Triple negative breast tumors contain heterogeneous cancer cells expressing distinct KRAS-dependent collective and disseminative invasion programs

Inter-patient and intra-tumoral heterogeneity complicate the identification of predictive biomarkers and effective treatments for basal triple negative breast cancer (b-TNBC). Invasion is the initiating event in metastasis and can occur by both collective and single-cell mechanisms. We cultured primary organoids from a b-TNBC genetically engineered mouse model in 3D collagen gels to characterize their invasive behavior. We observed that organoids from the same tumor presented different phenotypes that we classified as non-invasive, collective and disseminative. To identify molecular regulators driving these invasive phenotypes, we developed a workflow to isolate individual organoids from the collagen gels based on invasive morphology and perform RNA sequencing. We next tested the requirement of differentially regulated genes for invasion using shRNA knock-down. Strikingly, KRAS was required for both collective and disseminative phenotypes. We then performed a drug screen targeting signaling nodes upstream and downstream of KRAS. We found that inhibition of EGFR, MAPK/ERK, or PI3K/AKT signaling reduced invasion. Of these, ERK inhibition was striking for its ability to potently inhibit collective invasion and dissemination. We conclude that different cancer cells in the same b-TNBC tumor can express different metastatic molecular programs and identified KRAS and ERK as essential regulators of collective and single cell dissemination.

Mechano-induced cell metabolism promotes microtubule glutamylation to force metastasis

Mechanical signals from the tumor microenvironment modulate cell mechanics and influence cell metabolism to promote cancer aggressiveness. Cells withstand external forces by adjusting the stiffness of their cytoskeleton. Microtubules (MTs) act as compression-bearing elements. Yet how cancer cells regulate MT dynamic in response to the locally constrained environment has remained unclear. Using breast cancer as a model of a disease in which mechanical signaling promotes disease progression, we show that matrix stiffening rewires glutamine metabolism to promote MT glutamylation and force MT stabilization, thereby promoting cell invasion. Pharmacologic inhibition of glutamine metabolism decreased MT glutamylation and affected their mechanical stabilization. Similarly, decreased MT glutamylation by overexpressing tubulin mutants lacking glutamylation site(s) decreased MT stability, thereby hampering cancer aggressiveness in vitro and in vivo. Together, our results decipher part of the enigmatic tubulin code that coordinates the fine-tunable properties of MT and link cell metabolism to MT dynamics and cancer aggressiveness.

Abstract 3926: Establishment of patient-derived organoids as ex vivo tool to characterize the molecular mechanisms of SCLC chemo-radiation resistance

Small cell lung cancer (SCLC) is the most aggressive form of lung malignancies and accounts for 15-20% of all lung cancers. It has the tendency to metastasize early, thus limited-stage SCLC patients receive systemic chemo-radiotherapy (XRT) treatments. SCLC is exceptionally sensitive to XRT and exhibits high response rates; however, the recurrence rate is almost 100% and patients relapse with tumors that resist further chemotherapy. Clearly, elucidating the mechanisms of chemo-radiation resistance in SCLC will contribute to understanding how SCLC resists further treatments, to develop improved therapies and positively impact patient outcomes. Significant limitations for SCLC therapeutic development have been the lack of germane reliable and tractable model systems. Recent advances in establishing 3D organotypic culture have shown that this model can preserve the majority of pathways, key genes, histology and behavior of in situ tumors. Furthermore, patient-derived organoids (PDO) represent a powerful preclinical model that enable real-time cellular and molecular analysis of patient-derived xenograft (PDX) behavior ex vivo. Here, we present a novel patient-derived cancer organoid model to study the molecular underpinnings of XRT resistance in SCLC. Classic and variant SCLC PDX tumor tissues were isolated from mice and mechanically dissociated. Derived organoids were cultured in basal organoid medium. PDOs have been characterized using the SCLC molecular subtype classification reported in literature. RNA for transcriptomic analyses has been obtained to further characterize gene expression profiles of primary PDXs and PDOs, and to reconstruct gene regulatory network associated with XRT resistance. A SCLC PDX served as in vivo system to characterize the response to chemo-radiation resistance. Briefly, PDX tumor bearing mice were treated with: 1) vehicle control; 2) Cisplatin 5mg/kg on d1 plus Etoposide 8mg/kg on d1-2 (EP); 3) Radiotherapy 3Gy x1 on d3 (RT); and 4) both EP/RT. Whole transcriptome profiling among all treatments arms reveals molecular pathways and biological processes associated with XRT resistance. Also, by comparing our data with two previous SCLC patient cohort studies, we identified ideal candidates for functional analyses. SCLC XRT resistance candidate genes will be tested by either treating PDOs with small molecule inhibitors or by cDNA/shRNA lentiviral infection. To assess changes in chemo-radiation sensitivity, chemo-radiation protocols have been established and immunofluorescence staining for Ki67, γH2AX and cleaved caspase 3 served as markers for proliferation, DNA damage and apoptosis, respectively. Although further in-depth characterization is required, we aim to utilize our novel SCLC PDO model as a tool to identify candidate biomarkers to be used for developing therapy responses and translational research.

Citation Format: Francesca A. Carrieri, Nick Connis, Eloise M. Grasset, Isaac S. Chan, Eddie Luidy-Imada, Christine Lam, Hailun Wang, Andrew J. Ewald, Luigi Marchionni, Christine L. Hann, Phuoc T. Tran. Establishment of patient-derived organoids as ex vivo tool to characterize the molecular mechanisms of SCLC chemo-radiation resistance [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 3926.

Organotypic culture assays for murine and human primary and metastatic-site tumors

Cancer invasion and metastasis are challenging to study in vivo since they occur deep inside the body over extended time periods. Organotypic 3D culture of fresh tumor tissue enables convenient real-time imaging, genetic and microenvironmental manipulation and molecular analysis. Here, we provide detailed protocols to isolate and culture heterogenous organoids from murine and human primary and metastatic site tumors. The time required to isolate organoids can vary based on the tissue and organ type but typically takes <7 h. We describe a suite of assays that model specific aspects of metastasis, including proliferation, survival, invasion, dissemination and colony formation. We also specify comprehensive protocols for downstream applications of organotypic cultures that will allow users to (i) test the role of specific genes in regulating various cellular processes, (ii) distinguish the contributions of several microenvironmental factors and (iii) test the effects of novel therapeutics.