Multiple Hotspot Mutations Scanning by Single Droplet Digital PCR

BACKGROUND

Progress in the liquid biopsy field, combined with the development of droplet digital PCR (ddPCR), has enabled noninvasive monitoring of mutations with high detection accuracy. However, current assays detect a restricted number of mutations per reaction. ddPCR is a recognized method for detecting alterations previously characterized in tumor tissues, but its use as a discovery tool when the mutation is unknown a priori remains limited.

METHODS

We established 2 ddPCR assays detecting all genomic alterations within KRAS exon 2 and EGFR exon 19 mutation hotspots, which are of clinical importance in colorectal and lung cancer, with use of a unique pair of TaqMan® oligoprobes. The KRAS assay scanned for the 7 most common mutations in codons 12/13 but also all other mutations found in that region. The EGFR assay screened for all in-frame deletions of exon 19, which are frequent EGFR-activating events.

RESULTS

The KRAS and EGFR assays were highly specific and both reached a limit of detection of <0.1% in mutant allele frequency. We further validated their performance on multiple plasma and formalin-fixed and paraffin-embedded tumor samples harboring a panel of different KRAS or EGFR mutations.

CONCLUSIONS

This method presents the advantage of detecting a higher number of mutations with single-reaction ddPCRs while consuming a minimum of patient sample. This is particularly useful in the context of liquid biopsy because the amount of circulating tumor DNA is often low. This method should be useful as a discovery tool when the tumor tissue is unavailable or to monitor disease during therapy.

MYBL1 rearrangements and MYB amplification in breast adenoid cystic carcinomas lacking the MYB-NFIB fusion gene

Breast adenoid cystic carcinoma (AdCC), a rare type of triple-negative breast cancer, has been shown to be driven by MYB pathway activation, most often underpinned by the MYB-NFIB fusion gene. Alternative genetic mechanisms, such as MYBL1 rearrangements, have been reported in MYB-NFIB-negative salivary gland AdCCs. Here we report on the molecular characterization by massively parallel sequencing of four breast AdCCs lacking the MYB-NFIB fusion gene. In two cases, we identified MYBL1 rearrangements (MYBL1-ACTN1 and MYBL1-NFIB), which were associated with MYBL1 overexpression. A third AdCC harboured a high-level MYB amplification, which resulted in MYB overexpression at the mRNA and protein levels. RNA-sequencing and whole-genome sequencing revealed no definite alternative driver in the fourth AdCC studied, despite high levels of MYB expression and the activation of pathways similar to those activated in MYB-NFIB-positive AdCCs. In this case, a deletion encompassing the last intron and part of exon 15 of MYB, including the binding site of ERG-1, a transcription factor that may downregulate MYB, and the exon 15 splice site, was detected. In conclusion, we demonstrate that MYBL1 rearrangements and MYB amplification probably constitute alternative genetic drivers of breast AdCCs, functioning through MYBL1 or MYB overexpression. These observations emphasize that breast AdCCs probably constitute a convergent phenotype, whereby activation of MYB and MYBL1 and their downstream targets can be driven by the MYB-NFIB fusion gene, MYBL1 rearrangements, MYB amplification, or other yet to be identified mechanisms. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Lymphovascular invasion after neoadjuvant chemotherapy is strongly associated with poor prognosis in breast carcinoma

PURPOSE

Few studies evaluated the prognostic value of the presence of lymphovascular invasion (LVI) after neoadjuvant chemotherapy (NAC) for breast cancer (BC).

METHODS

The association between LVI and survival was evaluated in a cohort of BC patients treated by NAC between 2002 and 2011. Five post-NAC prognostic scores (ypAJCC, RCB, CPS, CPS + EG and Neo-Bioscore) were evaluated and compared with or without the addition of LVI.

RESULTS

Out of 1033 tumors, LVI was present on surgical specimens in 29.2% and absent in 70.8% of the cases. Post-NAC LVI was associated with impaired disease-free survival (DFS) (HR 2.54; 95% CI 1.96-3.31; P < 0.001), and the magnitude of this effect depended on BC subtype (P_interaction = 0.003), (luminal BC: HR 1.83; P = 0.003; triple negative BC: HR 3.73; P < 0.001; HER2-positive BC: HR 6.21; P < 0.001). Post-NAC LVI was an independent predictor of local relapse, distant metastasis, and overall survival; and increased the accuracy of all five post-NAC prognostic scoring systems.

CONCLUSIONS

Post-NAC LVI is a strong independent prognostic factor that: (i) should be systematically reported in pathology reports; (ii) should be used as stratification factor after NAC to propose inclusion in second-line trials or adjuvant treatment; (iii) should be included in post-NAC scoring systems.

Medullary Breast Carcinoma: Prognostic Implications of P53 Expression

Medullary breast carcinoma (MBC) is a rare pathological type of breast cancer. The rate of p53 protein accumulation is higher in MBC than in common invasive ductal carcinoma. Whether this particular feature of MBC influences the outcome after treatment is unknown. We retrospectively analyzed the characteristics, treatment and outcome of 71 patients with MBC treated between 1981 and 1996. The median age was 51 years (range 27–81) and the median clinical tumor size was 25 mm (range 0-70 mm). Breast-conserving treatment was offered when possible: 55 patients had undergone a tumorectomy and radiotherapy while 16 patients had undergone a mastectomy. p53 protein accumulation was determined by immunohistochemistry on paraffin-embedded tumor specimens from 58/71 samples available for this study. The median follow-up for the 56 survivors was 113 months (range 30–241). The 10-year survival and metastasis-free survival rates were 81% and 81.4%, respectively. The local recurrence rate was 16.4%. The two factors predicting outcome were pathological axillary node involvement in the 60 patients who underwent axillary dissection and adjuvant chemotherapy. p53 accumulation was found in 33/58 patients (57%). p53 status was not predictive of survival nor of distant or local recurrences. We confirm that medullary breast carcinoma has a favorable prognosis despite its aggressive pathological features. p53 protein accumulation, found in the majority of MBCs, was not related to outcome.

PET/CT imaging in management of concomitant Hodgkin lymphoma and tuberculosis - a problem solver tool

Infectious lymph nodes mimicking lymphoma is challenging for accurate staging. Although ¹⁸F-FDG is a nonspecific tracer accumulating not only in tumor cells but also in inflammatory tissues, the metabolic features and uptake kinetics give valuable information: ¹⁸F-FDG PET/CT appears as a useful problem solver tool in ambiguous situation.

Specific adaptive immune pattern induced by NBTXR3 exposed to radiation therapy in soft tissue sarcoma (STS) patients

e14615

Background: NBTXR3 are functionalized hafnium oxide nanoparticles, undergoing seven clinical trials for enhancing radiation therapy (RT). The high electron density of the nanoparticles, when exposed to radiotherapy (NBTXR3 + RT), allow absorption/deposition of a high radiation dose within the cancer cells to physically kill the cells, and possibly improve outcome. Besides, NBTXR3 + RT has shown subsequent ability to enhance immunogenic cell death and immune response in preclinics. We hypothesized that NBTXR3 + RT could trigger an enhanced immune response when compared to RT in patients with STS. Methods: Tumor tissues pre- (biopsy) and/or post-treatment (resection) were collected from patients (pts) with locally advanced STS, who received either NBTXR3 as intratumor injection and RT (14 pts) or RT (12 pts), as preoperative treatment (NCT02379845). Immunohistochemistry and Digital Pathology for immune biomarkers and for Immunoscore (CD3/CD8) were analyzed. Gene expression profiling and pre-optimized immune-gene signatures called Immunosign were also used. Results: A significant increase of T cells (CD3+, CD8+) and a marked increase of CD103+ immune cell infiltration post- vs pre-treatment were observed for NBTXR3 + RT ( P< 0.01), while no differences were seen for RT. Post-treatment, an increased Immunoscore (CD3 + CD8 cell densities) was observed for NBTXR3 + RT compared to RT (P < 0.07). Consistently, the up-regulation of pan immune genes expression and specifically expression of adaptive immunity genes between pre- and post-treatment, was pronounced for NBTXR3 + RT when compared to RT. Functional analysis of genes up-regulated in NBTXR3 + RT showed an enrichment of cytokine activity (IL7, IFNA, IL16, IL11, IFNG), adaptive immunity (RAG1, GZMA, TAP1, TAP2, TBX21, STAT4, IFNG, LCK, LTK, CD37, CD22) and T cell receptor signaling pathway (CD28, CTLA4, CD274, BTLA, TIGIT, CD40LG, CD5, CD3E, ZAP70). Conclusions: NBTXR3 + RT induces a specific adaptive immune pattern. As such, it may contribute to convert “cold” tumor into “hot” tumor and be effectively combined with immunotherapeutic agents across oncology. These data warrant more tissue samples evaluation to reinforce these findings.

HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures

Approximately 1-5% of breast cancers are attributed to inherited mutations in BRCA1 or BRCA2 and are selectively sensitive to poly(ADP-ribose) polymerase (PARP) inhibitors. In other cancer types, germline and/or somatic mutations in BRCA1 and/or BRCA2 (BRCA1/BRCA2) also confer selective sensitivity to PARP inhibitors. Thus, assays to detect BRCA1/BRCA2-deficient tumors have been sought. Recently, somatic substitution, insertion/deletion and rearrangement patterns, or 'mutational signatures', were associated with BRCA1/BRCA2 dysfunction. Herein we used a lasso logistic regression model to identify six distinguishing mutational signatures predictive of BRCA1/BRCA2 deficiency. A weighted model called HRDetect was developed to accurately detect BRCA1/BRCA2-deficient samples. HRDetect identifies BRCA1/BRCA2-deficient tumors with 98.7% sensitivity (area under the curve (AUC) = 0.98). Application of this model in a cohort of 560 individuals with breast cancer, of whom 22 were known to carry a germline BRCA1 or BRCA2 mutation, allowed us to identify an additional 22 tumors with somatic loss of BRCA1 or BRCA2 and 47 tumors with functional BRCA1/BRCA2 deficiency where no mutation was detected. We validated HRDetect on independent cohorts of breast, ovarian and pancreatic cancers and demonstrated its efficacy in alternative sequencing strategies. Integrating all of the classes of mutational signatures thus reveals a larger proportion of individuals with breast cancer harboring BRCA1/BRCA2 deficiency (up to 22%) than hitherto appreciated (∼1-5%) who could have selective therapeutic sensitivity to PARP inhibition.

Genetic Heterogeneity in Therapy-Naïve Synchronous Primary Breast Cancers and Their Metastases

Purpose: Paired primary breast cancers and metachronous metastases after adjuvant treatment are reported to differ in their clonal composition and genetic alterations, but it is unclear whether these differences stem from the selective pressures of the metastatic process, the systemic therapies, or both. We sought to define the repertoire of genetic alterations in breast cancer patients with de novo metastatic disease who had not received local or systemic therapy.Experimental Design: Up to two anatomically distinct core biopsies of primary breast cancers and synchronous distant metastases from nine patients who presented with metastatic disease were subjected to high-depth whole-exome sequencing. Mutations, copy number alterations and their cancer cell fractions, and mutation signatures were defined using state-of-the-art bioinformatics methods. All mutations identified were validated with orthogonal methods.Results: Genomic differences were observed between primary and metastatic deposits, with a median of 60% (range 6%-95%) of shared somatic mutations. Although mutations in known driver genes including TP53, PIK3CA, and GATA3 were preferentially clonal in both sites, primary breast cancers and their synchronous metastases displayed spatial intratumor heterogeneity. Likely pathogenic mutations affecting epithelial-to-mesenchymal transition-related genes, including SMAD4, TCF7L2, and TCF4 (ITF2), were found to be restricted to or enriched in the metastatic lesions. Mutational signatures of trunk mutations differed from those of mutations enriched in the primary tumor or the metastasis in six cases.Conclusions: Synchronous primary breast cancers and metastases differ in their repertoire of somatic genetic alterations even in the absence of systemic therapy. Mutational signature shifts might contribute to spatial intratumor genetic heterogeneity. Clin Cancer Res; 23(15); 4402-15. ©2017 AACR.

CXCR4 inhibitors could benefit to HER2 but not to triple-negative breast cancer patients

The CXCR4 receptor and its ligand CXCL12 (also named stromal cell-derived factor 1, SDF1) have a critical role in chemotaxis and homing, key steps in cancer metastasis. Although myofibroblasts expressing CXCL12 are associated with the presence of axillary metastases in HER2 breast cancers (BC), the therapeutic interest of targeting CXCR4/CXCL12 axis in the different BC subtypes remains unclear. Here, we investigate this question by testing antitumor activity of CXCR4 inhibitors in patient-derived xenografts (PDX), which faithfully reproduce human tumor properties. We observed that two CXCR4 inhibitors, AMD3100 and TN14003, efficiently impair tumor growth and metastasis dissemination in both Herceptin-sensitive and Herceptin-resistant HER2 BC. Conversely, blocking CXCR4/CXCL12 pathway in triple-negative (TN) BC does not reduce tumor growth, and can even increase metastatic spread. Moreover, although CXCR4 inhibitors significantly reduce myofibroblast content in all BC subtypes, they decrease angiogenesis only in HER2 BC. Thus, our findings suggest that targeting CXCR4 could provide some therapeutic interest for HER2 BC patients, whereas it has no impact or could even be detrimental for TN BC patients.

Patient-Specific Circulating Tumor DNA Detection during Neoadjuvant Chemotherapy in Triple-Negative Breast Cancer

BACKGROUND

In nonmetastatic triple-negative breast cancer (TNBC) patients, we investigated whether circulating tumor DNA (ctDNA) detection can reflect the tumor response to neoadjuvant chemotherapy (NCT) and detect minimal residual disease after surgery.

METHODS

Ten milliliters of plasma were collected at 4 time points: before NCT; after 1 cycle; before surgery; after surgery. Customized droplet digital PCR (ddPCR) assays were used to track tumor protein p53 (TP53) mutations previously characterized in tumor tissue by massively parallel sequencing (MPS).

RESULTS

Forty-six patients with nonmetastatic TNBC were enrolled. TP53 mutations were identified in 40 of them. Customized ddPCR probes were validated for 38 patients, with excellent correlation with MPS (r = 0.99), specificity (≥2 droplets/assay), and sensitivity (at least 0.1%). At baseline, ctDNA was detected in 27/36 patients (75%). Its detection was associated with mitotic index (P = 0.003), tumor grade (P = 0.003), and stage (P = 0.03). During treatment, we observed a drop of ctDNA levels in all patients but 1. No patient had detectable ctDNA after surgery. The patient with rising ctDNA levels experienced tumor progression during NCT. Pathological complete response (16/38 patients) was not correlated with ctDNA detection at any time point. ctDNA positivity after 1 cycle of NCT was correlated with shorter disease-free (P &lt; 0.001) and overall (P = 0.006) survival.

CONCLUSIONS

Customized ctDNA detection by ddPCR achieved a 75% detection rate at baseline. During NCT, ctDNA levels decreased quickly and minimal residual disease was not detected after surgery. However, a slow decrease of ctDNA level during NCT was strongly associated with shorter survival.

Pentraxin-3 is a PI3K signaling target that promotes stem cell-like traits in basal-like breast cancers

Basal-like breast cancers (BLBCs) exhibit hyperactivation of the phosphoinositide 3-kinase (PI3K) signaling pathway because of the frequent mutational activation of the PIK3CA catalytic subunit and the genetic loss of its negative regulators PTEN (phosphatase and tensin homolog) and INPP4B (inositol polyphosphate-4-phosphatase type II). However, PI3K inhibitors have had limited clinical efficacy in BLBC management because of compensatory amplification of PI3K downstream signaling loops. Therefore, identification of critical PI3K mediators is paramount to the development of effective BLBC therapeutics. Using transcriptomic analysis of activated PIK3CA-expressing BLBC cells, we identified the gene encoding the humoral pattern recognition molecule pentraxin-3 (PTX3) as a critical target of oncogenic PI3K signaling. We found that PTX3 abundance is stimulated, in part, through AKT- and nuclear factor κB (NF-κB)-dependent pathways and that presence of PTX3 is necessary for PI3K-induced stem cell-like traits. We further showed that PTX3 expression is greater in tumor samples from patients with BLBC and that it is prognostic of poor patient survival. Our results thus reveal PTX3 as a newly identified PI3K-regulated biomarker and a potential therapeutic target in BLBC.

Abstract PD1-06: Comparison of mutational landscapes of primary breast cancer and first metastatic relapse: Results from the ESOPE study

Background

Genomic profile of breast cancer metastases (M) may differ from that of the primary tumor (PT). In a multicenter prospective study (ESOPE, NCT 01956552) including 130 patients with biopsies of the first metastatic deposit, we have shown that luminal breast cancers are the most prone to phenotypical subtype changes (Comte et al, ASCO 2016#550). We report here the first results of a comparative PT/M targeted next generation sequencing (NGS) mutational analysis.

Methods

Of 130 patients, 117 paired PT/M samples obtained before any treatment were available for analysis. Targeted Sequencing was done using Illumina Hiseq2500 technology with a custom made 95 breast cancer associated genes panel. Sequence data were aligned to the human reference genome (hg19) using Bowtie2 algorithm. Median depth was 607X and 87% of targets achieved 100X depth. SNVs and indels were called using GATK UnifiedGenotyper. We retained COSMIC confirmed non synonymous, exonic/splice variants and observed at a frequency lower than 0,1% in population. Further confirmation of detected variants was performed with comparison to public databases (cbioportal, tumorportal), and potential pathogenicity was evaluated with 4 different public algorithms. We present here the results obtained from the first 35 matched PT/M samples (liver mets 68%), focusing analysis on 40 genes including PIK3CA (20 genes), ER (6 genes) and MAPK (11 genes) pathways, RUNX1, CDH1 and TP53 genes.

Results

Patients characteristics are representative of patients with first line metastatic breast cancer (Comte et al, ASCO 2016#550). Among the 40 genes analyzed in the 70 samples, we detected 134 somatic mutations (70 in PT and 64 in M) including 15 indels and 119 SNV. Among these 134 mutations there were 74 different mutations (66SNV and 8 indels) classified pathogenic for 26 and of unknown pathogenicity for 48 of them. We detected at least 1 mutation in 31 PT and in 28 M. Median numbers of mutations were 1 in PT (range 1-9) and 1 in M (range1-22) samples (p=0.295, Wilcoxon rank sum test). Top ten mutated genes in PT included PIK3CA, TP53, NCOR1, NF1, GATA3, CDH1, ERBB3, PTEN, HRAS, INPP4B. In M samples, the 10 top genes were PIK3CA, TP53, ERBB3, AKT3, CDH1, ERBB4, GATA3, INPP4B, MET, MTOR. Only 3 ESR1 mutations were detected, including 1 PT/M pair and 1 M. Beyond highly shared PIK3CA and TP53 mutations, overall crude PT/M discordance rate was 31%. Analysis by histological subtypes showed PT and M specific mutational profiles, suggesting a role in ERB gene family (notably ERBB3) and MAPK driven pathways in early metastatic progression. Specific metastatic site analysis suggested enrichment in MAPK pathway mutations in liver metastases when compared to other sites. Variant allelic fractions were globally not significantly different between PT and M samples.

Conclusion

In this prospective multicenter series of systematic biopsies of first metastases, we report a targeted mutational analysis of matched PT and M samples not modified by previous therapy exposure. Early analyses suggest specific genotypical changes according to tumor subtype and/or metastatic site. Extended and updated results will be reported at the meeting.

Citation Format: Cottu PH, Boulai A, Callens C, Baulande S, Legoix-Ne P, Bernard V, Vincent-Salomon A, Benhamo V, Brain EGC, Chemlali W, Campone M, Bachelot TD, Giacchetti S, Bonneterre J, Bidard F-C, Servois V, Comte A, Belin L, Sigal B, Bièche I. Comparison of mutational landscapes of primary breast cancer and first metastatic relapse: Results from the ESOPE study [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr PD1-06.

Abstract P1-03-05: A comprehensive molecular analysis of medullary breast carcinoma: A model of immunomodulatory triple negative breast cancer subtype

Medullary breast carcinoma (MBC) is a rare subtype of triple negative breast cancer (TNBC)with specific genomic features within the spectrum of basal-like carcinoma. The frequent association between BRCA constitutive mutation and MBC phenotype has been reported previously. In this study including 19 MBC and 36 non-MMB basal-like carcinoma (BLC), we refine the genomic and transcriptomic knowledge about this entity. Using pan genomic Affymetrix genome-wide human SNP6.0 array, we show that i/ MBC harbour more copy number alterations and losses of heterozygocity than BLC and that ii/ the high frequency of BRCAness genomic trait among MBC. Unsupervised and supervised analysis of GeneChip Uman Genome U133 Plus 2.0 Array transcriptomic generated data confirmed that MBC clearly differ from BLC in terms of gene expression level, with 92 genes overexpressed and 154 genes underexpressed in MBC over BLC. Immune response and inflammatory response are the most differentially represented pathways in MBC over BLC. Pro apoptotic gene BCLG is by far the more overexpressed gene in MBC. A validation study conducted with RT-QPCR among 526 breast tumors form all molecular subtype confirmed the specificity of BCLG overexpression in MBC, which was confirmed at protein level using immunohistochemisytry. Moreover, we show that a vast majority of MBC belong o the immunomodulatory TNBC subtype according to Lehman et al. Finally, we confirm the better prognosis of MBC toward BLC. Our observations epitomize the importance of developing DNA repair targeting drugs and immunotherapy based trials in order to improve the outcome of such a specific entity.

Citation Format: Romero P, Deniziaut G, Benhamo V, Fuhrmann L, Berger F, Bhalshankar J, Gruel N, MacGrogan G, Popova T, Manié E, Stern M-H, Stoppa-Lyonnet D, Rouzier R, Delattre O, Bieche I, Vincent-Salomon A. A comprehensive molecular analysis of medullary breast carcinoma: A model of immunomodulatory triple negative breast cancer subtype [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-03-05.

Abstract P1-05-03: The genomic landscape of breast metaplastic carcinoma

Introduction: Metaplastic breast carcinoma (MBC) is a rare histologic type of triple-negative breast cancer (TNBC), characterized by the presence of cells displaying squamous and/or mesenchymal differentiation. The transcriptomic profiles of MBCs have been reported to vary according to the type of metaplastic elements. The somatic genetic alterations that underpin this breast cancer subtype remain to be fully characterized. Here we sought to define the genomic landscape of MBCs, whether different subtypes of MBC would be driven by distinct constellations of genetic alterations, and to investigate functionally the impact of mutations affecting WNT pathway genes using non-malignant breast epithelial cells.

Methods: Thirty-five MBCs were retrieved from the pathology department of the authors' institutions and classified into the MBC histologic subtypes. All but one of the MBCs were of triple-negative phenotype. DNA was extracted from microdissected tumor-normal pairs and subjected to whole-exome sequencing. Somatic genetic alterations were identified using state-of-the-art bioinformatics algorithms. The genomic profiles of MBCs were compared to those of 69 common type TNBCs from The Cancer Genome Atlas. Overall mutation rates were compared using the Mann Whitney U test, and the frequency of mutations in each gene was compared using Fisher's exact test. RNA was extracted from a subset of MBCs and subjected to WNT signaling pathway activation analysis with the RT2 Profiler PCR Array. Triple-negative non-malignant breast epithelial cells (MCF10A and MCF12A) and cancer cell lines were utilized for 2D and 3D functional studies.

Results: Whole-exome analysis revealed that MBCs displayed a median of 103 (15-344) somatic mutations, which did not differ from the median number of somatic mutations in common type TNBCs (76, range 14-233). The most frequent recurrently mutated cancer genes included TP53 (69%) and PIK3CA (29%). MBCs more frequently harbored mutations in PI3K pathway genes than common type TNBCs (57% vs 22%, P&lt;0.05), including mutations affecting PIK3CA (29% vs 7%), PIK3R1 (11% vs 0) and PTEN (11% vs 1%). MBCs also more frequently harbored mutations affecting WNT signaling pathway genes (46% vs 26%, P&lt;0.05), including AXIN1 (6% vs 1%), WNT5A (6% vs 0) and APC (3% vs 0). MBC subtype analysis revealed that PIK3CA mutations were only detected in non-chondroid MBCs (53% vs 0), CHERP mutations were only found in chondroid MBCs (25% vs 0), whereas USP5 mutations only found in squamous MBCs (33% vs 0). MBCs with somatic mutations in WNT pathway genes had significantly higher WNT pathway activation than MBCs lacking mutations in these genes (P=0.0244). Consistent with the mesenchymal phenotype frequently exhibited by MBCs, in vitro experiments provided functional evidence that aberrant WNT pathway activation induces an epithelial-to-mesenchymal transition (EMT) phenotype, with downregulation of epithelial markers and upregulation of EMT transcriptional inducers.

Conclusions: MBCs are significantly enriched for mutations affecting PI3K and WNT pathways, highlighting the importance of the dysregulation of the WNT pathway in MBC carcinogenesis. Moreover, our findings suggest that specific mutations are significantly associated with distinct histologic subtypes of MBCs.

Citation Format: Geyer FC, Ng CK, Piscuoglio S, Wen YH, Wen H-C, Pareja F, Eberle CA, Burke KA, Lim RS, Natrajan R, Mariani O, Brogi E, Norton L, Vincent-Salomon A, Weigelt B, Reis-Filho JS. The genomic landscape of breast metaplastic carcinoma [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-05-03.

The Landscape of Somatic Genetic Alterations in Metaplastic Breast Carcinomas

Purpose: Metaplastic breast carcinoma (MBC) is a rare and aggressive histologic type of breast cancer, predominantly of triple-negative phenotype, and characterized by the presence of malignant cells showing squamous and/or mesenchymal differentiation. We sought to define the repertoire of somatic genetic alterations and the mutational signatures of MBCs.Experimental Design: Whole-exome sequencing was performed in 35 MBCs, with 16, 10, and 9 classified as harboring chondroid, spindle, and squamous metaplasia as the predominant metaplastic component. The genomic landscape of MBCs was compared with that of triple-negative invasive ductal carcinomas of no special type (IDC-NST) from The Cancer Genome Atlas. Wnt and PI3K/AKT/mTOR pathway activity was assessed using a qPCR assay.Results: MBCs harbored complex genomes with frequent TP53 (69%) mutations. In contrast to triple-negative IDC-NSTs, MBCs more frequently harbored mutations in PIK3CA (29%), PIK3R1 (11%), ARID1A (11%), FAT1 (11%), and PTEN (11%). PIK3CA mutations were not found in MBCs with chondroid metaplasia. Compared with triple-negative IDC-NSTs, MBCs significantly more frequently harbored mutations in PI3K/AKT/mTOR pathway-related (57% vs. 22%) and canonical Wnt pathway-related (51% vs. 28%) genes. MBCs with somatic mutations in PI3K/AKT/mTOR or Wnt pathway-related genes displayed increased activity of the respective pathway.Conclusions: MBCs are genetically complex and heterogeneous, and are driven by a repertoire of somatic mutations distinct from that of triple-negative IDC-NSTs. Our study highlights the genetic basis and the importance of PI3K/AKT/mTOR and Wnt pathway dysregulation in MBCs and provides a rationale for the metaplastic phenotype and the reported responses to PI3K/AKT/mTOR inhibitors in these tumors. Clin Cancer Res; 23(14); 3859-70. ©2017 AACR.

Evisceration and ocular tumors: What are the consequences?

PURPOSE

Evisceration can be performed for blind, painful eyes. This surgery can promote the dissemination of tumor cells within the orbit if an ocular tumor has been missed preoperatively.

METHODS

We reviewed the medical records of patients who were eviscerated for blind, painful eyes between 2009 and 2014 and who were referred after the surgery to the Institut Curie or the Rothschild Foundation in Paris. We included the patients with a histological diagnosis of ocular tumor or orbital recurrence. Cytogenetic analysis was performed whenever possible.

RESULTS

Four patients turned out to have an ocular tumor after evisceration (two choroidal melanomas, a rhabdoid tumor and an adenocarcinoma of the retinal pigment epithelium); two had a history of prior ocular trauma. The tumors were diagnosed either on histological analysis of the intraocular contents (2 patients) or biopsy of orbital recurrence (2 patients). Prior to evisceration, fundus examination was not performed in 3 patients. One had preoperative imaging but no intraocular tumor was suspected. At the time of this study, 3 patients had had an orbital recurrence and died. We also found 2 patients who had an evisceration despite a past history of choroidal melanoma treated with proton beam therapy.

CONCLUSION

We showed that evisceration of eyes with unsuspected ocular malignancies was associated with a poor prognosis due to orbital recurrence and metastasis. The evisceration specimen should therefore always be sent for histological analysis in order to perform prompt adjuvant orbital radiotherapy if an ocular tumor is found.

Genetic events in the progression of adenoid cystic carcinoma of the breast to high-grade triple-negative breast cancer

Adenoid cystic carcinoma of the breast is a rare histological type of triple-negative breast cancer with an indolent clinical behavior, often driven by the MYB-NFIB fusion gene. Here we sought to define the repertoire of somatic genetic alterations in two adenoid cystic carcinomas associated with high-grade triple-negative breast cancer. The different components of each case were subjected to copy number profiling and massively parallel sequencing targeting all exons and selected regulatory and intronic regions of 488 genes. Reverse transcription PCR and fluorescence in situ hybridization were employed to investigate the presence of the MYB-NFIB translocation. The MYB-NFIB fusion gene was detected in both adenoid cystic carcinomas and their associated high-grade triple-negative breast cancer components. Although the distinct components of both cases displayed similar patterns of gene copy number alterations, massively parallel sequencing analysis revealed intratumor genetic heterogeneity. In case 1, progression from the trabecular adenoid cystic carcinoma to the high-grade triple-negative breast cancer was found to involve clonal shifts with enrichment of mutations affecting EP300, NOTCH1, ERBB2 and FGFR1 in the high-grade triple-negative breast cancer. In case 2, a clonal KMT2C mutation was present in the cribriform adenoid cystic carcinoma, solid adenoid cystic carcinoma and high-grade triple-negative breast cancer components, whereas a mutation affecting MYB was present only in the solid and high-grade triple-negative breast cancer areas and additional three mutations targeting STAG2, KDM6A and CDK12 were restricted to the high-grade triple-negative breast cancer. In conclusion, adenoid cystic carcinomas of the breast with high-grade transformation are underpinned by the MYB-NFIB fusion gene and, akin to other forms of cancer, may be constituted by a mosaic of cancer cell clones at diagnosis. The progression from adenoid cystic carcinoma to high-grade triple-negative breast cancer of no special type may involve the selection of neoplastic clones and/or the acquisition of additional genetic alterations.

Choroidal melanoma and pregnancy

PURPOSE

Choroidal melanoma is a rare tumour in adults. The mean age at diagnosis is 60, but the tumour can affect women of childbearing age. A negative effect of pregnancy on patients' survival has not been formally excluded to date. The aim of the present study is to evaluate the effect of pregnancy on the prognosis of choroidal melanoma.

METHODS

We conducted a single-centre retrospective study at the Institut Curie on the population of women of childbearing age who were diagnosed with choroidal melanoma between June 1980 and October 2013. We took a particular interest in the prognosis of those who were pregnant at the time of diagnosis and in the prognosis of those who chose to get pregnant after the treatment.

RESULTS

We found 27 pregnant patients at the time of diagnosis and 13 patients who became pregnant after the treatment. There was no difference in the survival between these two groups of patients and the group of other women of childbearing age diagnosed with choroidal melanoma (p = 0.52). There was also no difference in metastasis-free survival (p = 0.91). Most women were able to carry their pregnancies to term (67% had a term pregnancy, and only 7% had an abortion). For women who were pregnant when they were diagnosed with choroidal melanoma, a conservative treatment was chosen in 85% of cases, and proton beam therapy was the most widely used treatment.

CONCLUSIONS

Survival in women of childbearing age does not appear to be influenced by pregnancy. We show that proton beam therapy can be used to treat women who are pregnant at the time of choroidal melanoma diagnosis.

AMOTL1 Promotes Breast Cancer Progression and Is Antagonized by Merlin

The Hippo signaling network is a key regulator of cell fate. In the recent years, it was shown that its implication in cancer goes well beyond the sole role of YAP transcriptional activity and its regulation by the canonical MST/LATS kinase cascade. Here we show that the motin family member AMOTL1 is an important effector of Hippo signaling in breast cancer. AMOTL1 connects Hippo signaling to tumor cell aggressiveness. We show that both canonical and noncanonical Hippo signaling modulates AMOTL1 levels. The tumor suppressor Merlin triggers AMOTL1 proteasomal degradation mediated by the NEDD family of ubiquitin ligases through direct interaction. In parallel, YAP stimulates AMOTL1 expression. The loss of Merlin expression and the induction of Yap activity that are frequently observed in breast cancers thus result in elevated AMOTL1 levels. AMOTL1 expression is sufficient to trigger tumor cell migration and stimulates proliferation by activating c-Src. In a large cohort of human breast tumors, we show that AMOTL1 protein levels are upregulated during cancer progression and that, importantly, the expression of AMOTL1 in lymph node metastasis appears predictive of the risk of relapse. Hence we uncover an important mechanism by which Hippo signaling promotes breast cancer progression by modulating the expression of AMOTL1.

Breast lesions of uncertain malignant nature and limited metastatic potential: proposals to improve their recognition and clinical management

Breast lesions comprise a family of heterogeneous entities with variable patterns of presentation, morphology and clinical behaviour. The majority of breast lesions are classified traditionally into benign and malignant conditions and their behaviour can, in the vast majority of cases, be predicted with a reasonable degree of accuracy. However, there remain lesions which show borderline features and lie in a grey zone between benign and malignant, as their behaviour cannot be predicted reliably. Defined pathological categorization of such lesions is challenging, and for some entities is recognized to be subjective and include a range of diagnoses, and forms of terminology, which may trigger over- or undertreatment. The rarity of these lesions makes the acquisition of clinical evidence problematic and limits the development of a sufficient evidence base to support informed decision-making by clinicians and patients. Emerging molecular evidence is providing a greater understanding of the biology of these lesions, but this may or may not be reflected in their clinical behaviour. Herein we discuss some breast lesions that are associated with uncertainty regarding classification and behaviour, and hence management. These include biologically invasive malignant lesions associated with uncertain metastatic potential, such as low-grade adenosquamous carcinoma, low-grade fibromatosis-like spindle cell carcinoma and encapsulated papillary carcinoma. Other lesions of uncertain malignant nature remain, such as mammary cylindroma, atypical microglandular adenosis, mammary pleomorphic adenoma and infiltrating epitheliosis. The concept of categories of (1) breast lesions of uncertain malignant nature and (2) breast lesions of limited metastatic potential are proposed with details of which histological entities could be included in each category, and their management implications are discussed.

Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration

A recent comprehensive whole genome analysis of a large breast cancer cohort was used to link known and novel drivers and substitution signatures to the transcriptome of 266 cases. Here, we validate that subtype-specific aberrations show concordant expression changes for, for example, TP53, PIK3CA, PTEN, CCND1 and CDH1. We find that CCND3 expression levels do not correlate with amplification, while increased GATA3 expression in mutant GATA3 cancers suggests GATA3 is an oncogene. In luminal cases the total number of substitutions, irrespective of type, associates with cell cycle gene expression and adverse outcome, whereas the number of mutations of signatures 3 and 13 associates with immune-response specific gene expression, increased numbers of tumour-infiltrating lymphocytes and better outcome. Thus, while earlier reports imply that the sheer number of somatic aberrations could trigger an immune-response, our data suggests that substitutions of a particular type are more effective in doing so than others.

A phenotypic and mechanistic perspective on heterogeneity of HER2-positive breast cancers

Analysis of gene expression and whole-genome features of 64 human epidermal growth factor 2 (HER2)-positive breast tumors supports the idea that their intrinsic heterogeneity actually reflects their cell of origin, suggesting that HER2 amplification is an embedded event in the natural history of these tumors. Possible mechanisms for this event involve breakage-fusion-bridge and chromothripsis.

First description of a sporadic breast cancer in a woman with BRCA1 germline mutation

We describe the case of a woman carrying a germline pathogenic BRCA1 mutation diagnosed with a breast cancer overexpressing HER2. Clinical presentation of the tumor, HER2-positivity, genomic profile and loss of the mutated BRCA1 allele in tumor evidence that BRCA1 is not inactivated in this breast cancer. It represents the first biological demonstration for the existence of a sporadic HER2-positive breast cancer independent from BRCA loss of function in a woman carrier of a deleterious BRCA1 mutation. In a context where targeted therapies based on BRCA loss of function in the tumor are developed, such case could have direct implications.

Direct Transcriptional Consequences of Somatic Mutation in Breast Cancer

Disordered transcriptomes of cancer encompass direct effects of somatic mutation on transcription, coordinated secondary pathway alterations, and increased transcriptional noise. To catalog the rules governing how somatic mutation exerts direct transcriptional effects, we developed an exhaustive pipeline for analyzing RNA sequencing data, which we integrated with whole genomes from 23 breast cancers. Using X-inactivation analyses, we found that cancer cells are more transcriptionally active than intermixed stromal cells. This is especially true in estrogen receptor (ER)-negative tumors. Overall, 59% of substitutions were expressed. Nonsense mutations showed lower expression levels than expected, with patterns characteristic of nonsense-mediated decay. 14% of 4,234 rearrangements caused transcriptional abnormalities, including exon skips, exon reusage, fusions, and premature polyadenylation. We found productive, stable transcription from sense-to-antisense gene fusions and gene-to-intergenic rearrangements, suggesting that these mutation classes drive more transcriptional disruption than previously suspected. Systematic integration of transcriptome with genome data reveals the rules by which transcriptional machinery interprets somatic mutation.

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Greater transcriptional activity in cancer than stromal cells, particularly when ER-ve

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Intron mutations only infrequently affect splicing, even at essential splice sites

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Distinctive RNA effects of sense-to-antisense and gene-to-intergenic rearrangements

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Exhaustive pipeline for identifying aberrant transcripts from RNA-sequencing data

Abstract 1524: Mutations and gene copy number variations landscape of metastases of various cancer types from patients enrolled in the SHIVA trial

Background

The molecular landscape of primary tumors of several cancer types is available and tissue-independent classification of tumors on the basis of genetic and epigenetic alterations is emerging1. The molecular profile of metastatic cancers remains to be unraveled. Here we present mutations and gene copy number variations (CNV) of metastases across tumor types from patients enrolled in the SHIVA trial2.

Patients and methods

The SHIVA trial is a multicentric randomized proof-of-concept phase II trial comparing molecularly targeted therapy based on tumor molecular profiling versus conventional therapy in patients with any type of refractory cancer. Mutations using targeted NGS (AmpliSeq cancer panel on Ion Torrent / PGM (Life)), and CNV using Cytoscan HD (Affymetrix) were assessed on a mandatory biopsy from a metastatic site with ≥30% of tumor cell content. Sequencing data were processed in order to detect actionable somatic mutations. Detected variants were filtered according to their frequency (≥4% for SNVs and 5% for indels), strand ratio (≥0.2), and reads coverage (≥30X for SNVs and 100X for indels). Non polymorphic deleterious mutations were reported. Copy number and allele difference profiles were processed taking into account% of tumor cells and ploidy of the sample. Homozygous and heterozygous deletions and focal amplifications were reported for tumor suppressor genes and oncogenes. Between October 2012 and July 2014, 741 patients with any type of solid cancer were enrolled in the SHIVA trial. Among these, 507 and 496 patients had high quality NGS and CNV profiling, respectively.

Results

Major cancer types for which molecular analyses were possible on a metastatic biopsy were: breast (14%), colorectal (11%), lung (11%), ovarian (11%), pancreatic (8%), sarcoma (6%), head and neck (4%), cervical (4%), urothelial (4%), endometrial (3%), oesogastric (3%) cancers, adenoid cystic carcinoma (3%) and others (18%). TP53 mutations were present in 44% of metastatic patients. Major mutated oncogenes were KRAS (20%), PIK3CA (12%), MET (6%), FGFR3 (5%), EGFR (2%) and BRAF (2%). Tumor suppressor genes PTEN, FBXW7 and CDKN2A were mutated in 3% of patients. Alternatively, homozygous and heterozygous deletions of PTEN, FBXW7 and CDKN2A were observed in around half of the patients analyzed (40%, 40% and 54%, respectively).

Conclusions

Mutations and CNV analyses on metastatic tumors from patients enrolled in the SHIVA trial showed similar results in terms of frequency of previously reported genetic alterations1,3. The frequency of KRAS mutations (20%) was however higher than the frequency (7%) reported in the pan cancer cohort of the tumors portal3. This result needs to be interpreted in accordance with tumor types before suggesting potential resistance mechanisms in heavily pretreated patients. Clustering of these alterations in specific signaling pathways is currently ongoing.

Citation Format: Maud Kamal, Nicolas Servant, Gaelle Pierron, Celine Callens, David Gentien, Alban Lermine, Georges Lucotte, Virginie Bernard, Anne Vincent-Salomon, Ivan Bièche, Christophe Le Tourneau. Mutations and gene copy number variations landscape of metastases of various cancer types from patients enrolled in the SHIVA trial. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1524.

Abstract 91: The mutational landscape of mucinous carcinomas of the breast

Background: Mucinous breast carcinoma (MBC) is a special histologic type of breast cancer, comprising approximately 2% of all invasive breast carcinomas. Morphologically, MBCs are characterized by clusters of tumor cells floating in large amounts of extracellular mucin. MBCs are preferentially of low histologic grade and estrogen receptor (ER)-positive and HER2-negative. MBCs have been shown to lack the hallmark 1q gains and 16q losses found in low-grade ER-positive invasive ductal carcinomas of no special type (IDC-NSTs). Here we sought to characterize the mutational landscape and copy number alterations (CNA) of MBCs by whole exome sequencing analysis.

Material and Methods: Frozen sections from 25 pure MBCs (n = 13 mucinous A (paucicellular), n = 12 mucinous B (hypercellular)) were subjected to microdissection to ensure a tumor cell content &gt;85%. In addition, five cases of mixed mucinous carcinomas composed of mucinous and IDC-NST components were included in this study. In these cases, the MBC and IDC-NST components were microdissected separately. DNA samples extracted from microdissected tumors and matched normal counterparts were subjected to whole exome sequencing on an Illumina HiSeq2000. Somatic single nucleotide variants (SNVs) were identified using MuTect and somatic insertions and deletions (indels) were identified using Strelka and Varscan2. Somatic CNAs were defined using FACETS. Mutational frequencies in MBCs were compared to those of luminal IDC-NSTs from The Cancer Genome Atlas.

Results: A median of 26 (range 5-71) non-synonymous SNVs and indels were identified per MBC. GATA3, mutated in 28% of cases, was the only significantly mutated gene as defined by MutSigCV (q&lt;0.1). Compared to IDC-NSTs of luminal molecular subtype, MBCs were found to harbor significantly fewer mutations in TP53 (3% vs 19%, p&lt;0.001) and PIK3CA (6% vs 41%, p&lt;0.001). Mucinous subtypes A and B did not differ in terms of mutations and/ or CNAs, whereas MBCs of mixed phenotype harbored a greater extent of genomic instability. While MBC and IDC-NST components of mixed MBCs shared the majority of the somatic genetic alterations, indicating their clonal relatedness, mutations and CNAs restricted to either the MBC or the IDC-NST components were also identified. Furthermore, CNA analysis confirmed our previous observations that MBCs, contrary to low-grade ER-positive IDC-NSTs, lack concurrent copy number gains of 1q and 16p and losses of 16q.

Conclusions: Our data suggest that the repertoires of somatic mutations and gene CNAs of MBCs are distinct from those of luminal IDC-NSTs, and that MBCs are an entity distinct from low-grade ER-positive IDC-NSTs not only at the morphologic but also at the genetic level.

Citation Format: Salvatore Piscuoglio, Charlotte KY Ng, Felipe C. Geyer, Carey A. Eberle, Elena Guerini-Rocco, Caterina Marchio, Anne Vincent-Salomon, Jorge S. Reis-Filho, Britta Weigelt. The mutational landscape of mucinous carcinomas of the breast. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 91.

A whole-genome sequence and transcriptome perspective on HER2-positive breast cancers

HER2-positive breast cancer has long proven to be a clinically distinct class of breast cancers for which several targeted therapies are now available. However, resistance to the treatment associated with specific gene expressions or mutations has been observed, revealing the underlying diversity of these cancers. Therefore, understanding the full extent of the HER2-positive disease heterogeneity still remains challenging. Here we carry out an in-depth genomic characterization of 64 HER2-positive breast tumour genomes that exhibit four subgroups, based on the expression data, with distinctive genomic features in terms of somatic mutations, copy-number changes or structural variations. The results suggest that, despite being clinically defined by a specific gene amplification, HER2-positive tumours melt into the whole luminal-basal breast cancer spectrum rather than standing apart. The results also lead to a refined ERBB2 amplicon of 106 kb and show that several cases of amplifications are compatible with a breakage-fusion-bridge mechanism.

Landscape of somatic mutations in 560 breast cancer whole-genome sequences

We analysed whole-genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. We found that 93 protein-coding cancer genes carried probable driver mutations. Some non-coding regions exhibited high mutation frequencies, but most have distinctive structural features probably causing elevated mutation rates and do not contain driver mutations. Mutational signature analysis was extended to genome rearrangements and revealed twelve base substitution and six rearrangement signatures. Three rearrangement signatures, characterized by tandem duplications or deletions, appear associated with defective homologous-recombination-based DNA repair: one with deficient BRCA1 function, another with deficient BRCA1 or BRCA2 function, the cause of the third is unknown. This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operating, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer.

Chronic oxidative stress promotes H2AX protein degradation and enhances chemosensitivity in breast cancer patients

Anti‐cancer drugs often increase reactive oxygen species (ROS) and cause DNA damage. Here, we highlight a new cross talk between chronic oxidative stress and the histone variant H2AX, a key player in DNA repair. We observe that persistent accumulation of ROS, due to a deficient JunD‐/Nrf2‐antioxidant response, reduces H2AX protein levels. This effect is mediated by an enhanced interaction of H2AX with the E3 ubiquitin ligase RNF168, which is associated with H2AX poly‐ubiquitination and promotes its degradation by the proteasome. ROS‐mediated H2AX decrease plays a crucial role in chemosensitivity. Indeed, cycles of chemotherapy that sustainably increase ROS reduce H2AX protein levels in Triple‐Negative breast cancer (TNBC) patients. H2AX decrease by such treatment is associated with an impaired NRF2‐antioxidant response and is indicative of the therapeutic efficiency and survival of TNBC patients. Thus, our data describe a novel ROS‐mediated regulation of H2AX turnover, which provides new insights into genetic instability and treatment efficacy in TNBC patients.

Microglandular adenosis associated with triple-negative breast cancer is a neoplastic lesion of triple-negative phenotype harbouring TP53 somatic mutations

Microglandular adenosis (MGA) is a rare proliferative lesion of the breast composed of small glands lacking myoepithelial cells and lined by S100-positive, oestrogen receptor (ER)-negative, progesterone receptor (PR)-negative, and HER2-negative epithelial cells. There is evidence to suggest that MGA may constitute a non-obligate precursor of triple-negative breast cancer (TNBC). We sought to define the genomic landscape of pure MGA and of MGA, atypical MGA (AMGA) and associated TNBCs, and to determine whether synchronous MGA, AMGA, and TNBCs would be clonally related. Two pure MGAs and eight cases of MGA and/or AMGA associated with in situ or invasive TNBC were collected, microdissected, and subjected to massively parallel sequencing targeting all coding regions of 236 genes recurrently mutated in breast cancer or related to DNA repair. Pure MGAs lacked clonal non-synonymous somatic mutations and displayed limited copy number alterations (CNAs); conversely, all MGAs (n = 7) and AMGAs (n = 3) associated with TNBC harboured at least one somatic non-synonymous mutation (range 3-14 and 1-10, respectively). In all cases where TNBCs were analyzed, identical TP53 mutations and similar patterns of gene CNAs were found in the MGA and/or AMGA and in the associated TNBC. In the MGA/AMGA associated with TNBC lacking TP53 mutations, somatic mutations affecting PI3K pathway-related genes (eg PTEN, PIK3CA, and INPP4B) and tyrosine kinase receptor signalling-related genes (eg ERBB3 and FGFR2) were identified. At diagnosis, MGAs associated with TNBC were found to display subclonal populations, and clonal shifts in the progression from MGA to AMGA and/or to TNBC were observed. Our results demonstrate the heterogeneity of MGAs, and that MGAs associated with TNBC, but not necessarily pure MGAs, are genetically advanced, clonal, and neoplastic lesions harbouring recurrent mutations in TP53 and/or other cancer genes, supporting the notion that a subset of MGAs and AMGAs may constitute non-obligate precursors of TNBCs.

ARF6-JIP3/4 regulate endosomal tubules for MT1-MMP exocytosis in cancer invasion

Interaction of plasma membrane ARF6 with JIP3/JIP4 effectors on MT1-MMP endosomes coordinates dynactin–dynein and kinesin-1 activity in a tug-of-war mechanism for endosome tubulation and MT1-MMP exocytosis to promote breast cancer cell invasion.

Invasion of cancer cells into collagen-rich extracellular matrix requires membrane-tethered membrane type 1–matrix metalloproteinase (MT1-MMP) as the key protease for collagen breakdown. Understanding how MT1-MMP is delivered to the surface of tumor cells is essential for cancer cell biology. In this study, we identify ARF6 together with c-Jun NH₂-terminal kinase–interacting protein 3 and 4 (JIP3 and JIP4) effectors as critical regulators of this process. Silencing ARF6 or JIP3/JIP4 in breast tumor cells results in MT1-MMP endosome mispositioning and reduces MT1-MMP exocytosis and tumor cell invasion. JIPs are recruited by Wiskott-Aldrich syndrome protein and scar homologue (WASH) on MT1-MMP endosomes on which they recruit dynein–dynactin and kinesin-1. The interaction of plasma membrane ARF6 with endosomal JIPs coordinates dynactin–dynein and kinesin-1 activity in a tug-of-war mechanism, leading to MT1-MMP endosome tubulation and exocytosis. In addition, we find that ARF6, MT1-MMP, and kinesin-1 are up-regulated in high-grade triple-negative breast cancers. These data identify a critical ARF6–JIP–MT1-MMP–dynein–dynactin–kinesin-1 axis promoting an invasive phenotype of breast cancer cells.

LIN7A is a major determinant of cell-polarity defects in breast carcinomas

Background

Polarity defects are a hallmark of most carcinomas. Cells from invasive micropapillary carcinomas (IMPCs) of the breast are characterized by a striking cell polarity inversion and represent an interesting model for the analysis of polarity abnormalities.

Methods

In-depth investigation of polarity proteins in 24 IMPCs and a gene expression profiling, comparing IMPC (n = 73) with invasive carcinomas of no special type (ICNST) (n = 51) have been performed.

Results

IMPCs showed a profound disorganization of the investigated polarity proteins and revealed major abnormalities in their subcellular localization. Gene expression profiling experiments highlighted a number of deregulated genes in the IMPCs that have a role in apico-basal polarity, adhesion and migration. LIN7A, a Crumbs-complex polarity gene, was one of the most differentially over-expressed genes in the IMPCs. Upon LIN7A over-expression, we observed hyperproliferation, invasion and a complete absence of lumen formation, revealing strong polarity defects.

Conclusion

This study therefore shows that LIN7A has a crucial role in the polarity abnormalities associated with breast carcinogenesis.

Electronic supplementary material

The online version of this article (doi:10.1186/s13058-016-0680-x) contains supplementary material, which is available to authorized users.

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&lt;0.05) and a lower frequency of PIK3CA somatic mutations (14% vs 42%, respectively, p&lt;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 P6-03-10: 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 P6-07-13: New insights on HER2 amplification from the constitutional and somatic standpoints: Results from the ICGC and SIGNAL/Phare studies

Background: HER2-positive (HER2+) breast cancers are defined by the amplification and/or overexpression of the human epidermal growth factor receptor (HER2/ERBB2) gene on chromosome region 17q12. Although anti-HER2 targeted therapies have greatly improved treatment of HER2+ breast cancer, the magnitude of benefit varies widely between patients. Deciphering the genomic and genetic heterogeneity of HER2+ breast cancer may provide a basis to better understand their natural history, opening new avenues of treatment.

Methods: As part of the ICGC Breast Cancer Working Group effort, we combined whole genome sequencing and transcriptomic analyses of 64 HER2+ primary invasive carcinomas, and a genome wide association study (GWAS) of over 9.836 breast cancer patients in the prospective SIGNAL/PHARE cohort (NCT00381901 – RECF1098).

Results: Using WGS data we precisely delineate the ERBB2 amplicon as a 106 kb region involving six genes and show that the amplification mechanism was consistent with breakage-fusion-bridge (BFB) cycles. Four RNA expression-based groups were identified, displaying specific genomic alterations in terms of amplification, rearrangements and mutations. On other hand, GWAS analyses failed to identify any constitutional variants associated with HER2 amplification.

Discussion: By combining whole genome sequencing and expression analysis, we provide evidence showing that HER2+ tumours display considerably more molecular heterogeneity than previously reported. These results are reinforced with the lack of association between any genetic variants and HER2 amplification from GWAS analyses. Taken as a whole, these results suggest that HER2+ breast cancers do not represent per se a homogeneous subtype, but are distributed along the whole breast cancer spectrum, from ER-positive luminal to ER-negative basal phenotype. Genome alterations present in HER2+ tumors are in accordance with these phenotypes, and it is likely that the HER2 amplification is a secondary event in the course of tumorigenesis, not favored by any particular constitutional or somatic genetic variants.

Citation Format: Vincent-Salomon A, Ferrari A, Pivot X, Macgrogan G, Arnould L, Treilleux I, Romieux G, Sertier A-S, Thomas E, Tonon L, Boyault S, Kielbassa J, Letexier V, Pauporte I, Birbaum D, Saintigny P, Cox D, Viari A. New insights on HER2 amplification from the constitutional and somatic standpoints: Results from the ICGC and SIGNAL/Phare studies. [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 P6-07-13.

Abstract P2-05-06: Clinical utility of systematic biopsy of first metastatic event in breast cancer: Results from a prospective multicenter trial

BACKGROUND: Cumulative evidence for phenotypic and molecular heterogeneity between primary breast cancer (BC) site and matched metastasis (mets) has been obtained in retrospective studies. Current expert consensus suggests performing biopsies of mets, but clinical utility and cost are unknown. The primary objective of the ESOPE study (NCT01956552) was to compare the phenotype and genotype of the primary tumor (PT) with those of matched mets at time of first distant relapse, before the start of any treatment, in order to optimize the treatment of mets

PATIENTS and METHODS: Between Nov. 2010 and Sept. 2013, we conducted a prospective multicenter study on BC patients (pts) with diagnosis of first mets. All pts were to have available Formalin-Fixed Paraffin-Embedded (FFPE) PT sample and mets accessible to either percutaneous or surgical sampling. All tissue samples were centrally analyzed with immunohistochemistry (ER, PgR, HER2, and Ki67) and FISH when indicated. Frozen samples were stored for further analyses. We recorded intended therapeutic decision before and after biopsy.

RESULTS: Of 93 pts included, 89 were eligible for biopsy. Median age was 57 years (28-81); median interval between PT and mets was 42 months (0-211), including 14 pts with novo metastatic breast cancer. Mets biopsy was performed in 85 pts (96%, refusal n=2, not feasible n=2). Toxicity was limited to only 1 grade 1 hemorrhage. Sampled sites were liver (44%), lung (16%), bone (13%), lymph node (13%), skin/muscle/chest wall (9%), ovary/peritoneum (4%), and adrenal gland (1%). PT was not available in 4 pts; mets biopsy was non contributive in 6 pts but led to a diagnosis of second primary cancer in 3 pts.

In 72 pts with matched PT and mets, PT were luminal A (n=11), luminal B (n=33), triple negative (n=13), HER2 (n=13), non-evaluable (n=2). Mets were luminal A (n=6), luminal B (n=30), triple negative (n=16), HER2 (n=14), non-evaluable (n=6). Discrepancy rates were: ER 18% [kappa for concordance =0.6, CI 95 % (0.42-0.77)], PgR: 39% [kappa=0.19, CI 95% (0.01-0.39)], Her2: 4% [kappa=0.86, CI 95% (0.7-1)], Ki67: 25% [kappa=0.19, CI 95% (-0.09; 0.49)].

The most frequent discrepancy rate was observed in pts with lum A PT, as only 3/10 developed Lum A mets. HER2 and triple negative were the most stable subtypes (12/13 and 12/12 respectively). Most importantly, mets biopsy led to a change in therapeutic decision in 25 pts (independent evaluation by 2 oncologists). Additional comparative targeted NGS analyses are ongoing on a first subset of 54 FFPE paired samples, and parallel whole exome sequencing is planned on 38 paired samples with available constitutional DNA.

CONCLUSION: Comparative analysis of breast cancer PT and first mets is routinely feasible, with very low morbidity and a significant impact for patients' management: 29% had a second cancer diagnosis or were proposed a therapeutic change. Furthermore, this study will provide additional data on quality and quantity of tissue available for molecular analysis, and ultimately in terms of cost-efficacy.

Citation Format: Comte A, Sigal-Zafrani B, Belin L, Bièche I, Callens C, Diéras V, Bidard F-C, Mariani O, Servois V, Szwarc D, Vincent-Salomon A, Brain ECG, Cottu PH. Clinical utility of systematic biopsy of first metastatic event in breast cancer: Results from a prospective multicenter trial. [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 P2-05-06.

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.

Estrogen-Receptor, Progesterone-Receptor and HER2 Status Determination in Invasive Breast Cancer. Concordance between Immuno-Histochemistry and MapQuant™ Microarray Based Assay

Background

Hormone receptor status and HER2 status are of critical interest in determining the prognosis of breast cancer patients. Their status is routinely assessed by immunohistochemistry (IHC). However, it is subject to intra-laboratory and inter-laboratory variability. The aim of our study was to compare the estrogen receptor, progesterone receptor and HER2 status as determined by the MapQuant™ test to the routine immuno-histochemical tests in early stage invasive breast cancer in a large comprehensive cancer center.

Patients and Methods

We retrospectively studied 163 invasive early-stage breast carcinoma with standard IHC status. The genomic status was determined using the MapQuant™ test providing the genomic grade index.

Results

We found only 4 tumours out of 161 (2.5%) with discrepant IHC and genomic results concerning ER status. The concordance rate between the two methods was 97.5% and the Cohen’s Kappa coefficient was 0.89.

Comparison between the MapQuant™ PR status and the PR IHC status gave more discrepancies. The concordance rate between the two methods was 91.4% and the Cohen’s Kappa coefficient was 0.74.

The HER2 MapQuant™ test was classified as « undetermined » in 2 out of 163 cases (1.2%). One HER2 IHC-negative tumour was found positive with a high HER2 MapQuant™ genomic score. The concordance rate between the two methods was 99.3% and the Cohen’s Kappa coefficient was 0.86.

Conclusion

Our results show that the MapQuant™ assay, based on mRNA expression assay, provides an objective and quantitative assessment of Estrogen receptor, Progesterone receptor and HER2 status in invasive breast cancer.

Satellite in transit metastases in rapidly fatal conjunctival melanoma: implications for angiotropism and extravascular migratory metastasis (description of a murine model for conjunctival melanoma)

Little information is currently available concerning loco-regional metastases such as satellite and in transit metastases and their natural history in conjunctival melanoma as compared to cutaneous melanoma. Angiotropism, a marker of extravascular migration of melanoma cells along vascular channels, often appears responsible for microscopic satellite, satellite and in transit metastases development in cutaneous melanoma. In addition, diffuse tissue microscopic satellites are correlated with widespread melanoma dissemination and death. Herein we report rapid conjunctival melanoma progression and a fatal outcome in four of five patients following recurrence as satellite in transit metastases. Five patients aged 31, 60, 63, 56, and 67 years developed primary conjunctival melanoma, histologically characterised by tumour thicknesses of 4, 4, 1.1, 3, and 2 mm. Two or more conjunctival melanomas manifested ulceration, significant mitotic rates, necrosis, angiotropism, and intralesional transformation. The conjunctival melanoma recurred in a matter of months as one or more discrete satellite in transit lesions in the vicinity of the primary melanoma. Histological examination revealed well-defined micronodules containing atypical melanocytes in the subepithelial connective tissue stroma. All lesions were extravascular and most appeared angiotropic. Four of five patients subsequently developed parotid or other loco-regional nodal disease and rapidly ensuing widespread metastases and death. The time course from diagnosis to the demise of the patients averaged about 13 (range 7-20) months. Our findings suggest that satellite in transit metastases constitute an important new risk marker for possible rapid metastatic disease progression and death in patients with conjunctival melanoma. This finding appears to take on even greater significance if such lesions develop rapidly, i.e., in a matter of weeks or months following diagnosis of primary conjunctival melanoma, and if the primary melanoma manifests additional high-risk features. Additional studies are underway in order to further elucidate the mechanism of these metastases.

Phyllodes tumours of the breast: a consensus review

Phyllodes tumours constitute an uncommon but complex group of mammary fibroepithelial lesions. Accurate and reproducible grading of these tumours has long been challenging, owing to the need to assess multiple stratified histological parameters, which may be weighted differently by individual pathologists. Distinction of benign phyllodes tumours from cellular fibroadenomas is fraught with difficulty, due to overlapping microscopic features. Similarly, separation of the malignant phyllodes tumour from spindle cell metaplastic carcinoma and primary breast sarcoma can be problematic. Phyllodes tumours are treated by surgical excision. However, there is no consensus on the definition of an appropriate surgical margin to ensure completeness of excision and reduction of recurrence risk. Interpretive subjectivity, overlapping histological diagnostic criteria, suboptimal correlation between histological classification and clinical behaviour and the lack of robust molecular predictors of outcome make further investigation of the pathogenesis of these fascinating tumours a matter of active research. This review consolidates the current understanding of their pathobiology and clinical behaviour, and includes proposals for a rational approach to the classification and management of phyllodes tumours.

Phyllodes tumours of the breast: a consensus review

Phyllodes tumours constitute an uncommon but complex group of mammary fibroepithelial lesions. Accurate and reproducible grading of these tumours has long been challenging, owing to the need to assess multiple stratified histological parameters, which may be weighted differently by individual pathologists. Distinction of benign phyllodes tumours from cellular fibroadenomas is fraught with difficulty, due to overlapping microscopic features. Similarly, separation of the malignant phyllodes tumour from spindle cell metaplastic carcinoma and primary breast sarcoma can be problematic. Phyllodes tumours are treated by surgical excision. However, there is no consensus on the definition of an appropriate surgical margin to ensure completeness of excision and reduction of recurrence risk. Interpretive subjectivity, overlapping histological diagnostic criteria, suboptimal correlation between histological classification and clinical behaviour and the lack of robust molecular predictors of outcome make further investigation of the pathogenesis of these fascinating tumours a matter of active research. This review consolidates the current understanding of their pathobiology and clinical behaviour, and includes proposals for a rational approach to the classification and management of phyllodes tumours.

[Perception of pT1a,b pN0 breast tumor prognosis by the French oncology community: Results of the EURISTIC national survey]

The prognosis of infracentimetric breast cancers (BC) is heterogeneous. The EURISTIC survey describes how French oncology specialists perceive the prognosis of pT1a,b pN0 BCs. A self-administered questionnaire has been sent to over 2000 French BC specialists. Six hundred and sixty-three physicians responded. Fifty-eight percent do not consider tumor size as a key prognostic criterion. They consider that the cutoff for poor prognosis is 22mm, 10mm and 7mm for hormone receptors (HRs)+, HER2+ and triple-negative (TN) tumors respectively. Eighty-three percent of respondents consider that a HR+ pT1a,b tumor has a good prognosis (21% and 8% for HER2+ and TN respectively). Factors perceived as most detrimental are: HER2 overexpression (29% of respondents); HR- (20%); high grade (20%); TN status (14%); high KI67 (5%); presence of lymphovascular invasion (3%); young age (2%) and high mitotic index (1%). For French specialists, immunohistochemical characteristics, in particular hormone and HER2 status, are strong prognostic factors in BCs below 1cm.

Inhibition of autophagy as a new means of improving chemotherapy efficiency in high-LC3B triple-negative breast cancers

The triple-negative breast cancer (TN BC) subtype is the most aggressive form of invasive BC. Despite intensive efforts to improve BC treatments, patients with TN BC continue to exhibit poor survival, with half developing resistance to chemotherapy. Here we identify autophagy as a key mechanism in the progression and chemoresistance of a subset of TN tumors. We demonstrate that LC3B, a protein involved in autophagosome formation, is a reliable marker of poor prognosis in TN BC, validating this prognostic value at both the mRNA and protein levels in several independent cohorts. We also show that LC3B has no prognostic value for other BC subtypes (Luminal or HER2 BC), thus revealing a specific impact of autophagy on TN tumors. Autophagy is essential for the proliferative and invasive properties in 3D of TN BC cells characterized by high LC3B levels. Interestingly, the activity of the transcriptional co-activator YAP1 (Yes-associated protein 1) is regulated by the autophagy process and we identify YAP1 as a new actor in the autophagy-dependent proliferative and invasive properties of high-LC3B TN BC. Finally, inhibiting autophagy by silencing ATG5 or ATG7 significantly impaired high-LC3B TN tumor growth in vivo. Moreover, using a patient-derived TN tumor transplanted into mice, we show that an autophagy inhibitor, chloroquine, potentiates the effects of chemotherapeutic agents. Overall, our data identify LC3B as a new prognostic marker for TN BC and the inhibition of autophagy as a promising therapeutic strategy for TN BC patients.