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Chen Q, Li D, Jiang L, Wu Y, Yuan H, Shi G, Liu F, Wu P, Jiang K. Biological functions and clinical significance of tRNA-derived small fragment (tsRNA) in tumors: Current state and future perspectives. Cancer Lett 2024; 587:216701. [PMID: 38369004 DOI: 10.1016/j.canlet.2024.216701] [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: 10/10/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/20/2024]
Abstract
A new class of noncoding RNAs, tsRNAs are not only abundant in humans but also have high tissue specificity. Recently, an increasing number of studies have explored the correlations between tsRNAs and tumors, showing that tsRNAs can affect biological behaviors of tumor cells, such as proliferation, apoptosis and metastasis, by modulating protein translation, RNA transcription or posttranscriptional regulation. In addition, tsRNAs are widely distributed and stably expressed, which endows them with broad application prospects in diagnosing and predicting the prognosis of tumors, and they are expected to become new biomarkers. However, notably, the current research on tsRNAs still faces problems that need to be solved. In this review, we describe the characteristics of tsRNAs as well as their unique features and functions in tumors. Moreover, we also discuss the potential opportunities and challenges in clinical applications and research of tsRNAs.
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Affiliation(s)
- Qun Chen
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Danrui Li
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Luyang Jiang
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yang Wu
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hao Yuan
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Guodong Shi
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Fengyuan Liu
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Pengfei Wu
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Kuirong Jiang
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
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Cabarcas-Petroski S, Olshefsky G, Schramm L. MAF1 is a predictive biomarker in HER2 positive breast cancer. PLoS One 2023; 18:e0291549. [PMID: 37801436 PMCID: PMC10558074 DOI: 10.1371/journal.pone.0291549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 09/01/2023] [Indexed: 10/08/2023] Open
Abstract
RNA polymerase III transcription is pivotal in regulating cellular growth and frequently deregulated in various cancers. MAF1 negatively regulates RNA polymerase III transcription. Currently, it is unclear if MAF1 is universally deregulated in human cancers. Recently, MAF1 expression has been demonstrated to be altered in colorectal and liver carcinomas and Luminal B breast cancers. In this study, we analyzed clinical breast cancer datasets to determine if MAF1 alterations correlate with clinical outcomes in HER2-positive breast cancer. Using various bioinformatics tools, we screened breast cancer datasets for alterations in MAF1 expression. We report that MAF1 is amplified in 39% of all breast cancer sub-types, and the observed amplification co-occurs with MYC. MAF1 amplification correlated with increased methylation of the MAF1 promoter and MAF1 protein expression is significantly decreased in luminal, HER2-positive, and TNBC breast cancer subtypes. MAF1 protein expression is also significantly reduced in stage 2 and 3 breast cancer compared to normal and significantly decreased in all breast cancer patients, regardless of race and age. In SKBR3 and BT474 breast cancer cell lines treated with anti-HER2 therapies, MAF1 mRNA expression is significantly increased. In HER2-positive breast cancer patients, MAF1 expression significantly increases and correlates with five years of relapse-free survival in response to trastuzumab treatment, suggesting MAF1 is a predictive biomarker in breast cancer. These data suggest a role for MAF1 alterations in HER2-positive breast cancer. More extensive studies are warranted to determine if MAF1 serves as a predictive and prognostic biomarker in breast cancer.
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Affiliation(s)
| | | | - Laura Schramm
- Department of Biology, St. John’s University, Queens, NY, United States of America
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3
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Kim S, Kim N, Kang HM, Jang HJ, Lee AC, Na KJ. Canine Somatic Mutations from Whole-Exome Sequencing of B-Cell Lymphomas in Six Canine Breeds-A Preliminary Study. Animals (Basel) 2023; 13:2846. [PMID: 37760246 PMCID: PMC10525272 DOI: 10.3390/ani13182846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/05/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Canine lymphoma (CL) is one of the most common malignant tumors in dogs. The cause of CL remains unclear. Genetic mutations that have been suggested as possible causes of CL are not fully understood. Whole-exome sequencing (WES) is a time- and cost-effective method for detecting genetic variants targeting only the protein-coding regions (exons) that are part of the entire genome region. A total of eight patients with B-cell lymphomas were recruited, and WES analysis was performed on whole blood and lymph node aspirate samples from each patient. A total of 17 somatic variants (GOLIM4, ITM2B, STN1, UNC79, PLEKHG4, BRF1, ENSCAFG00845007156, SEMA6B, DSC1, TNFAIP1, MYLK3, WAPL, ADORA2B, LOXHD1, GP6, AZIN1, and NCSTN) with moderate to high impact were identified by WES analysis. Through a Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of 17 genes with somatic mutations, a total of 16 pathways were identified. Overall, the somatic mutations identified in this study suggest novel candidate mutations for CL, and further studies are needed to confirm the role of these mutations.
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Affiliation(s)
- Sungryong Kim
- Laboratory of Veterinary Laboratory Medicine, College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea; (S.K.); (H.-M.K.)
| | - Namphil Kim
- Biophotonics and Nano Engineering Laboratory, Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, Republic of Korea;
| | - Hyo-Min Kang
- Laboratory of Veterinary Laboratory Medicine, College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea; (S.K.); (H.-M.K.)
| | - Hye-Jin Jang
- Department of Biomedical Laboratory Science, Daegu Health College, Daegu 41453, Republic of Korea;
| | | | - Ki-Jeong Na
- Laboratory of Veterinary Laboratory Medicine, College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea; (S.K.); (H.-M.K.)
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4
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Butterfield SP, Sizer RE, Rand E, White RJ. Selection of tRNA Genes in Human Breast Tumours Varies Substantially between Individuals. Cancers (Basel) 2023; 15:3576. [PMID: 37509247 PMCID: PMC10377016 DOI: 10.3390/cancers15143576] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/07/2023] [Accepted: 07/09/2023] [Indexed: 07/30/2023] Open
Abstract
Abnormally elevated expression of tRNA is a common feature of breast tumours. Rather than a uniform increase in all tRNAs, some are deregulated more strongly than others. Elevation of particular tRNAs has been associated with poor prognosis for patients, and experimental models have demonstrated the ability of some tRNAs to promote proliferation or metastasis. Each tRNA isoacceptor is encoded redundantly by multiple genes, which are commonly dispersed across several chromosomes. An unanswered question is whether the consistently high expression of a tRNA in a cancer type reflects the consistent activation of the same members of a gene family, or whether different family members are activated from one patient to the next. To address this question, we interrogated ChIP-seq data to determine which tRNA genes were active in individual breast tumours. This revealed that distinct sets of tRNA genes become activated in individual cancers, whereas there is much less variation in the expression patterns of families. Several pathways have been described that are likely to contribute to increases in tRNA gene transcription in breast tumours, but none of these can adequately explain the observed variation in the choice of genes between tumours. Current models may therefore lack at least one level of regulation.
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Affiliation(s)
| | - Rebecca E Sizer
- Department of Biology, University of York, York YO10 5DD, UK
| | - Emma Rand
- Department of Biology, University of York, York YO10 5DD, UK
| | - Robert J White
- Department of Biology, University of York, York YO10 5DD, UK
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5
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Cabarcas-Petroski S, Olshefsky G, Schramm L. BDP1 as a biomarker in serous ovarian cancer. Cancer Med 2023; 12:6401-6418. [PMID: 36305848 PMCID: PMC10028122 DOI: 10.1002/cam4.5388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 09/19/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND TFIIIB, an RNA polymerase III specific transcription factor has been found to be deregulated in human cancers with much of the research focused on the TBP, BRF1, and BRF2 subunits. To date, the TFIIIB specific subunit BDP1 has not been investigated in ovarian cancer but has previously been shown to be deregulated in neuroblastoma, breast cancer, and Non-Hodgkins lymphoma. RESULTS Using in silico analysis of clinically derived platforms, we report a decreased BDP1 expression as a result of deletion in serous ovarian cancer and a correlation with higher and advanced ovarian stages. Further analysis in the context of TP53 mutations, a major contributor to ovarian tumorigenesis, suggests that high BDP1 expression is unfavorable for overall survival and high BDP1 expression occurs in stages 2, 3 and 4 serous ovarian cancer. Additionally, high BDP1 expression is disadvantageous and unfavorable for progression-free survival. Lastly, BDP1 expression significantly decreased in patients treated with first-line chemotherapy, platin and taxane, at twelve-month relapse-free survival. CONCLUSIONS Taken together with a ROC analysis, the data suggest BDP1 could be of clinical relevance as a predictive biomarker in serous ovarian cancer. Lastly, this study further demonstrates that both the over- and under expression of BDP1 warrants further investigation and suggests BDP1 may exhibit dual function in the context of tumorigenesis.
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Affiliation(s)
| | | | - Laura Schramm
- Biology Department, St. John's University, Queens, New York, USA
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Wang J, Chen Q, Wang X, Zhao S, Deng H, Guo B, Zhang C, Song X, Deng W, Zhang T, Ni H. TFIIB-related factor 1 is a nucleolar protein that promotes RNA polymerase I-directed transcription and tumour cell growth. Hum Mol Genet 2023; 32:104-121. [PMID: 35925837 DOI: 10.1093/hmg/ddac152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 06/26/2022] [Accepted: 07/01/2022] [Indexed: 01/25/2023] Open
Abstract
Eukaryotic RNA polymerase I (Pol I) products play fundamental roles in ribosomal assembly, protein synthesis, metabolism and cell growth. Abnormal expression of both Pol I transcription-related factors and Pol I products causes a range of diseases, including ribosomopathies and cancers. However, the factors and mechanisms governing Pol I-dependent transcription remain to be elucidated. Here, we report that transcription factor IIB-related factor 1 (BRF1), a subunit of transcription factor IIIB required for RNA polymerase III (Pol III)-mediated transcription, is a nucleolar protein and modulates Pol I-mediated transcription. We showed that BRF1 can be localized to the nucleolus in several human cell types. BRF1 expression correlates positively with Pol I product levels and tumour cell growth in vitro and in vivo. Pol III transcription inhibition assays confirmed that BRF1 modulates Pol I-directed transcription in an independent manner rather than through a Pol III product-to-45S pre-rRNA feedback mode. Mechanistically, BRF1 binds to the Pol I transcription machinery components and can be recruited to the rDNA promoter along with them. Additionally, alteration of BRF1 expression affects the recruitment of Pol I transcription machinery components to the rDNA promoter and the expression of TBP and TAF1A. These findings indicate that BRF1 modulates Pol I-directed transcription by controlling the expression of selective factor 1 subunits. In summary, we identified a novel role of BRF1 in Pol I-directed transcription, suggesting that BRF1 can independently regulate both Pol I- and Pol III-mediated transcription and act as a key coordinator of Pol I and Pol III.
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Affiliation(s)
- Juan Wang
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan 430065, China.,School of Materials and Metallurgy, Wuhan University of Science and Technology, Wuhan 430081, China
| | - Qiyue Chen
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Xin Wang
- Faculty of Biology, Medicine, and Health, University of Manchester, Manchester M13 9PL, UK
| | - Shasha Zhao
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Huan Deng
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Baoqiang Guo
- School of Healthcare Science, Manchester Metropolitan University, Manchester M1 5GD, UK
| | - Cheng Zhang
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Xiaoye Song
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Wensheng Deng
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Tongcun Zhang
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Hongwei Ni
- School of Materials and Metallurgy, Wuhan University of Science and Technology, Wuhan 430081, China
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Malcolm JR, Leese NK, Lamond-Warner PI, Brackenbury WJ, White RJ. Widespread association of ERα with RMRP and tRNA genes in MCF-7 cells and breast cancers. Gene X 2022; 821:146280. [PMID: 35143945 PMCID: PMC8942118 DOI: 10.1016/j.gene.2022.146280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 01/21/2022] [Accepted: 02/03/2022] [Indexed: 12/04/2022] Open
Abstract
Estrogen receptor (ER) interacts with hundreds of tRNA genes (tDNAs) in MCF-7 cells. Hundreds of tDNAs are also targeted in primary breast tumours and metastases. Canonical estrogen response element is not found near top tDNA targets of ER. ER also targets non-coding breast cancer driver gene RMRP. ER also targets RN7SL1 gene that promotes breast cancer progression.
tRNA gene transcription by RNA polymerase III (Pol III) is a tightly regulated process, but dysregulated Pol III transcription is widely observed in cancers. Approximately 75% of all breast cancers are positive for expression of Estrogen Receptor alpha (ERα), which acts as a key driver of disease. MCF-7 cells rapidly upregulate tRNA gene transcription in response to estrogen and ChIP-PCR demonstrated ERα enrichment at tRNALeu and 5S rRNA genes in this breast cancer cell line. While these data implicate the ERα as a Pol III transcriptional regulator, how widespread this regulation is across the 631 tRNA genes has yet to be revealed. Through analyses of ERα ChIP-seq datasets, we show that ERα interacts with hundreds of tRNA genes, not only in MCF-7 cells, but also in primary human breast tumours and distant metastases. The extent of ERα association with tRNA genes varies between breast cancer cell lines and does not correlate with levels of ERα binding to its canonical target gene GREB1. Amongst other Pol III-transcribed genes, ERα is consistently enriched at the long non-coding RNA gene RMRP, a positive regulator of cell cycle progression that is subject to focal amplification in tumours. Another Pol III template targeted by ERα is the RN7SL1 gene, which is strongly implicated in breast cancer pathology by inducing inflammatory responses in tumours. Our data indicate that Pol III-transcribed non-coding genes should be added to the list of ERα targets in breast cancer.
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Affiliation(s)
- Jodie R Malcolm
- Department of Biology, The University of York, Heslington Road, YO10 5DD, United Kingdom
| | - Natasha K Leese
- Department of Biology, The University of York, Heslington Road, YO10 5DD, United Kingdom
| | | | - William J Brackenbury
- Department of Biology, The University of York, Heslington Road, YO10 5DD, United Kingdom
| | - Robert J White
- Department of Biology, The University of York, Heslington Road, YO10 5DD, United Kingdom.
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Goldkamp AK, Li Y, Rivera RM, Hagen DE. Characterization of tRNA expression profiles in large offspring syndrome. BMC Genomics 2022; 23:273. [PMID: 35392796 PMCID: PMC8988405 DOI: 10.1186/s12864-022-08496-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 03/23/2022] [Indexed: 11/10/2022] Open
Abstract
Background Assisted Reproductive Technologies (ART) use can increase the risk of congenital overgrowth syndromes, such as large offspring syndrome (LOS) in ruminants. Epigenetic variations are known to influence gene expression and differentially methylated regions (DMRs) were previously determined to be associated with LOS in cattle. We observed DMRs overlapping tRNA clusters which could affect tRNA abundance and be associated with tissue specificity or overgrowth. Variations in tRNA expression have been identified in several disease pathways suggesting an important role in the regulation of biological processes. Understanding the role of tRNA expression in cattle offers an opportunity to reveal mechanisms of regulation at the translational level. We analyzed tRNA expression in the skeletal muscle and liver tissues of day 105 artificial insemination-conceived, ART-conceived with a normal body weight, and ART-conceived bovine fetuses with a body weight above the 97th percentile compared to Control-AI. Results Despite the centrality of tRNAs to translation, in silico predictions have revealed dramatic differences in the number of tRNA genes between humans and cattle (597 vs 1,659). Consistent with reports in human, only a fraction of predicted tRNA genes are expressed. We detected the expression of 474 and 487 bovine tRNA genes in the muscle and liver with the remainder being unexpressed. 193 and 198 unique tRNA sequences were expressed in all treatment groups within muscle and liver respectively. In addition, an average of 193 tRNA sequences were expressed within the same treatment group in different tissues. Some tRNA isodecoders were differentially expressed between treatment groups. In the skeletal muscle and liver, we categorized 11 tRNA isoacceptors with undetected expression as well as an isodecoder that was unexpressed in the liver (SerGGA). Our results identified variation in the proportion of tRNA gene copies expressed between tissues and differences in the highest contributing tRNA anticodon within an amino acid family due to treatment and tissue type. Out of all amino acid families, roughly half of the most highly expressed tRNA isoacceptors correlated to their most frequent codon in the bovine genome. Conclusion Although the number of bovine tRNA genes is nearly triple of that of the tRNA genes in human, there is a shared occurrence of transcriptionally inactive tRNA genes in both species. We detected differential expression of tRNA genes as well as tissue- and treatment- specific tRNA transcripts with unique sequence variations that could modulate translation during protein homeostasis or cellular stress, and give rise to regulatory products targeting genes related to overgrowth in the skeletal muscle and/or tumor development in the liver of LOS individuals. While the absence of certain isodecoders may be relieved by wobble base pairing, missing tRNA species could increase the likelihood of mistranslation or mRNA degradation. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08496-7.
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Affiliation(s)
- Anna K Goldkamp
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Yahan Li
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Rocio M Rivera
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Darren E Hagen
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, USA.
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BDP1 Alterations Correlate with Clinical Outcomes in Breast Cancer. Cancers (Basel) 2022; 14:cancers14071658. [PMID: 35406430 PMCID: PMC8996959 DOI: 10.3390/cancers14071658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/21/2022] [Accepted: 03/21/2022] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Breast cancer accounts for 30% of all new cancer diagnoses in the United States. The most common type of breast cancer is invasive breast cancer. A hallmark trait of breast cancer is uncontrolled cell growth due to genetic alterations. TFIIIB-mediated RNA polymerase III transcription is specifically deregulated in human cancers. The TFIIIB BDP1 subunit is not well characterized in human cancer. The objective of this study was to analyze publicly available clinical cancer datasets to determine if BDP1 alterations correlate with clinical outcomes in available breast cancer datasets. BDP1 copy number and expression negatively correlate with breast cancer outcomes, including stage, grade, and mortality. Abstract TFIIIB is deregulated in a variety of cancers. However, few studies investigate the TFIIIB subunit BDP1 in cancer. BDP1 has not been studied in breast cancer patients. Herein, we analyzed clinical breast cancer datasets to determine if BDP1 alterations correlate with clinical outcomes. BDP1 copy number (n = 1602; p = 8.03 × 10−9) and mRNA expression (n = 130; p = 0.002) are specifically decreased in patients with invasive ductal carcinoma (IDC). In IDC, BDP1 copy number negatively correlates with high grade (n = 1992; p = 2.62 × 10−19) and advanced stage (n = 1992; p = 0.005). BDP1 mRNA expression also negatively correlated with high grade (n = 55; p = 6.81 × 10−4) and advanced stage (n = 593; p = 4.66 × 10−4) IDC. Decreased BDP1 expression correlated with poor clinical outcomes (n = 295 samples): a metastatic event at three years (p = 7.79 × 10−7) and cancer reoccurrence at three years (p = 4.81 × 10−7) in IDC. Decreased BDP1 mRNA correlates with patient death at three (p = 9.90 × 10−6) and five (p = 1.02 × 10−6) years. Both BDP1 copy number (n = 3785; p = 1.0 × 10−14) and mRNA expression (n = 2434; p = 5.23 × 10−6) are altered in triple-negative invasive breast cancer (TNBC). Together, these data suggest a role for BDP1 as potential biomarker in breast cancer and additional studies are warranted.
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Nsengimana B, Khan FA, Ngowi EE, Zhou X, Jin Y, Jia Y, Wei W, Ji S. Processing body (P-body) and its mediators in cancer. Mol Cell Biochem 2022; 477:1217-1238. [PMID: 35089528 DOI: 10.1007/s11010-022-04359-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 01/11/2022] [Indexed: 12/24/2022]
Abstract
In recent years, processing bodies (P-bodies) formed by liquid-liquid phase separation, have attracted growing scientific attention due to their involvement in numerous cellular activities, including the regulation of mRNAs decay or storage. These cytoplasmic dynamic membraneless granules contain mRNA storage and decay components such as deadenylase and decapping factors. In addition, different mRNA metabolic regulators, including m6A readers and gene-mediated miRNA-silencing, are also associated with such P-bodies. Cancerous cells may profit from these mRNA decay shredders by up-regulating the expression level of oncogenes and down-regulating tumor suppressor genes. The main challenges of cancer treatment are drug resistance, metastasis, and cancer relapse likely associated with cancer stem cells, heterogeneity, and plasticity features of different tumors. The mRNA metabolic regulators based on P-bodies play a great role in cancer development and progression. The dysregulation of P-bodies mediators affects mRNA metabolism. However, less is known about the relationship between P-bodies mediators and cancerous behavior. The current review summarizes the recent studies on P-bodies mediators, their contribution to tumor development, and their potential in the clinical setting, particularly highlighting the P-bodies as potential drug-carriers such as exosomes to anticancer in the future.
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Affiliation(s)
- Bernard Nsengimana
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Henan, 475004, People's Republic of China
| | - Faiz Ali Khan
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Henan, 475004, People's Republic of China
| | - Ebenezeri Erasto Ngowi
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Henan, 475004, People's Republic of China
| | - Xuefeng Zhou
- Department of Oncology, Dongtai Affiliated Hospital of Nantong University, Dongtai, 224200, Jiangsu, People's Republic of China
| | - Yu Jin
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Henan, 475004, People's Republic of China
| | - Yuting Jia
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Henan, 475004, People's Republic of China
| | - Wenqiang Wei
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Henan, 475004, People's Republic of China.
| | - Shaoping Ji
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Henan, 475004, People's Republic of China.
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Zhang C, Zhao H, Song X, Wang J, Zhao S, Deng H, He L, Zhou X, Yin X, Zhang K, Zhang Y, Wu Z, Chen Q, Du J, Yu D, Zhang S, Deng W. Transcription factor GATA4 drives RNA polymerase III-directed transcription and transformed cell proliferation through a filamin A/GATA4/SP1 pathway. J Biol Chem 2022; 298:101581. [PMID: 35038452 PMCID: PMC8857480 DOI: 10.1016/j.jbc.2022.101581] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/31/2021] [Accepted: 01/03/2022] [Indexed: 11/27/2022] Open
Abstract
RNA polymerase III (pol III) products play fundamental roles in a variety of cellular processes, including protein synthesis and cancer cell proliferation. In addition, dysregulation of pol III-directed transcription closely correlates with tumorigenesis. It is therefore of interest to identify novel pathways or factors governing pol III-directed transcription. Here, we show that transcription factor (TF) GATA binding protein 4 (GATA4) expression in SaOS2 cells was stimulated by the silencing of filamin A (FLNA), a repressor of pol III-directed transcription, suggesting that GATA4 is potentially associated with the regulation of pol III-directed transcription. Indeed, we show that GATA4 expression positively correlates with pol III-mediated transcription and tumor cell proliferation. Mechanistically, we found that GATA4 depletion inhibits the occupancies of the pol III transcription machinery factors at the loci of pol III target genes by reducing expression of both TFIIIB subunit TFIIB-related factor 1 and TFIIIC subunit general transcription factor 3C subunit 2 (GTF3C2). GATA4 has been shown to activate specificity factor 1 (Sp1) gene transcription by binding to the Sp1 gene promoter, and Sp1 has been confirmed to activate pol III gene transcription by directly binding to both Brf1 and Gtf3c2 gene promoters. Thus, the findings from this study suggest that GATA4 links FLNA and Sp1 signaling to form an FLNA/GATA4/Sp1 axis to modulate pol III-directed transcription and transformed cell proliferation. Taken together, these results provide novel insights into the regulatory mechanism of pol III-directed transcription.
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Affiliation(s)
- Cheng Zhang
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Houliang Zhao
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Xiaoye Song
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Juan Wang
- School of Materials and Metallurgy, Wuhan University of Science and Technology, Wuhan, China
| | - Shasha Zhao
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Huan Deng
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Liu He
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Xiangyu Zhou
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Xiaomei Yin
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Kewei Zhang
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Yue Zhang
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Zhongyu Wu
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Qiyue Chen
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Jiannan Du
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Deen Yu
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Shihua Zhang
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, China.
| | - Wensheng Deng
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, China.
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12
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Qiu Z, Wang Q, Liu L, Li G, Hao Y, Ning S, Zhang L, Zhang X, Chen Y, Wu J, Wang X, Yang S, Lin Y, Xu S. Riddle of the Sphinx: Emerging Role of Transfer RNAs in Human Cancer. Front Pharmacol 2021; 12:794986. [PMID: 34975491 PMCID: PMC8714751 DOI: 10.3389/fphar.2021.794986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/10/2021] [Indexed: 01/16/2023] Open
Abstract
The dysregulation of transfer RNA (tRNA) expression contributes to the diversity of proteomics, heterogeneity of cell populations, and instability of the genome, which may be related to human cancer susceptibility. However, the relationship between tRNA dysregulation and cancer susceptibility remains elusive because the landscape of cancer-associated tRNAs has not been portrayed yet. Furthermore, the molecular mechanisms of tRNAs involved in tumorigenesis and cancer progression have not been systematically understood. In this review, we detail current knowledge of cancer-related tRNAs and comprehensively summarize the basic characteristics and functions of these tRNAs, with a special focus on their role and involvement in human cancer. This review bridges the gap between tRNAs and cancer and broadens our understanding of their relationship, thus providing new insights and strategies to improve the potential clinical applications of tRNAs for cancer diagnosis and therapy.
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Affiliation(s)
- Zhilin Qiu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Qin Wang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Lei Liu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Guozheng Li
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yi Hao
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Shipeng Ning
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Lei Zhang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xin Zhang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yihai Chen
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jiale Wu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xinheng Wang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Shuai Yang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yaoxin Lin
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing, China
- *Correspondence: Yaoxin Lin, ; Shouping Xu,
| | - Shouping Xu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
- *Correspondence: Yaoxin Lin, ; Shouping Xu,
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13
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Zheng L, Lin Y, Zhong S. ROS Signaling-Mediated Novel Biological Targets: Brf1 and RNA Pol III Genes. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:5888432. [PMID: 34646425 PMCID: PMC8505076 DOI: 10.1155/2021/5888432] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 09/20/2021] [Indexed: 11/18/2022]
Abstract
Biomolecule metabolism produces ROS (reactive oxygen species) under physiological and pathophysiological conditions. Dietary factors (alcohol) and carcinogens (EGF, DEN, and MNNG) also induce the release of ROS. ROS often causes cell stress and tissue injury, eventually resulting in disorders or diseases of the body through different signaling pathways. Normal metabolism of protein is critically important to maintain cellular function and body health. Brf1 (transcript factor II B-related factor 1) and its target genes, RNA Pol III genes (RNA polymerase III-dependent genes), control the process of protein synthesis. Studies have demonstrated that the deregulation of Brf1 and its target genes is tightly linked to cell proliferation, cell transformation, tumor development, and human cancers, while alcohol, EGF, DEN, and MNNG are able to induce the deregulation of these genes through different signaling pathways. Therefore, it is very important to emphasize the roles of these signaling events mediating the processes of Brf1 and RNA Pol III gene transcription. In the present paper, we mainly summarize our studies on signaling events which mediate the deregulation of these genes in the past dozen years. These studies indicate that Brf1 and RNA Pol III genes are novel biological targets of ROS.
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Affiliation(s)
- Liling Zheng
- First Hospital of Quanzhou Affiliated to Fujian Medical University, China
| | - Yongluan Lin
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shuping Zhong
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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14
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Abstract
Increased proliferation and protein synthesis are characteristics of transformed and tumor cells. Although the components of the translation machinery are often dysregulated in cancer, the role of tRNAs in cancer cells has not been well studied. Nevertheless, the number of related studies has recently started increasing. With the development of high throughput technologies such as next-generation sequencing, genome-wide differential tRNA expression patterns in breast cancer-derived cell lines and breast tumors have been investigated. The genome-wide transcriptomics analyses have been linked with many studies for functional and phenotypic characterization, whereby tRNAs or tRNA-related fragments have been shown to play important roles in breast cancer regulation and as promising prognostic biomarkers. Here, we review their expression patterns, functions, prognostic value, and potential therapeutic use as well as related technologies.
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Sabit H, Abdel-Ghany S, Tombuloglu H, Cevik E, Alqosaibi A, Almulhim F, Al-Muhanaa A. New insights on CRISPR/Cas9-based therapy for breast Cancer. Genes Environ 2021; 43:15. [PMID: 33926574 PMCID: PMC8082964 DOI: 10.1186/s41021-021-00188-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/12/2021] [Indexed: 12/26/2022] Open
Abstract
CRISPR/Cas9 has revolutionized genome-editing techniques in various biological fields including human cancer research. Cancer is a multi-step process that encompasses the accumulation of mutations that result in the hallmark of the malignant state. The goal of cancer research is to identify these mutations and correlate them with the underlying tumorigenic process. Using CRISPR/Cas9 tool, specific mutations responsible for cancer initiation and/or progression could be corrected at least in animal models as a first step towards translational applications. In the present article, we review various novel strategies that employed CRISPR/Cas9 to treat breast cancer in both in vitro and in vivo systems.
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Affiliation(s)
- Hussein Sabit
- Department of Genetics, Institute for Medical Research and Consultations, Imam Abdulrahman Bin Faisal University, P. O. Box: 1982, Dammam, 31441, Saudi Arabia.
| | - Shaimaa Abdel-Ghany
- Department of Environmental Biotechnology, College of Biotechnology, Misr University for Science and Technology, P. O. Box 77, Giza, Egypt
| | - Huseyin Tombuloglu
- Department of Genetics, Institute for Medical Research and Consultations, Imam Abdulrahman Bin Faisal University, P. O. Box: 1982, Dammam, 31441, Saudi Arabia
| | - Emre Cevik
- Department of Genetics, Institute for Medical Research and Consultations, Imam Abdulrahman Bin Faisal University, P. O. Box: 1982, Dammam, 31441, Saudi Arabia
| | - Amany Alqosaibi
- Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University, P. O. 4 Box, Dammam, 1982, Saudi Arabia
| | - Fatma Almulhim
- Breast Imaging Division, KFHU, Imam Abdulrahman Bin Faisal University, P. O. 4 Box, Dammam, 1982, Saudi Arabia
| | - Afnan Al-Muhanaa
- Breast Imaging Division, KFHU, Imam Abdulrahman Bin Faisal University, P. O. 4 Box, Dammam, 1982, Saudi Arabia
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16
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Wu T, Zhang D, Lin M, Yu L, Dai T, Li S, Yu F, Lu L, Zheng L, Zhong S. Exploring the Role and Mechanism of pAMPK α-Mediated Dysregulation of Brf1 and RNA Pol III Genes. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:5554932. [PMID: 33995823 PMCID: PMC8081602 DOI: 10.1155/2021/5554932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/30/2021] [Accepted: 04/05/2021] [Indexed: 02/05/2023]
Abstract
TF IIB-related factor 1 (Brf1) is a key transcription factor of RNA polymerase III (Pol III) genes. Our early studies have demonstrated that Brf1 and Pol III genes are epigenetically modulated by histone H3 phosphorylation. Here, we have further investigated the relationship of the abnormal expression of Brf1 with a high level of phosphorylated AMPKα (pAMPKα) and explored the role and molecular mechanism of pAMPKα-mediated dysregulation of Brf1 and Pol III genes in lung cancer. Brf1 is significantly overexpressed in lung cancer cases. The cases with high Brf1 expression display short overall survival times. Elevation of Brf1 expression is accompanied by a high level of pAMPKα. Brf1 and pAMPKα colocalize in nuclei. Further analysis indicates that the carcinogen MNNG induces pAMPKα to upregulate Brf1 expression, resulting in the enhancement of Pol III transcription. In contrast, inhibiting pAMPKα decreases cellular levels of Brf1, resulting in the reduction of Pol III gene transcription to attenuate the rates of cell proliferation and colony formation of lung cancer cells. These outcomes demonstrate that high Brf1 expression reveals a worse prognosis in lung cancer patients. pAMPKα-mediated dysregulation of Brf1 and Pol III genes plays important roles in cell proliferation, colony formation, and tumor development of lung cancer. Brf1 may be a biomarker for establishing the prognosis of lung cancer. It is a new mechanism that pAMPKα mediates dysregulation of Brf1 and Pol III genes to promote lung cancer development.
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Affiliation(s)
- Teng Wu
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, China
| | - Dongkun Zhang
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Mingen Lin
- The First Affiliated Hospital of Shantou University Medical College, China
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Lihong Yu
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, China
| | - Ting Dai
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, China
| | - Shuai Li
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, China
| | - Fenghai Yu
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, China
| | - Lei Lu
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, China
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Liling Zheng
- First Hospital of Quanzhou Affiliated to Fujian Medical University, China
| | - Shuping Zhong
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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17
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Ho C, Lin CY. Genes Associated with Calcium Signaling are Involved in Alcohol-Induced Breast Cancer Growth. Alcohol Clin Exp Res 2020; 45:79-91. [PMID: 33222221 DOI: 10.1111/acer.14521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/26/2020] [Accepted: 11/16/2020] [Indexed: 11/27/2022]
Abstract
BACKGROUND Alcohol consumption is a risk factor for breast cancer, contributing to up to nearly 23,000 new cases each year. Mechanistic studies show that alcohol increases tumor aggressiveness and metastatic potential, promotes angiogenesis, induces chronic inflammation, and dysregulates RNA polymerase III-related genes. Alcohol has also been shown to affect estrogen signaling in breast cancer, including in our study of the transcriptomic effects of alcohol in breast cancer cells. METHODS To elucidate mechanisms of action of alcohol in breast cancer, we carried out secondary analyses of our alcohol-responsive transcriptome data using gene ontology and pathway databases and analysis tools and cistromic data analysis of candidate transcription factors which may mediate the transcriptomic alterations. Predicted alcohol-responsive pathways and mechanisms were perturbed and examined experimentally in breast cancer cells. The clinical relevance of identified genes was determined by expression profiles in patient samples and correlation with disease outcomes and alcohol consumption in previously published study cohorts. RESULTS Gene ontology analysis showed that alcohol alters the expression of many metabolism-related genes, and cistromic data of differentially expressed genes revealed the potential involvement of nuclear factor of activated T cells 3 (NFATC3) in mediating the transcriptomic effects of alcohol. Pathway analysis also predicted regulation of calcium signaling by alcohol in breast cancer cells. Chemical perturbation of this pathway reversed the effect of alcohol on breast cancer cell growth and reduced the elevated cytosolic Ca2+ levels induced by alcohol. Expression levels of alcohol-responsive genes in tumor samples from breast cancer patients are associated with poor disease outcomes. Moreover, expression of some of these genes was altered in breast cancer patients who consumed alcohol previously as compared to those who did not drink. CONCLUSION Alcohol alters expression of genes that regulate intracellular calcium levels and downstream signaling pathways which drive breast cancer cell proliferation and disease progression.
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Affiliation(s)
- Charles Ho
- From the, Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Science & Engineering Research Center, Houston, Texas, USA
| | - Chin-Yo Lin
- From the, Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Science & Engineering Research Center, Houston, Texas, USA
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18
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Liu Q, Lan T, Song Y, Cai J, Yu X, Chen W. Oncostatin M expression and TP53 mutation status regulate tumor-infiltration of immune cells and survival outcomes in cholangiocarcinoma. Aging (Albany NY) 2020; 12:21518-21543. [PMID: 33216732 DOI: 10.18632/aging.103936] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 08/01/2020] [Indexed: 11/25/2022]
Abstract
In this study, we used bioinformatics tools to analyze transcriptome data from cholangiocarcinoma (CCA) patients in multiple datasets (Sun Yat-sen University, TCGA and GSE32225 cohorts) to identify mechanisms that regulate tumor infiltration by immune cells and survival outcomes. We identified 96 differentially expressed genes (DEGs), including 13 upregulated and 83 downregulated genes, in CCA tissues as regulatory T cells were significantly higher and the proportions of activated natural killer cells and monocytes were significantly lower in CCA tissues than the precancerous tissues. The survival outcomes of CCA patients were associated with the TP53 gene mutation status, levels of Oncostatin M (OSM) expression, and the proportions of tumor-infiltrating immune cell types, including dendritic cells, monocytes, and T follicular helper cells. Functional enrichment analysis of the DEGs in the high OSM-expressing CCA tissues showed that pathways related to tumor progression and immune response were significantly upregulated. Our study demonstrates that OSM expression and TP53 mutation status regulate the tumor infiltration by immune cells and survival outcomes in CCA. OSM is thus a potential prognostic biomarker and therapeutic target in cholangiocarcinoma.
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Affiliation(s)
- Qi Liu
- Department of Pancreatico-Biliary Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, Guangdong Province, China
| | - Tian Lan
- Department of Pancreatico-Biliary Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, Guangdong Province, China
| | - Yuxuan Song
- Department of Urology, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Jianpeng Cai
- Department of Pancreatico-Biliary Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, Guangdong Province, China
| | - Xi Yu
- Department of Pancreatico-Biliary Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, Guangdong Province, China
| | - Wei Chen
- Department of Pancreatico-Biliary Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, Guangdong Province, China
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Abstract
In this review, Yeganeh et al. summarize different human diseases that have been linked to defects in the Pol III transcription apparatus or to Pol III products imbalance and discuss the possible underlying mechanisms. RNA polymerase (Pol) III is responsible for transcription of different noncoding genes in eukaryotic cells, whose RNA products have well-defined functions in translation and other biological processes for some, and functions that remain to be defined for others. For all of them, however, new functions are being described. For example, Pol III products have been reported to regulate certain proteins such as protein kinase R (PKR) by direct association, to constitute the source of very short RNAs with regulatory roles in gene expression, or to control microRNA levels by sequestration. Consistent with these many functions, deregulation of Pol III transcribed genes is associated with a large variety of human disorders. Here we review different human diseases that have been linked to defects in the Pol III transcription apparatus or to Pol III products imbalance and discuss the possible underlying mechanisms.
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Affiliation(s)
- Meghdad Yeganeh
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Nouria Hernandez
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
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20
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Hong Z, Lin M, Zhang Y, He Z, Zheng L, Zhong S. Role of betaine in inhibiting the induction of RNA Pol III gene transcription and cell growth caused by alcohol. Chem Biol Interact 2020; 325:109129. [PMID: 32418914 PMCID: PMC7323736 DOI: 10.1016/j.cbi.2020.109129] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 03/24/2020] [Accepted: 05/06/2020] [Indexed: 02/05/2023]
Abstract
Alcohol has been classified as carcinogenic to humans by the International Agency for Research on Cancer (IARC). Studies have demonstrated that alcohol intake increases the risk of breast cancer, and alcohol also stimulates breast cancer cell growth. Deregulation of Pol III genes is tightly associated with tumour development. Transcription factor II-B (TFIIB)-related factor 1 (Brf1) is a transcription factor that specifically regulates Pol III gene transcription. Our in vivo and in vitro studies have indicated that alcohol enhances the transcription of Pol III genes to cause an alteration of cellular phenotypes, which is closely related with human breast cancer. Betaine is a vegetable alkaloid and has antitumor functions. Most reports about betaine show that the consumption level of betaine is inversely associated with a risk of breast cancer. Although different mechanisms of betaine against tumour have been investigated, nothing has been reported on the effect of betaine on the deregulation of Brf1 and Pol III genes. In this study, we determine the role of betaine in breast cancer cell growth and colony formation and explore its mechanism. Our results indicate that alcohol increases the rates of growth and colony formation of breast cancer cells, whereas betaine is able to significantly inhibit the effects of alcohol on these cell phenotypes. Betaine decreases the induction of Brf1 expression and Pol III gene transcription caused by ethanol to reduce the rates of cell growth and colony formation. Together, these studies provide novel insights into the role of betaine in alcohol-caused breast cancer cell growth and deregulation of Brf1 and Pol III genes. These results suggest that betaine consumption is able to prevent alcohol-associated human cancer development.
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Affiliation(s)
- Zaifa Hong
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, China; Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Mingen Lin
- The First Hospital of Shantou University Medical College, China; Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Yanmei Zhang
- Department of Pharmacology of Shantou University Medical College, China; Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Zhimin He
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, China
| | - Liling Zheng
- First Hospital of Quanzhou Affiliated to Fujian Medical University, China.
| | - Shuping Zhong
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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21
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Mitogen- and Stress-Activated Protein Kinase 1 Mediates Alcohol-Upregulated Transcription of Brf1 and tRNA Genes to Cause Phenotypic Alteration. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:2067959. [PMID: 32685086 PMCID: PMC7336232 DOI: 10.1155/2020/2067959] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/20/2020] [Accepted: 06/08/2020] [Indexed: 02/06/2023]
Abstract
Upregulation of Brf1 (TFIIB-related factor 1) and Pol III gene (RNA polymerase III-dependent gene, such as tRNAs and 5S rRNA) activities is associated with cell transformation and tumor development. Alcohol intake causes liver injury, such as steatosis, inflammation, fibrosis, and cirrhosis, which enhances the risk of HCC development. However, the mechanism of alcohol-promoted HCC remains to be explored. We have designed the complementary research system, which is composed of cell lines, an animal model, human samples, and experiments in vivo and in vitro, to carry out this project by using molecular biological, biochemical, and cellular biological approaches. It is a unique system to explore the mechanism of alcohol-associated HCC. Our results indicate that alcohol upregulates Brf1 and Pol III gene (tRNAs and 5S rRNA) transcription in primary mouse hepatocytes, immortalized mouse hepatocyte-AML-12 cells, and engineered human HepG2-ADH cells. Alcohol activates MSK1 to upregulate expression of Brf1 and Pol III genes, while inhibiting MSK1 reduces transcription of Brf1 and Pol III genes in alcohol-treated cells. The inhibitor of MSK1, SB-747651A, decreases the rates of cell proliferation and colony formation. Alcohol feeding promotes liver tumor development of the mouse. These results, for the first time, show the identification of the alcohol-response promoter fragment of the Pol III gene key transcription factor, Brf1. Our studies demonstrate that Brf1 expression is elevated in HCC tumor tissues of mice and humans. Alcohol increases cellular levels of Brf1, resulting in enhancement of Pol III gene transcription in hepatocytes through MSK1. Our mechanism analysis has demonstrated that alcohol-caused high-response fragment of the Brf1 promoter is at p-382/+109bp. The MSK1 inhibitor SB-747651A is an effective reagent to repress alcohol-induced cell proliferation and colony formation, which is a potential pharmaceutical agent. Developing this inhibitor as a therapeutic approach will benefit alcohol-associated HCC patients.
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Zeng T, Hua Y, Sun C, Zhang Y, Yang F, Yang M, Yang Y, Li J, Huang X, Wu H, Fu Z, Li W, Yin Y. Relationship between tRNA-derived fragments and human cancers. Int J Cancer 2020; 147:3007-3018. [PMID: 32427348 DOI: 10.1002/ijc.33107] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 04/14/2020] [Accepted: 05/11/2020] [Indexed: 12/11/2022]
Abstract
tRNA-derived fragments, a class of small noncoding RNAs (sncRNAs), have been identified in numerous studies in recent years. tRNA-derived fragments are classified into two main groups, including tRNA halves (tiRNAs) and tRNA-derived small RNA fragments (tRFs), according to different cleavage positions of the precursor or mature tRNAs. Instead of random tRNA degradation debris, a growing body of evidence has shown that tRNA-derived fragments are precise products of specific tRNA modifications and play important roles in biological activities, such as regulating protein translation, affecting gene expression, and altering immune signaling. Recently, the relations between tRNA-derived fragments and the occurrence of human diseases, especially cancers, have generated wide interest. It has been demonstrated that tRNA-derived fragments are involved in cancer cell proliferation, metastasis, progression and survival. In this review, we will describe the biogenesis of tRNA-derived fragments, the distinct expression and function of tRNA-derived fragments in the development of cancers, and their emerging roles as diagnostic and prognostic biomarkers and precise targets of future treatments.
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Affiliation(s)
- Tianyu Zeng
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yijia Hua
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chunxiao Sun
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yuchen Zhang
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Fan Yang
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Mengzhu Yang
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yiqi Yang
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jun Li
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiang Huang
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hao Wu
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ziyi Fu
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Nanjing Maternal and Child Health Medical Institute, Obstetrics and Gynecology Hospital Affiliated of Nanjing Medical University, Nanjing, China
| | - Wei Li
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yongmei Yin
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
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23
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Hong Z, Fang Z, Lei J, Shi G, Zhang Y, He Z, Li B W, Zhong S. The significance of Runx2 mediating alcohol-induced Brf1 expression and RNA Pol III gene transcription. Chem Biol Interact 2020; 323:109057. [PMID: 32198086 PMCID: PMC7261693 DOI: 10.1016/j.cbi.2020.109057] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 03/10/2020] [Indexed: 02/05/2023]
Abstract
Runx2 (Runt-related transcription factor 2) is a key transcription factor which is associated with osteoblast differentiation and expressed in ER+ (estrogen receptor positive) human breast cancer cell lines. Runx2 also participates in mammary gland development. Deregulation of RNA Pol III genes (polymerase III-dependent genes) is tightly linked to tumor development, while Brf1 (TFIIB-related factor 1) specifically regulates these gene transcription. However, nothing is known about the effect of Runx2 on Brf1 expression and Pol III gene transcription. Expression of Runx2, Brf1 and Pol III genes from the samples of human breast cancer and cell culture model were determined by the assays of RT-qPCR, immunoblot, luciferase reporter activity, immunohistochemistry, chromatin immunoprecipitation and Immunofluorescence. High expression of Runx2 is observed in the cases of breast cancer. The patients of high Runx2 expression at early stages display longer survival period, whereas the cases of high Runx2 at advanced stages reveal faster recurrence. The identification of signaling pathway indicates that JNK1 and c-Jun mediate Runx2 transcription. Repression of Runx2 reduces Brf1 expression and Pol III gene transcription. Further analysis indicates that Runx2 is colocalized with Brf1 in nucleus of breast cancer tissue. Both Runx2 and Brf1 synergistically modulate Pol III gene transcription. These studies indicate that Brf1 overexpression is able to be used as an early diagnosis biomarker of breast cancer, while high Runx2 expression indicates long survival period and faster recurrence. Runx2 mediates the deregulation of Brf1 and Pol III genes and its abnormal expression predicts the worse prognosis of breast cancer.
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Affiliation(s)
- Zaifa Hong
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, China; Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Zeng Fang
- Laboratory of General Surgery and Department of Breast and Thyroid Surgery, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Junxia Lei
- School of Medicine, South China University of Technology, China; Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ganggang Shi
- Department of Pharmacology, Shantou University Medical College, China
| | - Yanmei Zhang
- Department of Pharmacology, Shantou University Medical College, China; Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Zhiming He
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, China
| | - Wen Li B
- Laboratory of General Surgery and Department of Breast and Thyroid Surgery, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
| | - Shuping Zhong
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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24
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Loveridge CJ, Slater S, Campbell KJ, Nam NA, Knight J, Ahmad I, Hedley A, Lilla S, Repiscak P, Patel R, Salji M, Fleming J, Mitchell L, Nixon C, Strathdee D, Neilson M, Ntala C, Bryson S, Zanivan S, Edwards J, Robson CN, Goodyear CS, Blyth K, Leung HY. BRF1 accelerates prostate tumourigenesis and perturbs immune infiltration. Oncogene 2020; 39:1797-1806. [PMID: 31740786 PMCID: PMC7033044 DOI: 10.1038/s41388-019-1106-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 10/22/2019] [Accepted: 11/06/2019] [Indexed: 01/10/2023]
Abstract
BRF1 is a rate-limiting factor for RNA Polymerase III-mediated transcription and is elevated in numerous cancers. Here, we report that elevated levels of BRF1 associate with poor prognosis in human prostate cancer. In vitro studies in human prostate cancer cell lines demonstrated that transient overexpression of BRF1 increased cell proliferation whereas the transient downregulation of BRF1 reduced proliferation and mediated cell cycle arrest. Consistent with our clinical observations, BRF1 overexpression in a Pten-deficient mouse (PtenΔ/Δ BRF1Tg) prostate cancer model accelerated prostate carcinogenesis and shortened survival. In PtenΔ/Δ BRF1Tg tumours, immune and inflammatory processes were altered, with reduced tumoral infiltration of neutrophils and CD4 positive T cells, which can be explained by decreased levels of complement factor D (CFD) and C7 components of the complement cascade, an innate immune pathway that influences the adaptive immune response. We tested if the secretome was involved in BRF1-driven tumorigenesis. Unbiased proteomic analysis on BRF1-overexpresing PC3 cells confirmed reduced levels of CFD in the secretome, implicating the complement system in prostate carcinogenesis. We further identify that expression of C7 significantly correlates with expression of CD4 and has the potential to alter clinical outcome in human prostate cancer, where low levels of C7 associate with poorer prognosis.
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Affiliation(s)
- Carolyn J Loveridge
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden, Glasgow, G61 1QH, UK
- CRUK Beatson Institute, Bearsden, Glasgow, G61 1BD, UK
| | - Sarah Slater
- CRUK Beatson Institute, Bearsden, Glasgow, G61 1BD, UK
| | - Kirsteen J Campbell
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden, Glasgow, G61 1QH, UK
- CRUK Beatson Institute, Bearsden, Glasgow, G61 1BD, UK
| | - Noor A Nam
- CRUK Beatson Institute, Bearsden, Glasgow, G61 1BD, UK
- Department of Basic Sciences and Oral Biology, Faculty of Dentistry, Universiti Sains Islam Malaysia, Kuala Lumpur, Malaysia
| | - John Knight
- CRUK Beatson Institute, Bearsden, Glasgow, G61 1BD, UK
| | - Imran Ahmad
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden, Glasgow, G61 1QH, UK
- CRUK Beatson Institute, Bearsden, Glasgow, G61 1BD, UK
| | - Ann Hedley
- CRUK Beatson Institute, Bearsden, Glasgow, G61 1BD, UK
| | - Sergio Lilla
- CRUK Beatson Institute, Bearsden, Glasgow, G61 1BD, UK
| | | | - Rachana Patel
- CRUK Beatson Institute, Bearsden, Glasgow, G61 1BD, UK
| | - Mark Salji
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden, Glasgow, G61 1QH, UK
- CRUK Beatson Institute, Bearsden, Glasgow, G61 1BD, UK
| | - Janis Fleming
- CRUK Beatson Institute, Bearsden, Glasgow, G61 1BD, UK
| | | | - Colin Nixon
- CRUK Beatson Institute, Bearsden, Glasgow, G61 1BD, UK
| | | | | | - Chara Ntala
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden, Glasgow, G61 1QH, UK
- CRUK Beatson Institute, Bearsden, Glasgow, G61 1BD, UK
| | - Sheila Bryson
- CRUK Beatson Institute, Bearsden, Glasgow, G61 1BD, UK
| | - Sara Zanivan
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden, Glasgow, G61 1QH, UK
- CRUK Beatson Institute, Bearsden, Glasgow, G61 1BD, UK
| | - Joanne Edwards
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden, Glasgow, G61 1QH, UK
| | - Craig N Robson
- Northern Institute for Cancer Research, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Carl S Goodyear
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Karen Blyth
- CRUK Beatson Institute, Bearsden, Glasgow, G61 1BD, UK
| | - Hing Y Leung
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden, Glasgow, G61 1QH, UK.
- CRUK Beatson Institute, Bearsden, Glasgow, G61 1BD, UK.
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25
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Liko D, Mitchell L, Campbell KJ, Ridgway RA, Jones C, Dudek K, King A, Bryson S, Stevenson D, Blyth K, Strathdee D, Morton JP, Bird TG, Knight JRP, Willis AE, Sansom OJ. Brf1 loss and not overexpression disrupts tissues homeostasis in the intestine, liver and pancreas. Cell Death Differ 2019; 26:2535-2550. [PMID: 30858608 PMCID: PMC6861133 DOI: 10.1038/s41418-019-0316-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 01/18/2019] [Accepted: 02/13/2019] [Indexed: 12/22/2022] Open
Abstract
RNA polymerase III (Pol-III) transcribes tRNAs and other small RNAs essential for protein synthesis and cell growth. Pol-III is deregulated during carcinogenesis; however, its role in vivo has not been studied. To address this issue, we manipulated levels of Brf1, a Pol-III transcription factor that is essential for recruitment of Pol-III holoenzyme at tRNA genes in vivo. Knockout of Brf1 led to embryonic lethality at blastocyst stage. In contrast, heterozygous Brf1 mice were viable, fertile and of a normal size. Conditional deletion of Brf1 in gastrointestinal epithelial tissues, intestine, liver and pancreas, was incompatible with organ homeostasis. Deletion of Brf1 in adult intestine and liver induced apoptosis. However, Brf1 heterozygosity neither had gross effects in these epithelia nor did it modify tumorigenesis in the intestine or pancreas. Overexpression of BRF1 rescued the phenotypes of Brf1 deletion in intestine and liver but was unable to initiate tumorigenesis. Thus, Brf1 and Pol-III activity are absolutely essential for normal homeostasis during development and in adult epithelia. However, Brf1 overexpression or heterozygosity are unable to modify tumorigenesis, suggesting a permissive, but not driving role for Brf1 in the development of epithelial cancers of the pancreas and gut.
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Affiliation(s)
- Dritan Liko
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Louise Mitchell
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Kirsteen J Campbell
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Rachel A Ridgway
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Carolyn Jones
- MRC Toxicology Unit, Hodgkin Building Lancaster Road, Leicester, LE1 9HN, UK
| | - Kate Dudek
- MRC Toxicology Unit, Hodgkin Building Lancaster Road, Leicester, LE1 9HN, UK
| | - Ayala King
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Sheila Bryson
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - David Stevenson
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Karen Blyth
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD, UK
| | - Douglas Strathdee
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Jennifer P Morton
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD, UK
| | - Thomas G Bird
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - John R P Knight
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK.
| | - Anne E Willis
- MRC Toxicology Unit, Hodgkin Building Lancaster Road, Leicester, LE1 9HN, UK
| | - Owen J Sansom
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK.
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD, UK.
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26
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Zhang K, Yang W, Yu H, Fu C, Liu X, Liu J. Double mutation of BRF1 and BRF2 leads to sterility in Arabidopsis thaliana. Biochem Biophys Res Commun 2019; 516:969-975. [PMID: 31277948 DOI: 10.1016/j.bbrc.2019.06.138] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 06/24/2019] [Indexed: 01/22/2023]
Abstract
The TFIIB-related factor (BRF) family plays vital roles in RNA polymerase (Pol) III transcription initiation. However, little is known about the role of BRF in plants. Here, we report BRF1 and BRF2 are involved in Arabidopsis reproduction. In this study, we generated BRF1 and BRF2 double mutant plants. We found that no homozygous double mutants of brf1brf2 were obtained when brf1 and brf2 were crossed, although brf1 and brf2 mutants individually developed and reproduced normally. Further experiments revealed that heterozygous brf1/ + brf2/ + produced abnormal pollen and had no seeds in some placentas of siliques. Genetic data derived from reciprocal crosses showed that BRF2 plays a dominant role in Arabidopsis reproduction. Taken together, a double mutation of BRF1 and BRF2 results in a high degree of aborted macrogametes and microgametes and complete failure in zygote generation, ultimately leading to sterility.
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Affiliation(s)
- Kaiyue Zhang
- College of Life Science, Shandong Normal University, Jinan, 250014, Shandong, China
| | - Wenwen Yang
- College of Life Science, Shandong Normal University, Jinan, 250014, Shandong, China
| | - Hongbin Yu
- College of Life Science, Shandong Normal University, Jinan, 250014, Shandong, China
| | - Can Fu
- College of Life Science, Shandong Normal University, Jinan, 250014, Shandong, China
| | - Xiaxia Liu
- College of Life Science, Shandong Normal University, Jinan, 250014, Shandong, China
| | - Jian Liu
- College of Life Science, Shandong Normal University, Jinan, 250014, Shandong, China.
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27
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Santos M, Fidalgo A, Varanda AS, Oliveira C, Santos MAS. tRNA Deregulation and Its Consequences in Cancer. Trends Mol Med 2019; 25:853-865. [PMID: 31248782 DOI: 10.1016/j.molmed.2019.05.011] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 05/24/2019] [Accepted: 05/28/2019] [Indexed: 02/06/2023]
Abstract
The expression of transfer RNAs (tRNAs) is deregulated in cancer cells but the mechanisms and functional meaning of such deregulation are poorly understood. The proteome of cancer cells is not fully encoded by their transcriptome, however, the contribution of mRNA translation to such diversity remains to be elucidated. We review data supporting the hypothesis that tRNA expression deregulation and translational error rate is an important contributor to proteome diversity and cell population heterogeneity, genome instability, and drug resistance in tumors. This hypothesis is aligned with recent data in various model organisms, showing unanticipated adaptive roles of translational errors (adaptive mistranslation), expression control of specific gene subsets by tRNAs, and proteome diversification by elevation of translational error rates in tumors.
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Affiliation(s)
- Mafalda Santos
- Expression Regulation in Cancer, Instituto de Investigação e Inovação em Saúde, University of Porto, Portugal; Institute of Molecular Pathology and Immunology University of Porto (IPATIMUP), Porto, Portugal; Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - Ana Fidalgo
- Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - A Sofia Varanda
- Expression Regulation in Cancer, Instituto de Investigação e Inovação em Saúde, University of Porto, Portugal; Institute of Molecular Pathology and Immunology University of Porto (IPATIMUP), Porto, Portugal; Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - Carla Oliveira
- Expression Regulation in Cancer, Instituto de Investigação e Inovação em Saúde, University of Porto, Portugal; Institute of Molecular Pathology and Immunology University of Porto (IPATIMUP), Porto, Portugal; Department of Pathology, Medical Faculty of Porto, Porto, Portugal.
| | - Manuel A S Santos
- Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal.
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28
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Chen S, Yi Y, Xia T, Hong Z, Zhang Y, Shi G, He Z, Zhong S. The influences of red wine in phenotypes of human cancer cells. Gene 2019; 702:194-204. [PMID: 30366081 PMCID: PMC6478559 DOI: 10.1016/j.gene.2018.10.049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/16/2018] [Accepted: 10/19/2018] [Indexed: 02/05/2023]
Abstract
Alcohol intake increases the risk of cancer development. Approximately 3.6% human cancers worldwide derive from chronic alcohol drinking, including oral, liver, breast and other organs. Our studies in vivo and in vitro have demonstrated that diluted ethanol increase RNA Pol III gene transcription and promotes cell proliferation and transformation, as well as tumor formation. However, it is unclear about the effect of red wines on the human cancer cells. In present study, we investigated the roles of red wine in human cancer cell growth, colony formation and RNA Pol III gene transcription. Low concentration (12.5 mM to 25 mM) of ethanol enhances cell proliferation of breast and esophageal cancer lines, whereas its higher concentration (100 mM to 200 mM) slightly decreases the rates. In contrast, red wines significantly repress cell proliferation of different human cancer lines from low dose to high dose. The results reveal that the red wine also inhibits colony formation of human breast cancer and esophageal carcinoma cells. The effects of repression on different human cancer lines are in a dose-dependent manner. Further analysis indicates that ethanol increases RNA Pol III gene transcription, whereas the red wines significantly reduce transcription of the genes. Interestingly, the effects of mature wine (brick red) on cancer cell phenotypes are much stronger than young wine (intense violet). Together, these new findings suggest that red wines may contain some bioactive components, which are able to inhibit human cancer cell growth and colony formation.
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Affiliation(s)
- Songlin Chen
- Department of Cardiothoracic Surgery, Xiamen University Affiliated Southeast Hospital, China
| | - Yunfeng Yi
- Department of Cardiothoracic Surgery, Xiamen University Affiliated Southeast Hospital, China
| | - Ting Xia
- Department of Cardiothoracic Surgery, Xiamen University Affiliated Southeast Hospital, China
| | - Zaifa Hong
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, China; Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Yanmei Zhang
- Department of Pharmacology, Shantou University Medical College, China; Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ganggang Shi
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, China
| | - Zhimin He
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, China
| | - Shuping Zhong
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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29
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Özcan Şimşek NÖ, Özgür A, Gürgen F. Statistical representation models for mutation information within genomic data. BMC Bioinformatics 2019; 20:324. [PMID: 31195961 PMCID: PMC6567431 DOI: 10.1186/s12859-019-2868-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 04/30/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND As DNA sequencing technologies are improving and getting cheaper, genomic data can be utilized for diagnosis of many diseases such as cancer. Human raw genome data is huge in size for computational systems. Therefore, there is a need for a compact and accurate representation of the valuable information in DNA. The occurrence of complex genetic disorders often results from multiple gene mutations. The effect of each mutation is not equal for the development of a disease. Inspired from the field of information retrieval, we propose using the term frequency (tf) and BM25 term weighting measures with the inverse document frequency (idf) and relevance frequency (rf) measures to weight genes based on their mutations. The underlying assumption is that the more mutations a gene has in patients with a certain disease and the less mutations it has in other patients, the more discriminative that gene is. RESULTS We evaluated the proposed representations on the task of cancer type classification. We applied various machine learning techniques using the tf-idf and tf-rf schemes and their BM25 versions. Our results show that the BM25-tf-rf representation leads to improved classification accuracy and f-score values compared to the other representations. The highest accuracy (76.44%) and f-score (76.95%) are achieved with the BM25-tf-rf based data representation. CONCLUSIONS As a result of our experiments, the BM25-tf-rf scheme and the proposed neural network model is shown to be the best performing classification system for our case study of cancer type classification. This system is further utilized for causal gene analysis. Examples from the most effective genes that are used for decision making are found to be in the literature as target or causal genes.
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Affiliation(s)
| | - Arzucan Özgür
- Department of Computer Engineering, Boğaziçi University, İstanbul, Turkey.
| | - Fikret Gürgen
- Department of Computer Engineering, Boğaziçi University, İstanbul, Turkey.
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30
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tRNA-derived fragments and tRNA halves: The new players in cancers. Cancer Lett 2019; 452:31-37. [DOI: 10.1016/j.canlet.2019.03.012] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 02/25/2019] [Accepted: 03/08/2019] [Indexed: 01/27/2023]
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31
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Huang C, Zhang Y, Zhong S. Alcohol Intake and Abnormal Expression of Brf1 in Breast Cancer. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:4818106. [PMID: 31781337 PMCID: PMC6874981 DOI: 10.1155/2019/4818106] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 09/28/2019] [Indexed: 02/07/2023]
Abstract
Breast cancer is the most common malignant disease of females. Overall, one woman in every nine will get breast cancer at some time in her life. Epidemiological studies have indicated that alcohol consumption has most consistently been associated with breast cancer risk. However, the mechanism of alcohol-associated breast cancer remains to be addressed. Little is known about the effects of alcohol consumption on Brf1 (TFIIIB-related factor 1) expression and RNA Pol III gene (RNA polymerase III-dependent gene) transcription, which are responsible for protein synthesis and tightly linked to cell proliferation, cell transformation, and tumor development. Emerging evidences have indicated that alcohol induces deregulation of Brf1 and Pol III genes to cause the alterations of cell phenotypes and tumor formation. In this paper, we summarize the progresses regarding alcohol-caused increase in the expression of Brf1 and Pol III genes and analysis of its molecular mechanism of breast cancer. As the earlier and accurate diagnosis approach of breast cancer is not available yet, exploring the molecular mechanism and identifying the biomarker of alcohol-associated breast cancer are especially important. Recent studies have demonstrated that Brf1 is overexpressed in most ER+ (estrogen receptor positive) cases of breast cancer and the change in cellular levels of Brf1 reflects the therapeutic efficacy and prognosis of this disease. It suggests that Brf1 may be a potential diagnosis biomarker and a therapeutic target of alcohol-associated breast cancer.
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Affiliation(s)
- Chenghao Huang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, China
| | - Yanmei Zhang
- Department of Pharmacology of Shantou University Medical College, China
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shuping Zhong
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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32
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Wang F, Zhao K, Yu S, Xu A, Han W, Mei Y. RNF12 catalyzes BRF1 ubiquitination and regulates RNA polymerase III-dependent transcription. J Biol Chem 2018; 294:130-141. [PMID: 30413534 DOI: 10.1074/jbc.ra118.004524] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/24/2018] [Indexed: 01/07/2023] Open
Abstract
RNA polymerase III (Pol III) is responsible for the production of small noncoding RNA species, including tRNAs and 5S rRNA. Pol III-dependent transcription is generally enhanced in transformed cells and tumors, but the underlying mechanisms remain not well-understood. It has been demonstrated that the BRF1 subunit of TFIIIB is essential for the accurate initiation of Pol III-dependent transcription. However, it is not known whether BRF1 undergoes ubiquitin modification and whether BRF1 ubiquitination regulates Pol III-dependent transcription. Here, we show that RNF12, a RING domain-containing ubiquitin E3 ligase, physically interacts with BRF1. Via direct interaction, RNF12 catalyzes Lys27- and Lys33-linked polyubiquitination of BRF1. Furthermore, RNF12 is able to negatively regulate Pol III-dependent transcription and cell proliferation via BRF1. These findings uncover a novel mechanism for the regulation of BRF1 and reveal RNF12 as an important regulator of Pol III-dependent transcription.
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Affiliation(s)
- Fang Wang
- Anhui Province Key Laboratory of Medical Physics and Technology/Center of Medical Physics and Technology, Hefei Institutes of Physical Sciences, Chinese Academy of Sciences, Hefei 230031, Anhui, China; Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230026, Anhui, China
| | - Kailiang Zhao
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230026, Anhui, China
| | - Sixiang Yu
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230026, Anhui, China
| | - An Xu
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230026, Anhui, China
| | - Wei Han
- Anhui Province Key Laboratory of Medical Physics and Technology/Center of Medical Physics and Technology, Hefei Institutes of Physical Sciences, Chinese Academy of Sciences, Hefei 230031, Anhui, China.
| | - Yide Mei
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230026, Anhui, China.
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33
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Huang SQ, Sun B, Xiong ZP, Shu Y, Zhou HH, Zhang W, Xiong J, Li Q. The dysregulation of tRNAs and tRNA derivatives in cancer. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2018; 37:101. [PMID: 29743091 PMCID: PMC5944149 DOI: 10.1186/s13046-018-0745-z] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 03/29/2018] [Indexed: 11/14/2022]
Abstract
Transfer RNAs (tRNAs), traditionally considered to participate in protein translation, were interspersed in the entire genome. Recent studies suggested that dysregulation was observed in not only tRNAs, but also tRNA derivatives generated by the specific cleavage of pre- and mature tRNAs in the progression of cancer. Accumulating evidence had identified that certain tRNAs and tRNA derivatives were involved in proliferation, metastasis and invasiveness of cancer cell, as well as tumor growth and angiogenesis in several malignant human tumors. This paper reviews the importance of the dysregulation of tRNAs and tRNA derivatives during the development of cancer, such as breast cancer, lung cancer, and melanoma, aiming at a better understanding of the tumorigenesis and providing new ideas for the treatment of these cancers.
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Affiliation(s)
- Shi-Qiong Huang
- Department of Clinical Pharmacology, Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, People's Republic of China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, 410078, People's Republic of China
| | - Bao Sun
- Department of Clinical Pharmacology, Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, People's Republic of China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, 410078, People's Republic of China
| | - Zong-Ping Xiong
- Department of Clinical Pharmacology, Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, People's Republic of China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, 410078, People's Republic of China
| | - Yan Shu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland at Baltimore, Baltimore, MD, USA
| | - Hong-Hao Zhou
- Department of Clinical Pharmacology, Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, People's Republic of China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, 410078, People's Republic of China
| | - Wei Zhang
- Department of Clinical Pharmacology, Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, People's Republic of China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, 410078, People's Republic of China
| | - Jing Xiong
- Department of gynaecology and obstetrics, The Second Xiangya Hospital of Central South University, Central South University, Changsha, 410078, People's Republic of China.
| | - Qing Li
- Department of Clinical Pharmacology, Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, People's Republic of China. .,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, 410078, People's Republic of China.
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34
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Yi Y, Lei J, Shi G, Chen S, Zhang Y, Hong Z, He Z, Zhong S. The Effects of Liquor Spirits on RNA Pol III Genes and Cell Growth of Human Cancer Lines. ACTA ACUST UNITED AC 2018. [DOI: 10.4236/fns.2018.93016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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