Showing papers by "Bernard J. Pope published in 2023"

Genotoxic colibactin mutational signature in colorectal cancer is associated with clinicopathological features, specific genomic alterations and better survival

Abstract: Background and Aims The microbiome has long been suspected of a role in colorectal cancer (CRC) tumorigenesis. The mutational signature SBS88 mechanistically links CRC development with the strain of Escherichia coli harboring the pks island that produces the genotoxin colibactin, but the genomic, pathological and survival characteristics associated with SBS88-positive tumors are unknown. Methods SBS88 positive CRCs were identified from targeted sequencing data from 5,292 CRCs from 17 studies and tested for their association with clinico-pathological features, oncogenic pathways, genomic characteristics and survival. Results In total, 7.5% (398/5,292) of the CRCs were SBS88 positive, of which 98.7% (392/398) were microsatellite stable/microsatellite instability low (MSS/MSI L), compared with 80% (3916/4894) of SBS88 negative tumors (p=1.5x10-28). Analysis of MSS/MSI-L CRCs demonstrated that SBS88 positive CRCs were associated with the distal colon (OR=1.84, 95% CI=1.40-2.42, p=1x10-5) and rectum (OR=1.90, 95% CI=1.44-2.51, p=6x10-6) tumor sites compared with the proximal colon. The top seven recurrent somatic mutations associated with SBS88-positive CRCs demonstrated mutational contexts associated with colibactin-induced DNA damage, the strongest of which was the APC:c.835 8A>G mutation (OR=65.5, 95%CI=39.0-110.0, p=3x10-80). Large copy number alterations (CNAs) including CNA loss on 14q and gains on 13q, 16q and 20p were significantly enriched in SBS88-positive CRCs. SBS88-positive CRCs were associated with better CRC-specific survival (p=0.007; hazard ratio of 0.69, 95% CI=0.52-0.90) when stratified by age, sex, study, and by stage. Conclusion SBS88-positivity, a biomarker of colibactin-induced DNA damage, can identify a novel subtype of CRC characterized by recurrent somatic mutations, copy number alterations and better survival. These findings provide new insights for treatment and prevention strategies for this subtype of CRC.

A tumor focused approach to resolving the etiology of DNA mismatch repair deficient tumors classified as suspected Lynch syndrome

Abstract: Abstract Routine screening of tumors for DNA mismatch repair (MMR) deficiency (dMMR) in colorectal (CRC), endometrial (EC) and sebaceous skin (SST) tumors leads to a significant proportion of unresolved cases classified as suspected Lynch syndrome (SLS). SLS cases (n = 135) were recruited from Family Cancer Clinics across Australia and New Zealand. Targeted panel sequencing was performed on tumor (n = 137; 80×CRCs, 33×ECs and 24xSSTs) and matched blood-derived DNA to assess for microsatellite instability status, tumor mutation burden, COSMIC tumor mutational signatures and to identify germline and somatic MMR gene variants. MMR immunohistochemistry (IHC) and MLH1 promoter methylation were repeated. In total, 86.9% of the 137 SLS tumors could be resolved into established subtypes. For 22.6% of these resolved SLS cases, primary MLH1 epimutations (2.2%) as well as previously undetected germline MMR pathogenic variants (1.5%), tumor MLH1 methylation (13.1%) or false positive dMMR IHC (5.8%) results were identified. Double somatic MMR gene mutations were the major cause of dMMR identified across each tumor type (73.9% of resolved cases, 64.2% overall, 70% of CRC, 45.5% of ECs and 70.8% of SSTs). The unresolved SLS tumors (13.1%) comprised tumors with only a single somatic (7.3%) or no somatic (5.8%) MMR gene mutations. A tumor-focused testing approach reclassified 86.9% of SLS into Lynch syndrome, sporadic dMMR or MMR-proficient cases. These findings support the incorporation of tumor sequencing and alternate MLH1 methylation assays into clinical diagnostics to reduce the number of SLS patients and provide more appropriate surveillance and screening recommendations.

A polygenic two-hit hypothesis for prostate cancer.

Abstract: Prostate cancer is one of the most heritable cancers. Hundreds of germline polymorphisms have been linked to prostate cancer diagnosis and prognosis. Polygenic risk scores can predict genetic risk of a prostate cancer diagnosis. While these scores inform on the probability of developing a tumor, it remains unknown how germline risk influences the tumor molecular evolution. We cultivated a cohort of 1,250 localized European-descent patients with germline and somatic DNA profiling. Men of European descent with higher genetic risk were diagnosed earlier, had less genomic instability, and fewer driver genes mutated. Higher genetic risk was associated with better outcome. These data imply a polygenic "two-hit" model where germline risk reduces the number of somatic alterations required for tumorigenesis. These findings support further clinical studies of PRS as inexpensive and minimally invasive adjuncts to standard risk stratification. Further studies are required to interrogate generalizability to more ancestrally and clinically diverse populations.

Abstract PR012: Ultra-sensitive detection of circulating tumour DNA enriches for patients with higher risk disease in clinically localised prostate cancer

Abstract: Purpose Circulating tumour DNA (ctDNA) analysis has demonstrated utility for diagnostic and prognostic applications in many cancer types, including metastatic prostate cancer. However, localised prostate cancer yields relatively low levels of ctDNA and therefore it has been difficult to detect in this context using conventional methods. We aimed to assess the limits of detection of ctDNA in localised prostate cancer by leveraging thousands of patient-specific mutations per case with the high-sensitivity INVAR method, and to test the hypothesis that ctDNA detection is associated with high risk disease. Experimental Procedures A total of 128 individuals with clinically localised prostate cancer at the time of sample collection were selected from cohorts in Australia (n=48) and the UK (n=80). Additionally, 27 healthy individuals without prostate cancer were included as negative controls. Primary tumour tissue and matched bloods from all cases were whole genome sequenced (WGS) and somatic variants were called using pipelines from the Pan Prostate Cancer Group. Plasma cell-free DNA (cfDNA) samples from cases and controls were profiled using custom targeted sequencing panels, with saturating coverage of patient-specific mutations identified by WGS. We assessed ctDNA detection in cases using the highly sensitive INVAR pipeline, that leverages consensus read sequencing alignments, background error modelling and integration of signals across thousands of patient-specific variants. Biochemical recurrence and metastasis-free survival curves were used to assess the relationship between ctDNA detection and disease progression. Results We analysed pre-treatment blood plasma ctDNA in a large cohort of localised prostate cancer patients, using error-suppressed targeted sequencing of over 280k patient-specific mutations. To comprehensively assess ctDNA mutation analysis in this context, we combined signals across the maximum number of genome-wide patient specific mutations and leveraged an established analysis pipeline (INVAR) that corrects for background error rates and calculates a global integrated mutant allele fraction. ctDNA was detected in 9.3% of localised prostate cancer patients. In cases where ctDNA was detected we found significant associations with biochemical recurrence (p=0.01) and shorter metastasis-free survival (p < 0.0001). Conclusions Our study provides clear insights into the required analytical sensitivity and potential utility of ctDNA mutation analysis in localised prostate cancer. We found that mutation-based ctDNA detection rates were low in localised prostate cancer (<10% cases), but in ctDNA positive cases there was a significant association with relapse after surgical intervention alone. This raises the potential for including ctDNA detection as an additional tool for patient stratification in future neo/adjuvant treatment trials aiming to assess the impact of treatment escalation in men at high risk of relapse with current standard of care treatment alone. Citation Format: Bernard J. Pope, Gahee Park, Edmund Lau, Jelena Belic, Radoslaw Lach, Anne George, Patrick McCoy, Anne Nguyen, Corrina Grima, Chol-hee Jung, Emma-Jane Ditter, Hui Zhao, David Wedge, Rosalind A Eeles, Daniel Brewer, Andy G. Lynch, Harveer Dev, Christopher M Hovens, Vincent J. Gnanpragasam, Nitzan Rosenfeld, Niall M. Corcoran, Charles E. Massie. Ultra-sensitive detection of circulating tumour DNA enriches for patients with higher risk disease in clinically localised prostate cancer [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr PR012.