UHRF1-mediated tumor suppressor gene inactivation in nonsmall cell lung cancer

BACKGROUND

The UHRF1 gene possesses an essential role in DNA methylation maintenance, but its contribution to tumor suppressor gene hypermethylation in primary human cancers currently remains unclear.

METHODS

mRNA expression levels of UHRF1, DNMT1, DNMT3A, DNMT3B, and E2F1 were evaluated in 105 primary nonsmall cell lung carcinomas by quantitative polymerase chain reaction. The methylation status of CDKN2A and RASSF1 promoters was examined by pyrosequencing. UHRF1 was knocked down by short hairpin RNA in A549 lung adenocarcinoma cells.

RESULTS

All 4 genes were overexpressed in a coordinated manner in the lung tumor tissues, and their expression correlated with that of E2F1. Higher UHRF1 expression in tumor tissues correlated with the hypermethylation of CDKN2A (P = .005) and RASSF1 promoters (P = .034), and the relationship with a combined epigenotype was even stronger (P = 2.3 × 10(-4) ). When UHRF1 was knocked down in A549 lung adenocarcinoma cells, lower methylation levels of RASSF1, CYGB, and CDH13 promoters were observed. Also, UHRF1 knockdown clones demonstrated reduced proliferation and decreased cell migration properties.

CONCLUSIONS

Our data demonstrate that UHRF1 is a key epigenetic switch, which controls cell cycle in nonsmall cell lung carcinoma through its ability to sustain the transcriptional silencing of tumor suppressor genes by maintaining their promoters in a hypermethylated status. Thus, UHRF1 should be considered, along with DNMTs, among the potential targets for cancer treatment and/or therapeutic stratification.

Sp1 binds to the external promoter of the p73 gene and induces the expression of TAp73gamma in lung cancer

The p73 gene possesses an extrinsic P1 promoter and an intrinsic P2 promoter, resulting in TAp73 and DeltaNup73 isoforms, respectively. The ultimate effect of p73 in oncogenesis is thought to depend on the apoptotic TA to antiapoptotic DeltaN isoforms' ratio. This study was aimed at identifying novel transcription factors that affect TA isoform synthesis. With the use of bioinformatics tools, in vitro binding assays, and chromatin immunoprecipitation analysis, a region extending -233 to -204 bp upstream of the transcription start site of the human p73 P1 promoter, containing conserved Sp1-binding sites, was characterized. Treatment of cells with Sp1 RNAi and Sp1 inhibitor functionally suppress TAp73 expression, indicating positive regulation of P1 by the Sp1 protein. Notably Sp1 inhibition or knockdown also reduces DeltaNup73 protein levels. Therefore, Sp1 directly regulates TAp73 transcription and affects DeltaNup73 levels in lung cancer. TAp73gamma was shown to be the only TA isoform overexpressed in several lung cancer cell lines and in 26 non-small cell lung cancers, consistent with Sp1 overexpression, thereby questioning the apoptotic role of this specific p73 isoform in lung cancer.

Abstract 163: DTMETH: A novel method for increased length quantitative CpG methylation analysis

DNA methylation analysis has been blooming in the last decade as there is increasing evidence for epigenetic control of new pathways involved in normal cell function as well as the pathogenesis of human disease. A large number of methods have been devised to address the needs of DNA methylation detection in clinical samples. A DNA methylation detection method of preference should be able to interrogate multiple CpGs over long stretches of DNA, quantify DNA methylation, include multiple bisulphite conversion controls, provide increased sensitivity and low background. Here we present DTMETH, a novel method for DNA methylation analysis that bears the above characteristics. In principle, the desired locus is amplified from bisulphite treated-DNA using primers at CpG-free areas. Primers bear short 5’ tails which contain two cytosines (forward) or guanines (reverse) that will serve as normalisation tools. After a spin-column cleanup process, the PCR product is subjected to DTMETH. This is a thermostable reaction utilising FS Taq and labelled ddC (Applied Biosystems). The latter will be only incorporated at methylated cytosines, as post-bisulphite unmethylated cytosines are converted to uracils. The DTMETH products are cleaned by ethanol precipitation and subjected to analysis on a capillary sequencer. ddC peak areas corresponding to methylated Cs are normalised by the peak areas of the control Cs on the primer tail. As proof of principle we present DNA methylation analysis for the p16 gene. We amplified a 269 bp region of the gene's 5’UTR containing 28 CpGs. The assays provide excellent linearity and reproducibility. We used it to screen 90 non-small cell lung carcinomas for p16 methylation in comparison to an established pyrosequencing assay. p16 hypermethylation was detected in 23 samples with both methods, 3 samples with DTMETH only, while 64 samples were negative. DTMETH combines the read lengths of dideoxy terminator sequencing, and enables quantitation without the need of cloning. It is highly versatile, offering easy assay design and due to its thermostable nature can easily overcome secondary structure issues arising from the low complexity bisulphite DNA sequence composition.

Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 163.

Hypomethylation of retrotransposable elements correlates with genomic instability in non-small cell lung cancer

LINE-1 and Alu elements are non-LTR retrotransposons, constituting together over 30% of the human genome and they are frequently hypomethylated in human tumors. A relationship between global hypomethylation and genomic instability has been shown, however, there is little evidence to suggest active role for hypomethylation-mediated reactivation of retroelements in human cancer. In our study, we examined by Pyrosequencing the methylation levels of LINE-1 and Alu sequences in 48 primary nonsmall cell carcinomas and their paired adjacent tissues. We demonstrate a significant reduction of the methylation levels of both elements (p = 7.7 x 10(-14) and 9.6 x 10(-7), respectively). The methylation indices of the 2 elements correlated (p = 0.006), suggesting a possible common mechanism for their methylation maintenance. Genomic instability was measured utilizing 11 fluorescent microsatellite markers located on lung cancer hot-spot regions such as 3p, 5q 9p, 13q and 17p. Hypomethylation of both transposable elements was associated with increased genomic instability (LINE, p = 7.1 x 10(-5); Alu, p = 0.008). The reduction of the methylation index of LINE-1 and Alu following treatment of 3 lung cell lines with 5-aza-2'-deoxycitidine, consistently resulted in increased expression of both elements. Our study demonstrates the strong link between hypomethylation of transposable elements with genomic instability in non-small cell lung cancer and provides early evidence for a potential active role of these elements in lung neoplasia. As demethylating agents are now entering lung cancer trials, it is imperative to gain a greater insight into the potential reactivation of silent retrotransposons in order to advance for the clinical utilization of epigenetics in cancer therapy.