Abstract PR20: A 53BP1 integrates DNA repair and p53-dependent cell fate decisions via distinct mechanisms

The tumor suppressor protein 53BP1 was first identified as a p53-interacting protein over two decades ago, however its direct contribution to p53-dependent cellular activities has remained enigmatic. Having reinvestigated the link between 53BP1 and p53, we now show 53BP1 plays an important role in directly stimulating genome-wide p53-dependent gene transactivation and repression events in response to ionizing radiation (IR) and synthetic p53 activation. We have also fine-mapped the domains in 53BP1 that modulate p53 activity and reveal it requires both auto-oligomerization and its tandem-BRCT domain-mediated bivalent interactions with p53 and the ubiquitin-specific protease USP28. Loss of 53BP1 or USP28 catalytic activities results in inefficient p53-dependent cell-cycle checkpoint and exit responses. Mechanistically, we show 53BP1-USP28 cooperation to be essential for stimulating normal p53-promoter element interactions and downstream gene transactivation-associated events, yet dispensable for 53BP1-dependent DSB repair regulation. Collectively, our data indicate a upstream role for 53BP1-USP28 complexes in priming p53's transcriptional potential, providing a mechanistic explanation for 53BP1-p53 cooperation in controlling anti-tumorigenic cell-fate decisions. Moreover, we reveal these activities to be distinct and separable from 53BP1's regulation of DNA double-strand break repair pathway choice, and establish the prime function for the 53BP1 BRCT domain and its interaction partner USP28. Our study therefore defines important and novel functions for 53BP1 in enforcing a vital tumor suppressor pathway that are likely to contribute to tumor suppression. In the meeting we will describe these findings and update on recent progress.

This abstract is also being presented as Poster B04.

Citation Format: Raquel Cuella-Martin, Catarina Oliveira, Helen E. Lockstone, Suzanne Snellenberg, Natalia Grolmusova, J Ross Chapman. A 53BP1 integrates DNA repair and p53-dependent cell fate decisions via distinct mechanisms [abstract]. In: Proceedings of the AACR Special Conference on DNA Repair: Tumor Development and Therapeutic Response; 2016 Nov 2-5; Montreal, QC, Canada. Philadelphia (PA): AACR; Mol Cancer Res 2017;15(4_Suppl):Abstract nr PR20.

53BP1 Integrates DNA Repair and p53-Dependent Cell Fate Decisions via Distinct Mechanisms

The tumor suppressor protein 53BP1, a pivotal regulator of DNA double-strand break (DSB) repair, was first identified as a p53-interacting protein over two decades ago. However, its direct contributions to p53-dependent cellular activities remain undefined. Here, we reveal that 53BP1 stimulates genome-wide p53-dependent gene transactivation and repression events in response to ionizing radiation (IR) and synthetic p53 activation. 53BP1-dependent p53 modulation requires both auto-oligomerization and tandem-BRCT domain-mediated bivalent interactions with p53 and the ubiquitin-specific protease USP28. Loss of these activities results in inefficient p53-dependent cell-cycle checkpoint and exit responses. Furthermore, we demonstrate 53BP1-USP28 cooperation to be essential for normal p53-promoter element interactions and gene transactivation-associated events, yet dispensable for 53BP1-dependent DSB repair regulation. Collectively, our data provide a mechanistic explanation for 53BP1-p53 cooperation in controlling anti-tumorigenic cell-fate decisions and reveal these activities to be distinct and separable from 53BP1's regulation of DNA double-strand break repair pathway choice.

Methylation-mediated repression of PRDM14 contributes to apoptosis evasion in HPV-positive cancers

Promoter methylation of the transcription factor PRDM14 (PRDI-BF1 and RIZ domain containing 14) represents a highly frequent event in human papillomavirus (HPV)-induced cervical cancers and cancer precursor lesions. Here, we aimed to assess the functional consequences of PRDM14 promoter methylation in HPV-induced carcinogenesis. PRDM14 promoter methylation, expression and consequences of ectopic PRDM14 expression were studied in HPV16-positive cervical and oral cancer cell lines (SiHa, CaSki and 93VU147T), human embryonic kidney 293 (HEK293T) cells and primary human foreskin keratinocytes (HFK). PRDM14 mRNA expression was restricted to HEK293T and HFK cells, and could be upregulated in SiHa cells upon DNA methylation inhibition. Ectopic expression of PRDM14 in SiHa, CaSki and 93VU147T cells resulted in significantly more apoptotic cells, as measured by annexin V labelling, compared to HEK293T and HFK cells. MRNA profiling of 41 apoptosis regulators identified NOXA and PUMA as candidate target genes involved in PRDM14-mediated apoptosis induction. Full-length PRDM14 transactivated both NOXA and PUMA promoters. Transactivation was abolished upon deletion of the PRDM14 DNA binding domain. This suggests that NOXA and PUMA expression is directly regulated by PRDM14, which in case of NOXA was linked to a consensus PRDM14 binding motif in the promoter region. Taken together, these results suggest that PRDM14 acts as a regulator of NOXA and PUMA-mediated apoptosis induction, thereby providing evidence for a tumour suppressive role in HPV-induced carcinogenesis. The contribution of methylation-mediated gene silencing of PRDM14 to apoptosis evasion in HPV-positive cancer cells offers novel therapeutic options for HPV-induced cancers.

Promoter methylation of Wnt-antagonists in polypoid and nonpolypoid colorectal adenomas

BACKGROUND

Nonpolypoid adenomas are a subgroup of colorectal adenomas that have been associated with a more aggressive clinical behaviour compared to their polypoid counterparts. A substantial proportion of nonpolypoid and polypoid adenomas lack APC mutations, APC methylation or chromosomal loss of the APC locus on chromosome 5q, suggesting the involvement of other Wnt-pathway genes. The present study investigated promoter methylation of several Wnt-pathway antagonists in both nonpolypoid and polypoid adenomas.

METHODS

Quantitative methylation-specific PCR (qMSP) was used to evaluate methylation of four Wnt-antagonists, SFRP2, WIF-1, DKK3 and SOX17 in 18 normal colorectal mucosa samples, 9 colorectal cancer cell lines, 18 carcinomas, 44 nonpolypoid and 44 polypoid adenomas. Results were integrated with previously obtained data on APC mutation, methylation and chromosome 5q status from the same samples.

RESULTS

Increased methylation of all genes was found in the majority of cell lines, adenomas and carcinomas compared to normal controls. WIF-1 and DKK3 showed a significantly lower level of methylation in nonpolypoid compared to polypoid adenomas (p < 0.01). Combining both adenoma types, a positive trend between APC mutation and both WIF-1 and DKK3 methylation was observed (p < 0.05).

CONCLUSIONS

Methylation of Wnt-pathway antagonists represents an additional mechanism of constitutive Wnt-pathway activation in colorectal adenomas. Current results further substantiate the existence of partially alternative Wnt-pathway disruption mechanisms in nonpolypoid compared to polypoid adenomas, in line with previous observations.

Abstract 4248: Methylation specific digital karyotyping of human papillomavirus type 16 E6E7 expressing keratinocytes identifies novel methylation targets in cervical carcinogenesis

Persistent infection with high-risk human papillomavirus (hrHPV) types is causally related to the development of cervical cancer and a subset of other anogenital and head and neck cancers. HrHPV-induced malignant transformation of epithelial cells is associated with (epi)genetic aberrations in host cell genes, including alterations in DNA methylation often affecting tumor suppressor gene expression. This study aimed to comprehensively unravel genome-wide DNA methylation events linked to a transforming hrHPV-infection, which is characterized by deregulated expression of the viral oncogenes E6 and E7 in dividing epithelial cells. Hereto, primary human keratinocytes transduced with HPV16E6E7 and their untransduced counterparts were subjected to methylation-specific digital karyotyping (MSDK) to screen for genome-wide DNA-methylation changes at different stages of HPV-induced transformation. Integration of the obtained methylation karyotype with genome-wide expression profiles of cervical carcinomas identified 34 genes with increased methylation in HPV-transformed cells and reduced expression in cervical carcinomas. For 12 genes (CLIC3, CREB3L1, FAM19A4, LFNG, LHX1, MRC2, NKX2-8, NPTX-1, PHACTR3, PRDM14, SOST and TNFSF13) specific methylation in HPV-containing cell lines was confirmed using a real-time methylation specific PCR (MSP) detection platform. Except from NPTX-1, methylation of none of these genes has to the best of our knowledge been linked to hrHPV-induced cancers before. Subsequent analysis of FAM19A4, LHX1, NKX2-8, NPTX-1, PHACTR3 and PRDM14 in cervical tissue specimens revealed an increase in methylation of all six genes with disease progression. All genes were commonly methylated in cervical carcinomas, with highest frequencies of up to 100% detected for FAM19A4, PHACTR3 and PRDM14. NKX2-8, PHACTR3 and PRDM14 were already methylated in approximately one third of precancerous lesions, indicating that their alterations represent relatively early events in cervical carcinogenesis.

In conclusion, MSDK analysis of HPV16 transduced keratinocytes at different stages of HPV-induced transformation resulted in the identification of novel methylation events in cervical carcinogenesis, including methylation of FAM19A4, LHX1, NKX2-8, PHACTR3 and PRDM14 gene promoters. These genes may provide promising triage markers for assessment of the presence of (pre)cancerous cervical lesions in hrHPV-positive women.

Citation Format: Renske D M Steenbergen, Maté Ongenaert, Suzanne Snellenberg, Chris JLM Meijer, Kornelia Polyak, Noga Bloushtain-Qimron, Peter JF Snijders, Wim van Criekinge. Methylation specific digital karyotyping of human papillomavirus type 16 E6E7 expressing keratinocytes identifies novel methylation targets in cervical carcinogenesis. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4248. doi:10.1158/1538-7445.AM2013-4248

Development of a multiplex methylation-specific PCR as candidate triage test for women with an HPV-positive cervical scrape

Background

Quantitative methylation-specific PCR (qMSP) analysis for determining the methylation status of (candidate) tumor suppressor genes has potential as objective and valuable test to triage high-risk human papillomavirus (hrHPV) positive women in cervical screening. Particularly combined methylation analysis of a panel of genes shows most promising clinical performance, with sensitivity levels that equal or exceed that of cytology. However, the wide application of such methylation marker panels is hampered by the lack of effective multiplex assays allowing simultaneous methylation detection of various targets in a single reaction. Here, we designed and analyzed a multiplex qMSP assay for three genes whose methylation was previously found to be informative for cervical (pre)cancer (i.e. CADM1, MAL and hsa-miR-124-2) as well as a reference gene β-actin. Based on our experience, we discuss the optimization of the parameters that provide a practical approach towards multiplex qMSP design.

Methods

Primers and PCR reagents were optimized for multiplex qMSP purposes and the resulting assay was analytically validated on serial dilutions of methylated DNA in unmethylated DNA, and compared with singleplex counterparts on hrHPV-positive cervical scrapings.

Results

Upon optimization, including primer redesign and primer limiting assays, the multiplex qMSP showed the same analytical performance as the singleplex qMSPs. A strong correlation between the obtained normalized ratios of the singleplex and multiplex qMSPs on cervical scrapes was found for all three markers: CADM1 (R²=0.985), MAL (R²=0.986) and hsa-miR-124-2 (R²=0.944).

Conclusion

Multiplex qMSP offers a promising approach for high-throughput diagnostic analysis of the methylation status of multiple genes, which after proper design and validation can be equally specific, sensitive and reproducible as its singleplex versions.

Promoter methylation analysis of WNT/β-catenin signaling pathway regulators to detect adenocarcinoma or its precursor lesion of the cervix

OBJECTIVE

Cervical adenocarcinoma (AdCA) and adenocarcinoma in situ (ACIS) are frequently missed in cytology-based screening programs. Testing for high-risk human papillomavirus (hrHPV) improves their detection, but novel ACIS/AdCA specific biomarkers are needed to increase specificity for these lesions. Novel markers may be deduced from the WNT/β-catenin signaling pathway, which is aberrantly activated during cervical carcinogenesis.

METHODS

Promoter methylation of nine WNT-antagonists (APC, AXIN2, DKK3, SFRP2, SFRP4, SFRP5, SOX17, WIF1 and WNT5A) was evaluated by methylation-specific PCR (MSP) on a small series of cervical tissue specimens, including AdCA and SCC. To estimate the diagnostic potential of the genes most frequently methylated in AdCA an extended series of ACIS, AdCA, CIN3, SCC, and normal cervical tissue specimens (n=131) as well as 49 hrHPV-positive scrapings were analyzed by quantitative MSP (qMSP).

RESULTS

The frequency of DKK3 and SFRP2 methylation was significantly higher in AdCA compared to SCC, i.e. 82% vs. 18% (p<0.01) and 84% vs. 39% (p<0.01), respectively, while SOX17 methylation frequency was significantly higher in SCC than AdCA, i.e. 89% vs. 62% (p<0.05). Methylation of WIF1 was common in both AdCA (71%) and SCC (54%). Methylation frequencies ranged from 4% to 55% in precursor lesions and from 0% to 5% in normal biopsies. When tested on HPV-positive cervical scrapings, qMSP of the best ACIS/AdCA discriminator genes, i.e. DKK3 and SFRP2, detected all women with underlying ACIS/AdCA, compared to 3% of controls.

CONCLUSIONS

DKK3 and SFRP2 promoter methylation is highly indicative for the presence of ACIS/AdCA, thereby providing promising triage markers for HPV-positive women at risk of ACIS/AdCA.