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Kritika C. Transforming 'Junk' DNA into Cancer Warriors: The Role of Pseudogenes in Hepatocellular Carcinoma. CANCER DIAGNOSIS & PROGNOSIS 2024; 4:214-222. [PMID: 38707729 PMCID: PMC11062172 DOI: 10.21873/cdp.10311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 02/07/2024] [Indexed: 05/07/2024]
Abstract
In the dynamic landscape of hepatocellular carcinoma (HCC) or the liver cancer research, pseudogenes have emerged from the shadows of genetic obscurity to become central figures, significantly influencing the disease molecular development and clinical trajectory. This review explores a transformative shift in perspective, recognizing pseudogenes not as genetic remnants without function, but as critical regulators in the molecular underpinnings of HCC. Engaging in complex interactions such as microRNA sponging, gene expression modulation, and signaling pathway disruptions, pseudogenes orchestrate a part of the molecular complexity driving tumor genesis, progression, and drug resistance in the liver cancer. Their unique expression patterns in hepatoma tissues herald new opportunities for early HCC detection, offering insights into patient prognosis, and identifying novel targets for therapeutic intervention of this disease. Such advancements underscore the importance of pseudogenes in enriching our understanding and management of HCC, paving the way for more effective diagnostic strategies and targeted therapies in the ongoing battle against this challenging malignancy.
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Affiliation(s)
- Chugh Kritika
- Graduate Student, School of Natural Sciences and Mathematics, University of Texas at Dallas, Richardson, TX, U.S.A
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Karimi B, Mokhtari K, Rozbahani H, Peymani M, Nabavi N, Entezari M, Rashidi M, Taheriazam A, Ghaedi K, Hashemi M. Pathological roles of miRNAs and pseudogene-derived lncRNAs in human cancers, and their comparison as prognosis/diagnosis biomarkers. Pathol Res Pract 2024; 253:155014. [PMID: 38128189 DOI: 10.1016/j.prp.2023.155014] [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: 10/23/2023] [Revised: 12/02/2023] [Accepted: 12/02/2023] [Indexed: 12/23/2023]
Abstract
This review examines and compares the diagnostic and prognostic capabilities of miRNAs and lncRNAs derived from pseudogenes in cancer patients. Additionally, it delves into their roles in cancer pathogenesis. Both miRNAs and pseudogene-derived lncRNAs have undergone thorough investigation as remarkably sensitive and specific cancer biomarkers, offering significant potential for cancer detection and monitoring. . Extensive research is essential to gain a complete understanding of the precise roles these non-coding RNAs play in cancer, allowing the development of novel targeted therapies and biomarkers for improved cancer detection and treatment approaches.
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Affiliation(s)
- Bahareh Karimi
- Department of Cellular and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Khatere Mokhtari
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Hossein Rozbahani
- Department of Psychology, North Tehran Branch, Islamic Azad University, Tehran, Iran; Department of Psychology, West Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Noushin Nabavi
- Department of Urologic Sciences and Vancouver Prostate Centre, University of British Columbia, Vancouver, BC V6H3Z6, Canada
| | - Maliheh Entezari
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Mohsen Rashidi
- Department Pharmacology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran; The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, Iran.
| | - Afshin Taheriazam
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Orthopedics, Faculty of medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Mehrdad Hashemi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
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Li J, Shaikh SN, Uqaili AA, Nasir H, Zia R, Akram MA, Jawad FA, Sohail S, AbdelGawwad MR, Almutairi SM, Elshikh MS, Jamil M, Rasheed RA. A pan-cancer analysis of pituitary tumor-transforming 3, pseudogene. Am J Transl Res 2023; 15:5408-5424. [PMID: 37692950 PMCID: PMC10492052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 08/14/2023] [Indexed: 09/12/2023]
Abstract
BACKGROUND Although evidence regarding pituitary tumor-transforming 3, pseudogene (PTTG3P) involvement in human cancers has been acquired via human and animal model-based molecular studies, there is a lack of pan-cancer analysis of this gene in human tumors. METHODS Tumor-causing effects of PTTG3P in 24 human tumors were explored using The Cancer Genome Atlas (TCGA) datasets from different bioinformatics databases and applying in silico tools such as The University of ALabama at Birmingham CANcer (UALCAN), Human Protein Atlas (HPA), Kaplan Meier (KM) plotter, cBioPortal, Search Tool for the Retrieval of Interacting Genes/Proteins (STRING), Cytoscape, Database for Annotation, Visualization, and Integrated Discovery (DAVID), Tumor IMmune Estimation Resource (TIMER), and Comparative Toxicogenomics Database (CTD). Then, via in vitro experiments, including RNA sequencing (RNA-seq) and targeted bisulfite sequencing (bisulfite-seq), expression and promoter methylation levels of PTTG3P were verified in cell lines. RESULTS The PTTG3P expression was overexpressed across 23 malignancies and its overexpression was further found significantly effecting the overall survival (OS) durations of the esophageal carcinoma (ESCA) and head and neck cancer (HNSC) patients. This important information helps us to understand that PTTG3P plays a significant role in the development and progression of ESCA and HNSC. As for PTTG3P functional mechanisms, this gene along with its other binding partners was significantly concentrated in "Oocyte meiosis", "Cell cycle", "Ubiquitin mediated proteolysis", and "Progesterone-mediated oocyte maturation". Moreover, ESCA and HNSC tissues having the higher expression of PTTG3P were found to have lower promoter methylation levels of PTTG3P and higher CD8+ T immune cells level. Additionally, PTTG3P expression-regulatory drugs were also explored in the current manuscript for designing appropriate treatment strategies for ESCA and HNSC with respect to PTTG3P expression. CONCLUSION Our pan-cancer based findings provided a comprehensive account of the oncogenic role and utilization of PTTG3P as a novel molecular biomarker of ESCA and HNSC.
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Affiliation(s)
- Jie Li
- The Second Affiliated Hospital of Hainan Medical University Health Management CenterHaikou 570311, Hainan, China
| | - Saima Naz Shaikh
- Department of Physiology, Liaquat University of Medical and Health SciencesJamshoro, Sindh 76090, Pakistan
| | - Arsalan Ahmed Uqaili
- Department of Physiology, Liaquat University of Medical and Health SciencesJamshoro, Sindh 76090, Pakistan
| | - Hilal Nasir
- Clinical and Translational Oncology, Scuola Superiore Meridionale, Naples Federico II UniversityNapoli 80138, Italy
| | - Rabeea Zia
- Pakistan Kidney and Liver Institute and ResearchLahore, Punjab 54000, Pakistan
| | - Muhammad Aitzaz Akram
- University Institute of Biochemistry and Biotechnology, PMAS-Arid Agriculture UniversityRawalpindi 46000, Pakistan
| | - Fahim Ali Jawad
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture FaisalabadFaisalabad 38000, Pakistan
| | - Salman Sohail
- Registrar Ophthalmology, Al Shifa Trust Eye HospitalRawalpindi 46000, Pakistan
| | - Mohamed Ragab AbdelGawwad
- Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, International University of SarajevoSarajevo 71210, Bosnia and Herzegovina
| | - Saeedah Musaed Almutairi
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. 2455, Riyadh 11451, Saudi Arabia
| | - Mohamed S Elshikh
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. 2455, Riyadh 11451, Saudi Arabia
| | - Muhammad Jamil
- PARC Arid Zone Research CenterDera Ismail Khan 29050, Pakistan
| | - Rabab Ahmed Rasheed
- Histology & Cell Biology Department, Faculty of Medicine, King Salman International UniversitySouth Sinai, Egypt
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Lin YC, Chang PC, Hueng DY, Huang SM, Li YF. Decoding the prognostic significance of integrator complex subunit 9 (INTS9) in glioma: links to TP53 mutations, E2F signaling, and inflammatory microenvironments. Cancer Cell Int 2023; 23:154. [PMID: 37537630 PMCID: PMC10401760 DOI: 10.1186/s12935-023-03006-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/26/2023] [Indexed: 08/05/2023] Open
Abstract
INTRODUCTION Gliomas, a type of brain neoplasm, are prevalent and often fatal. Molecular diagnostics have improved understanding, but treatment options are limited. This study investigates the role of INTS9 in processing small nuclear RNA (snRNA), which is crucial to generating mature messenger RNA (mRNA). We aim to employ advanced bioinformatics analyses with large-scale databases and conduct functional experiments to elucidate its potential role in glioma therapeutics. MATERIALS AND METHODS We collected genomic, proteomic, and Whole-Exon-Sequencing data from The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) for bioinformatic analyses. Then, we validated INTS9 protein expression through immunohistochemistry and assessed its correlation with P53 and KI67 protein expression. Gene Set Enrichment Analysis (GSEA) was performed to identify altered signaling pathways, and functional experiments were conducted on three cell lines treated with siINTS9. Then, we also investigate the impacts of tumor heterogeneity on INTS9 expression by integrating single-cell sequencing, 12-cell state prediction, and CIBERSORT analyses. Finally, we also observed longitudinal changes in INTS9 using the Glioma Longitudinal Analysis (GLASS) dataset. RESULTS Our findings showed increased INTS9 levels in tumor tissue compared to non-neoplastic components, correlating with high tumor grading and proliferation index. TP53 mutation was the most notable factor associated with upregulated INTS9, along with other potential contributors, such as combined chromosome 7 gain/10 loss, TERT promoter mutation, and increased Tumor Mutational Burden (TMB). In GSEA analyses, we also linked INTS9 with enhanced cell proliferation and inflammation signaling. Downregulating INTS9 impacted cellular proliferation and cell cycle regulation during the function validation. In the context of the 12 cell states, INTS9 correlated with tumor-stem and tumor-proliferative-stem cells. CIBERSORT analyses revealed increased INTS9 associated with increased macrophage M0 and M2 but depletion of monocytes. Longitudinally, we also noticed that the INTS9 expression declined during recurrence in IDH wildtype. CONCLUSION This study assessed the role of INTS9 protein in glioma development and its potential as a therapeutic target. Results indicated elevated INTS9 levels were linked to increased proliferation capacity, higher tumor grading, and poorer prognosis, potentially resulting from TP53 mutations. This research highlights the potential of INTS9 as a promising target for glioma treatment.
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Affiliation(s)
- Yu-Chieh Lin
- Department of Pathology and Laboratory Medicine, Taoyuan Armed Forces General Hospital, Taoyuan, 325, Taiwan, Republic of China
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipe, 114, Taiwan, Republic of China
| | - Pei-Chi Chang
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipe, 114, Taiwan, Republic of China
| | - Dueng-Yuan Hueng
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipe, 114, Taiwan, Republic of China
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipe, 114, Taiwan, Republic of China
- Department of Neurologic Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipe, 114, Taiwan, Republic of China
| | - Shih-Ming Huang
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipe, 114, Taiwan, Republic of China
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipe, 114, Taiwan, Republic of China
- Department of Biochemistry, National Defense Medical Center, Taipe, 114, Taiwan, Republic of China
| | - Yao-Feng Li
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipe, 114, Taiwan, Republic of China.
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipe, 114, Taiwan, Republic of China.
- Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipe, 114, Taiwan, Republic of China.
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Gu X, Wang S, Jin B, Qi Z, Deng J, Huang C, Yin X. A pathway analysis-based algorithm for calculating the participation degree of ncRNA in transcriptome. Sci Rep 2022; 12:22654. [PMID: 36587048 PMCID: PMC9805457 DOI: 10.1038/s41598-022-27178-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 12/27/2022] [Indexed: 01/01/2023] Open
Abstract
After sequencing, it is common to screen ncRNA according to expression differences. But this may lose a lot of valuable information and there is currently no indicator to characterize the regulatory function and participation degree of ncRNA on transcriptome. Based on existing pathway enrichment methods, we developed a new algorithm to calculating the participation degree of ncRNA in transcriptome (PDNT). Here we analyzed multiple data sets, and differentially expressed genes (DEGs) were used for pathway enrichment analysis. The PDNT algorithm was used to calculate the Contribution value (C value) of each ncRNA based on its target genes and the pathways they participates in. The results showed that compared with ncRNAs screened by log2 fold change (FC) and p-value, those screened by C value regulated more DEGs in IPA canonical pathways, and their target DEGs were more concentrated in the core region of the protein-protein interaction (PPI) network. The ranking of disease critical ncRNAs increased integrally after sorting with C value. Collectively, we found that the PDNT algorithm provides a measure from another view compared with the log2FC and p-value and it may provide more clues to effectively evaluate ncRNA.
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Affiliation(s)
- Xinyi Gu
- grid.411634.50000 0004 0632 4559Department of Orthopedics and Traumatology, Peking University People’s Hospital, Beijing, 100044 China ,grid.11135.370000 0001 2256 9319Key Laboratory of Trauma and Neural Regeneration (Peking University), Beijing, China
| | - Shen Wang
- grid.411634.50000 0004 0632 4559Department of Orthopedics and Traumatology, Peking University People’s Hospital, Beijing, 100044 China ,grid.11135.370000 0001 2256 9319Key Laboratory of Trauma and Neural Regeneration (Peking University), Beijing, China
| | - Bo Jin
- grid.411634.50000 0004 0632 4559Department of Orthopedics and Traumatology, Peking University People’s Hospital, Beijing, 100044 China ,grid.11135.370000 0001 2256 9319Key Laboratory of Trauma and Neural Regeneration (Peking University), Beijing, China
| | - Zhidan Qi
- grid.411634.50000 0004 0632 4559Department of Orthopedics and Traumatology, Peking University People’s Hospital, Beijing, 100044 China ,grid.11135.370000 0001 2256 9319Key Laboratory of Trauma and Neural Regeneration (Peking University), Beijing, China
| | - Jin Deng
- grid.411634.50000 0004 0632 4559Department of Orthopedics and Traumatology, Peking University People’s Hospital, Beijing, 100044 China ,grid.11135.370000 0001 2256 9319Key Laboratory of Trauma and Neural Regeneration (Peking University), Beijing, China
| | - Chen Huang
- grid.411634.50000 0004 0632 4559Department of Orthopedics and Traumatology, Peking University People’s Hospital, Beijing, 100044 China ,grid.11135.370000 0001 2256 9319Key Laboratory of Trauma and Neural Regeneration (Peking University), Beijing, China
| | - Xiaofeng Yin
- grid.411634.50000 0004 0632 4559Department of Orthopedics and Traumatology, Peking University People’s Hospital, Beijing, 100044 China ,grid.11135.370000 0001 2256 9319Key Laboratory of Trauma and Neural Regeneration (Peking University), Beijing, China
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ceRNAs in Cancer: Mechanism and Functions in a Comprehensive Regulatory Network. JOURNAL OF ONCOLOGY 2021; 2021:4279039. [PMID: 34659409 PMCID: PMC8516523 DOI: 10.1155/2021/4279039] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 12/15/2022]
Abstract
Noncoding RNAs have been shown with powerful ability in post-transcriptional regulation, enabling intertwined RNA crosstalk and global molecular interaction in a large amount of dysfunctional conditions including cancer. Competing endogenous RNAs (ceRNAs) are those competitively binding with shared microRNAs (miRNAs), freeing their counterparts from miRNA-induced degradation, thus actively influencing and connecting with each other. Constantly updated analytical approaches boost outstanding advancement achieved in this burgeoning hotspot in multilayered intracellular communication, providing new insights into pathogenesis and clinical treatment. Here, we summarize the mechanisms and correlated factors under this RNA interplay and deregulated transcription profile in neoplasm and tumor progression, underscoring the great significance of ceRNAs for diagnostic values, monitoring biomarkers, and prognosis evaluation in cancer.
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Ding X, Chen T, Shi Q, Nan P, Wang X, Xie D, Li J. INTS6 promotes colorectal cancer progression by activating of AKT and ERK signaling. Exp Cell Res 2021; 407:112826. [PMID: 34508742 DOI: 10.1016/j.yexcr.2021.112826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 08/12/2021] [Accepted: 09/05/2021] [Indexed: 10/20/2022]
Abstract
INTS6 (integrator complex subunit 6) has been reported as a tumor suppressor in many cancers. However, the expression and biological function of INTS6 in colorectal cancer (CRC) has not been investigated yet. In this study, we found that INTS6 expression was significantly increased in CRC tissues when compared with normal tissues and was associated with poor prognosis. Downregulation of INTS6 induced G1/S-phase cell cycle arrest, and markedly suppressed the growth of CRC cells and the derived tumors, while overexpression of INTS6 showed opposite effect. Mechanism study revealed that INTS6 increased the levels of phosphorylated AKT (p-AKT) and ERK (p-ERK), and the growth-promoting effect of INTS6 was inhibited by AKT and ERK inhibitors. Besides, INTS6 also affected the expression of two targets of PI3K/AKT and MAPK signaling, c-Myc and CDK2, which contributed to cell cycle alteration. Altogether, the present study has revealed the oncogenic role of INTS6 in CRC, providing a novel therapeutic target for this malignant cancer.
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Affiliation(s)
- Xufen Ding
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China; Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Tianwei Chen
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Qian Shi
- First People's Hospital of Huzhou, First Affiliated Hospital of Huzhou University, Huzhou, China
| | - Peng Nan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Xiang Wang
- First People's Hospital of Huzhou, First Affiliated Hospital of Huzhou University, Huzhou, China.
| | - Dong Xie
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, China; NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China.
| | - Jingjing Li
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China.
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Ciomborowska-Basheer J, Staszak K, Kubiak MR, Makałowska I. Not So Dead Genes-Retrocopies as Regulators of Their Disease-Related Progenitors and Hosts. Cells 2021; 10:cells10040912. [PMID: 33921034 PMCID: PMC8071448 DOI: 10.3390/cells10040912] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 03/30/2021] [Accepted: 04/13/2021] [Indexed: 12/12/2022] Open
Abstract
Retroposition is RNA-based gene duplication leading to the creation of single exon nonfunctional copies. Nevertheless, over time, many of these duplicates acquire transcriptional capabilities. In human in most cases, these so-called retrogenes do not code for proteins but function as regulatory long noncoding RNAs (lncRNAs). The mechanisms by which they can regulate other genes include microRNA sponging, modulation of alternative splicing, epigenetic regulation and competition for stabilizing factors, among others. Here, we summarize recent findings related to lncRNAs originating from retrocopies that are involved in human diseases such as cancer and neurodegenerative, mental or cardiovascular disorders. Special attention is given to retrocopies that regulate their progenitors or host genes. Presented evidence from the literature and our bioinformatics analyses demonstrates that these retrocopies, often described as unimportant pseudogenes, are significant players in the cell’s molecular machinery.
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Zhang H, Li L, Yu Y, Li L, Jiang Y, Liu R. Prenatal detection of a 7q11.21 microdeletion (517-605 kb): A variant with normal characteristics at birth (STROBE). Medicine (Baltimore) 2021; 100:e24560. [PMID: 33578551 PMCID: PMC7886492 DOI: 10.1097/md.0000000000024560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 01/11/2021] [Indexed: 01/05/2023] Open
Abstract
In the literature, 7q11 deletion was reported with various abnormalities. However, there were other genetic conditions combined with 7q11.21. It is necessary to have sufficient pure 7q11.21 microdeletions for classifying the pathogenic categories of variation.Chromosomal karyotyping analysis was performed on cultured amniotic fluid cells. Eighteen pregnant women took chromosomal microarray using prenatal amniotic fluid samples at our center by Affymetrix CytoScan750K_Array. We followed the outcome of these pregnancies and determined postnatal health conditions.Cytogenetic studies delineated that all patients had normal karyotypes. The exception was P17, who had 47, XN. Single nucleotide polymorphism array results showed 517 to 605 kb deletions of 7q11.21 (chr7: 64543313-65196780) in these cases. The microarray results were pure or combined 7q11.21 microdeletions. In 11 pure 7q11.21 microdeletions and 7 combined cases, there was no apparent abnormal phenotype associated with partial 7q11.21. Among them, only mothers of P10 and P17 decided to terminate the pregnancies due to 18 trisomy or ultrasound abnormal fetal strephenopodia. In the follow-up survey, the newborns had no apparent abnormalities.In this study, we described 11 pure and 7 combined 7q11.21 microdeletions associating with no apparent postnatal phenotypic abnormalities. From this study, we can learn that the partial 7q11.21 deletion (chr7: 64543313-65196780) might be benign and have no association with human disorders.
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Affiliation(s)
- Hongguo Zhang
- Center for Reproductive Medicine, Center for Prenatal Diagnosis, First Hospital, Jilin University
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Leilei Li
- Center for Reproductive Medicine, Center for Prenatal Diagnosis, First Hospital, Jilin University
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Yang Yu
- Center for Reproductive Medicine, Center for Prenatal Diagnosis, First Hospital, Jilin University
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Linlin Li
- Center for Reproductive Medicine, Center for Prenatal Diagnosis, First Hospital, Jilin University
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Yuting Jiang
- Center for Reproductive Medicine, Center for Prenatal Diagnosis, First Hospital, Jilin University
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Ruizhi Liu
- Center for Reproductive Medicine, Center for Prenatal Diagnosis, First Hospital, Jilin University
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
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Cancer, Retrogenes, and Evolution. Life (Basel) 2021; 11:life11010072. [PMID: 33478113 PMCID: PMC7835786 DOI: 10.3390/life11010072] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 12/18/2022] Open
Abstract
This review summarizes the knowledge about retrogenes in the context of cancer and evolution. The retroposition, in which the processed mRNA from parental genes undergoes reverse transcription and the resulting cDNA is integrated back into the genome, results in additional copies of existing genes. Despite the initial misconception, retroposition-derived copies can become functional, and due to their role in the molecular evolution of genomes, they have been named the “seeds of evolution”. It is convincing that retrogenes, as important elements involved in the evolution of species, also take part in the evolution of neoplastic tumors at the cell and species levels. The occurrence of specific “resistance mechanisms” to neoplastic transformation in some species has been noted. This phenomenon has been related to additional gene copies, including retrogenes. In addition, the role of retrogenes in the evolution of tumors has been described. Retrogene expression correlates with the occurrence of specific cancer subtypes, their stages, and their response to therapy. Phylogenetic insights into retrogenes show that most cancer-related retrocopies arose in the lineage of primates, and the number of identified cancer-related retrogenes demonstrates that these duplicates are quite important players in human carcinogenesis.
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Joshi H, Vastrad B, Joshi N, Vastrad C, Tengli A, Kotturshetti I. Identification of Key Pathways and Genes in Obesity Using Bioinformatics Analysis and Molecular Docking Studies. Front Endocrinol (Lausanne) 2021; 12:628907. [PMID: 34248836 PMCID: PMC8264660 DOI: 10.3389/fendo.2021.628907] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 05/19/2021] [Indexed: 01/01/2023] Open
Abstract
Obesity is an excess accumulation of body fat. Its progression rate has remained high in recent years. Therefore, the aim of this study was to diagnose important differentially expressed genes (DEGs) associated in its development, which may be used as novel biomarkers or potential therapeutic targets for obesity. The gene expression profile of E-MTAB-6728 was downloaded from the database. After screening DEGs in each ArrayExpress dataset, we further used the robust rank aggregation method to diagnose 876 significant DEGs including 438 up regulated and 438 down regulated genes. Functional enrichment analysis was performed. These DEGs were shown to be significantly enriched in different obesity related pathways and GO functions. Then protein-protein interaction network, target genes - miRNA regulatory network and target genes - TF regulatory network were constructed and analyzed. The module analysis was performed based on the whole PPI network. We finally filtered out STAT3, CORO1C, SERPINH1, MVP, ITGB5, PCM1, SIRT1, EEF1G, PTEN and RPS2 hub genes. Hub genes were validated by ICH analysis, receiver operating curve (ROC) analysis and RT-PCR. Finally a molecular docking study was performed to find small drug molecules. The robust DEGs linked with the development of obesity were screened through the expression profile, and integrated bioinformatics analysis was conducted. Our study provides reliable molecular biomarkers for screening and diagnosis, prognosis as well as novel therapeutic targets for obesity.
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Affiliation(s)
- Harish Joshi
- Department of Endocrinology, Endocrine and Diabetes Care Center, Hubbali, India
| | - Basavaraj Vastrad
- Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, India
| | - Nidhi Joshi
- Department of Medicine, Dr. D. Y. Patil Medical College, Kolhapur, India
| | - Chanabasayya Vastrad
- Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad, India
- *Correspondence: Chanabasayya Vastrad,
| | - Anandkumar Tengli
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, Mysuru and JSS Academy of Higher Education & Research, Mysuru, India
| | - Iranna Kotturshetti
- Department of Ayurveda, Rajiv Gandhi Education Society`s Ayurvedic Medical College, Ron, India
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Intermittent fasting from dawn to sunset for four consecutive weeks induces anticancer serum proteome response and improves metabolic syndrome. Sci Rep 2020; 10:18341. [PMID: 33110154 PMCID: PMC7592042 DOI: 10.1038/s41598-020-73767-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 09/18/2020] [Indexed: 12/11/2022] Open
Abstract
Metabolic syndrome is characterized by central obesity, insulin resistance, elevated blood pressure, and dyslipidemia. Metabolic syndrome is a significant risk factor for several common cancers (e.g., liver, colorectal, breast, pancreas). Pharmacologic treatments used for the components of the metabolic syndrome appear to be insufficient to control cancer development in subjects with metabolic syndrome. Murine models showed that cancer has the slowest progression when there is no food consumption during the daily activity phase. Intermittent fasting from dawn to sunset is a form of fasting practiced during human activity hours. To test the anticancer effect of intermittent fasting from dawn to sunset in metabolic syndrome, we conducted a pilot study in 14 subjects with metabolic syndrome who fasted (no eating or drinking) from dawn to sunset for more than 14 h daily for four consecutive weeks. We collected serum samples before 4-week intermittent fasting, at the end of 4th week during 4-week intermittent fasting and 1 week after 4-week intermittent fasting. We performed serum proteomic analysis using nano ultra-high performance liquid chromatography-tandem mass spectrometry. We found a significant fold increase in the levels of several tumor suppressor and DNA repair gene protein products (GP)s at the end of 4th week during 4-week intermittent fasting (CALU, INTS6, KIT, CROCC, PIGR), and 1 week after 4-week intermittent fasting (CALU, CALR, IGFBP4, SEMA4B) compared with the levels before 4-week intermittent fasting. We also found a significant reduction in the levels of tumor promoter GPs at the end of 4th week during 4-week intermittent fasting (POLK, CD109, CAMP, NIFK, SRGN), and 1 week after 4-week intermittent fasting (CAMP, PLAC1) compared with the levels before 4-week intermittent fasting. Fasting from dawn to sunset for four weeks also induced an anti-diabetes proteome response by upregulating the key regulatory proteins of insulin signaling at the end of 4th week during 4-week intermittent fasting (VPS8, POLRMT, IGFBP-5) and 1 week after 4-week intermittent fasting (PRKCSH), and an anti-aging proteome response by upregulating H2B histone proteins 1 week after 4-week intermittent fasting. Subjects had a significant reduction in body mass index, waist circumference, and improvement in blood pressure that co-occurred with the anticancer, anti-diabetes, and anti-aging serum proteome response. These findings suggest that intermittent fasting from dawn to sunset actively modulates the respective genes and can be an adjunct treatment in metabolic syndrome. Further studies are needed to test the intermittent fasting from dawn to sunset in the prevention and treatment of metabolic syndrome-induced cancers.
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Xu G, Xu WY, Xiao Y, Jin B, Du SD, Mao YL, Zhang ZT. The emerging roles of non-coding competing endogenous RNA in hepatocellular carcinoma. Cancer Cell Int 2020; 20:496. [PMID: 33061848 PMCID: PMC7552539 DOI: 10.1186/s12935-020-01581-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 09/28/2020] [Indexed: 01/17/2023] Open
Abstract
Accumulating evidence has emerged revealing that noncoding RNAs (ncRNAs) play essential roles in the occurrence and development of hepatocellular carcinoma (HCC). However, the complicated regulatory interactions among various ncRNAs in the development of HCC are not entirely understood. The newly discovered mechanism of competing endogenous RNAs (ceRNAs) uncovered regulatory interactions among different varieties of RNAs. In recent years, a growing number of studies have suggested that ncRNAs, including long ncRNAs, circular RNAs and pseudogenes, play major roles in the biological functions of the ceRNA network in HCC. These ncRNAs can share microRNA response elements to affect microRNA affinity with target RNAs, thus regulating gene expression at the transcriptional level and both physiological and pathological processes. The ncRNAs that function as ceRNAs are involved in diverse biological processes in HCC cells, such as tumor cell proliferation, epithelial-mesenchymal transition, invasion, metastasis and chemoresistance. Based on these findings, ncRNAs that act as ceRNAs may be promising candidates for clinical diagnosis and treatments. In this review, we discuss the mechanisms and research methods of ceRNA networks. We also reviewed the recent advances in studying the roles of ncRNAs as ceRNAs in HCC and highlight possible directions and possibilities of ceRNAs as diagnostic biomarkers or therapeutic targets. Finally, the limitations, gaps in knowledge and opportunities for future research are also discussed.
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Affiliation(s)
- Gang Xu
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital and Chinese Academy of Medical Sciences, 1# Shuaifuyuan, Wangfujing, Dong-Cheng District, Beijing, 100730 China
| | - Wei-Yu Xu
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University; Beijing Key Laboratory of Cancer Invasion and Metastasis Research & National Clinical Research Center for Digestive Diseases, No. 95 Yong-An Road, Xi-Cheng District, Beijing, 100050 People's Republic of China
| | - Yao Xiao
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital and Chinese Academy of Medical Sciences, 1# Shuaifuyuan, Wangfujing, Dong-Cheng District, Beijing, 100730 China
| | - Bao Jin
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital and Chinese Academy of Medical Sciences, 1# Shuaifuyuan, Wangfujing, Dong-Cheng District, Beijing, 100730 China
| | - Shun-Da Du
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital and Chinese Academy of Medical Sciences, 1# Shuaifuyuan, Wangfujing, Dong-Cheng District, Beijing, 100730 China
| | - Yi-Lei Mao
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital and Chinese Academy of Medical Sciences, 1# Shuaifuyuan, Wangfujing, Dong-Cheng District, Beijing, 100730 China
| | - Zhong-Tao Zhang
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University; Beijing Key Laboratory of Cancer Invasion and Metastasis Research & National Clinical Research Center for Digestive Diseases, No. 95 Yong-An Road, Xi-Cheng District, Beijing, 100050 People's Republic of China
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14
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Wang N, Hao F, Ren J, Fei X, Chen Y, Xu W, Wang J. Positive feedback loop of AKR1B10P1/miR-138/SOX4 promotes cell growth in hepatocellular carcinoma cells. Am J Transl Res 2020; 12:5465-5480. [PMID: 33042431 PMCID: PMC7540089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/26/2020] [Indexed: 06/11/2023]
Abstract
Potential functions of pseudogenes on tumorigenesis and development of human malignancies have been gradually revealed recently. However, the specific regulation and intracellular events associated with pseudogenes have not been illustrated clearly in hepatocellular carcinoma (HCC). AKR1B10P1 is an isoform pseudogene of oncogenic AKR1B10, and is barely transcribed in normal hepatocytes. In this study, anomalous transcript of AKR1B10P1 was detected in both HCC tissues and cell lines, and is positively correlated with its parental genes. High level of AKR1B10P1 transcript is correlated with dismal clinicopathologic features, including large tumor dimension, high level of serum Alpha-fetoprotein (AFP), advanced TNM stages, tumor microsatellite formation and venous invasion. Loss-of and gain-of function assays demonstrated the exact impact of AKR1B10P1 on promoting HCC cell proliferation. Furthermore, transcription factor SOX4 was discovered facilitating the activation of AKR1B10P1 transcription, and was validated as a down-stream target degraded by tumor-suppressing miR-138. Meanwhile, we discovered the existence of a positive feedback from AKR1B10P1, by which miR-138 interacts with AKR1B10P1 via a competing endogenous RNA (ceRNA) way. Thus, we suggest a positive feedback loop of AKR1B10P1/miR-138/SOX4, promoting HCC cell proliferation. In summary, the AKR1B10P1/miR-138/SOX4 loop in HCC cells provides us potential and probable targets contributing to HCC prevention and therapeutic treatment.
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Affiliation(s)
- Nan Wang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine197, Rui Jin Er Road, Shanghai 200025, People’s Republic of China
| | - Fengjie Hao
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine197, Rui Jin Er Road, Shanghai 200025, People’s Republic of China
| | - Jiajun Ren
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine197, Rui Jin Er Road, Shanghai 200025, People’s Republic of China
| | - Xiaochun Fei
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine197, Rui Jin Er Road, Shanghai 200025, People’s Republic of China
| | - Yongjun Chen
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine197, Rui Jin Er Road, Shanghai 200025, People’s Republic of China
| | - Wen Xu
- State Key Laboratory of Bioreactor Engineering and Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and TechnologyShanghai 200237, People’s Republic of China
| | - Junqing Wang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine197, Rui Jin Er Road, Shanghai 200025, People’s Republic of China
- Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine197, Rui Jin Er Road, Shanghai 200025, People’s Republic of China
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15
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Hao F, Fei X, Ren X, Xi Xiao J, Chen Y, Wang J. Pseudogene AKR1B10P1 enhances tumorigenicity and regulates epithelial-mesenchymal transition in hepatocellular carcinoma via stabilizing SOX4. J Cell Mol Med 2020; 24:11779-11790. [PMID: 32924268 PMCID: PMC7579691 DOI: 10.1111/jcmm.15790] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/25/2020] [Accepted: 07/30/2020] [Indexed: 12/20/2022] Open
Abstract
Pseudogenes exert potential functions in tumorigenicity and tumour process in human beings. In our previous research on oncogene AKR1B10 in hepatocellular carcinoma (HCC), its pseudogene, AKR1B10P1, was preliminarily noticed being anomalistic transcribed, whereas whether AKR1B10P1 plays any specific function in HCC is poorly understood. By using shRNA transfection and lentiviral infection, we regulated the expression of ARK1B10P1 transcript and the relative targets in two ways. As we discovered, pathological transcription of AKR1B10P1 in HCC cells significantly promotes cell growth and motility either in vitro or in vivo. AKR1B10P1 was correlated with relatively dismal features of HCC. The epithelial‐mesenchymal transition (EMT) was enhanced by up‐regulating AKR1B10P1. And, a potential sequence of AKR1B10P1 transcript was discovered directly interacting with miR‐138. SOX4, a pivotal promotor of EMT, was validated as the down‐streaming target of miR‐138. Mechanistically, degradation of SOX4 mRNA induced by miR‐138 was effectively abrogated by AKR1B10P1. In conclusion, pseudogene AKR1B10P1 exerts stabilizing effect on SOX4 in HCC, associated EMT process, by directly sponging miR‐138, which post‐transcriptionally modulates SOX4’s regulating gene.
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Affiliation(s)
- Fengjie Hao
- Department of General Surgery, Hepatobiliary Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Xiaochun Fei
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Xinping Ren
- Department of Ultrasound, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Joanna Xi Xiao
- Department of Ultrasound, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Yongjun Chen
- Department of General Surgery, Hepatobiliary Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Junqing Wang
- Department of General Surgery, Hepatobiliary Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.,Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
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16
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Lou W, Ding B, Fu P. Pseudogene-Derived lncRNAs and Their miRNA Sponging Mechanism in Human Cancer. Front Cell Dev Biol 2020; 8:85. [PMID: 32185172 PMCID: PMC7058547 DOI: 10.3389/fcell.2020.00085] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/30/2020] [Indexed: 12/28/2022] Open
Abstract
Pseudogenes, abundant in the human genome, are traditionally considered as non-functional “junk genes.” However, recent studies have revealed that pseudogenes act as key regulators at DNA, RNA or protein level in diverse human disorders (including cancer), among which pseudogene-derived long non-coding RNA (lncRNA) transcripts are extensively investigated and has been reported to be frequently dysregulated in various types of human cancer. Growing evidence demonstrates that pseudogene-derived lncRNAs play important roles in cancer initiation and progression by serving as competing endogenous RNAs (ceRNAs) through competitively binding to shared microRNAs (miRNAs), thus affecting both their cognate genes and unrelated genes. Herein, we retrospect those current findings about expression, functions and potential ceRNA mechanisms of pseudogene-derived lncRNAs in human cancer, which may provide us with some crucial clues in developing potential targets for cancer therapy in the future.
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Affiliation(s)
- Weiyang Lou
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Program of Innovative Cancer Therapeutics, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Key Laboratory of Organ Transplantation, Zhejiang University, Hangzhou, China
| | - Bisha Ding
- Program of Innovative Cancer Therapeutics, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Key Laboratory of Organ Transplantation, Zhejiang University, Hangzhou, China
| | - Peifen Fu
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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17
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Chen X, Wan L, Wang W, Xi WJ, Yang AG, Wang T. Re-recognition of pseudogenes: From molecular to clinical applications. Theranostics 2020; 10:1479-1499. [PMID: 32042317 PMCID: PMC6993246 DOI: 10.7150/thno.40659] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 11/12/2019] [Indexed: 12/14/2022] Open
Abstract
Pseudogenes were initially regarded as "nonfunctional" genomic elements that did not have protein-coding abilities due to several endogenous inactivating mutations. Although pseudogenes are widely expressed in prokaryotes and eukaryotes, for decades, they have been largely ignored and classified as gene "junk" or "relics". With the widespread availability of high-throughput sequencing analysis, especially omics technologies, knowledge concerning pseudogenes has substantially increased. Pseudogenes are evolutionarily conserved and derive primarily from a mutation or retrotransposon, conferring the pseudogene with a "gene repository" role to store and expand genetic information. In contrast to previous notions, pseudogenes have a variety of functions at the DNA, RNA and protein levels for broadly participating in gene regulation to influence the development and progression of certain diseases, especially cancer. Indeed, some pseudogenes have been proven to encode proteins, strongly contradicting their "trash" identification, and have been confirmed to have tissue-specific and disease subtype-specific expression, indicating their own value in disease diagnosis. Moreover, pseudogenes have been correlated with the life expectancy of patients and exhibit great potential for future use in disease treatment, suggesting that they are promising biomarkers and therapeutic targets for clinical applications. In this review, we summarize the natural properties, functions, disease involvement and clinical value of pseudogenes. Although our knowledge of pseudogenes remains nascent, this field deserves more attention and deeper exploration.
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18
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Bioinformatic Analysis of Circular RNA-Associated ceRNA Network Associated with Hepatocellular Carcinoma. BIOMED RESEARCH INTERNATIONAL 2019; 2019:8308694. [PMID: 31886256 PMCID: PMC6926424 DOI: 10.1155/2019/8308694] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 09/23/2019] [Accepted: 10/15/2019] [Indexed: 12/29/2022]
Abstract
Hepatocellular carcinoma (HCC) is the sixth most common cancer worldwide and is associated with a high mortality rate and poor treatment efficacy. In an attempt to investigate the mechanisms involved in the pathogenesis of HCC, bioinformatic analysis and validation by qRT-PCR were performed. Three circRNA GEO datasets and one miRNA GEO dataset were selected for this purpose. Upon combined biological prediction, a total of 11 differentially expressed circRNAs, 15 differentially expressed miRNAs, and 560 target genes were screened to construct a circRNA-related ceRNA network. GO analysis and KEGG pathway analysis were performed for the 560 target genes. To further screen key genes, a protein-protein interaction network of the target genes was constructed using STRING, and the genes and modules with higher degree were identified by MCODE and CytoHubba plugins of Cytoscape. Subsequently, a module was screened out and subjected to GO enrichment analysis and KEGG pathway analysis. This module included eight genes, which were further screened using TCGA. Finally, UBE2L3 was selected as a key gene and the hsa_circ_0009910-miR-1261-UBE2L3 regulatory axis was established. The relative expression of the regulatory axis members was confirmed by qRT-PCR in 30 pairs of samples, including HCC tissues and adjacent nontumor tissues. The results suggested that hsa_circ_0009910, which was upregulated in HCC tissues, participates in the pathogenesis of HCC by acting as a sponge of miR-1261 to regulate the expression of UBE2L3. Overall, this study provides support for the possible mechanisms of progression in HCC.
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He QL, Qin SY, Tao L, Ning HJ, Jiang HX. Prognostic value and prospective molecular mechanism of miR-100-5p in hepatocellular carcinoma: A comprehensive study based on 1,258 samples. Oncol Lett 2019; 18:6126-6142. [PMID: 31788087 PMCID: PMC6865135 DOI: 10.3892/ol.2019.10962] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 09/06/2019] [Indexed: 02/07/2023] Open
Abstract
The prognostic value and molecular mechanism of microRNA-100-5p (miR-100-5p) in hepatocellular carcinoma (HCC) are still unclear. To explore the prognostic value and the mechanism of miR-100-5p in HCC, the present study analyzed the results of 18 previous studies and bioinformatic datasets. The clinical significance of miR-100-5p and its targets in HCC were investigated using The Cancer Genome Atlas and the Gene Expression Omnibus, as well as relevant literature. In total, 12 online tools were used to predict the target genes of miR-100-5p. Bioinformatics analysis and Spearman correlation analysis were performed, and genomic alterations of the hub genes were evaluated. A meta-analysis with 1,258 samples revealed that miR-100-5p was significantly downregulated in HCC [standard mean difference (SMD), −0.94; 95% confidence interval (CI), −1.14 to −0.74; I2, 35.2%]. Lower miR-100-5p expression was associated with poorer clinical characteristics and a poorer prognosis for patients with HCC. Additionally, bioinformatics analysis revealed that the ‘regulation of transcription’, ‘chromatin remodeling complex’, ‘transcription regulator activity’, ‘pathways in cancer’ and ‘heparan sulfate biosynthesis’ were the most enriched terms. Furthermore, expression of histone deacetylase (HDAC)2, HDAC3, SHC-transforming protein 1 (SHC1), Ras-related protein Rac1 (RAC1) and E3 ubiquitin-protein ligase CBL (CBL) was negatively correlated with miR-100-5p expression. Among these, upregulated HDAC2 [hazard ratio (HR), 1.910; 95% CI, 1.309–2.787; P=0.0007], HDAC3 (HR, 1.474; 95% CI, 1.012–2.146; P=0.0435), SHC1 (HR, 1.52; 95% CI, 1.043–2.215; P=0.0281) and RAC1 (HR, 1.817; 95% CI, 1.248–2.645; P=0.0022) were associated with shorter survival. Alterations in HDAC2, SHC1, RAC1 and IGF1R were linked with a poorer outcome for HCC, and alternative splicing of SHC and RAC1 were significantly decreased and increased in HCC, respectively. In summary, the downregulation of miR-100-5p may be involved in the progression and prognosis of HCC. The upregulation of HDAC2, HDAC3, SHC1 and RAC1 may indicate a poorer survival rate for patients with HCC. Thus, miR-100-5p and these 4 potential target genes may provide novel therapeutic targets and prognostic predictors for patients with HCC.
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Affiliation(s)
- Qing-Lin He
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Shan-Yu Qin
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Lin Tao
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Hong-Jian Ning
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Hai-Xing Jiang
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
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20
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Chan JJ, Kwok ZH, Chew XH, Zhang B, Liu C, Soong TW, Yang H, Tay Y. A FTH1 gene:pseudogene:microRNA network regulates tumorigenesis in prostate cancer. Nucleic Acids Res 2019; 46:1998-2011. [PMID: 29240947 PMCID: PMC5829750 DOI: 10.1093/nar/gkx1248] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 12/02/2017] [Indexed: 12/27/2022] Open
Abstract
Non-coding RNAs play a vital role in diverse cellular processes. Pseudogenes, which are non-coding homologs of protein-coding genes, were once considered non-functional evolutional relics. However, recent studies have shown that pseudogene transcripts can regulate their parental transcripts by sequestering shared microRNAs (miRNAs), thus acting as competing endogenous RNAs (ceRNAs). In this study, we utilize an unbiased screen to identify the ferritin heavy chain 1 (FTH1) transcript and multiple FTH1 pseudogenes as targets of several oncogenic miRNAs in prostate cancer (PCa). We characterize the critical role of this FTH1 gene:pseudogene:miRNA network in regulating tumorigenesis in PCa, whereby oncogenic miRNAs downregulate the expression of FTH1 and its pseudogenes to drive oncogenesis. We further show that impairing miRNA binding and subsequent ceRNA crosstalk completely rescues the slow growth phenotype in vitro and in vivo. Our results also demonstrate the reciprocal regulation between the pseudogenes and intracellular iron levels, which are crucial for multiple physiological and pathophysiological processes. In summary, we describe an extensive gene:pseudogene network comprising multiple miRNAs and multiple pseudogenes derived from a single parental gene. The network could be regulated through multiple mechanisms to modulate iron storage in various signaling pathways, the deregulation of which results in PCa development and progression.
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Affiliation(s)
- Jia Jia Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Zhi Hao Kwok
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Xiao Hong Chew
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Bin Zhang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Chao Liu
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Tuck Wah Soong
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.,National Neuroscience Institute, Singapore 308433, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Yvonne Tay
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
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21
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Yue C, Liang C, Ge H, Yan L, Xu Y, Li G, Li P, Wei Z, Wu J. Pseudogene DUXAP10 acts as a diagnostic and prognostic marker and promotes cell proliferation by activating PI3K/AKT pathway in hepatocellular carcinoma. Onco Targets Ther 2019; 12:4555-4566. [PMID: 31354289 PMCID: PMC6572670 DOI: 10.2147/ott.s210623] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 05/16/2019] [Indexed: 01/10/2023] Open
Abstract
Background: Recently, the pseudogene DUXAP10 was shown to be overexpressed in various human cancers and emerged as a key cancer regulator. However, the roles of DUXAP10 in hepatocellular carcinoma (HCC) tumorigenesis and progression remain uncharacterized. Methods: Comprehensive analyses were performed to investigate DUXAP10 expression patterns, potential biologic functions, and clinical significance in HCC based on the data downloaded from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. DUXAP10 expression levels in HCC tissue sections and cells were verified using quantitative real-time PCR analysis. DUXAP10-siRNA was used to silence DUXAP10 in the Hep3B cell line to determine the roles of DUXAP10 in HCC cell proliferation. Results: DUXAP10 was significantly overexpressed in HCC, and DUXAP10 upregulation was closely associated with poor prognoses in HCC patients. DUXAP10 knockdown decreased cell proliferation and arrested HCC cells in the G1 phase of the cell cycle. Western blot analysis showed that DUXAP10 knockdown decreased p-AKT expression in HCC cells. Conclusion: Our study demonstrates that pseudogene DUXAP10 promotes HCC cell proliferation by activating PI3K/AKT pathway and could act as a potential diagnostic and prognostic biomarker for HCC patients.
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Affiliation(s)
- Chaosen Yue
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Chaojie Liang
- Department of General Surgery, First Hospital/First Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi, People's Republic of China
| | - Hua Ge
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Lijun Yan
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Yingchen Xu
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Guangming Li
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Pengyang Li
- Department of Medicine, Saint Vincent Hospital, Worcester, MA, USA
| | - Zhigang Wei
- Department of General Surgery, First Hospital/First Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi, People's Republic of China
| | - Jixiang Wu
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, People's Republic of China
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22
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Pseudogene RACGAP1P activates RACGAP1/Rho/ERK signalling axis as a competing endogenous RNA to promote hepatocellular carcinoma early recurrence. Cell Death Dis 2019; 10:426. [PMID: 31160556 PMCID: PMC6546712 DOI: 10.1038/s41419-019-1666-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 04/18/2019] [Accepted: 05/06/2019] [Indexed: 01/13/2023]
Abstract
Accumulating evidence has indicated crucial roles for pseudogenes in human cancers. However, the roles played by pseudogenes in the pathogenesis of HCC, particularly HCC early recurrence, still incompletely elucidated. Herein, we identify a novel early recurrence related pseudogene RACGAP1P which was significantly upregulated in HCC and was associated with larger tumour size, advanced clinical stage, abnormal AFP level and shorter survival time. In vitro and in vivo experiments have shown that RACGAP1P is a prerequisite for the development of malignant characteristics of HCC cells, including cell growth and migration. Mechanistic investigations indicated that RACGAP1P elicits its oncogenic activity as a ceRNA to sequestrate miR-15-5p from its endogenous target RACGAP1, thereby leading to the upregulation of RACGAP1 and the activation of RhoA/ERK signalling. These results may provide new insights into the functional crosstalk of the pseudogene/miRNA/parent-gene genetic network during HCC early relapse and may contribute to improving the clinical intervention for this subset of HCC patients.
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23
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Lou W, Ding B, Fan W. High Expression of Pseudogene PTTG3P Indicates a Poor Prognosis in Human Breast Cancer. MOLECULAR THERAPY-ONCOLYTICS 2019; 14:15-26. [PMID: 31011629 PMCID: PMC6463746 DOI: 10.1016/j.omto.2019.03.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 03/13/2019] [Indexed: 01/16/2023]
Abstract
Pseudogenes play pivotal roles in tumorigenesis. Previous studies have suggested that pituitary tumor-transforming 3, pseudogene (PTTG3P), serves as an oncogene in human cancers. However, its expression pattern, biological function, and underlying mechanism in breast cancer remain unknown. In this study, we demonstrated an elevated expression of PTTG3P in breast cancer and discovered that PTTG3P expression correlated negatively with estrogen receptor (ER) and progesterone receptor (PR) status, but linked positively to basal-like status, triple-negative breast cancer status, Nottingham prognostic index (NPI), and Scarff-Bloom-Richardson grade. High expression of PTTG3P was also found to be associated with a poor prognosis of breast cancer. To explore the potential mechanisms of PTTG3P, a PTTG3P-microRNA (miRNA)-mRNA regulatory network was established. Co-expressed genes of PTTG3P were also obtained. Enrichment analysis for these co-expressed genes revealed that they were significantly enriched in mitotic nuclear division and cell cycle. Subsequent research on mechanism of PTTG3P indicated that its expression correlated positively with PTTG1 expression. However, no significant expression correlation between PTTG3P and PTTG2 was observed. Taken together, our findings suggest that increased expression of pseudogene PTTG3P may be used as a promising prognostic biomarker and novel therapeutic target for breast cancer.
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Affiliation(s)
- Weiyang Lou
- Program of Innovative Cancer Therapeutics, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China.,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou 310003, China.,Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, Hangzhou 310000, China
| | - Bisha Ding
- Program of Innovative Cancer Therapeutics, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China.,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou 310003, China.,Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, Hangzhou 310000, China
| | - Weimin Fan
- Program of Innovative Cancer Therapeutics, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China.,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou 310003, China.,Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, Hangzhou 310000, China.,Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
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24
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Zhang F, Ding L, Cui L, Barber R, Deng B. Identification of long non-coding RNA-related and -coexpressed mRNA biomarkers for hepatocellular carcinoma. BMC Med Genomics 2019; 12:25. [PMID: 30704465 PMCID: PMC6357343 DOI: 10.1186/s12920-019-0472-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Background While changes in mRNA expression during tumorigenesis have been used widely as molecular biomarkers for the diagnosis of a number of cancers, the approach has limitations. For example, traditional methods do not consider the regulatory and positional relationship between mRNA and lncRNA. The latter has been largely shown to possess tumor suppressive or oncogenic properties. The combined analysis of mRNA and lncRNA is likely to facilitate the identification of biomarkers with higher confidence. Results Therefore, we have developed an lncRNA-related method to identify traditional mRNA biomarkers. First we identified mRNAs that are differentially expressed in Hepatocellular Carcinoma (HCC) by comparing cancer and matched adjacent non-tumorous liver tissues. Then, we performed mRNA-lncRNA relationship and coexpression analysis and obtained 41 lncRNA-related and -coexpressed mRNA biomarkers. Next, we performed network analysis, gene ontology analysis and pathway analysis to unravel the functional roles and molecular mechanisms of these lncRNA-related and -coexpressed mRNA biomarkers. Finally, we validated the prediction and performance of the 41 lncRNA-related and -coexpressed mRNA biomarkers using Support Vector Machine model with five-fold cross-validation in an independent HCC dataset from RNA-seq. Conclusions Our results suggested that mRNAs expression profiles coexpressed with positionally related lncRNAs can provide important insights into early diagnosis and specific targeted gene therapy of HCC.
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Affiliation(s)
- Fan Zhang
- Vermont Genetics Network, University of Vermont, Burlington, VT, 05405, USA. .,Department of Biology, University of Vermont, Burlington, VT, 05405, USA.
| | - Linda Ding
- School of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0606, USA
| | - Li Cui
- Department of Neurosciences, School of Medicine, University of California, San Diego, 9500 Gilman Drive #0949, La Jolla, CA, 92093, USA
| | - Robert Barber
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Bin Deng
- Vermont Genetics Network, University of Vermont, Burlington, VT, 05405, USA.,Department of Biology, University of Vermont, Burlington, VT, 05405, USA
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25
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Jurj A, Pop L, Petrushev B, Pasca S, Dima D, Frinc I, Deak D, Desmirean M, Trifa A, Fetica B, Gafencu G, Selicean S, Moisoiu V, Micu WT, Berce C, Sacu A, Moldovan A, Colita A, Bumbea H, Tanase A, Dascalescu A, Zdrenghea M, Stiufiuc R, Leopold N, Tetean R, Burzo E, Tomuleasa C, Berindan-Neagoe I. Exosome-carried microRNA-based signature as a cellular trigger for the evolution of chronic lymphocytic leukemia into Richter syndrome. Crit Rev Clin Lab Sci 2018; 55:501-515. [PMID: 30238808 DOI: 10.1080/10408363.2018.1499707] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Even if considered a cumulative and not a proliferative CD5+ B-cell neoplasm, chronic lymphocytic leukemia (CLL) has a proliferation rate higher than that recognized earlier, especially in the lymphoid tissues. Some patients with CLL develop a clinical syndrome entitled Richter syndrome (RS). Understanding CLL genetics and epigenetics may help to elucidate the molecular basics of the clinical heterogeneity of this type of malignancy. In the present project we aimed to identify a microRNA species that can predict the evolution of therapy-resistant CLL towards RS. In the first phase of our study, microRNA-19b was identified as a possible target, and in the second phase, we transfected three different CLL cell lines with microRNA-19b mimic and inhibitor and assessed the potential role on leukemia cells in vitro. The mechanism by which miR-19b acts were identified as the upregulation of Ki67 and downregulation of p53. This was further supported through RT-PCR and western blotting on CLL cell lines, as well as by next generation sequencing on two patients diagnosed with CLL that evolved into RS.
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Affiliation(s)
- Ancuta Jurj
- a Research Center for Functional Genomic, Biomedicine and Translational Medicine , Iuliu Hatieganu University of Medicine and Pharmacy , Cluj Napoca , Romania
| | - Laura Pop
- a Research Center for Functional Genomic, Biomedicine and Translational Medicine , Iuliu Hatieganu University of Medicine and Pharmacy , Cluj Napoca , Romania
| | - Bobe Petrushev
- b Department of Pathology , Ion Chiricuta Oncology Institute , Cluj Napoca , Romania
| | - Sergiu Pasca
- a Research Center for Functional Genomic, Biomedicine and Translational Medicine , Iuliu Hatieganu University of Medicine and Pharmacy , Cluj Napoca , Romania
| | - Delia Dima
- c Department of Hematology , Ion Chiricuta Oncology Institute , Cluj Napoca , Romania
| | - Ioana Frinc
- c Department of Hematology , Ion Chiricuta Oncology Institute , Cluj Napoca , Romania
| | - Dalma Deak
- c Department of Hematology , Ion Chiricuta Oncology Institute , Cluj Napoca , Romania
| | - Minodora Desmirean
- d Department of Hematology , Iuliu Hatieganu University of Medicine and Pharmacy , Cluj Napoca , Romania
| | - Adrian Trifa
- c Department of Hematology , Ion Chiricuta Oncology Institute , Cluj Napoca , Romania
| | - Bogdan Fetica
- b Department of Pathology , Ion Chiricuta Oncology Institute , Cluj Napoca , Romania
| | - Grigore Gafencu
- a Research Center for Functional Genomic, Biomedicine and Translational Medicine , Iuliu Hatieganu University of Medicine and Pharmacy , Cluj Napoca , Romania
| | - Sonia Selicean
- a Research Center for Functional Genomic, Biomedicine and Translational Medicine , Iuliu Hatieganu University of Medicine and Pharmacy , Cluj Napoca , Romania
| | - Vlad Moisoiu
- a Research Center for Functional Genomic, Biomedicine and Translational Medicine , Iuliu Hatieganu University of Medicine and Pharmacy , Cluj Napoca , Romania
| | - Wilhelm-Thomas Micu
- a Research Center for Functional Genomic, Biomedicine and Translational Medicine , Iuliu Hatieganu University of Medicine and Pharmacy , Cluj Napoca , Romania
| | - Cristian Berce
- e Center for Experimental Medicine , Iuliu Hatieganu University of Medicine and Pharmacy , Cluj Napoca , Romania
| | - Alexandra Sacu
- d Department of Hematology , Iuliu Hatieganu University of Medicine and Pharmacy , Cluj Napoca , Romania
| | - Alin Moldovan
- a Research Center for Functional Genomic, Biomedicine and Translational Medicine , Iuliu Hatieganu University of Medicine and Pharmacy , Cluj Napoca , Romania.,f Department of Hematology , Carol Davilla University of Medicine and Pharmacy , Bucharest , Romania
| | - Andrei Colita
- g Department of Hematology , Coltea Hospital , Bucharest , Romania
| | - Horia Bumbea
- f Department of Hematology , Carol Davilla University of Medicine and Pharmacy , Bucharest , Romania.,h Department of Hematology , University Hospital , Bucharest , Romania
| | - Alina Tanase
- h Department of Hematology , University Hospital , Bucharest , Romania.,i Department of Hematology , Fundeni Clinical Hospital , Bucharest , Romania
| | - Angela Dascalescu
- j Department of Hematology , Grigore T. Popa University of Medicine and Pharmacy , Iasi , Romania.,k Department of Hematology , Regional Institute of Oncology , Iasi , Romania
| | - Mihnea Zdrenghea
- d Department of Hematology , Iuliu Hatieganu University of Medicine and Pharmacy , Cluj Napoca , Romania
| | - Rares Stiufiuc
- d Department of Hematology , Iuliu Hatieganu University of Medicine and Pharmacy , Cluj Napoca , Romania
| | - Nicolae Leopold
- l Department of Physics , Babes Bolyai University , Cluj Napoca , Romania
| | - Romulus Tetean
- l Department of Physics , Babes Bolyai University , Cluj Napoca , Romania
| | - Emil Burzo
- l Department of Physics , Babes Bolyai University , Cluj Napoca , Romania.,m Romanian Academy , Romania
| | - Ciprian Tomuleasa
- a Research Center for Functional Genomic, Biomedicine and Translational Medicine , Iuliu Hatieganu University of Medicine and Pharmacy , Cluj Napoca , Romania.,c Department of Hematology , Ion Chiricuta Oncology Institute , Cluj Napoca , Romania
| | - Ioana Berindan-Neagoe
- a Research Center for Functional Genomic, Biomedicine and Translational Medicine , Iuliu Hatieganu University of Medicine and Pharmacy , Cluj Napoca , Romania
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26
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Liu S, Yao X, Zhang D, Sheng J, Wen X, Wang Q, Chen G, Li Z, Du Z, Zhang X. Analysis of Transcription Factor-Related Regulatory Networks Based on Bioinformatics Analysis and Validation in Hepatocellular Carcinoma. BIOMED RESEARCH INTERNATIONAL 2018; 2018:1431396. [PMID: 30228980 PMCID: PMC6136478 DOI: 10.1155/2018/1431396] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 07/03/2018] [Accepted: 07/25/2018] [Indexed: 02/07/2023]
Abstract
Hepatocellular carcinoma (HCC) accounts for a significant proportion of liver cancer, which has become the second most common cause of cancer-related mortality worldwide. To investigate the potential mechanisms of invasion and progression of HCC, bioinformatics analysis and validation by qRT-PCR were performed. We found 237 differentially expressed genes (DEGs) including EGR1, FOS, and FOSB, which were three cancer-related transcription factors. Subsequently, we constructed TF-gene network and miRNA-TF-mRNA network based on data obtained from mRNA and miRNA expression profiles for analysis of HCC. We found that 42 key genes from the TF-gene network including EGR1, FOS, and FOSB were most enriched in the p53 signaling pathway. The qRT-PCR data confirmed that mRNA levels of EGR1, FOS, and FOSB all were decreased in HCC tissues. In addition, we confirmed that the mRNA levels of CCNB1, CCNB2, and CHEK1, three key markers of the p53 signaling pathway, were all increased in HCC tissues by bioinformatics analysis and qRT-PCR validation. Therefore, we speculated that miR-181a-5p, which was upregulated in HCC tissues, could regulate FOS and EGR1 to promote the invasion and progression of HCC by p53 signaling pathway. Overall, the study provides support for the possible mechanisms of progression in HCC.
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Affiliation(s)
- Shui Liu
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun 130041, China
- Jilin Engineering Laboratory for Translational Medicine of Hepatobiliary and Pancreatic Diseases, The Second Hospital of Jilin University, Changchun 130041, China
| | - Xiaoxiao Yao
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun 130041, China
- Jilin Engineering Laboratory for Translational Medicine of Hepatobiliary and Pancreatic Diseases, The Second Hospital of Jilin University, Changchun 130041, China
| | - Dan Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun 130041, China
- Jilin Engineering Laboratory for Translational Medicine of Hepatobiliary and Pancreatic Diseases, The Second Hospital of Jilin University, Changchun 130041, China
| | - Jiyao Sheng
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun 130041, China
- Jilin Engineering Laboratory for Translational Medicine of Hepatobiliary and Pancreatic Diseases, The Second Hospital of Jilin University, Changchun 130041, China
| | - Xin Wen
- The Second Hospital of Jilin University, Changchun 130041, China
| | - Qingyu Wang
- Department of Orthopedics, The Second Hospital of Jilin University, Changchun 130041, China
| | - Gaoyang Chen
- Department of Orthopedics, The Second Hospital of Jilin University, Changchun 130041, China
| | - Zhaoyan Li
- Department of Orthopedics, The Second Hospital of Jilin University, Changchun 130041, China
| | - Zhenwu Du
- Department of Orthopedics, The Second Hospital of Jilin University, Changchun 130041, China
- Research Center of Second Clinical College, Jilin University, Changchun 130041, China
| | - Xuewen Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun 130041, China
- Jilin Engineering Laboratory for Translational Medicine of Hepatobiliary and Pancreatic Diseases, The Second Hospital of Jilin University, Changchun 130041, China
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27
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Chen H, Shen HX, Lin YW, Mao YQ, Liu B, Xie LP. Small RNA-induced INTS6 gene up-regulation suppresses castration-resistant prostate cancer cells by regulating β-catenin signaling. Cell Cycle 2018; 17:1602-1613. [PMID: 29895194 DOI: 10.1080/15384101.2018.1475825] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
Abstract
Small RNAs play an important role in gene regulatory networks. The gene suppressive effect of small RNAs was previously the dominant focus of studies, but during the recent decade, small RNA-induced gene activation has been reported and has become a notable gene manipulation technique. In this study, a putative tumor suppressor, INTS6, was activated by introducing a promoter-targeted small RNA (dsRNA-915) into castration-resistant prostate cancer (CRPC) cells. Unique dynamics associated with the gene upregulation phenomenon was observed. Following gene activation, cell proliferation and motility were suppressed in vitro. Downregulation of Wnt/β-catenin signaling was observed during the activation period, and the impairment of β-catenin degradation reversed the tumor suppressor effects of INTS6. These results suggest the potential application of small activating RNAs in targeted gene therapy for CRPC.
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Affiliation(s)
- Hong Chen
- a Department of Urology , The First Affiliated Hospital, School of Medicine, Zhejiang University , Hangzhou , Zhejiang Province , China
| | - Hai-Xiang Shen
- a Department of Urology , The First Affiliated Hospital, School of Medicine, Zhejiang University , Hangzhou , Zhejiang Province , China
| | - Yi-Wei Lin
- a Department of Urology , The First Affiliated Hospital, School of Medicine, Zhejiang University , Hangzhou , Zhejiang Province , China
| | - Ye-Qing Mao
- a Department of Urology , The First Affiliated Hospital, School of Medicine, Zhejiang University , Hangzhou , Zhejiang Province , China
| | - Ben Liu
- a Department of Urology , The First Affiliated Hospital, School of Medicine, Zhejiang University , Hangzhou , Zhejiang Province , China
| | - Li-Ping Xie
- a Department of Urology , The First Affiliated Hospital, School of Medicine, Zhejiang University , Hangzhou , Zhejiang Province , China
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28
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Noncoding RNA:RNA Regulatory Networks in Cancer. Int J Mol Sci 2018; 19:ijms19051310. [PMID: 29702599 PMCID: PMC5983611 DOI: 10.3390/ijms19051310] [Citation(s) in RCA: 771] [Impact Index Per Article: 128.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 04/20/2018] [Accepted: 04/25/2018] [Indexed: 02/08/2023] Open
Abstract
Noncoding RNAs (ncRNAs) constitute the majority of the human transcribed genome. This largest class of RNA transcripts plays diverse roles in a multitude of cellular processes, and has been implicated in many pathological conditions, especially cancer. The different subclasses of ncRNAs include microRNAs, a class of short ncRNAs; and a variety of long ncRNAs (lncRNAs), such as lincRNAs, antisense RNAs, pseudogenes, and circular RNAs. Many studies have demonstrated the involvement of these ncRNAs in competitive regulatory interactions, known as competing endogenous RNA (ceRNA) networks, whereby lncRNAs can act as microRNA decoys to modulate gene expression. These interactions are often interconnected, thus aberrant expression of any network component could derail the complex regulatory circuitry, culminating in cancer development and progression. Recent integrative analyses have provided evidence that new computational platforms and experimental approaches can be harnessed together to distinguish key ceRNA interactions in specific cancers, which could facilitate the identification of robust biomarkers and therapeutic targets, and hence, more effective cancer therapies and better patient outcome and survival.
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29
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Non-coding RNAs in hepatocellular carcinoma: molecular functions and pathological implications. Nat Rev Gastroenterol Hepatol 2018; 15:137-151. [PMID: 29317776 DOI: 10.1038/nrgastro.2017.169] [Citation(s) in RCA: 303] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hepatocellular carcinoma (HCC) is a leading lethal malignancy worldwide. However, the molecular mechanisms underlying liver carcinogenesis remain poorly understood. Over the past two decades, overwhelming evidence has demonstrated the regulatory roles of different classes of non-coding RNAs (ncRNAs) in liver carcinogenesis related to a number of aetiologies, including HBV, HCV and NAFLD. Among the ncRNAs, microRNAs, which belong to a distinct class of small ncRNAs, have been proven to play a crucial role in the post-transcriptional regulation of gene expression. Deregulation of microRNAs has been broadly implicated in the inactivation of tumour-suppressor genes and activation of oncogenes in HCC. Modern high-throughput sequencing analyses have unprecedentedly identified a very large number of non-coding transcripts. Divergent groups of long ncRNAs have been implicated in liver carcinogenesis through interactions with DNA, RNA or proteins. Overall, ncRNAs represent a burgeoning field of cancer research, and we are only beginning to understand the importance and complicity of the ncRNAs in liver carcinogenesis. In this Review, we summarize the common deregulation of small and long ncRNAs in human HCC. We also comprehensively review the pathological roles of ncRNAs in liver carcinogenesis, epithelial-to-mesenchymal transition and HCC metastasis and discuss the potential applications of ncRNAs as diagnostic tools and therapeutic targets in human HCC.
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30
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Downregulated pseudogene CTNNAP1 promote tumor growth in human cancer by downregulating its cognate gene CTNNA1 expression. Oncotarget 2018; 7:55518-55528. [PMID: 27487124 PMCID: PMC5342433 DOI: 10.18632/oncotarget.10833] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Accepted: 06/17/2016] [Indexed: 01/16/2023] Open
Abstract
Accumulating evidence indicates that deregulation of cancer-associated pseudogene is involved in the pathogenesis of cancer. In the study, we demonstrated that pseudogene CTNNAP1, for the CTNNA1 gene, was dysregulated in colorectal cancer and the degree of dysregulation was remarkably associated with tumor node metastasis (TNM) stage (P<0.05). The mechanistic experiments revealed that pseudogene CTNNAP1 played a pivotal role in the regulation of its cognate gene CTNNA1 by competition for microRNA-141. Moreover, gain-of-function approaches showed that overexpression of CTNNAP1 or CTNNA1 significantly inhibited cell proliferation and tumor growth in vitro and in vivo by inducing G0/G1 cell cycle arrest. Our findings add a new regulatory circuit via competing endogenous RNA (ceRNA) cross-talk between pseudogene CTNNAP1 and its cognate gene CTNNA1, and provide new insights into potential diagnostic biomarker for monitoring human colorectal cancer.
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31
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Xu Y, Yu X, Wei C, Nie F, Huang M, Sun M. Over-expression of oncigenic pesudogene DUXAP10 promotes cell proliferation and invasion by regulating LATS1 and β-catenin in gastric cancer. J Exp Clin Cancer Res 2018; 37:13. [PMID: 29374493 PMCID: PMC5787324 DOI: 10.1186/s13046-018-0684-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 01/19/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recently, the pesudogenes have emerged as critical regulators in human cancers tumorigenesis and progression, and been identified as a key revelation in post-genomic biology. However, the expression pattern, biological function and mechanisms responsible for these molecules in human gastric cancer (GC) are not fully understood. METHODS In this study, we globally assessed the transcriptomic differences of pesudogenes in gastric cancer using publicly available microarray data. DUXAP10 expression levels in GC tissues and cells was detected using quantitative real-time PCR (qPCR). DUXAP10 siRNAs and over-expression vector were transfected into GC cells to down-regulate or up-regulate DUXAP10 expression. Loss- and gain-of function assays were performed to investigate the role of DUXAP10 in GC cells cell proliferation, and invasion. RIP, RNA pulldown, and ChIP assays were used to determine the mechanism of DUXAP10's regulation of underlying targets. RESULTS The pesudogene DUXAP10 is the only pseudogene that significantly over-expressed in all four GEO datasets, and frequently over-expressed in many other cancers including Liver Hepatocellular carcinoma, Bladder cancer, and Esophageal Cancer. High DUXAP10 expression is associated with GC patients poor prognosis, and knockdown of DUXAP10 significantly inhibits cells proliferation, migration and invasion in GC. Mechanistic investigation shows that DUXAP10 can interact with PRC2 and LSD1 to repress LATS1 expression at transcriptional level, and bind with HuR to maintain the stability of β-catenin mRNA and increase its protein levels at post-transcriptional level. CONCLUSIONS Overall, our findings illuminate how increased DUXAP10 confers an oncogenic function in GC development and progression that may serve as a candidate prognostic biomarker and target for clinical management of GC.
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Affiliation(s)
- Yongcan Xu
- Department of General Surgery, Huzhou Central Hospital, Huzhou, People's Republic of China
| | - Xiang Yu
- Department of General Surgery, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, People's Republic of China
| | - Chenchen Wei
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Fengqi Nie
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, People's Republic of China.
- Department of Oncology, First Affiliated Hospital, Nanjing Medical University, Nanjing, People's Republic of China.
| | - Mingde Huang
- Department of Oncology, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, People's Republic of China.
| | - Ming Sun
- Department of Bioinformatics and computational biology, UT MD Anderson Cancer Center, 1400 Pressler Street, Unit 1410, Houston, TX, 77030, USA.
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32
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PIK3C2A mRNA functions as a miR-124 sponge to facilitate CD151 expression and enhance malignancy of hepatocellular carcinoma cells. Oncotarget 2017; 7:43376-43389. [PMID: 27270320 PMCID: PMC5190030 DOI: 10.18632/oncotarget.9716] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 05/09/2016] [Indexed: 01/17/2023] Open
Abstract
Competing endogenous RNAs (ceRNAs) are RNA transcripts that can crosstalk with each other by competing for shared microRNAs (miRNAs) through miRNA response elements (MREs). Involved in ceRNA networks, the RNA transcripts may be in a balance, disruption of which could lead to tumorigenesis. Here we reveal a ceRNA interaction between PIK3C2A and CD151 mRNAs in hepatocellular carcinoma (HCC) cells. PIK3C2A is a candidate ceRNA of CD151 because mRNA 3' untranslated regions (3'UTRs) of these two genes contain miR-124 binding sites. miR-124 is downregulated, while PIK3C2A and CD151 are upregulated in HCC cells compared with normal hepatocytes. Direct and negative regulation of PIK3C2A and CD151 by miR-124 was confirmed in HCC cells. miR-124 and the two potential ceRNAs are all recruited to the RNA-induced silencing complex (RISC). In HCC cell lines QGY- 7703 and SMMC-7721, and normal hepatic cell line HL-7702, miR-124 plays a tumor suppressor role by targeting PIK3C2A and CD151. The MREs within PIK3C2A 3'UTR can independently stimulate CD151 expression level by acting as miR-124 decoys. PIK3C2A MREs enhance HCC cell malignancy by absorbing endogenous miR-124 and activating CD151 in HCC cells. We conclude that PIK3C2A 3'UTR functions as a trans activator to stimulate CD151 by competing for miR-124 binding in HCC cells. The collaboration of PIK3C2A and CD151 through ceRNA mechanism may be implicated in HCC initiation and development.
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33
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Qian L, Dima D, Berce C, Liu Y, Rus I, Raduly LZ, Liu Y, Petrushev B, Berindan-Neagoe I, Irimie A, Tanase A, Jurj A, Shen J, Tomuleasa C. Protein dysregulation in graft versus host disease. Oncotarget 2017; 9:1483-1491. [PMID: 29416707 PMCID: PMC5787452 DOI: 10.18632/oncotarget.23276] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/05/2017] [Indexed: 12/15/2022] Open
Abstract
Allogeneic hematopoietic stem cell transplantation is a well-established treatment for many malignant and non-malignant hematological disorders. As a frequent complication in up to 50% of all patients, graft-versus-host disease is still the main cause for morbidity and non-relapse mortality. Diagnosis is usually done clinically, even though confirmation by pathology is often used to support the clinical findings. Effective treatment requires intensified immunosuppression as early as possible. Although several promising biomarkers have been proposed for an early diagnosis, no internationally-recognized consensus has yet been established. Protein-based biomarkers represent an interesting tool since they have been recently reported to be an important regulator of various cells, including immune cells such as T cells. Therefore, we assume that protein dysregulation is important in the pathogenesis of acute graft versus host disease and their detection might be an possibility in the early diagnosis and monitoring. In this review, we aim to summarize the previous reports of protein biomarkers, focusing on the pathogenesis of the disease and possible implications in diagnostic approaches.
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Affiliation(s)
- Liren Qian
- Department of Hematology, Navy General Hospital, Beijing, PR China
| | - Delia Dima
- Department of Hematology, Ion Chiricuta Oncology Institute, Cluj Napoca, Romania
| | - Cristian Berce
- Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Yu Liu
- Department of Hematology, Navy General Hospital, Beijing, PR China
| | - Ioana Rus
- Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Lajos-Zsolt Raduly
- Department of Hematology, Ion Chiricuta Oncology Institute, Cluj Napoca, Romania
| | - Yi Liu
- Department of Hematology, Navy General Hospital, Beijing, PR China
| | - Bobe Petrushev
- Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | | | - Alexandru Irimie
- Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Alina Tanase
- Department of Stem Cell Transplantation, Fundeni Clinical Institute, Bucharest, Romania
| | - Ancuta Jurj
- Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Jianliang Shen
- Department of Hematology, Navy General Hospital, Beijing, PR China
| | - Ciprian Tomuleasa
- Department of Hematology, Ion Chiricuta Oncology Institute, Cluj Napoca, Romania.,Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
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De Martino M, Forzati F, Arra C, Fusco A, Esposito F. HMGA1-pseudogenes and cancer. Oncotarget 2017; 7:28724-35. [PMID: 26895108 PMCID: PMC5053758 DOI: 10.18632/oncotarget.7427] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 02/05/2016] [Indexed: 12/25/2022] Open
Abstract
Pseudogenes are DNA sequences with high homology to the corresponding functional gene, but, because of the accumulation of various mutations, they have lost their initial functions to code for proteins. Consequently, pseudogenes have been considered until few years ago dysfunctional relatives of the corresponding ancestral genes, and then useless in the course of genome evolution. However, several studies have recently established that pseudogenes are owners of key biological functions. Indeed, some pseudogenes control the expression of functional genes by competitively binding to the miRNAs, some of them generate small interference RNAs to negatively modulate the expression of functional genes, and some of them even encode functional mutated proteins. Here, we concentrate our attention on the pseudogenes of the HMGA1 gene, that codes for the HMGA1a and HMGA1b proteins having a critical role in development and cancer progression. In this review, we analyze the family of HMGA1 pseudogenes through three aspects: classification, characterization, and their possible function and involvement in cancer.
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Affiliation(s)
- Marco De Martino
- Istituto di Endocrinologia ed Oncologia Sperimentale del CNR c/o Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Scuola di Medicina e Chirurgia di Napoli, Università degli Studi di Napoli "Federico II", Naples, Italy
| | - Floriana Forzati
- Istituto di Endocrinologia ed Oncologia Sperimentale del CNR c/o Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Scuola di Medicina e Chirurgia di Napoli, Università degli Studi di Napoli "Federico II", Naples, Italy
| | - Claudio Arra
- Istituto Nazionale dei Tumori, Fondazione Pascale, Naples, Italy
| | - Alfredo Fusco
- Istituto di Endocrinologia ed Oncologia Sperimentale del CNR c/o Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Scuola di Medicina e Chirurgia di Napoli, Università degli Studi di Napoli "Federico II", Naples, Italy
| | - Francesco Esposito
- Istituto di Endocrinologia ed Oncologia Sperimentale del CNR c/o Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Scuola di Medicina e Chirurgia di Napoli, Università degli Studi di Napoli "Federico II", Naples, Italy
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Lui KY, Zhao H, Qiu C, Li C, Zhang Z, Peng H, Fu R, Chen HA, Lu MQ. Integrator complex subunit 6 (INTS6) inhibits hepatocellular carcinoma growth by Wnt pathway and serve as a prognostic marker. BMC Cancer 2017; 17:644. [PMID: 28899352 PMCID: PMC5596937 DOI: 10.1186/s12885-017-3628-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 08/28/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Integrator complex subunit 6 (INTS6) was found to play a tumour suppressing role in certain types of solid tumours. In this study, we wanted to determine the expression level of INTS6 in hepatocellular carcinoma (HCC) and evaluate its clinical characteristics and mechanisms in HCC patients (Lui and Lu, European Journal of Cancer, 51:S94, 2015). METHODS First, we used a microarray analysis to explore the mRNA expression levels in HCC and paired normal liver tissues; second, we used qRT-PCR to measure the INTS6 mRNA levels in a cohort of 50 HCC tissues and adjacent normal liver tissues; third, we used Western blot analyses to detect the INTS6 protein levels in 20 paired HCC and normal liver tissues; fourth, we used immunohistochemistry to determine the INTS6 expression levels in 70 archived paraffin-embedded HCC samples. Finally, we investigated the suppressive function of INTS6 in the Wnt pathway. RESULTS Herein, according to the microarray data analysis, the expression levels of INTS6 were dramatically down-regulated in HCC tissues vs. those in normal liver tissues (p<0.05). qRT-PCR and Western blot analyses showed that the INTS6 mRNA and protein expression was significantly down-regulated in tumour tissues compared to the adjacent normal liver tissues (p<0.05). Immunohistochemical assays revealed that decreased INTS6 expression was present in 62.9% (44/70) of HCC patients. Correlation analyses showed that INTS6 expression was significantly correlated with serum alpha-fetoprotein levels (AFP, p =0.004), pathology grade (p =0.005), and tumour recurrence (p =0.04). Kaplan-Meier analysis revealed that patients with low INTS6 expression levels had shorter overall and disease-free survival rates than patients with high INTS6 expression levels (p =0.001 and p =0.001). Multivariate regression analysis indicated that INTS6 was an independent predictor of overall survival and disease-free survival rates. Mechanistically, INTS6 increased WIF-1 expression and then inhibited the Wnt/β-catenin signalling pathway. CONCLUSION The results of our study show that down-regulated INTS6 expression is associated with a poorer prognosis in HCC patients. This newly identified INTS6/WIF-1 axis indicates the molecular mechanism of HCC and may represent a therapeutic target in HCC patients.
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Affiliation(s)
- Ka Yin Lui
- Department of Critical Care Medicine, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Hui Zhao
- Department of Hepatic Surgery, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Chunhui Qiu
- Department of Hepatic Surgery, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Chuo Li
- Obstetric Laboratory, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Zhigang Zhang
- Department of Pathology, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Haoran Peng
- Transitional Year, Gwinnentt Medical Center, Lawrenceville, GA, USA
| | - Rongdang Fu
- Department of Hepatic Surgery, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Hu-An Chen
- Department of Hepatic Surgery, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China.
| | - Min-Qiang Lu
- Department of Hepatobiliary Surgery, Guangzhou First People's Hospital, Guangzhou, 510180, China.
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Tang L, Chen HY, Hao NB, Tang B, Guo H, Yong X, Dong H, Yang SM. microRNA inhibitors: Natural and artificial sequestration of microRNA. Cancer Lett 2017; 407:139-147. [PMID: 28602827 DOI: 10.1016/j.canlet.2017.05.025] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 05/16/2017] [Accepted: 05/31/2017] [Indexed: 12/14/2022]
Abstract
MicroRNA (miRNAs) is post-transcriptional regulator of mRNA. However, the prevalence and activity of miRNA are regulated by other regulators. miRNA inhibitors are natural or artificial RNA transcripts that sequestrate miRNAs and decrease or even eliminate miRNA activity. Competing endogenous RNAs (ceRNAs) are natural and intracellular miRNA inhibitors that compete to bind to shared miRNA recognition elements (MREs) to decrease microRNA availability and relieve the repression of target RNAs. In recent years, studies have revealed that ceRNA crosstalk is involved in many pathophysiological processes and adds a new dimension to miRNA regulation. Artificial miRNA inhibitors are RNA transcripts that are synthesized via chemical and genetic methods. Artificial miRNA inhibitors can be used in miRNA loss-of-function research and gene therapies for certain diseases. In this review, we summarize the recent advances in the two different types of miRNA inhibitors.
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Affiliation(s)
- Li Tang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Hong-Yan Chen
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Ning-Bo Hao
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Bo Tang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Hong Guo
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Xin Yong
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Hui Dong
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Shi-Ming Yang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China.
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Tomuleasa C, Selicean S, Gafencu G, Petrushev B, Pop L, Berce C, Jurj A, Trifa A, Rosu AM, Pasca S, Magdo L, Zdrenghea M, Dima D, Tanase A, Frinc I, Bojan A, Berindan-Neagoe I, Ghiaur G, Ciurea SO. Fibroblast dynamics as an in vitro screening platform for anti-fibrotic drugs in primary myelofibrosis. J Cell Physiol 2017; 233:422-433. [PMID: 28294327 DOI: 10.1002/jcp.25902] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 03/09/2017] [Indexed: 02/06/2023]
Abstract
Although the cause for bone marrow fibrosis in patients with myelofibrosis remains controversial, it has been hypothesized that it is caused by extensive fibroblast proliferation under the influence of cytokines generated by the malignant megakaryocytes. Moreover, there is no known drug therapy which could reverse the process. We studied the fibroblasts in a novel system using the hanging drop method, evaluated whether the fibroblasts obtain from patients are part of the malignant clone of not and, using this system, we screen a large library of FDA-approved drugs to identify potential drugs candidates that might be useful in the treatment of this disease, specifically which would inhibit fibroblast proliferation and the development of bone marrow fibrosis. We have found that the BM fibroblasts are not part of the malignant clone, as previously suspected and two immunosuppressive medications-cyclosporine and mycophenolate mophetil, as most potent suppressors of the fibroblast collagen production thus potentially inhibitors of bone marrow fibrosis production in myelofibrosis.
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Affiliation(s)
- Ciprian Tomuleasa
- Department of Hematology, Ion Chiricuta Oncology Institute, Cluj Napoca, Romania.,Research Center for Functional Genomics and Translational Medicine/Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Sonia Selicean
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Grigore Gafencu
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Bobe Petrushev
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Laura Pop
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Cristian Berce
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Anca Jurj
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Adrian Trifa
- Department of Genetics, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Ana-Maria Rosu
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Sergiu Pasca
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Lorand Magdo
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Mihnea Zdrenghea
- Department of Hematology, Ion Chiricuta Oncology Institute, Cluj Napoca, Romania
| | - Delia Dima
- Department of Hematology, Ion Chiricuta Oncology Institute, Cluj Napoca, Romania
| | - Alina Tanase
- Department of Stem Cell Transplantation, Fundeni Clinical Institute, Bucharest, Romania
| | - Ioana Frinc
- Department of Hematology, Ion Chiricuta Oncology Institute, Cluj Napoca, Romania
| | - Anca Bojan
- Department of Hematology, Ion Chiricuta Oncology Institute, Cluj Napoca, Romania
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Gabriel Ghiaur
- Division of Hematological Malignancies, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center-The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Stefan O Ciurea
- Division of Cancer Medicine, Department of Stem Cell Transplantation, The University of Texas MD Anderson Cancer Center, Houston, Texas
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Pan-Cancer Mutational and Transcriptional Analysis of the Integrator Complex. Int J Mol Sci 2017; 18:ijms18050936. [PMID: 28468258 PMCID: PMC5454849 DOI: 10.3390/ijms18050936] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 04/20/2017] [Accepted: 04/23/2017] [Indexed: 12/28/2022] Open
Abstract
The integrator complex has been recently identified as a key regulator of RNA Polymerase II-mediated transcription, with many functions including the processing of small nuclear RNAs, the pause-release and elongation of polymerase during the transcription of protein coding genes, and the biogenesis of enhancer derived transcripts. Moreover, some of its components also play a role in genome maintenance. Thus, it is reasonable to hypothesize that their functional impairment or altered expression can contribute to malignancies. Indeed, several studies have described the mutations or transcriptional alteration of some Integrator genes in different cancers. Here, to draw a comprehensive pan-cancer picture of the genomic and transcriptomic alterations for the members of the complex, we reanalyzed public data from The Cancer Genome Atlas. Somatic mutations affecting Integrator subunit genes and their transcriptional profiles have been investigated in about 11,000 patients and 31 tumor types. A general heterogeneity in the mutation frequencies was observed, mostly depending on tumor type. Despite the fact that we could not establish them as cancer drivers, INTS7 and INTS8 genes were highly mutated in specific cancers. A transcriptome analysis of paired (normal and tumor) samples revealed that the transcription of INTS7, INTS8, and INTS13 is significantly altered in several cancers. Experimental validation performed on primary tumors confirmed these findings.
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Protein-Coding Genes' Retrocopies and Their Functions. Viruses 2017; 9:v9040080. [PMID: 28406439 PMCID: PMC5408686 DOI: 10.3390/v9040080] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 04/07/2017] [Accepted: 04/11/2017] [Indexed: 12/11/2022] Open
Abstract
Transposable elements, often considered to be not important for survival, significantly contribute to the evolution of transcriptomes, promoters, and proteomes. Reverse transcriptase, encoded by some transposable elements, can be used in trans to produce a DNA copy of any RNA molecule in the cell. The retrotransposition of protein-coding genes requires the presence of reverse transcriptase, which could be delivered by either non-long terminal repeat (non-LTR) or LTR transposons. The majority of these copies are in a state of “relaxed” selection and remain “dormant” because they are lacking regulatory regions; however, many become functional. In the course of evolution, they may undergo subfunctionalization, neofunctionalization, or replace their progenitors. Functional retrocopies (retrogenes) can encode proteins, novel or similar to those encoded by their progenitors, can be used as alternative exons or create chimeric transcripts, and can also be involved in transcriptional interference and participate in the epigenetic regulation of parental gene expression. They can also act in trans as natural antisense transcripts, microRNA (miRNA) sponges, or a source of various small RNAs. Moreover, many retrocopies of protein-coding genes are linked to human diseases, especially various types of cancer.
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40
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Yu F, Chen B, Dong P, Zheng J. HOTAIR Epigenetically Modulates PTEN Expression via MicroRNA-29b: A Novel Mechanism in Regulation of Liver Fibrosis. Mol Ther 2017; 25:205-217. [PMID: 28129115 PMCID: PMC5363197 DOI: 10.1016/j.ymthe.2016.10.015] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 10/27/2016] [Accepted: 10/31/2016] [Indexed: 02/06/2023] Open
Abstract
Homeobox transcript antisense RNA (HOTAIR), as a long intergenic non-coding RNA (lincRNA), is upregulated in various cancers and involved in diverse cellular functions. However, its role in liver fibrosis is unclear. In this study, HOTAIR expression was upregulated in hepatic stellate cells (HSCs) in vivo and in vitro during liver fibrosis. HOTAIR knockdown suppressed HSC activation including α-smooth muscle actin (α-SMA) and typeIcollagen in vitro and in vivo. Both HSC proliferation and cell cycle were inhibited by HOTAIR knockdown. Notably, inhibition of HOTAIR led to an increase in PTEN, associated with the loss of DNA methylation. miR-29b-mediated control of PTEN methylation was involved in the effects of HOTAIR knockdown. HOTAIR was confirmed a target of miR-29b and lack of the miR-29b binding site in HOTAIR prevented the suppression of miR-29b, suggesting HOTAIR contributes to PTEN expression downregulation via sponging miR-29b. Interestingly, increased HOTAIR was also observed in hepatocytes during liver fibrosis. Loss of HOTAIR additionally led to the increase in PTEN and the reduction in typeIcollagen in hepatocytes. Collectively, we demonstrate that HOTAIR downregulates miR-29b expression and attenuates its control on epigenetic regulation, leading to enhanced PTEN methylation, which contributes to the progression of liver fibrosis.
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Affiliation(s)
- Fujun Yu
- Department of Infectious Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China; Department of Gastroenterology, Songjiang Hospital Affiliated Shanghai First People's Hospital, Shanghai Jiao Tong University, Shanghai 201600, China; Department of Gastroenterology, Shanghai Songjiang Hospital Affiliated to Nanjing Medical University, Nanjing 210029, China
| | - Bicheng Chen
- Key Laboratory of Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Peihong Dong
- Department of Infectious Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China.
| | - Jianjian Zheng
- Key Laboratory of Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China.
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An Y, Furber KL, Ji S. Pseudogenes regulate parental gene expression via ceRNA network. J Cell Mol Med 2017; 21:185-192. [PMID: 27561207 PMCID: PMC5192809 DOI: 10.1111/jcmm.12952] [Citation(s) in RCA: 166] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 07/14/2016] [Indexed: 12/14/2022] Open
Abstract
The concept of competitive endogenous RNA (ceRNA) was first proposed by Salmena and colleagues. Evidence suggests that pseudogene RNAs can act as a 'sponge' through competitive binding of common miRNA, releasing or attenuating repression through sequestering miRNAs away from parental mRNA. In theory, ceRNAs refer to all transcripts such as mRNA, tRNA, rRNA, long non-coding RNA, pseudogene RNA and circular RNA, because all of them may become the targets of miRNA depending on spatiotemporal situation. As binding of miRNA to the target RNA is not 100% complementary, it is possible that one miRNA can bind to multiple target RNAs and vice versa. All RNAs crosstalk through competitively binding to miRNAvia miRNA response elements (MREs) contained within the RNA sequences, thus forming a complex regulatory network. The ratio of a subset of miRNAs to the corresponding number of MREs determines repression strength on a given mRNA translation or stability. An increase in pseudogene RNA level can sequester miRNA and release repression on the parental gene, leading to an increase in parental gene expression. A massive number of transcripts constitute a complicated network that regulates each other through this proposed mechanism, though some regulatory significance may be mild or even undetectable. It is possible that the regulation of gene and pseudogene expression occurring in this manor involves all RNAs bearing common MREs. In this review, we will primarily discuss how pseudogene transcripts regulate expression of parental genes via ceRNA network and biological significance of regulation.
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Affiliation(s)
- Yang An
- Department of Biochemistry and Molecular BiologyMedical SchoolHenan UniversityHenan ProvinceChina
| | - Kendra L. Furber
- College of Pharmacy and NutritionUniversity of SaskatchewanSaskatchewanSKCanada
| | - Shaoping Ji
- Department of Biochemistry and Molecular BiologyMedical SchoolHenan UniversityHenan ProvinceChina
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Yu F, Lu Z, Huang K, Wang X, Xu Z, Chen B, Dong P, Zheng J. MicroRNA-17-5p-activated Wnt/β-catenin pathway contributes to the progression of liver fibrosis. Oncotarget 2016; 7:81-93. [PMID: 26637809 PMCID: PMC4807984 DOI: 10.18632/oncotarget.6447] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 11/22/2015] [Indexed: 01/02/2023] Open
Abstract
Aberrant Wnt/β-catenin pathway contributes to the development of liver fibrosis. MicroRNAs (MiRNAs) are found to act as regulators of the activation of hepatic stellate cell (HSC) in liver fibrosis. However, whether miRNAs activate Wnt/β-catenin pathway in activated HSCs during liver fibrosis is largely unknown. In this study, we found that Salvianolic acid B (Sal B) treatment significantly inhibited liver fibrosis in CCl4-treated rats, HSC-T6 cells and rat primary HSCs, resulting in the suppression of type I collagen and alpha-smooth muscle actin. Also, Sal B suppressed HSC activation and cell proliferation in vitro. Interestingly, Sal B treatment induced the inactivation of Wnt/β-catenin pathway, with an increase in P-β-catenin and Wnt inhibitory factor 1 (WIF1). We demonstrated that the anti-fibrotic effects caused by Sal B were, at least in part, via WIF1. Moreover, our study revealed that miR-17-5p was reduced in vivo and in vitro after Sal B treatment. As confirmed by luciferase activity assays, WIF1 was a direct target of miR-17-5p. Notably, the suppression of HSCs induced by Sal B was almost inhibited by miR-17-5p mimics. Collectively, we demonstrated that miR-17-5p activates Wnt/β-catenin pathway to result in HSC activation through inhibiting WIF1 expression.
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Affiliation(s)
- Fujun Yu
- Department of Infectious Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zhongqiu Lu
- Emergency Department, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Kate Huang
- Department of Pathology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiaodong Wang
- Department of Infectious Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Ziqiang Xu
- Institute of Organ Transplantation, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Bicheng Chen
- Key Laboratory of Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Peihong Dong
- Department of Infectious Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jianjian Zheng
- Key Laboratory of Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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Rienzo M, Casamassimi A. Integrator complex and transcription regulation: Recent findings and pathophysiology. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1859:1269-80. [PMID: 27427483 DOI: 10.1016/j.bbagrm.2016.07.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 07/08/2016] [Accepted: 07/12/2016] [Indexed: 12/20/2022]
Abstract
In the last decade, a novel molecular complex has been added to the RNA polymerase II-mediated transcription machinery as one of the major components. This multiprotein complex, named Integrator, plays a pivotal role in the regulation of most RNA Polymerase II-dependent genes. This complex consists of at least 14 different subunits. However, studies investigating its structure and composition are still lacking. Although it was originally discovered as a complex implicated in the 3'-end formation of noncoding small nuclear RNAs, recent studies indicate additional roles for Integrator in transcription regulation, for example during transcription pause-release and elongation of polymerase, in the biogenesis of transcripts derived from enhancers, as well as in DNA and RNA metabolism for some of its components. Noteworthy, several subunits have been emerging to play roles during development and differentiation; more importantly, their alterations are likely to be involved in several human pathologies, including cancer and lung diseases.
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Affiliation(s)
- Monica Rienzo
- Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Via L. De Crecchio 7, 80138 Naples, Italy
| | - Amelia Casamassimi
- Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Via L. De Crecchio 7, 80138 Naples, Italy.
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Li J, Tian H, Yang J, Gong Z. Long Noncoding RNAs Regulate Cell Growth, Proliferation, and Apoptosis. DNA Cell Biol 2016; 35:459-70. [PMID: 27213978 DOI: 10.1089/dna.2015.3187] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The revolutionary findings in nonprotein-coding part of human genome analysis have revealed a large number of RNA transcripts longer than 200 nucleotides that lack coding protein function, termed long noncoding RNAs (lncRNAs). Recently, accumulating shreds of evidence suggest that lncRNAs are widely distributed in human genome and deeply involved in cellular activities such as cell growth, proliferation, and apoptosis. Generally, lncRNAs regulate cell behaviors by targeting cell cycle-associated cyclins, cyclin-dependent kinases (CDKs), and/or CDK inhibitors. Specifically, lncRNAs serve as scaffolds or guides for chromatin-modifying complexes and act as signals in response to DNA damage. In addition, lncRNAs function as protein decoys and microRNA decoys, as well as interveners in cell division by modulating oncogenes and/or tumor suppressors. In this review, we mainly focus on the current understanding of the molecular mechanisms, how lncRNAs influence cellular processes and cancer progression. Finally, we also prospect the limitations of lncRNAs in cell behaviors and the novel roles of lncRNAs in epigenetic regulations.
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Affiliation(s)
- Jingqiu Li
- 1 Department of Biochemistry and Molecular Biology, Ningbo University School of Medicine , Ningbo, China .,2 Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine , Ningbo, China
| | - Haihua Tian
- 1 Department of Biochemistry and Molecular Biology, Ningbo University School of Medicine , Ningbo, China .,2 Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine , Ningbo, China .,3 Department of Laboratory Medicine, Ningbo Kangning Hospital , Ningbo, China
| | - Jie Yang
- 1 Department of Biochemistry and Molecular Biology, Ningbo University School of Medicine , Ningbo, China .,2 Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine , Ningbo, China
| | - Zhaohui Gong
- 1 Department of Biochemistry and Molecular Biology, Ningbo University School of Medicine , Ningbo, China .,2 Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine , Ningbo, China
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45
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Wang Y, Hou J, He D, Sun M, Zhang P, Yu Y, Chen Y. The Emerging Function and Mechanism of ceRNAs in Cancer. Trends Genet 2016; 32:211-224. [PMID: 26922301 PMCID: PMC4805481 DOI: 10.1016/j.tig.2016.02.001] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 01/19/2016] [Accepted: 02/02/2016] [Indexed: 01/17/2023]
Abstract
Complex diseases, such as cancer, are often associated with aberrant gene expression at both the transcriptional and post-transcriptional level. Over the past several years, competing endogenous RNAs (ceRNAs) have emerged as an important class of post-transcriptional regulators that alter gene expression through a miRNA-mediated mechanism. Recent studies in both solid tumors and hematopoietic malignancies showed that ceRNAs have significant roles in cancer pathogenesis by altering the expression of key tumorigenic or tumor-suppressive genes. Characterizing the identity, function, and mechanism of the ceRNAs will not only further our fundamental understanding of RNA-mediated cancer pathogenesis, but may also shed light on the development of new RNA-based therapeutic strategies for treating cancer.
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Affiliation(s)
- Yunfei Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jiakai Hou
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dandan He
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ming Sun
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Peng Zhang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yonghao Yu
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yiwen Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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Petrushev B, Boca S, Simon T, Berce C, Frinc I, Dima D, Selicean S, Gafencu GA, Tanase A, Zdrenghea M, Florea A, Suarasan S, Dima L, Stanciu R, Jurj A, Buzoianu A, Cucuianu A, Astilean S, Irimie A, Tomuleasa C, Berindan-Neagoe I. Gold nanoparticles enhance the effect of tyrosine kinase inhibitors in acute myeloid leukemia therapy. Int J Nanomedicine 2016; 11:641-60. [PMID: 26929621 PMCID: PMC4760658 DOI: 10.2147/ijn.s94064] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND AND AIMS Every year, in Europe, acute myeloid leukemia (AML) is diagnosed in thousands of adults. For most subtypes of AML, the backbone of treatment was introduced nearly 40 years ago as a combination of cytosine arabinoside with an anthracycline. This therapy is still the worldwide standard of care. Two-thirds of patients achieve complete remission, although most of them ultimately relapse. Since the FLT3 mutation is the most frequent, it serves as a key molecular target for tyrosine kinase inhibitors (TKIs) that inhibit FLT3 kinase. In this study, we report the conjugation of TKIs onto spherical gold nanoparticles. MATERIALS AND METHODS The internalization of TKI-nanocarriers was proved by the strongly scattered light from gold nanoparticles and was correlated with the results obtained by transmission electron microscopy and dark-field microscopy. The therapeutic effect of the newly designed drugs was investigated by several methods including cell counting assay as well as the MTT assay. RESULTS We report the newly described bioconjugates to be superior when compared with the drug alone, with data confirmed by state-of-the-art analyses of internalization, cell biology, gene analysis for FLT3-IDT gene, and Western blotting to assess degradation of the FLT3 protein. CONCLUSION The effective transmembrane delivery and increased efficacy validate its use as a potential therapeutic.
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Affiliation(s)
- Bobe Petrushev
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Sanda Boca
- Nanobiophotonics and Laser Microscopy Center, Babes Bolyai University, Cluj-Napoca, Romania
| | - Timea Simon
- Nanobiophotonics and Laser Microscopy Center, Babes Bolyai University, Cluj-Napoca, Romania
| | - Cristian Berce
- Department of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ioana Frinc
- Department of Hematology, Ion Chiricuta Oncology Institute, Cluj-Napoca, Romania
| | - Delia Dima
- Department of Hematology, Ion Chiricuta Oncology Institute, Cluj-Napoca, Romania
| | - Sonia Selicean
- Department of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Grigore-Aristide Gafencu
- Department of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Alina Tanase
- Department of Stem Cell Transplantation, Fundeni Clinical Institute, Bucharest, Romania
| | - Mihnea Zdrenghea
- Department of Hematology, Ion Chiricuta Oncology Institute, Cluj-Napoca, Romania; Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Adrian Florea
- Department of Cell and Molecular Biology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Sorina Suarasan
- Nanobiophotonics and Laser Microscopy Center, Babes Bolyai University, Cluj-Napoca, Romania
| | - Liana Dima
- School of Dentistry, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Raluca Stanciu
- Department of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ancuta Jurj
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Anca Buzoianu
- Department of Pharmacology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Andrei Cucuianu
- Department of Hematology, Ion Chiricuta Oncology Institute, Cluj-Napoca, Romania; Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Simion Astilean
- Nanobiophotonics and Laser Microscopy Center, Babes Bolyai University, Cluj-Napoca, Romania; Faculty of Physics, Babes Bolyai University, Cluj-Napoca, Romania
| | - Alexandru Irimie
- Department of Surgery, Ion Chiricuta Oncology Institute, Cluj-Napoca, Romania; Department of Surgery, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ciprian Tomuleasa
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania; Department of Hematology, Ion Chiricuta Oncology Institute, Cluj-Napoca, Romania
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania; Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Zhang X, Zhang J, Ping X, Wang QL, Lu X. Pseudogene transcripts: Participants in tumorigenicity and promising therapeutic targets. Leuk Res 2015; 42:105-6. [PMID: 26818436 DOI: 10.1016/j.leukres.2015.12.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 12/22/2015] [Indexed: 12/23/2022]
Affiliation(s)
- Xin Zhang
- Department of Radiology, the Fourth People's Hospital of Huai'an, 128 Yanan east road, Huai'an, Jiangsu 223300, China
| | - Juan Zhang
- Department of Rehabilitation, The Affiliated Huai'an Hospital of Xuzhou Medical College and The Second People's Hospital of Huai'an, Huai'an, China
| | - Xu Ping
- Department of Gynecology, Jiangsu Huai'an Maternity and Children Hospital, Huai'an, China
| | - Qi-Long Wang
- Department of Clinical Oncology, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, China.
| | - Xiaojie Lu
- Department of Radiology, Zhong-da Hospital, Medical School, Southeast University, Nanjing, China.
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48
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Shi X, Nie F, Wang Z, Sun M. Pseudogene-expressed RNAs: a new frontier in cancers. Tumour Biol 2015; 37:1471-8. [PMID: 26662308 DOI: 10.1007/s13277-015-4482-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 11/19/2015] [Indexed: 01/26/2023] Open
Abstract
Over the past decade, the importance of non-protein-coding functional elements in the human genome has emerged from the water and been identified as a key revelation in post-genomic biology. Since the completion of the ENCODE (Encyclopedia of DNA Elements) and FANTOM (Functional Annotation of Mammals) project, tens of thousands of pseudogenes as well as numerous long non-coding RNA (lncRNA) genes were identified. However, while pseudogenes were initially regarded as non-functional relics littering the human genome during evolution, recent studies have revealed that they play critical roles at multiple levels in diverse physiological and pathological processes, especially in cancer through parental-gene-dependent or parental-gene-independent regulation. Herein, we review the current knowledge of pseudogenes and synthesize the nascent evidence for functional properties and regulatory modalities exerted by pseudogene-transcribed RNAs in human cancers and prospect the potential as molecular signatures in cancer reclassification and tailored therapy.
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Affiliation(s)
- Xuefei Shi
- Department of Respiratory Medicine, Huzhou Central Hospital, Huzhou, China
| | - Fengqi Nie
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, 210029, China
| | - Zhaoxia Wang
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, 210029, China.
| | - Ming Sun
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, 210029, China.
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49
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Takahashi H, Ishikawa T, Ishiguro M, Okazaki S, Mogushi K, Kobayashi H, Iida S, Mizushima H, Tanaka H, Uetake H, Sugihara K. Prognostic significance of Traf2- and Nck- interacting kinase (TNIK) in colorectal cancer. BMC Cancer 2015; 15:794. [PMID: 26499327 PMCID: PMC4619995 DOI: 10.1186/s12885-015-1783-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 10/12/2015] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The potential of expression profiling using microarray analysis as a tool to predict the prognosis for different types of cancer has been realized. This study aimed to identify a novel biomarker for colorectal cancer (CRC). METHODS The expression profiles of cancer cells in 152 patients with stage I-III CRC were examined using microarray analysis. High expression in CRC cells, especially in patients with distant recurrences, was a prerequisite to select candidate genes. Thus, we identified seventeen candidate genes, and selected Traf2- and Nck-interacting kinase (TNIK), which was known to be associated with progression in CRC through Wnt signaling pathways. We analyzed the protein expression of TNIK using immunohistochemistry (IHC) and investigated the relationship between protein expression and patient characteristics in 220 stage I-III CRC patients. RESULTS Relapse-free survival was significantly worse in the TNIK high expression group than in the TNIK low expression group in stage II (p = 0.028) and stage III (p = 0.006) patients. In multivariate analysis, high TNIK expression was identified as a significant independent risk factor of distant recurrence in stage III patients. CONCLUSION This study is the first to demonstrate the prognostic significance of intratumoral TNIK protein expression in clinical tissue samples of CRC, in that high expression of TNIK protein in primary tumors was associated with distant recurrence in stage II and III CRC patients. This TNIK IHC study might contribute to practical decision-making in the treatment of these patients.
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Affiliation(s)
- Hidenori Takahashi
- Department of Surgical Oncology, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8519, Japan.
| | - Toshiaki Ishikawa
- Department of Surgical Oncology, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8519, Japan.
| | - Megumi Ishiguro
- Department of Translational Oncology, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, Japan.
| | - Satoshi Okazaki
- Department of Surgical Oncology, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8519, Japan.
| | - Kaoru Mogushi
- Department of Systems Biology, Graduate School of Biochemical Science, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, Japan.
| | - Hirotoshi Kobayashi
- Center for Minimally Invasive Surgery, Division of Colorectal Surgery, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8519, Japan.
| | - Satoru Iida
- Department of Surgical Oncology, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8519, Japan.
| | - Hiroshi Mizushima
- Center for Public Health Informatics, National Institute of Public Health, 2-3-6 Minami, Wako-shi, Saitama, 351-0197, Japan.
| | - Hiroshi Tanaka
- Department of Systems Biology, Graduate School of Biochemical Science, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, Japan.
| | - Hiroyuki Uetake
- Department of Translational Oncology, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, Japan.
| | - Kenichi Sugihara
- Department of Surgical Oncology, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8519, Japan.
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50
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Poliseno L, Marranci A, Pandolfi PP. Pseudogenes in Human Cancer. Front Med (Lausanne) 2015; 2:68. [PMID: 26442270 PMCID: PMC4585173 DOI: 10.3389/fmed.2015.00068] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 09/03/2015] [Indexed: 12/14/2022] Open
Abstract
Recent advances in the analysis of RNA sequencing data have shown that pseudogenes are highly specific markers of cell identity and can be used as diagnostic and prognostic markers. Furthermore, genetically engineered mouse models have recently provided compelling support for a causal link between altered pseudogene expression and cancer. In this review, we discuss the most recent milestones reached in the pseudogene field and the use of pseudogenes as cancer classifiers.
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Affiliation(s)
- Laura Poliseno
- Oncogenomics Unit, Core Research Laboratory, Istituto Toscano Tumori , Pisa , Italy ; Institute of Clinical Physiology, Consiglio Nazionale delle Ricerche , Pisa , Italy
| | - Andrea Marranci
- Oncogenomics Unit, Core Research Laboratory, Istituto Toscano Tumori , Pisa , Italy ; University of Siena , Siena , Italy
| | - Pier Paolo Pandolfi
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Departments of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School , Boston, MA , USA
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