Abstract PR002: Genomic predictor can discriminate between high- and low-risk DCIS

Introduction: Ductal carcinoma in situ (DCIS) is considered a non-obligate precursor of invasive ductal carcinoma. With the aim of preventing a subsequent invasive cancer, all DCIS lesions are currently treated with surgical excision often supplemented with radiotherapy (RT). To prevent DCIS over- or undertreatment, a reliable marker of DCIS invasiveness risk is urgently needed. Methods: We studied two large DCIS cohorts: the Sloane cohort, a prospective breast screening cohort from the UK (median follow-up of 11 years), and a Dutch population-based cohort (NKI, median follow-up of 13 years). FFPE tissue specimens from patients with pure primary DCIS after breast-conserving surgery (BCS) +/- RT that did develop a subsequent ipsilateral event (DCIS or invasive) were considered as cases, whereas patients that did not develop any form of recurrence up to the last follow-up or death were considered as controls. We performed copy number analysis (CNA) and RNAseq analysis on 229 cases (80 DCIS only recurrences) and 344 controls. Results: DCIS was classified into the PAM50 subtypes using RNAseq data which revealed an enrichment of luminal A phenotype in DCIS that did not recur (P = 0.01, Fisher Exact test). No single copy number aberration was more common in cases compared to controls. RNAseq data did not reveal any genes significantly over/under-expressed in cases versus controls after FDR correction. However, by limiting the analysis to samples that had not had RT and excluding pure DCIS recurrences, we could develop a penalized Cox model from RNAseq data. The model was trained on weighted samples (to correct for the biased sampling of the case-control dataset) from the NKI series with double loop cross-validation. The genes were selected using the Elastic net framework of penalization. Using this predicted hazard ratio, the samples were split into high, medium, and low-risk quantiles, with a recurrence risk of 23%, 7% and 2%, respectively at 5 years (p = 10-10, Wald test). The NKI-trained predictor was independently validated in the Sloane No RT no DCIS recurrence cohort (p = 0.02, Wald test). GSEA analysis revealed proliferation hallmarks enriched in the recurrence predictor (FDR = 0.058). The RNAseq predictor was more predictive of recurrence than PAM50, clinical features (Grade, Her2 and ER) and the 12-gene Oncotype DCIS score (p < 0.001, permutation test using the Wald statistic) in both the NKI and Sloane series. Conclusion: Genomic profiling of two independent series of DCIS with outcome data did not reveal any clear associations with recurrence until analysis was limited to a set of samples who had not had radiotherapy and DCIS recurrences were excluded. We then identified an RNAseq-based classifier that could differentiate primary DCIS in low-, medium-, and high-risk groups, and validated it in an independent cohort. This classifier, if validated in other datasets, will allow us to identify women who do not need intensive treatment for their DCIS.

Citation Format: Maria Roman Escorza, Michael Sheinman, Tycho Bismeijer, Ahmed A. Ahmed, Vandna Shah, Jeffrey R. Marks, Lorraine M. King, Anargyros Megalios, Lindy L. Visser, Marlous Hoogstrat, Helen R. Davies, Tapsi Kumar, Deborah Collyar, Hilary Stobart, Sarah Pinder, Nicholas N. Navin, Andrew Futreal, Serena Nik-Zainal, E. Shelley Hwang, Esther H. Lips, Alastair Thompson, Lodewyk F.A. Wessels, Jelle Wesseling, Elinor J. Sawyer. Genomic predictor can discriminate between high- and low-risk DCIS [abstract]. In: Proceedings of the AACR Special Conference on Rethinking DCIS: An Opportunity for Prevention?; 2022 Sep 8-11; Philadelphia, PA. Philadelphia (PA): AACR; Can Prev Res 2022;15(12 Suppl_1): Abstract nr PR002.

Abstract 5108: Copy number analysis of pure DCIS and association with recurrence

With the widespread adoption of breast cancer screening the incidence of pure ductal carcinoma in situ (DCIS) has increased. As DCIS is considered a non-obligate precursor of invasive ductal carcinoma most women with pure DCIS are treated with breast conserving surgery (BCS) +/- radiotherapy. However, for many this is likely to be overtreatment as only a minority will develop a subsequent ipsilateral recurrence. Studies also show that only ~60% of these ipsilateral recurrences are invasive disease with the remainder being pure DCIS. To predict which women are most likely to benefit from interventions, there is a need to identify biomarkers that are associated with invasive recurrence. Our aim was to assess whether copy number aberrations (CNAs) could be used to identify DCIS that was likely to recur as invasive disease or remain recurrence-free during long-time follow up.

We performed somatic copy number profiling on 309 pure DCIS samples that had not developed an ipsilateral event (controls), 198 that had developed subsequent ipsilateral invasive disease (INV-cases) and 58 that had developed subsequent ipsilateral pure DCIS (DCIS-cases). The samples were obtained from two large nation-wide cohorts: the Sloane cohort, a prospective breast screening cohort from the UK with a median follow up of 12.5 years and a Dutch population based cohort, with a median follow up of 13 years. CNAs were assessed using the CytoSNP array or low pass whole genome sequencing and analyzed using GISTIC.

Integrative cluster (IntClust) subtyping revealed that only 5 subtypes were well represented in DCIS compared to 10 in invasive disease and the distribution of clusters between INV-cases and controls was similar with the exception of IntClust 4, which was significantly more common in controls (P= 0.025, Fishers exact test). IntClust 4 is characterized to have low levels of genomic instability and a CNA-devoid. INV-cases were globally more aberrant than controls (P = 0.006, Wilcoxon test) as assessed by the chromosomal instability index (CIN) score. GISTIC identified 17 recurrent amplifications, 21 recurrent gains and 22 recurrent losses in the whole cohort. Six of these regions were more common in INV-cases compared to controls: amplifications at 17q24.1 and 8p11.23, losses at 1p36.13 and 11q23.2 ​and gains at 17q21.33​ and 16p (Nominal P < 0.05 and FDR < 0.1, Fishers exact test). Subgroup analysis of ER+, Her2- INV-cases versus controls revealed an additional differential CNA, amplification at 11q13.3 more common in cases.

DCIS-cases had similar CNAs to INV-cases and were more aberrant than controls in terms of CIN score (P < 0.037, Wilcoxon test) but not as aberrant as INV-cases.

In conclusion, we have identified potential CNAs that are associated with invasive recurrence. Further analysis will integrate gene expression with copy number data to identify which genes are being targeted by these CNAs in order to identify pathways important in progression of DCIS.

Citation Format: Ahmed A. Ahmed, Maria Roman-Escorza, Tycho Bismeijer, Michael Sheinman, Vandna Shah, Rana Shami, Jeffrey R. Marks, Lorraine M. King, Anargyros Megalios, Lindy L. Visser, Marlous Hoogstraat, Helen R. Davies, Tapsi Kumar, Deborah Collyar, Hilary Stobart, Sarah Pinder, Nicholas N. Navin, Andrew Futreal, Serena Nik-Zainal, E. Shelley Hwang, Lodewyk F. Wessels, Esther H. Lips, Alastair Thompson, Jelle Wesseling, Elinor J. Sawyer. Copy number analysis of pure DCIS and association with recurrence [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5108.

Genomic analysis defines clonal relationships of ductal carcinoma in situ and recurrent invasive breast cancer

Ductal carcinoma in situ (DCIS) is the most common form of preinvasive breast cancer and, despite treatment, a small fraction (5-10%) of DCIS patients develop subsequent invasive disease. A fundamental biologic question is whether the invasive disease arises from tumor cells in the initial DCIS or represents new unrelated disease. To address this question, we performed genomic analyses on the initial DCIS lesion and paired invasive recurrent tumors in 95 patients together with single-cell DNA sequencing in a subset of cases. Our data show that in 75% of cases the invasive recurrence was clonally related to the initial DCIS, suggesting that tumor cells were not eliminated during the initial treatment. Surprisingly, however, 18% were clonally unrelated to the DCIS, representing new independent lineages and 7% of cases were ambiguous. This knowledge is essential for accurate risk evaluation of DCIS, treatment de-escalation strategies and the identification of predictive biomarkers.

Abstract P1-22-05: Identifying predictors of invasive recurrence based on molecular profiles of DCIS lesions

Introduction Ductal carcinoma in situ (DCIS) is a non-obligate precursor of invasive breast cancer. Patients with DCIS are routinely treated by breast-conserving surgery often supplemented by radiotherapy, although many will never develop invasive disease. To date, no robust predictors of invasive breast cancer recurrence following DCIS have been identified. In our efforts to find such predictors, we performed gene expression, copy number and mutation analysis on two large DCIS cohorts with long-term follow-up. Methods Two nested case control series were analyzed, where cases are defined as DCIS with a subsequent invasive breast cancer and controls remained disease free during follow up. Cases and controls were matched on age and on follow up duration and were derived from two nation-wide cohort studies. The Sloane cohort is a prospective breast screening cohort from the UK, median follow up is 6 years (range 1-10). The Dutch cohort is population-based and had a median follow up of 13 years (range 2-23). We performed copy number analysis using CytoSNP array or low pass whole genome sequencing (lpWGS) on 310 controls and 196 cases, and RNA-seq on 295 controls and 206 cases. Results First analyses on the copy number data suggest that cases are genetically more aberrant with multiple regions of amplification compared to controls (p < 0.05). RNA-seq was used to classify DCIS into the PAM50 subtypes which did not appear to be predictive of recurrence. Initial RNA-seq analysis did not show consistent gene expression differences between cases and controls in the Sloane or Dutch cohorts, possibly explained by differences in clinical characteristics of the cohorts. A new computational method has been developed accounting for the differences in follow-up times, results will be presented at SABCS. Targeted sequencing revealed that the most common mutations were in PIK3CA and TP53, but there was no association with recurrence. Conclusion Only small molecular differences were identified between DCIS that recurs as invasive breast cancer and DCIS that remains disease-free. Currently, we are seeking to identify reproducible differences by a combined analysis of two population-based cohorts in a time dependent fashion. These will be presented at the SABCS. This work was supported by Cancer Research UK and by KWF Dutch Cancer Society (ref.C38317/A24043)

Citation Format: Tycho Bismeijer, Ahmed A Ahmed, Michael Sheinman, Maria Roman-Escorza, Vandna Shah, Jeffrey R Marks, Lorraine M King, Anargyros Megalios, Lindy L Visser, Marlous Hoogstraat, Helen R Davies, Tapsi Kumar, Deborah Collyar, Hilary Stobart, Nicholas N Navin, Andrew Futreal, Serena Nik-Zainal, Shelley Hwang, Esther H Lips, Alastair Thompson, Lodewyk FA Wessels, Elinor J Sawyer, Jelle Wesseling, Grand Challenge PRECISION Consortium. Identifying predictors of invasive recurrence based on molecular profiles of DCIS lesions [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P1-22-05.

Abstract PS16-03: Clonal relatedness of LCIS with synchronous and asynchronous invasive disease

Background: Lobular carcinoma in situ (LCIS) is typically clinically undetectable but is being increasingly diagnosed as a result of breast screening mammography and is often found associated with other breast pathologies such as invasive lobular breast cancer (ILC), invasive carcinoma of ductal /no special type (IDC) and ductal carcinoma in situ (DCIS). It is also considered a risk factor for the development of subsequent invasive breast disease. The aim of this study was to understand the genetic relationship between LCIS that presents with synchronous DCIS, IDC and/or ILC in order to ascertain whether the components have common precursors and also to understand the clonal relationship between LCIS and subsequent invasive disease. Methods: 25 cases of LCIS with synchronous ILC, 7 cases of LCIS with synchronous DCIS & IDC, and 8 pure LCIS that developed a subsequent invasive recurrence were identified from the GLACIER study (MREC 06/Q1702/64). DNA was extracted from archival paraffin embedded tissue and underwent copy number analysis using either the Oncoscan™ Array (Affymetrix) or HumanCytoSNP FFPE-12 BeadChip (Illumina). Four of 7 cases of LCIS with synchronous DCIS & IDC also underwent targeted sequencing using a custom 121 breast cancer-associated gene panel (SureSelectXT HS kit, Agilent Technologies). Clonal relatedness was assessed using a novel methodology based on the presence of shared copy number aberration breakpoints and mutations. Results: Of the 25 synchronous LCIS and ILC cases, 17 appeared related, 4 were ambiguous (sharing the typical lobular signature of 1q gain and 16q loss) and 4 demonstrated no evidence of relatedness. Of the 7 cases with synchronous LCIS, DCIS and IDC, all had copy number data available and 4 had mutation data available. In 3 cases the synchronous LCIS, DCIS and IDC were clonally related according to copy number and for two there was mutation data that supported this (one sharing PIK3CA and CDH1 mutations, the other a TP53 mutation). In two cases the LCIS was not related to the DCIS or IDC, but the DCIS and IDC were related to each other; while in one case LCIS was related to IDC but not to the DCIS by copy number but all components shared the same CHEK2 mutation. Finally in one case none of the three components were related to each other by copy number but the LCIS and IDC shared a PIK3CA mutation, albeit at much lower allele frequency in LCIS than in IDC. Of the 8 patients with pure LCIS, 4 developed an ipsilateral invasive recurrence of various combinations of morphologies: 1 ILC & LCIS, 1 ILC & DCIS, 1 IDC & DCIS, 1 ILC & IDC, and 4 a contralateral recurrence (1 tubular, 1 IDC, 2 ILC), with a median time to recurrence of 69 months (range 34-175). The primary LCIS was related to at least one component of the recurrent disease in all four ipsilateral cases; in two the primary LCIS and all components of the recurrent disease were related, and in the remainder we observed a variety of putative evolutionary patterns. Conclusions: The majority (68%) of cases of synchronous LCIS and ILC appeared to be clonally related by copy number. 50% of cases of co-existing LCIS and IDC appeared to have a common clonal origin by either copy number or targeted sequencing. As these are genomically stable tumours, copy number data may also be underestimating relatedness. In the four cases of pure primary LCIS that developed an ipsilateral recurrence, different subtypes of breast cancer were noted as the recurrence morphology, supporting the historical view that LCIS is a risk lesion rather than a true precursor. However, in all cases the preceding LCIS was found to be related to at least one component of the subsequent invasive tumour including DCIS and IDC. This data shows that clonal relatedness between LCIS and both synchronous and asynchronous invasive disease and DCIS is more complex than previously thought, with LCIS acting as a precursor lesion even in some cases of IDC.

Citation Format: Elinor Sawyer, Mateja Sborchia, Anargyros Megalios, Vandna Shah, Salpie Nowinski, Cloe Vassart, Anita Grigoriadis, Alastair Thompson, Ian Tomlinson, Rebecca Roylance, Sarah Pinder. Clonal relatedness of LCIS with synchronous and asynchronous invasive disease [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS16-03.

Abstract P4-06-05: Heterogeneity of DCIS does not appear to be a biomarker for development of subsequent invasive cancer

Genomic instability is a key feature of carcinogenesis, giving rise to tumour promoting aberrations. The inherent unpredictability of these processes leads to a high degree of intratumour heterogeneity, previously shown to be advantageous for cancer progression in a series of cancer types.

We sought to explore the role of genomic instability and intratumour heterogeneity in the progression of ductal carcinoma in situ (DCIS) to invasive disease, in a cohort of 49 women with pure DCIS that developed subsequent ipsilateral invasive disease and 90 women with pure DCIS with no evidence of recurrence with a median follow up of 5.4 years. All samples were identified from within the Sloane project, a prospective national cohort study of DCIS within the UK National Health Service Breast Screening Programme. DNA extracted from bulk tissue samples was processed on the HumanCytoSNP array, and allele-specific copy number aberration (CNA) data was obtained from ASCAT. We measured genomic instability using Scores Of Chromosomal Instability Scarring (SCINS), as well as by calculating the Shannon diversity index for the different copy number states occurring in the tumour genome. We also attempted to deconvolute the clonal structure of the tumours by applying the Shannon diversity index on the raw copy number estimates provided by ASCAT. Non-integer copy number states were interpreted as indicative of the presence of subclonal CNAs.

As a positive control, we compared ER+ and ER- DCIS in a larger cohort of 173 DCIS samples (129 ER+ and 44 ER-), using the same methods. We expect ER- tumours to be more genomically unstable, and consequentially more clonally diverse. Measured using SCINS, both copy-neutral loss of heterozygosity (≥ 4 Mbp) and allelic-imbalanced CNAs (≥ 8 Mbp) were shown to be higher in ER- tumours (Fisher’s exact test, p = 0.014 and p = 0.034, respectively). Overall genomic instability was also shown to be higher in ER- tumours using the Shannon diversity index (Fisher’s exact test, p = 0.0085). Our attempt at clonal structure deconvolution also indicates increased heterogeneity in ER- tumours (Fisher’s exact test, p = 0.027). However, no significant difference was identified in the genomic instability or heterogeneity of DCIS that developed subsequent invasive disease compared to that of indolent DCIS, using any of the aforementioned measures.

We were therefore unable to identify evidence of a direct link between DCIS heterogeneity and progression to invasive cancer. Our methods did, however, demonstrate that DCIS in general is highly genomically diverse, with ER- tumours exhibiting increased diversity compared to ER+ ones. We aim to validate these findings using spatial sampling data from our cohort, as well as integrating mutation data to allow the use of established clonal heterogeneity deconvolution pipelines.

Citation Format: Anargyros Megalios, Vandna Shah, Rana Shami, Salpie Nowinski, Jelmar Quist, Mathini Sridharan, Carolina Salinas de Souza, Karen Clements, Anita Grigoriadis, Sarah Pinder, Alastair Thompson, Elinor Sawyer. Heterogeneity of DCIS does not appear to be a biomarker for development of subsequent invasive cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-06-05.

MetaboCraft: building a Minecraft plugin for metabolomics

Motivation

The rapid advances in metabolomics pose a significant challenge in presentation and interpretation of results. Development of new, engaging visual aids is crucial to advancing our understanding of new findings.

Results

We have developed MetaboCraft, a Minecraft plugin which creates immersive visualizations of metabolic networks and pathways in a 3D environment and allows the results of user experiments to be viewed in this context, presenting a novel approach to exploring the metabolome.

Availability and implementation

https://github.com/argymeg/MetaboCraft/; https://hub.docker.com/r/ronandaly/metabocraft/

Supplementary information

Supplementary data are available at Bioinformatics online.

Frequency of pathogenic germline variants in BRCA1, BRCA2, PALB2, CHEK2 and TP53 in ductal carcinoma in situ diagnosed in women under the age of 50 years

INTRODUCTION

Ductal carcinoma in situ (DCIS) is a non-obligate precursor of invasive ductal breast cancer, and approximately 20% of screen-detected tumours are pure DCIS. Most risk factors for breast cancer have similar associations with DCIS and IDC; however, there is limited data on the prevalence of the known high and moderate penetrance breast cancer predisposition genes in DCIS and which women with DCIS should be referred for genetic screening. The aim of this study was to assess the frequency of germline variants in BRCA2, BRCA1, CHEK2, PALB2 and TP53 in DCIS in women aged less than 50 years of age.

METHODS

After DNA extraction from the peripheral blood, Access Array technology (Fluidigm) was used to amplify all exons of these five known breast cancer predisposition genes using a custom made targeted sequencing panel in 655 cases of pure DCIS presenting in women under the age of 50 years together with 1611 controls.

RESULTS

Case-control analysis revealed an excess of pathogenic variants in BRCA2 (OR = 27.96, 95%CI 6.56-119.26, P = 2.0 × 10^-10) and CHEK2 (OR = 8.04, 95%CI 2.93-22.05, P = 9.0 × 10^-6), with weaker associations with PALB2 (P = 0.003), BRCA1 (P = 0.007) and TP53 (P = 0.02). For oestrogen receptor (ER)-positive DCIS the frequency of pathogenic variants was 9% under the age of 50 (14% with a family history of breast cancer) and 29% under the age of 40 (42% with a family history of breast cancer). For ER-negative DCIS, the frequency was 9% (16% with a family history of breast cancer) and 8% (11% with a family history of breast cancer) under the ages of 50 and 40, respectively.

CONCLUSIONS

This study has shown that breast tumourigenesis in women with pathogenic variants in BRCA2, CHEK2, PALB2, BRCA1 and TP53 can involve a DCIS precursor stage and that the focus of genetic testing in DCIS should be on women under the age of 40 with ER-positive DCIS.