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Chen W, Geng D, Chen J, Han X, Xie Q, Guo G, Chen X, Zhang W, Tang S, Zhong X. Roles and mechanisms of aberrant alternative splicing in melanoma - implications for targeted therapy and immunotherapy resistance. Cancer Cell Int 2024; 24:101. [PMID: 38462618 PMCID: PMC10926661 DOI: 10.1186/s12935-024-03280-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 02/22/2024] [Indexed: 03/12/2024] Open
Abstract
BACKGROUND Despite advances in therapeutic strategies, resistance to immunotherapy and the off-target effects of targeted therapy have significantly weakened the benefits for patients with melanoma. MAIN BODY Alternative splicing plays a crucial role in transcriptional reprogramming during melanoma development. In particular, aberrant alternative splicing is involved in the efficacy of immunotherapy, targeted therapy, and melanoma metastasis. Abnormal expression of splicing factors and variants may serve as biomarkers or therapeutic targets for the diagnosis and prognosis of melanoma. Therefore, comprehensively integrating their roles and related mechanisms is essential. This review provides the first detailed summary of the splicing process in melanoma and the changes occurring in this pathway. CONCLUSION The focus of this review is to provide strategies for developing novel diagnostic biomarkers and summarize their potential to alter resistance to targeted therapies and immunotherapy.
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Affiliation(s)
- Wanxian Chen
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Deyi Geng
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Jiasheng Chen
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Xiaosha Han
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Qihu Xie
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Genghong Guo
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Xuefen Chen
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Wancong Zhang
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Shijie Tang
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Xiaoping Zhong
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China.
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China.
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Nguyen JQ, Drabarek W, Vaarwater J, Yavuzyigitoglu S, Verdijk RM, Paridaens D, Naus NC, de Klein A, Brosens E, Kiliç E. 8q Gain Has No Additional Predictive Value in SF3B1MUT Uveal Melanoma but Is Predictive for a Worse Prognosis in Patients with BAP1MUT Uveal Melanoma. OPHTHALMOLOGY SCIENCE 2024; 4:100413. [PMID: 38187129 PMCID: PMC10767501 DOI: 10.1016/j.xops.2023.100413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/03/2023] [Accepted: 10/11/2023] [Indexed: 01/09/2024]
Abstract
Purpose Gain of chromosome 8q has been associated with poor prognosis in uveal melanoma (UM), and an increase in the absolute number of 8q-copies correlated with an even shorter survival. Splicing factor 3b subunit 1 (SF3B1)-mutated (SF3B1MUT) tumors display structural chromosomal anomalies and frequently show a partial gain of chromosome 8qter. A recent subset of SF3B1MUT UM with early-onset metastases has been identified, prompting the investigation of the relationship between survival, 8q gain, and SF3B1MUT UM. Design Retrospective cohort study. Subjects Patients diagnosed with UM who underwent enucleation or received a biopsy at the Erasmus MC Cancer Institute or the Rotterdam Eye Hospital, The Netherlands were included. Methods Fifty-nine patients with SF3B1MUT tumors and 211 patients with BRCA1 associated protein 1 (BAP1)-mutated (BAP1MUT) tumors were included in this study. Copy number status and gene expression were assessed using either a single nucleotide polymorphism array, fluorescence in situ hybridization, and karyotyping, or a combination of these techniques. Disease-free survival was determined and a cut-off of 60 months was used to define early-onset metastatic disease. Main Outcome Measures Disease-free survival. Results Forty-eight patients with SF3B1MUT UM (81%) had chromosome 8q gain (3 copies, 78%; 4 copies, 22%). Kaplan-Meier analysis of SF3B1MUT UM did not indicate a difference in survival in patients with or without gain of 8q (P = 0.99). Furthermore, the number of 8q copies was not associated with survival when comparing early (P = 0.97) versus late (P = 0.23) metastases group. In contrast, the presence of 8q gain (86%) was correlated with a decreased survival in BAP1MUT UM (P = 0.013). Conclusions We did not find a correlation between 8q gain and early-onset metastasis in SF3B1MUT tumors. Gain of 8q has no additional predictive value in SF3B1MUT tumors. In contrast, 8q gain is predictive of a worse prognosis in patients with BAP1MUT tumors. Thus, gain of chromosome 8q has additional predictive value for BAP1MUT tumors, but not for SF3B1MUT tumors. Financial Disclosures The author(s) have no proprietary or commercial interest in any materials discussed in this article.
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Affiliation(s)
- Josephine Q.N. Nguyen
- Department of Ophthalmology, Erasmus MC Cancer Institute, Erasmus MC Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus MC Cancer Institute, Erasmus MC Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Wojtek Drabarek
- Department of Ophthalmology, Erasmus MC Cancer Institute, Erasmus MC Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus MC Cancer Institute, Erasmus MC Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
- Department of Ophthalmic Oncology, The Rotterdam Eye Hospital, 3011 BH, Rotterdam, The Netherlands
| | - Jolanda Vaarwater
- Department of Ophthalmology, Erasmus MC Cancer Institute, Erasmus MC Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus MC Cancer Institute, Erasmus MC Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Serdar Yavuzyigitoglu
- Department of Ophthalmology, Erasmus MC Cancer Institute, Erasmus MC Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Robert M. Verdijk
- Department of Pathology, Section Ophthalmic Pathology, Erasmus MC Cancer Institute, Erasmus MC Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Dion Paridaens
- Department of Ophthalmology, Erasmus MC Cancer Institute, Erasmus MC Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
- Department of Ophthalmic Oncology, The Rotterdam Eye Hospital, 3011 BH, Rotterdam, The Netherlands
| | - Nicole C. Naus
- Department of Ophthalmology, Erasmus MC Cancer Institute, Erasmus MC Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus MC Cancer Institute, Erasmus MC Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus MC Cancer Institute, Erasmus MC Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Emine Kiliç
- Department of Ophthalmology, Erasmus MC Cancer Institute, Erasmus MC Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
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Analysis of Alternative mRNA Splicing in Vemurafenib-Resistant Melanoma Cells. Biomolecules 2022; 12:biom12070993. [PMID: 35883549 PMCID: PMC9312936 DOI: 10.3390/biom12070993] [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: 06/24/2022] [Revised: 07/11/2022] [Accepted: 07/14/2022] [Indexed: 01/09/2023] Open
Abstract
Alternative mRNA splicing is common in cancers. In BRAF V600E-mutated malignant melanoma, a frequent mechanism of acquired resistance to BRAF inhibitors involves alternative splicing (AS) of BRAF. The resulting shortened BRAF protein constitutively dimerizes and conveys drug resistance. Here, we have analysed AS in SK-MEL-239 melanoma cells and a BRAF inhibitor (vemurafenib)-resistant derivative that expresses an AS, shortened BRAF V600E transcript. Transcriptome analysis showed differential expression of spliceosome components between the two cell lines. As there is no consensus approach to analysing AS events, we used and compared four common AS softwares based on different principles, DEXSeq, rMATS, ASpli, and LeafCutter. Two of them correctly identified the BRAF V600E AS in the vemurafenib-resistant cells. Only 12 AS events were identified by all four softwares. Testing the AS predictions experimentally showed that these overlapping predictions are highly accurate. Interestingly, they identified AS caused alterations in the expression of melanin synthesis and cell migration genes in the vemurafenib-resistant cells. This analysis shows that combining different AS analysis approaches produces reliable results and meaningful, biologically testable hypotheses.
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Ye Z, Bing A, Zhao S, Yi S, Zhan X. Comprehensive analysis of spliceosome genes and their mutants across 27 cancer types in 9070 patients: clinically relevant outcomes in the context of 3P medicine. EPMA J 2022; 13:335-350. [DOI: 10.1007/s13167-022-00279-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 04/25/2022] [Indexed: 12/19/2022]
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de Bruyn DP, Beasley AB, Verdijk RM, van Poppelen NM, Paridaens D, de Keizer ROB, Naus NC, Gray ES, de Klein A, Brosens E, Kiliç E. Is Tissue Still the Issue? The Promise of Liquid Biopsy in Uveal Melanoma. Biomedicines 2022; 10:biomedicines10020506. [PMID: 35203714 PMCID: PMC8962331 DOI: 10.3390/biomedicines10020506] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 12/18/2022] Open
Abstract
Uveal melanoma (UM) is the second most frequent type of melanoma. Therapeutic options for UM favor minimally invasive techniques such as irradiation for vision preservation. As a consequence, no tumor material is obtained. Without available tissue, molecular analyses for gene expression, mutation or copy number analysis cannot be performed. Thus, proper patient stratification is impossible and patients’ uncertainty about their prognosis rises. Minimally invasive techniques have been studied for prognostication in UM. Blood-based biomarker analysis has become more common in recent years; however, no clinically standardized protocol exists. This review summarizes insights in biomarker analysis, addressing new insights in circulating tumor cells, circulating tumor DNA, extracellular vesicles, proteomics, and metabolomics. Additionally, medical imaging can play a significant role in staging, surveillance, and prognostication of UM and is addressed in this review. We propose that combining multiple minimally invasive modalities using tumor biomarkers should be the way forward and warrant more attention in the coming years.
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Affiliation(s)
- Daniël P. de Bruyn
- Department of Ophthalmology, Erasmus MC Rotterdam, 3000 CA Rotterdam, The Netherlands; (D.P.d.B.); (N.M.v.P.); (D.P.); (N.C.N.)
- Department of Clinical Genetics, Erasmus MC Rotterdam, 3000 CA Rotterdam, The Netherlands; (A.d.K.); (E.B.)
- Erasmus MC Cancer Institute, 3000 CA Rotterdam, The Netherlands
| | - Aaron B. Beasley
- Centre for Precision Health, School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA 6027, Australia; (A.B.B.); (E.S.G.)
| | - Robert M. Verdijk
- The Rotterdam Eye Hospital, 3011 BH Rotterdam, The Netherlands; (R.M.V.); (R.O.B.d.K.)
- Department of Pathology, Section Ophthalmic Pathology, Erasmus MC Rotterdam, 3000 CA Rotterdam, The Netherlands
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Natasha M. van Poppelen
- Department of Ophthalmology, Erasmus MC Rotterdam, 3000 CA Rotterdam, The Netherlands; (D.P.d.B.); (N.M.v.P.); (D.P.); (N.C.N.)
- Department of Clinical Genetics, Erasmus MC Rotterdam, 3000 CA Rotterdam, The Netherlands; (A.d.K.); (E.B.)
- Erasmus MC Cancer Institute, 3000 CA Rotterdam, The Netherlands
| | - Dion Paridaens
- Department of Ophthalmology, Erasmus MC Rotterdam, 3000 CA Rotterdam, The Netherlands; (D.P.d.B.); (N.M.v.P.); (D.P.); (N.C.N.)
- The Rotterdam Eye Hospital, 3011 BH Rotterdam, The Netherlands; (R.M.V.); (R.O.B.d.K.)
| | | | - Nicole C. Naus
- Department of Ophthalmology, Erasmus MC Rotterdam, 3000 CA Rotterdam, The Netherlands; (D.P.d.B.); (N.M.v.P.); (D.P.); (N.C.N.)
- Erasmus MC Cancer Institute, 3000 CA Rotterdam, The Netherlands
| | - Elin S. Gray
- Centre for Precision Health, School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA 6027, Australia; (A.B.B.); (E.S.G.)
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus MC Rotterdam, 3000 CA Rotterdam, The Netherlands; (A.d.K.); (E.B.)
- Erasmus MC Cancer Institute, 3000 CA Rotterdam, The Netherlands
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus MC Rotterdam, 3000 CA Rotterdam, The Netherlands; (A.d.K.); (E.B.)
- Erasmus MC Cancer Institute, 3000 CA Rotterdam, The Netherlands
| | - Emine Kiliç
- Department of Ophthalmology, Erasmus MC Rotterdam, 3000 CA Rotterdam, The Netherlands; (D.P.d.B.); (N.M.v.P.); (D.P.); (N.C.N.)
- Erasmus MC Cancer Institute, 3000 CA Rotterdam, The Netherlands
- Correspondence: ; Tel.: +31-107030683
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Prognostic Biomarkers in Uveal Melanoma: The Status Quo, Recent Advances and Future Directions. Cancers (Basel) 2021; 14:cancers14010096. [PMID: 35008260 PMCID: PMC8749988 DOI: 10.3390/cancers14010096] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/15/2021] [Accepted: 12/23/2021] [Indexed: 01/18/2023] Open
Abstract
Simple Summary Although rare, uveal melanoma (UM) is the most common cancer that develops inside adult eyes. The prognosis is poor, since 50% of patients will develop lethal metastases in the first decade, especially to the liver. Once metastases are detected, life expectancy is limited, given that the available treatments are mostly unsuccessful. Thus, there is a need to find methods that can accurately predict UM prognosis and also effective therapeutic strategies to treat this cancer. In this manuscript, we initially compile the current knowledge on epidemiological, clinical, pathological and molecular features of UM. Then, we cover the most relevant prognostic factors currently used for the evaluation and follow-up of UM patients. Afterwards, we highlight emerging molecular markers in UM published over the last three years. Finally, we discuss the problems preventing meaningful advances in the treatment and prognostication of UM patients, as well as forecast new roadblocks and paths of UM-related research. Abstract Uveal melanoma (UM) is the most common malignant intraocular tumour in the adult population. It is a rare cancer with an incidence of nearly five cases per million inhabitants per year, which develops from the uncontrolled proliferation of melanocytes in the choroid (≈90%), ciliary body (≈6%) or iris (≈4%). Patients initially present either with symptoms like blurred vision or photopsia, or without symptoms, with the tumour being detected in routine eye exams. Over the course of the disease, metastases, which are initially dormant, develop in nearly 50% of patients, preferentially in the liver. Despite decades of intensive research, the only approach proven to mildly control disease spread are early treatments directed to ablate liver metastases, such as surgical excision or chemoembolization. However, most patients have a limited life expectancy once metastases are detected, since there are limited therapeutic approaches for the metastatic disease, including immunotherapy, which unlike in cutaneous melanoma, has been mostly ineffective for UM patients. Therefore, in order to offer the best care possible to these patients, there is an urgent need to find robust models that can accurately predict the prognosis of UM, as well as therapeutic strategies that effectively block and/or limit the spread of the metastatic disease. Here, we initially summarized the current knowledge about UM by compiling the most relevant epidemiological, clinical, pathological and molecular data. Then, we revisited the most important prognostic factors currently used for the evaluation and follow-up of primary UM cases. Afterwards, we addressed emerging prognostic biomarkers in UM, by comprehensively reviewing gene signatures, immunohistochemistry-based markers and proteomic markers resulting from research studies conducted over the past three years. Finally, we discussed the current hurdles in the field and anticipated the future challenges and novel avenues of research in UM.
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Yavuzyigitoglu S, Tang MCY, Jansen M, Geul KW, Dwarkasing RS, Vaarwater J, Drabarek W, Verdijk RM, Paridaens D, Naus NC, Brosens E, de Klein A, Kilic E. Radiological Patterns of Uveal Melanoma Liver Metastases in Correlation to Genetic Status. Cancers (Basel) 2021; 13:cancers13215316. [PMID: 34771480 PMCID: PMC8582397 DOI: 10.3390/cancers13215316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 10/15/2021] [Indexed: 11/16/2022] Open
Abstract
This study reports the role played by the mutation status of Uveal Melanoma (UM) in relation to hepatic metastatic patterns as seen on imaging modalities. Radiological images were obtained from 123 patients treated at the Erasmus Medical Center Rotterdam or the Rotterdam Eye Hospital. Radiological images were derived from either computed tomography or magnetic resonance imaging. Hepatic metastatic patterns were classified by counting the number of metastases found in the liver. Miliary metastatic pattern (innumerable small metastases in the entire liver) was analyzed separately. Mutation status was determined in 85 patients. Median disease-free survival (DFS) and survival with metastases differed significantly between each of the metastatic patterns (respectively, p = 0.009, p < 0.001), both in favor of patients with less hepatic metastases. The mutation status of the primary tumor was not correlated with any hepatic tumor profiles (p = 0.296). Of the patients who had a solitary metastasis (n = 18), 11 originated from a primary BAP1-mutated tumors and one from a primary SF3B1-mutated tumor. Of the patients who had a miliary metastasis pattern (n = 24), 17 had a primary BAP1-mutated tumor and two had a primary SF3B1-mutated tumor. Chromosome 8p loss was significantly more in patients with more metastases (p = 0.045). Moreover, the primary UMs of patients with miliary metastases harbored more chromosome 8p and 1p loss, compared to patients with single solitary metastasis (p = 0.035 and p = 0.026, respectively). In conclusion, our study shows that there is an inverse correlation of the number of metastasis with the DFS and metastasized survival, indicating separate growth patterns. We also revealed that the number and type of metastases is irrelevant to the prognostic mutation status of the tumor, showing that both BAP1- and SF3B1-mutated UM can result in solitary and miliary metastases, indicating that other processes lay ground to the different metastatic patterns.
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Affiliation(s)
- Serdar Yavuzyigitoglu
- Department of Ophthalmology, Erasmus Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands; (S.Y.); (M.C.Y.T.); (M.J.); (J.V.); (W.D.); (D.P.); (N.C.N.)
- Department of Clinical Genetics, Erasmus Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands; (E.B.); (A.d.K.)
| | - Michael C. Y. Tang
- Department of Ophthalmology, Erasmus Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands; (S.Y.); (M.C.Y.T.); (M.J.); (J.V.); (W.D.); (D.P.); (N.C.N.)
| | - Miguel Jansen
- Department of Ophthalmology, Erasmus Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands; (S.Y.); (M.C.Y.T.); (M.J.); (J.V.); (W.D.); (D.P.); (N.C.N.)
| | - Kaspar W. Geul
- Department of Internal Medicine, Sint Franciscus Gasthuis Rotterdam, 3045 PM Rotterdam, The Netherlands;
| | - Roy S. Dwarkasing
- Department of Radiology, Erasmus Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands;
| | - Jolanda Vaarwater
- Department of Ophthalmology, Erasmus Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands; (S.Y.); (M.C.Y.T.); (M.J.); (J.V.); (W.D.); (D.P.); (N.C.N.)
- Department of Clinical Genetics, Erasmus Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands; (E.B.); (A.d.K.)
| | - Wojtek Drabarek
- Department of Ophthalmology, Erasmus Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands; (S.Y.); (M.C.Y.T.); (M.J.); (J.V.); (W.D.); (D.P.); (N.C.N.)
- Department of Clinical Genetics, Erasmus Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands; (E.B.); (A.d.K.)
| | - Robert M. Verdijk
- Department of Pathology, Erasmus Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands;
| | - Dion Paridaens
- Department of Ophthalmology, Erasmus Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands; (S.Y.); (M.C.Y.T.); (M.J.); (J.V.); (W.D.); (D.P.); (N.C.N.)
- The Rotterdam Eye Hospital, 3011 BH Rotterdam, The Netherlands
| | - Nicole C. Naus
- Department of Ophthalmology, Erasmus Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands; (S.Y.); (M.C.Y.T.); (M.J.); (J.V.); (W.D.); (D.P.); (N.C.N.)
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands; (E.B.); (A.d.K.)
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands; (E.B.); (A.d.K.)
| | - Emine Kilic
- Department of Ophthalmology, Erasmus Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands; (S.Y.); (M.C.Y.T.); (M.J.); (J.V.); (W.D.); (D.P.); (N.C.N.)
- Correspondence:
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Yang X, Han B, He Z, Zhang Y, Lin K, Su H, Hosseini DK, Sun H, Yang M, Chen X. RNA-Binding Proteins CLK1 and POP7 as Biomarkers for Diagnosis and Prognosis of Esophageal Squamous Cell Carcinoma. Front Cell Dev Biol 2021; 9:715027. [PMID: 34568328 PMCID: PMC8458940 DOI: 10.3389/fcell.2021.715027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/09/2021] [Indexed: 12/24/2022] Open
Abstract
The abnormality of RNA-binding proteins (RBPs) is closely related to the tumorigenesis and development of esophageal squamous cell carcinoma (ESCC), and has been an area of interest for research recently. In this study, 162 tumors and 11 normal samples are obtained from The Cancer Genome Atlas database, among which 218 differentially expressed RBPs are screened. Finally, a prognostic model including seven RBPs (CLK1, DDX39A, EEF2, ELAC1, NKRF, POP7, and SMN1) is established. Further analysis reveals that the overall survival (OS) rate of the high-risk group is lower than that of the low-risk group. The area under the receiver operating characteristic (ROC) curve (AUC) of the training group and testing group is significant (AUCs of 3 years are 0.815 and 0.694, respectively, AUCs of 5 years are 0.737 and 0.725, respectively). In addition, a comprehensive analysis of seven identified RBPs shows that most RBPs are related to OS in patients with ESCC, among which EEF2 and ELCA1 are differentially expressed at the protein level of ESCC and control tissues. CLK1 and POP7 expressions in esophageal cancer tumor samples are undertaken using the tissue microarray, and show that CLK1 mRNA levels are relatively lower, and POP7 mRNA levels are higher compared with non-cancerous esophageal tissues. Survival analysis reveals that a higher expression of CLK1 predicts a significant worse prognosis, and a lower expression of POP7 predicts a worse prognosis in esophageal cancer. These results suggest that CLK1 may promote tumor progression, and POP7 may hinder the development of esophageal cancer. In addition, gene set enrichment analysis reveals that abnormal biological processes related to ribosomes and abnormalities in classic tumor signaling pathways such as TGF-β are important driving forces for the occurrence and development of ESCC. Our results provide new insights into the pathogenesis of ESCC, and seven RBPs have potential application value in the clinical prognosis prediction of ESCC.
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Affiliation(s)
- Xiuping Yang
- Department of Otorhinolaryngology, Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Baoai Han
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zuhong He
- Department of Otorhinolaryngology, Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ya Zhang
- Department of Otorhinolaryngology, Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Kun Lin
- Department of Otorhinolaryngology, Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hongguo Su
- Department of Otorhinolaryngology, Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Davood K Hosseini
- Department of Internal Medicine, Hackensack University Medical Center, Hackensack, NJ, United States
| | - Haiying Sun
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Minlan Yang
- Department of Otorhinolaryngology, Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xiong Chen
- Department of Otorhinolaryngology, Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
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Akin-Bali DF. Bioinformatics analysis of GNAQ, GNA11, BAP1, SF3B1,SRSF2, EIF1AX, PLCB4, and CYSLTR2 genes and their role in the pathogenesis of Uveal Melanoma. Ophthalmic Genet 2021; 42:732-743. [PMID: 34353217 DOI: 10.1080/13816810.2021.1961280] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Uveal melanoma (UM) is the most common primary intraocular malignancy in adults, and its metastases are known to be fatal. It is critical to identify molecular markers to be used in potential prognostic evaluation for early diagnosis, treatment, and metastasis or to investigate all aspects of known genetic anomalies. Therefore, this study aimed to analyze the eight genes (GNAQ, GNA11, BAP1, SF3B1, SRSF2, EIF1AX, PLCB4, and CYSLTR2) that are associated with the most common genetic anomalies in UM from a molecular perspective. The genome sequences and expression profiles of 108 UM patients were obtained via bioinformatics tools that provide data from TCGA. The overall mutational load and the mutation patterns for eight genes, in particular, were thoroughly determined. Moreover, PolyPhen2 and SNAP2 tools were used to estimate the oncogenic/pathogenic properties of identified mutations for UM. In addition to the mutation profile, the effects of the presence of a mutation on gene expression and survival were determined. Finally, STRING network analysis was performed to better understand the functional relationships of mutated proteins in cellular processes. There were 27 missense mutations, 16 frameshift mutations, six nonsense mutations, and three splice region mutations among the 52 mutations found in eight genes, and 26 of them had pathogenic properties. BAP1 m-RNA expression was significantly lower in tumors with the mutant genotype (p = .001). The impact of gene expression, which has poor prognostic importance, on survival is statistically significant for high-expressed BAP1 (p = .0015) and low-expressed CYSLTR2 (p = .0021). To assess the current state of this potentially devastating disease, a molecular perspective has been evaluated. Defining this molecular perspective can be useful in developing targeted drug therapies and personalized medicine.
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Goenka A, Tiek D, Song X, Huang T, Hu B, Cheng SY. The Many Facets of Therapy Resistance and Tumor Recurrence in Glioblastoma. Cells 2021; 10:cells10030484. [PMID: 33668200 PMCID: PMC7995978 DOI: 10.3390/cells10030484] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/19/2021] [Accepted: 02/19/2021] [Indexed: 12/14/2022] Open
Abstract
Glioblastoma (GBM) is the most lethal type of primary brain cancer. Standard care using chemo- and radio-therapy modestly increases the overall survival of patients; however, recurrence is inevitable, due to treatment resistance and lack of response to targeted therapies. GBM therapy resistance has been attributed to several extrinsic and intrinsic factors which affect the dynamics of tumor evolution and physiology thus creating clinical challenges. Tumor-intrinsic factors such as tumor heterogeneity, hypermutation, altered metabolomics and oncologically activated alternative splicing pathways change the tumor landscape to facilitate therapy failure and tumor progression. Moreover, tumor-extrinsic factors such as hypoxia and an immune-suppressive tumor microenvironment (TME) are the chief causes of immunotherapy failure in GBM. Amid the success of immunotherapy in other cancers, GBM has occurred as a model of resistance, thus focusing current efforts on not only alleviating the immunotolerance but also evading the escape mechanisms of tumor cells to therapy, caused by inter- and intra-tumoral heterogeneity. Here we review the various mechanisms of therapy resistance in GBM, caused by the continuously evolving tumor dynamics as well as the complex TME, which cumulatively contribute to GBM malignancy and therapy failure; in an attempt to understand and identify effective therapies for recurrent GBM.
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Affiliation(s)
| | | | | | | | | | - Shi-Yuan Cheng
- Correspondence: ; Tel.: +1-312-503-3043; Fax: +1-312-503-5603
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