Abstract S4-04: Lobular carcinoma in situ displays intra-lesion genetic heterogeneity and its progression to invasive disease involves clonal selection and variations in mutational processes

Introduction: Lobular carcinoma in situ (LCIS) is considered both a risk factor and non-obligate precursor of invasive breast cancer. We sought to determine the genomic landscape of LCIS and the mutational processes involved in the clonal evolution and progression from LCIS to ductal carcinoma in situ (DCIS) and invasive lobular carcinoma (ILC).

Methods: Patients with a history of LCIS undergoing therapeutic or prophylactic mastectomy were prospectively enrolled in an IRB approved protocol. Frozen tissue blocks were collected, screened for lesions of interest (LCIS, DCIS, ILC, invasive ductal carcinomas (IDC)) and subjected to microdissection and DNA/RNA extraction. Matched germline DNA was available for all cases. Whole exome sequencing was performed on a HiSeq2000 and data were aligned to the reference human genome and processed using GATK. Single nucleotide variants (SNVs) and small insertions/deletions were identified using MuTect and Varscan, respectively. Purity and ploidy estimates were calculated using ABSOLUTE. Clonal frequencies were estimated using Pyclone and the clonal structure of each sample was reconstructed using SubcloneSeeker. Shannon index and Simpson index metrics were used to calculate heterogeneity levels. Mutational signatures were defined according to their mutational trinucleotide context, and the expression levels of APOBEC gene family members were assessed by quantitative reverse transcription (qRT)-PCR.

Results: 30 LCIS, 10 ILCs, 7 DCIS and 5 IDCs from 15 patients qualified for data analysis. CDH1 was the most frequently mutated gene and found to be targeted by mutations in 26 LCIS samples (23 somatic, 3 germline). The repertoire of somatic mutations in LCIS was similar to that of luminal A breast cancers, with the exception of the significantly higher frequency of CDH1 mutations and the lower prevalence of TP53 mutations. ILCs were clonally related to at least one LCIS in 10 patients, and in 3/7 patients, DCIS was clonally related to at least one LCIS. Clonal composition analysis revealed that the presence of a minor clone(s) in LCIS, and the levels of intra-tumor genetic heterogeneity were significantly higher in LCIS clonally related with DCIS/ILC than in LCIS unrelated to DCIS/ILC. In two cases, a minor LCIS subclone constituted the major clone in the associated DCIS/ILC. A comparative analysis of the mutational signatures in the truncal and branch mutations of these cases revealed that whilst the truncal mutations displayed an aging signature, branch mutations were enriched for the APOBEC signature. qRT-PCR analysis demonstrated that cases displaying the APOBEC signature also harbored significantly higher levels of APOBEC3B expression than samples with the aging signature.

Conclusions: LCIS displays intra-lesion genetic heterogeneity, and the progression from LCIS to DCIS or ILC may involve the selection of clones resulting from distinct mutational processes during clonal evolution. Our findings also suggest that cytodine deamination driven by the overexpression of APOBEC3B may drive the progression of LCIS to DCIS/ILC in a subset of cases.

Citation Format: Reis-Filho JS, Schizas M, Piscuoglio S, Sakr RA, Ng CKY, Lim RS, Carniello JVS, Towers R, Martelotto L, Giri DD, de Andrade VP, Viale A, Solit DB, Weigelt B, King TA. Lobular carcinoma in situ displays intra-lesion genetic heterogeneity and its progression to invasive disease involves clonal selection and variations in mutational processes. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr S4-04.

Abstract P6-07-04: Distinct repertoires of somatic mutations affecting driver genes in mucinous and neuroendocrine carcinomas of the breast

Introduction: Mucinous carcinoma of the breast (MCB) is a rare histologic type, which accounts for approximately 2% of all invasive breast cancers (IBCs) and is characterized by clusters of tumor cells floating in large amounts of extracellular mucin. MCB comprises two main subtypes based on architectural and cytologic features: mucinous A (paucicellular) and mucinous B (hypercellular). Although MCBs are low-grade ER-positive/HER2-negative tumors of luminal molecular subtype, these cancers lack concurrent losses of 16q and gains of 1q, the hallmark genetic features of low-grade ER+/HER2- breast cancers, and have low levels of genetic instability. Neuroendocrine carcinoma of the breast (NCB) accounts for 2% - 5% of IBCs and displays morphologic features similar to those of neuroendocrine tumors of other organs. Previous transcriptomic analyses have revealed that NCBs and mucinous B, but not mucinous A, breast cancers display similar gene expression profiles. The aims of this study were to determine whether MCBs and NCBs share a similar repertoire of somatic genetic alterations and if these aberrations are distinct from those reported in common forms of ER+/HER2- IBCs.

Material and methods: DNA extracted from microdissected MCBs (n=7 mucinous A, n=6 mucinous B), NCBs (n=14) and adjacent normal tissues were subjected to massively parallel sequencing targeting all exons of 254 genes most frequently mutated in IBC or related to DNA repair. Somatic point mutations were identified using MuTect and somatic insertions and deletions (indels) were defined using Strelka and Varscan2. We retrieved mutations in the same 254 genes in common forms of ER+/HER2- IBC (n=252) from The Cancer Genome Atlas (TCGA).

Results: The most frequently mutated genes in MCBs were GATA3 (31% of cases, 4/13, all frame-shift indels), followed by KMT2C (MLL3) and MAP3K1 (both 23%). GATA3 and KMT2C (29%) were the most frequently mutated genes in mucinous A cancers, whereas MAP3K1 (33%) was the most frequently mutated gene in mucinous B cancers. ARID1A mutations were found in three of 14 (21%) NCBs, of which 2 were truncating mutations. A comparative analysis of the repertoire of somatic mutations found in mucinous A, mucinous B and NCBs did not reveal any statistically significant differences. As compared to common forms of ER+/HER2- IBCs, MCBs were found to have a significantly lower frequency of PIK3CA (8% vs 42%, p=0.02) mutations, which was particularly evident in mucinous A cancers (0% vs 42%, p=0.04). NCBs displayed significantly higher frequencies of somatic mutations affecting ARID1A (21% vs 2%, respectively, p=0.006), FOXA1 (14% vs 2%, respectively, p<0.05) and a lower frequency of PIK3CA somatic mutations (14% vs 42%, respectively, p<0.05) than common forms of ER+/HER2- IBCs.

Conclusion: The frequency of mutations affecting bona fide breast cancer genes differed among mucinous A, mucinous B and NCBs. The repertoire of somatic mutations found in MCBs and NCBs differed from that of common forms of ER+/HER2- IBCs, in particular by the low frequency of somatic mutations affecting PIK3CA.

Citation Format: Piscuoglio S, Ng CKY, Marchio C, Eberle CA, Guerini-Rocco E, Mariani O, Vincent-Salomon A, Reis-Filho JS, Weigelt B. Distinct repertoires of somatic mutations affecting driver genes in mucinous and neuroendocrine carcinomas of the breast. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-07-04.

Abstract P6-06-02: Germline CDH1 mutations in lobular carcinoma in situ

BACKGROUND: Germline CDH1 mutations are responsible for the increased risk of both gastric cancer and invasive lobular breast cancer (ILC) in families with hereditary diffuse gastric cancer syndrome; yet germline CDH1 mutations in women with ILC without a family history (FH) of gastric cancer are rare. Lobular carcinoma in situ (LCIS) is both a risk factor and non-obligate precursor of ILC and recent data suggest that germline CDH1 mutations may be present in up to 8% of patients with bilateral LCIS +/- ILC; raising questions about the role of genetic testing in this context. The purpose of this study was to determine the frequency of germline CDH1 mutations in a large prospectively followed cohort of patients with pathologically confirmed bilateral LCIS.

METHODS: Patients with a biopsy proven history of LCIS, entering surveillance or presenting for surgery (prophylactic or therapeutic mastectomy), between 2005 and 2013 were prospectively identified and enrolled in IRB approved protocols at Memorial Sloan-Kettering Cancer Center for the collection of tissue and/or germline DNA (IRB 01-135, 99-030). All biopsies were reviewed to confirm LCIS and mastectomy specimens were subject to extensive sampling of all quadrants. Cases with confirmed bilateral LCIS were chosen for the primary analysis. Cases where bilateral mastectomy tissue sampling confirmed only unilateral LCIS were included for comparison. Germline DNA was anonymized and analyzed for CDH1 mutations using targeted capture sequencing with baits for all exons of CDH1 on HiSeq2000. Germline single nucleotide variants were called using GATK HaplotypeCaller and insertions/deletions by Varscan and Scalpel. Mutations were manually inspected using the Integrative Genomics Viewer (IGV). Clinical data were abstracted prior to anonymization.

RESULTS: Germline DNA was available for 114 patients; 78 underwent bilateral mastectomy for breast cancer (BC), 8 chose prophylactic mastectomy and 28 patients with biopsy proven bilateral LCIS were identified in surveillance. Following mastectomy, tissue sampling confirmed bilateral LCIS in 67/86 (78%) patients, and ruled out bilateral LCIS in 19 patients; yielding 95 patients with bilateral LCIS for the primary analysis. Median age at LCIS diagnosis for bilateral and unilateral cases respectively was 48yrs (range 36-70) and 44 yrs (range 38-63). One patient with bilateral LCIS also reported a FH of gastric cancer. Pathogenic germline CDH1 mutations (D72N (missense) and E35* (nonsense)) were identified in 2/95 (2%) patients with bilateral LCIS, one of whom also had invasive breast cancer (ILC). A germline CDH1 mutation was not identified in the patient with bilateral LCIS and a FH of gastric cancer, nor were CDH1 mutations identified among the 19 patients with unilateral LCIS.

CONCLUSIONS: In this cohort of 95 patients with pathologically documented bilateral LCIS +/- BC, the overall frequency of CDH1 germline mutations was 2%; considerably lower than previously reported. To our knowledge this is the largest series to address this question and these findings do not support germline testing for CDH1 mutations in women with bilateral LCIS.

Citation Format: Reyes SA, Sakr RA, Schizas M, Towers R, Park AY, Ng CKY, Weigelt B, Reis-Filho JS, King TA. Germline CDH1 mutations in lobular carcinoma in situ. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-06-02.

Abstract P6-03-10: Genomic and transcriptomic heterogeneity in metaplastic breast carcinomas

Introduction: Metaplastic breast carcinoma (MBC) is a rare form of triple-negative breast cancer (TNBC), accounting for approximately 0.2%-5% of all invasive breast cancers. These tumors are characterized by the presence of neoplastic cells displaying differentiation towards squamous epithelium or mesenchymal elements. MBCs are reported to have an aggressive clinical behavior, to exhibit a worse prognosis and to respond less frequently to conventional chemotherapy regimens than common forms of TNBCs. In this study, we sought to define whether morphologically distinct subgroups of MBCs would be underpinned by distinct gene expression or copy number profiles, and whether MBCs, akin to other special histologic types of TNBC (e.g. secretory carcinoma and adenoid cystic carcinoma), would be underpinned by a highly recurrent fusion gene.

Methods: RNA and DNA samples were extracted from microdissected frozen MBCs (5 squamous, 5 spindle and 7 chondroid) and subjected to gene expression profiling using the Illumina Human HT-12 v4 platform and gene copy number profiling using the Affymetrix Human SNP 6.0 arrays, respectively. Genes differentially expressed between MBC subtypes were identified using SAM, and functional annotation of these genes was performed using Ingenuity Pathway Analysis. Intrinsic molecular subtypes were determined using the PAM50 and claudin-low intrinsic gene lists. In addition, all cases were subjected to paired-end massively parallel RNA-sequencing (Illumina GAIIx). Putative expressed fusion transcripts were identified using a validated algorithm (i.e. ChimeraScan), and confirmed by means of RT-PCR.

Results: MBCs with spindle cell morphology were all classified as of claudin-low intrinsic subtype, whereas MBCs with chondroid or squamous cell metaplasia were classified as of normal breast-like, basal-like or claudin-low subtypes, suggesting that these morphologic subgroups are heterogeneous. Unsupervised analysis of microarray and RNA-sequencing gene expression data further demonstrated that MBCs with spindle cell differentiation displayed distinctive transcriptomic profiles, and formed clusters distinct from those enriched for MBCs with chondroid and squamous cell metaplasia. MBCs with spindle cell morphology preferentially expressed regulators of epithelial-to-mesenchymal transition including lower expression of E-cadherin and EpCAM. At the genomic level, MBC subtypes displayed patterns of gene copy number alterations similar to those of common forms of TNBCs from The Cancer Genome Atlas, and no significant differences were found among the distinct MBC subtypes. Nine in-frame fusion genes, TBL1XR1-PIK3CA, WAPL-CDHR1, MAP2K3-HMGCLL, PARG-BMS1, FN1-ICAM1, TNKS1BP1-SPARC, AAK1-ARNT2, MBTPS1-TCEANC2 and PSMA6-SHMT1 were identified and validated in the index cases, however none of these was found to be recurrent in the cases analyzed in this study.

Conclusion: MBC subtypes, despite harboring similar patterns of gene copy number alterations, display significant transcriptomic differences, which may account for their distinct histologic features. Our findings also demonstrate that unlike other histologic special types of TNBC, MBCs are not underpinned by a highly recurrent expressed fusion gene.

Citation Format: Piscuoglio S, Ng CKY, Cowell CF, Mariani O, Martelotto L, Natrajan R, Lim RS, Maher CA, Vincent-Salomon A, Weigelt B, Reis-Filho JS. Genomic and transcriptomic heterogeneity in metaplastic breast carcinomas. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-03-10.

Abstract P2-01-02: Capturing intra-tumor genetic heterogeneity in cell-free plasma DNA from patients with oligometastatic breast cancer

Background: The analysis of cell-free tumor DNA (ctDNA) from plasma has been heralded as a non-invasive technique for disease monitoring and as a means to overcome the challenges posed by intra-tumor genetic heterogeneity. ctDNA levels have been shown to correlate with tumor burden in breast cancer patients. Hence, we sought to define whether massively parallel sequencing of cell-free plasma DNA would capture the entire repertoire of somatic mutations present in the primary tumors and/ or metastases from patients with oligometastatic breast cancer.

Methods: Frozen diagnostic biopsies from primary tumors and their distant metastases were obtained from five prospectively accrued treatment-naïve patients with stage IV breast cancer at presentation (1 estrogen receptor (ER)+/HER2+, 2 ER+/HER2-, 2 ER-/HER2+). A second, independent formalin-fixed paraffin-embedded (FFPE) diagnostic biopsy was obtained from the primary tumor and metastasis from 4 patients. Plasma samples were obtained from all patients. DNA samples from microdissected frozen tumors and peripheral blood, as well as plasma from one patient, were subjected to high-depth whole exome sequencing. DNA samples from all biopsies (frozen/FFPE), plasma and peripheral blood were subjected to targeted capture massively parallel sequencing, with baits for all somatic mutations detected by whole exome sequencing and all exons of the 100 genes most frequently mutated in breast cancer. Driver mutations were defined by state-of-the-art bioinformatic methods and literature search.

Results: We identified and confirmed a median of 54 (range 25-75) and 53 (range 26-85) non-synonymous mutations in the primary tumors and metastases from the 5 cases analyzed, respectively. By sequencing the plasma DNA to a median depth of 248x (range 92-431x), state-of-the-art mutation callers revealed 0-4 mutations (0%-8% of mutations) per patient, and direct interrogation of the sequencing data, based on prior knowledge of the mutations present in the lesions, resulted in the identification of 2-18 mutations (3%-38% of mutations) per patient. Of the bona fide driver mutations, 2/3 TP53 mutations, 0/1 PIK3CA hotspot mutation, 0/1 BRCA2 frameshift mutation, 0/1 GATA3 frameshift mutation and 0/1 ERBB3 activating mutation were captured in the plasma DNA. A SMAD4 pathogenic mutation and a TCF7L2 truncating mutation were found in two diagnostic biopsies of metastatic lesions but not in two biopsies of the primary tumors in one patient each. Whilst the SMAD4 mutation was detected in the plasma DNA from the respective patient, the TCF7L2 mutation was not. Of the 62 mutations restricted to the primary tumors (0-42 per patient) and 74 restricted to the metastatic tumors (1-41 per patient), 4 and 7, respectively, were captured in the plasma DNA.

Conclusions: Massively parallel sequencing assessment of plasma DNA allows for the identification of mutations found in primary tumors and/ or their metastases, however, only a subset of these could be detected at up to 431x depth. These observations suggest that current approaches for whole exome or targeted massively parallel sequencing may not be sufficient to capture the genetic heterogeneity of breast cancers in patients with oligometastatic disease.

Citation Format: Ng CKY, Bidard F-C, Piscuoglio S, Lim RS, Pierga J-Y, Cottu P, Vincent-Salomon A, Viale A, Norton L, Sigal B, Weigelt B, Reis-Filho JS. Capturing intra-tumor genetic heterogeneity in cell-free plasma DNA from patients with oligometastatic breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P2-01-02.