Combined PARP and WEE1 inhibition triggers anti-tumor immune response in BRCA1/2 wildtype triple-negative breast cancer

Novel therapeutic strategies that can effectively combine with immunotherapies are needed in the treatment of triple-negative breast cancer (TNBC). We demonstrate that combined PARP and WEE1 inhibition are synergistic in controlling tumour growth in BRCA1/2 wild-type TNBC preclinical models. The PARP inhibitor (PARPi) olaparib combined with the WEE1 inhibitor (WEE1i) adavosertib triggered increases in anti-tumour immune responses, including STING pathway activation. Combinations with a STING agonist resulted in further improved durable tumour regression and significant improvements in survival outcomes in murine tumour models of BRCA1/2 wild-type TNBC. In addition, we have identified baseline tumour-infiltrating lymphocyte (TIL) levels as a potential predictive biomarker of response to PARPi, WEE1i and immunotherapies in BRCA1/2 wild-type TNBC.

Tucatinib promotes immune activation and synergises with PD-1/PD-L1 inhibition in HER2-positive breast cancer

BACKGROUND

PD-1 and PD-L1 inhibitors have poor efficacy in patients with trastuzumab-resistant advanced HER2-positive breast cancer. Tucatinib is a potent, selective anti-HER2 tyrosine kinase inhibitor with proven clinical benefit in the advanced setting in patients with trastuzumab resistance. We investigated if tucatinib can alter the tumor microenvironment and if this could be harnessed for therapeutic efficacy.

METHODS

We investigated the anti-tumor efficacy and contribution of the immune response of tucatinib using two immunocompetent, HER2-positive murine breast cancer models (trastuzumab-sensitive H2N113; trastuzumab-resistant Fo5) and the efficacy of tucatinib with trastuzumab and PD-1/PD-L1 checkpoint inhibitors.

RESULTS

In both models, tucatinib significantly inhibited tumor growth and demonstrated dose-dependent efficacy. Ex vivo analysis by flow cytometry of TILs in mice treated with tucatinib showed increased frequency, higher proliferation and enhanced effector function of CD8+ effector memory T cells (TEM). Tucatinib treatment also increased frequency of CD8+PD-1+ and CD8+TIM3+ T cells, CD49+ NK cells, monocytes, and MHC II expression on dendritic cells and macrophages, and a decrease in myeloid derived suppressor cells. Gene expression analysis revealed significant enrichment in pathways associated with immune activation, type I and II interferon response, adaptive immune response and antigen receptor signalling. In vivo, tucatinib and α-PD-L1 or α-PD-1 demonstrated significantly increased efficacy and improved survival of mice compared with tucatinib alone.

CONCLUSION

Tucatinib modulates the immune microenvironment favourably and combination treatment with α-PD-L1 or α-PD-1 demonstrated increased efficacy in preclinical HER2-positive tumor models. These findings provide a rationale for investigation of tucatinib and immune checkpoint inhibition in the clinic.

Intratumoral CD8+ T cells with a tissue-resident memory phenotype mediate local immunity and immune checkpoint responses in breast cancer

CD8⁺ tumor-infiltrating lymphocytes with a tissue-resident memory T (T_RM) cell phenotype are associated with favorable prognosis in patients with triple-negative breast cancer (TNBC). However, the relative contribution of CD8⁺ T_RM cells to anti-tumor immunity and immune checkpoint blockade efficacy in breast cancer remains unknown. Here, we show that intratumoral CD8⁺ T cells in murine mammary tumors transcriptionally resemble those from TNBC patients. Phenotypic and transcriptional studies established two intratumoral sub-populations: one more enriched in markers of terminal exhaustion (T_EX-like) and the other with a bona fide resident phenotype (T_RM-like). Treatment with anti-PD-1 and anti-CTLA-4 therapy resulted in expansion of these intratumoral populations, with the T_RM-like subset displaying significantly enhanced cytotoxic capacity. T_RM-like CD8⁺ T cells could also provide local immune protection against tumor rechallenge and a T_RM gene signature extracted from tumor-free tissue was significantly associated with improved clinical outcomes in TNBC patients treated with checkpoint inhibitors.

Abstract P5-02-16: SPEN is a biomarker for CDK4/6 inhibitor resistance in patients with metastatic hormone receptor positive (HR+)/HER2- breast cancer

Background: Despite significant improvements in the treatment of breast cancer (BC), metastatic disease remains the principal cause of BC-related death. Through analysis of rapid autopsy collected biospecimens, we have previously identified Split Ends (SPEN) alterations in patients with metastatic HR+/HER2- BC (Savas et al. 2016). The role of SPEN in BC is poorly defined. Here we aimed to further explore the function of this gene in metastatic HR+/HER2- metastatic BC (mBC). Methods: We explored the clinical and genomic characteristics of SPEN altered mBC in human sequencing datasets. We created a model of SPEN loss using a gene knockdown (KD) via siRNA in MCF7 cells. Flow cytometry and western blot analysis was utilized to investigate the molecular impact of SPEN loss. The KD and non-targeting control cells were then subjected to a high throughput kinase inhibitor screen (n=480 compounds) to identify sensitive and resistant therapeutics. Finally, we used an in-house metastatic HR+/HER2- BC patient cohort treated with CDK (cyclin-dependent kinase) 4/6 inhibitors to validate SPEN loss as a marker of resistance. Results: Using a cohort of 7519 BC samples, SPEN alterations (mutation and copy number deletions) were found to be significantly enriched in HR+ mBC vs primary HR+ disease (29% vs 7%, respectively p< 0.0001). SPEN altered compared with SPEN wild type (WT) HR+ mBCs were significantly associated with higher tumor mutational burden (median 4.6 vs 1.7, p < 0.0001), more large-scale transitions (median 20 vs 14, p= 0.006), increased fraction of genome altered (52% vs 35%, p< 0.0001), and enrichment of APOBEC-induced mutations (65% vs 42%, p=0.004) respectively. Taken together, these results suggest greater genomic instability in patients with tumors with SPEN loss compared with WT. This hypothesis was further supported when SPEN KD cells showed significantly increased growth rate (p= 0.04), and significantly greater DNA damage by γH2Ax staining (p=0.03) compared with control cells. In a kinase inhibitor compound screen, SPEN KD cells displayed significant resistance to the CDK4/6 inhibitor palbociclib (p< 0.0001) compared with WT cells. We validated this finding in vitro by demonstrating SPEN KD cell resistance to other CDK4/6 inhibitors ribociclib and abemaciclib (p= 0.02 and 0.0004 respectively). In our in-house cohort of 56 patients with HR+ mBC treated with CDK4/6 inhibitors, we found that the HR+ mBC patients with a SPEN alteration have significantly decreased overall survival (OS) compared with WT patients, (median OS 34 months vs not reached, respectively; HR 3.18, 95%CI 0.94-10.73, p=0.049). Conclusion: These results provide the first clinical evidence that SPEN alterations are enriched in HR+ mBC. Additionally, SPEN may be a biomarker for CDK4/6 inhibitor resistance in this subtype. These results warrant further analysis into the role of SPEN in BC and its relevance in clinical management. Reference: Savas P, Teo ZL, Lefevre C, et al. The subclonal architecture of metastatic breast cancer: Results from a prospective community-based rapid autopsy program "cascade". PLoS medicine 2016;13:e1002204.

Citation Format: Courtney T. van Geelen, Zhi Ling Teo, Peter Savas, Stephen J. Luen, Kylie A. Clarke, Sneha Sant, Karla J. Cowley, Franco Caramia, Kaylene J. Simpson, Fabrice Andre, Sarah-Jane Dawson, Richard Pearson, Sherene Loi. SPEN is a biomarker for CDK4/6 inhibitor resistance in patients with metastatic hormone receptor positive (HR+)/HER2- breast cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-02-16.

Clinical implications of prospective genomic profiling of metastatic breast cancer patients

Background

Metastatic breast cancer remains incurable. Next-generation sequencing (NGS) offers the ability to identify actionable genomic alterations in tumours which may then be matched with targeted therapies, but the implementation and utility of this approach is not well defined for patients with metastatic breast cancer.

Methods

We recruited patients with advanced breast cancer of any subtype for prospective targeted NGS of their most recent tumour samples, using a panel of 108 breast cancer-specific genes. Genes were classified as actionable or non-actionable using the European Society of Medical Oncology Scale for Clinical Actionability of Molecular Targets (ESCAT) guidelines.

Results

Between February 2014 and May 2019, 322 patients were enrolled onto the study, with 72% (n = 234) of patients successfully sequenced (n = 357 samples). The majority (74%, n = 171) of sequenced patients were found to carry a potentially actionable alteration, the most common being a PIK3CA mutation. Forty-three percent (n = 74) of patients with actionable alterations were referred for a clinical trial or referred for confirmatory germline testing or had a change in therapy outside of clinical trials. We found alterations in AKT1, BRCA2, CHEK2, ESR1, FGFR1, KMT2C, NCOR1, PIK3CA and TSC2 to be significantly enriched in our metastatic population compared with primary breast cancers. Concordance between primary and metastatic samples for key driver genes (TP53, ERBB2 amplification) was > 75%. Additionally, we found that patients with a higher number of mutations had a significantly worse overall survival.

Conclusion

Genomic profiling of patients with metastatic breast cancer can have clinical implications and should be considered in all suitable patients.

Abstract PD5-03: Characterization of high TIL breast cancers reveals a prognostic and functionally distinct tissue-resident memory subpopulation

Background: Tumor infiltrating lymphocytes (TILs) assessed via light microscopy are prognostic and predictive in the early stage and advanced triple negative and HER2-amplified breast cancer (BC). Higher TILs can also identify patients more likely to benefit from anti-PD-1 therapy. In this study we interrogated T cell subsets that comprise high TILs to determine if distinct subpopulations are key mediators of anti-tumor immunity.

Methods: We characterised TILs with a focus on CD3+ T cells in 129 primary and metastatic BC samples using flow cytometry, bulk RNASeq on flow sorted T cell populations, multiplex immunohistochemistry and microdroplet based single cell 3' mRNA sequencing on the 10X Genomics Chromium platform. Cell type specific gene expression signatures were determined from differential expression between putative T cell subpopulations. These signatures were investigated in clinical cohorts, including trial cohorts treated with pembrolizumab.

Results: High TIL Infiltrates consisted primarily of CD3+ T cells, with both CD8 and CD4 populations. Unsupervised clustering of single cell sequencing identified 9 CD8 and CD4 subpopulations with distinct gene expression profiles. In addition to Tregs and CD8 effector memory (TEM) T cells, we found a CD8+ tissue resident memory (TRM) population expressing greater levels of T-cell checkpoints and cytotoxic markers compared to effector memory cells. In 2 primary tumours and 1 liver metastasis, bulk RNASeq of flow sorted TEM and TRM corroborated the single cell mRNASeq results. T cell receptor profiling (TCR) in the 3 samples found non-overlapping repertoires in the 2 primary tumours, but overlap in one metastatic lesion, suggesting divergent developmental origins in the breast, but the potential for nascent TRM differentiation in a metastatic niche. Clustering of these TCRs suggested differing antigen specificities between TRM and non-TRM CD8 T cells. Using Metabric data, the CD8 TRM gene expression signature was prognostic for disease free survival (DFS) in primary TNBCs (n=329, log-rank p=0.003), and was able to further stratify cases with high and low CD8A expression for DFS (log-rank p = 0.03). The CD8 TRM signature was enriched in baseline tumour samples of responders (n = 9) compared with non-responders (n=36) in 45 patients with metastatic melanoma treated with T cell checkpoint blockade (p < 0.0001). Additional single cell sequencing data with TCR sequencing will be combined with these initial results, and an independent data set of single cell mRNASeq and TCR Seq on CD3+ BC TILs will be used to confirm our findings. Cell type specific signatures will be explored in additional clinical cohorts including KEYNOTE-086, and presented at the meeting.

Conclusion: Using single cell profiling of the immune microenvironment in BC we demonstrate that high TIL BCs contain multiple T cell subpopulations with different functional and prognostic significance. Our approach identified a CD8 TRM population with a distinct gene expression profile and strong expression of key immune checkpoints likely representing the presence of true tumor specific immunity. This population may be a key target of immune checkpoint blockade.

Citation Format: Savas P, Virassamy B, Ye C, Salim A, Mintoff CP, Caramia F, Salgado R, Teo ZL, Dushyanthen S, Byrne A, Luen SJ, Fox SB, Speed TP, Mackay LK, Neeson PJ, Loi S. Characterization of high TIL breast cancers reveals a prognostic and functionally distinct tissue-resident memory subpopulation [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 PD5-03.

Advancing Immunotherapy in Metastatic Breast Cancer

OPINION STATEMENT

Despite many advances in the treatment of breast cancer, the development of metastatic disease remains an incurable and frequent cause of cancer death for women worldwide. An improved understanding of the role of host immunosurveillance in modulating breast cancer disease biology, as well as impressive survival benefits seen to checkpoint blockade in other malignancies have provided great hope for an expanding role of immunotherapies in breast cancer management. While these novel therapies are currently being investigated in clinical trials, signals of efficacy, and tolerability in early phase studies suggest these will eventually make their way into standard practice algorithms. Ongoing research has highlighted a high degree of intertumoural heterogeneity in tumour lymphocytic infiltrates, suggesting some tumours or subtypes are more immunogenic than others. Furthermore, tumour intrinsic mechanisms of immune evasion are beginning to be uncovered, potentially representing key therapeutic targets to use in combination with checkpoint blockade, exemplifying the emerging concept of personalised medicine approaches to immune therapies. Subsequently, different immunotherapeutic strategies may be required based on stratification by these factors-for the minority of tumours with a high level of pre-existing immunity, immune checkpoint blockade monotherapy may be sufficient. However, for the majority of tumours with lower levels of pre-existing immunity, combination approaches will likely be required to achieve maximal therapeutic effect. Results of ongoing clinical trials including combinations with chemotherapy, radiation therapy, and targeted therapies are eagerly awaited.

Agonist immunotherapy restores T cell function following MEK inhibition improving efficacy in breast cancer

The presence of tumor-infiltrating lymphocytes in triple-negative breast cancers is correlated with improved outcomes. Ras/MAPK pathway activation is associated with significantly lower levels of tumor-infiltrating lymphocytes in triple-negative breast cancers and while MEK inhibition can promote recruitment of tumor-infiltrating lymphocytes to the tumor, here we show that MEK inhibition adversely affects early onset T-cell effector function. We show that α-4-1BB and α-OX-40 T-cell agonist antibodies can rescue the adverse effects of MEK inhibition on T cells in both mouse and human T cells, which results in augmented anti-tumor effects in vivo. This effect is dependent upon increased downstream p38/JNK pathway activation. Taken together, our data suggest that although Ras/MAPK pathway inhibition can increase tumor immunogenicity, the negative impact on T-cell activity is functionally important. This undesirable impact is effectively prevented by combination with T-cell immune agonist immunotherapies resulting in superior therapeutic efficacy.MEK inhibition in breast cancer is associated with increased tumour infiltrating lymphocytes (TILs), however, MAPK activity is required for T cells function. Here the authors show that TILs activity following MEK inhibition can be enhanced by agonist immunotherapy resulting in synergic therapeutic effects.

Correction: The Subclonal Architecture of Metastatic Breast Cancer: Results from a Prospective Community-Based Rapid Autopsy Program "CASCADE"

[This corrects the article DOI: 10.1371/journal.pmed.1002204.].

The Subclonal Architecture of Metastatic Breast Cancer: Results from a Prospective Community-Based Rapid Autopsy Program "CASCADE"

BACKGROUND

Understanding the cancer genome is seen as a key step in improving outcomes for cancer patients. Genomic assays are emerging as a possible avenue to personalised medicine in breast cancer. However, evolution of the cancer genome during the natural history of breast cancer is largely unknown, as is the profile of disease at death. We sought to study in detail these aspects of advanced breast cancers that have resulted in lethal disease.

METHODS AND FINDINGS

Three patients with oestrogen-receptor (ER)-positive, human epidermal growth factor receptor 2 (HER2)-negative breast cancer and one patient with triple negative breast cancer underwent rapid autopsy as part of an institutional prospective community-based rapid autopsy program (CASCADE). Cases represented a range of management problems in breast cancer, including late relapse after early stage disease, de novo metastatic disease, discordant disease response, and disease refractory to treatment. Between 5 and 12 metastatic sites were collected at autopsy together with available primary tumours and longitudinal metastatic biopsies taken during life. Samples underwent paired tumour-normal whole exome sequencing and single nucleotide polymorphism (SNP) arrays. Subclonal architectures were inferred by jointly analysing all samples from each patient. Mutations were validated using high depth amplicon sequencing. Between cases, there were significant differences in mutational burden, driver mutations, mutational processes, and copy number variation. Within each case, we found dramatic heterogeneity in subclonal structure from primary to metastatic disease and between metastatic sites, such that no single lesion captured the breadth of disease. Metastatic cross-seeding was found in each case, and treatment drove subclonal diversification. Subclones displayed parallel evolution of treatment resistance in some cases and apparent augmentation of key oncogenic drivers as an alternative resistance mechanism. We also observed the role of mutational processes in subclonal evolution. Limitations of this study include the potential for bias introduced by joint analysis of formalin-fixed archival specimens with fresh specimens and the difficulties in resolving subclones with whole exome sequencing. Other alterations that could define subclones such as structural variants or epigenetic modifications were not assessed.

CONCLUSIONS

This study highlights various mechanisms that shape the genome of metastatic breast cancer and the value of studying advanced disease in detail. Treatment drives significant genomic heterogeneity in breast cancers which has implications for disease monitoring and treatment selection in the personalised medicine paradigm.

PALB2, CHEK2 and ATM rare variants and cancer risk: data from COGS

BACKGROUND

The rarity of mutations in PALB2, CHEK2 and ATM make it difficult to estimate precisely associated cancer risks. Population-based family studies have provided evidence that at least some of these mutations are associated with breast cancer risk as high as those associated with rare BRCA2 mutations. We aimed to estimate the relative risks associated with specific rare variants in PALB2, CHEK2 and ATM via a multicentre case-control study.

METHODS

We genotyped 10 rare mutations using the custom iCOGS array: PALB2 c.1592delT, c.2816T>G and c.3113G>A, CHEK2 c.349A>G, c.538C>T, c.715G>A, c.1036C>T, c.1312G>T, and c.1343T>G and ATM c.7271T>G. We assessed associations with breast cancer risk (42 671 cases and 42 164 controls), as well as prostate (22 301 cases and 22 320 controls) and ovarian (14 542 cases and 23 491 controls) cancer risk, for each variant.

RESULTS

For European women, strong evidence of association with breast cancer risk was observed for PALB2 c.1592delT OR 3.44 (95% CI 1.39 to 8.52, p=7.1×10-5), PALB2 c.3113G>A OR 4.21 (95% CI 1.84 to 9.60, p=6.9×10-8) and ATM c.7271T>G OR 11.0 (95% CI 1.42 to 85.7, p=0.0012). We also found evidence of association with breast cancer risk for three variants in CHEK2, c.349A>G OR 2.26 (95% CI 1.29 to 3.95), c.1036C>T OR 5.06 (95% CI 1.09 to 23.5) and c.538C>T OR 1.33 (95% CI 1.05 to 1.67) (p≤0.017). Evidence for prostate cancer risk was observed for CHEK2 c.1343T>G OR 3.03 (95% CI 1.53 to 6.03, p=0.0006) for African men and CHEK2 c.1312G>T OR 2.21 (95% CI 1.06 to 4.63, p=0.030) for European men. No evidence of association with ovarian cancer was found for any of these variants.

CONCLUSIONS

This report adds to accumulating evidence that at least some variants in these genes are associated with an increased risk of breast cancer that is clinically important.

Relevance of tumor-infiltrating lymphocytes in breast cancer

While breast cancer has not been considered a cancer amenable to immunotherapeutic approaches, recent studies have demonstrated evidence of significant immune cell infiltration via tumor-infiltrating lymphocytes in a subset of patient tumors. In this review we present the current evidence highlighting the clinical relevance and utility of tumor-infiltrating lymphocytes in breast cancer. Retrospective and prospective studies have shown that the presence of tumor-infiltrating lymphocytes is a prognostic marker for higher responses to neoadjuvant chemotherapy and better survival, particularly in triple negative and HER2-positive early breast cancer. Further work is required to determine the immune subsets important in this response and to discover ways of encouraging immune infiltrate in tumor-infiltrating lymphocytes-negative patients.

Molecular segmentation of luminal breast: Reality in 2015?

PURPOSE

With the advent of next generation sequencing, we are beginning to get a clearer picture of the landscape of genetic alterations in primary breast cancer. One of the key findings has been the heterogeneity of mutational profiles, with no two primary breast tumors being alike. How these genetic alterations will help us manage patients is currently unclear. Studies are ongoing to determine which genetic alterations will signify "oncogenic addiction" and which ones will determine resistance and relapse to current standard therapies.

Integrin linked kinase (ILK) is required for lens epithelial cell survival, proliferation and differentiation

While the role of growth factors in lens development has been investigated extensively, the role of extracellular matrix signalling is less well understood. The developing lens expresses predominantly laminin-binding integrins (such as α3β1, α6β1), which are cooperatively required in the lens epithelium during development. We investigated the role of ILK, a downstream mediator of integrin signalling in mice conditionally null for Ilk. Mutant lenses showed epithelial thinning at E17.5 with reduced proliferation and epithelial cell number and aberrant fibre differentiation. There was complete loss of the central epithelium from postnatal day (P) 2 due to cell death followed by fibre cell degeneration and death by P10 as well as rupture of the lens capsule between P10 and P21. At E17.5 there was significant inhibition (∼50%) of epithelial cell cycle progression, as shown by BrdU incorporation, cyclin D1/D2 and phospho-histone H3 immunostaining. The epithelial marker, E-cadherin, was decreased progressively from E17.5 to P2, in the central epithelium, but there was no significant change in Pax6 expression. Analyses of ERK and Akt phosphorylation indicated marked depression of MAPK and PI3K-Akt signalling, which correlated with decreased phosphorylation of FRS2α and Shp2, indicating altered activation of FGF receptors. At later postnatal stages there was reduced or delayed expression of fibre cell markers (β-crystallin and p57(kip2)). Loss of Ilk also affected deposition of extracellular matrix, with marked retention of collagen IV within differentiating fibre cells. By quantitative RT-PCR array there was significantly decreased expression of 19 genes associated with focal adhesions, actin filament stability and MAPK and PI3K/Akt signalling. Overall, these data indicate that ILK is required for complete activation of signalling cascades downstream of the FGF receptor in lens epithelium and fibre cells during development and thus is involved in epithelial proliferation, survival and subsequent fibre differentiation.