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Jahanbani I, Almoualem N, Al-Abdallah A. Evaluation of reference genes suitable for studying mRNAs and microRNAs expression in thyroid neoplasms. Pathol Res Pract 2024; 262:155519. [PMID: 39173468 DOI: 10.1016/j.prp.2024.155519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 07/31/2024] [Accepted: 08/09/2024] [Indexed: 08/24/2024]
Abstract
Analysis of gene expression is a pivotal method at the core of biomarkers studies and cancer research. Currently, RT-qPCR is the most commonly used technique to investigate the expression of certain genes. The accurate and reliable result relies on an effective normalization step using suitable reference genes. The present study was designed to evaluate the eligibility of a set of candidate mRNAs and snoRNA as reference genes in the most common human thyroid neoplasms. We tested the expression levels of eleven mRNA and small RNA housekeeping genes in thyroid samples. The stability of the candidate genes was examined in different thyroid lesions and under different experimental conditions. Results were compared to the reported data in the TCGA database. Our results suggested HPRT1 and ACTB as the best mRNA reference genes, SNORD96A, and SNORD95 as the best miRNA reference genes in thyroid tissues. These genes showed the most stable expression pattern among different thyroid lesions as well as different experimental conditions. The findings in this study highlight the effect of reference genes selection on data interpretation and emphasize the importance of testing for suitable reference genes to be used in specific types of cells and experimental conditions to ensure the validity and accuracy of results.
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Affiliation(s)
- Iman Jahanbani
- Pathology Department, Faculty of Medicine, Kuwait University, Kuwait.
| | - Nada Almoualem
- Pathology Department, Faculty of Medicine, Kuwait University, Kuwait.
| | - Abeer Al-Abdallah
- Pathology Department, Faculty of Medicine, Kuwait University, Kuwait.
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2
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Jusic A, Erpapazoglou Z, Dalgaard LT, Lakkisto P, de Gonzalo-Calvo D, Benczik B, Ágg B, Ferdinandy P, Fiedorowicz K, Schroen B, Lazou A, Devaux Y. Guidelines for mitochondrial RNA analysis. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102262. [PMID: 39091381 PMCID: PMC11292373 DOI: 10.1016/j.omtn.2024.102262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Mitochondria are the energy-producing organelles of mammalian cells with critical involvement in metabolism and signaling. Studying their regulation in pathological conditions may lead to the discovery of novel drugs to treat, for instance, cardiovascular or neurological diseases, which affect high-energy-consuming cells such as cardiomyocytes, hepatocytes, or neurons. Mitochondria possess both protein-coding and noncoding RNAs, such as microRNAs, long noncoding RNAs, circular RNAs, and piwi-interacting RNAs, encoded by the mitochondria or the nuclear genome. Mitochondrial RNAs are involved in anterograde-retrograde communication between the nucleus and mitochondria and play an important role in physiological and pathological conditions. Despite accumulating evidence on the presence and biogenesis of mitochondrial RNAs, their study continues to pose significant challenges. Currently, there are no standardized protocols and guidelines to conduct deep functional characterization and expression profiling of mitochondrial RNAs. To overcome major obstacles in this emerging field, the EU-CardioRNA and AtheroNET COST Action networks summarize currently available techniques and emphasize critical points that may constitute sources of variability and explain discrepancies between published results. Standardized methods and adherence to guidelines to quantify and study mitochondrial RNAs in normal and disease states will improve research outputs, their reproducibility, and translation potential to clinical application.
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Affiliation(s)
- Amela Jusic
- HAYA Therapeutics SA, Route De La Corniche 6, SuperLab Suisse - Batiment Serine, 1066 Epalinges, Switzerland
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, 1445 Strassen, Luxembourg
| | - Zoi Erpapazoglou
- Ιnstitute for Fundamental Biomedical Research, B.S.R.C. “Alexander Fleming”, Vari, 16672 Athens, Greece
| | - Louise Torp Dalgaard
- Department of Science and Environment, Roskilde University, 4000 Roskilde, Denmark
| | - Päivi Lakkisto
- Minerva Foundation Institute for Medical Research, 00290 Helsinki, Finland
- Department of Clinical Chemistry, University of Helsinki and Helsinki University Hospital, 00014 Helsinki, Finland
| | - David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, 25198 Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Bettina Benczik
- Cardiometabolic and HUN-REN-SU System Pharmacology Research Group, Center for Pharmacology and Drug Research & Development, Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1089 Budapest, Hungary
- Pharmahungary Group, 6722 Szeged, Hungary
| | - Bence Ágg
- Cardiometabolic and HUN-REN-SU System Pharmacology Research Group, Center for Pharmacology and Drug Research & Development, Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1089 Budapest, Hungary
- Pharmahungary Group, 6722 Szeged, Hungary
| | - Péter Ferdinandy
- Cardiometabolic and HUN-REN-SU System Pharmacology Research Group, Center for Pharmacology and Drug Research & Development, Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1089 Budapest, Hungary
- Pharmahungary Group, 6722 Szeged, Hungary
| | | | - Blanche Schroen
- Department of Physiology, Cardiovascular Research Institute Maastricht, Maastricht University, ER 6229 Maastricht, the Netherlands
| | - Antigone Lazou
- School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, 1445 Strassen, Luxembourg
| | - on behalf of EU-CardioRNA COST Action CA17129
- HAYA Therapeutics SA, Route De La Corniche 6, SuperLab Suisse - Batiment Serine, 1066 Epalinges, Switzerland
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, 1445 Strassen, Luxembourg
- Ιnstitute for Fundamental Biomedical Research, B.S.R.C. “Alexander Fleming”, Vari, 16672 Athens, Greece
- Department of Science and Environment, Roskilde University, 4000 Roskilde, Denmark
- Minerva Foundation Institute for Medical Research, 00290 Helsinki, Finland
- Department of Clinical Chemistry, University of Helsinki and Helsinki University Hospital, 00014 Helsinki, Finland
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, 25198 Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain
- Cardiometabolic and HUN-REN-SU System Pharmacology Research Group, Center for Pharmacology and Drug Research & Development, Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1089 Budapest, Hungary
- Pharmahungary Group, 6722 Szeged, Hungary
- NanoBioMedical Centre, Adam Mickiewicz University in Poznan, 61614 Poznan, Poland
- Department of Physiology, Cardiovascular Research Institute Maastricht, Maastricht University, ER 6229 Maastricht, the Netherlands
- School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - AtheroNET COST Action CA21153
- HAYA Therapeutics SA, Route De La Corniche 6, SuperLab Suisse - Batiment Serine, 1066 Epalinges, Switzerland
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, 1445 Strassen, Luxembourg
- Ιnstitute for Fundamental Biomedical Research, B.S.R.C. “Alexander Fleming”, Vari, 16672 Athens, Greece
- Department of Science and Environment, Roskilde University, 4000 Roskilde, Denmark
- Minerva Foundation Institute for Medical Research, 00290 Helsinki, Finland
- Department of Clinical Chemistry, University of Helsinki and Helsinki University Hospital, 00014 Helsinki, Finland
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, 25198 Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain
- Cardiometabolic and HUN-REN-SU System Pharmacology Research Group, Center for Pharmacology and Drug Research & Development, Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1089 Budapest, Hungary
- Pharmahungary Group, 6722 Szeged, Hungary
- NanoBioMedical Centre, Adam Mickiewicz University in Poznan, 61614 Poznan, Poland
- Department of Physiology, Cardiovascular Research Institute Maastricht, Maastricht University, ER 6229 Maastricht, the Netherlands
- School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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Lee EJ, Jeong M, Lee H, Je MA, Park K, Lee DG, Xuan X, Kim S, Park S, Kim J. MiR-122, miR-133a, and miR-206 as potential biomarkers for post-mortem interval estimation. Genes Genomics 2024:10.1007/s13258-024-01559-x. [PMID: 39207675 DOI: 10.1007/s13258-024-01559-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Accepted: 08/12/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUD Accurate estimation of post-mortem interval (PMI) is crucial in forensic investigations. MicroRNAs (miRNAs or miRs) are small non-coding RNAs that remain relatively stable within the cell nucleus despite post-mortem changes. OBJECTIVE We assessed three target genes (miR-122, miR-133a, and miR-206) for PMI estimation using 72 healthy adult male BALB/c mice exposed to two different temperatures (4 and 21℃) at nine different time points over 10 days. METHODS Initially, the stability of the two reference genes (RNU6B and 5 srRNA) was evaluated using gene stability analysis tools (Delta Ct, Best Keeper, and Genorm) to select the optimal reference gene. RNU6B was found to be the most stable endogenous control. Subsequently, the expression patterns of miR-122, miR-133a, and miR-206 were analyzed within a 10-day PMI period using the heart, skeletal muscle, liver, and brain tissues. RESULTS At 4℃, miR-122 levels significantly decreased on days 8 and 10 in all tissues, with only the liver showing significant changes at 21℃. MiR-133a decreased over time in the heart, muscles, and brain, showing a dramatic decrease on days 8 and 10 in the heart and muscles at both temperatures. Although miR-206 levels decreased over time in muscles and liver at 4 ℃, these increased in the brain at 21 ℃, with no expression changes in other organs. CONCLUSION In summary, miR-122, miR-133a, and miR-206 are potential PMI markers in heart and skeletal muscle tissues.
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Affiliation(s)
- Eun Ju Lee
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan, 46252, Republic of Korea
- Department of Research and Development, Korea Mycobacterium Resource Center (KMRC), The Korean Institute of Tuberculosis, Osong, 28158, Republic of Korea
| | - Mingyoung Jeong
- Department of Forensic Science, Graduate School, Catholic University of Pusan, Busan, 46252, Republic of Korea
| | - Haneul Lee
- Department of Forensic Science, Graduate School, Catholic University of Pusan, Busan, 46252, Republic of Korea
- Next-Generation Industrial Field-Based Specialist Program for Molecular Diagnostics, Brain Busan 21 Plus Project, Graduate School, Catholic University of Pusan, Busan, 46252, Republic of Korea
| | - Min-A Je
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan, 46252, Republic of Korea
| | - Kwangmin Park
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan, 46252, Republic of Korea
- Next-Generation Industrial Field-Based Specialist Program for Molecular Diagnostics, Brain Busan 21 Plus Project, Graduate School, Catholic University of Pusan, Busan, 46252, Republic of Korea
| | - Dong Geon Lee
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan, 46252, Republic of Korea
- Next-Generation Industrial Field-Based Specialist Program for Molecular Diagnostics, Brain Busan 21 Plus Project, Graduate School, Catholic University of Pusan, Busan, 46252, Republic of Korea
| | - Xianglan Xuan
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan, 46252, Republic of Korea
- Next-Generation Industrial Field-Based Specialist Program for Molecular Diagnostics, Brain Busan 21 Plus Project, Graduate School, Catholic University of Pusan, Busan, 46252, Republic of Korea
| | - Sunghyun Kim
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan, 46252, Republic of Korea
- Department of Forensic Science, Graduate School, Catholic University of Pusan, Busan, 46252, Republic of Korea
- Next-Generation Industrial Field-Based Specialist Program for Molecular Diagnostics, Brain Busan 21 Plus Project, Graduate School, Catholic University of Pusan, Busan, 46252, Republic of Korea
| | - Sunyoung Park
- School of Mechanical Engineering, Yonsei University, Seoul, 03772, Republic of Korea.
| | - Jungho Kim
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan, 46252, Republic of Korea.
- Department of Forensic Science, Graduate School, Catholic University of Pusan, Busan, 46252, Republic of Korea.
- Next-Generation Industrial Field-Based Specialist Program for Molecular Diagnostics, Brain Busan 21 Plus Project, Graduate School, Catholic University of Pusan, Busan, 46252, Republic of Korea.
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Chung J, Xiao S, Gao Y, Soung YH. Recent Technologies towards Diagnostic and Therapeutic Applications of Circulating Nucleic Acids in Colorectal Cancers. Int J Mol Sci 2024; 25:8703. [PMID: 39201393 PMCID: PMC11354501 DOI: 10.3390/ijms25168703] [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: 07/12/2024] [Revised: 07/30/2024] [Accepted: 08/05/2024] [Indexed: 09/02/2024] Open
Abstract
Liquid biopsy has emerged as a promising noninvasive approach for colorectal cancer (CRC) management. This review focuses on technologies detecting circulating nucleic acids, specifically circulating tumor DNA (ctDNA) and circulating RNA (cfRNA), as CRC biomarkers. Recent advancements in molecular technologies have enabled sensitive and specific detection of tumor-derived genetic material in bodily fluids. These include quantitative real-time PCR, digital PCR, next-generation sequencing (NGS), and emerging nanotechnology-based methods. For ctDNA analysis, techniques such as BEAMing and droplet digital PCR offer high sensitivity in detecting rare mutant alleles, while NGS approaches provide comprehensive genomic profiling. cfRNA detection primarily utilizes qRT-PCR arrays, microarray platforms, and RNA sequencing for profiling circulating microRNAs and discovering novel RNA biomarkers. These technologies show potential in early CRC detection, treatment response monitoring, minimal residual disease assessment, and tumor evolution tracking. However, challenges remain in standardizing procedures, optimizing detection limits, and establishing clinical utility across disease stages. This review summarizes current circulating nucleic acid detection technologies, their CRC applications, and discusses future directions for clinical implementation.
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Affiliation(s)
| | | | | | - Young Hwa Soung
- Department of Pathology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA; (J.C.); (S.X.); (Y.G.)
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Hacimoto SYS, Cressoni ACL, da Silva LECM, Padovan CC, Ferriani RA, Rosa-e-Silva JC, Meola J. Selection of reference miRNAs for RT-qPCR assays in endometriosis menstrual blood-derived mesenchymal stem cells. PLoS One 2024; 19:e0306657. [PMID: 39078824 PMCID: PMC11288454 DOI: 10.1371/journal.pone.0306657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 06/20/2024] [Indexed: 08/02/2024] Open
Abstract
Choosing appropriate reference genes or internal controls to normalize RT-qPCR data is mandatory for the interexperimental reproducibility of gene expression data obtained by RT-qPCR in most studies, including those on endometriosis. Particularly for miRNAs, the choice for reference genes is challenging because of their physicochemical and biological characteristics. Moreover, the retrograde menstruation theory, mesenchymal stem cells in menstrual blood (MenSCs), and changes in post-transcriptional regulatory processes through miRNAs have gained prominence in the scientific community as important players in endometriosis. Therefore, we originally explored the stability of 10 miRNAs expressions as internal control candidates in conditions involving the two-dimensional culture of MenSCs from healthy women and patients with endometriosis. Here, we applied multiple algorithms (geNorm, NormFinder, Bestkeeper, and delta Ct) to screen reference genes and assessed the comprehensive stability classification of miRNAs using RefFinder. Pairwise variation calculated using geNorm identified three miRNAs as a sufficient number of reference genes for accurate normalization. MiR-191-5p, miR-24-3p, and miR-103a-3p were the best combination for suitable gene expression normalization. This study will benefit similar research, but is also attractive for regenerative medicine and clinics that use MenSCs, miRNA expression, and RT-qPCR.
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Affiliation(s)
- Sabrina Yukari Santos Hacimoto
- Department of Gynecology and Obstetrics of Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Ana Clara Lagazzi Cressoni
- Department of Gynecology and Obstetrics of Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | | | - Cristiana Carolina Padovan
- Department of Gynecology and Obstetrics of Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Rui Alberto Ferriani
- Department of Gynecology and Obstetrics of Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- National Institute of Hormones and Women’s Health (Hormona), CNPq, Porto Alegre, Rio Grande do Sul, Brazil
| | - Júlio César Rosa-e-Silva
- Department of Gynecology and Obstetrics of Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Juliana Meola
- Department of Gynecology and Obstetrics of Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- National Institute of Hormones and Women’s Health (Hormona), CNPq, Porto Alegre, Rio Grande do Sul, Brazil
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6
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Chauhan W, Sudharshan SJ, Kafle S, Zennadi R. SnoRNAs: Exploring Their Implication in Human Diseases. Int J Mol Sci 2024; 25:7202. [PMID: 39000310 PMCID: PMC11240930 DOI: 10.3390/ijms25137202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 07/16/2024] Open
Abstract
Small nucleolar RNAs (snoRNAs) are earning increasing attention from research communities due to their critical role in the post-transcriptional modification of various RNAs. These snoRNAs, along with their associated proteins, are crucial in regulating the expression of a vast array of genes in different human diseases. Primarily, snoRNAs facilitate modifications such as 2'-O-methylation, N-4-acetylation, and pseudouridylation, which impact not only ribosomal RNA (rRNA) and their synthesis but also different RNAs. Functionally, snoRNAs bind with core proteins to form small nucleolar ribonucleoproteins (snoRNPs). These snoRNAs then direct the protein complex to specific sites on target RNA molecules where modifications are necessary for either standard cellular operations or the regulation of pathological mechanisms. At these targeted sites, the proteins coupled with snoRNPs perform the modification processes that are vital for controlling cellular functions. The unique characteristics of snoRNAs and their involvement in various non-metabolic and metabolic diseases highlight their potential as therapeutic targets. Moreover, the precise targeting capability of snoRNAs might be harnessed as a molecular tool to therapeutically address various disease conditions. This review delves into the role of snoRNAs in health and disease and explores the broad potential of these snoRNAs as therapeutic agents in human pathologies.
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Affiliation(s)
| | | | | | - Rahima Zennadi
- Department of Physiology, University of Tennessee Health Science Center, 71 S. Manassas St., Memphis, TN 38103, USA; (W.C.); (S.S.); (S.K.)
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Corell-Sierra J, Marquez-Molins J, Marqués MC, Hernandez-Azurdia AG, Montagud-Martínez R, Cebriá-Mendoza M, Cuevas JM, Albert E, Navarro D, Rodrigo G, Gómez G. SARS-CoV-2 remodels the landscape of small non-coding RNAs with infection time and symptom severity. NPJ Syst Biol Appl 2024; 10:41. [PMID: 38632240 PMCID: PMC11024147 DOI: 10.1038/s41540-024-00367-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
The COVID-19 pandemic caused by the coronavirus SARS-CoV-2 has significantly impacted global health, stressing the necessity of basic understanding of the host response to this viral infection. In this study, we investigated how SARS-CoV-2 remodels the landscape of small non-coding RNAs (sncRNA) from a large collection of nasopharyngeal swab samples taken at various time points from patients with distinct symptom severity. High-throughput RNA sequencing analysis revealed a global alteration of the sncRNA landscape, with abundance peaks related to species of 21-23 and 32-33 nucleotides. Host-derived sncRNAs, including microRNAs (miRNAs), transfer RNA-derived small RNAs (tsRNAs), and small nucleolar RNA-derived small RNAs (sdRNAs) exhibited significant differential expression in infected patients compared to controls. Importantly, miRNA expression was predominantly down-regulated in response to SARS-CoV-2 infection, especially in patients with severe symptoms. Furthermore, we identified specific tsRNAs derived from Glu- and Gly-tRNAs as major altered elements upon infection, with 5' tRNA halves being the most abundant species and suggesting their potential as biomarkers for viral presence and disease severity prediction. Additionally, down-regulation of C/D-box sdRNAs and altered expression of tinyRNAs (tyRNAs) were observed in infected patients. These findings provide valuable insights into the host sncRNA response to SARS-CoV-2 infection and may contribute to the development of further diagnostic and therapeutic strategies in the clinic.
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Affiliation(s)
- Julia Corell-Sierra
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain
| | - Joan Marquez-Molins
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - María-Carmen Marqués
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain
| | | | - Roser Montagud-Martínez
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain
| | - María Cebriá-Mendoza
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain
| | - José M Cuevas
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain
| | - Eliseo Albert
- Microbiology Service, Clinic University Hospital, INCLIVA Biomedical Research Institute, 46010, Valencia, Spain
| | - David Navarro
- Microbiology Service, Clinic University Hospital, INCLIVA Biomedical Research Institute, 46010, Valencia, Spain
- Department of Microbiology, School of Medicine, University of Valencia, 46010, Valencia, Spain
| | - Guillermo Rodrigo
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain.
| | - Gustavo Gómez
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain.
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Li X, Zhao X, Xie L, Song X, Song X. Identification of four snoRNAs (SNORD16, SNORA73B, SCARNA4, and SNORD49B) as novel non-invasive biomarkers for diagnosis of breast cancer. Cancer Cell Int 2024; 24:55. [PMID: 38311725 PMCID: PMC10840236 DOI: 10.1186/s12935-024-03237-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 01/20/2024] [Indexed: 02/06/2024] Open
Abstract
BACKGROUND Emerging data point to the critical role of snoRNA in the emergence of different types of cancer, but scarcely in breast cancer (BC). This study aimed to clarify the differential expressions and potential diagnostic value of SNORD16, SNORA73B, SCARNA4, and SNORD49B in BC. METHODS We screened differential snoRNAs in BC tissues and adjacent tissues through SNORic datasets, and then we further verified them in the plasma of BC patients and healthy volunteers by quantitative polymerase chain reaction (qPCR). RESULTS These four snoRNAs: SNORD16, SNORA73B, SCARNA4, and SNORD49B were considerably more abundant in cancerous tissues than in neighboring tissues in the TCGA database. Their plasma levels were also higher in BC and early-stage BC patients when compared to healthy controls. Furthermore, the ROC curve demonstrated that BC (AUC = 0.7521) and early-stage BC (AUC = 0.7305) might be successfully distinguished from healthy people by SNORD16, SNORA73B, SCARNA4, and SNORD49B. CONCLUSION Plasma snoRNAs: SNORD16, SNORA73B, SCARNA4, and SNORD49B were upregulated in BC and early-stage BC and can be used as potential diagnostic markers for BC and early-stage BC.
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Affiliation(s)
- Xiao Li
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University, Shandong Academy of Medical Sciences, 440 Ji-Yan Road, Jinan, 250117, Shandong Province, China
| | - Xuan Zhao
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University, Shandong Academy of Medical Sciences, 440 Ji-Yan Road, Jinan, 250117, Shandong Province, China
| | - Li Xie
- Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Xingguo Song
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University, Shandong Academy of Medical Sciences, 440 Ji-Yan Road, Jinan, 250117, Shandong Province, China
| | - Xianrang Song
- Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, Shandong Academy of Medical Sciences, Jinan, Shandong, China.
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Yu L, Zhang M, Ma Z, Wu S. Expression of small nucleolar RNA SNORA51 and its clinical significance in hepatocellular carcinoma. Oncol Lett 2024; 27:55. [PMID: 38192654 PMCID: PMC10773229 DOI: 10.3892/ol.2023.14188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/09/2023] [Indexed: 01/10/2024] Open
Abstract
Small nucleolar RNA H/ACA Box 51 (SNORA51) is involved in progression of multiple cancers. However, its role in hepatocellular carcinoma (HCC) is still unclear. The aim of the present study was to analyze the expression of SNORA51 in HCC and its clinical significance. A total of 136 patients with HCC who underwent surgery from January 1, 2016 to December 31, 2018 were included. The expression of SNORA51 in cancer tissues and adjacent tissues was compared using reverse transcription-quantitative PCR and bioinformatics methods. Methylation of the SNORA51 promoter in cancer and adjacent tissues was compared using bioinformatics. The relationship between SNORA51 expression levels and clinicopathological characteristics of patients with HCC, in addition to prognosis, was analyzed. The expression of SNORA51 in HCC was significantly higher compared with that in adjacent tissues (P<0.05). starBase demonstrated that higher expression levels of SNORA51 were associated with a significantly worse prognosis of patients with HCC compared with those who had lower expression levels of SNORA51 (P<0.05). Bioinformatics analysis using The University of Alabama at Birmingham Cancer Data Analysis Portal demonstrated that methylation of the SNORA51 promoter region in HCC was significantly decreased compared with adjacent tissues (P<0.05). A high expression of SNORA51 was significantly associated with portal vein tumor thrombus, vascular invasion and TNM stage (P<0.05). The median survival time of patients with high SNORA51 expression was significantly lower compared with those who had low SNORA51 expression (P<0.05). Both uni- and multivariate Cox regression analysis demonstrated that SNORA51 expression was an independent risk factor that significantly worsened the prognosis of patients with HCC (P<0.05). The overexpression of SNORA51 in patients with HCC was significantly associated with a poor prognosis and may be related to the reduced methylation of the SNORA51 promoter region. Therefore, SNORA51 may be a promising biomarker for prediction of the prognosis of patients with HCC and may be a therapeutic target for the treatment of HCC in future.
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Affiliation(s)
- Liang Yu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Mei Zhang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Zhenhua Ma
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Shengli Wu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
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10
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Atwan QS, Al-Ogaidi I. Enhancing the therapeutic potential of curcumin: a novel nanoformulation for targeted anticancer therapy to colorectal cancer with reduced miR20a and miR21 expression. Biomed Mater 2024; 19:025020. [PMID: 38215475 DOI: 10.1088/1748-605x/ad1dfc] [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: 09/09/2023] [Accepted: 01/12/2024] [Indexed: 01/14/2024]
Abstract
Curcumin (Cur) possesses remarkable pharmacological properties, including cardioprotective, neuroprotective, antimicrobial, and anticancer activities. However, the utilization of Cur in pharmaceuticals faces constraints owing to its inadequate water solubility and limited bioavailability. To overcome these hurdles, there has been notable focus on exploring innovative formulations, with nanobiotechnology emerging as a promising avenue to enhance the therapeutic effectiveness of these complex compounds. We report a novel safe, effective method for improving the incorporation of anticancer curcumin to induce apoptosis by reducing the expression levels of miR20a and miR21. The established method features three aspects that, to our knowledge, have not been formally verified: (1) use of a novel formula to incorporate curcumin, (2) use of all biocompatible biodegradable materials to produce this formula without leaving harmful residues, and (3) an incorporation process at temperatures of approximately 50 °C. The formula was prepared from lecithin (LE), and chitosan (CH) with an eco-friendly emulsifying agent and olive oil as the curcumin solvent. The formula was converted to nanoscale through ultrasonication and probe sonication at a frequency of 20 kHz. Transmission electron microscopy showed that the nano formula was spherical in shape with sizes ranging between 49.7 nm in diameter and negative zeta potentials ranging from 28 to 34 mV. Primers miR20a and miR21 were designed for molecular studies. Nearly complete curcumin with an encapsulation efficiency of 91.1% was established using a straight-line equation. The nano formula incorporated with curcumin was used to prepare formulations that exhibited anticancer activities. The apoptosis pathway in cancer cells was activated by the minimum inhibitory concentration of the nano formula. These findings suggest the potential of this nanoformulation as an effective and selective cancer treatment that does not affect the normal cells.
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Affiliation(s)
- Qusay S Atwan
- Department of Biotechnology, College of Science, University of Baghdad, Baghdad, Iraq
| | - Israa Al-Ogaidi
- Department of Biotechnology, College of Science, University of Baghdad, Baghdad, Iraq
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11
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Atwan QS, Al-Ogaidi I. Improving the targeted delivery of curcumin to esophageal cancer cells via a novel formulation of biodegradable lecithin/chitosan nanoparticles with downregulated miR-20a and miR-21 expression. NANOTECHNOLOGY 2024; 35:135103. [PMID: 38096580 DOI: 10.1088/1361-6528/ad15b9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 12/14/2023] [Indexed: 01/12/2024]
Abstract
Nanoencapsulation, employing safe materials, holds substantial promise for enhancing bioactive compounds' delivery, stability, and bioactivity. In this study, we present an innovative and safe methodology for augmenting the incorporation of the anticancer agent, curcumin, thereby inducing apoptosis by downregulating miR20a and miR21 expression. Our established methodology introduces three pivotal elements that, to our knowledge, have not undergone formal validation: (1) Novel formulation: We introduce a unique formula for curcumin incorporation. (2) Biocompatibility and biodegradability: our formulation exclusively consists of biocompatible and biodegradable constituents, ensuring the absence of detrimental residues or undesirable reactions under varying conditions. (3) Low-temperature incorporation: Curcumin is incorporated into the formulation at temperatures approximating 50 °C. The formulation comprises lecithin (LE), chitosan (CH), an eco-friendly emulsifying agent, and olive oil as the solvent for curcumin. Nanoscale conversion is achieved through ultrasonication and probe sonication (20 kHz). Transmission electron microscopy (TEM) reveals spherical nanoparticles with diameters ranging from 29.33 nm and negative zeta potentials within the -28 to -34 mV range. Molecular studies involve the design of primers for miR20a and miR21. Our findings showcase a remarkable encapsulation efficiency of 91.1% for curcumin, as determined through a linear equation. The curcumin-loaded nanoformulation demonstrates potent anticancer activity, effectively activating the apoptosis pathway in cancer cells at the minimum inhibitory concentration. These results underscore the potential of our nanoformulation as a compelling, cancer-selective treatment strategy, preserving the integrity of normal cells, and thus, warranting further exploration in the field of cancer therapy.
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Affiliation(s)
- Qusay S Atwan
- Department of Biotechnology, College of Science, University of Baghdad, Baghdad, Iraq
| | - Israa Al-Ogaidi
- Department of Biotechnology, College of Science, University of Baghdad, Baghdad, Iraq
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12
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Gao L, Fan J, He J, Che X, Wang X, Han C. Small Nucleolar RNAs as Diagnostic and Prognostic Biomarkers in Cancer: A Systematic Review and Meta-Analysis. Technol Cancer Res Treat 2024; 23:15330338241245939. [PMID: 38752263 PMCID: PMC11102679 DOI: 10.1177/15330338241245939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 01/14/2024] [Accepted: 02/12/2024] [Indexed: 05/21/2024] Open
Abstract
OBJECTIVES Small nucleolar RNAs (snoRNAs) form clusters within the genome, representing a mysterious category of small non-coding RNAs. Research has demonstrated that aberrant snoRNAs can contribute to the development of various types of cancers. Recent studies have identified snoRNAs as potentially valuable biomarkers for the diagnosis or/and prognosis of cancers. However, there has been a lack of comprehensive reviews on prognostic and diagnostic snoRNAs across different types of cancers. METHODS We conducted a systematic search of various databases including Google Scholar, Medline, Cochrane, Scopus, PubMed, Embase, ScienceDirect, Ovid-Medline, Chinese National Knowledge Infrastructure, WanFang, and SinoMed with a time frame reception to December 30, 2022. A total of 49 relevant articles were included in our analysis, consisting of 21 articles focusing on diagnostic aspects and 41 articles focusing on prognostic aspects. Pooled odds ratio, 95% confidence intervals (CIs), and hazard ratio (HR) were utilized to evaluate clinical parameters and overall survival (OS), respectively. RESULT The findings indicated that area under the curve, sensitivity, and specificity were 0.85, 75%, and 80% in cancer, respectively. There was a possibility that snoRNAs had a positive impact on the diagnosis (risk ratio, RR = 2.95, 95% CI: 2.75-3.16, P = 0.000) and OS (HR = 1) in cancer. Additionally, abnormally expressed snoRNAs were associated with a positive impact on OS time for chronic lymphocytic leukemia (HR: 0.88, 95%Cl: 0.69-1.11, P < 0.00001), colon adenocarcinoma (HR: 0.97, 95%Cl: 0.91-1.03, P < 0.0001), and ovarian cancer (HR: 0.98, 95%Cl: 0.98-0.99, P < 0.00001). However, dysregulated snoRNAs of colon cancer and colorectal cancer had a negative impact on OS time (HR = 3.01 and 1.01 respectively, P < 0.0001). CONCLUSION The results strongly suggested that snoRNAs could serve as potential novel indicators for prognosis and diagnosis in cancers. This systematic review followed the guidelines of the Transparent Reporting of Systematic Review and Meta-Analyses (PROSPERO register: CRD42020209096).
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Affiliation(s)
- Liyun Gao
- Laboratory of Precision Preventive Medicine, School of Basic Medicine, Jiujiang University, Jiujiang, China
- Jiangxi Provincial Key Laboratory of Cell Precision Therapy, School of Basic Medical Sciences, Jiujiang University, China
| | - Junfei Fan
- School of Humanities, Shangluo University, Shangluo, China
| | - Jiayin He
- School of Literature and Journalism, South-central Minzu University, Wuhan, China
| | - Xiangxin Che
- Laboratory of Precision Preventive Medicine, School of Basic Medicine, Jiujiang University, Jiujiang, China
| | - Xin Wang
- Laboratory of Precision Preventive Medicine, School of Basic Medicine, Jiujiang University, Jiujiang, China
| | - Chunhua Han
- Internal Medicine, Jiujiang First People's Hospital, Jiujiang, China
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Guimaraes GJ, Saad JG, Annavarapu V, Bartlett MG. Mobile Phase Aging and Its Impact on Electrospray Ionization of Oligonucleotides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2691-2699. [PMID: 37978939 DOI: 10.1021/jasms.3c00264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
The implementation of fluoroalcohol/alkylamine mobile phase systems in oligonucleotide LC-MS provides a good balance between chromatographic separations and MS sensitivity. Since its introduction, several parameters including mobile phase composition, additive concentration, alkylamine hydrophobicity, and different fluoroalcohols have been carefully evaluated and optimized. While our understanding of this mobile phase system has increased over the years, there are challenges that continue to hinder method performance and remain poorly understood. One of these challenges is the constant loss of MS sensitivity over time, commonly termed mobile phase aging. This study investigates two aging mechanisms associated with loss of MS sensitivity: alkylamine oxidation and aggregate formation. The relationship between pH, organic solvent, oxygen, and mobile phase aging is characterized, and mitigation strategies to extend mobile phase lifetime are discussed.
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Affiliation(s)
- Guilherme J Guimaraes
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia College of Pharmacy, Athens, Georgia 30602, United States
| | - Jack G Saad
- Micromeritics Instrument Company, 4356 Communications Drive, Norcross, Georgia 30093, United States
| | - Vidya Annavarapu
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia College of Pharmacy, Athens, Georgia 30602, United States
| | - Michael G Bartlett
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia College of Pharmacy, Athens, Georgia 30602, United States
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Xu R, Wang L, Hou J, Wang X, Wang Y, Wang K. Knowledge mapping and current trends of global research on snoRNA in the field of cancer. J Cancer 2023; 14:2596-2607. [PMID: 37779878 PMCID: PMC10539387 DOI: 10.7150/jca.87196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 07/31/2023] [Indexed: 10/03/2023] Open
Abstract
Cancer is a major health hazard for humans. Recent studies have indicated the involvement of small nucleolar RNAs (snoRNAs) in the occurrence and development of cancer and indicated its potential role as a diagnostic/prognostic marker and therapeutic target. The purpose of this study was to use the bibliometrics method to analyze the published literature on this subject. We collected articles pertaining to the field of snoRNA and cancer from the Web of Science Core Collection database. The data were analyzed to identify the research hotspots and frontiers. The number of articles in this field was low in the early period. Chu Liang and Montanaro Lorenzo were the most prolific authors on this subject, while Jiang and Feng were the most frequently cited authors. In China, three institutions published the most articles, namely Wuhan Univ, China Med Univ, and Guangxi Med Univ. The journal with the highest number of articles on this subject was Oncotarget. The country with the most published articles was China. Analysis of keywords and burst words indicated that early studies mainly focused on molecular mechanisms. Available evidence suggests the involvement of snoRNAs in the molecular mechanism of cancer development and their potential role as a diagnostic and prognostic biomarker.
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Affiliation(s)
- Runsen Xu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Lina Wang
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Junhui Hou
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Xia Wang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Yibing Wang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Kefeng Wang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang 110004, China
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Komoto TT, Nishimura FG, Evangelista AF, de Freitas AJA, da Silva G, Silva WA, Peronni K, Marques MMC, Marins M, Fachin AL. Exploring the Therapeutic Potential of trans-Chalcone: Modulation of MicroRNAs Linked to Breast Cancer Progression in MCF-7 Cells. Int J Mol Sci 2023; 24:10785. [PMID: 37445965 DOI: 10.3390/ijms241310785] [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: 05/05/2023] [Revised: 06/10/2023] [Accepted: 06/16/2023] [Indexed: 07/15/2023] Open
Abstract
Breast cancer is responsible for 25% of all cancers that affect women. Due to its high heterogeneity pattern in clinical diagnosis and its molecular profile differences, researchers have been seeking new targets and therapies, with more specificity and fewer side effects. Thus, one compound that has garnered our attention is trans-chalcone, which is naturally occurring in various plants and possesses promising biological properties, including antitumor effects. MiRNA is an extensive class of non-coding small, endogenous, and single-stranded RNAs, and it is involved in post-translational gene regulation. Therefore, the objective of this study was to investigate the effects of TChal on miRNAs expression and its relationship with anticancer activity against MCF-7. Initially, the trans-chalcone IC50 value was established by MTT assay for MCF-7and HaCat (non-cancer cell), in which we found out that it was 53.73 and 44.18 μM, respectively. Subsequently, we treated MCF-7 cells with trans-chalcone at its IC50 concentration and performed Mi-seq analysis, which unveiled 23 differentially expressed miRNAs. From this set, we selected five miRNAs (miR-25-5p, miR-27a-3p, miR-891a, miR-449a, and miR-4485) for further validation using qRT-PCR, guided by in silico analysis and their known association with tumorigenesis. In conclusion, our research provides valuable insights into the potential use of TChal to reveal MicroRNAs molecular targets that can be applied in breast cancer therapy.
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Affiliation(s)
- Tatiana Takahasi Komoto
- Biotechnology Unit, University of Ribeirão Preto, SP, Av. Costábile Romano, 2201, Ribeirão Preto 14096-900, Brazil
- Molecular Oncology Research Center, Barretos Cancer Hospital, Teaching and Research Institute, Barretos 14784-400, Brazil
| | - Felipe Garcia Nishimura
- Biotechnology Unit, University of Ribeirão Preto, SP, Av. Costábile Romano, 2201, Ribeirão Preto 14096-900, Brazil
| | - Adriane Feijó Evangelista
- Sergio Arouca National School of Public Health, Oswaldo Cruz Foundation, Manguinhos, Rio de Janeiro 21040-361, Brazil
| | - Ana Julia Aguiar de Freitas
- Molecular Oncology Research Center, Barretos Cancer Hospital, Teaching and Research Institute, Barretos 14784-400, Brazil
| | - Gabriel da Silva
- Biotechnology Unit, University of Ribeirão Preto, SP, Av. Costábile Romano, 2201, Ribeirão Preto 14096-900, Brazil
| | - Wilson Araujo Silva
- Center for Medical Genomics at the Clinics Hospital of Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil
| | - Kamila Peronni
- Center for Medical Genomics at the Clinics Hospital of Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil
| | | | - Mozart Marins
- Biotechnology Unit, University of Ribeirão Preto, SP, Av. Costábile Romano, 2201, Ribeirão Preto 14096-900, Brazil
| | - Ana Lucia Fachin
- Biotechnology Unit, University of Ribeirão Preto, SP, Av. Costábile Romano, 2201, Ribeirão Preto 14096-900, Brazil
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16
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Liu Z, Ke S, Wang Q, Gu X, Zhai G, Shao H, He M, Guo J. Analyzing roles of small nucleolar RNA host gene 25 from clinical, molecular target and tumor formation in prostate cancer. Exp Cell Res 2023:113686. [PMID: 37307941 DOI: 10.1016/j.yexcr.2023.113686] [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: 01/17/2023] [Revised: 06/04/2023] [Accepted: 06/06/2023] [Indexed: 06/14/2023]
Abstract
BACKGROUND Prostate cancer (PCa) is one of the most deadly and metastatic cancers of the urinary tract. Latest studies have confirmed that long non-coding RNAs (lncRNAs) play a crucial role in a variety of cancers. Some of these lncRNAs code for small nucleolar RNAs (snoRNAs), called small nucleolar RNA host genes (SNHGs), which exert some value in predicting the prognosis of certain cancer patients, but little is known regarding the function of SNHGs within the PCa. AIM OF THE STUDY To explore the expression distribution and differential analysis of SNHGs in different tumors using RNA-seq and survival data from TCGA and GTEx, and to assess the potential impacts of the lncRNA SNHG25 on human PCa. To validate the expression of SNHG25 using experimental data and to investigate in detail its particular molecular biological function on PCa both in vivo and in vitro. METHODS LncRNA SNHG25 expression was analyzed by bioinformatic prediction and qPCR. CCK-8, EdU, transwell, wound healing, and western blotting assays were conducted to investigate the main role of lncRNA SNHG25 in PCa. Xenograft tumour growth model in nude mice was surveyed by in vivo imaging and Ki-67 staining. AKT pathway activator (SC79) was used to verify the interaction among SNHG25 and PI3K/AKT signaling pathway. RESULTS Bioinformatics analysis and experimental research illuminated that the expression of lncRNA SNHG25 was observably up-regulated in PCa tissues and cells. Moreover, SNHG25 knockdown restrained PCa cell proliferation, invasion and migration, while promoting apoptosis. Xenografts model confirmed that the si-SNHG25 group had a significant inhibitory effect on PCa tumour growth in vivo. Additionally, a series of gain-of-function analyses suggested that SNHG25 could activate the PI3K/AKT pathway to accelerate PCa progression. CONCLUSIONS These in vitro and in vivo findings demonstrate that SNHG25 is highly expressed in PCa and facilitates PCa development through regulation of PI3K/AKT signaling pathway. SNHG25 acts as an oncogene to predict tumour malignancy and survival in PCa patients and may therefore become a promising potential molecular target for early detection and therapy of lethal PCa.
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Affiliation(s)
- Zelin Liu
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, 430060, China; Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Shuai Ke
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Qinghua Wang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Xuhang Gu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410000, China
| | - Guanzhong Zhai
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Haoren Shao
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Mu He
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Jia Guo
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
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17
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Kniazeva M, Zabegina L, Shalaev A, Smirnova O, Lavrinovich O, Berlev I, Malek A. NOVAprep-miR-Cervix: New Method for Evaluation of Cervical Dysplasia Severity Based on Analysis of Six miRNAs. Int J Mol Sci 2023; 24:ijms24119114. [PMID: 37298066 DOI: 10.3390/ijms24119114] [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: 03/30/2023] [Revised: 05/12/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
Cervical cancer is one of the most common gynecological malignancies and it is preventable through the yearly diagnosis and management of pre-cancerous cervical disease. The profile of miRNA expression in cervical epithelium cells is altered with cervical dysplasia development and further progression. The NOVAprep-miR-CERVIX is a new approach for the assessment of cervical dysplasia through the analysis of six marker miRNAs. This study aims to evaluate theperformance and diagnostic potency of the new method. Cytological smears from 226 women (NILM, n.114; HSIL, n.112) were included in the study. A VPH test was performed with RealBest DNAHPV HR screen Kit, six marker miRNAs (miR-21, -29b, -145, -451a, -1246, -1290) were assayed using NOVAprep-miR-CERVIX kit. Obtained data were analyzed using the Delta Ct method and random forest machine learning algorithm. The results of the quantitative analysis of six microRNAs were expressed as a miR-CERVIX parameter, which ranged from 0 to 1, where "0" corresponded to the healthy cervical epithelium, while "1" corresponded to high-grade squamous intraepithelial dysplasia. The average value of miR-CERVIX differed in groups of NILM and HSIL samples (0.34 vs. 0.72; p < 0.000005). An estimation of miR-CERVIX allowed for the differentiation between healthy and pre-cancerous samples with sensitivity of 0.79 and specificity of 0.79, as well as to confirm HSIL with specificity of 0.98. Interestingly, the HSIL group included HPV(+) and HPV(-) samples, which were statistically significantly different in terms of miR-CERVIX value. Analysis of CC-associated miRNAs in material of cervical smear might serve as an additional method for the evaluation of cervical dysplasia severity.
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Affiliation(s)
- Margarita Kniazeva
- Subcellular Technology Lab., N.N. Petrov National Medical Research Center of Oncology, 197758 St. Petersburg, Russia
| | - Lidia Zabegina
- Subcellular Technology Lab., N.N. Petrov National Medical Research Center of Oncology, 197758 St. Petersburg, Russia
| | - Andrey Shalaev
- Subcellular Technology Lab., N.N. Petrov National Medical Research Center of Oncology, 197758 St. Petersburg, Russia
| | - Olga Smirnova
- Department of Gynecological Oncology, N.N. Petrov National Medical Research Center of Oncology, 197758 St. Petersburg, Russia
| | - Olga Lavrinovich
- Department of Gynecological Oncology, N.N. Petrov National Medical Research Center of Oncology, 197758 St. Petersburg, Russia
| | - Igor Berlev
- Department of Gynecological Oncology, N.N. Petrov National Medical Research Center of Oncology, 197758 St. Petersburg, Russia
| | - Anastasia Malek
- Subcellular Technology Lab., N.N. Petrov National Medical Research Center of Oncology, 197758 St. Petersburg, Russia
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18
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Su M, Huang P, Li Q. Long noncoding RNA SNHG6 promotes the malignant phenotypes of ovarian cancer cells via miR-543/YAP1 pathway. Heliyon 2023; 9:e16291. [PMID: 37234669 PMCID: PMC10208841 DOI: 10.1016/j.heliyon.2023.e16291] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
The long non-coding RNA small nucleolar RNA host gene 6 (SNHG6) acts as an oncogene in several cancers, and is highly expressed in ovarian cancer. MiR-543, a tumor suppressor, was expressed lowly in ovarian cancer. However, whether SNHG6 performed its oncogenic role via miR-543 in ovarian cancer, as well as the underlying mechanism is still not clear. In this study, we showed that the levels of SNHG6 and Yes-associated protein 1 (YAP1) were significantly elevated, while the level of miR-543 was significantly decreased, in ovarian cancer tissues compared with adjacent normal samples. We demonstrated that overexpression of SNHG6 significantly promoted the proliferation, migration, invasion and epithelial-mesenchymal transition (EMT) of ovarian cancer cells SKOV3 and A2780. Knockdown of SNHG6 showed the opposite effects. MiR-543 level was negatively correlated with the SNHG6 level in ovarian cancer tissues. SHNG6 overexpression significantly inhibited the expression of miR-543, and SHNG6 knockdown significantly elevated the expression of miR-543 in ovarian cancer cells. The effects of SNHG6 on ovarian cancer cells were abrogated by miR-543 mimic, and strengthened by anti-miR-543. YAP1 was identified as a target of miR-543. Forced expression of miR-543 significantly inhibited the expression of YAP1. Moreover, YAP1 overexpression could reverse the effects of SNHG6 downregulation on the malignant phenotypes of ovarian cancer cells. In summary, our study showed that SNHG6 promoted the malignant phenotypes of ovarian cancer cells via miR-543/YAP1 pathway.
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Affiliation(s)
- Mengya Su
- Department of Reproductive Medicine, Cangzhou Central Hospital, Cangzhou, 061000, Hebei Province, China
| | - Ping Huang
- Department of Gynecology, Cangzhou Central Hospital, Cangzhou, 061000, Hebei Province, China
| | - Qian Li
- Department of Gynecology, Cangzhou Central Hospital, Cangzhou, 061000, Hebei Province, China
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19
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Wischmann FJ, Troschel FM, Frankenberg M, Kemper B, Vijaya Kumar A, Sicking M, Ibrahim SA, Kiesel L, Götte M, Eich HT, Greve B. Tumor suppressor miR-218 directly targets epidermal growth factor receptor (EGFR) expression in triple-negative breast cancer, sensitizing cells to irradiation. J Cancer Res Clin Oncol 2023:10.1007/s00432-023-04750-x. [PMID: 37088795 PMCID: PMC10374822 DOI: 10.1007/s00432-023-04750-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/05/2023] [Indexed: 04/25/2023]
Abstract
PURPOSE MicroRNA-218 (miR-218) is a key regulator of numerous processes relevant to tumor progression. In the present study, we aimed to characterize the relationship between miR-218 and the Epidermal Growth Factor Receptor (EGFR) as well as to understand downstream effects in triple-negative breast cancer (TNBC). METHODS We assessed miR-218 and EGFR expression in cell lines and publicly available primary breast cancer gene expression data. We then overexpressed miR-218 in two TNBC cell lines and investigated effects on EGFR and downstream mitogen-activated protein (MAP) kinase signaling. Luciferase reporter assay was used to characterize a direct binding interaction between miR-218 and EGFR mRNA. Digital holographic microscopy helped investigate cell migration and dry mass after miR-218 overexpression. Cell division and invasion were assessed microscopically, while radiation response after miR-218 overexpression alone or combined with additional EGFR knockdown was investigated via clonogenic assays. RESULTS We found an inverse correlation between EGFR expression and miR-218 levels in cell lines and primary breast cancer tissues. MiR-218 overexpression resulted in a downregulation of EGFR via direct binding of the mRNA. Activation of EGFR and downstream p44/42 MAPK signaling were reduced after pre-miR-218 transfection. Cell proliferation, motility and invasiveness were inhibited whereas cell death and mitotic catastrophe were upregulated in miR-218 overexpressing cells compared to controls. MiR-218 overexpressing and EGFR siRNA-treated cells were sensitized to irradiation, more than miR-218 overexpressing cells alone. CONCLUSION This study characterizes the antagonistic relationship between miR-218 and EGFR. It also demonstrates downstream functional effects of miR-218 overexpression, leading to anti-tumorigenic cellular changes.
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Affiliation(s)
- Franz-Josef Wischmann
- Department of Radiation Oncology, University Hospital Münster, Albert-Schweitzer-Campus 1, Gebäude A1, 48149, Münster, Germany
| | - Fabian M Troschel
- Department of Radiation Oncology, University Hospital Münster, Albert-Schweitzer-Campus 1, Gebäude A1, 48149, Münster, Germany.
| | - Maj Frankenberg
- Department of Radiation Oncology, University Hospital Münster, Albert-Schweitzer-Campus 1, Gebäude A1, 48149, Münster, Germany
| | - Björn Kemper
- Biomedical Technology Center, Medical Faculty, University of Münster, Münster, Germany
| | - Archana Vijaya Kumar
- Department of Gynecology and Obstetrics, University Hospital Münster, Münster, Germany
| | - Mark Sicking
- Department of Radiation Oncology, University Hospital Münster, Albert-Schweitzer-Campus 1, Gebäude A1, 48149, Münster, Germany
| | | | - Ludwig Kiesel
- Department of Gynecology and Obstetrics, University Hospital Münster, Münster, Germany
| | - Martin Götte
- Department of Gynecology and Obstetrics, University Hospital Münster, Münster, Germany
| | - Hans Theodor Eich
- Department of Radiation Oncology, University Hospital Münster, Albert-Schweitzer-Campus 1, Gebäude A1, 48149, Münster, Germany
| | - Burkhard Greve
- Department of Radiation Oncology, University Hospital Münster, Albert-Schweitzer-Campus 1, Gebäude A1, 48149, Münster, Germany.
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MicroRNA Profiling of Cell Lines and Xenografts by Quantitative PCR : MicroRNA Expression Level Determination by qPCR. Methods Mol Biol 2023; 2595:101-114. [PMID: 36441457 DOI: 10.1007/978-1-0716-2823-2_7] [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: 11/29/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that play essential roles in regulating gene expression at the post-transcriptional level, possibly at any level of the cellular physiology. Furthermore, their deregulation has been observed in a myriad of human diseases including cancer. Therefore, miRNA-based therapies are directed to inhibit the function of oncogenic miRNA or to restore the function of tumor-suppressive miRNAs. Here, we describe how to analyze miRNA levels after the transfection of miRNAs of interest using different transfection reagents or intravenous administration of miRNAs conjugated to lipid nanoparticles in cell lines and in mouse xenograft models.
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21
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Stverakova T, Baranova I, Mikyskova P, Gajdosova B, Vosmikova H, Laco J, Palicka V, Parova H. Selection of endogenous control and identification of significant microRNA deregulations in cervical cancer. Front Oncol 2023; 13:1143691. [PMID: 37168377 PMCID: PMC10164982 DOI: 10.3389/fonc.2023.1143691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/11/2023] [Indexed: 05/13/2023] Open
Abstract
Introduction Cervical cancer causes approximately 350,000 deaths each year. The availability of sensitive and specific diagnostic tests to detect cervical cancer in its early stages is essential to improve survival rates. Methods In this study, we compared two strategies for selecting endogenous controls: miRNA profiling by small-RNA sequencing and a commercially available microfluidic card with 30 recommended endogenous controls preloaded by the manufacturer. We used the RefFinder algorithm and coefficient of variation to select endogenous controls. We selected the combination of miR-181a-5p and miR-423-3p as the most optimal normalizer. In the second part of this study, we determined the differential expression (between tumor/non-tumor groups) of microRNA in cervical cancer FFPE tissue samples. We determined the comprehensive miRNA expression profile using small-RNA sequencing technology and verified the results by real-time PCR. We determined the relative expression of selected miRNAs using the 2-ΔΔCt method. Results We detected statistically significant upregulation of miR-320a-3p, miR-7704, and downregulation of miR-26a-5p in the tumor group compared to the control group. The combination of these miRNAs may have the potential to be utilized as a diagnostic panel for cervical cancer. Using ROC curve analysis, the proposed panel showed 93.33% specificity and 96.97% sensitivity with AUC = 0.985. Conclusions We proposed a combination of miR-181a-5p and miR-423-3p as optimal endogenous control and detected potentially significant miRNAs (miR-320a-3p, miR-7704, miR-26a-5p). After further validation of our results, these miRNAs could be used in a diagnostic panel for cervical cancer.
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Affiliation(s)
- T. Stverakova
- Department of Clinical Biochemistry and Diagnostics, Charles University, Faculty of Medicine in Hradec Králové and University Hospital Hradec Králové, Hradec Králové, Czechia
| | - I. Baranova
- Department of Clinical Biochemistry and Diagnostics, Charles University, Faculty of Medicine in Hradec Králové and University Hospital Hradec Králové, Hradec Králové, Czechia
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - P. Mikyskova
- Department of Clinical Biochemistry and Diagnostics, Charles University, Faculty of Medicine in Hradec Králové and University Hospital Hradec Králové, Hradec Králové, Czechia
| | - B. Gajdosova
- The Fingerland Department of Pathology, Charles University, Faculty of Medicine in Hradec Králové and University Hospital Hradec Králové, Hradec Králové, Czechia
| | - H. Vosmikova
- The Fingerland Department of Pathology, Charles University, Faculty of Medicine in Hradec Králové and University Hospital Hradec Králové, Hradec Králové, Czechia
| | - J. Laco
- The Fingerland Department of Pathology, Charles University, Faculty of Medicine in Hradec Králové and University Hospital Hradec Králové, Hradec Králové, Czechia
| | - V. Palicka
- Department of Clinical Biochemistry and Diagnostics, Charles University, Faculty of Medicine in Hradec Králové and University Hospital Hradec Králové, Hradec Králové, Czechia
| | - H. Parova
- Department of Clinical Biochemistry and Diagnostics, Charles University, Faculty of Medicine in Hradec Králové and University Hospital Hradec Králové, Hradec Králové, Czechia
- *Correspondence: H. Parova,
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Gu W, Tu X, Lu W, Yin Y, Meng Q, Wang X, Zhang F, Fu Y. Identification of RNU44 as an Endogenous Reference Gene for Normalizing Cell-Free RNA in Tuberculosis. Open Forum Infect Dis 2022; 9:ofac540. [DOI: 10.1093/ofid/ofac540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/11/2022] [Indexed: 12/13/2022] Open
Abstract
Abstract
Background
Normalization of cell-free RNA (cf-RNA) concentration can be affected by variable experimental conditions and thus impact the performance of their diagnostic potential. Our study aimed to identify appropriate endogenous reference genes for cf-RNA biomarker evaluation in the diagnosis of tuberculosis (TB).
Methods
Subjects consisting of patients with TB with and without malignancy, patients with pneumonia, and healthy controls were recruited. Candidate reference genes were screened and identified by literature reviewing and RNA-Seq analysis. Expression levels of the candidate genes were determined by reverse-transcription real-time quantitative polymerase chain reaction in plasma from patients with TB and healthy controls. The stability of gene expression was assessed by geNorm, NormFinder, BestKeeper, the Comparative Delta Ct method, and RefFinder. Differential expression of 2 small RNAs (sRNAs) encoding by genome of Mycobacterium tuberculosis in plasma of patients with TB were determined by both absolute quantification and relative quantification with candidate reference genes.
Results
According to the stability ranking analyzed with the 5 computational programs, the top 4 candidates—miR-93, RNU44, miR-16, and glyceraldehyde 3-phosphate dehydrogenase—were used to normalize the transcript levels of 2 mycobacterial sRNAs, MTS2823 and MTS1338, which were observed to have higher copy numbers in the plasma of patients with TB. Normalization with RNU44 displayed significantly higher levels of the 2 M tuberculosis sRNAs in the patients’ plasma than those of healthy controls.
Conclusions
RNU44 was demonstrated as a proper endogenous gene for cf-RNA normalization in TB diagnosis.
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Affiliation(s)
- Wei Gu
- Department of Microbiology, Harbin Medical University , Harbin , China
| | - Xilin Tu
- Department of Respiratory Medicine, First Affiliated Hospital, Harbin Medical University , Harbin , China
| | - Weinan Lu
- Department of Microbiology, Harbin Medical University , Harbin , China
| | - Yian Yin
- Department of Microbiology, Harbin Medical University , Harbin , China
| | - Qingtai Meng
- Department of Microbiology, Harbin Medical University , Harbin , China
| | - Xinyang Wang
- Department of Microbiology, Harbin Medical University , Harbin , China
| | - Fengmin Zhang
- Department of Microbiology, Harbin Medical University , Harbin , China
| | - Yingmei Fu
- Department of Microbiology, Harbin Medical University , Harbin , China
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Zhang Z, Yu H, Yao W, Zhu N, Miao R, Liu Z, Song X, Xue C, Cai C, Cheng M, Lin K, Qi D. RRP9 promotes gemcitabine resistance in pancreatic cancer via activating AKT signaling pathway. Cell Commun Signal 2022; 20:188. [PMID: 36434608 PMCID: PMC9700947 DOI: 10.1186/s12964-022-00974-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 09/18/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Pancreatic cancer (PC) is a highly lethal malignancy regarding digestive system, which is the fourth leading factor of cancer-related mortalities in the globe. Prognosis is poor due to diagnosis at advanced disease stage, low rates of surgical resection, and resistance to traditional radiotherapy and chemotherapy. In order to develop novel therapeutic strategies, further elucidation of the molecular mechanisms underlying PC chemoresistance is required. Ribosomal RNA biogenesis has been implicated in tumorigenesis. Small nucleolar RNAs (snoRNAs) is responsible for post-transcriptional modifications of ribosomal RNAs during biogenesis, which have been identified as potential markers of various cancers. Here, we investigate the U3 snoRNA-associated protein RRP9/U3-55 K along with its role in the development of PC and gemcitabine resistance. METHODS qRT-PCR, western blot and immunohistochemical staining assays were employed to detect RRP9 expression in human PC tissue samples and cell lines. RRP9-overexpression and siRNA-RRP9 plasmids were constructed to test the effects of RRP9 overexpression and knockdown on cell viability investigated by MTT assay, colony formation, and apoptosis measured by FACS and western blot assays. Immunoprecipitation and immunofluorescence staining were utilized to demonstrate a relationship between RRP9 and IGF2BP1. A subcutaneous xenograft tumor model was elucidated in BALB/c nude mice to examine the RRP9 role in PC in vivo. RESULTS Significantly elevated RRP9 expression was observed in PC tissues than normal tissues, which was negatively correlated with patient prognosis. We found that RRP9 promoted gemcitabine resistance in PC in vivo and in vitro. Mechanistically, RRP9 activated AKT signaling pathway through interacting with DNA binding region of IGF2BP1 in PC cells, thereby promoting PC progression, and inducing gemcitabine resistance through a reduction in DNA damage and inhibition of apoptosis. Treatment with a combination of the AKT inhibitor MK-2206 and gemcitabine significantly inhibited tumor proliferation induced by overexpression of RRP9 in vitro and in vivo. CONCLUSIONS Our data reveal that RRP9 has a critical function to induce gemcitabine chemoresistance in PC through the IGF2BP1/AKT signaling pathway activation, which might be a candidate to sensitize PC cells to gemcitabine. Video abstract.
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Affiliation(s)
- Zhiqi Zhang
- grid.24516.340000000123704535Department of Hepatic-Biliary-Pancreatic Surgery, Shanghai Fourth People’s Hospital, School of Medicine, Tongji University, No.1279 Sanmen Road, Hongkou District, Shanghai, 200434 China
| | - Haitao Yu
- grid.415468.a0000 0004 1761 4893Intensive Care Unit, Qingdao Municipal Hospital, Qingdao, 266001 Shandong Province China
| | - Wenyan Yao
- grid.24516.340000000123704535Department of Hepatic-Biliary-Pancreatic Surgery, Shanghai Fourth People’s Hospital, School of Medicine, Tongji University, No.1279 Sanmen Road, Hongkou District, Shanghai, 200434 China
| | - Na Zhu
- grid.24516.340000000123704535Department of Hepatic-Biliary-Pancreatic Surgery, Shanghai Fourth People’s Hospital, School of Medicine, Tongji University, No.1279 Sanmen Road, Hongkou District, Shanghai, 200434 China
| | - Ran Miao
- grid.24516.340000000123704535Department of Hepatic-Biliary-Pancreatic Surgery, Shanghai Fourth People’s Hospital, School of Medicine, Tongji University, No.1279 Sanmen Road, Hongkou District, Shanghai, 200434 China
| | - Zhiquan Liu
- grid.24516.340000000123704535Department of Hepatic-Biliary-Pancreatic Surgery, Shanghai Fourth People’s Hospital, School of Medicine, Tongji University, No.1279 Sanmen Road, Hongkou District, Shanghai, 200434 China
| | - Xuwei Song
- grid.24516.340000000123704535Department of Hepatic-Biliary-Pancreatic Surgery, Shanghai Fourth People’s Hospital, School of Medicine, Tongji University, No.1279 Sanmen Road, Hongkou District, Shanghai, 200434 China
| | - Chunhua Xue
- grid.24516.340000000123704535Department of Hepatic-Biliary-Pancreatic Surgery, Shanghai Fourth People’s Hospital, School of Medicine, Tongji University, No.1279 Sanmen Road, Hongkou District, Shanghai, 200434 China
| | - Cheng Cai
- grid.24516.340000000123704535Department of Hepatic-Biliary-Pancreatic Surgery, Shanghai Fourth People’s Hospital, School of Medicine, Tongji University, No.1279 Sanmen Road, Hongkou District, Shanghai, 200434 China
| | - Ming Cheng
- grid.24516.340000000123704535Department of Hepatic-Biliary-Pancreatic Surgery, Shanghai Fourth People’s Hospital, School of Medicine, Tongji University, No.1279 Sanmen Road, Hongkou District, Shanghai, 200434 China
| | - Ke Lin
- grid.203458.80000 0000 8653 0555Intensive Care Unit, University-Town Hospital of Chongqing Medical University, Chongqing, 401331 China
| | - Dachuan Qi
- grid.24516.340000000123704535Department of Hepatic-Biliary-Pancreatic Surgery, Shanghai Fourth People’s Hospital, School of Medicine, Tongji University, No.1279 Sanmen Road, Hongkou District, Shanghai, 200434 China
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Sullivan R, Montgomery A, Scipioni A, Jhaveri P, Schmidt AT, Hicks SD. Confounding Factors Impacting microRNA Expression in Human Saliva: Methodological and Biological Considerations. Genes (Basel) 2022; 13:genes13101874. [PMID: 36292760 PMCID: PMC9602126 DOI: 10.3390/genes13101874] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/04/2022] Open
Abstract
There is growing interest in saliva microRNAs (miRNAs) as non-invasive biomarkers for human disease. Such an approach requires understanding how differences in experimental design affect miRNA expression. Variations in technical methodologies, coupled with inter-individual variability may reduce study reproducibility and generalizability. Another barrier facing salivary miRNA biomarker research is a lack of recognized “control miRNAs”. In one of the largest studies of human salivary miRNA to date (922 healthy individuals), we utilized 1225 saliva samples to quantify variability in miRNA expression resulting from aligner selection (Bowtie1 vs. Bowtie2), saliva collection method (expectorated vs. swabbed), RNA stabilizer (presence vs. absence), and individual biological factors (sex, age, body mass index, exercise, caloric intake). Differential expression analyses revealed that absence of RNA stabilizer introduced the greatest variability, followed by differences in methods of collection and aligner. Biological factors generally affected a smaller number of miRNAs. We also reported coefficients of variations for 643 miRNAs consistently present in saliva, highlighting several salivary miRNAs to serve as reference genes. Thus, the results of this analysis can be used by researchers to optimize parameters of salivary miRNA measurement, exclude miRNAs confounded by numerous biologic factors, and identify appropriate miRNA controls.
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Affiliation(s)
- Rhea Sullivan
- Department of Pediatrics, Penn State Hershey College of Medicine, Hershey, PA 17033, USA
| | - Austin Montgomery
- Department of Pediatrics, Penn State Hershey College of Medicine, Hershey, PA 17033, USA
| | - Anna Scipioni
- Department of Pediatrics, Penn State Hershey College of Medicine, Hershey, PA 17033, USA
- Department of Obstetrics, Morsani College of Medicine, University of Southern Florida, Tampa, FL 33606, USA
| | - Pooja Jhaveri
- Department of Pediatrics, Penn State Hershey College of Medicine, Hershey, PA 17033, USA
| | - Adam T. Schmidt
- Department of Psychological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Steven D. Hicks
- Department of Pediatrics, Penn State Hershey College of Medicine, Hershey, PA 17033, USA
- Correspondence: ; Tel.: +1-717-531-0003
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25
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Song J, Zheng A, Li S, Zhang W, Zhang M, Li X, Jin F, Ji Z. Clinical significance and prognostic value of small nucleolar RNA SNORA38 in breast cancer. Front Oncol 2022; 12:930024. [PMID: 36158687 PMCID: PMC9500313 DOI: 10.3389/fonc.2022.930024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/10/2022] [Indexed: 12/24/2022] Open
Abstract
BackgroundBreast cancer is the most common malignant tumor among women worldwide, and breast cancer stem cells (BCSCs) are believed to be the source of tumorigenesis. New findings suggest that small nucleolar RNAs (snoRNAs) play a significant role in tumor development.MethodsThe Cancer Genome Atlas (TCGA) and Kaplan–Meier survival analysis were used to demonstrate expression and survival of SNORA38 signature. In situ hybridization (ISH) and immunohistochemical (IHC) were conducted to analyze the correlation between SNORA38 and stemness biomarker in 77 BC samples. Gene Set Enrichment Analysis (GSEA) was performed to investigate the mechanisms related to SNORA38 expression in BC. Real-time qPCR was employed to evaluate the expression of SNORA38 in breast cancer cell lines.ResultsIn the public database and patients’ biopsies, SNORA38 was significantly up-regulated in breast cancer. Furthermore, the expression of SNORA38 was significantly correlated with tumor size, lymph node metastasis, and TNM stage, among which tumor size was an independent factor for SNORA38 expression. Higher SNORA38 expression was associated with shorter overall survival (OS). Meanwhile, SNORA38 was positively associated with the stem cell marker OCT-4, which suggested that SNORA38 might be related to breast cancer stemness.ConclusionsSNORA38 is an important carcinogenic snoRNA in breast cancer and might be a prognostic biomarker for breast cancer.
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Affiliation(s)
- Jian Song
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, China
| | - Ang Zheng
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, China
| | - Shan Li
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, China
| | - Wenrong Zhang
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, China
| | - Meilin Zhang
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, China
| | - Xingzhe Li
- Department of Ultrasound, The First Hospital of China Medical University, Shenyang, China
| | - Feng Jin
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, China
- *Correspondence: Feng Jin, ; Ziyao Ji,
| | - Ziyao Ji
- Department of Ultrasound, The First Hospital of China Medical University, Shenyang, China
- *Correspondence: Feng Jin, ; Ziyao Ji,
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26
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Non-Coding RNAs in Hepatocellular Carcinoma. LIVERS 2022. [DOI: 10.3390/livers2030017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Liver cancer ranks as the fourth leading cause of cancer-related deaths. Despite extensive research efforts aiming to evaluate the biological mechanisms underlying hepatocellular carcinoma (HCC) development, little has been translated towards new diagnostic and treatment options for HCC patients. Historically, the focus has been centered on coding RNAs and their respective proteins. However, significant advances in sequencing and RNA detection technologies have shifted the research focus towards non-coding RNAs (ncRNA), as well as their impact on HCC development and progression. A number of studies reported complex post-transcriptional interactions between various ncRNA and coding RNA molecules. These interactions offer insights into the role of ncRNAs in both the known pathways leading to oncogenesis, such as dysregulation of p53, and lesser-known mechanisms, such as small nucleolar RNA methylation. Studies investigating these mechanisms have identified prevalent ncRNA changes in microRNAs, snoRNAs, and long non-coding RNAs that can both pre- and post-translationally regulate key factors in HCC progression. In this review, we present relevant publications describing ncRNAs to summarize the impact of different ncRNA species on liver cancer development and progression and to evaluate recent attempts at clinical translation.
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27
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Dome A, Dymova M, Richter V, Stepanov G. Post-Transcriptional Modifications of RNA as Regulators of Apoptosis in Glioblastoma. Int J Mol Sci 2022; 23:9272. [PMID: 36012529 PMCID: PMC9408889 DOI: 10.3390/ijms23169272] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/16/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
This review is devoted to changes in the post-transcriptional maturation of RNA in human glioblastoma cells, which leads to disruption of the normal course of apoptosis in them. The review thoroughly highlights the latest information on both post-transcriptional modifications of certain regulatory RNAs, associated with the process of apoptosis, presents data on the features of apoptosis in glioblastoma cells, and shows the relationship between regulatory RNAs and the apoptosis in tumor cells. In conclusion, potential target candidates are presented that are necessary for the development of new drugs for the treatment of glioblastoma.
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Affiliation(s)
| | - Maya Dymova
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
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28
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Cerneckis J, Cui Q, He C, Yi C, Shi Y. Decoding pseudouridine: an emerging target for therapeutic development. Trends Pharmacol Sci 2022; 43:522-535. [DOI: 10.1016/j.tips.2022.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/12/2022] [Accepted: 03/22/2022] [Indexed: 01/18/2023]
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Small non-coding RNA profiling in breast cancer: plasma U6 snRNA, miR-451a and miR-548b-5p as novel diagnostic and prognostic biomarkers. Mol Biol Rep 2022; 49:1955-1971. [PMID: 34993725 DOI: 10.1007/s11033-021-07010-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 11/24/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Breast cancer is a leading cause of cancer-related death in women. Most cases are invasive ductal carcinomas of no special type (NST breast carcinomas). METHODS AND RESULTS In this prospective, multicentric biomarker discovery study, we analyzed the expression of small non-coding RNAs (mainly microRNAs) in plasma by qPCR and evaluated their association with NST breast cancer. Large-scale expression profiling and subsequent validations have been performed in patient and control groups and compared with clinicopathological data. Small nuclear U6 snRNA, miR-548b-5p and miR-451a have been identified as candidate biomarkers. U6 snRNA was remarkably overexpressed in all the validations, miR-548b-5p levels were generally elevated and miR-451a expression was mostly downregulated in breast cancer groups. Combined U6 snRNA/miR-548b-5p signature demonstrated the best diagnostic performance based on the ROC curve analysis with AUC of 0.813, sensitivity 73.1% and specificity 82.6%. There was a trend towards increased expression of both miR-548b-5p and U6 snRNA in more advanced stages. Further, increased miR-548b-5p levels have been partially associated with higher grades, multifocality, Ki-67 positivity, and luminal B rather than luminal A samples. On the other hand, an association has been observed between high miR-451a expression and progesterone receptor positivity, lower grade, unifocal samples, Ki-67-negativity, luminal A rather than luminal B samples as well as improved progression-free survival and overall survival. CONCLUSIONS Our results indicated that U6 snRNA and miR-548b-5p may have pro-oncogenic functions, while miR-451a may act as tumor suppressor in breast cancer.
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Zhou J, Zhu X, Long J. Insights into the Prognostic Value of Small Nucleolar RNA U81 and SNORA7B in Breast Cancer. Int J Gen Med 2022. [DOI: 10.2147/ijgm.s345945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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31
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Santos P, Nunes S, Franchi F, Giroto A, Fontes P, Pinheiro V, Castilho A. Expression of bta-miR-222 and LHCGR in bovine cultured granulosa cells: Impact of follicle deviation and regulation by FSH/insulin in vitro. Theriogenology 2022; 182:71-77. [DOI: 10.1016/j.theriogenology.2022.01.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 10/19/2022]
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32
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Wan R, Bai L, Cai C, Ya W, Jiang J, Hu C, Chen Q, Zhao B, Li Y. Discovery of tumor immune infiltration-related snoRNAs for predicting tumor immune microenvironment status and prognosis in lung adenocarcinoma. Comput Struct Biotechnol J 2021; 19:6386-6399. [PMID: 34938414 PMCID: PMC8649667 DOI: 10.1016/j.csbj.2021.11.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/15/2021] [Accepted: 11/20/2021] [Indexed: 11/17/2022] Open
Abstract
Lung adenocarcinoma (LUAD) has a high mortality rate and is difficult to diagnose and treat in its early stage. Previous studies have demonstrated that small nucleolar RNAs (snoRNAs) play a critical role in tumor immune infiltration and the development of a variety of solid tumors. However, there have been no studies on the correlation between tumor-infiltrating immune-related snoRNAs (TIISRs) and LUAD. In this study, we filtered six immune-related snoRNAs based on the tissue specificity index (TSI) and expression profile of all snoRNAs between all LUAD cell lines from the Cancer Cell Line Encyclopedia and 21 types of immune cells from the Gene Expression Omnibus database. Further, we performed real-time quantitative polymerase chain reaction (RT-qPCR) to validate the expression status of these snoRNAs on peripheral blood mononuclear cells (PBMCs) and lung cancer cell lines. Next, we developed a TIISR signature based on the expression profiles of snoRNAs from 479 LUAD patients filtered by the random survival forest algorithm. We then analyzed the value of this TIISR signature (TIISR risk score) for assessing tumor immune infiltration, immune checkpoint inhibitor (ICI) treatment response, and the prognosis of LUAD between groups with high and low TIISR risk score. Further, we found that the TIISR risk score groups showed significant differences in biological characteristics and that the risk score could be used to assess the level of tumor immune cell infiltration, thereby predicting prognosis and responsiveness to immunotherapy in LUAD patients.
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Key Words
- AUC, area under the curve
- CCLE, Cancer Cell Line Encyclopedia
- FPKM, fragments per kilobase of transcript per million
- GEO, Gene Expression Omnibus
- GO, gene ontology
- GSVA, gene set variation analysis
- HIC, immunohistochemistry
- HR, hazard ratio
- ICIs, immune checkpoints inhibitors
- IF, immunofluorescence
- Immune checkpoints
- LUAD, lung adenocarcinoma
- Lung adenocarcinoma
- NK cell, natural killer cell
- PBMC, Peripheral Blood Mononuclear Cell
- ROC, receiver operating characteristic
- RSF, random survival forest
- RT-qPCR, Real-time Quantitative Polymerase Chain Reaction
- Small nucleolar RNAs
- TCGA, The Cancer Genome Atlas
- TIISR signature
- TIISR, tumor-infiltrating immune-related snoRNA
- TIME, tumor immune microenvironment
- TPM, transcripts per kilobase million
- TSI, tissue specificity index
- Tumor cell immune infiltration
- ncRNA, noncoding RNA
- snoRNAs, small nucleolar RNAs
- ssGSEA, single-sample gene set enrichment analysis
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Affiliation(s)
- Rongjun Wan
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China, 410008
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China. 410008
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China. 410008
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China. 410008
- National Clinical Research Center for Geriatric Disorders,Xiangya Hospital, Changsha, Hunan, P.R. China, 410008
| | - Lu Bai
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China, 410008
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China. 410008
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China. 410008
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China. 410008
- National Clinical Research Center for Geriatric Disorders,Xiangya Hospital, Changsha, Hunan, P.R. China, 410008
| | - Changjing Cai
- National Clinical Research Center for Geriatric Disorders,Xiangya Hospital, Changsha, Hunan, P.R. China, 410008
| | - Wang Ya
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China, 410008
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China. 410008
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China. 410008
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China. 410008
- National Clinical Research Center for Geriatric Disorders,Xiangya Hospital, Changsha, Hunan, P.R. China, 410008
| | - Juan Jiang
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China, 410008
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China. 410008
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China. 410008
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China. 410008
- National Clinical Research Center for Geriatric Disorders,Xiangya Hospital, Changsha, Hunan, P.R. China, 410008
| | - Chengping Hu
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China, 410008
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China. 410008
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China. 410008
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China. 410008
- National Clinical Research Center for Geriatric Disorders,Xiangya Hospital, Changsha, Hunan, P.R. China, 410008
| | - Qiong Chen
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China, 410008
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China. 410008
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China. 410008
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China. 410008
- National Clinical Research Center for Geriatric Disorders,Xiangya Hospital, Changsha, Hunan, P.R. China, 410008
| | - Bingrong Zhao
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China, 410008
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China. 410008
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China. 410008
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China. 410008
- National Clinical Research Center for Geriatric Disorders,Xiangya Hospital, Changsha, Hunan, P.R. China, 410008
| | - Yuanyuan Li
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China, 410008
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China. 410008
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China. 410008
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China. 410008
- National Clinical Research Center for Geriatric Disorders,Xiangya Hospital, Changsha, Hunan, P.R. China, 410008
- Corresponding author.
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James V, Nizamudeen ZA, Lea D, Dottorini T, Holmes TL, Johnson BB, Arkill KP, Denning C, Smith JGW. Transcriptomic Analysis of Cardiomyocyte Extracellular Vesicles in Hypertrophic Cardiomyopathy Reveals Differential snoRNA Cargo. Stem Cells Dev 2021; 30:1215-1227. [PMID: 34806414 PMCID: PMC8742282 DOI: 10.1089/scd.2021.0202] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is characterized by increased left ventricular wall thickness that can lead to devastating conditions such as heart failure and sudden cardiac death. Despite extensive study, the mechanisms mediating many of the associated clinical manifestations remain unknown and human models are required. To address this, human-induced pluripotent stem cell (hiPSC) lines were generated from patients with a HCM-associated mutation (c.ACTC1G301A) and isogenic controls created by correcting the mutation using CRISPR/Cas9 gene editing technology. Cardiomyocytes (hiPSC-CMs) were differentiated from these hiPSCs and analyzed at baseline, and at increased contractile workload (2 Hz electrical stimulation). Released extracellular vesicles (EVs) were isolated and characterized after a 24-h culture period and transcriptomic analysis performed on both hiPSC-CMs and released EVs. Transcriptomic analysis of cellular mRNA showed the HCM mutation caused differential splicing within known HCM pathways, and disrupted metabolic pathways. Analysis at increasing contraction frequency showed further disruption of metabolic gene expression, with an additive effect in the HCM background. Intriguingly, we observed differences in snoRNA cargo within HCM released EVs that specifically altered when HCM hiPSC-CMs were subjected to increased workload. These snoRNAs were predicted to have roles in post-translational modifications and alternative splicing, processes differentially regulated in HCM. As such, the snoRNAs identified in this study may unveil mechanistic insight into unexplained HCM phenotypes and offer potential future use as HCM biomarkers or as targets in future RNA-targeting therapies.
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Affiliation(s)
- Victoria James
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom
| | - Zubair A Nizamudeen
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom
| | - Daniel Lea
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom
| | - Tania Dottorini
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom
| | - Terri L Holmes
- Faculty of Medicine and Health Sciences, Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - Benjamin B Johnson
- Faculty of Medicine and Health Sciences, Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - Kenton P Arkill
- School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Chris Denning
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - James G W Smith
- Faculty of Medicine and Health Sciences, Norwich Medical School, University of East Anglia, Norwich, United Kingdom
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Barros-Silva D, Klavert J, Jenster G, Jerónimo C, Lafontaine DLJ, Martens-Uzunova ES. The role of OncoSnoRNAs and Ribosomal RNA 2'-O-methylation in Cancer. RNA Biol 2021; 18:61-74. [PMID: 34775914 PMCID: PMC8677010 DOI: 10.1080/15476286.2021.1991167] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Ribosomes are essential nanomachines responsible for all protein production in cells. Ribosome biogenesis and function are energy costly processes, they are tightly regulated to match cellular needs. In cancer, major pathways that control ribosome biogenesis and function are often deregulated to ensure cell survival and to accommodate the continuous proliferation of tumour cells. Ribosomal RNAs (rRNAs) are abundantly modified with 2'-O-methylation (Nm, ribomethylation) being one of the most common modifications. In eukaryotic ribosomes, ribomethylation is performed by the methyltransferase Fibrillarin guided by box C/D small nucleolar RNAs (snoRNAs). Accumulating evidences indicate that snoRNA expression and ribosome methylation profiles are altered in cancer. Here we review our current knowledge on differential snoRNA expression and rRNA 2ʹ-O methylation in the context of human malignancies, and discuss the consequences and opportunities for cancer diagnostics, prognostics, and therapeutics.
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Affiliation(s)
- Daniela Barros-Silva
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands.,Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), Porto, Portugal
| | - Jonathan Klavert
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Guido Jenster
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (Icbas-up), Porto, Portugal
| | - Denis L J Lafontaine
- Rna Molecular Biology, Fonds De La Recherche Scientifique (F.r.s./fnrs), Université Libre De Bruxelles (Ulb), BioPark Campus, Gosselies, Belgium
| | - Elena S Martens-Uzunova
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
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Small nucleolar RNA is potential as a novel player in leukemogenesis and clinical application. BLOOD SCIENCE 2021; 3:122-131. [PMID: 35402848 PMCID: PMC8975097 DOI: 10.1097/bs9.0000000000000091] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/21/2021] [Indexed: 12/19/2022] Open
Abstract
Lack of clarity of the mechanisms that underlie leukemogenesis obstructs the diagnosis, prognosis, and treatment of leukemia. Research has found that small nuclear RNA (snoRNA) plays an essential role in leukemia. These small non-coding RNAs are involved in ribosome biogenesis, including the 2′-O-methylation and pseudouridylation of precursor ribosomal RNA (pre-rRNA), and pre-rRNA splicing. Recently, many snoRNAs were found to be orphans that have no predictable RNA modification targets, but these RNAs have always been found to be located in different subcellular organelles, and they play diverse roles. Using high-throughput technology, snoRNA expression profiles have been revealed in leukemia, and some of the deregulated snoRNAs may regulate the cell cycle, differentiation, proliferation, and apoptosis in leukemic cells and confer drug resistance during leukemia treatment. In this review, we discuss the expression profiles and functions of snoRNAs, particularly orphan snoRNAs, in leukemia. It is possible that the dysregulated snoRNAs are promising diagnosis and prognosis markers for leukemia, which may serve as potential therapeutic targets in leukemia treatment.
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Circulating Exosomal miRNAs as Biomarkers in Epithelial Ovarian Cancer. Biomedicines 2021; 9:biomedicines9101433. [PMID: 34680550 PMCID: PMC8533168 DOI: 10.3390/biomedicines9101433] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 09/17/2021] [Accepted: 09/20/2021] [Indexed: 12/15/2022] Open
Abstract
Failure to detect early-stage epithelial ovarian cancer (EOC) is a major contributing factor to its low survival rate. Increasing evidence suggests that different subtypes of EOC may behave as distinct diseases due to their different cells of origins, histology and treatment responses. Therefore, the identification of EOC subtype-specific biomarkers that can early detect the disease should be clinically beneficial. Exosomes are extracellular vesicles secreted by different types of cells and carry biological molecules, which play important roles in cell-cell communication and regulation of various biological processes. Multiple studies have proposed that exosomal miRNAs present in the circulation are good biomarkers for non-invasive early detection of cancer. In this review, the potential use of exosomal miRNAs as early detection biomarkers for EOCs and their accuracy are discussed. We also review the differential expression of circulating exosomal miRNAs and cell-free miRNAs between different biofluid sources, i.e., plasma and serum, and touch on the issue of endogenous reference miRNA selection. Additionally, the current clinical trials using miRNAs for detecting EOCs are summarized. In conclusion, circulating exosomal miRNAs as the non-invasive biomarkers have a high potential for early detection of EOC and its subtypes, and are likely to be clinically important in the future.
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Kochhar P, Dwarkanath P, Ravikumar G, Thomas A, Crasta J, Thomas T, Kurpad AV, Mukhopadhyay A. Placental expression of RNU44, RNU48 and miR-16-5p: stability and relations with fetoplacental growth. Eur J Clin Nutr 2021; 76:722-729. [PMID: 34508256 DOI: 10.1038/s41430-021-01003-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 08/04/2021] [Accepted: 08/24/2021] [Indexed: 11/09/2022]
Abstract
BACKGROUND/OBJECTIVES The current study aimed to identify suitable reference miRNA for placental miRNA expression analysis in a set of well-characterized and fetal-sex balanced small- (SGA) and appropriate- (AGA) for gestational age full-term singleton pregnancies. SUBJECTS/METHODS In this retrospective study, placental samples (n = 106) from 35 SGA (19 male and 16 female) and 71 AGA (30 male and 41 female) full-term singleton pregnancies were utilized. Placental transcript abundance of three widely used reference miRNAs [miR-16-5p and Small nucleolar RNAs (snoRNAs) RNU44 and RNU48] were assessed by real-time quantitative PCR. Raw cycle threshold (Ct) analysis and RefFinder tool analysis were conducted for evaluating stability of expression of these miRNAs. RESULTS Raw Ct values of miR-16-5p were similar between SGA and AGA births (P = 0.140) and between male and female births within SGA (P = 0.159) and AGA (P = 0.060) births while that of RNU44 and RNU48 were higher in SGA births (P = 0.008 and 0.006 respectively) and in male births within the SGA group (P = 0.005) for RNU44 and in female births within the AGA group (P = 0.048) for RNU48. Across all 106 samples tested using the RefFinder tool, miR-16-5p and RNU44 were equally stable reference miRNAs. CONCLUSION We recommend miR-16-5p and RNU44 as suitable reference miRNAs for placental samples from settings similar to our study.
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Affiliation(s)
- P Kochhar
- Division of Nutrition, St. John's Research Institute, A recognized research centre of University of Mysore, Bangalore, Karnataka, India
| | - P Dwarkanath
- Division of Nutrition, St. John's Research Institute, A recognized research centre of University of Mysore, Bangalore, Karnataka, India
| | - G Ravikumar
- Department of Pathology, St John's Medical College Hospital, Bangalore, Karnataka, India
| | - A Thomas
- Department of Obstetrics and Gynaecology, St John's Medical College Hospital, Bangalore, Karnataka, India
| | - J Crasta
- Department of Pathology, St John's Medical College Hospital, Bangalore, Karnataka, India
| | - T Thomas
- Department of Biostatistics, St. John's Medical College Hospital, Bangalore, Karnataka, India
| | - A V Kurpad
- Division of Nutrition, St. John's Research Institute, A recognized research centre of University of Mysore, Bangalore, Karnataka, India
| | - A Mukhopadhyay
- Division of Nutrition, St. John's Research Institute, A recognized research centre of University of Mysore, Bangalore, Karnataka, India.
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Lambert M, Benmoussa A, Diallo I, Ouellet-Boutin K, Dorval V, Majeau N, Joly-Beauparlant C, Droit A, Bergeron A, Têtu B, Fradet Y, Pouliot F, Provost P. Identification of Abundant and Functional dodecaRNAs (doRNAs) Derived from Ribosomal RNA. Int J Mol Sci 2021; 22:9757. [PMID: 34575920 PMCID: PMC8467515 DOI: 10.3390/ijms22189757] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/02/2021] [Accepted: 09/05/2021] [Indexed: 12/17/2022] Open
Abstract
Using a modified RNA-sequencing (RNA-seq) approach, we discovered a new family of unusually short RNAs mapping to ribosomal RNA 5.8S, which we named dodecaRNAs (doRNAs), according to the number of core nucleotides (12 nt) their members contain. Using a new quantitative detection method that we developed, we confirmed our RNA-seq data and determined that the minimal core doRNA sequence and its 13-nt variant C-doRNA (doRNA with a 5' Cytosine) are the two most abundant doRNAs, which, together, may outnumber microRNAs. The C-doRNA/doRNA ratio is stable within species but differed between species. doRNA and C-doRNA are mainly cytoplasmic and interact with heterogeneous nuclear ribonucleoproteins (hnRNP) A0, A1 and A2B1, but not Argonaute 2. Reporter gene activity assays suggest that C-doRNA may function as a regulator of Annexin II receptor (AXIIR) expression. doRNAs are differentially expressed in prostate cancer cells/tissues and may control cell migration. These findings suggest that unusually short RNAs may be more abundant and important than previously thought.
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Affiliation(s)
- Marine Lambert
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Department of Microbiology, Infectious Diseases and Immunology, Université Laval, Quebec City, QC G1V 4G2, Canada
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Abderrahim Benmoussa
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Department of Microbiology, Infectious Diseases and Immunology, Université Laval, Quebec City, QC G1V 4G2, Canada
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Idrissa Diallo
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Department of Microbiology, Infectious Diseases and Immunology, Université Laval, Quebec City, QC G1V 4G2, Canada
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Katheryn Ouellet-Boutin
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Department of Microbiology, Infectious Diseases and Immunology, Université Laval, Quebec City, QC G1V 4G2, Canada
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Véronique Dorval
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
| | - Nathalie Majeau
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
| | - Charles Joly-Beauparlant
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
- Department of Molecular Medicine, Université Laval, Quebec City, QC G1V 4G2, Canada
| | - Arnaud Droit
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
- Department of Molecular Medicine, Université Laval, Quebec City, QC G1V 4G2, Canada
| | - Alain Bergeron
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
- Department of Surgery, Université Laval, Quebec City, QC G1R 2J6, Canada
| | - Bernard Têtu
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Yves Fradet
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
- Department of Surgery, Université Laval, Quebec City, QC G1R 2J6, Canada
| | - Frédéric Pouliot
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
- Department of Surgery, Université Laval, Quebec City, QC G1R 2J6, Canada
| | - Patrick Provost
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Department of Microbiology, Infectious Diseases and Immunology, Université Laval, Quebec City, QC G1V 4G2, Canada
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
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Baptista B, Riscado M, Queiroz J, Pichon C, Sousa F. Non-coding RNAs: Emerging from the discovery to therapeutic applications. Biochem Pharmacol 2021. [DOI: 10.1016/j.bcp.2021.114469 order by 22025--] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2022]
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40
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Garcia A, Dunoyer-Geindre S, Fontana P. Do miRNAs Have a Role in Platelet Function Regulation? Hamostaseologie 2021; 41:217-224. [PMID: 34192780 DOI: 10.1055/a-1478-2105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of non-coding RNAs known to repress mRNA translation and subsequent protein production. miRNAs are predicted to modulate many targets and are involved in regulating various cellular processes. Identifying their role in cell function regulation may allow circulating miRNAs to be used as diagnostic or prognostic markers of various diseases. Increasing numbers of clinical studies have shown associations between circulating miRNA levels and platelet reactivity or the recurrence of cardiovascular events. However, these studies differed regarding population selection, sample types used, miRNA quantification procedures, and platelet function assays. Furthermore, they often lacked functional validation of the miRNA identified in such studies. The latter step is essential to identifying causal relationships and understanding if and how miRNAs regulate platelet function. This review describes recent advances in translational research dedicated to identifying miRNAs' roles in platelet function regulation.
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Affiliation(s)
- A Garcia
- Geneva Platelet Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | | | - P Fontana
- Geneva Platelet Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Division of Angiology and Haemostasis, Geneva University Hospitals, Geneva, Switzerland
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Ghanbari S, Salimi A, Rahmani S, Nafissi N, Sharifi-Zarchi A, Mowla SJ. miR-361-5p as a promising qRT-PCR internal control for tumor and normal breast tissues. PLoS One 2021; 16:e0253009. [PMID: 34101749 PMCID: PMC8186776 DOI: 10.1371/journal.pone.0253009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 05/27/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND One of the most widely used evaluation methods in miRNA experiments is qRT-PCR. However, selecting suitable internal controls (IC) is crucial for qRT-PCR experiments. Currently, there is no consensus on the ICs for miRNA qRT-PCR experiments in breast cancer. To this end, we tried to identify the most stable (the least expression alteration) and promising miRNAs in normal and tumor breast tissues by employing TCGA miRNA-Seq data and then experimentally validated them on fresh clinical samples. METHODS A multi-component scoring system was used which takes into account multiple expression stability criteria as well as correlation with clinical characteristics. Furthermore, we extended the scoring system for more than two biological sub-groups. TCGA BRCA samples were analyzed based on two grouping criteria: Tumor & Normal samples and Tumor subtypes. The top 10 most stable miRNAs were further investigated by differential expression and survival analysis. Then, we examined the expression level of the top scored miRNA (hsa-miR-361-5p) along with two commonly used ICs hsa-miR-16-5p and U48 on 34 pairs of Primary breast tumor and their adjacent normal tissues using qRT-PCR. RESULTS According to our multi-component scoring system, hsa-miR-361-5p had the highest stability score in both grouping criteria and hsa-miR-16-5p showed significantly lower scores. Based on our qRT-PCR assay, while U48 was the most abundant IC, hsa-miR-361-5p had lower standard deviation and also was the only IC capable of detecting a significant up-regulation of hsa-miR-21-5p in breast tumor tissue. CONCLUSIONS miRNA-Seq data is a great source to discover stable ICs. Our results demonstrated that hsa-miR-361-5p is a highly stable miRNA in tumor and non-tumor breast tissue and we recommend it as a suitable reference gene for miRNA expression studies in breast cancer. Additionally, although hsa-miR-16-5p is a commonly used IC, it's not a suitable one for breast cancer studies.
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Affiliation(s)
- Sogol Ghanbari
- Molecular Genetics Department, Biological Sciences Faculty, Tarbiat Modares University, Tehran, Iran
| | - Adel Salimi
- Computer Engineering Department, Sharif University of Technology, Tehran, Iran
| | - Saeid Rahmani
- Computer Engineering Department, Sharif University of Technology, Tehran, Iran
| | - Nahid Nafissi
- Surgical Department, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Ali Sharifi-Zarchi
- Computer Engineering Department, Sharif University of Technology, Tehran, Iran
| | - Seyed Javad Mowla
- Molecular Genetics Department, Biological Sciences Faculty, Tarbiat Modares University, Tehran, Iran
- * E-mail:
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Wang J, Huang R, Huang Y, Chen Y, Chen F. Overexpression of NOP58 as a Prognostic Marker in Hepatocellular Carcinoma: A TCGA Data-Based Analysis. Adv Ther 2021; 38:3342-3361. [PMID: 34014550 DOI: 10.1007/s12325-021-01762-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/27/2021] [Indexed: 12/24/2022]
Abstract
INTRODUCTION NOP58 ribonucleoprotein, a core component of box C/D small nucleolar ribonucleoproteins, is involved in various cell physiological processes. However, its role in hepatocellular carcinoma (HCC) remains very unclear. We aim to investigate NOP58 expression and its probable prognostic value in patients with HCC based on The Cancer Genome Atlas (TCGA) database. METHODS RNA sequencing data and clinicopathological characteristics of patients with HCC were collected from TCGA database. Expression of NOP58 in HCC tissues and normal tissues was analyzed by Wilcoxon rank-sum test. Patients were divided into high and low subgroups according to median expression of NOP58. Logistic regression, gene set enrichment analysis (GSEA), and single-sample gene set enrichment analysis (ssGSEA) were conducted to annotate biological function and immune infiltration of NOP58. RESULTS NOP58 was significantly overexpressed in HCC tissues and correlated with significantly high tumor stage [odds ratio (OR) 10.01, 95% confidence interval (CI) 10.01-10.03; P = 0.003], advanced pathologic stage (OR 10.02, 95% CI 10.01-10.03; P < 0.001), advanced histologic stage (OR 10.03, 95% CI 10.02-10.04; P < 0.001), vascular invasion (OR 10.02, 95% CI 10.01-10.03; P = 0.003), poor performance status (OR 10.01, 95% CI 10.01-10.03; P = 0.003), and Mut-TP53 status (OR 10.02, 95% CI 10.01-10.03; P < 0.001). Elevated NOP58 expression had poor disease-specific survival (DSS; P < 0.001), progression-free interval (P = 0.006), and overall survival (OS; P < 0.001). NOP58 expression was independently correlated with OS (HR 1.731, 95% CI 10.037-2.890; P = 0.036). GSEA demonstrated that various cell cycle pathways along with RB-1 pathway, interleukin-10 signaling, regulation of TP53 activity, and P53 downstream pathway were differentially enriched in NOP58 high expression phenotype. NOP58 expression was positively correlated with infiltrating the levels of T helper type 2 (Th2) cells. CONCLUSIONS Overexpression of NOP58 is negatively correlated with overall survival in patients with HCC and might be a potential biomarker for prognosis of HCC.
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Papadaki C, Thomopoulou K, Monastirioti A, Koronakis G, Papadaki MA, Rounis K, Vamvakas L, Nikolaou C, Mavroudis D, Agelaki S. MicroRNAs Regulating Tumor and Immune Cell Interactions in the Prediction of Relapse in Early Stage Breast Cancer. Biomedicines 2021; 9:biomedicines9040421. [PMID: 33924670 PMCID: PMC8069787 DOI: 10.3390/biomedicines9040421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/10/2021] [Accepted: 04/11/2021] [Indexed: 11/20/2022] Open
Abstract
MicroRNAs (miRNAs) are involved in the regulation of immune response and hold an important role in tumor immune escape. We investigated the differential expression of the immunomodulatory miR-10b, miR-19a, miR-20a, miR-126, and miR-155 in the plasma of healthy women and patients with early stage breast cancer and interrogated their role in the prediction of patients’ relapse. Blood samples were obtained from healthy women (n = 20) and patients with early stage breast cancer (n = 140) before adjuvant chemotherapy. Plasma miRNA expression levels were assessed by RT-qPCR. Relapse predicting models were developed using binary logistic regression and receiver operating curves (ROC) were constructed to determine miRNA sensitivity and specificity. Only miR-155 expression was lower in patients compared with healthy women (p = 0.023), whereas miR-155 and miR-10b were lower in patients who relapsed compared with healthy women (p = 0.039 and p = 0.002, respectively). MiR-155 expression combined with axillary lymph node infiltration and tumor grade demonstrated increased capability in distinguishing relapsed from non-relapsed patients [(area under the curve, (AUC = 0.861; p < 0.001)]. Combined miR-19a and miR-20a expression had the highest performance in discriminating patients with early relapse (AUC = 0.816; p < 0.001). Finally, miR-10b in combination with lymph node status and grade had the highest accuracy to discriminate patients with late relapse (AUC = 0.971; p < 0.001). The robustness of the relapse predicting models was further confirmed in a 10-fold cross validation. Deregulation of circulating miRNAs involved in tumor-immune interactions may predict relapse in early stage breast cancer. Their successful clinical integration could potentially address the significance challenge of treatment escalation or de-escalation according to the risk of recurrence.
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Affiliation(s)
- Chara Papadaki
- Laboratory of Translational Oncology, School of Medicine, University of Crete, Heraklion, Vassilika Vouton, 71003 Crete, Greece; (C.P.); (A.M.); (M.A.P.); (D.M.)
| | - Konstantina Thomopoulou
- Department of Medical Oncology, University General Hospital of Heraklion, Vassilika Vouton, 71110 Crete, Greece; (K.T.); (G.K.); (K.R.); (L.V.)
| | - Alexia Monastirioti
- Laboratory of Translational Oncology, School of Medicine, University of Crete, Heraklion, Vassilika Vouton, 71003 Crete, Greece; (C.P.); (A.M.); (M.A.P.); (D.M.)
| | - George Koronakis
- Department of Medical Oncology, University General Hospital of Heraklion, Vassilika Vouton, 71110 Crete, Greece; (K.T.); (G.K.); (K.R.); (L.V.)
| | - Maria A. Papadaki
- Laboratory of Translational Oncology, School of Medicine, University of Crete, Heraklion, Vassilika Vouton, 71003 Crete, Greece; (C.P.); (A.M.); (M.A.P.); (D.M.)
| | - Konstantinos Rounis
- Department of Medical Oncology, University General Hospital of Heraklion, Vassilika Vouton, 71110 Crete, Greece; (K.T.); (G.K.); (K.R.); (L.V.)
| | - Lambros Vamvakas
- Department of Medical Oncology, University General Hospital of Heraklion, Vassilika Vouton, 71110 Crete, Greece; (K.T.); (G.K.); (K.R.); (L.V.)
| | - Christoforos Nikolaou
- Department of Biology, University of Crete, Heraklion, Vassilika Vouton, 70013 Crete, Greece;
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation of Research and Technology (FORTH), Heraklion, Vassilika Vouton, 70013 Crete, Greece
- Biomedical Science Research Center “Alexander Fleming”, Institute of Bioinnovation, 16672 Athens, Greece
| | - Dimitrios Mavroudis
- Laboratory of Translational Oncology, School of Medicine, University of Crete, Heraklion, Vassilika Vouton, 71003 Crete, Greece; (C.P.); (A.M.); (M.A.P.); (D.M.)
- Department of Medical Oncology, University General Hospital of Heraklion, Vassilika Vouton, 71110 Crete, Greece; (K.T.); (G.K.); (K.R.); (L.V.)
| | - Sofia Agelaki
- Laboratory of Translational Oncology, School of Medicine, University of Crete, Heraklion, Vassilika Vouton, 71003 Crete, Greece; (C.P.); (A.M.); (M.A.P.); (D.M.)
- Department of Medical Oncology, University General Hospital of Heraklion, Vassilika Vouton, 71110 Crete, Greece; (K.T.); (G.K.); (K.R.); (L.V.)
- Correspondence: ; Tel.: +30-281-039-2438
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Tölle A, Jung K, Friedersdorff F, Maxeiner A, Lein M, Fendler A, Stephan C. The discriminative ability of Prostate Health Index to detect prostate cancer is enhanced in combination with miR-222-3p. Cancer Biomark 2021; 30:381-393. [PMID: 33361585 DOI: 10.3233/cbm-201600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
BACKGROUND There is an urgent need for better prostate cancer (PCa) biomarkers due to the low specificity of prostate specific antigen (PSA). OBJECTIVE Prostate Health Index (PHI) is an advanced PSA-based test for early detection of PCa. The present study aim was to investigate the potential improvement of diagnostic accuracy of PHI by its combination with suitable discriminative microRNAs (miRNAs). METHODS A two-phase study was performed. In a discovery phase, a panel of 177 miRNAs was measured in ten men with biopsy proven PCa and ten men with histologically no evidence of malignancy (NEM). These results were validated in a second phase including 25 patients in each group. The patients of all groups were matched regarding their PSA values and PHI were measured. RESULTS Based on data in the discovery phase, four elevated miRNAs were selected as potential miRNA candidates for further validation. A combination of miR-222-3p as the best discriminative miRNA with PHI extended the diagnostic accuracy of PHI from an AUC value of 0.690 to 0.787 and resulted in a sensitivity of 72.0% and a specificity of 84.0%. CONCLUSION Circulating microRNAs show useful diagnostic potential in combination with common used biomarkers to enhance their diagnostic power.
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Affiliation(s)
- Angelika Tölle
- Department of Urology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Klaus Jung
- Department of Urology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute for Urologic Research, Berlin, Germany
| | - Frank Friedersdorff
- Department of Urology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Andreas Maxeiner
- Department of Urology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Michael Lein
- Berlin Institute for Urologic Research, Berlin, Germany.,Department of Urology, Sana Medical Center Offenbach, Offenbach/Main, Germany
| | - Annika Fendler
- Department of Urology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Max Delbrueck Center for Molecular Medicine in the Helmholtz Association, Cancer Research Program, Berlin, Germany.,Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Carsten Stephan
- Department of Urology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute for Urologic Research, Berlin, Germany
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Breast Cancer and the Other Non-Coding RNAs. Int J Mol Sci 2021; 22:ijms22063280. [PMID: 33807045 PMCID: PMC8005115 DOI: 10.3390/ijms22063280] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 03/19/2021] [Indexed: 12/12/2022] Open
Abstract
Breast cancer is very heterogenous and the most common gynaecological cancer, with various factors affecting its development. While its impact on human lives and national health budgets is still rising in almost all global areas, many molecular mechanisms affecting its onset and development remain unclear. Conventional treatments still prove inadequate in some aspects, and appropriate molecular therapeutic targets are required for improved outcomes. Recent scientific interest has therefore focused on the non-coding RNAs roles in tumour development and their potential as therapeutic targets. These RNAs comprise the majority of the human transcript and their broad action mechanisms range from gene silencing to chromatin remodelling. Many non-coding RNAs also have altered expression in breast cancer cell lines and tissues, and this is often connected with increased proliferation, a degraded extracellular environment, and higher endothelial to mesenchymal transition. Herein, we summarise the known abnormalities in the function and expression of long non-coding RNAs, Piwi interacting RNAs, small nucleolar RNAs and small nuclear RNAs in breast cancer, and how these abnormalities affect the development of this deadly disease. Finally, the use of RNA interference to suppress breast cancer growth is summarised.
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Yasser MB, Abdellatif M, Emad E, Jafer A, Ahmed S, Nageb L, Abdelshafy H, Al-Anany AM, Al-Arab MAE, Gibriel AA. Circulatory miR-221 & miR-542 expression profiles as potential molecular biomarkers in Hepatitis C Virus mediated liver cirrhosis and hepatocellular carcinoma. Virus Res 2021; 296:198341. [PMID: 33607184 DOI: 10.1016/j.virusres.2021.198341] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 01/05/2021] [Accepted: 02/10/2021] [Indexed: 02/06/2023]
Abstract
Chronic hepatitis C virus (cHCV) is a leading cause for liver cirrhosis (LC) and hepatocellular carcinoma (HCC) globally. So far, there is no optimal non-invasive biomarker for diagnosing HCV associated hepatic disorders. Circulatory miRNAs have drawn great attention as potential non-invasive biomarkers in various diseases. We quantified miR-221 and miR-542 levels in the plasma of 153 Egyptian patients (38 healthy controls (HC), 36 cHCV, 39 HCV-LC and 40 HCV mediated HCC groups) using qRT-PCR. All diseased groups exhibited significant upregulation in miR-221 expression (P < 0.001) with an increasing trend towards late stages (HCV-LC+HCV-HCC) as compared to early stages (cHCV). MiR-221 could significantly discriminate HCC patients from cHCV and HCV-LC with (AUC=0.698; P = 0.002) and (AUC=0.644; P = 0.032) respectively. Furthermore, miR-221 could significantly discriminate between HCC and non-HCC groups (AUC=0.670, P<0.001). HCV-LC & cHCV groups showed significant upregulation in miR-542 with remarkable downregulation in HCC group (P = 0.004). MiR-542 exhibited diagnostic power of (AUC=0.640; P = 0.044) and (AUC= 0.644; P = 0.040) for discriminating HCV-LC from HCC and cHCV groups respectively. Both miR-221 and miR-542 were significantly upregulated in cirrhotic group (HCV-LC) (P = 0.046 and P = 0.002 respectively) as compared to non-cirrhotic group (cHCV+HC). Combining both miRNAs in a panel significantly improved diagnostic performance as follows; HC and HCC (AUC=0.714, P < 0.001); HCC and LC (AUC=0.714, P = 0.001); HC and LC (AUC=0.710, P = 0.002) and also cHCV and HCC (AUC=0.672, P = 0.006). In conclusion, both miR-221 & miR-542 could stand as a standalone biomarker for staging various HCV associated disorders. Combining them would greatly enhance their diagnostic potential.
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Affiliation(s)
- Montaser Bellah Yasser
- Final year undergraduate students, Faculty of Pharmacy, The British University in Egypt, Egypt
| | - Mahmoud Abdellatif
- Final year undergraduate students, Faculty of Pharmacy, The British University in Egypt, Egypt
| | - Esraa Emad
- Final year undergraduate students, Faculty of Pharmacy, The British University in Egypt, Egypt
| | - Afnan Jafer
- Final year undergraduate students, Faculty of Pharmacy, The British University in Egypt, Egypt
| | - Samar Ahmed
- Final year undergraduate students, Faculty of Pharmacy, The British University in Egypt, Egypt
| | - Lobna Nageb
- Final year undergraduate students, Faculty of Pharmacy, The British University in Egypt, Egypt
| | - Hanan Abdelshafy
- Final year undergraduate students, Faculty of Pharmacy, The British University in Egypt, Egypt
| | - Amany Mohamed Al-Anany
- Biochemistry & Molecular Biology Department, Faculty of Pharmacy, The British University in Egypt (BUE), Suez Rd, El Sherouk City, Cairo Governorate, 11837 Egypt
| | - Mohamed Ali Ezz Al-Arab
- National Hepatology &Tropical Medicine Research Institute (NHTMRI), 10 El-Sayeda Zainab, Cairo Governorate, Egypt
| | - Abdullah Ahmed Gibriel
- Biochemistry & Molecular Biology Department, Faculty of Pharmacy, The British University in Egypt (BUE), Suez Rd, El Sherouk City, Cairo Governorate, 11837 Egypt.
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Wan Q, Tang M, Sun SL, Hu J, Sun ZJ, Fang YT, He TC, Zhang Y. SNHG3 promotes migration, invasion, and epithelial-mesenchymal transition of breast cancer cells through the miR-186-5p/ZEB1 axis. Am J Transl Res 2021; 13:585-600. [PMID: 33594311 PMCID: PMC7868844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 12/11/2020] [Indexed: 06/12/2023]
Abstract
Increasing evidence suggests that the long non-coding RNAs (lncRNAs) participate in the development and progression of breast cancer. The lncRNA small nucleolar RNA host gene 3 (SNHG3) reportedly acts as an oncogene in hepatocellular carcinoma and colorectal cancer; however, little is known about the biological function and oncogenic mechanisms of SNHG3 in breast cancer. We demonstrated that the expression of SNHG3 was abnormally high in breast cancer tissues and cells, and transgenic expression of SNHG3 promoted the proliferation, migration, and invasion of breast cancer cell lines (MCF-7 and MDA-MB-231). The mean volume of the xenografts from the SNHG3-knockdown MCF-7 cells was lower than that of the control tumor cells. Moreover, the expression of zinc finger E-box binding homeobox 1 (ZEB1) increased after SNHG3 overexpression and vice versa. Overexpression of ZEB1 triggered cellular migration and invasion behaviors. Analysis of the mechanism underlying these effects suggested that SNHG3 is an effective sink for miR-186-5p and modulates ZEB1 repression, conferring an additional level to its post-transcriptional regulation. In conclusion, SNHG3 promotes the migration and invasion of breast cancer cells through miR-186-5p/ZEB1 regulation and the induction of the epithelial to mesenchymal transition, indicating that SNHG3 is a potential treatment target for breast cancer.
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Affiliation(s)
- Qun Wan
- Key Laboratory of Diagnostic Medicine Designated by The Chinese Ministry of Education, Chongqing Medical UniversityChongqing 400000, China
| | - Min Tang
- Key Laboratory of Diagnostic Medicine Designated by The Chinese Ministry of Education, Chongqing Medical UniversityChongqing 400000, China
| | - Shi-Lei Sun
- Key Laboratory of Diagnostic Medicine Designated by The Chinese Ministry of Education, Chongqing Medical UniversityChongqing 400000, China
| | - Jing Hu
- Key Laboratory of Diagnostic Medicine Designated by The Chinese Ministry of Education, Chongqing Medical UniversityChongqing 400000, China
| | - Zi-Jiu Sun
- Key Laboratory of Diagnostic Medicine Designated by The Chinese Ministry of Education, Chongqing Medical UniversityChongqing 400000, China
| | - Yu-Ting Fang
- Key Laboratory of Diagnostic Medicine Designated by The Chinese Ministry of Education, Chongqing Medical UniversityChongqing 400000, China
| | - Tong-Chuan He
- Molecular Oncology Laboratory, Department of Surgery, University of Chicago Medical CenterChicago, IL 60637, USA
| | - Yan Zhang
- Key Laboratory of Diagnostic Medicine Designated by The Chinese Ministry of Education, Chongqing Medical UniversityChongqing 400000, China
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Baptista B, Riscado M, Queiroz JA, Pichon C, Sousa F. Non-coding RNAs: Emerging from the discovery to therapeutic applications. Biochem Pharmacol 2021; 189:114469. [PMID: 33577888 DOI: 10.1016/j.bcp.2021.114469] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/03/2021] [Accepted: 02/04/2021] [Indexed: 02/06/2023]
Abstract
The knowledge about non-coding RNAs (ncRNAs) is rapidly increasing with new data continuously emerging, regarding their diverse types, applications, and roles. Particular attention has been given to ncRNA with regulatory functions, which may have a critical role both in biological and pathological conditions. As a result of the diversity of ncRNAs and their ubiquitous involvement in several biologic processes, ncRNA started to be considered in the biomedical field, with immense potential to be exploited either as biomarkers or as therapeutic agents in certain pathologies. Indeed, ncRNA-based therapeutics have been proposed in many disorders and some even reached clinical trials. However, to prepare an RNA product suitable for pharmacological applications, certain criteria must be fulfilled, and it has to be guaranteed RNA purity, stability, and bioactivity. So, in this review, the different types of ncRNAs are identified and characterized, by describing their biogenesis, functions, and applications. A perspective on the main challenges and innovative approaches for the future and broad therapeutic application of RNA is also presented.
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Affiliation(s)
- B Baptista
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Avenida Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - M Riscado
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Avenida Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - J A Queiroz
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Avenida Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - C Pichon
- Centre de Biophysique Moléculaire (CBM), UPR 4301 CNRS & University of Orléans Orléans, France
| | - F Sousa
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Avenida Infante D. Henrique, 6200-506 Covilhã, Portugal.
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Dsouza VL, Adiga D, Sriharikrishnaa S, Suresh PS, Chatterjee A, Kabekkodu SP. Small nucleolar RNA and its potential role in breast cancer - A comprehensive review. Biochim Biophys Acta Rev Cancer 2021; 1875:188501. [PMID: 33400969 DOI: 10.1016/j.bbcan.2020.188501] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/07/2020] [Accepted: 12/28/2020] [Indexed: 02/07/2023]
Abstract
Small Nucleolar RNAs (snoRNAs) are known for their canonical functions, including ribosome biogenesis and RNA modification. snoRNAs act as endogenous sponges that regulate miRNA expression. Thus, precise snoRNA expression is critical for fine-tuning miRNA expression. snoRNAs processed into miRNA-like sequences play a crucial role in regulating the expression of protein-coding genes similar to that of miRNAs. Recent studies have linked snoRNA deregulation to breast cancer (BC). Inappropriate snoRNA expression contributes to BC pathology by facilitating breast cells to acquire cancer hallmarks. Since snoRNAs show significant differential expression in normal and cancer conditions, measuring snoRNA levels could be useful for BC prognosis and diagnosis. The present article provides a comprehensive overview of the role of snoRNAs in breast cancer pathology. More specifically, we have discussed the regulation, biological function, signaling pathways, and clinical utility of abnormally expressed snoRNAs in BC. Besides, we have also discussed the role of snoRNA host genes in breast tumorigenesis and emerging and future research directions in the field of snoRNA and cancer.
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Affiliation(s)
- Venzil Lavie Dsouza
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Divya Adiga
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - S Sriharikrishnaa
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Padmanaban S Suresh
- School of Biotechnology, National Institute of Technology, Calicut, Kerala 673601, India
| | - Aniruddha Chatterjee
- Department of Pathology, Otago Medical School, Dunedin Campus, University of Otago, Dunedin, New Zealand
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
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50
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Toden S, Zumwalt TJ, Goel A. Non-coding RNAs and potential therapeutic targeting in cancer. Biochim Biophys Acta Rev Cancer 2021; 1875:188491. [PMID: 33316377 PMCID: PMC7856203 DOI: 10.1016/j.bbcan.2020.188491] [Citation(s) in RCA: 120] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 12/02/2020] [Accepted: 12/02/2020] [Indexed: 12/11/2022]
Abstract
Recent advances have begun to clarify the physiological and pathological roles of non-coding RNAs (ncRNAs) in various diseases, including cancer. Among these, microRNAs (miRNAs) have been the most studied and have emerged as key players that are involved in the regulation of important growth regulatory pathways in cancer pathogenesis. The ability of a single ncRNA to modulate the expression of multiple downstream gene targets and associated pathways, have provided a rationale to pursue them for therapeutic drug development in cancer. In this context, early data from pre-clinical studies have demonstrated that synthetic miRNA-based therapeutic molecules, along with various protective coating approaches, has allowed for their efficient delivery and anti-tumor activity. In fact, some of the miRNA-based cancer therapeutic strategies have shown promising results even in early-phase human clinical trials. While the enthusiasm for ncRNA-based cancer therapeutics continue to evolve, the field is still in the midst of unraveling a more precise understanding of the molecular mechanisms and specific downstream therapeutic targets of other lesser studied ncRNAs such as the long-non-coding RNAs, transfer RNAs, circular RNAs, small nucleolar RNAs, and piwi-interacting RNAs. This review article provides the current state of knowledge and the evolving principles for ncRNA-based therapeutic approaches in cancer, and specifically highlights the importance of data to date and the approaches that are being developed to overcome the challenges associated with their delivery and mitigating the off-target effects in human cancers.
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Affiliation(s)
- Shusuke Toden
- Center for Gastrointestinal Research; Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor Research Institute and Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas, USA
| | - Timothy J Zumwalt
- Center for Gastrointestinal Research; Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor Research Institute and Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas, USA
| | - Ajay Goel
- Center for Gastrointestinal Research; Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor Research Institute and Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas, USA; Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Duarte, CA, USA.
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