Projects

Mechanogenomics of epithelial homeostasis and colorectal cancer onset and progression

Here we aim to uncover mechanistic principles of mammalian tissue architecture maintenance and decipher its role in genome integrity and proper cellular function and how this cross-talk breaks down with cancer onset and progression. Our particular interest it to test if there is a mechanistic coupling between the co-evolving cellular states which drive tumor heterogeneity and worsen patient outcome with the mechanical and architectural properties of the tumor and stroma microenvironments. This is a highly interdisciplinary research strategy that builds on stem cell biology, combining scale-bridging tools of bioengineering and biophysics, machine learning-based quantitative imaging, genome-wide analyses, spatial transcriptomics, and computational modeling. Discovering these regulatory principles will deepen our understanding of cancer progression/aggression and facilitate the development of regenerative therapies and more effective diagnostics and treatments against cancers.

Fundaments of mechano-osmotic control of transcriptional bursting

Cells are continuously exposed to a range of biomechanical forces emanating from their dynamic, topologically complex microenvironments. Emerging evidence suggests that transcription is not only regulated by the activity of promoters and enhancers but is also sensitive to mechanical forces which have profound effects on gene transcription. The mechanisms by which forces alter the highly organized and tightly-controlled transcriptional processes are thought to involve nuclear deformation. However, virtually nothing is known about the direct effects of nuclear deformation and changes in chromatin biophysics on global transcriptional kinetics in real time. To address this gap, we combine genetic approaches with single cell live imaging, mathematical modeling, optogenetics, sequencing, and biophysical approaches to determine the effect of mechanical forces and nuclear deformation on gene and enhancer activities and coordination.

Mechanical cues and dimensionality in cell fate transitions

Cell fate transitions during mammalian development tend to coincide with profound changes in cell/nuclear shapes driven by morphogens but also mechanical forces emanating from cell divisions, death, and morphogenetic movements that ultimately deform and shape the embryo. For instance, during gastrulation, a morphogenetic process that leads to the formation of the three germ layers (ectoderm, mesoderm, and definitive endoderm), cells of the epiblast simultaneously differentiate and spatially segregate into the three germ layers. This process relies on cell- and tissue-level forces and geometrical cues to properly couple cell identity and fate with correct positioning within developing tissue of the organism. Inability to do so would compromise development. Yet, the precise mechanisms by which cells sense, integrate, and respond to mechanical and topological cues to inform their cell fate specification and rearrangement during early embryogenesis remains poorly understood. How the nucleus, which is the largest and stiffest organelle, manages such stress while simultaneously coordinating profound loci rearrangement between actively transcribed and transcriptionally silenced genomic regions to match the needs of the embryo with single-cell resolution is also unknown. To address these questions, we use rudimentary but interpretable 2- and 3-dimensional models of embryonic development that we interrogate with high spatio-temporal resolution using advanced imaging modalities (lightsheet and spinning disc live microscopy) coupled to biophysical characterization and manipulation devices (atomic force microscopy, microfluidic devices and bioreactors) to measure and apply forces to our cellular systems while simultaneously monitoring their state. We further utilize genetic and optogentic tools to perturb development in order to understand it and ultimately employ various ‘omics approaches to identify key molecular players and critical genomic/epigenetic regions in the process. 

Nuclear/chromatin architecture and mechanics in genome integrity

Tight regulation of the 3-dimensional organization of the genome, its transcriptional output, and ability to engage fast and efficient DNA damage repair in case of insults is fundamental to the maintenance of genome integrity, homeostasis, and ultimately to organismal survival. In this arm of our research, we aim to uncover the biophysical principles of genome maintenance and remodeling in response to extrinsically-applied environmental insults. In particular we focus on the spatial organization of the heterochromatin and lamina-associated domains (LADs), the mechanical/tensional state of the nuclear periphery, as well as physical properties and macromolecular crowding of the nucleoplasm to the maintenance of genome architecture.