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Deng L, Liao L, Zhang YL, Hu SY, Yang SY, Ma XY, Huang MY, Zhang FL, Li DQ. MYC-driven U2SURP regulates alternative splicing of SAT1 to promote triple-negative breast cancer progression. Cancer Lett 2023; 560:216124. [PMID: 36907504 DOI: 10.1016/j.canlet.2023.216124] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/27/2023] [Accepted: 03/09/2023] [Indexed: 03/12/2023]
Abstract
Triple-negative breast cancer (TNBC), although highly lethal, lacks validated therapeutic targets. Here, we report that U2 snRNP-associated SURP motif-containing protein (U2SURP), a poorly defined member of the serine/arginine rich protein family, was significantly upregulated in TNBC tissues, and its high expression was associated with poor prognosis of TNBC patients. MYC, a frequently amplified oncogene in TNBC tissues, enhanced U2SURP translation through an eIF3D (eukaryotic translation initiation factor 3 subunit D)-dependent mechanism, resulting in the accumulation of U2SURP in TNBC tissues. Functional assays revealed that U2SURP played an important role in facilitating tumorigenesis and metastasis of TNBC cells both in vitro and in vivo. Intriguingly, U2SURP had no significant effects on proliferative, migratory, and invasive potential of normal mammary epithelial cells. Furthermore, we found that U2SURP promoted alternative splicing of spermidine/spermine N1-acetyltransferase 1 (SAT1) pre-mRNA by removal of intron 3, resulting in an increase in the stability of SAT1 mRNA and subsequent protein expression levels. Importantly, spliced SAT1 promoted the oncogenic properties of TNBC cells, and re-expression of SAT1 in U2SURP-depleted cells partially rescued the impaired malignant phenotypes of TNBC cells caused by U2SURP knockdown both in vitro and in mice. Collectively, these findings reveal previously unknown functional and mechanism roles of the MYC-U2SURP-SAT1 signaling axis in TNBC progression and highlight U2SURP as a potential therapy target for TNBC.
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Affiliation(s)
- Ling Deng
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Li Liao
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China; Cancer Institute, Shanghai Medical College, Fudan University, Shanghai, 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yin-Ling Zhang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China; Cancer Institute, Shanghai Medical College, Fudan University, Shanghai, 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Shu-Yuan Hu
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Shao-Ying Yang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Xiao-Yan Ma
- Department of Breast Surgery, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Min-Ying Huang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Fang-Lin Zhang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China; Cancer Institute, Shanghai Medical College, Fudan University, Shanghai, 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Da-Qiang Li
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China; Cancer Institute, Shanghai Medical College, Fudan University, Shanghai, 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China; Department of Breast Surgery, Shanghai Medical College, Fudan University, Shanghai, 200032, China; Shanghai Key Laboratory of Breast Cancer, Shanghai Medical College, Fudan University, Shanghai, 200032, China; Shanghai Key Laboratory of Radiation Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
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2
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Fanelli A, Marconato L, Licenziato L, Minoli L, Rouquet N, Aresu L. POT1 mutations are frequent and associated with Ki-67 index in canine diffuse large B-cell lymphoma. Front Vet Sci 2022; 9:968807. [PMID: 36016811 PMCID: PMC9396242 DOI: 10.3389/fvets.2022.968807] [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: 06/14/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) represents one of the most frequent and deadliest neoplasia in dogs worldwide and is characterized by a remarkable degree of clinical heterogeneity, with poor chances to anticipate the outcome. Even if in the last years some recurrently mutated genes have been identified, the genetic origin of canine DLBCL (cDLBCL) is not yet completely understood. The aim of the present study was to assess the prevalence of POT1 mutations in cDLBCL and to elucidate the role of such gene in the pathogenesis of this tumor. Mutations in POT1 were retrieved in 34% of cases, in line with previous reports, but no significant associations with any clinico-pathological variable were identified. Likewise, POT1 mutations are not predictive of worse prognosis. Interestingly, Ki-67 index was significantly higher in dogs harboring POT1 mutations compared to wild-type ones. These results suggest that POT1 mutations may exert their pathogenic role in cDLBCL by promoting cellular proliferation.
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Affiliation(s)
- Antonella Fanelli
- Department of Veterinary Sciences, University of Turin, Turin, Italy
- *Correspondence: Antonella Fanelli
| | - Laura Marconato
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Luca Licenziato
- Department of Veterinary Sciences, University of Turin, Turin, Italy
| | - Lucia Minoli
- Department of Veterinary Sciences, University of Turin, Turin, Italy
| | | | - Luca Aresu
- Department of Veterinary Sciences, University of Turin, Turin, Italy
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3
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Wnt/β-Catenin Signalling and Its Cofactor BCL9L Have an Oncogenic Effect in Bladder Cancer Cells. Int J Mol Sci 2022; 23:ijms23105319. [PMID: 35628130 PMCID: PMC9141496 DOI: 10.3390/ijms23105319] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 12/12/2022] Open
Abstract
Bladder cancer (BC) is characterised by a high recurrence and progression rate. However, the molecular mechanisms of BC progression remain poorly understood. BCL9L, a coactivator of β-catenin was mutated in the 5′ and 3′ untranslated regions (UTRs). We assessed the influence of UTRs mutations on BCL9L, and the role of BCL9L and Wnt/β-catenin signalling in BC cells. UTR mutations were analysed by a luciferase reporter. BCL9L protein was assessed by immunohistochemistry in BC tissues. Cell proliferation was examined by crystal violet staining and by the spheroid model. Moreover, migration and invasion were analysed in real-time using the xCelligence RTCA system. The A > T mutation at 3′ UTR of BCL9L reduces the luciferase reporter mRNA expression and activity. BCL9L is predominantly increased in dysplastic urothelial cells and muscle-invasive BC. Knockdown of BCL9L and inhibition of Wnt/β-catenin signalling significantly repress the proliferation, migration and invasion of Cal29 and T24. In addition, BCL9L knockdown reduces mRNA level of Wnt/β-catenin target genes in Cal29 but not in T24 cells. BCL9L and Wnt/β-catenin signalling play an oncogenic role in bladder cancer cells and seems to be associated with BC progression. Nevertheless, the involvement of BCL9L in Wnt/β-catenin signalling is cell-line specific.
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4
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Aoude LG, Bonazzi VF, Brosda S, Patel K, Koufariotis LT, Oey H, Nones K, Wood S, Pearson JV, Lonie JM, Arneil M, Atkinson V, Smithers BM, Waddell N, Barbour AP. Pathogenic germline variants are associated with poor survival in stage III/IV melanoma patients. Sci Rep 2020; 10:17687. [PMID: 33077847 PMCID: PMC7572377 DOI: 10.1038/s41598-020-74956-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/08/2020] [Indexed: 12/11/2022] Open
Abstract
Patients with late stage resected cutaneous melanoma have poor overall survival (OS) and experience irreversible adverse events from systemic therapy. There is a clinical need to identify biomarkers to predict outcome. Performing germline/tumour whole-exome sequencing of 44 stage III/IV melanoma patients we identified pathogenic germline mutations in CDKN2A, CDK4, ATM, POLH, MRE11A, RECQL4 and XPC, affecting 7/44 patients. These mutations were associated with poor OS (p = 0.0082). We confirmed our findings in The Cancer Genome Atlas (TCGA) human skin cutaneous melanoma cohort where we identified pathogenic variants in 40/455 patients (p = 0.0203). Combining these cohorts (n = 499) further strengthened these findings showing germline carriers had worse OS (p = 0.0009). Additionally, we determined whether tumour mutation burden (TMB) or BRAF status were prognostic markers of survival. Low TMB rate (< 20 Mut/Mb; p = 0.0034) and BRAF p.V600 mutation (p = 0.0355) were associated with worse progression-free survival. Combining these biomarkers indicated that V600 mutant patients had significantly lower TMB (p = 0.0155). This was confirmed in the TCGA (n = 443, p = 0.0007). Integrative analysis showed germline mutation status conferred the highest risk (HR 5.2, 95% CI 1.72–15.7). Stage IV (HR 2.5, 0.74–8.6) and low TMB (HR 2.3, 0.57–9.4) were similar, whereas BRAF V600 status was the weakest prognostic biomarker (HR 1.5, 95% CI 0.44–5.2).
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Affiliation(s)
- Lauren G Aoude
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia.
| | - Vanessa F Bonazzi
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - Sandra Brosda
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - Kalpana Patel
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia
| | | | - Harald Oey
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - Katia Nones
- QIMR Berghofer Medical Research Institute, Herston, QLD, 4006, Australia
| | - Scott Wood
- QIMR Berghofer Medical Research Institute, Herston, QLD, 4006, Australia
| | - John V Pearson
- QIMR Berghofer Medical Research Institute, Herston, QLD, 4006, Australia
| | - James M Lonie
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - Melissa Arneil
- Division of Cancer Services, Princess Alexandra Hospital, Woolloongabba, QLD, 4102, Australia
| | - Victoria Atkinson
- Queensland Melanoma Project, Princess Alexandra Hospital, Woolloongabba, QLD, 4102, Australia.,Faculty of Medicine, University of Queensland, St Lucia, QLD, 4067, Australia
| | - B Mark Smithers
- Queensland Melanoma Project, Princess Alexandra Hospital, Woolloongabba, QLD, 4102, Australia.,Faculty of Medicine, University of Queensland, St Lucia, QLD, 4067, Australia
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Herston, QLD, 4006, Australia
| | - Andrew P Barbour
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia.,Queensland Melanoma Project, Princess Alexandra Hospital, Woolloongabba, QLD, 4102, Australia
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5
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Variants in the 5'UTR reduce SHOX expression and contribute to SHOX haploinsufficiency. Eur J Hum Genet 2020; 29:110-121. [PMID: 32647378 PMCID: PMC7852508 DOI: 10.1038/s41431-020-0676-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 06/08/2020] [Accepted: 06/23/2020] [Indexed: 11/08/2022] Open
Abstract
SHOX haploinsufficiency causes 70-90% of Léri-Weill dyschondrosteosis (LWD) and 2-10% of idiopathic short stature (ISS). Deletions removing the entire gene or enhancers and point mutations in the coding region represent a well-established cause of haploinsufficiency. During diagnostic genetic testing on ISS/LWD patients, in addition to classic SHOX defects, five 5'UTR variants (c.-58G > T, c.-55C > T, c.-51G > A, c.-19G > A, and c.-9del), were detected whose pathogenetic role was unclear and were thus classified as VUS (Variants of Uncertain Significance). The purpose of the present study was to investigate the role of these noncoding variations in SHOX haploinsufficiency. The variants were tested for their ability to interfere with correct gene expression of a regulated reporter gene (luciferase assay). The negative effect on the mRNA splicing predicted in silico for c.-19G > A was assayed in vitro through a minigene splicing assay. The luciferase assay showed that c.-51G > A, c.-19G > A, and c.-9del significantly reduce luciferase activity by 60, 35, and 40% at the homozygous state. Quantification of the luciferase mRNA showed that c.-51G > A and c.-9del might interfere with the correct SHOX expression mainly at the post-transcriptional level. The exon trapping assay demonstrated that c.-19G > A determines the creation of a new branch site causing an aberrant mRNA splicing. In conclusion, this study allowed us to reclassify two of the 5'UTR variants identified during SHOX diagnostic screening as likely pathogenic, one remains as a VUS, and two as likely benign variants. This analysis for the first time expands the spectrum of the genetic causes of SHOX haploinsufficiency to noncoding variations in the 5'UTR.
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6
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DNA Methylation Changes in Human Papillomavirus-Driven Head and Neck Cancers. Cells 2020; 9:cells9061359. [PMID: 32486347 PMCID: PMC7348958 DOI: 10.3390/cells9061359] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/25/2020] [Accepted: 05/28/2020] [Indexed: 12/12/2022] Open
Abstract
Disruption of DNA methylation patterns is one of the hallmarks of cancer. Similar to other cancer types, human papillomavirus (HPV)-driven head and neck cancer (HNC) also reveals alterations in its methylation profile. The intrinsic ability of HPV oncoproteins E6 and E7 to interfere with DNA methyltransferase activity contributes to these methylation changes. There are many genes that have been reported to be differentially methylated in HPV-driven HNC. Some of these genes are involved in major cellular pathways, indicating that DNA methylation, at least in certain instances, may contribute to the development and progression of HPV-driven HNC. Furthermore, the HPV genome itself becomes a target of the cellular DNA methylation machinery. Some of these methylation changes appearing in the viral long control region (LCR) may contribute to uncontrolled oncoprotein expression, leading to carcinogenesis. Consistent with these observations, demethylation therapy appears to have significant effects on HPV-driven HNC. This review article comprehensively summarizes DNA methylation changes and their diagnostic and therapeutic indications in HPV-driven HNC.
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7
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Insights into Genetic Susceptibility to Melanoma by Gene Panel Testing: Potential Pathogenic Variants in ACD, ATM, BAP1, and POT1. Cancers (Basel) 2020; 12:cancers12041007. [PMID: 32325837 PMCID: PMC7226507 DOI: 10.3390/cancers12041007] [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: 03/24/2020] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 12/20/2022] Open
Abstract
The contribution of recently established or candidate susceptibility genes to melanoma missing heritability has yet to be determined. Multigene panel testing could increase diagnostic yield and better define the role of candidate genes. We characterized 273 CDKN2A/ARF and CDK4-negative probands through a custom-designed targeted gene panel that included CDKN2A/ARF, CDK4, ACD, BAP1, MITF, POT1, TERF2IP, ATM, and PALB2. Co-segregation, loss of heterozygosity (LOH)/protein expression analysis, and splicing characterization were performed to improve variant classification. We identified 16 (5.9%) pathogenic and likely pathogenic variants in established high/medium penetrance cutaneous melanoma susceptibility genes (BAP1, POT1, ACD, MITF, and TERF2IP), including two novel variants in BAP1 and 4 in POT1. We also found four deleterious and five likely deleterious variants in ATM (3.3%). Thus, including potentially deleterious variants in ATM increased the diagnostic yield to about 9%. Inclusion of rare variants of uncertain significance would increase the overall detection yield to 14%. At least 10% of melanoma missing heritability may be explained through panel testing in our population. To our knowledge, this is the highest frequency of putative ATM deleterious variants reported in melanoma families, suggesting a possible role in melanoma susceptibility, which needs further investigation.
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8
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Suganuma M, Kono M, Yamanaka M, Akiyama M. Pathogenesis of a variant in the 5′ untranslated region of ADAR1 in dyschromatosis symmetrica hereditaria. Pigment Cell Melanoma Res 2020; 33:591-600. [DOI: 10.1111/pcmr.12863] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/30/2019] [Accepted: 01/08/2020] [Indexed: 12/31/2022]
Affiliation(s)
- Mutsumi Suganuma
- Department of Dermatology Nagoya University Graduate School of Medicine Nagoya Japan
| | - Michihiro Kono
- Department of Dermatology Nagoya University Graduate School of Medicine Nagoya Japan
| | | | - Masashi Akiyama
- Department of Dermatology Nagoya University Graduate School of Medicine Nagoya Japan
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9
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Silva J, Fernandes R, Romão L. Translational Regulation by Upstream Open Reading Frames and Human Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1157:99-116. [DOI: 10.1007/978-3-030-19966-1_5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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10
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Fan Z, Zheng J, Xue Y, Liu X, Wang D, Yang C, Ma J, Liu L, Ruan X, Wang Z, Liu Y. NR2C2-uORF targeting UCA1-miR-627-5p-NR2C2 feedback loop to regulate the malignant behaviors of glioma cells. Cell Death Dis 2018; 9:1165. [PMID: 30518750 PMCID: PMC6281640 DOI: 10.1038/s41419-018-1149-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 09/25/2018] [Accepted: 10/01/2018] [Indexed: 12/15/2022]
Abstract
Accumulating evidence has highlighted the potential role of non-coding RNAs (ncRNAs) and upstream open-reading frames (uORFs) in the biological behaviors of glioblastoma. Here, we elucidated the function and possible molecular mechanisms of the effect of some ncRNAs and NR2C2-uORF on the biological behaviors of gliomas. Quantitative real-time PCR was conducted to profile the cell expression of lnc-UCA1 and microRNA-627-5p (miR-627-5p) in glioma tissues and cells. Western blot assay was used to determine the expression levels of NR2C2, SPOCK1, and NR2C2-uORF in glioma tissues and cells. Stable knockdown of lnc-UCA1 or overexpression of miR-627-5p in glioma cell lines (U87 and U251) were established to explore the function of lnc-UCA1 and miR-627-5p in glioma cells. Further, Dual luciferase report assay was used to investigate the correlation between lnc-UCA1 and miR-627-5p. Cell Counting Kit-8, transwell assays, and flow cytometry were used to investigate lnc-UCA1 and miR-627-5p function including cell proliferation, migration and invasion, and apoptosis, respectively. ChIP assays were used to ascertain the correlations between NR2C2 and SPOCK1 as well as NR2C2 between lnc-UCA1. This study confirmed that lnc-UCA1 was up-regulated in glioma tissues and cells. UCA1 knockdown inhibited the malignancies of glioma cells by reducing proliferation, migration, and invasion, but inducing apoptosis. We found that lnc-UCA1 acted as miR-627-5p sponge in a sequence-specific manner. Meanwhile, upregulated lnc-UCA1 inhibited miR-627-5p expression. In addition, miR-627-5p targeted 3'UTR of NR2C2 and down-regulated its expression. Moreover, UCA1 knockdown impaired NR2C2 expression by upregulating miR-627-5p. An uORF was identified in mRNA 5'UTR of NR2C2 and overexpression of whom negatively regulated NR2C2 expression. Remarkably, lnc-UCA1 knockdown combined with uORF overepression and NR2C2 knockdown led to severe tumor suppression in vivo. This study demonstrated that the NR2C2-uORF impaired the pivotal roles that UCA1-miR-627-5p-NR2C2 feedback loop had in regulating the malignancies of glioma cells by targeting NR2C2 directly. And this may provide a potential therapeutic strategy for treating glioma.
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MESH Headings
- Animals
- Apoptosis/genetics
- Brain Neoplasms/genetics
- Brain Neoplasms/metabolism
- Brain Neoplasms/mortality
- Brain Neoplasms/pathology
- Cell Line, Tumor
- Cell Movement
- Cell Proliferation
- Feedback, Physiological
- Gene Expression Regulation, Neoplastic
- Glioblastoma/genetics
- Glioblastoma/metabolism
- Glioblastoma/mortality
- Glioblastoma/pathology
- Humans
- Mice
- Mice, Nude
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Open Reading Frames
- Promoter Regions, Genetic
- Proteoglycans/genetics
- Proteoglycans/metabolism
- RNA, Long Noncoding/antagonists & inhibitors
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Receptors, Steroid/genetics
- Receptors, Steroid/metabolism
- Receptors, Thyroid Hormone/genetics
- Receptors, Thyroid Hormone/metabolism
- Signal Transduction
- Survival Analysis
- Tumor Burden
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Zirong Fan
- Department of Neurosurgery, Shengjing Hospital of China Medical University, 110004, Shenyang, China
- Liaoning Clinical Medical Research Center in Nervous System Disease, 110004, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, 110004, Shenyang, China
| | - Jian Zheng
- Department of Neurosurgery, Shengjing Hospital of China Medical University, 110004, Shenyang, China
- Liaoning Clinical Medical Research Center in Nervous System Disease, 110004, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, 110004, Shenyang, China
| | - Yixue Xue
- Department of Neurobiology, College of Basic Medicine, China Medical University, 110122, Shenyang, China
- Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, 110122, Shenyang, China
- Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, 110122, Shenyang, China
| | - Xiaobai Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, 110004, Shenyang, China
- Liaoning Clinical Medical Research Center in Nervous System Disease, 110004, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, 110004, Shenyang, China
| | - Di Wang
- Department of Neurosurgery, Shengjing Hospital of China Medical University, 110004, Shenyang, China
- Liaoning Clinical Medical Research Center in Nervous System Disease, 110004, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, 110004, Shenyang, China
| | - Chunqing Yang
- Department of Neurosurgery, Shengjing Hospital of China Medical University, 110004, Shenyang, China
- Liaoning Clinical Medical Research Center in Nervous System Disease, 110004, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, 110004, Shenyang, China
| | - Jun Ma
- Department of Neurobiology, College of Basic Medicine, China Medical University, 110122, Shenyang, China
- Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, 110122, Shenyang, China
- Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, 110122, Shenyang, China
| | - Libo Liu
- Department of Neurobiology, College of Basic Medicine, China Medical University, 110122, Shenyang, China
- Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, 110122, Shenyang, China
- Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, 110122, Shenyang, China
| | - Xuelei Ruan
- Department of Neurobiology, College of Basic Medicine, China Medical University, 110122, Shenyang, China
- Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, 110122, Shenyang, China
- Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, 110122, Shenyang, China
| | - Zhenhua Wang
- Department of Physiology, College of Basic Medicine, China Medical University, 110122, Shenyang, Liaoning, China
| | - Yunhui Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, 110004, Shenyang, China.
- Liaoning Clinical Medical Research Center in Nervous System Disease, 110004, Shenyang, China.
- Key Laboratory of Neuro-oncology in Liaoning Province, 110004, Shenyang, China.
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Sriram A, Bohlen J, Teleman AA. Translation acrobatics: how cancer cells exploit alternate modes of translational initiation. EMBO Rep 2018; 19:embr.201845947. [PMID: 30224410 DOI: 10.15252/embr.201845947] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 07/09/2018] [Accepted: 08/16/2018] [Indexed: 12/11/2022] Open
Abstract
Recent work has brought to light many different mechanisms of translation initiation that function in cells in parallel to canonical cap-dependent initiation. This has important implications for cancer. Canonical cap-dependent translation initiation is inhibited by many stresses such as hypoxia, nutrient limitation, proteotoxic stress, or genotoxic stress. Since cancer cells are often exposed to these stresses, they rely on alternate modes of translation initiation for protein synthesis and cell growth. Cancer mutations are now being identified in components of the translation machinery and in cis-regulatory elements of mRNAs, which both control translation of cancer-relevant genes. In this review, we provide an overview on the various modes of non-canonical translation initiation, such as leaky scanning, translation re-initiation, ribosome shunting, IRES-dependent translation, and m6A-dependent translation, and then discuss the influence of stress on these different modes of translation. Finally, we present examples of how these modes of translation are dysregulated in cancer cells, allowing them to grow, to proliferate, and to survive, thereby highlighting the importance of translational control in cancer.
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Affiliation(s)
- Ashwin Sriram
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg University, Heidelberg, Germany
| | - Jonathan Bohlen
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg University, Heidelberg, Germany
| | - Aurelio A Teleman
- German Cancer Research Center (DKFZ), Heidelberg, Germany .,Heidelberg University, Heidelberg, Germany
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12
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Overlapping open reading frames strongly reduce human and yeast STN1 gene expression and affect telomere function. PLoS Genet 2018; 14:e1007523. [PMID: 30067734 PMCID: PMC6089452 DOI: 10.1371/journal.pgen.1007523] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 08/13/2018] [Accepted: 06/28/2018] [Indexed: 12/18/2022] Open
Abstract
The levels of telomeric proteins, such as telomerase, can have profound effects on telomere function, cell division and human disease. Here we demonstrate how levels of Stn1, a component of the conserved telomere capping CST (Cdc13, Stn1, Ten1) complex, are tightly regulated by an upstream overlapping open reading frame (oORF). In budding yeast inactivation of the STN1 oORF leads to a 10-fold increase in Stn1 levels, reduced telomere length, suppression of cdc13-1 and enhancement of yku70Δ growth defects. The STN1 oORF impedes translation of the main ORF and reduces STN1 mRNA via the nonsense mediated mRNA decay (NMD) pathway. Interestingly, the homologs of the translation re-initiation factors, MCT-1Tma20/DENRTma22 also reduce Stn1 levels via the oORF. Human STN1 also contains oORFs, which reduce expression, demonstrating that oORFs are a conserved mechanism for reducing Stn1 levels. Bioinformatic analyses of the yeast and human transcriptomes show that oORFs are more underrepresented than upstream ORFs (uORFs) and associated with lower protein abundance. We propose that oORFs are an important mechanism to control expression of a subset of the proteome. Telomeres are special structures at the ends of linear chromosomes that help protect the genetic information that chromosomes carry. The levels of telomere proteins are important and can affect diseases such as cancer and ageing. The CST complex is comprised of three proteins and binds human and yeast telomeres. Levels of Stn1, a very low abundance protein, are of particular importance to telomere function in yeast cells. There are many ways to affect protein levels but little was understood about how Stn1 levels are controlled. We show that levels of Stn1 in yeast and human cells are reduced by the presence of an upstream overlapping open reading frame (oORF). Cells lacking the oORF have short telomeres and increased fitness when combined with a defect in the Stn1-partner protein, Cdc13. Interestingly, in another telomere defective context, yku70Δ cells missing the STN1-oORF are less fit. We show that the oORF reduces Stn1 levels by stimulating nonsense mediated mRNA decay and by reducing translation. More generally, genome-wide computational analysis shows that oORFs were strongly selected against during evolution and when present are associated with low protein abundance. We propose that oORFs are a powerful mechanism to regulate protein expression and function.
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13
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Zhang H, Dou S, He F, Luo J, Wei L, Lu J. Genome-wide maps of ribosomal occupancy provide insights into adaptive evolution and regulatory roles of uORFs during Drosophila development. PLoS Biol 2018; 16:e2003903. [PMID: 30028832 PMCID: PMC6070289 DOI: 10.1371/journal.pbio.2003903] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 08/01/2018] [Accepted: 07/03/2018] [Indexed: 11/19/2022] Open
Abstract
Upstream open reading frames (uORFs) play important roles in regulating the main coding DNA sequences (CDSs) via translational repression. Despite their prevalence in the genomes, uORFs are overall discriminated against by natural selection. However, it remains unclear why in the genomes there are so many uORFs more conserved than expected under the assumption of neutral evolution. Here, we generated genome-wide maps of translational efficiency (TE) at the codon level throughout the life cycle of Drosophila melanogaster. We identified 35,735 uORFs that were expressed, and 32,224 (90.2%) of them showed evidence of ribosome occupancy during Drosophila development. The ribosome occupancy of uORFs is determined by genomic features, such as optimized sequence contexts around their start codons, a shorter distance to CDSs, and higher coding potentials. Our population genomic analysis suggests the segregating mutations that create or disrupt uORFs are overall deleterious in D. melanogaster. However, we found for the first time that many (68.3% of) newly fixed uORFs that are associated with ribosomes in D. melanogaster are driven by positive Darwinian selection. Our findings also suggest that uORFs play a vital role in controlling the translational program in Drosophila. Moreover, we found that many uORFs are transcribed or translated in a developmental stage-, sex-, or tissue-specific manner, suggesting that selective transcription or translation of uORFs could potentially modulate the TE of the downstream CDSs during Drosophila development. Upstream open reading frames (uORFs) in the 5′ untranslated regions (UTRs) of messenger RNAs can potentially inhibit translation of the downstream regions that encode proteins by sequestering protein-making machinery the ribosome. Moreover, mutations that destroy existing uORFs or create new ones are known to cause human disease. Although mutations that create new uORFs are generally deleterious and are selected against, many uORFs are evolutionarily conserved across eukaryotic species. To resolve this dilemma, we used extensive mRNA-Seq and ribosome profiling to generate high-resolution genome-wide maps of ribosome occupancy and translational efficiency (TE) during the life cycle of the fruit fly D. melanogaster. This allowed us to identify the sequence features of uORFs that influence their ability to associate with ribosomes. We demonstrate for the first time that the majority of the newly fixed uORFs in D. melanogaster, especially the translated ones, are under positive Darwinian selection. We also show that uORFs exert widespread repressive effects on the translation of the downstream protein-coding region. We find that many uORFs are transcribed or translated in a developmental stage-, sex-, or tissue-specific manner. Our results suggest that during Drosophila development, changes in the TE of uORFs, as well as the inclusion/exclusion of uORFs, are frequently exploited to inversely influence the translation of the downstream protein-coding regions. Our study provides novel insights into the molecular mechanisms and functional consequences of uORF-mediated regulation.
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Affiliation(s)
- Hong Zhang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
| | - Shengqian Dou
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
| | - Feng He
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Junjie Luo
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
| | - Liping Wei
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- * E-mail:
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14
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Schrenk C, Fetz V, Vallet C, Heiselmayer C, Schröder E, Hensel A, Hahlbrock A, Wünsch D, Goesswein D, Bier C, Habtemichael N, Schneider G, Stauber RH, Knauer SK. TFIIA transcriptional activity is controlled by a 'cleave-and-run' Exportin-1/Taspase 1-switch. J Mol Cell Biol 2018; 10:33-47. [PMID: 28992066 DOI: 10.1093/jmcb/mjx025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 07/09/2017] [Indexed: 12/24/2022] Open
Abstract
Transcription factor TFIIA is controlled by complex regulatory networks including proteolysis by the protease Taspase 1, though the full impact of cleavage remains elusive. Here, we demonstrate that in contrast to the general assumption, de novo produced TFIIA is rapidly confined to the cytoplasm via an evolutionary conserved nuclear export signal (NES, amino acids 21VINDVRDIFL30), interacting with the nuclear export receptor Exportin-1/chromosomal region maintenance 1 (Crm1). Chemical export inhibition or genetic inactivation of the NES not only promotes TFIIA's nuclear localization but also affects its transcriptional activity. Notably, Taspase 1 processing promotes TFIIA's nuclear accumulation by NES masking, and modulates its transcriptional activity. Moreover, TFIIA complex formation with the TATA box binding protein (TBP) is cooperatively enhanced by inhibition of proteolysis and nuclear export, leading to an increase of the cell cycle inhibitor p16INK, which is counteracted by prevention of TBP binding. We here identified a novel mechanism how proteolysis and nuclear transport cooperatively fine-tune transcriptional programs.
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Affiliation(s)
- Christian Schrenk
- Molecular and Cellular Oncology/ENT, University Hospital of Mainz, 55101 Mainz, Germany
| | - Verena Fetz
- Molecular and Cellular Oncology/ENT, University Hospital of Mainz, 55101 Mainz, Germany
| | - Cecilia Vallet
- Molecular Biology, Centre for Medical Biotechnology (ZMB), University Duisburg-Essen, 45141 Essen, Germany
| | - Christina Heiselmayer
- Molecular Biology, Centre for Medical Biotechnology (ZMB), University Duisburg-Essen, 45141 Essen, Germany
| | - Elisabeth Schröder
- Molecular Biology, Centre for Medical Biotechnology (ZMB), University Duisburg-Essen, 45141 Essen, Germany
| | - Astrid Hensel
- Molecular Biology, Centre for Medical Biotechnology (ZMB), University Duisburg-Essen, 45141 Essen, Germany
| | - Angelina Hahlbrock
- Molecular and Cellular Oncology/ENT, University Hospital of Mainz, 55101 Mainz, Germany
| | - Désirée Wünsch
- Molecular and Cellular Oncology/ENT, University Hospital of Mainz, 55101 Mainz, Germany
| | - Dorothee Goesswein
- Molecular and Cellular Oncology/ENT, University Hospital of Mainz, 55101 Mainz, Germany
| | - Carolin Bier
- Molecular and Cellular Oncology/ENT, University Hospital of Mainz, 55101 Mainz, Germany
| | - Negusse Habtemichael
- Molecular and Cellular Oncology/ENT, University Hospital of Mainz, 55101 Mainz, Germany
| | - Günter Schneider
- University Hospital Klinikum rechts der Isar, II. Medizinische Klinik, Technical University München, 81675 Munich, Germany
| | - Roland H Stauber
- Molecular and Cellular Oncology/ENT, University Hospital of Mainz, 55101 Mainz, Germany
| | - Shirley K Knauer
- Molecular Biology, Centre for Medical Biotechnology (ZMB), University Duisburg-Essen, 45141 Essen, Germany
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15
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Bruno W, Andreotti V, Bisio A, Pastorino L, Fornarini G, Sciallero S, Bianchi-Scarrà G, Inga A, Ghiorzo P. Functional analysis of a CDKN2A 5'UTR germline variant associated with pancreatic cancer development. PLoS One 2017; 12:e0189123. [PMID: 29216274 PMCID: PMC5720692 DOI: 10.1371/journal.pone.0189123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 11/20/2017] [Indexed: 11/18/2022] Open
Abstract
CDKN2A coding region germline variants are associated with pancreatic adenocarcinoma (PC) susceptibility. Recently, we described functional germline 5’UTR CDKN2A variants from melanoma patients affecting the post-transcriptional regulation of p16INK4a mRNA that is dependent, at least in part, on an Internal Ribosome Entry Site (IRES) in the 5’UTR region. Here we describe a 5’UTR c.-201_-198delinsCTTT CDKN2A variant (frequency 0.0028 based on 350 PC patients), which seems to be private to PC, since it has never been found in public databases nor in thousands of melanoma patients tested. Functional analyses confirmed IRES activity of the 5’UTR in BX-PC3 PC cells and revealed a functional impact of the identified variant. Using gene reporter assays we observed reduced translation potential in cells treated with the mTOR inhibitor Torin1, a condition that favors the assessment of IRES activity. At the endogenous gene level we quantified allelic imbalance among polysome-associated mRNAs using a patient-derived cell line heterozygous for the c.-201_-198delinsCTTT. Overall, we conclude that this very rare private variant can be considered a potential mutation, specifically associated with PC. Our data indicate that sequencing of the entire 5'UTR of CDKN2A should be included in routine screening of PC cases with suspected inherited susceptibility.
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Affiliation(s)
- William Bruno
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and Ospedale Policlinico San Martino, Genoa, Italy
| | - Virginia Andreotti
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and Ospedale Policlinico San Martino, Genoa, Italy
| | - Alessandra Bisio
- Centre for Integrative Biology (CIBIO) and University of Trento, Trento, Italy
| | - Lorenza Pastorino
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and Ospedale Policlinico San Martino, Genoa, Italy
| | | | | | - Giovanna Bianchi-Scarrà
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and Ospedale Policlinico San Martino, Genoa, Italy
| | - Alberto Inga
- Centre for Integrative Biology (CIBIO) and University of Trento, Trento, Italy
| | - Paola Ghiorzo
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and Ospedale Policlinico San Martino, Genoa, Italy
- * E-mail:
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16
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Oncogenic BRAF mutations and p16 expression in melanocytic nevi and melanoma in the Polish population. Postepy Dermatol Alergol 2017; 34:490-498. [PMID: 29507566 PMCID: PMC5831287 DOI: 10.5114/ada.2017.71119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 10/17/2017] [Indexed: 01/07/2023] Open
Abstract
Introduction Twenty-five - fifty percent of skin melanomas arise from nevi. Melanocyte proliferation is activated by BRAFV600E, then is arrested, but single nevi transform to melanomas. p16 controls arrest, and p16 loss may promote transformation. Aim To analyze BRAFV600E, p16 expression and melanocyte proliferation in dermal, compound and dysplastic nevi, cells of primary and metastatic melanoma in the Polish population. Material and methods One hundred and thirty-two nevi (dermal, compound, dysplastic) and 41 melanomas (in situ, primary, metastatic) were studied. BRAF was assessed by cobas® 4800 BRAFV600 Mutation Test, High Resolution Melting Assay validated with: pyrosequencing and immunohistochemistry. p16 and Ki67 expression was analyzed by IHC. Results Eighty-two percent of nevi and 57% of melanomas display BRAFV600E expression. Most dermal and compound nevi had > 50% of p16(+) cells. BRAFV600E dysplastic nevi had a low number of p16(+) cells. Nevi without BRAFV600E (WT), had 90% of cells p16(+). In 60% of in situ and primary melanomas, there was a low number of cells of p16(+). Fifty percent of WT metastatic melanoma and 33% of BRAFV600E showed a high level of p16. The number of Ki67(+) cells in dysplastic nevi was very low. In 25% of BRAFV600E melanomas in situ and 55% of WT, > 10% cells were Ki67(+). All BRAFV600E primary melanomas and 66% of WT had > 10% Ki67(+) cells. Twenty percent of BRAFV600E and WT metastases had > 10% of Ki67(+), however, 62% of BRAFV600E and 32% of WT samples had > 50% of Ki67(+) cells. Conclusions BRAFV600E and p16 are more frequent in nevi than in melanoma in vivo. A significantly higher p16 expression was observed in mutated nevi than in WT, while in melanoma it was just the opposite. The proliferation rate of melanoma cells negatively correlated with p16 expression.
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17
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Heidenreich B, Kumar R. Altered TERT promoter and other genomic regulatory elements: occurrence and impact. Int J Cancer 2017; 141:867-876. [PMID: 28407294 DOI: 10.1002/ijc.30735] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 03/28/2017] [Accepted: 03/31/2017] [Indexed: 12/19/2022]
Abstract
Study of genetic alterations, inherited or acquired, that increase the risk or drive cancers and many other diseases had remained mostly confined to coding sequences of the human genome. Data from genome wide associations studies, development of the Encyclopedia of DNA Elements (ENCODE), and a spurt in detection of driver somatic mutations have shifted focus towards noncoding regions of the human genome. The majority of genetic variants robustly associated with cancers and other syndromes identified through genome wide studies are located within noncoding regulatory regions of the genome. Genome wide techniques have put an emphasis on the role of three-dimensional chromosomal structures and cis-acting elements in regulations of different genes. The variants within noncoding genomic regions can potentially alter a number of regulatory elements including promoters, enhancers, insulators, noncoding long RNAs and others that affect cancers and various diseases through altered expression of critical genes. With effect of genetic alterations within regulatory elements dependent on other partner molecules like transcription factors and histone marks, an understanding of such modifications can potentially identify extended therapeutic targets. That concept has been augmented by the detection of driver somatic noncoding mutations within the promoter region of the telomerase reverse transcriptase (TERT) gene in different cancers. The acquired somatic noncoding mutations within different regulatory elements are now being reported in different cancers with an increased regularity. In this review we discuss the occurrence and impact of germline and somatic alterations within the TERT promoter and other genomic regulatory elements.
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Affiliation(s)
- Barbara Heidenreich
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Rajiv Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany.,German Consortium for Translational Research (DKTK), German Cancer Research Center, Heidelberg, Germany
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18
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Soares J, Raimundo L, Pereira NAL, Monteiro Â, Gomes S, Bessa C, Pereira C, Queiroz G, Bisio A, Fernandes J, Gomes C, Reis F, Gonçalves J, Inga A, Santos MMM, Saraiva L. Reactivation of wild-type and mutant p53 by tryptophanolderived oxazoloisoindolinone SLMP53-1, a novel anticancer small-molecule. Oncotarget 2016; 7:4326-43. [PMID: 26735173 PMCID: PMC4826208 DOI: 10.18632/oncotarget.6775] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 11/28/2015] [Indexed: 12/28/2022] Open
Abstract
Restoration of the p53 pathway, namely by reactivation of mutant (mut) p53, represents a valuable anticancer strategy. Herein, we report the identification of the enantiopure tryptophanol-derived oxazoloisoindolinone SLMP53-1 as a novel reactivator of wild-type (wt) and mut p53, using a yeast-based screening strategy. SLMP53-1 has a p53-dependent anti-proliferative activity in human wt and mut p53R280K-expressing tumor cells. Additionally, SLMP53-1 enhances p53 transcriptional activity and restores wt-like DNA binding ability to mut p53R280K. In wt/mut p53-expressing tumor cells, SLMP53-1 triggers p53 transcription-dependent and mitochondrial apoptotic pathways involving BAX, and wt/mut p53 mitochondrial translocation. SLMP53-1 inhibits the migration of wt/mut p53-expressing tumor cells, and it shows promising p53-dependent synergistic effects with conventional chemotherapeutics. In xenograft mice models, SLMP53-1 inhibits the growth of wt/mut p53-expressing tumors, but not of p53-null tumors, without apparent toxicity. Collectively, besides the potential use of SLMP53-1 as anticancer drug, the tryptophanol-derived oxazoloisoindolinone scaffold represents a promissing starting point for the development of effective p53-reactivating drugs.
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Affiliation(s)
- Joana Soares
- UCIBIO/REQUIMTE, Universidade do Porto, Porto, Portugal.,Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Liliana Raimundo
- UCIBIO/REQUIMTE, Universidade do Porto, Porto, Portugal.,Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Nuno A L Pereira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
| | - Ângelo Monteiro
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
| | - Sara Gomes
- UCIBIO/REQUIMTE, Universidade do Porto, Porto, Portugal.,Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Cláudia Bessa
- UCIBIO/REQUIMTE, Universidade do Porto, Porto, Portugal.,Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Clara Pereira
- UCIBIO/REQUIMTE, Universidade do Porto, Porto, Portugal.,Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Glória Queiroz
- Laboratório de Farmacologia, Departamento de Ciências do Medicamento, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Alessandra Bisio
- CIBIO, Centre for Integrative Biology, Laboratory of Transcriptional Networks, University of Trento, Trento, Italy
| | - João Fernandes
- Laboratório de Farmacologia e Terapêutica Experimental, IBILI, Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal
| | - Célia Gomes
- Laboratório de Farmacologia e Terapêutica Experimental, IBILI, Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal
| | - Flávio Reis
- Laboratório de Farmacologia e Terapêutica Experimental, IBILI, Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal
| | - Jorge Gonçalves
- Laboratório de Farmacologia, Departamento de Ciências do Medicamento, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Alberto Inga
- CIBIO, Centre for Integrative Biology, Laboratory of Transcriptional Networks, University of Trento, Trento, Italy
| | - Maria M M Santos
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
| | - Lucília Saraiva
- UCIBIO/REQUIMTE, Universidade do Porto, Porto, Portugal.,Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
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19
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Bisio A, Latorre E, Andreotti V, Bressac-de Paillerets B, Harland M, Scarra GB, Ghiorzo P, Spitale RC, Provenzani A, Inga A. The 5'-untranslated region of p16INK4a melanoma tumor suppressor acts as a cellular IRES, controlling mRNA translation under hypoxia through YBX1 binding. Oncotarget 2016; 6:39980-94. [PMID: 26498684 PMCID: PMC4741874 DOI: 10.18632/oncotarget.5387] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 10/05/2015] [Indexed: 12/20/2022] Open
Abstract
CDKN2A/p16INK4a is an essential tumor suppressor gene that controls cell cycle progression and replicative senescence. It is also the main melanoma susceptibility gene. Here we report that p16INK4a 5'UTR mRNA acts as a cellular Internal Ribosome Entry Site (IRES). The potential for p16INK4a 5'UTR to drive cap-independent translation was evaluated by dual-luciferase assays using bicistronic and monocistronic vectors. Results of reporters' relative activities coupled to control analyses for actual bicistronic mRNA transcription, indicated that the wild type p16INK4a 5'UTR could stimulate cap-independent translation. Notably, hypoxic stress and the treatment with mTOR inhibitors enhanced the translation-stimulating property of p16INK4a 5'UTR. RNA immunoprecipitation performed in melanoma-derived SK-Mel-28 and in a patient-derived lymphoblastoid cell line indicated that YBX1 can bind the wild type p16INK4a mRNA increasing its translation efficiency, particularly during hypoxic stress. Modulation of YBX1 expression further supported its involvement in cap-independent translation of the wild type p16INK4a but not a c.-42T>A variant. RNA SHAPE assays revealed local flexibility changes for the c.-42T>A variant at the predicted YBX1 binding site region. Our results indicate that p16INK4a 5'UTR contains a cellular IRES that can enhance mRNA translation efficiency, in part through YBX1.
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Affiliation(s)
- Alessandra Bisio
- Laboratory of Transcriptional Networks, Centre for Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Elisa Latorre
- Laboratory of Genomic Screening, Centre for Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Virginia Andreotti
- Laboratory of Genetics of Rare Hereditary Cancers, DiMI, University of Genoa, Italy and IRCCS AOU San Martino-IST, Genoa, Italy
| | | | - Mark Harland
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Giovanna Bianchi Scarra
- Laboratory of Genetics of Rare Hereditary Cancers, DiMI, University of Genoa, Italy and IRCCS AOU San Martino-IST, Genoa, Italy
| | - Paola Ghiorzo
- Laboratory of Genetics of Rare Hereditary Cancers, DiMI, University of Genoa, Italy and IRCCS AOU San Martino-IST, Genoa, Italy
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, USA
| | - Alessandro Provenzani
- Laboratory of Genomic Screening, Centre for Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Alberto Inga
- Laboratory of Transcriptional Networks, Centre for Integrative Biology, CIBIO, University of Trento, Trento, Italy
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20
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Al-Ali R, González-Sarmiento R. Proximity of AUG sequences to initiation codon in genomic 5' UTR regulates mammalian protein expression. Gene 2016; 594:268-271. [PMID: 27613142 DOI: 10.1016/j.gene.2016.08.052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 08/24/2016] [Accepted: 08/31/2016] [Indexed: 01/28/2023]
Abstract
Protein expression can be controlled via AUG sequences located upstream to the initiation codon in the 5' end untranslated region (5' UTR). Our study was focused on the effect of distance between the initiation codon and the first upstream AUG. An inhibitory effect on protein expression was established when AUG exists in 5' UTR, and this effect is increased when multiple AUG sequences occur there. The study was performed with ATG16L2, a non-lethal gene with no introns or upstream AUG sequence to avoid any interference. New mutations were generated at different locations within the promoter region of ATG16L2 gene and added to a plasmid construct containing a luciferase gene reporter gene. The results show a clear relationship between the distance of the novel AUGs from initiation codon and protein expression. The inhibitory effect was even stronger when multiple AUG sequences were present in 5' UTR.
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Affiliation(s)
- Ruslan Al-Ali
- Unidad de Medicina Molecular-IBSAL, Departamento de Medicina, Universidad de Salamanca-Hospital Universitario de Salamanca-CSIC, Salamanca, Spain
| | - Rogelio González-Sarmiento
- Unidad de Medicina Molecular-IBSAL, Departamento de Medicina, Universidad de Salamanca-Hospital Universitario de Salamanca-CSIC, Salamanca, Spain; Instituto de Biología Molecular y Celular del Cáncer (IBMCC), Universidad de Salamanca-CSIC, Salamanca, Spain.
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21
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Bruno W, Pastorino L, Ghiorzo P, Andreotti V, Martinuzzi C, Menin C, Elefanti L, Stagni C, Vecchiato A, Rodolfo M, Maurichi A, Manoukian S, De Giorgi V, Savarese I, Gensini F, Borgognoni L, Testori A, Spadola G, Mandalà M, Imberti G, Savoia P, Astrua C, Ronco AM, Farnetti A, Tibiletti MG, Lombardo M, Palmieri G, Ayala F, Ascierto P, Ghigliotti G, Muggianu M, Spagnolo F, Picasso V, Tanda ET, Queirolo P, Bianchi-Scarrà G. Multiple primary melanomas (MPMs) and criteria for genetic assessment: MultiMEL, a multicenter study of the Italian Melanoma Intergroup. J Am Acad Dermatol 2016; 74:325-32. [PMID: 26775776 DOI: 10.1016/j.jaad.2015.09.053] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 09/24/2015] [Accepted: 09/29/2015] [Indexed: 12/20/2022]
Abstract
BACKGROUND Multiple primary melanoma (MPM), in concert with a positive family history, is a predictor of cyclin-dependent kinase (CDK) inhibitor 2A (CDKN2A) germline mutations. A rule regarding the presence of either 2 or 3 or more cancer events (melanoma and pancreatic cancer) in low or high melanoma incidence populations, respectively, has been established to select patients for genetic referral. OBJECTIVE We sought to determine the CDKN2A/CDK4/microphthalmia-associated transcription factor mutation rate among Italian patients with MPM to appropriately direct genetic counseling regardless of family history. METHODS In all, 587 patients with MPM and an equal number with single primary melanomas and control subjects were consecutively enrolled at the participating centers and tested for CDKN2A, CDK4, and microphthalmia-associated transcription factor. RESULTS CDKN2A germline mutations were found in 19% of patients with MPM versus 4.4% of patients with single primary melanoma. In familial MPM cases the mutation rate varied from 36.6% to 58.8%, whereas in sporadic MPM cases it varied from 8.2% to 17.6% in patients with 2 and 3 or more melanomas, respectively. The microphthalmia-associated transcription factor E318K mutation accounted for 3% of MPM cases altogether. LIMITATIONS The study was hospital based, not population based. Rare novel susceptibility genes were not tested. CONCLUSION Italian patients who developed 2 melanomas, even in situ, should be referred for genetic counseling even in the absence of family history.
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Affiliation(s)
- William Bruno
- Department of Internal Medicine, Medical Specialties and Surgical Science and Integrated Diagnostics, University of Genoa, Genoa, Italy; Genetics of Rare Cancers, IRCCS AOU San Martino-IST Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - Lorenza Pastorino
- Department of Internal Medicine, Medical Specialties and Surgical Science and Integrated Diagnostics, University of Genoa, Genoa, Italy; Genetics of Rare Cancers, IRCCS AOU San Martino-IST Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy.
| | - Paola Ghiorzo
- Department of Internal Medicine, Medical Specialties and Surgical Science and Integrated Diagnostics, University of Genoa, Genoa, Italy; Genetics of Rare Cancers, IRCCS AOU San Martino-IST Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - Virginia Andreotti
- Department of Internal Medicine, Medical Specialties and Surgical Science and Integrated Diagnostics, University of Genoa, Genoa, Italy
| | - Claudia Martinuzzi
- Department of Internal Medicine, Medical Specialties and Surgical Science and Integrated Diagnostics, University of Genoa, Genoa, Italy; Department of Internal Medicine, Medical Specialties and Surgical Science and Integrated Diagnostics, University of Genoa, Genoa, Italy
| | - Chiara Menin
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, Istituto Oncologico Veneto (IOV)-IRCCS, Padua, Italy
| | - Lisa Elefanti
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, Istituto Oncologico Veneto (IOV)-IRCCS, Padua, Italy
| | - Camilla Stagni
- Section of Oncology and Immunology, Department of Surgery, Oncology, and Gastroenterology, University of Padua, Padua, Italy
| | - Antonella Vecchiato
- Melanoma and Soft Tissue Sarcoma Unit, Veneto Institute of Oncology, IOV-IRCCS, Padua, Italy
| | - Monica Rodolfo
- Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Andrea Maurichi
- Melanoma and Sarcoma Surgery Unit, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Siranoush Manoukian
- Medical Genetics Unit, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | | | - Imma Savarese
- Department of Dermatology, University of Florence, Florence, Italy
| | - Francesca Gensini
- Unit of Medical Genetics, Department of Biomedical Experimental and Clinical Sciences, University of Florence, Florence, Italy
| | - Lorenzo Borgognoni
- Plastic Surgery Unit, Regional Melanoma Referral Center, Santa Maria Annunziata Hospital, Florence, Italy
| | - Alessandro Testori
- Division of Dermatoncological Surgery, European Institute of Oncology, Milan, Italy
| | - Giuseppe Spadola
- Division of Dermatoncological Surgery, European Institute of Oncology, Milan, Italy
| | - Mario Mandalà
- Medical Oncology Unit, Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | | | - Paola Savoia
- Department of Medical Sciences, Dermatology Section, University of Turin, Turin, Italy
| | - Chiara Astrua
- Department of Medical Sciences, Dermatology Section, University of Turin, Turin, Italy
| | - Anna Maria Ronco
- Dermatoncological Surgery Unit, Presidio Sanitario Gradenigo, Turin, Italy
| | | | | | | | - Giuseppe Palmieri
- Cancer Genetics Unit, Institute of Biomolecular Chemistry, National Research Council, Sassari, Italy
| | - Fabrizio Ayala
- Department of Melanoma, National Cancer Institute Pascale Foundation, Naples, Italy
| | - Paolo Ascierto
- Department of Melanoma, National Cancer Institute Pascale Foundation, Naples, Italy
| | - Giovanni Ghigliotti
- Dermatology Unit, IRCCS AOU San Martino-IST Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - Marisa Muggianu
- Department of Plastic and Reconstructive Surgery, IRCCS AOU San Martino-IST Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - Francesco Spagnolo
- Department of Plastic and Reconstructive Surgery, IRCCS AOU San Martino-IST Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - Virginia Picasso
- Department of Medical Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Azienda Ospedaliera Universitaria (AOU) San Martino-Istituto Nazionale dei Tumori (IST) Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - Enrica Teresa Tanda
- Department of Medical Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Azienda Ospedaliera Universitaria (AOU) San Martino-Istituto Nazionale dei Tumori (IST) Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - Paola Queirolo
- Department of Medical Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Azienda Ospedaliera Universitaria (AOU) San Martino-Istituto Nazionale dei Tumori (IST) Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - Giovanna Bianchi-Scarrà
- Department of Internal Medicine, Medical Specialties and Surgical Science and Integrated Diagnostics, University of Genoa, Genoa, Italy; Genetics of Rare Cancers, IRCCS AOU San Martino-IST Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
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22
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Zhang T, Dutton-Regester K, Brown KM, Hayward NK. The genomic landscape of cutaneous melanoma. Pigment Cell Melanoma Res 2016; 29:266-83. [PMID: 26833684 DOI: 10.1111/pcmr.12459] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 01/25/2016] [Indexed: 12/31/2022]
Abstract
Somatic mutation analysis of melanoma has been performed at the single gene level extensively over the past several decades. This has provided considerable insight into the critical pathways controlling melanoma initiation and progression. During the last 5 yr, next-generation sequencing (NGS) has enabled even more comprehensive mutational screening at the level of multigene panels, exomes and genomes. These studies have uncovered many new and unexpected players in melanoma development. The recent landmark study from The Cancer Genome Atlas (TCGA) consortium describing the genomic architecture of 333 cutaneous melanomas provides the largest and broadest analysis to date on the somatic aberrations underlying melanoma genesis. It thus seems timely to review the mutational landscape of melanoma and highlight the key genes and cellular pathways that appear to drive this cancer.
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Affiliation(s)
- Tongwu Zhang
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Ken Dutton-Regester
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
- Oncogenomics Laboratory, QIMR Berghofer Medical Research Institute, Herston, Qld, Australia
| | - Kevin M Brown
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Nicholas K Hayward
- Oncogenomics Laboratory, QIMR Berghofer Medical Research Institute, Herston, Qld, Australia
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23
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Mucaki EJ, Caminsky NG, Perri AM, Lu R, Laederach A, Halvorsen M, Knoll JHM, Rogan PK. A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer. BMC Med Genomics 2016; 9:19. [PMID: 27067391 PMCID: PMC4828881 DOI: 10.1186/s12920-016-0178-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 03/15/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Sequencing of both healthy and disease singletons yields many novel and low frequency variants of uncertain significance (VUS). Complete gene and genome sequencing by next generation sequencing (NGS) significantly increases the number of VUS detected. While prior studies have emphasized protein coding variants, non-coding sequence variants have also been proven to significantly contribute to high penetrance disorders, such as hereditary breast and ovarian cancer (HBOC). We present a strategy for analyzing different functional classes of non-coding variants based on information theory (IT) and prioritizing patients with large intragenic deletions. METHODS We captured and enriched for coding and non-coding variants in genes known to harbor mutations that increase HBOC risk. Custom oligonucleotide baits spanning the complete coding, non-coding, and intergenic regions 10 kb up- and downstream of ATM, BRCA1, BRCA2, CDH1, CHEK2, PALB2, and TP53 were synthesized for solution hybridization enrichment. Unique and divergent repetitive sequences were sequenced in 102 high-risk, anonymized patients without identified mutations in BRCA1/2. Aside from protein coding and copy number changes, IT-based sequence analysis was used to identify and prioritize pathogenic non-coding variants that occurred within sequence elements predicted to be recognized by proteins or protein complexes involved in mRNA splicing, transcription, and untranslated region (UTR) binding and structure. This approach was supplemented by in silico and laboratory analysis of UTR structure. RESULTS 15,311 unique variants were identified, of which 245 occurred in coding regions. With the unified IT-framework, 132 variants were identified and 87 functionally significant VUS were further prioritized. An intragenic 32.1 kb interval in BRCA2 that was likely hemizygous was detected in one patient. We also identified 4 stop-gain variants and 3 reading-frame altering exonic insertions/deletions (indels). CONCLUSIONS We have presented a strategy for complete gene sequence analysis followed by a unified framework for interpreting non-coding variants that may affect gene expression. This approach distills large numbers of variants detected by NGS to a limited set of variants prioritized as potential deleterious changes.
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Affiliation(s)
- Eliseos J Mucaki
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada
| | - Natasha G Caminsky
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada
| | - Ami M Perri
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada
| | - Ruipeng Lu
- Department of Computer Science, Faculty of Science, Western University, London, N6A 2C1, Canada
| | - Alain Laederach
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599-3290, USA
| | - Matthew Halvorsen
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Joan H M Knoll
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, N6A 2C1, Canada
- Cytognomix Inc., London, Canada
| | - Peter K Rogan
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada.
- Department of Computer Science, Faculty of Science, Western University, London, N6A 2C1, Canada.
- Cytognomix Inc., London, Canada.
- Department of Oncology, Schulich School of Medicine and Dentistry, Western University, London, N6A 2C1, Canada.
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24
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Andreotti V, Bisio A, Bressac-de Paillerets B, Harland M, Cabaret O, Newton-Bishop J, Pastorino L, Bruno W, Bertorelli R, De Sanctis V, Provenzani A, Menin C, Fronza G, Queirolo P, Spitale RC, Bianchi-Scarrà G, Inga A, Ghiorzo P. The CDKN2A/p16(INK) (4a) 5'UTR sequence and translational regulation: impact of novel variants predisposing to melanoma. Pigment Cell Melanoma Res 2016; 29:210-21. [PMID: 26581427 DOI: 10.1111/pcmr.12444] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/13/2015] [Indexed: 12/20/2022]
Abstract
Many variants of uncertain functional significance in cancer susceptibility genes lie in regulatory regions, and clarifying their association with disease risk poses significant challenges. We studied 17 germline variants (nine of which were novel) in the CDKN2A 5'UTR with independent approaches, which included mono and bicistronic reporter assays, Western blot of endogenous protein, and allelic representation after polysomal profiling to investigate their impact on CDKN2A mRNA translation regulation. Two of the novel variants (c.-27del23, c.-93-91delAGG) were classified as causal mutations (score ≥3), along with the c.-21C>T, c.-34G>T, and c.-56G>T, which had already been studied by a subset of assays. The novel c.-42T>A as well as the previously described c.-67G>C were classified as potential mutations (score 1 or 2). The remaining variants (c.-14C>T, c.-20A>G, c.-25C>T+c.-180G>A, c.-30G>A, c.-40C>T, c.-45G>A, c.-59C>G, c.-87T>A, c.-252A>T) were classified as neutral (score 0). In conclusion, we found evidence that nearly half of the variants found in this region had a negative impact on CDKN2A mRNA translation, supporting the hypothesis that 5'UTR can act as a cellular Internal Ribosome Entry Site (IRES) to modulate p16(INK) (4a) translation.
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Affiliation(s)
- Virginia Andreotti
- Department of Internal Medicine and Medical Specialties, DiMI, University of Genoa, Genoa, Italy
- Genetics of Rare Cancers, IRCCS AOU San Martino-IST, Genoa, Italy
| | - Alessandra Bisio
- Laboratory of Transcriptional Networks, Centre for Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | | | - Mark Harland
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Odile Cabaret
- Department of Biopathology and INSERM U1186, Gustave Roussy, Villejuif, France
| | - Julia Newton-Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Lorenza Pastorino
- Department of Internal Medicine and Medical Specialties, DiMI, University of Genoa, Genoa, Italy
- Genetics of Rare Cancers, IRCCS AOU San Martino-IST, Genoa, Italy
| | - William Bruno
- Department of Internal Medicine and Medical Specialties, DiMI, University of Genoa, Genoa, Italy
- Genetics of Rare Cancers, IRCCS AOU San Martino-IST, Genoa, Italy
| | - Roberto Bertorelli
- NGS Core Facility, Centre for Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Veronica De Sanctis
- NGS Core Facility, Centre for Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Alessandro Provenzani
- Laboratory of Genomic Screening, Centre for Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Chiara Menin
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | | | - Paola Queirolo
- Medical Oncology Unit, IRCCS AOU San Martino-IST, Genoa, Italy
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, USA
| | - Giovanna Bianchi-Scarrà
- Department of Internal Medicine and Medical Specialties, DiMI, University of Genoa, Genoa, Italy
- Genetics of Rare Cancers, IRCCS AOU San Martino-IST, Genoa, Italy
| | - Alberto Inga
- Laboratory of Transcriptional Networks, Centre for Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Paola Ghiorzo
- Department of Internal Medicine and Medical Specialties, DiMI, University of Genoa, Genoa, Italy
- Genetics of Rare Cancers, IRCCS AOU San Martino-IST, Genoa, Italy
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25
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D'Agostino VG, Lal P, Mantelli B, Tiedje C, Zucal C, Thongon N, Gaestel M, Latorre E, Marinelli L, Seneci P, Amadio M, Provenzani A. Dihydrotanshinone-I interferes with the RNA-binding activity of HuR affecting its post-transcriptional function. Sci Rep 2015; 5:16478. [PMID: 26553968 PMCID: PMC4639722 DOI: 10.1038/srep16478] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 10/14/2015] [Indexed: 01/07/2023] Open
Abstract
Post-transcriptional regulation is an essential determinant of gene expression programs in physiological and pathological conditions. HuR is a RNA-binding protein that orchestrates the stabilization and translation of mRNAs, critical in inflammation and tumor progression, including tumor necrosis factor-alpha (TNF). We identified the low molecular weight compound 15,16-dihydrotanshinone-I (DHTS), well known in traditional Chinese medicine practice, through a validated high throughput screening on a set of anti-inflammatory agents for its ability to prevent HuR:RNA complex formation. We found that DHTS interferes with the association step between HuR and the RNA with an equilibrium dissociation constant in the nanomolar range in vitro (Ki = 3.74 ± 1.63 nM). In breast cancer cell lines, short term exposure to DHTS influences mRNA stability and translational efficiency of TNF in a HuR-dependent manner and also other functional readouts of its post-transcriptional control, such as the stability of selected pre-mRNAs. Importantly, we show that migration and sensitivity of breast cancer cells to DHTS are modulated by HuR expression, indicating that HuR is among the preferential intracellular targets of DHTS. Here, we disclose a previously unrecognized molecular mechanism exerted by DHTS, opening new perspectives to therapeutically target the HuR mediated, post-transcriptional control in inflammation and cancer cells.
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Affiliation(s)
| | - Preet Lal
- Centre For Integrative Biology (CIBIO), University of Trento, Trento, 38123, Italy
| | - Barbara Mantelli
- Centre For Integrative Biology (CIBIO), University of Trento, Trento, 38123, Italy
| | - Christopher Tiedje
- Department of Biochemistry, Hannover Medical University, Hannover, D-30625, Germany
| | - Chiara Zucal
- Centre For Integrative Biology (CIBIO), University of Trento, Trento, 38123, Italy
| | - Natthakan Thongon
- Centre For Integrative Biology (CIBIO), University of Trento, Trento, 38123, Italy
| | - Matthias Gaestel
- Department of Biochemistry, Hannover Medical University, Hannover, D-30625, Germany
| | - Elisa Latorre
- Centre For Integrative Biology (CIBIO), University of Trento, Trento, 38123, Italy
| | - Luciana Marinelli
- Department of Pharmacy, University of Naples "Federico II", Naples, 80131, Italy
| | | | - Marialaura Amadio
- Department of Drug Sciences, University of Pavia, Pavia, 27100, Italy
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Burgstaller-Muehlbacher S, Marko M, Müller C, Wendt J, Pehamberger H, Okamoto I. Novel CDKN2A mutations in Austrian melanoma patients. Melanoma Res 2015; 25:412-20. [PMID: 26225579 DOI: 10.1097/cmr.0000000000000179] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
CDKN2A is the most prominent familial melanoma gene, with mutations occurring in up to 40% of the families. Numerous mutations in the gene are known, several of them representing regional founder mutations. We sought to determine, for the first time, germline mutations in CDKN2A in Austria to identify novel mutations. In total, 700 individuals (136 patients with a positive family history and 164 with at least two primary melanomas as the high-risk groups; 200 with single primary melanomas; and 200 healthy individuals as the control groups) were Sanger sequenced for CDKN2A exon 1α, 1β, and 2. The 136 patients with affected relatives were also sequenced for CDK4 exon 2. We found the disease-associated mutations p.R24P (8×), p.N71T (1×), p.G101W (1×), and p.V126D (1×) in the group with affected relatives and p.R24P (2×) in the group with several primary melanomas. Furthermore, we discovered four mutations of unknown significance, two of which were novel: p.A34V and c.151-4 G>C, respectively. Computational effect prediction suggested p.A34V as conferring a high risk for melanoma, whereas c.151-4 G>C, although being predicted as a splice site mutation by MutationTaster, could not functionally be confirmed to alter splicing. Moreover, computational effect prediction confirmed accumulation of high-penetrance mutations in high-risk groups, whereas mutations of unknown significance were distributed across all groups. p.R24P is the most common high-risk mutation in Austria. In addition, we discovered two new mutations in Austrian melanoma patients, p.A34V and c.151-4 G>C, respectively.
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Analysis of sequence variants in the 3'UTR of CDKN2A gene in melanoma patients. Contemp Oncol (Pozn) 2015; 19:276-9. [PMID: 26557774 PMCID: PMC4631302 DOI: 10.5114/wo.2015.54227] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 07/15/2015] [Accepted: 08/20/2015] [Indexed: 12/28/2022] Open
Abstract
Background The 3'UTR region plays a crucial role in regulating gene expression at posttranscriptional levels. Any changes in sequence in this region can cause numerous pathologies and can also lead to tumour development. The most common changes reported in in the CDKN2A gene are the 148Ala/Thr in exon 2 and 500C>G and 540C>T in the 3'UTR region. They are suspected of having a great impact on cancer progression. Since the role of these sequence variants in the Polish population in the development of melanoma has not been confirmed, the importance of 3'UTR polymorphisms in the regulation of gene expression was tested. Material and methods First, genetic analysis in a group of 285 melanoma patients was performed and the obtained results were correlated with the clinical course of melanoma. Then vectors carrying 3'UTR sequence variants were prepared and the level expression of the reported gene was measured. Results Within this study no correlation between the presence of 148Ala/Thr polymorphism and cancer in the family was observed. There was a correlation between the presence of this polymorphism and breast cancer and melanoma in the same patient. There was no correlation between 500C>G polymorphism and tumour localisation, age of diagnosis, and type of cancer in patients’ family, but a correlation between the percentage of patients dying and the 500C>G variant was observed. Conclusion The results of functional tests indicated that the presence of polymorphism in the 3'UTR region of the CDKN2A gene resulted in changes in the level of reporter gene expression.
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28
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Palmieri G, Colombino M, Casula M, Budroni M, Manca A, Sini MC, Lissia A, Stanganelli I, Ascierto PA, Cossu A. Epidemiological and genetic factors underlying melanoma development in Italy. Melanoma Manag 2015; 2:149-163. [PMID: 30190844 PMCID: PMC6094587 DOI: 10.2217/mmt.15.12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Among human cancers, melanoma remains one of the malignancies with an ever-growing incidence in white populations. Recent advances in biological and immunological therapeutic approaches as well as increased efforts for secondary prevention are contributing to improve the survival rates. It is likely that a significant fall in mortality rates for melanoma will be achieved by further increase of the early detection through a more accurate selection of the higher-risk individuals (i.e., carriers of predisposing genetic alterations). A similar scenario occurs in Italy. In the present review, we have considered data on incidence, survival and mortality rates of melanoma in Italian population, including evaluation of the main risk factors and genetic mutations underlying disease susceptibility.
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Affiliation(s)
- Giuseppe Palmieri
- Institute of Biomolecular Chemistry, National Research Council (CNR), Sassari, Italy
| | - Maria Colombino
- Institute of Biomolecular Chemistry, National Research Council (CNR), Sassari, Italy
| | - Milena Casula
- Institute of Biomolecular Chemistry, National Research Council (CNR), Sassari, Italy
| | - Mario Budroni
- Department of Pathology, Hospital-University Health Unit (AOU), Sassari, Italy
| | - Antonella Manca
- Institute of Biomolecular Chemistry, National Research Council (CNR), Sassari, Italy
| | - Maria Cristina Sini
- Institute of Biomolecular Chemistry, National Research Council (CNR), Sassari, Italy
| | - Amelia Lissia
- Department of Pathology, Hospital-University Health Unit (AOU), Sassari, Italy
| | - Ignazio Stanganelli
- Skin Cancer Unit, Istituto Scientifico Romagnolo Tumori (IRST), Meldola, Italy
| | - Paolo A Ascierto
- Istituto Nazionale Tumori (INT), Fondazione G. Pascale, Naples, Italy
| | - Antonio Cossu
- Department of Pathology, Hospital-University Health Unit (AOU), Sassari, Italy
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Re-annotation of presumed noncoding disease/trait-associated genetic variants by integrative analyses. Sci Rep 2015; 5:9453. [PMID: 25819875 PMCID: PMC4377585 DOI: 10.1038/srep09453] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 03/02/2015] [Indexed: 11/08/2022] Open
Abstract
Using RefSeq annotations, most disease/trait-associated genetic variants identified by genome-wide association studies (GWAS) appear to be located within intronic or intergenic regions, which makes it difficult to interpret their functions. We reassessed GWAS-Associated single-nucleotide polymorphisms (herein termed as GASs) for their potential functionalities using integrative approaches. 8834 of 9184 RefSeq “noncoding” GASs were reassessed to have potential regulatory functionalities. As examples, 3 variants (rs3130320, rs3806932 and rs6890853) were shown to have regulatory properties in HepG2, A549 and 293T cells. Except rs3130320 as a known expression quantitative trait loci (eQTL), rs3806932 and rs6890853 were not reported as eQTLs in previous reports. 1999 of 9184 “noncoding” GASs were re-annotated to the promoters or intragenic regions using Ensembl, UCSC and AceView gene annotations but they were not annotated into corresponding regions in RefSeq database. Moreover, these GAS-harboring genes were broadly expressed across different tissues and a portion of them was expressed in a tissue-specific manner, suggesting that they could be functional. Collectively, our study demonstrates the benefits of using integrative analyses to interpret genetic variants and may help to predict or explain disease susceptibility more accurately and comprehensively.
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Ozretić P, Bisio A, Musani V, Trnski D, Sabol M, Levanat S, Inga A. Regulation of human PTCH1b expression by different 5' untranslated region cis-regulatory elements. RNA Biol 2015; 12:290-304. [PMID: 25826662 PMCID: PMC4615190 DOI: 10.1080/15476286.2015.1008929] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
PTCH1 gene codes for a 12-pass transmembrane receptor with a negative regulatory role in the Hedgehog-Gli signaling pathway. PTCH1 germline mutations cause Gorlin syndrome, a disorder characterized by developmental abnormalities and tumor susceptibility. The autosomal dominant inheritance, and the evidence for PTCH1 haploinsufficiency, suggests that fine-tuning systems of protein patched homolog 1 (PTC1) levels exist to properly regulate the pathway. Given the role of 5' untranslated region (5'UTR) in protein expression, our aim was to thoroughly explore cis-regulatory elements in the 5'UTR of PTCH1 transcript 1b. The (CGG)n polymorphism was the main potential regulatory element studied so far but with inconsistent results and no clear association between repeat number and disease risk. Using luciferase reporter constructs in human cell lines here we show that the number of CGG repeats has no strong impact on gene expression, both at mRNA and protein levels. We observed variability in the length of 5'UTR and changes in abundance of the associated transcripts after pathway activation. We show that upstream AUG codons (uAUGs) present only in longer 5'UTRs could negatively regulate the amount of PTC1 isoform L (PTC1-L). The existence of an internal ribosome entry site (IRES) observed using different approaches and mapped in the region comprising the CGG repeats, would counteract the effect of the uAUGs and enable synthesis of PTC1-L under stressful conditions, such as during hypoxia. Higher relative translation efficiency of PTCH1b mRNA in HEK 293T cultured hypoxia was observed by polysomal profiling and Western blot analyses. All our results point to an exceptionally complex and so far unexplored role of 5'UTR PTCH1b cis-element features in the regulation of the Hedgehog-Gli signaling pathway.
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Key Words
- 5'UTR
- 5′UTR, 5′ untranslated region
- CGG repeats
- Fluc, Firefly luciferase
- Hedgehog-Gli
- Hh-Gli, Hedgehog-Gli
- IRES
- IRES, internal ribosome entry site
- POL, polysome-associated
- PTC1-L, protein patched homolog 1
- PTCH1
- Rluc, Renilla luciferase
- SUB, subpolysomal
- isoform L PTCH1b, Patched 1 gene, transcript variant 1b
- uAUG
- uAUG, upstream AUG codon
- uORF
- uORF, upstream open reading frame
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Affiliation(s)
- Petar Ozretić
- Laboratory for Hereditary Cancer; Division of Molecular Medicine; Ruđer Bošković Institute; Zagreb, Croatia
| | - Alessandra Bisio
- Laboratory of Transcriptional Networks; Center for Integrative Biology; University of Trento; Mattarello, Trento, Italy
| | - Vesna Musani
- Laboratory for Hereditary Cancer; Division of Molecular Medicine; Ruđer Bošković Institute; Zagreb, Croatia
| | - Diana Trnski
- Laboratory for Hereditary Cancer; Division of Molecular Medicine; Ruđer Bošković Institute; Zagreb, Croatia
| | - Maja Sabol
- Laboratory for Hereditary Cancer; Division of Molecular Medicine; Ruđer Bošković Institute; Zagreb, Croatia
| | - Sonja Levanat
- Laboratory for Hereditary Cancer; Division of Molecular Medicine; Ruđer Bošković Institute; Zagreb, Croatia
- Correspondence to: Sonja Levanat; ; Alberto Inga;
| | - Alberto Inga
- Laboratory of Transcriptional Networks; Center for Integrative Biology; University of Trento; Mattarello, Trento, Italy
- Correspondence to: Sonja Levanat; ; Alberto Inga;
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Prabhakara S, Anbazhagan K. Molecular analysis of PRRT2 gene in a case of paroxysmal kinesigenic dyskinesia patient. Ann Indian Acad Neurol 2014; 17:459-62. [PMID: 25506174 PMCID: PMC4251026 DOI: 10.4103/0972-2327.144039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 02/03/2014] [Accepted: 02/26/2014] [Indexed: 12/03/2022] Open
Abstract
Paroxysmal kinesigenic dyskinesia (PKD) is an abnormal involuntary movement that is episodic or intermittent, with sudden onset, and the attacks are induced by sudden movement. Mutations in proline-rich transmembrane protein 2 (PRRT2) gene have been implicated in the cause of this disorder. This study presents a case of PKD on the basis of clinical findings supported and evidences obtained through a mutational analysis. Sequencing of all the exons of PRRT2 gene revealed a frameshift mutation (p.R217Pfs*8) in exon 2 and a novel transition mutation (c.244C > T) in 5′-untranslated region (UTR). Though mutations in PRRT2 gene are well-established in PKD, this study for the first time presents a novel transition mutation in the exon 2 region.
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Affiliation(s)
- S Prabhakara
- Department of Research and Development, Genomics and Central Research Laboratory, Sri Devaraj Urs Academy of Higher Education and Research, Tamaka, Kolar, India ; Central Research Lab, Raja Rajeswari Medical College and Hospital, Bangalore, Karnataka, India
| | - Kolandaswamy Anbazhagan
- INSERM U844, Institute for Neurosciences of Montpellier, Hospital St. Eloi, 34295 Montpellier, France
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p53-directed translational control can shape and expand the universe of p53 target genes. Cell Death Differ 2014; 21:1522-34. [PMID: 24926617 DOI: 10.1038/cdd.2014.79] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 04/23/2014] [Accepted: 04/30/2014] [Indexed: 01/20/2023] Open
Abstract
The increasing number of genome-wide transcriptome analyses focusing on p53-induced cellular responses in many cellular contexts keeps adding to the already numerous p53-regulated transcriptional networks. To investigate post-transcriptional controls as an additional dimension of p53-directed gene expression responses, we performed a translatome analysis through polysomal profiling on MCF7 cells upon 16 hours of doxorubicin or nutlin-3a treatment. The comparison between the transcriptome and the translatome revealed a considerable level of uncoupling, characterized by genes whose transcription variations did not correlate with translation variations. Interestingly, uncoupled genes were associated with apoptosis, DNA and RNA metabolism and cell cycle functions, suggesting that post-transcriptional control can modulate classical p53-regulated responses. Furthermore, even for well-established p53 targets that were differentially expressed both at the transcriptional and translational levels, quantitative differences between the transcriptome, subpolysomal and polysomal RNAs were evident. As we searched mechanisms underlying gene expression uncoupling, we identified the p53-dependent modulation of six RNA-binding proteins, where hnRNPD (AUF1) and CPEB4 are direct p53 transcriptional targets, whereas SRSF1, DDX17, YBX1 and TARDBP are indirect targets (genes modulated preferentially in the subpolysomal or polysomal mRNA level) modulated at the translational level in a p53-dependent manner. In particular, YBX1 translation appeared to be reduced by p53 via two different mechanisms, one related to mTOR inhibition and the other to miR-34a expression. Overall, we established p53 as a master regulator of translational control and identified new p53-regulated genes affecting translation that can contribute to p53-dependent cellular responses.
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Abstract
Upstream open reading frames (uORFs) are major gene expression regulatory elements. In many eukaryotic mRNAs, one or more uORFs precede the initiation codon of the main coding region. Indeed, several studies have revealed that almost half of human transcripts present uORFs. Very interesting examples have shown that these uORFs can impact gene expression of the downstream main ORF by triggering mRNA decay or by regulating translation. Also, evidence from recent genetic and bioinformatic studies implicates disturbed uORF-mediated translational control in the etiology of many human diseases, including malignancies, metabolic or neurologic disorders, and inherited syndromes. In this review, we will briefly present the mechanisms through which uORFs regulate gene expression and how they can impact on the organism's response to different cell stress conditions. Then, we will emphasize the importance of these structures by illustrating, with specific examples, how disturbed uORF-mediated translational control can be involved in the etiology of human diseases, giving special importance to genotype-phenotype correlations. Identifying and studying more cases of uORF-altering mutations will help us to understand and establish genotype-phenotype associations, leading to advancements in diagnosis, prognosis, and treatment of many human disorders.
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Affiliation(s)
- Cristina Barbosa
- Departamento de Genética Humana, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisboa, Portugal
- Center for Biodiversity, Functional and Integrative Genomics, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Isabel Peixeiro
- Departamento de Genética Humana, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisboa, Portugal
- Center for Biodiversity, Functional and Integrative Genomics, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Luísa Romão
- Departamento de Genética Humana, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisboa, Portugal
- Center for Biodiversity, Functional and Integrative Genomics, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- * E-mail:
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Leão M, Pereira C, Bisio A, Ciribilli Y, Paiva AM, Machado N, Palmeira A, Fernandes MX, Sousa E, Pinto M, Inga A, Saraiva L. Discovery of a new small-molecule inhibitor of p53-MDM2 interaction using a yeast-based approach. Biochem Pharmacol 2013; 85:1234-45. [PMID: 23428467 DOI: 10.1016/j.bcp.2013.01.032] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 01/28/2013] [Accepted: 01/30/2013] [Indexed: 10/27/2022]
Abstract
The virtual screening of a library of xanthone derivatives led us to the identification of potential novel MDM2 ligands. The activity of these compounds as inhibitors of p53-MDM2 interaction was investigated using a yeast phenotypic assay, herein developed for the initial screening. Using this approach, in association with a yeast p53 transactivation assay, the pyranoxanthone (3,4-dihydro-12-hydroxy-2,2-dimethyl-2H,6H-pyrano[3,2-b]xanthen-6-one) (1) was identified as a putative small-molecule inhibitor of p53-MDM2 interaction. The activity of the pyranoxanthone 1 as inhibitor of p53-MDM2 interaction was further investigated in human tumor cells with wild-type p53 and overexpressed MDM2. Notably, the pyranoxanthone 1 mimicked the activity of known p53 activators, leading to p53 stabilization and activation of p53-dependent transcriptional activity. Additionally, it led to increased protein levels of p21 and Bax, and to caspase-7 cleavage. By computational docking studies, it was predicted that, like nutlin-3a, a known small-molecule inhibitor of p53-MDM2 interaction, pyranoxanthone 1 binds to the p53-binding site of MDM2. Overall, in this work, a novel small-molecule inhibitor of p53-MDM2 interaction with a xanthone scaffold was identified for the first time. Besides its potential use as molecular probe and possible lead to develop anticancer agents, the pyranoxanthone 1 will pave the way for the structure-based design of a new class of p53-MDM2 inhibitors.
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Affiliation(s)
- Mariana Leão
- REQUIMTE, Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira n.° 164, 4050-313 Porto, Portugal
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Abstract
A host of data on genetic variation from the Human Genome and International HapMap projects, and advances in high-throughput genotyping technologies, have made genome-wide association (GWA) studies technically feasible. GWA studies help in the discovery and quantification of the genetic components of disease risks, many of which have not been unveiled before and have opened a new avenue to understanding disease, treatment, and prevention. This chapter presents an overview of GWA, an important tool for discovering regions of the genome that harbor common genetic variants to confer susceptibility for various diseases or health outcomes in the post-Human Genome Project era. A tutorial on how to conduct a GWA study and some practical challenges specifically related to the GWA design is presented, followed by a detailed GWA case study involving the identification of loci associated with glioma as an example and an illustration of current technologies.
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Ward LD, Kellis M. Interpreting noncoding genetic variation in complex traits and human disease. Nat Biotechnol 2012; 30:1095-106. [PMID: 23138309 PMCID: PMC3703467 DOI: 10.1038/nbt.2422] [Citation(s) in RCA: 340] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 10/16/2012] [Indexed: 12/13/2022]
Abstract
Association studies provide genome-wide information about the genetic basis of complex disease, but medical research has primarily focused on protein-coding variants, due to the difficulty of interpreting non-coding mutations. This picture has changed with advances in the systematic annotation of functional non-coding elements. Evolutionary conservation, functional genomics, chromatin state, sequence motifs, and molecular quantitative trait loci all provide complementary information about non-coding function. These functional maps can help prioritize variants on risk haplotypes, filter mutations encountered in the clinic, and perform systems-level analyses to reveal processes underlying disease associations. Advances in predictive modeling can enable dataset integration to reveal pathways shared across loci and alleles, and richer regulatory models can guide the search for epistatic interactions. Lastly, new massively parallel reporter experiments can systematically validate regulatory predictions. Ultimately, advances in regulatory and systems genomics can help unleash the value of whole-genome sequencing for personalized genomic risk assessment, diagnosis, and treatment.
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Affiliation(s)
- Lucas D Ward
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
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Nikolaou V, Kang X, Stratigos A, Gogas H, Latorre MC, Gabree M, Plaka M, Njauw CN, Kypreou K, Mirmigi I, Stefanaki I, Tsao H. Comprehensive mutational analysis of CDKN2A and CDK4 in Greek patients with cutaneous melanoma. Br J Dermatol 2011; 165:1219-22. [PMID: 21801156 PMCID: PMC3225501 DOI: 10.1111/j.1365-2133.2011.10551.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND The penetrance of CDKN2A mutations is subject to geographical and latitudinal variation and is presumably dictated by ultraviolet radiation exposure and possibly other co-inherited genetic factors. The frequency of mutations increases with the number of family members affected and the number of primary tumours, and also fluctuates with geography. To date, little is known about the prevalence of CDKN2A mutations in patients with melanoma from Greece. OBJECTIVE To characterize the frequency of CDKN2A and CDK4 mutations in a hospital-based population of Greek patients with melanoma. METHODS Three hundred and four consecutive single primary melanoma (SPM), nine familial melanoma (FM) and seven multiple primary melanoma cases (MPM) were assessed for sequence variants in exons 1α, 1β and 2 of CDKN2A and exon 2 of CDK4. RESULTS Germline CDKN2A mutations were detected in 10 of 304 SPM (3·3%), in four of seven MPM (57%) and in two of nine FM (22%) cases. The most common mutation was a Northern European allele (p16 p.R24P) detected in eight individuals. Five previously unreported CDKN2A variants were also identified: -34G>C, c.41_43delins20bp, c.301G>C (p.G101R), c.301G>A (p.G101E) and c.296_297insGACC. We also describe the first report of a CDK4 p.R24H substitution in a Greek family. CONCLUSIONS The Greek population appears to harbour a higher prevalence of the CDKN2A mutation than other reported cohorts. This supports the notion that genetic susceptibility may play a stronger influence in a country with a relatively low incidence of melanoma. Furthermore, the identification of Northern European alleles suggests that gene migration may be responsible, in part, for the observed cases in Greece.
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Affiliation(s)
- V Nikolaou
- Department of Dermatology, University of Athens Medical School, 'A. Sygros' Hospital, I Dragoumi 5, 16121 Athens, Greece
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Yang TH, Kon M, Hung JH, Delisi C. Combinations of newly confirmed Glioma-Associated loci link regions on chromosomes 1 and 9 to increased disease risk. BMC Med Genomics 2011; 4:63. [PMID: 21827660 PMCID: PMC3212919 DOI: 10.1186/1755-8794-4-63] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Accepted: 08/09/2011] [Indexed: 01/15/2023] Open
Abstract
Background Glioblastoma multiforme (GBM) tends to occur between the ages of 45 and 70. This relatively early onset and its poor prognosis make the impact of GBM on public health far greater than would be suggested by its relatively low frequency. Tissue and blood samples have now been collected for a number of populations, and predisposing alleles have been sought by several different genome-wide association (GWA) studies. The Cancer Genome Atlas (TCGA) at NIH has also collected a considerable amount of data. Because of the low concordance between the results obtained using different populations, only 14 predisposing single nucleotide polymorphism (SNP) candidates in five genomic regions have been replicated in two or more studies. The purpose of this paper is to present an improved approach to biomarker identification. Methods Association analysis was performed with control of population stratifications using the EIGENSTRAT package, under the null hypothesis of "no association between GBM and control SNP genotypes," based on an additive inheritance model. Genes that are strongly correlated with identified SNPs were determined by linkage disequilibrium (LD) or expression quantitative trait locus (eQTL) analysis. A new approach that combines meta-analysis and pathway enrichment analysis identified additional genes. Results (i) A meta-analysis of SNP data from TCGA and the Adult Glioma Study identifies 12 predisposing SNP candidates, seven of which are reported for the first time. These SNPs fall in five genomic regions (5p15.33, 9p21.3, 1p21.2, 3q26.2 and 7p15.3), three of which have not been previously reported. (ii) 25 genes are strongly correlated with these 12 SNPs, eight of which are known to be cancer-associated. (iii) The relative risk for GBM is highest for risk allele combinations on chromosomes 1 and 9. (iv) A combined meta-analysis/pathway analysis identified an additional four genes. All of these have been identified as cancer-related, but have not been previously associated with glioma. (v) Some SNPs that do not occur reproducibly across populations are in reproducible (invariant) pathways, suggesting that they affect the same biological process, and that population discordance can be partially resolved by evaluating processes rather than genes. Conclusion We have uncovered 29 glioma-associated gene candidates; 12 of them known to be cancer related (p = 1. 4 × 10-6), providing additional statistical support for the relevance of the new candidates. This additional information on risk loci is potentially important for identifying Caucasian individuals at risk for glioma, and for assessing relative risk.
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Affiliation(s)
- Tun-Hsiang Yang
- Bioinformatics Program, Boston University, 24 Cummington Street, Boston, MA 02215, USA
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Khan N, Khan MK, Almasan A, Singh AD, Macklis R. The evolving role of radiation therapy in the management of malignant melanoma. Int J Radiat Oncol Biol Phys 2011; 80:645-54. [PMID: 21489712 DOI: 10.1016/j.ijrobp.2010.12.071] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Revised: 12/19/2010] [Accepted: 12/26/2010] [Indexed: 02/01/2023]
Abstract
The incidence of melanoma is rising in the United States, leading to an estimated 68,720 new diagnoses and 8,650 deaths annually. The natural history involves metastases to lymph nodes, lung, liver, brain, and often to other sites. Primary treatment for melanoma is surgical excision of the primary tumor and affected lymph nodes. The role of adjuvant or definitive radiation therapy in the treatment of melanoma remains controversial, because melanoma has traditionally been viewed as a prototypical radioresistant cancer. However, recent studies suggest that under certain clinical circumstances, there may be a significant role for radiation therapy in melanoma treatment. Stereotactic radiosurgery for brain metastases has shown effective local control. High dose per fraction radiation therapy has been associated with a lower rate of locoregional recurrence of sinonasal melanoma. Plaque brachytherapy has evolved into a promising alternative to enucleation at the expense of moderate reduction in visual acuity. Adjuvant radiation therapy following lymphadenectomy in node-positive melanoma prevents local and regional recurrence. The newer clinical data along with emerging radiobiological data indicate that radiotherapy is likely to play a greater role in melanoma management and should be considered as a treatment option.
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Affiliation(s)
- Niloufer Khan
- Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
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