PROACTING: predicting pathological complete response to neoadjuvant chemotherapy in breast cancer from routine diagnostic histopathology biopsies with deep learning

BACKGROUND

Invasive breast cancer patients are increasingly being treated with neoadjuvant chemotherapy; however, only a fraction of the patients respond to it completely. To prevent overtreatment, there is an urgent need for biomarkers to predict treatment response before administering the therapy.

METHODS

In this retrospective study, we developed hypothesis-driven interpretable biomarkers based on deep learning, to predict the pathological complete response (pCR, i.e., the absence of tumor cells in the surgical resection specimens) to neoadjuvant chemotherapy solely using digital pathology H&E images of pre-treatment breast biopsies. Our approach consists of two steps: First, we use deep learning to characterize aspects of the tumor micro-environment by detecting mitoses and segmenting tissue into several morphology compartments including tumor, lymphocytes and stroma. Second, we derive computational biomarkers from the segmentation and detection output to encode slide-level relationships of components of the tumor microenvironment, such as tumor and mitoses, stroma, and tumor infiltrating lymphocytes (TILs).

RESULTS

We developed and evaluated our method on slides from n = 721 patients from three European medical centers with triple-negative and Luminal B breast cancers and performed external independent validation on n = 126 patients from a public dataset. We report the predictive value of the investigated biomarkers for predicting pCR with areas under the receiver operating characteristic curve between 0.66 and 0.88 across the tested cohorts.

CONCLUSION

The proposed computational biomarkers predict pCR, but will require more evaluation and finetuning for clinical application. Our results further corroborate the potential role of deep learning to automate TILs quantification, and their predictive value in breast cancer neoadjuvant treatment planning, along with automated mitoses quantification. We made our method publicly available to extract segmentation-based biomarkers for research purposes.

High-dose alkylating chemotherapy in BRCA-altered triple-negative breast cancer: the randomized phase III NeoTN trial

Exploratory analyses of high-dose alkylating chemotherapy trials have suggested that BRCA1 or BRCA2-pathway altered (BRCA-altered) breast cancer might be particularly sensitive to this type of treatment. In this study, patients with BRCA-altered tumors who had received three initial courses of dose-dense doxorubicin and cyclophosphamide (ddAC), were randomized between a fourth ddAC course followed by high-dose carboplatin-thiotepa-cyclophosphamide or conventional chemotherapy (initially ddAC only or ddAC-capecitabine/decetaxel [CD] depending on MRI response, after amendment ddAC-carboplatin/paclitaxel [CP] for everyone). The primary endpoint was the neoadjuvant response index (NRI). Secondary endpoints included recurrence-free survival (RFS) and overall survival (OS). In total, 122 patients were randomized. No difference in NRI-score distribution (p = 0.41) was found. A statistically non-significant RFS difference was found (HR 0.54; 95% CI 0.23-1.25; p = 0.15). Exploratory RFS analyses showed benefit in stage III (n = 35; HR 0.16; 95% CI 0.03-0.75), but not stage II (n = 86; HR 1.00; 95% CI 0.30-3.30) patients. For stage III, 4-year RFS was 46% (95% CI 24-87%), 71% (95% CI 48-100%) and 88% (95% CI 74-100%), for ddAC/ddAC-CD, ddAC-CP and high-dose chemotherapy, respectively. No significant differences were found between high-dose and conventional chemotherapy in stage II-III, triple-negative, BRCA-altered breast cancer patients. Further research is needed to establish if there are patients with stage III, triple negative BRCA-altered breast cancer for whom outcomes can be improved with high-dose alkylating chemotherapy or whether the current standard neoadjuvant therapy including carboplatin and an immune checkpoint inhibitor is sufficient. Trial Registration: NCT01057069.

A living biobank of patient-derived ductal carcinoma in situ mouse-intraductal xenografts identifies risk factors for invasive progression

Ductal carcinoma in situ (DCIS) is a non-obligate precursor of invasive breast cancer (IBC). Due to a lack of biomarkers able to distinguish high- from low-risk cases, DCIS is treated similar to early IBC even though the minority of untreated cases eventually become invasive. Here, we characterized 115 patient-derived mouse-intraductal (MIND) DCIS models reflecting the full spectrum of DCIS observed in patients. Utilizing the possibility to follow the natural progression of DCIS combined with omics and imaging data, we reveal multiple prognostic factors for high-risk DCIS including high grade, HER2 amplification, expansive 3D growth, and high burden of copy number aberrations. In addition, sequential transplantation of xenografts showed minimal phenotypic and genotypic changes over time, indicating that invasive behavior is an intrinsic phenotype of DCIS and supporting a multiclonal evolution model. Moreover, this study provides a collection of 19 distributable DCIS-MIND models spanning all molecular subtypes.

Tumour-educated platelets for breast cancer detection: biological and technical insights

BACKGROUND

Studies have shown that blood platelets contain tumour-specific mRNA profiles tumour-educated platelets (TEPs). Here, we aim to train a TEP-based breast cancer detection classifier.

METHODS

Platelet mRNA was sequenced from 266 women with stage I-IV breast cancer and 212 female controls from 6 hospitals. A particle swarm optimised support vector machine (PSO-SVM) and an elastic net-based classifier (EN) were trained on 71% of the study population. Classifier performance was evaluated in the remainder (29%) of the population, followed by validation in an independent set (37 cases and 36 controls). Potential confounding was assessed in post hoc analyses.

RESULTS

Both classifiers reached an area under the curve (AUC) of 0.85 upon internal validation. Reproducibility in the independent validation set was poor with an AUC of 0.55 and 0.54 for the PSO-SVM and EN classifier, respectively. Post hoc analyses indicated that 19% of the variance in gene expression was associated with hospital. Genes related to platelet activity were differentially expressed between hospitals.

CONCLUSIONS

We could not validate two TEP-based breast cancer classifiers in an independent validation cohort. The TEP protocol is sensitive to within-protocol variation and revision might be necessary before TEPs can be reconsidered for breast cancer detection.

Abstract PR006: A living biobank of patient-derived ductal carcinoma in situ (DCIS) Mouse-INtraDuctal (MIND) xenografts identifies multiple risk factors of invasive progression

Ductal Carcinoma in Situ (DCIS) is a non-invasive non-obligate precursor of invasive breast cancer (IBC). DCIS is usually treated by surgery combined with radiotherapy, which can have a large impact on the life of patients. However, many of these DCIS lesions would never progress into IBC. To reduce the overtreatment of DCIS, but assure proper treatment for high risk DCIS, it is crucial to understand the biology underlying DCIS. To study the biology of DCIS we established Mouse INtraDuctal (MIND) patient-derived xenograft (PDX) models by intraductally injecting patient DCIS material into the mammary ducts of female immunocompromised mice. We engrafted 130 samples, which have been incubated in vivo for a period of 12 months. We obtain a take rate of 88% with 46% of our models showing invasive progression. Histology and molecular subtyping by PAM50 classification are well preserved in the MIND models compared to the primary counterpart, ensuring that our MIND models represent the patient disease well. For 102 primary samples we obtained RNAseq profiles as well as for 64 matched MIND-PDX models. In addition whole exome-/panel sequencing data is generated from the same primary DCIS samples together with 12 matched MIND-PDX WES profiles as well as 60 matched Copy Number Variation (CNV) MIND-PDX profiles. Together these data revealed multiple biomarkers related to invasive progression, including factors such as high grade, solid growth, a high copy number aberrations burden, HER2, PTK6 & MYC amplifications and a high Ki67. On top of this we used whole mount imaging of the injected mammary glands extracted from our MIND-PDX models, showing two distinct growth patterns correlated with invasion. And as this is all done in the context of the PRECISION consortium this allows us to confirm and validate our findings in larger sequencing and imaging efforts of human samples. We have also successfully passaged 42 MIND-PDX models which showed minimal changes in pheno- and genotype over time indicating invasive behavior is an intrinsic phenotype of DCIS with minimal evolution, supporting a multiclonal evolution model. Moreover, this provided a collection of 19 stable sequentially transplantable DCIS MIND models including Luminal A, Luminal B, ER+/HER2+ and ER-/HER2+ models. Ultimately these models can be used to validate the biomarkers found to be related to invasive progression, as an example we proved the direct role of HER2 overexpression in invasive progression by inhibiting the HER2 receptor or by overexpressing HER2. In conclusion all this data together enabled us to create a well-characterized biobank of DCIS models with the unique opportunity to follow the natural progression, sequentially transplant 42 models, find genomic and transcriptomic profiles related to high risk DCIS and manipulate gene expression to validate the role of genes in DCIS progression.

Citation Format: Stefan J. Hutten, Roebi de Bruijn, Catrin Lutz, Madelon Badoux, Timo Eijkman, Xue Chao, Marta Ciwinska, Andrea Herencia-Ropero, Petra Kristel, Lennart Mulder, Joyce Sanders, Mathilde Almekinders, Alba Llop-Gueverra, Helen R. Davies, Fariba Behbod, Serena Nik-Zainal, Violeta Serra, Jacco van Rheenen, Esther H. Lips, Lodewyk F.A. Wessels, Jelle Wesseling, Colinda Scheele, Jos Jonkers. A living biobank of patient-derived ductal carcinoma in situ (DCIS) Mouse-INtraDuctal (MIND) xenografts identifies multiple risk factors of invasive progression [abstract]. In: Proceedings of the AACR Special Conference on Rethinking DCIS: An Opportunity for Prevention?; 2022 Sep 8-11; Philadelphia, PA. Philadelphia (PA): AACR; Can Prev Res 2022;15(12 Suppl_1): Abstract nr PR006.

Abstract A016: Identification of methylated regions in ductal carcinoma in situ and association with disease progression

Background: The advent of breast screening has led to a 4-fold increase in the diagnosis of ductal carcinoma in situ (DCIS). Studies following the clinical outcomes of patients show variable progression free survival rates, with only up to 35% of patients progressing to invasive disease without treatment. This highlights the need to find a biomarker to accurately predict which DCIS lesions will recur as invasive tumors. Epigenetics changes are events which occur early in tumorigenesis, this makes DNA methylation a potential biomarker of DCIS progression. However, a lack of DCIS methylation profiling with long term follow-up data exists. This study investigates genome-wide methylation profiles in women with primary DCIS and associates the data with their overall recurrence free survival. Methods: DCIS was macrodissected from 89 formalin-fixed paraffin embedded (FFPE) to extract tumor enriched DNA from patients with DCIS and long term follow up. 39 women had developed an ipsilateral invasive recurrence (classified as cases) and 50 had no evidence of recurrent disease (classified as controls). Genome wide methylation was assessed using the human methylation EPIC BeadChip which, interrogates over 850,000 methylation sites. Data was assessed for quality both at the sample and probe level by the wateRmelon. Further analysis was performed in ChAMP to identify differentially methylated regions (DMR) and by DMRcate packages in R to identify variably methylated regions (VMR). Genes annotated in the most significant VMRs were analysed through Metascape, a web-based tool to perform functional gene set enrichment analysis (GSEA). A cox proportional hazards model was used to calculate the association between the methylation of the VMRs and recurrence free survival. This model was adjusted for DCIS receptor status and grade. Results: 59 samples passed data quality assessment (35 controls and 24 cases). 10 differentially methylated regions were identified. The most significant of which, was a hypomethylated region on chromosome 4, containing CDKL2 (p = 0.001), known to promote the epithelial-mesenchymal transition in breast cancer progression. 5813 VMRs were identified across the genome, (P-value range between 0 and 10-321). 82% of the VMRs aligned to the body of the gene or the surrounding regulatory features. GSEA revealed that VMRs were predominantly involved in pathways involved in cell adhesion (GO:0007156) Assessment of the significant VMRs by COX proportional hazards model showed that a VMR on chromosome 6p was associated with the development of invasive disease after adjusting for oestrogen receptor, human epidermal growth factor 2 status and grade (p=0.001). Conclusions: This preliminary study shows altered sites of methylation could be observed across the genome, in DCIS. The function of the VMRs is currently being investigated to understand how methylation in this region predisposes to invasive recurrence of DCIS. Correlation of methylation status and RNA expression data will be used to understand the biological relevance.

Citation Format: Vandna Shah, Maria Roman-Escorza, Karen Clements Clements, Lennart Mulder, Esther H. Lips, Jelle Wesseling, Sarah Pinder, Alastair M. Thompson, Elinor J. Sawyer. Identification of methylated regions in ductal carcinoma in situ and association with disease progression [abstract]. In: Proceedings of the AACR Special Conference on Rethinking DCIS: An Opportunity for Prevention?; 2022 Sep 8-11; Philadelphia, PA. Philadelphia (PA): AACR; Can Prev Res 2022;15(12 Suppl_1): Abstract nr A016.

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.

Structured Solicitation: A Standardized Method for Gaining Travel Information

Travelers must be able to obtain locational information if they are to travel successfully to unfamiliar places. Three subjectives were asked to call a number of businesses to pinpoint their location. After establishing a baseline rate, the subjects were introduced to a structured solicitation procedure, which consisted of asking seven specific questions in a particular order. The completeness of information obtained increased dramatically with the use of this procedure.

Abstract 751: Ductal carcinoma in situ of the breast: Cancer precursor or not

Background. Ductal carcinoma in situ (DCIS) is a potential precursor of invasive breast cancer (IBC). However, the natural course of a particular DCIS lesion is unknown, because almost all women with DCIS are treated. Furthermore, most studies are biased because these comprise DCIS adjacent to IBC, also known as synchronous DCIS and IBC, indicating that such DCIS lesions already have the capacity to progress to IBC. It is still unknown which proportion and type of subsequent ipsilateral IBCs (iIBC) are related to the initial primary “pure” DCIS lesion. Therefore, we performed an extensive molecular characterization of DCIS and matched subsequent iIBC, to better understand the natural course of DCIS.

Patients and methods. We used a unique series of 78 women diagnosed with DCIS and treated by breast conserving surgery (BCS) alone, which subsequently developed iIBC. Mean time to iIBC event was 6.3 years (range 0.5-17.0). These 78 women are a representative sample of a case-control series, nested in a nation-wide, population-based cohort including all patients diagnosed with DCIS between 1989 and 2005 in the Netherlands (Visser, et al Clin Can Res 2018). Data on tumor location (ICD-10) was available for all lesions. DNA and RNA was simultaneously extracted for 78 DCIS lesions and 78 matched subsequent iIBC (DNA >20ng; RNA >100ng), and RNA sequencing (RNAseq) and low coverage whole genome sequencing (CNVseq) was performed. Panel sequencing (PanelSeq), using a custom panel of 53 breast cancer driver genes, was performed with the remaining DNA of 42 DCIS and iIBC matched pairs. We determined if the iIBC lesion and DCIS lesion were related, by comparing tumor location and genomic features.

Results. Based on tumor location and histological grade, >95% of the subsequent iIBC reflected outgrowth of residual disease. Based on RNAseq data, 77% of all DCIS and IBC lesions classified into the same PAM50 subtypes. The CNVseq data showed that the DCIS lesions contained copy number aberrations on typical breast cancer-associated loci, such as 1q gain, 8q gain, 16q loss, 20q gain. However, when we compared DCIS with their matched iIBC, we observed in 41% of the cases very distinct copy number profiles, indicating either outgrow of a different tumor (minority) subclone or a second primary tumor. Analysis of PanelSeq mutation data supported this clonal or independent origin of the subsequent iIBC.

Conclusion. To our knowledge, our study is the first to investigate if subsequent iIBC is likely to originate from the initial primary “pure” DCIS in a large series with long-term follow-up.

Surprisingly, our CNVseq and PanelSeq results indicate that more than one third of the subsequent iIBCs after BCS alone treated primary DCIS are likely to be second primary tumors or represent selective outgrowth of a minority DCIS subclone.

Citation Format: Lindy Visser, Marlous Hoogstraat, Tycho Bismeijer, Lotte Elshof, Koen van de Vijver, Emilie Groen, Mathilde Almekinders, Joyce Sanders, Carolien Bierman, Dennis Peters, Ingrid Hofland, Frank Nieboer, Michiel de Maaker, Petra Kristel, Lennart Mulder, Annegien Broeks, Michael Schaapveld, Marjanka Schmidt, Lodewyk Wessels, Esther Lips, Jelle Wesseling, On behalf of the PRECISION team. Ductal carcinoma in situ of the breast: Cancer precursor or not [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 751.

Abstract PD8-09: Approximately 40% of invasive recurrences after treatment of ductal carcinoma in situ is likely to be a second primary tumor

Background. Ductal carcinoma in situ (DCIS) is a potential precursor of invasive breast cancer, because: DCIS often accompanies invasive breast cancer; its risk factors are similar to those of invasive breast cancer; and genetic markers found in DCIS are similar to the ones found in invasive breast cancer. However, clinical behavior of DCIS is still poorly understood, as there is only limited information on its long-term natural history. Altogether, this makes it difficult to understand the relatedness of DCIS and its subsequent ipsilateral invasive breast cancer (iIBC). Here, we set-up a comparison between primary DCIS and matched subsequent iIBC, by making use of pathological and molecular data.

Patients and methods. For this study, we used a unique series of 155 DCIS cases which developed a subsequent iIBC during a median follow up period of 12.6 years. We assessed histological characteristics, tumor location, estrogen and progesterone receptor status, p16 expression, and HER2 and p53 overexpression. RNA sequencing and copy number sequencing was done on 78 DCIS lesions and 78 matched invasive breast cancer relapses. We determined if the iIBC lesion and DCIS lesion were related, with respect to tumor location, immunohistochemical (IHC) markers, and genomic features.

Results. Based on tumor location and histological grade, >95% of the subsequent invasive breast cancers reflected outgrowth of residual disease. HER2 was the only IHC marker that showed a significant difference in expression between DCIS and matched iIBC: 40% of the HER2 positive DCIS was followed by a HER2 negative invasive recurrence. In addition, RNAseq data was used to classify DCIS and IBC lesions into PAM50 subtypes. 77% of the DCIS IBC pair belonged to the same subtype. The DCIS lesions showed copy number aberrations on typical breast cancer-associated loci. However, when we compared the DCIS with its matched iIBC, we saw in 41% of the cases very distinct copy number profiles, indicating either outgrow of a different tumor subclone or a second primary.

Conclusion. This is the first time that a sound comparison could be made between primary DCIS and its subsequent invasive breast cancer with such a large patient group, integrating pathological and molecular data. Our results strongly suggest that many subsequent iIBCs after treatment of pure DCIS could be considered as second primary breast cancer lesions. To provide definite proof for this, in depth DNA sequencing and heterogeneity studies will be presented at SABCS 2018.

Citation Format: Visser LL, Hoogstraat M, Elshof LE, van de Vijver K, Groen EJ, Almekinders MM, Bierman C, Nieboer F, de Maaker M, Kristel P, Mulder L, Schaapveld M, Schmidt MK, Lips E, Wesseling J. Approximately 40% of invasive recurrences after treatment of ductal carcinoma in situ is likely to be a second primary tumor [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 PD8-09.

Evaluation of the EGFR polymorphism R497K in two cohorts of neoadjuvantly treated breast cancer patients

Pathological response of breast cancer to neoadjuvant chemotherapy (NAC) presents great variability, and new prognostic biomarkers are needed. Our aim was to evaluate the association of the epidermal growth factor receptor gene (EGFR) polymorphism R497K (rs2227983) with prognostic features and clinical outcomes of breast cancer, including the pathological response to NAC and the recurrence-free survival (RFS). Tumoral complete response (tCR) was defined by no remaining invasive cancer in the excised breast, whereas pathological complete response (pCR) was defined by no remaining invasive cancer both in the excised breast and lymph nodes. Two independent cohorts were analyzed: one from Brazil (INCA, n = 288) and one from The Netherlands (NKI-AVL, n = 255). In the INCA cohort, the variant (Lys-containing) genotypes were significantly associated with lower proportion of tCR (ORadj = 0.92; 95%CI = 0.85-0.99), whereas in the NKI-AVL cohort they were associated with tumor grade 3 (p = 0.035) and with triple-negative subtype (p = 0.032), but not with clinical outcomes. Such distinct prognostic associations may have arisen due to different neoadjuvant protocols (p < 0.001), or to lower age at diagnosis (p < 0.001) and higher proportion of tumor grade 3 (p = 0.018) at the NKI-AVL cohort. Moreover, NKI-AVL patients achieved better proportion of pCR (21.2% vs 8.3%, p < 0.001) and better RFS (HRadj = 0.48; 95% adjCI = 0.26-0.86) than patients from INCA. In conclusion, large scale studies comprehending different populations are needed to evaluate the impact of genome variants on breast cancer outcomes.

Abstract 1751: Systematic bias in genomic breast cancer classification due to selecting cases with high tumor percentage and good RNA quality

Background

Cancer classification, prognostication, and prediction of treatment sensitivity increasingly rely on DNA and RNA-based tests. This approach requires sufficiently high tumor cell percentages to yield enough DNA or RNA for reliable test results. As a consequence, samples of insufficient quality may drop out, e.g. due to poor cellularity or high numbers of tumor infiltrating lymphocytes. We hypothesized that requiring a high tumor cell percentage and high quality RNA causes systemic bias when interpreting genomic test results in breast cancer, as specific breast cancer subgroups may be over- or underrepresented.

Patients and methods

For this analysis, we used pre-treatment frozen samples from patients included in neoadjuvant chemotherapy trials at the Netherlands Cancer Institute between 2004 and 2012. Histological features and tumor cell percentage were reviewed and assessed by a consultant breast pathologist. Gene expression profiling was done if the tumor cell percentage exceeded 50% and RNA quantity (&gt;1 µg) and quality (RIN value≥ 6.5) were sufficient. We compared patient and tumor characteristics between patients in whom gene expression profiling could be performed and those in whom it could not be performed. In addition, we performed a systematic review on gene expression profiling for breast cancer, to assess the percentage of sample dropout in published studies.

Results

Frozen biopsies were available from 658 patients (79% of the total study population) and gene expression profiling could be performed in 60% of the cases, a percentage comparable to what is reported in the literature. Reasons for drop out were a low cellularity, poor quality and quantity of the RNA, or a too small biopsy for processing. These patients had more grade 3 tumors (43% versus 34%, p=0.04) and were more node positive (76% versus 69%, p=0.03). Analysis of neoadjuvant chemotherapy response and survival in these patients is ongoing and will be presented at the AACR Annual Meeting 2017.

Conclusion

Breast cancers for which gene expression data were successfully obtained were associated with a higher grade and with lymph node metastasis. Such tumors represent a more aggressive phenotype and have a relatively poor prognosis, compared to the patients for whom gene expression data could not be measured. As gene expression arrays are now broadly used in a clinical context, it is important to acknowledge this systematic bias, and to be cautious in applying gene expression based tests on different patient populations than a test was developed on.

Citation Format: Esther H. Lips, Antien L. Mooyaart, Maartje van Seijen, Lennart Mulder, Marlous Hoogstraat, Petra M. Nederlof, Lodewyk F. Wessels, Sjoerd Rodenhuis, Gabe S. Sonke, Jelle Wesseling. Systematic bias in genomic breast cancer classification due to selecting cases with high tumor percentage and good RNA quality [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1751. doi:10.1158/1538-7445.AM2017-1751

Abstract P4-12-03: Estrogen receptor-positive breast cancer in BRCA1 mutation carriers shows a BRCAness profile, suggesting sensitivity to drugs targeting homologous recombination deficiency

Background

As estrogen receptor (ER)-positive breast cancer in BRCA1 mutation carriers arises at an older age with less aggressive tumor characteristics than ER negative BRCA1 mutated breast cancer, it has been suggested that these tumors are 'sporadic' and not BRCA1-driven. With the introduction of targeted treatments specific for tumors with a non-functioning BRCA1 or BRCA2 gene, the question whether the BRCA genes are impaired in the tumor, is highly relevant. Therefore, we performed genomic profiling of BRCA1-mutated ER+ tumors.

Methods

Genomic profiling, BRCA1 promoter methylation assessment, and loss of heterozygosity (LOH) analysis were done on 16 BRCA1-mutated ER+ tumors. Results were compared with 57 BRCA1-mutated ER- tumors, 36 BRCA2-mutated ER+ associated tumors, and 182 sporadic ER+ tumors.

Results

The genomic profile of BRCA1-mutated ER+ tumors was different from BRCA1-mutated ER- breast tumors, but highly similar to BRCA2-mutated ER+ tumors. In 83% of the BRCA1-mutated ER+ tumors, loss of the wildtype BRCA1 allele was observed. Clinico-pathological variables in BRCA1-mutated ER+ cancer were more similar to BRCA2-mutated ER+ and sporadic ER+ breast cancer than to BRCA1 mutated ER- cancers.

Conclusions

As BRCA1-mutated ER+ tumors showed a BRCAness copy number profile and LOH, it is likely that the loss of a functional BRCA1 protein plays a role in tumorigenesis in BRCA1-mutated ER+ tumors. Therefore, we hypothesize that these tumors are sensitive to drugs targeting the BRCA1 gene defect.

Citation Format: Lips EH, Debipersad R, Scheerman E, Mulder L, Sonke GS, van der Kolk LE, Wessling J, Hogervorst FBL, Nederlof PM. Estrogen receptor-positive breast cancer in BRCA1 mutation carriers shows a BRCAness profile, suggesting sensitivity to drugs targeting homologous recombination deficiency [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 P4-12-03.

Abstract PD1-07: Comprehensive characterization of matched pre-treatment biopsies and residual disease of doxorubicin treated breast cancer

Background

Neoadjuvant chemotherapy is standard of care for locally advanced breast cancer. Unfortunately not all patients benefit from this treatment. Even after decades of research, we still cannot predict which tumor will or will not respond. This may in part be due to tumor heterogeneity, as the sample taken before treatment not necessarily represents the tumor cell population that causes therapy resistance.

Methods

To test this hypothesis, we collected pre-treatment biopsies, resection specimens, and matched blood from 21 breast cancer patients treated with doxorubicin and cyclophosphamide in a neoadjuvant setting. Specifically, tumors were selected with a tumor percentage &gt;50% after chemotherapy to enrich for resistant samples and ensure high quality data. RNA and whole exome sequencing were performed to characterize somatic mutations, copy number alterations and gene expression profiles. Histopathological characteristics were determined to obtain a comprehensive profile of all tumor samples.

Results

The comparisons of somatic variants and copy number alterations revealed a very diverse image: in several cases, high-level amplifications, large genomic gains or losses, and mutations in known oncogenes or tumor suppressors such as MAP3K1 and RUNX1 were either lost or gained during treatment, while in other cases no such changes were detected. We observed a remarkable number of genetic alterations involved in cell cycle progression and DNA damage checkpoints, including amplification of MDM2, CCND1 and CDK4, and copy number loss or mutations in CDKN1B and ATM. Strikingly, both cases of CDKN1B loss were identified in pre-treatment biopsies and no longer detectable in the surgery specimen. In contrast, CCND1, CDK4 and MDM2 amplifications were retained, although CCND1 expression decreased significantly in CCND1 amplified tumors.

In addition, eighty percent of tumors showed a decreased cell proliferation after chemotherapy, where the high-proliferative ER+ (Luminal B) tumors were most strongly affected. This trend was also visible in a validation cohort of 94 ER+ samples, but the prognosis of Luminal B tumors that showed a decrease in proliferation was still significantly worse than that of Luminal A tumors that did not show an altered proliferation rate.

Conclusion

Our results confirm that biologically relevant genomic alterations can differ between pre- and post-treatment samples, which greatly impacts biomarker discovery. In addition, our findings emphasize the chemotherapy insensitivity of CCND1 amplified ER+ breast cancers, and stress the need for better treatment regimens for these patients. In contrast, genomic loss of CDKN1B may be a marker for sensitivity to doxorubicin.

Citation Format: Lips EH, Hoogstraat M, Mulder L, Nederlof PM, Sonke GS, Rodenhuis S, Wesseling J, Wessels LFA. Comprehensive characterization of matched pre-treatment biopsies and residual disease of doxorubicin treated 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 PD1-07.

Structural and Mechanical Properties of Mandibular Condylar Bone

The trabecular bone of the mandibular condyle is structurally anisotropic and heterogeneous. We hypothesized that its apparent elastic moduli are also anisotropic and heterogeneous, and depend on trabecular density and orientation. Eleven condyles were scanned with a micro-CT system. Volumes of interest were selected for the construction of finite element models. We simulated compressive and shear tests to determine the principal mechanical directions and the apparent elastic moduli. Compressive moduli were relatively large in directions acting in the sagittal plane, and small in the mediolateral direction. The degree of mechanical anisotropy ranged from 4.7 to 10.8. Shear moduli were largest in the sagittal plane and smallest in the transverse plane. The magnitudes of the moduli varied with the condylar region and were proportional to the bone volume fraction. Furthermore, principal mechanical direction correlated significantly with principal structural direction. It was concluded that variation in trabecular structure coincides with variation in apparent mechanical properties.

BRCA1-Mutated Estrogen Receptor-Positive Breast Cancer Shows BRCAness, Suggesting Sensitivity to Drugs Targeting Homologous Recombination Deficiency

Purpose: As estrogen receptor-positive (ER⁺) breast cancer in BRCA1 mutation carriers arises at an older age with less aggressive tumor characteristics than ER-negative (ER^-) BRCA1-mutated breast cancer, it has been suggested that these tumors are "sporadic" and not BRCA1 driven. With the introduction of targeted treatments specific for tumors with a nonfunctioning BRCA1 or BRCA2 gene, the question whether the BRCA genes are impaired in the tumor is highly relevant. Therefore, we performed genomic profiling of BRCA1-mutated ER⁺ tumors.Experimental Design: Genomic profiling, BRCA1 promoter methylation assessment, and loss of heterozygosity analysis were done on 16 BRCA1-mutated ER⁺ tumors. Results were compared with 57 BRCA1-mutated ER^- tumors, 36 BRCA2-mutated ER⁺-associated tumors, and 182 sporadic ER⁺ tumors.Results: The genomic profile of BRCA1-mutated ER⁺ tumors was different from BRCA1-mutated ER^- breast tumors, but highly similar to BRCA2-mutated ER⁺ tumors. In 83% of the BRCA1-mutated ER⁺ tumors, loss of the wild-type BRCA1 allele was observed. In addition, clinicopathologic variables in BRCA1-mutated ER⁺ cancer were also more similar to BRCA2-mutated ER⁺ and sporadic ER⁺ breast cancer than to BRCA1-mutated ER^- cancers.Conclusions: As BRCA1-mutated ER⁺ tumors show a BRCAness copy number profile and LOH, it is likely that the loss of a functional BRCA1 protein plays a role in tumorigenesis in BRCA1-mutated ER⁺ tumors. Therefore, we hypothesize that these tumors are sensitive to drugs targeting the BRCA1 gene defect, providing new targeted treatment modalities for advanced BRCA-deficient, ER⁺ breast cancer. Clin Cancer Res; 23(5); 1236-41. ©2016 AACR.

Mechanisms of Therapy Resistance in Patient-Derived Xenograft Models of BRCA1-Deficient Breast Cancer

BACKGROUND

Although BRCA1-deficient tumors are extremely sensitive to DNA-damaging drugs and poly(ADP-ribose) polymerase (PARP) inhibitors, recurrences do occur and, consequently, resistance to therapy remains a serious clinical problem. To study the underlying mechanisms, we induced therapy resistance in patient-derived xenograft (PDX) models of BRCA1-mutated and BRCA1-methylated triple-negative breast cancer.

METHODS

A cohort of 75 mice carrying BRCA1-deficient breast PDX tumors was treated with cisplatin, melphalan, nimustine, or olaparib, and treatment sensitivity was determined. In tumors that acquired therapy resistance, BRCA1 expression was investigated using quantitative real-time polymerase chain reaction and immunoblotting. Next-generation sequencing, methylation-specific multiplex ligation-dependent probe amplification (MLPA) and Target Locus Amplification (TLA)-based sequencing were used to determine mechanisms of BRCA1 re-expression in therapy-resistant tumors.

RESULTS

BRCA1 protein was not detected in therapy-sensitive tumors but was found in 31 out of 42 resistant cases. Apart from previously described mechanisms involving BRCA1-intragenic deletions and loss of BRCA1 promoter hypermethylation, a novel resistance mechanism was identified in four out of seven BRCA1-methylated PDX tumors that re-expressed BRCA1 but retained BRCA1 promoter hypermethylation. In these tumors, we found de novo gene fusions that placed BRCA1 under the transcriptional control of a heterologous promoter, resulting in re-expression of BRCA1 and acquisition of therapy resistance.

CONCLUSIONS

In addition to previously described clinically relevant resistance mechanisms in BRCA1-deficient tumors, we describe a novel resistance mechanism in BRCA1-methylated PDX tumors involving de novo rearrangements at the BRCA1 locus, demonstrating that BRCA1-methylated breast cancers may acquire therapy resistance via both epigenetic and genetic mechanisms.

Next generation sequencing of triple negative breast cancer to find predictors for chemotherapy response

Introduction

In triple negative breast cancers (TNBC) the initial response to chemotherapy is often favorable, but relapse and chemotherapy resistance frequently occur in advanced disease. Hence there is an urgent need for targeted treatments in this breast cancer subtype. In the current study we deep sequenced DNA of tumors prior to chemotherapy to search for predictors of response or resistance.

Methods

Next generation sequencing (NGS) was performed for 1,977 genes involved in tumorigenesis. DNA from 56 pre-treatment TNBC-biopsies was sequenced, as well as matched normal DNA. Following their tumor biopsy, patients started neoadjuvant chemotherapy with doxorubicin and cyclophosphamide. We studied associations between genetic alterations and three clinical variables: chemotherapy response, relapse-free survival and BRCA proficiency.

Results

The mutations observed were diverse and few recurrent mutations were detected. Most mutations were in TP53, TTN, and PIK3CA (55 %, 14 %, and 9 %, respectively). The mutation rates were similar between responders and non-responders (average mutation rate 9 vs 8 mutations). No recurrent mutations were associated with chemotherapy response or relapse. Interestingly, PIK3CA mutations were exclusively observed in patients proficient for BRCA1. Samples with a relapse had a higher copy number alteration rate, and amplifications of TTK and TP53BP2 were associated with a poor chemotherapy response.

Conclusions

In this homogenous cohort of TNBCs few recurrent mutations were found. However, PIK3CA mutations were associated with BRCA proficiency, which can have clinical consequences in the near future.

Electronic supplementary material

The online version of this article (doi:10.1186/s13058-015-0642-8) contains supplementary material, which is available to authorized users.

Randomized clinical trial on the effect of a multispecies probiotic on visceroperception in hypersensitive IBS patients

BACKGROUND

Irritable bowel syndrome (IBS) is characterized by heterogeneous pathophysiology and low response to treatment. Up to 60% of IBS patients suffers from visceral hypersensitivity, which is associated with symptom severity and underlying pathophysiological mechanisms. Recently, positive effects of probiotics in IBS have been reported, but overall the response was modest. We performed a study in IBS patients, characterized by visceral hypersensitivity measured with the rectal barostat, aiming to assess the effect of 6 weeks of multispecies probiotic mix on visceral pain perception.

METHODS

We conducted a randomized, placebo-controlled, double-blind trial in forty Rome III IBS patients with visceral hypersensitivity. Prior to intake, patients kept a 2-week symptom diary and underwent a rectal barostat measurement. When hypersensitivity was confirmed, participation was allowed and patients received a multispecies probiotic with in vitro proven potential beneficial effects on mechanisms contributing to visceral hypersensitivity (six different probiotic strains; 10(9)  cfu/g), or a placebo product of one sachet (5 g) per day for 6 weeks. At the end of the intervention period, visceroperception and symptoms were reassessed.

KEY RESULTS

Thirty-five patients completed the trial. The percentage of patients with visceral hypersensitivity decreased significantly in the probiotic and placebo group (76.5% and 71.4%, respectively; N.S. between groups). Improvement in pain scores and mean symptom score did not differ between the probiotic and placebo group.

CONCLUSIONS & INFERENCES

In this placebo-controlled trial in IBS patients with visceral hypersensitivity, no significant effect of a multispecies probiotic on viscerperception was observed. The study has been registered in the US National Library of Medicine (http://www.clinicaltrials.gov, NCT00702026).

Contrast-enhanced microCT (EPIC-μCT) ex vivo applied to the mouse and human jaw joint

OBJECTIVES

The temporomandibular joint (TMJ) is susceptive to the development of osteoarthritis (OA). More detailed knowledge of its development is essential to improve our insight into TMJ-OA. It is imperative to have a standardized reliable three-dimensional (3D) imaging method that allows for detailed assessment of both bone and cartilage in healthy and diseased joints. We aimed to determine the applicability of a contrast-enhanced microCT (µCT) technique for ex vivo research of mouse and human TMJs.

METHODS

Equilibrium partitioning of an ionic contrast agent via µCT (EPIC-µCT) was previously applied for cartilage assessment in the knee joint. The method was ex vivo, applied to the mouse TMJ and adapted for the human TMJ.

RESULTS

EPIC-µCT (30-min immersion time) was applied to mouse mandibular condyles, and 3D imaging revealed an average cartilage thickness of 110 ± 16 µm. These measurements via EPIC-µCT were similar to the histomorphometric measures (113 ± 19 µm). For human healthy OA-affected TMJ samples, the protocol was adjusted to an immersion time of 1 h. 3D imaging revealed a significant thicker cartilage layer in joints with early signs of OA compared with healthy joints (414.2 ± 122.6 and 239.7 ± 50.5 µm, respectively). A subsequent significant thinner layer was found in human joints with late signs of OA (197.4 ± 159.7 µm).

CONCLUSIONS

The EPIC-µCT technique is effective for the ex vivo assessment of 3D cartilage morphology in the mouse as well as human TMJ and allows bone-cartilage interaction research in TMJ-OA.

Breast cancer subtyping by immunohistochemistry and histological grade outperforms breast cancer intrinsic subtypes in predicting neoadjuvant chemotherapy response

Intrinsic subtypes are widely accepted for the classification of breast cancer. Lacking gene expression data, surrogate classifications based on immunohistochemistry (IHC) have been proposed. A recent St. Gallen consensus meeting recommends to use this "surrogate intrinsic subtypes" for predicting adjuvant chemotherapy resistance, implying that "Surrogate Luminal A" breast cancers should only receive endocrine therapy. In this study we assessed both gene expression based intrinsic subtypes as well as surrogate intrinsic subtypes regarding their power to predict neoadjuvant chemotherapy benefit. Single institution data of 560 breast cancer patients were reviewed. Gene expression data was available for 247 patients. Subtypes were determined on the basis of IHC, Ki67, histological grade, endocrine responsiveness, and gene expression, and were correlated with chemotherapy response and recurrence-free survival. In ER+/HER2- tumors, a high histological grade was the best predictor for chemotherapy benefit, both in terms of pCR (p = 0.004) and recurrence-free survival (p = 0.002). The gene expression based and surrogate intrinsic subtype based on Ki67 had no predictive or prognostic value in ER+/HER2- tumors. Histological grade, ER, PR, and HER2 were the best predictive factors for chemotherapy response in breast cancer. We propose to continue the conventional use of these markers.

Next-generation sequencing to find predictors for chemotherapy response in triple-negative breast cancer (TNBC)

1010

Background: In TNBC initial response to chemotherapy is often favorable, but relapse and chemotherapy resistance frequently occur in advanced disease. Hence there is an urgent need for targeted treatments in this breast cancer subtype. Methods: To identify biomarkers of chemotherapy resistance and putative directed treatment targets, we performed next generation sequencing (NGS) of 2,000 genes implicated in oncogenesis. DNA from 31 pre-treatment biopsies and matched normal blood was sequenced. Biopsies were derived from patients scheduled to receive neoadjuvant chemotherapy with doxorubicin/cyclophosphamide. For the analysis, the tumors were divided in responders and non-responders, depending on whether or not a pathological complete remission (pCR) was achieved. Two definitions of pCR were employed: either the complete absence of infiltrating tumor cells in the breast (n=18) or a pCR of both the breast and lymph nodes (n=15). Tumors with partial or no responses were grouped in the non-responder category. Results: As a positive control, we verified that all patients with a known germline BRCA1 mutation (n=8) could be detected by the NGS analysis. In further analyses, we focused only on somatic mutations. Overall, the mutation rate was slightly higher in the non-responders (per tumor, average=12, range=[3-25]) than in the responders (average=8, range=[3-19]) (p=0.17). The analysis of individual genes did not reveal significant differences between responders and non-responders. However, pathway analysis showed that mutations in phosphatidylinositol signaling (e.g., PIK3CA, CALML5) were significantly more frequent in the non-responders, with mutations present in 10/13 non-responders and 2/18 responders (adjusted p=0.013). The chemokine and integrin signaling pathways also revealed a significantly higher mutation rate in the non-responders. Conclusions: Mutations in genes of the phosphatidylinositol pathway occur frequently in TNBCs that do not achieve a pCR on a neoadjuvant chemotherapy regimen consisting of doxorubicin and cyclophosphamide. After validation, alternative chemotherapy regimens and targeted agents should be investigated for these tumors.

Platform comparisons for identification of breast cancers with a BRCA-like copy number profile

Previously, we employed bacterial artificial chromosome (BAC) array comparative genomic hybridization (aCGH) profiles from BRCA1 and -2 mutation carriers and sporadic tumours to construct classifiers that identify tumour samples most likely to harbour BRCA1 and -2 mutations, designated 'BRCA1 and -2-like' tumours, respectively. The classifiers are used in clinical genetics to evaluate unclassified variants, and patients for which no good quality germline DNA is available. Furthermore, we have shown that breast cancer patients with BRCA-like tumour aCGH profiles benefit substantially from platinum-based chemotherapy, potentially due to their inability to repair DNA double strand breaks (DSB), providing a further important clinical application for the classifiers. The BAC array technology has been replaced with oligonucleotide arrays. To continue clinical use of existing classifiers, we mapped oligonucleotide aCGH data to the BAC domain, such that the oligonucleotide profiles can be employed as in the BAC classifier. We demonstrate that segmented profiles derived from oligonucleotide aCGH show high correlation with BAC aCGH profiles. Furthermore, we trained a support vector machine score to objectify aCGH profile quality. Using the mapped oligonucleotide aCGH data, we show equivalence in classification of biologically relevant cases between BAC and oligonucleotide data. Furthermore, the predicted benefit of DSB inducing chemotherapy due to a homologous recombination defect is retained. We conclude that oligonucleotide aCGH data can be mapped to and used in the previously developed and validated BAC aCGH classifiers. Our findings suggest that it is possible to map copy number data from any other technology in a similar way.

Abstract 1192: Triple negative breast cancer: BRCAness and concordance of clinical features and treatment response with BRCA1 mutation carriers

Introduction

Previous work from our group and other groups has shown that triple negative breast cancers (TNBC) frequently show BRCAness, the phenotype that some sporadic tumors share with BRCA-mutated cancers. We propose the use of a BRCA1-like genomic profile and of BRCA1 promoter methylation as indicators of BRCAness. In a randomized trial, tumors with this BRCA1-like profile responded more favorably to intensified alkylating chemotherapy. We now assessed the frequency of BRCAness in a large cohort of TNBCs. In addition, we determined the association with clinicopathological variables and treatment response.

Methods

A total of 388 TNBCs were included in this study. These were obtained from three different sources: a neoadjuvant chemotherapy trial (n=152), a series of patients from breast cancer families but without germline mutations (n=145), and a series of patients treated with adjuvant chemotherapy (n=91). Two assays for BRCAness were employed: array Comparative Genomic Hybridization (aCGH) to asses a BRCA1-like profile and methylation specific Multiplex Ligation-dependent Probe Amplification (MLPA) to determine BRCA1 promoter methylation. BRCA1 germline mutation status was known for half of the patients. Clinicopathological characteristics were available for most patients, and chemotherapy response data was available for the neoadjuvant series.

Results

In the three series, 66% to 69% of the tumors had an aCGH BRCA1-like profile and 27% to 37% showed BRCA1 promoter methylation. 87% of the tumors with promoter methylation showed a BRCA1-like aCGH profile. A germline mutation in BRCA1 and somatic BRCA1 promoter methylation did not occut together (n=155; p = 10-6). Patients with aCGH BRCA1-like or BRCA1 methylated tumors were younger than patients with non-BRCA1-like or unmethylated tumors (p=0.02 and p&lt;0.01, respectively). BRCA1 mutated tumors and aCGH BRCA1-like tumors were more often of histological grade 3 (97% vs. 74% (p&lt;0.01) for BRCA1-mutated vs. BRCA1 wildtype and 86% vs 67% (p&lt;0.01) for aCGH BRCA1-like vs. non-BRCA1-like tumors). BRCA1-mutated tumors had a higher response rate to neoadjuvant chemotherapy than BRCA1 wildtype tumors (71% vs. 37% (p=0.04) pathological complete remission rate). For aCGH BRCA1-like and BRCA1 methylated tumors, a non-significant trend for a better chemtherapy response was observed.

Conclusion

The majority of the TNBCs in this study show signs of BRCAness, and these tumors share clinicopathological characteristics with BRCA1 mutated tumors. Somatic BRCA1 promoter methylation and BRCA1 germline mutations are mutually exclusive events. A better characterization of TNBC and the presence of BRCAness will not only have consequences for treatment, but also for hereditary breast cancer screening.

Citation Format: Esther H. Lips, Lennart Mulder, Lizet E. van der Kolk, Anne M.M. Oonk, Alex L.T. Imholz, Frans B.L. Hogervorst, Jelle Wesseling, Sjoerd Rodenhuis, Petra M. Nederlof. Triple negative breast cancer: BRCAness and concordance of clinical features and treatment response with BRCA1 mutation carriers. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1192. doi:10.1158/1538-7445.AM2013-1192

Triple-negative breast cancer: BRCAness and concordance of clinical features with BRCA1-mutation carriers

Background:

BRCAness is defined as shared tumour characteristics between sporadic and BRCA-mutated cancers. However, how to exactly measure BRCAness and its frequency in breast cancer is not known. Assays to establish BRCAness would be extremely valuable for the clinical management of these tumours. We assessed BRCAness characteristics frequencies in a large cohort of triple-negative breast cancers (TNBCs).

Methods:

As a measure of BRCAness, we determined a specific BRCA1-like pattern by array Comparative Genomic Hybridisation (aCGH), and BRCA1 promoter methylation in 377 TNBCs, obtained from 3 different patient cohorts. Clinicopathological data were available for all tumours, BRCA1-germline mutation status and chemotherapy response data were available for a subset.

Results:

Of the tumours, 66–69% had a BRCA1-like aCGH profile and 27–37% showed BRCA1 promoter methylation. BRCA1-germline mutations and BRCA1 promoter methylation were mutually exclusive events (P=1 × 10⁻⁵). BRCAness was associated with younger age and grade 3 tumours. Chemotherapy response was significantly higher in BRCA1-mutated tumours, but not in tumours with BRCAness (63% (12 out of 19) vs 35% (18 out of 52) pathological complete remission rate, respectively).

Conclusion:

The majority of the TNBCs show BRCAness, and those tumours share clinicopathological characteristics with BRCA1-mutated tumours. A better characterisation of TNBC and the presence of BRCAness could have consequences for both hereditary breast cancer screening and the treatment of these tumours.

SERPINA6, BEX1, AGTR1, SLC26A3, and LAPTM4B are markers of resistance to neoadjuvant chemotherapy in HER2-negative breast cancer

Response rates to chemotherapy remain highly variable in breast cancer patients. We set out to identify genes associated with chemotherapy resistance. We analyzed what is currently the largest single-institute set of gene expression profiles derived from breast cancers prior to a single neoadjuvant chemotherapy regimen (dose-dense doxorubicin and cyclophosphamide). We collected, gene expression-profiled, and analyzed 178 HER2-negative breast tumor biopsies ("NKI dataset"). We employed a recently developed approach for detecting imbalanced differential signal (DIDS) to identify markers of resistance to treatment. In contrast to traditional methods, DIDS is able to identify markers that show aberrant expression in only a small subgroup of the non-responder samples. We found a number of markers of resistance to anthracycline-based chemotherapy. We validated our findings in three external datasets, totaling 456 HER2-negative samples. Since these external sets included patients who received differing treatment regimens, the validated markers represent markers of general chemotherapy resistance. There was a highly significant overlap in the markers identified in the NKI dataset and the other three datasets. Five resistance markers, SERPINA6, BEX1, AGTR1, SLC26A3, and LAPTM4B, were identified in three of the four datasets (p value overlap < 1 × 10(-6)). These five genes identified resistant tumors that could not have been identified by merely taking ER status or proliferation into account. The identification of these genes might lead to a better understanding of the mechanisms involved in (clinically) observed chemotherapy resistance and could possibly assist in the recognition of breast cancers in which chemotherapy does not contribute to response or survival.

Clinical correlates of 'BRCAness' in triple-negative breast cancer of patients receiving adjuvant chemotherapy

BACKGROUND

We have previously reported an array comparative genomic hybridization profile that identifies triple-negative breast cancers (TNBC), with BRCA1 dysfunction and a high sensitivity to intensified dose bifunctional alkylating agents. To determine the effect of conventional-dose chemotherapy in patients with this so-called BRCA1-like profile, clinical characteristics and survival were studied in a large group of TNBC patients.

PATIENTS AND METHODS

DNA was isolated and BRCA1-like status was assessed in 101 patients with early-stage TNBC receiving adjuvant cyclophosphamide-based chemotherapy. Clinical characteristics and survival were compared between BRCA1-like and non-BRCA1-like groups. Results Sixty-six tumors (65%) had a BRCA1-like profile. Patients with BRCA1-like tumors tended to be younger and had more often node-negative disease (P = 0.06 and P = 0.03, respectively). Five-year recurrence-free survival was 80% for the BRCA1-like group and 75% for the non-BRCA1-like group (P = 0.35). T stage was the only variable significantly associated with survival.

CONCLUSIONS

BRCA1-like tumors share clinical features, like young age at diagnosis and similar nodal status, with breast cancers in BRCA1 mutation carriers. Their prognosis is similar to that of non-BRCA1-like tumors when conventional-dose chemotherapy is administered. TNBCs that are classified as BRCA1-like may contain a defect in homologous recombination and could, in theory, benefit from the addition of poly ADP ribose polymerase inhibitors.

PD03-08: BRCA1-Like Triple Negative Tumors: Clinicopathological Variables and Chemosensitivity to Alkylating Agents

Background

Our group has previously employed array Comparative Genomic Hybridization (aCGH) to assess the genomic patterns of BRCA1-mutated breast cancers. It is reasonable to assume that this pattern indicates ‘BRCAness’ and thus serves as a marker for homologous recombination deficiency. This BRCA1-like aCGH profile is also present in about half of all triple negative sporadic breast cancers and has been shown to be predictive for benefit from intensive chemotherapy with DNA crosslinking agents. To study BRCA1-like tumors and conventional dose chemotherapy sensitivity in more detail, we compared clinical factors and survival rates in a uniform cohort of triple negative breast tumors treated with alkylating agents.

Patients and methods

103 patients with triple negative tumors received conventional dose adjuvant chemotherapy with doxorubicin/cyclophosphamide. DNA was extracted from tumor samples and BRCA1-like profiles were assessed. Tumors were classified as BRCA1 -like or non-BRCA1-like. Standard clinical and histopathological factors were determined and compared between both groups. Relapse free survival (RFS), disease specific survival (DSS) and overall survival (OS) after diagnosis were compared between BRCA1-like and non-BRCA1-like tumors.

Results

66 tumors (65%) had a BRCA1-like profile, while 35 tumors (35%) did not show such a profile. Patients with BRCA1-like tumors tended to be younger and had more often node-negative disease compared to the patients with non-BRCA1-like tumors (p=0.058 and p=0.034, respectively). There was no significant difference in survival between BRCA1-like and non BRCA1-like patients after treatment with alkylating agents: the median RFS was 121 vs. 109 months, median DSS was 129 vs. 114 months and OS was 127 vs. 110 months, for BRCA1-like versus non-BRCA1-like tumors. T-stage was the only variable significantly associated with survival.

Conclusion

BRCA1-like tumors occurred in younger patients and were more often node negative, which are features shared with tumors in BRCA1-mutation carriers. We did not observe a difference in survival between BRCA1-like and non-BRCA1-like triple negative breast cancers after treatment with conventional dose chemotherapy with alkylating agents. These results confirm our previous findings that BRCA1-like tumors have similar sensitivity to anthracycline-based adjuvant chemotherapy as other triple-negative tumors. It will be important to establish whether BRCA1-like tumors also share the exquisite sensitivity of BRCA-mutated tumors to PARP-inhibitors.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr PD03-08.

Abstract 22: Identifying chemotherapy resistance genes using outlier detection

Motivation: Breast cancer is a heterogeneous disease and although gene expression analysis or immuno histo chemistry can be used to subclassify tumors into distinct subgroups, even within these subgroups there exist significant differences at the molecular level. When it comes to chemotherapy resistance, it appears highly unlikely that all resistant tumors share the same mechanism of action. Classical approaches have been unsuccessful in finding reliable biomarkers for therapy resistance and this may be due to the fact that these approaches are not sensitive to changes in small subgroups of samples.

Methods: Traditional analyses approaches, like a t-test or using the SAM approach, compare the two groups of samples for each gene, and identify genes with a significant difference in expression between the two groups. If only a small subset of the resistant tumors would show aberrant expression indicative of a resistance mechanism, then this would not be picked up by such approaches. Using a novel algorithm we try to circumvent this problem and specifically aim to find relatively small subgroups of tumors within the resistant group that show differential expression compared to the sensitive group.

Results: Using a positive control set, where we mixed in a small set of HER2-positive tumors in a larger HER2-negative set and by generating an artificial dataset we show that our algorithm is able to pick up all positive controls. These controls are not picked up by either a t-test or the SAM algorithm. Next, we applied the algorithm on a gene expression set of 195 patients that were neoadjuvantly treated and identified a number of genes that show an expression pattern that suggests a role in chemotherapy resistance in ER+ tumors. We validate our findings on a separate set of 90 patients.

Discussion: We have developed a novel algorithm that allows the identification of genes that show aberrant expression, relative to the reference group, in a small subset of the samples. Using this approach we identified a number of genes that are linked to chemotherapy resistance. The algorithm can be used in any type of analysis that involves the detection of small subsets of samples within one of the labeled classes, where the small subset shows behavior different from the average behavior of the remaining samples. Our approach can therefore be applied to a wide range of problems.

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 22. doi:10.1158/1538-7445.AM2011-22

Abstract 3134: Neoadjuvant chemotherapy in ER+HER2- breast cancer: Response prediction based on immunohistochemical and molecular characteristics

Introduction: A pathological complete remission (pCR) is rarely achieved by neoadjuvant chemotherapy (NAC) in ER+HER2- tumors. Therefore, its use might be questionable in specific groups of this tumor type. To select which patients benefit and which could be withheld from NAC, we tested standard pathology and molecular markers in ER+HER2- breast tumors.

Methods: Pre-treatment biopsies were available from 211 ER+HER2- tumors, which had been treated with NAC. mRNA expression and aCGH data were available for 132 tumors. We determined progesterone receptor (PR)expression, endocrine responsiveness, histology, proliferation, molecular subtypes and BRCAness aCGH profiles. We correlated these data with chemotherapy response using pCR rates and the neoadjuvant response index (NRI).

Results: PR-negative tumors (n = 65, 30.8%) and Luminal B type tumors (n=43, 20.4%) responded significantly better to NAC than other tumors, for both pCR breast and the NRI as outcome measure (table 1). The associations remained significant in multivariate analysis. However, even in the subgroup of patients with the lowest response rate (tumors with both a positive PR and of the Luminal A type (n=58, 44 %)), the majority showed downstaging (median NRI=0.25)(table 1). For endocrine responsiveness and the BRCAness aCGH profile only an association with pCR breast was observed. Histology (lobular versus ductal) and proliferation did not show an association with chemotherapy response (table 1).

Discussion: PR expression and molecular subtype are associated with a better response to NAC. However, both markers had only weak predictive power and it was not possible to identify a subgroup with no or only minimal chemotherapy benefit. Therefore, the decision to refrain patients from NAC in ER+HER2- breast tumors should not be based on predictive markers, but exclusively on estimates of prognosis.

Neoadjuvant chemotherapy in ER+ HER2- breast cancer: response prediction based on immunohistochemical and molecular characteristics

A pathological complete remission (pCR) is rarely achieved by neoadjuvant chemotherapy in estrogen receptor-positive (ER+) HER2-negative (HER2-) tumors. Therefore, its use might be questionable in specific groups of this tumor type. To select which patients benefit and which could be spared neoadjuvant chemotherapy, we tested standard pathology and molecular markers in ER+ HER2- breast tumors. Pretreatment biopsies were available from 211 ER+ HER2- tumors, who had been treated with neoadjuvant chemotherapy (adriamycin/cyclophosphamide). mRNA expression data were available for 132 tumors. We determined progesterone receptor expression (PR), endocrine sensitivity, HER2 expression, histology, proliferation, and molecular subtypes. We correlated these data to chemotherapy response using pCR rates and the previously published neoadjuvant response index (NRI). PR-negative tumors (n = 65, 30.8%) and luminal B type tumors (n = 43, 20.4%) responded significantly better to chemotherapy than other tumors. These associations remained significant in multivariate analysis. However, even in the subgroup of patients with the lowest response rate, comprising tumors that had both a positive-PR expression and the luminal A subtype (n = 58, 44%), the majority of the patients had downstaging because of chemotherapy. For histology (lobular vs. ductal), endocrine sensitivity, and proliferation, no associations with chemotherapy response were observed. Gene expression array analysis resulted in 28 significant genes (FDR < 0.1). PR expression and luminal B status are associated with a better response to neoadjuvant chemotherapy. However, both markers had only weak response predictive power, and it was not possible to identify a subgroup with no or only minimal chemotherapy benefit. Therefore, the decision to refrain from neoadjuvant chemotherapy to ER+ HER2- breast tumors should not be based on predictive markers, but exclusively on estimates of prognosis.

Genomic signature of BRCA1 deficiency in sporadic basal-like breast tumors

About 10-20% of all breast carcinomas show a basal-like phenotype, while ∼ 90% of breast tumors from BRCA1-mutation carriers are of this subtype. There is growing evidence that BRCA1-mutated tumors are not just a specific subset of the basal-like tumors, but that (the majority of) basal-like tumors show a dysfunctional BRCA1 pathway. This has major treatment implications, because emerging regimens specifically targeting DNA repair mechanisms would then be most effective against these tumors. To further understand the involvement of BRCA1 deficiency in sporadic basal-like tumors, we investigated 41 basal-like tumors for BRCA1 mRNA expression by quantitative real-time polymerase chain reaction, BRCA1 promoter methylation, their genomic profile by array-CGH, and gene expression levels by whole genome expression arrays. Array-CGH results were compared to those of 34 proven BRCA1-mutated tumors. Basal-like tumors were subdivided into two equal groups: deficient and proficient in BRCA1 gene expression. The chromosomal makeup of BRCA1 deficient sporadic basal-like tumors was similar to that of BRCA1-mutated tumors. BRCA1 proficient sporadic basal-like tumors were more similar to nonbasal-like tumors. Only half of the basal-like breast tumors are actually deficient in BRCA1 expression. Gain of chromosome arm 3q is a marker for BRCA1 deficiency in hereditary and sporadic breast tumors.

Abstract PD07-07: Indicators of Homologous Recombination Deficiency in Breast Cancer and Association with Response to Neoadjuvant Chemotherapy

Background: Tumors with homologous recombination (HR) deficiency are highly sensitive to DNA double strand break (DSB) inducing agents, such as alkylating agents and poly (ADP-ribose) polymerase (PARP)-inhibitors. BRCA1 or BRCA2- mutated tumors, which are HR deficient, have characteristic DNA gains and losses that can be assessed by an array Comparative Genomic Hybridization (aCGH) classifier, one for BRCA1 mutations and one for BRCA2 mutations. We have studied these aCGH profiles together with several other HR deficiency indicators in sporadic breast cancers and we have correlated their presence to neoadjuvant chemotherapy response.

Material and Methods: A total of 163 HER2-negative pre-treatment biopsies were examined, procured from sporadic breast cancer patients scheduled to receive neoadjuvant therapy with doxorubicin and cyclophosphamide. Triple negative (TN) and estrogen receptor positive (ER+/HER2-) tumors were analyzed separately. aCGH was performed to assess BRCA1-like and BRCA2-like profiles. In addition, BRCA1 promoter methylation, BRCA1 mRNA expression and amplification of the BRCA2-inhibiting gene EMSY were analyzed. Response to neoadjuvant treatment was assessed by measuring pathological complete remission (pCR) and near pCR at the time of surgery.

Results: Inactivation of BRCA1 was frequent in TN tumors: 57% of these tumors showed a BRCA1-like profile at aCGH. BRCA 1 promoter methylation and reduced BRCA1 mRNA expression were observed in 25% and 36% of the TN tumors, respectively. The BRCA1-like aCGH profile was not clearly associated with a better neoadjuvant treatment response (58% vs. 48%, p=0.47). In ER+ tumors, a BRCA2-like aCGH profile and the amplification of the BRCA2 inhibiting gene EMSY were frequently observed (43% and 13% respectively). A BRCA2-like aCGH profile was associated with a significantly higher response rate (35% vs. 14%, p=0.014). EMSY amplification and a BRCA2-like aCGH profile occurred together in only one case, suggesting mutual exclusivity. EMSY was not associated with treatment response, questioning the role of EMSY in HR deficiency.

Conclusion: Alterations associated with BRCA1 inactivation are present in about half of the TN breast cancers, but were not predictive of chemotherapy response. In ER+/HER2- tumors, the BRCA2-like aCGH profile predicts sensitivity to DSB-inducing chemotherapy, and possibly as well to new targeted agents, such as the PARP inhibitors. After validation in independent series the aCGH classifiers may lead to a diagnostic test that could assist in neoadjuvant treatment selection.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr PD07-07.

Indicators of homologous recombination deficiency in breast cancer and association with response to neoadjuvant chemotherapy

BACKGROUND

Tumors with homologous recombination deficiency (HRD), such as BRCA1-associated breast cancers, are not able to reliably repair DNA double-strand breaks (DSBs) and are therefore highly sensitive to both DSB-inducing chemotherapy and poly (ADP-ribose) polymerase inhibitors. We have studied markers that may indicate the presence of HRD in HER2-negative breast cancers and related them to neoadjuvant chemotherapy response.

PATIENTS AND METHODS

Array comparative genomic hybridization (aCGH), BRCA1 promoter methylation, BRCA1 messenger RNA (mRNA) expression and EMSY amplification were assessed in 163 HER2-negative pretreatment biopsies from patients scheduled for neoadjuvant chemotherapy.

RESULTS

Features of BRCA1 dysfunction were frequent in triple-negative (TN) tumors: a BRCA1-like aCGH pattern, promoter methylation and reduced mRNA expression were observed in, respectively, 57%, 25% and 36% of the TN tumors. In ER+ tumors, a BRCA2-like aCGH pattern and the amplification of the BRCA2 inhibiting gene EMSY were frequently observed (43% and 13%, respectively) and this BRCA2-like profile was associated with a better response to neoadjuvant chemotherapy.

CONCLUSIONS

Abnormalities associated with BRCA1 inactivation are present in about half of the TN breast cancers but were not predictive of chemotherapy response. In ER+/HER2- tumors, a BRCA2-like aCGH pattern was predictive of chemotherapy response. These findings should be confirmed in independent series.

BRCA1 loss preexisting in small subpopulations of prostate cancer is associated with advanced disease and metastatic spread to lymph nodes and peripheral blood

PURPOSE

A preliminary study performed on a small cohort of multifocal prostate cancer (PCa) detected BRCA1 allelic imbalances among circulating tumor cells (CTC). The present analysis was aimed to elucidate the biological and clinical roles of BRCA1 losses in metastatic spread and tumor progression in PCa patients.

EXPERIMENTAL DESIGN

To map molecular progression in PCa outgrowth, we used fluorescence in situ hybridization analysis of primary tumors and lymph node sections, and CTCs from peripheral blood.

RESULTS

We found that 14% of 133 tested patients carried monoallelic BRCA1 loss in at least one tumor focus. Extended molecular analysis of chr17q revealed that this aberration was often a part of larger cytogenetic rearrangement involving chr17q21 accompanied by allelic imbalance of the tumor suppressor gene PTEN and lack of BRCA1 promoter methylation. The BRCA1 losses correlated with advanced T stage (P < 0.05), invasion to pelvic lymph nodes (P < 0.05), as well as biochemical recurrence (P < 0.01). Their prevalence was twice as high within 62 lymph node metastases (LNM) as in primary tumors (27%, P < 0.01). The analysis of 11 matched primary PCa-LNM pairs confirmed the suspected transmission of genetic abnormalities between these two sites. In four of seven patients with metastatic disease, BRCA1 losses appeared in a minute fraction of cytokeratin- and vimentin-positive CTCs.

CONCLUSIONS

Small subpopulations of PCa cells bearing BRCA1 losses might be one confounding factor initiating tumor dissemination and might provide an early indicator of shortened disease-free survival.

Biomechanical effect of mineral heterogeneity in trabecular bone

Due to daily loading, trabecular bone is subjected to deformations (i.e., strain), which lead to stress in the bone tissue. When stress and/or strain deviate from the normal range, the remodeling process leads to adaptation of the bone architecture and its degree of mineralization to effectively withstand the sustained altered loading. As the apparent mechanical properties of bone are assumed to depend on the degree and distribution of mineralization, the goal of the present study was examine the influences of mineral heterogeneity on the biomechanical properties of trabecular bone in the human mandibular condyle. For this purpose nine right condyles from human dentate mandibles were scanned and evaluated with a microCT system. Cubic regional volumes of interest were defined, and each was transformed into two different types of finite element (FE) models, one homogeneous and one heterogeneous. In the heterogeneous models the element tissue moduli were scaled to the local degree of mineralization, which was determined using microCT. Compression and shear tests were simulated to determine the apparent elastic moduli in both model types. The incorporation of mineralization variation decreased the apparent Young's and shear moduli by maximally 21% in comparison to the homogeneous models. The heterogeneous model apparent moduli correlated significantly with bone volume fraction and degree of mineralization. It was concluded that disregarding mineral heterogeneity may lead to considerable overestimation of apparent elastic moduli in FE models.

The anion exchanger Ae2 is required for enamel maturation in mouse teeth

One of the mechanisms by which epithelial cells regulate intracellular pH is exchanging bicarbonate for Cl(-). We tested the hypothesis that in ameloblasts the anion exchanger-2 (Ae2) is involved in pH regulation during maturation stage amelogenesis. Quantitative X-ray microprobe mineral content analysis, scanning electron microscopy, histology, micro-computed tomography and Ae2 immuno-localisation analyses were applied to Ae2-deficient and wild-type mouse mandibles. Immuno-localisation of Ae2 in wild-type mouse incisors showed a very strong expression of Ae2 in the basolateral membranes of the maturation stage ameloblasts. Strikingly, zones of contiguous ameloblasts were found within the maturation stage in which Ae2 expression was extremely low as opposed to neighbouring cells. Maturation stage ameloblasts of the Ae2(a,b)(-/-) mice failed to stain for Ae2 and showed progressive disorganisation as enamel development advanced. Maturation stage enamel of the Ae2(a,b)(-/-) mice contained substantially less mineral and more protein than wild-type enamel as determined by quantitative X-ray microanalysis. Incisor enamel was more severely affected than molar enamel. Scanning electron microscopy revealed that the rod-inter-rod structures of the Ae2(a,b)(-/-) mice incisor enamel were absent. Mineral content of dentine and bone of Ae2(a,b)(-/-) mice was not significantly different from wild-type mice. The enamel from knockout mouse teeth wore down much faster than that from wild-type litter mates. Basolateral bicarbonate secretion via the anionic exchanger Ae2 is essential for mineral growth in the maturation stage enamel. The observed zonal expression of Ae2 in the maturation stage ameloblasts is in line with a model for cyclic proton secretion during maturation stage amelogenesis.

Porosity of human mandibular condylar bone

Quantification of porosity and degree of mineralization of bone facilitates a better understanding of the possible effects of adaptive bone remodelling and the possible consequences for its mechanical properties. The present study set out first to give a three-dimensional description of the cortical canalicular network in the human mandibular condyle, in order to obtain more information about the principal directions of stresses and strains during loading. Our second aim was to determine whether the amount of remodelling was larger in the trabecular bone than in cortical bone of the condyle and to establish whether the variation in the amount of remodelling was related to the surface area of the cortical canals and trabeculae. We hypothesized that there were differences in porosity and orientation of cortical canals between various cortical regions. In addition, as greater cortical and trabecular porosities are likely to coincide with a greater surface area of cortical canals and trabeculae available for osteoblastic and osteoclastic activity, we hypothesized that this surface area would be inversely proportional to the degree of mineralization of cortical and trabecular bone, respectively. Micro-computed tomography was used to quantify porosity and mineralization in cortical and trabecular bone of ten human mandibular condyles. The cortical canals in the subchondral cortex of the condyle were orientated in the mediolateral direction, and in the anterior and posterior cortex in the superoinferior direction. Cortical porosity (average 3.5%) did not differ significantly between the cortical regions. It correlated significantly with the diameter and number of cortical canals, but not with cortical degree of mineralization. In trabecular bone (average porosity 79.3%) there was a significant negative correlation between surface area of the trabeculae and degree of mineralization; such a correlation was not found between the surface area of the cortical canals and the degree of mineralization of cortical bone. No relationship between trabecular and cortical porosity, nor between trabecular degree of mineralization and cortical degree of mineralization was found, suggesting that adaptive remodelling is independent and different between trabecular and cortical bone. We conclude (1) that the principal directions of stresses and strains are presumably directed mediolaterally in the subchondral cortex and superoinferiorly in the anterior and posterior cortex, (2) that the amount of remodelling is larger in the trabecular than in the cortical bone of the mandibular condyle; in trabecular bone variation in the amount of remodelling is related to the available surface area of the trabeculae.

Variations in mineralization affect the stress and strain distributions in cortical and trabecular bone

The mechanical properties of bone depend largely on its degree and distribution of mineralization. The present study analyzes the effect of an inhomogeneous distribution of mineralization on the stress and strain distributions in the human mandibular condyle during static clenching. A condyle was scanned with a micro-CT scanner to create a finite element model. For every voxel the degree of mineralization (DMB) was determined from the micro-CT scan. The Young's moduli of the elements were calculated from the DMB using constant, linear, and cubic relations, respectively. Stresses, strains, and displacements in cortical and trabecular bone, as well as the condylar deformation (extension along the antero-posterion axis) and compliance were compared. Over 90% of the bone mineral was located in the cortical bone. The DMB showed large variations in both cortical bone (mean: 884, SD: 111 mg/cm(3)) and trabecular bone (mean: 738, SD: 101 mg/cm(3)). Variations of the stresses and the strains were small in cortical bone, but large in trabecular bone. In the cortical bone an inhomogeneous mineral distribution increased the stresses and the strains. In the trabecular bone, however, it decreased the stresses and increased the strains. Furthermore, the condylar compliance remained relatively constant, but the condylar deformation doubled. It was concluded that neglect of the inhomogeneity of the mineral distribution results in a large underestimation of the stresses and strains of possibly more than 50%. The stiffness of trabecular bone strongly influences the condylar deformation. Vice versa, the condylar deformation largely determines the magnitude of the strains in the trabecular bone.