Clinical patterns and genomic profiling of recurrent 'ultra-low risk' endometrial cancer

OBJECTIVE

Despite good prognosis for patients with low-risk endometrial cancer, a small subset of women with low-grade/low-stage endometrial cancer experience disease recurrence and death. The aim of this study was to characterize clinical features and mutational profiles of recurrent, low-grade, non-myoinvasive, 'ultra-low risk' endometrioid endometrial adenocarcinomas.

METHODS

We retrospectively identified patients with International Federation of Gynecology and Obstetrics (FIGO) stage IA endometrioid endometrial cancers who underwent primary surgery at our institution, between January 2009 and February 2017, with follow-up of ≥12 months. 'Ultra-low risk' was defined as FIGO tumor grade 1, non-myoinvasive, and lacking lymphovascular space invasion. Tumor-normal profiling using massively parallel sequencing targeting 468 genes was performed. Microsatellite instability was assessed using MSIsensor. DNA mismatch repair (MMR) protein proficiency was determined by immunohistochemistry.

RESULTS

A total of 486 patients with ultra-low risk endometrioid endometrial cancers were identified: 14 (2.9%) of 486 patients developed a recurrence. Median follow-up for non-recurrent endometrioid endometrial cancers: 34 (range 12-116) months; for recurrent endometrioid endometrial cancers: 50.5 (range 20-116) months. Patients with recurrent disease were older, had lower body mass index, and were most commonly non-White (p=0.025, p<0.001, and p<0.001, respectively). Other clinical characteristics did not differ. MMR immunohistochemistry was obtained for 211 (43%) tumors: 158 (75%) MMR-proficient and 53 (25%) MMR-deficient. Primary tumors of 9 recurrent and 27 non-recurrent endometrioid endometrial cancers underwent mutational profiling. Most were microsatellite stable (6/9, 67% recurrent; 25/27, 93% non-recurrent). Recurrent PTEN and PIK3CA mutations were present in both groups. Exon 3 CTNNB1 hotspot mutations were found in 4/9 (44%) recurrent and 8/27 (30%) non-recurrent (p=0.44).

CONCLUSIONS

Patients diagnosed with ultra-low risk endometrioid endometrial cancers have an overall excellent prognosis. However, in our study, 2.9% of patients with no identifiable clinical or pathologic risk factors developed recurrence. Further work is warranted to elucidate the mechanism for recurrence in this population.

Unraveling tumor-immune heterogeneity in advanced ovarian cancer uncovers immunogenic effect of chemotherapy

In metastatic cancer, the degree of heterogeneity of the tumor microenvironment (TME) and its molecular underpinnings remain largely unstudied. To characterize the tumor-immune interface at baseline and during neoadjuvant chemotherapy (NACT) in high-grade serous ovarian cancer (HGSOC), we performed immunogenomic analysis of treatment-naive and paired samples from before and after treatment with chemotherapy. In treatment-naive HGSOC, we found that immune-cell-excluded and inflammatory microenvironments coexist within the same individuals and within the same tumor sites, indicating ubiquitous variability in immune cell infiltration. Analysis of TME cell composition, DNA copy number, mutations and gene expression showed that immune cell exclusion was associated with amplification of Myc target genes and increased expression of canonical Wnt signaling in treatment-naive HGSOC. Following NACT, increased natural killer (NK) cell infiltration and oligoclonal expansion of T cells were detected. We demonstrate that the tumor-immune microenvironment of advanced HGSOC is intrinsically heterogeneous and that chemotherapy induces local immune activation, suggesting that chemotherapy can potentiate the immunogenicity of immune-excluded HGSOC tumors.

Alterations in PTEN and ESR1 promote clinical resistance to alpelisib plus aromatase inhibitors

Alpelisib is a selective inhibitor of PI3Kα, shown to improve outcomes for PIK3CA mutant, hormone receptor positive (HR+) metastatic breast cancers (MBC) when combined with antiestrogen therapy. To uncover mechanisms of resistance, we conducted a detailed, longitudinal analysis of tumor and plasma circulating tumor DNA among such patients from a phase I/II trial combining alpelisib with an aromatase inhibitor (AI) (NCT01870505). The trial's primary objective was to establish safety with maculopapular rash emerging as the most common grade 3 adverse event (33%). Among 44 evaluable patients, the observed clinical benefit rate was 52%. Correlating genetic alterations with outcome, we identified loss-of-function PTEN mutations in 25% of patients with resistance. ESR1 activating mutations also expanded in number and allele fraction during treatment and were associated with resistance. These data indicate that genomic alterations that mediate resistance to alpelisib or antiestrogen may promote disease progression and highlight PTEN loss as a recurrent mechanism of resistance to PI3Kα inhibition.

Whole-Exome Sequencing Analysis of the Progression from Non-Low-Grade Ductal Carcinoma In Situ to Invasive Ductal Carcinoma

PURPOSE

Ductal carcinoma in situ (DCIS) is a nonobligate precursor of invasive breast cancer. Here, we sought to investigate the level of intralesion genetic heterogeneity in DCIS and the patterns of clonal architecture changes in the progression from DCIS to invasive disease.

EXPERIMENTAL DESIGN

Synchronous DCIS (n = 27) and invasive ductal carcinomas of no special type (IDC-NSTs; n = 26) from 25 patients, and pure DCIS (n = 7) from 7 patients were microdissected separately and subjected to high-depth whole-exome (n = 56) or massively parallel sequencing targeting ≥410 key cancer-related genes (n = 4). Somatic genetic alterations, mutational signatures, clonal composition, and phylogenetic analyses were defined using validated computational methods.

RESULTS

DCIS revealed genetic alterations similar to those of synchronously diagnosed IDC-NSTs and of non-related IDC-NSTs from The Cancer Genome Atlas (TCGA), whereas pure DCIS lacked PIK3CA mutations. Clonal decomposition and phylogenetic analyses based on somatic mutations and copy number alterations revealed that the mechanisms of progression of DCIS to invasive carcinoma are diverse, and that clonal selection might have constituted the mechanism of progression from DCIS to invasive disease in 28% (7/25) of patients. DCIS displaying a pattern of clonal selection in the progression to invasive cancer harbored higher levels of intralesion genetic heterogeneity than DCIS where no clonal selection was observed.

CONCLUSIONS

Intralesion genetic heterogeneity is a common feature in DCIS synchronously diagnosed with IDC-NST. DCIS is a nonobligate precursor of IDC-NST, whose mechanisms of progression to invasive breast cancer are diverse and vary from case to case.

Sclerosing epithelioid mesenchymal neoplasm of the pancreas - a proposed new entity

We have encountered pancreatic tumors with unique histologic features, which do not conform to any of the known tumors of the pancreas or other anatomical sites. We aimed to define their clinicopathologic features and whether they are characterized by recurrent molecular signatures. Eight cases were identified; studied histologically and by immunohistochemistry. Selected cases were also subjected to whole-exome sequencing (WES; n = 4), RNA-sequencing (n = 6), Archer FusionPlex assay (n = 5), methylation profiling using the Illumina MethylationEPIC (850k) array platform (n = 6), and TERT promoter sequencing (n = 5). Six neoplasms occurred in females. The mean age was 43 years (range: 26-75). Five occurred in the head/neck of the pancreas. All patients were treated surgically; none received neoadjuvant/adjuvant therapy. All patients are free of disease after 53 months of median follow-up (range: 8-94). The tumors were well-circumscribed, and the median size was 1.8 cm (range: 1.3-5.8). Microscopically, the unencapsulated tumors had a geographic pattern of epithelioid cell nests alternating with spindle cell fascicles. Some areas showed dense fibrosis, in which enmeshed tumor cells imparted a slit-like pattern. The predominant epithelioid cells had scant cytoplasm and round-oval nuclei with open chromatin. The spindle cells displayed irregular, hyperchromatic nuclei. Mitoses were rare. No lymph node metastases were identified. All tumors were positive for vimentin, CD99 and cytokeratin (patchy), while negative for markers of solid pseudopapillary neoplasm, neuroendocrine, acinar, myogenic/rhabdoid, vascular, melanocytic, or lymphoid differentiation, gastrointestinal stromal tumor as well as MUC4. Whole-exome sequencing revealed no recurrent somatic mutations or amplifications/homozygous deletions in any known oncogenes or tumor suppressor genes. RNA-sequencing and the Archer FusionPlex assay did not detect any recurrent likely pathogenic gene fusions. Single sample gene set enrichment analysis revealed that these tumors display a likely mesenchymal transcriptomic program. Unsupervised analysis (t-SNE) of their methylation profiles against a set of different mesenchymal neoplasms demonstrated a distinct methylation pattern. Here, we describe pancreatic neoplasms with unique morphologic/immunophenotypic features and a distinct methylation pattern, along with a lack of abnormalities in any of key genetic drivers, supporting that these neoplasms represent a novel entity with an indolent clinical course. Given their mesenchymal transcriptomic features, we propose the designation of "sclerosing epithelioid mesenchymal neoplasm" of the pancreas.

Abstract PD7-01: Identification of a high FOXA1-induced pro-metastatic enhancer signature in endocrine-resistant and metastatic breast cancer

Background: Forkhead box A1 (FOXA1) is a pioneer transcription factor (TF) for chromatin binding and function of other lineage-specific TFs essential for the normal development of endoderm-derived organs. Aberrant FOXA1 signaling, due to genetic amplification or mutations and/or overexpression, has been frequently detected in metastatic tumors of the breast, prostate, pancreas, bladder and thyroid, suggesting a general role and mechanism of FOXA1-driven tumorigenesis and disease progression. We recently reported that high levels of FOXA1 (H-FOXA1) promote endocrine-resistant (EndoR) and metastatic phenotypes in estrogen receptor (ER)+ breast cancer (BC) cells. Here we sought to uncover the role and the mechanisms by which H-FOXA1 promotes EndoR metastatic BC.

Methods: Genomic sequencing data from an ER+/HER2- metastatic BC cohort (n=781, MSK-IMPACT; cBioportal) were used to compare mutations and copy number alterations of FOXA1 and ESR1. Genome-wide FOXA1-chromatin binding (cistrome) and distribution of the enhancer marks histone H3 lysine 27 acetylation (H3K27ac) and lysine 4 mono-methylation (H3K4me1) were analyzed by ChIP-seq in MCF7 cell model with inducible H-FOXA1. FOXA1 cistrome, H3K27ac distribution, and transcriptome of a FOXA1-overexpressing pancreatic ductal adenocarcinoma cell model (PDA-hT2) were obtained from NCBI GEO (GSE99311). The core regulatory circuitry (CRC) Mapper was used to identify auto-regulatory loop of TFs induced by H-FOXA1. Gene Ontology was used for gene set functional annotation. FOXA1-associated enhancers of ER+ metastatic vs. primary tumors were analyzed using the H3K27ac epigenome data (European Nucleotide Archive, PRJEB22757).

Results: The FOXA1 and ESR1 genetic amplification and mutations displayed a largely mutually exclusive pattern in ER+/HER2- metastatic BC, suggesting a role of hyperactive FOXA1 signaling in promoting EndoR and metastatic BC distinct from that of the ESR1 mutations. FOXA1 overexpression in BC cells resulted in increased FOXA1 DNA binding and the establishment of more regions with gained H3K27ac and/or H3K4me1, suggesting a more accessible and active chromatin state. H-FOXA1-induced upregulated genes were enriched for the gained H3K27ac or H3K4me1, especially for the enhancers with both marks. An enhancer signature with gained and overlapped H3K27ac and H3K4me1 predicts genes enriched for proliferation, anti-apoptosis and developmental signaling. Upregulated genes induced by H-FOXA1 with gained enhancers were further enriched for pro-metastatic processes, sharing the same characteristics of cellular morphogenesis during embryonic development. Similar results were obtained using integrated data from the PDA-hT2 cell model, sharing enriched pro-metastatic genes predicted by the H-FOXA1-induced enhancer signature. A CRC auto-regulatory TF loop, comprising components of the AP-1 and SMAD families, was predicted to amplify the impact of this enhancer signature on activation of the pro-metastatic transcriptional programs. In line with our preclinical findings, epigenetic changes of active enhancers in ER+ metastatic vs. primary BC were associated with the H-FOXA1-induced enhancer signature.

Conclusions: Our study suggests that in ER+ metastatic BC, genetic alterations of FOXA1 leading to hyperactive FOXA1 signaling involves epigenetic evolution to promote a pro-metastatic enhancer signature. This genome-wide H-FOXA1-induced enhancer signature supports the role of H-FOXA1 in unleashing oncogenic activities of lineage-specific TFs in many types of metastatic tumors. Developing therapeutics targeting FOXA1 itself or key components of the H-FOXA1-induced CRC is warranted to treat or prevent EndoR and metastatic BC effectively via targeting the entire aberrant transcriptional programs.

Citation Format: Xiaoyong Fu, Resel Pereira, Carmine De Angelis, Sarmistha Nanda, Lanfang Qin, Jamunarani Veeraraghavan, Pier Selenica, Britta Weigelt, Jorge S Reis-Filho, Agostina Nardone, Rinath Jeselsohn, Myles Brown, Mothaffar F Rimawi, C Kent Osborne, Rachel Schiff. Identification of a high FOXA1-induced pro-metastatic enhancer signature in endocrine-resistant and metastatic breast 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 PD7-01.

Abstract P4-05-11: Methylation profiling of mucinous breast cancer

Introduction: Mucinous carcinoma of the breast (MCB) is a rare histologic form of estrogen receptor (ER)-positive/HER2-negative breast cancer characterized by tumor cells floating in lakes of mucin. As compared to invasive ductal carcinoma of no special type (IDC-NST), we have recently shown that MCBs harbor a lower frequency of PIK3CA mutations and lack concurrent 1q gains and 16q losses, hallmark genetic alterations of ER-positive breast cancer. Despite their distinctive phenotype and previous efforts to characterize their genomic landscape by whole-genome, whole-exome and RNA-sequencing, no pathognomonic somatic mutation or fusion gene underpinning MCBs or the mucinous phenotype have been identified. In this study we sought to determine whether MCBs would be defined by specific epigenetic changes.

Materials and methods: Thirty-six MCBs were subjected to DNA methylation profiling using Infinium MethylationEPIC arrays. Following quantile normalization, low quality probe filtering, and data background and dye bias correction using the ‘noob’ algorithm, methylation profiling data of MCBs were compared to those of ER-positive/HER2-negative IDC-NSTs from The Cancer Genome Atlas (TCGA) lacking concurrent 1q gains/16q losses or PIK3CA hotspot mutations and matched according to age and menopausal status at a 1:2 ratio (n=72). An enrichment analysis of the differentially methylated targets in gene promoters and enhancers was conducted using Minfi and MethylGSEA R packages. A subset of 12 MCBs of this cohort was subjected to RNA-sequencing and compared to age, menopausal status and molecular features-matched ER-positive/HER2-negative IDC-NSTs from TCGA (1:2 ratio; n=24) using gene set enrichment analysis (GSEA).

Results: Enrichment analysis of differentially methylated probes revealed a significant enrichment of targets in promoters and enhancers of mucin-encoding genes and in genes of the mTOR signaling pathway between MCBs and matched IDC-NSTs from TCGA (P&lt;0.01). Compared to matched IDC-NSTs, MCBs displayed promoter/enhancer hypomethylation of mucin-encoding genes, such as MUC1, MUC2 and MUCL1. We also observed promoter/enhancer hypomethylation of mTOR signaling pathway genes including MTOR, which encodes for the catalytic subunit of the mTORC complex, RPTOR, which codes for an mTOR binding protein that positively regulates the downstream effector S6 Kinase 1, EIF4E and EIF4B, key downstream effectors of the mTOR signaling pathway, and the oncogenes PIK3R2 and PIK3R3, which encode for regulatory isoforms of PI3K, in MCBs. Our gene expression analysis revealed that the mucin-encoding genes MUC1, MUC2 and MUCL1, and the mTOR signaling genes MTOR, RPTOR, EIF4E, EPIF4B, PIK3R1 and PIK3R2, found to be hypomethylated in MCBs, displayed a significantly higher gene expression in MCBs (P&lt;0.001, each) compared to clinically and molecularly matched IDC-NSTs.

Conclusions: Taken together, our data suggest that MCBs display a high expression of mucin-encoding genes, due to hypomethylation of promoters and enhancers and could provide the basis for their distinctive phenotype. Moreover, our findings suggest that despite the lack of genetic alterations affecting genes of the PI3K/mTOR signaling pathway in MCBs, mTOR signaling might be constitutively active in these tumors via epigenetic mechanisms, supporting the notion that, in the absence of pathognomonic genetic alterations, a disruption of the epigenetic landscape is a critical driver in the development of this rare breast cancer type.

Citation Format: Fresia Pareja, Lorenzo Ferrando, Edaise M da Silva, Arnaud Da Cruz Paula, Anthe Stylianou, David N Brown, Pier Selenica, Jonathan Serrano, Hannah Y Wen, Hong Zhang, Edi Brogi, Larry Norton, Matjia Snuderl, Jorge S Reis-Filho, Britta Weigelt. Methylation profiling of mucinous breast 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 P4-05-11.

Abstract PD8-06: The genomic landscape of metastatic special histologic types of breast cancer

Introduction: Breast cancer (BC) is heterogeneous and comprises diverse entities with distinctive phenotypes, biology and clinical presentations. There are 21 special histologic types, accounting for approximately 20% of invasive BCs. Large-scale sequencing studies have focused preferentially on common histologic forms, and data on the genomic landscape of special histologic types, particularly in the metastatic setting, are scarce. Here, we sought to define the repertoire of somatic genetic alterations of metastatic special histologic types of BC.

Materials and methods: We conducted a reanalysis of MSK-IMPACT targeted sequencing data of 346 special histologic types of BC from Razavi et al (Cancer Cell 2018), including invasive lobular (ILC; primary, n=129; metastasis, n=150), mucinous (primary n=11, metastasis n=5), micropapillary (primary n=8, metastasis n=13) and metaplastic carcinomas (primary, n=6; metastasis, n=11). Somatic single nucleotide variants (SNVs) and copy number alterations (CNAs) were inferred using a validated bioinformatics pipeline, and mutational signatures were assessed with SigMA. Genetic alterations of metastatic special histologic type BCs were compared to those of primary tumors and metastatic invasive ductal carcinomas of no special type (IDC-NSTs) matched by age, menopausal status and estrogen receptor (ER)/HER2 status at a 1:2 ratio for ILCs and at a 1:3 ratio for the remaining BCs.

Results: The most frequently mutated genes in metastatic ILCs were CDH1 (71%), PIK3CA (49%), ESR1 (20%) and KMT2C (19%). ESR1 mutations were more frequent in metastatic than in primary ILCs (20% vs 3%; P&lt;0.01). Metastatic ILCs, as compared to matched metastatic IDC-NSTs, had a higher frequency of mutations in CDH1 (71% vs 2%; P&lt;0.001), KMT2C (19% vs 10%; P&lt;0.05), TBX3 (16% vs 5%; P&lt;0.001), ERBB2 (12% vs 3%; P&lt;0.01) and FOXA1 (10% vs 2%; P&lt;0.05), and a lower frequency of mutations in TP53 (16% vs 36%; P&lt;0.001) and GATA3 (6% vs 16%; P&lt;0.01). GATA3, NCOR1 and ESR1 (each, 40%) were the most frequently mutated genes in metastatic mucinous BCs. ESR1 and NCOR were numerically more frequent in metastatic than in primary mucinous BCs (40% vs 0%; P&gt;0.05). Metastatic mucinous BCs had a numerically higher frequency of mutations in ESR1 (40% vs 6%; P&gt;0.05) and GATA3 (40% vs 0%; P&gt;0.05), and lower frequency of TP53 mutations (20% vs 53%; P&gt;0.05) than matched metastatic IDC-NSTs. PIK3CA and TP53 were the most recurrently mutated genes in metastatic micropapillary BCs and were numerically more frequent in metastatic than in primary tumors (PIK3CA, 61% vs 25%; TP53, 46% vs 25%; P&gt;0.05). PIK3CA was more frequently mutated in metastatic micropapillary BCs than IDC-NSTs (61% vs 23%; P&lt;0.05). Metastatic metaplastic BCs most frequently harbored mutations in TP53 (72%) and PIK3CA (45%), with comparable frequencies in primary metaplastic BCs. ATM (27% vs 3%; P&lt;0.05), MAP3K13 and YAP1 (27% vs 0%; P&lt;0.05) were more frequently mutated in metastatic metaplastic BCs than in matched IDC-NSTs. No differences in the frequency of CNAs were seen between metastatic BCs of special histologic type and matched primary tumors or metastatic IDC-NSTs. Akin to metastatic IDC-NSTs, aging or APOBEC were the predominant mutational SNV signatures in metastatic ILCs, micropapillary and metaplastic BCs.

Conclusions: The repertoire of somatic genetic alterations of primary and metastatic special histologic type BCs markedly overlaps. Nonetheless, there is an enrichment of mutations in ESR1 in metastatic BCs of typically ER-positive special histologic type. Metastatic BCs of special histologic type show an enrichment of similar genetic alterations as primary tumors, such as a higher frequency of mutations in CDH1, FOXA1 and TBX3 in ILCs, a lower frequency of PIK3CA and TP53 mutations in mucinous BCs and a higher frequency of PIK3CA and TP53 mutations in micropapillary and metaplastic BCs.

Citation Format: Fresia Pareja, Simon SK Lee, Francisco Beca, Lorenzo Ferrando, Pier Selenica, David N Brown, Hannah Y Wen, Hong Zhang, Edi Brogi, Pedram Razavi, Sarat Chandarlapaty, Britta Weigelt, Jorge S Reis-Filho. The genomic landscape of metastatic special histologic types of breast 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 PD8-06.

Abstract P6-09-01: RAD51B loss-of-function variants confer susceptibility to hereditary breast and ovarian cancers and result in tumors with genomic features of homologous recombination repair defects

Introduction: Germline pathogenic variants in genes in the homologous recombination (HR) pathway such as BRCA1, BRCA2, ATM, PALB2, RAD51C and RAD51D confer an increased risk of breast and ovarian cancers. Screening for germline variants in these cancer susceptibility genes is critical as prophylactic measures and monitoring can be performed in these individuals to minimize their risk of developing breast and/or ovarian cancers. More recently, it has been recognized that cancers arising in carriers of germline pathogenic (P)/ likely pathogenic (LP) variants in HR genes often show a homologous recombination (HR) deficient (HRD) phenotype and can be targeted with platinum agents or PARP inhibitors. RAD51B is a RAD51 paralog that binds to RAD51C and functions as a heterodimer in the HR pathway. Whilst RAD51B germline variants have been reported in isolated cases of breast and ovarian cancers, it is unclear as to whether RAD51B P/LP germline variants would confer predisposition to these cancer types. Materials and Methods: We screened 9,287 consecutive unselected cancer patients who consented for both tumor and germline testing using the MSK-IMPACT platform for the presence of RAD51B germline truncating variants. Selected RAD51B germline mutant breast cancers identified by MSK-IMPACT were subjected to whole-exome sequencing (WES) analysis to determine the dominant mutational signatures using DeconstructSigs. Functional assays were performed to ascertain the impact of RAD51B loss on HR DNA repair and PARP inhibitor sensitivity using genome editing methods in non-malignant breast epithelial cell lines. Results: Out of the 9,287 cancer patients, we detected likely pathogenic loss of function RAD51B germline variants in 11 patients (0.12%), which was similar to the frequency detected in the gnomAD database (0.09%). All female carriers of RAD51B loss of function variants (n=8) had breast or ovarian cancers (8/1,619 breast or ovarian cancers, 0.5%). The observed carrier frequencies of germline truncating variants in RAD51B was statistically enriched in breast and ovarian cancer patients compared to individuals in the gnomAD database (0.5% vs 0.09% P=0.0003; odds ratio = 5.06 (95% CI: 2.1-10.3)). Although segregation studies were not available, 9/11 of the RAD51B germline loss of function variant carriers had a personal or family history of breast or ovarian cancers. All five breast and ovarian cancers from RAD51B mutation carriers investigated by WES were found to harbor RAD51B bi-allelic inactivation through loss of heterozygosity of the RAD51B wild-type allele. In addition, these five cases were found to display genomic features of HRD including high large-scale state transition scores and a dominant mutational signature 3. CRISPR/Cas9 genome editing of RAD51B in a non-malignant breast epithelial cell model revealed that RAD51B deficient cells display PARP inhibitor sensitivity similar to that reported in BRCA1 and BRCA2 deficient cell lines. Conclusion: RAD51B loss-of-function germline variants confer susceptibility to breast and ovarian cancer development. Breast and ovarian cancers occurring in the context of RAD51B germline mutations harbor bi-allelic inactivation of RAD51B through loss-of-heterozygosity of the wild-type allele, genomic features of HRD and are likely sensitive to PARP inhibition. Albeit rarely germline mutated, RAD51B should be considered as an addition to clinical germline testing panels for hereditary breast and ovarian cancer syndrome patients. &lt;!–EndFragment→

Citation Format: Diana SReis-FilhoReis-Filho Mandelker, Semanti Mukherjee, Jeremy Setton, Pier Selenica, Yelena Kemel, Ozge Ceyhan-Birsoy, Margaret Sheehan, Kaitlyn Tkachuk, David N Brown, Simon Powell, Britta Weigelt, Mark E Robson, Nadeem Riaz, Kenneth Offit, Jorge S Reis-Filho. RAD51B loss-of-function variants confer susceptibility to hereditary breast and ovarian cancers and result in tumors with genomic features of homologous recombination repair defects [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 P6-09-01.

Abstract P4-05-01: Massively parallel sequencing analysis of microsatellite instability in breast cancer

Introduction: Breast cancers (BCs) with microsatellite instability (MSI)/DNA mismatch repair (MMR) deficiency are rare. Their identification is key, given that these tumors might be sensitive to immune checkpoint blockade. Here we sought to define the characteristics of primary and metastatic MSI-high (MSI-H) BCs using massively parallel sequencing.

Materials and methods: To define MSI, MSISensor was applied to MSK-IMPACT targeted sequencing data of 918 primary BCs (pBCs) and 1,000 metastatic BCs (mBCs), and MSISensor and MANTIS to whole-exome sequencing (WES) data of 1,084 pBCs from The Cancer Genome Atlas (TCGA) BC project. BCs were classified as MSI-H if they displayed an MSISensor score ≥3.5 for WES or ≥10 for targeted sequencing data, or a MANTIS score ≥0.4 for WES data. The dominant mutational signature was inferred using SigMA in cases harboring at least 5 single nucleotide variants (SNVs). Mann-Whitney U and Fisher’s exact t-tests were employed for statistical analyses.

Results: MSISensor classified 0.3% (3/903) of pBCs and 0.3% (3/965) of the mBCs subjected to MSK-IMPACT sequencing as MSI-H. The MSI-H pBCs were invasive ductal carcinomas (IDC), preferentially ER-positive/HER2-negative (66.6%). Compared to MSS pBCs, MSI-H pBCs displayed a higher tumor mutational burden (TMB; 11.2 vs 2.6 somatic mutations) and were enriched for dominant MMR mutational signatures 20 or 26 (33% vs 1.1%). MSI-H mBCs were all ER-positive/HER2-negative IDCs, displayed similar TMBs, percentage of small insertions and deletions (indels) and fraction of the genome altered (FGA) as compared to MSS mBCs. Only one of the three MSI-H mBCs had enough SNVs for inference of a dominant mutational signature, which was aging. MSISensor and MANTIS classified 1.5% (11/735) and 1.8% (15/836) of pBCs from TCGA as MSI-H. We observed a moderate agreement between MSISensor and MANTIS (Cohen’s Kappa = 0.552) with 1% (7/735) of pBCs being classified as MSI-H by both algorithms. pBCs from TCGA classified as MSI by either MSISensor or MANTIS were IDCs (90.9% and 85.7%, respectively) and invasive lobular carcinoma (ILC; 9.1% and 14.3%, respectively), and were either ER-positive/HER2-negative (45.5% and 42.9%, respectively) or ER-negative/HER2-negative (45.5% and 42.9%, respectively). These MSI-H pBCs (TCGA) displayed a higher TMB (MSISensor: 12.7 vs 0.8; MANTIS: 3.6 vs 0.8; both P&lt;0.01), percentage of indels (MSISensor: 8.2% vs 4.7%; MANTIS: 8.1% vs 4.8%, both P&lt;0.01) and were enriched for dominant MMR mutational signatures 15, 20 or 26 (MSISensor: 63.6% vs 1.4%, MANTIS: 46.7% vs 1.2%, both P&lt;0.01) than MSS pBCs. pBCs from TCGA classified as MSI by both MSISensor and MANTIS were IDCs (85.7%) and ILCs (14.3%), and were preferentially ER-positive/HER2-negative or ER-negative/HER2-negative (42.9%, each). Compared to MSS pBCs, MSI-H pBCs from TCGA displayed a higher TMB (17.4 MSI-H vs 0.8 MSS; P&lt;0.01), percentage of indels (12.1% MSI-H vs 4.7% MSS; P&lt;0.01) and an enrichment for dominant MMR mutational signatures 15, 20 or 26 (87.5% MSI-H vs 1.4% MSS; P&lt;0.01).

Conclusions: We observed a moderate agreement between different MSI detection algorithms in the classification of pBCs as MSI-H based on WES analysis. pBCs classified as MSI-H were of common histologic types, either ER-positive/HER2-negative or ER-negative/HER2-negative, and displayed features characteristic of MSI, including a high TMB, high percentage of indels and an enrichment for MMR deficiency mutational signatures. mBCs classified as MSI-H by targeted capture sequencing were found to be of ER-positive/HER2-negative phenotype.

Citation Format: Pier Selenica, Fresia Pareja, Lorenzo Ferrando, David N Brown, Nadeem Riaz, Britta Weigelt, Joshua Z Drago, Mark E Robson, Pedram Razavi, Sarat Chandarlapaty, Jorge S Reis-Filho. Massively parallel sequencing analysis of microsatellite instability in breast 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 P4-05-01.

Abstract GS2-01: High levels of interferon-response gene signatures are associated with de novo and acquired resistance to CDK4/6 inhibitors in ER+ breast cancer

Background: The CDK4/6 inhibitors (i) palbociclib (Palbo), ribociclib, and abemaciclib remarkably improved the outcome of patients with metastatic ER+/HER2- breast cancer (BC) and are now under clinical investigation in early BC. Despite high efficacy, de novo and acquired resistance to CDK4/6i is common. Elucidating the molecular basis for sensitivity and resistance to CDK4/6i is crucial to identify predictive biomarkers and novel therapeutic targets to improve patient outcome. Materials and Methods: MCF7, T47D and ZR75-1 parental (P) BC cells and their derivatives made resistant to tamoxifen, estrogen deprivation (EDR), or fulvestrant were used. The P and EDR models of MCF7 and T47D cells were chronically exposed to increasing concentrations of Palbo to generate derivatives with acquired resistance to Palbo (PalboR). The transcriptomic profiles of P, endocrine-resistant (EndoR) and PalboR models were determined by RNA-seq. IC50s were determined by exposing MCF7, T47D, and ZR75-1 P and EndoR lines (n=12) to increasing concentrations of Palbo. Cell growth was assessed by methylene blue staining, and changes in the mRNA and protein levels of key cell cycle molecules were assessed by RT-PCR and Western blot, respectively. Gene expression data from the Cancer Dependency Map (DepMap), baseline tumors from the NeoPalAna (NCT01723774) and neoMONARCH (NCT02441946) neoadjuvant trials, as well as the TCGA and METABRIC datasets were interrogated for correlations of gene signatures and patient outcome (by KMPlot). Results: Palbo treatment resulted in a dose-dependent inhibition of the growth of P and EndoR BC cell lines, with varying degree of sensitivity among the models. GSEA analysis comparing the least sensitive (IC50&gt;350nM) vs. the most sensitive (IC50&lt;100) cell lines identified the ‘interferon gamma response’ (IFNg) and ‘interferon alpha response’ (IFNa) as the top-ranked hallmark enriched signatures. Likewise, DepMap analysis of ER+/HER2- BC cell lines (n=11) revealed that cells with low CDK4 dependency scores displayed high IFN-signaling. We derived a 35-gene signature (termed ‘IFN-Related Palbociclib-Resistance Signature’, IRPS) comprised of genes belonging to the INFg and INFa gene sets that positively correlated with the Palbo IC50 values of our collection of P and EndoR lines. To extend these findings to primary ER+ BC, we interrogated transcriptomic data from the NeoPalAna and neoMONARCH trials that evaluated neoadjuvant CDK4/6i with endocrine therapy. In both trials, the IFNg, IFNa, and IRPS gene signatures were highly enriched in patients with tumors exhibiting intrinsic resistance to CDK4/6i. We next investigated the underlying molecular changes and their association with IFN-signaling in our acquired resistant PalboR cell lines. Compared to the untreated cells, the PalboR models commonly displayed alterations in several components of the cyclin D-CDK4/6-Rb axis, including elevated expression of cyclin-D1, -E1, and CDK6, and reduced levels of Rb. Notably, the PalboR derivatives commonly displayed a dramatic activation of IFN/STAT1-signaling compared to their short-term treated or untreated counterparts. In primary ER+/HER2- tumors, the IRPS score was significantly higher in lumB vs. lumA subtype and correlated with increased gene expression of immune checkpoints (PD-1, PD-L1, CTLA-4), endocrine-resistance, and poor prognosis. Conclusion: Aberrant IFN-signaling predicts resistance to CDK4/6i in both ER+/HER2- BC cell lines and in primary BCs from neoadjuvant clinical trials. Experimentally, acquired resistance to Palbo is associated with activation of the IFN-pathway suggesting its involvement in resistance to CDK4/6i. Future studies are warranted to provide mechanistic insights into the association of IFN-signaling with response to CDK4/6i.

Citation Format: Carmine De Angelis, Xiaoyong Fu, Maria Letizia Cataldo, Agostina Nardone, Valerie M. Jansen, Jamunarani Veeraraghavan, Sarmistha Nanda, Lanfang Qin, Vidyalakshmi Sethunath, Resel Pereira, Matteo Benelli, Ilenia Migliaccio, Luca Malorni, Joshua Donaldson, Pier Selenica, David N. Brown, Britta Weigelt, Jorge S. Reis-Filho, Ben H. Park, Sara A. Hurvitz, Dennis J. Slamon, Mothaffar F. Rimawi, Rinath Jeselsohn, Kent Osborne, Rachel Schiff. High levels of interferon-response gene signatures are associated with de novo and acquired resistance to CDK4/6 inhibitors in ER+ breast 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 GS2-01.

Abstract P4-05-08: Genomic landscape of breast cancer occurring in elderly individuals

Introduction: There is evidence to suggest that the biology of breast cancer (BC) might vary according to age, as BCs in elderly patients might be associated with accumulation of DNA damage and BCs in younger individuals might be enriched for genetic alterations affecting cancer predisposition genes. Whether the genetic landscape of BC in elderly individuals differs is yet to be determined. Here, we sought to describe the spectrum of somatic genetic alterations and mutational signatures in BC according to age.

Materials and Methods: We conducted a re-analysis of two cohorts of BC: i) MSK-IMPACT targeted sequencing cohort (primary, n=918; metastatic, n=1,000) and ii) whole-exome sequencing data of primary BCs from The Cancer Genome Atlas (TCGA) BC study (n=1087). BCs of younger (&lt;65 years old) and elderly individuals (≥ 65 years old) were compared, matched by estrogen receptor (ER)/HER2 status at a 2:1 ratio (MSK-IMPACT) or a 1:1 ratio (TCGA). Somatic single nucleotide variants and copy number alterations (CNAs) were determined using a validated bioinformatics pipeline, and mutational signatures were defined using DeconstructSigs and SigMA. Two-tailed Fisher’s exact test was performed.

Results: Primary BCs in elderly and younger patients, matched by ER/HER2 status, from the MSK-IMPACT (n=220 and n=440) and TCGA (n=290, each) cohorts, and metastatic BCs from elderly (n=98) and younger (n=196) patients from the MSK-IMPACT cohort, matched by ER/HER2 status, were compared. In both cohorts of primary BCs, PIK3CA, TP53 and CDH1 were the most frequently mutated genes. Compared to younger patients, primary BCs in elderly patients from the MSK-IMPACT cohort displayed a lower frequency of mutations in TP53 (23% vs 34%, P&lt;0.01), AKT1 (2% vs 6%, P&lt;0.05) and MAP2K4 (0.4% vs 4%, P&lt;0.01). In the TCGA cohort, somatic mutations in AKT1 were found to be less frequent in elderly than in younger patients (1% vs 5%, P&lt;0.05), whereas NF1 (2% vs 6%, P&lt;0.05) mutations were more frequent in elderly than in younger patients with primary BCs. Our analyses of BC metastases subjected to MSK-IMPACT revealed that elderly patients harbored a higher frequency of mutations in NCOR1 (11% vs 4%, P&lt;0.05) and RUNX1 (9% vs 2%, P&lt;0.05) than younger patients. The frequency of bi-allelic inactivation of homologous recombination DNA repair deficiency (HRD) genes (i.e. BRCA1, BRCA2, PALB2, RAD51C and RAD51D) in primary BCs of elderly and younger individuals in the TCGA cohort was 2% and 5%, respectively. No differences in the frequency of CNAs were observed between the two groups. The most frequent mutational signatures found in primary BCs of elderly and younger patients were aging, APOBEC and HRD in the MSK-IMPACT cohort, and aging, APOBEC and HRD in primary BCs of the TCGA cohort, with APOBEC being enriched in younger patients compared to elderly patients. The most frequent mutational signatures in metastatic BCs in elderly and younger individuals of the MSK-IMPACT cohort were APOBEC followed by aging and HRD.

Conclusion: Our findings show that BCs in elderly patients harbor a lower frequency of somatic mutations in TP53, AKT1 and MAP2K4 than younger individuals. In contrast, BCs in elderly patients more frequently harbor somatic mutations in the transcription factors RUNX1 and NCOR1. Bi-allelic alterations affecting HRD-related genes was numerically more frequent in younger than in older patients. As expected, BCs in elderly patients show a numerically higher incidence of the aging signature, whereas primary BCs affecting younger patients displayed a higher frequency of the APOBEC signature than primary BCs from elderly individuals.

Citation Format: Pier Selenica, Fresia Pareja, Audree Tadros, Lorenzo Ferrando, David N Brown, Hong Zhang, Pedram Razavi, Diana Mandelker, Mark E Robson, Sarat Chandarlapaty, Britta Weigelt, Jorge S Reis-Filho. Genomic landscape of breast cancer occurring in elderly individuals [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 P4-05-08.

Abstract P4-05-07: Whole-exome and RNA-sequencing analyses of acinic cell carcinomas of the breast

Introduction: Acinic cell carcinoma of the breast (ACC) is an exceedingly rare histologic form of triple-negative breast cancer (TNBC) with a generally good clinical behavior. Despite its unique histology, targeted sequencing analysis of ACC has failed to identify recurrent genetic alterations other than those found in common forms of TNBC. Here, we subjected three breast ACCs to whole-exome and RNA-sequencing, seeking to define whether they would be underpinned by a pathognomonic genetic alteration that would distinguish them from common forms of TNBC.

Materials and methods: Three breast ACCs were subjected to whole-exome sequencing (WES) and RNA-sequencing. Somatic mutations, copy number alterations, mutational signatures and fusion genes were determined using a validated bioinformatics pipeline. We also estimated DNA-based measures of genomic instability including mutational signatures (using SigMA), large-scale state transition (LST) and telomeric allelic imbalance (NtAI).

Results: No oncogenic in-frame fusion transcript was identified in the breast ACCs analyzed. ACCs displayed a median of 173 (range, 92-230) non-synonymous somatic mutations as defined by WES. We detected clonal TP53 hotspot mutations associated with loss of heterozygosity (LOH) of the wild-type allele in two ACCs (ACC1 and ACC18). In contrast, the TP53 wild-type ACC (ACC12) harbored a pathogenic MLH1 germline mutation (p.Glu227_Ser295del) and a clonal hotspot mutation in CTNNB1 (p.Lys335Ile). No cancer gene other than TP53 was found to be mutated in &gt;1 case. Copy number analysis revealed that ACC18 harbored a BRCA1 homozygous deletion and focal amplification of 20p12.3 encompassing PCNA. Moreover, the TP53-mutant cases, ACC1 and ACC18, displayed complex copy number profiles, with multiple gains and losses and focal high-level amplifications. Consistent with the BRCA1 homozygous deletion, ACC18 displayed genomic features of homologous recombination DNA repair deficiency (HRD), such as a dominant mutational signature 3, a high LST score (24), a high NtAI score (23) and a high number of ‘small deletions’ &gt;5bps. In contrast, and consistent with its DNA mismatch repair (MMR) deficiency, ACC12 had a simple genome without detectable copy number alterations, displayed a dominant mutational signature 6 associated with defective MMR, microsatellite instability (MSI) as determined by MSIsensor and loss of MLH1 expression by immunohistochemical analysis.

Conclusions: Our findings lend further support to the notion that ACCs of the breast are genetically heterogeneous and display genomic features overlapping with those of common forms of TNBCs. Although no pathognomonic genetic alterations were detected in these cases, our data suggest that at least some ACCs of the breast may arise in the setting of HRD or MSI through distinct molecular mechanisms. Our data also suggest the possibility that both BRCA1 and TP53 loss of function may not be sufficient for a TNBC to display high-grade features and that inactivation of these two genes may not necessarily result in the development of high-grade TNBC.

Citation Format: Francisco Beca, Simon SK Lee, Fresia Pareja, Arnaud Da Cruz Paula, Pier Selenica, Lorenzo Ferrando, Hannah Y Wen, Hong Zhang, Elena Guerini-Rocco, Emad A Rakha, Britta Weigelt, Jorge S Reis-Filho. Whole-exome and RNA-sequencing analyses of acinic cell carcinomas of the breast [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 P4-05-07.

Molecular Characterization of a Rare Dedifferentiated Liposarcoma With Rhabdomyosarcomatous Differentiation in a 24 Year Old

Aims. The aim of this study was to identify potential driver genetic alterations in a dedifferentiated liposarcoma (DDLPS) with rhabdomyosarcomatous differentiation. Methods and Results. A 24-year-old female underwent resection of an abdominal mass, which on a previous biopsy demonstrated rhabdomyosarcomatous differentiation concerning for embryonal rhabdomyosarcoma. Histologically the resected tumor displayed a high-grade sarcoma with rhabdomyosarcomatous differentiation in the background of well-differentiated liposarcoma consistent with DDLPS. Fluorescence in situ hybridization confirmed MDM2 amplification, as did array-based copy number profiling. Whole-exome sequencing revealed a somatic FGFR1 hotspot mutation and RNA sequencing an LMNB2-MAP2K6 fusion only within the dedifferentiated component. Conclusions. This study represents an in-depth examination of a rare DDLPS with rhabdomyosarcomatous differentiation in a young individual. Additionally, it is also instructive of a potential pitfall when assessing for MDM2 amplification in small biopsies. Despite exhaustive analysis, mutation and gene copy number analysis did not identify any molecular events that would underlie the rhabdomyoblastic differentiation. Our understanding of what causes some tumors to dedifferentiate as well as undergo divergent differentiation is limited, and larger studies are needed.

Whole-exome sequencing and RNA sequencing analyses of acinic cell carcinomas of the breast

AIMS

Acinic cell carcinoma (ACC) of the breast is a rare histological form of triple-negative breast cancer (TNBC). Despite its unique histology, targeted sequencing analysis has failed to identify recurrent genetic alterations other than those found in common forms of TNBC. Here we subjected three breast ACCs to whole-exome and RNA sequencing to determine whether they would harbour a pathognomonic genetic alteration.

METHODS AND RESULTS

DNA and RNA samples from three breast ACCs were subjected to whole-exome sequencing and RNA-sequencing, respectively. Somatic mutations, copy number alterations, mutational signatures and fusion genes were determined with state-of-the-art bioinformatics methods. Our analyses revealed TP53 hotspot mutations associated with loss of heterozygosity of the wild-type allele in two cases. Mutations affecting homologous recombination DNA repair-related genes were found in two cases, and an MLH1 pathogenic germline variant was found in one case. In addition, copy number analysis revealed the presence of a somatic BRCA1 homozygous deletion and focal amplification of 12q14.3-12q21.1, encompassing MDM2, HMGA2, FRS2, and PTPRB. No oncogenic in-frame fusion transcript was identified in the three breast ACCs analysed.

CONCLUSIONS

No pathognomonic genetic alterations were detected in the breast ACCs analysed. These tumours have somatic genetic alterations similar to those of common forms of TNBC, and may show homologous recombination deficiency or microsatellite instability. These findings provide further insights into why breast ACCs, which are usually clinically indolent, may evolve into or in parallel with high-grade TNBC.

The molecular genetic make-up of male breast cancer

Male breast cancer (MBC) is extremely rare and accounts for less than 1% of all breast malignancies. Therefore, clinical management of MBC is currently guided by research on the disease in females. In this study, DNA obtained from 45 formalin-fixed paraffin-embedded (FFPE) MBCs with and 90 MBCs (52 FFPE and 38 fresh-frozen) without matched normal tissues was subjected to massively parallel sequencing targeting all exons of 1943 cancer-related genes. The landscape of mutations and copy number alterations was compared to that of publicly available estrogen receptor (ER)-positive female breast cancers (smFBCs) and correlated to prognosis. From the 135 MBCs, 90% showed ductal histology, 96% were ER-positive, 66% were progesterone receptor (PR)-positive, and 2% HER2-positive, resulting in 50, 46 and 4% luminal A-like, luminal B-like and basal-like cases, respectively. Five patients had Klinefelter syndrome (4%) and 11% of patients harbored pathogenic BRCA2 germline mutations. The genomic landscape of MBC to some extent recapitulated that of smFBC, with recurrent PIK3CA (36%) and GATA3 (15%) somatic mutations, and with 40% of the most frequently amplified genes overlapping between both sexes. TP53 (3%) somatic mutations were significantly less frequent in MBC compared to smFBC, whereas somatic mutations in genes regulating chromatin function and homologous recombination deficiency-related signatures were more prevalent. MDM2 amplifications were frequent (13%), correlated with protein overexpression (P = 0.001) and predicted poor outcome (P = 0.007). In conclusion, despite similarities in the genomic landscape between MBC and smFBC, MBC is a molecularly unique and heterogeneous disease requiring its own clinical trials and treatment guidelines.

Homologous recombination DNA repair defects in PALB2-associated breast cancers

Mono-allelic germline pathogenic variants in the Partner And Localizer of BRCA2 (PALB2) gene predispose to a high-risk of breast cancer development, consistent with the role of PALB2 in homologous recombination (HR) DNA repair. Here, we sought to define the repertoire of somatic genetic alterations in PALB2-associated breast cancers (BCs), and whether PALB2-associated BCs display bi-allelic inactivation of PALB2 and/or genomic features of HR-deficiency (HRD). Twenty-four breast cancer patients with pathogenic PALB2 germline mutations were analyzed by whole-exome sequencing (WES, n = 16) or targeted capture massively parallel sequencing (410 cancer genes, n = 8). Somatic genetic alterations, loss of heterozygosity (LOH) of the PALB2 wild-type allele, large-scale state transitions (LSTs) and mutational signatures were defined. PALB2-associated BCs were found to be heterogeneous at the genetic level, with PIK3CA (29%), PALB2 (21%), TP53 (21%), and NOTCH3 (17%) being the genes most frequently affected by somatic mutations. Bi-allelic PALB2 inactivation was found in 16 of the 24 cases (67%), either through LOH (n = 11) or second somatic mutations (n = 5) of the wild-type allele. High LST scores were found in all 12 PALB2-associated BCs with bi-allelic PALB2 inactivation sequenced by WES, of which eight displayed the HRD-related mutational signature 3. In addition, bi-allelic inactivation of PALB2 was significantly associated with high LST scores. Our findings suggest that the identification of bi-allelic PALB2 inactivation in PALB2-associated BCs is required for the personalization of HR-directed therapies, such as platinum salts and/or PARP inhibitors, as the vast majority of PALB2-associated BCs without PALB2 bi-allelic inactivation lack genomic features of HRD.

Solid pseudopapillary neoplasms of the pancreas are dependent on the Wnt pathway

Solid pseudopapillary neoplasms (SPNs) are rare and relatively indolent tumors of the pancreas. While primary SPNs can be surgically resected, there are currently no therapies available for patients with advanced stage disease. Given that these tumors frequently carry CTNNB1 hotspot (recurrently mutated loci in a gene) mutations resulting in β‐catenin nuclear accumulation, it has been speculated that the Wnt pathway may be a driver in this disease. Here, we present a comprehensive “multi‐omics” study where the genome, transcriptome, and methylome of SPNs were analyzed. We found that SPNs are characterized by a low‐complexity genome where somatic mutations in CTNNB1, present in 100% of the cases, are the only actionable genomic lesions. Compared to more common subtypes of pancreatic tumors (adenocarcinomas and pancreatic neuroendocrine tumors), SPNs show high expression levels of genes belonging to the Wnt pathway. Their methylome was consistent with an epithelial cell origin and a general upregulation of Wnt pathway genes. Clinical studies to evaluate the exquisite sensitivity of SPNs to inhibitors of the Wnt pathway are warranted.

Micropapillary variant of mucinous carcinoma of the breast shows genetic alterations intermediate between those of mucinous carcinoma and micropapillary carcinoma

AIMS

Micropapillary variant of mucinous carcinoma of the breast (MPMC) is a rare histological form of oestrogen receptor (ER)-positive invasive carcinoma that is characterised by micropapillary clusters of tumour cells in lakes of extracellular mucin. The aims of this study were to determine the genetic alterations underpinning MPMCs, and to determine whether they overlap with those of mucinous carcinomas and/or invasive micropapillary carcinomas.

METHODS AND RESULTS

DNA from five MPMCs was subjected to whole-exome sequencing. Somatic mutations, copy number alterations and mutational signatures were determined with state-of-the-art bioinformatics methods. No mutations in genes significantly mutated in breast cancer, including TP53, PIK3CA, GATA3, and MAP3K1, were detected. We identified copy number alterations that have been reported in invasive micropapillary carcinomas, such as recurrent gains in 1q, 6p, 8q, and 10q, and recurrent losses in 16q, 11q, and 13q, as well as a recurrent 8p12-8p11.2 amplification encompassing FGFR1. Like mucinous carcinomas, three of the five MPMCs analysed lacked PIK3CA mutations, 1q gains, and 16q losses, which are the hallmark genetic alterations of ER-positive breast cancers, whereas two MPMCs harboured 16q losses and/or a complex pattern of copy number alterations similar to those found in breast-invasive micropapillary carcinomas.

CONCLUSIONS

MPMCs are heterogeneous at the genetic level; some tumours show a pattern of somatic genetic alterations similar to those of mucinous carcinomas, whereas others resemble invasive micropapillary carcinomas at the genetic level. These findings suggest that MPMCs may not constitute one histological subtype, but rather a convergent phenotype that can stem from mucinous carcinomas or invasive micropapillary carcinomas.

Massively parallel sequencing analysis of benign melanocytic naevi

AIMS

Melanocytic naevi are benign lesions of the skin or mucosa that may constitute non-obligate precursors of malignant melanoma, particularly when they show lentiginous and dysplastic features. The aim of this study was to investigate the repertoire of somatic genetic alterations in melanocytic naevi.

METHODS AND RESULTS

DNA extracted from 12 melanocytic naevi and DNA from matching normal tissue were separately microdissected and subjected to targeted massively parallel sequencing of ≥300 cancer genes. A median of 5.5 (range 1-12) non-synonymous somatic mutations were detected, with 10 cases harbouring mutually exclusive BRAF V600E (6/12) or NRAS (4/12) clonal hotspot mutations. One of the two cases lacking BRAF and NRAS mutations was a dysplastic naevus harbouring an HRAS Q61L hotspot mutation. Analysis of the laser-capture microdissected components of a naevus synchronously diagnosed with in-situ and invasive malignant melanoma revealed a truncal, clonal BRAF V600E mutation, and the acquisition of a CDKN2A homozygous deletion in the invasive component, in conjunction with additional clonal mutations affecting NF2, FAT4 and KDR in both in-situ and invasive malignant components.

CONCLUSION

Melanocytic naevi harbour recurrent BRAF V600E or NRAS hotspot mutations with low mutational burdens. Our findings also show that progression from naevi to malignant melanoma may be driven by the acquisition of additional genetic alterations, including CDKN2A homozygous deletions.

The Landscape of Somatic Genetic Alterations in Breast Cancers from CHEK2 Germline Mutation Carriers

Pathogenic germline variants in checkpoint kinase 2 (CHEK2), which plays pivotal roles in DNA damage response and cell cycle regulation, confer an increased breast cancer (BC) risk. Here, we investigated the phenotypic and genomic characteristics of 33 BCs from CHEK2 germline mutation carriers (16 high-risk variants and 17 low-risk p.Ile157Thr variants). CHEK2-associated BCs from patients with high-risk germline variants were largely hormone receptor-positive (87%, 13/15), and 81% (13/16) exhibited loss of heterozygosity (LOH) of the CHEK2 wild-type allele. Conversely, CHEK2-associated BCs from patients with the low-risk p.Ile157Thr variant displayed less-frequent loss of heterozygosity (5/17, 29%) and higher levels of CHEK2 protein expression than those with high-risk germline variants. CHEK2-associated BCs lacked a dominant mutational signature 3, a genomics feature of homologous recombination DNA repair deficiency (HRD). Our findings indicate that CHEK2-associated BCs are generally hormone receptor-positive and lack HRD-related mutational signatures, recapitulating the features of ATM-associated BCs. Specific CHEK2 germline variants may have a distinct impact on tumor biology.

Somatic genetic alterations in synchronous and metachronous low-grade serous tumours and high-grade carcinomas of the adnexa

AIMS

Low-grade serous carcinomas (LGSCs) and their precursors serous borderline tumours (SBTs) characteristically harbour mutations in BRAF, KRAS or NRAS but rarely in TP53, whereas high-grade serous carcinomas (HGSCs) are characterised by frequent TP53 mutations but rare BRAF, KRAS or NRAS mutations. In a small subset of cases, LGSCs and/or SBTs develop into high-grade tumours, including HGSCs and poorly differentiated carcinomas (PDCs). Here, we sought to define the repertoire of somatic genetic alterations in low-grade serous tumours and synchronous or metachronous high-grade adnexal carcinomas.

METHODS AND RESULTS

DNA extracted from five SBTs/LGSCs and synchronous or metachronous HGSCs/PDCs and matched normal tissue was subjected to massively parallel sequencing targeting all exons and selected non-coding regions of 341 cancer-related genes. The low-grade and high-grade tumours from a given case were related, and shared mutations and copy number alterations. Progression from low-grade to high-grade lesions was observed, and involved the acquisition of additional mutations and/or copy number alterations, or shifts from subclonal to clonal mutations. Only two (an HGSC and a PDC) of the five high-grade tumours investigated harboured TP53 mutations, whereas NRAS and KRAS hotspot mutations were seen in two HGSCs and one HGSC, respectively.

CONCLUSIONS

Our results suggest that progression from SBT to HGSC may take place in a subset of cases, and that at least some of the rare HGSCs lacking TP53 mutations may be derived from a low-grade serous precursor.

Abstract P4-04-01: The landscape of somatic genetic alterations in breast cancers from CHEK2 germline mutation carriers

Introduction: Checkpoint kinase 2 (CHEK2) is a tumor suppressor gene, which regulates cell cycle in response to DNA damage response. Selected CHEK2 germline mutations have been shown to confer an increased risk of breast cancer development. Multiple founder mutations in CHEK2 have been identified, and meta analyses have shown that CHEK2 truncating variants confer a higher breast cancer risk than missense variants. Here, we assessed the phenotype and repertoire of genetic alterations of breast cancers from 33 patients with CHEK2 pathogenic germline variants.

Materials and methods: We performed targeted capture massively parallel sequencing (≥410 genes) of tumor and normal samples from 13 patients with CHEK2 pathogenic germline variants, and retrieved whole exome sequencing (WES) data (BAM files) of tumor and normal samples from 20 patients with CHEK2 germline pathogenic variants included in the TCGA breast cancer study. In addition, we retrieved WES data of BRCA1, BRCA2 and ATM associated breast cancers from TCGA and Weigelt et al. (JNCI 2018). Somatic mutations, copy number alterations, mutational signatures and large-scale transitions (LSTs) were defined using state-of-the-art bioinformatics algorithms.

Results: Of the 33 CHEK2-associated breast cancers included in this study, 21 had missense and 12 had loss-of-function (LoF) germline mutations, and 81% were ER-positive and 12% HER2-positive. CHEK2-associated breast cancers statistically significantly less frequently displayed an ER-negative/HER2-negative phenotype (0%) than BRCA1- (80%) or BRCA2-associated (33%) breast cancers (BRCA1, p&lt;0.0001 for both comparisons), but were similar to ATM-associated breast cancers. Biallelic inactivation of CHEK2 through loss of heterozygosity (LOH) of the wild-type allele was present in 17 of 33 samples (52%). LOH of the CHEK2 wild-type allele was significantly more frequent in tumors with LOF mutations than in those with missense mutations (78% vs 36%, respectively; p=0.0394). PIK3CA (36%) and GATA3 (33%) were the two most recurrently mutated genes in these samples. TP53 somatic mutations were detected in five cases, four of which harbored missense CHEK2 germline mutations. Unlike BRCA1- and BRCA2-associated breast cancers, but akin to ATM-associated breast cancers, CHEK2-associated breast cancers lacked the mutational signature associated with homologous recombination (HR) DNA repair defects (i.e. signature 3) and only five cases displayed high LST scores.

Conclusion:CHEK2-associated breast cancers are phenotypically and genetically distinct from BRCA1- and BRCA2-associated breast cancers, but similar to ATM-associated breast cancers. Akin to ATM-associated breast cancers, CHEK2-associated breast cancers are preferentially ER-positive, lack genomics features consistent with defective HR, and have a repertoire of somatic genetic alterations similar to those of non-BRCA1/2 ER-positive breast cancers. Our results suggest that either CHEK2 germline mutations contribute to an increased risk of breast cancer independently of the HR DNA repair defects or that the mutational signatures caused by CHEK2 pathogenic germline mutations differ from those caused by pathogenic germline mutations affecting bona fide HR-related genes (e.g. BRCA1, BRCA2 and PALB2).

Citation Format: Kumar R, Pei X, Selenica P, Wen HY, Powell S, Robson M, Riaz N, Reis-Filho JS, Weigelt B, Mandelker D. The landscape of somatic genetic alterations in breast cancers from CHEK2 germline mutation carriers [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-04-01.