MSC-regulated microRNAs converge on the transcription factor FOXP2 and promote breast cancer metastasis

Mesenchymal stem/stromal cells (MSCs) are progenitor cells shown to participate in breast tumor stroma formation and to promote metastasis. Despite expanding knowledge of their contributions to breast malignancy, the underlying molecular responses of breast cancer cells (BCCs) to MSC influences remain incompletely understood. Here, we show that MSCs cause aberrant expression of microRNAs, which, led by microRNA-199a, provide BCCs with enhanced cancer stem cell (CSC) properties. We demonstrate that such MSC-deregulated microRNAs constitute a network that converges on and represses the expression of FOXP2, a forkhead transcription factor tightly associated with speech and language development. FOXP2 knockdown in BCCs was sufficient in promoting CSC propagation, tumor initiation, and metastasis. Importantly, elevated microRNA-199a and depressed FOXP2 expression levels are prominent features of malignant clinical breast cancer and are associated significantly with poor survival. Our results identify molecular determinants of cancer progression of potential utility in the prognosis and therapy of breast cancer.

Fine-needle aspiration of low-grade adenosquamous carcinomas of the breast: a report of three new cases

OBJECTIVES

To describe cytology patterns in low-grade adenosquamous carcinomas (LGASCs) of the breast.

STUDY DESIGN

Low-grade adenosquamous carcinomas of the breast are a recently described rare variant of primary metaplastic carcinomas characterized by clinical indolence, slow evolution and excellent survival. To date, only 7 cases of LGASC were studied cytologically, and it was demonstrated that LGASC identification was difficult because its cellular components exhibited unspecific and nonsuspicious features. They consisted of irregularly clustered cells without prominent cytonuclear atypia, mitosis or necrosis. The presence of metaplastic cells or keratin debris was helpful in accurate tumor typing. We report here 3 additional cases of LGASC that were initially studied by fine-needle aspiration.

RESULTS

We have also encountered diagnostic difficulties and misdiagnosed tumors, since 2 cases were underdiagnosed as 'suspicious' and only 1 was accurately diagnosed as malignancy.

CONCLUSION

The review of our cases and the literature confirms that, despite its putative metaplastic origin, LGASC is an entity which is difficult to diagnose using classical cytological methods. Moreover, core-needle biopsy as well as frozen sections may also misdiagnose LGASC as a benign breast lesion.

Abstract LB-30: Membrane-anchored MT1-MMP downstream of p63 is essential for the transition of in situ to invasive breast carcinoma

Understanding breast tumor progression requires insights both at the molecular and cellular levels. In particular, the transition of ductal carcinoma in situ (DCIS) to invasive ductal carcinoma (IDC) is a key, yet poorly understood event. Membrane-Type 1 matrix metalloproteinase (MT1-MMP) is critical for pericellular remodelling of the basement membrane and interstitial collagen during invasion by carcinoma cells.

The role of MT1-MMP during the transition from DCIS to IDC was investigated using an intraductal human-in-mouse xenograft model. Breast tumor-derived MCF10.DCIS.com cells, which express MT1-MMP were injected into the primary mammary ducts of female SCID mice. Histological analysis revealed a progression from DCIS, to microinvasive and invasive lesions by 5, 7-8 and 10-12 weeks post-injection, respectively. Immunohistochemistry (IHC) staining showed homogeneous expression of MT1-MMP over the tumor section at DCIS stage, and up-regulation at the edge of the tumours at microinvasive and invasive states. In microinvasives lesion, up-regulation of MT1-MMP in tumour cells coincided with disruption of the basement membrane. At later stages, one characteristic of invasive lesions is the increase in collagen fibers deposition. Interestingly, MT1-MMP expression was also increased at the front of infiltrating tumours in contact with the stroma.

After 10 weeks, intraductally injected cells knocked down for MT1-MMP developed invasive tumours only in 20% of injected mammary glands, while 100% of glands injected with control cells developed infiltrating lesions. All together, these results demonstrated that MT1-MMP is instrumental for the transition from in situ to invasive breast tumours.

IHC staining revealed a strong correlation of the expression of the basal marker p63 and MT1-MMP in tumour cells both at the microinvasive and invasive stages. One hypothesis was that contact of tumor cells with the stroma triggered induction of p63 that in turn up-regulated MT1-MMP. Along this line, we found that MCF10.DCIS.com cells plated on type I collagen up-regulated p63 and MT1-MMP, both at the mRNA and protein levels, while silencing of p63 abolished collagen-dependent MT1-MMP increase. At the functional level, silencing of MT1-MMP or p63 inhibited invasion of multicellular spheroids into 3D type collagen as well as the cells capacity to degrade collagen I fibers.

Finally, MT1-MMP expression was analysed by IHC staining on human tissue microarray comprising 432 IDCs, 40 microinfiltrated lesions and 68 DCIS. MT1-MMP was upregulated in IDC as compared to DCIS. Invasive triple-negative breast (TNBC) and grade III tumours expressed highest MT1-MMP levels. To our knowledge, this is the first demonstration that up-regulation of MT1-MMP is associated with invasiveness, histopathologic grade and molecular subtypes in human breast cancer. We also observed 10% of TNBC expressing p63 and found a positive correlation with MT1-MMP expression suggesting an interplay between p63 and MT1-MMP during progression.

Citation Format: Catalina Lodillinsky, Elvira Infante, Laetitia Fuhrmann, Alan Guichard, Joanna Cyrta, Emilie Lagoutte, Marie Irondelle, Sophie Vacher, Ivan Bieche, Marina Glukhova, Anne Vincent-Salomon, Philippe Chavrier. Membrane-anchored MT1-MMP downstream of p63 is essential for the transition of in situ to invasive breast carcinoma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr LB-30. doi:10.1158/1538-7445.AM2014-LB-30

Mobile DNA in cancer. Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes

Long interspersed nuclear element-1 (L1) retrotransposons are mobile repetitive elements that are abundant in the human genome. L1 elements propagate through RNA intermediates. In the germ line, neighboring, nonrepetitive sequences are occasionally mobilized by the L1 machinery, a process called 3' transduction. Because 3' transductions are potentially mutagenic, we explored the extent to which they occur somatically during tumorigenesis. Studying cancer genomes from 244 patients, we found that tumors from 53% of the patients had somatic retrotranspositions, of which 24% were 3' transductions. Fingerprinting of donor L1s revealed that a handful of source L1 elements in a tumor can spawn from tens to hundreds of 3' transductions, which can themselves seed further retrotranspositions. The activity of individual L1 elements fluctuated during tumor evolution and correlated with L1 promoter hypomethylation. The 3' transductions disseminated genes, exons, and regulatory elements to new locations, most often to heterochromatic regions of the genome.

Integrative genomic and transcriptomic characterization of papillary carcinomas of the breast

Papillary carcinoma (PC) is a rare type of breast cancer, which comprises three histologic subtypes: encapsulated PC (EPC), solid PC (SPC) and invasive PC (IPC). Microarray‐based gene expression and Affymetrix SNP 6.0 gene copy number profiling, and RNA‐sequencing revealed that PCs are luminal breast cancers that display transcriptomic profiles distinct from those of grade‐ and estrogen receptor (ER)‐matched invasive ductal carcinomas of no special type (IDC‐NSTs), and that the papillary histologic pattern is unlikely to be underpinned by a highly recurrent expressed fusion gene or a highly recurrent expressed mutation. Despite displaying similar patterns of gene copy number alterations, significant differences in the transcriptomic profiles of EPCs, SPCs and IPCs were found, and may account for their different histologic features.

Papillary carcinomas of the breast display distinctive transcriptomic profiles.

Proliferation‐related genes are expressed at low levels in papillary carcinomas.

Papillary carcinomas are unlikely to be underpinned by a highly recurrent fusion gene.

Papillary carcinomas are unlikely to be underpinned by a highly recurrent expressed mutation.

Polarity gene alterations in pure invasive micropapillary carcinomas of the breast

INTRODUCTION

Pure invasive micropapillary carcinoma (IMPC) is a special type of breast carcinoma characterised by clusters of cells presenting polarity abnormalities. The biological alterations underlying this pattern remain unknown.

METHODS

Pangenomic analysis (n=39), TP53 (n=43) and PIK3CA (n=41) sequencing in a series of IMPCs were performed. A subset of cases was also analysed with whole-exome sequencing (n=4) and RNA sequencing (n=6). Copy number variation profiles were compared with those of oestrogen receptors and grade-matched invasive ductal carcinomas (IDCs) of no special type.

RESULTS

Unsupervised analysis of genomic data distinguished two IMPC subsets: one (Sawtooth/8/16) exhibited a significant increase in 16p gains (71%), and the other (Firestorm/Amplifier) was characterised by a high frequency of 8q (35%), 17q (20% to 46%) and 20q (23% to 30%) amplifications and 17p loss (74%). TP53 mutations (10%) were more frequently identified in the amplifier subset, and PIK3CA mutations (4%) were detected in both subsets. Compared to IDC, IMPC exhibited specific loss of the 6q16-q22 region (45%), which is associated with downregulation of FOXO3 and SEC63 gene expression. SEC63 and FOXO3 missense mutations were identified in one case each (2%). Whole-exome sequencing combined with RNA sequencing of IMPC allowed us to identify somatic mutations in genes involved in polarity, DNAH9 and FMN2 (8% and 2%, respectively) or ciliogenesis, BBS12 and BBS9 (2% each) or genes coding for endoplasmic reticulum protein, HSP90B1 and SPTLC3 (2% each) and cytoskeleton, UBR4 and PTPN21 (2% each), regardless of the genomic subset. The intracellular biological function of the mutated genes identified by gene ontology analysis suggests a driving role in the clinicopathological characteristics of IMPC.

CONCLUSION

In our comprehensive molecular analysis of IMPC, we identified numerous genomic alterations without any recurrent fusion genes. Recurrent somatic mutations of genes participating in cellular polarity and shape suggest that they, together with other biological alterations (such as epigenetic modifications and stromal alterations), could contribute to the morphological pattern of IMPC. Though none of the individual abnormalities demonstrated specificity for IMPC, whether their combination in IMPC may have a cumulative effect that drives the abnormal polarity of IMPC needs to be examined further with in vitro experiments.

Control of MT1-MMP transport by atypical PKC during breast-cancer progression

Dissemination of carcinoma cells requires the pericellular degradation of the extracellular matrix, which is mediated by membrane type 1-matrix metalloproteinase (MT1-MMP). In this article, we report a co-up-regulation and colocalization of MT1-MMP and atypical protein kinase C iota (aPKCι) in hormone receptor-negative breast tumors in association with a higher risk of metastasis. Silencing of aPKC in invasive breast-tumor cell lines impaired the delivery of MT1-MMP from late endocytic storage compartments to the surface and inhibited matrix degradation and invasion. We provide evidence that aPKCι, in association with MT1-MMP-containing endosomes, phosphorylates cortactin, which is present in F-actin-rich puncta on MT1-MMP-positive endosomes and regulates cortactin association with the membrane scission protein dynamin-2. Thus, cell line-based observations and clinical data reveal the concerted activity of aPKC, cortactin, and dynamin-2, which control the trafficking of MT1-MMP from late endosome to the plasma membrane and play an important role in the invasive potential of breast-cancer cells.

Randomised proof-of-concept phase II trial comparing targeted therapy based on tumour molecular profiling vs conventional therapy in patients with refractory cancer: results of the feasibility part of the SHIVA trial

Background:

The SHIVA trial is a multicentric randomised proof-of-concept phase II trial comparing molecularly targeted therapy based on tumour molecular profiling vs conventional therapy in patients with any type of refractory cancer. Results of the feasibility study on the first 100 enrolled patients are presented.

Methods:

Adult patients with any type of metastatic cancer who failed standard therapy were eligible for the study. The molecular profile was performed on a mandatory biopsy, and included mutations and gene copy number alteration analyses using high-throughput technologies, as well as the determination of oestrogen, progesterone, and androgen receptors by immunohistochemistry (IHC).

Results:

Biopsy was safely performed in 95 of the first 100 included patients. Median time between the biopsy and the therapeutic decision taken during a weekly molecular biology board was 26 days. Mutations, gene copy number alterations, and IHC analyses were successful in 63 (66%), 65 (68%), and 87 (92%) patients, respectively. A druggable molecular abnormality was present in 38 patients (40%).

Conclusions:

The establishment of a comprehensive tumour molecular profile was safe, feasible, and compatible with clinical practice in refractory cancer patients.

High numbers of differentiated effector CD4 T cells are found in patients with cancer and correlate with clinical response after neoadjuvant therapy of breast cancer

CD4(+) T cells influence tumor immunity in complex ways that are not fully understood. In this study, we characterized a population of human differentiated effector CD4(+) T cells that is defined by low levels of the interleukin (IL)-2 and IL-7 receptors (CD25(-)CD127(-)). We found that this cell population expands in patients with various types of cancer, including breast cancer, to represent 2% to 20% of total CD4(+) blood T lymphocytes as compared with only 0.2% to 2% in healthy individuals. Notably, these CD25(-)CD127(-)CD4 T cells expressed effector markers such as CD244 and CD11b with low levels of CD27, contrasting with the memory phenotype dominating this population in healthy individuals. These cells did not cycle in patients, nor did they secrete IL-10 or IL-17, but instead displayed cytotoxic features. Moreover, they encompassed oligoclonal expansions paralleling an expansion of effector CD8(+) T cells that included tumor antigen-specific T cells. During neoadjuvant chemotherapy in patients with breast cancer, we found that the increase in CD25(-)CD127(-) CD4(+) T cells correlated with tumor regression. This observation suggested that CD4(+) T cells included tumor antigen-specific cells, which may be generated by or participate in tumor regressions during chemotherapy. In summary, our results lend support to the hypothesis that CD4(+) T cells are involved in human antitumor responses.

Abstract P4-04-05: Molecular subtyping reveals the heterogeneity of metaplastic breast cancers

Introduction: Metaplastic breast carcinoma (MBC) is a rare (1%) and aggressive histological special type of breast cancer, which often (>90%) displays a triple-negative (TN) phenotype. Microarray-based gene expression classifications of breast cancer have been described, including the ‘intrinsic subtypes’ (i.e. luminal A, luminal B, basal-like, HER2-enriched, normal breast-like and claudin-low) and the six TN molecular subtypes with therapeutic implications in preclinical models (i.e. basal-like I, basal-like II, mesenchymal-like, mesenchymal stem-like, immunomodulatory and luminal androgen receptor). In addition, single nucleotide polymorphism (SNP) array analyses have led to the development of classifiers to define whether TN breast cancers would have genomic aberrations consistent with those found in tumors arising in BRCA1 germline mutation carriers. Here we sought to define i) the heterogeneity of MBCs using distinct microarray-based classifiers and ii) whether MBCs display gene copy number profiles consistent with those of BRCA1 breast cancers.

Material and Methods: Thirty consecutive MBCs were retrieved from the tumor banks of the authors’ institutions, reviewed by two pathologists and classified into three groups: carcinomas with spindle cell metaplasia (n = 12), with squamous metaplasia (n = 10), and with heterologous elements (n = 8). RNA and DNA were extracted from representative frozen sections containing >50% of cancer cells from each tumor and subjected to gene expression profiling using the HumanHT-12 v4 platform (Illumina) and gene copy number analysis using SNP 6.0 arrays (Affymetrix), respectively. ‘Intrinsic subtyping’ was performed according to the UNC guidelines, and subtyping into the six TN types using a dedicated website (https://cbc.mc.vanderbilt.edu/tnbc/). Classification of MBCs into BRCA1-like or non-BRCA1-like was performed using an algorithm to identify and quantify large-scale state transitions.

Results: PAM50/claudin-low subtyping of MBCs revealed that all spindle cell carcinomas (n = 12) were consistently of claudin-low subtype, whereas MBCs with heterologous elements were classified as of basal-like (n = 6) and normal breast-like (n = 2), and squamous cell carcinomas as of basal-like (n = 5), claudin-low (n = 4) and normal-like (n = 1). Using the six TN subtypes, spindle cell MBCs were classified as mesenchymal stem-like (n = 4), immunomodulatory (n = 3), basal-like 2 (n = 3), or mesenchymal (n = 2) subtype. Carcinomas with heterologous elements were classified as basal-like 1 (n = 5) or mesenchymal (n = 3) subtype, whereas carcinomas with squamous metaplasia were of immunomodulatory (n = 5), basal-like 1 (n = 2), basal-like 2 (n = 2) or mesenchymal (n = 1) subtype. Out of the 26 samples where SNP 6.0 arrays were successfully performed, only 9 (35%) were classified as BRCA1-like, including two spindle cell carcinomas, two carcinomas with heterologous elements and five carcinomas with squamous metaplasia.

Conclusion: MBCs constitute a heterogeneous group of tumors and the histological subclassification of these cancers is of importance, given that tumors with distinct metaplastic elements are classified differently according to current molecular subtyping methods. Only 35% of MBCs display BRCA1-like patterns of gene copy number aberrations.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-04-05.

Abstract P4-04-08: Genomic and transcriptomic characterization of papillary carcinomas of the breast

Introduction: Papillary carcinomas (PCs) are a rare (<1%) special histological type of breast cancer that often affects postmenopausal women, and has an overall favorable outcome. Based on their histological characteristics, these tumors are classified into three different subtypes, namely encapsulated papillary carcinomas (EPC), solid papillary carcinomas (SPC) and invasive papillary carcinomas (IPC). In this study, we sought i) to investigate whether PCs constitute a molecular entity distinct from grade- and ER-matched invasive ductal carcinomas of no special type (IDC-NST) at the transcriptomic level, ii) to investigate whether EPC, SPC and IPC display distinct transcriptomic profiles, iii) to characterize the repertoire of copy number alterations in the different subtypes of PC, and iv) to identify recurrent fusion genes that may be potential drivers of this disease.

Material and methods: DNA and RNA were extracted from microdissected PCs (4 SPCs, 5 IPCs and 7 EPCs) and grade- and ER-matched IDC-NSTs (RNA only). 16 PCs and 16 grade- and ER-matched IDC-NSTs were subjected to gene expression profiling using the Illumina Human HT-12 v4 platform. Genes differentially expressed between the PC subtypes were identified using SAM, and functional annotation of these genes was performed using DAVID. Intrinsic molecular subtypes were determined using the PAM50 single sample predictor. Copy number profiling was performed using Affymetrix Human SNP 6.0 arrays with DNA extracted from 16 PCs. In addition, 8 PCs (3 IPCs, 3 EPCs, 2 SPCs) were subjected to paired-end massively parallel RNA sequencing (Illumina GAIIx). Putative expressed fusion transcripts were identified using validated algorithms (i.e. deFuse and Chimerascan), and confirmed by reverse transcription PCR.

Results: PCs were preferentially of histological grade I/II (82%) and ER-positive (100%). Unsupervised analysis revealed that PC subtypes show a high degree of similarity at the transcriptomic level, and form clusters distinct from grade- and ER-matched IDC-NSTs. Compared with IDC-NSTs, PCs displayed reduced expression of genes related to cell motility, adhesion and extracellular matrix. PAM50 subtyping classified 87.5%, 50% and 100% of EPCs, SPCs and IPCs as of luminal subtypes, respectively. 12.5% of EPCs were classified as of basal-like subtype, and 50% of SPCs as of HER2-enriched subtype. At the genomic level, PC subtypes displayed similar patterns of gene copy number aberrations. Five in-frame fusion genes, USF1-CCDC38, MDC1-SFTA2, DLD-LMBR1, PDCL-DENND1A and SUGT1-NOL6, were identified and validated in PCs, however none of these were recurrent in the cases included in this study.

Conclusion: Our results demonstrate that the majority of PCs are of luminal subtype, and support the contention that at the transcriptomic level, PCs are distinct from grade- and ER-matched IDC-NSTs. Our findings also demonstrate that unlike some other histological special types of breast cancer, PCs are not underpinned by a highly recurrent expressed fusion gene.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-04-08.

Abstract B233: The depletion of LRP5, unlike that of LRP6, promotes apoptosis in triple-negative breast cancer cells, making it an interesting therapeutic target

Introduction. Treatment of patients with triple-negative breast cancers (TNBCs) remains a major challenge for oncologists. Although they respond well to the current therapeutic strategies based on conventional chemotherapies, they represent a large proportion of breast cancer death due to a high recurrence rate. Alternative treatments are needed to improve survival of these patients. The Wnt/beta-catenin signaling, recently reported to be activated in TNBCs, may represent an interesting pathway to target.

Methods. We analyzed mRNA, DNA and protein levels for the LRP5 and LRP6 Wnt coreceptors in our cohort of breast tumor biopsy specimens. We then identified which TNBC cell lines display the most similarity to TNBC tumors regarding the Wnt pathway status using a centroid approach. We investigated the effects of modulating LRP5 or LRP6 expression on Wnt signaling, cell viability and apoptosis. We evaluated the potential therapeutic value of targeting LRP5 and LRP6 in TNBCs, by performing depletion experiments and treating cells with a mixture of doxorubicin/cyclophosphamide. We also examined whether the depletion of LRP5 or LRP6 had an impact on tumorigenicicy in vitro, in soft-agar assays, and in vivo, in xenograft models.

Results. Gene expression analyses revealed that both LRP5 and LRP6 Wnt coreceptors were more strongly expressed in TNBCs than in other breast tumor subtypes. HCC38 and MDA-MB-468 TNBC cells were more similar to TNBC biopsy specimens in terms of Wnt pathway gene expression profiles than any other tested cell line. Unlike LRP5, LRP6 was involved in activating the canonical Wnt pathway in response to Wnt3a. LRP5 knockdown induced caspase-dependent apoptosis, whereas LRP6 knockdown had no such effect. LRP5-depleted cells were also more sensitive to conventional chemotherapy than cells depleted of LRP6. The knockdown of LRP5 or LRP6 decreased tumorigenesis both in vitro and in vivo.

Conclusions. These data indicate that the LRP5 and LRP6 have different functions in TNBCs, with LRP5 playing a preponderant role in survival control. Our data suggest that both coreceptors are potential treatment targets in TNBCs, but that LRP5 may be the most useful target, given the impact of its depletion on cell survival and the response to anti-cancer drugs.

Citation Information: Mol Cancer Ther 2013;12(11 Suppl):B233.

Citation Format: Sylvie Maubant, Virginie Maire, Bruno Tesson, Fariba Némati, Aurélie Dumont, David Gentien, Bérengère Marty-Prouvost, Guillem Rigaill, Leanne De Koning, Anne Vincent-Salomon, Emmanuel Barillot, Didier Decaudin, Alain Pierré, Stéphane Depil, Francisco Cruzalegui, Gordon C. Tucker, Sergio Roman-Roman, Thierry Dubois. The depletion of LRP5, unlike that of LRP6, promotes apoptosis in triple-negative breast cancer cells, making it an interesting therapeutic target. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr B233.

A siRNA screen identifies RAD21, EIF3H, CHRAC1 and TANC2 as driver genes within the 8q23, 8q24.3 and 17q23 amplicons in breast cancer with effects on cell growth, survival and transformation

RNA interference has boosted the field of functional genomics, by making it possible to carry out 'loss-of-function' screens in cultured cells. Here, we performed a small interfering RNA screening, in three breast cancer cell lines, for 101 candidate driver genes overexpressed in amplified breast tumors and belonging to eight amplicons on chromosomes 8q and 17q, investigating their role in cell survival/proliferation. This screening identified eight driver genes that were amplified, overexpressed and critical for breast tumor cell proliferation or survival. They included the well-described oncogenic driver genes for the 17q12 amplicon, ERBB2 and GRB7. Four of six other candidate driver genes-RAD21 and EIF3H, both on chromosome 8q23, CHRAC1 on chromosome 8q24.3 and TANC2 on chromosome 17q23-were confirmed to be driver genes regulating the proliferation/survival of clonogenic breast cancer cells presenting an amplification of the corresponding region. Indeed, knockdown of the expression of these genes decreased cell viability, through both cell cycle arrest and apoptosis induction, and inhibited the formation of colonies in anchorage-independent conditions, in soft agar. Strategies for inhibiting the expression of these genes or the function of the proteins they encode are therefore of potential value for the treatment of breast cancers presenting amplifications of the corresponding genomic region.

Signatures of mutational processes in human cancer

All cancers are caused by somatic mutations; however, understanding of the biological processes generating these mutations is limited. The catalogue of somatic mutations from a cancer genome bears the signatures of the mutational processes that have been operative. Here we analysed 4,938,362 mutations from 7,042 cancers and extracted more than 20 distinct mutational signatures. Some are present in many cancer types, notably a signature attributed to the APOBEC family of cytidine deaminases, whereas others are confined to a single cancer class. Certain signatures are associated with age of the patient at cancer diagnosis, known mutagenic exposures or defects in DNA maintenance, but many are of cryptic origin. In addition to these genome-wide mutational signatures, hypermutation localized to small genomic regions, 'kataegis', is found in many cancer types. The results reveal the diversity of mutational processes underlying the development of cancer, with potential implications for understanding of cancer aetiology, prevention and therapy.

Signatures of mutational processes in human cancer

All cancers are caused by somatic mutations; however, understanding of the biological processes generating these mutations is limited. The catalogue of somatic mutations from a cancer genome bears the signatures of the mutational processes that have been operative. Here we analysed 4,938,362 mutations from 7,042 cancers and extracted more than 20 distinct mutational signatures. Some are present in many cancer types, notably a signature attributed to the APOBEC family of cytidine deaminases, whereas others are confined to a single cancer class. Certain signatures are associated with age of the patient at cancer diagnosis, known mutagenic exposures or defects in DNA maintenance, but many are of cryptic origin. In addition to these genome-wide mutational signatures, hypermutation localized to small genomic regions, 'kataegis', is found in many cancer types. The results reveal the diversity of mutational processes underlying the development of cancer, with potential implications for understanding of cancer aetiology, prevention and therapy.

Loss of heterozygosity at 13q13 and 14q32 predicts BRCA2 inactivation in luminal breast carcinomas

BRCA2 is the major high-penetrance predisposition gene for luminal (estrogen receptor [ER] positive) breast cancers. However, many BRCA2 mutant carriers lack family history of breast/ovarian cancers and do not benefit from genetic testing. Specific genomic features associated with BRCA2 inactivation in tumors could help identify patients for whom a genetic test for BRCA2 may be proposed. A series of ER-positive invasive ductal carcinomas (IDCs) including 30 carriers of BRCA2 mutations and 215 control cases was studied by single-nucleotide polymorphism (SNP) arrays. Cases and controls were stratified by grade and HER2 status. Independently, 7 BRCA2 and 51 control cases were used for validation. Absolute copy number and Loss of heterozygosity (LOH) profiles were obtained from SNP arrays by the genome alteration print (GAP) method. BRCA2 tumors were observed to display a discriminatively greater number of chromosomal breaks calculated after filtering out and smoothing <3 Mb variations. This argues for a BRCA2-associated genomic instability responsible for long-segment aberrations. Co-occurrence of two genomic features-LOH of 13q13 and 14q32-was found to predict BRCA2 status with 90% of sensitivity and 87% of specificity in discovery series of high-grade HER2-negative IDCs and 100% of sensitivity and 88% of specificity in an independent series of 58 IDCs. Estimated positive predictive value was 17.2% (confidence interval: 6.7-33.5) in the whole series. In conclusion, the simplified BRCA2 classifier based on the co-occurrence of LOH at 13q13 and 14q32 could provide an indication to test for BRCA2 mutation in patients with ER-positive IDC.

Prognosis of pT1a,bN0 breast cancer: Perception from the French oncology community—Results from the EURISTIC survey

e11607

Background: Although most early-stage breast tumors have a favourable outcome, some subgroups carry a higher recurrence risk. The objective of the EURISTIC Survey was to evaluate the perception French physicians have of the prognostic risk associated with the biopathological characteristics of tumors in pT1a,b N0 breast cancer. Methods: This 38 item postal survey was developed by an expert panel. 2,000 physicians involved in breast cancer treatment were contacted. Specialities involved were medical and radiation oncologists, surgeons, radiologists and pathologists. Results: The survey was conducted between September and December 2012. A total of 663 physicians responded (response rate = 33%). They stated treating an average of 50 breast cancer patients per month. 58% of physicians reported that tumour size was not considered a major parameter in this clinical setting. In the absence of an adjuvant treatment, the prognosis of T1a,bN0 carcinoma was perceived better if HR-positive rather than HER2-positive or triple-negative with a "positive" prognosis perception rated by 83%, 21% and 8% of physicians respectively. For pT1a,bN0 tumors, the criteria with the highest perceived prognostic risk were ranked as follows: HER2+ (29%), HR- (20%) elevated tumor grade (20%) and triple negative tumor (14%). The average size threshold for a "negative" prognostic rated tumor was 18 mm. This threshold was scaled up for HR-positive carcinoma (22 mm) and scaled down for HER2-positive (10mm) or triple negative carcinoma (7mm). Between 4 and 17 mm, there was a linear correlation between tumor size and perceived risk of recurrence with HER2-positive tumors always carrying a worse prognostic than HR-positive tumor (Table). Conclusions: French physicians have the perception that HER2-positivity and triple negative tumor biology strongly impact the prognosis of pT1a,b N0 carcinoma, independent of tumor size. [Table: see text]

TTK/hMPS1 is an attractive therapeutic target for triple-negative breast cancer

Triple-negative breast cancer (TNBC) represents a subgroup of breast cancers (BC) associated with the most aggressive clinical behavior. No targeted therapy is currently available for the treatment of patients with TNBC. In order to discover potential therapeutic targets, we searched for protein kinases that are overexpressed in human TNBC biopsies and whose silencing in TNBC cell lines causes cell death. A cohort including human BC biopsies obtained at Institut Curie as well as normal tissues has been analyzed at a gene-expression level. The data revealed that the human protein kinase monopolar spindle 1 (hMPS1), also known as TTK and involved in mitotic checkpoint, is specifically overexpressed in TNBC, compared to the other BC subgroups and healthy tissues. We confirmed by immunohistochemistry and reverse phase protein array that TNBC expressed higher levels of TTK protein compared to the other BC subgroups. We then determined the biological effects of TTK depletion by RNA interference, through analyses of tumorigenic capacity and cell viability in different human TNBC cell lines. We found that RNAi-mediated depletion of TTK in various TNBC cell lines severely compromised their viability and their ability to form colonies in an anchorage-independent manner. Moreover, we observed that TTK silencing led to an increase in H2AX phosphorylation, activation of caspases 3/7, sub-G1 cell population accumulation and high annexin V staining, as well as to a decrease in G1 phase cell population and an increased aneuploidy. Altogether, these data indicate that TTK depletion in TNBC cells induces apoptosis. These results point out TTK as a protein kinase overexpressed in TNBC that may represent an attractive therapeutic target specifically for this poor prognosis associated subgroup of breast cancer.