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Zhao X, Chen Z, Wang H, Sun H. Occlusion enhanced pan-cancer classification via deep learning. BMC Bioinformatics 2024; 25:260. [PMID: 39118043 PMCID: PMC11308240 DOI: 10.1186/s12859-024-05870-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 07/12/2024] [Indexed: 08/10/2024] Open
Abstract
Quantitative measurement of RNA expression levels through RNA-Seq is an ideal replacement for conventional cancer diagnosis via microscope examination. Currently, cancer-related RNA-Seq studies focus on two aspects: classifying the status and tissue of origin of a sample and discovering marker genes. Existing studies typically identify marker genes by statistically comparing healthy and cancer samples. However, this approach overlooks marker genes with low expression level differences and may be influenced by experimental results. This paper introduces "GENESO," a novel framework for pan-cancer classification and marker gene discovery using the occlusion method in conjunction with deep learning. we first trained a baseline deep LSTM neural network capable of distinguishing the origins and statuses of samples utilizing RNA-Seq data. Then, we propose a novel marker gene discovery method called "Symmetrical Occlusion (SO)". It collaborates with the baseline LSTM network, mimicking the "gain of function" and "loss of function" of genes to evaluate their importance in pan-cancer classification quantitatively. By identifying the genes of utmost importance, we then isolate them to train new neural networks, resulting in higher-performance LSTM models that utilize only a reduced set of highly relevant genes. The baseline neural network achieves an impressive validation accuracy of 96.59% in pan-cancer classification. With the help of SO, the accuracy of the second network reaches 98.30%, while using 67% fewer genes. Notably, our method excels in identifying marker genes that are not differentially expressed. Moreover, we assessed the feasibility of our method using single-cell RNA-Seq data, employing known marker genes as a validation test.
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Grants
- 14106521 General Research Funds (GRF) from the Research Grants Council (RGC), University Grants Committee of the Hong Kong Special Administrative Region, China.
- 14100620 General Research Funds (GRF) from the Research Grants Council (RGC), University Grants Committee of the Hong Kong Special Administrative Region, China.
- 14105823 General Research Funds (GRF) from the Research Grants Council (RGC), University Grants Committee of the Hong Kong Special Administrative Region, China.
- 14115319 General Research Funds (GRF) from the Research Grants Council (RGC), University Grants Committee of the Hong Kong Special Administrative Region, China.
- 2141109 General Research Funds (GRF) from the Research Grants Council (RGC), University Grants Committee of the Hong Kong Special Administrative Region, China.
- 2141157 General Research Funds (GRF) from the Research Grants Council (RGC), University Grants Committee of the Hong Kong Special Administrative Region, China.
- 2141261 General Research Funds (GRF) from the Research Grants Council (RGC), University Grants Committee of the Hong Kong Special Administrative Region, China.
- 14105123 General Research Funds (GRF) from the Research Grants Council (RGC), University Grants Committee of the Hong Kong Special Administrative Region, China.
- 14103522 General Research Funds (GRF) from the Research Grants Council (RGC), University Grants Committee of the Hong Kong Special Administrative Region, China.
- 14120420 General Research Funds (GRF) from the Research Grants Council (RGC), University Grants Committee of the Hong Kong Special Administrative Region, China.
- 14120619 General Research Funds (GRF) from the Research Grants Council (RGC), University Grants Committee of the Hong Kong Special Administrative Region, China.
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Affiliation(s)
- Xing Zhao
- Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Guangdong, People's Republic of China
| | - Zigui Chen
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Huating Wang
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Hao Sun
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Guangdong, People's Republic of China.
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, People's Republic of China.
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2
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Su L, Luo H, Yan Y, Yang Z, Lu J, Xu D, Du L, Liu J, Yang G, Chi H. Exploiting gender-based biomarkers and drug targets: advancing personalized therapeutic strategies in hepatocellular carcinoma. Front Pharmacol 2024; 15:1433540. [PMID: 38966543 PMCID: PMC11222576 DOI: 10.3389/fphar.2024.1433540] [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: 05/16/2024] [Accepted: 06/04/2024] [Indexed: 07/06/2024] Open
Abstract
This review systematically examines gender differences in hepatocellular carcinoma (HCC), identifying the influence of sex hormones, genetic variance, and environmental factors on the disease's epidemiology and treatment outcomes. Recognizing the liver as a sexually dimorphic organ, we highlight how gender-specific risk factors, such as alcohol consumption and obesity, contribute differently to hepatocarcinogenesis in men and women. We explore molecular mechanisms, including the differential expression of androgen and estrogen receptors, which mediate diverse pathways in tumor biology such as cell proliferation, apoptosis, and DNA repair. Our analysis underscores the critical need for gender-specific research in liver cancer, from molecular studies to clinical trials, to improve diagnostic accuracy and therapeutic effectiveness. By incorporating a gender perspective into all facets of liver cancer research, we advocate for a more precise and personalized approach to cancer treatment that acknowledges gender as a significant factor in both the progression of HCC and its response to treatment. This review aims to foster a deeper understanding of the biological and molecular bases of gender differences in HCC and to promote the development of tailored interventions that enhance outcomes for all patients.
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Affiliation(s)
- Lanqian Su
- Clinical Medical College, Southwest Medical University, Luzhou, China
| | - Huanyu Luo
- Clinical Medical College, Southwest Medical University, Luzhou, China
| | - Yalan Yan
- Clinical Medical College, Southwest Medical University, Luzhou, China
| | - Zhongqiu Yang
- Department of General Surgery, Dazhou Central Hospital, Dazhou, China
| | - Jiaan Lu
- Clinical Medical College, Southwest Medical University, Luzhou, China
| | - Danqi Xu
- Clinical Medical College, Southwest Medical University, Luzhou, China
| | - Linjuan Du
- Department of Oncology, Dazhou Central Hospital, Dazhou, China
| | - Jie Liu
- Department of General Surgery, Dazhou Central Hospital, Dazhou, China
| | - Guanhu Yang
- Department of Specialty Medicine, Ohio University, Athens, OH, United States
| | - Hao Chi
- Clinical Medical College, Southwest Medical University, Luzhou, China
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3
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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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4
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Li H, Cheng Z, Yang P, Huang W, Li X, Xiang D, Wu X. Endothelial Nogo-B Suppresses Cancer Cell Proliferation via a Paracrine TGF-β/Smad Signaling. Cells 2022; 11:cells11193084. [PMID: 36231046 PMCID: PMC9564156 DOI: 10.3390/cells11193084] [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] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 09/12/2022] [Accepted: 09/20/2022] [Indexed: 11/20/2022] Open
Abstract
Nogo-B has been reported to play a critical role in angiogenesis and the repair of damaged blood vessels; however, its role in the tumor microenvironment remains unclear. Here, we observed the differential expression of Nogo-B in endothelial cells from hepatocellular carcinoma (HCC) and glioma samples. Downregulation of Nogo-B expression correlated with the malignant phenotype of cancer and a poor prognosis for patients. In subsequent studies, endothelial Nogo-B inhibition robustly promoted the growth of HCC or glioma xenografts in nude mice. Intriguingly, endothelial Nogo-B silencing dramatically suppressed endothelial cell expansion and tumor angiogenesis, but potently enhanced the proliferation of neighboring HCC and glioma cells. Based on the results of the ELISA assay, Nogo-B silencing reduced TGF-β production in endothelial cells, which attenuated the phosphorylation and nuclear translocation of Smad in neighboring cancer cells. The endothelial Nogo-B silencing-mediated increase in cancer cell proliferation was abolished by either a TGF-β neutralizing antibody or TGF-β receptor inhibitor, indicating the essential role for TGF-β in endothelial Nogo-B-mediated suppression of cancer growth. These findings not only broaden our understanding of the crosstalk between cancer cells and endothelial cells but also provide a novel prognostic biomarker and a therapeutic target for cancer treatments.
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Affiliation(s)
- Hengyu Li
- Department of Breast and Thyroid Surgery, Changhai Hospital, Naval Military Medical University, Shanghai 200433, China
- Correspondence: (H.L.); (X.L.); (D.X.); (X.W.)
| | - Zhuo Cheng
- Department of Oncology, Third Affiliated Hospital of Naval Military Medical University, Shanghai 200438, China
| | - Pinghua Yang
- Department of Hepatic Surgery, Third Affiliated Hospital of Naval Military Medical University, Shanghai 200438, China
| | - Wei Huang
- Department of Neurosurgery, The First People’s Hospital of Yunnan Province, Kunming 650032, China
| | - Xizhou Li
- Department of Breast and Thyroid Surgery, Changhai Hospital, Naval Military Medical University, Shanghai 200433, China
- Correspondence: (H.L.); (X.L.); (D.X.); (X.W.)
| | - Daimin Xiang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
- Correspondence: (H.L.); (X.L.); (D.X.); (X.W.)
| | - Xiaojun Wu
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Correspondence: (H.L.); (X.L.); (D.X.); (X.W.)
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5
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Carron J, Della Coletta R, Lourenço GJ. Pseudogene Transcripts in Head and Neck Cancer: Literature Review and In Silico Analysis. Genes (Basel) 2021; 12:genes12081254. [PMID: 34440428 PMCID: PMC8391979 DOI: 10.3390/genes12081254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/10/2021] [Accepted: 08/12/2021] [Indexed: 12/25/2022] Open
Abstract
Once considered nonfunctional, pseudogene transcripts are now known to provide valuable information for cancer susceptibility, including head and neck cancer (HNC), a serious health problem worldwide, with about 50% unimproved overall survival over the last decades. The present review focuses on the role of pseudogene transcripts involved in HNC risk and prognosis. We combined current literature and in silico analyses from The Cancer Genome Atlas (TCGA) database to identify the most deregulated pseudogene transcripts in HNC and their genetic variations. We then built a co-expression network and performed gene ontology enrichment analysis to better understand the pseudogenes’ interactions and pathways in HNC. In the literature, few pseudogenes have been studied in HNC. Our in silico analysis identified 370 pseudogene transcripts associated with HNC, where SPATA31D5P, HERC2P3, SPATA31C2, MAGEB6P1, SLC25A51P1, BAGE2, DNM1P47, SPATA31C1, ZNF733P and OR2W5 were found to be the most deregulated and presented several genetic alterations. NBPF25P, HSP90AB2P, ZNF658B and DPY19L2P3 pseudogenes were predicted to interact with 12 genes known to participate in HNC, DNM1P47 was predicted to interact with the TP53 gene, and HLA-H pseudogene was predicted to interact with HLA-A and HLA-B genes. The identified pseudogenes were associated with cancer biology pathways involving cell communication, response to stress, cell death, regulation of the immune system, regulation of gene expression, and Wnt signaling. Finally, we assessed the prognostic values of the pseudogenes with the Kaplan–Meier Plotter database, and found that expression of SPATA31D5P, SPATA31C2, BAGE2, SPATA31C1, ZNF733P and OR2W5 pseudogenes were associated with patients’ survival. Due to pseudogene transcripts’ potential for cancer diagnosis, progression, and as therapeutic targets, our study can guide new research to HNC understanding and development of new target therapies.
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Affiliation(s)
- Juliana Carron
- Laboratory of Cancer Genetics, School of Medical Sciences, University of Campinas, Campinas 13083-888, São Paulo, Brazil;
| | - Rafael Della Coletta
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA;
| | - Gustavo Jacob Lourenço
- Laboratory of Cancer Genetics, School of Medical Sciences, University of Campinas, Campinas 13083-888, São Paulo, Brazil;
- Correspondence: ; Tel.: +55-19-3521-9120
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6
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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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7
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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: 4] [Impact Index Per Article: 1.3] [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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8
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Abstract
Pseudogenes are commonly labeled as "junk DNA" given their perceived nonfunctional status. However, the advent of large-scale genomics projects prompted a revisit of pseudogene biology, highlighting their key functional and regulatory roles in numerous diseases, including cancers. Integrative analyses of cancer data have shown that pseudogenes can be transcribed and even translated, and that pseudogenic DNA, RNA, and proteins can interfere with the activity and function of key protein coding genes, acting as regulators of oncogenes and tumor suppressors. Capitalizing on the available clinical research, we are able to get an insight into the spread and variety of pseudogene biomarker and therapeutic potential. In this chapter, we describe pseudogenes that fulfill their role as diagnostic or prognostic biomarkers, both as unique elements and in collaboration with other genes or pseudogenes. We also report that the majority of prognostic pseudogenes are overexpressed and exert an oncogenic role in colorectal, liver, lung, and gastric cancers. Finally, we highlight a number of pseudogenes that can establish future therapeutic avenues.
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9
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Sousa D, Matthiesen R, Lima RT, Vasconcelos MH. Deep Sequencing Analysis Reveals Distinctive Non-Coding RNAs When Comparing Tumor Multidrug-Resistant Cells and Extracellular Vesicles with Drug-Sensitive Counterparts. Cancers (Basel) 2020; 12:cancers12010200. [PMID: 31947507 PMCID: PMC7016831 DOI: 10.3390/cancers12010200] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/07/2020] [Accepted: 01/09/2020] [Indexed: 12/12/2022] Open
Abstract
Multidrug resistance (MDR) is one of the main limitations of cancer treatment. The overexpression of drug-efflux pumps, such as P-glycoprotein (P-gp), is a major cause of MDR. Importantly, different studies have shown that extracellular vesicles (EVs) participate in the communication between MDR cells and drug-sensitive counterparts, promoting dissemination of the MDR phenotype. In the present work, we aimed to identify RNA species present in MDR cells and in EVs released by those cells, which may be associated with the MDR phenotype. The RNA content from two pairs (leukemia and lung cancer) of MDR (P-gp overexpressing) cells and their drug-sensitive counterparts, as well as from their EVs, was analyzed by deep sequencing. Our results showed distinctive transcripts for MDR cells and their EVs, when compared with their drug-sensitive counterparts. Remarkably, two pseudogenes (a novel pseudogene and RNA 5.8S ribosomal pseudogene 2) were found to be increased in EVs released by MDR cells in both leukemia and lung cancer models. Moreover, six miRs (miR-204-5p, miR-139-5p, miR-29c-5p, miR-551b-3p, miR-29b-2-5p, and miR-204-3p) exhibited altered levels in lung cancer MDR cells and their EVs. This study provides insights into the contribution of EVs to MDR.
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Affiliation(s)
- Diana Sousa
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (D.S.); (R.T.L.)
- Cancer Drug Resistance Group, IPATIMUP—Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal
- Department of Biological Sciences, FFUP—Faculty of Pharmacy of the University of Porto, 4050-313 Porto, Portugal
| | - Rune Matthiesen
- Computational and Experimental Biology Group, CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 130, 1169-056 Lisboa, Portugal
- Correspondence: (R.M.); (M.H.V.); Tel.: +351-939-218-696 (R.M.); +351-225-570-772 (M.H.V.)
| | - Raquel T. Lima
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (D.S.); (R.T.L.)
- Department of Pathology, FMUP—Faculty of Medicine of the University of Porto, 4200-319 Porto, Portugal
- Cancer Signalling & Metabolism Group, IPATIMUP—Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal
| | - M. Helena Vasconcelos
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (D.S.); (R.T.L.)
- Cancer Drug Resistance Group, IPATIMUP—Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal
- Department of Biological Sciences, FFUP—Faculty of Pharmacy of the University of Porto, 4050-313 Porto, Portugal
- Correspondence: (R.M.); (M.H.V.); Tel.: +351-939-218-696 (R.M.); +351-225-570-772 (M.H.V.)
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10
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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: 52] [Impact Index Per Article: 13.0] [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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11
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Wang B, Yong H, Zhu H, Ni D, Tang S, Zhang S, Wang W, Zhou Y, Zhao W, Ding G, Zhu J, Li X, Feng Z. Abnormal amphiregulin expression correlates with gastric cancer prognosis. Oncotarget 2016; 7:76684-76692. [PMID: 27713123 PMCID: PMC5363540 DOI: 10.18632/oncotarget.12436] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 09/27/2016] [Indexed: 12/13/2022] Open
Abstract
Gastric cancer (GC) is a global health issue with a high mortality rate. Early diagnosis and tracking of GC is a challenge due to a lack of reliable tools. Amphiregulin (AREG) is a member of the epidermal growth factor (EGF) family that activates growth signaling upon binding of EGF receptors. Elevated AREG expression is associated with various pathological conditions, including cancer. Here, we investigated whether increased AREG expression is a disease indicator and/or prognostic biomarker for GC. We used tissue microarray and quantitative real-time polymerase chain reaction to assess AREG expression in clinical tissue specimens at various stages of GC and a conducted bioinformatics analysis to evaluate the value of AREG over-expression as a GC biomarker. We found that both mRNA and protein expression of AREG were increased in the tissues of GC patients when compared to tissues from non-cancer patients or normal tissues. High expression of AREG was also associated with GC clinicopathological characteristics and poor survival. Thus, over-expression of AREG could serve as a novel GC biomarker, and active surveillance of its expression could be a novel approach to GC diagnosis and monitoring.
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Affiliation(s)
- Bing Wang
- Center for Pathology and Laboratory Medicine, Zhangjiagang Ao Yang Hospital, Zhangjiagang, Jiangsu, China
- Department of Oncology, Zhangjiagang Ao Yang Hospital, Zhangjiagang, Jiangsu, China
| | - Hongmei Yong
- Department of Oncology, Huai'an Hospital Affiliated of Xuzhou Medical College and Huai'an Second People's Hospital, Huai'an, Jiangsu, China
| | - Huijun Zhu
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Daguang Ni
- Center for Pathology and Laboratory Medicine, Zhangjiagang Ao Yang Hospital, Zhangjiagang, Jiangsu, China
| | - Sijie Tang
- Center for Pathology and Laboratory Medicine, Zhangjiagang Ao Yang Hospital, Zhangjiagang, Jiangsu, China
| | - Shu Zhang
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Wei Wang
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Yan Zhou
- Department of Oncology, Zhangjiagang Ao Yang Hospital, Zhangjiagang, Jiangsu, China
| | - Wei Zhao
- Department of Pathology, Nanjing Medical University, Nanjing, China
| | - Guipeng Ding
- Department of Pathology, Nanjing Medical University, Nanjing, China
| | - Jin Zhu
- Huadong Medical Institute of Biotechniques, Nanjing, China
| | - Xiaohua Li
- Center for Pathology and Laboratory Medicine, Zhangjiagang Ao Yang Hospital, Zhangjiagang, Jiangsu, China
- School of Medicine, Jiangsu University, Jiangsu, China
- The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhenqing Feng
- Department of Oncology, Zhangjiagang Ao Yang Hospital, Zhangjiagang, Jiangsu, China
- Department of Pathology, Nanjing Medical University, Nanjing, China
- Key Laboratory of Antibody Technique of Ministry of Health, Nanjing Medical University, Nanjing, China
- Jiangsu Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
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12
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Shen L, Wen J, Zhao T, Hu Z, Song C, Gu D, He M, Lee NP, Xu Z, Chen J. A genetic variant in large tumor suppressor kinase 2 of Hippo signaling pathway contributes to prognosis of hepatocellular carcinoma. Onco Targets Ther 2016; 9:1945-51. [PMID: 27110123 PMCID: PMC4831600 DOI: 10.2147/ott.s100699] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The Hippo pathway plays an important role in the development of hepatocellular carcinoma (HCC). The present study aimed at exploring the genetic variants of Hippo pathway-related genes and their association with HCC prognosis. A total of 331 HCC patients who tested positive for hepatitis B surface antigen were recruited in this study. None of the patients had prior surgical treatment. Twelve potentially functional single-nucleotide polymorphisms (rs7317471 and rs9509492 in LATS2; rs4810446, rs2267853, rs8000, and rs6073627 in MST1; rs10955176 in MST2; and rs16861979, rs2043550, rs16861985, rs1055153, and rs7630434 in TAZ) in the Hippo pathway were genotyped from patients’ peripheral leukocytes using the Sequenom MassARRAY iPLEX platform. Cox proportional hazard models and log-rank test were used for the survival analyses. LATS2 rs7317471 C>T polymorphism was significantly associated with decreased risk of death in HCC using the dominant model (adjusted hazard ratio [HR] =0.63, 95% confidence interval [CI] =0.46–0.87, P=0.004). Furthermore, using stratified analysis, LATS2 rs7317471 CT/TT genotypes were found to be significantly associated with decreased risk of death in patients who were below 53 years of age (adjusted HR =0.50), females (adjusted HR =0.60), smokers (adjusted HR =0.56), drinkers (adjusted HR =0.58), have Barcelona clinic liver cancer stage B (adjusted HR =0.62), and received no prior chemotherapy or transcatheter hepatic arterial chemoembolization (adjusted HR =0.48). Our results suggested that LATS2 rs7317471 could be used as a potential biomarker for the prediction of HCC prognosis.
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Affiliation(s)
- Lili Shen
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, People's Republic of China; Department of Oncology, Haimen People's Hospital, Haimen, People's Republic of China
| | - Juan Wen
- Nanjing Maternity and Child Health Care Institute, Nanjing Maternity and Child Health Care Hospital Affiliated with Nanjing Medical University, Nanjing, People's Republic of China; Department of Epidemiology and Biostatistics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Cancer Center, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Tingting Zhao
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Cancer Center, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China; State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, People's Republic of China
| | - Ci Song
- Department of Epidemiology and Biostatistics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Cancer Center, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Dongying Gu
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Mingliang He
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, People's Republic of China
| | - Nikki P Lee
- Department of Surgery, The University of Hong Kong, Hong Kong, People's Republic of China
| | - Zhi Xu
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Jinfei Chen
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, People's Republic of China
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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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