1
|
Mattos FMG, Dreyer N, Fong CL, Wen YHV, Jain D, De Vivo M, Huang YS, Mwihaki JK, Wang TY, Ho MJ, Tsai IJ, Wang J, Chan BKK, Machida RJ. Potential PCR amplification bias in identifying complex ecological patterns: Higher species compositional homogeneity revealed in smaller-size coral reef zooplankton by metatranscriptomics. Mol Ecol Resour 2024; 24:e13911. [PMID: 38063371 DOI: 10.1111/1755-0998.13911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 11/13/2023] [Accepted: 11/20/2023] [Indexed: 03/06/2024]
Abstract
PCR-based high-throughput sequencing has permitted comprehensive resolution analyses of zooplankton diversity dynamics. However, significant methodological issues still surround analyses of complex bulk community samples, not least as in prevailing PCR-based approaches. Marine drifting animals-zooplankton-play essential ecological roles in the pelagic ecosystem, transferring energy and elements to higher trophic levels, such as fishes, cetaceans and others. In the present study, we collected 48 size-fractionated zooplankton samples in the vicinity of a coral reef island with environmental gradients. To investigate the spatiotemporal dynamics of zooplankton diversity patterns and the effect of PCR amplification biases across these complex communities, we first took metatranscriptomics approach. Comprehensive computational analyses revealed a clear pattern of higher/lower homogeneity in smaller/larger zooplankton compositions across samples respectively. Our study thus suggests changes in the role of dispersal across the sizes. Next, we applied in silico PCR to the metatranscriptomics datasets, in order to estimate the extent of PCR amplification bias. Irrespective of stringency criteria, we observed clear separations of size fraction sample clusters in both metatranscriptomics and in silico datasets. In contrast, the pattern-smaller-fractioned communities had higher compositional homogeneity than larger ones-was observed in the metatranscriptomics data but not in the in silico datasets. To investigate this discrepancy further, we analysed the mismatches of widely used mitochondrial CO1 primers and identified priming site mismatches likely driving PCR-based biases. Our results suggest the use of metatranscriptomics or, although less ideal, redesigning the CO1 primers is necessary to circumvent these issues.
Collapse
Affiliation(s)
- Felipe M G Mattos
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
| | - Niklas Dreyer
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
- Natural History Museum of Denmark, Invertebrate Zoology, University of Copenhagen, Copenhagen, Denmark
| | - Chia-Ling Fong
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
| | - Yung-Hui Victoria Wen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taipei, Taiwan
| | - Dharmesh Jain
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
- Molecular and Biological Agricultural Sciences, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei, Taiwan
| | - Mattia De Vivo
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
| | - Yu-Sin Huang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
| | - John Karichu Mwihaki
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
| | - Tzi-Yuan Wang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Ming-Jay Ho
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | | | - John Wang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Benny K K Chan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Ryuji J Machida
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| |
Collapse
|
2
|
Alshabeeb MA, Alwadaani D, Al Qahtani FH, Abohelaika S, Alzahrani M, Al Zayed A, Al Saeed HH, Al Ajmi H, Alsomaie B, Rashid M, Daly AK. Impact of Genetic Variations on Thromboembolic Risk in Saudis with Sickle Cell Disease. Genes (Basel) 2023; 14:1919. [PMID: 37895268 PMCID: PMC10606407 DOI: 10.3390/genes14101919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 10/04/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Sickle cell disease (SCD) is a Mendelian disease characterized by multigenic phenotypes. Previous reports indicated a higher rate of thromboembolic events (TEEs) in SCD patients. A number of candidate polymorphisms in certain genes (e.g., FVL, PRT, and MTHFR) were previously reported as risk factors for TEEs in different clinical conditions. This study aimed to genotype these genes and other loci predicted to underlie TEEs in SCD patients. METHODOLOGY A multi-center genome-wide association study (GWAS) involving Saudi SCD adult patients with a history of TEEs (n = 65) and control patients without TEE history (n = 285) was performed. Genotyping used the 10× Affymetrix Axiom array, which includes 683,030 markers. Fisher's exact test was used to generate p-values of TEE associations with each single-nucleotide polymorphism (SNP). The haplotype analysis software tool version 1.05, designed by the University of Göttingen, Germany, was used to identify the common inherited haplotypes. RESULTS No association was identified between the targeted single-nucleotide polymorphism rs1801133 in MTHFR and TEEs in SCD (p = 0.79). The allele frequency of rs6025 in FVL and rs1799963 in PRT in our cohort was extremely low (<0.01); thus, both variants were excluded from the analysis as no meaningful comparison was possible. In contrast, the GWAS analysis showed novel genome-wide associations (p < 5 × 10-8) with seven signals; five of them were located on Chr 11 (rs35390334, rs331532, rs317777, rs147062602, and rs372091), one SNP on Chr 20 (rs139341092), and another on Chr 9 (rs76076035). The other 34 SNPs located on known genes were also detected at a signal threshold of p < 5 × 10-6. Seven of the identified variants are located in olfactory receptor family 51 genes (OR51B5, OR51V1, OR51A1P, and OR51E2), and five variants were related to family 52 genes (OR52A5, OR52K1, OR52K2, and OR52T1P). The previously reported association between rs5006884-A in OR51B5 and fetal hemoglobin (HbF) levels was confirmed in our study, which showed significantly lower levels of HbF (p = 0.002) and less allele frequency (p = 0.003) in the TEE cases than in the controls. The assessment of the haplotype inheritance pattern involved the top ten significant markers with no LD (rs353988334, rs317777, rs14788626882, rs49188823, rs139349992, rs76076035, rs73395847, rs1368823, rs8888834548, and rs1455957). A haplotype analysis revealed significant associations between two haplotypes (a risk, TT-AA-del-AA-ins-CT-TT-CC-CC-AA, and a reverse protective, CC-GG-ins-GG-del-TT-CC-TT-GG-GG) and TEEs in SCD (p = 0.024, OR = 6.16, CI = 1.34-28.24, and p = 0.019, OR = 0.33, CI = 0.13-0.85, respectively). CONCLUSIONS Seven markers showed novel genome-wide associations; two of them were exonic variants (rs317777 in OLFM5P and rs147062602 in OR51B5), and less significant associations (p < 5 × 10-6) were identified for 34 other variants in known genes with TEEs in SCD. Moreover, two 10-SNP common haplotypes were determined with contradictory effects. Further replication of these findings is needed.
Collapse
Affiliation(s)
- Mohammad A. Alshabeeb
- King Abdullah International Medical Research Center (KAIMRC), Riyadh 11426, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia (M.A.)
| | - Deemah Alwadaani
- King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia (M.A.)
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Riyadh 11481, Saudi Arabia
| | - Farjah H. Al Qahtani
- Hematology/Oncology Center, King Saud University Medical City (KSUMC), Riyadh 11411, Saudi Arabia;
| | - Salah Abohelaika
- Research Department, Qatif Central Hospital (QCH), Qatif 32654, Saudi Arabia;
- Pharmacy Department, Qatif Central Hospital (QCH), Qatif 32654, Saudi Arabia
| | - Mohsen Alzahrani
- King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia (M.A.)
- King Fahad Hospital, Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia
| | - Abdullah Al Zayed
- Hematology Department, Qatif Central Hospital (QCH), Qatif 32654, Saudi Arabia; (A.A.Z.); (H.H.A.S.)
| | - Hussain H. Al Saeed
- Hematology Department, Qatif Central Hospital (QCH), Qatif 32654, Saudi Arabia; (A.A.Z.); (H.H.A.S.)
| | - Hala Al Ajmi
- King Abdullah International Medical Research Center (KAIMRC), Riyadh 11426, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia (M.A.)
| | - Barrak Alsomaie
- King Abdullah International Medical Research Center (KAIMRC), Riyadh 11426, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia (M.A.)
| | - Mamoon Rashid
- King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia (M.A.)
- Department of AI and Bioinformatics, King Abdullah International Medical Research Center (KAIMRC), Riyadh 11481, Saudi Arabia
| | - Ann K. Daly
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, UK
| |
Collapse
|
3
|
Abrahim M, Machado E, Alvarez-Valín F, de Miranda AB, Catanho M. Uncovering Pseudogenes and Intergenic Protein-coding Sequences in TriTryps' Genomes. Genome Biol Evol 2022; 14:6754225. [PMID: 36208292 PMCID: PMC9576210 DOI: 10.1093/gbe/evac142] [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: 08/10/2022] [Revised: 09/14/2022] [Accepted: 09/20/2022] [Indexed: 01/24/2023] Open
Abstract
Trypanosomatids belong to a remarkable group of unicellular, parasitic organisms of the order Kinetoplastida, an early diverging branch of the phylogenetic tree of eukaryotes, exhibiting intriguing biological characteristics affecting gene expression (intronless polycistronic transcription, trans-splicing, and RNA editing), metabolism, surface molecules, and organelles (compartmentalization of glycolysis, variation of the surface molecules, and unique mitochondrial DNA), cell biology and life cycle (phagocytic vacuoles evasion and intricate patterns of cell morphogenesis). With numerous genomic-scale data of several trypanosomatids becoming available since 2005 (genomes, transcriptomes, and proteomes), the scientific community can further investigate the mechanisms underlying these unusual features and address other unexplored phenomena possibly revealing biological aspects of the early evolution of eukaryotes. One fundamental aspect comprises the processes and mechanisms involved in the acquisition and loss of genes throughout the evolutionary history of these primitive microorganisms. Here, we present a comprehensive in silico analysis of pseudogenes in three major representatives of this group: Leishmania major, Trypanosoma brucei, and Trypanosoma cruzi. Pseudogenes, DNA segments originating from altered genes that lost their original function, are genomic relics that can offer an essential record of the evolutionary history of functional genes, as well as clues about the dynamics and evolution of hosting genomes. Scanning these genomes with functional proteins as proxies to reveal intergenic regions with protein-coding features, relying on a customized threshold to distinguish statistically and biologically significant sequence similarities, and reassembling remnant sequences from their debris, we found thousands of pseudogenes and hundreds of open reading frames, with particular characteristics in each trypanosomatid: mutation profile, number, content, density, codon bias, average size, single- or multi-copy gene origin, number and type of mutations, putative primitive function, and transcriptional activity. These features suggest a common process of pseudogene formation, different patterns of pseudogene evolution and extant biological functions, and/or distinct genome organization undertaken by those parasites during evolution, as well as different evolutionary and/or selective pressures acting on distinct lineages.
Collapse
Affiliation(s)
- Mayla Abrahim
- Laboratório de Tecnologia Imunológica, Instituto de Tecnologia em Imunobiológicos, Vice-Diretoria de Desenvolvimento Tecnológico, Bio-Manguinhos, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Edson Machado
- Laboratório de Biologia Molecular Aplicada a Micobactérias, Instituto Oswaldo Cruz, Fiocruz, Brazil
| | - Fernando Alvarez-Valín
- Unidad de Genómica Evolutiva, Sección Biomatemática, Universidad de la República del Uruguay, Montevideo, Uruguay
| | | | | |
Collapse
|
4
|
Najari-Hanjani P, Farazmandfar T, Golalipour M. PER3P1 pseudogene modulates PER3 oscillation: a new player in the molecular clock network. BIOL RHYTHM RES 2022. [DOI: 10.1080/09291016.2022.2050978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Parisa Najari-Hanjani
- Department of Medical Genetics, Faculty of Advanced Technologies in Medicine, Golestan University of Medical Science, Gorgan, Iran
| | - Touraj Farazmandfar
- Department of Medical Genetics, Faculty of Advanced Technologies in Medicine, Golestan University of Medical Science, Gorgan, Iran
- Cellular and Molecular Research Center, Golestan University of Medical Science, Gorgan, Iran
| | - Masoud Golalipour
- Department of Medical Genetics, Faculty of Advanced Technologies in Medicine, Golestan University of Medical Science, Gorgan, Iran
- Cellular and Molecular Research Center, Golestan University of Medical Science, Gorgan, Iran
| |
Collapse
|
5
|
Abbasi S, Parmar G, Kelly RD, Balasuriya N, Schild-Poulter C. The Ku complex: recent advances and emerging roles outside of non-homologous end-joining. Cell Mol Life Sci 2021; 78:4589-4613. [PMID: 33855626 PMCID: PMC11071882 DOI: 10.1007/s00018-021-03801-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/29/2021] [Accepted: 02/24/2021] [Indexed: 12/15/2022]
Abstract
Since its discovery in 1981, the Ku complex has been extensively studied under multiple cellular contexts, with most work focusing on Ku in terms of its essential role in non-homologous end-joining (NHEJ). In this process, Ku is well-known as the DNA-binding subunit for DNA-PK, which is central to the NHEJ repair process. However, in addition to the extensive study of Ku's role in DNA repair, Ku has also been implicated in various other cellular processes including transcription, the DNA damage response, DNA replication, telomere maintenance, and has since been studied in multiple contexts, growing into a multidisciplinary point of research across various fields. Some advances have been driven by clarification of Ku's structure, including the original Ku crystal structure and the more recent Ku-DNA-PKcs crystallography, cryogenic electron microscopy (cryoEM) studies, and the identification of various post-translational modifications. Here, we focus on the advances made in understanding the Ku heterodimer outside of non-homologous end-joining, and across a variety of model organisms. We explore unique structural and functional aspects, detail Ku expression, conservation, and essentiality in different species, discuss the evidence for its involvement in a diverse range of cellular functions, highlight Ku protein interactions and recent work concerning Ku-binding motifs, and finally, we summarize the clinical Ku-related research to date.
Collapse
Affiliation(s)
- Sanna Abbasi
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Gursimran Parmar
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Rachel D Kelly
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Nileeka Balasuriya
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Caroline Schild-Poulter
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 5B7, Canada.
| |
Collapse
|
6
|
Hou X, Tang W. Pseudogene PA2G4P4 promotes oncogene PA2G4 expression and nuclear translocation to affect glioblastoma cell viability and apoptosis. Life Sci 2020; 265:118793. [PMID: 33220287 DOI: 10.1016/j.lfs.2020.118793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 10/02/2020] [Accepted: 11/15/2020] [Indexed: 12/21/2022]
Abstract
Dysregulation of pseudogenes is involved in the progression of various types of cancer, including glioblastoma (GBM). Proliferation associated-2G4 (PA2G4) pseudogene 4 (PA2G4P4) has been shown to play an oncogenic role in bladder cancer development. Our study aimed to explore the role and mechanism of PA2G4P4 in GBM progression. PA2G4P4 and PA2G4 expression in GBM tissues was analyzed using the GEPIA database. Cell viability, apoptosis, and activities of caspase-3 and caspase-9 in GBM cells were explored by CCK-8, flow cytometry analysis, and colorimetric activity assay kits, respectively. GEPIA database showed that PA2G4P4 and PA2G4 were both upregulated in GBM tissues. PA2G4P4 expression was also boosted in GBM cells. Knockdown of PA2G4P4 or PA2G4 inhibited cell viability, induced apoptosis, and increased caspase-3 and caspase-9 activities in GBM cells. Data from UALCAN database showed that among top 15 genes correlated with PA2G4P4, PA2G4 had the highest correlation coefficient. Additionally, knockdown of PA2G4P4 inhibited PA2G4 expression and nuclear translocation in GBM cells. Overexpression of PA2G4 abolished the functions of PA2G4P4 knockdown on viability and apoptosis in GBM cells. Summarily, pseudogene PA2G4P4 promotes oncogene PA2G4 expression and nuclear translocation to affect cell viability and apoptosis in GBM cells.
Collapse
Affiliation(s)
- Xiaofeng Hou
- Department of Neurosurgery, The First Affiliated Hospital of Baotou Medical College, Inner Mongolia University of Science and Technology, Baotou 014010, China
| | - Wenhai Tang
- Department of Neurosurgery, Shanxian Central Hospital, Heze 274300, China.
| |
Collapse
|
7
|
Zhou Z, Wang B. Identification of male infertility-related long non-coding RNAs and their functions based on a competing endogenous RNA network. J Int Med Res 2020; 48:300060520961277. [PMID: 33054493 PMCID: PMC7580164 DOI: 10.1177/0300060520961277] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
OBJECTIVE To identify male infertility-related long non-coding (lnc)RNAs and an lncRNA-related competing endogenous (ce)RNA network. METHODS Expression data including 13 normospermic and eight teratozoospermic samples from postmortem donors were downloaded from the GEO database (GSE6872). The limma R package was used to discriminate dysregulated lncRNA and micro (m)RNA profiles. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of differentially expressed (DE) mRNAs were performed using the clusterProfiler R package. The ceRNA network of dysregulated genes was visualized by Cytoscape. RESULTS A total of 101 DE lncRNAs and 1722 mRNAs were identified as male infertility-specific RNAs with thresholds of |log2FoldChange| >2.0 and adjusted P-value <0.05. GO and KEGG pathways were analyzed for DE mRNAs. Gene set enrichment analysis revealed that DE genes were enriched in embryonic skeletal system development and cytokine-cytokine receptor interactions. A ceRNA network was constructed with 26 key lncRNAs, 33 microRNAs, and 133 mRNAs. DE lncRNAs in male sterility were mainly associated with transferring phosphorus-containing groups and complexes of histone methyltransferases, methyltransferases, PcG proteins, and serine/threonine protein kinases. CONCLUSION This provides a novel perspective to study lncRNA-related ceRNA networks in male infertility and assist in identifying new potential biomarkers for diagnostic purposes.
Collapse
Affiliation(s)
- Zuo Zhou
- Department of Obstetrics, Maternal and Child Health Hospital of Zibo City, Shandong Province, China
| | - Bing Wang
- Center of Reproductive Medicine, Maternal and Child Health Hospital of Zibo City, Shandong Province, China
| |
Collapse
|
8
|
Taylor LW, French JE, Robbins ZG, Boyer JC, Nylander-French LA. Influence of Genetic Variance on Biomarker Levels After Occupational Exposure to 1,6-Hexamethylene Diisocyanate Monomer and 1,6-Hexamethylene Diisocyanate Isocyanurate. Front Genet 2020; 11:836. [PMID: 32973864 PMCID: PMC7466756 DOI: 10.3389/fgene.2020.00836] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/10/2020] [Indexed: 12/15/2022] Open
Abstract
We evaluated the impact of genetic variance on biomarker levels in a population of workers in the automotive repair and refinishing industry who were exposed to respiratory sensitizers 1,6-hexamethylene diisocyanate (HDI) monomer and one of its trimers, HDI isocyanurate. The exposures and respective urine and plasma biomarkers 1,6-diaminohexane (HDA) and trisaminohexyl isocyanurate (TAHI) were measured in 33 workers; and genome-wide microarrays (Affymetrix 6.0) were used to genotype the workers' single-nucleotide polymorphisms (SNPs). Linear mixed model analyses have indicated that interindividual variations in both inhalation and skin exposures influenced these biomarker levels. Using exposure values as covariates and a false discovery rate < 0.10 to assess statistical significance, we observed that seven SNPs were associated with HDA in plasma, five were associated with HDA in urine, none reached significance for TAHI in plasma, and eight were associated with TAHI levels in urine. The different genotypes for the 20 significant SNPs accounted for 4- to 16-fold changes observed in biomarker levels. Associated gene functions include transcription regulation, calcium ion transport, vascular morphogenesis, and transforming growth factor beta signaling pathway, which may impact toxicokinetics indirectly by altering inflammation levels. Additionally, in an expanded analysis using a minor allele cutoff of 0.05 instead of 0.10, there were biomarker-associated SNPs within three genes that have been associated with isocyanate-induced asthma: ALK, DOCK2, and LHPP. We demonstrate that genetic variance impacts the biomarker levels in workers exposed to HDI monomer and HDI isocyanurate and that genetics can be used to refine exposure predictions in small cohorts when quantitative personal exposure and biomarker measurements are included in the models.
Collapse
Affiliation(s)
- Laura W. Taylor
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - John E. French
- Nutrition Research Institute, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Zachary G. Robbins
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jayne C. Boyer
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Leena A. Nylander-French
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Paula DP, Menger J, Andow DA, Koch RL. Diverse patterns of constitutive and inducible overexpression of detoxifying enzyme genes among resistant Aphis glycines populations. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2020; 164:100-114. [PMID: 32284115 DOI: 10.1016/j.pestbp.2019.12.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/21/2019] [Accepted: 12/30/2019] [Indexed: 06/11/2023]
Abstract
Understanding the mechanisms of pyrethroid resistance is essential to the effective management of pesticide resistance in Aphis glycines Matsumura (Hemiptera: Aphididae). We mined putative detoxifying enzyme genes in the draft genome sequence of A. glycines for cytochrome oxidase P450 (CYP), glutathione-S-transferase (GST) and esterases (E4 and carboxylesterases-CES). Aphids from clonal populations resistant to pyrethroids from three sites in Minnesota, USA, were screened against a diagnostic LC99 concentration of either λ-cyhalothrin or bifenthrin and detoxifying enzyme genes expression in survivors was analyzed by qPCR. Their expression profiles were compared relative to a susceptible clonal population. We found 61 CYP (40 full-length), seven GST (all full-length), seven E4 (five full-length) and three CES (two full-length) genes, including 24 possible pseudogenes. The detoxifying enzymes had different expression profiles across resistant aphid populations, possibly reflecting differences in the genetic background and pyrethroid selection pressures as the number of constitutively overexpressed detoxifying enzyme genes was correlated with the level of resistance. Our findings will strengthen the understanding of the pyrethroid resistance mechanisms in A. glycines.
Collapse
Affiliation(s)
- Débora Pires Paula
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, W5 Norte, P.O. Box 02372, Brasília, DF 70770-917, Brazil.
| | - James Menger
- Department of Entomology, University of Minnesota, 219 Hodson Hall, 1980 Folwell Ave., St. Paul, MN 55108, USA
| | - David A Andow
- Department of Entomology, University of Minnesota, 219 Hodson Hall, 1980 Folwell Ave., St. Paul, MN 55108, USA
| | - Robert L Koch
- Department of Entomology, University of Minnesota, 219 Hodson Hall, 1980 Folwell Ave., St. Paul, MN 55108, USA
| |
Collapse
|
11
|
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]
|
12
|
Pseudogene RACGAP1P activates RACGAP1/Rho/ERK signalling axis as a competing endogenous RNA to promote hepatocellular carcinoma early recurrence. Cell Death Dis 2019; 10:426. [PMID: 31160556 PMCID: PMC6546712 DOI: 10.1038/s41419-019-1666-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 04/18/2019] [Accepted: 05/06/2019] [Indexed: 01/13/2023]
Abstract
Accumulating evidence has indicated crucial roles for pseudogenes in human cancers. However, the roles played by pseudogenes in the pathogenesis of HCC, particularly HCC early recurrence, still incompletely elucidated. Herein, we identify a novel early recurrence related pseudogene RACGAP1P which was significantly upregulated in HCC and was associated with larger tumour size, advanced clinical stage, abnormal AFP level and shorter survival time. In vitro and in vivo experiments have shown that RACGAP1P is a prerequisite for the development of malignant characteristics of HCC cells, including cell growth and migration. Mechanistic investigations indicated that RACGAP1P elicits its oncogenic activity as a ceRNA to sequestrate miR-15-5p from its endogenous target RACGAP1, thereby leading to the upregulation of RACGAP1 and the activation of RhoA/ERK signalling. These results may provide new insights into the functional crosstalk of the pseudogene/miRNA/parent-gene genetic network during HCC early relapse and may contribute to improving the clinical intervention for this subset of HCC patients.
Collapse
|
13
|
Wu Q, Shi M, Meng W, Wang Y, Hui P, Ma J. Long noncoding RNA FOXD3‐AS1 promotes colon adenocarcinoma progression and functions as a competing endogenous RNA to regulate SIRT1 by sponging miR‐135a‐5p. J Cell Physiol 2019; 234:21889-21902. [PMID: 31058315 DOI: 10.1002/jcp.28752] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 04/12/2019] [Accepted: 04/15/2019] [Indexed: 12/30/2022]
Affiliation(s)
- Qiong Wu
- Department of Gastroenterology, Tongren Hospital Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Min Shi
- Department of Gastroenterology, Tongren Hospital Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Wenying Meng
- Department of Gastroenterology, Tongren Hospital Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Yugang Wang
- Department of Gastroenterology, Tongren Hospital Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Pingping Hui
- Department of Gastroenterology, Tongren Hospital Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Jiali Ma
- Department of Gastroenterology, Tongren Hospital Shanghai Jiao Tong University School of Medicine Shanghai China
| |
Collapse
|
14
|
Yu J, Zhang J, Zhou L, Li H, Deng ZQ, Meng B. The Octamer-Binding Transcription Factor 4 (OCT4) Pseudogene, POU Domain Class 5 Transcription Factor 1B (POU5F1B), is Upregulated in Cervical Cancer and Down-Regulation Inhibits Cell Proliferation and Migration and Induces Apoptosis in Cervical Cancer Cell Lines. Med Sci Monit 2019; 25:1204-1213. [PMID: 30762028 PMCID: PMC6383437 DOI: 10.12659/msm.912109] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Background The POU domain class 5 transcription factor 1B (POU5F1B), is a pseudogene that is homologous to octamer-binding transcription factor 4 (OCT4), and is located adjacent to the MYC gene on human chromosome 8q24. POU5F1B has been reported to be transcribed in several types of cancer, but its role in cervical cancer remains unclear. This study aimed to investigate the expression and function of POU5F1B in tissue samples of human cervical cancer and in cervical cancer cell lines in vitro. Material/Methods Quantitative reverse transcription polymerase chain reaction (qRT-PCR) was used to quantify POU5F1B expression in cervical cancer tissues and in SiHa, HeLa, CaSki, and C33A human cervical cancer cell lines. Functional in vitro studies included analysis of the effects of POU5F1B expression on cervical cancer cell proliferation, migration, and apoptosis using a Cell Counting Kit-8 (CCK-8) assay, cell migration assays, and flow cytometry. Luciferase activity assays, qRT-PCR, and Western blot were performed to confirm the expression of POU5F1B. Results POU5F1B was significantly upregulated in cervical cancer tissues and cell lines. Interference with the expression of POU5F1B significantly inhibited cell proliferation, apoptosis, migration and invasion, and induced apoptosis in vitro. Western blot demonstrated that POU5F1B could modulate the expression of the OCT4 protein. Conclusions POU5F1B was upregulated in cervical cancer and down-regulation inhibited cell proliferation and migration and induced apoptosis in cervical cancer cell lines by modulating OCT4. Further studies are required to determine whether POU5F1B might be a diagnostic or prognostic biomarker or therapeutic target in cervical cancer.
Collapse
Affiliation(s)
- Jingwen Yu
- Taixing Peoples' Hospital Affiliated to Bengbu Medical College, Taixing, Jiangsu, China (mainland)
| | - Jingling Zhang
- Taixing Peoples' Hospital Affiliated to Bengbu Medical College, Taixing, Jiangsu, China (mainland)
| | - Liulin Zhou
- Department of Gynaecology and Obstetrics, Taixing Peoples' Hospital Affiliated to Bengbu Medical College, Taixing, Jiangsu, China (mainland)
| | - Hao Li
- Clinical Laboratory, Taixing Peoples' Hospital Affiliated to Bengbu Medical College, Taixing, Jiangsu, China (mainland)
| | - Zhao-Qun Deng
- Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China (mainland)
| | - Bi Meng
- Taixing Peoples' Hospital Affiliated to Bengbu Medical College, Taixing, Jiangsu, China (mainland)
| |
Collapse
|
15
|
Shang J, Wang Z, Chen W, Yang Z, Zheng L, Wang S, Li S. Pseudogene CHIAP2 inhibits proliferation and invasion of lung adenocarcinoma cells by means of the WNT pathway. J Cell Physiol 2019; 234:13735-13746. [PMID: 30623445 DOI: 10.1002/jcp.28053] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 12/03/2018] [Indexed: 12/23/2022]
Abstract
Recently, pseudogenes have emerged as critical regulators in the onset of human neoplasia. Here, we present a comprehensive analysis of pseudogene alterations at transcriptional levels in lung adenocarcinoma (LUAD) from The Cancer Genome Atlas. By combinations of differential expression analysis, survival analysis, and univariate and multivariable Cox proportional hazards regression models, we identified four dysregulated pseudogenes, whose expression level was closely related to LUAD patients' prognosis and the four pseudogene signature could act as an independent prognostic indicator for LUAD patients. We further characterized CHIAP2, one of those four pseudogenes, whose expression level was the most closely linked to LUAD patients' prognosis. Consistent with our analysis, the expression of CHIAP2 was abnormally downregulated in LUAD tissues compared with that in normal tissues in our 50 pairs of clinical samples. Functional assays demonstrated that upregulation of CHIAP2 significantly impaired cell proliferation and invasion. After performing RNA sequencing (RNA-seq) and small RNA-seq between CHIAP2 overexpression and negative control LUAD cell lines, we identified differentially expressed messenger RNAs and microRNAs (miRNAs), among which six miRNAs were downregulated. Target genes of six downregulated miRNAs were predicted with online miRNA target prediction tools and significant pathways including the WNT signal pathway were identified with Gene Set Enrichment Analysis. By combining predictor genes of six downregulated miRNAs and dysregulated genes of the WNT pathway, we inferred that overexpression of CHAP2 may inhibit LUAD cell proliferation and invasion via modulation of NFATC2 or GSK3B (WNT signal pathway) targeted by miR-3614-5p or miR-873-3p.
Collapse
Affiliation(s)
- Jun Shang
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Zhongyu Wang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenjie Chen
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Zuyi Yang
- Department of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China
| | - Liping Zheng
- Department of Anesthesia Catheter Room, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Sihua Wang
- Department of Thoracic Surgery, Union Hospital Tongji Medical College Huazhong University of Science and Technology, Wuhan, China
| | - Shikang Li
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| |
Collapse
|
16
|
Nuerzhati Y, Dong R, Song Z, Zheng S. Role of the long non‑coding RNA‑Annexin A2 pseudogene 3/Annexin A2 signaling pathway in biliary atresia‑associated hepatic injury. Int J Mol Med 2018; 43:739-748. [PMID: 30569159 PMCID: PMC6317672 DOI: 10.3892/ijmm.2018.4023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 11/21/2018] [Indexed: 12/29/2022] Open
Abstract
Biliary atresia (BA) is the most common cause of chronic cholestasis in children. The long non‑coding RNA (lncRNA) Annexin A2 pseudogene 3 (ANXA2P3) and Annexin A2 (ANXA2) have been suggested to serve pivotal roles in BA; however, the clinical significance and biological roles of ANXA2P3 and ANXA2 in BA remain to be elucidated. The present study aimed to elucidate the function of ANAX2P3 and ANXA2 in BA‑induced liver injury using a human liver cell line and liver tissues from patients with BA. Reverse transcription‑quantitative polymerase chain reaction, western blotting and immunohistochemistry were conducted to determine the expression levels of ANXA2 and ANXA2P3 in liver tissues from patients with BA. Classification of fibrosis was analyzed by Masson staining. The functional roles of ANXA2 and ANXA2P3 in liver cells were determined by Cell Counting kit‑8 assay, and flow cytometric and cell cycle analyses. Activation of the ANXA2/ANXA2P3 signaling pathway in liver cells was evaluated by western blot analysis. According to the present results, the expression levels of ANXA2 and ANXA2P3 were significantly increased in liver tissues from patients with BA. In addition, knocking down the expression of ANXA2P3 and ANXA2 may result in reduced liver cell proliferation, cell cycle arrest in G1 phase and increased apoptosis of liver cells in vitro. Furthermore, in cells in which ANXA2 and ANXA2P3 were overexpressed, cell apoptosis was reduced and cell cycle arrest in G2 phase. Taken together, these results indicated that ANXA2P3 and ANXA2 may have protective effects against liver injury progression and may be considered biomarkers in patients with BA.
Collapse
Affiliation(s)
- Yeletai Nuerzhati
- Department of Pediatric Hepatobiliary Surgery, Children's Hospital of Fudan University, Shanghai 201102, P.R. China
| | - Rui Dong
- Department of Pediatric Hepatobiliary Surgery, Children's Hospital of Fudan University, Shanghai 201102, P.R. China
| | - Zai Song
- Department of Pediatric Hepatobiliary Surgery, Children's Hospital of Fudan University, Shanghai 201102, P.R. China
| | - Shan Zheng
- Department of Pediatric Hepatobiliary Surgery, Children's Hospital of Fudan University, Shanghai 201102, P.R. China
| |
Collapse
|
17
|
Lian Y, Yang J, Lian Y, Xiao C, Hu X, Xu H. DUXAP8, a pseudogene derived lncRNA, promotes growth of pancreatic carcinoma cells by epigenetically silencing CDKN1A and KLF2. Cancer Commun (Lond) 2018; 38:64. [PMID: 30367681 PMCID: PMC6235391 DOI: 10.1186/s40880-018-0333-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 10/08/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Recent studies highlight pseudogene derived long non-coding RNAs (lncRNAs) as key regulators of cancer biology. However, few of them have been well characterized in pancreatic cancer. Here, we aimed to identify the association between pseudogene derived lncRNA DUXAP8 and growth of pancreatic cancer cells. METHODS We screened for pseudogene derived lncRNAs associated with human pancreatic cancer by comparative analysis of three independent datasets from GEO. Quantitative real-time reverse transcription polymerase chain reaction was used to assess the relative expression of DUXAP8 in pancreatic cancer tissues and cells. Loss-of-function approaches were used to investigate the potential functional roles of DUXAP8 in pancreatic cancer cell proliferation and apoptosis in vitro and in vivo. RNA immunoprecipitation, chromosome immunoprecipitation assay and rescue experiments were performed to analyze the association of DUXAP8 with target proteins and genes in pancreatic cancer cells. RESULTS Pancreatic cancer tissues had significantly higher DUXAP8 levels than paired adjacent normal tissues. High DUXAP8 expression was associated with a larger tumor size, advanced pathological stage and shorter overall survival of pancreatic cancer patients. Moreover, silencing DUXAP8 expression by siRNA or shRNA inhibited pancreatic cancer cell proliferation and promoted apoptosis in vitro and in vivo. Mechanistic analyses indicated that DUXAP8 regulates PC cell proliferation partly through downregulation of tumor suppressor CDKN1A and KLF2 expression. CONCLUSION Our results suggest that tumor expression of pseudogene derived lncRNA DUXAP8 plays an important role in pancreatic cancer progression. DUXAP8 may serve as a candidate biomarker and represent a novel therapeutic target of pancreatic cancer.
Collapse
Affiliation(s)
- Yifan Lian
- Department of Gastroenterology, Zhongshan Hospital, Xiamen University, Xiamen, 361005, Fujian, P. R. China.,Institute for Microbial Ecology, Xiamen University, Xiamen, 361005, Fujian, P. R. China
| | - Jiebin Yang
- Department of Gastroenterology, Zhongshan Hospital, Xiamen University, Xiamen, 361005, Fujian, P. R. China.,Institute for Microbial Ecology, Xiamen University, Xiamen, 361005, Fujian, P. R. China
| | - Yikai Lian
- Department of Gastroenterology, Zhongshan Hospital, Xiamen University, Xiamen, 361005, Fujian, P. R. China.,Institute for Microbial Ecology, Xiamen University, Xiamen, 361005, Fujian, P. R. China
| | - Chuangxing Xiao
- Department of Gastroenterology, Zhongshan Hospital, Xiamen University, Xiamen, 361005, Fujian, P. R. China.,Institute for Microbial Ecology, Xiamen University, Xiamen, 361005, Fujian, P. R. China
| | - Xuezhen Hu
- Jiangsu Province Hospital of TCM, Affiliated Hospital of Nanjing University of TCM, Nanjing, 210029, Jiangsu, P. R. China.
| | - Hongzhi Xu
- Department of Gastroenterology, Zhongshan Hospital, Xiamen University, Xiamen, 361005, Fujian, P. R. China. .,Institute for Microbial Ecology, Xiamen University, Xiamen, 361005, Fujian, P. R. China.
| |
Collapse
|
18
|
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.
Collapse
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.
| |
Collapse
|
19
|
The pseudogene-derived long non-coding RNA SFTA1P suppresses cell proliferation, migration, and invasion in gastric cancer. Biosci Rep 2018. [PMID: 29523596 PMCID: PMC5968191 DOI: 10.1042/bsr20171193] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Pseudogenes were once regarded as transcriptionally inactive and without specific molecular function. However, current evidence shows that pseudogene-derived long non-coding RNAs (lncRNAs) may be crucial regulators of human cancer development, including gastric cancer (GC). In the present study, we report that a pseudogene-derived lncRNA named surfactant associated 1, pseudogene (SFTA1P), which is 693-nt long, was significantly down-regulated in GC tissues compared with that in the adjacent normal tissues. In addition, decreased SFTA1P expression was strongly correlated with advanced tumor lymph node metastasis (TNM) stage, larger tumor size, lymphatic metastasis, and poor prognosis of patients with GC. Moreover, gain-of-function experiments revealed that the overexpression of SFTA1P inhibits cell proliferation, migration, and invasion, thus verifying the tumor inhibitory role of SFTA1P in GC. Furthermore, we investigated the potential action mechanism of SFTA1P. Our results showed that down-regulation of SFTA1P may be associated with decreased TP53 expression. In summary, our work suggests that the pseudogene-derived lncRNA SFTA1P functions as a tumor suppressor in GC and thus may act as a potential diagnostic and therapeutic target of GC.
Collapse
|
20
|
Zhao G, Zou C, Li K, Wang K, Li T, Gao L, Zhang X, Wang H, Yang Z, Liu X, Jiang W, Mao L, Kong X, Jiao Y, Jia J. The Aegilops tauschii genome reveals multiple impacts of transposons. NATURE PLANTS 2017; 3:946-955. [PMID: 29158546 DOI: 10.1038/s41477-017-0067-8] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 10/30/2017] [Indexed: 05/19/2023]
Abstract
Wheat is an important global crop with an extremely large and complex genome that contains more transposable elements (TEs) than any other known crop species. Here, we generated a chromosome-scale, high-quality reference genome of Aegilops tauschii, the donor of the wheat D genome, in which 92.5% sequences have been anchored to chromosomes. Using this assembly, we accurately characterized genic loci, gene expression, pseudogenes, methylation, recombination ratios, microRNAs and especially TEs on chromosomes. In addition to the discovery of a wave of very recent gene duplications, we detected that TEs occurred in about half of the genes, and found that such genes are expressed at lower levels than those without TEs, presumably because of their elevated methylation levels. We mapped all wheat molecular markers and constructed a high-resolution integrated genetic map corresponding to genome sequences, thereby placing previously detected agronomically important genes/quantitative trait loci (QTLs) on the Ae. tauschii genome for the first time.
Collapse
Affiliation(s)
- Guangyao Zhao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Cheng Zou
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Kui Li
- Novogene Bioinformatics Institute, 100083, Beijing, China
| | - Kai Wang
- Novogene Bioinformatics Institute, 100083, Beijing, China
| | - Tianbao Li
- Agronomy College, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, 450002, Zhengzhou, China
| | - Lifeng Gao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Xiaoxia Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, 100093, Beijing, China
| | - Hongjin Wang
- Center for Information in Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, 610054, Chengdu, China
| | - Zujun Yang
- Center for Information in Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, 610054, Chengdu, China
| | - Xu Liu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Wenkai Jiang
- Novogene Bioinformatics Institute, 100083, Beijing, China.
| | - Long Mao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, China.
| | - Xiuying Kong
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, China.
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, 100093, Beijing, China.
| | - Jizeng Jia
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, China.
| |
Collapse
|
21
|
Samuel P, Fabbri M, Carter DRF. Mechanisms of Drug Resistance in Cancer: The Role of Extracellular Vesicles. Proteomics 2017; 17. [PMID: 28941129 DOI: 10.1002/pmic.201600375] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 09/11/2017] [Indexed: 12/11/2022]
Abstract
Drug resistance remains a major barrier to the successful treatment of cancer. The mechanisms by which therapeutic resistance arises are multifactorial. Recent evidence has shown that extracellular vesicles (EVs) play a role in mediating drug resistance. EVs are small vesicles carrying a variety of macromolecular cargo released by cells into the extracellular space and can be taken up into recipient cells, resulting in transfer of cellular material. EVs can mediate drug resistance by several mechanisms. They can serve as a pathway for sequestration of cytotoxic drugs, reducing the effective concentration at target sites. They can act as decoys carrying membrane proteins and capturing monoclonal antibodies intended to target receptors at the cell surface. EVs from resistant tumor cells can deliver mRNA, miRNA, long noncoding RNA, and protein inducing resistance in sensitive cells. This provides a new model for how resistance that arises can then spread through a heterogeneous tumor. EVs also mediate cross-talk between cancer cells and stromal cells in the tumor microenvironment, leading to tumor progression and acquisition of therapeutic resistance. In this review, we will describe what is known about how EVs can induce drug resistance, and discuss the ways in which EVs could be used as therapeutic targets or diagnostic markers for managing cancer treatment. While further characterization of the vesiculome and the mechanisms of EV function are still required, EVs offer an exciting opportunity in the fight against cancer.
Collapse
Affiliation(s)
- Priya Samuel
- Department of Biological and Medical Sciences Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Muller Fabbri
- Department of Pediatrics and Microbiology & Molecular Immunology University of Southern California-Keck School of Medicine Norris Comprehensive Cancer Center Children's Center for Cancer and Blood Diseases, Children's Hospital, Los Angeles, CA, USA
| | - David Raul Francisco Carter
- Department of Biological and Medical Sciences Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| |
Collapse
|
22
|
Lian Y, Xu Y, Xiao C, Xia R, Gong H, Yang P, Chen T, Wu D, Cai Z, Zhang J, Wang K. The pseudogene derived from long non-coding RNA DUXAP10 promotes colorectal cancer cell growth through epigenetically silencing of p21 and PTEN. Sci Rep 2017; 7:7312. [PMID: 28779166 PMCID: PMC5544748 DOI: 10.1038/s41598-017-07954-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 07/03/2017] [Indexed: 12/24/2022] Open
Abstract
Recently, substantial evidence has demonstrated that pseudogene derived lncRNAs are crucial regulators of cancer development and progression. DUXAP10,a pseudogene derived long non-coding RNA(lncRNA), is overexpression in colorectal cancer (CRC), but its expression pattern, biological function and underlying mechanism in CRC is still undetermined. In this study, we observed that DUXAP10 was up-regulated in CRC tissues which was positively correlated with advanced pathological stages, larger tumor sizes and lymph node metastasis. Additionally, knockdown of DUXAP10 inhibited cell proliferation, induced cell apoptosis and increase the number of G0/G1 cells significantly in the HCT116 and SW480 cell lines. Moreover, DUXAP10 silencing inhibited tumor growth in vivo. Further mechanism study showed that, by binding to histone demethylase lysine-specific demethylase 1 (LSD1), DUXAP10 promote CRC cell growth and reduced cell apoptosis through silencing the expression of p21 and phosphatase and tensin homolog (PTEN) tumor suppressor. Our findings suggested that the pseudogene-derived from lncRNA DUXAP10 promotes the biological progression of CRC and is likely to be a potential therapeutic target for CRC intervention.
Collapse
Affiliation(s)
- Yifan Lian
- Department of Gastroenterology, Zhongshan Hospital affiliated to Xiamen University, Xiamen, 361004, Fujian, People's Republic of China.,Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, 210000, Jiangsu, People's Republic of China
| | - Yetao Xu
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, Jiangsu, People's Republic of China
| | - Chuanxing Xiao
- Department of Gastroenterology, Zhongshan Hospital affiliated to Xiamen University, Xiamen, 361004, Fujian, People's Republic of China
| | - Rui Xia
- Department of Laboratory, Nanjing Chest Hospital, Nanjing, 210029, Jiangsu, People's Republic of China
| | - Huangbo Gong
- Department of General Surgery, Second Affiliated Hospital, Nanjing Medical University, Nanjing, 210000, Jiangsu, People's Republic of China
| | - Peng Yang
- Department of General Surgery, Second Affiliated Hospital, Nanjing Medical University, Nanjing, 210000, Jiangsu, People's Republic of China
| | - Tao Chen
- Department of General Surgery, Second Affiliated Hospital, Nanjing Medical University, Nanjing, 210000, Jiangsu, People's Republic of China
| | - Dongdong Wu
- Department of General Surgery, Second Affiliated Hospital, Nanjing Medical University, Nanjing, 210000, Jiangsu, People's Republic of China
| | - Zeling Cai
- Department of General Surgery, Second Affiliated Hospital, Nanjing Medical University, Nanjing, 210000, Jiangsu, People's Republic of China
| | - Jianping Zhang
- Department of General Surgery, Second Affiliated Hospital, Nanjing Medical University, Nanjing, 210000, Jiangsu, People's Republic of China
| | - Keming Wang
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, 210000, Jiangsu, People's Republic of China.
| |
Collapse
|
23
|
Dykstra-Aiello C, Jickling GC, Ander BP, Shroff N, Zhan X, Liu D, Hull H, Orantia M, Stamova BS, Sharp FR. Altered Expression of Long Noncoding RNAs in Blood After Ischemic Stroke and Proximity to Putative Stroke Risk Loci. Stroke 2016; 47:2896-2903. [PMID: 27834745 DOI: 10.1161/strokeaha.116.013869] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 09/20/2016] [Accepted: 10/04/2016] [Indexed: 01/01/2023]
Abstract
BACKGROUND AND PURPOSE Although peripheral blood mRNA and micro-RNA change after ischemic stroke, any role for long noncoding RNA (lncRNA), which comprise most of the genome and have been implicated in various diseases, is unknown. Thus, we hypothesized that lncRNA expression also changes after stroke. METHODS lncRNA expression was assessed in 266 whole-blood RNA samples drawn once per individual from patients with ischemic stroke and matched with vascular risk factor controls. Differential lncRNA expression was assessed by ANCOVA (P<0.005; fold change>|1.2|), principal components analysis, and hierarchical clustering on a derivation set (n=176) and confirmed on a validation set (n=90). Poststroke temporal lncRNA expression changes were assessed using ANCOVA with confounding factor correction (P<0.005; partial correlation with time since event >|0.4|). Because sexual dimorphism exists in stroke, analyses were performed for each sex separately. RESULTS A total of 299 lncRNAs were differentially expressed between stroke and control males, whereas 97 lncRNAs were differentially expressed between stroke and control females. Significant changes of lncRNA expression with time after stroke were detected for 49 lncRNAs in men and 31 lncRNAs in women. Some differentially expressed lncRNAs mapped close to genomic locations of previously identified putative stroke-risk genes, including lipoprotein, lipoprotein(a)-like 2, ABO (transferase A, α1-3-N-acetylgalactosaminyltransferase; transferase B, α1-3-galactosyltransferase) blood group, prostaglandin 12 synthase, and α-adducins. CONCLUSIONS This study provides evidence of altered and sexually dimorphic lncRNA expression in peripheral blood of patients with stroke compared with that of controls and suggests that lncRNAs have potential for stroke biomarker development. Some regulated lncRNA could regulate some previously identified putative stroke-risk genes.
Collapse
Affiliation(s)
| | - Glen C Jickling
- From the Department of Neurology, University of California at Davis, Sacramento
| | - Bradley P Ander
- From the Department of Neurology, University of California at Davis, Sacramento
| | - Natasha Shroff
- From the Department of Neurology, University of California at Davis, Sacramento
| | - Xinhua Zhan
- From the Department of Neurology, University of California at Davis, Sacramento
| | - DaZhi Liu
- From the Department of Neurology, University of California at Davis, Sacramento
| | - Heather Hull
- From the Department of Neurology, University of California at Davis, Sacramento
| | - Miles Orantia
- From the Department of Neurology, University of California at Davis, Sacramento
| | - Boryana S Stamova
- From the Department of Neurology, University of California at Davis, Sacramento.
| | - Frank R Sharp
- From the Department of Neurology, University of California at Davis, Sacramento
| |
Collapse
|
24
|
McCabe MJ, Hu Y, Gregory LC, Gaston-Massuet C, Alatzoglou KS, Saldanha JW, Gualtieri A, Thankamony A, Hughes I, Townshend S, Martinez-Barbera JP, Bouloux PM, Dattani MT. Novel application of luciferase assay for the in vitro functional assessment of KAL1 variants in three females with septo-optic dysplasia (SOD). Mol Cell Endocrinol 2015; 417:63-72. [PMID: 26375424 PMCID: PMC4646839 DOI: 10.1016/j.mce.2015.09.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 09/10/2015] [Accepted: 09/10/2015] [Indexed: 01/13/2023]
Abstract
KAL1 is implicated in 5% of Kallmann syndrome cases, a disorder which genotypically overlaps with septo-optic dysplasia (SOD). To date, a reporter-based assay to assess the functional consequences of KAL1 mutations is lacking. We aimed to develop a luciferase assay for novel application to functional assessment of rare KAL1 mutations detected in a screen of 422 patients with SOD. Quantitative analysis was performed using L6-myoblasts stably expressing FGFR1, transfected with a luciferase-reporter vector containing elements of the FGF-responsive osteocalcin promoter. The two variants assayed [p.K185N, p.P291T], were detected in three females with SOD (presenting with optic nerve hypoplasia, midline and pituitary defects). Our novel assay revealed significant decreases in transcriptional activity [p.K185N: 21% (p < 0.01); p.P291T: 40% (p < 0.001)]. Our luciferase-reporter assay, developed for assessment of KAL1 mutations, determined that two variants in females with hypopituitarism/SOD are loss-of-function; demonstrating that this assay is suitable for quantitative assessment of mutations in this gene.
Collapse
Affiliation(s)
- Mark J McCabe
- Section of Genetics and Epigenetics in Health and Disease, Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK; Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia; St Vincent's Clinical School, UNSW Australia, Sydney, NSW, Australia
| | - Youli Hu
- Centre for Neuroendocrinology, Royal Free Hospital and University College Medical School, University College London, London, UK; Department of Anaesthesiology, Nanjing Medical University First Affiliated Hospital, Jiangsu Province Hospital, Nanjing 210029, China
| | - Louise C Gregory
- Section of Genetics and Epigenetics in Health and Disease, Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK
| | - Carles Gaston-Massuet
- Neural Development Unit, UCL Institute of Child Health, London, UK; Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, UK
| | - Kyriaki S Alatzoglou
- Section of Genetics and Epigenetics in Health and Disease, Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK
| | - José W Saldanha
- Division of Mathematical Biology, National Institute for Medical Research, London, UK
| | - Angelica Gualtieri
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, UK
| | - Ajay Thankamony
- University of Cambridge, Addenbrookes Hospital, Cambridge, UK
| | - Ieuan Hughes
- University of Cambridge, Addenbrookes Hospital, Cambridge, UK
| | - Sharron Townshend
- Princess Margaret Hospital for Children, Subiaco, Western Australia, Australia
| | | | - Pierre-Marc Bouloux
- Centre for Neuroendocrinology, Royal Free Hospital and University College Medical School, University College London, London, UK
| | - Mehul T Dattani
- Section of Genetics and Epigenetics in Health and Disease, Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK.
| |
Collapse
|
25
|
Ko YJ, Yang EC, Lee JH, Lee KW, Jeong JY, Park K, Chung O, Bhak J, Lee JH, Yim HS. Characterization of cetacean Numt and its application into cetacean phylogeny. Genes Genomics 2015. [DOI: 10.1007/s13258-015-0353-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
|
26
|
A ceRNA approach may unveil unexpected contributors to deletion syndromes, the model of 5q- syndrome. Oncoscience 2015; 2:872-9. [PMID: 26682279 PMCID: PMC4671954 DOI: 10.18632/oncoscience.261] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/09/2015] [Indexed: 02/06/2023] Open
Abstract
In genomic deletions, gene haploinsufficiency might directly configure a specific disease phenotype. Nevertheless, in some cases no functional association can be identified between haploinsufficient genes and the deletion-associated phenotype. Transcripts can act as microRNA sponges. The reduction of transcripts from the hemizygous region may increase the availability of specific microRNAs, which in turn may exert in-trans regulation of target genes outside the deleted region, eventually contributing to the phenotype. Here we prospect a competing endogenous RNA (ceRNA) approach for the identification of candidate genes target of epigenetic regulation in deletion syndromes. As a model, we analyzed the 5q- myelodysplastic syndrome. Genes in haploinsufficiency within the common 5q deleted region in CD34+ blasts were identified in silico. Using the miRWalk 2.0 platform, we predicted microRNAs whose availability, and thus activity, could be enhanced by the deletion, and performed a genomewide analysis of the genes outside the 5q deleted region that could be targeted by the predicted miRNAs. The analysis pointed to two genes with altered expression in 5q- transcriptome, which have never been related with 5q- before. The prospected approach allows investigating the global transcriptional effect of genomic deletions, possibly prompting discovery of unsuspected contributors in the deletion-associated phenotype. Moreover, it may help in functionally characterizing previously reported unexpected interactions.
Collapse
|
27
|
Epigenetic silencing of Oct4 by a complex containing SUV39H1 and Oct4 pseudogene lncRNA. Nat Commun 2015; 6:7631. [PMID: 26158551 PMCID: PMC4510692 DOI: 10.1038/ncomms8631] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 05/27/2015] [Indexed: 12/19/2022] Open
Abstract
Pseudogene-derived, long non-coding RNAs (lncRNAs) act as epigenetic regulators of gene expression. Here we present a panel of new mouse Oct4 pseudogenes and demonstrate that the X-linked Oct4 pseudogene Oct4P4 critically impacts mouse embryonic stem cells (mESCs) self-renewal. Sense Oct4P4 transcription produces a spliced, nuclear-restricted lncRNA that is efficiently upregulated during mESC differentiation. Oct4P4 lncRNA forms a complex with the SUV39H1 HMTase to direct the imposition of H3K9me3 and HP1α to the promoter of the ancestral Oct4 gene, located on chromosome 17, leading to gene silencing and reduced mESC self-renewal. Targeting Oct4P4 expression in primary mouse embryonic fibroblasts causes the re-acquisition of self-renewing features of mESC. We demonstrate that Oct4P4 lncRNA plays an important role in inducing and maintaining silencing of the ancestral Oct4 gene in differentiating mESCs. Our data introduces a sense pseudogene–lncRNA-based mechanism of epigenetic gene regulation that controls the cross-talk between pseudogenes and their ancestral genes. Pseudogene derived long non-coding RNAs (lncRNAs) can regulate the expression of their ancestral genes. Here, the authors show that the Oct4 pseudogene OctP4 lncRNA plays an important role in inducing and maintaining silencing of the ancestral Oct4 gene in differentiating mouse embryonic stem cells.
Collapse
|
28
|
Telonis AG, Loher P, Kirino Y, Rigoutsos I. Nuclear and mitochondrial tRNA-lookalikes in the human genome. Front Genet 2014; 5:344. [PMID: 25339973 PMCID: PMC4189335 DOI: 10.3389/fgene.2014.00344] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 09/13/2014] [Indexed: 02/03/2023] Open
Abstract
We are interested in identifying and characterizing loci of the human genome that harbor sequences resembling known mitochondrial and nuclear tRNAs. To this end, we used the known nuclear and mitochondrial tRNA genes (the “tRNA-Reference” set) to search for “tRNA-lookalikes” and found many such loci at different levels of sequence conservation. We find that the large majority of these tRNA-lookalikes resemble mitochondrial tRNAs and exhibit a skewed over-representation in favor of some mitochondrial anticodons. Our analysis shows that the tRNA-lookalikes have infiltrated specific chromosomes and are preferentially located in close proximity to known nuclear tRNAs (z-score ≤ −2.54, P-value ≤ 0.00394). Examination of the transcriptional potential of these tRNA-lookalike loci using public transcript annotations revealed that more than 20% of the lookalikes are transcribed as part of either known protein-coding pre-mRNAs, known lncRNAs, or known non-protein-coding RNAs, while public RNA-seq data perfectly agreed with the endpoints of tRNA-lookalikes. Interestingly, we found that tRNA-lookalikes are significantly depleted in known genetic variations associated with human health and disease whereas the known tRNAs are enriched in such variations. Lastly, a manual comparative analysis of the cloverleaf structure of several of the transcribed tRNA-lookalikes revealed no disruptive mutations suggesting the possibility that these loci give rise to functioning tRNA molecules.
Collapse
Affiliation(s)
- Aristeidis G Telonis
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University Philadelphia, PA, USA
| | - Phillipe Loher
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University Philadelphia, PA, USA
| | - Yohei Kirino
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University Philadelphia, PA, USA
| | - Isidore Rigoutsos
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University Philadelphia, PA, USA
| |
Collapse
|
29
|
Goralska M, Fleisher LN, McGahan MC. Hypoxia induced changes in expression of proteins involved in iron uptake and storage in cultured lens epithelial cells. Exp Eye Res 2014; 125:135-41. [PMID: 24877740 DOI: 10.1016/j.exer.2014.05.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Revised: 05/14/2014] [Accepted: 05/15/2014] [Indexed: 12/11/2022]
Abstract
Hypoxia inducible factor (HIF) regulates expression of over 60 genes by binding to hypoxia response elements (HRE) located upstream of the transcriptional start sites. Many genes encoding proteins involved in iron transport and homeostasis are regulated by HIF. Expression of iron handling proteins can also be translationally regulated by binding of iron regulatory protein (IRP) to iron responsive elements (IREs) on the mRNA of ferritin chains and transferrin receptor (TfR). Lens epithelial cells (LEC) function in a low oxygen environment. This increases the risk of iron catalyzed formation of reactive oxygen species (ROS) and oxidative cell damage. We examined changes in expression of ferritin (iron storage protein) and Tf/TfR1 (iron uptake proteins) in LEC cultured under hypoxic conditions. Ferritin consists of 24 subunits of two types, heavy (H-chain) and light (L-chain) assembled in a cell specific ratio. Real-time PCR showed that 24 h exposure to hypoxia lowered transcription of both ferritin chains by over 50% when compared with normoxic LEC. However it increased the level of ferritin chain proteins (20% average). We previously found that 6 h exposure of LEC to hypoxia increased the concentration of cytosolic iron which would stimulate translation of ferritin chains. This elevated ferritin concentration increased the iron storage capacity of LEC. Hypoxic LEC labeled with 59FeTf incorporated 70% more iron into ferritin after 6 h as compared to normoxic LEC. Exposure of LEC to hypoxia for 24 h reduced the concentration of TfR1 in cell lysates. As a result, hypoxic LEC internalized less Tf at this later time point. Incorporation of 59Fe into ferritin of hypoxic LEC after 24 h did not differ from that of normoxic LEC due to lower 59FeTf uptake. This study showed that hypoxia acutely increased iron storage capacity and lowered iron uptake due to changes in expression of iron handling proteins. These changes may better protect LEC against oxidative stress by limiting iron-catalyzed ROS formation in the low oxygen environment in which the lens resides.
Collapse
Affiliation(s)
- Małgorzata Goralska
- Department of Molecular Biomedical Sciences, North Carolina State University, 1060 William Moore Dr Raleigh, NC 27607, USA.
| | - Lloyd N Fleisher
- Department of Molecular Biomedical Sciences, North Carolina State University, 1060 William Moore Dr Raleigh, NC 27607, USA.
| | - M Christine McGahan
- Department of Molecular Biomedical Sciences, North Carolina State University, 1060 William Moore Dr Raleigh, NC 27607, USA.
| |
Collapse
|