Fall 2018 Research Projects

A microfluidic model of immune responses in dense tissues: toward optimal cancer immunotherapies

Principal Investigators:

Don L. DeVoe, Department of Mechanical Engineering, University of Maryland

Grégoire Altan-Bonnet, Center for Cancer Research - National Cancer Institute

Ph.D. Student:

Supriya Padmanabhan, Department of Chemical and Biomolecular Engineering ,supriya@umd.edu

Competition for cytokines among T cells is a key mechanism regulating immunologic response, and plays a critical role in the efficacy of cancer immunotherapies based on cytokine manipulation. Because cytokine communication is highly localized within the dense and structured lymphoid or tumor tissues, conventional cell culture cannot properly model the dynamics of T cells during an immune response. Here we propose a microfluidic platform mimicking the geometric and cellular complexity of dense tissues, enabling cytokine dynamics and communication to be accurately probed, and serving as a model for optimizing cytokine immunotherapy. Ultimately, we envision that the “artificial lymph chips” may be employed for therapeutic applications by engineering an immunologic response co-located with the targeted tumor tissue.

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Probing the role of physical properties of the microenvironment on metastatic tumor outgrowth

Principal Investigators:

Giuliano Scarcelli, Fischell Department of Bioengineering, University of Maryland

Kandice Tanner, Center for Cancer Research - National Cancer Institute

Ph.D. Student:

Milos Nikolic, Biophysics Program, University of Maryland, mnikolic@umd.edu

The mechanisms that govern the behavior of metastatic tumor cells in secondary organs and why in some cases they remain quiescent while in other cases they aggressively proliferate are not well understood. In particular, the role of the microenvironment biophysics on tumor outgrowth is not known. Yet, in other realms, biophysical cues of the tissue microenvironment (e.g. mechanics and topography) have been shown to drive cellular response; moreover, the mechanical response of cells to the physical cues of the microenvironment is known to be linked to the metastatic potential. In this proposal, we will close this gap by studying how the dynamic interaction between tumor cell and physical cues of the microenvironment affects tumor outgrowth. We hypothesize that cells’ ability to adapt to the mechanical and topographical challenges posed by the microenvironment is necessary for successful tumor outgrowth. To test this hypothesis, we will use isogenic breast cancer cells that are either “dormant” or aggressive when cultured in 3D matrices and measure their mechanical response to the changing environment. This will lead to the identification of the crucial regulatory pathways that regulate cell response to physical cues and how they are affected by malignancy transformation. The proposal is based on the synergistic expertise of Tanner Lab at NCI and Scarcelli Lab at UMD. Tanner lab has developed a biomimetic 3D culture system that allows for independent control of mechanical and topographical cues; Scarcelli Lab has developed Brillouin microscopy to map cell elastic modulus within 3D cultures without contact. The successful completion of the proposed research will both provide new insights on the biophysics of metastatic cells and develop a new comprehensive platform to study the complex and dynamic interplay between metastatic cells and their changing microenvironments.

Brillouin stiffness map of a fibroblast. The high 3D resolution of Brillouin technology enables identifying a stiffer nucleus within an intact cell without contact or perturbations.

Brillouin stiffness map of a fibroblast. The high 3D resolution of Brillouin technology enables identifying a stiffer nucleus within an intact cell without contact or perturbations.


Demystifying sequence-specific DNA-protein interactions with statistical mechanics and deep learning based all-atom simulations

Principal Investigators:

Pratyush Tiwary, Department of Chemistry & Biochemistry, University of Maryland

Charles Vinson, Center for Cancer Research - National Cancer Institute

Ph.D. Student:

Yihang Wang, Biophysics Program, University of Maryland, yhwang17@terpmail.umd.edu

Quantifying and understanding DNA-protein interactions is a key challenge in understanding complex biological processes related to cancer and beyond. Experiments can now rank a given series of interactions, but it is hard to gain atomistic-scale insight into the how’s, why’s and when’s, which is crucial from the perspective of better understanding the complex regulatory networks underlying cancer. In this collaborative project, experimentalists from NCI will team up with computational chemists from UMD to apply and refine molecular dynamics based simulations for the study of such systems, guided by experiments performed at NCI. The first year of the project will focus on the Epstein-Barr Virus B-ZIP Protein Zta shown below binding a DNA sequence, but the technologies developed here should be applicable to additional DNA-protein systems.

Pictorial summary of this project: Understanding the how’s, why’s and when’s of DNA-protein interactions using all-atom simulations and protein binding microarrays

Pictorial summary of this project: Understanding the how’s, why’s and when’s of DNA-protein interactions using all-atom simulations and protein binding microarrays


Roles of RNA localization during migration of tumor cells in confined spaces

Principal Investigators:

Kimberly Stroka, Fischell Department of Bioengineering, University of Maryland

Stavroula Mili, Center for Cancer Research - National Cancer Institute

Ph.D. Student:

Rebecca Moriarty, Fischell Department of Bioengineering, University of Maryland, rmoriart@terpmail.umd.edu

Tumor cell metastasis, which accounts for 90% of all cancer deaths, involves tumor cell migration and invasion through biochemically and mechanically heterogeneous microenvironments, including through preexisting longitudinal microtracks in tissues and along anatomical features. RNA localization, and localized translation, is emerging as a mechanism required for persistent and directional cell movement, and recent work from our groups has revealed that localization of RNAs is influenced by the mechanical properties of the environment. Using an integrated approach combining novel biophysical, bioengineering, and biological methods pioneered by the labs of the PIs, this proposal seeks to explore the role of RNA localization in tumor cells during entrance into, migration through, and exit from physically confining spaces. Overall, we seek to understand how cell mechanics influence mRNA localization in tumor cells during migration through physically confined spaces and the functional importance of these events, thus providing important new insights into cancer metastasis.

Schematic summarizing our hypothesis about RNA localization during tumor cell migration in unconfined versus confined spaces. RNA groups A and B represent distinct sets of RNAs that localize to the leading edge in unconfined or confined cells, respectively, depending on cell tension state. We hypothesize that these localization events functionally contribute to migration speed and persistence in the respective environments.

Schematic summarizing our hypothesis about RNA localization during tumor cell migration in unconfined versus confined spaces. RNA groups A and B represent distinct sets of RNAs that localize to the leading edge in unconfined or confined cells, respectively, depending on cell tension state. We hypothesize that these localization events functionally contribute to migration speed and persistence in the respective environments.