Homologous recombination deficiency derived from whole-genome sequencing predicts platinum response in triple-negative breast cancers

The high frequency of homologous recombination deficiency (HRD) is the main rationale of testing platinum-based chemotherapy in triple-negative breast cancer (TNBC), however, the existing methods to identify HRD are controversial and there is a medical need for predictive biomarkers. We assess the in vivo response to platinum agents in 55 patient-derived xenografts (PDX) of TNBC to identify determinants of response. The HRD status, determined from whole genome sequencing, is highly predictive of platinum response. BRCA1 promoter methylation is not associated with response, in part due to residual BRCA1 gene expression and homologous recombination proficiency in different tumours showing mono-allelic methylation. Finally, in 2 cisplatin sensitive tumours we identify mutations in XRCC3 and ORC1 genes that are functionally validated in vitro. In conclusion, our results demonstrate that the genomic HRD is predictive of platinum response in a large cohort of TNBC PDX and identify alterations in XRCC3 and ORC1 genes driving cisplatin response.

Abstract A21: Dissecting MYC immunoregulatory activity in BRCA1-associated breast cancer

Breast cancer is the most common cancer among women in the Western world. Approximately 8% of all breast cancer cases may be caused by inheritance of mutations in breast cancer susceptibility genes. Of these, BRCA1 is the most important one, contributing to approximately half of all familial breast cancer cases. BRCA1-related breast tumors show a triple-negative (TBNC) basal-like phenotype, which correlates with aggressive characteristics and poor prognosis. MYC has been identified as a potential driver gene in BRCA1-associated breast cancer. In line with this, we found MYC to be frequently amplified in both mouse and human BRCA1-deficient breast cancers. Thus, evaluating the contribution of MYC to BRCA1-associated breast cancer might unravel new mechanistic insights and potentially open the way to new therapeutic approaches.

To investigate a causal role of MYC in BRCA1-associated breast cancer, we generated WAPCre;Brca1F/F;Trp53F/F (WB1P) and WAPCre;Brca1F/F;Trp53F/F;invCAG-Myc (WB1P-Myc) mouse models, which were monitored for tumor development. Whereas WB1P female mice developed mammary tumors after 300 days, WB1P-Myc mice showed a dramatic acceleration in tumor development with a median survival of 100 days. Tumors of both models were histopathologically classified as poorly differentiated solid carcinomas resembling TNBC. To characterize the differences between the WB1P and WB1P-Myc tumors, we performed whole-transcriptome analysis using RNAseq. Unsupervised hierarchical cluster analysis showed that WB1P and WB1P-Myc tumors cluster separately. Interestingly, Gene Set Enrichment Analysis (GSEA) showed that the most significant deregulated pathway is the cytokine-cytokine interaction pathway. Compared to WB1P tumors, WB1P-Myc tumors showed downregulation of different molecules involved in immune cell chemoattraction and antigen presentation. Characterization of the immune infiltrate of WB1P and WB1P-Myc tumors showed that MYC overexpression leads to depletion of different tumor-infiltrating immune cells, including leukocytes, T cells, myeloid cells, and NK cells.

To further investigate the role of MYC on the tumor microenvironment, we generated different Myc inducible platforms, including a “double-layered” system for Cre-conditional and doxycycline-regulatable overexpression of the MYC gene in WB1P mice. We also obtained tumor organoids from the WB1P and WB1P-Myc tumors which can be manipulated in vitro and orthotopically transplanted in vivo. We transduced the WB1P organoids with a lentiviral MycERT2 construct, enabling us to switch on and off MYC in organoids and study if its overexpression is the cause of the differences observed in the WB1P-Myc tumors. In addition, we are studying if MYC upregulation induces secretion of immune-suppressive factors and/or upregulation of molecules that can create an immunosuppressive microenvironment. Moreover, we are studying the secretome of WB1P and WB1P-Myc organoids in vitro.

Of note, we discovered that WB1P-Myc tumors strongly downregulate the CIITA-CD74-MHCII axis, which is important for T-cell mediated antitumor activity. Taking advantage of the aforementioned Myc-inducible platforms, we are currently investigating if this axis is the underlying cause of the immune-depleted microenvironment we observed in WB1P-Myc tumors. In addition, we are somatically inducing CIITA expression in the mammary epithelium of WB1P-Myc mice to investigate if this leads to delayed mammary tumor formation and/or increased influx of immune cells in the resulting tumors.

Citation Format: Chiara Svetlana Brambillasca, Linda Henneman, Julian de Ruiter, Max Wellenstein, Anne Paulien Drenth, Karin de Visser, Jos Jonkers. Dissecting MYC immunoregulatory activity in BRCA1-associated breast cancer [abstract]. In: Proceedings of the AACR Special Conference: Advances in Modeling Cancer in Mice: Technology, Biology, and Beyond; 2017 Sep 24-27; Orlando, Florida. Philadelphia (PA): AACR; Cancer Res 2018;78(10 Suppl):Abstract nr A21.

Abstract 673: The role of MYPT1/2, ASPP2 and MYH9 in invasive lobular carcinoma

Invasive lobular carcinoma (ILC) accounts for 10-15% of breast cancer cases in women. One of the characteristics of this type of cancer is the loss of intercellular adhesion which is facilitated by inactivating mutations in E-cadherin. However the loss of E-cadherin alone is not enough to induce ILC. An in vivo Sleeping Beauty insertional mutagenesis screen was performed to identify genes that together with E-cadherin loss contribute to ILC development in mice. In around 85% of the tumors that were analyzed during this screen one of four hits were observed, namely MYPT1, MYPT2, ASPP2 and MYH9. Interestingly these four hits appear to be mutually exclusive indicating a shared mechanism of action.

To investigate how these genes might affect tumorigenesis we first looked at the location of the transposon insertions. This revealed that for MYPT1, MYPT2 and ASPP2 the transposons appeared to localize to a specific region in the gene indicating that these insertions could result in a truncation variant. In the case of MYH9 no clear localization of insertions was found which in combination with the recently published data indicates a loss of function. Northern blot analysis revealed the presence of truncation variants for MYPT1/2 and ASPP2 which for MYPT1 were confirmed to also result in truncated protein variants.

In order to identify the tumorigenic potential of truncated MYPT1 and ASPP2 we overexpressed them in spontaneously immortalized mammary epithelial cell lines HC11 and NMuMG. We are using these cell lines to analyse differences in cell proliferation, anchorage independent growth, sensitivity to apoptosis in vitro and tumor formation in vivo. To further analyse the hits in an E-cadherin negative setting we made use of primary mammary epithelial cells (MECs) isolated from genetically engineered mice with mammary gland specific E-cadherin loss. These MECs normally do not grow past several passages in vitro. However, these MECs when we overexpress truncated MYPT1 or ASPP2, or use shRNA mediated knockdown of MYH9 can be passaged and grown in vitro consistently.

Finally we are generating conditional mouse models with mammary gland specific E-cadherin loss in combination of expression of the truncated variants of MYPT1 or ASPP2, or loss of MYH9. We will to monitor whether these mice are prone to developing ILC.

Citation Format: Koen Schipper, Julian de Ruiter, Sjors Kas, Eva Schut, Marco Koudijs, David Addams, Jos Jonkers. The role of MYPT1/2, ASPP2 and MYH9 in invasive lobular carcinoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 673.

Abstract 889: Dissecting the role of MYC in BRCA1-associated breast cancer

Breast cancer is the most common cancer among women in the Western world. Approximately 8% of all breast cancer cases may be caused by inheritance of mutations in breast cancer susceptibility genes. Of these, BRCA1 is the most important one, contributing to approximately half of all familial breast cancer cases. BRCA1-related breast tumors show a triple-negative (TBNC) basal like phenotype, that correlates with aggressive characteristics and bad prognosis. A number of BRCA1 associated genes have been identified; among those MYC overexpression seems to have an important role in aggressive TBNC. In line with this, we found MYC to be frequently amplified in both mouse and human BRCA1-deficient breast cancers. Thus, evaluating the contribution of MYC to BRCA1-associated breast cancer might unravel new mechanistic insights and potentially open the way to new therapeutic approaches.

To pursue this, we generated a WAPCre;Brca1F/F;Trp53F/F;Myc (WB1P-MYC) mouse model to monitor tumor development. Whereas the WAPCre;Brca1F/F;Trp53F/F (WB1P) mouse model develops tumors after 300 days, Cre-conditional overexpression of the MYC transgene leads to a dramatic acceleration in tumor development with a median survival of 100 days. Tumors of both models were histopathologically classified as solid carcinomas. Further characterization revealed that WB1P-MYC tumors show higher levels of apoptosis and DNA damage. Moreover, we also observed a strong difference in immune infiltrate between WB1P and WB1P-MYC tumors. To better characterize these differences between WB1P and WB1P-MYC tumors we obtained tumor organoids. Importantly, these tumor organoids maintained characteristics of the original tumor like Brca1, P53 deletion status and MYC overexpression. Moreover, they can be orthotopically transplanted in vivo, leading to formation of solid carcinomas. Therefore, they represent a versatile platform to test new drug combinations both in vitro and in vivo.

To test if MYC overexpression is also required for maintenance of established tumors, we are developing a “double-layered” system for Cre-conditional and doxycycline-regulatable overexpression of the MYC gene in the WAPCre;Brca1F/F;Trp53F/F model. By administering doxycycline we will induce MYC only in Cre-expressing mammary epithelial cells. After tumor formation MYC will be switched-off to assess its role in tumor maintenance and progression. Furthermore, we would like to test new therapeutic approaches, like combining Myc down-regulation with administration of PARP inhibitors. In addition, tumor organoids of this inducible WB1P-MYC model will be a powerful system to study the MYC-associated phenotype, drugs combinations and forward genetic screens.

Citation Format: Chiara Svetlana Brambillasca, Linda Henneman, Julian de Ruiter, Anne Paulien Drenth, Jos Jonkers. Dissecting the role of MYC in BRCA1-associated breast cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 889.

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.

CopywriteR: DNA copy number detection from off-target sequence data

Current methods for detection of copy number variants (CNV) and aberrations (CNA) from targeted sequencing data are based on the depth of coverage of captured exons. Accurate CNA determination is complicated by uneven genomic distribution and non-uniform capture efficiency of targeted exons. Here we present CopywriteR, which eludes these problems by exploiting 'off-target' sequence reads. CopywriteR allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. CopywriteR outperforms existing methods and constitutes a widely applicable alternative to available tools.