Search

Multicellular tumor spheroid (MCTS) systems provide an in vitro cell culture model system which mimics many of the complexities of an in vivo solid tumor and tumor microenvironment, and are often used to study cancer cell growth and drug efficacy. Here, we present a coupled experimental-computational framework to estimate phenotypic growth and biophysical tumor microenvironment properties. This novel framework utilizes standard microscopy imaging of MCTS systems to drive a biophysical mathematical model of MCTS growth and mechanical interactions. By extending our previous in vivo mechanically-coupled reaction-diffusion modeling framework we developed a microscopy image processing framework capable of mechanistic characterization of MCTS systems. Using MDA-MB-231 breast cancer MCTS, we estimated biophysical parameters of cellular diffusion, rate of cellular proliferation, and cellular tractions forces. We found significant differences in these model-based biophysical parameters throughout the treatment time course between untreated and treated MCTS systems, whereas traditional size-based morphometric parameters were inconclusive. The proposed experimental-computational framework estimates mechanistic MCTS growth and invasion parameters with significant potential to assist in better and more precise assessment of in vitro drug efficacy through the development of computational analysis methodologies for three-dimensional cell culture systems to improve the development and evaluation of antineoplastic drugs. National Institutes of Health - National Cancer InstituteUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Cancer Institute (NCI) [K25CA204599, P30CA012197]; Wake Forest Baptist Medical Center Comprehensive Cancer Center Signaling and Biotechnology Program Pilot Grant National Institutes of Health - National Cancer Institute K25CA204599 and P30CA012197. Wake Forest Baptist Medical Center Comprehensive Cancer Center Signaling and Biotechnology Program Pilot Grant.

Introduction: Conventional 2D monolayer cell culture methods have distinct weaknesses in mimicking in vivo tumors as they ignore major phenotypic physical tumor microenvironment (TME) factors. 3D multicellular tumor spheroid (MTS) systems have been developed to study cancer cell growth in the presence of such TME factors, including cell-cell and cell-extracellular matrix (ECM) mechanical interactions. However, the development of analysis methodologies for these complex culture systems has considerably lagged. We hypothesize that a coupled experimental-computational framework using a microscopy image-driven biophysical mathematical model of MTS systems can accurately estimate phenotypic growth and biophysical TME properties, revealing significantly more mechanistic information than traditional morphometric analysis methods. Materials and Methods: MDA-MB-231 triple-negative breast cancer cells were used to generate spheroids. A single 3D MTS embedded in Collagen I ECM was used as a 3D culture tumor model system as they exhibit cell-cell and cell-ECM interactions that mimic in vivo tumors. Fluorescent fiducial microspheres were placed in the ECM to track displacement induced by the MTS. Time-lapse fluorescence microscopy images were taken of the MTS and microspheres for 72 hours on an automated fluorescent microscope every 12-hours. Images were compiled using a customized fully-automated tiling/stitching/image processing software in MATLAB. Time-lapse images of the MTS and microspheres are used in conjunction with subsequent mathematical modeling analysis for biophysical parameter estimation. We assess MTS using a mathematical model based on two coupled partial differential equations describing growth/motility and mechanical equilibrium in response to cellular-induced forces. Parameters describing cell proliferation rate (k), cell diffusion (D), and cellular mechanical forces (λ) are estimated based on fitting acquired microscopy images to the model via an iterative least-squares parameter estimation. Experiments and model-based analyses were performed in triplicate to define the reproducibility of biophysical parameter estimation. Results and Discussion: In this preliminary study, our modeling framework is able to estimate biophysical parameters of cell diffusion, proliferation rate, and cellular mechanical force in a 3D breast cancer cell culture system of invading MTS embedded in ECM with coefficients of variation across all parameters less than 15% on average. The model predictions accurately represent changes in cellular density and ECM deformation induced by cellular traction forces throughout the observed time series, demonstrating that this model is capable of representing MTS/ECM growth behavior and parameterizing the driving biophysical properties. Conclusions: These results indicate that our imaging-driven mathematical modeling framework for estimating biophysical model parameters has potential to reliably characterize 3D MTS growth and invasion. With reproducibility established, we plan to extend the method to investigate these phenotypic biophysical TME properties in a range of culture and treatment condition interventions. These biophysical properties could be utilized in developing anti-neoplastic drug sensitivity assays to improve cancer therapy by enabling patient-specific estimation/prediction of response to agents and dosing conditions. Acknowledgements: NIH-NCI K25CA204599 and P30CA012197 Citation Format: Haley Brooke Johnson, Emily E. Fannin, Alexandra Thomas, Jared A Weis. Image driven biophysical mathematical modeling of multicellular breast tumor spheroids [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P1-06-05.

MicroRNAs (miRNAs) have emerged as biomarkers of metabolic status, etiological factors in complex disease, and promising drug targets. Recent reports suggest that miRNAs are critical regulators of pathways underlying the pathophysiology of type 2 diabetes. In this study, we demonstrate by deep sequencing and real-time quantitative PCR that hepatic levels of Foxa2 mRNA and miR-29 are elevated in a mouse model of diet-induced insulin resistance. We also show that Foxa2 and miR-29 are significantly upregulated in the livers of Zucker diabetic fatty (fa/fa) rats and that the levels of both returned to normal upon treatment with the insulin-sensitizing agent pioglitazone. We present evidence that miR-29 expression in human hepatoma cells is controlled in part by FOXA2, which is known to play a critical role in hepatic energy homeostasis. Moreover, we demonstrate that miR-29 fine-tunes FOXA2-mediated activation of key lipid metabolism genes, including PPARGC1A, HMGCS2, and ABHD5. These results suggest that miR-29 is an important regulatory factor in normal metabolism and may represent a novel therapeutic target in type 2 diabetes and related metabolic syndromes.

The breast cancer susceptibility gene 1 (BRCA1) encodes a tumor-suppressor protein that maintains genetic stability through DNA damage response pathways. Specifically, BRCA1 has a well-established role in double-strand DNA break repair, and emerging evidence supports a role for BRCA1 in repair of oxidative DNA damage via the base-excision repair (BER) pathway. We and others have shown that cells with mutant/deficient BRCA1 harbor defective BER of oxidative DNA damage. Interestingly, defective BER of oxidative DNA damage in breast cancer cells rendered sensitivity to elesclomol, an experimental therapeutic that induces reactive oxygen species to levels beyond a viable threshold. Given that BRCA1-mutated cancers associate with a poor prognosis and are in need of targeted treatment options, we hypothesized that breast or ovarian cancer cells with mutant BRCA1 would exhibit selective sensitivity to elesclomol or treatment regimens containing elesclomol. First, we determined the effect of BRCA1 on the cellular response to oxidative stress and elesclomol using human ovarian cancer cells isogenic for BRCA1. Compared to mutant BRCA1 cells (UWB1.289), wild-type BRCA1 cells (UWB1.289+BRCA1) produced significantly greater levels of BRCA1 mRNA (p=0.009), expressed markedly higher levels of BRCA1 protein in the nucleus, and showed significantly greater sensitivity to hydrogen peroxide (p=0.002) as evidenced by RTqPCR, Western blot analysis, and MTT assay, respectively. Importantly, mutant BRCA1 cells displayed an approximate 100-fold greater sensitivity to elesclomol compared to wild-type BRCA1 cells as determined by MTT assay. These data suggest that the oxidative stress induced by elesclomol may be used to selectively target cancer cells with mutant BRCA1 due to their defective BER phenotype. We next asked whether elesclomol may be combined with other agents used clinically or experimentally for the treatment of BRCA1-mutated cancers, including standard chemotherapy drugs and PARP inhibitors. Elesclomol exhibited synergistic sensitivity when combined with DNA-damaging agents, including doxorubicin or cisplatin, in breast cancer cells with mutant BRCA1 (SUM149) as determined by combination index and isobologram analysis. On the other hand, a synergistic effect was not observed with the anti-microtubule agent paclitaxel, which is consistent with a phase III study that evaluated this combination for the treatment of advanced melanoma. However, elesclomol in combination with PARP inhibitors, including rucaparib or talazoparib, indeed showed synergism in breast cancer cells with mutant BRCA1. These data suggest that elesclomol may be used in combination with other anticancer agents to further exploit defects in DNA repair due to mutant BRCA1. In conclusion, elesclomol may be explored as a novel component of treatment regimens for targeting BRCA1-mutated breast and ovarian cancers. Citation Format: Maria Kammire, Emily Fannin, James M. Ford, Elizabeth Alli. Targeting BRCA1-mutated cancer cells with elesclomol [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4846.

MicroRNAs (miRNAs) are important regulators and potential therapeutic targets of metabolic disease. In this study we show by in vivo administration of locked nucleic acid (LNA) inhibitors that suppression of endogenous miR-29 lowers plasma cholesterol levels by ~40%, commensurate with the effect of statins and reduces fatty acid content in the liver by ~20%. Whole transcriptome sequencing of the liver reveals 883 genes dysregulated (612 down, 271 up) by inhibition of miR-29. The set of 612 down-regulated genes are most significantly over-represented in lipid synthesis pathways. Among the up-regulated genes are the anti-lipogenic deacetylase sirtuin 1 (Sirt1) and the anti-lipogenic transcription factor aryl hydrocarbon receptor (Ahr), the latter of which we demonstrate is a direct target of miR-29. In vitro radiolabeled acetate incorporation assays confirm that pharmacologic inhibition of miR-29 significantly reduces de novo cholesterol and fatty acid synthesis. Our findings indicate that miR-29 controls hepatic lipogenic programs, likely in part through regulation of Ahr and Sirt1 and therefore may represent a candidate therapeutic target for metabolic disorders such as dyslipidemia.

Persistent infections with hepatitis B virus (HBV) or hepatitis C virus (HCV) account for the majority of cases of hepatic cirrhosis and hepatocellular carcinoma (HCC) worldwide. Small, non-coding RNAs play important roles in virus-host interactions. We used high throughput sequencing to conduct an unbiased profiling of small (14-40 nts) RNAs in liver from Japanese subjects with advanced hepatitis B or C and hepatocellular carcinoma (HCC). Small RNAs derived from tRNAs, specifically 30-35 nucleotide-long 5' tRNA-halves (5' tRHs), were abundant in non-malignant liver and significantly increased in humans and chimpanzees with chronic viral hepatitis. 5' tRH abundance exceeded microRNA abundance in most infected non-cancerous tissues. In contrast, in matched cancer tissue, 5' tRH abundance was reduced, and relative abundance of individual 5' tRHs was altered. In hepatitis B-associated HCC, 5' tRH abundance correlated with expression of the tRNA-cleaving ribonuclease, angiogenin. These results demonstrate that tRHs are the most abundant small RNAs in chronically infected liver and that their abundance is altered in liver cancer.

Recent advances in sequencing technology have helped unveil the unexpected complexity and diversity of small RNAs. A critical step in small RNA library preparation for sequencing is the ligation of adapter sequences to both the 5’ and 3’ ends of small RNAs. Two widely used protocols for small RNA library preparation, Illumina v1.5 and Illumina TruSeq, use different pairs of adapter sequences. In this study, we compare the results of small RNA-sequencing between v1.5 and TruSeq and observe a striking differential bias. Nearly 100 highly expressed microRNAs (miRNAs) are >5-fold differentially detected and 48 miRNAs are >10-fold differentially detected between the two methods of library preparation. In fact, some miRNAs, such as miR-24-3p, are over 30-fold differentially detected. The results are reproducible across different sequencing centers (NIH and UNC) and both major Illumina sequencing platforms, GAIIx and HiSeq. While some level of bias in library preparation is not surprising, the apparent massive differential bias between these two widely used adapter sets is not well appreciated. As increasingly more laboratories transition to the newer TruSeq-based library preparation for small RNAs, researchers should be aware of the extent to which the results may differ from previously published results using v1.5.