RESEARCH

My research interests lie in understanding the fundamental mechanobiology principles of complex diseases which govern both the phenotype and genotype of these diseases. The development and use of novel biophysical assays to interrogate diseased states at scales ranging from cell to tissue is what excites me. This not only helps understand the mechanisms behind why some diseases are so deadly but also develop solutions and therapeutic targets for that increases the overall survivability rates of the patients. Currently, I'm working on understanding the 'Emperor of all Maladies' (Link), specifically brain cancer. The details about my current project can be found below. In addition, recently I have been extensively reading about designing hydrogel-based 3D in-vitro models to understand and recapitulate complex diseases in general. To sum up (although I don't particularly appreciate summing up since it limits our horizons), I love solving challenging problems at the interface of biology and engineering.

I have highlighted below some of my projects done during my undergraduate, later as a research assistant, and now as a graduate student at UC San Diego. The publications that resulted from some of these works are mentioned under the Publications tab at the top.

Biophysical interrogation of intrinsic and extrinsic signals that drive glioblastoma multiforme (GBM) invasion

A lack of biological markers has limited our ability to identify the invasive cells responsible for glioblastoma multiforme (GBM). To become migratory and invasive, cells must downregulate matrix adhesions, which could be a physical marker of invasive potential. We engineered murine astrocytes with common GBM mutations, e.g. Ink4a (Ink) or PTEN deletion and expressing a constitutively active EGF receptor truncation (EGFRvIII), to elucidate their effect on adhesion. While loss of Ink or PTEN did not affect adhesion, counterparts expressing EGFRvIII were significantly less adhesive. EGFRvIII reduced focal adhesion size and number, and these cells – with more labile adhesions – displayed enhanced migration. Regulation appears to depend not on physical receptor association to integrins but, rather, on the activity of the receptor kinase, resulting in transcriptional integrin repression. Interestingly, EGFRvIII intrinsic signals can be propagated by cytokine crosstalk to cells expressing wild-type EGFR, resulting in reduced adhesion and enhanced migration. These data identify potential intrinsic and extrinsic mechanisms that gliomas use to invade surrounding parenchyma. We are interrogating further into the crosstalk mechanisms between the wtEGFR and EGFRvIII cells.

Poster Presentations:

Banerjee, A., Banasidar, A., Furnari, F., Engler, A., 2023. Biophysical interrogation of intrinsic and extrinsic signals that drive glioblastoma multiforme (GBM) invasion. Poster Presentation, Sanford Stem Cell Institute Symposium Link

Characterization and modeling of cell-substrate interaction under external stimuli

Quantitatively understanding the cellular interaction with the extracellular matrix (ECM) is important to develop better therapies for diseases like cancer. Mechanical and chemical cues of the ECM direct cellular functions like growth, proliferation, and migration. The macroscopic behavior observed from collective cells is in fact due to individual cell-matrix crosstalk. These are regulated by the contribution of different cytoskeleton elements present inside the cell. For example, it is known that actin filaments inside the cell align themselves during cell shape changes and acts as stress fibers.

Here, in this study, we designed, developed, validated, and analyzed two separate three-dimensional models of circular and hemispherical cap-shaped single cells adhered to the ECM substrate. The substrate roughness was varied, and the models were subjected to two different types of biologically relevant loading, i.e. nano-indentation and cyclic loading. Our model predicted the strain induced on individual cytoskeleton elements, overall deformation of the cell, and loading-unloading plastic behavior of the cell. As an improvement, we took cytoskeleton degradation into consideration, providing a good approximation of the actual in-vivo interaction between cells and substrate.

Publications:

Banerjee, A. *, Khan, Md. Parvez*, Barui, A, Dutta, P., Chowdhury, A. Roy, Bhowmik, K, 2021. Finite Element Analysis of the Influence of Cyclic Strain on Cells Anchored to Substrates with Varying Properties. Medical & Biological Engineering & Computing. Link

Fabrication, characterization, and microscale modeling of cell-seeded 3D bioprinted hydrogels

Extrusion-based bioprinting is a popular fabrication technique to bioprint patient-specific tissue constructs. The bioinks used contain not only biocompatible hydrogels but also spatially controlled seeded cells, depending upon the post-printing application. The current approach of bioink properties optimization is trial and error printing which is costly, time-consuming, tedious, and also not standardized across various laboratories. Alternate approaches include numerical models based on linear, non-linear regression and Navier’s Stokes equation.

However, the presence of cells in the hydrogel requires micro-scale modeling to predict accurate post-printing properties of the bioinks. Although more resource exhaustive and complex, we have developed 3D micro-scale FE models of both strand and honeycomb-shaped Alginate-HeLa cell bioink composite subjected to mechanical loading. We fabricated HeLa cell-seeded Alginate strands using a 3D bioprinter and did its mechanical characterization to obtain the non-linear hyperelastic material properties. The work was extended for GelMa, collagen, and spider silk hydrogels. In the end, we validated the developed model with experiments for three different stoichiometric fractions of HeLa cells and predicted the honeycomb-shaped scaffold response for the distinct pre-defined spatial distribution of cells within the scaffold volume.

Publications:

Banerjee, A.*, Datta, S.*, Chowdhury, A. Roy, Dutta, P., 2022. A micro-scale finite element model to optimize the mechanical behavior of bioprinted constructs. 3D Printing and Additive Manufacturing. Link
Banerjee A et al, Cell-Laden Alginate Hydrogel Modeling using Three-Dimensional (3D) Microscale Finite Element Technique, Oral Presentation in ICRTST-2021. (Paper published in the Journal of The Institution of Engineers (India): Series C). Link