Mechano-Genomics Group Projects

Major research themes of the mechano-genomics group:   

• Probing the nuclear mechanotransduction pathways and 3D genome regulation during cellular ageing, partial reprogramming, and rejuvenation:
  Cellular ageing results in major alterations in nuclear mechanotransduction pathways and genome programs leading to progressive decline in tissue homeostasis. In recent work, we demonstrated that mechanical signals could partially reprogram and rejuvenate ageing human fibroblasts, although the epigenetic mechanisms and the underlying mechanical checkpoints in driving such cell-state transitions are still unclear. Towards this, we study the cytoskeletal remodeling mechanisms to activate specific nuclear mechanotransduction pathways. Using high-resolution fluorescence microscopy combined with sequencing methods, we analyze how actin and microtubule links to the nuclear membrane could provide a mechanical code to reorganize 3D chromatin organization at the nuclear envelope. Furthermore, using chromosome capture assays combined with RNA sequencing and chromosome painting, we assess the transcription dependent alterations in chromatin conformations during fibroblast ageing and rejuvenation. The final goal of these experiments, using well-controlled microfabricated platforms and time-course single-cell and multi-cell lineage tracing experiments, is to construct a phase diagram linking the mechano-genomic regulatory modules in cellular ageing, partial reprogramming and re-differentiation of ageing fibroblasts and the resulting cell-fate choices.
   
• Unraveling the ultrastructure, mechanics, and dynamics of nuclear and chromatin states during cellular ageing, partial reprogramming, and rejuvenation:
  In recent studies, we showed that the extracellular matrix dependent gene expression programs are regulated by cellular mechanical state and the 3D genome organization. DNA is differentially packed into heterochromatin (condensed and repressive) and euchromatin (open and active), determining its accessibility within living cells. Cellular ageing leads to alterations in such differential packing, regulated by post-translational chromatin modifications, although the underlying principles are still unclear. Towards this, we use single cell fluorescence imaging combined with micromanipulation experiments, to map the mechanics and dynamics of the mesoscale states of chromatin. In addition, we are exploring if correlative fluorescence and soft X-ray tomography, combined with chromatin conformation data, could provide additional insights on the mesoscale ultrastructure of chromatin. Furthermore, we are developing theoretical models derived from soft-matter physics, to understand the biophysical basis of mesoscale chromatin states during cellular ageing, partial reprogramming, and rejuvenation.
   
• Implanting the mechanically reprogrammed fibroblasts into ageing tissue models, including wound healing, for applications in regenerative medicine:
  Ageing leads to accumulation of senescent cells resulting in loss of tissue integrity and homeostasis. For example, wounding leads to the activation of dermal fibroblasts by local mechanical signals and growth factors resulting in increased extracellular matrix deposition to clear the wound. However, with ageing, the fibroblast cell number and the synthesis of collagen and elastin is reduced leading to altered mechanical integrity of the skin dermis and reduced wound healing responses of the resident ageing dermal fibroblasts. In this context, cell-based therapies have become popular to rejuvenate ageing tissues and improve wound healing properties, although major bottlenecks remain. To address this, we implant the partially reprogrammed aged fibroblasts into sites of wound. The process of rejuvenation, through partial reprogramming, also depends on the local matrix stiffness constraints, highlighting the existence of mechanical checkpoints to induce cell-state transitions. Understanding such checkpoints could also determine ageing cell transitions between rejuvenation, fibrotic, senescent, or oncogenic transformations at sites of wound. Collectively, these experiments are aimed at demonstrating if implanting partially reprogrammed aged fibroblasts could provide novel avenues for wound healing and more generally for ageing tissue regeneration and repair.
   
• Developing single-cell imaging-AI based analysis of functional chromatin states as biomarkers of cellular ageing, rejuvenation and ageing associated diseases:
  Abnormalities in nuclear and chromatin organization are hallmarks of cellular ageing and many ageing related diseases including fibrosis, cancer, and neurodegeneration. However, quantitative methods to analyze nuclear and chromatin abnormalities for early disease diagnostics are still missing. In recent studies, we showed that single-cell fluorescence imaging combined with machine learning based analysis of nuclear and chromatin condensation patterns provide robust biomarkers for healthy and diseased cell states. In addition, we are testing if multi-domain data translation methods could be implemented to infer the functional coupling between chromatin organization, gene expression and genome regulatory networks of cells. Furthermore, in ongoing studies, we are exploring if the imaging-AI based chromatin biomarkers of healthy cells could serve as robust methods to analyze the secretome of ageing and diseased cells. These studies also provide avenues to setup secondary drug screens to assess how the ageing and diseased cell secretome signals could be circumvented for healthy ageing. Taken together, our studies are aimed at using mesoscale chromatin organization as a biomarker for cell states and their fates in health and disease.

Clinical trials: In collaboration with the Center for Proton Therapy at PSI, we have started a clinical trial to analyze if chromatin biomarkers in liquid biopsies could help determine the efficacy and toxicity of proton radiation therapy in human patients. In addition, together with the local Health Center, we are starting a clinical trial to assess if our chromatin biomarkers could provide robust methods for early disease diagnostics.