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Jagielski NP, Rai AK, Rajan KS, Mangal V, Garikipati VNS. A contemporary review of snoRNAs in cardiovascular health: RNA modification and beyond. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102087. [PMID: 38178918 PMCID: PMC10765057 DOI: 10.1016/j.omtn.2023.102087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
As cardiovascular diseases continue to be the leading cause of death worldwide, groundbreaking research is being conducted to mitigate their effects. This review looks into the potential of small nucleolar RNAs (snoRNAs) and the opportunity to use these molecular agents as therapeutic biomarkers for cardiovascular issues specific to the heart. Through an investigation of snoRNA biogenesis, functionality, and roles in cardiovascular diseases, this review relates our past and present knowledge of snoRNAs to the current scientific literature. Considering the initial discovery of snoRNAs and the studies thereafter analyzing the roles of snoRNAs in disease, we look forward to uncovering many other noncanonical functions that could lead researchers closer to finding preventive and curative solutions for cardiovascular diseases.
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Affiliation(s)
- Noah Peter Jagielski
- Aging + Cardiovascular Discovery Center, Department of Cardiovascular Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Amit Kumar Rai
- Aging + Cardiovascular Discovery Center, Department of Cardiovascular Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - K. Shanmugha Rajan
- Department of Chemical and Structural Biology, Weizmann Institute, Rehovot 76100 001, Israel
| | - Vatsal Mangal
- Aging + Cardiovascular Discovery Center, Department of Cardiovascular Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Venkata Naga Srikanth Garikipati
- Aging + Cardiovascular Discovery Center, Department of Cardiovascular Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
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Radhakrishnan S, Martin CA, Rammohan A, Vij M, Chandrasekar M, Rela M. Significance of nucleologenesis, ribogenesis, and nucleolar proteome in the pathogenesis and recurrence of hepatocellular carcinoma. Expert Rev Gastroenterol Hepatol 2023; 17:363-378. [PMID: 36919496 DOI: 10.1080/17474124.2023.2191189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
INTRODUCTION Emerging evidence suggests that enhanced ribosome biogenesis, increased size, and quantitative distribution of nucleoli are associated with dysregulated transcription, which in turn drives a cell into aberrant cellular proliferation and malignancy. Nucleolar alterations have been considered a prognostic histological marker for aggressive tumors. More recently, advancements in the understanding of chromatin network (nucleoplasm viscosity) regulated liquid-liquid phase separation mechanism of nucleolus formation and their multifunctional role shed light on other regulatory processes, apart from ribosomal biogenesis of the nucleolus. AREAS COVERED Using hepatocellular carcinoma as a model to study the role of nucleoli in tumor progression, we review the potential of nucleolus coalescence in the onset and development of tumors through non-ribosomal biogenesis pathways, thereby providing new avenues for early diagnosis and cancer therapy. EXPERT OPINION Molecular-based classifications have failed to identify the nucleolar-based molecular targets that facilitate cell-cycle progression. However, the algorithm-based tumor risk identification with high-resolution medical images suggests prominent nucleoli, karyotheca, and increased nucleus/cytoplasm ratio as largely associated with tumor recurrence. Nonetheless, the role of the non-ribosomal functions of nucleoli in tumorigenesis remains elusive. This clearly indicates the lacunae in the study of the nucleolar proteins pertaining to cancer. [Figure: see text].
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Affiliation(s)
| | | | - Ashwin Rammohan
- The Institute of Liver Disease & Transplantation, Dr. Rela Institute & Medical Centre, Chennai, India
| | - Mukul Vij
- Department of Pathology, Dr. Rela Institute & Medical Centre, Chennai, India
| | - Mani Chandrasekar
- Department of Oncology, Dr. Rela Institute & Medical Centre, Chennai, India
| | - Mohamed Rela
- Cell Laboratory, National Foundation for Liver Research, Chennai, India
- The Institute of Liver Disease & Transplantation, Dr. Rela Institute & Medical Centre, Chennai, India
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3
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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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Rai AK, Rajan KS, Bisserier M, Brojakowska A, Sebastian A, Evans AC, Coleman MA, Mills PJ, Arakelyan A, Uchida S, Hadri L, Goukassian DA, Garikipati VNS. Spaceflight-Associated Changes of snoRNAs in Peripheral Blood Mononuclear Cells and Plasma Exosomes-A Pilot Study. Front Cardiovasc Med 2022; 9:886689. [PMID: 35811715 PMCID: PMC9267956 DOI: 10.3389/fcvm.2022.886689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
During spaceflight, astronauts are exposed to various physiological and psychological stressors that have been associated with adverse health effects. Therefore, there is an unmet need to develop novel diagnostic tools to predict early alterations in astronauts' health. Small nucleolar RNA (snoRNA) is a type of short non-coding RNA (60-300 nucleotides) known to guide 2'-O-methylation (Nm) or pseudouridine (ψ) of ribosomal RNA (rRNA), small nuclear RNA (snRNA), or messenger RNA (mRNA). Emerging evidence suggests that dysregulated snoRNAs may be key players in regulating fundamental cellular mechanisms and in the pathogenesis of cancer, heart, and neurological disease. Therefore, we sought to determine whether the spaceflight-induced snoRNA changes in astronaut's peripheral blood (PB) plasma extracellular vesicles (PB-EV) and peripheral blood mononuclear cells (PBMCs). Using unbiased small RNA sequencing (sRNAseq), we evaluated changes in PB-EV snoRNA content isolated from astronauts (n = 5/group) who underwent median 12-day long Shuttle missions between 1998 and 2001. Using stringent cutoff (fold change > 2 or log2-fold change >1, FDR < 0.05), we detected 21 down-and 9-up-regulated snoRNAs in PB-EVs 3 days after return (R + 3) compared to 10 days before launch (L-10). qPCR validation revealed that SNORA74A was significantly down-regulated at R + 3 compared to L-10. We next determined snoRNA expression levels in astronauts' PBMCs at R + 3 and L-10 (n = 6/group). qPCR analysis further confirmed a significant increase in SNORA19 and SNORA47 in astronauts' PBMCs at R + 3 compared to L-10. Notably, many downregulated snoRNA-guided rRNA modifications, including four Nms and five ψs. Our findings revealed that spaceflight induced changes in PB-EV and PBMCs snoRNA expression, thus suggesting snoRNAs may serve as potential novel biomarkers for monitoring astronauts' health.
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Affiliation(s)
- Amit Kumar Rai
- Department of Emergency Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - K. Shanmugha Rajan
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Malik Bisserier
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Agnieszka Brojakowska
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Aimy Sebastian
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Angela C. Evans
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
- Department of Radiation Oncology, University of California, Davis, Sacramento, CA, United States
| | - Matthew A. Coleman
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
- Department of Radiation Oncology, University of California, Davis, Sacramento, CA, United States
| | - Paul J. Mills
- Center of Excellence for Research and Training in Integrative Health, University of California, San Diego, La Jolla, CA, United States
| | - Arsen Arakelyan
- Group of Bioinformatics, Institute of Molecular Biology, National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia
| | - Shizuka Uchida
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
| | - Lahouaria Hadri
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - David A. Goukassian
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Venkata Naga Srikanth Garikipati
- Department of Emergency Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Dorothy M. Davis Heart Lung and Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, United States
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Braghini MR, Lo Re O, Romito I, Fernandez-Barrena MG, Barbaro B, Pomella S, Rota R, Vinciguerra M, Avila MA, Alisi A. Epigenetic remodelling in human hepatocellular carcinoma. J Exp Clin Cancer Res 2022; 41:107. [PMID: 35331312 PMCID: PMC8943959 DOI: 10.1186/s13046-022-02297-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/19/2022] [Indexed: 04/13/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the most frequent primary liver cancer, being the sixth most commonly diagnosed cancer and the fourth leading cause of cancer-related death. As other heterogeneous solid tumours, HCC results from a unique synergistic combination of genetic alterations mixed with epigenetic modifications.In HCC the patterns and frequencies of somatic variations change depending on the nearby chromatin. On the other hand, epigenetic alterations often induce genomic instability prone to mutations. Epigenetics refers to heritable states of gene expression without alteration to the DNA sequence itself and, unlike genetic changes, the epigenetic modifications are reversible and affect gene expression more extensively than genetic changes. Thus, studies of epigenetic regulation and the involved molecular machinery are greatly contributing to the understanding of the mechanisms that underline HCC onset and heterogeneity. Moreover, this knowledge may help to identify biomarkers for HCC diagnosis and prognosis, as well as future new targets for more efficacious therapeutic approaches.In this comprehensive review we will discuss the state-of-the-art knowledge about the epigenetic landscape in hepatocarcinogenesis, including evidence on the diagnostic and prognostic role of non-coding RNAs, modifications occurring at the chromatin level, and their role in the era of precision medicine.Apart from other better-known risk factors that predispose to the development of HCC, characterization of the epigenetic remodelling that occurs during hepatocarcinogenesis could open the way to the identification of personalized biomarkers. It may also enable a more accurate diagnosis and stratification of patients, and the discovery of new targets for more efficient therapeutic approaches.
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Affiliation(s)
- Maria Rita Braghini
- Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children's Hospital, IRCCS, Viale S. Paolo, 15, 00146, Rome, Italy
| | - Oriana Lo Re
- Department of Translational Stem Cell Biology, Research Institute of the Medical University of Varna, Varna, Bulgaria
| | - Ilaria Romito
- Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children's Hospital, IRCCS, Viale S. Paolo, 15, 00146, Rome, Italy
| | - Maite G Fernandez-Barrena
- Hepatology Program, CIMA, University of Navarra, Pamplona, Spain
- Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, Madrid, Spain
| | - Barbara Barbaro
- Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children's Hospital, IRCCS, Viale S. Paolo, 15, 00146, Rome, Italy
| | - Silvia Pomella
- Department of Paediatric Haematology/Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Rossella Rota
- Department of Paediatric Haematology/Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Manlio Vinciguerra
- Department of Translational Stem Cell Biology, Research Institute of the Medical University of Varna, Varna, Bulgaria
| | - Matias A Avila
- Hepatology Program, CIMA, University of Navarra, Pamplona, Spain
- Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, Madrid, Spain
| | - Anna Alisi
- Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children's Hospital, IRCCS, Viale S. Paolo, 15, 00146, Rome, Italy.
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Liu Z, Pang Y, Jia Y, Qin Q, Wang R, Li W, Jing J, Liu H, Liu S. SNORA23 inhibits HCC tumorigenesis by impairing the 2'-O-ribose methylation level of 28S rRNA. Cancer Biol Med 2021; 19:j.issn.2095-3941.2020.0343. [PMID: 33710804 PMCID: PMC8763008 DOI: 10.20892/j.issn.2095-3941.2020.0343] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 11/11/2020] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVE The dysregulation of ribosome biogenesis is associated with the progression of numerous tumors, including hepatocellular carcinoma (HCC). Small nucleolar RNAs (snoRNAs) regulate ribosome biogenesis by guiding the modification of ribosomal RNAs (rRNAs). However, the underlying mechanism of this process in HCC remains elusive. METHODS RNA immunoprecipitation and sequencing were used to analyze RNAs targeted by ribosome proteins. The biological functions of SNORA23 were examined in HCC cells and a xenograft mouse model. To elucidate the underlying mechanisms, the 2'-O-ribose methylation level of rRNAs was evaluated by qPCR, and the key proteins in the PI3K/Akt/mTOR pathway were detected using Western blot. RESULTS Twelve snoRNAs were found to co-exist in 4 cancer cell lines using RPS6 pull-down assays. SNORA23 was downregulated in HCC and correlated with the poor prognoses of HCC patients. SNORA23 inhibited the proliferation, migration, and invasion of HCC cells both in vitro and in vivo. We also found that SNORA23 regulated ribosome biogenesis by impairing 2'-O-ribose methylation of cytidine4506 of 28S rRNA. Furthermore, SNORA23, which is regulated by the PI3K/Akt/mTOR signaling pathway, significantly inhibited the phosphorylation of 4E binding protein 1. SNORA23 and rapamycin blocked the PI3K/AKT/mTOR signaling pathway and impaired HCC growth in vivo. CONCLUSIONS SNORA23 exhibited antitumor effects in HCC and together with rapamycin, provided a promising therapeutic strategy for HCC treatment.
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Affiliation(s)
- Zhiyong Liu
- Department of Laboratory Diagnostics, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yanan Pang
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
- Shanghai Institute of Pancreatic Diseases, Shanghai 200433, China
| | - Yin Jia
- Department of Laboratory Diagnostics, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Qin Qin
- Department of Laboratory Diagnostics, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Rui Wang
- Department of Chemistry and State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433 China
| | - Wei Li
- Department of General Surgery, Changzheng Hospital, Second Military Medical University, Shanghai 200433, China
| | - Jie Jing
- Department of Laboratory Diagnostics, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Haidong Liu
- Department of Laboratory Diagnostics, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Shanrong Liu
- Department of Laboratory Diagnostics, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
- Shanghai Fourth People’s Hospital, Tongji University School of Medicine, Shanghai 200081, China
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Wu J, Nagy LE, Liangpunsakul S, Wang L. Non-coding RNA crosstalk with nuclear receptors in liver disease. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166083. [PMID: 33497819 DOI: 10.1016/j.bbadis.2021.166083] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 12/28/2020] [Accepted: 01/16/2021] [Indexed: 02/06/2023]
Abstract
The dysregulation of nuclear receptors (NRs) underlies the pathogenesis of a variety of liver disorders. Non-coding RNAs (ncRNAs) are defined as RNA molecules transcribed from DNA but not translated into proteins. MicroRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are two types of ncRNAs that have been extensively studied for regulating gene expression during diverse cellular processes. NRs as therapeutic targets in liver disease have been exemplified by the successful application of their pharmacological ligands in clinics. MiRNA-based reagents or drugs are emerging as flagship products in clinical trials. Advancing our understanding of the crosstalk between NRs and ncRNAs is critical to the development of diagnostic and therapeutic strategies. This review summarizes recent findings on the reciprocal regulation between NRs and ncRNAs (mainly on miRNAs and lncRNAs) and their implication in liver pathophysiology, which might be informative to the translational medicine of targeting NRs and ncRNAs in liver disease.
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Affiliation(s)
- Jianguo Wu
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States of America; Department of Molecular Medicine, Case Western Reserve University, Cleveland, OH, United States of America.
| | - Laura E Nagy
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States of America; Department of Gastroenterology and Hepatology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States of America; Department of Molecular Medicine, Case Western Reserve University, Cleveland, OH, United States of America
| | - Suthat Liangpunsakul
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States of America; Roudebush Veterans Administration Medical Center, Indianapolis, IN, United States of America; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States of America
| | - Li Wang
- Department of Internal Medicine, Section of Digestive Diseases, Yale University, New Haven, CT, United States of America
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Zhu Y, Wang S, Xi X, Zhang M, Liu X, Tang W, Cai P, Xing S, Bao P, Jin Y, Zhao W, Chen Y, Zhao H, Jia X, Lu S, Lu Y, Chen L, Yin J, Lu ZJ. Integrative analysis of long extracellular RNAs reveals a detection panel of noncoding RNAs for liver cancer. Theranostics 2021; 11:181-193. [PMID: 33391469 PMCID: PMC7681086 DOI: 10.7150/thno.48206] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 09/06/2020] [Indexed: 12/11/2022] Open
Abstract
Rationale: Long extracellular RNAs (exRNAs) in plasma can be profiled by new sequencing technologies, even with low abundance. However, cancer-related exRNAs and their variations remain understudied. Methods: We investigated different variations (i.e. differential expression, alternative splicing, alternative polyadenylation, and differential editing) in diverse long exRNA species (e.g. long noncoding RNAs and circular RNAs) using 79 plasma exosomal RNA-seq (exoRNA-seq) datasets of multiple cancer types. We then integrated 53 exoRNA-seq datasets and 65 self-profiled cell-free RNA-seq (cfRNA-seq) datasets to identify recurrent variations in liver cancer patients. We further combined TCGA tissue RNA-seq datasets and validated biomarker candidates by RT-qPCR in an individual cohort of more than 100 plasma samples. Finally, we used machine learning models to identify a signature of 3 noncoding RNAs for the detection of liver cancer. Results: We found that different types of RNA variations identified from exoRNA-seq data were enriched in pathways related to tumorigenesis and metastasis, immune, and metabolism, suggesting that cancer signals can be detected from long exRNAs. Subsequently, we identified more than 100 recurrent variations in plasma from liver cancer patients by integrating exoRNA-seq and cfRNA-seq datasets. From these datasets, 5 significantly up-regulated long exRNAs were confirmed by TCGA data and validated by RT-qPCR in an independent cohort. When using machine learning models to combine two of these validated circular and structured RNAs (SNORD3B-1, circ-0080695) with a miRNA (miR-122) as a panel to classify liver cancer patients from healthy donors, the average AUROC of the cross-validation was 89.4%. The selected 3-RNA panel successfully detected 79.2% AFP-negative samples and 77.1% early-stage liver cancer samples in the testing and validation sets. Conclusions: Our study revealed that different types of RNA variations related to cancer can be detected in plasma and identified a 3-RNA detection panel for liver cancer, especially for AFP-negative and early-stage patients.
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Affiliation(s)
- Yumin Zhu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, MOE Key Laboratory of Population Health Across Life Cycle, NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Provincial Key Laboratory of Population Health and Aristogenics, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Siqi Wang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaochen Xi
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Minfeng Zhang
- Department of Surgery, Eastern Hepatobiliary Surgery Hospital, Navy Medical University, Shanghai 200433, China
| | - Xiaofan Liu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Weina Tang
- Department of Epidemiology, Faculty of Navy Medicine, Navy Medical University, Shanghai 200433, China
| | - Peng Cai
- Department of Epidemiology, Faculty of Navy Medicine, Navy Medical University, Shanghai 200433, China
| | - Shaozhen Xing
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Pengfei Bao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yunfan Jin
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Weihao Zhao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yinghui Chen
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Huanan Zhao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaodong Jia
- International Co-operation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military medical University, Shanghai 200438, China
| | - Shanshan Lu
- International Co-operation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military medical University, Shanghai 200438, China
| | - Yinying Lu
- International Co-operation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military medical University, Shanghai 200438, China
| | - Lei Chen
- International Co-operation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military medical University, Shanghai 200438, China
- National Center for Liver Cancer, Shanghai 201805, China
| | - Jianhua Yin
- Department of Epidemiology, Faculty of Navy Medicine, Navy Medical University, Shanghai 200433, China
| | - Zhi John Lu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
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Identification of snoRNA SNORA71A as a Novel Biomarker in Prognosis of Hepatocellular Carcinoma. DISEASE MARKERS 2020; 2020:8879944. [PMID: 33062075 PMCID: PMC7537701 DOI: 10.1155/2020/8879944] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 08/02/2020] [Accepted: 09/10/2020] [Indexed: 12/21/2022]
Abstract
Background Small nucleolar RNAs (snoRNAs) have been proved to play important roles in various cellular physiological process. Recently, dysregulation of snoRNA SNORA71A has been found involved in tumorigenesis of various malignant cancers. However, the emerging effects of SNORA71A in hepatocellular carcinoma (HCC) remain largely unclear. In this study, we aimed to explore the SNORA71A expression and its underlying significance in HCC. Methods Expression of SNORA71A in cell lines and clinical specimens was measured by quantitative real-time PCR. Then, all enrolled HCC patients were divided into low and high SNORA71A expression subgroups and then they were compared in the aspects of clinical features as well as survival outcome by respective statistical analysis methods. Results SNORA71A was significantly downexpressed in SK-HEP-1 (P = 0.001), Huh-7 (P < 0.001), Hep3B (P < 0.001), and clinical HCC specimens (P = 0.006). Comparing the clinical features between SNORA71A expression subgroups, it showed that low SNORA71A expression was significantly associated with large tumor diameter, multiple lesions, capsular invasion, bad tumor differentiation, and TNM stage (P < 0.05). Furthermore, it was found that HCC patients with lower SNORA71A expression had higher risk in postoperative tumor relapse (median time: 9.5 vs. 35.2 months; low vs. high; P < 0.001) and poor overall survival (median time: 36.8 vs. 52.9 months; low vs. high; P < 0.001). Besides, SNORA71A expression served as independent risk factors for tumor-free (HR = 0.450; 95% CI [0.263-0.770]; P = 0.004) and long-term survival (HR = 0.289; 95% CI [0.127-0.657]; P = 0.003). Conclusions Our study for the first time demonstrated that downregulation of SNORA71A could serve as a novel biomarker for clinical assessment and prognostic prediction of HCC patients.
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10
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Kakihara Y, Kiguchi T, Ohazama A, Saeki M. R2TP/PAQosome as a promising chemotherapeutic target in cancer. JAPANESE DENTAL SCIENCE REVIEW 2020; 56:38-42. [PMID: 31890057 PMCID: PMC6926247 DOI: 10.1016/j.jdsr.2019.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/27/2019] [Accepted: 08/21/2019] [Indexed: 11/30/2022] Open
Abstract
R2TP/PAQosome (particle for arrangement of quaternary structure) is a novel multisubunit chaperone specialized in the assembly/maturation of protein complexes that are involved in essential cellular processes such as PIKKs (phosphatidylinositol 3-kinase-like kinases) signaling, snoRNP (small nucleolar ribonucleoprotein) biogenesis, and RNAP II (RNA polymerase II) complex formation. In this review article, we describe the current understanding of R2TP/PAQosome functions and characteristics as well as how the chaperone complex is involved in oncogenesis, highlighting DNA damage response, mTOR (mammalian target of rapamycin) pathway as well as snoRNP biogenesis. Also, we discuss its possible involvement in HNSCC (head and neck squamous cell carcinoma) including OSCC (oral squamous cell carcinoma). Finally, we provide an overview of current anti-cancer drug development efforts targeting R2TP/PAQosome.
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Affiliation(s)
- Yoshito Kakihara
- Division of Dental Pharmacology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Tetsuo Kiguchi
- Division of Dental Pharmacology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Atsushi Ohazama
- Division of Oral Anatomy, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Makio Saeki
- Division of Dental Pharmacology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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Mjelle R, Dima SO, Bacalbasa N, Chawla K, Sorop A, Cucu D, Herlea V, Sætrom P, Popescu I. Comprehensive transcriptomic analyses of tissue, serum, and serum exosomes from hepatocellular carcinoma patients. BMC Cancer 2019; 19:1007. [PMID: 31660891 PMCID: PMC6816220 DOI: 10.1186/s12885-019-6249-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 10/10/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The expression of microRNAs (miRNAs) is a promising prognostic and diagnostic tool in hepatocellular carcinoma (HCC). Here we performed small RNA sequencing (sRNA-seq) of tissue, serum and serum exosomes to investigate changes in miRNA expression between the different sample types and correlated the expression with clinical parameters. We also performed gene expression arrays on tumor and normal tissue. RESULTS Paired tissue, serum and serum exosomes sequencing revealed consistent positive correlation of miR-21 between serum exosomes and tumor tissue, indicating that miR-21 could be exported from tissue to circulation via exosomes. We found that let-7 miRNAs are generally upregulated in serum exosomes compared to whole serum, indicating that these miRNAs could be preferentially loaded into exosomes. Comparing serum from HCC patients with serum from healthy individuals revealed a global increase of miRNAs in serum from HCC patients, including an almost 4-fold increase of several miRNAs, including the liver-specific miR-122. When correlating miRNA expression with clinical parameters we detected significant association between hepatitis B virus (HBV) infection and miR-122 in serum as well as several serum and tissue-miRNAs that correlated with surgery type. We found that miR-141 and miR-146 correlated with cirrhosis in tumor tissue and normal tissue, respectively. Finally, high expression of miR-21 in tumors were associated with poor survival. Focusing on gene expression we found several significant messenger RNAs (mRNAs) between tumor and normal tissue and a Gene Ontology (GO) analysis revealed that these changes were mainly related to cell cycle and metabolism. Further, we detected mRNAs that correlated with cirrhosis and HBV infection in tissue. Finally, GO analysis of predicted targets for miRNAs down-regulated in tumor found that these were enriched for functions related to collagen synthesis. CONCLUSIONS Our combined data point to altered miRNA and mRNA expression contributing to both generally impaired lipid metabolism and increased cell proliferation and a miRNA-driven increase in collagen synthesis in HCC. Our results further indicate a correlation in miRNA expression between exosomes, serum, and tissue samples suggesting export from tumors via exosomes. This correlation could provide a basis for a more tumor-specific miRNA profile in serum.
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Affiliation(s)
- Robin Mjelle
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Erling Skjalgssons gt 1, 7030, Trondheim, Norway. .,Department of Computer Science, Norwegian University of Science and Technology, NTNU, Trondheim, Norway.
| | - Simona O Dima
- Center of Digestive Diseases and Liver Transplantation, Fundeni Clinical Institute, Bucharest, Romania.,Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
| | - Nicolae Bacalbasa
- Center of Digestive Diseases and Liver Transplantation, Fundeni Clinical Institute, Bucharest, Romania.,Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
| | - Konika Chawla
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Erling Skjalgssons gt 1, 7030, Trondheim, Norway.,Bioinformatics Core Facility-BioCore, Norwegian University of Science and Technology, NTNU, Trondheim, Norway
| | - Andrei Sorop
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
| | - Dana Cucu
- Department of Anatomy, Physiology, and Biophysics, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | - Vlad Herlea
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania.,K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, NTNU, Trondheim, Norway
| | - Pål Sætrom
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Erling Skjalgssons gt 1, 7030, Trondheim, Norway.,Department of Computer Science, Norwegian University of Science and Technology, NTNU, Trondheim, Norway.,Bioinformatics Core Facility-BioCore, Norwegian University of Science and Technology, NTNU, Trondheim, Norway.,K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, NTNU, Trondheim, Norway
| | - Irinel Popescu
- Center of Digestive Diseases and Liver Transplantation, Fundeni Clinical Institute, Bucharest, Romania.,Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania.,Acad. Nicolae Cajal Institute of Medical Scientific Research, Titu Maiorescu University, Bucharest, Romania
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Non-Coding RNAs and Hepatitis C Virus-Induced Hepatocellular Carcinoma. Viruses 2018; 10:v10110591. [PMID: 30380697 PMCID: PMC6265700 DOI: 10.3390/v10110591] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 10/27/2018] [Accepted: 10/29/2018] [Indexed: 02/06/2023] Open
Abstract
Hepatitis C virus (HCV) infection is a worldwide health problem and is one of the main causes of chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma (HCC). Despite recent improvements, effective treatments for HCC are still missing and new tools for early detection are needed. Non-coding RNAs (ncRNAs) have emerged as important regulators of gene expression and key players in human carcinogenesis, including HCC. Aberrant expression of ncRNAs is associated with HCC metastasis, invasion, dissemination, and recurrence. This review will focus on the recent advances in ncRNA expression profiles, their dysregulation in HCV-related HCC, and the clinical perspective of ncRNA signatures for the early detection of HCC.
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