Alternative product of the p16/CKDN2A locus connects the Rb and p53 tumor suppressors

Oxidative Stress in Genetic Cataract Formation

BACKGROUND

Cataracts are the leading cause of blindness worldwide, and age-related cataracts are the result of environmental insults that largely lead to oxidative stress imposed on a genetic background that determines susceptibility to these stresses.

METHODS

A comprehensive literature review was performed to identify GWAS, targeted association studies, and TWAS that identified genes associated with age-related cataract. Additional genes associated with age-related cataracts were identified through the CAT-MAP online database. Pathway analysis was performed using Qiagen Ingenuity Pathway Analysis and pathways related to oxidative stress were analyzed using the same program.

RESULTS

A large number of genes have been identified as causes of both Mendelian and complex cataracts. Of these, 10 genes related to oxidative stress were identified, and all were associated with age-related cataracts. These genes fall into seven canonical pathways primarily related to glutathione metabolism and other pathways related to detoxifying reactive oxygen species.

CONCLUSIONS

While a relatively small number of antioxidant related genes were identified as being associated with cataracts, they allow the identification of redox pathways important for lens metabolism and homeostasis. These are largely related to glutathione and its metabolism, other pathways for detoxification of reactive oxygen species, and the transcriptional systems that control their expression.

Cell Senescence and the Genetics of Melanoma Development

Cutaneous malignant melanoma is an aggressive skin cancer with an approximate lifetime risk of 1 in 38 in the UK. While exposure to ultraviolet radiation is a key environmental risk factor for melanoma, up to ~10% of patients report a family history of melanoma, and ~1% have a strong family history. The understanding of causal mutations in melanoma has been critical to the development of novel targeted therapies that have contributed to improved outcomes for late-stage patients. Here, we review current knowledge of the genes affected by familial melanoma mutations and their partial overlap with driver genes commonly mutated in sporadic melanoma development. One theme linking a set of susceptibility loci/genes is the regulation of skin pigmentation and suntanning. The largest functional set of susceptibility variants, typically with high penetrance, includes CDKN2A, RB1, and telomerase reverse transcriptase (TERT) mutations, associated with attenuation of cell senescence. We discuss the mechanisms of action of these gene sets in the biology and progression of nevi and melanoma.

Regulation of p14ARF expression by HPV-18 E6 variants

A common causative agent for uterine cervical cancer is the human papillomavirus type 18 (HPV-18) which has three phylogenic variants: Asian-Amerindian, European, and African. Each variant shows significant molecular differences in the E6 gene. E6 oncoprotein is a negative regulator of tumor suppressor protein p53, hence, this oncoprotein indirectly regulates the expression of tumor-suppressor p14(ARF) . p14(ARF) and p16(INK4A) genes are overexpressed in--and have been proposed as markers for--HPV-related cervical cancer. In order to dissect the role of E6 on the regulation of p14(ARF) expression, separating it from that of other intervening factors, transfection of E6 variants to MCF-7 cells was performed, assessing cDNA transcript levels by RT-PCR, whereas p14(ARF) and p53 expression were evaluated by immunocytochemistry and Western blot. E6 transfected cells differentially expressed transcripts of two molecular forms: E6 and E6*. The ratio of these two forms varied with the transfected E6 variant. With the Asian-Amerindian variant, the ratio was E6 > E6*, whereas with the European and the African the ratio was E6* > E6. As expected with the E6* construct, E6* transcripts were solely observed. In addition, when E6 > E6* and p53 expression was low, p14(ARF) was high and when E6* > E6 and p53 expression was high, p14(ARF) was low. In conclusion, each E6 variant distinctively affects p53 levels and consequently p14(ARF) expression, finding that could be related with the differences in oncogenic effect of infection with the diverse high-risk HPV variants.

Measurement of relative copy number of CDKN2A/ARF and CDKN2B in bladder cancer by real-time quantitative PCR and multiplex ligation-dependent probe amplification

Many tumors have large homozygous deletions of the CDKN2A locus (encoding p14(ARF) and p16) and of CDKN2B (p15). Our aim was to determine which gene is the major target in bladder cancer. We used quantitative real-time PCR (RTQ-PCR) to determine copy number of p15, of p14(ARF) exon 1beta, and p16 exon 2 in 22 tumor cell lines and 83 bladder tumors, some of which had been assessed previously by duplex PCR. Titration experiments showed that homozygous deletion could be detected in the presence of up to 30% normal DNA. Results for cell lines were compatible with previous cytogenetic analyses. Ten cell lines and 32 tumors (38.5%) had homozygous deletion of at least one target. Thirteen tumors (15.7%) had deletion of all three targets. Two tumors had deletion of p14(ARF) exon 1beta alone and four of p16 exon 2 alone. RTQ-PCR detected more homozygous deletions than duplex PCR. Finally we used a multiplex ligation-dependent probe amplification kit to provide independent confirmation of results. We conclude that with appropriate controls RTQ-PCR is a sensitive and robust method to detect copy number changes in tumors even in the presence of contaminating normal cell DNA.

Alternative reading frame protein (ARF)-independent function of CARF (collaborator of ARF) involves its interactions with p53: evidence for a novel p53-activation pathway and its negative feedback control

CARF, a collaborator of ARF (alternative reading frame protein), was cloned as a novel ARF-binding protein from a yeast-interaction screen. It potentiated ARF-mediated p53 function, and also caused a moderate increase in p53 activity in the absence of ARF. We herein report the molecular mechanism of ARF-independent function of CARF. By employing a variety of approaches, including overexpression of CARF, its suppression by small interfering RNA and use of protease inhibitors, we demonstrate that: (i) CARF directly interacts with wild-type p53, causing its stabilization and functional activation; and (ii) CARF and p53 levels show an inverse relationship that is instigated by a negative-feedback control via a proteasome-mediated degradation pathway.

Myc pathways provoking cell suicide and cancer

A paradox for the cancer biology field has been the revelation that oncogenes, once thought to simply provide advantages to a cancer cell, actually put it at dire risk of cell suicide. Myc is the quintessential oncogene in this respect, as in normal cells it is required for cell cycle traverse, whereas in cancers it is overexpressed and functions as the angiogenic switch. Nonetheless, Myc overexpression kills normal cells dead in their tracks. Here we review Myc-induced pathways that contribute to the apoptotic response. Molecular analysis of Myc-induced tumors has established that some of these apoptotic pathways are essential checkpoints that guard the cell from cancer, as they are selectively bypassed during tumorigenesis. The precise mechanism(s) by which Myc targets these pathways are largely unresolved, but we propose that they involve crosstalk and feedback regulatory loops between arbiters of cell death.

CARF is a novel protein that cooperates with mouse p19ARF (human p14ARF) in activating p53

The INK4a locus on chromosome 9p21 encodes two structurally distinct tumor suppressor proteins, p16(INK4a) and the alternative reading frame protein, ARF (p19(ARF) in mouse and p14(ARF) in human). Each of these proteins has a role in senescence of primary cells and activates pathways for cell cycle control and tumor suppression. The current prevailing model proposes that p19(ARF) activates p53 function by antagonizing its degradation by MDM2. It was, however, recently shown that stabilization of p53 by p14(ARF) occurs independent of the relocalization of MDM2 to the nucleolus. We have identified a novel collaborator of ARF, CARF. It co-localizes and interacts with ARF in the nucleolus. We demonstrate that CARF is co-regulated with ARF, cooperates with it in activating p53, and thus acts as a novel component of the ARF-p53-p21 pathway.

A major functional difference between the mouse and human ARF tumor suppressor proteins

Suppression of tumorigenesis is considerably more stringent in the human than in the much shorter lived mouse species, and the reasons for this difference are poorly understood. We investigated functional differences in the control of the ARF (alternative reading frame) protein that acts upstream of p53 and is encoded along with p16(INK4a) at a major tumor suppressor locus in both the human and mouse genomes. The mouse and human ARF proteins are substantially divergent at their carboxyl termini. We have shown that the mouse ARF protein (p19ARF) interacts with Pex19p in the cell cytoplasm leading to its nuclear exclusion and repression of its p53 activation function. The human ARF protein (p14ARF) is substantially smaller than its mouse counterpart and is not subject to this functional inactivation by Pex19p. In an identical cellular background, ribozymes directed against Pex19p enhanced p19ARF- but not p14ARF-activated p53 function. This is the first demonstration of a functional difference between the mouse and human ARF proteins. In view of the major role of ARF in tumor suppression, this distinction may contribute to the different levels of tumor proneness of these species.

P53 gene mutations: case study of a clinical marker for solid tumors

P53 is a tumor-suppressor gene that codes for a multifunctional DNA-binding protein involved in cell cycle arrest, DNA repair, differentiation, and apoptosis. The P53 gene is mutated in approximately 50% of human cancers and in germline DNA of families with inherited cancer syndromes. The role of P53 mutations in the program of carcinogenic genetic alterations differs among tumor sites ranging from the earliest mutations that can be detected in premalignant cells to mutations that trigger malignant transformation of a benign neoplasm. P53 mutations can cause expression of abnormal proteins or result in complete absence of P53 expression. For these reasons the role of P53 genetic disruption has different implications in different tumor types and may vary depending on the effect of the mutation on P53 protein function. Immunohistochemical detection of P53, commonly used as a surrogate for identification of a mutant gene, has imperfect sensitivity and specificity, further complicating correlations between P53 gene status and clinical outcomes. The presence of P53 mutations has been shown to affect prognosis of some cancers. The identity of P53 mutations can be used to determine tumor clonality. The detection of P53 mutations suggests the severity of premalignant lesions. Evolving technology for more accurate identification of P53 mutations, better understanding of the function of mutant P53 protein, and more detailed analysis of individual tumor types may expand the relevance of P53 gene analysis for clinical outcomes and therapeutic response.

Profiling alternative splicing on fiber-optic arrays

The human transcriptome is marked by extensive alternative mRNA splicing and the expression of many closely related genes, which may be difficult to distinguish using standard microarray techniques. Here we describe a sensitive and specific assay for parallel analysis of mRNA isoforms on a fiber-optic microarray platform. The method permits analysis of mRNA transcripts without prior RNA purification or cDNA synthesis. Using an endogenously expressed viral transcript as a model, we demonstrated that the assay readily detects mRNA isoforms from as little as 10-100 pg of total cellular RNA or directly from a few cells. Multiplexed analysis of human cancer cell lines revealed differences in mRNA splicing and suggested a potential autocrine mechanism in the development of choriocarcinomas. Our approach may be useful in the large-scale analysis of the role of alternative splicing in development and disease.

Stabilization of p53 by p14ARF without relocation of MDM2 to the nucleolus

The alternative product of the human INK4a/ARF locus, p14ARF, has the potential to act as a tumour suppressor by binding to and inhibiting the p53 antagonist MDM2. Current models propose that ARF function depends on its ability to sequester MDM2 in the nucleolus. Here we describe situations in which stabilization of MDM2 and p53 occur without relocalization of endogenous MDM2 from the nucleoplasm. Conversely, forms of ARF that do not accumulate in the nucleolus retain the capacity to stabilize MDM2 and p53. We therefore propose that nucleolar localization is not essential for ARF function but may enhance the availability of ARF to inhibit MDM2.