Abstract 4053: NGY-B is a novel inhibitor of MCT transporters blocking lactate and glucose metabolisms

Aberrant glycolytic flux and mitochondrial respiration are known to drive tumor progression and metastasis. Therefore, targeting metabolic alterations in cancer is critical for developing novel cancer therapeutics. We have developed NGY-B as a first-in-Class small molecule inhibitor of the lactate transporters, MCT1 and MCT4, that also decreases mitochondrial respiration. These transporters play a crucial role in regulating both glycolysis and oxidative phosphorylation in cancer cells. NGY-B treatment exhibited potent in vitro cytotoxicity in cancer cells with various levels of MCT1 and MCT4 expression. The on-target activity of NGY-B was validated by measuring intracellular and extracellular lactate levels. NGY-B blocks lactate import through MCT1 under high lactate conditions and lactate export through MCT4 in high glucose conditions. Seahorse and U-13C-glucose tracing analysis demonstrated NGY-B treatment modulates glycolysis and oxidative phosphorylation consistent with the lactate measurement data. Therefore, NGY-B is a novel inhibitor of MCT1/4 while also exhibiting inhibition of mitochondrial respiration.

Citation Format: Sambad Sharma, Gregory Goreczny, Nicole Bowman, Jennifer Duffy, Daliya Banerjee, Sanath Wijerathna, John Dzuris, Jaime Escobedo, Vincent Sandanayaka. NGY-B is a novel inhibitor of MCT transporters blocking lactate and glucose metabolisms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4053.

Abstract 1702: SunCatcher: Clonal barcoding with qPCR-based detection enables live cell functional analyses and generation of custom cell pools

Single cell “omics” and lineage tracing analyses are valuable tools for studying heterogeneity and clonal dynamics. However, current clonal analyses do not easily enable live cell retrieval. That is a particular issue when further study of cells that were targeted for elimination or otherwise not selected during an experiment could provide critical information. We report a clonal molecular barcoding method, called SunCatcher, that enables longitudinal tracking and retrieval of live cells. Single cell-derived clonal populations are generated from complex cell population, each is infected with a unique, heritable molecular barcode, and stocks of each individual barcoded clone (BC) are retained. BCs can be combined to create a version of the original cell population or to generate custom BC pools. We developed a highly sensitive, accurate, rapid, and inexpensive qPCR-based method for identifying and quantifying BCs in vitro and in vivo.We applied SunCatcher to various breast cancer cell lines, including murine Met1 triple negative breast cancer line. A heterogeneous pool comprised of 31 Met1 BCs reliably reproduced the proliferation rate, tumor-forming capacity, and cancer progression as the original parental cell line. Individual BCs, however, displayed significant differences in proliferation, tumor formation, and breast cancer cell hallmarks: cytokeratin 8/14, Zeb1 (mesenchymal marker), EpCAM (epithelial marker) PD-L1 (immune checkpoint protein) and MHC-I (antigen presentation). Five BCs consistently dominated the primary tumors at the ethical end point of 21 days: BC2, BC8, BC25, BC53, BC67. Interestingly, not all 5 BCs were the fastest growing clones, suggesting in vitro proliferation does not correlate with clone expansion in vivo. Two clones (BC43, 18) were not detected in the primary tumors at ethical endpoint, yet when injected alone, had tumor-forming capacity after a long latency (~60 days). Therefore, SunCatcher enabled identification of clones that are consequential for disease progression that would otherwise not be identified during pre-clinical experimentation. Using SunCatcher, we successfully detected Met1 spontaneous metastases as early as 3 weeks in the lung, long bone, and mandible. Long bone had the highest incidence and metastatic burden and were dominated by BC53 and 8 in 3/5 mice. Lung had lower metastatic burden and BC53 was the dominant clone in 4/4 mice. BC8 was exclusive to bone, suggesting site-specific metastasis capacity for different tumor clones. SunCatcher is a reliable, inexpensive, and rapid clonal barcoding method that enables deeper understanding of heterogeneity and clonal dynamics. We identified and analyzed BCs that were responsible for cancer progression, and, for the first time, could analyze BCs that were negatively selected during cancer progression. We envision that SunCatcher will be a useful cancer research tool.

Citation Format: Qiuchen Guo, Milos Spasic, Adam Maynard, Gregory Goreczny, Amanuel Bizuayehu, Jessica Olive, Sandra McAllister. SunCatcher: Clonal barcoding with qPCR-based detection enables live cell functional analyses and generation of custom cell pools [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1702.

Abstract 1773: Overcoming paclitaxel resistance in triple-negative breast cancer using a novel barcoding technology

Triple-negative breast cancer (TNBC) is an aggressive breast cancer subtype for which chemotherapy remains a part of standard treatment. Although pathologic complete response (pCR) after neoadjuvant chemotherapy, including paclitaxel (PTX), is associated with good outcomes, 50-60% of TNBC patients do not experience pCR and suffer poor long-term outcomes, often due to chemotherapy resistance. Identifying and analyzing the tumor cells responsible for chemotherapy resistance will lead to improved treatment strategies.

We developed a model of TNBC resistance to neoadjuvant PTX using Met1 murine mammary carcinoma cells. To study clonal dynamics in response to PTX we developed a barcoding method, SunCatcher. First, 31 single-cell derived clonal populations were generated from parental Met1 cells. Each clone was infected with a lentiviral vector containing a unique DNA barcode detectable by qPCR. All barcoded clones (BCs) were mixed in equivalent numbers to generate a BC pool that we confirmed captures the parental Met1 heterogeneity and tumor growth kinetics.

First, PTX responses were tested in vitro. The BC pool had an IC50 of ~100 nM, while individual BCs ranged in IC50 from 5 nM to 25 µM. We maintained the BC pool in 100 nM PTX for 39 days (termed long-term PTX; LTP), at which point it became clonal for BC25, suggesting that BC25 (IC50 of 100 nM) is uniquely PTX resistant, despite being the most proliferative and Zeb1hi/EpCAMlow clone in vitro. BC25 was not detected in the control-treated BC pool at 39 days.

Next, the BC pool was orthotopically injected into FVB/NJ mice and treated the mice with 20 mg/kg PTX on days 7, 11, and 15. At the day 18 experimental endpoint, tumor volume significantly decreased by 56% in response to PTX compared to control. BC25 composition increased from 7.7% (controls) to 15% (PTX treated) within the tumors at endpoint. We also injected BC25 and LTP cells alone and administered the same PTX regimen once tumors reached 50 mm3. Both BC25 and LTP tumors were unresponsive to PTX and had a longer latency period (35d) than BC pool (10d).

We performed a drug screen of 2313 compounds spanning FDA-approved cancer therapeutics on the LTP cells to identify compounds to target the PTX-resistant clone. HDAC inhibitors were the most potent class of hits and one, Panobinostat, killed LTP cells with an IC50 of 4.3 nM.

Utilizing SunCatcher, we identified a unique PTX-resistant TNBC subclone that represents residual disease associated with poor long-term outcome. Typical in vivo experiments would have reached ethical endpoint before BC25 had a chance to grow, given its long latency, therefore this PTX-resistant clone would not have been identified. This is an important finding because therapeutic resistance can emerge after a protracted period, longer than typical pre-clinical experiments. Further work will explore mechanisms of resistance and the potential for combination therapies to prevent recurrent disease.

Citation Format: Milos Spasic, Qiuchen Guo, Adam Maynard, Gregory Goreczny, Adrienne Waks, Sara Tolaney, Elizabeth Mittendorf, Sandra McAllister. Overcoming paclitaxel resistance in triple-negative breast cancer using a novel barcoding technology [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1773.

Abstract 2652: Efficacy of a small molecule MCT1 and MCT4 transporter inhibitor in cancer

Targeting metabolic pathways has been a major clinical interest to effectively treat cancer patients. FDA approval of TIVSOVO(R) (IDH1 inhibitor) has validated the clinical importance of targeting tumor metabolism in cancer. Although MCT1-targeting small molecule inhibitor is currently under investigation for lymphoid cancers, the therapeutic efficacy of this compound is compromised by compensatory overexpression of MCT4 by tumor cells. Therefore, there is a need for a dual MCT1/4 inhibitor to target cancer. We have developed a first-in-class orally bioavailable small molecule inhibitor that targets lactate transport through MCT1 and MCT4 transporters. In 4T1 syngeneic model, we observed a significant dose-dependent reduction of tumor growth by NGY-B treatment that also correlated with serum lactate levels. Immunoprofiling of tumors revealed that NGY-B promoted anti-tumor immune response in 4T1 tumor bearing mice indicating simultaneous immune activation. Also, the combination of NGY-B with a checkpoint inhibitor led to greater efficacy and overall survival in this model suggesting a potential combination therapy in the clinic. Furthermore, we demonstrated the direct tumor cell killing effect of NGY-B in multiple human CDX and PDX models. Therefore, NGY-B intervenes two key hallmarks of cancer - tumor metabolism and anti-tumor immunity, and provides a novel modality to therapeutically target cancer.

Citation Format: Sambad Sharma, Gregory Goreczny, Nicole Bowman, Jennifer Duffy, Daliya Banerjee, Sanath Wijerathna, John Dzuris, Kerui Wu, Shih-Ying Wu, Abhishek Tyagi, Kounosuke Watabe, Jaime Escobedo, Vincent Sandanayaka. Efficacy of a small molecule MCT1 and MCT4 transporter inhibitor in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2652.

Abstract 1268: A novel treatment approach for melanoma by dually targeting MCT1 and MCT4 lactate transporters

Cancer cells are metabolically rewired to activate glycolysis, which results in the generation and excretion of lactate as a byproduct. Although lactate was previously thought to be a waste product of anaerobic respiration, increasing evidence has revealed that distinct cell populations within tumors use lactate as a source of energy through TCA cycle. This metabolic symbiosis between distinct cell populations, hypoxic lactate consumers, and oxidative glycolytic lactate exporters within the tumor is regulated by differential expression of lactate transporters, mainly MCT1 and MCT4. Therefore, dual targeting of MCT1 and MCT4 is a novel approach to treat cancer. We have developed a compound, NGY-B, which binds and inhibits both MCT1 and MCT4 transporters. This compound has shown to significantly increase intracellular lactate levels in melanoma models and thereby decreasing in vitro cell proliferation. When cultured in the media with exogenous lactate to mimic the tumor microenvironment, NGY-B greatly reduced lactate uptake by cancer cells. Mechanistically, NGY-B deactivated glycolytic pathway by reducing hexokinase 2 (HK2), phosphoglycerate dehydrogenase (PHGDH), and pyruvate dehydrogenase kinase 1 (PDK1) expression. Additionally, NGY-B treatment strongly decreased STAT3 and mTOR signaling pathways. Furthermore, the in vivo therapeutic efficacy of NGY-B was validated in xenograft and syngeneic mouse models of melanoma. While a significant reduction in tumor size was observed in A375 xenograft model treated with NGY-B, a robust tumor growth reduction was evident in SM1 immunocompetent syngeneic melanoma mouse model, suggesting the involvement of immune cells for higher response in this model. Supporting this premise, we also found that NGY-B treated cells showed a decrease in PD-L1, B7-H3, and B7-H4 expression. Overall, our results indicate that NGY-B inhibits melanoma by targeting metabolic symbiosis and activating antitumor immune response mechanisms.

Citation Format: Sambad Sharma, Gregory Goreczny, Satish Kumar Noonepalle, Erica Palmer, Maria Garcia-Hernandez, Daliya Banerjee, Jaime Escobedo, Alejandro Villagra, Vincent Sandanayaka. A novel treatment approach for melanoma by dually targeting MCT1 and MCT4 lactate transporters [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1268.

Abstract 1955: Investigating anti-tumor immunity with CDK4/6 inhibition in triple negative breast cancer

The purpose of our study is to evaluate the immunological effects of CDK4/6 inhibitors in pre-clinical models of triple negative breast cancer (TNBC). CDK4/6 inhibitors, including abemaciclib, are currently approved to treat patients with metastatic hormone receptor-positive (HR+), Her2-negative breast cancer. We previously reported in our HR+ model that CDK4/6 inhibitors promote anti-tumor immunity by inducing tumor cell antigen presentation via activating tumor endogenous retroviral elements, which induce type III interferon production and MHC-I upregulation (Goel, DeCristo, et al., Nature, 2017). We also uncovered important anti-tumor effects on the immune system: CDK4/6 inhibitors decrease T regulatory cell proliferation without affecting cytotoxic CD8 T cell numbers. TNBC has been considered a poor candidate for CDK4/6 inhibitor therapy, as tumors often lose retinoblastoma (Rb) protein expression/function, which is critical for CDK4/6 inhibitor-induced cell cycle arrest. However, Rb mutation or loss occurs in only ~20% of TNBC cases and we found Rb expressing murine and human TNBC cell lines decreased proliferation in vitro in response to abemaciclib. In our preclinical model of TNBC, abemaciclib suppressed tumor growth Consistent with previous findings, TNBC tumor cells upregulated MHC-I upon abemaciclib treatment, suggesting increased antigen presentation. Tumor cell-surface PD-L1 was also increased with abemaciclib both in vitro and in vivo, as assessed by flow cytometry and RT-qPCR. These results are encouraging, given that αPD-L1 therapy (Atezolizumab) in combination with chemotherapy (nab-paclitaxel) has recently been approved as standard care for metastatic TNBC and the IMpassion130 trial reported enhanced progression-free and overall survival in patients with PD-L1+ tumors. However, treatment with Palbociclib did not increase tumor PD-L1 level, suggesting the potential functional variances between different CDK4/6 inhibitors. Our data therefore suggest the potential efficacy of abemaciclib in combination with αPD-L1 in the treatment of Rb+ TNBC. We also found that abemaciclib increased CD8+ and CD4+ T cells and decreased PD1+ CD8 and CD4 cells in the spleen. Furthermore, total numbers of naïve CD8+ and CD4+ T cells increased with abemaciclib treatment, suggesting a favorable anti-tumor systemic immunological effect. We recently performed RNAseq on abemaciclib-treated TNBC and while we do not have the results at this time, they will be analyzed and prepared for presentation at the meeting. Deeper analysis of the mechanisms involved in regulation of PD-L1 expression and enhancement of naïve T cells should enable us to evaluate combination therapies using CDK4/6 inhibitors for this particularly deadly breast cancer subtype.

Citation Format: Qiuchen Guo, Milos Spasic, Gregory Goreczny, Adam Maynard, Sandra McAllister. Investigating anti-tumor immunity with CDK4/6 inhibition in triple negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1955.

The focal adhesion scaffold protein Hic-5 regulates vimentin organization in fibroblasts

Focal adhesion (FA)-stimulated reorganization of the F-actin cytoskeleton regulates cellular size, shape, and mechanical properties. However, FA cross-talk with the intermediate filament cytoskeleton is poorly understood. Genetic ablation of the FA-associated scaffold protein Hic-5 in mouse cancer-associated fibroblasts (CAFs) promoted a dramatic collapse of the vimentin network, which was rescued following EGFP-Hic-5 expression. Vimentin collapse correlated with a loss of detergent-soluble vimentin filament precursors and decreased vimentin S72/S82 phosphorylation. Additionally, fluorescence recovery after photobleaching analysis indicated impaired vimentin dynamics. Microtubule (MT)-associated EB1 tracking and Western blotting of MT posttranslational modifications indicated no change in MT dynamics that could explain the vimentin collapse. However, pharmacological inhibition of the RhoGTPase Cdc42 in Hic-5 knockout CAFs rescued the vimentin collapse, while pan-formin inhibition with SMIFH2 promoted vimentin collapse in Hic-5 heterozygous CAFs. Our results reveal novel regulation of vimentin organization/dynamics by the FA scaffold protein Hic-5 via modulation of RhoGTPases and downstream formin activity.