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Bok I, Karreth FA. Strategies to Study the Functions of Pseudogenes in Mouse Models of Cancer. Methods Mol Biol 2021; 2324:287-304. [PMID: 34165722 DOI: 10.1007/978-1-0716-1503-4_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Aberrant expression of pseudogenes has been observed in many cancer types. Deregulated pseudogenes engage in a multitude of biological processes at the DNA, RNA, and protein levels and eventually facilitate disease progression. To investigate pseudogene functions in cancer, cell lines and cell line transplantation models have been widely used. However, cancer biology is best studied in the context of an intact organism. Here, we present various strategies to investigate pseudogenes in genetically engineered mouse models and discuss advantages and disadvantages of the different approaches.
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Affiliation(s)
- Ilah Bok
- Cancer Biology Ph.D. Program, University of South Florida, Tampa, FL, USA
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Florian A Karreth
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.
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52
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Lister NC, Johnsson P, Waters PD, Morris KV. Pseudogenes: A Novel Source of Trans-Acting Antisense RNAs. Methods Mol Biol 2021; 2324:219-236. [PMID: 34165718 DOI: 10.1007/978-1-0716-1503-4_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Several recent studies support a functional role for pseudogenes, a copy of a parent gene that has lost protein-coding potential, which was for a long time thought to represent only "junk" DNA. Several hundreds of pseudogenes have now been reported as transcribed RNAs in a large variety of tissues and tumor types. Most studies have focused on pseudogenes expressed in sense direction, relative to their protein-coding gene counterpart, but some reports suggest that pseudogenes can be also transcribed as antisense RNAs (asRNAs). Key regulatory genes, such as PTEN and OCT4, have in fact been reported to be under the regulation of pseudogene-expressed asRNAs. Here, we review what is known about pseudogene-expressed asRNAs, we discuss the functional role that these transcripts may have in gene regulation and we summarize the techniques that are available to study them.
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Affiliation(s)
- Nicholas C Lister
- School of Biotechnology and Biomedical Sciences, The University of New South Wales, Sydney, NSW, Australia.
| | - Per Johnsson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Paul D Waters
- School of Biotechnology and Biomedical Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Kevin V Morris
- Menzies Health Institute and School of Pharmacology and Medical Sciences, Griffith University, Southport, QLD, Australia
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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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54
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Tan L, He X, Shen G. Identification of a 15-pseudogene based prognostic signature for predicting survival and antitumor immune response in breast cancer. Aging (Albany NY) 2020; 13:14499-14521. [PMID: 33378744 PMCID: PMC8202842 DOI: 10.18632/aging.103735] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 07/07/2020] [Indexed: 12/04/2022]
Abstract
Pseudogenes are noncoding RNAs that have been revealed to play critical roles in oncogenesis and tumor progression. However, their functional roles have not been comprehensively clarified in breast cancer. Here, we systematically analyzed the RNA sequencing data of 13931 pseudogenes in 775 breast cancer patients from The Cancer Genome Atlas dataset, and ultimately identified 15 prognostic pseudogenes by univariate Cox proportional hazard regression. A risk score model was constructed based on the prognostic pseudogenes via LASSO analysis and dichotomized patients into low- and high-risk subgroups. Patients in the high-risk group had a significantly shorter overall survival than those in the low-risk group. The prognostic value of these 15 pseudogenes and the risk score model were further validated in the European Genome-Phenome Archive dataset. Furthermore, we performed consensus clustering of the 15 prognostic pseudogenes and found that their expression pattern was significantly associated with tumor malignancy and host antitumor immune response, in terms of infiltrating immune cell compositions, antigen presenting genes expression, cytolytic activity and T-cell exhausted markers. This study indicated that these 15 prognostic pseudogenes were significantly correlated with tumor malignancy and host antitumor immune response in breast cancer, and might serve as potential targets for immunotherapy.
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Affiliation(s)
- Liqiang Tan
- Department of Medical Bioinformatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.,Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Xiaofang He
- Department of Radiation Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Guoping Shen
- Department of Radiation Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
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55
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Zhou B, Yang H, Yang C, Bao YL, Yang SM, Liu J, Xiao YF. Translation of noncoding RNAs and cancer. Cancer Lett 2020; 497:89-99. [PMID: 33038492 DOI: 10.1016/j.canlet.2020.10.002] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 02/07/2023]
Abstract
The human genome contains thousands of noncoding RNAs (ncRNAs), which are thought to lack open reading frames (ORFs) and cannot be translated. Some ncRNAs reportedly have important functions, including epigenetic regulation, chromatin remolding, protein modification, and RNA degradation, but the functions of most ncRNAs remain elusive. Through the application and development of ribosome profiling and sequencing technologies, an increasing number of studies have discovered the translation of ncRNAs. Although ncRNAs were initially defined as noncoding RNAs, a number of ncRNAs actually contain ORFs that are translated into peptides. Here, we summarize the available methods, tools, and databases for identifying and validating ncRNA-encoded peptides/proteins, and the recent findings regarding ncRNA-encoded small peptides/proteins in cancer are compiled and synthesized. Importantly, the role of ncRNA-encoding peptides/proteins has application prospects in cancer research, but some potential challenges remain unresolved. The aim of this review is to provide a theoretical basis that might promote the discovery of more peptides/proteins encoded by ncRNAs and aid the further development of novel diagnostic and prognostic cancer markers and therapeutic targets.
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Affiliation(s)
- Bo Zhou
- Department of Gastroenterology, Xinqiao Hospital, Chongqing, 400037, China
| | - Huan Yang
- Department of Gastroenterology, Xinqiao Hospital, Chongqing, 400037, China
| | - Chuan Yang
- Department of Gastroenterology, Xinqiao Hospital, Chongqing, 400037, China
| | - Yu-Lu Bao
- Department of Gastroenterology, Xinqiao Hospital, Chongqing, 400037, China
| | - Shi-Ming Yang
- Department of Gastroenterology, Xinqiao Hospital, Chongqing, 400037, China
| | - Jiao Liu
- Department of Endoscope, General Hospital of Northern Theater Command, Shenyang, 110016, Liaoning, China.
| | - Yu-Feng Xiao
- Department of Gastroenterology, Xinqiao Hospital, Chongqing, 400037, China.
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56
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Lin W, Liu H, Tang Y, Wei Y, Wei W, Zhang L, Chen J. The development and controversy of competitive endogenous RNA hypothesis in non-coding genes. Mol Cell Biochem 2020; 476:109-123. [PMID: 32975695 DOI: 10.1007/s11010-020-03889-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 08/14/2020] [Indexed: 02/07/2023]
Abstract
As a momentous post-transcriptional regulator, microRNAs (miRNAs) are attracting more and more attention. The classical miRNAs regulated mechanism shows it binds to the targets' 3'UTR thus play the role in post-transcription. Meanwhile, single miRNA can target multiple genes, so those should compete to bind that miRNA. Vice versa, single gene can sponge mass of miRNAs as well. Thus the competitive endogenous RNAs (ceRNAs) hypothesis was put forward in 2011. The ceRNA hypothesis has made huge achievements, in particular in non-coding genes, which including long non-coding RNAs (lncRNAs), circle RNAs (circRNAs) and pseudogenes, even viral transcripts. It also contributed greatly to epigenetics development. However, an increasing number of controversies have occurred with applause. Based on this situation, this review introduces something in detail about the ceRNAs hypothesis achieved in lncRNAs, circRNAs, pseudogenes and viral transcripts, respectively. Meanwhile, it also covers controversy of the ceRNAs hypothesis.
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Affiliation(s)
- Weimin Lin
- Nanjing Agricultural University, Nanjing, China
| | | | | | - Yuchen Wei
- Nanjing Agricultural University, Nanjing, China
| | - Wei Wei
- Nanjing Agricultural University, Nanjing, China
| | - Lifan Zhang
- Nanjing Agricultural University, Nanjing, China
| | - Jie Chen
- Nanjing Agricultural University, Nanjing, China.
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57
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Rubanov LI, Zverkov OA, Shilovsky GA, Seliverstov AV, Lyubetsky VA. Protein-Coding Genes in Euarchontoglires with Pseudogene Homologs in Humans. Life (Basel) 2020; 10:life10090192. [PMID: 32927891 PMCID: PMC7555810 DOI: 10.3390/life10090192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/23/2020] [Accepted: 09/08/2020] [Indexed: 12/02/2022] Open
Abstract
An original bioinformatics technique is developed to identify the protein-coding genes in rodents, lagomorphs and nonhuman primates that are pseudogenized in humans. The method is based on per-gene verification of local synteny, similarity of exon-intronic structures and orthology in a set of genomes. It is applicable to any genome set, even with the number of genomes exceeding 100, and efficiently implemented using fast computer software. Only 50 evolutionary recent human pseudogenes were predicted. Their functional homologs in model species are often associated with the immune system or digestion and mainly express in the testes. According to current evidence, knockout of most of these genes leads to an abnormal phenotype. Some genes were pseudogenized or lost independently in human and nonhuman hominoids.
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Affiliation(s)
- Lev I. Rubanov
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow 127051, Russia; (L.I.R.); (O.A.Z.); (G.A.S.); (A.V.S.)
| | - Oleg A. Zverkov
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow 127051, Russia; (L.I.R.); (O.A.Z.); (G.A.S.); (A.V.S.)
| | - Gregory A. Shilovsky
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow 127051, Russia; (L.I.R.); (O.A.Z.); (G.A.S.); (A.V.S.)
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119192, Russia
| | - Alexandr V. Seliverstov
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow 127051, Russia; (L.I.R.); (O.A.Z.); (G.A.S.); (A.V.S.)
| | - Vassily A. Lyubetsky
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow 127051, Russia; (L.I.R.); (O.A.Z.); (G.A.S.); (A.V.S.)
- Correspondence:
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58
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Li J, Jiang L, Liu Z, Li Y, Xu Y, Liu H. Oncogenic pseudogene DUXAP10 knockdown suppresses proliferation and invasion and induces apoptosis of papillary thyroid carcinoma cells by inhibition of Akt/mTOR pathway. Clin Exp Pharmacol Physiol 2020; 47:1473-1483. [PMID: 32215944 DOI: 10.1111/1440-1681.13310] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/15/2020] [Accepted: 03/19/2020] [Indexed: 12/13/2022]
Abstract
Pseudogenes, another novel group of non-coding segments without protein-coding capacity, are closely associated with tumourigenesis and cancer progression. Double homeoboxA pseudogene 10 (DUXAP10) is reported to be robustly expressed in thyroid carcinoma. However, the functional role and underlying mechanism of DUXAP10 in papillary thyroid carcinoma (PTC) progression remain undefined. DUXAP10 expression in PTC cells was detected by qRT-PCR. Cell proliferation and invasion were determined using 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide (MTT) and Transwell invasion assay, respectively. Apoptosis was evaluated using flow cytometry. Protein expression of matrix metalloproteinase (MMP)-2, MMP-9, protein kinase B (Akt), phosphorylated Akt, mammalian target of rapamycin (mTOR), and phosphorylated mTOR was examined by western blot. Results showed that DUXAP10 was significantly overexpressed in PTC cells compared with normal thyroid follicular epithelium cells. DUXAP10 silencing suppressed cell proliferation and invasive ability, reduced the expression of MMP-2 and MMP-9, and increased apoptotic rate and caspase-3 activity in PTC cells. Additionally, the Akt/mTOR pathway was inhibited following DUXAP10 knockdown in PTC cells. Activation of the Akt/mTOR pathway by 740Y-P and MHY1485 attenuated DUXAP10 knockdown-induced proliferation reduction, invasion suppression and apoptosis in PTC cells. In conclusion, DUXAP10 knockdown suppressed proliferation and invasion and induced apoptosis in PTC cells at least partially by inhibition of the Akt/mTOR pathway.
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Affiliation(s)
- Jian Li
- Department of Head and Neck Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, China
| | - Li Jiang
- Department of Head and Neck Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, China
| | - Zhu Liu
- Department of Head and Neck Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, China
| | - Yanguo Li
- Department of Head and Neck Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, China
| | - Yang Xu
- Department of Head and Neck Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, China
| | - Hongwei Liu
- Department of Head and Neck Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, China
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59
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Ribeiro JMC, Mans BJ. TickSialoFam (TSFam): A Database That Helps to Classify Tick Salivary Proteins, a Review on Tick Salivary Protein Function and Evolution, With Considerations on the Tick Sialome Switching Phenomenon. Front Cell Infect Microbiol 2020; 10:374. [PMID: 32850476 PMCID: PMC7396615 DOI: 10.3389/fcimb.2020.00374] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 06/17/2020] [Indexed: 01/09/2023] Open
Abstract
Tick saliva contains a complex mixture of peptides and non-peptides that counteract their hosts' hemostasis, immunity, and tissue-repair reactions. Recent transcriptomic studies have revealed over one thousand different transcripts coding for secreted polypeptides in a single tick species. Not only do these gene products belong to many expanded families, such as the lipocalins, metalloproteases, Antigen-5, cystatins, and apyrases, but also families that are found exclusively in ticks, such as the evasins, Isac, DAP36, and many others. Phylogenetic analysis of the deduced protein sequences indicate that the salivary genes exhibit an increased rate of evolution due to a lower evolutionary constraint and/or positive selection, allowing for a large diversity of tick salivary proteins. Thus, for each new tick species that has its salivary transcriptome sequenced and assembled, a formidable task of annotation of these transcripts awaits. Currently, as of November 2019, there are over 287 thousand coding sequences deposited at the National Center for Biotechnology Information (NCBI) that are derived from tick salivary gland mRNA. Here, from these 287 thousand sequences we identified 45,264 potential secretory proteins which possess a signal peptide and no transmembrane domains on the mature peptide. By using the psiblast tools, position-specific matrices were constructed and assembled into the TickSialoFam (TSF) database. The TSF is a rpsblastable database that can help with the annotation of tick sialotranscriptomes. The TSA database identified 136 tick salivary secreted protein families, as well as 80 families of endosomal-related products, mostly having a protein modification function. As the number of sequences increases, and new annotation details become available, new releases of the TSF database may become available.
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Affiliation(s)
- José M. C. Ribeiro
- Section of Vector Biology, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Rockville, MD, United States
| | - Ben J. Mans
- Epidemiology, Parasites and Vectors, Agricultural Research Council - Onderstepoort Veterinary Research, Pretoria, South Africa
- The Department of Veterinary Tropical Diseases, University of Pretoria, Pretoria, South Africa
- Department of Life and Consumer Sciences, University of South Africa, Pretoria, South Africa
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60
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Slack FJ, Chinnaiyan AM. The Role of Non-coding RNAs in Oncology. Cell 2020; 179:1033-1055. [PMID: 31730848 DOI: 10.1016/j.cell.2019.10.017] [Citation(s) in RCA: 908] [Impact Index Per Article: 227.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 10/09/2019] [Accepted: 10/18/2019] [Indexed: 02/07/2023]
Abstract
For decades, research into cancer biology focused on the involvement of protein-coding genes. Only recently was it discovered that an entire class of molecules, termed non-coding RNA (ncRNA), plays key regulatory roles in shaping cellular activity. An explosion of studies into ncRNA biology has since shown that they represent a diverse and prevalent group of RNAs, including both oncogenic molecules and those that work in a tumor suppressive manner. As a result, hundreds of cancer-focused clinical trials involving ncRNAs as novel biomarkers or therapies have begun and these are likely just the beginning.
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Affiliation(s)
- Frank J Slack
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02215, USA; Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA.
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA.
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61
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Complex Analysis of Retroposed Genes' Contribution to Human Genome, Proteome and Transcriptome. Genes (Basel) 2020; 11:genes11050542. [PMID: 32408516 PMCID: PMC7290577 DOI: 10.3390/genes11050542] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/06/2020] [Accepted: 05/08/2020] [Indexed: 02/07/2023] Open
Abstract
Gene duplication is a major driver of organismal evolution. One of the main mechanisms of gene duplications is retroposition, a process in which mRNA is first transcribed into DNA and then reintegrated into the genome. Most gene retrocopies are depleted of the regulatory regions. Nevertheless, examples of functional retrogenes are rapidly increasing. These functions come from the gain of new spatio-temporal expression patterns, imposed by the content of the genomic sequence surrounding inserted cDNA and/or by selectively advantageous mutations, which may lead to the switch from protein coding to regulatory RNA. As recent studies have shown, these genes may lead to new protein domain formation through fusion with other genes, new regulatory RNAs or other regulatory elements. We utilized existing data from high-throughput technologies to create a complex description of retrogenes functionality. Our analysis led to the identification of human retroposed genes that substantially contributed to transcriptome and proteome. These retrocopies demonstrated the potential to encode proteins or short peptides, act as cis- and trans- Natural Antisense Transcripts (NATs), regulate their progenitors’ expression by competing for the same microRNAs, and provide a sequence to lncRNA and novel exons to existing protein-coding genes. Our study also revealed that retrocopies, similarly to retrotransposons, may act as recombination hot spots. To our best knowledge this is the first complex analysis of these functions of retrocopies.
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Abstract
The partial success of a study to reproduce experiments that linked pseudogenes and cancer proves that understanding RNA networks is more complicated than expected.
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Affiliation(s)
- George A Calin
- Translational Molecular Pathology Department, University of Texas MD Anderson Cancer CenterHoustonUnited States
- Center for RNA Interference and Non-Coding RNAs, University of Texas MD Anderson Cancer CenterHoustonUnited States
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63
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Molecular fossils “pseudogenes” as functional signature in biological system. Genes Genomics 2020; 42:619-630. [DOI: 10.1007/s13258-020-00935-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 04/03/2020] [Indexed: 12/11/2022]
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Smerekanych S, Johnson TS, Huang K, Zhang Y. Pseudogene-gene functional networks are prognostic of patient survival in breast cancer. BMC Med Genomics 2020; 13:51. [PMID: 32241256 PMCID: PMC7118805 DOI: 10.1186/s12920-020-0687-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Given the vast range of molecular mechanisms giving rise to breast cancer, it is unlikely universal cures exist. However, by providing a more precise prognosis for breast cancer patients through integrative models, treatments can become more individualized, resulting in more successful outcomes. Specifically, we combine gene expression, pseudogene expression, miRNA expression, clinical factors, and pseudogene-gene functional networks to generate these models for breast cancer prognostics. Establishing a LASSO-generated molecular gene signature revealed that the increased expression of genes STXBP5, GALP and LOC387646 indicate a poor prognosis for a breast cancer patient. We also found that increased CTSLP8 and RPS10P20 and decreased HLA-K pseudogene expression indicate poor prognosis for a patient. Perhaps most importantly we identified a pseudogene-gene interaction, GPS2-GPS2P1 (improved prognosis) that is prognostic where neither the gene nor pseudogene alone is prognostic of survival. Besides, miR-3923 was predicted to target GPS2 using miRanda, PicTar, and TargetScan, which imply modules of gene-pseudogene-miRNAs that are potentially functionally related to patient survival. RESULTS In our LASSO-based model, we take into account features including pseudogenes, genes and candidate pseudogene-gene interactions. Key biomarkers were identified from the features. The identification of key biomarkers in combination with significant clinical factors (such as stage and radiation therapy status) should be considered as well, enabling a specific prognostic prediction and future treatment plan for an individual patient. Here we used our PseudoFuN web application to identify the candidate pseudogene-gene interactions as candidate features in our integrative models. We further identified potential miRNAs targeting those features in our models using PseudoFuN as well. From this study, we present an interpretable survival model based on LASSO and decision trees, we also provide a novel feature set which includes pseudogene-gene interaction terms that have been ignored by previous prognostic models. We find that some interaction terms for pseudogenes and genes are significantly prognostic of survival. These interactions are cross-over interactions, where the impact of the gene expression on survival changes with pseudogene expression and vice versa. These may imply more complicated regulation mechanisms than previously understood. CONCLUSIONS We recommend these novel feature sets be considered when training other types of prognostic models as well, which may provide more comprehensive insights into personalized treatment decisions.
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Affiliation(s)
- Sasha Smerekanych
- Kenyon College, Gambier, OH, 43022, USA
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Travis S Johnson
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
- Department of Medicine, School of Medicine, Indiana University, Indianapolis, IN, 46202, USA
| | - Kun Huang
- Department of Medicine, School of Medicine, Indiana University, Indianapolis, IN, 46202, USA
- Regenstrief Institute, Indiana University, Indianapolis, IN, 46202, USA
| | - Yan Zhang
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA.
- The Ohio State University Comprehensive Cancer Center (OSUCCC - James), Columbus, OH, 43210, USA.
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65
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Pisapia L, Terreri S, Barba P, Mastroianni M, Donnini M, Mercadante V, Palmieri A, Verze P, Mirone V, Altieri V, Califano G, Liguori GL, Strazzullo M, Cimmino A, Del Pozzo G. Role of PA2G4P4 pseudogene in bladder cancer tumorigenesis. BIOLOGY 2020; 9:E66. [PMID: 32244410 PMCID: PMC7235711 DOI: 10.3390/biology9040066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 03/23/2020] [Accepted: 03/26/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND Many pseudogenes possess biological activities and play important roles in the pathogenesis of various types of cancer including bladder cancer (BlCa), which still lacks suitable molecular biomarkers. Recently, pseudogenes were found to be significantly enriched in a pan-cancer classification based on the Cancer Genome Atlas gene expression data. Among them, the top-ranking pseudogene was the proliferation-associated 2G4 pseudogene 4 (PA2G4P4). METHODS Genomic and transcript features of PA2G4P4 were determined by GeneBank database analysis followed by 5' RACE experiments. Therefore, we conducted a retrospective molecular study on a cohort of 45 patients of BlCa. PA2G4P4 expression was measured by RT-qPCR, whereas PA2G4P4 transcript distribution was analyzed by in situ hybridization on both normal and cancerous histological sections and compared to the immunolocalization of its parental PA2G4/EBP1 protein. Finally, we tested the effects of PA2G4P4 depletion on proliferation, migration, and death of BlCa cells. RESULTS We showed for the first time PA2G4P4 overexpression in BlCa tissues and in cell lines. PA2G4P4 distribution strictly overlaps PA2G4/EBP1 protein localization. Moreover, we showed that PA2G4P4 knockdown affects both proliferation and migration of BlCa cells, highlighting its potential oncogenic role. CONCLUSIONS PA2G4P4 may play a functional role as an oncogene in BlCa development, suggesting it as a good candidate for future investigation and new clinical applications.
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Affiliation(s)
- Laura Pisapia
- Institute of Genetics and Biophysics, CNR, 80131 Naples, Italy; (L.P.); (S.T.); (P.B.); (M.M.); (M.D.); (V.M.); (A.C.)
| | - Sara Terreri
- Institute of Genetics and Biophysics, CNR, 80131 Naples, Italy; (L.P.); (S.T.); (P.B.); (M.M.); (M.D.); (V.M.); (A.C.)
- B Cell Pathophysiology Unit, IRCCS Bambino Gesù Children’s Hospital, 00146 Rome, Italy
| | - Pasquale Barba
- Institute of Genetics and Biophysics, CNR, 80131 Naples, Italy; (L.P.); (S.T.); (P.B.); (M.M.); (M.D.); (V.M.); (A.C.)
| | - Marianna Mastroianni
- Institute of Genetics and Biophysics, CNR, 80131 Naples, Italy; (L.P.); (S.T.); (P.B.); (M.M.); (M.D.); (V.M.); (A.C.)
| | - Maria Donnini
- Institute of Genetics and Biophysics, CNR, 80131 Naples, Italy; (L.P.); (S.T.); (P.B.); (M.M.); (M.D.); (V.M.); (A.C.)
| | - Vincenzo Mercadante
- Institute of Genetics and Biophysics, CNR, 80131 Naples, Italy; (L.P.); (S.T.); (P.B.); (M.M.); (M.D.); (V.M.); (A.C.)
| | - Alessandro Palmieri
- Department of Neurosciences, Reproductive Sciences and Odontostomatology, University of Naples Federico II, 80131 Naples, Italy; (A.P.); (V.M.); (G.C.)
| | - Paolo Verze
- Department of Medicine and Surgery “Scuola medica Salernitana” University of Salerno, 84084 Salerno, Italy; (P.V.); (V.A.)
| | - Vincenzo Mirone
- Department of Neurosciences, Reproductive Sciences and Odontostomatology, University of Naples Federico II, 80131 Naples, Italy; (A.P.); (V.M.); (G.C.)
| | - Vincenzo Altieri
- Department of Medicine and Surgery “Scuola medica Salernitana” University of Salerno, 84084 Salerno, Italy; (P.V.); (V.A.)
| | - Gianluigi Califano
- Department of Neurosciences, Reproductive Sciences and Odontostomatology, University of Naples Federico II, 80131 Naples, Italy; (A.P.); (V.M.); (G.C.)
| | - Giovanna Lucia Liguori
- Institute of Genetics and Biophysics, CNR, 80131 Naples, Italy; (L.P.); (S.T.); (P.B.); (M.M.); (M.D.); (V.M.); (A.C.)
| | - Maria Strazzullo
- Institute of Genetics and Biophysics, CNR, 80131 Naples, Italy; (L.P.); (S.T.); (P.B.); (M.M.); (M.D.); (V.M.); (A.C.)
| | - Amelia Cimmino
- Institute of Genetics and Biophysics, CNR, 80131 Naples, Italy; (L.P.); (S.T.); (P.B.); (M.M.); (M.D.); (V.M.); (A.C.)
| | - Giovanna Del Pozzo
- Institute of Genetics and Biophysics, CNR, 80131 Naples, Italy; (L.P.); (S.T.); (P.B.); (M.M.); (M.D.); (V.M.); (A.C.)
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Yan L, Yue C, Xu Y, Jiang X, Zhang L, Wu J. Prognostic Value and Molecular Regulatory Mechanism of MSTO2P in Hepatocellular Carcinoma: A Comprehensive Study Based on Bioinformatics, Clinical Analysis and in vitro Validation. Onco Targets Ther 2020; 13:2583-2598. [PMID: 32273728 PMCID: PMC7109319 DOI: 10.2147/ott.s245741] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 03/10/2020] [Indexed: 11/30/2022] Open
Abstract
Background Accumulating studies have shown that pseudogenes could become key regulators in human cancers. Misato family member 2, pseudogene (MSTO2P) is overexpressed in lung and gastric cancer and affects the biological functions of tumor cells. However, the role of MSTO2P in hepatocellular carcinoma (HCC) is unreported. Purpose This study aimed to examine the diagnostic and prognostic value of MSTO2P in HCC, to investigate the effects of MSTO2P on the biological functions of HCC cells, and to explore the potential mechanisms of MSTO2P in HCC. Methods Relevant data on HCC were downloaded from the Gene Expression Omnibus database and the Cancer Genome Atlas database and used to analyze MSTO2P expression and the role of MSTO2P in HCC prognosis. MSTO2P in HCC cell lines was knocked down by shRNA to study the effects of MSTO2P on cell proliferation, apoptosis, metastasis and invasion in HCC. Expressions of the main proteins involved in epithelial–mesenchymal transition and the PI3K/AKT/mTOR signaling pathway in HCC were examined via Western blot analysis. Results MSTO2P had significant diagnostic and prognostic value in HCC. MSTO2P was highly expressed in HCC tissues and cells, and MSTO2P increased HCC cell proliferation, invasion and metastasis. MSTO2P knockdown also increased E-cadherin expression and decreased N-cadherin and Vimentin expression. Additionally, MSTO2P increased the expressions of proteins in the PI3K/AKT/mTOR pathway, including PI3K, p-AKT and p-mTOR. Conclusion MSTO2P might be used as a potential target for diagnosing and curing HCC. MSTO2P may affect HCC cell proliferation, apoptosis, metastasis and invasion through the PI3K/AKT/mTOR pathway.
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Affiliation(s)
- Lijun Yan
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Chaosen Yue
- Department of Breast Center, 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
| | - Xinceng Jiang
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Lijun Zhang
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, 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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67
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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: 103] [Impact Index Per Article: 25.8] [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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68
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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: 48] [Impact Index Per Article: 12.0] [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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69
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Johnson TS, Li S, Franz E, Huang Z, Dan Li S, Campbell MJ, Huang K, Zhang Y. PseudoFuN: Deriving functional potentials of pseudogenes from integrative relationships with genes and microRNAs across 32 cancers. Gigascience 2019; 8:5480571. [PMID: 31029062 PMCID: PMC6486473 DOI: 10.1093/gigascience/giz046] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 12/13/2018] [Accepted: 03/29/2019] [Indexed: 12/14/2022] Open
Abstract
Background Long thought “relics” of evolution, not until recently have pseudogenes been of medical interest regarding regulation in cancer. Often, these regulatory roles are a direct by-product of their close sequence homology to protein-coding genes. Novel pseudogene-gene (PGG) functional associations can be identified through the integration of biomedical data, such as sequence homology, functional pathways, gene expression, pseudogene expression, and microRNA expression. However, not all of the information has been integrated, and almost all previous pseudogene studies relied on 1:1 pseudogene–parent gene relationships without leveraging other homologous genes/pseudogenes. Results We produce PGG families that expand beyond the current 1:1 paradigm. First, we construct expansive PGG databases by (i) CUDAlign graphics processing unit (GPU) accelerated local alignment of all pseudogenes to gene families (totaling 1.6 billion individual local alignments and >40,000 GPU hours) and (ii) BLAST-based assignment of pseudogenes to gene families. Second, we create an open-source web application (PseudoFuN [Pseudogene Functional Networks]) to search for integrative functional relationships of sequence homology, microRNA expression, gene expression, pseudogene expression, and gene ontology. We produce four “flavors” of CUDAlign-based databases (>462,000,000 PGG pairwise alignments and 133,770 PGG families) that can be queried and downloaded using PseudoFuN. These databases are consistent with previous 1:1 PGG annotation and also are much more powerful including millions of de novo PGG associations. For example, we find multiple known (e.g., miR-20a-PTEN-PTENP1) and novel (e.g., miR-375-SOX15-PPP4R1L) microRNA-gene-pseudogene associations in prostate cancer. PseudoFuN provides a “one stop shop” for identifying and visualizing thousands of potential regulatory relationships related to pseudogenes in The Cancer Genome Atlas cancers. Conclusions Thousands of new PGG associations can be explored in the context of microRNA-gene-pseudogene co-expression and differential expression with a simple-to-use online tool by bioinformaticians and oncologists alike.
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Affiliation(s)
- Travis S Johnson
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, 1800 Cannon Drive, Columbus, OH 43210, USA.,Department of Medicine, Indiana University School of Medicine, 545 Barnhill Drive, Indianapolis, IN 46202, USA
| | - Sihong Li
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, 1800 Cannon Drive, Columbus, OH 43210, USA
| | - Eric Franz
- Ohio Supercomputer Center, 1224 Kinnear Road, Columbus, OH 43212, USA
| | - Zhi Huang
- School of Electrical and Computer Engineering, Purdue University, 465 Northwestern Avenue, West Lafayette, IN 47907, USA.,Department of Medicine, Indiana University School of Medicine, 545 Barnhill Drive, Indianapolis, IN 46202, USA
| | - Shuyu Dan Li
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Moray J Campbell
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, 500 West 12 th Avenue, Columbus, OH 43210, USA
| | - Kun Huang
- Department of Medicine, Indiana University School of Medicine, 545 Barnhill Drive, Indianapolis, IN 46202, USA.,Regenstrief Institute, Indiana University, 1101 West 10 th Street, Indianapolis, IN 46262, USA
| | - Yan Zhang
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, 1800 Cannon Drive, Columbus, OH 43210, USA.,The Ohio State University Comprehensive Cancer Center (OSUCCC - James), 460 West 10 th Avenue, Columbus, OH 43210, USA
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70
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Overcoming challenges and dogmas to understand the functions of pseudogenes. Nat Rev Genet 2019; 21:191-201. [DOI: 10.1038/s41576-019-0196-1] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2019] [Indexed: 01/08/2023]
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71
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Wang S, Mao C, Liu S. Peptides encoded by noncoding genes: challenges and perspectives. Signal Transduct Target Ther 2019; 4:57. [PMID: 31871775 PMCID: PMC6908703 DOI: 10.1038/s41392-019-0092-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 10/17/2019] [Accepted: 10/27/2019] [Indexed: 01/01/2023] Open
Abstract
In recent years, noncoding gene (NCG) translation events have been frequently discovered. The resultant peptides, as novel findings in the life sciences, perform unexpected functions of increasingly recognized importance in many fundamental biological and pathological processes. The emergence of these novel peptides, in turn, has advanced the field of genomics while indispensably aiding living organisms. The peptides from NCGs serve as important links between extracellular stimuli and intracellular adjustment mechanisms. These peptides are also important entry points for further exploration of the mysteries of life that may trigger a new round of revolutionary biotechnological discoveries. Insights into NCG-derived peptides will assist in understanding the secrets of life and the causes of diseases, and will also open up new paths to the treatment of diseases such as cancer. Here, a critical review is presented on the action modes and biological functions of the peptides encoded by NCGs. The challenges and future trends in searching for and studying NCG peptides are also critically discussed.
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Affiliation(s)
- Shuo Wang
- Changhai Hospital, Shanghai, 200433 China
| | - Chuanbin Mao
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, Institute for Biomedical Engineering, Science and Technology, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019-5300 USA
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Hatje K, Mühlhausen S, Simm D, Kollmar M. The Protein-Coding Human Genome: Annotating High-Hanging Fruits. Bioessays 2019; 41:e1900066. [PMID: 31544971 DOI: 10.1002/bies.201900066] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/07/2019] [Indexed: 12/19/2022]
Abstract
The major transcript variants of human protein-coding genes are annotated to a certain degree of accuracy combining manual curation, transcript data, and proteomics evidence. However, there is considerable disagreement on the annotation of about 2000 genes-they can be protein-coding, noncoding, or pseudogenes-and on the annotation of most of the predicted alternative transcripts. Pure transcriptome mapping approaches seem to be limited in discriminating functional expression from noise. These limitations have partially been overcome by dedicated algorithms to detect alternative spliced micro-exons and wobble splice variants. Recently, knowledge about splice mechanism and protein structure are incorporated into an algorithm to predict neighboring homologous exons, often spliced in a mutually exclusive manner. Predicted exons are evaluated by transcript data, structural compatibility, and evolutionary conservation, revealing hundreds of novel coding exons and splice mechanism re-assignments. The emerging human pan-genome is necessitating distinctive annotations incorporating differences between individuals and between populations.
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Affiliation(s)
- Klas Hatje
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstr. 124, 4070, Basel, Switzerland
| | - Stefanie Mühlhausen
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Dominic Simm
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.,Theoretical Computer Science and Algorithmic Methods, Institute of Computer Science, Georg-August-University Göttingen, Goldschmidtstr. 7, 37077, Göttingen, Germany
| | - Martin Kollmar
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
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73
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Pseudogene Associated Recurrent Gene Fusion in Prostate Cancer. Neoplasia 2019; 21:989-1002. [PMID: 31446281 PMCID: PMC6713813 DOI: 10.1016/j.neo.2019.07.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 02/08/2023] Open
Abstract
We present the functional characterization of a pseudogene associated recurrent gene fusion in prostate cancer. The fusion gene KLK4-KLKP1 is formed by the fusion of the protein coding gene KLK4 with the noncoding pseudogene KLKP1. Screening of a cohort of 659 patients (380 Caucasian American; 250 African American, and 29 patients from other races) revealed that the KLK4-KLKP1 is expressed in about 32% of prostate cancer patients. Correlative analysis with other ETS gene fusions and SPINK1 revealed a concomitant expression pattern of KLK4-KLKP1 with ERG and a mutually exclusive expression pattern with SPINK1, ETV1, ETV4, and ETV5. Development of an antibody specific to KLK4-KLKP1 fusion protein confirmed the expression of the full-length KLK4-KLKP1 protein in prostate tissues. The in vitro and in vivo functional assays to study the oncogenic properties of KLK4-KLKP1 confirmed its role in cell proliferation, cell invasion, intravasation, and tumor formation. Presence of strong ERG and AR binding sites located at the fusion junction in KLK4-KLKP1 suggests that the fusion gene is regulated by ERG and AR. Correlative analysis of clinical data showed an association of KLK4-KLKP1 with lower preoperative PSA values and in young men (<50 years) with prostate cancer. Screening of patient urine samples showed that KLK4-KLKP1 can be detected noninvasively in urine. Taken together, we present KLK4-KLKP1 as a class of pseudogene associated fusion transcript in cancer with potential applications as a biomarker for routine screening of prostate cancer.
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74
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Zheng LL, Zhou KR, Liu S, Zhang DY, Wang ZL, Chen ZR, Yang JH, Qu LH. dreamBase: DNA modification, RNA regulation and protein binding of expressed pseudogenes in human health and disease. Nucleic Acids Res 2019; 46:D85-D91. [PMID: 29059382 PMCID: PMC5753186 DOI: 10.1093/nar/gkx972] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/12/2017] [Indexed: 12/28/2022] Open
Abstract
Although thousands of pseudogenes have been annotated in the human genome, their transcriptional regulation, expression profiles and functional mechanisms are largely unknown. In this study, we developed dreamBase (http://rna.sysu.edu.cn/dreamBase) to facilitate the investigation of DNA modification, RNA regulation and protein binding of potential expressed pseudogenes from multidimensional high-throughput sequencing data. Based on ∼5500 ChIP-seq and DNase-seq datasets, we identified genome-wide binding profiles of various transcription-associated factors around pseudogene loci. By integrating ∼18 000 RNA-seq data, we analysed the expression profiles of pseudogenes and explored their co-expression patterns with their parent genes in 32 cancers and 31 normal tissues. By combining microRNA binding sites, we demonstrated complex post-transcriptional regulation networks involving 275 microRNAs and 1201 pseudogenes. We generated ceRNA networks to illustrate the crosstalk between pseudogenes and their parent genes through competitive binding of microRNAs. In addition, we studied transcriptome-wide interactions between RNA binding proteins (RBPs) and pseudogenes based on 458 CLIP-seq datasets. In conjunction with epitranscriptome sequencing data, we also mapped 1039 RNA modification sites onto 635 pseudogenes. This database will provide insights into the transcriptional regulation, expression, functions and mechanisms of pseudogenes as well as their roles in biological processes and diseases.
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Affiliation(s)
- Ling-Ling Zheng
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Ke-Ren Zhou
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Shun Liu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Ding-Yao Zhang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Ze-Lin Wang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Zhi-Rong Chen
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Jian-Hua Yang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Liang-Hu Qu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China
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75
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Gebert D, Zischler H, Rosenkranz D. Primate piRNA Cluster Evolution Suggests Limited Relevance of Pseudogenes in piRNA-Mediated Gene Regulation. Genome Biol Evol 2019; 11:1088-1104. [PMID: 30888404 PMCID: PMC6461890 DOI: 10.1093/gbe/evz060] [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] [Accepted: 03/16/2019] [Indexed: 12/11/2022] Open
Abstract
PIWI proteins and their guiding Piwi-interacting (pi-) RNAs direct the silencing of target nucleic acids in the animal germline and soma. Although in mammal testes fetal piRNAs are involved in extensive silencing of transposons, pachytene piRNAs have additionally been shown to act in post-transcriptional gene regulation. The bulk of pachytene piRNAs is produced from large genomic loci, named piRNA clusters. Recently, the presence of reversed pseudogenes within piRNA clusters prompted the idea that piRNAs derived from such sequences might direct regulation of their parent genes. Here, we examine primate piRNA clusters and integrated pseudogenes in a comparative approach to gain a deeper understanding about mammalian piRNA cluster evolution and the presumed gene-regulatory role of pseudogene-derived piRNAs. Initially, we provide a broad analysis of the evolutionary relationships of piRNA clusters and their differential activity among six primate species. Subsequently, we show that pseudogenes in reserve orientation relative to piRNA cluster transcription direction generally do not exhibit signs of selection pressure and cause weakly conserved targeting of homologous genes among species, suggesting a lack of functional constraints and thus only a minor significance for gene regulation in most cases. Finally, we report that piRNA-producing loci generally tend to be located in active genomic regions with elevated gene and pseudogene density. Thus, we conclude that the presence of most pseudogenes in piRNA clusters might be regarded as a byproduct of piRNA cluster generation, whereas this does not exclude that some pseudogenes nevertheless play critical roles in individual cases.
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Affiliation(s)
- Daniel Gebert
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University, Mainz, Germany
| | - Hans Zischler
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University, Mainz, Germany
| | - David Rosenkranz
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University, Mainz, Germany
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76
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Feng J, Yang G, Liu Y, Gao Y, Zhao M, Bu Y, Yuan H, Yuan Y, Yun H, Sun M, Gao H, Zhang S, Liu Z, Yin M, Song X, Miao Z, Lin Z, Zhang X. LncRNA PCNAP1 modulates hepatitis B virus replication and enhances tumor growth of liver cancer. Am J Cancer Res 2019; 9:5227-5245. [PMID: 31410212 PMCID: PMC6691589 DOI: 10.7150/thno.34273] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 06/06/2019] [Indexed: 02/06/2023] Open
Abstract
Rationale: Hepatitis B virus (HBV) is a major risk factor for liver cancer, in which HBV covalently closed circular DNA (cccDNA) plays crucial roles. However, the effect of pseudogene-derived long noncoding RNAs (lncRNAs) acting as functional regulators of their ancestral gene expression on HBV replication and hepatocellular carcinoma (HCC) remains unclear. In this study, we speculated that the pseudogene-derived lncRNA PCNAP1 and its ancestor PCNA might modulate HBV replication and promote hepatocarcinogenesis. Methods: We investigated the roles of lncRNA PCNAP1 in contribution of HBV replication through modulating miR-154/PCNA/HBV cccDNA signaling in hepatocarcinogenesis by using CRISPR/Cas9, Southern blot analysis, confocal assays, et al. in primary human hepatocytes (PHH), HepaRG cells, HepG2-NTCP cells, hepatoma carcinoma cells, human liver-chimeric mice model, transgenetic mice model, in vitro tumorigenicity and clinical patients. Results: Interestingly, the expression levels of PCNAP1 and PCNA were significantly elevated in the liver of HBV-infectious human liver-chimeric mice. Clinically, the mRNA levels of PCNAP1 and PCNA were increased in the liver of HBV-positive/HBV cccDNA-positive HCC patients. Mechanistically, PCNA interacted with HBV cccDNA in a HBc-dependent manner. PCNAP1 enhanced PCNA through sponging miR-154 targeting PCNA mRNA 3′UTR. Functionally, PCNAP1 or PCNA remarkably enhanced HBV replication and accelerated the growth of HCC in vitro and in vivo. Conclusion: We conclude that lncRNA PCNAP1 enhances the HBV replication through modulating miR-154/PCNA/HBV cccDNA signaling and the PCNAP1/PCNA signaling drives the hepatocarcinogenesis. Our finding provides new insights into the mechanism by which lncRNA PCNAP1 enhances HBV replication and hepatocarcinogenesis.
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77
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Heyer EE, Deveson IW, Wooi D, Selinger CI, Lyons RJ, Hayes VM, O'Toole SA, Ballinger ML, Gill D, Thomas DM, Mercer TR, Blackburn J. Diagnosis of fusion genes using targeted RNA sequencing. Nat Commun 2019; 10:1388. [PMID: 30918253 PMCID: PMC6437215 DOI: 10.1038/s41467-019-09374-9] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 02/22/2019] [Indexed: 01/05/2023] Open
Abstract
Fusion genes are a major cause of cancer. Their rapid and accurate diagnosis can inform clinical action, but current molecular diagnostic assays are restricted in resolution and throughput. Here, we show that targeted RNA sequencing (RNAseq) can overcome these limitations. First, we establish that fusion gene detection with targeted RNAseq is both sensitive and quantitative by optimising laboratory and bioinformatic variables using spike-in standards and cell lines. Next, we analyse a clinical patient cohort and improve the overall fusion gene diagnostic rate from 63% with conventional approaches to 76% with targeted RNAseq while demonstrating high concordance for patient samples with previous diagnoses. Finally, we show that targeted RNAseq offers additional advantages by simultaneously measuring gene expression levels and profiling the immune-receptor repertoire. We anticipate that targeted RNAseq will improve clinical fusion gene detection, and its increasing use will provide a deeper understanding of fusion gene biology. Rapid and accurate detection of fusion genes is important in cancer diagnostics. Here, the authors demonstrate that targeted RNA sequencing provides fast, sensitive and quantitative gene fusion detection and overcomes the limitations of approaches currently in clinical use.
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Affiliation(s)
- Erin E Heyer
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia
| | - Ira W Deveson
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia.,St. Vincent's Clinical School, UNSW Australia, Sydney, 2031, NSW, Australia
| | - Danson Wooi
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia.,St. Vincent's Clinical School, UNSW Australia, Sydney, 2031, NSW, Australia
| | - Christina I Selinger
- Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Sydney, 2050, NSW, Australia
| | - Ruth J Lyons
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia
| | - Vanessa M Hayes
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia.,St. Vincent's Clinical School, UNSW Australia, Sydney, 2031, NSW, Australia.,Faculty of Health Sciences, University of Limpopo, Turfloop Campus, Mankweng, 0727, South Africa.,School of Health Systems and Public Health, University of Pretoria, Pretoria, 0002, South Africa.,Central Clinical School, University of Sydney, Sydney, 2006, NSW, Australia
| | - Sandra A O'Toole
- St. Vincent's Clinical School, UNSW Australia, Sydney, 2031, NSW, Australia.,Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Sydney, 2050, NSW, Australia.,Central Clinical School, University of Sydney, Sydney, 2006, NSW, Australia.,The Kinghorn Cancer Centre and Cancer Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia.,Australian Clinical Labs, Sydney, 2010, NSW, Australia
| | - Mandy L Ballinger
- The Kinghorn Cancer Centre and Cancer Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia
| | - Devinder Gill
- Department of Haematology, Princess Alexandra Hospital, Brisbane, 4102, QLD, Australia
| | - David M Thomas
- The Kinghorn Cancer Centre and Cancer Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia
| | - Tim R Mercer
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia. .,St. Vincent's Clinical School, UNSW Australia, Sydney, 2031, NSW, Australia. .,Altius Institute for Biomedical Sciences, Seattle, 98121, WA, USA.
| | - James Blackburn
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia. .,St. Vincent's Clinical School, UNSW Australia, Sydney, 2031, NSW, Australia.
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High Expression of ANXA2 Pseudogene ANXA2P2 Promotes an Aggressive Phenotype in Hepatocellular Carcinoma. DISEASE MARKERS 2019; 2019:9267046. [PMID: 30881525 PMCID: PMC6387700 DOI: 10.1155/2019/9267046] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 11/09/2018] [Accepted: 11/19/2018] [Indexed: 12/12/2022]
Abstract
Objective Accumulating evidence suggests that pseudogenes play potential roles in the regulation of their cognate wild-type genes, oncogenes, and tumor suppressor genes. ANXA2P2 (annexin A2 pseudogene 2) is one of three pseudogenes of annexin A2 that have recently been shown to be aberrantly transcribed in hepatocellular carcinoma (HCC) cells. However, its clinical meaning and biological function in HCC have remained unclear. Therefore, the present study was aimed at exploring the prognostic value of a high expression of ANXA2P2 in HCC tissue and at identifying whether it can affect the efficacy of targeted drugs (sorafenib, regorafenib, and lenvatinib). Methods We obtained ANXA2P2 mRNA expression levels from The Cancer Genome Atlas (TCGA) RNA sequence database. The expression levels of ANXA2P2 in 49 pairs of intratumoral and peritumoral liver tissues were examined by RT-PCR. Wound healing and transwell assays were performed to confirm the tumor-promoting properties of ANXA2P2 in HCC cells. CCK8 assay was conducted to identify whether ANXA2P2 can affect the growth of HCC cells when administered with targeted drugs (sorafenib, regorafenib, and lenvatinib). Results The expression of ANXA2P2 in HCC tissues was significantly higher than that in adjacent cancerous tissues from TCGA database and validation group. Additionally, patients with high ANXA2P2 expression in HCC tissue had a shorter overall survival, whereas no statistically significant correlation was found between ANXA2P2 expression and disease-free survival (p = 0.08) as well as other clinical parameters, such as age, gender, histological grade, T classification, stage, albumin level, alpha-fetoprotein, and vascular invasion (p = 0.7323, 0.8807, 0.5762, 0.8515, 0.7113, 0.242, 1.0000, and 0.7685, respectively). Furthermore, in vitro experiments showed that knockdown of ANXA2P2 inhibited migration and invasion of HCC cells but did not have an influence on the HCC cell proliferation when treated with targeted drugs (sorafenib, regorafenib, and lenvatinib). Conclusion Our study confirmed elevated ANXA2P2 expression levels in HCC tissue compared with adjacent noncancerous tissue and a worse prognosis of patients with high ANXA2P2 levels in the HCC tissue. The newly found properties of promoting migration and invasion of ANXA2P2 in HCC help to explain this phenomenon. ANXA2P2 could be a novel and suitable predicative biomarker for the risk assessment of recurrence or metastasis of HCC patients but may not be effective to predict the efficacy of targeted drugs.
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Vo JN, Cieslik M, Zhang Y, Shukla S, Xiao L, Zhang Y, Wu YM, Dhanasekaran SM, Engelke CG, Cao X, Robinson DR, Nesvizhskii AI, Chinnaiyan AM. The Landscape of Circular RNA in Cancer. Cell 2019; 176:869-881.e13. [PMID: 30735636 PMCID: PMC6601354 DOI: 10.1016/j.cell.2018.12.021] [Citation(s) in RCA: 1052] [Impact Index Per Article: 210.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 10/05/2018] [Accepted: 12/12/2018] [Indexed: 12/17/2022]
Abstract
Circular RNAs (circRNAs) are an intriguing class of RNA due to their covalently closed structure, high stability, and implicated roles in gene regulation. Here, we used an exome capture RNA sequencing protocol to detect and characterize circRNAs across >2,000 cancer samples. When compared against Ribo-Zero and RNase R, capture sequencing significantly enhanced the enrichment of circRNAs and preserved accurate circular-to-linear ratios. Using capture sequencing, we built the most comprehensive catalog of circRNA species to date: MiOncoCirc, the first database to be composed primarily of circRNAs directly detected in tumor tissues. Using MiOncoCirc, we identified candidate circRNAs to serve as biomarkers for prostate cancer and were able to detect circRNAs in urine. We further detected a novel class of circular transcripts, termed read-through circRNAs, that involved exons originating from different genes. MiOncoCirc will serve as a valuable resource for the development of circRNAs as diagnostic or therapeutic targets across cancer types.
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Affiliation(s)
- Josh N Vo
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marcin Cieslik
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yajia Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sudhanshu Shukla
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, 580011, India
| | - Lanbo Xiao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yuping Zhang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yi-Mi Wu
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Saravana M Dhanasekaran
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Carl G Engelke
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dan R Robinson
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alexey I Nesvizhskii
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Arul M Chinnaiyan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan, Ann Arbor, MI 48109, USA.
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Rao MS, Van Vleet TR, Ciurlionis R, Buck WR, Mittelstadt SW, Blomme EAG, Liguori MJ. Comparison of RNA-Seq and Microarray Gene Expression Platforms for the Toxicogenomic Evaluation of Liver From Short-Term Rat Toxicity Studies. Front Genet 2019; 9:636. [PMID: 30723492 PMCID: PMC6349826 DOI: 10.3389/fgene.2018.00636] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 11/27/2018] [Indexed: 12/12/2022] Open
Abstract
Gene expression profiling is a useful tool to predict and interrogate mechanisms of toxicity. RNA-Seq technology has emerged as an attractive alternative to traditional microarray platforms for conducting transcriptional profiling. The objective of this work was to compare both transcriptomic platforms to determine whether RNA-Seq offered significant advantages over microarrays for toxicogenomic studies. RNA samples from the livers of rats treated for 5 days with five tool hepatotoxicants (α-naphthylisothiocyanate/ANIT, carbon tetrachloride/CCl4, methylenedianiline/MDA, acetaminophen/APAP, and diclofenac/DCLF) were analyzed with both gene expression platforms (RNA-Seq and microarray). Data were compared to determine any potential added scientific (i.e., better biological or toxicological insight) value offered by RNA-Seq compared to microarrays. RNA-Seq identified more differentially expressed protein-coding genes and provided a wider quantitative range of expression level changes when compared to microarrays. Both platforms identified a larger number of differentially expressed genes (DEGs) in livers of rats treated with ANIT, MDA, and CCl4 compared to APAP and DCLF, in agreement with the severity of histopathological findings. Approximately 78% of DEGs identified with microarrays overlapped with RNA-Seq data, with a Spearman’s correlation of 0.7 to 0.83. Consistent with the mechanisms of toxicity of ANIT, APAP, MDA and CCl4, both platforms identified dysregulation of liver relevant pathways such as Nrf2, cholesterol biosynthesis, eiF2, hepatic cholestasis, glutathione and LPS/IL-1 mediated RXR inhibition. RNA-Seq data showed additional DEGs that not only significantly enriched these pathways, but also suggested modulation of additional liver relevant pathways. In addition, RNA-Seq enabled the identification of non-coding DEGs that offer a potential for improved mechanistic clarity. Overall, these results indicate that RNA-Seq is an acceptable alternative platform to microarrays for rat toxicogenomic studies with several advantages. Because of its wider dynamic range as well as its ability to identify a larger number of DEGs, RNA-Seq may generate more insight into mechanisms of toxicity. However, more extensive reference data will be necessary to fully leverage these additional RNA-Seq data, especially for non-coding sequences.
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Affiliation(s)
- Mohan S Rao
- Investigative Toxicology and Pathology, Global Preclinical Safety, AbbVie, North Chicago, IL, United States
| | - Terry R Van Vleet
- Investigative Toxicology and Pathology, Global Preclinical Safety, AbbVie, North Chicago, IL, United States
| | - Rita Ciurlionis
- Investigative Toxicology and Pathology, Global Preclinical Safety, AbbVie, North Chicago, IL, United States
| | - Wayne R Buck
- Investigative Toxicology and Pathology, Global Preclinical Safety, AbbVie, North Chicago, IL, United States
| | - Scott W Mittelstadt
- Investigative Toxicology and Pathology, Global Preclinical Safety, AbbVie, North Chicago, IL, United States
| | - Eric A G Blomme
- Investigative Toxicology and Pathology, Global Preclinical Safety, AbbVie, North Chicago, IL, United States
| | - Michael J Liguori
- Investigative Toxicology and Pathology, Global Preclinical Safety, AbbVie, North Chicago, IL, United States
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81
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Estrogen affects the negative feedback loop of PTENP1-miR200c to inhibit PTEN expression in the development of endometrioid endometrial carcinoma. Cell Death Dis 2018; 10:4. [PMID: 30584245 PMCID: PMC6315040 DOI: 10.1038/s41419-018-1207-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 10/10/2018] [Accepted: 11/05/2018] [Indexed: 01/15/2023]
Abstract
Endometrial carcinoma is one of the most common malignancies in the female reproductive system. It is well-known that estrogen plays an important role in the pathogenesis of endometrioid endometrial carcinoma (EEC), and induces the cancer suppressor gene PTEN deletion. However, how estrogen affects PTEN expression remains unknown. In the present study, we found in 40 EEC specimens, miR-200c level was higher in most cancer areas than that in the adjacent normal endometrium, while PTEN and PTENP1 were lower. Moreover, the expression of PTEN/PTENP1 and miR-200c also showed a converse relationship in EEC cell lines. In addition, we demonstrated that miR-200c bound directly to PTEN and PTENP1, and PTENP1 could reverse miR-200c inhibition function to PTEN using a dual-luciferase reporter and RNA binding protein immunoprecipitation (RIP) assays. Next, 17β-estradiol (E2) treatment could improve miR-200c and drop the PTEN level, which caused a consequential increase of the phospho-PI3K-AKT pathway genes. When we stably knocked down estrogen receptor α (ERα) expression in the EEC cell line, the effects of E2 on miR-200c and PTEN declined. In addition, it was demonstrated that E2 might modulate cell proliferation, migration and invasion relying on the expression of miR-200c. Taken together, it can be concluded that estrogen improves the miR-200c level by combining with ER, PTENP1 and PTEN could be inhibited by miR-200c, and then activate the PI3K-AKT pathway. This work provided a new mechanism of EEC development and a new potential therapeutic target.
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82
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Kovalenko TF, Patrushev LI. Pseudogenes as Functionally Significant Elements of the Genome. BIOCHEMISTRY (MOSCOW) 2018; 83:1332-1349. [PMID: 30482145 DOI: 10.1134/s0006297918110044] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Pseudogene is a gene copy that has lost its original function. For a long time, pseudogenes have been considered as "junk DNA" that inevitably arises as a result of ongoing evolutionary process. However, experimental data obtained during recent years indicate this understanding of the nature of pseudogenes is not entirely correct, and many pseudogenes perform important genetic functions. In the review, we have addressed classification of pseudogenes, methods of their detection in the genome, and the problem of their evolutionary conservatism and prevalence among species belonging to different taxonomic groups in the light of modern data. The mechanisms of gene expression regulation by pseudogenes and the role of pseudogenes in pathogenesis of various human diseases are discussed.
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Affiliation(s)
- T F Kovalenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - L I Patrushev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
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83
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Abdollahzadeh R, Daraei A, Mansoori Y, Sepahvand M, Amoli MM, Tavakkoly-Bazzaz J. Competing endogenous RNA (ceRNA) cross talk and language in ceRNA regulatory networks: A new look at hallmarks of breast cancer. J Cell Physiol 2018; 234:10080-10100. [PMID: 30537129 DOI: 10.1002/jcp.27941] [Citation(s) in RCA: 194] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 11/16/2018] [Indexed: 02/06/2023]
Abstract
Breast cancer (BC) is the most frequently occurring malignancy in women worldwide. Despite the substantial advancement in understanding the molecular mechanisms and management of BC, it remains the leading cause of cancer death in women. One of the main reasons for this obstacle is that we have not been able to find the Achilles heel for the BC as a highly heterogeneous disease. Accumulating evidence has revealed that noncoding RNAs (ncRNAs), play key roles in the development of BC; however, the involving of complex regulatory interactions between the different varieties of ncRNAs in the development of this cancer has been poorly understood. In the recent years, the newly discovered mechanism in the RNA world is "competing endogenous RNA (ceRNA)" which proposes regulatory dialogues between different RNAs, including long ncRNAs (lncRNAs), microRNAs (miRNAs), transcribed pseudogenes, and circular RNAs (circRNAs). In the latest BC research, various studies have revealed that dysregulation of several ceRNA networks (ceRNETs) between these ncRNAs has fundamental roles in establishing the hallmarks of BC development. And it is thought that such a discovery could open a new window for a better understanding of the hidden aspects of breast tumors. Besides, it probably can provide new biomarkers and potential efficient therapeutic targets for BC. This review will discuss the existing body of knowledge regarding the key functions of ceRNETs and then highlights the emerging roles of some recently discovered ceRNETs in several hallmarks of BC. Moreover, we propose for the first time the "ceRnome" as a new term in the present article for RNA research.
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Affiliation(s)
- Rasoul Abdollahzadeh
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Abdolreza Daraei
- Department of Genetics, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Yaser Mansoori
- Department of Medical Genetics, Fasa University of Medical Sciences, Fasa, Iran
| | - Masoumeh Sepahvand
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahsa M Amoli
- Endocrinology and Metabolism Molecular Cellular Sciences Institute, Metabolic Disorders Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Javad Tavakkoly-Bazzaz
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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84
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Lee MH, Siddoway B, Kaeser GE, Segota I, Rivera R, Romanow WJ, Liu CS, Park C, Kennedy G, Long T, Chun J. Somatic APP gene recombination in Alzheimer's disease and normal neurons. Nature 2018; 563:639-645. [PMID: 30464338 DOI: 10.1038/s41586-018-0718-6] [Citation(s) in RCA: 139] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 10/09/2018] [Indexed: 11/09/2022]
Abstract
The diversity and complexity of the human brain are widely assumed to be encoded within a constant genome. Somatic gene recombination, which changes germline DNA sequences to increase molecular diversity, could theoretically alter this code but has not been documented in the brain, to our knowledge. Here we describe recombination of the Alzheimer's disease-related gene APP, which encodes amyloid precursor protein, in human neurons, occurring mosaically as thousands of variant 'genomic cDNAs' (gencDNAs). gencDNAs lacked introns and ranged from full-length cDNA copies of expressed, brain-specific RNA splice variants to myriad smaller forms that contained intra-exonic junctions, insertions, deletions, and/or single nucleotide variations. DNA in situ hybridization identified gencDNAs within single neurons that were distinct from wild-type loci and absent from non-neuronal cells. Mechanistic studies supported neuronal 'retro-insertion' of RNA to produce gencDNAs; this process involved transcription, DNA breaks, reverse transcriptase activity, and age. Neurons from individuals with sporadic Alzheimer's disease showed increased gencDNA diversity, including eleven mutations known to be associated with familial Alzheimer's disease that were absent from healthy neurons. Neuronal gene recombination may allow 'recording' of neural activity for selective 'playback' of preferred gene variants whose expression bypasses splicing; this has implications for cellular diversity, learning and memory, plasticity, and diseases of the human brain.
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Affiliation(s)
- Ming-Hsiang Lee
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Benjamin Siddoway
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Gwendolyn E Kaeser
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.,Biomedical Sciences Program, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Igor Segota
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Richard Rivera
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - William J Romanow
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Christine S Liu
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.,Biomedical Sciences Program, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Chris Park
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.,Biomedical Sciences Program, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Grace Kennedy
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Tao Long
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Jerold Chun
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
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85
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Xiang Y, Ye Y, Zhang Z, Han L. Maximizing the Utility of Cancer Transcriptomic Data. Trends Cancer 2018; 4:823-837. [PMID: 30470304 DOI: 10.1016/j.trecan.2018.09.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 09/23/2018] [Accepted: 09/24/2018] [Indexed: 12/13/2022]
Abstract
Transcriptomic profiling has been applied to large numbers of cancer samples, by large-scale consortia, including The Cancer Genome Atlas, International Cancer Genome Consortium, and Cancer Cell Line Encyclopedia. Advances in mining cancer transcriptomic data enable us to understand the endless complexity of the cancer transcriptome and thereby to discover new biomarkers and therapeutic targets. In this paper, we review computational resources for deep mining of transcriptomic data to identify, quantify, and determine the functional effects and clinical utility of transcriptomic events, including noncoding RNAs, post-transcriptional regulation, exogenous RNAs, and transcribed genetic variants. These approaches can be applied to other complex diseases, thereby greatly leveraging the impact of this work.
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Affiliation(s)
- Yu Xiang
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; These authors contributed equally
| | - Youqiong Ye
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; These authors contributed equally
| | - Zhao Zhang
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Leng Han
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Center for Precision Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
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86
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Liu F, Gong R, He B, Chen F, Hu Z. TUSC2P suppresses the tumor function of esophageal squamous cell carcinoma by regulating TUSC2 expression and correlates with disease prognosis. BMC Cancer 2018; 18:894. [PMID: 30219035 PMCID: PMC6139140 DOI: 10.1186/s12885-018-4804-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 09/06/2018] [Indexed: 12/13/2022] Open
Abstract
Background Pseudogenes are RNA transcripts with high homology with its parent protein-coding genes. Although pseudogenes lost the ability to produce protein, it still exert import biological function, and play important role in the pathogenesis of a wide varity of tumors; However, the role of pseudogenes in esophageal squamous cell carcinoma (ESCC) is poorly understood. Methods TUSC2P function in ESCC were explored using both in vitro and in vivo experiments cell proliferation, invasion and apoptosis assay was performed to evaluated the effect of TUSC2P on the tumor biology of ESCC. Expression of relative genes was assessed by quantitative real-time PCR (qRT-PCR) and western blotting in EC109 and TE-1 cell, as well as ESCC patients. 3’UTR luciferase assay was used to confirm the direct binding of miRNAs with TUSC2 and TUSC2P 3’UTR. Relation betweenTUSC2P, TUSC2 and ESCC prognosis was predicted by survival analysis (n = 56). Results Pseudogene TUSC2P was down regulated in ESCC tissues compared with paired normal adjacent tissues, and the expression of TUSC2P was significantly correlated with survivalof ESCC patients. Over expression of TUSC2P in EC109 and TE-1 cells resulted in altered expression of TUSC2, thus inhibited proliferation, invasion and promoted apoptosis. Dual luciferase assay demonstrated that TUSC2P 3’UTR decoyed miR-17-5p, miR-520a-3p, miR-608, miR-661 from binding to TUSC2. Conclusions TUSC2P can suppresses the tumor function of esophageal squamous cell carcinoma by regulating TUSC2 expression and may also serve as a prognostic factor for ESCC patients. Electronic supplementary material The online version of this article (10.1186/s12885-018-4804-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fengqiong Liu
- Fujian Provincial Key Laboratory of Environment factors and Cancer, School of Public Health, Fujian Medical University, 1 Xuefubei Road, Fuzhou, Fujian, 350108, People's Republic of China.,Department of Epidemiology and Health Statistic, School of Public Health, Fujian Medical University, 1 Xuefubei Road, Fuzhou, Fujian, China
| | - Ruijie Gong
- Fujian Provincial Key Laboratory of Environment factors and Cancer, School of Public Health, Fujian Medical University, 1 Xuefubei Road, Fuzhou, Fujian, 350108, People's Republic of China
| | - Baochang He
- Fujian Provincial Key Laboratory of Environment factors and Cancer, School of Public Health, Fujian Medical University, 1 Xuefubei Road, Fuzhou, Fujian, 350108, People's Republic of China.,Department of Epidemiology and Health Statistic, School of Public Health, Fujian Medical University, 1 Xuefubei Road, Fuzhou, Fujian, China
| | - Fa Chen
- Fujian Provincial Key Laboratory of Environment factors and Cancer, School of Public Health, Fujian Medical University, 1 Xuefubei Road, Fuzhou, Fujian, 350108, People's Republic of China.,Department of Epidemiology and Health Statistic, School of Public Health, Fujian Medical University, 1 Xuefubei Road, Fuzhou, Fujian, China
| | - Zhijian Hu
- Fujian Provincial Key Laboratory of Environment factors and Cancer, School of Public Health, Fujian Medical University, 1 Xuefubei Road, Fuzhou, Fujian, 350108, People's Republic of China. .,Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, 1 Xuefubei Road, Fuzhou, Fujian, China. .,Department of Epidemiology and Health Statistic, School of Public Health, Fujian Medical University, 1 Xuefubei Road, Fuzhou, Fujian, China.
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87
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Single nucleotide polymorphisms in the MYLKP1 pseudogene are associated with increased colon cancer risk in African Americans. PLoS One 2018; 13:e0200916. [PMID: 30161129 PMCID: PMC6116948 DOI: 10.1371/journal.pone.0200916] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/04/2018] [Indexed: 12/18/2022] Open
Abstract
INTRODUCTION Pseudogenes are paralogues of functional genes historically viewed as defunct due to either the lack of regulatory elements or the presence of frameshift mutations. Recent evidence, however, suggests that pseudogenes may regulate gene expression, although the functional role of pseudogenes remains largely unknown. We previously reported that MYLKP1, the pseudogene of MYLK that encodes myosin light chain kinase (MLCK), is highly expressed in lung and colon cancer cell lines and tissues but not in normal lung or colon. The MYLKP1 promoter is minimally active in normal bronchial epithelial cells but highly active in lung adenocarcinoma cells. In this study, we further validate MYLKP1 as an oncogene via elucidation of the functional role of MYLKP1 genetic variants in colon cancer risk. METHODS Proliferation and migration assays were performed in MYLKP1-transfected colon and lung cancer cell lines (H441, A549) and commercially-available normal lung and colon cells. Fourteen MYLKP1 SNPs (MAFs >0.01) residing within the 4 kb MYLKP1 promoter region, the core 1.4 kb of MYLKP1 gene, and a 4 kb enhancer region were selected and genotyped in a colorectal cancer cohort. MYLKP1 SNP influences on activity of MYLKP1 promoter (2kb) was assessed by dual luciferase reporter assay. RESULTS Cancer cell lines, H441 and A549, exhibited increased MYLKP1 expression, increased MYLKP1 luciferase promoter activity, increased proliferation and migration. Genotyping studies identified two MYLKP1 SNPs (rs12490683; rs12497343) that significantly increase risk of colon cancer in African Americans compared to African American controls. Rs12490683 and rs12497343 further increase MYLKP1 promoter activity compared to the wild type MYLKP1 promoter. CONCLUSION MYLKP1 is a cancer-promoting pseudogene whose genetic variants differentially enhance cancer risk in African American populations.
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88
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Xu S, Zhou L, Ponnusamy M, Zhang L, Dong Y, Zhang Y, Wang Q, Liu J, Wang K. A comprehensive review of circRNA: from purification and identification to disease marker potential. PeerJ 2018; 6:e5503. [PMID: 30155370 PMCID: PMC6110255 DOI: 10.7717/peerj.5503] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/01/2018] [Indexed: 12/14/2022] Open
Abstract
Circular RNA (circRNA) is an endogenous noncoding RNA with a covalently closed cyclic structure. Based on their components, circRNAs are divided into exonic circRNAs, intronic circRNAs, and exon-intron circRNAs. CircRNAs have well-conserved sequences and often have high stability due to their resistance to exonucleases. Depending on their sequence, circRNAs are involved in different biological functions, including microRNA sponge activity, modulation of alternative splicing or transcription, interaction with RNA-binding proteins, and rolling translation, and are a derivative of pseudogenes. CircRNAs are involved in the development of a variety of pathological conditions, such as cardiovascular diseases, diabetes, neurological diseases, and cancer. Emerging evidence has shown that circRNAs are likely to be new potential clinical diagnostic markers or treatments for many diseases. Here we describe circRNA research methods and biological functions, and discuss the potential relationship between circRNAs and disease progression.
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Affiliation(s)
- Sheng Xu
- Center for Developmental Cardiology, Institute of Translational Medicine and School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - LuYu Zhou
- Center for Developmental Cardiology, Institute of Translational Medicine and School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Murugavel Ponnusamy
- Center for Developmental Cardiology, Institute of Translational Medicine and School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - LiXia Zhang
- Department of Inspection, The Medical Faculty of Qingdao University, Qingdao, Shandong, China
| | - YanHan Dong
- Center for Developmental Cardiology, Institute of Translational Medicine and School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - YanHui Zhang
- Center for Developmental Cardiology, Institute of Translational Medicine and School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Qi Wang
- Center for Developmental Cardiology, Institute of Translational Medicine and School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Jing Liu
- Center for Developmental Cardiology, Institute of Translational Medicine and School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Kun Wang
- Center for Developmental Cardiology, Institute of Translational Medicine and School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
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89
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Emadi-Baygi M, Sedighi R, Nourbakhsh N, Nikpour P. Pseudogenes in gastric cancer pathogenesis: a review article. Brief Funct Genomics 2018; 16:348-360. [PMID: 28459995 DOI: 10.1093/bfgp/elx004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Cancer burden rises globally at an alarming pace. According to GLOBOCAN 2012, gastric cancer (GC) is regarded as the fifth most common malignancy in the world. Being twice as high in men as in women, GC is the third leading cause of cancer mortality in both sexes globally. Being labeled as 'junk DNA', pseudogenes were considered as nonfunctional 'trash', which contribute nothing to survival of the organism; therefore, a number of strategies have been developed to circumvent their accidental detection. Recent progresses have confirmed that pseudogenes can have broad and multifaceted spectrum of activities in human cancers in general and GC in particular. Furthermore, the mentioned functions are parental gene-dependent and/or -independent. Therefore, pseudogenes can be regarded as the emerging class of elaborate modulators of gene expression involved in pathogenesis of human cancers including gastric adenocarcinoma.
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90
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Booth KT, Azaiez H, Jahan I, Smith RJH, Fritzsch B. Intracellular Regulome Variability Along the Organ of Corti: Evidence, Approaches, Challenges, and Perspective. Front Genet 2018; 9:156. [PMID: 29868110 PMCID: PMC5951964 DOI: 10.3389/fgene.2018.00156] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/13/2018] [Indexed: 12/13/2022] Open
Abstract
The mammalian hearing organ is a regular array of two types of hair cells (HCs) surrounded by six types of supporting cells. Along the tonotopic axis, this conserved radial array of cell types shows longitudinal variations to enhance the tuning properties of basilar membrane. We present the current evidence supporting the hypothesis that quantitative local variations in gene expression profiles are responsible for local cell responses to global gene manipulations. With the advent of next generation sequencing and the unprecedented array of technologies offering high throughput analyses at the single cell level, transcriptomics will become a common tool to enhance our understanding of the inner ear. We provide an overview of the approaches and landmark studies undertaken to date to analyze single cell variations in the organ of Corti and discuss the current limitations. We next provide an overview of the complexity of known regulatory mechanisms in the inner ear. These mechanisms are tightly regulated temporally and spatially at the transcription, RNA-splicing, mRNA-regulation, and translation levels. Understanding the intricacies of regulatory mechanisms at play in the inner ear will require the use of complementary approaches, and most probably, a combinatorial strategy coupling transcriptomics, proteomics, and epigenomics technologies. We highlight how these data, in conjunction with recent insights into molecular cell transformation, can advance attempts to restore lost hair cells.
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Affiliation(s)
- Kevin T Booth
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa, Iowa City, IA, United States.,Interdisciplinary Graduate Program in Molecular Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Hela Azaiez
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa, Iowa City, IA, United States
| | - Israt Jahan
- Department of Biology, University of Iowa, Iowa City, IA, United States
| | - Richard J H Smith
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa, Iowa City, IA, United States
| | - Bernd Fritzsch
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa, Iowa City, IA, United States.,Department of Biology, University of Iowa, Iowa City, IA, United States
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91
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Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow. Nat Commun 2018; 9:903. [PMID: 29500430 PMCID: PMC5834625 DOI: 10.1038/s41467-018-03311-y] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 02/02/2018] [Indexed: 01/23/2023] Open
Abstract
Proteogenomics enable the discovery of novel peptides (from unannotated genomic protein-coding loci) and single amino acid variant peptides (derived from single-nucleotide polymorphisms and mutations). Increasing the reliability of these identifications is crucial to ensure their usefulness for genome annotation and potential application as neoantigens in cancer immunotherapy. We here present integrated proteogenomics analysis workflow (IPAW), which combines peptide discovery, curation, and validation. IPAW includes the SpectrumAI tool for automated inspection of MS/MS spectra, eliminating false identifications of single-residue substitution peptides. We employ IPAW to analyze two proteomics data sets acquired from A431 cells and five normal human tissues using extended (pH range, 3–10) high-resolution isoelectric focusing (HiRIEF) pre-fractionation and TMT-based peptide quantitation. The IPAW results provide evidence for the translation of pseudogenes, lncRNAs, short ORFs, alternative ORFs, N-terminal extensions, and intronic sequences. Moreover, our quantitative analysis indicates that protein production from certain pseudogenes and lncRNAs is tissue specific. Proteogenomics enables the discovery of protein coding regions and disease-relevant mutations but their verification remains challenging. Here, the authors combine peptide discovery, curation and validation in an integrated proteogenomics workflow, robustly identifying unknown coding regions and mutations.
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92
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Wei CC, Nie FQ, Jiang LL, Chen QN, Chen ZY, Chen X, Pan X, Liu ZL, Lu BB, Wang ZX. The pseudogene DUXAP10 promotes an aggressive phenotype through binding with LSD1 and repressing LATS2 and RRAD in non small cell lung cancer. Oncotarget 2018; 8:5233-5246. [PMID: 28029651 PMCID: PMC5354904 DOI: 10.18632/oncotarget.14125] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 11/21/2016] [Indexed: 01/04/2023] Open
Abstract
Pseudogenes have been considered as non-functional transcriptional relics of human genomic for long time. However, recent studies revealed that they play a plethora of roles in diverse physiological and pathological processes, especially in cancer, and many pseudogenes are transcribed into long noncoding RNAs and emerging as a novel class of lncRNAs. However, the biological roles and underlying mechanism of pseudogenes in the pathogenesis of non small cell lung cancer are still incompletely elucidated. This study identifies a putative oncogenic pseudogene DUXAP10 in NSCLC, which is located in 14q11.2 and 2398 nt in length. Firstly, we found that DUXAP10 was significantly up-regulated in 93 human NSCLC tissues and cell lines, and increased DUXAP10 was associated with patients poorer prognosis and short survival time. Furthermore, the loss and gain of functional studies including growth curves, migration, invasion assays and in vivo studies verify the oncogenic roles of DUXAP10 in NSCLC. Finally, the mechanistic experiments indicate that DUXAP10 could interact with Histone demethylase Lysine specific demethylase1 (LSD1) and repress tumor suppressors Large tumor suppressor 2 (LATS2) and Ras-related associated with diabetes (RRAD) transcription in NSCLC cells. Taken together, these findings demonstrate DUXAP10 exerts the oncogenic roles through binding with LSD1 and epigenetic silencing LATS2 and RRAD expression. Our investigation reveals the novel roles of pseudogene in NSCLC, which may serve as new target for NSCLC diagnosis and therapy.
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Affiliation(s)
- Chen-Chen Wei
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Feng-Qi Nie
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Li-Li Jiang
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, People's Republic of China.,Department of Oncology, Haimen People's Hospital, Haimen, People's Republic of China
| | - Qin-Nan Chen
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Zhen-Yao Chen
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Xin Chen
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Xuan Pan
- Department of Medical Oncology, Nanjing Medical University Affiliated Cancer Hospital of Jiangsu Province, Cancer Institution of Jiangsu Province, Nanjing, People's Republic of China
| | - Zhi-Li Liu
- Department of Oncology, The Affiliated Jiangyin Hospital, School of Medicine, Southeast University, Jiangyin, People's Republic of China
| | - Bin-Bin Lu
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Zhao-Xia Wang
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, People's Republic of China
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93
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Toffalorio F, Santarpia M, Radice D, Jaramillo CA, Spitaleri G, Manzotti M, Catania C, Jordheim LP, Pelosi G, Peters GJ, Tibaldi C, Funel N, Spaggiari L, de Braud F, De Pas T, Giovannetti E. 5'-nucleotidase cN-II emerges as a new predictive biomarker of response to gemcitabine/platinum combination chemotherapy in non-small cell lung cancer. Oncotarget 2018; 9:16437-16450. [PMID: 29662657 PMCID: PMC5893252 DOI: 10.18632/oncotarget.24505] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 02/02/2018] [Indexed: 02/04/2023] Open
Abstract
A number of pharmacogenetic studies have been carried out in non-small-cell lung cancer (NSCLC) to identify and characterize genes involved in chemotherapy activity. However, the results obtained so far are controversial and no reliable biomarker is currently used to predict clinical benefit from platinum-based chemotherapy, which represents the cornerstone of treatment of advanced NSCLC. This study investigated the expression levels of ERCC1 and of six genes (RRM1, RRM2, hENT1, dCK, cN-II and CDA) involved in gemcitabine metabolism in locally/advanced NSCLC patients treated with gemcitabine/platinum combination. Gene expression was assessed by quantitative-PCR in laser-microdissected specimens and correlated with tumor response. Frequency distribution of responses above and below the median expression level of biomarkers was compared using a two-sided Fisher’s test. 5′-nucleotidase (cN-II) was the only gene differently expressed (p = 0.016) in the responders (complete/partial-response) compared to non-responders (stable/progressive disease). In the multivariate analysis, overexpression of this catabolic enzyme of gemcitabine remained a significant negative predictive factor. Patients with low cN-II had a modest trend toward increased survival, while both survival and progression-free survival were significantly longer in a more homogenous validation cohort of 40 advanced NSCLC (8.0 vs. 5.1 months, p = 0.026). Moreover, in vitro studies showed that silencing or pharmacological inhibition of cN-II increased the cytotoxicity of gemcitabine. This is the first study demonstrating the role of cN-II as a predictor of response to gemcitabine/platinum combinations in NSCLC. Its validation in prospective studies may improve clinical outcome of selected patients.
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Affiliation(s)
- Francesca Toffalorio
- Medical Oncology Unit of Respiratory Tract and Sarcomas, New Drugs Development Division, European Institute of Oncology, Milan, Italy.,Medical Affairs, Roche Spa, Monza, Italy
| | - Mariacarmela Santarpia
- Medical Oncology Unit of Respiratory Tract and Sarcomas, New Drugs Development Division, European Institute of Oncology, Milan, Italy.,Medical Oncology Unit, Department of Human Pathology, University of Messina, Messina, Italy
| | - Davide Radice
- Epidemiology and Biostatistics Division, European Institute of Oncology, Milan, Italy
| | | | - Gianluca Spitaleri
- Medical Oncology Unit of Respiratory Tract and Sarcomas, New Drugs Development Division, European Institute of Oncology, Milan, Italy.,Thoracic Oncology Division, European Institute of Oncology, Milan, Italy
| | - Michela Manzotti
- Division of Pathology and Laboratory Medicine, European Institute of Oncology, Milan, Italy
| | - Chiara Catania
- Medical Oncology Unit of Respiratory Tract and Sarcomas, New Drugs Development Division, European Institute of Oncology, Milan, Italy.,Thoracic Oncology Division, European Institute of Oncology, Milan, Italy
| | - Lars Petter Jordheim
- Centre de Recherche en Cancérologie de Lyon, INSERM 1052/CNRS UMR 5286, Lyon, France
| | - Giuseppe Pelosi
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy.,Inter-Hospital Pathology Division, Science and Technology Park, IRCCS MultiMedica, Milan, Italy
| | - Godefridus J Peters
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Carmelo Tibaldi
- Division of Oncology, Department of Oncology, S. Luca Hospital, Lucca, Italy
| | - Niccola Funel
- CNR-Nano, Institute of Nanoscience and Nanotechnology, Pisa, Italy.,Cancer Pharmacology Laboratory, AIRC Start-Up Unit, University of Pisa, Pisa, Italy
| | - Lorenzo Spaggiari
- Thoracic Surgery Division, European Institute of Oncology, Milan, Italy
| | - Filippo de Braud
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy.,Inter-Hospital Pathology Division, Science and Technology Park, IRCCS MultiMedica, Milan, Italy
| | - Tommaso De Pas
- Medical Oncology Unit of Respiratory Tract and Sarcomas, New Drugs Development Division, European Institute of Oncology, Milan, Italy
| | - Elisa Giovannetti
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands.,CNR-Nano, Institute of Nanoscience and Nanotechnology, Pisa, Italy.,Cancer Pharmacology Laboratory, AIRC Start-Up Unit, University of Pisa, Pisa, Italy
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94
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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: 33] [Impact Index Per Article: 5.5] [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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95
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Abstract
Our understanding of cancer pathways has been changed by the determination of noncoding transcripts in the human genome in recent years. miRNAs and pseudogenes are key players of the noncoding transcripts from the genome, and alteration of their expression levels provides clues for significant biomarkers in pathogenesis of diseases. Especially, miRNAs and pseudogenes have both oncogenic and tumor-suppressive roles in each step of cancer tumorigenesis. In this current study, association between oncogenes and miRNAs-pseudogenes was reviewed and determined in human cancer by the CellMiner web-tool.
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Affiliation(s)
- Lütfi Tutar
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Ahi Evran University, Kırşehir, Turkey
| | - Aykut Özgür
- Division of Biochemistry, Department of Basic Sciences, Faculty of Pharmacy, Cumhuriyet University, 58140, Sivas, Turkey
| | - Yusuf Tutar
- Division of Biochemistry, Department of Basic Sciences, Faculty of Pharmacy, Cumhuriyet University, 58140, Sivas, Turkey.
- Department of Nutrition and Dietetics, Health Sciences Faculty, University of Health Sciences, Üsküdar, Istanbul, 34668, Turkey.
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96
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Manem VSK, Salgado R, Aftimos P, Sotiriou C, Haibe-Kains B. Network science in clinical trials: A patient-centered approach. Semin Cancer Biol 2017; 52:135-150. [PMID: 29278737 DOI: 10.1016/j.semcancer.2017.12.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/12/2017] [Accepted: 12/13/2017] [Indexed: 02/08/2023]
Abstract
There has been a paradigm shift in translational oncology with the advent of novel molecular diagnostic tools in the clinic. However, several challenges are associated with the integration of these sophisticated tools into clinical oncology and daily practice. High-throughput profiling at the DNA, RNA and protein levels (omics) generate a massive amount of data. The analysis and interpretation of these is non-trivial but will allow a more thorough understanding of cancer. Linear modelling of the data as it is often used today is likely to limit our understanding of cancer as a complex disease, and at times under-performs to capture a phenotype of interest. Network science and systems biology-based approaches, using machine learning and network science principles, that integrate multiple data sources, can uncover complex changes in a biological system. This approach will integrate a large number of potential biomarkers in preclinical studies to better inform therapeutic decisions and ultimately make substantial progress towards precision medicine. It will however require development of a new generation of clinical trials. Beyond discussing the challenges of high-throughput technologies, this review will develop a framework on how to implement a network science approach in new clinical trial designs in order to advance cancer care.
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Affiliation(s)
- Venkata S K Manem
- Bioinformatics and Computational Genomics Laboratory, Princess Margaret Cancer Center, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Roberto Salgado
- Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Brussels, Belgium; Department of Pathology, GZA Hospitals Antwerp, Belgium
| | - Philippe Aftimos
- Medical Oncology Clinic, Institut Jules Bordet - Université Libre de Bruxelles, Brussels, Belgium
| | - Christos Sotiriou
- Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Brussels, Belgium; Medical Oncology Clinic, Institut Jules Bordet - Université Libre de Bruxelles, Brussels, Belgium
| | - Benjamin Haibe-Kains
- Bioinformatics and Computational Genomics Laboratory, Princess Margaret Cancer Center, Toronto, ON, Canada; Department of Computer Science, University of Toronto, Toronto, ON, Canada; Ontario Institute of Cancer Research, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
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97
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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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98
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Capobianco E, Valdes C, Sarti S, Jiang Z, Poliseno L, Tsinoremas NF. Ensemble Modeling Approach Targeting Heterogeneous RNA-Seq data: Application to Melanoma Pseudogenes. Sci Rep 2017; 7:17344. [PMID: 29229974 PMCID: PMC5725464 DOI: 10.1038/s41598-017-17337-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 11/23/2017] [Indexed: 01/28/2023] Open
Abstract
We studied the transcriptome landscape of skin cutaneous melanoma (SKCM) using 103 primary tumor samples from TCGA, and measured the expression levels of both protein coding genes and non-coding RNAs (ncRNAs). In particular, we emphasized pseudogenes potentially relevant to this cancer. While cataloguing the profiles based on the known biotypes, all the employed RNA-Seq methods generated just a small consensus of significant biotypes. We thus designed an approach to reconcile the profiles from all methods following a simple strategy: we selected genes that were confirmed as differentially expressed by the ensemble predictions obtained in a regression model. The main advantages of this approach are: 1) Selection of a high-confidence gene set identifying relevant pathways; 2) Use of a regression model whose covariates embed all method-driven outcomes to predict an averaged profile; 3) Method-specific assessment of prediction power and significance. Furthermore, the approach can be generalized to any biological system for which noisy RNA-Seq profiles are computed. As our analyses concerned bio-annotations of both high-quality protein coding genes and ncRNAs, we considered the associations between pseudogenes and parental genes (targets). Among the candidate targets that were validated, we identified PINK1, which is studied in patients with Parkinson and cancer (especially melanoma).
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Affiliation(s)
- Enrico Capobianco
- Center for Computational Science, University of Miami, Miami, FL, USA.
| | - Camilo Valdes
- Center for Computational Science, University of Miami, Miami, FL, USA
| | | | - Zhijie Jiang
- Center for Computational Science, University of Miami, Miami, FL, USA
| | - Laura Poliseno
- Istituto Toscano Tumori Oncogenomics Unit, Institute of Clinical Physiology-National Research Council, Pisa, Italy
| | - Nicolas F Tsinoremas
- Center for Computational Science, University of Miami, Miami, FL, USA
- Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL, USA
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99
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Dhaygude K, Trontti K, Paviala J, Morandin C, Wheat C, Sundström L, Helanterä H. Transcriptome sequencing reveals high isoform diversity in the ant Formica exsecta. PeerJ 2017; 5:e3998. [PMID: 29177112 PMCID: PMC5701548 DOI: 10.7717/peerj.3998] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 10/17/2017] [Indexed: 12/21/2022] Open
Abstract
Transcriptome resources for social insects have the potential to provide new insight into polyphenism, i.e., how divergent phenotypes arise from the same genome. Here we present a transcriptome based on paired-end RNA sequencing data for the ant Formica exsecta (Formicidae, Hymenoptera). The RNA sequencing libraries were constructed from samples of several life stages of both sexes and female castes of queens and workers, in order to maximize representation of expressed genes. We first compare the performance of common assembly and scaffolding software (Trinity, Velvet-Oases, and SOAPdenovo-trans), in producing de novo assemblies. Second, we annotate the resulting expressed contigs to the currently published genomes of ants, and other insects, including the honeybee, to filter genes that have annotation evidence of being true genes. Our pipeline resulted in a final assembly of altogether 39,262 mRNA transcripts, with an average coverage of >300X, belonging to 17,496 unique genes with annotation in the related ant species. From these genes, 536 genes were unique to one caste or sex only, highlighting the importance of comprehensive sampling. Our final assembly also showed expression of several splice variants in 6,975 genes, and we show that accounting for splice variants affects the outcome of downstream analyses such as gene ontologies. Our transcriptome provides an outstanding resource for future genetic studies on F. exsecta and other ant species, and the presented transcriptome assembly can be adapted to any non-model species that has genomic resources available from a related taxon.
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Affiliation(s)
- Kishor Dhaygude
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Kalevi Trontti
- Department of Biosciences, Neurogenomics Laboratory, University of Helsinki, Helsinki, Finland
| | - Jenni Paviala
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Claire Morandin
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Christopher Wheat
- Department of Zoology Ecology, Stockholm University, Stockholm, Sweden
| | - Liselotte Sundström
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland
- Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
| | - Heikki Helanterä
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland
- Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
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Sanabria NM, Gulumian M. The presence of residual gold nanoparticles in samples interferes with the RT-qPCR assay used for gene expression profiling. J Nanobiotechnology 2017. [PMID: 29017502 DOI: 10.1186/s12951-017-0299-9.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND RT-qPCR is routinely used in expression profiling of toxicity pathway genes. However, genetic and molecular level studies used to determine, understand and clarify potential risks of engineered nanomaterials (ENMs) are still incomplete. Concerns regarding possible interference caused by intracellular ENMs during analyses have been raised. The aim of this study was to verify a qPCR procedure for gene expression assays, which can be used in toxicity and exposure assessments. RESULTS Amplification of ten reference genes was performed to test the expression stability. A preliminary study was performed on RNA from BEAS-2B cells that had been treated with AuNPs. Also, a reference total RNA standard from ten cell lines was spiked with various amounts of the same AuNP. This treatment mimics exposure assessment studies, where assay-interference may be caused by intracellular residual ENMs still being present in the biological samples (during and after isolation/purification procedures). Both types of RNA samples were reverse transcribed and then amplified by qPCR. The qPCR-related software and statistical programs used included BestKeeper, NormFinder, REST and qBase+. These results proved that using standard qPCR analysis and statistical programs should not be the only procedure applied to verify the assay for gene expression assessment related to ENMs. A comparison of SYBR Green to EVA Green was discussed, in addition to a comparison to the latest reports regarding the influence of ENM thermal conductivity, surface interactions with ENMs, effects of ENM size and charge, as well as, the limit of detection in a qPCR assay. CONCLUSIONS AuNPs have the potential to interfere with the assay mechanism of RT-qPCR, thus, assay verification is required for AuNP-related gene expression studies used to evaluate toxicity. It is recommended to use HSP90 and YWHAZ as reference genes, i.e. these were the most stable in our study, irrespective of the source of the RNA, or, the point at which the AuNPs interacted with the assay. This report describes steps that can be utilised to generate a suitable method for gene expression studies associated with toxicity testing of various ENMs. For example, RNA standards that have been spiked with known amounts of ENMs should be run in conjunction with the unknown samples, in order to verify any RT-qPCR assay and determine the degree of error.
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Affiliation(s)
| | - Mary Gulumian
- National Institute for Occupational Health, Johannesburg, South Africa. .,Haematology and Molecular Medicine Department, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa.
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