INHBA is a mediator of aggressive tumor behavior in HER2+ basal breast cancer

Background

Resistance to HER2-targeted therapeutics remains a significant clinical problem in HER2+ breast cancer patients with advanced disease. This may be particularly true for HER2+ patients with basal subtype disease, as recent evidence suggests they receive limited benefit from standard of care HER2-targeted therapies. Identification of drivers of resistance and aggressive disease that can be targeted clinically has the potential to impact patient outcomes.

Methods

We performed siRNA knockdown screens of genes differentially expressed between lapatinib-responsive and -resistant HER2+ breast cancer cells, which corresponded largely to luminal versus basal subtypes. We then validated hits in 2-d and 3-d cell culture systems.

Results

Knockdown of one of the genes, INHBA, significantly slowed growth and increased sensitivity to lapatinib in multiple basal HER2+ cell lines in both 2-d and 3-d cultures, but had no effect in luminal HER2+ cells. Loss of INHBA altered metabolism, eliciting a shift from glycolytic to oxidative phosphorylative metabolism, which was also associated with a decrease in tumor invasiveness. Analysis of breast cancer datasets showed that patients with HER2+ breast cancer and high levels of INHBA expression had worse outcomes than patients with low levels of INHBA expression.

Conclusions

Our data suggest that INHBA is associated with aggressiveness of the basal subtype of HER2+ tumors, resulting in poor response to HER2-targeted therapy and an invasive phenotype. We hypothesize that targeting this pathway could be an effective therapeutic strategy to reduce invasiveness of tumor cells and to improve therapeutic response.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13058-022-01512-4.

Sensitivity to targeted therapy differs between HER2-amplified breast cancer cells harboring kinase and helical domain mutations in PIK3CA

BACKGROUND

HER2-amplified breast cancer is a clinically defined subtype of breast cancer for which there are multiple viable targeted therapies. Resistance to these targeted therapies is a common problem, but the mechanisms by which resistance occurs remain incompletely defined. One mechanism that has been proposed is through mutation of genes in the PI3-kinase pathway. Intracellular signaling from the HER2 pathway can occur through PI3-kinase, and mutations of the encoding gene PIK3CA are known to be oncogenic. Mutations in PIK3CA co-occur with HER2-amplification in ~ 20% of cases within the HER2-amplified subtype.

METHODS

We generated isogenic knockin mutants of each PIK3CA hotspot mutation in HER2-amplified breast cancer cells using adeno-associated virus-mediated gene targeting. Isogenic clones were analyzed using a combinatorial drug screen to determine differential responses to HER2-targeted therapy. Western blot analysis and immunofluorescence uncovered unique intracellular signaling dynamics in cells resistant to HER2-targeted therapy. Subsequent combinatorial drug screens were used to explore neuregulin-1-mediated resistance to HER2-targeted therapy. Finally, results from in vitro experiments were extrapolated to publicly available datasets.

RESULTS

Treatment with HER2-targeted therapy reveals that mutations in the kinase domain (H1047R) but not the helical domain (E545K) increase resistance to lapatinib. Mechanistically, sustained AKT signaling drives lapatinib resistance in cells with the kinase domain mutation, as demonstrated by staining for the intracellular product of PI3-kinase, PIP3. This resistance can be overcome by co-treatment with an inhibitor to the downstream kinase AKT. Additionally, knockout of the PIP3 phosphatase, PTEN, phenocopies this result. We also show that neuregulin-1, a ligand for HER-family receptors, confers resistance to cells harboring either hotspot mutation and modulates response to combinatorial therapy. Finally, we show clinical evidence that the hotspot mutations have distinct expression profiles related to therapeutic resistance through analysis of TCGA and METABRIC data cohorts.

CONCLUSION

Our results demonstrate unique intracellular signaling differences depending on which mutation in PIK3CA the cell harbors. Only mutations in the kinase domain fully activate the PI3-kinase signaling pathway and maintain downstream signaling in the presence of HER2 inhibition. Moreover, we show there is potentially clinical importance in understanding both the PIK3CA mutational status and levels of neuregulin-1 expression in patients with HER2-amplified breast cancer treated with targeted therapy and that these problems warrant further pre-clinical and clinical testing.

Abstract 1870: The impact of the microenvironment on heterogeneity and trametinib response in HCC1143 triple negative breast cancer cells

Triple negative breast cancer (TNBC) lacks expression of hormone receptors (ER and PR) and HER2 and is characterized by aggressive disease with poor outcomes. Recent work suggests that TNBC also has a high degree of intratumoral heterogeneity, as measured by lineage differentiation status. This heterogeneity may impact therapeutic response, as it has been shown that treatment with PI3K/mTOR (BEZ235) or MEK (trametinib) inhibitors can drive TNBC cells into more homogeneous states, but that the surviving cells are resistant to the targeted therapy. In this study, we sought to understand how the microenvironment impacts differentiation state heterogeneity and response to targeted therapeutics in HCC1143 cells using our microenvironment microarray (MEMA) platform. Under low serum growth conditions, we found that several ligands could drive the growth of HCC1143, particularly EGF family ligands like AREG and EGF. With respect to differentiation state and heterogeneity, EGF and TGFB1 drove HCC1143 cells into a more mesenchymal like state, with increased expression of VIM and decreased expression of KRT14. In contrast, BMP2 led to higher levels of KRT14 and lower levels of VIM, leading to a more basal-like state. We also grew HCC1143 on MEMA with trametinib treatment. Here we found that combinations of collagen-based substrates and NRG1, HGF, and EGF ligands all led to higher cell counts and EdU incorporation rates compared to PBS-control treated cells. However, the levels of resistance conferred by the microenvironment was less than we had previously seen in HER2 positive MEMA, as the GR50 values (dose required to inhibit growth by 50%) only increased modestly (18 nM for untreated cells, 40 nM for NRG1, 45 nM for HGF). Interestingly, in that HER2 positive MEMA study, we identified HGF and NRG1 as potent resistance factors to lapatinib, but that they functioned in a subtype specific manner. HGF was effective in basal subtype cells and NRG1 in luminal, but not vice versa. We postulated that the modest resistance we observed was due to ligands acting on subsets of cells. We thus treated cells with a combination of NRG1 plus HGF, and found that this resulted in increased resistance (GR50= 91 nM). Imaging showed that trametinib drove HCC1143 cells to a homogenous KRT14 positive state, but surprisingly, addition of ligands reverted the cells to a more heterogeneous state that was resistant to trametinib. These data demonstrate that the microenvironment can impact the differentiation state of TNBC cells and is also capable of conferring resistance within subsets of the heterogeneous cell populations.

Citation Format: Rebecca Smith, Kaylyn Devlin, Moqing Liu, Tiera Liby, David Kilburn, Elmar Bucher, Damir Sudar, Guillaume Thibault, Mark Dane, Joe Gray, Laura Heiser, James E. Korkola. The impact of the microenvironment on heterogeneity and trametinib response in HCC1143 triple negative breast cancer cells [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1870.

Abstract B04: Palbociclib-based combinatorial drug screening in ER-positive cell lines identifies efficacious single agents and novel combinations with synergistic interactions

Estrogen receptor (ER)-positive breast cancer is associated with a good prognosis, but when ER+ breast tumors progress, treatment options are limited. The combination of the CDK inhibitor palbociclib plus the ER degrader fulvestrant was recently approved for patients who have recurrences of ER+ disease. However, durable responses are not typically seen with this combination, and patients eventually progress on therapy. We sought to test other drug combinations using palbociclib as the backbone of therapy. We tested 13 different FDA-approved drugs in combination with palbocilib in a panel of 7 ER+ breast cancer cell lines (600MPE, MDAMB134vii, MDAMB415, ZR75-1, ZR75B, and MCF7). Molecularly, all lines were characterized by amplification of the CCND1 region, high levels of expression of ER, and low RNA expression of EGFR. CAMA1 showed general resistance to the drugs used, never reaching a GR50 (growth rate inhibition of 50%) even at the highest dose tested with palbociclib. CAMA1 was also resistant to the majority of the other 13 drugs, with the exception of panobinostat, vorinostat, and everolimus. Across the entire cell line set, these three compounds were the most effective as single agents. For example, the HDAC inhibitors panobinostat and vorinostat had low nanomolar GR50 values in 7/7 and 4/7 cell lines, respectively. However, significant antagonism was observed between both HDAC inhibitors and palbociclib in MCF7, ZR75B, and ZR75-1, indicating that combining these agents may not be clinically effective. Everolimus plus palbociclib and trametinib plus palbociclib combinations were significantly synergistic in 3/7 cell lines (600MPE, ZR75B, and MCF7 in both cases). Interestingly, CAMA1 and MDAMB134 never showed any evidence of synergistic interactions with any of the combinations tested, suggesting that they may be a distinct subset of ER+ breast cancers. This study indicates that HDAC inhibitors may be effective for treating ER+ tumors that have progressed on antiestrogen therapy, and that combinations of palbociclib plus everolimus or trametinib may also have efficacy.

Citation Format: Rebecca Smith, Tiera Liby, Joe Gray, James Korkola. Palbociclib-based combinatorial drug screening in ER-positive cell lines identifies efficacious single agents and novel combinations with synergistic interactions [abstract]. In: Proceedings of the AACR Special Conference: Advances in Breast Cancer Research; 2017 Oct 7-10; Hollywood, CA. Philadelphia (PA): AACR; Mol Cancer Res 2018;16(8_Suppl):Abstract nr B04.

Microenvironment-Mediated Mechanisms of Resistance to HER2 Inhibitors Differ between HER2+ Breast Cancer Subtypes

Extrinsic signals are implicated in breast cancer resistance to HER2-targeted tyrosine kinase inhibitors (TKIs). To examine how microenvironmental signals influence resistance, we monitored TKI-treated breast cancer cell lines grown on microenvironment microarrays composed of printed extracellular matrix proteins supplemented with soluble proteins. We tested ~2,500 combinations of 56 soluble and 46 matrix microenvironmental proteins on basal-like HER2+ (HER2E) or luminal-like HER2+ (L-HER2+) cells treated with the TKIs lapatinib or neratinib. In HER2E cells, hepatocyte growth factor, a ligand for MET, induced resistance that could be reversed with crizotinib, an inhibitor of MET. In L-HER2+ cells, neuregulin1-β1 (NRG1β), a ligand for HER3, induced resistance that could be reversed with pertuzumab, an inhibitor of HER2-HER3 heterodimerization. The subtype-specific responses were also observed in 3D cultures and murine xenografts. These results, along with bioinformatic pathway analysis and siRNA knockdown experiments, suggest different mechanisms of resistance specific to each HER2+ subtype: MET signaling for HER2E and HER2-HER3 heterodimerization for L-HER2+ cells.

Pathway-Enriched Gene Signature Associated with 53BP1 Response to PARP Inhibition in Triple-Negative Breast Cancer

Effective treatment of patients with triple-negative (ER-negative, PR-negative, HER2-negative) breast cancer remains a challenge. Although PARP inhibitors are being evaluated in clinical trials, biomarkers are needed to identify patients who will most benefit from anti-PARP therapy. We determined the responses of three PARP inhibitors (veliparib, olaparib, and talazoparib) in a panel of eight triple-negative breast cancer cell lines. Therapeutic responses and cellular phenotypes were elucidated using high-content imaging and quantitative immunofluorescence to assess markers of DNA damage (53BP1) and apoptosis (cleaved PARP). We determined the pharmacodynamic changes as percentage of cells positive for 53BP1, mean number of 53BP1 foci per cell, and percentage of cells positive for cleaved PARP. Inspired by traditional dose-response measures of cell viability, an EC₅₀ value was calculated for each cellular phenotype and each PARP inhibitor. The EC₅₀ values for both 53BP1 metrics strongly correlated with IC₅₀ values for each PARP inhibitor. Pathway enrichment analysis identified a set of DNA repair and cell cycle-associated genes that were associated with 53BP1 response following PARP inhibition. The overall accuracy of our 63 gene set in predicting response to olaparib in seven breast cancer patient-derived xenograft tumors was 86%. In triple-negative breast cancer patients who had not received anti-PARP therapy, the predicted response rate of our gene signature was 45%. These results indicate that 53BP1 is a biomarker of response to anti-PARP therapy in the laboratory, and our DNA damage response gene signature may be used to identify patients who are most likely to respond to PARP inhibition. Mol Cancer Ther; 16(12); 2892-901. ©2017 AACR.

Abstract PD5-01: Microenvironment microarrays show that microenvironment mediated resistance mechanisms to lapatinib differ between basal and luminal HER2+ cells

Cell lines represent a valuable model system for the study of breast cancer, as they capture the cellular diversity, mutational spectrum, expression subtypes, and genomic alterations that are observed in clinical specimens. However, like any model system, cell lines are imperfect, particularly when it comes to capturing the effects of the myriad of signals and interactions they encounter in their microenvironment (ME). We are utilizing a technology known as microenvironment microarrays (MEMA) to begin to unravel the consequences of interactions of breast cancer cells with the ME. MEMA consist of thousands of unique combinations of insoluble matrix proteins that are printed to form growth pads with ligands added to the media. Cells are grown on the MEMA spots and the effects of the specific ME that they are exposed to can be read out using immunofluorescent stains of interest. When combined with automated imaging and sophisticated image processing and analysis, the MEMA platform enables the identification of specific ME conditions that alter the phenotypes of cells. We have applied MEMA to understand both baseline responses to the ME as well as how the ME might mediate response to therapeutics. We performed a pilot experiment to investigate the effects of the ME on the response to the HER2-targeted inhibitor lapatinib. We found that HCC1954 cells continued to proliferate robustly in the presence of HGF when treated with 500 nM lapatinib. In contrast, AU565 cells were proliferative in the presence of NRG1 and lapatinib, but not HGF. Focused follow up studies showed that HGF is effective in rescuing only basal HER2+ cells, while NRG1 is effective in rescuing only luminal subtype HER2+cells. Rescue with the relevant growth factor was also observed in 3-d matrigel studies, showing this was not an artifact of the 2-d culture system. We investigated the effects of drug combinations using lapatinib plus drugs that target either MET (Crizotinib) or HER3-HER2 dimers (pertuzumab). These drug combinations were able to overcome the resistance mediated by HGF and NRG1 in basal and luminal cells respectively. We found the effectiveness of pertuzumab particularly interesting, given that lapatinib should still be inhibiting HER2 kinase activity. Parallel studies found that inhibitors targeting other kinase receptors such as IGF1R partially restored sensitivity to HER2 in the presence of NRG1, suggesting a role for such receptors in the resistance. Immunoprecipitation studies showed that IGF1R co-immunoprecipitated with HER2/HER3 when pertuzumab was absent, but that additional of pertuzumab abrogated the binding of IGF1R to HER3, suggesting the formation of HER2-dependent higher order structures that can signal even when HER2 is inhibited. These studies highlight the importance of understanding the effects of the ME on cancer cells, and demonstrate the differences between ME factors that can confer resistance to HER2 targeted inhibitors in basal and luminal HER2+ cells. These findings suggest that both subtype and ME composition may be important in determining response to combinatorial treatments and may be useful to inform clinical decision making.

Citation Format: Korkola JE, Watson S, Smith R, Thompson W, Dame M, Liby T, Bucher E, Sudar D, Nederlof M, Heiser L, Gray JW. Microenvironment microarrays show that microenvironment mediated resistance mechanisms to lapatinib differ between basal and luminal HER2+ cells [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 PD5-01.

Abstract 1347: NTRK1/TRKA as a therapeutic target in castration resistant prostate cancer

Treatment options remain limited for men with castration resistant prostate cancer, with current chemotherapy offering mainly palliative benefits. Thus, there is an urgent need to identify new targets for therapeutic intervention in men who have progressed on anti-androgen therapy. We have compiled a panel of 20 prostate cancer cell lines that has been extensively characterized at the molecular level that enables us to perform high throughput drug and siRNA screens to identify novel therapeutic targets. We performed an siRNA screen targeting kinases using eight representative lines, both in the presence and absence of the anti-androgen MDV3100. Knockdown of NTRK1 (TRKA) significantly inhibited growth in 4/8 of the cell lines tested. To confirm this, we screened the entire panel of cell lines with the inhibitor CEP-701, which targets FLT3, JAK2, and TRK-A/B/C. CEP-701 showed GI50 values (dose required to inhibit growth by 50%) less than 400 nM in 8/20 cell lines. Since this drug had already been tested in clinical trials for prostate cancer and the trials were discontinued due to lack of PSA decline, we looked for other drugs that also inhibit TRKA. Both BIBF-1120 and GSK-1363089 are also known to inhibit TRKA, but neither have been tested in prostate cancer expressing TRKA. We tested GSK-136089 in a subset of 9 prostate cell lines, and found that 4/9 lines reached GI50 at 1 uM or less, including AR mutant or null lines such as 22rv1 and PC3 that are non-responsive to MDV3100. Additional tests with BIBF-1120 and GSK-1363089 are underway. These data suggest that NTRK1 may be a potential target for patients with castration resistant prostate cancer.

Citation Format: James E. Korkola, Moqing Liu, Rebecca Smith, Tiera Liby, Joe W. Gray. NTRK1/TRKA as a therapeutic target in castration resistant prostate 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 1347.

Abstract S6-07: Detrimental effects of sequential compared to concurrent treatment of pertuzumab plus T-DM1 in HER2+ breast cancer cell lines

Background. Pertuzumab and T-DM1 are two recently approved monoclonal antibody based therapies targeting HER2+ breast cancer. Pertuzumab interferes with dimerization of HER family members, while T-DM1 binds to HER2 and interferes with its oncogenic function while also specifically delivering a cytotoxic agent (emtansine). One arm of the I-SPY 2 clinical trial is to investigate the efficacy of a combination Pertuzumab plus T-DM1 in HER2+ breast cancer patients. Methods. We performed pre-clinical screening of response to each agent alone and in combination in a set of 21 HER2+ breast cancer cell lines, with an end goal of identifying markers of response to the therapies. There were five treatment regimens employed in the initial screen: i) pertuzumab alone for 72 h; ii) T-DM1 alone for 72h; iii) pertuzumab plus T-DM1 concurrently for 72h; iv) pertuzumab for 24h followed by addition of T-DM1 for 48h more; and iv) T-DM1 for 24h followed by addition of pertuzumab for 48h more. Response was assessed using the Cell Titer Glo assay as a measure of cell viability. To assess the effects of drug combinations, we used a stringent measure of synergy and antagonism employing the median effect method of Chou and Talalay that included 95% confidence intervals to determine significance. Results. Initial screens showed that concurrent treatment of cells with pertuzumab plus T-DM1 gave significant synergistic interactions in 15/21 cell lines as measured by the median effect method, with combination indices (CI) less than 0.5 (and 95% upper confidence levels less than 1.0) for at least one drug concentration. However, 24h pretreatment with pertuzumab followed by T-DM1 significantly diminished the response of cells to T-DM1, resulting in significant antagonism in 17/21 cell lines test (CI>1.5, lower confidence level greater than 1). Since this could be due to a shorter exposure time to T-DM1, and since patients are scheduled to be treated with pertuzumab first followed by T-DM1 one hour later, we repeated the experiment with one hour between pertuzumab and T-DM1 rather than 24h. While the inhibitory effect was diminished, this treatment regimen still resulted in significant antagonism when T-DM1 was given 1 hour after pertuzumab in 5/5 cell lines tested, in contrast to concurrent pertuzumab plus T-DM1 treatment, which showed synergy. Conclusions. Pertuzumab plus T-DM1 appears to be beneficial when given concurrently, but pretreatment with pertuzumab appears to blunt the efficacy of T-DM1. This has important potential ramifications for patient treatment, and may further elucidate mechanisms of action for both compounds. Further testing will be necessary to determine whether these timing effects are operational in vivo and whether immune effects mitigate the antagonism.

Citation Format: James E Korkola, Moqing Liu, Tiera Liby, Laura Heiser, Heidi Feiler, Joe W Gray. Detrimental effects of sequential compared to concurrent treatment of pertuzumab plus T-DM1 in HER2+ breast cancer cell lines [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr S6-07.