Immunity in Breast Cancer: Charting T cell evasion and exploring new targets for T cells

Cancer immunotherapy of breast cancer is currently challenged by low response rates and lack of predictive markers for immune therapies; lack of druggable targets that counteract T cell evasion; and lack of safe and effective target antigens for adoptive T cell therapies. In Part 1 of this thesis (Chapter2-4) we focused on the knowledge gap regarding T cell evasive mechanisms, which, provides a basis for patient stratification and selection of combination therapies. In Part 2 of this thesis (Chapter 5-7) we focused on the identification and selection of safe and effective target antigens and corresponding TCRs for adoptive T cell therapy for TNBC (one of the subtypes of breast cancer

Association of microRNA-7 and its binding partner CDR1-AS with the prognosis and prediction of 1st-line tamoxifen therapy in breast cancer

The large number of non-coding RNAs (ncRNAs) and their breadth of functionalities has fuelled many studies on their roles in cancer. We previously linked four microRNAs to breast cancer prognosis. One of these microRNAs, hsa-miR-7, was found to be regulated by another type of ncRNA, the circular non-coding RNA (circRNA) CDR1-AS, which contains multiple hsa-miR-7 binding sites. Based on this finding, we studied the potential clinical value of this circRNA on breast cancer prognosis in a cohort based on a cohort that was previously analysed for hsa-miR-7 and in an adjuvant hormone-naïve cohort for 1st-line tamoxifen treatment outcomes, in which we also analysed hsa-miR-7. A negative correlation was observed between hsa-miR-7 and CDR1-AS in both cohorts. Despite associations with various clinical metrics (e.g., tumour grade, tumour size, and relapse location), CDR1-AS was neither prognostic nor predictive of relevant outcomes in our cohorts. However, we did observe stromal CDR1-AS expression, suggesting a possible cell-type specific interaction. Next to the known association of hsa-miR-7 expression with poor prognosis in primary breast cancer, we found that high hsa-miR-7 expression was predictive of an adverse response to tamoxifen therapy and poor progression-free and post-relapse overall survival in patients with recurrent disease

Breast cancer genomics and immuno-oncological markers to guide immune therapies

There is an increasing awareness of the importance of tumor – immune cell interactions to the evolution and therapy responses of breast cancer (BC). Not surprisingly, numerous studies are currently assessing the clinical value of immune modulation for BC patients. However, till now durable clinical responses are only rarely observed. It is important to reali

Transcriptomic properties of her2+ ductal carcinoma in situ of the breast associate with absence of immune cells

SIMPLE SUMMARY: Tumor-infiltrating lymphocytes (TILs) are likely to play a role in the biological behavior of HER2+ ductal carcinoma in situ (DCIS). To prevent invasiveness, the potential of targeted immune-modulating treatment of HER2+ DCIS has been explored. We identified a 29-gene expression profile that was associated with the density of TILs. These genes included CCND3, DUSP10 and RAP1GAP, which may guide towards more rationalized choices with respect to immune-mediated therapy in HER2+ DCIS, such as targeted vaccine therapy. ABSTRACT: The identification of transcriptomic alterations of HER2+ ductal carcinoma in situ (DCIS) that are associated with the density of tumor-infiltrating lymphocytes (TILs) could contribute to optimizing choices regarding the potential benefit of immune therapy. We compared the gene expression profile of TIL-poor HER2+ DCIS to that of TIL-rich HER2+ DCIS. Tumor cells from 11 TIL-rich and 12 TIL-poor DCIS cases were micro-dissected for RNA isolation. The Ion AmpliSeq Transcriptome Human Gene Expression Kit was used for RNA sequencing. After normalization, a Mann–Whitney rank sum test was used to analyze differentially expressed genes between TIL-poor and TIL-rich HER2+ DCIS. Whole tissue sections were immunostained for validation of protein expression. We identified a 29-gene expression profile that differentiated TIL-rich from TIL-poor HER2+ DCIS. These genes included CCND3, DUSP10 and RAP1GAP, which were previously described in breast cancer and cancer immunity and were more highly expressed in TIL-rich DCIS. Using immunohistochemistry, we found lower protein expression in TIL-rich DCIS. This suggests regulation of protein expression at the posttranslational level. We identified a gene expression profile of HER2+ DCIS cells that was associated with the density of TILs. This classifier may guide towards more rationalized choices regarding immune-mediated therapy in HER2+ DCIS, such as targeted vaccine therapy

Detection of Low-Frequency Epitope-Specific T Cells in Blood of Healthy Individuals according to an Optimized In Vitro Amplification System

Detection and amplification of epitope-specific T cells hold great promise for diagnosis and therapy of cancer patients. Currently, measurement and retrieval of epitope-specific T cells is hampered by limited availability of patients’ biomaterials and lack of sensitive and easy-to-implement T cell priming and expansion. We have developed an in vitro T cell amplification system starting from healthy donor blood and tested different subsets and ratios of autologous T cells and APCs as well as the resting period between amplification cycles. We demonstrated in 10 different donors significantly enhanced frequency of T cells specific for MelanA/HLA-A2, which relied on coculturing of naive T cells and CD11c+ dendritic cells in a 1:1 ratio followed by three weekly amplification cycles using the effluent of the naive T cell sort as APCs, a 24-h rest period prior to every reamplification cycle, and IFN-γ production as a readout for epitope-specific T cells. Using this system, MelanA/HLA-A2-specific T cells were enriched by 200-fold, measuring up to 20-60% of all T cells. We extended this system to enrich NY-ESO-1/HLA-A2- and BMLF-1/HLAA2-specific T cells, examples of a cancer germline Ag and an oncoviral Ag differing in their ability to bind to HLA-A2 and the presence of specific T cells in the naive and, in case of BMLF-1, also the Ag-experienced repertoire. Collectively, we have developed a sensitive and easy-to-implement in vitro T cell amplification method to enrich epitope-specific T cells that is expected to facilitate research and clinical utility regarding T cell diagnosis and treatments

Cancer germline antigens and tumor-agnostic CD8+ T cell evasion

Cancer germline antigens (CGAs) are expressed in immune-privileged germline tissues, while epigenetically silenced in somatic tissues. CGAs become re-expressed in tumors and can promote oncogenesis. Tumors prominently exploit mechanisms similar to those in germline tissues to shield from immunosurveillance. We hypothesize that CGAs contribute towards tumor escape from immune effector CD8+ T cells. For illustrative purposes, we assessed the co-presence or -absence of CGAs with these cells in multiple tumor types. Considering a broad array of CD8+ T cell evasive mechanisms, we exemplify the co-occurrence of gene transcripts of eight CGAs with those of adhesion molecules, endothelial cells, and/or the Wnt pathway. We present a novel concept of CGAs and their association with CD8+ T cell evasion, which may be relevant for future immunotherapeutic interventions