AbstractPurpose: Ovarian high-grade serous carcinoma (HGSC) is usually diagnosed at late stage. We investigated whether late-stage HGSC has unique genomic characteristics consistent with acquisition of evolutionary advantage compared with early-stage tumors. Experimental Design: We performed targeted next-generation sequencing and shallow whole-genome sequencing (sWGS) on pretreatment samples from 43 patients with FIGO stage I–IIA HGSC to investigate somatic mutations and copy-number (CN) alterations (SCNA). We compared results to pretreatment samples from 52 patients with stage IIIC/IV HGSC from the BriTROC-1 study. Results: Age of diagnosis did not differ between early-stage and late-stage patients (median 61.3 years vs. 62.3 years, respectively). TP53 mutations were near-universal in both cohorts (89% early-stage, 100% late-stage), and there were no significant differences in the rates of other somatic mutations, including BRCA1 and BRCA2. We also did not observe cohort-specific focal SCNA that could explain biological behavior. However, ploidy was higher in late-stage (median, 3.0) than early-stage (median, 1.9) samples. CN signature exposures were significantly different between cohorts, with greater relative signature 3 exposure in early-stage and greater signature 4 in late-stage. Unsupervised clustering based on CN signatures identified three clusters that were prognostic. Conclusions: Early-stage and late-stage HGSCs have highly similar patterns of mutation and focal SCNA. However, CN signature analysis showed that late-stage disease has distinct signature exposures consistent with whole-genome duplication. Further analyses will be required to ascertain whether these differences reflect genuine biological differences between early-stage and late-stage or simply time-related markers of evolutionary fitness. See related commentary by Yang et al., p. 2730

Dataset containing pre-processed data files required to replicate analysis performed in the publication "The genomic landscape of recurrent ovarian high grade serous carcinoma: the BriTROC-1 study" (Smith & Bradley et al. 2023).

Background: Median overall survival (OS) for women with high-grade serous ovarian cancer (HGSOC) is similar to 4 years, yet survival varies widely between patients. There are no well-established, gene expression signatures associated with prognosis. The aim of this study was to develop a robust prognostic signature for OS in patients with HGSOC. Patients and methods: Expression of 513 genes, selected from a meta-analysis of 1455 tumours and other candidates, was measured using NanoString technology from formalin-fixed paraffin-embedded tumour tissue collected from 3769 women with HGSOC from multiple studies. Elastic net regularization for survival analysis was applied to develop a prognostic model for 5-year OS, trained on 2702 tumours from 15 studies and evaluated on an independent set of 1067 tumours from six studies. Results: Expression levels of 276 genes were associated with OS (false discovery rate < 0.05) in covariate-adjusted single-gene analyses. The top five genes were TAP1, ZFHX4, CXCL9, FBN1 and PTGER3 (P < 0.001). The best performing prognostic signature included 101 genes enriched in pathways with treatment implications. Each gain of one standard deviation in the gene expression score conferred a greater than twofold increase in risk of death [hazard ratio (HR) 2.35, 95% confidence interval (CI) 2.02-2.71; P < 0.001]. Median survival [HR (95% CI)] by gene expression score quintile was 9.5 (8.3 to -), 5.4 (4.6-7.0), 3.8 (3.3-4.6), 3.2 (2.9-3.7) and 2.3 (2.1-2.6) years. Conclusion: The OTTA-SPOT (Ovarian Tumor Tissue Analysis consortium - Stratified Prognosis of Ovarian Tumours) gene expression signature may improve risk stratification in clinical trials by identifying patients who are least likely to achieve 5-year survival. The identified novel genes associated with the outcome may also yield opportunities for the development of targeted therapeutic approaches.

This article was originally published under a CC BY NC SA License, but has now been made available under a CC BY 4.0 License.

Introduction High-grade serous ovarian carcinoma (HGSOC) is characterised by ubiquitous TP53 mutations and significant copy-number alterations. Current ctDNA assays for HGSOC have focused on detection of TP53 mutations. In patients with low-stage disease or during therapy, the amount of ctDNA may be below the threshold of reliable detection. We tested whether sensitivity for ctDNA detection could be increased by combining TP53 mutations with focal genomic amplifications. Material and methods Targeted TP53 sequencing was performed on 264 plasma samples of 137 patients from the BriTROC-1 study with relapsed HGSOC tissue samples. Four patients had no somatic TP53 mutation detected and were excluded from analysis. Shallow WGS (0.1x) was performed on 256 plasma samples and matched tumour samples. The length-adjusted Z-score was calculated for each genomic segment and was used to distinguish significant focal amplifications (FA). Results and discussions TP53 mutations were detected in 180 plasma samples with median mutant allele fraction (MAF) of 5% (IQR 1.4%–16%). Twenty-five patients had at least one plasma sample with MAF >20%, which could be used for genomic profiling. Focal amplifications were observed in 151 plasma samples with a median of 4 amplifications per sample. The FA with the maximum observed Z-score per sample was significantly correlated with TP53 MAF. Both approaches detected ctDNA in about half of the samples. However, in some plasma samples ctDNA could be detected only by one of the used methods. Conclusion Combining targeted TP53 sequencing with shallow WGS may be a more sensitive approach for ctDNA detection.

Introduction Large screening studies in ovarian cancer (OC) using CA125 and transvaginal ultrasound have not shown a significant improvement in mortality. There is a need for new diagnostic biomarkers in OC. High-grade serous ovarian cancer (HGSOC) is characterised by ubiquitous TP53 mutations and extreme genomic rearrangement. Circulating tumour DNA (ctDNA) can be detected in plasma in >80% of women with relapsed HGSOC. However, detection of ctDNA in untreated, early stage patients is more challenging due to small disease volume and low levels of ctDNA. We aim to assess the proportion of women with newly diagnosed HGSOC with detectable ctDNA using a combination of sequencing assays including a new, sensitive, whole genome sequencing analysis method. Material and methods Targeted sequencing for TP53 and shallow whole genome sequencing (sWGS) were performed on 148 plasma samples collected from women with newly diagnosed, untreated HGSOC. Results and discussions Using targeted sequencing for TP53 ctDNA can be detected in 50% of newly diagnosed HGSOC. The addition of a genome wide measure of copy number aberration (t-MAD) and in-silico size selection of DNA fragments between 90–150 bp increases rates of ctDNA detection. Using the size selected t-MAD score we see a sensitivity of 80% for a specificity of 95% to discriminate HGSOC cases from healthy controls. Conclusion Plasma ctDNA can be detected in women with newly diagnosed HGSOC using targeted sequencing for TP53 and sWGS. By combining these low cost, high throughput sequencing assays we show that ctDNA has the potential be used in a diagnostic setting in HGSOC.

Laryngeal cancer is the most common type of malignant head and neck tumor worldwide. A lot of factors turn it from a disease with very good opportunities for prevention, early diagnosis, successful treatment and good prognosis into a disabling one with high death rate. The five years survival from 52% for the period from 1950 to 1954 has changed to only 64.4% for the period from 2003 to 2009. What underlies this unsatisfactory progress? As a matter of fact while the etiological factors are well known, the molecular basis of laryngeal carcinogenesis remains unrevealed

ABSTRACT Aim: Laryngeal squamous cell carcinomas (LSCC) are frequently occurring cancers with a high risk of local recurrences or second primary tumours developing within the first two years of diagnosis. A common feature of LSCC is the epigenetic inactivation of certain genes by promoter hypermethylation. In a previous study we found associations of promoter methylation with some clinical features of LSCC. The present study aimed at assessing promoter hypermethylation of CDKN2A, MGMT and MLH1 as prognostic factors in LSCC patients. Methods: We examined the methylation status of the selected three genes in 61 laryngeal tumours by Methylation-specific High-Resolution Melting and analyzed its association with the overall survival of the patients. Results: We observed promoter hypermethylation of MGMT, CDKN2A and MLH1 genes in 31 (50.8%), 25 (40.9%) and 24 (39.3%) patients, respectively. Kaplan-Meier survival analysis showed significant association of methylation status of MGMT gene with overall survival (p = 0.018). Patients with unmethylated MGMT had longer median survival (35.1 months) compared to those with methylation (25.7 months). Multivariate Cox regression confirmed that the association was independent of other clinical factors and/or smoking history of the patients. Conclusions: Our results showed that MGMT promoter methylation is a promising prognostic factor for LSCC patients. Disclosure: All authors have declared no conflicts of interest.

studied by immunoprecipitation and chromatin structure by nuclease digestion, with HepG2 as a control.Results: Expression of both DLK1 (p = 0.004) and MEG3 (p = 0.01) was significantly diminished in UC tissues and low to undectable in UC cell lines, independent of changes in gene copy numbers.Concomitant loss of expression was accompanied by distinctive methylation patterns at the DMRs and the DLK1 promoter that differed from those of either parental allele.In UC lines, histones at these sites carried modifications indicative of silencing and fixed nucleosomes.In comparison to HepG2 cells, chromatin was poorly accessible to nuclease digestion throughout the region.Conclusions: Decreased expression of DLK1 and MEG3 is highly prevalent in urothelial carcinoma.While allelic losses at 14q32 do occur in UC, the concomitant downregulation of these normally oppositely regulated imprinted genes is probably achieved by epigenetic mechanisms imposing a novel epigenetic state across the region.

negative feedback loop due to the induction of AHR pathway by dioxin-like compounds.Our results regarding a key gene in the AHR pathway will have relevance beyond tobacco smoke exposure given the key role played by this pathway in the metabolism of many environmental carcinogens.

The expression of two tumor suppressor genes, fragile histidine triad (FHIT) and WW domain containing oxidoreductase (WWOX), encompassing common chromosome fragile regions, FRA3B at 3p14.2 and FRA16D at 16q23, is altered in many epithelial tumors. Since DNA sequence search shows that the FHIT gene has the E2F-1 recognition site in 5′ region, which regulates cell cycle, we tested the effect of E2F-1 overexpression in tumor cells. Ectopic E2F-1 expression led to an increase of Fhit and Wwox expression in allele remaining tumor cells and resulted in induction of apoptosis. Reporter assay showed that the E2F-1 site in FHIT 5′ region was involved in the down-stream transcription after exogenous E2F-1 introduction. Chromatin immunoprecipitation detected exogenous E2F-1 binding to the recognition site in FHIT 5′ region. The data suggest that E2F-1 overexpression plays a role in suppression of tumor, at least in part trough transcriptional regulation of FHIT and relevant activation of WWOX.