Programmed ribosomal frameshifting (PRF) is a gene expression mechanism which enables the translation of two N-terminally coincident, C-terminally distinct protein products from a single mRNA. Many ...viruses utilize PRF to control or regulate gene expression, but very few phylogenetically conserved examples are known in vertebrate genes. Additional sex combs-like (ASXL) genes 1 and 2 encode important epigenetic and transcriptional regulatory proteins that control the expression of homeotic genes during key developmental stages. Here we describe an ~150-codon overlapping ORF (termed TF) in ASXL1 and ASXL2 that, with few exceptions, is conserved throughout vertebrates.
Conservation of the TF ORF, strong suppression of synonymous site variation in the overlap region, and the completely conserved presence of an EHN/SY motif (a known binding site for Host Cell Factor-1, HCF-1, an epigenetic regulatory factor), all indicate that TF is a protein-coding sequence. A highly conserved UCC_UUU_CGU sequence (identical to the known site of +1 ribosomal frameshifting for influenza virus PA-X expression) occurs at the 5' end of the region of enhanced synonymous site conservation in ASXL1. Similarly, a highly conserved RG_GUC_UCU sequence (identical to a known site of -2 ribosomal frameshifting for arterivirus nsp2TF expression) occurs at the 5' end of the region of enhanced synonymous site conservation in ASXL2.
Due to a lack of appropriate splice forms, or initiation sites, the most plausible mechanism for translation of the ASXL1 and 2 TF regions is ribosomal frameshifting, resulting in a transframe fusion of the N-terminal half of ASXL1 or 2 to the TF product, termed ASXL-TF. Truncation or frameshift mutants of ASXL are linked to myeloid malignancies and genetic diseases, such as Bohring-Opitz syndrome, likely at least in part as a result of gain-of-function or dominant-negative effects. Our hypothesis now indicates that these disease-associated mutant forms represent overexpressed defective versions of ASXL-TF.
This article was reviewed by Laurence Hurst and Eugene Koonin.
Prostate cancer (PrCa) progression and mortality are associated with calcium metabolism, parathyroid hormone level, and vitamin D level. However, the lack of comprehensive understanding on the ...molecular rationale of calcium intake, serum homeostasis, and cytoplasmic function, is critically hindering our ability to propose a mechanism based technique for targeting calcium in PrCa. Recently, studies performed on PrCa samples have shown that calcium-sensing receptor regulates cytoplasmic calcium levels in relation to extracellular calcium concentrations. Recent publications have also revealed the role of BAP1 and FBXL2 associated endoplasmic reticular IP3Rs in controlling the trafficking of calcium from cytosol into the mitochondria of PrCa cells. Competitive binding between BAP1, PTEN and FBXL2 to IP3Rs regulates the calcium flux of mitochondria and thereby controls apoptosis. Analysis of data released by Prostate Adenocarcinoma (Provisional TCGA) reveals that calcium related proteins play critical role in the development of PrCa. From this constantly expanding appreciation for the role of calcium outside the muscle, we predict that calcium-induced-calcium-release ryanodine receptors could also be involved in determining cell fate. Keywords: Prostate cancer, CaSR, RyR, IP3R, BAP1, FBXL2, PTEN
The prognostic value of BRCA1-associated protein 1 (BAP1) expression in different cancer types remains controversial. The aim of this study was to identify the prognostic and clinicopathological ...significance of BAP1 gene expression.
The PubMed, Web of Science, and Embase databases were searched comprehensively for relevant studies. The pooled effects were calculated to investigate the association of BAP1 expression with cancer prognosis and clinicopathological features. The χ
and I
tests were performed to evaluate heterogeneity among the enrolled articles. If the p > 0.05 and I
< 50%, a fixed-effects model was applied; and if the p < 0.05 and I
> 50%, we used a random-effects model.
A total of 26 studies covering 8043 patients were included in the meta-analysis. The correlation between BAP1 expression and patient survival was evaluated for 10 different cancer types. The pooled hazard ratio (HR) of BAP1 expression and overall survival (OS) was 0.83 (95% confidence interval CI: 0.61-1.12) with heterogeneity (I
= 85.8%, p < 0.001), which indicated that the expression of BAP1 had no obvious impact on patient survival in the all-cancer cohort. However, subgroup analyses indicated that cancer type, rather than other parameters (geographic region, detection method, sample size, or comparison method), lead to this heterogeneity. BAP1 expression was a favorable predicative factor for OS in clear cell renal cell carcinoma (HR = 0.57, 95% CI: 0.47-0.69), non-small cell lung cancer (HR = 0.55, 95% CI: 0.32-0.96), and uveal melanoma (HR = 0.41, 95% CI: 0.27-0.62), while high expression of BAP1 was associated with poorer outcome in malignant pleural mesothelioma (HR = 2.03, 95% CI: 1.67-2.47).
Our study revealed that BAP1 expression tends to have different prognostic values in different cancer types. Clinically, BAP1 may serve as a promising marker for prognostic prediction for certain cancer types.
Germline mutations of the oncosuppressor gene breast cancer 1-associated protein 1 (BAP1) were recently related to an autosomal-dominant tumor predisposition syndrome (BAP1-TPDS), characterized by ...uveal melanoma, malignant mesothelioma (MM), cutaneous melanoma, and other malignancies. The demonstration that BAP1 mutations are strongly associated with MM has provided a real breakthrough in the study of genetic predisposition in MM, that may explain why only a fraction of asbestos-exposed individuals go on to develop MM.
To evaluate the possible role of BAP1 mutations in the epidemiology of sporadic MM, and their relationship with asbestos exposure, we determined the prevalence of germline BAP1 mutations by the Sanger method in a group of 29 asbestos-exposed patients, 21 of which were diagnosed with MM. They were residents of Trieste, a ship-building town in Northeast Italy with a very high incidence of mesothelioma.
We identified non-obviously pathogenetic germline sequence variants of BAP1 in 3/29 patients and in 2/21 MM cases (10%).
Non obviously pathogenic germline sequence variants of BAP1 were found. Nevertheless, limitations of predictive web tools allowed us to comment on some interesting peculiarities of our findings.
Abstract
Background: To evaluate the prevalence of BAP1 germline mutations in a series of young patients with uveal melanoma (UM), diagnosed before age 30.
Materials and Methods: The study was ...carried out on 14 young uveal melanoma patients (average age 21.4 years, range 3 months to 29 years). Germline DNA was extracted from peripheral blood. BAP1 sequencing was carried out using direct sequencing of all exons and adjacent intronic sequences. We also tested for germline mutations in additional melanoma-associated candidate genes CDKN2A and CDK4 (exon 4).
Results: We identified one patient with a pathogenic mutation (c. 1717delC, p.L573fs*3) in BAP1. This patient was diagnosed with UM at age 18 years and had a family history of a father with UM and a paternal grandfather with cancer of unknown origin. One additional patient had an intronic variant of uncertain significance (c.123-48T > G) in BAP1 while the remaining 12 patients had no alteration. None of the patients had CDKN2A or CDK4 (Exon 4) mutations. Family history was positive for a number of additional malignancies in this series, in particular for cutaneous melanoma, prostate, breast and colon cancers. There were no families with a history of mesothelioma or renal cell carcinoma.
Conclusions: This study suggests that a small subset of patients with early onset UM has germline mutation in BAP1. While young patients with UM should be screened for germline BAP1 mutations, our results suggest that there is a need to identify other candidate genes which are responsible for UM in young patients.
Malignant mesothelioma (MM) is a malignancy arising from the mesothelial cells lining the thoracic and abdominal serosal cavities. The pleural space is the most commonly affected site, accounting for ...about 80% of cases, while peritoneum makes up the majority of the remaining 20%. The different types of mesotheliomas are generally considered as distinct diseases with specific risk factors, therapeutic strategies and prognoses. Epidemiological and clinical differences between pleural and peritoneal MM raise questions about the involvement of different molecular mechanisms. Since the
gene is involved in the BAP1 cancer syndrome and seems to be a prognostic factor in MM, this review presents an overview of BAP1 alterations in mesothelioma comparing pleural and peritoneal localizations.
Post-translational modifications of the histones are centrally involved in the regulation of all DNA-templated processes, including gene transcription, DNA replication, recombination, and repair. ...These modifications are often dynamic, and their removal is just as important as their addition in proper regulation of cellular functions. Although histone acetylation/deacetylation and histone methylation/demethylation are highly studied, the functions and regulation of histone ubiquitination and deubiquitination are less well understood. This review highlights our current understanding of how histone ubiquitination impacts gene transcription, DNA repair, and cell cycle progression, and stresses the importance of deubiquitinases to normal cellular functions as well as to disease states such as cancer.
The Hippo signalling pathway is dysregulated across a wide range of cancer types and, although driver mutations that directly affect the core Hippo components are rare, a handful is found within ...pleural mesothelioma (PM). PM is a deadly disease of the lining of the lung caused by asbestos exposure. By pooling the largest‐scale clinical datasets publicly available, we here interrogate associations between the most prevalent driver mutations within PM and Hippo pathway disruption in patients, while assessing correlations with a variety of clinical markers. This analysis reveals a consistent worse outcome in patients exhibiting transcriptional markers of YAP/TAZ activation, pointing to the potential of leveraging Hippo pathway transcriptional activation status as a metric by which patients may be meaningfully stratified. Preclinical models recapitulating disease are transformative in order to develop new therapeutic strategies. We here establish an isogenic cell‐line model of PM, which represents the most frequently mutated genes and which faithfully recapitulates the molecular features of clinical PM. This preclinical model is developed to probe the molecular basis by which the Hippo pathway and key driver mutations affect cancer initiation and progression. Implementing this approach, we reveal the role of NF2 as a mechanosensory component of the Hippo pathway in mesothelial cells. Cellular NF2 loss upon physiological stiffnesses analogous to the tumour niche drive YAP/TAZ‐dependent anchorage‐independent growth. Consequently, the development and characterisation of this cellular model provide a unique resource to obtain molecular insights into the disease and progress new drug discovery programs together with future stratification of PM patients.
Stratifying pleural mesothelioma (PM) patients reveals active YAP/TAZ is associated with poor clinical outcomes.
An isogenic cell‐line model of PM driver mutations is developed that faithfully recapitulates clinical PM characteristics.
NF2 regulates YAP/TAZ mesothelial activity in response to stresses, including sensing mechanical cues, while BAP1 appears to regulate a stem‐cell‐like transcriptional program.
Multiple Uveal Melanoma Kheir, Wajiha J.; Kim, Jane S.; Materin, Miguel Angel
Ocular oncology and pathology,
10/2020, Volume:
6, Issue:
5
Journal Article
Open access
Introduction: Multiple uveal melanoma is a rare occurrence and includes bilateral melanoma, unilateral multiple/multifocal melanoma, or melanoma with metastasis to the ipsilateral or contralateral ...eye. Methods: A chart review of patients diagnosed with uveal melanoma between January 2013 and January 2019 at the Duke University Eye Center Ophthalmic Oncology Service was performed. Results: Three patients with multiple, sequential melanoma were identified; patient 1 had bilateral choroidal melanoma and patients 2 and 3 had 2 choroidal melanomas occurring in the same eye. In all 3 patients, both the first and sequential choroidal melanomas were treated with I-125 radioactive plaque brachytherapy (PBT). Two patients were found to have developed secondary metastatic uveal melanoma as a presenting sign of systemic metastases. Patient 4, initially treated with PBT, was diagnosed with ipsilateral metastatic choroidal melanoma, also treated with PBT. Patient 5 had right eye enucleation for choroidal melanoma and developed vision-threatening metastasis in the left eye, which was treated with PBRT. None of the patients had history of cancer prior to their first diagnosis. Patients 1 and 5 were tested with a systemic melanoma panel; both were negative for BAP1, but patient 1 had a variant of unknown significance in BRCA2. Patient 3 had oculodermal melanocytosis, an established risk factor of uveal melanoma. Conclusion: Although rare, the possibility of multiple uveal melanoma does exist. Examination of the treated and contralateral eye on a regular basis is crucial, not only to identify local failure but also new metastases from the primary tumor and additional primary tumors.
Recent sequencing studies of clear cell (conventional) renal cell carcinoma (ccRCC) have identified inactivating point mutations in the chromatin-modifying genes PBRM1, KDM6A/UTX, KDM5C/JARID1C, ...SETD2, MLL2 and BAP1. To investigate whether aberrant hypermethylation is a mechanism of inactivation of these tumor suppressor genes in ccRCC, we sequenced the promoter region within a bona fide CpG island of PBRM1, KDM6A, SETD2 and BAP1 in bisulfite-modified DNA of a representative series of 50 primary ccRCC, 4 normal renal parenchyma specimens and 5 RCC cell lines. We also interrogated the promoter methylation status of KDM5C and ARID1A in the Cancer Genome Atlas (TCGA) ccRCC Infinium data set. PBRM1, KDM6A, SETD2 and BAP1 were unmethylated in all tumor and normal specimens. KDM5C and ARID1A were unmethylated in the TCGA 219 ccRCC and 119 adjacent normal specimens. Aberrant promoter hypermethylation of PBRM1, BAP1 and the other chromatin-modifying genes examined here is therefore absent or rare in ccRCC.
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