PAK6 acts downstream of IQGAP3 to promote contractility in triple negative breast cancer cells

Breast cancer is a heterogeneous disease that remains the most common malignancy among women worldwide. During genomic analysis of breast tumours, mRNA levels of IQGAP3 were found to be upregulated in triple negative tumours. IQGAP3 was subsequently found to be expressed across a panel of triple negative breast cancer (TNBC) cell lines. Depleting expression levels of IQGAP3 delivered elongated cells, disrupted cell migration, and inhibited the ability of cells to form specialised invasive adhesion structures, termed invadopodia. The morphological changes induced by IQGAP3 depletion were found to be dependent on RhoA. Indeed, reduced expression of IQGAP3 disrupted RhoA activity and actomyosin contractility. Interestingly, IQGAP3 was also found to interact with p-21 activated kinase 6 (PAK6); a protein already associated with the regulation of cell morphology. Moreover, PAK6 depletion phenocopied IQGAP3 depletion in these cells. Whereas PAK6 overexpression rescued the IQGAP3 depletion phenotype. Our work points to an important PAK6-IQGAP3-RhoA pathway that drives the cellular contractility of breast cancer cells promoting both cell migration and adhesive invasion of these cells. As this phenotype is relevant to the process of metastasis and re-seeding of metastasis, the pharmacological targeting of PAK6 could lead to clinical benefit in TNBC patients.

Natural History of Germline BRCA1 Mutated and BRCA Wild-type Triple-negative Breast Cancer

We report a deep next-generation sequencing analysis of 13 sequentially obtained tumor samples, eight sequentially obtained circulating tumor DNA (ctDNA) samples and three germline DNA samples over the life history of 3 patients with triple-negative breast cancer (TNBC), 2 of whom had germline pathogenic BRCA1 mutation, to unravel tumor evolution. Tumor tissue from all timepoints and germline DNA was subjected to whole-exome sequencing (WES), custom amplicon deep sequencing (30,000X) of a WES-derived somatic mutation panel, and SNP arrays for copy-number variation (CNV), while whole transcriptome sequencing (RNA-seq) was performed only on somatic tumor.There was enrichment of homologous recombination deficiency signature in all tumors and widespread CNV, which remained largely stable over time. Somatic tumor mutation numbers varied between patients and within each patient (range: 70-216, one outlier). There was minimal mutational overlap between patients with TP53 being the sole commonly mutated gene, but there was substantial overlap in sequential samples in each patient. Each patient's tumor contained a founding ("stem") clone at diagnosis, which persisted over time, from which all other clones ("subclone") were derived ("branching evolution"), which contained mutations in well-characterized cancer-related genes like PDGFRB, ARID2, TP53 (Patient_02), TP53, BRAF, BRIP1, CSF3R (Patient_04), and TP53, APC, EZH2 (Patient_07). Including stem and subclones, tumors from all patients were polyclonal at diagnosis and during disease progression. ctDNA recapitulated most tissue-derived stem clonal and subclonal mutations while detecting some additional subclonal mutations. RNA-seq revealed a stable basal-like pattern, with most highly expressed variants belonging to stem clone.

SIGNIFICANCE

In germline BRCA1 mutated and BRCA wild-type patients, TNBC shows a branching evolutionary pattern of mutations with a single founding clone, are polyclonal throughout their disease course, and have widespread copy-number aberrations. This evolutionary pattern may be associated with treatment resistance or sensitivity and could be therapeutically exploited.

Adipose-enriched peri-tumoral stroma, in contrast to myofibroblast-enriched stroma, prognosticates poorer survival in breast cancers

Despite our understanding of the genetic basis of intra-tumoral heterogeneity, the role of stromal heterogeneity arising from an altered tumor microenvironment in affecting tumorigenesis is poorly understood. In particular, extensive study on the peri-tumoral stroma in the morphologically normal tissues surrounding the tumor is lacking. Here, we examine the heterogeneity in tumors and peri-tumoral stroma from 8 ER+/PR+/HER2- invasive breast carcinomas, through multi-region transcriptomic profiling by microarray. We describe the regional heterogeneity observed at the intrinsic molecular subtype, pathway enrichment, and cell type composition levels within each tumor and its peri-tumoral region, up to 7 cm from the tumor margins. Moreover, we identify a pro-inflammatory adipose-enriched peri-tumoral subtype which was significantly associated with poorer overall survival in breast cancer patients, in contrast to an adaptive immune cell- and myofibroblast-enriched subtype. These data together suggest that peri-tumoral heterogeneity may be an important determinant of the evolution and treatment of breast cancers.

Integrated Multimodal Analyses of DNA Damage Response and Immune Markers as Predictors of Response in Metastatic Triple-Negative Breast Cancer in the TNT Trial (NCT00532727)

PURPOSE

The TNT trial (NCT00532727) showed no evidence of carboplatin superiority over docetaxel in metastatic triple-negative breast cancer (mTNBC), but carboplatin benefit was observed in the germline BRCA1/2 mutation subgroup. Broader response-predictive biomarkers are needed. We explored the predictive ability of DNA damage response (DDR) and immune markers.

EXPERIMENTAL DESIGN

Tumor-infiltrating lymphocytes were evaluated for 222 of 376 patients. Primary tumors (PT) from 186 TNT participants (13 matched recurrences) were profiled using total RNA sequencing. Four transcriptional DDR-related and 25 immune-related signatures were evaluated. We assessed their association with objective response rate (ORR) and progression-free survival (PFS). Conditional inference forest clustering was applied to integrate multimodal data. The biology of subgroups was characterized by 693 gene expression modules and other markers.

RESULTS

Transcriptional DDR-related biomarkers were not predictive of ORR to either treatment overall. Changes from PT to recurrence were demonstrated; in chemotherapy-naïve patients, transcriptional DDR markers separated carboplatin responders from nonresponders (P values = 0.017; 0.046). High immune infiltration was associated with docetaxel ORR (interaction P values < 0.05). Six subgroups were identified; the immune-enriched cluster had preferential docetaxel response [62.5% (D) vs. 29.4% (C); P = 0.016]. The immune-depleted cluster had preferential carboplatin response [8.0% (D) vs. 40.0% (C); P = 0.011]. DDR-related subgroups were too small to assess ORR.

CONCLUSIONS

High immune features predict docetaxel response, and high DDR signature scores predict carboplatin response in treatment-naïve mTNBC. Integrating multimodal DDR and immune-related markers identifies subgroups with differential treatment sensitivity. Treatment options for patients with immune-low and DDR-proficient tumors remains an outstanding need. Caution is needed using PT-derived transcriptional signatures to direct treatment in mTNBC, particularly DDR-related markers following prior chemotherapy.

Abstract PD9-06: Histopathological and molecular immune landscape and DNA damage response signatures to predict response to carboplatin and docetaxel in TNT trial TNBC cohort

Background The TNT trial (NCT00532727) showed no evidence of carboplatin (C) superiority over docetaxel (D) overall in metastatic triple negative breast cancers (TNBC), but a C benefit was observed in the pre-specified sub-group analysis in patients with a gBRCA1/2 mutation (Tutt et al, Nat Med 2018). Given only ~30% of patients have a gBRCA1/2 mutation, broader predictive biomarkers of response are needed. In this cohort we previously found that DNA Damage Response (DDR) signatures were associated with improved C response in chemotherapy (CT) naïve patients only (Tovey et al, ASCO 2020). Since DDR activities influence tumour immune-microenvironment, we explored the predictive ability of immune cell markers and performed integrative analyses on multi-omics features to identify novel TNBC subgroups. Patients and Methods Tumour infiltrating lymphocytes (TILs) were evaluated on haematoxylin and eosin stained primary tumour (PT) slides for 222/376 TNT patients. Formalin-fixed paraffin-embedded PT tissues from 186/376 TNT patients were successfully profiled using total RNA-sequencing. Matched recurrence (REC) was also sequenced for 13 patients. Twenty-five immune signatures were assessed. Logistic regression and restricted mean progression free survival (PFS) were applied to delineate the relationship of these features with treatment outcomes. Random forest clustering of multi-omics DDR and immune biology markers, including gene expression signatures and mutation/methylation status, was applied to identify subgroups. We further molecularly characterised these clusters through supervised clustering of 693 gene expression “modules” (sets of co-expressed genes), immune cell deconvolution and genomic scars. Results Immune gene expression signatures and TILs were highly correlated. Average immune infiltration based on ConsensusTME was lower in mutated/methylated tumours compared with BRCA1 wildtype tumours (p=0.04). Immune signature score markers decreased from PT to REC, demonstrating a dynamic immune microenvironment. In the overall population and when restricting to prior CT treated patients, high immune infiltration (gene expression based & TILs) was associated with response to D while C response rates were not associated with immune scores (interaction p-values&lt; 0.05). This did not translate to a PFS benefit. Multi-omics clustering identified 6 biological subgroups including immune enriched, immune depleted, DDR deficient and proficient clusters as well as 2 small clusters with no obvious distinguishing features. Immune enriched TNBC were predominantly basal-like immune activated with high B-cell/T-cell diversity. Immune depleted TNBC showed higher activity of proliferation and DDR pathway modules. DDR proficient tumours had low expression of immune markers and enrichment for ESR1/PGR expression, markers of extra cellular formation, cell structure, lipid metabolism and proliferation. The DDR deficient cluster was enriched for proliferation and demonstrated high number of TILs despite no apparent enrichment for gene expression-based immune modules. In the prior CT treated cohort, the immune enriched cluster had preferential response to D (62.5% (D) vs. 29.4% (C); p=0.02). The immune depleted cluster had preferential response to C (8.0% (D) vs. 40.0% (C); p=0.01). Numbers were too small to assess differential response within the other clusters or in the CT naïve cohort. Conclusions Tumours with high immune features have high response to D while those with low immune features have preferential response to C in advanced TNBC. Combining multi-omics markers of DDR deficiency and immune biology can identify clusters of patients with distinct biological profiles and differential treatment specific response rates.

Citation Format: Holly Tovey, Orsolya Sipos, Katherine A Hoadley, Joel S Parker, Jelmar Quist, Sarah Kernaghan, Lucy Kilburn, Roberto Salgado, Sherene Loi, Richard D Kennedy, Ioannis Roxanis, Patrycja Gazinska, Sarah E. Pinder, Judith Bliss, Charles M. Perou, Syed Haider, Andrew Tutt, Anita Grigoriadis, Maggie Chon U Cheang. Histopathological and molecular immune landscape and DNA damage response signatures to predict response to carboplatin and docetaxel in TNT trial TNBC cohort [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD9-06.

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

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

Predictive value of ectopic HORMAD1 tumor expression for high-dose platinum-based chemotherapy benefit in patients with high-risk HER2-negative breast cancer

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Background: The meiotic DNA break regulator HORMAD1 is aberrantly expressed in many cancers and is associated with increased genomic instability. The susceptibility of HORMAD1 expressing tumors to agents targeting DNA damage repair (DDR) pathways is poorly understood since clinical data within the context of a randomized clinical trial (RCT) is lacking. Here, we retrospectively studied HORMAD1 expression as a putative predictive biomarker in an RCT for benefit of adjuvant high-dose platinum-based chemotherapy (HDCT) with autologous stem cell support in patients with high-risk HER2-negative early breast cancer (BC). Methods: Patients with stage III BC participated in an RCT comparing HDCT to conventional chemotherapy (CDCT; Rodenhuis et all, NEJM, 2003; Steenbruggen et all, JAMA Oncol, 2020). We studied the subgroup with HER2-negative BC for whom tumor BRCA1-like classification was previously determined using a validated DNA comparative genomic hybridization algorithm (Vollebergh et all, BCR, 2014). Tumor HORMAD1 expression was determined on FFPE samples using RNAscope, an RNA in situ hybridization method, and classified as negative (no expression) or positive (any expression detected). Results: For 195/246 (79.3%) HER2-negative patients treated according to protocol, HORMAD1 RNAscope status was available; dropout was due to absence or insufficient quality of tumor specimens. HORMAD1 positivity was enriched in triple-negative breast cancer (TNBC) (23/47; 48.9%). Furthermore, in all HER2-negative BCs, HORMAD1 positivity (45/195; 23.1%) was associated with age ≤40 years, histological grade III, <10 positive lymph nodes, breast-conserving surgery, BRCA1-like profile, and tumor-infiltrating lymphocytes (TILs) >10%. Such association, although not significant, was also observed within TNBC. During a median follow-up of 20.3 years, 124 (63.6%) recurrences and 115 deaths (59.0%) occurred. The prognostic effect of HORMAD1 positivity on overall survival (OS) varied with follow-up time and was borderline significant at 10 years and significant thereafter (10-year: adjusted (adj.) HR 0.47, 95% CI 0.21-1.04; 15-year: adj. HR 0.25, 95% CI 0.07-0.91). Benefit on RFS from HDCT over CDCT was stronger in patients with HORMAD1-positive tumors (adj. HR 0.18, 95% CI 0.06-0.54) than in patients with HORMAD1-negative tumors (adj. HR 0.69, 95% CI 0.46-1.02) (P-interaction = 0.02). Similar results were observed for OS. Conclusions: In this retrospective sub study of 195 patients with high-risk HER2-negative BC participating in an RCT, tumor HORMAD1 expression is predictive for benefit of high-dose platinum-based chemotherapy. Our observations are consistent with the prior observations that HORMAD1 expression is associated with genomic instability and impaired DDR pathways. Further research is warranted to validate our findings. Clinical trial information: NCT03087409.

TGF-β1 potentiates Vγ9Vδ2 T cell adoptive immunotherapy of cancer

Despite its role in cancer surveillance, adoptive immunotherapy using γδ T cells has achieved limited efficacy. To enhance trafficking to bone marrow, circulating Vγ9Vδ2 T cells are expanded in serum-free medium containing TGF-β1 and IL-2 (γδ[T2] cells) or medium containing IL-2 alone (γδ[2] cells, as the control). Unexpectedly, the yield and viability of γδ[T2] cells are also increased by TGF-β1, when compared to γδ[2] controls. γδ[T2] cells are less differentiated and yet display increased cytolytic activity, cytokine release, and antitumor activity in several leukemic and solid tumor models. Efficacy is further enhanced by cancer cell sensitization using aminobisphosphonates or Ara-C. A number of contributory effects of TGF-β are described, including prostaglandin E2 receptor downmodulation, TGF-β insensitivity, and upregulated integrin activity. Biological relevance is supported by the identification of a favorable γδ[T2] signature in acute myeloid leukemia (AML). Given their enhanced therapeutic activity and compatibility with allogeneic use, γδ[T2] cells warrant evaluation in cancer immunotherapy.

Tumor-Infiltrating B Lymphocyte Profiling Identifies IgG-Biased, Clonally Expanded Prognostic Phenotypes in Triple-Negative Breast Cancer

In breast cancer, humoral immune responses may contribute to clinical outcomes, especially in more immunogenic subtypes. Here, we investigated B lymphocyte subsets, immunoglobulin expression, and clonal features in breast tumors, focusing on aggressive triple-negative breast cancers (TNBC). In samples from patients with TNBC and healthy volunteers, circulating and tumor-infiltrating B lymphocytes (TIL-B) were evaluated. CD20+CD27+IgD- isotype-switched B lymphocytes were increased in tumors, compared with matched blood. TIL-B frequently formed stromal clusters with T lymphocytes and engaged in bidirectional functional cross-talk, consistent with gene signatures associated with lymphoid assembly, costimulation, cytokine-cytokine receptor interactions, cytotoxic T-cell activation, and T-cell-dependent B-cell activation. TIL-B-upregulated B-cell receptor (BCR) pathway molecules FOS and JUN, germinal center chemokine regulator RGS1, activation marker CD69, and TNFα signal transduction via NFκB, suggesting BCR-immune complex formation. Expression of genes associated with B lymphocyte recruitment and lymphoid assembly, including CXCL13, CXCR4, and DC-LAMP, was elevated in TNBC compared with other subtypes and normal breast. TIL-B-rich tumors showed expansion of IgG but not IgA isotypes, and IgG isotype switching positively associated with survival outcomes in TNBC. Clonal expansion was biased toward IgG, showing expansive clonal families with specific variable region gene combinations and narrow repertoires. Stronger positive selection pressure was present in the complementarity determining regions of IgG compared with their clonally related IgA in tumor samples. Overall, class-switched B lymphocyte lineage traits were conspicuous in TNBC, associated with improved clinical outcomes, and conferred IgG-biased, clonally expanded, and likely antigen-driven humoral responses. SIGNIFICANCE: Tumor-infiltrating B lymphocytes assemble in clusters, undergoing B-cell receptor-driven activation, proliferation, and isotype switching. Clonally expanded, IgG isotype-biased humoral immunity associates with favorable prognosis primarily in triple-negative breast cancers.

Systemic immune reaction in axillary lymph nodes adds to tumor-infiltrating lymphocytes in triple-negative breast cancer prognostication

The level of stromal tumor-infiltrating lymphocytes (sTILs) in triple-negative (TNBC) and HER2-positive breast cancers convey prognostic information. The importance of systemic immunity to local immunity is unknown in breast cancer. We previously demonstrated that histological alterations in axillary lymph nodes (LNs) carry clinical relevance. Here, we capture local immune responses by scoring TILs at the primary tumor and systemic immune responses by recording the formation of secondary follicles, also known as germinal centers, in 2,857 cancer-free and involved axillary LNs on haematoxylin and eosin (H&E) stained sections from a retrospective cohort of 161 LN-positive triple-negative and HER2-positive breast cancer patients. Our data demonstrate that the number of germinal center formations across all cancer-free LNs, similar to high levels of TILs, is associated with a good prognosis in low TILs TNBC. This highlights the importance of assessing both primary and LN immune responses for prognostication and for future breast cancer research.

Random Forest Modelling of High-Dimensional Mixed-Type Data for Breast Cancer Classification

Advances in high-throughput technologies encourage the generation of large amounts of multiomics data to investigate complex diseases, including breast cancer. Given that the aetiologies of such diseases extend beyond a single biological entity, and that essential biological information can be carried by all data regardless of data type, integrative analyses are needed to identify clinically relevant patterns. To facilitate such analyses, we present a permutation-based framework for random forest methods which simultaneously allows the unbiased integration of mixed-type data and assessment of relative feature importance. Through simulation studies and machine learning datasets, the performance of the approach was evaluated. The results showed minimal multicollinearity and limited overfitting. To further assess the performance, the permutation-based framework was applied to high-dimensional mixed-type data from two independent breast cancer cohorts. Reproducibility and robustness of our approach was demonstrated by the concordance in relative feature importance between the cohorts, along with consistencies in clustering profiles. One of the identified clusters was shown to be prognostic for clinical outcome after standard-of-care adjuvant chemotherapy and outperformed current intrinsic molecular breast cancer classifications.

Abstract PS6-36: The formation of GCs in cancer-free ALNs, a non-monotonic prognostic factor in HR-negative invasive breast cancer patients

Purpose: To assess the frequency and prognostic relevance of germinal centres (GC) in cancer-free axillary lymph nodes (ALNs), in relation to stromal tumour-infiltrating lymphocytes (sTILs) and the presence of tertiary lymphoid structures (TLS) in the primary carcinoma, in LN-positive Hormone Receptor (HR)-negative invasive breast cancer patients.

Patients and methods: A cohort of 161 patients with HR-negative invasive breast cancer of no special type (NST) and LN-positive status treated between 2005-10 at Tianjin Medical University (China) was identified. sTILs and TLS at the primary tumour site and GC in 2,841 involved and cancer-free ALNs were evaluated on H&E stained sections. Markers were tested for prognostic value for invasive Disease-Free Survival (iDFS), distant Disease-Free Survival (dDFS) and Overall Survival (OS), using Cox regression models adjusted for clinico-pathological factors.

Results: Among the 161 HR-negative breast cancers, 47% (n=75) had &gt;=20% sTILs and 24% (n=38) peritumoural TLS. 75% (121/161) and 76% (122/161), respectively, displayed GCs in their cancer-free and involved ALNs. Significantly higher numbers of GCs were seen in both cancer-free and involved ALNs when the primary tumours showed &gt;=20% sTILs. The presence of TLS was significantly associated with increased GC numbers in involved but to a lesser extend in cancer-free ALNs (Kruskal-Wallis rank sum test, p&lt;0.001 and P_value=0.07, respectively). As expected, increased sTILs and presence of TLS were associated with improved outcome for all endpoints.

Using an iterative process to determine an optimal cut off point by a minimal P value approach, a non-monotonic relationship between the frequency of GC in cancer-free ALNs and all endpoints was observed. Patients with &gt;2 GC but less than the top 5% (= 62 GC) in cancer-free ALNs showed improved iDFS, dDFS and OS, whilst patients with &lt;=2 GC or &gt;62 GC across all assessed cancer-free ALNs had poorer iDFS, dDFS and OS (see Table). In the multivariate models, the frequency of GC in cancer-free ALNs added independent prognostic information for all endpoints across all patients.

In patients with &gt;=20% sTILS, cancer-free ALNs within the top 5% for GC remained associated with a worse dDFS and iDFS (see Table). Cancer-free ALNs with &lt;=2 GC in total identified a subgroup of patients with &lt;20% sTILs tumours having the worst iDFS, dDFS and OS in multivariate models.

Five-year iDFS, dDFS and OS in patients with &lt;20% sTILs were 39%, 39% and 48% respectively for those with &lt;=2 GC in total, in comparison those with &gt;2 GC whose five-year iDFS, dDFS and OS were 65%, 65% and 69%, respectively.

Conclusions: The prognostic importance of GC assessment in cancer-free ALNs in women with LN-positive HR-negative breast cancers is demonstrated. A better outcome in patients with GC formation in their cancer-free ALNs, despite low sTILs in the primary carcinoma, may suggest a systemic anticancer immune response. High sTILs but with extreme GC formation in the cancer-free ALNs could potentially reflect an overdriving but less effective immune response. The assessment of the combination of primary and nodal immune response in HR-negative breast cancers is imperative in these high-risk patients.

Table 1. Univariate and Multivariate Cox Regression Analysis of Outcome by GC in Cancer-Free ALNsiDFSUnivariateAll cases&lt;20% sTIL&gt;=20% sTILTotal GCs number - binnedModel PHRCIModel PHRCIModel PHRCI&lt;=23.581.95 - 6.572.871.48 - 5.571.310.15 - 11.262&gt;GC&lt;624.86E-05reference7.64E-03reference4.66E-03reference&gt;624.631.75 - 12.41.930.26 - 14.5612.793.34 - 48.97MultivariateCorrected for: pNstage, sTILS & TLSCorrected for: pTstage & TLSCorrected for: pNstageTotal GCs number - binnedCovariate PModel PHRCICovariate PModel PHRCICovariate PModel PHRCI&lt;=22.90E-022.00E-082.102.08 - 4.103.13E-037.00E-042.831.42 - 5.658.45E-011.00E-031.240.14 - 10.622&gt;GC&lt;62NAreferenceNAreferenceNAreference&gt;624.15E-059.583.25 - 28.201.94E-014.070.49 - 33.876.62E-038.861.83 - 42.82dDFSUnivariateAll cases&lt;20% sTIL&gt;=20% sTILTotal GCs number - binnedModel PHRCIModel PHRCIModel PHRCI&lt;=24.762.48 - 9.143.681.82 - 7.432,130.22 - 20.442&gt;GC&lt;622.46E-06reference1.10E-03reference2.19E-03reference&gt;625.872.14 - 16.082.490.32 - 19.0718.434.04 - 84.03MultivariateCorrected for: pTstage, pNstage, sTILS & TLSCorrected for: Age, pTstage, TLSCorrected for: pNstageTotal GCs number - binnedCovariate PModel PHRCICovariate PModel PHRCICovariate PModel PHRCI&lt;=24.30E-033.00E-092.911.40 - 6.059.01E-042.00E-053.451.66 - 7.165.51E-011.00E-031.990.21 - 19.132&gt;GC&lt;62NAreferenceNAreferenceNAreference&gt;622.49E-0615.304.91 - 47.635.19E-028.610.98 - 75.553.11E-0313.302.39 - 73.89OSUnivariateAll cases&lt;20% sTIL&gt;=20% sTILTotal GCs number - binnedModel PHRCIModel PHRCIModel PHRCI&lt;=24.142.03 - 8.412.931.38 - 6.223.130.28 - 34.512&gt;GC&lt;622.62E-04reference1.78E-02reference7.52E-02reference&gt;624.131.18 - 14.42.570.33 - 19.8311.891.65 - 85.45MultivariateCorrected for: Age, pTstage, pNstage, sTILS & TLSCorrected for: Age & TLSCorrected for: pNstage, LVI & TLSTotal GCs number - binnedCovariate PModel PHRCICovariate PModel PHRCICovariate PModel PHRCI&lt;=21.50E-013.00E-091.820.80 - 4.122.28E-024.00E-042.411.13 - 5.12*3.00E-04**2&gt;GC&lt;62NAreferenceNAreferenceNAreference&gt;628.62E-0516.064.02 - 64.247.01E-027.050.85 - 58.342.80E-012.970.41 - 21.43*too few events

Citation Format: Fangfang Liu, Thomas Hardiman, Patrycja Gazinska, Jelmar Quist, Sarah Pinder, Anita Grigoriadis. The formation of GCs in cancer-free ALNs, a non-monotonic prognostic factor in HR-negative invasive breast cancer patients [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS6-36.

Assessment of structural chromosomal instability phenotypes as biomarkers of carboplatin response in triple negative breast cancer: the TNT trial

BACKGROUND

In the TNT trial of triple negative breast cancer (NCT00532727), germline BRCA1/2 mutations were present in 28% of carboplatin responders. We assessed quantitative measures of structural chromosomal instability (CIN) to identify a wider patient subgroup within TNT with preferential benefit from carboplatin over docetaxel.

PATIENTS AND METHODS

Copy number aberrations (CNAs) were established from 135 formalin-fixed paraffin-embedded primary carcinomas using Illumina OmniExpress SNP-arrays. Seven published [allelic imbalanced CNA (AiCNA); allelic balanced CNA (AbCNA); copy number neutral loss of heterozygosity (CnLOH); number of telomeric allelic imbalances (NtAI); BRCA1-like status; percentage of genome altered (PGA); homologous recombination deficiency (HRD) scores] and two novel [Shannon diversity index (SI); high-level amplifications (HLAMP)] CIN-measurements were derived. HLAMP was defined based on the presence of at least one of the top 5% amplified cytobands located on 1q, 8q and 10p. Continuous CIN-measurements were divided into tertiles. All nine CIN-measurements were used to analyse objective response rate (ORR) and progression-free survival (PFS).

RESULTS

Patients with tumours without HLAMP had a numerically higher ORR and significantly longer PFS in the carboplatin (C) than in the docetaxel (D) arm [56% (C) versus 29% (D), PHLAMP,quiet = 0.085; PFS 6.1 months (C) versus 4.1 months (D), Pinteraction/HLAMP = 0.047]. In the carboplatin arm, patients with tumours showing intermediate telomeric NtAI and AiCNA had higher ORR [54% (C) versus 20% (D), PNtAI,intermediate = 0.03; 62% (C) versus 33% (D), PAiCNA,intermediate = 0.076]. Patients with high AiCNA and PGA had shorter PFS in the carboplatin arm [3.4 months (high) versus 5.7 months (low/intermediate); and 3.8 months (high) versus 5.6 months (low/intermediate), respectively; Pinteraction/AiCNA = 0.027, Padj.interaction/AiCNA = 0.125 and Pinteraction/PGA = 0.053, Padj.interaction/PGA = 0.176], whilst no difference was observed in the docetaxel arm.

CONCLUSIONS

Patients with tumours lacking HLAMP and demonstrating intermediate CIN-measurements formed a subgroup benefitting from carboplatin relative to docetaxel treatment within the TNT trial. This suggests a complex and paradoxical relationship between the extent of genomic instability in primary tumours and treatment response in the metastatic setting.

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

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

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

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

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

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

Pan-cancer transcriptomic analysis dissects immune and proliferative functions of APOBEC3 cytidine deaminases

APOBEC3 cytidine deaminases are largely known for their innate immune protection from viral infections. Recently, members of the family have been associated with a distinct mutational activity in some cancer types. We report a pan-tissue, pan-cancer analysis of RNA-seq data specific to the APOBEC3 genes in 8,951 tumours, 786 cancer cell lines and 6,119 normal tissues. By deconvolution of levels of different cell types in tumour admixtures, we demonstrate that APOBEC3B (A3B), the primary candidate as a cancer mutagen, shows little association with immune cell types compared to its paralogues. We present a pipeline called RESPECTEx (REconstituting SPecific Cell-Type Expression) and use it to deconvolute cell-type specific expression levels in a given cohort of tumour samples. We functionally annotate APOBEC3 co-expressing genes, and create an interactive visualization tool which 'barcodes' the functional enrichment (http://fraternalilab.kcl.ac.uk/apobec-barcodes/). These analyses reveal that A3B expression correlates with cell cycle and DNA repair genes, whereas the other APOBEC3 members display specificity for immune processes and immune cell populations. We offer molecular insights into the functions of individual APOBEC3 proteins in antiviral and proliferative contexts, and demonstrate the diversification this family of enzymes displays at the transcriptomic level, despite their high similarity in protein sequences and structures.

Abstract P1-06-07: Characterization of chromosomal instability in the TNT trial: A randomized phase III trial of carboplatin compared with docetaxel for patients with metastatic or recurrent locally advanced triple negative or BRCA1/2 breast cancer (CRUK/07/012)

Background

A distinctive trait of triple negative breast cancer (TNBC) is the acquisition of genome wide highly aberrant copy number states, which is more evident in metastatic settings. The level of copy number alterations can be characterized by quantitative estimates of chromosomal instability, such as allelic imbalanced copy number aberrations, telomeric allelic imbalance (NtAI), homologous recombination deficiency (HRD) score, referred here as genomic scars. Several of these scars are reported as being indicative of BRCAness and potential predictive and/or prognostic biomarkers of chemotherapy response, currently mostly demonstrated in neoadjuvant settings in TNBC.

Aims

Using several genomic scar measures, we aim to capture chromosomal instability and test their predictive and prognostic value in metastatic or recurrent locally advanced triple negative or BRCA1/2 mutated breast cancer in the TNT trial.

Methods

Patients recruited to TNT (n=376) had ER-/PR-/Her2- breast cancer or were germline BRCA mutation carriers. Genome-wide copy numbers (CN) were derived from FFPE samples including primary tumours and positive lymph nodes (n=183, docetaxel=93, carboplatin=90; BRCA1 mut=25). Genomic scars were generated using ASCAT (Van loo et al., PNAS 2010) CN profiles. HRD scores were established by Myriad Genetics, Inc. assay (n=272). BRCA1-like classifier was applied as described in Schouten et al., Mol Onc 2015. Shannon diversity index was calculated using ASCAT raw CN profiles. Association of genomic scars with PAM50 subtypes and BRCA1 deficiency status were evaluated using Kruskal-Wallis test; p-values were adjusted for multiple comparisons (Dunn's test). Statistical significance was defined as p&lt;0.05. Association of genomic scars with objective tumour response rate (ORR) and Progression Free Survival (PFS) was assessed using logistic regression and restricted mean survival analysis, respectively.

Results

HRD and NtAI scores were higher in basal like samples compared to non-basal like (median diff. HRD=11.5, p=0.005; NtAI=3, p=0.04). HRD (p=2e-14) and NtAI (p=0.003) scores were also higher in BRCA1 deficient (BRCA1 germline/somatic mutant or BRCA1 methylated) samples compared to non-deficient. Using the BRCA1-like classifier, 42 out of 50 BRCA1 deficient samples and 93 out of 133 BRCA1 non-deficient/undetermined samples were identified as BRCA1-like. The Shannon diversity index, measuring CN heterogeneity, clustered samples into 3 groups. Analysis of ORR showed non-significant trends to preferential response rates with docetaxel in cluster 1 and 3. Membership of cluster 2 predicted higher ORR to carboplatin over docetaxel (interaction p=0.017). PFS indicated a treatment effect in cluster 2, but not in cluster 1 or 3; there was no evidence of interaction between subgroups and treatment (p=0.15).

Conclusions

Our results suggest that the overall heterogeneity of the copy number landscape is a promising area for seeking predictive/prognostic biomarkers in metastatic TNBC, and combined with other modalities of high-dimensional omics data could provide essential treatment response information.

Citation Format: Sipos O, Tovey H, Quist J, Haider S, Nowinski S, Gazinska P, Kernaghan S, Toms C, Timms KM, Lanchbury JS, Linn SC, Pinder SE, Bliss JM, Tutt A, Cheang MC, Grigoriadis A, On behalf of the TNT Trial Management Group and Investigators. Characterization of chromosomal instability in the TNT trial: A randomized phase III trial of carboplatin compared with docetaxel for patients with metastatic or recurrent locally advanced triple negative or BRCA1/2 breast cancer (CRUK/07/012) [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-06-07.

A Four-gene Decision Tree Signature Classification of Triple-negative Breast Cancer: Implications for Targeted Therapeutics

The molecular complexity of triple-negative breast cancers (TNBCs) provides a challenge for patient management. We set out to characterize this heterogeneous disease by combining transcriptomics and genomics data, with the aim of revealing convergent pathway dependencies with the potential for treatment intervention. A Bayesian algorithm was used to integrate molecular profiles in two TNBC cohorts, followed by validation using five independent cohorts (n = 1,168), including three clinical trials. A four-gene decision tree signature was identified, which robustly classified TNBCs into six subtypes. All four genes in the signature (EXO1, TP53BP2, FOXM1, and RSU1) are associated with either genomic instability, malignant growth, or treatment response. One of the six subtypes, MC6, encompassed the largest proportion of tumors (∼50%) in early diagnosed TNBCs. In TNBC patients with metastatic disease, the MC6 proportion was reduced to 25%, and was independently associated with a higher response rate to platinum-based chemotherapy. In TNBC cell line data, platinum sensitivity was recapitulated, and a sensitivity to the inhibition of the phosphatase PPM1D was revealed. Molecularly, MC6-TNBCs displayed high levels of telomeric allelic imbalances, enrichment of CD4+ and CD8+ immune signatures, and reduced expression of genes negatively regulating the MAPK signaling pathway. These observations suggest that our integrative classification approach may identify TNBC patients with discernible and theoretically pharmacologically tractable features that merit further studies in prospective trials.

Integrated genomics and functional validation identifies malignant cell specific dependencies in triple negative breast cancer

Triple negative breast cancers (TNBCs) lack recurrent targetable driver mutations but demonstrate frequent copy number aberrations (CNAs). Here, we describe an integrative genomic and RNAi-based approach that identifies and validates gene addictions in TNBCs. CNAs and gene expression alterations are integrated and genes scored for pre-specified target features revealing 130 candidate genes. We test functional dependence on each of these genes using RNAi in breast cancer and non-malignant cells, validating malignant cell selective dependence upon 37 of 130 genes. Further analysis reveals a cluster of 13 TNBC addiction genes frequently co-upregulated that includes genes regulating cell cycle checkpoints, DNA damage response, and malignant cell selective mitotic genes. We validate the mechanism of addiction to a potential drug target: the mitotic kinesin family member C1 (KIFC1/HSET), essential for successful bipolar division of centrosome-amplified malignant cells and develop a potential selection biomarker to identify patients with tumors exhibiting centrosome amplification.

Association of a four-gene decision tree signature with response to platinum-based chemotherapy in patients with triple negative breast cancer

1006

Background: Approaches to capture the molecular complexity of triple negative breast cancers (TNBCs) are lacking. We sought to classify TNBCs into subgroups with common biological features based on transcriptomic and genomic data using a Bayesian algorithm. Methods: Matched gene expression and copy number microarray data was available for the Guy’s (n = 88) and METABRIC (n = 112) TNBC cohorts. CONEXIC was used to derive a decision tree signature for classification. Performance of the signature was tested in 7 TNBC cohorts (total n: 1,368), including 2 clinical trials assessing the efficacy of gemcitabine and carboplatin with and without iniparib. In the early-stage PrECOG 0105 Phase II neoadjuvant trial (n = 43), subtypes were evaluated in relation to response by residual cancer burden (RCB). In the metastatic Sanofi Phase III trial (n = 224), subtypes were assessed by RECIST. Results were compared to the BL1 TNBCtype-4 subtype and assessed using a multivariate analysis. Results: The integrative analysis using CONEXIC identified a four-gene signature. Across 7 TNBC cohorts this classification identified 6 entities, including 5 smaller groups and 1 major. Characterisation of the latter subgroup, referred to as MC6, revealed enrichment of CD4+ and CD8+ immune signatures, increased genomic instability and reduction in negative regulation of the MAPK signalling pathway. In PrECOG, 25 out of 41 MC6-TNBCs (61%, OR = 1.19, 95% CI = 0.37 to 3.81, P = 0.79) had RCB 0/I. Similarly, 65% of the BL1-TNBCs had an RCB 0/I, however in a smaller population (11 out of 17, OR = 1.30, 95% CI = 0.35 to 5.31), P = 0.77). In Sanofi Phase III, the objective response rate (ORR) in MC6-TNBCs was 46% versus 30% in non-MC6-TNBCs (OR = 1.97, 95% CI = 1.03 to 3.77, P = 0.04), in comparison to BL1-TNBCs with an ORR of 41% versus 32% in non-BL1-TNBCs (OR = 1.47, 95% CI = 0.75 to 2.86), P = 0.26). Conclusions: These results demonstrate that a four-gene signature can identify a subgroup of TNBCs responsive to platinum-based chemotherapy in the metastatic setting. The distinct features of these TNBCs suggest investigation of alternative actionable interventions with immunotherapy or MEK inhibitors in relation to this signature.

Functional redundancy between Apc and Apc2 regulates tissue homeostasis and prevents tumorigenesis in murine mammary epithelium

Aberrant Wnt signaling within breast cancer is associated with poor prognosis, but regulation of this pathway in breast tissue remains poorly understood and the consequences of immediate or long-term dysregulation remain elusive. The exact contribution of the Wnt-regulating proteins adenomatous polyposis coli (APC) and APC2 in the pathogenesis of human breast cancer are ill-defined, but our analysis of publically available array data sets indicates that tumors with concomitant low expression of both proteins occurs more frequently in the 'triple negative' phenotype, which is a subtype of breast cancer with particularly poor prognosis. We have used mouse transgenics to delete Apc and/or Apc2 from mouse mammary epithelium to elucidate the significance of these proteins in mammary homeostasis and delineate their influences on Wnt signaling and tumorigenesis. Loss of either protein alone failed to affect Wnt signaling levels or tissue homeostasis. Strikingly, concomitant loss led to local disruption of β-catenin status, disruption in epithelial integrity, cohesion and polarity, increased cell division and a distinctive form of ductal hyperplasia with 'squamoid' ghost cell nodules in young animals. Upon aging, the development of Wnt activated mammary carcinomas with squamous differentiation was accompanied by a significantly reduced survival. This novel Wnt-driven mammary tumor model highlights the importance of functional redundancies existing between the Apc proteins both in normal homeostasis and in tumorigenesis.

Abstract P1-07-03: Mesenchymal subtype negatively associates with the presence of immune infiltrates within a triple negative breast cancer classifier

Introduction: Lehmann and colleagues (Lehmann et al., 2011) devised a gene expression classification system for triple negative breast cancer (TNBC) consisting of seven subtypes—IM, BL1, BL2, LAR, M, MSL, and UNS (unselected). We (Ring et al., 2016) recently modified this original algorithm of 2188 gene subtyping into a 101-gene algorithm. In addition to a reduction of genes, the 101-gene algorithm has two methodological differences: first, the immunomodulatory (IM) signature was treated not as a subtype but rather as a binary feature of one of the other subtypes (e.g. BL1/IM+, LAR/IM-); second, when tumors—by a predefined correlation coefficient—showed traits of more than one subtype, both subtypes were reported as “dual subtypes.”

Aim: Our aim was to apply the 101-gene algorithm for TNBC subtyping and to establish the relation of TNBC subtypes with their IM-status across several independent data sets.

Methods: 951 patients from four independent TNBC cohorts with available gene expression data were analyzed by the 101-gene algorithm. Of these 848 were classified with at least one subtype.

Results: The distribution of the 5 TNBC subtypes in both single and dual subtypes was 47%,10%,15%,18%,11%, for BL1, BL2, LAR, M, and MSL respectively. The majority of cases gave only one subtype (572, 67%) with M (Mesenchymal) being 9% (n=54) of these. Given this frequency of 9% of M as a baseline, in the remaining 276 (33%) cases with dual subtypes, the expectation that M would be one of the two is 11% (64 subtype calls). However, M is one of the two of the dual subtypes at a much higher frequency of 40% (222 subtype calls, Chi-Squared, P&lt;0.0001). IM+ is a common feature across these cohorts (n=310 or 37%). When examining the IM feature within the patients exhibiting the M subtype as either a single subtype or one of the two dual subtypes (n=276, 33%), IM positive tumors are never of the M phenotype (Chi-Squared, p&lt;0.0001).

Conclusions: We further have confirmed with the 101-gene algorithm that the IM signature inversely associates with the M subtype as it has been observed with the 2188 gene algorithm (Lehmann et al., 2016). Moreover, the M signature is occasionally a confounder of other subtypes however still identifies those tumors negative for immune infiltrates. This raises important opportunities to understand the relationships between intrinsic tumor biology reflected in TNBC subtypes and their interaction with variable immune cell stroma which are the subject of ongoing analyses.

Citation Format: Grigoriadis A, Quist J, Mirza H, Cheang MC, Ring BZ, Hout DR, Bailey DB, Seitz RS, Tutt AN. Mesenchymal subtype negatively associates with the presence of immune infiltrates within a triple negative breast cancer classifier [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 P1-07-03.

Abstract P1-05-14: Copy number aberration-induced gene breakage analysis identifies recurrent FOXP1 fusions in breast cancer

Background: Genomic instability is a critical feature of breast cancers, which manifests in genome-wide copy number aberrations (CNA), often causing “gene breakage” and the generation of fusion genes. We aimed to identify aborted transcripts with underlying CNAs and to investigate the molecular landscape of breast cancers harbouring such events.

Methods: A walking student's t-test algorithm was applied to Affymetrix Exon 1.0ST array data of 123 breast cancers to identify regions of aborted transcription and overlaid with DNA breakpoints derived from matched Affymetrix SNP6 ASCAT-segmented copy number. Aborted transcripts were investigated as potential fusion gene partners through RNA-seq analysis of 151 breast cancer samples (TCGA) and 51 breast cancer cell lines (BCCL) using ChimeraScan. Clinical correlates were established for clinicopathological features, genomic instability measures, and gene expression-based molecular classifiers including PAM50, TNBCtype, IntClust subtypes and immune signatures.

Results: One hundred and six genes with recurrent CNA-induced aborted transcription were identified. Aborted transcription showed hormone receptor subtype-specificity for 7 genes (nTNBC=1, nNon-TNBC=6) and was less prevalent in samples of IntClust 2 and IntClust 4 subtypes (p: 0.0043, 0.0011). Aborted transcripts were more frequently observed in samples with greater copy-neutral loss of heterozygosity (p=0.012), while aborted transcription of 54/106 genes significantly affected enrichment of 27 tumor-infiltrating lymphocyte subpopulations.14 aborted transcripts were found as a fusion gene with one partner in RNA-seq of TCGA and BCCL, while 19 were involved in multiple fusion events (range=1-6, median=2). Nine of 106 genes displayed gene breakage and fusion events exclusively in samples with an enriched tandem duplication phenotype. Notably, FOXP1, localised to a tumour suppressor locus at 3p14.1, reported the highest number of fusion configurations (n=6) with concurrent aborted transcription across all RNA-seq datasets (nPRADA=9, nTCGA=38, nBCCL=6).

Conclusion: CNA-induced gene breakage affects the molecular landscape of breast cancers and is linked with many genomic configurations of interest including copy-neutral loss of heterozygosity and tandem duplications. In particular, the role of recurrent gene fusions of the tumour suppressor, FOXP1, in tumourigenesis warrants further investigation.

Citation Format: Mohd Noor A, Maguire S, Watkins J, Quist J, Mirza H, Tutt A, Gillett C, Natrajan R, Grigoriadis A. Copy number aberration-induced gene breakage analysis identifies recurrent FOXP1 fusions in breast cancer [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 P1-05-14.

Functional and prognostic significance of the genomic amplification of frizzled 6 (FZD6) in breast cancer

Frizzled receptors mediate Wnt ligand signalling, which is crucially involved in regulating tissue development and differentiation, and is often deregulated in cancer. In this study, we found that the gene encoding the Wnt receptor frizzled 6 (FZD6) is frequently amplified in breast cancer, with an increased incidence in the triple‐negative breast cancer (TNBC) subtype. Ablation of FZD6 expression in mammary cancer cell lines: (1) inhibited motility and invasion; (2) induced a more symmetrical shape of organoid three‐dimensional cultures; and (3) inhibited bone and liver metastasis in vivo. Mechanistically, FZD6 signalling is required for the assembly of the fibronectin matrix, interfering with the organization of the actin cytoskeleton. Ectopic delivery of fibronectin in FZD6‐depleted, triple‐negative MDA‐MB‐231 cells rearranged the actin cytoskeleton and restored epidermal growth factor‐mediated invasion. In patients with localized, lymph node‐negative (early) breast cancer, positivity of tumour cells for FZD6 protein identified patients with reduced distant relapse‐free survival. Multivariate analysis indicated an independent prognostic significance of FZD6 expression in TNBC tumours, predicting distant, but not local, relapse. We conclude that the FZD6–fibronectin actin axis identified in our study could be exploited for drug development in highly metastatic forms of breast cancer, such as TNBC. © 2016 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.

PIM1 kinase regulates cell death, tumor growth and chemotherapy response in triple-negative breast cancer

Triple-negative breast cancers (TNBCs) have poor prognosis and lack targeted therapies. Here we identified increased copy number and expression of the PIM1 proto-oncogene in genomic data sets of patients with TNBC. TNBC cells, but not nonmalignant mammary epithelial cells, were dependent on PIM1 for proliferation and protection from apoptosis. PIM1 knockdown reduced expression of the anti-apoptotic factor BCL2, and dynamic BH3 profiling of apoptotic priming revealed that PIM1 prevents mitochondrial-mediated apoptosis in TNBC cell lines. In TNBC tumors and their cellular models, PIM1 expression was associated with several transcriptional signatures involving the transcription factor MYC, and PIM1 depletion in TNBC cell lines decreased, in a MYC-dependent manner, cell population growth and expression of the MYC target gene MCL1. Treatment with the pan-PIM kinase inhibitor AZD1208 impaired the growth of both cell line and patient-derived xenografts and sensitized them to standard-of-care chemotherapy. This work identifies PIM1 as a malignant-cell-selective target in TNBC and the potential use of PIM1 inhibitors for sensitizing TNBC to chemotherapy-induced apoptotic cell death.

Abstract 178: PIM1, a novel target in chemotherapy-resistant triple-negative breast cancer

Triple-Negative Breast Cancers (TNBCs) are aggressive, associated with poor prognosis and lack targeted therapies, mainly due to the absence of suitable molecular targets. The genomic region 6p21-p25 is recurrently amplified in TNBCs and encompasses the PIM1 oncogene.

This study interrogated genomic breast cancer datasets and identified gene copy number-driven increase of PIM1 expression in TNBC. To understand the role of PIM1 in malignant phenotypes of TNBCs, functional studies were carried out in breast cancer and non-malignant mammary epithelial cell line models. RNA interference and rescue-of-function experiments revealed addiction to PIM1 kinase for cell population growth and apoptosis protection in TNBC cells, absent in non-malignant cells. In cells sensitive to PIM1 knockdown, we observed a subsequent reduction of the expression of the anti-apoptotic proteins BCL2 and MCL1. Moreover, exogenous expression of BCL2 prevented apoptosis caused by PIM1 knockdown. BH3-profiling analysis further confirmed that PIM1 blocks apoptosis elicited through the mitochondrial pathway in TNBC cell lines. The activity of PIM1 in other cancers has been closely linked to the regulation of c-MYC, an “un-targetable” oncogene that drives malignancy and that is frequently amplified and highly expressed in primary TNBCs and post-chemotherapy residual disease. Importantly, we found that PIM1 expression associates with several MYC-transcriptional signatures in TNBCs and mediates phosphorylation of c-MYC Ser62 and Histone-H3 Ser10, key targets for MYC-driven transcription. Exogenous expression of MYC rescued the phenotypes caused by PIM1 knockdown, providing mechanistic insights for the observed addiction. Finally, the therapeutic potential of targeting PIM1 was assessed using AZD1208, a small molecule inhibitor of the PIM kinase family. AZD1208 inhibited growth and sensitized TNBC derived cell lines, cell line xenografts and PDXs to chemotherapy by increasing apoptosis.

We therefore identify PIM1 as a driver of malignancy in TNBC, illustrating relationships with MYC-activation and regulation of anti-apoptotic BCL2 and MCL1 proteins. PIM1 inhibitors could provide a potential therapeutic to abrogate chemotherapy resistance in TNBCs.

Citation Format: Fara Braso-Maristany, Simone Filosto, Steven Catchpole, Rebecca Marlow, Jelmar Quist, Erika Francesch Domenech, Gianmaria Liccardi, Leila Zakka, Violeta Serra, Albert Gris, Maggie Cheang, Nirmesh Patel, Anna Perdrix Rosell, Patrycja Gazinska, Elodie Noel, Jonathan Watkins, Pierfrancesco Marra, Anita Grigoriadis, Andrew Tutt. PIM1, a novel target in chemotherapy-resistant triple-negative breast cancer. [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 178.

Abstract 67: An integrated copy number and gene expression genomics analysis and RNAi approach identifies and validates the KIFC1 kinesin as a malignant cell selective target in triple negative breast cancer

Triple negative breast cancers (TNBCs) lack oestrogen (ER), progesterone (PR) and human epidermal growth factor 2 (HER2) receptors, and have limited targeted treatment options. Large scale genomic and transcriptomic studies have advanced our understanding of the changes which occur in TNBCs. However, the substantial number of copy number and gene expression alterations present in TNBCs makes it difficult to identify putative drivers, biomarkers and/or therapeutic targets of the disease. To overcome this problem, we have carried out an integrative computational and RNAi based approach to identify genes required for proliferation of TNBC.

Copy number and gene expression alterations were analysed using Affymetrix Human Exon HTS1.0 and SNP6.0 data of 152 primary breast tumours enriched for a TNBC phenotype and 9 normal breast epithelium. These analyses revealed 141 candidate genes whose upregulated gene expression is copy number driven in TNBC. The functional dependence on each of these genes was subsequently examined using RNAi in an array of 17 breast cancer and non-malignant cell lines using 6-8 cell lines per gene covering the widest possible range of expression levels for that gene. We validated a malignant cell specific functional dependence on 37 of the 141 genes using this method.

STRING analysis of validated hits reveals a subset of genes involved in the process of cell division and mitosis including the previously characterised mitotic kinase TTK. Of these, we further validated KIFC1 (HSET) which is known to play a role in clustering supernumerary centrosomes, a common occurrence in breast cancer. We show that siRNA and shRNA mediated depletion of KIFC1 decreases cell viability and clonogenic ability specifically in centrosome amplified cell lines, which can be rescued upon introduction of an si/shRNA resistant KIFC1. KIFC1 depletion also produces a high level of catastrophic multipolar mitoses in centrosome amplified but not in non-amplified cell lines. Furthermore, in-vivo studies show that inducible depletion of KIFC1 suppresses tumour growth of centrosome amplified cell line xenografts.

Our work has identified and functionally validated novel drivers, and potential therapeutic targets in TNBC. The data presented here shows KIFC1, a druggable kinesin motor protein is a promising target for therapeutic intervention being expressed through gene copy gain in a significant proportion of TNBCs. We validate its role in cancer-specific amplified centrosome clustering showing KIFC1 plays an essential role in aiding the survival of breast cancer cells that have supernumerary centrosomes in both in-vitro and in-vivo contexts.

Citation Format: Nirmesh S. Patel, Konstantinos Drosopoulos, Daniel Weekes, Elodie Noel, Hasan Mirza, Mamunur Rashid, Emanuele de Rinaldis, Fara Brasó Maristany, Sumi Mathew, Erika Francesch Domenech, Patrycja Gazinska, Farzana Noor, Jelmar Quist, Rebecca Marlow, Anita Grigoriadis, Spiros Linardopoulos, Andrew N. Tutt. An integrated copy number and gene expression genomics analysis and RNAi approach identifies and validates the KIFC1 kinesin as a malignant cell selective target in triple negative breast cancer. [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 67.

Pharmacokinetic profile of methotrexate in psoriatic skin via the oral or subcutaneous route using dermal microdialysis showing higher methotrexate bioavailability in psoriasis plaques than in non-lesional skin

AIMS

The aim of this pilot study was to use microdialysis to evaluate levels of Methotrexate (MTX) directly in psoriatic skin following oral or subcutaneous administration of MTX to elaborate a complete pharmacokinetic profile within the dermal skin.

METHODS

Six patients with chronic plaque psoriasis on the arm undergoing treatment with MTX were included in a mono-centre clinical trial. Patients were under treatment with p.o. or s.c. MTX (7.5 and 15 mg) for at least 3 months. Interstitial fluid was collected ex vivo via dermal microdialysis from lesional or non-lesional skin and via intravenous microdialysis as well as blood serum every hour up to 10 h after methotrexate administration every hour. MTX was analysed via liquid chromatography.

RESULTS

The area under the curve (AUC) of methotrexate from peripheral blood was up to four times higher than from microdiaylsis, which detection of free unbound MTX. The AUC from dialysates in psoriatic lesional skin was higher than in non-lesional psoriatic skin, and the AUC levels from i.v. microdialysis were non-significantly higher than those from lesional psoriatic skin. Pharmacokinetic profiles were individually quite different and did not primarily depend on the dose or the means (p.o. vs. s.c.) in which it was administered.

CONCLUSION

Dermal microdialysis is a valid tool to evaluate levels of methotrexate in the skin of psoriasis patients. Drug levels and bioavailability of methotrexate were higher in lesional than non-lesional psoriatic skin. The individual AUC of MTX was not primarily dependent on the route or dose of administration.

Do Genetic Susceptibility Variants Associate with Disease Severity in Early Active Rheumatoid Arthritis?

OBJECTIVE

Genetic variants affect both the development and severity of rheumatoid arthritis (RA). Recent studies have expanded the number of RA susceptibility variants. We tested the hypothesis that these associated with disease severity in a clinical trial cohort of patients with early, active RA.

METHODS

We evaluated 524 patients with RA enrolled in the Combination Anti-Rheumatic Drugs in Early RA (CARDERA) trials. We tested validated susceptibility variants - 69 single-nucleotide polymorphisms (SNP), 15 HLA-DRB1 alleles, and amino acid polymorphisms in 6 HLA molecule positions - for their associations with progression in Larsen scoring, 28-joint Disease Activity Scores, and Health Assessment Questionnaire (HAQ) scores over 2 years using linear mixed-effects and latent growth curve models.

RESULTS

HLA variants were associated with joint destruction. The *04:01 SNP (rs660895, p = 0.0003), *04:01 allele (p = 0.0002), and HLA-DRβ1 amino acids histidine at position 13 (p = 0.0005) and valine at position 11 (p = 0.0012) significantly associated with radiological progression. This association was only significant in anticitrullinated protein antibody (ACPA)-positive patients, suggesting that while their effects were not mediated by ACPA, they only predicted joint damage in ACPA-positive RA. Non-HLA variants did not associate with radiograph damage (assessed individually and cumulatively as a weighted genetic risk score). Two SNP - rs11889341 (STAT4, p = 0.0001) and rs653178 (SH2B3-PTPN11, p = 0.0004) - associated with HAQ scores over 6-24 months.

CONCLUSION

HLA susceptibility variants play an important role in determining radiological progression in early, active ACPA-positive RA. Genome-wide and HLA-wide analyses across large populations are required to better characterize the genetic architecture of radiological progression in RA.

Mouse mammary stem cells express prognostic markers for triple-negative breast cancer

INTRODUCTION

Triple-negative breast cancer (TNBC) is a heterogeneous group of tumours in which chemotherapy, the current mainstay of systemic treatment, is often initially beneficial but with a high risk of relapse and metastasis. There is currently no means of predicting which TNBC will relapse. We tested the hypothesis that the biological properties of normal stem cells are re-activated in tumour metastasis and that, therefore, the activation of normal mammary stem cell-associated gene sets in primary TNBC would be highly prognostic for relapse and metastasis.

METHODS

Mammary basal stem and myoepithelial cells were isolated by flow cytometry and tested in low-dose transplant assays. Gene expression microarrays were used to establish expression profiles of the stem and myoepithelial populations; these were compared to each other and to our previously established mammary epithelial gene expression profiles. Stem cell genes were classified by Gene Ontology (GO) analysis and the expression of a subset analysed in the stem cell population at single cell resolution. Activation of stem cell genes was interrogated across different breast cancer cohorts and within specific subtypes and tested for clinical prognostic power.

RESULTS

A set of 323 genes was identified that was expressed significantly more highly in the purified basal stem cells compared to all other cells of the mammary epithelium. A total of 109 out of 323 genes had been associated with stem cell features in at least one other study in addition to our own, providing further support for their involvement in the biology of this cell type. GO analysis demonstrated an enrichment of these genes for an association with cell migration, cytoskeletal regulation and tissue morphogenesis, consistent with a role in invasion and metastasis. Single cell resolution analysis showed that individual cells co-expressed both epithelial- and mesenchymal-associated genes/proteins. Most strikingly, we demonstrated that strong activity of this stem cell gene set in TNBCs identified those tumours most likely to rapidly progress to metastasis.

CONCLUSIONS

Our findings support the hypothesis that the biological properties of normal stem cells are drivers of metastasis and that these properties can be used to stratify patients with a highly heterogeneous disease such as TNBC.

Abstract 2259: Identifying causative genes and prognostic markers for bladder cancer

Upon presentation 70% of the bladder tumors are confined to the epithelial (stage pTa) and stromal layers (stage pT1) of the bladder. These non-muscle invasive tumors (NMI-BC) frequently recur and 10-15% will eventually invade the detrusor muscle and may cause metastases. The management of these tumors is characaterized by the difficult choice between transurethral resection (TURB) or total bladder removal by cystectomy. Our first objective was to identify DNA copy number changes as biomarkers predicting tumor progression in high grade NMI-BC to aid decision making. A set of 18 DNA samples isolated from fresh frozen high grade NMI-BC was hybridized on Illumina SNP arrays. Analysis of alterations was done with Nexus software. Hierarchical clustering of significantly differing SNPs showed that tumors that progressed and those that did not clustered separately. A comparison of the differential alterations between tumor groups resulted in many chromosomal locations encompassing chromosome 1p, 2-6, 8-10, 12p, 13q, 17q, 18p and 22q that were fit for inclusion in a validation assay. A custom Agilent 15K array was designed to include probes for these locations. We collected a retrospective series of 96 high grade NMI-BC paraffin embedded tumors with a median follow-up of 5 years. Half of these samples were from patients who developed a muscle-invasive tumor at a later time. Preliminary results show an interesting region on chromosome 8 with the best independent prognostic value. This region and the genes therein will be studied in more detail. This and other validated regions will be used to design a definitive prognostic assay.

Complex losses on chromosome 9 characterize bladder tumors regardless of stage. We hypothesized that the complex rearrangements on this chromosome in BC are the results of attempts of the tumor cell to loose tumor suppressor genes whilst struggling to retain other (onco)genes. Therefore, the second aim was to identify pivotal tumor suppressor and/or oncogenes on chromosome 9 for development of bladder cancer, with the aim to exploit these genes or the pathways in which they function as potential targets for therapy for tumors from all stage categories. A custom Agilent 44K array was designed, containing probes for all genes on chromosome 9 (and 8p). DNA from a series of 144 tumors from different stages was hybridized to the arrays. Analysis of alterations was done with Nexus software. We found many regions of loss as expected but also a region that appeared amplified in most tumors. Several candidate regions were validated of their copy number status with specific MLPA assays. Two potential candidate genes from chromosome 9 were selected for mutational and functional analysis. In one of those genes we found several mutations affecting protein function, suggesting that this gene is a new tumor suppressor gene for bladder cancer.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2259. doi:10.1158/1538-7445.AM2011-2259