Identification of Topological Features in Renal Tumor Microenvironment Associated with Patient Survival

Motivation As a highly heterogeneous disease, the progression of tumor is not only achieved by unlimited growth of the tumor cells, but also supported, stimulated, and nurtured by the microenvironment around it. However, traditional qualitative and/or semi-quantitative parameters obtained by pathologist’s visual examination have very limited capability to capture this interaction between tumor and its microenvironment. With the advent of digital pathology, computerized image analysis may provide a better tumor characterization and give new insights into this problem. Results We propose a novel bioimage informatics pipeline for automatically characterizing the topological organization of different cell patterns in the tumor microenvironment. We apply this pipeline to the only publicly available large histopathology image dataset for a cohort of 190 patients with papillary renal cell carcinoma obtained from The Cancer Genome Atlas project. Experimental results show that the proposed topological features can successfully stratify early- and middle-stage patients with distinct survival, and show superior performance to traditional clinical features and cellular morphological and intensity features. The proposed features not only provide new insights into the topological organizations of cancers, but also can be integrated with genomic data in future studies to develop new integrative biomarkers

Deconstructing tumor heterogeneity: The stromal perspective

Significant advances have been made towards understanding the role of immune cell-tumor interplay in either suppressing or promoting tumor growth, progression, and recurrence, however, the roles of additional stromal elements, cell types and/or cell states remain ill-defined. The overarching goal of this NCI-sponsored workshop was to highlight and integrate the critical functions of non-immune stromal components in regulating tumor heterogeneity and its impact on tumor initiation, progression, and resistance to therapy. The workshop explored the opposing roles of tumor supportiv

Three-Dimensional Microfluidic Based Tumor-Vascular Model to Study Cancer Cell Invasion and Intravasation

abstract: Breast cancer is the second leading cause of disease related death in women, contributing over 40,000 fatalities annually. The severe impact of breast cancer can be attributed to a poor understanding of the mechanisms underlying cancer metastasis. A primary aspect of cancer metastasis includes the invasion and intravasation that results in cancer cells disseminating from the primary tumor and colonizing distant organs. However, the integrated study of invasion and intravasation has proven to be challenging due to the difficulties in establishing a combined tumor and vascular microenvironments. Compared to traditional in vitro assays, microfluidic models enable spatial organization of 3D cell-laden and/or acellular matrices to better mimic human physiology. Thus, microfluidics can be leveraged to model complex steps of metastasis. The fundamental aim of this thesis was to develop a three-dimensional microfluidic model to study the mechanism through which breast cancer cells invade the surrounding stroma and intravasate into outerlying blood vessels, with a primary focus on evaluating cancer cell motility and vascular function in response to biochemical cues. A novel concentric three-layer microfluidic device was developed, which allowed for simultaneous observation of tumor formation, vascular network maturation, and cancer cell invasion/intravasation. Initially, MDA-MB-231 disseminated from the primary tumor and invaded the acellular collagen present in the adjacent second layer. The presence of an endothelial network in the third layer of the device drastically increased cancer cell invasion. Furthermore, by day 6 of culture, cancer cells could be visually observed intravasating into the vascular network. Additionally, the effect of tumor cells on the formation of the surrounding microvascular network within the vascular layer was evaluated. Results indicated that the presence of the tumor significantly reduced vessel diameter and increased permeability, which correlates with prior in vivo data. The novel three-layer platform mimicked the in vivo spatial organization of the tumor and its surrounding vasculature, which enabled investigations of cell-cell interactions during cancer invasion and intravasation. This approach will provide insight into the cascade of events leading up to intravasation, which could provide a basis for developing more effective therapeutics.Dissertation/ThesisMasters Thesis Biomedical Engineering 201

3D bioprinting for reconstituting the cancer microenvironment.

The cancer microenvironment is known for its complexity, both in its content as well as its dynamic nature, which is difficult to study using two-dimensional (2D) cell culture models. Several advances in tissue engineering have allowed more physiologically relevant three-dimensional (3D) in vitro cancer models, such as spheroid cultures, biopolymer scaffolds, and cancer-on-a-chip devices. Although these models serve as powerful tools for dissecting the roles of various biochemical and biophysical cues in carcinoma initiation and progression, they lack the ability to control the organization of multiple cell types in a complex dynamic 3D architecture. By virtue of its ability to precisely define perfusable networks and position of various cell types in a high-throughput manner, 3D bioprinting has the potential to more closely recapitulate the cancer microenvironment, relative to current methods. In this review, we discuss the applications of 3D bioprinting in mimicking cancer microenvironment, their use in immunotherapy as prescreening tools, and overview of current bioprinted cancer models

Pathomimetic cancer avatars for live-cell imaging of protease activity

Proteases are essential for normal physiology as well as multiple diseases, e.g., playing a causative role in cancer progression, including in tumor angiogenesis, invasion, and metastasis. Identification of dynamic alterations in protease activity may allow us to detect early stage cancers and to assess the efficacy of anti-cancer therapies. Despite the clinical importance of proteases in cancer progression, their functional roles individually and within the context of complex protease networks have not yet been well defined. These gaps in our understanding might be addressed with: 1) accurate and sensitive tools and methods to directly identify changes in protease activities in live cells, and 2) pathomimetic avatars for cancer that recapitulate in vitro the tumor in the context of its cellular and non-cellular microenvironment. Such avatars should be designed to facilitate mechanistic studies that can be translated to animal models and ultimately the clinic. Here, we will describe basic principles and recent applications of live-cell imaging for identification of active proteases. The avatars optimized by our laboratory are three-dimensional (3D) human breast cancer models in a matrix of reconstituted basement membrane (rBM). They are designated mammary architecture and microenvironment engineering (MAME) models as they have been designed to mimic the structural and functional interactions among cell types in the normal and cancerous human breast. We have demonstrated the usefulness of these pathomimetic avatars for following dynamic and temporal changes in cell:cell interactions and quantifying changes in protease activity associated with these interactions in real-time (4D). We also briefly describe adaptation of the avatars to custom-designed and fabricated tissue architecture and microenvironment engineering (TAME) chambers that enhance our ability to analyze concomitant changes in the malignant phenotype and the associated tumor microenvironment

Microfluidic Models of Tumor-Stroma Interactions to Study the Interplay of Cancer Cells with their Surrounding Microenvironment

abstract: According to the World Health Organization, cancer is one of the leading causes of death around the world. Although early diagnostics using biomarkers and improved treatments with targeted therapy have reduced the rate of cancer related mortalities, there remain many unknowns regarding the contributions of the tumor microenvironment to cancer progression and therapeutic resistance. The tumor microenvironment plays a significant role by manipulating the progression of cancer cells through biochemical and biophysical signals from the surrounding stromal cells along with the extracellular matrix. As such, there is a critical need to understand how the tumor microenvironment influences the molecular mechanisms underlying cancer metastasis to facilitate the discovery of better therapies. This thesis described the development of microfluidic technologies to study the interplay of cancer cells with their surrounding microenvironment. The microfluidic model was used to assess how exposure to chemoattractant, epidermal growth factor (EGF), impacted 3D breast cancer cell invasion and enhanced cell motility speed was noted in the presence of EGF validating physiological cell behavior. Additionally, breast cancer and patient-derived cancer-associated fibroblast (CAF) cells were co-cultured to study cell-cell crosstalk and how it affected cancer invasion. GPNMB was identified as a novel gene of interest and it was shown that CAFs enhanced breast cancer invasion by up-regulating the expression of GPNMB on breast cancer cells resulting in increased migration speed. Lastly, this thesis described the design, biological validation, and use of this microfluidic platform as a new in vitro 3D organotypic model to study mechanisms of glioma stem cell (GSC) invasion in the context of a vascular niche. It was confirmed that CXCL12-CXCR4 signaling is involved in promoting GSC invasion in a 3D vascular microenvironment, while also demonstrating the effectiveness of the microfluidic as a drug screening assay. Taken together, the broader impacts of the microfluidic model developed in this dissertation include, a possible alternative platform to animal testing that is focused on mimicking human physiology, a potential ex vivo platform using patient-derived cells for studying the interplay of cancer cells with its surrounding microenvironment, and development of future therapeutic strategies tailored toward disrupting key molecular pathways involved in regulatory mechanisms of cancer invasion.Dissertation/ThesisMovie D.2Movie D.1Movie D.3Movie D.4Movie D.5Movie D.6Movie D.7Movie D.8Movie D.9Movie D.10Movie D.12Movie D.11Movie D.13Movie D.14Movie D.15Doctoral Dissertation Biomedical Engineering 201

Pathomimetic avatars reveal divergent roles of microenvironment in invasive transition of ductal carcinoma in situ

The breast tumor microenvironment regulates progression of ductal carcinoma in situ (DCIS) to invasive ductal carcinoma (IDC). However, it is unclear how interactions between breast epithelial and stromal cells can drive this progression and whether there are reliable microenvironmental biomarkers to predict transition of DCIS to IDC

Recapitulating the tumor ecosystem along the metastatic cascade using 3D culture models

Advances in cancer research have shown that a tumor can be likened to a foreign species that disrupts delicately balanced ecological interactions, compromising the survival of normal tissue ecosystems. In efforts to mitigate tumor expansion and metastasis, experimental approaches from ecology are becoming more frequently and successfully applied by researchers from diverse disciplines to reverse engineer and re-engineer biological systems in order to normalize the tumor ecosystem. We present a review on the use of 3D biomimetic platforms to recapitulate biotic and abiotic components of the tumor ecosystem, in efforts to delineate the underlying mechanisms that drive evolution of tumor heterogeneity, tumor dissemination, and acquisition of drug resistance.ope