Abstract PD4-04: PD4-04 A quantitative spatial analysis of microenvironmental biomarkers for breast cancer outcome

Background: Understanding breast cancer progression and the relationships among biomarkers in the tumor and tumor microenvironment could go beyond established prognostic markers of breast cancer. Poor response and recurrence may indeed be a consequence of the highly heterogeneous spatial distribution of biomarkers within cancers, and/or the synergistic and antagonistic relationship between co-localized biomarkers. Recently, mechanical and physical microenvironmental signatures have emerged as relevant in determining cancer aggressiveness and invasiveness. This suggests that physical structures in the tumor tissue may drive favorable immune-tumor-stroma cell patterns. However, current assessment of tumor biopsies is limited in the ability to quantify and spatially resolve several different subtypes of cells and biomarkers within tumors. Methods: We developed a 60-marker imaging mass cytometry panel to resolve high-plex spatial patterns of cells, signaling, and microenvironmental biomarkers within tumor tissues. Our panel includes 16 tumor markers, 20 immune markers and 24 microenvironmental markers. We built an innovative computational tool to identify recurring spatial patterns of these markers within the tumor microenvironment, and define the spatial scale of heterogeneity of such patterns. We correlated the results from this spatial analysis to prospectively collected long term clinical outcome variables (e.g. 10 year survival, local and distant recurrence) in primary breast cancers sampled at baseline. Our patient cohort comprised 287 samples of patients treated with surgery and a radiation, chemotherapy, endocrine therapy, or combinations of these post-surgery. Of these, 174 were from patients alive 5 years post diagnosis, and 113 from patients lost to breast cancer deaths. Living patients were evaluated for recurrence, and of these 94% were disease free at the end of the study, while 4% had local recurrence and 2% distant metastasis. Of the dead patients, 59% had local recurrence while 27% had distant metastasis. Results: We investigated first all patients independent of tumor subtype; in this analysis the presence of both endothelial (CD31+) or HLADR+ cells were consistently associated with long term survival. We further investigated the distribution of all 60 markers in Lum A, Lum B, Lum like, Her2+ and triple negative subtypes. Among the results we confirmed the prognostic role of known biomarkers such as p53+ as a biomarker for poor survival in Luminal B. We also identified complex microenvironmental patterns associated with outcome. For example, the presence of PD1+ cells in collagen rich environments were generally associated with long terms survival in Luminal B patients. With our spatial analysis tool we further investigated intra-patient and inter-patient spatial distribution and classified clusters predictive of outcome beyond heterogeneity. We found that beyond the mere positivity of each marker, the spatial distribution and co-localization of different immune, tumor and mechanical markers determines long term outcome in different subtypes. Specifically, we investigated the role of vimentin within different microenvironments and tumor subtypes. We identified the co-localization of hCa9 and vimentin as strongly associated with poor 5 year outcome, independent of tumor subtype. Moreover, in Luminal A patients while the presence of clusters exclusively positive for vimentin was associated with poor survival, vimentin co-expression with β actin and co-localization of XBP1+ cancer cells and immune cells in a collagen matrix was associated with longer survival. Conclusion: These results suggest the importance of mechanics and physics in determining spatial distribution of tumor-promoting and tumor-inhibiting immune cells, offering new avenues of physics-based therapeutic targets.

Citation Format: Sara Nizzero, Maria Pelaez Soni, Yitian Xu, Licheng Zhang, Junjun Zheng, Brian A. Menegaz, Lee B Jordan, Colin A Purdie, Philip R Quinlan, Chandandeep Nagi, Karla A Sepulveda, Philipp Oertle, Tobias A Appenzeller, Marko Loparic, Zhihui Wang, Shu-Hsia Chen, Vittorio Cristini, Marija Plodinec, Alastair M. Thompson. PD4-04 A quantitative spatial analysis of microenvironmental biomarkers for breast cancer outcome [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 PD4-04.

The frequency and clinical significance of centromere enumeration probe 17 alterations in HER2 immunohistochemistry-equivocal invasive breast cancer

Background and aims

Chromosome 17 alterations affect the assessment of HER2 gene amplification in breast cancer (BC), but its clinical significance remains unclear. This study aimed to identify the prevalence of centromere enumeration probe 17 (CEP17) alterations, and its correlation with response to neoadjuvant therapy (NAT) in BC patients with human epidermal growth factor receptor 2 (HER2) immunohistochemistry‐equivocal score.

Methods and results

A large BC cohort (n = 6049) with HER2 immunohistochemistry score 2+ and florescent in‐situ hybridisation (FISH) results was included to assess the prevalence of CEP17 alterations. Another cohort (n = 885) with available clinicopathological data was used to evaluate the effect of CEP17 in the setting of NAT. HER2‐amplified tumours with monosomy 17 (CEP17 copy number < 1.5 per nucleus), normal 17 (CEP17 1.5–< 3.0) and polysomy 17 (CEP17 ≥ 3.0) were observed in 16, 59 and 25%, respectively, compared with 3, 74 and 23%, respectively, in HER2‐non‐amplified tumours. There was no significant relationship between CEP17 alterations and pathological complete response (pCR) rate in both HER2‐amplified and HER2‐non‐amplified tumours. The independent predictors of pCR were oestrogen (ER) negativity in HER2‐amplified tumours [ER negative versus positive; odds ratio (OR) = 11.80; 95% confidence interval (CI) = 1.37–102.00; P = 0.02], and histological grade 3 in HER2 non‐amplified tumours (3 versus 1, 2; OR = 5.54; 95% CI = 1.61–19.00; P = 0.007).

Conclusion

The impacts of CEP17 alterations are not as strong as those of HER2/CEP17 ratio and HER2 copy number. The hormonal receptors status and tumour histological grade are more useful to identify BC patients with a HER2 immunohistochemistry‐equivocal score who would benefit from NAT.

Abstract 1963: Spatial patterns of microenvironmental biomarkers drive long-term breast cancer outcome

Determining early biomarkers of long-term survival remain a significant challenge for solid tumors. Certain spatial patterns of immune and stroma cells within tumors have been correlated with treatment response across cancer types, including breast cancer. Mechanical and physical microenvironmental signatures have emerged as drivers of cancer aggressiveness and invasiveness. This suggests that physio/mechanical structures may drive the formation of favorable immune-tumor-stroma cell patterns. In this work, we use a novel 60-marker imaging mass cytometry panel that included 16 tumor markers, 20 immune markers and 24 microenvironmental markers to resolve spatial patterns of cells, mechanical, structural, and other biomarkers within 700 clinical tumor samples (tissue microarrays from untreated primary breast cancers). Table 1 Sample distribution, patients were also treated surgically.

Imaging and clinical data (eg. pathology, treatment, 10+ years survival) were integrated and analyzed to extract cell phenotypes, neighboring cells/markers and establish cell density, microenvironmental marker presence, and repeating spatial cell/marker patterns in all samples. Several markers showed significant increased expression in the survival group including CD3, CD44, CD20 for cellular markers, α-SMA, Pan-Cytokeratin, Cytokeratin 5, MMP2, LOX, and HIF1α for mechanical/microenvironmental markers. Conversely, breast cancer death samples exhibited upregulation of Na+/K+ ATPase, hCA9, and Ki67. Moreover, we identified that the co-localization of mechanical markers such as Integrin β1 and Plakoglobin is a signature of tumors with poor outcome, while the individual presence of either does not affect survival. For each of the cells/markers studied, we investigated functional relationships and identified clusters that drive survival such as Vimentin+/β-actin+ B cells, which suggests that the role of mechanics is critical to the tumor-controlling functions of immune cells.

Long-term survival Cohort Survival Breast cancer death N samples 174 113 Long-term disease status Disease-free 94% 14% Local reoccurrence 4% 59% Distant reoccurrence 2% 27% Treatment No adjuvant treatment 3% 10% Adj. radiation 3% 4% Adj. chemo 0% 4% Adj. endocrine 28% 7% Adj .rad + chemo 13% 30% Adj. rad + endocrine 25% 35% Adj. chemo + endocrine 6% 4% Adj. rad + chemo + endocrine 21% 6%

Citation Format: Sara Nizzero, Licheng Zhang, Yitian Xu, Maria J. Pelaez-Soni, Prashant Dogra, Brian A. Menegaz, Lee B. Jordan, Colin A. Purdie, Philip R. Quinlan, Chandandeep Nagi, Karla A. Sepulveda, Philipp Oertle, Tobias A. Appenzeller, Shu-Hsia Chen, Marko Loparic, Zhihui Wang, Vittorio Cristini, Marija Plodinec, Alastair M. Thompson. Spatial patterns of microenvironmental biomarkers drive long-term breast cancer outcome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1963.

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.

Mode of presentation and skin thickening on ultrasound may predict nodal burden in breast cancer patients with a positive axillary core biopsy

OBJECTIVE

A number of pre-operative factors predicting nodal burden in females with breast cancer have recently been identified. The aim of this study is to assess if these factors independently influence nodal burden in females with a positive axillary core biopsy.

METHODS

All node positive patients detected on axillary core biopsy were identified in our cancer audit database. Mode of presentation, age, core tumour grade, core tumour type, ER and HER2 status were evaluated. Tumours were assessed for ultrasound size, distance of tumour-to-skin, presence of invasion of skin and diffuse skin thickening. Axillary lymph nodes were assessed for cortical thickness and presence of ultrasound replaced nodes. Statistical significance was ascertained using univariate logistic regression. A predictive model was produced following a multiple logistic regression model incorporating cross-validation and assessed using receiving operating characteristic curve.

RESULTS

115 patients' data were analysed. Patients referred because of symptoms (70% vs 38%, p = 0.005), and those with ultrasound skin thickening (87% vs 59%, p = 0.055) have higher nodal burden than those referred from screening or without skin thickening. These factors were significant after multivariate analysis. The final predictive model included mode of presentation, ultrasound tumour size, cortical thickness and presence of ultrasound skin thickening. The area under curve is 0.77.

CONCLUSION

We have shown that mode of presentation and ultrasound skin thickening are independent predictors of high nodal burden at surgery. A model has been developed to predict nodal burden pre-operatively, which may lead to avoidance of axillary node clearance in patients with lower nodal burden.

ADVANCES IN KNOWLEDGE

Method of presentation and skin involvement/proximity to skin by the primary tumour are known to influence outcome and nodal involvement respectively but have not been studied with regard to nodal burden. We have shown that mode of presentation and skin thickening at ultrasound are independent predictors of high nodal burden at surgery.

Breast MRI and tumour biology predict axillary lymph node response to neoadjuvant chemotherapy for breast cancer

BACKGROUND

In patients who have had axillary nodal metastasis diagnosed prior to neoadjuvant chemotherapy for breast cancer, there is little consensus on how to manage the axilla subsequently. The aim of this study was to explore whether a combination of breast magnetic resonance imaging (MRI) assessed response and primary tumour pathology factors could identify a subset of patients that might be spared axillary node clearance.

METHODS

A retrospective data analysis was performed of patients with core biopsy-proven axillary nodal metastasis prior to commencement of neoadjuvant chemotherapy (NAC) who had subsequent axillary node clearance (ANC) at definitive breast surgery. Breast tumour and axillary response at MRI before, during and on completion of NAC, core biopsy tumour grade, tumour type and immunophenotype were correlated with pathological response in the breast and the number of metastatic nodes in the ANC specimens.

RESULTS

Of 87 consecutive patients with MRI at baseline, interim and after neoadjuvant chemotherapy who underwent ANC at time of breast surgery, 33 (38%) had no residual macrometastatic axillary disease, 28 (32%) had 1-2 metastatic nodes and 26 (30%) had more than 2 metastatic nodes. Factors that predicted axillary nodal complete response were MRI complete response in the breast (p < 0.0001), HER2 positivity (p = 0.02) and non-lobular tumour type (p = 0.015).

CONCLUSION

MRI assessment of breast tumour response to NAC and core biopsy factors are predictive of response in axillary nodes, and can be used to guide decision making regarding appropriate axillary surgery.

∆Np63/p40 correlates with the location and phenotype of basal/mesenchymal cancer stem-like cells in human ER+ and HER2+ breast cancers

ΔNp63, also known as p40, regulates stemness of normal mammary gland epithelium and provides stem cell characteristics in basal and HER2‐driven murine breast cancer models. Whilst ΔNp63/p40 is a characteristic feature of normal basal cells and basal‐type triple‐negative breast cancer, some receptor‐positive breast cancers express ΔNp63/p40 and its overexpression imparts cancer stem cell‐like properties in ER⁺ cell lines. However, the incidence of ER⁺ and HER2⁺ tumours that express ΔNp63/p40 is unclear and the phenotype of ΔNp63/p40⁺ cells in these tumours remains uncertain. Using immunohistochemistry with p63 isoform‐specific antibodies, we identified a ΔNp63/p40⁺ tumour cell subpopulation in 100 of 173 (58%) non‐triple negative breast cancers and the presence of this population associated with improved survival in patients with ER⁻/HER2⁺ tumours (p = 0.006). Furthermore, 41% of ER⁺/PR⁺ and/or HER2⁺ locally metastatic breast cancers expressed ΔNp63/p40, and these cells commonly accounted for <1% of the metastatic tumour cell population that localised to the tumour/stroma interface, exhibited an undifferentiated phenotype and were CD44⁺/ALDH⁻. In vitro studies revealed that MCF7 and T47D (ER⁺) and BT‐474 (HER2⁺) breast cancer cell lines similarly contained a small subpopulation of ΔNp63/p40⁺ cells that increased in mammospheres. In vivo, MCF7 xenografts contained ΔNp63/p40⁺ cells with a similar phenotype to primary ER⁺ cancers. Consistent with tumour samples, these cells also showed a distinct location at the tumour/stroma interface, suggesting a role for paracrine factors in the induction or maintenance of ΔNp63/p40. Thus, ΔNp63/p40 is commonly present in a small population of tumour cells with a distinct phenotype and location in ER⁺ and/or HER2⁺ human breast cancers.

Are baseline ultrasound and mammographic features associated with rates of pathological completes response in patients receiving neoadjuvant chemotherapy for breast cancer?

Background

Increasing numbers of breast cancer patients receive neoadjuvant chemotherapy (NACT). We seek to investigate whether baseline mammographic and ultrasound features are associated with complete pathological response (pCR) after NACT.

Methods

A database of NACT patients was reviewed. Baseline imaging parameters assessed were ultrasound: posterior effect; echo pattern; margin and lesion diameter; mammography: spiculation and microcalcification. Core biopsy grade and immunophenotype were documented. Data were analysed for the whole study group and by immunophenotype.

Results

Of the 222 cancers, 83 (37%) were triple negative (TN), 61 (27%) ER positive/HER-2 negative and 78 (35%) HER-2 positive. A pCR occurred in 46 of 222 cancers (21%). For the whole group, response was associated with high core biopsy grade (grade 3 vs. grade 1 or 2) (26% vs. 9%, p = 0.0044), absence of posterior shadowing on ultrasound (26% vs. 10%, p <  0.001) and the absence of mammographic spiculation (26 vs. 6%, p <  0.001). Within the HER-2 positive group; the absence of shadowing and spiculation remained highly associated with pCR, in addition to small ultrasound size (AUC = 0.71, p < 0.001) and the absence of microcalcification (39% vs. 21%, p < 0.02). On multivariable analysis absence of spiculation and core grade remained significant for the whole cohort, size and absence of spiculation remained significant for HER-2 positive tumours. No feature predicted pCR in TN tumours.

Conclusion

A pCR is less likely when there is mammographic spiculation. Small ultrasound size is associated with pCR in HER-2 positive tumours. These findings may be helpful when discussing NACT and surgical options with patients.

Trial registration

UK Clinical Trials Gateway: registration number 16712.

Metformin Promotes Antitumor Immunity via Endoplasmic-Reticulum-Associated Degradation of PD-L1

Metformin has been reported to possess antitumor activity and maintain high cytotoxic T lymphocyte (CTL) immune surveillance. However, the functions and detailed mechanisms of metformin's role in cancer immunity are not fully understood. Here, we show that metformin increases CTL activity by reducing the stability and membrane localization of programmed death ligand-1 (PD-L1). Furthermore, we discover that AMP-activated protein kinase (AMPK) activated by metformin directly phosphorylates S195 of PD-L1. S195 phosphorylation induces abnormal PD-L1 glycosylation, resulting in its ER accumulation and ER-associated protein degradation (ERAD). Consistently, tumor tissues from metformin-treated breast cancer patients exhibit reduced PD-L1 levels with AMPK activation. Blocking the inhibitory signal of PD-L1 by metformin enhances CTL activity against cancer cells. Our findings identify a new regulatory mechanism of PD-L1 expression through the ERAD pathway and suggest that the metformin-CTLA4 blockade combination has the potential to increase the efficacy of immunotherapy.

The circular RNome of primary breast cancer

Circular RNAs (circRNAs) are a class of RNAs that is under increasing scrutiny, although their functional roles are debated. We analyzed RNA-seq data of 348 primary breast cancers and developed a method to identify circRNAs that does not rely on unmapped reads or known splice junctions. We identified 95,843 circRNAs, of which 20,441 were found recurrently. Of the circRNAs that match exon boundaries of the same gene, 668 showed a poor or even negative (R < 0.2) correlation with the expression level of the linear gene. In silico analysis showed only a minority (8.5%) of circRNAs could be explained by known splicing events. Both these observations suggest that specific regulatory processes for circRNAs exist. We confirmed the presence of circRNAs of CNOT2, CREBBP, and RERE in an independent pool of primary breast cancers. We identified circRNA profiles associated with subgroups of breast cancers and with biological and clinical features, such as amount of tumor lymphocytic infiltrate and proliferation index. siRNA-mediated knockdown of circCNOT2 was shown to significantly reduce viability of the breast cancer cell lines MCF-7 and BT-474, further underlining the biological relevance of circRNAs. Furthermore, we found that circular, and not linear, CNOT2 levels are predictive for progression-free survival time to aromatase inhibitor (AI) therapy in advanced breast cancer patients, and found that circCNOT2 is detectable in cell-free RNA from plasma. We showed that circRNAs are abundantly present, show characteristics of being specifically regulated, are associated with clinical and biological properties, and thus are relevant in breast cancer.

Abstract 787: Cytosolic TRIM24 characterizes an aggressive subset of ER- PR- and TP53 mutant breast cancer

Introduction: Tripartite Motif Containing 24 (TRIM24) is a PhD/Bromodomain containing steroid receptor co-activator that targets p53 for proteosomal degradation, transforms human mammary epithelial cells, and promotes treatment resistance in preclinical models. While bromodomain inhibitors and proteolysis targeting chimeras have been developed against TRIM24, the disease subtype it is most relevant to remains under explored. In this study, we characterize a uniquely annotated cohort of invasive ductal carcinomas for tumor expression of TRIM24 protein by immunohistochemistry (IHC) to assess its relationship with molecular and clinicopathological features.

Methods: Tissue microarrays (TMAs) representing 198 tumors with 6 cores/tumor were obtained from the Tayside Biospecimen Repository and stained by IHC for TRIM24. TMAs were scored for nuclear and cytosolic intensity and the proportion of tumor cells with staining. These values were combined into Histo-scores (H-Scores) and averaged as a semi-quantitative metric for tumor TRIM24 expression. Statistical associations between TRIM24 H-Scores, clinicopathological annotations, and existing molecular profiles generated from the same TMA were determined using SciPy and SPSS.

Results: TRIM24 has four distinct expression patterns in the 170 tumors with scorable cores on the TMA: nuclear (55), cytosolic (38), nuclear and cytosolic (35), and negative (42). Non-parametric analysis revealed associations between TRIM24 expression pattern and ER (χ2=21.3, p=0.000), PR (χ2=14.8, p=0.002), invasive grade (χ2=14.9, p=0.021), and TP53 mutation (χ2=9.55, p=0.023). No significant association was found with HER2 (χ2=1.51, p=0.68). Higher nuclear H-scores are observed in ER+ (p=0.0008) and PR+ (p=0.001) tumors. Higher cytosolic but not nuclear H-scores are observed in Grade 3 (p=0.003), triple negative (TNBC, p=0.004), and TP53 mutant (p=0.0289) cases. Kaplan-Meier analysis revealed high cytosolic (p=0.037) but not nuclear (p=0.601) H-scores associated with poor survival in ER- patients. No significant survival difference was found in ER+ patients stratified by nuclear (p=0.781) or cytosolic (p=0.683) H-scores. Similar analysis of TNBC was underpowered. TP53 mutant (p=0.142) but not TP53 wild type (p=0.378) disease with high cytosolic H-scores trend toward diminished survival. No such trend is observed in cases stratified by nuclear H-scores and TP53 status.

Conclusions: TRIM24 is overexpressed in most human breast cancers. Nuclear expression is more common in ER+/PR+ tumors but does not stratify outcome. Cytosolic expression occurs in Grade 3, ER-, and TP53 mutant tumors and associates with poor clinical outcome in ER- disease. This suggests TRIM24 may be a more relevant drug target in ER-/PR- than luminal breast cancer and emphasizes the need for studies investigating the cytosolic functions of TRIM24 in ER-/PR- and TP53-mutant breast cancer.

Citation Format: Lalit R. Patel, Jurgen Mitsch, Grazziela P. Figueredo, Philip Quinlan, Lee B. Jordan, Colin A. Purdie, Savitri Krishnamurthy, Michelle C. Barton, Alastair M. Thompson. Cytosolic TRIM24 characterizes an aggressive subset of ER- PR- and TP53 mutant breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 787.

Breast cancer: influence of tumour volume estimation method at MRI on prediction of pathological response to neoadjuvant chemotherapy

OBJECTIVE

Does method of tumour volume measurement on MRI influence prediction of treatment outcome in patients with primary breast cancer undergoing neoadjuvant chemotherapy (NAC)?.

METHOD

The study comprised of 136 women with biopsy-proven breast cancer scheduled for MRI monitoring during NAC treatment. Dynamic contrast-enhanced images were acquired at baseline (pre-NAC) and interim (post three NAC cycles) time points. Functional tumour volumes (FTVs), automatically derived using vendor software and enhancing tumour volumes (ETVs), user-derived using a semi-automated thresholding technique, were calculated at each time point and percentage changes calculated. Response, assessed using residual cancer burden (RCB) score on surgically resected specimens, was compared statistically with volumetric changes and receiver operating characteristic analysis performed.

RESULTS

Mean volumetric differences for each RCB response category were (FTV/ETV): pathological complete response (pCR) 95.5/96.8%, RCB-I 69.8/66.7%, RCB-II 64.0/65.5%, RCB-III 25.4/24.0%. Differences were significant between pCR and RCB-II/RCB-III categories (p < 0.040; unpaired t-test) using FTV measures and between pCR and RCB-I/RCB-II/RCB-III categories (p < 0.006; unpaired t-test) when ETV was used. Receiver operating characteristic analysis for pCR identification post-NAC yielded area under the curve for FTV/ETV of 0.834/0.920 respectively. Sensitivity and specificity for FTV was 80.0 and 76.8% for FTV and 81.0 and 91.8% for ETV.

CONCLUSION

ETV changes can identify patients likely to achieve a complete response to NAC. Potentially, this could impact patient management regarding the possible avoidance of post-NAC surgery. Advances in Knowledge: Interim changes in ETV are more useful than FTV in predicting final pathological response to NAC. ETV differentiates patients who will achieve a complete response from those who will have residual disease.

Corrigendum: A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers

This corrects the article DOI: 10.1038/ng.3771.

Whole-Genome Sequencing Reveals Breast Cancers with Mismatch Repair Deficiency

Mismatch repair (MMR)-deficient cancers have been discovered to be highly responsive to immune therapies such as PD-1 checkpoint blockade, making their definition in patients, where they may be relatively rare, paramount for treatment decisions. In this study, we utilized patterns of mutagenesis known as mutational signatures, which are imprints of the mutagenic processes associated with MMR deficiency, to identify MMR-deficient breast tumors from a whole-genome sequencing dataset comprising a cohort of 640 patients. We identified 11 of 640 tumors as MMR deficient, but only 2 of 11 exhibited germline mutations in MMR genes or Lynch Syndrome. Two additional tumors had a substantially reduced proportion of mutations attributed to MMR deficiency, where the predominant mutational signatures were related to APOBEC enzymatic activity. Overall, 6 of 11 of the MMR-deficient cases in this cohort were confirmed genetically or epigenetically as having abrogation of MMR genes. However, IHC analysis of MMR-related proteins revealed all but one of 10 samples available for testing as MMR deficient. Thus, the mutational signatures more faithfully reported MMR deficiency than sequencing of MMR genes, because they represent a direct pathophysiologic readout of repair pathway abnormalities. As whole-genome sequencing continues to become more affordable, it could be used to expose individually abnormal tumors in tissue types where MMR deficiency has been rarely detected, but also rarely sought. Cancer Res; 77(18); 4755-62. ©2017 AACR.

Somatic mutations reveal asymmetric cellular dynamics in the early human embryo

Somatic cells acquire mutations throughout the course of an individual's life. Mutations occurring early in embryogenesis are often present in a substantial proportion of, but not all, cells in postnatal humans and thus have particular characteristics and effects. Depending on their location in the genome and the proportion of cells they are present in, these mosaic mutations can cause a wide range of genetic disease syndromes and predispose carriers to cancer. They have a high chance of being transmitted to offspring as de novo germline mutations and, in principle, can provide insights into early human embryonic cell lineages and their contributions to adult tissues. Although it is known that gross chromosomal abnormalities are remarkably common in early human embryos, our understanding of early embryonic somatic mutations is very limited. Here we use whole-genome sequences of normal blood from 241 adults to identify 163 early embryonic mutations. We estimate that approximately three base substitution mutations occur per cell per cell-doubling event in early human embryogenesis and these are mainly attributable to two known mutational signatures. We used the mutations to reconstruct developmental lineages of adult cells and demonstrate that the two daughter cells of many early embryonic cell-doubling events contribute asymmetrically to adult blood at an approximately 2:1 ratio. This study therefore provides insights into the mutation rates, mutational processes and developmental outcomes of cell dynamics that operate during early human embryogenesis.

A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers

Somatic rearrangements contribute to the mutagenized landscape of cancer genomes. Here, we systematically interrogated rearrangements in 560 breast cancers by using a piecewise constant fitting approach. We identified 33 hotspots of large (>100 kb) tandem duplications, a mutational signature associated with homologous-recombination-repair deficiency. Notably, these tandem-duplication hotspots were enriched in breast cancer germline susceptibility loci (odds ratio (OR) = 4.28) and breast-specific 'super-enhancer' regulatory elements (OR = 3.54). These hotspots may be sites of selective susceptibility to double-strand-break damage due to high transcriptional activity or, through incrementally increasing copy number, may be sites of secondary selective pressure. The transcriptomic consequences ranged from strong individual oncogene effects to weak but quantifiable multigene expression effects. We thus present a somatic-rearrangement mutational process affecting coding sequences and noncoding regulatory elements and contributing a continuum of driver consequences, from modest to strong effects, thereby supporting a polygenic model of cancer development.

Abstract PD3-04: Which measure of the interim changes in breast tumoral volume at breast MRI in response to neoadjuvant chemotherapy best predicts final pathological response?

BACKGROUND: Interim changes in breast tumour volume at magnetic resonance imaging (MRI) can predict ultimate response to neoadjuvant chemotherapy (NAC), but there is little data on the best measure of volumetric change.

PURPOSE: To assess whether changes in measurements of semi-automated enhancing tumour volume (ETV) or fully automated functional tumour volume (FTV) between baseline and interim contrast-enhanced MRI are equivalent in predicting ultimate pathological response to neoadjuvant chemotherapy (NAC) for primary breast cancer, assessed using the residual cancer burden (RCB) score.

MATERIALS & METHODS: 78 patients undergoing treatment with NAC for primary breast cancer underwent contrast-enhanced MRI on a 1.5T or 3.0T MRI scanner using a dedicated bilateral breast coil before and after two or three cycles of NAC. Image analysis was performed using either semi-automated, user-defined thresholding (ITK-Snap; ETV) or fully-automated (Siemens SyngoVia BreVis; FTV) approaches. For ETV, the two-minute post-contrast subtracted volumes were analysed, with enhancing pixels thresholded to define tumour volume. FTV was measured using a manufacturer default setting of 50% enhancement threshold, relative to pre-contrast signal intensity, to define tumour volume. ETV intra-observer reproducibility was assessed by repeat analysis one month after initial analysis and a second observer also repeated the measure. Coefficient of reproducibility (CoR) and intraclass correlation coefficents (ICC) were calculated for intra- and inter-observer repeatability.

ETV and FTV percentage reduction between baseline and interim examinations was compared with final pathological response, as assessed using the residual cancer burden (RCB) score on resected cancer specimens.

Correlation of the two volumetric measures was performed using a Pearson Intra-class Correlation Coefficient (ICC) and pair-wise comparisons of ETV and FTV changes between RCB groups carried out using a Mann-Whitney U test. All statistical assessment was performed using SPSS, v21, with p&lt;0.05 considered significant.

RESULTS: There was significant correlation between ETV and FTV (ICC= 0.744, p&lt;0.05). Intra and inter observer reproducibility for ETV was excellent, with ICC 0.940 and 0.861 respectively and corresponding CoRs of 11.6% and 14.8%.

Average percentage reductions in ETV for each pathological response category were: pCR 96.4% (n=12), RCB-I 66.6% (n=10), RCB-II 62.9% (n=39) and RCB-III 27.3% (n=17). Corresponding values for FTV were 88.8%, 70.6%, 54.6% and 20.8%.

Significant differences in percentage ETV changes were found for pCR vs. RCB-I (p&lt;0.008), II (p&lt;0.001) & III (p&lt;0.001) and RCB-II vs. RCB-III (p&lt;0.001). For FTV, significant differences were measured only for pCR vs. RCB-II & III (p&lt;0.001).

CONCLUSION: changes in the semi-automated ETV measuement between baseline and interim MRI may provide more useful predictive information on final pathological response to NAC than FTV, as the changes are better able to discriminate between pCR and minimal residual disease (RCB-I). The ability to confidently predict pCR versus all other residual disease categories could facilitate planning of enhanced approaches to surgical management.

Citation Format: Thompson AM, Vinnicombe SJ, Waugh SA, Purdie CA, Evans AJ, Brunton T, Fuller-Pace FV. Which measure of the interim changes in breast tumoral volume at breast MRI in response to neoadjuvant chemotherapy best predicts final pathological response? [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 PD3-04.

A prospective comparison of ER, PR, Ki67 and gene expression in paired sequential core biopsies of primary, untreated breast cancer

BACKGROUND

Sequential biopsy of breast cancer is used to assess biomarker effects and drug efficacy. The preoperative "window of opportunity" setting is advantageous to test biomarker changes in response to therapeutic agents in previously untreated primary cancers. This study tested the consistency over time of paired, sequential biomarker measurements on primary, operable breast cancer in the absence of drug therapy.

METHODS

Immunohistochemistry was performed for ER, PR and Ki67 on paired preoperative/operative tumor samples taken from untreated patients within 2 weeks of each other. Microarray analysis on mRNA extracted from formalin fixed paraffin embedded cores was performed using Affymetrix based arrays on paired core biopsies analysed using Ingenuity Pathway Analysis (IPA) and Gene Set Analysis (GSA).

RESULTS

In 41 core/resection pairs, the recognised trend to lower ER, PR and Ki67 score on resected material was confirmed. Concordance for ER, PR and Ki67 without changing biomarker status (e.g. ER+ to ER-) was 90, 74 and 80 % respectively. However, in 23 paired core samples (diagnostic core v on table core), Ki67 using a cut off of 13.25 % was concordant in 22/23 (96 %) and differences in ER and PR immunohistochemistry by Allred or Quickscore between the pairs did not impact hormone receptor status. IPA and GSA demonstrated substantial gene expression changes between paired cores at the mRNA level, including reduced expression of ER pathway analysis on the second core, despite the absence of drug intervention.

CONCLUSIONS

Sequential core biopsies of primary breast cancer (but not core versus resection) was consistent and is appropriate to assess the effects of drug therapy in vivo on ER, PR and Ki67 using immunohistochemistry. Conversely, studies utilising mRNA expression may require non-treatment controls to distinguish therapeutic from biopsy differences.

TP53 drives invasion through expression of its Δ133p53β variant

TP53 is conventionally thought to prevent cancer formation and progression to metastasis, while mutant TP53 has transforming activities. However, in the clinic, TP53 mutation status does not accurately predict cancer progression. Here we report, based on clinical analysis corroborated with experimental data, that the p53 isoform Δ133p53β promotes cancer cell invasion, regardless of TP53 mutation status. Δ133p53β increases risk of cancer recurrence and death in breast cancer patients. Furthermore Δ133p53β is critical to define invasiveness in a panel of breast and colon cell lines, expressing WT or mutant TP53. Endogenous mutant Δ133p53β depletion prevents invasiveness without affecting mutant full-length p53 protein expression. Mechanistically WT and mutant Δ133p53β induces EMT. Our findings provide explanations to 2 long-lasting and important clinical conundrums: how WT TP53 can promote cancer cell invasion and reciprocally why mutant TP53 gene does not systematically induce cancer progression.

DOI:http://dx.doi.org/10.7554/eLife.14734.001

Most cancers are caused by a build-up of mutations that are acquired throughout life. One gene in particular, called TP53, is the most commonly mutated gene in many types of human cancers. This suggests that TP53 mutations play an important role in cancer development.

It is widely considered that the TP53 gene normally stops tumors from forming, while mutant forms of the gene somehow promote cancer growth. Evidence from patients with cancer has shown, however, that the relationship between TP53 mutations and cancer is not that simple. Some very aggressive cancers that resist treatment and spread have a normal TP53 gene. Some cancers with a mutated gene do not spread and respond well to cancer treatments. Recent studies have shown that the normal TP53 gene produces many different versions of its protein, and that some of these naturally occurring forms are found more often in tumors that others. However, it was not clear if certain versions of TP53’s proteins contributed to the development of cancer.

Now, Gadea, Arsic, Fernandes et al. show that Δ133p53β, one version of the protein produced by the TP53 gene in human cells, helps tumor cells to spread to other organs. Tests of 273 tumors taken from patients with breast cancer revealed that tumors with the Δ133p53β protein were more likely to spread. Patients with these Δ133p53β-containing tumors were also more likely to develop secondary tumors at other sites in the body and to die within five years.

Next, a series of experiments showed that removing Δ133p53β from breast cancer cells grown in the laboratory made them less likely to invade, while adding it back had the opposite effect. The same thing happened in colon cancer cells grown in the laboratory. The experiments showed that Δ133p53β causes tumor cells with the normal TP53 gene or a mutated TP53 gene to spread to other organs.

Together the new findings help explain why some aggressive cancers develop even with a normal version of the tumor-suppressing TP53 gene. They also help explain why not all cancers with a mutant version of the TP53 gene go on to spread. Future studies will be needed to determine whether drugs that prevent the production of the Δ133p53β protein can help to treat aggressive cancers.

DOI:http://dx.doi.org/10.7554/eLife.14734.002

Expression profiling of nuclear receptors in breast cancer identifies TLX as a mediator of growth and invasion in triple-negative breast cancer

The Nuclear Receptor (NR) superfamily of transcription factors comprises 48 members, several of which have been implicated in breast cancer. Most important is estrogen receptor-α (ERα), which is a key therapeutic target. ERα action is facilitated by co-operativity with other NR and there is evidence that ERα function may be recapitulated by other NRs in ERα-negative breast cancer. In order to examine the inter-relationships between nuclear receptors, and to obtain evidence for previously unsuspected roles for any NRs, we undertook quantitative RT-PCR and bioinformatics analysis to examine their expression in breast cancer. While most NRs were expressed, bioinformatic analyses differentiated tumours into distinct prognostic groups that were validated by analyzing public microarray data sets. Although ERα and progesterone receptor were dominant in distinguishing prognostic groups, other NR strengthened these groups. Clustering analysis identified several family members with potential importance in breast cancer. Specifically, RORγ is identified as being co-expressed with ERα, whilst several NRs are preferentially expressed in ERα-negative disease, with TLX expression being prognostic in this subtype. Functional studies demonstrated the importance of TLX in regulating growth and invasion in ERα-negative breast cancer cells.

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

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

Abstract P5-07-15: Breast cancer estrogen receptor scoring in tissue microarrays: Specialist breast pathologist versus automation

Rationale: Tissue microarrays (TMAs) have become a valuable resource for biomarker expression in translational research. Immunohistochemical (IHC) assessment of TMAs is the principal method for analyzing protein expression in large numbers of patient samples efficient with conservation of tissue. However, manual IHC assessment of TMAs remains a challenging and laborious task. With advances in image analysis, computer generated analyses of TMAs have the potential to lessen the burden of expert pathologist review. Computerized ER scoring relies on tumor localization.

Aim: The objective of this study was to compare the effectiveness of a locally developed automated invasive tumor location system with the skills of specialist breast pathologists.

Methods: In this study, tumor localization for estrogen receptor (ER) scoring was evaluated comparing computer- generated segmentation masks with those of two specialist breast pathologists. Automated tumor localization was achieved using a novel image analysis algorithm, which labeled compact groups of pixels called superpixels. Machine learning techniques were adopted to model color, shape and textural properties of superpixels in a rotation invariant manner, suitable for histopathology images. The resulting automatically and manually-obtained segmentation masks were used to obtain IHC scores for thirty-two ER stained invasive breast cancer TMA samples using FDA-approved IHC scoring software.

Results: Pixel-level comparisons showed lower agreement between automated and manual segmentation masks (κ = 0.84) than between pathologists' masks (κ = 0.91). However, this had little impact on computed IHC scores (Allred method; κ = 0.91, Quickscore method; κ = 0.92).

Conclusion: The automated system provides sufficiently consistent measurements for standardized IHC analysis of nuclear staining in TMAs from large clinical trials.

Citation Format: Jordan LB, Akbar S, Purdie CA, Thompson AM, McKenna SJ. Breast cancer estrogen receptor scoring in tissue microarrays: Specialist breast pathologist versus automation. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P5-07-15.

The Informatics Challenges Facing Biobanks: A Perspective from a United Kingdom Biobanking Network

The challenges facing biobanks are changing from simple collections of materials to quality-assured fit-for-purpose clinically annotated samples. As a result, informatics awareness and capabilities of a biobank are now intrinsically related to quality. A biobank may be considered a data repository, in the form of raw data (the unprocessed samples), data surrounding the samples (processing and storage conditions), supplementary data (such as clinical annotations), and an increasing ethical requirement for biobanks to have a mechanism for researchers to return their data. The informatics capabilities of a biobank are no longer simply knowing sample locations; instead the capabilities will become a distinguishing factor in the ability of a biobank to provide appropriate samples. There is an increasing requirement for biobanking systems (whether in-house or commercially sourced) to ensure the informatics systems stay apace with the changes being experienced by the biobanking community. In turn, there is a requirement for the biobanks to have a clear informatics policy and directive that is embedded into the wider decision making process. As an example, the Breast Cancer Campaign Tissue Bank in the UK was a collaboration between four individual and diverse biobanks in the UK, and an informatics platform has been developed to address the challenges of running a distributed network. From developing such a system there are key observations about what can or cannot be achieved by informatics in isolation. This article will highlight some of the lessons learned during this development process.

Comparing computer-generated and pathologist-generated tumour segmentations for immunohistochemical scoring of breast tissue microarrays

Background:

Tissue microarrays (TMAs) have become a valuable resource for biomarker expression in translational research. Immunohistochemical (IHC) assessment of TMAs is the principal method for analysing large numbers of patient samples, but manual IHC assessment of TMAs remains a challenging and laborious task. With advances in image analysis, computer-generated analyses of TMAs have the potential to lessen the burden of expert pathologist review.

Methods:

In current commercial software computerised oestrogen receptor (ER) scoring relies on tumour localisation in the form of hand-drawn annotations. In this study, tumour localisation for ER scoring was evaluated comparing computer-generated segmentation masks with those of two specialist breast pathologists. Automatically and manually obtained segmentation masks were used to obtain IHC scores for thirty-two ER-stained invasive breast cancer TMA samples using FDA-approved IHC scoring software.

Results:

Although pixel-level comparisons showed lower agreement between automated and manual segmentation masks (κ=0.81) than between pathologists' masks (κ=0.91), this had little impact on computed IHC scores (Allred; =0.91, Quickscore; =0.92).

Conclusions:

The proposed automated system provides consistent measurements thus ensuring standardisation, and shows promise for increasing IHC analysis of nuclear staining in TMAs from large clinical trials.

Magnetic resonance imaging texture analysis classification of primary breast cancer

OBJECTIVES

Patient-tailored treatments for breast cancer are based on histological and immunohistochemical (IHC) subtypes. Magnetic Resonance Imaging (MRI) texture analysis (TA) may be useful in non-invasive lesion subtype classification.

METHODS

Women with newly diagnosed primary breast cancer underwent pre-treatment dynamic contrast-enhanced breast MRI. TA was performed using co-occurrence matrix (COM) features, by creating a model on retrospective training data, then prospectively applying to a test set. Analyses were blinded to breast pathology. Subtype classifications were performed using a cross-validated k-nearest-neighbour (k = 3) technique, with accuracy relative to pathology assessed and receiver operator curve (AUROC) calculated. Mann-Whitney U and Kruskal-Wallis tests were used to assess raw entropy feature values.

RESULTS

Histological subtype classifications were similar across training (n = 148 cancers) and test sets (n = 73 lesions) using all COM features (training: 75%, AUROC = 0.816; test: 72.5%, AUROC = 0.823). Entropy features were significantly different between lobular and ductal cancers (p < 0.001; Mann-Whitney U). IHC classifications using COM features were also similar for training and test data (training: 57.2%, AUROC = 0.754; test: 57.0%, AUROC = 0.750). Hormone receptor positive and negative cancers demonstrated significantly different entropy features. Entropy features alone were unable to create a robust classification model.

CONCLUSION

Textural differences on contrast-enhanced MR images may reflect underlying lesion subtypes, which merits testing against treatment response.

KEY POINTS

• MR-derived entropy features, representing heterogeneity, provide important information on tissue composition. • Entropy features can differentiate between histological and immunohistochemical subtypes of breast cancer. • Differing entropy features between breast cancer subtypes implies differences in lesion heterogeneity. • Texture analysis of breast cancer potentially provides added information for decision making.

Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells

Mitochondrial genomes are separated from the nuclear genome for most of the cell cycle by the nuclear double membrane, intervening cytoplasm, and the mitochondrial double membrane. Despite these physical barriers, we show that somatically acquired mitochondrial-nuclear genome fusion sequences are present in cancer cells. Most occur in conjunction with intranuclear genomic rearrangements, and the features of the fusion fragments indicate that nonhomologous end joining and/or replication-dependent DNA double-strand break repair are the dominant mechanisms involved. Remarkably, mitochondrial-nuclear genome fusions occur at a similar rate per base pair of DNA as interchromosomal nuclear rearrangements, indicating the presence of a high frequency of contact between mitochondrial and nuclear DNA in some somatic cells. Transmission of mitochondrial DNA to the nuclear genome occurs in neoplastically transformed cells, but we do not exclude the possibility that some mitochondrial-nuclear DNA fusions observed in cancer occurred years earlier in normal somatic cells.

Macroscopic handling and reporting of breast cancer specimens pre- and post-neoadjuvant chemotherapy treatment: review of pathological issues and suggested approaches

Neoadjuvant chemotherapy (NACT) is used increasingly in the treatment of invasive breast cancer and presents challenges for the pathologist in the handling and interpretation of tissues. Potential issues include pathological identification and localization of the residual tumour site; how best to assess pathological response (given the diversity of scoring systems described); the timing and assessment of axillary node biopsy; and the value of retesting any residual tumour for dissonance between core biopsy and post-treatment residual cancer cells for biomarker expression such as oestrogen and progesterone receptors and human epidermal growth factor receptor 2 (HER2). The role of the pathologist is critical in modern NACT approaches to breast cancer and is likely to remain challenging as novel agents and newer biomarkers become available. In this manuscript we review these issues and describe some practical approaches to handling and reporting these samples in the routine histopathology laboratory.

Mutant p53 accumulation in human breast cancer is not an intrinsic property or dependent on structural or functional disruption but is regulated by exogenous stress and receptor status

Many human cancers contain missense TP53 mutations that result in p53 protein accumulation. Although generally considered as a single class of mutations that abrogate wild-type function, individual TP53 mutations may have specific properties and prognostic effects. Tumours that contain missense TP53 mutations show variable p53 stabilization patterns, which may reflect the specific mutation and/or aspects of tumour biology. We used immunohistochemistry on cell lines and human breast cancers with known TP53 missense mutations and assessed the effects of each mutation with four structure-function prediction methods. Cell lines with missense TP53 mutations show variable percentages of cells with p53 stabilization under normal growth conditions, ranging from approximately 50% to almost 100%. Stabilization is not related to structural or functional disruption, but agents that stabilize wild-type p53 increase the percentages of cells showing missense mutant p53 accumulation in cell lines with heterogeneous stabilization. The same heterogeneity of p53 stabilization occurs in primary breast cancers, independent of the effect of the mutation on structural properties or functional disruption. Heterogeneous accumulation is more common in steroid receptor-positive or HER2-positive breast cancers and cell lines than in triple-negative samples. Immunohistochemcal staining patterns associate with Mdm2 levels, proliferation, grade and overall survival, whilst the type of mutation reflects downstream target activity. Inhibiting Mdm2 activity increases the extent of p53 stabilization in some, but not all, breast cancer cell lines. The data indicate that missense mutant p53 stabilization is a complex and variable process in human breast cancers that associates with disease characteristics but is unrelated to structural or functional properties. That agents which stabilize wild-type p53 also stabilize mutant p53 has implications for patients with heterogeneous mutant p53 accumulation, where therapy may activate mutant p53 oncogenic function.

What are the characteristics of breast cancers misclassified as benign by quantitative ultrasound shear wave elastography?

OBJECTIVES

Shear wave elastography (SWE) is a promising adjunct to greyscale ultrasound in differentiating benign from malignant breast masses. The purpose of this study was to characterise breast cancers which are not stiff on quantitative SWE, to elucidate potential sources of error in clinical application of SWE to evaluation of breast masses.

METHODS

Three hundred and two consecutive patients examined by SWE who underwent immediate surgery for breast cancer were included. Characteristics of 280 lesions with suspicious SWE values (mean stiffness >50 kPa) were compared with 22 lesions with benign SWE values (<50 kPa). Statistical significance of the differences was assessed using non-parametric goodness-of-fit tests.

RESULTS

Pure ductal carcinoma in situ (DCIS) masses were more often soft on SWE than masses representing invasive breast cancer. Invasive cancers that were soft were more frequently: histological grade 1, tubular subtype, ≤10 mm invasive size and detected at screening mammography. No significant differences were found with respect to the presence of invasive lobular cancer, vascular invasion, hormone and HER-2 receptor status. Lymph node positivity was less common in soft cancers.

CONCLUSION

Malignant breast masses classified as benign by quantitative SWE tend to have better prognostic features than those correctly classified as malignant.

KEY POINTS

• Over 90 % of cancers assessable with ultrasound have a mean stiffness >50 kPa. • 'Soft' invasive cancers are frequently small (≤10 mm), low grade and screen-detected. • Pure DCIS masses are more often soft than invasive cancers (>40 %). • Large symptomatic masses are better evaluated with SWE than small clinically occult lesions. • When assessing small lesions, 'softness' should not raise the threshold for biopsy.

Does shear wave ultrasound independently predict axillary lymph node metastasis in women with invasive breast cancer?

Shear wave elastography (SWE) shows promise as an adjunct to greyscale ultrasound examination in assessing breast masses. In breast cancer, higher lesion stiffness on SWE has been shown to be associated with features of poor prognosis. The purpose of this study was to assess whether lesion stiffness at SWE is an independent predictor of lymph node involvement. Patients with invasive breast cancer treated by primary surgery, who had undergone SWE examination were eligible. Data were retrospectively analysed from 396 consecutive patients. The mean stiffness values were obtained using the Aixplorer^® ultrasound machine from SuperSonic Imagine Ltd. Measurements were taken from a region of interest positioned over the stiffest part of the abnormality. The average of the mean stiffness value obtained from each of two orthogonal image planes was used for analysis. Associations between lymph node involvement and mean lesion stiffness, invasive cancer size, histologic grade, tumour type, ER expression, HER-2 status and vascular invasion were assessed using univariate and multivariate logistic regression. At univariate analysis, invasive size, histologic grade, HER-2 status, vascular invasion, tumour type and mean stiffness were significantly associated with nodal involvement. Nodal involvement rates ranged from 7 % for tumours with mean stiffness <50 kPa to 41 % for tumours with a mean stiffness of >150 kPa. At multivariate analysis, invasive size, tumour type, vascular invasion, and mean stiffness maintained independent significance. Mean stiffness at SWE is an independent predictor of lymph node metastasis and thus can confer prognostic information additional to that provided by conventional preoperative tumour assessment and staging.

Abstract PD03-02: Evidence for the anti-cancer action of metformin mediated via tumor AMPK, Akt and Ki67, in a preoperative window of opportunity trial

Background: Metformin reduces the overall risk of cancer incidence by 31%, improves cancer-related mortality and enhances response to neoadjuvant chemotherapy in type 2-diabetics receiving metformin. There is evidence that metformin works through activation of Adenosine Monophosphate Protein Kinase (AMPK), an energy-sensing kinase that maintains cellular energy homeostasis. In a pre-operative window-of-opportunity randomized trial we have demonstrated that metformin significantly reduces proliferation and blunts the insulin response in primary operable breast cancer. This study further analysed cancer tissue from the trial to dissect the molecular mechanisms involved.

Methodology: Non-diabetic women with operable invasive breast cancer were randomised to receive pre-operative metformin or no drug. Forty seven patients had core biopsy at diagnosis then were randomized to metformin (metformin 500mg o.d. for 1 week increased to 1g b.d for a further week continued to surgery) or no drug, and 2 weeks later had core biopsy at surgery. Insulin receptor, phospho-AMPK (pAMPK), phospho-Akt (pAkt) and Ki67 immunohistochemistry was performed on formalin-fixed paraffin-embedded cores and scored blinded to treatment. Paired t-test was used for analysis.

Results: Significant up-regulation of pAMPK (p = 0.04) and down-regulation of pAkt (p = 0.04) in metformin treated patients was demonstrated compared to the control group. No change in insulin receptor expression was identified but, as previously reported, there was a fall in ki67. Changes were independent of Body Mass Index. Seven patients (7/24) receiving metformin withdrew because of gastro-intestinal upset and were excluded from the immunohistochemical analyses.

Conclusion: These findings suggest that metformin works in vivo in breast cancer patients via up-regulation of tumor pAMPK and down-regulation of pAkt and proliferation. Since down-regulation of pAMPK is a feature of breast cancer, this suggests mechanistic evidence for the therapeutic effect of metformin.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr PD03-02.

The manufacture and assessment of tissue microarrays: suggestions and criteria for analysis, with breast cancer as an example

Tissue microarray (TMA) is an established and valuable tool, particularly in translational research and clinical trials, allowing resource-efficient use, and high-throughput profiling, of large numbers of tumours. Despite this, there is little evidence, or guidance, on the optimum manufacture, use and assessment of TMAs. Here we review some of the literature, using breast cancer as an example, to highlight good practice and pitfalls in the design and manufacture of TMAs. Issues, such as the size, number, spacing and layout of cores, as well as the assessment and reporting of studies using TMAs are addressed. We make some suggestions regarding these challenges, and propose a checklist of features that should be considered in order to stimulate debate and improve the quality of data produced by TMA analysis.

Immunohistochemical detection of Polo-like kinase-1 (PLK1) in primary breast cancer is associated with TP53 mutation and poor clinical outcom

INTRODUCTION

Polo-like kinase-1 (PLK1) is a crucial driver of cell cycle progression and its down-regulation plays an important checkpoint role in response to DNA damage. Mechanistically, this is mediated by p53 which represses PLK1 expression through chromatin remodelling. Consistent with this model, cultured cells lacking p53 fail to repress PLK1 expression. This study examined PLK1 expression, p53 mutation and clinical outcome in breast cancer.

METHODS

Immunohistochemistry was performed using antibodies to PLK1, MDM2 and Ki67 on Tissue Micro-Array (TMA) slides of a cohort of 215 primary breast cancers. The TP53 gene (encoding p53) was sequenced in all tumour samples. Protein expression scored using the "Quickscore" method was compared with clinical and pathological data, including survival.

RESULTS

Staining of PLK1 was observed in 11% of primary breast tumours and was significantly associated with the presence of TP53 mutation (P = 0.0063). Moreover, patients with both PLK1 expression and TP53 mutation showed a significantly worse survival than those with either PLK1 expression or TP53 mutation alone. There was also a close association of elevated PLK1 with triple negative tumours, considered to be poor prognosis breast cancers that generally harbour TP53 mutation. Further association was observed between elevated PLK1 levels and the major p53 negative regulator, MDM2.

CONCLUSIONS

The significant association between elevated PLK1 and TP53 mutation in women with breast cancer is consistent with escape from repression of PLK1 expression by mutant p53. Tumours expressing elevated PLK1, but lacking functional p53, may be potential targets for novel anti-PLK1-targeted drugs.

High frequency of complex TP53 mutations in CNS metastases from breast cancer

Background:

Brain metastasis from breast cancer is usually associated with a poor prognosis and early death. Alteration of p53 may contribute to malignant progression by abrogation of apoptosis induced by oncogene activation and by acquisition of gain-of-function properties, which promote tumour aggression. Mutation in TP53 occurs at high frequency in carcinomas of the lung and gastro-intestinal tract, but is much less frequent, at 25%, in primary breast cancer. The frequency of TP53 alteration in the central nervous system (CNS) metastatic breast cancer is not known.

Methods:

In all, 23 cases of histologically confirmed CNS metastatic breast cancer were identified and the coding sequence of TP53 determined. TP53 was also sequenced in two control series of primary breast carcinomas from independent clinical centres.

Results:

We demonstrate a strikingly high frequency of TP53 mutation in the CNS metastatic lesions with an over-representation of complex mutations (non-sense/deletions/insertions). Complex mutations occur in metastatic lesions in both triple-negative breast cancer and hormone receptor/HER2-positive cases. Analysis of paired primary carcinomas and brain metastatic lesions revealed evidence for both clonal selection and generation of new mutations (missense and complex) in progression from a primary breast carcinoma to brain metastasis.

Conclusion:

Mutation in TP53 is the most common genetic alteration reported during metastasis to the brain in breast cancer.

P4-02-06: Progesterone Receptor Expression Predicts Poor Outcome in Estrogen Receptor Positive, Lymph Node Negative Breast Cancer – A Population Based Study

Background: Estrogen receptor (ER) positive, lymph node (LN) negative breast cancer usually carries a good prognosis; endocrine therapy is often the only adjuvant treatment. However, a small proportion of such patients do badly (possibly representing those with luminal B cancers identified by gene expression profiling). A clinically applicable method for identifying this subgroup of poor prognosis ER+, LN- patients is required to offer them more intensive adjuvant therapy.

Material and methods: A consecutive, unselected series of 1072 new, operable breast cancer patients diagnosed between 2000 and 2004 was studied for ER and progesterone receptor (PR) expression, HER2 status and standard pathological and demographic parameters. ER and PR expression were scored on immunohistochemistry (IHC) on preoperative, diagnostic core biopsies using the “Quickscore” method. This ensured optimal fixation and tissue processing avoiding the variable fixation of resection specimens and the well-described sampling error of tissue micro-array (TMA) methodologies. PR expression is frequently heterogeneous resulting in false negative scores in at least 12% of cases by TMA analysis. HER2 status was assessed using IHC with dual color FISH for cases scoring 2+. Adjuvant therapy was prescribed using standard protocols; all patients with ER+ disease received adjuvant endocrine therapy. Follow up data were obtained from the oncology database, and the registrar of deaths for the date and cause of death. All deaths not attributable to breast cancer were censored at the date of death. Accordingly, the primary end-point was breast cancer-specific overall survival. Survival analysis was carried out by Kaplan-Meier survival curves analysed by the Log-Rank test. Multivariate analysis was carried out using Cox's regression.

Results: Overall, PR- cancers had a worse prognosis than PR+ (p&lt;10−12, Hazard Ratio 3.40), even in the ER+ (p=0.006, HR 1.86), LN- (p=10−8, HR=5.33) and LN+ (p=10−11, HR=3.26) sub-groups. In the ER+ LN- group, the absence of PR expression predicted worse prognosis (88% vs 96% 8 year survival, p=0.0003) with a hazard ratio of 3.75. This is considerably more significant than Ki67 IHC scoring reported for a similar group of patients in other studies (HR 2.22). Multivariate analysis demonstrated that PR expression was an independent prognostic variable second only to LN status and more powerful than ER.

Discussion: Patients with ER+, LN-, PR- breast cancers have a significantly worse prognosis than those with ER+, LN-, PR+ cancers. Unlike Ki67, PR IHC uses a simple, cost effective, standard methodology (as for ER) and should identify patients who may require chemotherapy in addition to endocrine therapy in this group of otherwise good prognosis patients.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P4-02-06.

FGFR2 protein expression in breast cancer: nuclear localisation and correlation with patient genotype

BACKGROUND

Single Nucleotide Polymorphisms (SNPs) in intron 2 of the Fibroblast Growth Factor Receptor Type 2 (FGFR2) gene, including rs2981582, contribute to multifactorial breast cancer susceptibility. The high risk polymorphism haplotype in the FGFR2 gene has been associated with increased mRNA transcription and altered transcription factor binding but the effect on FGFR2 protein expression is unknown. 40 breast tumours were identified from individuals with known rs2981582 genotype. Tumour sections were stained for FGFR2 protein expression, and scored for nuclear and cytoplasmic staining in tumour and surrounding normal tissue.

FINDINGS

FGFR2 immunohistochemistry demonstrated variable nuclear staining in normal tissue and tumour tissue, as well as consistent cytoplasmic staining. We did not find an association between nuclear staining for FGFR2 and genotype, and there was no association between FGFR2 staining and estrogen or progestogen receptor status. There was an association between presence of nuclear staining for FGFR2 in normal tissue and presence of nuclear staining in the adjacent tumour (Fishers exact test, p = 0.002).

CONCLUSIONS

Variable nuclear staining for FGFR2 in breast cancer, but an absence of correlation with rs2981582 genotype suggests that the mechanism of action of polymorphisms at the FGFR2 locus may be more complex than a direct effect on mRNA expression levels in the final cancer. The effect may relate to FGFR2 function or localisation during breast development or tumourigenesis. Nuclear localisation of FGFR2 suggests an important additional role for this protein in breast development and breast cancer, in addition to its function as a classical cell surface receptor.

p53 mutant breast cancer patients expressing p53γ have as good a prognosis as wild-type p53 breast cancer patients

INTRODUCTION

Normal function of the p53 network is lost in most cancers, often through p53 mutation. The clinical impact of p53 mutations in breast cancer remains uncertain, especially where p53 isoforms may modify the effects of these p53 mutations.

METHODS

Expression of p53β and p53γ isoforms, the isoforms identified in normal breast tissue, was detected by reverse transcription polymerase chain reaction from a cohort of 127 primary breast tumours. Expression of p53β and p53γ isoforms was analysed in relation to clinical markers and clinical outcomes (5 years) by binary logistic regression, Cox proportional hazards regression and Kaplan-Meier survival analyses.

RESULTS

p53β and p53γ were not randomly expressed in breast cancer. p53β was associated with tumour oestrogen receptor (ER) expression, and p53γ was associated with mutation of the p53 gene. The patient group with the mutant p53 breast tumour-expressing p53γ isoform had low cancer recurrence and an overall survival as good as that of patients with wild-type p53 breast cancer. Conversely, patients expressing only mutant p53, without p53γ isoform expression, had a particularly poor prognosis.

CONCLUSIONS

The determination of p53γ expression may allow the identification, independently of the ER status, of two subpopulations of mutant p53 breast cancer patients, one expressing p53γ with a prognosis as good as the wild-type p53 breast cancer patients and a second one not expressing p53γ with a particularly poor prognosis. The p53γ isoform may provide an explanation of the hitherto inconsistent relationship between p53 mutation, treatment response and outcome in breast cancer.

Differential contextual responses of normal human breast epithelium to ionizing radiation in a mouse xenograft model

Radiotherapy is a key treatment option for breast cancer, yet the molecular responses of normal human breast epithelial cells to ionizing radiation are unclear. A murine subcutaneous xenograft model was developed in which nonneoplastic human breast tissue was maintained with the preservation of normal tissue architecture, allowing us to study for the first time the radiation response of normal human breast tissue in situ. Ionizing radiation induced dose-dependent p53 stabilization and p53 phosphorylation, together with the induction of p21(CDKN1A) and apoptosis of normal breast epithelium. Although p53 was stabilized in both luminal and basal cells, induction of Ser392-phosphorylated p53 and p21 was higher in basal cells and varied along the length of the ductal system. Basal breast epithelial cells expressed ΔNp63, which was unchanged on irradiation. Although stromal responses themselves were minimal, the response of normal breast epithelium to ionizing radiation differed according to the stromal setting. We also demonstrated a dose-dependent induction of γ-H2AX foci in epithelial cells that was similarly dependent on the stromal environment and differed between basal and luminal epithelial cells. The intrinsic differences between human mammary cell types in response to in vivo irradiation are consistent with clinical observation that therapeutic ionizing radiation is associated with the development of basal-type breast carcinomas. Furthermore, there may be clinically important stromal-epithelial interactions that influence DNA damage responses in the normal breast. These findings demonstrate highly complex responses of normal human breast epithelium following ionizing radiation exposure and emphasize the importance of studying whole-tissue effects rather than single-cell systems.

Prospective comparison of switches in biomarker status between primary and recurrent breast cancer: the Breast Recurrence In Tissues Study (BRITS)

Introduction

Immunohistochemistry of primary breast cancer is routinely used to guide changes in therapy at the time of relapse. Retrospective reviews suggest that the estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor type 2 (HER2) receptor may differ between the primary and loco-regional recurrence or distant metastases. The Breast Recurrence In Tissues Study (BRITS) was a large, multicentre, prospective study to examine changes in ER, PR and HER2.

Methods

Matched primary and recurrent breast cancer tissue samples were prospectively collected from 205 women attending 20 institutions. Central laboratory immunohistochemical analysis of core biopsies and tissue microarrays of ER and PR using the Allred and Quickscore methods and HER2 (confirmed by fluorescence in situ hybridisation (FISH) for HER2 2+) were performed.

Results

From 205 consenting women, 18 (8.8%) did not have recurrent disease on biopsy, 35 were ineligible, 13 had insufficient paired tissue and 2 were excluded for safety reasons. Paired samples from 137 women, mean age 62.6 years (range 27-87 years), 83/137 (60.6%) postmenopausal with a median 92.2 months (range 5-327 months) from primary to recurrence and 88 (64.2%) as locoregional recurrence were successfully analysed. A switch in receptor status, in either direction, by Allred score, was identified for ER in 14 patients (10.2%; P = 0.983 Wilcoxon sign rank test), PR in 34 (24.8%; P = 0.003 Wilcoxon sign rank test) and HER2 in 4 (2.9%; P = 0.074 Wilcoxon sign rank test). There was no difference between locoregional or distant recurrence in the proportion who switched. The switch in receptor status led to a change in the subsequent treatment plan for 24 patients (17.5%).

Conclusions

This prospective study confirms retrospective evidence that the management of relapsed breast cancer should include confirmatory tissue sampling and identify switches of ER, PR or HER2 which change therapeutic management for one in six patients.

Comprehensive CYP2D6 genotype and adherence affect outcome in breast cancer patients treated with tamoxifen monotherapy

The association between CYP2D6 genotype and outcome in breast cancer patients treated with adjuvant tamoxifen remains controversial. We assessed the influence of comprehensive versus limited CYP2D6 genotype in the context of tamoxifen adherence and co-medication in a large cohort of 618 patients. Genotyping of 33 CYP2D6 alleles used two archival cohorts from tamoxifen-treated women with invasive breast cancer (Dundee, n = 391; Manchester, n = 227). Estimates for recurrence-free survival (RFS) were calculated based on inferred CYP2D6 phenotypes using Kaplan-Meier and Cox proportional hazard models, adjusted for nodal status and tumour size. Patients with at least one reduced function CYP2D6 allele (60%) or no functional alleles (6%) had a non-significant trend for worse RFS: hazard ratio (HR) 1.52 (CI 0.98-2.36, P = 0.06). For post-menopausal women on tamoxifen monotherapy, the HR for recurrence in patients with reduced functional alleles was 1.96 (CI 1.05-3.66, P = 0.036). However, RFS analysis limited to four common CYP2D6 allelic variants was no longer significant (P = 0.39). The effect of CYP2D6 genotype was increased by adjusting for adherence to tamoxifen therapy, but not significantly changed when adjusted for co-administration of potent inhibitors of CYP2D6. Comprehensive genotyping of CYP2D6 and adherence to tamoxifen therapy may be useful to identify breast cancer patients most likely to benefit from adjuvant tamoxifen.

Increased mortality in HER2 positive, oestrogen receptor positive invasive breast cancer: a population-based study

BACKGROUND

This study assessed the impact of human epidermal growth factor receptor 2 (HER2) status on the outcomes in an unselected population of breast cancer patients who did not receive HER2-targeted therapy.

METHODS

HER2 status by immunohistochemistry and fluorescence in situ hybridisation was compared with clinicopathological data, overall survival (OS) and disease-free survival (DFS) for all patients presenting with breast cancer over 3 years.

RESULTS

In 865 patients (median follow up 6.02 years), HER2 positivity was identified in 13.3% of all cancers and was associated with higher tumour grade (P<10(-8)), lymphovascular invasion (P<0.001) and axillary nodal metastasis (P=0.003). There was a negative association with oestrogen-receptor (ER) and progesterone-receptor expression (P<10(-8)), but the majority (57%) of HER2+tumours were ER+HER2 positivity was associated with poorer OS (P=0.0046) and DFS (P=0.0001) confined to the lymph node-positive (LN+) and ER+ subgroups.

CONCLUSION

HER2-positive cancers were less common in this population-based cohort than most selected series. The association of HER2 positivity with poor prognosis was confined to the ER+ and LN+ subgroups. The survival deficit for the 7.5% of patients with ER+/HER2+ cancer compared with ER+/HER2- patients points to a significant subgroup of women who may not (currently) be considered for HER2-directed therapy.

High CCND1 amplification identifies a group of poor prognosis women with estrogen receptor positive breast cancer

CCND1 encodes for the cyclin D1 protein involved in G1/S cell cycle transition. In breast cancer the mechanism of CCND1 amplification, relationship between cyclin D1 protein expression and the key clinical markers estrogen receptor (ER) and HER2 requires elucidation. Tissue microarrays of primary invasive breast cancer from 93 women were evaluated for CCND1 amplification by fluorescent in-situ hybridization and cyclin D1 protein overexpression by immunohistochemistry. CCND1 amplification was identified in 27/93 (30%) cancers and 59/93 (63%) cancers had overexpression of cyclin D1. CCND1 amplification was significantly associated with cyclin D1 protein overexpression (p < 0.001; Fisher's exact test) and both CCND1 amplification and cyclin D1 protein expression with oestrogen receptor (ER) expression (p = 0.003 and p < 0.001; Fishers exact test). Neither CCND1 amplification nor cyclinD1 expression was associated with tumor size, pathological node status or HER2 amplification, but high CCND1 amplification (Copy Number Gain (CNG) > or = 8) was associated with high tumor grade (p = 0.005; chi square 7.915, 2 df) and worse prognosis by Nottingham Prognostic Index (p = 0.001; 2 sample t-test). High CCND1 amplification (CNG > or = 8) may identify a subset of patients with poor prognosis ER-positive breast cancers who should be considered for additional therapy.