna Mission Vivekananda Educational Research Institute (RKMVERI), Kolkata, India
| | - Rajesh Kumar Kar
- Department of Neurosurgery, School of Medicine, Yale University, New Haven, CT, USA
| | - Jawed Akhtar Siddiqui
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
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27
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Sun Y, Jiang H, Pan L, Han Y, Chen Y, Jiang Y, Wang Y. LncRNA OIP5-AS1/miR-410-3p/Wnt7b axis promotes the proliferation of rheumatoid arthritis fibroblast-like synoviocytes via regulating the Wnt/β-catenin pathway. Autoimmunity 2023; 56:2189136. [PMID: 36942896 DOI: 10.1080/08916934.2023.2189136] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
LncRNA OIP5-AS1 has a common gene imbalance in various cancers and tumours, which plays an important role in regulating its biological function. However, there are few studies on lncRNA OIP5-AS1 in rheumatoid arthritis (RA). The purpose of the present study was to investigate the role of lncRNA OIP5-AS1 in the pathogenesis of RA. In the present study, we established an adjuvant arthritis (AA) rat model to obtain primary fibroblast-like synoviocytes (FLSs);The subcellular localisation of lncRNA OIP5-AS1 was detected by fluorescence in situ hybridisation (FISH) assay; Cell proliferation of FLSs was determined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide(MTT) assay;IL-1β, IL-6 and TNF-α concentrations were measured by enzyme-linked immunosorbent assay (ELISA);Quantitative real-time PCR (qRT-PCR), Western blots(WB) and immunofluorescence were used to detect the expression of lncRNA OIP5-AS1/miR-410-3p/wnt7b signal axis and Wnt/β-catenin signal pathway related indicators in FLSs. FISH assay confirmed the presence of lncRNA OIP5-AS1 in the cytoplasm, suggesting that it acts as a competing endogenous RNA (ceRNA). qRT-PCR showed that the expression of lncRNA OIP5-AS1 was upregulated in FLSs, while the expression of miR-410-3p was downregulated in FLSs. We also found that lncRNA OIP5-AS1 knockdown inhibited the proliferation and inflammation of FLSs. Moreover, the expression of Wnt7b, the downstream target gene of miR-410-3p, and the activation of the Wnt/β-catenin signalling pathway were also inhibited by lncRNA OIP5-AS1 knockdown. These results suggested that lncRNA OIP5-AS1 promotes the activation of the Wnt/β-catenin signalling pathway by regulating the miR-410-3p/Wnt7b signalling axis, thereby participating in the occurrence and development of RA.
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Affiliation(s)
- Yuan Sun
- Pharmacy Department, The First Affiliated Hospital of Anhui University of Traditional Chinese Medicine, Hefei, Anhui, P.R. China
- School of Pharmacy, Anhui University of Traditional Chinese Medicine, Hefei, Anhui, P.R. China
- Pharmacy Department, ShangHai East Hospital, Shanghai, P.R. China
| | - Hui Jiang
- Pharmacy Department, The First Affiliated Hospital of Anhui University of Traditional Chinese Medicine, Hefei, Anhui, P.R. China
| | - LingYu Pan
- Pharmacy Department, The First Affiliated Hospital of Anhui University of Traditional Chinese Medicine, Hefei, Anhui, P.R. China
| | - YanQuan Han
- Pharmacy Department, The First Affiliated Hospital of Anhui University of Traditional Chinese Medicine, Hefei, Anhui, P.R. China
| | - Yan Chen
- School of Pharmacy, Anhui University of Traditional Chinese Medicine, Hefei, Anhui, P.R. China
| | - Yeke Jiang
- School of Pharmacy, Anhui University of Traditional Chinese Medicine, Hefei, Anhui, P.R. China
| | - Yongzhong Wang
- Pharmacy Department, The First Affiliated Hospital of Anhui University of Traditional Chinese Medicine, Hefei, Anhui, P.R. China
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28
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Feichtenschlager V, Chen L, Zheng YJ, Ho W, Sanlorenzo M, Vujic I, Fewings E, Lee A, Chen C, Callanan C, Lin K, Qu T, Hohlova D, Vujic M, Hwang Y, Lai K, Chen S, Nguyen T, Muñoz DP, Kohwi Y, Posch C, Daud A, Rappersberger K, Kohwi-Shigematsu T, Coppé JP, Ortiz-Urda S. The therapeutically actionable long non-coding RNA ' T-RECS' is essential to cancer cells' survival in NRAS/MAPK-driven melanoma. RESEARCH SQUARE 2023:rs.3.rs-1297358. [PMID: 38077055 PMCID: PMC10705697 DOI: 10.21203/rs.3.rs-1297358/v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Finding effective therapeutic targets to treat NRAS-mutated melanoma remains a challenge. Long non-coding RNAs (lncRNAs) recently emerged as essential regulators of tumorigenesis. Using a discovery approach combining experimental models and unbiased computational analysis complemented by validation in patient biospecimens, we identified a nuclear-enriched lncRNA (AC004540.4) that is upregulated in NRAS/MAPK-dependent melanoma, and that we named T-RECS. Considering potential innovative treatment strategies, we designed antisense oligonucleotides (ASOs) to target T-RECS. T-RECS ASOs reduced the growth of melanoma cells and induced apoptotic cell death, while having minimal impacton normal primary melanocytes. Mechanistically, treatment with T-RECS ASOs downregulated the activity of pro-survival kinases and reduced the protein stability of hnRNPA2/B1, a pro-oncogenic regulator of MAPK signaling. Using patient- and cell line- derived tumor xenograft mouse models, we demonstrated that systemic treatment with T-RECS ASOs significantly suppressed the growth of melanoma tumors, with no noticeable toxicity. ASO-mediated T-RECS inhibition represents a promising RNA-targeting approach to improve the outcome of MAPK pathway-activated melanoma.
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Affiliation(s)
| | | | | | - Wilson Ho
- University of California San Francisco
| | | | - Igor Vujic
- Department of Dermatology and Venerology, Medical Institution Rudolfstiftung, Vienna, Austria
| | | | | | | | | | - Kevin Lin
- University of California San Francisco
| | - Tiange Qu
- University of California San Francisco
| | | | | | | | - Kevin Lai
- University of California San Francisco
| | | | | | | | | | | | - Adil Daud
- University of California at San Francisco
| | - Klemens Rappersberger
- Department of Dermatology, Clinic Landstrasse Vienna, Academic Teaching Hospital, Medical University Vienna, Vienna, Austria
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29
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Yue Q, Liu Y, Ji J, Hu T, Lin T, Yu S, Li S, Wu N. Down-regulation of OIP5-AS1 inhibits obesity-induced myocardial pyroptosis and miR-22/NLRP3 inflammasome axis. Immun Inflamm Dis 2023; 11:e1066. [PMID: 37904706 PMCID: PMC10611552 DOI: 10.1002/iid3.1066] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 11/01/2023] Open
Abstract
BACKGROUND Obesity can induce myocardial pyroptosis, but the exact mechanism is still unknown. A recent study reported the association of opa-interacting protein 5-antisense transcript 1 (OIP5-AS1), an evolutionarily conserved long noncoding RNA, with pyroptosis. Therefore, this study aimed to investigate the role of OIP5-AS1 in obesity-induced myocardial pyroptosis. METHODS OIP5-AS1 was downregulated in H9c2 cells, followed by treatment with 400 μM palmitic acid (PA). Propidium iodide (PI) staining, lactic dehydrogenase (LDH) release assay, caspase-1 activity assay, IL-1β, and IL-18 activity assay were performed to detect pyroptotic phenotype. The interaction between OIP5-AS1 and microRNAs (miRNAs) was analyzed using RNA pull-down and luciferase assay. The effect of OIP5-AS1 knockdown in high-fat diet (HFD)-induced obesity rat on cardiac function, myocardial hypertrophy, fibrosis, and remodeling was evaluated. RESULTS Fat deposition was observed in cardiomyocytes 24 h after PA treatment; moreover, PA-treated cardiomyocytes showed significant increase in the rate of pyroptotic cells, release of LDH, protein expressions of NLRP3 and cleaved caspase-1, and the activity of caspase-1, IL-1β, and IL-18 as well as OIP5-AS1 expression. These findings suggested that PA activated pyroptosis and induced OIP5-AS1 expression in cardiomyocytes. Moreover, OIP5-AS1 knockdown inhibited PA-induced pyroptosis. Mechanistically, OIP5-AS1 was found to specifically bind to miR-22 and to regulate NLRP3 inflammasome-mediated pyroptosis via miR-22. Furthermore, OIP5-AS1 knockdown ameliorated HFD-induced cardiac dysfunction, myocardial hypertrophy, fibrosis, remodeling, and pyroptosis. CONCLUSION Our results revealed that downregulation of OIP5-AS1 can inhibit obesity-induced myocardial pyroptosis via miR-22/NLRP3 inflammasome axis. This finding lays a foundation of gene therapy for heart disease targeting OIP5-AS1.
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Affiliation(s)
- Qingxiong Yue
- Department of UltrasoundDalian Municipal Central HospitalDalianLiaoning ProvinceChina
| | - Yan Liu
- Department of UltrasoundDalian Women and Children's Medical GroupDalianLiaoning ProvinceChina
| | - Jun Ji
- Department of Central LaboratoryDalian Municipal Central HospitalDalianLiaoning ProvinceChina
| | - Tao Hu
- Department of UltrasoundDalian Municipal Central HospitalDalianLiaoning ProvinceChina
| | - Tong Lin
- Department of UltrasoundDalian Municipal Central HospitalDalianLiaoning ProvinceChina
| | - Shuang Yu
- Department of Central LaboratoryFirst Affiliated Hospital of China Medical UniversityShenyangLiaoning ProvinceChina
| | - Shijun Li
- Department of CardiologyDalian Municipal Central HospitalDalianLiaoning ProvinceChina
| | - Nan Wu
- Department of Central LaboratoryFirst Affiliated Hospital of China Medical UniversityShenyangLiaoning ProvinceChina
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30
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Liao L, Chen X, Huang H, Li Y, Huang Q, Song Z, Luo J, Yuan T, Deng S. Long non-coding RNA CASC7 is a promising serum biomarker for hepatocellular carcinoma. BMC Gastroenterol 2023; 23:324. [PMID: 37735632 PMCID: PMC10514991 DOI: 10.1186/s12876-023-02961-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 09/17/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND At present, a large number of studies have found that long non-coding RNAs (lncRNAs) can be used as biomarkers for diagnosis and monitoring prognosis of hepatocellular carcinoma (HCC). The expression of lncRNA cancer susceptibility candidate 7 (CASC7) in HCC has rarely been studied. The purpose of this study was to explore the expression of CASC7 and its correlation with clinical features, and to further analyze its diagnostic value in HCC. METHODS Serum samples were collected from 80 patients with HCC, 80 patients with chronic hepatitis B (CHB), and 80 healthy people. The expression level of serum CASC7 was detected by droplet digital PCR. Appropriate parametric and nonparametric tests were used for data analysis. RESULTS The results showed that the expression of CASC7 in serum of patients with HCC was significantly higher than that of patients with CHB (median: 8.8 versus 2.2 copies/µl, p < 0.001) and healthy controls (median: 8.8 versus 3.8 copies/µl, p < 0.001). High expression of serum CASC7 was significantly correlated with tumor number (p = 0.005), intrahepatic metastasis (IM) (p < 0.001), tumor size (p = 0.007) and tumor-node-metastasis (TNM) stage (p = 0.008). The area under the curve (AUC) of CASC7 to distinguish HCC patients from CHB patients and healthy controls was 0.808 (95% CI: 0.742-0.874) at the cut-off value of 7.24 copies/µl with 63.8% sensitivity and 95.2% specificity. CONCLUSIONS This study suggested that CASC7 was significantly up-regulated in serum of patients with HCC and closely related to tumor number, IM, tumor size and TNM stage, which may serve as a promising diagnostic biomarker.
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Affiliation(s)
- Ling Liao
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Third Military Medical University, No. 10, Changjiang Zhilu, DaPing, Yuzhong District, Chongqing, 400042, China
- Department of Clinical Laboratory, Chongqing University Hospital, Chongqing University, Chongqing, 400044, China
| | - Xia Chen
- Department of Laboratory Medicine, The First Branch of the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hengliu Huang
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Third Military Medical University, No. 10, Changjiang Zhilu, DaPing, Yuzhong District, Chongqing, 400042, China
| | - Yuwei Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Third Military Medical University, No. 10, Changjiang Zhilu, DaPing, Yuzhong District, Chongqing, 400042, China
| | - Qing Huang
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Third Military Medical University, No. 10, Changjiang Zhilu, DaPing, Yuzhong District, Chongqing, 400042, China
| | - Zhen Song
- Department of Clinical Laboratory, The 954th Hospital of Chinese People's Liberation Army, No. 80, Naidong Road, Naidong District, Shannan, 856000, China
| | - Jie Luo
- Department of Clinical Laboratory, The 954th Hospital of Chinese People's Liberation Army, No. 80, Naidong Road, Naidong District, Shannan, 856000, China.
| | - Tao Yuan
- Department of Hepatobiliary Surgery, Daping Hospital, Army Medical University, Third Military Medical University, No. 10, Changjiang Zhilu, DaPing, Yuzhong District, Chongqing, 400042, China.
| | - Shaoli Deng
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Third Military Medical University, No. 10, Changjiang Zhilu, DaPing, Yuzhong District, Chongqing, 400042, China.
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Balmas E, Sozza F, Bottini S, Ratto ML, Savorè G, Becca S, Snijders KE, Bertero A. Manipulating and studying gene function in human pluripotent stem cell models. FEBS Lett 2023; 597:2250-2287. [PMID: 37519013 DOI: 10.1002/1873-3468.14709] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 08/01/2023]
Abstract
Human pluripotent stem cells (hPSCs) are uniquely suited to study human development and disease and promise to revolutionize regenerative medicine. These applications rely on robust methods to manipulate gene function in hPSC models. This comprehensive review aims to both empower scientists approaching the field and update experienced stem cell biologists. We begin by highlighting challenges with manipulating gene expression in hPSCs and their differentiated derivatives, and relevant solutions (transfection, transduction, transposition, and genomic safe harbor editing). We then outline how to perform robust constitutive or inducible loss-, gain-, and change-of-function experiments in hPSCs models, both using historical methods (RNA interference, transgenesis, and homologous recombination) and modern programmable nucleases (particularly CRISPR/Cas9 and its derivatives, i.e., CRISPR interference, activation, base editing, and prime editing). We further describe extension of these approaches for arrayed or pooled functional studies, including emerging single-cell genomic methods, and the related design and analytical bioinformatic tools. Finally, we suggest some directions for future advancements in all of these areas. Mastering the combination of these transformative technologies will empower unprecedented advances in human biology and medicine.
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Affiliation(s)
- Elisa Balmas
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Federica Sozza
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Sveva Bottini
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Maria Luisa Ratto
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Giulia Savorè
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Silvia Becca
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Kirsten Esmee Snijders
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Alessandro Bertero
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
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Zhou W, Feng Y, Lin C, CHAO CK, He Z, Zhao S, Xue J, Zhao X, Cao W. Yin Yang 1-Induced Long Noncoding RNA DUXAP9 Drives the Progression of Oral Squamous Cell Carcinoma by Blocking CDK1-Mediated EZH2 Degradation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2207549. [PMID: 37401236 PMCID: PMC10477890 DOI: 10.1002/advs.202207549] [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: 12/20/2022] [Revised: 04/04/2023] [Indexed: 07/05/2023]
Abstract
LncRNAs play a critical role in oral squamous cell carcinoma (OSCC) progression. However, the function and detailed molecular mechanism of most lncRNAs in OSCC are not fully understood. Here, a novel nuclear-localized lncRNA, DUXAP9 (DUXAP9), that is highly expressed in OSCC is identified. A high level of DUXAP9 is positively associated with lymph node metastasis, poor pathological differentiation, advanced clinical stage, worse overall survival, and worse disease-specific survival in OSCC patients. Overexpression of DUXAP9 significantly promotes OSCC cell proliferation, migration, invasion, and xenograft tumor growth and metastasis, and upregulates N-cadherin, Vimentin, Ki67, PCNA, and EZH2 expression and downregulates E-cadherin in vitro and in vivo, whereas knockdown of DUXAP9 remarkably suppresses OSCC cell proliferation, migration, invasion, and xenograft tumor growth in vitro and in vivo in an EZH2-dependent manner. Yin Yang 1 (YY1) is found to activate the transcriptional expression of DUXAP9 in OSCC. Furthermore, DUXAP9 physically interacts with EZH2 and inhibits EZH2 degradation via the suppression of EZH2 phosphorylation, thereby blocking EZH2 translocation from the nucleus to the cytoplasm. Thus, DUXAP9 can serve as a promising target for OSCC therapy.
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Affiliation(s)
- Wenkai Zhou
- Department of Oral and Maxillofacial & Head and Neck OncologyShanghai Ninth People's HospitalCollege of StomatologyShanghai Jiao Tong University School of MedicineShanghai200011China
- National Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghai200011China
| | - Yisheng Feng
- National Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghai200011China
| | - Chengzhong Lin
- National Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghai200011China
- The 2nd Dental CenterShanghai Ninth People's HospitalCollege of StomatologyShanghai Jiao Tong University School of MedicineCollege of StomatologyShanghai Jiao Tong UniversityShanghai200011China
| | - Chi Kuan CHAO
- National Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghai200011China
| | - Ziqi He
- National Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghai200011China
| | - Shiyao Zhao
- National Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghai200011China
| | - Jieyuan Xue
- Department of CardiologyShanghai Chest HospitalShanghai Jiao Tong UniversityShanghai200030China
| | - Xu‐Yun Zhao
- Department of Biochemistry and Molecular Cell BiologyShanghai Key Laboratory for Tumor Microenvironment and InflammationKey Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of EducationShanghai Jiao Tong University School of MedicineShanghai200025China
| | - Wei Cao
- Department of Oral and Maxillofacial & Head and Neck OncologyShanghai Ninth People's HospitalCollege of StomatologyShanghai Jiao Tong University School of MedicineShanghai200011China
- National Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghai200011China
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Li GZ, Meng GX, Pan GQ, Zhang X, Yan LJ, Li RZ, Ding ZN, Tan SY, Wang DX, Tian BW, Yan YC, Dong ZR, Hong JG, Li T. MALAT1/ mir-1-3p mediated BRF2 expression promotes HCC progression via inhibiting the LKB1/AMPK signaling pathway. Cancer Cell Int 2023; 23:188. [PMID: 37653482 PMCID: PMC10472681 DOI: 10.1186/s12935-023-03034-1] [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: 06/12/2023] [Accepted: 08/19/2023] [Indexed: 09/02/2023] Open
Abstract
BACKGROUND The long non-coding RNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) has been reported to play a vital role in the occurrence and development of various tumors. However, the underlying mechanism of MALAT1 in hepatocellular carcinoma (HCC) has not been thoroughly elucidated. METHODS The expression levels of MALAT1 in HCC tissues and different cell lines were detected by qRT-PCR. Antisense oligonucleotides (ASO)-MALAT1 transfected cells were used to explore the biological effects of MALAT1 in HCC cells by cell counting kit 8 (CCK-8), colony formation, transwell, wound healing, and flow cytometry analysis. Western blotting was performed to measure AMPK and apoptosis-related protein levels. Dual-luciferase reporter assay was performed to verify the relationship between MALAT1 and its specific targets. RESULTS We found that MALAT1 was upregulated in HCC, and MALAT1 knockdown in HCC cells inhibited cell proliferation, migration, and invasion and inhibited apoptosis in vitro. Further studies demonstrated that MALAT1 positively regulated the expression of transcription factor II B‑related factor 2 (BRF2), which was associated with tumor recurrence, large tumor size, and poor prognosis in HCC. Mechanistically, MALAT1 was found to act as a competitive endogenous RNA to sponge has-miR-1-3p, which upregulated BRF2 expression. Knockdown of BRF2 inhibited the progression of HCC by activating the LKB1/AMPK signaling pathway. Overexpression of BRF2 reversed the inhibitory effect of MALAT1 knockdown on HCC cell viability. Moreover, ASO targeting MALAT1 inhibited the growth of xenograft tumors. CONCLUSIONS Our results demonstrate a novel MALAT1/miR-1-3p/BRF2/LKB1/AMPK regulatory axis in HCC, which may provide new molecular therapeutic targets for HCC in the future.
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Affiliation(s)
- Guang-Zhen Li
- Medical Integration and Practice Center, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of General Surgery, Qilu Hospital of Shandong University, 107 West Wen Hua Road, Jinan, 250012, China
| | - Guang-Xiao Meng
- Department of General Surgery, Qilu Hospital of Shandong University, 107 West Wen Hua Road, Jinan, 250012, China
- Laboratory of Basic Medical Sciences, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Guo-Qiang Pan
- Department of General Surgery, Qilu Hospital of Shandong University, 107 West Wen Hua Road, Jinan, 250012, China
- Laboratory of Basic Medical Sciences, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Xiao Zhang
- Department of General Surgery, Qilu Hospital of Shandong University, 107 West Wen Hua Road, Jinan, 250012, China
- Laboratory of Basic Medical Sciences, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Lun-Jie Yan
- Department of General Surgery, Qilu Hospital of Shandong University, 107 West Wen Hua Road, Jinan, 250012, China
- Laboratory of Basic Medical Sciences, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Rui-Zhe Li
- Department of General Surgery, Qilu Hospital of Shandong University, 107 West Wen Hua Road, Jinan, 250012, China
- Laboratory of Basic Medical Sciences, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Zi-Niu Ding
- Department of General Surgery, Qilu Hospital of Shandong University, 107 West Wen Hua Road, Jinan, 250012, China
| | - Si-Yu Tan
- Department of General Surgery, Qilu Hospital of Shandong University, 107 West Wen Hua Road, Jinan, 250012, China
| | - Dong-Xu Wang
- Department of General Surgery, Qilu Hospital of Shandong University, 107 West Wen Hua Road, Jinan, 250012, China
| | - Bao-Wen Tian
- Department of General Surgery, Qilu Hospital of Shandong University, 107 West Wen Hua Road, Jinan, 250012, China
| | - Yu-Chuan Yan
- Department of General Surgery, Qilu Hospital of Shandong University, 107 West Wen Hua Road, Jinan, 250012, China
- Laboratory of Basic Medical Sciences, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Zhao-Ru Dong
- Department of General Surgery, Qilu Hospital of Shandong University, 107 West Wen Hua Road, Jinan, 250012, China
| | - Jian-Guo Hong
- Department of General Surgery, Qilu Hospital of Shandong University, 107 West Wen Hua Road, Jinan, 250012, China.
| | - Tao Li
- Department of General Surgery, Qilu Hospital of Shandong University, 107 West Wen Hua Road, Jinan, 250012, China.
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Lyu QR, Zhang S, Zhang Z, Tang Z. Functional knockout of long non-coding RNAs with genome editing. Front Genet 2023; 14:1242129. [PMID: 37705609 PMCID: PMC10495571 DOI: 10.3389/fgene.2023.1242129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 08/16/2023] [Indexed: 09/15/2023] Open
Abstract
An effective loss-of-function study is necessary to investigate the biological function of long non-coding RNA (lncRNA). Various approaches are available, including RNA silencing, antisense oligos, and CRISPR-based genome editing. CRISPR-based genome editing is the most widely used for inactivating lncRNA function at the genomic level. Knocking out the lncRNA function can be achieved by removing the promoter and the first exon (PE1), introducing pre-termination poly(A) signals, or deleting the entire locus, unlike frameshift strategies used for messenger RNA (mRNA). However, the intricate genomic interplay between lncRNA and neighbor genes makes it challenging to interpret lncRNA function accurately. This article discusses the advantages and disadvantages of each lncRNA knockout method and envisions the potential future directions to facilitate lncRNA functional study.
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Affiliation(s)
- Qing Rex Lyu
- Medical Research Center, Chongqing General Hospital, Chongqing, China
- Chongqing Academy of Medical Sciences, Chongqing, China
| | - Shikuan Zhang
- Key Lab in Healthy Science and Technology of Shenzhen, Tsinghua Shenzhen International Graduate School, Shenzhen, China
| | - Zhe Zhang
- Department of Chinese Medical Gastrointestinal of China-Japan Friendship Hospital, Beijing, China
| | - Zhiyu Tang
- Medical Research Center, Chongqing General Hospital, Chongqing, China
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Haghighi R, Castillo-Acobo RY, H Amin A, Ehymayed HM, Alhili F, Mirzaei M, Mohammadzadeh Saliani S, Kheradjoo H. A thorough understanding of the role of lncRNA in prostate cancer pathogenesis; Current knowledge and future research directions. Pathol Res Pract 2023; 248:154666. [PMID: 37487316 DOI: 10.1016/j.prp.2023.154666] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/01/2023] [Accepted: 07/02/2023] [Indexed: 07/26/2023]
Abstract
In the entire world, prostate cancer (PCa) is one of the most common and deadly cancers. Treatment failure is still common among patients, despite PCa diagnosis and treatment improvements. Inadequate early diagnostic markers and the emergence of resistance to conventional therapeutic approaches, particularly androgen-deprivation therapy, are the causes of this. Long non-coding RNAs (lncRNAs), as an essential group of regulatory molecules, have been reported to be dysregulated through prostate tumorigenesis and hold great promise as diagnostic targets. Besides, lncRNAs regulate the malignant features of PCa cells, such as proliferation, invasion, metastasis, and drug resistance. These multifunctional RNA molecules interact with other molecular effectors like miRNAs and transcription factors to modulate various signaling pathways, including AR signaling. This study aimed to compile new knowledge regarding the role of lncRNA through prostate tumorigenesis in terms of their effects on the various malignant characteristics of PCa cells; in light of these characteristics and the significant potential of lncRNAs as diagnostic and therapeutic targets for PCa. AVAILABILITY OF DATA AND MATERIALS: Not applicable.
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Affiliation(s)
- Ramin Haghighi
- Department of Urology, Faculty of Medicine, North Khorasan University of Medical Sciences, Bojnord, Iran
| | | | - Ali H Amin
- Deanship of Scientific Research, Umm Al-Qura University, Makkah 21955, Saudi Arabia.
| | | | - Farah Alhili
- Medical technical college, Al-Farahidi University, Iraq
| | - Mojgan Mirzaei
- Department of Anatomy, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
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He T, Zhang Q, Xu P, Tao W, Lin F, Liu R, Li M, Duan X, Cai C, Gu D, Zeng G, Liu Y. Extracellular vesicle-circEHD2 promotes the progression of renal cell carcinoma by activating cancer-associated fibroblasts. Mol Cancer 2023; 22:117. [PMID: 37481520 PMCID: PMC10362694 DOI: 10.1186/s12943-023-01824-9] [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: 05/24/2023] [Accepted: 07/13/2023] [Indexed: 07/24/2023] Open
Abstract
BACKGROUND The encapsulation of circular RNAs (circRNAs) into extracellular vesicles (EVs) enables their involvement in intercellular communication and exerts an influence on the malignant advancement of various tumors. However, the regulatory role of EVs-circRNA in renal cell carcinoma (RCC) remains elusive. METHODS The in vitro and in vivo functional experiments were implemented to measure the effects of circEHD2 on the phenotype of RCC. The functional role of EVs-circEHD2 on the activation of fibroblasts was assessed by collagen contraction assay, western blotting, and enzyme-linked immunosorbent assay (ELISA). The mechanism was investigated by RNA pull-down assay, RNA immunoprecipitation, chromatin isolation by RNA purification, luciferase assay, and co-immunoprecipitation assay. RESULTS We demonstrated that circEHD2 was upregulated in RCC tissues and serum EVs of RCC patients with metastasis. Silencing circEHD2 inhibited tumor growth in vitro and in vivo. Mechanistic studies indicated that FUS RNA -binding protein (FUS) accelerated the cyclization of circEHD2, then circEHD2 interacts with tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein eta (YWHAH), which acts as a bridge to recruit circEHD2 and Yes1-associated transcriptional regulator (YAP) to the promoter of SRY-box transcription factor 9 (SOX9); this results in the sustained activation of SOX9. Heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNPA2B1) regulates the package of circEHD2 into EVs, then EVs-circEHD2 transmits to fibroblasts, converting fibroblasts to cancer-associated fibroblasts (CAFs). Activated CAFs promote the metastasis of RCC by secreting pro-inflammatory cytokines such as IL-6. Furthermore, antisense oligonucleotides (ASOs) targeting circEHD2 exhibited a strong inhibition of tumor growth in vivo. CONCLUSIONS The circEHD2/YWHAH/YAP/SOX9 signaling pathway accelerates the growth of RCC. EVs-circEHD2 facilitates the metastasis of RCC by converting fibroblasts to CAFs. Our results suggest that EVs-circEHD2 may be a useful biomarker and therapeutic target for RCC.
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Affiliation(s)
- Tao He
- Department of Urology, The First Affiliated Hospital of Guangzhou Medical University, 151 West Yanjiang Road, Guangzhou, 510120, China
- Urology Key Laboratory of Guangdong Province, Guangzhou, 510120, China
| | - Qiansheng Zhang
- Department of Urology, The First Affiliated Hospital of Guangzhou Medical University, 151 West Yanjiang Road, Guangzhou, 510120, China
- Urology Key Laboratory of Guangdong Province, Guangzhou, 510120, China
| | - Peng Xu
- Urology Key Laboratory of Guangdong Province, Guangzhou, 510120, China
- Department of Urology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Wen Tao
- Department of Urology, The First Affiliated Hospital of Guangzhou Medical University, 151 West Yanjiang Road, Guangzhou, 510120, China
- Urology Key Laboratory of Guangdong Province, Guangzhou, 510120, China
| | - Fuyang Lin
- Department of Urology, The First Affiliated Hospital of Guangzhou Medical University, 151 West Yanjiang Road, Guangzhou, 510120, China
- Urology Key Laboratory of Guangdong Province, Guangzhou, 510120, China
| | - Renfei Liu
- Department of Urology, The First Affiliated Hospital of Guangzhou Medical University, 151 West Yanjiang Road, Guangzhou, 510120, China
- Urology Key Laboratory of Guangdong Province, Guangzhou, 510120, China
| | - Mingzhao Li
- Department of Urology, The First Affiliated Hospital of Guangzhou Medical University, 151 West Yanjiang Road, Guangzhou, 510120, China
- Urology Key Laboratory of Guangdong Province, Guangzhou, 510120, China
| | - Xiaolu Duan
- Department of Urology, The First Affiliated Hospital of Guangzhou Medical University, 151 West Yanjiang Road, Guangzhou, 510120, China
- Urology Key Laboratory of Guangdong Province, Guangzhou, 510120, China
| | - Chao Cai
- Department of Urology, The First Affiliated Hospital of Guangzhou Medical University, 151 West Yanjiang Road, Guangzhou, 510120, China
- Urology Key Laboratory of Guangdong Province, Guangzhou, 510120, China
| | - Di Gu
- Department of Urology, The First Affiliated Hospital of Guangzhou Medical University, 151 West Yanjiang Road, Guangzhou, 510120, China
- Urology Key Laboratory of Guangdong Province, Guangzhou, 510120, China
| | - Guohua Zeng
- Department of Urology, The First Affiliated Hospital of Guangzhou Medical University, 151 West Yanjiang Road, Guangzhou, 510120, China
- Urology Key Laboratory of Guangdong Province, Guangzhou, 510120, China
| | - Yongda Liu
- Department of Urology, The First Affiliated Hospital of Guangzhou Medical University, 151 West Yanjiang Road, Guangzhou, 510120, China.
- Urology Key Laboratory of Guangdong Province, Guangzhou, 510120, China.
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Ivanov KI, Samuilova OV, Zamyatnin AA. The emerging roles of long noncoding RNAs in lymphatic vascular development and disease. Cell Mol Life Sci 2023; 80:197. [PMID: 37407839 PMCID: PMC10322780 DOI: 10.1007/s00018-023-04842-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 06/06/2023] [Accepted: 06/19/2023] [Indexed: 07/07/2023]
Abstract
Recent advances in RNA sequencing technologies helped uncover what was once uncharted territory in the human genome-the complex and versatile world of long noncoding RNAs (lncRNAs). Previously thought of as merely transcriptional "noise", lncRNAs have now emerged as essential regulators of gene expression networks controlling development, homeostasis and disease progression. The regulatory functions of lncRNAs are broad and diverse, and the underlying molecular mechanisms are highly variable, acting at the transcriptional, post-transcriptional, translational, and post-translational levels. In recent years, evidence has accumulated to support the important role of lncRNAs in the development and functioning of the lymphatic vasculature and associated pathological processes such as tumor-induced lymphangiogenesis and cancer metastasis. In this review, we summarize the current knowledge on the role of lncRNAs in regulating the key genes and pathways involved in lymphatic vascular development and disease. Furthermore, we discuss the potential of lncRNAs as novel therapeutic targets and outline possible strategies for the development of lncRNA-based therapeutics to treat diseases of the lymphatic system.
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Affiliation(s)
- Konstantin I Ivanov
- Research Center for Translational Medicine, Sirius University of Science and Technology, Sochi, Russian Federation.
- Department of Microbiology, University of Helsinki, Helsinki, Finland.
| | - Olga V Samuilova
- Department of Biochemistry, Sechenov First Moscow State Medical University, Moscow, Russian Federation
- HSE University, Moscow, Russian Federation
| | - Andrey A Zamyatnin
- Research Center for Translational Medicine, Sirius University of Science and Technology, Sochi, Russian Federation
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russian Federation
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
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38
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Li Y, Zhai H, Tong L, Wang C, Xie Z, Zheng K. LncRNA Functional Screening in Organismal Development. Noncoding RNA 2023; 9:36. [PMID: 37489456 PMCID: PMC10366883 DOI: 10.3390/ncrna9040036] [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: 05/10/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/26/2023] Open
Abstract
Controversy continues over the functional prevalence of long non-coding RNAs (lncRNAs) despite their being widely investigated in all kinds of cells and organisms. In animals, lncRNAs have aroused general interest from exponentially increasing transcriptomic repertoires reporting their highly tissue-specific and developmentally dynamic expression, and more importantly, from growing experimental evidence supporting their functionality in facilitating organogenesis and individual fitness. In mammalian testes, while a great multitude of lncRNA species are identified, only a minority of them have been shown to be useful, and even fewer have been demonstrated as true requirements for male fertility using knockout models to date. This noticeable gap is attributed to the virtual existence of a large number of junk lncRNAs, the lack of an ideal germline culture system, difficulty in loss-of-function interrogation, and limited screening strategies. Facing these challenges, in this review, we discuss lncRNA functionality in organismal development and especially in mouse testis, with a focus on lncRNAs with functional screening.
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Affiliation(s)
- Yang Li
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
| | - Huicong Zhai
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
| | - Lingxiu Tong
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
| | - Cuicui Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
| | - Zhiming Xie
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
| | - Ke Zheng
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
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Yin Q, Ma H, Bamunuarachchi G, Zheng X, Ma Y. Long Non-Coding RNAs, Cell Cycle, and Human Breast Cancer. Hum Gene Ther 2023; 34:481-494. [PMID: 37243445 PMCID: PMC10398747 DOI: 10.1089/hum.2023.074] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 05/25/2023] [Indexed: 05/28/2023] Open
Abstract
The long non-coding RNAs (lncRNAs) constitute an important class of the human transcriptome. The discovery of lncRNAs provided one of many unexpected results of the post-genomic era and uncovered a huge number of previously ignored transcriptional events. In recent years, lncRNAs are known to be linked with human diseases, with particular focus on cancer. Growing evidence has indicated that dysregulation of lncRNAs in breast cancer (BC) is strongly associated with the occurrence, development, and progress. Increasing numbers of lncRNAs have been found to interact with cell cycle progression and tumorigenesis in BC. The lncRNAs can exert their effect as a tumor suppressor or oncogene and regulate tumor development through direct or indirect regulation of cancer-related modulators and signaling pathways. What is more, lncRNAs are excellent candidates for promising therapeutic targets in BC due to the features of high tissue and cell-type specific expression. However, the underlying mechanisms of lncRNAs in BC still remain largely undefined. Here, we concisely summarize and sort out the current understanding of research progress in relationships of the roles for lncRNA in regulating the cell cycle. We also summarize the evidence for aberrant lncRNA expression in BC, and the potential for lncRNA to improve BC therapy is also discussed. Together, lncRNAs can be considered as exciting therapeutic candidates whose expression can be altered to impede BC progression.
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Affiliation(s)
- Qinan Yin
- Precision Medicine Laboratory, College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
| | - Haodi Ma
- Precision Medicine Laboratory, College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
| | - Gayan Bamunuarachchi
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Xuewei Zheng
- Precision Medicine Laboratory, College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
| | - Yan Ma
- Spatial Navigation and Memory Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
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40
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Wang T, Xie ZH, Wang L, Luo H, Zhang J, Dong WT, Zheng XH, Ye C, Tian XB, Liu G, Zhu XS, Li YL, Kang QL, Zhang F, Peng WX. LncAABR07053481 inhibits bone marrow mesenchymal stem cell apoptosis and promotes repair following steroid-induced avascular necrosis. Commun Biol 2023; 6:365. [PMID: 37012358 PMCID: PMC10070412 DOI: 10.1038/s42003-023-04661-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 03/03/2023] [Indexed: 04/05/2023] Open
Abstract
The osteonecrotic area of steroid-induced avascular necrosis of the femoral head (SANFH) is a hypoxic microenvironment that leads to apoptosis of transplanted bone marrow mesenchymal stem cells (BMSCs). However, the underlying mechanism remains unclear. Here, we explore the mechanism of hypoxic-induced apoptosis of BMSCs, and use the mechanism to improve the transplantation efficacy of BMSCs. Our results show that the long non-coding RNA AABR07053481 (LncAABR07053481) is downregulated in BMSCs and closely related to the degree of hypoxia. Overexpression of LncAABR07053481 could increase the survival rate of BMSCs. Further exploration of the downstream target gene indicates that LncAABR07053481 acts as a molecular "sponge" of miR-664-2-5p to relieve the silencing effect of miR-664-2-5p on the target gene Notch1. Importantly, the survival rate of BMSCs overexpressing LncAABR07053481 is significantly improved after transplantation, and the repair effect of BMSCs in the osteonecrotic area is also improved. This study reveal the mechanism by which LncAABR07053481 inhibits hypoxia-induced apoptosis of BMSCs by regulating the miR-664-2-5p/Notch1 pathway and its therapeutic effect on SANFH.
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Affiliation(s)
- Tao Wang
- Department of Orthopedics and Traumatology, The Affliated Hospital of Guizhou Medical University, Guiyang, Guizhou, 550004, P.R. China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou, 550004, P.R. China
| | - Zhi-Hong Xie
- School of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou, 550004, P.R. China
| | - Lei Wang
- Department of Orthopedics and Traumatology, The Affliated Hospital of Guizhou Medical University, Guiyang, Guizhou, 550004, P.R. China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou, 550004, P.R. China
| | - Hong Luo
- School of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou, 550004, P.R. China
| | - Jian Zhang
- Department of Orthopedics and Traumatology, The Affliated Hospital of Guizhou Medical University, Guiyang, Guizhou, 550004, P.R. China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou, 550004, P.R. China
| | - Wen-Tao Dong
- Department of Orthopedics and Traumatology, The Affliated Hospital of Guizhou Medical University, Guiyang, Guizhou, 550004, P.R. China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou, 550004, P.R. China
| | - Xiao-Han Zheng
- Department of Orthopedics and Traumatology, The Affliated Hospital of Guizhou Medical University, Guiyang, Guizhou, 550004, P.R. China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou, 550004, P.R. China
| | - Chuan Ye
- Department of Orthopedics and Traumatology, The Affliated Hospital of Guizhou Medical University, Guiyang, Guizhou, 550004, P.R. China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou, 550004, P.R. China
| | - Xiao-Bin Tian
- Department of Orthopedics and Traumatology, The Affliated Hospital of Guizhou Medical University, Guiyang, Guizhou, 550004, P.R. China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou, 550004, P.R. China
| | - Gang Liu
- Department of Orthopedics and Traumatology, The Affliated Hospital of Guizhou Medical University, Guiyang, Guizhou, 550004, P.R. China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou, 550004, P.R. China
| | - Xue-Song Zhu
- Department of Orthopedic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215000, P.R. China
| | - Yan-Lin Li
- Department of Sports Medicine, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650000, P.R. China
| | - Qing-Lin Kang
- Department of Orthopedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, P.R. China
| | - Fei Zhang
- Department of Orthopedics and Traumatology, The Affliated Hospital of Guizhou Medical University, Guiyang, Guizhou, 550004, P.R. China.
- School of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou, 550004, P.R. China.
| | - Wu-Xun Peng
- Department of Orthopedics and Traumatology, The Affliated Hospital of Guizhou Medical University, Guiyang, Guizhou, 550004, P.R. China.
- School of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou, 550004, P.R. China.
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Johnson KC, Corey DR. RNAi in cell nuclei: potential for a new layer of biological regulation and a new strategy for therapeutic discovery. RNA (NEW YORK, N.Y.) 2023; 29:415-422. [PMID: 36657971 PMCID: PMC10019369 DOI: 10.1261/rna.079500.122] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
RNA interference is almost always associated with post-transcriptional silencing in the cytoplasm. MicroRNAs (miRNAs) and critical RNAi protein factors like argonaute (AGO) and trinucleotide repeat binding containing 6 protein (TNRC6), however, are also found in cell nuclei, suggesting that nuclear miRNAs may be targets for gene regulation. Designed small duplex RNAs (dsRNAs) can modulate nuclear processes such as transcription and splicing, suggesting that they can also provide leads for therapeutic discovery. The goal of this Perspective is to provide the background on nuclear RNAi necessary to guide discussions on whether nuclear RNAi can play a role in therapeutic development programs.
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Affiliation(s)
- Krystal C Johnson
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, Texas 75205, USA
| | - David R Corey
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, Texas 75205, USA
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42
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Kulkarni V, Jayakumar S, Mohan M, Kulkarni S. Aid or Antagonize: Nuclear Long Noncoding RNAs Regulate Host Responses and Outcomes of Viral Infections. Cells 2023; 12:987. [PMID: 37048060 PMCID: PMC10093752 DOI: 10.3390/cells12070987] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 03/12/2023] [Accepted: 03/15/2023] [Indexed: 04/14/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are transcripts measuring >200 bp in length and devoid of protein-coding potential. LncRNAs exceed the number of protein-coding mRNAs and regulate cellular, developmental, and immune pathways through diverse molecular mechanisms. In recent years, lncRNAs have emerged as epigenetic regulators with prominent roles in health and disease. Many lncRNAs, either host or virus-encoded, have been implicated in critical cellular defense processes, such as cytokine and antiviral gene expression, the regulation of cell signaling pathways, and the activation of transcription factors. In addition, cellular and viral lncRNAs regulate virus gene expression. Viral infections and associated immune responses alter the expression of host lncRNAs regulating immune responses, host metabolism, and viral replication. The influence of lncRNAs on the pathogenesis and outcomes of viral infections is being widely explored because virus-induced lncRNAs can serve as diagnostic and therapeutic targets. Future studies should focus on thoroughly characterizing lncRNA expressions in virus-infected primary cells, investigating their role in disease prognosis, and developing biologically relevant animal or organoid models to determine their suitability for specific therapeutic targeting. Many cellular and viral lncRNAs localize in the nucleus and epigenetically modulate viral transcription, latency, and host responses to infection. In this review, we provide an overview of the role of nuclear lncRNAs in the pathogenesis and outcomes of viral infections, such as the Influenza A virus, Sendai Virus, Respiratory Syncytial Virus, Hepatitis C virus, Human Immunodeficiency Virus, and Herpes Simplex Virus. We also address significant advances and barriers in characterizing lncRNA function and explore the potential of lncRNAs as therapeutic targets.
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Affiliation(s)
- Viraj Kulkarni
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA;
| | - Sahana Jayakumar
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (S.J.); (M.M.)
| | - Mahesh Mohan
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (S.J.); (M.M.)
| | - Smita Kulkarni
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (S.J.); (M.M.)
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43
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Fellah S, Larrue R, Truchi M, Vassaux G, Mari B, Cauffiez C, Pottier N. Pervasive role of the long noncoding RNA DNM3OS in development and diseases. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1736. [PMID: 35491542 DOI: 10.1002/wrna.1736] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/04/2022] [Accepted: 04/11/2022] [Indexed: 11/08/2022]
Abstract
Thousands of unique noncoding RNAs (ncRNAs) are expressed in human cells, some are tissue or cell type specific whereas others are considered as house-keeping molecules. Studies over the last decade have modified our perception of ncRNAs from transcriptional noise to functional regulatory transcripts that influence a variety of molecular processes such as chromatin remodeling, transcription, post-transcriptional modifications, or signal transduction. Consequently, aberrant expression of many ncRNAs plays a causative role in the initiation and progression of various diseases. Since the identification of its developmental role, the long ncRNA DNM3OS (Dynamin 3 Opposite Strand) has attracted attention of researchers in distinct fields including oncology, fibroproliferative diseases, or bone disorders. Mechanistic studies have in particular revealed the multifaceted nature of DNM3OS and its important pathogenic role in several human disorders. In this review, we summarize the current knowledge of DNM3OS functions in diseases, with an emphasis on its potential as a novel therapeutic target. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Sandy Fellah
- University of Lille, CNRS, Inserm, CHU Lille, UMR9020-UMR-S 1277, Lille, France
| | - Romain Larrue
- University of Lille, CNRS, Inserm, CHU Lille, UMR9020-UMR-S 1277, Lille, France
| | - Marin Truchi
- Université Côte d'Azur, CNRS UMR7275, IPMC, Valbonne, France
| | - Georges Vassaux
- Université Côte d'Azur, CNRS UMR7275, IPMC, Valbonne, France
| | - Bernard Mari
- Université Côte d'Azur, CNRS UMR7275, IPMC, Valbonne, France
| | - Christelle Cauffiez
- University of Lille, CNRS, Inserm, CHU Lille, UMR9020-UMR-S 1277, Lille, France
| | - Nicolas Pottier
- University of Lille, CNRS, Inserm, CHU Lille, UMR9020-UMR-S 1277, Lille, France
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Emerging RNA-Based Therapeutic and Diagnostic Options: Recent Advances and Future Challenges in Genitourinary Cancers. Int J Mol Sci 2023; 24:ijms24054601. [PMID: 36902032 PMCID: PMC10003365 DOI: 10.3390/ijms24054601] [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: 12/01/2022] [Revised: 02/15/2023] [Accepted: 02/23/2023] [Indexed: 03/02/2023] Open
Abstract
Renal cell carcinoma, bladder cancer, and prostate cancer are the most widespread genitourinary tumors. Their treatment and diagnosis have significantly evolved over recent years, due to an increasing understanding of oncogenic factors and the molecular mechanisms involved. Using sophisticated genome sequencing technologies, the non-coding RNAs, such as microRNAs, long non-coding RNAs, and circular RNAs, have all been implicated in the occurrence and progression of genitourinary cancers. Interestingly, DNA, protein, and RNA interactions with lncRNAs and other biological macromolecules drive some of these cancer phenotypes. Studies on the molecular mechanisms of lncRNAs have identified new functional markers that could be potentially useful as biomarkers for effective diagnosis and/or as targets for therapeutic intervention. This review focuses on the mechanisms underlying abnormal lncRNA expression in genitourinary tumors and discusses their role in diagnostics, prognosis, and treatment.
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45
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Tang J, Wang X, Xiao D, Liu S, Tao Y. The chromatin-associated RNAs in gene regulation and cancer. Mol Cancer 2023; 22:27. [PMID: 36750826 PMCID: PMC9903551 DOI: 10.1186/s12943-023-01724-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/16/2023] [Indexed: 02/09/2023] Open
Abstract
Eukaryotic genomes are prevalently transcribed into many types of RNAs that translate into proteins or execute gene regulatory functions. Many RNAs associate with chromatin directly or indirectly and are called chromatin-associated RNAs (caRNAs). To date, caRNAs have been found to be involved in gene and transcriptional regulation through multiple mechanisms and have important roles in different types of cancers. In this review, we first present different categories of caRNAs and the modes of interaction between caRNAs and chromatin. We then detail the mechanisms of chromatin-associated nascent RNAs, chromatin-associated noncoding RNAs and emerging m6A on caRNAs in transcription and gene regulation. Finally, we discuss the roles of caRNAs in cancer as well as epigenetic and epitranscriptomic mechanisms contributing to cancer, which could provide insights into the relationship between different caRNAs and cancer, as well as tumor treatment and intervention.
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Affiliation(s)
- Jun Tang
- grid.216417.70000 0001 0379 7164Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078 Hunan China ,grid.216417.70000 0001 0379 7164Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, 410078 Hunan China
| | - Xiang Wang
- grid.216417.70000 0001 0379 7164Department of Thoracic Surgery, Hunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung Cancer, Second Xiangya Hospital, Central South University, Changsha, 410011 China
| | - Desheng Xiao
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Shuang Liu
- Department of Oncology, Institute of Medical Sciences, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Yongguang Tao
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, Hunan, China. .,Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, 410078, Hunan, China. .,Department of Thoracic Surgery, Hunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung Cancer, Second Xiangya Hospital, Central South University, Changsha, 410011, China. .,Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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46
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Wang H, Su Y, Chen D, Li Q, Shi S, Huang X, Fang M, Yang M. Advances in the mechanisms and applications of inhibitory oligodeoxynucleotides against immune-mediated inflammatory diseases. Front Pharmacol 2023; 14:1119431. [PMID: 36825156 PMCID: PMC9941346 DOI: 10.3389/fphar.2023.1119431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/26/2023] [Indexed: 02/09/2023] Open
Abstract
Inhibitory oligodeoxynucleotides (ODNs) are short single-stranded DNA, which capable of folding into complex structures, enabling them to bind to a large variety of targets. With appropriate modifications, the inhibitory oligodeoxynucleotides exhibited many features of long half-life time, simple production, low toxicity and immunogenicity. In recent years, inhibitory oligodeoxynucleotides have received considerable attention for their potential therapeutic applications in immune-mediated inflammatory diseases (IMIDs). Inhibitory oligodeoxynucleotides could be divided into three categories according to its mechanisms and targets, including antisense ODNs (AS-ODNs), DNA aptamers and immunosuppressive ODNs (iSup ODNs). As a synthetic tool with immunomodulatory activity, it can target RNAs or proteins in a specific way, resulting in the reduction, increase or recovery of protein expression, and then regulate the state of immune activation. More importantly, inhibitory oligodeoxynucleotides have been used to treat immune-mediated inflammatory diseases, including inflammatory disorders and autoimmune diseases. Several inhibitory oligodeoxynucleotide drugs have been developed and approved on the market already. These drugs vary in their chemical structures, action mechanisms and cellular targets, but all of them could be capable of inhibiting excessive inflammatory responses. This review summarized their chemical modifications, action mechanisms and applications of the three kinds of inhibitory oligodeoxynucleotidesin the precise treatment of immune-mediated inflammatory diseases.
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Affiliation(s)
- Hongrui Wang
- Department of Molecular Biology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, China
| | - Yingying Su
- Department of Anatomy, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, China
| | - Duoduo Chen
- Department of Molecular Biology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, China
| | - Qi Li
- Department of Molecular Biology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, China
| | - Shuyou Shi
- Department of Molecular Biology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, China
| | - Xin Huang
- Department of Molecular Biology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, China
| | - Mingli Fang
- Department of Molecular Biology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, China,*Correspondence: Mingli Fang, ; Ming Yang,
| | - Ming Yang
- Department of Molecular Biology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, China,*Correspondence: Mingli Fang, ; Ming Yang,
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47
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Emami Meybodi SM, Soleimani N, Yari A, Javadifar A, Tollabi M, Karimi B, Emami Meybodi M, Seyedhossaini S, Brouki Milan P, Dehghani Firoozabadi A. Circulatory long noncoding RNAs (circulatory-LNC-RNAs) as novel biomarkers and therapeutic targets in cardiovascular diseases: Implications for cardiovascular diseases complications. Int J Biol Macromol 2023; 225:1049-1071. [PMID: 36414082 DOI: 10.1016/j.ijbiomac.2022.11.167] [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: 09/28/2022] [Accepted: 11/16/2022] [Indexed: 11/21/2022]
Abstract
Cardiovascular diseases (CVDs) are a group of disorders with major global health consequences. The prevalence of CVDs continues to grow due to population-aging and lifestyle modifications. Non-coding RNAs (ncRNAs) as key regulators of cell signaling pathways have gained attention in the occurrence and development of CVDs. Exosomal-lncRNAs (exos-lncRNAs) are emerging biomarkers due to their high sensitivity and specificity, stability, accuracy and accessibility in the biological fluids. Recently, circulatory and exos-based-lncRNAs are emerging and novel bio-tools in various pathogenic conditions. It is worth mentioning that dysregulation of these molecules has been found in different types of CVDs. In this regard, we aimed to discuss the knowledge gaps and suggest research priorities regarding circulatory and exos-lncRNAs as novel bio-tools and therapeutic targets for CVDs.
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Affiliation(s)
- Seyed Mahdi Emami Meybodi
- Yazd Cardiovascular Research Center, Non-communicable Diseases Research Institute, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
| | - Nafiseh Soleimani
- Yazd Cardiovascular Research Center, Non-communicable Diseases Research Institute, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
| | - Abolfazl Yari
- Cellular and Molecular Research Center, Birjand University of Medical Mciences, Birjand, Iran.
| | - Amin Javadifar
- Immunology Research Center, Inflammation and Inflammatory Disease Division, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Mohammad Tollabi
- Department of Tissue Engineering & Regenerative Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran; Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran.
| | - Bahareh Karimi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Mahmoud Emami Meybodi
- Yazd Cardiovascular Research Center, Non-communicable Diseases Research Institute, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
| | - Seyedmostafa Seyedhossaini
- Yazd Cardiovascular Research Center, Non-communicable Diseases Research Institute, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
| | - Peiman Brouki Milan
- Department of Tissue Engineering & Regenerative Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran; Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran.
| | - Ali Dehghani Firoozabadi
- Department of Tissue Engineering & Regenerative Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran; Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran.
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48
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Kumar D, Sahoo SS, Chauss D, Kazemian M, Afzali B. Non-coding RNAs in immunoregulation and autoimmunity: Technological advances and critical limitations. J Autoimmun 2023; 134:102982. [PMID: 36592512 PMCID: PMC9908861 DOI: 10.1016/j.jaut.2022.102982] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/11/2022] [Accepted: 12/15/2022] [Indexed: 01/02/2023]
Abstract
Immune cell function is critically dependent on precise control over transcriptional output from the genome. In this respect, integration of environmental signals that regulate gene expression, specifically by transcription factors, enhancer DNA elements, genome topography and non-coding RNAs (ncRNAs), are key components. The first three have been extensively investigated. Even though non-coding RNAs represent the vast majority of cellular RNA species, this class of RNA remains historically understudied. This is partly because of a lag in technological and bioinformatic innovations specifically capable of identifying and accurately measuring their expression. Nevertheless, recent progress in this domain has enabled a profusion of publications identifying novel sub-types of ncRNAs and studies directly addressing the function of ncRNAs in human health and disease. Many ncRNAs, including circular and enhancer RNAs, have now been demonstrated to play key functions in the regulation of immune cells and to show associations with immune-mediated diseases. Some ncRNAs may function as biomarkers of disease, aiding in diagnostics and in estimating response to treatment, while others may play a direct role in the pathogenesis of disease. Importantly, some are relatively stable and are amenable to therapeutic targeting, for example through gene therapy. Here, we provide an overview of ncRNAs and review technological advances that enable their study and hold substantial promise for the future. We provide context-specific examples by examining the associations of ncRNAs with four prototypical human autoimmune diseases, specifically rheumatoid arthritis, psoriasis, inflammatory bowel disease and multiple sclerosis. We anticipate that the utility and mechanistic roles of these ncRNAs in autoimmunity will be further elucidated in the near future.
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Affiliation(s)
- Dhaneshwar Kumar
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA
| | - Subhransu Sekhar Sahoo
- Departments of Biochemistry and Computer Science, Purdue University, West Lafayette, IN, USA
| | - Daniel Chauss
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA
| | - Majid Kazemian
- Departments of Biochemistry and Computer Science, Purdue University, West Lafayette, IN, USA
| | - Behdad Afzali
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA.
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49
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Løvendorf MB, Holm A, Petri A, Thrue CA, Uchida S, Venø MT, Kauppinen S. Knockdown of Circular RNAs Using LNA-Modified Antisense Oligonucleotides. Nucleic Acid Ther 2023; 33:45-57. [PMID: 36445751 DOI: 10.1089/nat.2022.0040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Circular RNAs (circRNAs) constitute an abundant class of covalently closed noncoding RNA molecules that are formed by backsplicing from eukaryotic protein-coding genes. Recent studies have shown that circRNAs can act as microRNA or protein decoys, as well as transcriptional regulators. However, the functions of most circRNAs are still poorly understood. Because circRNA sequences overlap with their linear parent transcripts, depleting specific circRNAs without affecting host gene expression remains a challenge. In this study, we assessed the utility of LNA-modified antisense oligonucleotides (ASOs) to knock down circRNAs for loss-of-function studies. We found that, while most RNase H-dependent gapmer ASOs mediate effective knockdown of their target circRNAs, some gapmers reduce the levels of the linear parent transcript. The circRNA targeting specificity can be enhanced using design-optimized gapmer ASOs, which display potent and specific circRNA knockdown with a minimal effect on the host genes. In summary, our results demonstrate that LNA-modified ASOs complementary to backsplice-junction sequences mediate robust knockdown of circRNAs in vitro and, thus, represent a useful tool to explore the biological roles of circRNAs in loss-of-function studies in cultured cells and animal models.
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Affiliation(s)
| | - Anja Holm
- Department of Clinical Medicine, Center for RNA Medicine, Aalborg University, Copenhagen, Denmark.,Department of Clinical Experimental Research, Rigshopitalet, Glostrup, Denmark
| | - Andreas Petri
- Department of Clinical Medicine, Center for RNA Medicine, Aalborg University, Copenhagen, Denmark
| | - Charlotte Albæk Thrue
- Department of Clinical Medicine, Center for RNA Medicine, Aalborg University, Copenhagen, Denmark
| | - Shizuka Uchida
- Department of Clinical Medicine, Center for RNA Medicine, Aalborg University, Copenhagen, Denmark
| | | | - Sakari Kauppinen
- Department of Clinical Medicine, Center for RNA Medicine, Aalborg University, Copenhagen, Denmark
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50
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Yip CW, Hon CC, Yasuzawa K, Sivaraman DM, Ramilowski JA, Shibayama Y, Agrawal S, Prabhu AV, Parr C, Severin J, Lan YJ, Dostie J, Petri A, Nishiyori-Sueki H, Tagami M, Itoh M, López-Redondo F, Kouno T, Chang JC, Luginbühl J, Kato M, Murata M, Yip WH, Shu X, Abugessaisa I, Hasegawa A, Suzuki H, Kauppinen S, Yagi K, Okazaki Y, Kasukawa T, de Hoon M, Carninci P, Shin JW. Antisense-oligonucleotide-mediated perturbation of long non-coding RNA reveals functional features in stem cells and across cell types. Cell Rep 2022; 41:111893. [PMID: 36577377 DOI: 10.1016/j.celrep.2022.111893] [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: 04/12/2022] [Revised: 08/30/2022] [Accepted: 12/07/2022] [Indexed: 12/28/2022] Open
Abstract
Within the scope of the FANTOM6 consortium, we perform a large-scale knockdown of 200 long non-coding RNAs (lncRNAs) in human induced pluripotent stem cells (iPSCs) and systematically characterize their roles in self-renewal and pluripotency. We find 36 lncRNAs (18%) exhibiting cell growth inhibition. From the knockdown of 123 lncRNAs with transcriptome profiling, 36 lncRNAs (29.3%) show molecular phenotypes. Integrating the molecular phenotypes with chromatin-interaction assays further reveals cis- and trans-interacting partners as potential primary targets. Additionally, cell-type enrichment analysis identifies lncRNAs associated with pluripotency, while the knockdown of LINC02595, CATG00000090305.1, and RP11-148B6.2 modulates colony formation of iPSCs. We compare our results with previously published fibroblasts phenotyping data and find that 2.9% of the lncRNAs exhibit a consistent cell growth phenotype, whereas we observe 58.3% agreement in molecular phenotypes. This highlights that molecular phenotyping is more comprehensive in revealing affected pathways.
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Affiliation(s)
- Chi Wai Yip
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Chung-Chau Hon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Kayoko Yasuzawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Divya M Sivaraman
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695 011, India
| | - Jordan A Ramilowski
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Advanced Medical Research Center, Yokohama City University, Yokohama, Kanagawa 236-0004, Japan
| | - Youtaro Shibayama
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Saumya Agrawal
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Anika V Prabhu
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Callum Parr
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Jessica Severin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Yan Jun Lan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Josée Dostie
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Research Center, McGill University, Montréal, QC, Canada
| | - Andreas Petri
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen 2450, Denmark
| | | | - Michihira Tagami
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Masayoshi Itoh
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | | | - Tsukasa Kouno
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Jen-Chien Chang
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Joachim Luginbühl
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Masaki Kato
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Mitsuyoshi Murata
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Wing Hin Yip
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Xufeng Shu
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Department of Computational Biology and Medical Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Imad Abugessaisa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Akira Hasegawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Harukazu Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Sakari Kauppinen
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen 2450, Denmark
| | - Ken Yagi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Yasushi Okazaki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Michiel de Hoon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Human Technopole, via Rita Levi Montalcini 1, Milan, Italy
| | - Jay W Shin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672, Singapore.
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