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Liu Q, Huang J, Yan W, Liu Z, Liu S, Fang W. FGFR families: biological functions and therapeutic interventions in tumors. MedComm (Beijing) 2023; 4:e367. [PMID: 37750089 PMCID: PMC10518040 DOI: 10.1002/mco2.367] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 07/28/2023] [Accepted: 08/11/2023] [Indexed: 09/27/2023] Open
Abstract
There are five fibroblast growth factor receptors (FGFRs), namely, FGFR1-FGFR5. When FGFR binds to its ligand, namely, fibroblast growth factor (FGF), it dimerizes and autophosphorylates, thereby activating several key downstream pathways that play an important role in normal physiology, such as the Ras/Raf/mitogen-activated protein kinase kinase/extracellular signal-regulated kinase, phosphoinositide 3-kinase (PI3K)/AKT, phospholipase C gamma/diacylglycerol/protein kinase c, and signal transducer and activator of transcription pathways. Furthermore, as an oncogene, FGFR genetic alterations were found in 7.1% of tumors, and these alterations include gene amplification, gene mutations, gene fusions or rearrangements. Therefore, FGFR amplification, mutations, rearrangements, or fusions are considered as potential biomarkers of FGFR therapeutic response for tyrosine kinase inhibitors (TKIs). However, it is worth noting that with increased use, resistance to TKIs inevitably develops, such as the well-known gatekeeper mutations. Thus, overcoming the development of drug resistance becomes a serious problem. This review mainly outlines the FGFR family functions, related pathways, and therapeutic agents in tumors with the aim of obtaining better outcomes for cancer patients with FGFR changes. The information provided in this review may provide additional therapeutic ideas for tumor patients with FGFR abnormalities.
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Affiliation(s)
- Qing Liu
- Cancer CenterIntegrated Hospital of Traditional Chinese MedicineSouthern Medical UniversityGuangzhouGuangdongChina
| | - Jiyu Huang
- Cancer CenterIntegrated Hospital of Traditional Chinese MedicineSouthern Medical UniversityGuangzhouGuangdongChina
| | - Weiwei Yan
- Cancer CenterIntegrated Hospital of Traditional Chinese MedicineSouthern Medical UniversityGuangzhouGuangdongChina
| | - Zhen Liu
- Cancer CenterIntegrated Hospital of Traditional Chinese MedicineSouthern Medical UniversityGuangzhouGuangdongChina
- Key Laboratory of Protein Modification and DegradationBasic School of Guangzhou Medical UniversityGuangzhouGuangdongChina
| | - Shu Liu
- Department of Breast SurgeryThe Affiliated Hospital of Guizhou Medical UniversityGuiyangGuizhouChina
| | - Weiyi Fang
- Cancer CenterIntegrated Hospital of Traditional Chinese MedicineSouthern Medical UniversityGuangzhouGuangdongChina
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Maebele LT, Mulaudzi TV, Yasasve M, Dlamini Z, Damane BP. Immunomodulatory Gene-Splicing Dysregulation in Tumorigenesis: Unmasking the Complexity. Molecules 2023; 28:5984. [PMID: 37630236 PMCID: PMC10458946 DOI: 10.3390/molecules28165984] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/05/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Cancer is a global health concern with rising incidence, morbidity, and mortality. The interaction between the tumor and immune cells within the tumor microenvironment is facilitated by signaling pathways driven by immunomodulatory proteins. Alternative splicing regulates the production of multiple immunomodulatory proteins with diverse functionality from a single mRNA transcript. Splicing factors are pivotal in modulating alternative splicing processes but are also subject to regulation. The dysregulation of alternative splicing may result from splicing factor (SF) abnormal expression levels and mutations in the cis and trans-acting elements and small nuclear RNA (snRNA) molecules. Aberrant splicing may generate abnormal mRNA transcripts encoding isoforms with altered functions that contribute to tumorigenesis or cancer progression. This review uncovers the complexity of immunomodulatory genes splicing dysregulation in oncogenesis. Identifying specific immunomodulatory splicing isoforms that contribute to cancer could be utilized to improve current immunotherapeutic drugs or develop novel therapeutic interventions for cancer.
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Affiliation(s)
| | - Thanyani Victor Mulaudzi
- Department of Surgery, Steve Biko Academic Hospital, University of Pretoria, Hatfield 0028, South Africa
| | - Madhavan Yasasve
- Department of Oral Medicine and Radiology, Sri Ramachandra Institute of Higher Education and Research, Chennai 600116, India
| | - Zodwa Dlamini
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Cancer Research Institute (PACRI), University of Pretoria, Hatfield 0028, South Africa
| | - Botle Precious Damane
- Department of Surgery, Steve Biko Academic Hospital, University of Pretoria, Hatfield 0028, South Africa
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Karakulak T, Szklarczyk D, Saylan CC, Moch H, von Mering C, Kahraman A. CanIsoNet: a database to study the functional impact of isoform switching events in diseases. BIOINFORMATICS ADVANCES 2023; 3:vbad050. [PMID: 37123454 PMCID: PMC10133402 DOI: 10.1093/bioadv/vbad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 03/30/2023] [Accepted: 04/13/2023] [Indexed: 05/02/2023]
Abstract
Motivation Alternative splicing, as an essential regulatory mechanism in normal mammalian cells, is frequently disturbed in cancer and other diseases. Switches in the expression of most dominant alternative isoforms can alter protein interaction networks of associated genes giving rise to disease and disease progression. Here, we present CanIsoNet, a database to view, browse and search isoform switching events in diseases. CanIsoNet is the first webserver that incorporates isoform expression data with STRING interaction networks and ClinVar annotations to predict the pathogenic impact of isoform switching events in various diseases. Results Data in CanIsoNet can be browsed by disease or searched by genes or isoforms in annotation-rich data tables. Various annotations for 11 811 isoforms and 14 357 unique isoform switching events across 31 different disease types are available. The network density score for each disease-specific isoform, PFAM domain IDs of disrupted interactions, domain structure visualization of transcripts and expression data of switched isoforms for each sample is given. Additionally, the genes annotated in ClinVar are highlighted in interactive interaction networks. Availability and implementation CanIsoNet is freely available at https://www.caniso.net. The source codes can be found under a Creative Common License at https://github.com/kahramanlab/CanIsoNet_Web. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Tülay Karakulak
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich, 8057, Switzerland
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Schmelzbergstrasse 12, Zurich, 8091, Switzerland
- Swiss Institute of Bioinformatics, Amphipôle, Quartier UNIL-Sorge, Lausanne, 1015, Switzerland
| | - Damian Szklarczyk
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich, 8057, Switzerland
- Swiss Institute of Bioinformatics, Amphipôle, Quartier UNIL-Sorge, Lausanne, 1015, Switzerland
| | - Cemil Can Saylan
- Computational Science and Engineering Department, Informatics Institute, Istanbul Technical University, Reşitpaşa, İTÜ Ayazağa Kampüsü, Istanbul, 34467, Türkiye
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Schmelzbergstrasse 12, Zurich, 8091, Switzerland
- Faculty of Medicine, University of Zurich, Zurich, 8006, Switzerland
| | - Christian von Mering
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich, 8057, Switzerland
- Swiss Institute of Bioinformatics, Amphipôle, Quartier UNIL-Sorge, Lausanne, 1015, Switzerland
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[Expression and significance of fibroblast growth factor receptor 2 in clear cell renal cell carcinoma]. BEIJING DA XUE XUE BAO. YI XUE BAN = JOURNAL OF PEKING UNIVERSITY. HEALTH SCIENCES 2022; 54. [PMID: 35950384 PMCID: PMC9385531 DOI: 10.19723/j.issn.1671-167x.2022.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
OBJECTIVE To investigate the expression of fibroblast growth factor receptor 2 (FGFR2) in clear cell renal cell carcinoma (ccRCC; or kidney renal clear cell carcinoma, KIRC), to analyze the relationship between the expression of FGFR2 and the clinical pathological features and prognosis of ccRCC, to study the relationship between the expression of FGFR2 and other molecules, and to explore its role in the development of ccRCC. METHODS Gene expressional and clinical information of ccRCC patients were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus(GEO) database. Next, the data were transformed and collated. In the study, 104 clinical ccRCC samples and corresponding paracancerous normal tissue samples were collected from Department of Urology, Peking University First Hospital. Immunohistochemistry (IHC) was performed and the staining results were scored, so as to compare the expression of FGFR2 in ccRCC and paracancerous normal tissues. Besides, quantify real-time polymerase chain reaction (qRT-PCR) was used to detect the mRNA expression level of FGFR2 in normal renal epithelial cell lines (293) and ccRCC cell lines (786-O, 769-P, OSRC-2, Caki-1, ACHN, and A498). In addition, the relationship between FGFR2 expression and clinical pathological characteristics (including TNM staging and pathological grading) and survival prognosis in ccRCC patients was further analyzed. Furthermore, the relationship between FGFR2 expression and B cells, T cells, natural killer (NK) cells and neutrophil infiltration in the ccRCC patients was analyzed, and the Biological General Repository for Interactionh Datasets (BioGRID) was used to builds protein-protein interaction (PPI) networks to study molecules that interacted with the FGFR2 protein. RESULTS In the TCGA database, the expression of FGFR2 was down-regulated in ccRCC tissue samples compared with normal tissue samples, and the expression in the GEO database also showed this differences. Furthermore, FGFR2 expression was downregulated in ccRCC clinical samples and ccRCC cell lines, compared with corresponding paracancerous normal tissue or normal renal epithelial cell lines. In addition, FGFR2 high expression was associated with earlier, lower-level ccRCC and was associated with a better prognosis in the patients with ccRCC. Moreover, FGFR2 expression was not significantly related to B cells, T cells, NK cells and neutrophil infiltration, and the PPI network showed that FGFR2 protein interacted with certain molecules. CONCLUSION Our work sheds light on the potential role of FGFR2 in the development of ccRCC, suggesting that FGFR2 may serve as a prognostic marker and potential therapeutic target for patients with ccRCC.
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Pan YJ, Liu BW, Pei DS. The Role of Alternative Splicing in Cancer: Regulatory Mechanism, Therapeutic Strategy, and Bioinformatics Application. DNA Cell Biol 2022; 41:790-809. [PMID: 35947859 DOI: 10.1089/dna.2022.0322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
[Formula: see text] Alternative splicing (AS) can generate distinct transcripts and subsequent isoforms that play differential functions from the same pre-mRNA. Recently, increasing numbers of studies have emerged, unmasking the association between AS and cancer. In this review, we arranged AS events that are closely related to cancer progression and presented promising treatments based on AS for cancer therapy. Obtaining proliferative capacity, acquiring invasive properties, gaining angiogenic features, shifting metabolic ability, and getting immune escape inclination are all splicing events involved in biological processes. Spliceosome-targeted and antisense oligonucleotide technologies are two novel strategies that are hopeful in tumor therapy. In addition, bioinformatics applications based on AS were summarized for better prediction and elucidation of regulatory routines mingled in. Together, we aimed to provide a better understanding of complicated AS events associated with cancer biology and reveal AS a promising target of cancer treatment in the future.
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Affiliation(s)
- Yao-Jie Pan
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, China
| | - Bo-Wen Liu
- Department of General Surgery, Xuzhou Medical University, Xuzhou, China
| | - Dong-Sheng Pei
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, China
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Sengal AT, Smith D, Snell CE, Leung S, Talhouk A, Williams ED, McAlpine JN, Pollock PM. Spatial expression of the FGFR2b splice isoform and its prognostic significance in endometrioid endometrial carcinoma. J Pathol Clin Res 2022; 8:521-537. [PMID: 35866380 PMCID: PMC9535101 DOI: 10.1002/cjp2.286] [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: 01/19/2022] [Revised: 05/19/2022] [Accepted: 06/07/2022] [Indexed: 12/29/2022]
Abstract
Endometrial carcinoma (EC) is the most common gynecological malignancy and fibroblast growth factor receptor 2 (FGFR2) is a frequently dysregulated receptor tyrosine kinase. FGFR2b and FGFR2c are the two main splice isoforms of FGFR2 and are normally localized in epithelial and mesenchymal cells, respectively. Previously, we demonstrated that FGFR2c mRNA expression was associated with aggressive tumor characteristics, shorter progression-free survival (PFS), and disease-specific survival (DSS) in endometrioid ECs (EECs). The objectives of this study were to investigate the spatial expression of FGFR2b in normal and hyperplasia with and without atypia of human endometrium and to assess the prognostic significance of FGFR2b expression in EC. FGFR2b and FGFR2c mRNA expression was evaluated in normal (proliferative [n = 10], secretory [n = 15], and atrophic [n = 10] endometrium), hyperplasia with and without atypia (n = 19) as well as two patient cohorts of EC samples (discovery [n = 78] and Vancouver [n = 460]) using isoform-specific BaseScope RNA in situ hybridization assays. Tumors were categorized based on FGFR2 isoform expression (one, both, or neither) and categories were correlated with clinicopathologic markers, molecular subtypes, and clinical outcomes. The FGFR2b splice isoform was exclusively expressed in the epithelial compartment of normal endometrium and hyperplasia without atypia. We observed FGFR2c expression at the basalis layer of glands in 33% (3/9) of hyperplasia with atypia. In patients with EEC, FGFR2b+/FGFR2c- expression was found in 48% of the discovery cohort and 35% of the validation Vancouver cohort. In univariate analyses, tumors with FGFR2b+/FGFR2c- expression had longer PFS (hazard ratio [HR] 0.265; 95% CI 0.145-0.423; log-rank p < 0.019) and DSS (HR 0.31; 95% CI 0.149-0.622; log-rank p < 0.001) compared to tumors with FGFR2b-/FGFR2c+ expression in the large EEC Vancouver cohort. In multivariable Cox regression analyses, tumors with FGFR2b+/FGFR2c- expression were significantly associated with longer DSS (HR 0.37; 95% CI 0.153-0.872; log-rank p < 0.023) compared to FGFR2b-/FGFR2c+ tumors. In conclusion, FGFR2b+/FGFR2c- expression is associated with favorable clinicopathologic markers and clinical outcomes suggesting that FGFR2b could play a role in tailoring the management of EEC patients in the clinic if these findings are confirmed in an independent cohort.
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Affiliation(s)
- Asmerom T Sengal
- School of Biomedical Sciences, Faculty of HealthQueensland University of Technology (QUT) located at the Translational Research Institute (TRI)BrisbaneAustralia
| | - Deborah Smith
- Mater PathologyMater Research and University of QueenslandBrisbaneAustralia
| | - Cameron E Snell
- Mater PathologyMater Research and University of QueenslandBrisbaneAustralia
| | - Samuel Leung
- Department of Pathology and Laboratory Medicine, Genetic Pathology Evaluation CentreUniversity of British ColumbiaVancouverBCCanada
| | - Aline Talhouk
- Department of Gynaecology and Obstetrics, Division of Gynaecologic OncologyUniversity of British ColumbiaVancouverBCCanada
| | - Elizabeth D Williams
- School of Biomedical Sciences, Faculty of HealthQueensland University of Technology (QUT) located at the Translational Research Institute (TRI)BrisbaneAustralia
| | - Jessica N McAlpine
- Department of Gynaecology and Obstetrics, Division of Gynaecologic OncologyUniversity of British ColumbiaVancouverBCCanada
| | - Pamela M Pollock
- School of Biomedical Sciences, Faculty of HealthQueensland University of Technology (QUT) located at the Translational Research Institute (TRI)BrisbaneAustralia
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Hua J, Ma C, Wang CH, Wang Y, Feng S, Xiao T, Zhu C. Abnormal GRHL2 Methylation Confers Malignant Progression to Acute Leukemia. Appl Bionics Biomech 2022; 2022:9708829. [PMID: 35855840 PMCID: PMC9288345 DOI: 10.1155/2022/9708829] [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: 05/28/2022] [Revised: 06/16/2022] [Accepted: 06/24/2022] [Indexed: 11/17/2022] Open
Abstract
Purpose Abnormal methylation of Grainyhead-like 2 (GRHL2) is associated with a substantial role in the malignant phenotype of tumor patients. Our present research is aimed at studying the abnormal expression of GRHL2 and the association of methylation in patients with acute leukemia and its relationship with prognosis. Materials and Methods We used quantitative real-time polymerase chain reaction (qRT-PCR) for detecting the aberrant expression level of GRHL2 in 60 patients with acute leukemia and 60 normal controls. We analyzed the significant correlation between the expression level of GRHL2 with clinicopathological features and patients' prognosis in acute leukemia using the corresponding statistical methods. Secondly, we employed qRT-PCR and Western blotting to detect the mRNA and protein levels of GRHL2 in leukemia cell lines. Next, we used methylation-specific polymerase chain reaction (MSP) technology for detecting the methylation of GRHL2 in clinical samples with acute leukemia and cell lines. Then we investigated the demethylating effect of arsenic trioxide and 5-azacitidine on the mRNA and protein expression levels of GRHL2 in cell lines of acute leukemia. Finally, we studied the effects of arsenide trioxide and 5-azacitidine on the proliferation of leukemia cells and the TGF-β signaling pathway. Results We found a lower level of GRHL2 expression not only in acute leukemia patients but also in cell lines when compared with normal controls. At the same time, the expression level of GRHL2 in patients with acute leukemia was significantly correlated with leukocyte count, platelet count, and cytogenetic risk grouping. In addition, the lower GRHL2 expression group showed a significantly lower overall survival rate in acute leukemia patients than that of patients with a higher GRHL2 expression group. Univariate and multivariate analyses revealed that the expression of GRHL2 is an independent risk factor in acute leukemia patients. The methylation level of the GRHL2 promoter region in acute leukemia patients and cell lines was significantly higher than the normal control group, and we found the elevated mRNA and protein levels of GRHL2 in acute leukemia cell lines after the use of the demethylation drug arsenic trioxide and 5-azacitidine. At the same time, arsenide trioxide and 5-azacitidine are associated with the inhibition of cellular proliferation of acute leukemia cells and also promote the elevated expression of TGF-β signaling pathway-linked proteins, including TGF-β, Smad2, Smad3, and Smad4. Conclusion Increased expression and methylation level of GRHL2 are closely associated with the prognosis and malignant phenotype of acute leukemia patients and play an irreplaceable role in the occurrence and development of patients with acute leukemia.
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Affiliation(s)
- Jing Hua
- Department of Hematology, Shandong Provincial Qianfoshan Hospital, Shandong University, China
| | - Congcong Ma
- Department of Hematology, Liaocheng People's Hospital, Shandong University, China
| | - Chao Hui Wang
- Department of Hematology, Qingdao Haici Medical Group, China
| | - Yan Wang
- Department of Hematology, Shandong Provincial Qianfoshan Hospital, Shandong University, China
| | - Saran Feng
- Department of Hematology, Shandong Provincial Qianfoshan Hospital, Shandong University, China
| | - Taiwu Xiao
- Department of Hematology, Liaocheng People's Hospital, Shandong University, China
| | - ChuanSheng Zhu
- Department of Hematology, Shandong Provincial Qianfoshan Hospital, Shandong University, China
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Li L, Zheng J, Stevens M, Oltean S. A repositioning screen using an FGFR2 splicing reporter reveals compounds that regulate epithelial-mesenchymal transitions and inhibit growth of prostate cancer xenografts. Mol Ther Methods Clin Dev 2022; 25:147-157. [PMID: 35402635 PMCID: PMC8971352 DOI: 10.1016/j.omtm.2022.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 03/13/2022] [Indexed: 12/13/2022]
Abstract
Research in the area of hallmarks of cancer has opened the possibility of designing new therapies based on modulating these cancer properties. We present here a screen designed to find chemicals that modulate epithelial-mesenchymal transitions (EMTs) in prostate cancer. For screening, we used a repurposing library and, as a readout, an FGFR2-based splicing reporter, which has been shown previously to be a sensor for EMTs. Various properties of cancer cells were assessed, signaling pathways investigated, and in vivo experiments in nude mice xenografts performed. The screen yielded three hit compounds (a T-type Ca channel inhibitor, an L-type Ca channel inhibitor, and an opioid antagonist) that switch FGFR2 splicing and induce an epithelial phenotype in prostate cancer cells. The compounds affected differently various properties of cancer cells, but all of them decreased cell migration, which is in line with modulating EMTs. We further present mechanistic insights into one of the compounds, nemadipine-A. The administration of nemadipine-A intraperitoneally in a nude mouse xenograft model of prostate cancer slowed tumor growth. To conclude, we show that knowledge of the molecular mechanisms that connect alternative splicing and various cancer properties may be used as a platform for drug development.
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Affiliation(s)
- Ling Li
- Institute of Biomedical & Clinical Sciences, Medical School, College of Medicine and Health, University of Exeter, St Luke’s Campus, Exeter EX1 2LU, UK
| | - Jinxia Zheng
- Institute of Biomedical & Clinical Sciences, Medical School, College of Medicine and Health, University of Exeter, St Luke’s Campus, Exeter EX1 2LU, UK
| | - Megan Stevens
- Institute of Biomedical & Clinical Sciences, Medical School, College of Medicine and Health, University of Exeter, St Luke’s Campus, Exeter EX1 2LU, UK
| | - Sebastian Oltean
- Institute of Biomedical & Clinical Sciences, Medical School, College of Medicine and Health, University of Exeter, St Luke’s Campus, Exeter EX1 2LU, UK
- Corresponding author Sebastian Oltean, MD, PhD, Institute of Biomedical & Clinical Sciences, Medical School, College of Medicine and Health, University of Exeter, St Luke’s Campus, Exeter, EX1 2LU, UK.
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Shen D, Ding L, Lu Z, Wang R, Yu C, Wang H, Zheng Q, Wang X, Xu W, Yu H, Xu L, Wang M, Yu S, Zhu S, Qian J, Xia L, Li G. METTL14-mediated Lnc-LSG1 m6A modification inhibits clear cell renal cell carcinoma metastasis via regulating ESRP2 ubiquitination. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:547-561. [PMID: 35036065 PMCID: PMC8738955 DOI: 10.1016/j.omtn.2021.12.024] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 12/15/2021] [Indexed: 12/29/2022]
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most lethal urological cancer and is characterized by a high rate of metastasis and relapse. N6-Methyladenosine (m6A) is implicated in various stages of cancer development. However, a thorough understanding of m6A-modified lncRNAs in ccRCC is lacking. The results showed that METTL14 had decreased expression in ccRCC tissues. In addition, the expression of METTL14 was negatively correlated to the prognosis, stage, and ccRCC tumor grade. The silencing of METTL14 was shown to significantly increase metastasis in vitro and in vivo. High-throughput methylated RNA immunoprecipitation sequencing (MeRIP-seq) showed that the m6A levels of Lnc-LSG1 could be regulated by METTL14. Lnc-LSG1 can directly bind to ESRP2 protein and promote ESRP2 degradation via facilitating ESRP2 ubiquitination. However, m6A modification on Lnc-LSG1 can block the interaction between Lnc-LSG1 and ESRP2 via the m6A reader, YTHDC1. Taken together, our findings unraveled the novel mechanism of METTL14 inhibiting ccRCC progression, and explored the correlation between m6A and lncRNA in ccRCC for the first time.
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Affiliation(s)
- Danyang Shen
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China.,Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Lifeng Ding
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Zeyi Lu
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Ruyue Wang
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Chenhao Yu
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Huan Wang
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Qiming Zheng
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Xuliang Wang
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Wanjiang Xu
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Haifeng Yu
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Liwei Xu
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Mingchao Wang
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Shicheng Yu
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Shibin Zhu
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Jun Qian
- State Key Laboratory of Modern Optical Instrumentations, Centre for Optical and Electromagnetic Research, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310058, China
| | - Liqun Xia
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Gonghui Li
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
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Öther-Gee Pohl S, Myant KB. Alternative RNA splicing in tumour heterogeneity, plasticity and therapy. Dis Model Mech 2022; 15:dmm049233. [PMID: 35014671 PMCID: PMC8764416 DOI: 10.1242/dmm.049233] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Alternative splicing is a process by which a single gene is able to encode multiple different protein isoforms. It is regulated by the inclusion or exclusion of introns and exons that are joined in different patterns prior to protein translation, thus enabling transcriptomic and proteomic diversity. It is now widely accepted that alternative splicing is dysregulated across nearly all cancer types. This widespread dysregulation means that nearly all cellular processes are affected - these include processes synonymous with the hallmarks of cancer - evasion of apoptosis, tissue invasion and metastasis, altered cellular metabolism, genome instability and drug resistance. Emerging evidence indicates that the dysregulation of alternative splicing also promotes a permissive environment for increased tumour heterogeneity and cellular plasticity. These are fundamental regulators of a patient's response to therapy. In this Review, we introduce the mechanisms of alternative splicing and the role of aberrant splicing in cancer, with particular focus on newfound evidence of alternative splicing promoting tumour heterogeneity, cellular plasticity and altered metabolism. We discuss recent in vivo models generated to study alternative splicing and the importance of these for understanding complex tumourigenic processes. Finally, we review the effects of alternative splicing on immune evasion, cell death and genome instability, and how targeting these might enhance therapeutic efficacy.
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Affiliation(s)
| | - Kevin B. Myant
- Cancer Research UK Edinburgh Centre, Institute of Genetics of Cancer, The University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
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11
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Lyu J, Cheng C. Regulation of Alternative Splicing during Epithelial-Mesenchymal Transition. Cells Tissues Organs 2022; 211:238-251. [PMID: 34348273 PMCID: PMC8741878 DOI: 10.1159/000518249] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 06/28/2021] [Indexed: 01/03/2023] Open
Abstract
Alternative splicing is an essential mechanism of gene regulation, giving rise to remarkable protein diversity in higher eukaryotes. Epithelial-mesenchymal transition (EMT) is a developmental process that plays an essential role in metazoan embryogenesis. Recent studies have revealed that alternative splicing serves as a fundamental layer of regulation that governs cells to undergo EMT. In this review, we summarize recent findings on the functional impact of alternative splicing in EMT and EMT-associated activities. We then discuss the regulatory mechanisms that control alternative splicing changes during EMT.
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Affiliation(s)
- Jingyi Lyu
- Lester and Sue Smith Breast Center, Department of Molecular
& Human Genetics, Department of Molecular & Cellular Biology, Baylor College
of Medicine, Houston, TX 77030, USA,Integrative Molecular and Biomedical Sciences Graduate
Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chonghui Cheng
- Lester and Sue Smith Breast Center, Department of Molecular
& Human Genetics, Department of Molecular & Cellular Biology, Baylor College
of Medicine, Houston, TX 77030, USA,Integrative Molecular and Biomedical Sciences Graduate
Program, Baylor College of Medicine, Houston, TX 77030, USA.,To whom correspondence should be addressed:
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12
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Ebrahimie E, Rahimirad S, Tahsili M, Mohammadi-Dehcheshmeh M. Alternative RNA splicing in stem cells and cancer stem cells: Importance of transcript-based expression analysis. World J Stem Cells 2021; 13:1394-1416. [PMID: 34786151 PMCID: PMC8567453 DOI: 10.4252/wjsc.v13.i10.1394] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/21/2021] [Accepted: 09/14/2021] [Indexed: 02/06/2023] Open
Abstract
Alternative ribonucleic acid (RNA) splicing can lead to the assembly of different protein isoforms with distinctive functions. The outcome of alternative splicing (AS) can result in a complete loss of function or the acquisition of new functions. There is a gap in knowledge of abnormal RNA splice variants promoting cancer stem cells (CSCs), and their prospective contribution in cancer progression. AS directly regulates the self-renewal features of stem cells (SCs) and stem-like cancer cells. Notably, octamer-binding transcription factor 4A spliced variant of octamer-binding transcription factor 4 contributes to maintaining stemness properties in both SCs and CSCs. The epithelial to mesenchymal transition pathway regulates the AS events in CSCs to maintain stemness. The alternative spliced variants of CSCs markers, including cluster of differentiation 44, aldehyde dehydrogenase, and doublecortin-like kinase, α6β1 integrin, have pivotal roles in increasing self-renewal properties and maintaining the pluripotency of CSCs. Various splicing analysis tools are considered in this study. LeafCutter software can be considered as the best tool for differential splicing analysis and identification of the type of splicing events. Additionally, LeafCutter can be used for efficient mapping splicing quantitative trait loci. Altogether, the accumulating evidence re-enforces the fact that gene and protein expression need to be investigated in parallel with alternative splice variants.
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Affiliation(s)
- Esmaeil Ebrahimie
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide 5005, South Australia, Australia
- La Trobe Genomics Research Platform, School of Life Sciences, College of Science, Health and Engineering, La Trobe University, Melbourne 3086, Australia
- School of Biosciences, The University of Melbourne, Melbourne 3010, Australia,
| | - Samira Rahimirad
- Department of Medical Genetics, National Institute of Genetic Engineering and Biotechnology, Tehran 1497716316, Iran
- Division of Urology, Department of Surgery, McGill University and the Research Institute of the McGill University Health Centre, Montreal H4A 3J1, Quebec, Canada
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13
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Vadlamudi Y, Dey DK, Kang SC. Emerging Multi-cancer Regulatory Role of ESRP1: Orchestration of Alternative Splicing to Control EMT. Curr Cancer Drug Targets 2021; 20:654-665. [PMID: 32564755 DOI: 10.2174/1568009620666200621153831] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/30/2020] [Accepted: 05/06/2020] [Indexed: 02/06/2023]
Abstract
RNA binding proteins (RBPs) associate with nascent and mature RNAs to perform biological functions such as alternative splicing and RNA stability. Having unique RNA recognition binding motifs, RBPs form complexes with RNA in a sequence- and structure-based manner. Aberrant expressions of several RBPs have been identified in tumorigenesis and cancer progression. These uncontrolled RBPs affect several mechanisms, including cell proliferation, tumor growth, invasion, metastasis and chemoresistance. Epithelial splicing regulatory protein 1 (ESRP1) is a member of the hnRNP family of proteins that play a crucial role in regulating numerous cellular processes, including alternative splicing and translation of multiple genes during organogenesis. Abnormal expression of ESRP1 alters the cell morphology, and leads to cell proliferation and tumor growth during cancer progression. ESRP1 mediated alternative splicing of target genes, including CD44, FGFR, PTBP1, LYN, ENAH, SPAG1 and ZMYND8, results in cancer progression. In addition, ESRP1 also regulates circularization and biogenesis of circular RNAs such as circUHRF1, circNOL10 and circANKS1B, whose expressions have been identified as key factors in various cancers. This multi-functional protein is also involved in imposing stability of target mRNAs such as cyclin A2, and thereby cell cycle regulation. The scope of this review is to examine recent scientific data, outcomes of the up- and down-regulated proteins, and the role of ESRP1 in various cancers. We conclude by summarizing ESRP1 dysregulation and its consequences on target genes in various human cancers. Collectively, the consequences of ESRP1 mediated splicing in cancer cells suggest the role of ESRP1 in cell proliferation and chemoresistance via apoptosis and autophagy modulation, which could, therefore, be potential targets for cancer therapeutics.
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Affiliation(s)
| | - Debasish K Dey
- Department of Biotechnology, Daegu University, Gyeongsan, Gyeongbuk-38453, Korea
| | - Sun C Kang
- Department of Biotechnology, Daegu University, Gyeongsan, Gyeongbuk-38453, Korea
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14
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Epstein RJ, Tian LJ, Gu YF. 2b or Not 2b: How Opposing FGF Receptor Splice Variants Are Blocking Progress in Precision Oncology. JOURNAL OF ONCOLOGY 2021; 2021:9955456. [PMID: 34007277 PMCID: PMC8110382 DOI: 10.1155/2021/9955456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 04/21/2021] [Indexed: 01/16/2023]
Abstract
More than ten thousand peer-reviewed studies have assessed the role of fibroblast growth factors (FGFs) and their receptors (FGFRs) in cancer, but few patients have yet benefited from drugs targeting this molecular family. Strategizing how best to use FGFR-targeted drugs is complicated by multiple variables, including RNA splicing events that alter the affinity of ligands for FGFRs and hence change the outcomes of stromal-epithelial interactions. The effects of splicing are most relevant to FGFR2; expression of the FGFR2b splice isoform can restore apoptotic sensitivity to cancer cells, whereas switching to FGFR2c may drive tumor progression by triggering epithelial-mesenchymal transition. The differentiating and regulatory actions of wild-type FGFR2b contrast with the proliferative actions of FGFR1 and FGFR3, and may be converted to mitogenicity either by splice switching or by silencing of tumor suppressor genes such as CDH1 or PTEN. Exclusive use of small-molecule pan-FGFR inhibitors may thus cause nonselective blockade of FGFR2 isoforms with opposing actions, undermining the rationale of FGFR2 drug targeting. This splice-dependent ability of FGFR2 to switch between tumor-suppressing and -driving functions highlights an unmet oncologic need for isoform-specific drug targeting, e.g., by antibody inhibition of ligand-FGFR2c binding, as well as for more nuanced molecular pathology prediction of FGFR2 actions in different stromal-tumor contexts.
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Affiliation(s)
- Richard J. Epstein
- New Hope Cancer Center, Beijing United Hospital, 9-11 Jiangtai West Rd, Chaoyang, Beijing 100015, China
- Garvan Institute of Medical Research and UNSW Clinical School, 84 Victoria St, Darlinghurst 2010 Sydney, Australia
| | - Li Jun Tian
- New Hope Cancer Center, Beijing United Hospital, 9-11 Jiangtai West Rd, Chaoyang, Beijing 100015, China
| | - Yan Fei Gu
- New Hope Cancer Center, Beijing United Hospital, 9-11 Jiangtai West Rd, Chaoyang, Beijing 100015, China
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15
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Sbiera I, Kircher S, Altieri B, Fassnacht M, Kroiss M, Sbiera S. Epithelial and Mesenchymal Markers in Adrenocortical Tissues: How Mesenchymal Are Adrenocortical Tissues? Cancers (Basel) 2021; 13:1736. [PMID: 33917436 PMCID: PMC8038668 DOI: 10.3390/cancers13071736] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/02/2021] [Accepted: 04/04/2021] [Indexed: 12/22/2022] Open
Abstract
A clinically relevant proportion of adrenocortical carcinoma (ACC) cases shows a tendency to metastatic spread. The objective was to determine whether the epithelial to mesenchymal transition (EMT), a mechanism associated with metastasizing in several epithelial cancers, might play a crucial role in ACC. 138 ACC, 29 adrenocortical adenomas (ACA), three normal adrenal glands (NAG), and control tissue samples were assessed for the expression of epithelial (E-cadherin and EpCAM) and mesenchymal (N-cadherin, SLUG and SNAIL) markers by immunohistochemistry. Using real-time RT-PCR we quantified the alternative isoform splicing of FGFR 2 and 3, another known indicator of EMT. We also assessed the impact of these markers on clinical outcome. Results show that both normal and neoplastic adrenocortical tissues lacked expression of epithelial markers but strongly expressed mesenchymal markers N-cadherin and SLUG. FGFR isoform splicing confirmed higher similarity of adrenocortical tissues to mesenchymal compared to epithelial tissues. In ACC, higher SLUG expression was associated with clinical markers indicating aggressiveness, while N-cadherin expression inversely associated with these markers. In conclusion, we could not find any indication of EMT as all adrenocortical tissues lacked expression of epithelial markers and exhibited closer similarity to mesenchymal tissues. However, while N-cadherin might play a positive role in tissue structure upkeep, SLUG seems to be associated with a more aggressive phenotype.
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Affiliation(s)
- Iuliu Sbiera
- Department of Internal Medicine I, Division of Endocrinology and Diabetes, University Hospital Würzburg, 97080 Würzburg, Germany; (I.S.); (B.A.); (M.F.)
| | - Stefan Kircher
- Institute for Pathology, University of Würzburg, 97080 Würzburg, Germany;
| | - Barbara Altieri
- Department of Internal Medicine I, Division of Endocrinology and Diabetes, University Hospital Würzburg, 97080 Würzburg, Germany; (I.S.); (B.A.); (M.F.)
| | - Martin Fassnacht
- Department of Internal Medicine I, Division of Endocrinology and Diabetes, University Hospital Würzburg, 97080 Würzburg, Germany; (I.S.); (B.A.); (M.F.)
- Clinical Chemistry and Laboratory Medicine, University Hospital Würzburg, 97080 Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, University of Würzburg, 97080 Würzburg, Germany
| | - Matthias Kroiss
- Department of Internal Medicine I, Division of Endocrinology and Diabetes, University Hospital Würzburg, 97080 Würzburg, Germany; (I.S.); (B.A.); (M.F.)
- Comprehensive Cancer Center Mainfranken, University of Würzburg, 97080 Würzburg, Germany
- Department of Internal Medicine IV, University Hospital Munich, Ludwig-Maximilians-Universität München, 80336 Munich, Germany
| | - Silviu Sbiera
- Department of Internal Medicine I, Division of Endocrinology and Diabetes, University Hospital Würzburg, 97080 Würzburg, Germany; (I.S.); (B.A.); (M.F.)
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16
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Alternative splicing modulates cancer aggressiveness: role in EMT/metastasis and chemoresistance. Mol Biol Rep 2021; 48:897-914. [PMID: 33400075 DOI: 10.1007/s11033-020-06094-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 12/15/2020] [Indexed: 12/11/2022]
Abstract
Enhanced metastasis and disease recurrence accounts for the high mortality rates associated with cancer. The process of Epithelial-Mesenchymal Transition (EMT) contributes towards the augmentation of cancer invasiveness along with the gain of stem-like and the subsequent drug-resistant behavior. Apart from the well-established transcriptional regulation, EMT is also controlled post-transcriptionally by virtue of alternative splicing (AS). Numerous genes including Fibroblast Growth Factor receptor (FGFR) as well as CD44 are differentially spliced during this trans-differentiation process which, in turn, governs cancer progression. These splicing alterations are controlled by various splicing factors including ESRP, RBFOX2 as well as hnRNPs. Here, we have depicted the mechanisms governing the splice isoform switching of FGFR and CD44. Moreover, the role of the splice variants generated by AS of these gene transcripts in modulating the metastatic potential and stem-like/chemoresistant behavior of cancer cells has also been highlighted. Additionally, the involvement of splicing factors in regulating EMT/invasiveness along with drug-resistance as well as the metabolic properties of the cells has been emphasized. Tumorigenesis is accompanied by a remodeling of the cellular splicing profile generating diverse protein isoforms which, in turn, control the cancer-associated hallmarks. Therefore, we have also briefly discussed about a wide variety of genes which are differentially spliced in the tumor cells and promote cancer progression. We have also outlined different strategies for targeting the tumor-associated splicing events which have shown promising results and therefore this approach might be useful in developing therapies to reduce cancer aggressiveness in a more specific manner.
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17
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Landry-Truchon K, Houde N, Lhuillier M, Charron L, Hadchouel A, Delacourt C, Foulkes WD, Galmiche-Rolland L, Jeannotte L. Deletion of Yy1 in mouse lung epithelium unveils molecular mechanisms governing pleuropulmonary blastoma pathogenesis. Dis Model Mech 2020; 13:dmm045989. [PMID: 33158935 PMCID: PMC7790197 DOI: 10.1242/dmm.045989] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 10/21/2020] [Indexed: 12/11/2022] Open
Abstract
Pleuropulmonary blastoma (PPB) is a very rare pediatric lung disease. It can progress from abnormal epithelial cysts to an aggressive sarcoma with poor survival. PPB is difficult to diagnose as it can be confounded with other cystic lung disorders, such as congenital pulmonary airway malformation (CPAM). PPB is associated with mutations in DICER1 that perturb the microRNA (miRNA) profile in lung. How DICER1 and miRNAs act during PPB pathogenesis remains unsolved. Lung epithelial deletion of the Yin Yang1 (Yy1) gene in mice causes a phenotype mimicking the cystic form of PPB and affects the expression of key regulators of lung development. Similar changes in expression were observed in PPB but not in CPAM lung biopsies, revealing a distinctive PPB molecular signature. Deregulation of molecules promoting epithelial-mesenchymal transition (EMT) was detected in PPB specimens, suggesting that EMT might participate in tumor progression. Changes in miRNA expression also occurred in PPB lung biopsies. miR-125a-3p, a candidate to regulate YY1 expression and lung branching, was abnormally highly expressed in PPB samples. Together, these findings support the concept that reduced expression of YY1, due to the abnormal miRNA profile resulting from DICER1 mutations, contributes to PPB development via its impact on the expression of key lung developmental genes.This article has an associated First Person interview with the joint first authors of the paper.
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Affiliation(s)
- Kim Landry-Truchon
- Centre de recherche sur le cancer de l'Université Laval, Centre de recherche du CHU de Québec-Université Laval (Oncology Axis), Québec, Canada G1R 3S3
| | - Nicolas Houde
- Centre de recherche sur le cancer de l'Université Laval, Centre de recherche du CHU de Québec-Université Laval (Oncology Axis), Québec, Canada G1R 3S3
| | - Mickaël Lhuillier
- Inserm U1151, Institut Necker-Enfants Malades, Université de Paris, 75743 Paris, Cedex15, France
| | - Louis Charron
- Centre de recherche sur le cancer de l'Université Laval, Centre de recherche du CHU de Québec-Université Laval (Oncology Axis), Québec, Canada G1R 3S3
| | - Alice Hadchouel
- Inserm U1151, Institut Necker-Enfants Malades, Université de Paris, 75743 Paris, Cedex15, France
- AP-HP, Hôpital Necker-Enfants Malades, 75743 Paris, Cedex15, France
| | - Christophe Delacourt
- Inserm U1151, Institut Necker-Enfants Malades, Université de Paris, 75743 Paris, Cedex15, France
- AP-HP, Hôpital Necker-Enfants Malades, 75743 Paris, Cedex15, France
| | - William D Foulkes
- Department of Medical Genetics, Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, Montréal, Canada H3T 1E2
| | | | - Lucie Jeannotte
- Centre de recherche sur le cancer de l'Université Laval, Centre de recherche du CHU de Québec-Université Laval (Oncology Axis), Québec, Canada G1R 3S3
- Department of Molecular Biology, Medical Biochemistry & Pathology, Université Laval, Québec, Canada G1V 0A6
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18
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Role of PKCε in the epithelial-mesenchymal transition induced by FGFR2 isoform switch. Cell Commun Signal 2020; 18:76. [PMID: 32429937 PMCID: PMC7238605 DOI: 10.1186/s12964-020-00582-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/16/2020] [Indexed: 01/09/2023] Open
Abstract
Background The epithelial isoform of the fibroblast growth factor receptor 2 (FGFR2b) controls the entire program of keratinocyte differentiation via the sequential involvement of protein kinase C (PKC) δ and PKCα. In contrast, the FGFR2 isoform switch and the aberrant expression of the mesenchymal FGFR2c isoform leads to impairment of differentiation, epithelial-mesenchymal transition (EMT) and tumorigenic features. Aim of our present study was to contribute in clarifying the complex network of signaling pathways involved in the FGFR2c-mediated oncogenic outcomes focusing on PKCε, which appears to be involved in the induction of EMT and tumorigenesis in several epithelial contexts. Methods Biochemical and molecular analysis, as well as in vitro invasion assays, combined with the use of specific small interfering RNA (siRNA), were performed in human keratinocytes stably expressing FGFR2c or FGFR2b isoforms. Results Our results showed that aberrant expression and signaling of FGFR2c, but not those of FGFR2b, in human keratinocytes induced a strong phosphorylation/activation of PKCε. The use of siRNA approach showed that PKCε is the hub signaling downstream FGFR2c responsible for the modulation of EMT markers and for the induction of the EMT-related transcription factors STAT3, Snail1 and FRA1, as well as for the acquisition of the invasive behavior. Moreover, experiments of depletion of ESRP1, responsible for FGFR2 splicing in epithelial cells, indicated that the activation of PKCε is the key molecular event triggered by FGFR2 isoform switch and underlying EMT induction. Conclusions Overall, our results point to the identification of the downstream PKC isoform responsible for the FGFR signaling deregulation occurring in epithelial tissues from the physiological oncosoppressive to the pathological oncogenic profile. Video Abstract
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19
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Sengal AT, Patch AM, Snell CE, Smith DS, Leung SCY, Talhouk A, Williams ED, McAlpine JN, Pollock PM. FGFR2c Mesenchymal Isoform Expression Is Associated with Poor Prognosis and Further Refines Risk Stratification within Endometrial Cancer Molecular Subtypes. Clin Cancer Res 2020; 26:4569-4580. [PMID: 32414751 DOI: 10.1158/1078-0432.ccr-19-4088] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/17/2020] [Accepted: 05/11/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE The two most common molecular subtypes of endometrial cancers, mismatch repair deficient (MMRd) and p53 wild-type (p53wt) comprise the majority of endometrial cancers and have intermediate prognoses where additional risk stratification biomarkers are needed. Isoform switching of FGFR2 from FGFR2b to FGFR2c (normally expressed in mesenchymal cells), has been reported in other solid carcinomas. The objective of this study was to investigate the role of FGFR2c in risk stratification of endometrial cancer. EXPERIMENTAL DESIGN We have developed and optimized a BaseScope RNA ISH assay to detect FGFR2c. FGFR2c expression was determined in a preliminary screening cohort of 78 endometrial cancers and a clinically and molecularly annotated Vancouver cohort (n = 465). Cox regression model analyses were performed to assess the prognostic value of FGFR2c. RESULTS Univariate and multivariate analyses revealed FGFR2c expression was significantly associated with shorter disease-specific survival (DSS) and progression-free survival (PFS) in endometrioid endometrial cancer (EEC, n = 302). Notably, FGFR2c expression was significantly associated with shorter PFS and DSS in patients with grade 3 EECs (P < 0.003 and P < 0.002) and the European Society Medical Oncology (ESMO) high-risk group (P < 0.0001 and P < 0.002), respectively. Moreover, within the MMRd subtype, FGFR2c expression was significantly associated with shorter PFS (P < 0.048) and DSS (P < 0.001). CONCLUSIONS FGFR2c expression appears an independent prognostic biomarker in patients with EEC and further discerns the outcomes within grade 3 tumors, ESMO high-risk groups, as well as within the MMRd and p53wt subtypes. FGFR2c inclusion into future molecular subtyping can further refine risk stratification of EEC.
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Affiliation(s)
- Asmerom T Sengal
- Queensland University of Technology, School of Biomedical Sciences, Faculty of Health, Institute of Health and Biomedical Innovation, located at the Translational Research Institute, PA Hospital Campus, 37 Kent St Woolloongabba, Brisbane, Queensland, Australia
| | - Ann-Marie Patch
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Cameron E Snell
- Mater Pathology, Mater Research and University of Queensland, Brisbane, Queensland, Australia
| | - Deborah S Smith
- Mater Pathology, Mater Research and University of Queensland, Brisbane, Queensland, Australia
| | - Samuel C Y Leung
- Department of Pathology and Laboratory Medicine, Genetic Pathology Evaluation Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Aline Talhouk
- Division of Gynaecologic Oncology, Department of Gynaecology and Obstetrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Elizabeth D Williams
- Queensland University of Technology, School of Biomedical Sciences, Faculty of Health, Institute of Health and Biomedical Innovation, located at the Translational Research Institute, PA Hospital Campus, 37 Kent St Woolloongabba, Brisbane, Queensland, Australia
| | - Jessica N McAlpine
- Division of Gynaecologic Oncology, Department of Gynaecology and Obstetrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Pamela M Pollock
- Queensland University of Technology, School of Biomedical Sciences, Faculty of Health, Institute of Health and Biomedical Innovation, located at the Translational Research Institute, PA Hospital Campus, 37 Kent St Woolloongabba, Brisbane, Queensland, Australia.
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20
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Fujikura K, Yoshida M, Uesaka K. Transcriptome complexity in intravascular NK/T-cell lymphoma. J Clin Pathol 2020; 73:671-675. [PMID: 32188628 DOI: 10.1136/jclinpath-2020-206461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/23/2020] [Accepted: 02/25/2020] [Indexed: 11/04/2022]
Abstract
AIMS Intravascular NK/T-cell lymphoma (IVNKTCL) is a rare disease, which is characterised by exclusive growth of large cells within the lumen of small vessels, Epstein-Barr virus infection and somatic mutations in epigenetic regulator genes. Here, we elucidate the transcriptomic complexity of IVNKTCL. METHODS IVNKTCL cases were retrieved from a single-centre cohort of 25 intravascular lymphomas. RNA-seq and whole exome sequencing (WES) were performed to analyse transcriptomic abnormalities and mutations in splicing factors. RESULTS Approximately 88% of the total reads from the RNA-seq were considered exonic, while the remaining reads (12%) were mapped to intronic or intergenic regions. We detected 28,941 alternative splicing events, some of which would produce abnormal proteins rarely found in normal cells. The detected events also included tumour-specific splicing alterations in oncogenes and tumour suppressors (e.g., HRAS, MDM2 and VEGFA). WES identified premature termination mutations or copy number losses in a total of 15 splicing regulator genes, including SF3B5, SRSF12 and TNPO3. CONCLUSIONS This study raises the possibility that IVNKTCL may be driven by multiple complex regulatory loops, including non-exonic expression and aberrant splicing, in addition to defects in epigenetic regulation.
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Affiliation(s)
- Kohei Fujikura
- Department of Pathology, Kobe City Medical Center General Hospital, Kobe, Japan .,Department of Diagnostic Pathology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Makoto Yoshida
- Department of Pathology, Kobe City Medical Center General Hospital, Kobe, Japan
| | - Kazuma Uesaka
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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21
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Hu X, Harvey SE, Zheng R, Lyu J, Grzeskowiak CL, Powell E, Piwnica-Worms H, Scott KL, Cheng C. The RNA-binding protein AKAP8 suppresses tumor metastasis by antagonizing EMT-associated alternative splicing. Nat Commun 2020; 11:486. [PMID: 31980632 PMCID: PMC6981122 DOI: 10.1038/s41467-020-14304-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 12/17/2019] [Indexed: 01/01/2023] Open
Abstract
Alternative splicing has been shown to causally contribute to the epithelial–mesenchymal transition (EMT) and tumor metastasis. However, the scope of splicing factors that govern alternative splicing in these processes remains largely unexplored. Here we report the identification of A-Kinase Anchor Protein (AKAP8) as a splicing regulatory factor that impedes EMT and breast cancer metastasis. AKAP8 not only is capable of inhibiting splicing activity of the EMT-promoting splicing regulator hnRNPM through protein–protein interaction, it also directly binds to RNA and alters splicing outcomes. Genome-wide analysis shows that AKAP8 promotes an epithelial cell state splicing program. Experimental manipulation of an AKAP8 splicing target CLSTN1 revealed that splice isoform switching of CLSTN1 is crucial for EMT. Moreover, AKAP8 expression and the alternative splicing of CLSTN1 predict breast cancer patient survival. Together, our work demonstrates the essentiality of RNA metabolism that impinges on metastatic breast cancer. Splice isoform switching regulated by the heterogeneous nuclear ribonucleoprotein M (hnRNPM) induces EMT and metastasis. Here, the authors report that AKAP8 is a metastasis suppressor that inhibits the splicing activity of hnRNPM and antagonizes genome-wide EMT-associated alternative splicing to maintain epithelial cell state.
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Affiliation(s)
- Xiaohui Hu
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Samuel E Harvey
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Rong Zheng
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jingyi Lyu
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Caitlin L Grzeskowiak
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Emily Powell
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Helen Piwnica-Worms
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Kenneth L Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chonghui Cheng
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
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22
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Gao L, He RQ, Huang ZG, Dang YW, Gu YY, Yan HB, Li SH, Chen G. Genome-wide Analysis of the Alternative Splicing Profiles Revealed Novel Prognostic Index for Kidney Renal Cell Clear Cell Carcinoma. J Cancer 2020; 11:1542-1554. [PMID: 32047561 PMCID: PMC6995393 DOI: 10.7150/jca.36998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 12/13/2019] [Indexed: 11/21/2022] Open
Abstract
Alternative splicing (AS) is a major mechanism that greatly enhanced the diversity of proteome. Mounting evidence demonstrated that aberration of AS are important steps for the initiation and progression of human cancers. Here, we comprehensively investigated the association between whole landscape of AS profiles and the survival outcome of renal cell carcinoma (RCC) patients using RNA-seq data from TCGA SpliceSeq. Because of the limited number size of deaths in kidney chromophobe renal cell carcinoma (KICH) and papillary renal cell carcinoma (KIRP) TCGA cohorts, we only conducted survival analysis in kidney clear renal cell carcinoma (KIRC). We further constructed prognostic index (PI) based on prognosis-related AS events and built correlation network for splicing factors and prognosis-related AS events. According to the results, a total of 5351 AS events in 3522 genes were significantly correlated with the overall survival (OS) of kidney clear cell renal cell carcinoma (KIRC) patients. Seven of the PI models exhibited preferable prognosis-predicting capacity for KIRC with PI-ALL reaching the highest area under curve value of 0.875. The splicing regulatory network between splicing factors and prognosis-related AS events depicted a tangled web of relationships between them. One of the splicing factors: KHDRBS3 was validated by immunohistochemistry to be down-regulated in KIRC tissues. In conclusion, the powerful efficiency of risk stratification of PI models indicated the potential of AS signature as promising prognostic markers for KIRC and the splicing regulation network provided possible genetic mechanism of KIRC.
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Affiliation(s)
- Li Gao
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P. R. China
| | - Rong-Quan He
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P. R. China
| | - Zhi-Guang Huang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P. R. China
| | - Yi-Wu Dang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P. R. China
| | - Yong-Yao Gu
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P. R. China
| | - Hai-Biao Yan
- Department of Urology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P. R. China
| | - Sheng-Hua Li
- Department of Urology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P. R. China
| | - Gang Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P. R. China
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Wang H, Zhu N, Ye X, Wang L, Wang B, Shan W, Lai X, Tan Y, Fu S, Xiao H, Huang H. PTPN21-CDS long isoform inhibits the response of acute lymphoblastic leukemia cells to NK-mediated lysis via the KIR/HLA-I axis. J Cell Biochem 2020; 121:3298-3312. [PMID: 31898344 DOI: 10.1002/jcb.29601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 12/11/2019] [Indexed: 12/11/2022]
Abstract
Protein tyrosine phosphatase non-receptor type 21 (PTPN21) is a member of the non-receptor tyrosine phosphatase family. We have found that PTPN21 is mutated in relapsed Philadelphia chromosome-negative acute lymphoblastic leukemia (ALL) after allogeneic hematopoietic stem cell transplantation. PTPN21 consists of three types of isoforms according to the length of the protein encoded. However, the roles of different isoforms in leukemic cells have not been elucidated. In the study, PTPN21 isoform constitution in five ALL cell lines were identified by transcriptome polymerase chain reaction combined with Sanger sequencing, and the relationship between PTPN21 isoforms and sensitivity to natural killer (NK) cells mediated killing in ALL cell lines were further assessed by knock-out of different isoforms of PTPN21 using CRISPR-Cas9 technique. Subsequently, we explored the functional mechanisms through RNA sequencing and confirmatory testing. The results showed that there was no significant change when all PTPN21 isoforms were knocked out in ALL cells, but the sensitivity of NALM6 cells with PTPN21-CDSlong knock-out (NALM6-PTPN21lk ) to NK-mediated killing was significantly increased. Whole transcriptome sequencing and further validation testing showed that human leukocyte antigen class I (HLA-I) molecules were significantly decreased, accompanied by a significantly downregulated expression of antigen presenting-related chaperones in NALM6-PTPN21lk cells. Our results uncovered a previously unknown mechanism that PTPN21-CDSlong and CDSshort isoforms may play opposite roles in NK-mediated killing in ALL cells, and showed that the endogenous PTPN21-CDSlong isoform inhibited ALL cells to NK cell-mediated lysis by regulating the KIR-HLA-I axis.
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Affiliation(s)
- Huafang Wang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, China.,Zhejiang Engineering Laboratory for Stem cell and Immunotherapy, Hangzhou, Zhejiang, China
| | - Ni Zhu
- Department of Hematology, The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Xiaohang Ye
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Limengmeng Wang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, China.,Zhejiang Engineering Laboratory for Stem cell and Immunotherapy, Hangzhou, Zhejiang, China
| | - Binsheng Wang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, China.,Zhejiang Engineering Laboratory for Stem cell and Immunotherapy, Hangzhou, Zhejiang, China
| | - Wei Shan
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, China.,Zhejiang Engineering Laboratory for Stem cell and Immunotherapy, Hangzhou, Zhejiang, China
| | - Xiaoyu Lai
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yamin Tan
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Shan Fu
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Haowen Xiao
- Department of Hematology, The Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, China
| | - He Huang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, China.,Zhejiang Engineering Laboratory for Stem cell and Immunotherapy, Hangzhou, Zhejiang, China
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24
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Teles SP, Oliveira P, Ferreira M, Carvalho J, Ferreira P, Oliveira C. Integrated Analysis of Structural Variation and RNA Expression of FGFR2 and Its Splicing Modulator ESRP1 Highlight the ESRP1amp- FGFR2norm- FGFR2-IIIchigh Axis in Diffuse Gastric Cancer. Cancers (Basel) 2019; 12:cancers12010070. [PMID: 31881796 PMCID: PMC7017189 DOI: 10.3390/cancers12010070] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/15/2019] [Accepted: 12/23/2019] [Indexed: 01/11/2023] Open
Abstract
Gastric Cancer (GC) is one of the most common and deadliest types of cancer in the world. To improve GC prognosis, increasing efforts are being made to develop new targeted therapies. Although FGFR2 genetic amplification and protein overexpression in GC have been targeted in clinical trials, so far no improvement in patient overall survival has been found. To address this issue, we studied genetic and epigenetic events affecting FGFR2 and its splicing regulator ESRP1 in GC that could be used as new therapeutic targets or predictive biomarkers. We performed copy number variation (CNV), DNA methylation, and RNA expression analyses of FGFR2/ESRP1 across several cohorts. We discovered that both genes were frequently amplified and demethylated in GC, resulting in increased ESRP1 expression and of a specific FGFR2 isoform: FGFR2-IIIb. We also showed that ESRP1 amplification in GC correlated with a significant decreased expression of FGFR2-IIIc, an alternative FGFR2 splicing isoform. Furthermore, when we performed a survival analysis, we observed that patients harboring diffuse-type tumors with low FGFR2-IIIc expression revealed a better overall survival than patients with FGFR2-IIIc high-expressing diffuse tumors. Our results encourage further studies on the role of ESRP1 in GC and support FGFR2-IIIc as a relevant biomarker in GC.
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Affiliation(s)
- Sara Pinto Teles
- Ipatimup—Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Master in Oncology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
| | - Patrícia Oliveira
- Ipatimup—Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Marta Ferreira
- Ipatimup—Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Joana Carvalho
- Ipatimup—Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Pedro Ferreira
- Ipatimup—Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Department of Computer Science, Faculty of Sciences, University of Porto, Rua Campo Alegre 1021/1055, 4169-007 Porto, Portugal
| | - Carla Oliveira
- Ipatimup—Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Department Pathology and Oncology Faculty of Medicine University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
- Correspondence:
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25
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Rahhal R, Seto E. Emerging roles of histone modifications and HDACs in RNA splicing. Nucleic Acids Res 2019; 47:4911-4926. [PMID: 31162605 PMCID: PMC6547430 DOI: 10.1093/nar/gkz292] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 04/09/2019] [Accepted: 04/11/2019] [Indexed: 12/13/2022] Open
Abstract
Histone modifications and RNA splicing, two seemingly unrelated gene regulatory processes, greatly increase proteome diversity and profoundly influence normal as well as pathological eukaryotic cellular functions. Like many histone modifying enzymes, histone deacetylases (HDACs) play critical roles in governing cellular behaviors and are indispensable in numerous biological processes. While the association between RNA splicing and histone modifications is beginning to be recognized, a lack of knowledge exists regarding the role of HDACs in splicing. Recent studies however, reveal that HDACs interact with spliceosomal and ribonucleoprotein complexes, actively control the acetylation states of splicing-associated histone marks and splicing factors, and thereby unexpectedly could modulate splicing. Here, we review the role of histone/protein modifications and HDACs in RNA splicing and discuss the convergence of two parallel fields, which supports the argument that HDACs, and perhaps most histone modifying enzymes, are much more versatile and far more complicated than their initially proposed functions. Analogously, an HDAC-RNA splicing connection suggests that splicing is regulated by additional upstream factors and pathways yet to be defined or not fully characterized. Some human diseases share common underlying causes of aberrant HDACs and dysregulated RNA splicing and, thus, further support the potential link between HDACs and RNA splicing.
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Affiliation(s)
- Raneen Rahhal
- George Washington Cancer Center, Department of Biochemistry & Molecular Medicine, George Washington University School of Medicine & Health Sciences, Washington, DC 20037, USA
| | - Edward Seto
- George Washington Cancer Center, Department of Biochemistry & Molecular Medicine, George Washington University School of Medicine & Health Sciences, Washington, DC 20037, USA
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26
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Mohibi S, Chen X, Zhang J. Cancer the'RBP'eutics-RNA-binding proteins as therapeutic targets for cancer. Pharmacol Ther 2019; 203:107390. [PMID: 31302171 DOI: 10.1016/j.pharmthera.2019.07.001] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/02/2019] [Indexed: 12/11/2022]
Abstract
RNA-binding proteins (RBPs) play a critical role in the regulation of various RNA processes, including splicing, cleavage and polyadenylation, transport, translation and degradation of coding RNAs, non-coding RNAs and microRNAs. Recent studies indicate that RBPs not only play an instrumental role in normal cellular processes but have also emerged as major players in the development and spread of cancer. Herein, we review the current knowledge about RNA binding proteins and their role in tumorigenesis as well as the potential to target RBPs for cancer therapeutics.
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Affiliation(s)
- Shakur Mohibi
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, United States
| | - Xinbin Chen
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, United States
| | - Jin Zhang
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, United States.
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Nanni M, Ranieri D, Persechino F, Torrisi MR, Belleudi F. The Aberrant Expression of the Mesenchymal Variant of FGFR2 in the Epithelial Context Inhibits Autophagy. Cells 2019; 8:cells8070653. [PMID: 31261937 PMCID: PMC6678203 DOI: 10.3390/cells8070653] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 06/27/2019] [Accepted: 06/28/2019] [Indexed: 12/23/2022] Open
Abstract
Signaling of the epithelial splice variant of fibroblast growth factor receptor 2 (FGFR2b) triggers both differentiation and autophagy, while the aberrant expression of the mesenchymal FGFR2c isoform in epithelial cells induces impaired differentiation, epithelial mesenchymal transition (EMT) and tumorigenic features. Here we analyzed in the human keratinocyte cell line, as well as in primary cultured cells, the possible impact of FGFR2c forced expression on the autophagic process. Biochemical and quantitative immunofluorescence analysis, coupled to the use of autophagic flux sensors, specific substrate inhibitors or silencing approaches, showed that ectopic expression and the activation of FGFR2c inhibit the autophagosome formation and that AKT/MTOR is the downstream signaling mainly involved. Interestingly, the selective inhibition of AKT or MTOR substrates caused a reversion of the effects of FGFR2c on autophagy, which could also arise from the imbalance of the interplay between AKT/MTOR pathway and JNK1 signaling in favor of JNK1 activation, BCL-2 phosphorylation and possibly phagophore nucleation. Finally, silencing experiments of depletion of ESRP1, responsible for FGFR2 splicing and consequent FGFR2b expression, indicated that the switching from FGFR2b to FGFR2c isoform could represent the key event underlying the inhibition of the autophagic process in the epithelial context. Our results provide the first evidence of a negative impact of the out-of-context expression of FGFR2c on autophagy, suggesting a possible role of this receptor in the modulation of the recently proposed negative loop between autophagy and EMT during carcinogenesis.
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Affiliation(s)
- Monica Nanni
- Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Department of Clinical and Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy
| | - Danilo Ranieri
- Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Department of Clinical and Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy
| | - Flavia Persechino
- Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Department of Clinical and Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy
| | - Maria Rosaria Torrisi
- Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Department of Clinical and Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy.
- S. Andrea University Hospital, 00189 Rome, Italy.
| | - Francesca Belleudi
- Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Department of Clinical and Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy
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28
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Cause-and-Effect relationship between FGFR1 expression and epithelial-mesenchymal transition in EGFR-mutated non-small cell lung cancer cells. Lung Cancer 2019; 132:132-140. [PMID: 31097086 DOI: 10.1016/j.lungcan.2019.04.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 04/15/2019] [Accepted: 04/18/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVES Increased FGFR1 expression is associated with resistance to tyrosine kinase inhibitors (TKIs) in EGFR-mutated NSCLC cells and often concomitant with epithelial to mesenchymal transition (EMT). However, the cause-and-effect relationship between increased FGFR1 expression and EMT in the genetic background of EGFR-mutated non-small cell lung cancer (NSCLC) cells is not clear. Previous studies have specifically addressed the relationship between EMT and increased FGFR1 expression in the context of simultaneous TKI-mediated blocking of EGFR-signaling. Here, in the context of EGFR-mutated NSCLC cells with active EGFR-signaling, we have examined whether increased FGFR1 expression drives EMT or is an EMT passenger event. MATERIALS AND METHODS For cause-and-effect analyses between EMT and FGFR1 expression, including expression of alternative spliced FGFR1 isoforms, we used CRISPR-dCAS9-SAM-mediated induction of the endogenous FGFR1 and ZEB1 genes, as well as biochemical EMT-induction, in PC9 and HCC827 NSCLC cell lines harboring activating EGFR-mutations. RESULTS We find that FGFR1 expression correlates with a ZEB1-associated EMT gene expression profile in NSCLC cells. In experiments using NSCLC cell lines harboring activating EGFR-mutations we show that CRISPR-dCAS9-SAM-mediated induction of FGFR1 expression is neither driving an increase in ZEB1 expression nor EMT characteristics. However, CRISPR-dCAS9-SAM-mediated induction of ZEB1 expression drives EMT characteristics and an increase in FGFR1 expression. Biochemical induction of EMT also drives an increase in FGFR1 expression. CONCLUSION From our findings concerning the cause-and-effect relationship in the genetic background of EGFR-mutated NSCLC cells, we conclude that an increase in ZEB1 expression is a driver of EMT resulting in concomitant increased FGFR1 expression, whereas an increase in FGFR1 expression is insufficient to drive concomitant EMT.
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29
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Wang G, Pan J, Zhang L, Wang C. Overexpression of grainyhead-like transcription factor 2 is associated with poor prognosis in human pancreatic carcinoma. Oncol Lett 2018; 17:1491-1496. [PMID: 30675204 PMCID: PMC6341798 DOI: 10.3892/ol.2018.9741] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 10/03/2018] [Indexed: 12/23/2022] Open
Abstract
Recent studies have demonstrated that the abnormal expression of the grainyhead-like transcription factor 2 (GRHL2) gene contributes to the progression and poor prognosis of cancer through multiple mechanisms, but little is known about its expression status and prognostic value in pancreatic carcinoma (PC). The aim of the present study was to investigate the expression of GRHL2 in PC and to evaluate its clinicopathological and prognostic significance. Immunohistochemistry and western blotting were used to detect the expression of GRHL2 in PC tissues and cell lines, respectively. The expression of GRHL2 was investigated in 92 PC tissue samples by immunohistochemistry. High expression of GRHL2 was significantly associated with histological differentiation (P=0.018) and lymphatic metastasis (P=0.024). A Kaplan-Meier analysis revealed that high expression of GRHL2 was associated with worsened overall survival time (P<0.001). Multivariate analysis indicated that GRHL2 may be an independent prognostic factor for poor overall survival time (P=0.001). Additionally, western blot analysis demonstrated that the GRHL2 protein was highly expressed in PC cell lines. GRHL2 may serve an important role in the tumourigenesis of PC and serve as a potential therapeutic target for the prevention of PC progression.
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Affiliation(s)
- Gang Wang
- Department of General Surgery, Anhui Provincial Hospital Affiliated with Anhui Medical University, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, Hefei, Anhui 230001, P.R. China
| | - Jingen Pan
- Department of General Surgery, Anhui Provincial Hospital Affiliated with Anhui Medical University, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, Hefei, Anhui 230001, P.R. China
| | - Lu Zhang
- Department of General Surgery, Anhui Provincial Hospital Affiliated with Anhui Medical University, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, Hefei, Anhui 230001, P.R. China
| | - Cheng Wang
- Department of General Surgery, Anhui Provincial Hospital Affiliated with Anhui Medical University, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, Hefei, Anhui 230001, P.R. China
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El Marabti E, Younis I. The Cancer Spliceome: Reprograming of Alternative Splicing in Cancer. Front Mol Biosci 2018; 5:80. [PMID: 30246013 PMCID: PMC6137424 DOI: 10.3389/fmolb.2018.00080] [Citation(s) in RCA: 151] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/09/2018] [Indexed: 12/15/2022] Open
Abstract
Alternative splicing allows for the expression of multiple RNA and protein isoforms from one gene, making it a major contributor to transcriptome and proteome diversification in eukaryotes. Advances in next generation sequencing technologies and genome-wide analyses have recently underscored the fact that the vast majority of multi-exon genes under normal physiology engage in alternative splicing in tissue-specific and developmental-specific manner. On the other hand, cancer cells exhibit remarkable transcriptome alterations partly by adopting cancer-specific splicing isoforms. These isoforms and their encoded proteins are not insignificant byproducts of the abnormal physiology of cancer cells, but either drivers of cancer progression or small but significant contributors to specific cancer hallmarks. Thus, it is paramount that the pathways that regulate alternative splicing in cancer, including the splicing factors that bind to pre-mRNAs and modulate spliceosome recruitment. In this review, we present a few distinct cases of alternative splicing in cancer, with an emphasis on their regulation as well as their contribution to cancer cell phenotype. Several categories of splicing aberrations are highlighted, including alterations in cancer-related genes that directly affect their pre-mRNA splicing, mutations in genes encoding splicing factors or core spliceosomal subunits, and the seemingly mutation-free disruptions in the balance of the expression of RNA-binding proteins, including components of both the major (U2-dependent) and minor (U12-dependent) spliceosomes. Given that the latter two classes cause global alterations in splicing that affect a wide range of genes, it remains a challenge to identify the ones that contribute to cancer progression. These challenges necessitate a systematic approach to decipher these aberrations and their impact on cancer. Ultimately, a sufficient understanding of splicing deregulation in cancer is predicted to pave the way for novel and innovative RNA-based therapies.
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Affiliation(s)
- Ettaib El Marabti
- Biological Sciences Program, Carnegie Mellon University in Qatar, Doha, Qatar
| | - Ihab Younis
- Biological Sciences Program, Carnegie Mellon University in Qatar, Doha, Qatar
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Teng H, Mao F, Liang J, Xue M, Wei W, Li X, Zhang K, Feng D, Liu B, Sun Z. Transcriptomic signature associated with carcinogenesis and aggressiveness of papillary thyroid carcinoma. Theranostics 2018; 8:4345-4358. [PMID: 30214625 PMCID: PMC6134936 DOI: 10.7150/thno.26862] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/16/2018] [Indexed: 01/27/2023] Open
Abstract
Papillary thyroid carcinoma (PTC) is the fastest-growing disease caused by numerous molecular alterations in addition to previously reported DNA mutations. There is a compelling need to identify novel transcriptomic alterations that are associated with the pathogenesis of PTC with potential diagnostic and prognostic implications. Methods: We gathered and compared 242 expression profiles between paired PTC and adjacent normal tissues and identified and validated the coding and long non-coding RNAs (lncRNAs) associated with the extrathyroidal extension (ETE) of 655 PTC patients in two independent cohorts, followed by predicting their interactions with drugs. Co-expression, RNA interaction, Kaplan-Meier survival and multivariate Cox proportional regression analyses were performed to identify dysregulated lncRNAs and genes that correlated with clinical outcomes of PTC. Alternative splicing (AS), RNA circularization, and editing were also compared between transcriptomes to expand the repertoire of molecular alterations in PTC. Results: Numerous genes related to cellular microenvironment and steroid hormone response were associated with the ETE of PTC. Drug susceptibility predictions of the expression signature revealed two highly ranked compounds, 6-bromoindirubin-3'-oxime and lovastatin. Co-expression and RNA interaction analysis revealed the essential role of lncRNAs in PTC pathogenesis by modulating extracellular matrix and cell adhesion. Eight genes and two novel lncRNAs were identified that correlated with the aggressive nature and disease-free survival of PTC. Furthermore, this study provided the transcriptome-wide landscape of circRNAs in PTC and uncovered dissimilar expression profiles among circRNAs originating from the same host gene, suggesting the functional complexity of circRNAs in PTC carcinogenesis. The newly identified AS events in the SERPINA1 and FN1 genes may improve the sensitivity and specificity of these diagnostic biomarkers. Conclusions: Our study uncovered a comprehensive transcriptomic signature associated with the carcinogenesis and aggressive behavior of PTC, as well as presents a catalog of 10 potential biomarkers, which would facilitate PTC prognosis and development of new therapeutic strategies for this cancer.
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Affiliation(s)
- Huajing Teng
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Fengbiao Mao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Jialong Liang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Meiying Xue
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wenqing Wei
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xianfeng Li
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Kun Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Dongdong Feng
- Department of Head and Neck Surgery, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China
| | - Baoguo Liu
- Department of Head and Neck Surgery, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China
| | - Zhongsheng Sun
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
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32
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Urbanski L, Leclair N, Anczuków O. Alternative-splicing defects in cancer: Splicing regulators and their downstream targets, guiding the way to novel cancer therapeutics. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9:e1476. [PMID: 29693319 PMCID: PMC6002934 DOI: 10.1002/wrna.1476] [Citation(s) in RCA: 221] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/27/2018] [Accepted: 03/01/2018] [Indexed: 12/14/2022]
Abstract
Defects in alternative splicing are frequently found in human tumors and result either from mutations in splicing-regulatory elements of specific cancer genes or from changes in the regulatory splicing machinery. RNA splicing regulators have emerged as a new class of oncoproteins and tumor suppressors, and contribute to disease progression by modulating RNA isoforms involved in the hallmark cancer pathways. Thus, dysregulation of alternative RNA splicing is fundamental to cancer and provides a potentially rich source of novel therapeutic targets. Here, we review the alterations in splicing regulatory factors detected in human tumors, as well as the resulting alternatively spliced isoforms that impact cancer hallmarks, and discuss how they contribute to disease pathogenesis. RNA splicing is a highly regulated process and, as such, the regulators are themselves tightly regulated. Differential transcriptional and posttranscriptional regulation of splicing factors modulates their levels and activities in tumor cells. Furthermore, the composition of the tumor microenvironment can also influence which isoforms are expressed in a given cell type and impact drug responses. Finally, we summarize current efforts in targeting alternative splicing, including global splicing inhibition using small molecules blocking the spliceosome or splicing-factor-modifying enzymes, as well as splice-switching RNA-based therapeutics to modulate cancer-specific splicing isoforms. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing.
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Hamilton MJ, Girke T, Martinez E. Global isoform-specific transcript alterations and deregulated networks in clear cell renal cell carcinoma. Oncotarget 2018; 9:23670-23680. [PMID: 29805765 PMCID: PMC5955119 DOI: 10.18632/oncotarget.25330] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 04/19/2018] [Indexed: 11/25/2022] Open
Abstract
Extensive genome-wide analyses of deregulated gene expression have now been performed for many types of cancer. However, most studies have focused on deregulation at the gene-level, which may overlook the alterations of specific transcripts for a given gene. Clear cell renal cell carcinoma (ccRCC) is one of the best-characterized and most pervasive renal cancers, and ccRCCs are well-documented to have aberrant RNA processing. In the present study, we examine the extent of aberrant isoform-specific RNA expression by reporting a comprehensive transcript-level analysis, using the new kallisto-sleuth-RATs pipeline, investigating coding and non-coding differential transcript expression in ccRCC. We analyzed 50 ccRCC tumors and their matched normal samples from The Cancer Genome Altas datasets. We identified 7,339 differentially expressed transcripts and 94 genes exhibiting differential transcript isoform usage in ccRCC. Additionally, transcript-level coexpression network analyses identified vasculature development and the tricarboxylic acid cycle as the most significantly deregulated networks correlating with ccRCC progression. These analyses uncovered several uncharacterized transcripts, including lncRNAs FGD5-AS1 and AL035661.1, as potential regulators of the tricarboxylic acid cycle associated with ccRCC progression. As ccRCC still presents treatment challenges, our results provide a new resource of potential therapeutics targets and highlight the importance of exploring alternative methodologies in transcriptome-wide studies.
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Affiliation(s)
- Michael J. Hamilton
- Department of Biochemistry, University of California at Riverside, Riverside, CA, USA
| | - Thomas Girke
- Department of Botany and Plant Sciences, University of California at Riverside, Riverside, CA, USA
| | - Ernest Martinez
- Department of Biochemistry, University of California at Riverside, Riverside, CA, USA
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Rosato B, Ranieri D, Nanni M, Torrisi MR, Belleudi F. Role of FGFR2b expression and signaling in keratinocyte differentiation: sequential involvement of PKCδ and PKCα. Cell Death Dis 2018; 9:565. [PMID: 29752438 PMCID: PMC5948219 DOI: 10.1038/s41419-018-0509-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 02/16/2018] [Accepted: 03/15/2018] [Indexed: 12/13/2022]
Abstract
The tumor suppressor epithelial isoform of the fibroblast growth factor receptor 2 (FGFR2b) induces human keratinocyte early differentiation. Moreover, protein kinases C (PKCs) are known to regulate the differentiation program in several cellular contexts, including keratinocytes. Therefore, in this paper we propose to clarify if FGFR2b could play a role also in the late steps of keratinocyte differentiation and to assess if this receptor-induced process would sequentially involve PKCδ and PKCα isoforms. Immunofluorescence, biochemical, and molecular approaches, performed on 2D cultures or 3D organotypic rafts of human keratinocytes overexpressing FGFR2b by stable transduction, showed that receptor signaling induced the precocious onset and an accelerated progression of keratinocyte differentiation, indicating that FGFR2b is a crucial regulator of the entire program of keratinocyte differentiation. In addition, the use of specific inhibitors and gene silencing approaches through specific siRNA demonstrated that PKCδ controls the onset of FGFR2b-triggered differentiation, while PKCα plays a role restricted to the terminal stages of the process. Molecular analysis revealed that the two PKC isoforms sequentially act via induction of KLF4 and DLX3, two transcription factors linked by negative loops to p63, suggesting that p63 would represent the hub molecule at the crossroad of an intricate signaling network downstream FGFR2b, involving multiple PKC-induced transcription factors.
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Affiliation(s)
- Benedetta Rosato
- Department of Clinical and Molecular Medicine,Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Roma, Italy
| | - Danilo Ranieri
- Department of Clinical and Molecular Medicine,Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Roma, Italy
| | - Monica Nanni
- Department of Clinical and Molecular Medicine,Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Roma, Italy
| | - Maria Rosaria Torrisi
- Department of Clinical and Molecular Medicine,Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Roma, Italy.,S. Andrea University Hospital, Rome, Italy
| | - Francesca Belleudi
- Department of Clinical and Molecular Medicine,Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Roma, Italy.
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35
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Deloria AJ, Höflmayer D, Kienzl P, Łopatecka J, Sampl S, Klimpfinger M, Braunschmid T, Bastian F, Lu L, Marian B, Stättner S, Holzmann K. Epithelial splicing regulatory protein 1 and 2 paralogues correlate with splice signatures and favorable outcome in human colorectal cancer. Oncotarget 2018; 7:73800-73816. [PMID: 27650542 PMCID: PMC5342015 DOI: 10.18632/oncotarget.12070] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 09/02/2016] [Indexed: 12/21/2022] Open
Abstract
ESRPs are master splice regulators implicated in alternative mRNA splicing programs important for epithelial-mesenchymal transition (EMT) and tumor progression. ESRP1 was identified in some tumors as good or worse predictor of outcome, but in colorectal cancer (CRC) the prognostic value of ESRPs and relation with mesenchymal splice variants is not clear. Here, we studied 68 CRC cases, compared tissue expression of ESRPs with clinical data and with EMT gene splice patterns of conditional CRC cells with deficient ESRP1 expression.Around 72% of patients showed global decreased transcript expression of both ESRPs in tumor as compared to matched non-neoplastic colorectal epithelium. Reduction of ESRP1 in tumor cells was evaluated by immunohistochemistry, associated with microsatellite stability and switch to mesenchymal splice signatures of FGFRs, CD44, ENAH and CTNND1(p120-catenin). Expression of ESRPs was significantly associated with favorable overall survival (log-rank test, P=0.0186 and 0.0408), better than prognostic stratification by tumor staging; and for ESRP1 confirmed with second TCGA cohort (log-rank test, P=0.0435). Prognostic value is independent of the pathological stage and microsatellite instability (ESRP1: HR=0.36, 95%CI 0.15-0.91, P=0.032; ESRP2: HR=0.23, 95%CI 0.08-0.65, P=0.006).Our study supports the role of ESRP1 as tumor suppressor and strongly suggests that ESRPs are candidate markers for early detection, diagnosis, and prognosis of CRC.
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Affiliation(s)
- Abigail J Deloria
- Division of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University Vienna, Austria
| | - Doris Höflmayer
- Department of Pathology and Bacteriology, Social Medical Center South, Kaiser Franz Josef Hospital, Vienna, Austria.,Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Philip Kienzl
- Division of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University Vienna, Austria
| | - Justyna Łopatecka
- Division of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University Vienna, Austria
| | - Sandra Sampl
- Division of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University Vienna, Austria
| | - Martin Klimpfinger
- Department of Pathology and Bacteriology, Social Medical Center South, Kaiser Franz Josef Hospital, Vienna, Austria
| | - Tamara Braunschmid
- Department of Surgery, Social Medical Center South, Kaiser Franz Josef Hospital, Vienna, Austria
| | - Fabienne Bastian
- Department of Surgery, Social Medical Center South, Kaiser Franz Josef Hospital, Vienna, Austria
| | - Lingeng Lu
- Department of Chronic Disease Epidemiology, Yale School of Public Health, School of Medicine, Yale Cancer Center, Yale University, New Haven, USA
| | - Brigitte Marian
- Division of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University Vienna, Austria
| | - Stefan Stättner
- Department of Surgery, Social Medical Center South, Kaiser Franz Josef Hospital, Vienna, Austria.,Department of Visceral, Transplantation and Thoracic Surgery, Innsbruck, Austria
| | - Klaus Holzmann
- Division of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University Vienna, Austria
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36
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Böttcher R, Dulla K, van Strijp D, Dits N, Verhoef EI, Baillie GS, van Leenders GJLH, Houslay MD, Jenster G, Hoffmann R. Human PDE4D isoform composition is deregulated in primary prostate cancer and indicative for disease progression and development of distant metastases. Oncotarget 2018; 7:70669-70684. [PMID: 27683107 PMCID: PMC5342582 DOI: 10.18632/oncotarget.12204] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 09/12/2016] [Indexed: 02/07/2023] Open
Abstract
Phosphodiesterase 4D7 was recently shown to be specifically over-expressed in localized prostate cancer, raising the question as to which regulatory mechanisms are involved and whether other isoforms of this gene family (PDE4D) are affected under the same conditions.We investigated PDE4D isoform composition in prostatic tissues using a total of seven independent expression datasets and also included data on DNA methylation, copy number and AR and ERG binding in PDE4D promoters to gain insight into their effect on PDE4D transcription.We show that expression of PDE4D isoforms is consistently altered in primary human prostate cancer compared to benign tissue, with PDE4D7 being up-regulated while PDE4D5 and PDE4D9 are down-regulated. Disease progression is marked by an overall down-regulation of long PDE4D isoforms, while short isoforms (PDE4D1/2) appear to be relatively unaffected. While these alterations seem to be independent of copy number alterations in the PDE4D locus and driven by AR and ERG binding, we also observed increased DNA methylation in the promoter region of PDE4D5, indicating a long lasting alteration of the isoform composition in prostate cancer tissues.We propose two independent metrics that may serve as diagnostic and prognostic markers for prostate disease: (PDE4D7 - PDE4D5) provides an effective means for distinguishing PCa from normal adjacent prostate, whereas PDE4D1/2 - (PDE4D5 + PDE4D7 + PDE4D9) offers strong prognostic potential to detect aggressive forms of PCa and is associated with metastasis free survival. Overall, our findings highlight the relevance of PDE4D as prostate cancer biomarker and potential drug target.
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Affiliation(s)
- René Böttcher
- Department of Urology, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Bioinformatics, Technical University of Applied Sciences Wildau, Wildau, Germany
| | - Kalyan Dulla
- Department of Oncology Solutions and Precision Diagnostics, Philips Research Europe, Eindhoven, The Netherlands
| | - Dianne van Strijp
- Department of Oncology Solutions and Precision Diagnostics, Philips Research Europe, Eindhoven, The Netherlands
| | - Natasja Dits
- Department of Urology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Esther I Verhoef
- Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - George S Baillie
- Institute of Cardiovascular and Medical Science, University of Glasgow, Glasgow, Scotland, UK
| | | | - Miles D Houslay
- Institute of Pharmaceutical Science, King's College London, London, UK
| | - Guido Jenster
- Department of Urology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ralf Hoffmann
- Department of Oncology Solutions and Precision Diagnostics, Philips Research Europe, Eindhoven, The Netherlands.,Institute of Cardiovascular and Medical Science, University of Glasgow, Glasgow, Scotland, UK
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37
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Li Z, Chen Y, Hu S, Zhang J, Wu J, Ren W, Shao N, Ying X. Integrative analysis of protein-coding and non-coding RNAs identifies clinically relevant subtypes of clear cell renal cell carcinoma. Oncotarget 2018; 7:82671-82685. [PMID: 27705920 PMCID: PMC5347723 DOI: 10.18632/oncotarget.12340] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 09/20/2016] [Indexed: 12/25/2022] Open
Abstract
Protein-coding genes and non-coding RNAs cooperate mutually in cells. Integrative analysis of protein-coding and non-coding RNAs may facilitate characterizing tumor heterogeneity. We introduced integrated consensus clustering (ICC) method to integrate mRNA, miRNA and lncRNA expression profiles of 431 primary clear cell renal cell carcinomas (ccRCCs). We identified one RCC subgroup easily misdiagnosed as ccRCC in clinic and four robust ccRCC subtypes associated with distinct clinicopathologic and molecular features. In subtype R1, AMPK signaling pathway is significantly upregulated, which may improve the oncologic-metabolic shift and partially account for its best prognosis. Subtype R2 has more chromosomal abnormities, higher expression of cell cycle genes and less expression of genes in various metabolism pathways, which may explain its more aggressive characteristic and the worst prognosis. Moreover, much more miRNAs and lncRNAs are significantly upregulated in R2 and R4 respectively, suggesting more important roles of miRNAs in R2 and lncRNAs in R4. Triple-color co-expression network analysis identified 28 differentially expressed modules, indicating the importance of cooperative regulation of mRNAs, miRNAs and lncRNAs in ccRCC. This study establishes an integrated transcriptomic classification which may contribute to understanding the heterogeneity and implicating the treatment of ccRCC.
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Affiliation(s)
- Zongcheng Li
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China.,Translational Medicine Center of Stem Cells, 307-Ivy Translational Medicine Center, Laboratory of Oncology, Affiliated Hospital, Academy of Military Medical Sciences, Beijing 100071, China
| | - Yaowen Chen
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China.,Department of Obstetrics and Gynecology, Fuzhou General Hospital of Nanjing Military Command, Fuzhou, Fujian 350025, China
| | - Shuofeng Hu
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Jian Zhang
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Jiaqi Wu
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Wu Ren
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China.,Department of Gastrointestinal Surgery, The First Affiliated Hospital of Jilin University, Changchun 130021, China
| | - Ningsheng Shao
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Xiaomin Ying
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
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38
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Ranieri D, Rosato B, Nanni M, Belleudi F, Torrisi MR. Expression of the FGFR2c mesenchymal splicing variant in human keratinocytes inhibits differentiation and promotes invasion. Mol Carcinog 2017; 57:272-283. [PMID: 29068468 PMCID: PMC5813158 DOI: 10.1002/mc.22754] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 10/02/2017] [Accepted: 10/23/2017] [Indexed: 12/02/2022]
Abstract
The altered isoform switching of the fibroblast growth factor receptor 2 (FGFR2) and aberrant expression of the mesenchymal FGFR2c isoform in epithelial cells is involved in cancer progression. We have recently described that the ectopic expression of FGFR2c in normal human keratinocytes induces epithelial‐mesenchymal transition and leads to invasiveness and anchorage‐independent growth. Here, we extended our analysis to the effects of this FGFR2c forced expression on human keratinocyte differentiation and stratification. Our findings demonstrated that, differently from cells overexpressing the epithelial splicing variant FGFR2b, keratinocytes ectopically expressing FGFR2c are not able to form a monolayer and display decreased expression of early differentiation markers. This impaired ability to enter the differentiation program is related to the up‐modulation of the transcription factor ΔNp63. In addition, FGFR2c‐expressing keratinocytes undergo defective stratification and invasion of the collagen matrix in 3D organotypic cultures, further suggesting their tumorigenic potential. Taken together, our results support the hypothesis that the receptor switching and the consequent appearance of the mesenchymal FGFR2c variant in the epithelial context would drive early steps of carcinogenesis, unbalancing the p63/FGFR interplay, and altering the paracrine response to the microenvironment.
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Affiliation(s)
- Danilo Ranieri
- Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Department of Clinical and Molecular Medicine, Sapienza University of Rome, Roma, Lazio, Italy
| | - Benedetta Rosato
- Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Department of Clinical and Molecular Medicine, Sapienza University of Rome, Roma, Lazio, Italy
| | - Monica Nanni
- Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Department of Clinical and Molecular Medicine, Sapienza University of Rome, Roma, Lazio, Italy
| | - Francesca Belleudi
- Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Department of Clinical and Molecular Medicine, Sapienza University of Rome, Roma, Lazio, Italy
| | - Maria Rosaria Torrisi
- Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Department of Clinical and Molecular Medicine, Sapienza University of Rome, Roma, Lazio, Italy.,S. Andrea University Hospital, Rome, Italy
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39
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Neumann DP, Goodall GJ, Gregory PA. Regulation of splicing and circularisation of RNA in epithelial mesenchymal plasticity. Semin Cell Dev Biol 2017; 75:50-60. [PMID: 28789987 DOI: 10.1016/j.semcdb.2017.08.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 07/28/2017] [Accepted: 08/03/2017] [Indexed: 12/13/2022]
Abstract
Interconversions between epithelial and mesenchymal states, often referred to as epithelial mesenchymal transition (EMT) and its reverse MET, play important roles in embryonic development and are recapitulated in various adult pathologies including cancer progression. These conversions are regulated by complex transcriptional and post-transcriptional mechanisms including programs of alternative splicing which are orchestrated by specific splicing factors. This review will focus on the latest developments in our understanding of the splicing factors regulating epithelial mesenchymal plasticity associated with cancer progression and the induction of pluripotency, including potential roles for circular RNAs (circRNAs) which have been recently implicated in these processes.
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Affiliation(s)
- Daniel P Neumann
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, 5000, Australia
| | - Gregory J Goodall
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, 5000, Australia; Discipline of Medicine, The University of Adelaide, Adelaide, SA 5005, Australia; School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Philip A Gregory
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, 5000, Australia; Discipline of Medicine, The University of Adelaide, Adelaide, SA 5005, Australia.
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40
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Zhou B, Wang GZ, Wen ZS, Zhou YC, Huang YC, Chen Y, Zhou GB. Somatic Mutations and Splicing Variants of Focal Adhesion Kinase in Non–Small Cell Lung Cancer. J Natl Cancer Inst 2017; 110:4565750. [PMID: 29087503 DOI: 10.1093/jnci/djx157] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 06/30/2017] [Indexed: 12/17/2022] Open
Affiliation(s)
- Bo Zhou
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences, Beijing, China
| | - Gui-Zhen Wang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences, Beijing, China
| | - Zhe-Sheng Wen
- Department of Thoracic Surgery, the Cancer Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yong-Chun Zhou
- Department of Thoracic Surgery, the Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yun-Chao Huang
- Department of Thoracic Surgery, the Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Ying Chen
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Guang-Biao Zhou
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences, Beijing, China
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41
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Pereira B, Billaud M, Almeida R. RNA-Binding Proteins in Cancer: Old Players and New Actors. Trends Cancer 2017; 3:506-528. [PMID: 28718405 DOI: 10.1016/j.trecan.2017.05.003] [Citation(s) in RCA: 459] [Impact Index Per Article: 65.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 05/04/2017] [Accepted: 05/05/2017] [Indexed: 12/15/2022]
Abstract
RNA-binding proteins (RBPs) are key players in post-transcriptional events. The combination of versatility of their RNA-binding domains with structural flexibility enables RBPs to control the metabolism of a large array of transcripts. Perturbations in RBP-RNA networks activity have been causally associated with cancer development, but the rational framework describing these contributions remains fragmented. We review here the evidence that RBPs modulate multiple cancer traits, emphasize their functional diversity, and assess future trends in the study of RBPs in cancer.
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Affiliation(s)
- Bruno Pereira
- i3S - Institute for Research and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-465 Porto, Portugal.
| | - Marc Billaud
- Clinical and Experimental Model of Lymphomagenesis, Institut National de la Santé et de la Recherche Médicale (INSERM) Unité 1052, Centre National de la Recherche Scientifique (CNRS) Unité 5286, Centre Léon Bérard, Université Claude Bernard Lyon 1, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Raquel Almeida
- i3S - Institute for Research and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-465 Porto, Portugal; Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal; Biology Department, Faculty of Sciences of the University of Porto, 4169-007 Porto, Portugal
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42
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Abstract
The cell-surface glycoprotein CD56 has three major isoforms that play important roles in cell adhesion and signaling, which may promote cell proliferation, differentiation, survival, or migration. It is an important molecule in normal kidney development and acts as a key marker in Wilms tumor stem and progenitor cells. Here, we review the structural and genetic features of the CD56 glycoprotein, and summarize its roles in the normal versus diseased metanephric blastema. We discuss areas of CD56-related research that may complement or improve existing Wilms tumor treatment strategies, including the antibody-drug conjugate lorvotuzumab mertansine that binds to CD56.
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Affiliation(s)
- Li-Wei Yap
- a Department of Life Sciences , Imperial College London , London , UK
| | - Jesper Brok
- b University College London Institute of Child Health, Cancer Section , London , UK
- c Rigshospitalet , Kobenhavn , Denmark
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43
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EMT and stemness: flexible processes tuned by alternative splicing in development and cancer progression. Mol Cancer 2017; 16:8. [PMID: 28137272 PMCID: PMC5282733 DOI: 10.1186/s12943-016-0579-2] [Citation(s) in RCA: 198] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 12/25/2016] [Indexed: 12/17/2022] Open
Abstract
Epithelial-to-mesenchymal transition (EMT) is associated with metastasis formation as well as with generation and maintenance of cancer stem cells. In this way, EMT contributes to tumor invasion, heterogeneity and chemoresistance. Morphological and functional changes involved in these processes require robust reprogramming of gene expression, which is only partially accomplished at the transcriptional level. Alternative splicing is another essential layer of gene expression regulation that expands the cell proteome. This step in post-transcriptional regulation of gene expression tightly controls cell identity between epithelial and mesenchymal states and during stem cell differentiation. Importantly, dysregulation of splicing factor function and cancer-specific splicing isoform expression frequently occurs in human tumors, suggesting the importance of alternative splicing regulation for cancer biology. In this review, we briefly discuss the role of EMT programs in development, stem cell differentiation and cancer progression. Next, we focus on selected examples of key factors involved in EMT and stem cell differentiation that are regulated post-transcriptionally through alternative splicing mechanisms. Lastly, we describe relevant oncogenic splice-variants that directly orchestrate cancer stem cell biology and tumor EMT, which may be envisioned as novel targets for therapeutic intervention.
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44
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Ranieri D, Rosato B, Nanni M, Magenta A, Belleudi F, Torrisi MR. Expression of the FGFR2 mesenchymal splicing variant in epithelial cells drives epithelial-mesenchymal transition. Oncotarget 2016; 7:5440-60. [PMID: 26713601 PMCID: PMC4868697 DOI: 10.18632/oncotarget.6706] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 12/07/2015] [Indexed: 11/25/2022] Open
Abstract
The FGFRs are receptor tyrosine kinases expressed by tissue-specific alternative splicing in epithelial IIIb or mesenchymal IIIc isoforms. Deregulation of FGF/FGFR signaling unbalances the epithelial-stromal homeostasis and may lead to cancer development. In the epithelial-context, while FGFR2b/KGFR acts as tumor suppressor, FGFR2c appears to play an oncogenic role. Based on our recent observation that the switching of FGFR2b versus FGFR2c induces EMT, here we investigated the biological outcome of the ectopic expression of FGFR2c in normal human keratinocytes. Morphological analysis showed that, differently from FGFR2b overexpression, the forced expression and activation of FGFR2c drive the epithelial cells to acquire a mesenchymal-like shape and actin reorganization. Moreover, the appearance of invasiveness and anchorage-independent growth ability in FGFR2c transfected keratinocytes was consistent with the potential tumorigenic role proposed for this receptor variant. Biochemical and molecular approaches revealed that the observed phenotypic changes were accompanied by modulation of EMT biomarkers and indicated the involvement of EMT transcription factors and miRs. Finally, the analysis of the expression pattern of discriminating markers strongly suggested that activation of FGFR2c triggers a process corresponding to the initiation of the pathological type III EMT, but not to the more physiological type II EMT occurring during FGFR2b-mediated wound healing.
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Affiliation(s)
- Danilo Ranieri
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Medicina Clinica e Molecolare, Sapienza Università di Roma, Rome, Italy
| | - Benedetta Rosato
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Medicina Clinica e Molecolare, Sapienza Università di Roma, Rome, Italy
| | - Monica Nanni
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Medicina Clinica e Molecolare, Sapienza Università di Roma, Rome, Italy
| | - Alessandra Magenta
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Medicina Clinica e Molecolare, Sapienza Università di Roma, Rome, Italy
| | - Francesca Belleudi
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Medicina Clinica e Molecolare, Sapienza Università di Roma, Rome, Italy
| | - Maria Rosaria Torrisi
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Medicina Clinica e Molecolare, Sapienza Università di Roma, Rome, Italy.,Azienda Ospedaliera S. Andrea, Rome, Italy
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Yang IS, Son H, Kim S, Kim S. ISOexpresso: a web-based platform for isoform-level expression analysis in human cancer. BMC Genomics 2016; 17:631. [PMID: 27519173 PMCID: PMC4983006 DOI: 10.1186/s12864-016-2852-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 06/20/2016] [Indexed: 11/21/2022] Open
Abstract
Background Alternative splicing events that result in the production of multiple gene isoforms reveals important molecular mechanisms. Gene isoforms are often differentially expressed across organs and tissues, developmental stages, and disease conditions. Specifically, recent studies show that aberrant regulation of alternative splicing frequently occurs in cancer to affect tumor cell transformation and growth. While analysis of isoform expression is important for discovering tumor-specific isoform signatures and interpreting relevant genomic mutations, there is currently no web-based, easy-to-use, and publicly available platform for this purpose. Description We developed ISOexpresso to provide information regarding isoform existence and expression, which can be grouped by cancer vs. normal conditions, cancer types, and tissue types. ISOexpresso implements two main functions: First, the Isoform Expression View function creates visualizations for condition-specific RNA/isoform expression patterns upon query of a gene of interest. With this function, users can easily determine the major isoform (the most expressed isoform in a sample) of a gene with respect to the condition and check whether it matches the known canonical isoform. ISOexpresso outputs expression levels of all known transcripts to check alterations of expression landscape and to find potential tumor-specific isoforms. Second, the User Data Annotation function supports annotation of genomic variants to determine the most plausible consequence of a variation (e.g., an amino acid change) among many possible interpretations. As most coding sequence mutations are effective through the subsequent transcription and translation, ISOexpresso automatically prioritizes transcripts that act as backbones for mutation effect prediction by their relative expression. By employing ISOexpresso, we could investigate the consistency between the most expressed and known canonical/principal isoforms, as well as infer candidate tumor-specific isoforms based on their expression levels. In addition, we confirmed that ISOexpresso could easily reproduce previously known isoform expression patterns: recurrent observation of a major isoform across tissues, differential isoform expression patterns in a given tissue, and switching of major isoform during tumorigenesis. Conclusions ISOexpresso serves as a web-based, easy-to-use platform for isoform expression and alteration analysis based on large-scale cancer database. We anticipate that ISOexpresso will expedite formulation and confirmation of novel hypotheses by providing isoform-level perspectives on cancer research. The ISOexpresso database is available online at http://wiki.tgilab.org/ISOexpresso/. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2852-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- In Seok Yang
- Severance Biomedical Science Institute, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seoul, 03722, Korea
| | - Hyeonju Son
- Severance Biomedical Science Institute, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seoul, 03722, Korea.,Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seoul, 03722, Korea
| | - Sora Kim
- Severance Biomedical Science Institute, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seoul, 03722, Korea.,Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seoul, 03722, Korea
| | - Sangwoo Kim
- Severance Biomedical Science Institute, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seoul, 03722, Korea. .,Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seoul, 03722, Korea.
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Tsimafeyeu I, Ludes-Meyers J, Stepanova E, Daeyaert F, Khochenkov D, Joose JB, Solomko E, Van Akene K, Peretolchina N, Yin W, Ryabaya O, Byakhov M, Tjulandin S. Targeting FGFR2 with alofanib (RPT835) shows potent activity in tumour models. Eur J Cancer 2016; 61:20-8. [DOI: 10.1016/j.ejca.2016.03.068] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 01/24/2016] [Accepted: 03/17/2016] [Indexed: 12/18/2022]
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Shen S, Wang Y, Wang C, Wu YN, Xing Y. SURVIV for survival analysis of mRNA isoform variation. Nat Commun 2016; 7:11548. [PMID: 27279334 PMCID: PMC4906168 DOI: 10.1038/ncomms11548] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 04/07/2016] [Indexed: 01/07/2023] Open
Abstract
The rapid accumulation of clinical RNA-seq data sets has provided the opportunity to associate mRNA isoform variations to clinical outcomes. Here we report a statistical method SURVIV (Survival analysis of mRNA Isoform Variation), designed for identifying mRNA isoform variation associated with patient survival time. A unique feature and major strength of SURVIV is that it models the measurement uncertainty of mRNA isoform ratio in RNA-seq data. Simulation studies suggest that SURVIV outperforms the conventional Cox regression survival analysis, especially for data sets with modest sequencing depth. We applied SURVIV to TCGA RNA-seq data of invasive ductal carcinoma as well as five additional cancer types. Alternative splicing-based survival predictors consistently outperform gene expression-based survival predictors, and the integration of clinical, gene expression and alternative splicing profiles leads to the best survival prediction. We anticipate that SURVIV will have broad utilities for analysing diverse types of mRNA isoform variation in large-scale clinical RNA-seq projects.
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Affiliation(s)
- Shihao Shen
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Yuanyuan Wang
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Chengyang Wang
- Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Ying Nian Wu
- Department of Statistics, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Yi Xing
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA
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48
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Zhang J, Li Y. Therapeutic uses of FGFs. Semin Cell Dev Biol 2016; 53:144-54. [DOI: 10.1016/j.semcdb.2015.09.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 09/07/2015] [Indexed: 01/23/2023]
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49
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Yao J, Caballero OL, Huang Y, Lin C, Rimoldi D, Behren A, Cebon JS, Hung MC, Weinstein JN, Strausberg RL, Zhao Q. Altered Expression and Splicing of ESRP1 in Malignant Melanoma Correlates with Epithelial-Mesenchymal Status and Tumor-Associated Immune Cytolytic Activity. Cancer Immunol Res 2016; 4:552-61. [PMID: 27045022 DOI: 10.1158/2326-6066.cir-15-0255] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 03/03/2016] [Indexed: 11/16/2022]
Abstract
Melanoma is one of the major cancer types for which new immune-based cancer treatments have achieved promising results. However, anti-PD-1 and anti-CTLA-4 therapies are effective only in some patients. Hence, predictive molecular markers for the development of clinical strategies targeting immune checkpoints are needed. Using The Cancer Genome Atlas (TCGA) RNAseq data, we found that expression of ESRP1, encoding a master splicing regulator in the epithelial-mesenchymal transition (EMT), was inversely correlated with tumor-associated immune cytolytic activity. That association holds up across multiple TCGA tumor types, suggesting a link between tumor EMT status and infiltrating lymphocyte activity. In melanoma, ESRP1 mainly exists in a melanocyte-specific truncated form transcribed from exon 13. This was validated by analyzing CCLE cell line data, public CAGE data, and RT-PCR in primary cultured melanoma cell lines. Based on ESRP1 expression, we divided TCGA melanoma cases into ESRP1-low, -truncated, and -full-length groups. ESRP1-truncated tumors comprise approximately two thirds of melanoma samples and reside in an apparent transitional state between epithelial and mesenchymal phenotypes. ESRP1 full-length tumors express epithelial markers and constitute about 5% of melanoma samples. In contrast, ESRP1-low tumors express mesenchymal markers and are high in immune cytolytic activity as well as PD-L2 and CTLA-4 expression. Those tumors are associated with better patient survival. Results from our study suggest a path toward the use of ESRP1 and other EMT markers as informative biomarkers for immunotherapy. Cancer Immunol Res; 4(6); 552-61. ©2016 AACR.
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Affiliation(s)
- Jun Yao
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Otavia L Caballero
- Ludwig Collaborative Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland. Orygen Biotecnologia, SA., São Paulo, SP, Brazil
| | - Ying Huang
- Regeneron Pharmaceuticals Inc., Tarrytown, New York
| | - Calvin Lin
- Regeneron Pharmaceuticals Inc., Tarrytown, New York
| | - Donata Rimoldi
- Clinical Tumor Biology and Immunotherapy Unit, Ludwig Center, University of Lausanne, Switzerland, Lausanne, Switzerland
| | - Andreas Behren
- Cancer Immunobiology Laboratory, Olivia Newton-John Cancer Research Institute, Victoria, Australia
| | - Jonathan S Cebon
- Cancer Immunobiology Laboratory, Olivia Newton-John Cancer Research Institute, Victoria, Australia
| | - Mien-Chie Hung
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - John N Weinstein
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Qi Zhao
- Ludwig Collaborative Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland. Regeneron Pharmaceuticals Inc., Tarrytown, New York.
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Christinat Y, Pawłowski R, Krek W. jSplice: a high-performance method for accurate prediction of alternative splicing events and its application to large-scale renal cancer transcriptome data. Bioinformatics 2016; 32:2111-9. [PMID: 27153587 DOI: 10.1093/bioinformatics/btw145] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 03/11/2016] [Indexed: 01/01/2023] Open
Abstract
MOTIVATION Alternative splicing represents a prime mechanism of post-transcriptional gene regulation whose misregulation is associated with a broad range of human diseases. Despite the vast availability of transcriptome data from different cell types and diseases, bioinformatics-based surveys of alternative splicing patterns remain a major challenge due to limited availability of analytical tools that combine high accuracy and rapidity. RESULTS We describe here a novel junction-centric method, jSplice, that enables de novo extraction of alternative splicing events from RNA-sequencing data with high accuracy, reliability and speed. Application to clear cell renal carcinoma (ccRCC) cell lines and 65 ccRCC patients revealed experimentally validatable alternative splicing changes and signatures able to prognosticate ccRCC outcome. In the aggregate, our results propose jSplice as a key analytic tool for the derivation of cell context-dependent alternative splicing patterns from large-scale RNA-sequencing datasets. AVAILABILITY AND IMPLEMENTATION jSplice is a standalone Python application freely available at http://www.mhs.biol.ethz.ch/research/krek/jsplice CONTACT wilhelm.krek@biol.ethz.ch SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yann Christinat
- Institute of Molecular Health Sciences, ETH Zurich, Zurich 8093, Switzerland
| | - Rafał Pawłowski
- Institute of Molecular Health Sciences, ETH Zurich, Zurich 8093, Switzerland
| | - Wilhelm Krek
- Institute of Molecular Health Sciences, ETH Zurich, Zurich 8093, Switzerland
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