1
|
Luna R, Gómez-González B, Aguilera A. RNA biogenesis and RNA metabolism factors as R-loop suppressors: a hidden role in genome integrity. Genes Dev 2024; 38:504-527. [PMID: 38986581 PMCID: PMC11293400 DOI: 10.1101/gad.351853.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Genome integrity relies on the accuracy of DNA metabolism, but as appreciated for more than four decades, transcription enhances mutation and recombination frequencies. More recent research provided evidence for a previously unforeseen link between RNA and DNA metabolism, which is often related to the accumulation of DNA-RNA hybrids and R-loops. In addition to physiological roles, R-loops interfere with DNA replication and repair, providing a molecular scenario for the origin of genome instability. Here, we review current knowledge on the multiple RNA factors that prevent or resolve R-loops and consequent transcription-replication conflicts and thus act as modulators of genome dynamics.
Collapse
Affiliation(s)
- Rosa Luna
- Andalusian Center of Molecular Biology and Regenerative Medicine (CABIMER), Universidad de Sevilla-Spanish National Research Council (CSIC), 41092 Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Belén Gómez-González
- Andalusian Center of Molecular Biology and Regenerative Medicine (CABIMER), Universidad de Sevilla-Spanish National Research Council (CSIC), 41092 Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Andrés Aguilera
- Andalusian Center of Molecular Biology and Regenerative Medicine (CABIMER), Universidad de Sevilla-Spanish National Research Council (CSIC), 41092 Seville, Spain;
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| |
Collapse
|
2
|
Li S, Wang W, Yu H, Zhang S, Bi W, Sun S, Hong B, Fang Z, Chen X. Characterization of genomic instability-related genes predicts survival and therapeutic response in lung adenocarcinoma. BMC Cancer 2023; 23:1115. [PMID: 37974107 PMCID: PMC10655275 DOI: 10.1186/s12885-023-11580-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 10/27/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is the most common subtype of non-small cell lung cancer (NSCLC) and is the leading cause of cancer death worldwide. Its progression is characterized by genomic instability. In turn, the level of genomic instability affects the prognosis and immune status of patients with LUAD. However, the impact of molecular features associated with genomic instability on the tumor microenvironment (TME) has not been well characterized. In addition, the effect of the genes related to genomic instability in LUAD on individualized treatment of LUAD is unknown. METHODS The RNA-Sequencing, somatic mutation, and clinical data of LUAD patients were downloaded from publicly available databases. A genetic signature associated with genomic instability (GSAGI) was constructed by univariate Cox regression, Lasso regression, and multivariate Cox regression analysis. Bioinformatics analysis investigated the differences in prognosis, immune characteristics, and the most appropriate treatment strategy among different subtypes of LUAD patients. CCK-8 and colony formation verified the various effects of Etoposide on different subtypes of LUAD cell lines. Cell-to-cell communication analysis was performed using the "CellChat" R package. The expression of the risk factors in the GSAGI was verified using real-time quantitative PCR (qRT-PCR) and Immunohistochemistry (IHC). RESULTS We constructed and validated the GSAGI, consisting of five genes: ANLN, RHOV, KRT6A, SIGLEC6, and KLRG2. The GSAGI was an independent prognostic factor for LUAD patients. Patients in the high-risk group distinguished by the GSAGI are more suitable for chemotherapy. More immune cells are infiltrating the tumor microenvironment of patients in the low-risk group, especially B cells. Low-risk group patients are more suitable for receiving immunotherapy. The single-cell level analysis confirmed the influence of the GSAGI on TME and revealed the Mode of action between tumor cells and other types of cells. qRT-PCR and IHC showed increased ANLN, RHOV, and KRT6A expression in the LUAD cells and tumor tissues. CONCLUSION This study confirms that genes related to genomic instability can affect the prognosis and immune status of LUAD patients. The GSAGI we identified has the potential to guide clinicians in predicting clinical outcomes, assessing immunological status, and even developing personalized treatment plans for LUAD patients.
Collapse
Affiliation(s)
- Shuyang Li
- School of Basic Medicine, Anhui Medical University, No. 81, Meishan Road, Hefei, 230032, Anhui, China
- Hefei Cancer Hospital of CAS, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences (CAS), No. 350, Shushan Hu Road, Hefei, 230031, Anhui, China
| | - Wei Wang
- School of Basic Medicine, Anhui Medical University, No. 81, Meishan Road, Hefei, 230032, Anhui, China
- Hefei Cancer Hospital of CAS, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences (CAS), No. 350, Shushan Hu Road, Hefei, 230031, Anhui, China
| | - Huihan Yu
- School of Basic Medicine, Anhui Medical University, No. 81, Meishan Road, Hefei, 230032, Anhui, China
- Hefei Cancer Hospital of CAS, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences (CAS), No. 350, Shushan Hu Road, Hefei, 230031, Anhui, China
| | - Siyu Zhang
- Hefei Cancer Hospital of CAS, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences (CAS), No. 350, Shushan Hu Road, Hefei, 230031, Anhui, China
| | - Wenxu Bi
- Hefei Cancer Hospital of CAS, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences (CAS), No. 350, Shushan Hu Road, Hefei, 230031, Anhui, China
| | - Suling Sun
- Hefei Cancer Hospital of CAS, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences (CAS), No. 350, Shushan Hu Road, Hefei, 230031, Anhui, China
| | - Bo Hong
- Hefei Cancer Hospital of CAS, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences (CAS), No. 350, Shushan Hu Road, Hefei, 230031, Anhui, China
| | - Zhiyou Fang
- School of Basic Medicine, Anhui Medical University, No. 81, Meishan Road, Hefei, 230032, Anhui, China.
- Hefei Cancer Hospital of CAS, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences (CAS), No. 350, Shushan Hu Road, Hefei, 230031, Anhui, China.
| | - Xueran Chen
- School of Basic Medicine, Anhui Medical University, No. 81, Meishan Road, Hefei, 230032, Anhui, China.
- Hefei Cancer Hospital of CAS, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences (CAS), No. 350, Shushan Hu Road, Hefei, 230031, Anhui, China.
| |
Collapse
|
3
|
Zhang Y, Wang Y, He X, Yao R, Fan L, Zhao L, Lu B, Pang Z. Genome instability-related LINC02577, LINC01133 and AC107464.2 are lncRNA prognostic markers correlated with immune microenvironment in pancreatic adenocarcinoma. BMC Cancer 2023; 23:430. [PMID: 37173624 PMCID: PMC10176692 DOI: 10.1186/s12885-023-10831-4] [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: 05/11/2022] [Accepted: 04/09/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Pancreatic adenocarcinoma (PAAD) is a leading cause of malignancy-related deaths worldwide, and the efficacy of immunotherapy on PAAD is limited. Studies report that long non-coding RNAs (lncRNAs) play an important role in modulating genomic instability and immunotherapy. However, the identification of genome instability-related lncRNAs and their clinical significance has not been investigated in PAAD. METHODS The current study developed a computational framework for mutation hypothesis based on lncRNA expression profile and somatic mutation spectrum in pancreatic adenocarcinoma genome. We explored the potential of GInLncRNAs(genome instability-related lncRNAs) through co-expression analysis and function enrichment analysis. We further analyzed GInLncRNAs by Cox regression and used the results to construct a prognostic lncRNA signature. Finally, we analyzed the relationship between GILncSig (genomic instability derived 3-lncRNA signature) and immunotherapy. RESULTS A GILncSig was developed using bioinformatics analyses. It could divide patients into high-risk and low-risk groups, and there was a significant difference in OS between the two groups. In addition, GILncSig was associated with genome mutation rate in pancreatic adenocarcinoma, indicating its potential value as a marker for genomic instability. The GILncSig accurately grouped wild type patients of KRAS into two risk groups. The prognosis of the low-risk group was significantly improved. GILncSig was significantly correlated with the level of immune cell infiltration and immune checkpoint. CONCLUSIONS In summary, the current study provides a basis for further studies on the role of lncRNA in genomic instability and immunotherapy. The study provides a novel method for identification of cancer biomarkers related to genomic instability and immunotherapy.
Collapse
Affiliation(s)
- Yinjiang Zhang
- School of Pharmacy, Minzu University of China, No. 27, Zhongguancunnan Street, Haidian District, Beijing, 100081, People's Republic of China
- Key Laboratory of Ethnomedicine, Ministry of Education, Minzu University of China), Beijing, People's Republic of China
| | - Yao Wang
- Department of Radiation Oncology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Xu He
- School of Pharmacy, Minzu University of China, No. 27, Zhongguancunnan Street, Haidian District, Beijing, 100081, People's Republic of China
- Key Laboratory of Ethnomedicine, Ministry of Education, Minzu University of China), Beijing, People's Republic of China
| | - Rongfei Yao
- School of Pharmacy, Minzu University of China, No. 27, Zhongguancunnan Street, Haidian District, Beijing, 100081, People's Republic of China
- Key Laboratory of Ethnomedicine, Ministry of Education, Minzu University of China), Beijing, People's Republic of China
| | - Lu Fan
- School of Pharmacy, Minzu University of China, No. 27, Zhongguancunnan Street, Haidian District, Beijing, 100081, People's Republic of China
- Key Laboratory of Ethnomedicine, Ministry of Education, Minzu University of China), Beijing, People's Republic of China
| | - Linyi Zhao
- School of Pharmacy, Minzu University of China, No. 27, Zhongguancunnan Street, Haidian District, Beijing, 100081, People's Republic of China
- Key Laboratory of Ethnomedicine, Ministry of Education, Minzu University of China), Beijing, People's Republic of China
| | - Binan Lu
- School of Pharmacy, Minzu University of China, No. 27, Zhongguancunnan Street, Haidian District, Beijing, 100081, People's Republic of China.
- Key Laboratory of Ethnomedicine, Ministry of Education, Minzu University of China), Beijing, People's Republic of China.
| | - Zongran Pang
- School of Pharmacy, Minzu University of China, No. 27, Zhongguancunnan Street, Haidian District, Beijing, 100081, People's Republic of China.
- Key Laboratory of Ethnomedicine, Ministry of Education, Minzu University of China), Beijing, People's Republic of China.
| |
Collapse
|
4
|
Franco PIR, Neto JRDC, de Menezes LB, Machado JR, Miguel MP. Revisiting the hallmarks of cancer: A new look at long noncoding RNAs in breast cancer. Pathol Res Pract 2023; 243:154381. [PMID: 36857948 DOI: 10.1016/j.prp.2023.154381] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/16/2023] [Indexed: 02/19/2023]
Abstract
Breast cancer is one of the leading causes of death in women worldwide. The increasing understanding of the molecular mechanisms underlying its heterogeneity favors a better understanding of tumor biology and consequently the development of better diagnostic and treatment techniques. The advent of tumor genome sequencing techniques has highlighted more participants in the process, in addition to protein-coding genes. Thus, it is now known that long noncoding RNAs, previously described as transcriptional noise with no biological function, are intimately associated with tumor development. In breast cancer, they are abnormally expressed and closely associated with tumor progression, which makes them attractive diagnostic biomarkers and prognostic and specific therapeutic targets. Therefore, a thorough understanding of the regulatory mechanisms of long noncoding RNAs in breast cancer is essential for the search for new treatment strategies. In this review, we summarize the major long noncoding RNAs and their association with the cancer characteristics of the ability to sustain proliferative signaling, evasion of growth suppressors, replicative immortality, activation of invasion and metastasis, induction of angiogenesis, resistance to cell death, reprogramming of energy metabolism, genomic instability and sustained mutations, promotion of tumor inflammation, and evasion of the immune system. In addition, we report and suggest how they can be used as prognostic biomarkers and possible therapeutic targets.
Collapse
Affiliation(s)
- Pablo Igor Ribeiro Franco
- Instituto de Patologia Tropical e Saúde Pública, Programa de Pós-Graduação em Medicina Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, GO, Brazil.
| | - José Rodrigues do Carmo Neto
- Instituto de Patologia Tropical e Saúde Pública, Programa de Pós-Graduação em Medicina Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Liliana Borges de Menezes
- Setor de Patologia Geral, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, GO, Brazil; Escola de Veterinária e Zootecnia, Programa de Pós-Graduação em Ciência Animal, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Juliana Reis Machado
- Instituto de Patologia Tropical e Saúde Pública, Programa de Pós-Graduação em Medicina Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, GO, Brazil; Departamento de Patologia, Genética e Evolução, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, MG, Brazil
| | - Marina Pacheco Miguel
- Setor de Patologia Geral, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, GO, Brazil; Escola de Veterinária e Zootecnia, Programa de Pós-Graduação em Ciência Animal, Universidade Federal de Goiás, Goiânia, GO, Brazil
| |
Collapse
|
5
|
Kumar A, Fournier LA, Stirling PC. Integrative analysis and prediction of human R-loop binding proteins. G3 (BETHESDA, MD.) 2022; 12:jkac142. [PMID: 35666183 PMCID: PMC9339281 DOI: 10.1093/g3journal/jkac142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
In the past decade, there has been a growing appreciation for R-loop structures as important regulators of the epigenome, telomere maintenance, DNA repair, and replication. Given these numerous functions, dozens, or potentially hundreds, of proteins could serve as direct or indirect regulators of R-loop writing, reading, and erasing. In order to understand common properties shared amongst potential R-loop binding proteins, we mined published proteomic studies and distilled 10 features that were enriched in R-loop binding proteins compared with the rest of the proteome. Applying an easy-ensemble machine learning approach, we used these R-loop binding protein-specific features along with their amino acid composition to create random forest classifiers that predict the likelihood of a protein to bind to R-loops. Known R-loop regulating pathways such as splicing, DNA damage repair and chromatin remodeling are highly enriched in our datasets, and we validate 2 new R-loop binding proteins LIG1 and FXR1 in human cells. Together these datasets provide a reference to pursue analyses of novel R-loop regulatory proteins.
Collapse
Affiliation(s)
| | | | - Peter C Stirling
- Corresponding author: Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z1L3, Canada.
| |
Collapse
|
6
|
Tang L, Li W, Xu H, Zheng X, Qiu S, He W, Wei Q, Ai J, Yang L, Liu J. Mutator-Derived lncRNA Landscape: A Novel Insight Into the Genomic Instability of Prostate Cancer. Front Oncol 2022; 12:876531. [PMID: 35860569 PMCID: PMC9291324 DOI: 10.3389/fonc.2022.876531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/23/2022] [Indexed: 11/17/2022] Open
Abstract
Background Increasing evidence has emerged to reveal the correlation between genomic instability and long non-coding RNAs (lncRNAs). The genomic instability-derived lncRNA landscape of prostate cancer (PCa) and its critical clinical implications remain to be understood. Methods Patients diagnosed with PCa were recruited from The Cancer Genome Atlas (TCGA) program. Genomic instability-associated lncRNAs were identified by a mutator hypothesis-originated calculative approach. A signature (GILncSig) was derived from genomic instability-associated lncRNAs to classify PCa patients into high-risk and low-risk groups. The biochemical recurrence (BCR) model of a genomic instability-derived lncRNA signature (GILncSig) was established by Cox regression and stratified analysis in the train set. Then its prognostic value and association with clinical features were verified by Kaplan–Meier (K-M) analysis and receiver operating characteristic (ROC) curve in the test set and the total patient set. The regulatory network of transcription factors (TFs) and lncRNAs was established to evaluate TF–lncRNA interactions. Results A total of 95 genomic instability-associated lncRNAs of PCa were identified. We constructed the GILncSig based on 10 lncRNAs with independent prognostic value. GILncSig separated patients into the high-risk (n = 121) group and the low-risk (n = 121) group in the train set. Patients with high GILncSig score suffered from more frequent BCR than those with low GILncSig score. The results were further validated in the test set, the whole TCGA cohort, and different subgroups stratified by age and Gleason score (GS). A high GILncSig risk score was significantly associated with a high mutation burden and a low critical gene expression (PTEN and CDK12) in PCa. The predictive performance of our BCR model based on GILncSig outperformed other existing BCR models of PCa based on lncRNAs. The GILncSig also showed a remarkable ability to predict BCR in the subgroup of patients with TP53 mutation or wild type. Transcription factors, such as FOXA1, JUND, and SRF, were found to participate in the regulation of lncRNAs with prognostic value. Conclusion In summary, we developed a prognostic signature of BCR based on genomic instability-associated lncRNAs for PCa, which may provide new insights into the epigenetic mechanism of BCR.
Collapse
Affiliation(s)
- Liansha Tang
- Department of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
- West China Medical School of Sichuan University, Chengdu, China
| | - Wanjiang Li
- Department of Radiology, West China Hospital of Sichuan University, Chengdu, China
| | - Hang Xu
- Department of Urology, Institute of Urology, West China Hospital of Sichuan University, Chengdu, China
- Institute of System Genetics, West China Hospital of Sichuan University, Chengdu, China
| | - Xiaonan Zheng
- Department of Urology, Institute of Urology, West China Hospital of Sichuan University, Chengdu, China
- Institute of System Genetics, West China Hospital of Sichuan University, Chengdu, China
| | - Shi Qiu
- Department of Urology, Institute of Urology, West China Hospital of Sichuan University, Chengdu, China
| | - Wenbo He
- West China Medical School of Sichuan University, Chengdu, China
| | - Qiang Wei
- Department of Urology, Institute of Urology, West China Hospital of Sichuan University, Chengdu, China
| | - Jianzhong Ai
- Department of Urology, Institute of Urology, West China Hospital of Sichuan University, Chengdu, China
| | - Lu Yang
- Department of Urology, Institute of Urology, West China Hospital of Sichuan University, Chengdu, China
- *Correspondence: Lu Yang, ; Jiyan Liu,
| | - Jiyan Liu
- Department of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Lu Yang, ; Jiyan Liu,
| |
Collapse
|
7
|
Li J, Wei S, Zhang Y, Lu S, Zhang X, Wang Q, Yan J, Yang S, Chen L, Liu Y, Huang Z. Comprehensive Analyses of Mutation-Derived Long-Chain Noncoding RNA Signatures of Genome Instability in Kidney Renal Papillary Cell Carcinoma. Front Genet 2022; 13:874673. [PMID: 35547247 PMCID: PMC9082950 DOI: 10.3389/fgene.2022.874673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 04/05/2022] [Indexed: 11/13/2022] Open
Abstract
Background: The role of long-chain noncoding RNA (lncRNA) in genomic instability has been demonstrated to be increasingly importance. Therefore, in this study, lncRNAs associated with genomic instability were identified and kidney renal papillary cell carcinoma (KIRP)-associated predictive features were analysed to classify high-risk patients and improve individualised treatment. Methods: The training (n = 142) and test (n = 144) sets were created using raw RNA-seq and patient’s clinical data of KIRP obtained from The Cancer Genome Atlas (TCGA).There are 27 long-chain noncoding RNAs (lncRNAs) that are connected with genomic instability, these lncRNAs were identified using the ‘limma’ R package based on the numbers of somatic mutations and lncRNA expression profiles acquired from KIRP TCGA cohort. Furthermore, Cox regression analysis was carried out to develop a genome instability-derived lncRNA-based gene signature (GILncSig), whose prognostic value was confirmed in the test cohort as well as across the entire KIRP TCGA dataset. Results: A GILncSig derived from three lncRNAs (BOLA3-AS1, AC004870, and LINC00839), which were related with poor KIRP survival, was identified, which was split up into high- and low-risk groups. Additionally, the GILncSig was found to be an independent prognostic predictive index in KIRP using univariate and multivariate Cox analysis. Furthermore, the prognostic significance and characteristics of GilncSig were confirmed in the training test and TCGA sets. GilncSig also showed better predictive performance than other prognostic lncRNA features. Conclusion: The function of lncRNAs in genomic instability and the genetic diversity of KIRP were elucidated in this work. Moreover, three lncRNAs were screened for prediction of the outcome of KIRP survival and novel insights into identifying cancer biomarkers related to genomic instability were discussed.
Collapse
Affiliation(s)
- Jian Li
- Department of Pediatrics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Shimei Wei
- Department of Pediatrics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Yan Zhang
- Department of Pediatrics, Shanxi Children's Hospital, Taiyuan, China
| | - Shuangshuang Lu
- Department of Pediatrics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Xiaoxu Zhang
- Department of Pediatrics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Qiong Wang
- Department of Pediatrics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Jiawei Yan
- Department of Pediatrics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Sanju Yang
- Graduate School of Youjiang Medical University for Nationalities, Baise, China
| | - Liying Chen
- Graduate School of Youjiang Medical University for Nationalities, Baise, China
| | - Yunguang Liu
- Department of Pediatrics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Zhijing Huang
- Department of Pediatrics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| |
Collapse
|
8
|
Osadska M, Selicky T, Kretova M, Jurcik J, Sivakova B, Cipakova I, Cipak L. The Interplay of Cohesin and RNA Processing Factors: The Impact of Their Alterations on Genome Stability. Int J Mol Sci 2022; 23:3939. [PMID: 35409298 PMCID: PMC8999970 DOI: 10.3390/ijms23073939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/28/2022] [Accepted: 03/31/2022] [Indexed: 12/01/2022] Open
Abstract
Cohesin, a multi-subunit protein complex, plays important roles in sister chromatid cohesion, DNA replication, chromatin organization, gene expression, transcription regulation, and the recombination or repair of DNA damage. Recently, several studies suggested that the functions of cohesin rely not only on cohesin-related protein-protein interactions, their post-translational modifications or specific DNA modifications, but that some RNA processing factors also play an important role in the regulation of cohesin functions. Therefore, the mutations and changes in the expression of cohesin subunits or alterations in the interactions between cohesin and RNA processing factors have been shown to have an impact on cohesion, the fidelity of chromosome segregation and, ultimately, on genome stability. In this review, we provide an overview of the cohesin complex and its role in chromosome segregation, highlight the causes and consequences of mutations and changes in the expression of cohesin subunits, and discuss the RNA processing factors that participate in the regulation of the processes involved in chromosome segregation. Overall, an understanding of the molecular determinants of the interplay between cohesin and RNA processing factors might help us to better understand the molecular mechanisms ensuring the integrity of the genome.
Collapse
Affiliation(s)
- Michaela Osadska
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| | - Tomas Selicky
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| | - Miroslava Kretova
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| | - Jan Jurcik
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| | - Barbara Sivakova
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska Cesta 9, 845 38 Bratislava, Slovakia;
| | - Ingrid Cipakova
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| | - Lubos Cipak
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| |
Collapse
|
9
|
Guo CR, Mao Y, Jiang F, Juan CX, Zhou GP, Li N. Computational detection of a genome instability-derived lncRNA signature for predicting the clinical outcome of lung adenocarcinoma. Cancer Med 2021; 11:864-879. [PMID: 34866362 PMCID: PMC8817082 DOI: 10.1002/cam4.4471] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 07/30/2021] [Accepted: 10/03/2021] [Indexed: 12/13/2022] Open
Abstract
Evidence has been emerging of the importance of long non-coding RNAs (lncRNAs) in genome instability. However, no study has established how to classify such lncRNAs linked to genomic instability, and whether that connection poses a therapeutic significance. Here, we established a computational frame derived from mutator hypothesis by combining profiles of lncRNA expression and those of somatic mutations in a tumor genome, and identified 185 candidate lncRNAs associated with genomic instability in lung adenocarcinoma (LUAD). Through further studies, we established a six lncRNA-based signature, which assigned patients to the high- and low-risk groups with different prognosis. Further validation of this signature was performed in a number of separate cohorts of LUAD patients. In addition, the signature was found closely linked to genomic mutation rates in patients, indicating it could be a useful way to quantify genomic instability. In summary, this research offered a novel method by through which more studies may explore the function of lncRNAs and presented a possible new way for detecting biomarkers associated with genomic instability in cancers.
Collapse
Affiliation(s)
- Chen-Rui Guo
- Department of Abdominal Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Yan Mao
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Feng Jiang
- Department of Neonatology,, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Chen-Xia Juan
- Department of Nephrology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Guo-Ping Zhou
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ning Li
- Department of Abdominal Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, China
| |
Collapse
|
10
|
Identification of Mutator-Derived lncRNA Signatures of Genomic Instability for Promoting the Clinical Outcome in Hepatocellular Carcinoma. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2021:1205029. [PMID: 34840594 PMCID: PMC8613502 DOI: 10.1155/2021/1205029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/13/2021] [Accepted: 10/28/2021] [Indexed: 02/07/2023]
Abstract
Background Accumulating evidence proves that long noncoding RNA (lncRNA) plays a crucial role in maintaining genomic instability. However, it is significantly absent from exploring genomic instability-associated lncRNAs and discovering their clinical significance. Objective To identify crucial mutator-derived lncRNAs and construct a predictive model for prognosis and genomic instability in hepatocellular carcinoma. Methods First, we constructed a mutator hypothesis-derived calculative framework through uniting the lncRNA expression level and somatic mutation number to screen for genomic instability-associated lncRNA in hepatocellular carcinoma. We then selected mutator-derived lncRNA from the genome instability-associated lncRNA by univariate Cox analysis and Lasso regression analysis. Next, we created a prognosis model with the mutator-derived lncRNA signature. Furthermore, we verified the vital role of the model in the prognosis and genomic instability of hepatocellular carcinoma patients. Finally, we examined the potential relationship between the model and the mutation status of TP53. Results In this study, we screened 88 genome instability-associated lncRNAs and built a prognosis model with four mutator-derived lncRNAs. Moreover, the model was an independent predictor of prognosis and an accurate indicator of genomic instability in hepatocellular carcinoma. Finally, the model could catch the TP53 mutation status, and the model was a more effective indicator than the mutation status of TP53 for hepatocellular carcinoma patients. Conclusion This research adopted a reliable method to analyze the role of lncRNA in genomic instability. Besides, the prognostic model with four mutator-derived lncRNAs is an excellent new indicator of prognosis and genomic instability in hepatocellular carcinoma. In addition, this finding may help clinicians develop therapeutic systems.
Collapse
|
11
|
Huang DP, Liao MM, Tong JJ, Yuan WQ, Peng DT, Lai JP, Zeng YH, Qiu YJ, Tong GD. Construction of a genome instability-derived lncRNA-based risk scoring system for the prognosis of hepatocellular carcinoma. Aging (Albany NY) 2021. [PMID: 34799469 DOI: 10.1863/aging.203698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023]
Abstract
Emerging evidence revealed the critical roles of long non-coding RNAs (lncRNAs) in maintaining genomic instability. However, genome instability-associated lncRNAs (GILncRNAs) and their performance in clinical prognostic significance in hepatocellular carcinoma (HCC) are rarely reported. Our study constructed a computational framework integrating somatic mutation information and lncRNA expression profiles of HCC genome and we identified 88 GILncRNAs of HCC. Function enrichment analysis revealed that GILncRNAs were involved in various metabolism processes and genome instability of cancer. A genome instability-derived lncRNA-based gene signature (GILncSig) was constructed using training set data. The performance of GILncSig for outcome prediction was validated in testing set and The Cancer Genome Atlas (TCGA) set. The multivariate cox regression analysis and stratification analysis demonstrated GILncSig could serve as an independent prognostic factor for the overall survival of HCC patients. The time-dependent Receiver Operating Characteristic (ROC) curve illustrated GILncSig outperformed two recently published lncRNA signatures for overall survival prediction. The combination of GILncSig and tumor protein p53 (TP53) mutation status exhibited better prognostic performance in survival evaluation compared to TP53 mutation status alone. AC145343.1 was further validated to be a risk factor for HCC in vitro among GILncSig. Overall, our study provided a novel approach for identification of genome instability-associated lncRNAs and established an independent risk score system for outcome prediction of HCC patients, which provided a new insight for exploring in-depth mechanism and potential therapy strategy.
Collapse
Affiliation(s)
- Dan-Ping Huang
- Department of Hepatology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen 518033, Guangdong Province, China
| | - Mian-Mian Liao
- Department of Hepatology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen 518033, Guangdong Province, China.,College of Basic Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510403, Guangdong, China
| | - Jing-Jing Tong
- The Affiliated Chencun Hospital of Shunde Hospital, Southern Medical University, Shunde 528300, Guangdong Province, China
| | - Wei-Qu Yuan
- Department of Acupuncture, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen 518033, Guangdong Province, China
| | - De-Ti Peng
- Department of Hepatology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen 518033, Guangdong Province, China
| | - Jian-Ping Lai
- Department of Hepatology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen 518033, Guangdong Province, China
| | - Yi-Hao Zeng
- College of Basic Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510403, Guangdong, China
| | - Yi-Jun Qiu
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510403, Guangdong Province, China
| | - Guang-Dong Tong
- Department of Hepatology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen 518033, Guangdong Province, China
| |
Collapse
|
12
|
Huang DP, Liao MM, Tong JJ, Yuan WQ, Peng DT, Lai JP, Zeng YH, Qiu YJ, Tong GD. Construction of a genome instability-derived lncRNA-based risk scoring system for the prognosis of hepatocellular carcinoma. Aging (Albany NY) 2021; 13:24621-24639. [PMID: 34799469 PMCID: PMC8660619 DOI: 10.18632/aging.203698] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 10/25/2021] [Indexed: 12/25/2022]
Abstract
Emerging evidence revealed the critical roles of long non-coding RNAs (lncRNAs) in maintaining genomic instability. However, genome instability-associated lncRNAs (GILncRNAs) and their performance in clinical prognostic significance in hepatocellular carcinoma (HCC) are rarely reported. Our study constructed a computational framework integrating somatic mutation information and lncRNA expression profiles of HCC genome and we identified 88 GILncRNAs of HCC. Function enrichment analysis revealed that GILncRNAs were involved in various metabolism processes and genome instability of cancer. A genome instability-derived lncRNA-based gene signature (GILncSig) was constructed using training set data. The performance of GILncSig for outcome prediction was validated in testing set and The Cancer Genome Atlas (TCGA) set. The multivariate cox regression analysis and stratification analysis demonstrated GILncSig could serve as an independent prognostic factor for the overall survival of HCC patients. The time-dependent Receiver Operating Characteristic (ROC) curve illustrated GILncSig outperformed two recently published lncRNA signatures for overall survival prediction. The combination of GILncSig and tumor protein p53 (TP53) mutation status exhibited better prognostic performance in survival evaluation compared to TP53 mutation status alone. AC145343.1 was further validated to be a risk factor for HCC in vitro among GILncSig. Overall, our study provided a novel approach for identification of genome instability-associated lncRNAs and established an independent risk score system for outcome prediction of HCC patients, which provided a new insight for exploring in-depth mechanism and potential therapy strategy.
Collapse
Affiliation(s)
- Dan-Ping Huang
- Department of Hepatology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen 518033, Guangdong Province, China
| | - Mian-Mian Liao
- Department of Hepatology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen 518033, Guangdong Province, China.,College of Basic Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510403, Guangdong, China
| | - Jing-Jing Tong
- The Affiliated Chencun Hospital of Shunde Hospital, Southern Medical University, Shunde 528300, Guangdong Province, China
| | - Wei-Qu Yuan
- Department of Acupuncture, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen 518033, Guangdong Province, China
| | - De-Ti Peng
- Department of Hepatology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen 518033, Guangdong Province, China
| | - Jian-Ping Lai
- Department of Hepatology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen 518033, Guangdong Province, China
| | - Yi-Hao Zeng
- College of Basic Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510403, Guangdong, China
| | - Yi-Jun Qiu
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510403, Guangdong Province, China
| | - Guang-Dong Tong
- Department of Hepatology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen 518033, Guangdong Province, China
| |
Collapse
|
13
|
Tu G, Peng W, Cai Q, Zhao Z, Peng X, He B, Zhang P, Shi S, Wang X. A Novel Model Based on Genomic Instability-Associated Long Non-Coding RNAs for Predicting Prognosis and Response to Immunotherapy in Patients With Lung Adenocarcinoma. Front Genet 2021; 12:720013. [PMID: 34777461 PMCID: PMC8585772 DOI: 10.3389/fgene.2021.720013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 10/04/2021] [Indexed: 02/05/2023] Open
Abstract
Background: Emerging scientific evidence has shown that long non-coding RNAs (lncRNAs) exert critical roles in genomic instability (GI), which is considered a hallmark of cancer. To date, the prognostic value of GI-associated lncRNAs (GI-lncRNAs) remains largely unexplored in lung adenocarcinoma (LUAC). The aims of this study were to identify GI-lncRNAs associated with the survival of LUAC patients, and to develop a novel GI-lncRNA-based prognostic model (GI-lncRNA model) for LUAC. Methods: Clinicopathological data of LUAC patients, and their expression profiles of lncRNAs and somatic mutations were obtained from The Cancer Genome Atlas database. Pearson correlation analysis was conducted to identify the co-expressed mRNAs of GI-lncRNAs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were conducted to determine the main biological function and molecular pathways of the differentially expressed GI-lncRNAs. Univariate and multivariate Cox proportional hazard regression analyses were performed to identify GI-lncRNAs significantly related to overall survival (OS) for construction of the GI-lncRNA model. Kaplan–Meier survival analysis and receiver operating characteristic curve analysis were performed to evaluate the predictive accuracy. The performance of the newly developed GI-lncRNA model was compared with the recently published lncRNA-based prognostic index models. Results: A total of 19 GI-lncRNAs were found to be significantly associated with OS, of which 9 were identified by multivariate analysis to construct the GI-lncRNA model. Notably, the GI-lncRNA model showed a prognostic value independent of key clinical characteristics. Further performance evaluation indicated that the area under the curve (AUC) of the GI-lncRNA model was 0.771, which was greater than that of the TP53 mutation status and three existing lncRNA-based models in predicting the prognosis of patients with LUAC. In addition, the GI-lncRNA model was highly correlated with programed death ligand 1 (PD-L1) expression and tumor mutational burden in immunotherapy for LUAC. Conclusion: The GI-lncRNA model was established and its performance was found to be superior to existing lncRNA-based models. As such, the GI-lncRNA model holds promise as a more accurate prognostic tool for the prediction of prognosis and response to immunotherapy in patients with LUAC.
Collapse
Affiliation(s)
- Guangxu Tu
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy of Lung Cancer, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Weilin Peng
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy of Lung Cancer, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Qidong Cai
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy of Lung Cancer, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Zhenyu Zhao
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy of Lung Cancer, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Xiong Peng
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy of Lung Cancer, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Boxue He
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy of Lung Cancer, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Pengfei Zhang
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy of Lung Cancer, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Shuai Shi
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy of Lung Cancer, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Xiang Wang
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy of Lung Cancer, The Second Xiangya Hospital, Central South University, Changsha, China
| |
Collapse
|
14
|
Calculated identification of mutator-derived lncRNA signatures of genomic instability to predict the clinical outcome of muscle-invasive bladder cancer. Cancer Cell Int 2021; 21:476. [PMID: 34496843 PMCID: PMC8424867 DOI: 10.1186/s12935-021-02185-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/29/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Muscle-invasive bladder cancer (MIBC) is one of the most important type of bladder cancer, with a high morbidity and mortality rate. Studies have found that long non-coding RNA (lncRNA) plays a key role in maintaining genomic instability. However, Identification of lncRNAs related to genomic instability (GIlncRNAs) and their clinical significance in cancers have not been extensively studied yet. METHODS Here, we downloaded the lncRNA expression profiles, somatic mutation profiles and clinical related data in MIBC patients from The Cancer Genome Atlas (TCGA) database. A lncRNA computational framework was used to find differentially expressed GIlncRNAs. Multivariate Cox regression analysis was used to construct a genomic instability-related lncRNA signature (GIlncSig). Univariate and multivariate Cox analyses were used to assess the independent prognostic for the GIlncSig and other key clinical factors. RESULTS We found 43 differentially expressed GIlncRNAs and constructed the GIlncSig with 6 GIlncRNAs in the training cohort. The patients were divided into two risk groups. The overall survival of patients in the high-risk group was lower than that in the low-risk group (P < 0.001), which were further verified in the testing cohort and the entire TCGA cohort. Univariate and multivariate Cox regression showed that the GIlncSig was an independent prognostic factor. In addition, the GIlncSig correlated with the genomic mutation rate of MIBC, indicating its potential as a measure of the degree of genomic instability. The GIlncSig was able to divide FGFR3 wild- and mutant-type patients into two risk groups, and effectively enhanced the prediction effect. CONCLUSION Our study introduced an important reference for further research on the role of GIlncRNAs, and provided prognostic indicators and potential biological therapy targets for MIBC.
Collapse
|
15
|
Peng B, Li H, Na R, Lu T, Li Y, Zhao J, Zhang H, Zhang L. Identification of a Novel Prognostic Signature of Genome Instability-Related LncRNAs in Early Stage Lung Adenocarcinoma. Front Cell Dev Biol 2021; 9:706454. [PMID: 34336859 PMCID: PMC8324209 DOI: 10.3389/fcell.2021.706454] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/21/2021] [Indexed: 01/22/2023] Open
Abstract
Background Increasing evidence has demonstrated that long non-coding RNAs (lncRNAs) play a crucial part in maintaining genomic instability. We therefore identified genome instability-related lncRNAs and constructed a prediction signature for early stage lung adenocarcinoma (LUAD) as well in order for classification of high-risk group of patients and improvement of individualized therapies. Methods Early stage LUAD RNA-seq and clinical data from The Cancer Genome Atlas (TCGA) were randomly divided into training set (n = 177) and testing set (n = 176). A total of 146 genomic instability-associated lncRNAs were identified based on somatic mutation profiles combining lncRNA expression profiles from TCGA by the “limma R” package. We performed Cox regression analysis to develop this predictive indicator. We validated the prognostic signature by an external independent LUAD cohort with microarray platform acquired from the Gene Expression Omnibus (GEO). Results A genome instability-related six-lncRNA-based gene signature (GILncSig) was established to divide subjects into high-risk and low-risk groups with different outcomes at statistically significant levels. According to the multivariate Cox regression and stratification analysis, the GILncSig was an independent predictive factor. Furthermore, the six-lncRNA signature achieved AUC values of 0.745, 0.659, and 0.708 in the training set, testing set, and TCGA set, respectively. When compared with other prognostic lncRNA signatures, the GILncSig also exhibited better prediction performance. Conclusion The prognostic lncRNA signature is a potent tool for risk stratification of early stage LUAD patients. Our study also provided new insights for identifying genome instability-related cancer biomarkers.
Collapse
Affiliation(s)
- Bo Peng
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Huawei Li
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Ruisi Na
- Second Clinical College of Medicine, Harbin Medical University, Harbin, China
| | - Tong Lu
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yongchao Li
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jiaying Zhao
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Han Zhang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Linyou Zhang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| |
Collapse
|
16
|
Mathew V, Kumar A, Jiang YK, West K, Tam AS, Stirling PC. Cdc48 regulates intranuclear quality control sequestration of the Hsh155 splicing factor in budding yeast. J Cell Sci 2020; 133:jcs.252551. [PMID: 33172985 DOI: 10.1242/jcs.252551] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/30/2020] [Indexed: 11/20/2022] Open
Abstract
Cdc48 (known as VCP in mammals) is a highly conserved ATPase chaperone that plays an essential role in the assembly and disassembly of protein-DNA complexes and in degradation of misfolded proteins. We find that in Saccharomyces cerevisiae budding yeast, Cdc48 accumulates during cellular stress at intranuclear protein quality control sites (INQ). We show that Cdc48 function is required to suppress INQ formation under non-stress conditions and to promote recovery following genotoxic stress. Cdc48 physically associates with the INQ substrate and splicing factor Hsh155, and regulates its assembly with partner proteins. Accordingly, cdc48 mutants have defects in splicing and show spontaneous distribution of Hsh155 to INQ aggregates, where it is stabilized. Overall, this study shows that Cdc48 regulates deposition of proteins at INQ and suggests a previously unknown role for Cdc48 in the regulation or stabilization of splicing subcomplexes.This article has an associated First Person interview with the first author of the paper.
Collapse
Affiliation(s)
- Veena Mathew
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver V5Z 1L3, Canada
| | - Arun Kumar
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver V5Z 1L3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver V6H 3N1, Canada
| | - Yangyang K Jiang
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver V5Z 1L3, Canada
| | - Kyra West
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver V5Z 1L3, Canada
| | - Annie S Tam
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver V5Z 1L3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver V6H 3N1, Canada
| | - Peter C Stirling
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver V5Z 1L3, Canada .,Department of Medical Genetics, University of British Columbia, Vancouver V6H 3N1, Canada
| |
Collapse
|
17
|
Depletion of the MFAP1/SPP381 Splicing Factor Causes R-Loop-Independent Genome Instability. Cell Rep 2020; 28:1551-1563.e7. [PMID: 31390568 PMCID: PMC6693559 DOI: 10.1016/j.celrep.2019.07.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 03/18/2019] [Accepted: 07/01/2019] [Indexed: 01/19/2023] Open
Abstract
THO/TREX is a conserved complex with a role in messenger ribonucleoprotein biogenesis that links gene expression and genome instability. Here, we show that human THO interacts with MFAP1 (microfibrillar-associated protein 1), a spliceosome-associated factor. Interestingly, MFAP1 depletion impairs cell proliferation and genome integrity, increasing γH2AX foci and DNA breaks. This phenotype is not dependent on either transcription or RNA-DNA hybrids. Mutations in the yeast orthologous gene SPP381 cause similar transcription-independent genome instability, supporting a conserved role. MFAP1 depletion has a wide effect on splicing and gene expression in human cells, determined by transcriptome analyses. MFAP1 depletion affects a number of DNA damage response (DDR) genes, which supports an indirect role of MFAP1 on genome integrity. Our work defines a functional interaction between THO and RNA processing and argues that splicing factors may contribute to genome integrity indirectly by regulating the expression of DDR genes rather than by a direct role.
Collapse
|
18
|
Bao S, Zhao H, Yuan J, Fan D, Zhang Z, Su J, Zhou M. Computational identification of mutator-derived lncRNA signatures of genome instability for improving the clinical outcome of cancers: a case study in breast cancer. Brief Bioinform 2019; 21:1742-1755. [PMID: 31665214 DOI: 10.1093/bib/bbz118] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/29/2019] [Accepted: 08/12/2019] [Indexed: 12/24/2022] Open
Abstract
Emerging evidence revealed the critical roles of long non-coding RNAs (lncRNAs) in maintaining genomic instability. However, identification of genome instability-associated lncRNAs and their clinical significance in cancers remain largely unexplored. Here, we developed a mutator hypothesis-derived computational frame combining lncRNA expression profiles and somatic mutation profiles in a tumor genome and identified 128 novel genomic instability-associated lncRNAs in breast cancer as a case study. We then identified a genome instability-derived two lncRNA-based gene signature (GILncSig) that stratified patients into high- and low-risk groups with significantly different outcome and was further validated in multiple independent patient cohorts. Furthermore, the GILncSig correlated with genomic mutation rate in both ovarian cancer and breast cancer, indicating its potential as a measurement of the degree of genome instability. The GILncSig was able to divide TP53 wide-type patients into two risk groups, with the low-risk group showing significantly improved outcome and the high-risk group showing no significant difference compared with those with TP53 mutation. In summary, this study provided a critical approach and resource for further studies examining the role of lncRNAs in genome instability and introduced a potential new avenue for identifying genomic instability-associated cancer biomarkers.
Collapse
Affiliation(s)
- Siqi Bao
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Hengqiang Zhao
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Jian Yuan
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Dandan Fan
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Zicheng Zhang
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Jianzhong Su
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Meng Zhou
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou 325027, P. R. China
| |
Collapse
|
19
|
Tam AS, Stirling PC. Splicing, genome stability and disease: splice like your genome depends on it! Curr Genet 2019; 65:905-912. [PMID: 30953124 DOI: 10.1007/s00294-019-00964-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 03/27/2019] [Accepted: 03/28/2019] [Indexed: 12/21/2022]
Abstract
The spliceosome has been implicated in genome maintenance for decades. Recently, a surge in discoveries in cancer has suggested that the oncogenic mechanism of spliceosomal defects may involve defective genome stability. The action of the core spliceosome prevents R-loop accumulation, and regulates the expression of genome stability factors. At the same time, specific spliceosomal components have non-canonical functions in genome maintenance. Here we review these different models, highlighting their discovery in different model systems, and describing their potential impact on human disease states.
Collapse
Affiliation(s)
- Annie S Tam
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Peter C Stirling
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
| |
Collapse
|