Associate Professor of Neuroscience
Developmental Biology and Aging Program
Del E. Webb Neuroscience, Aging and Stem Cell Research Center
Sanford Burnham Prebys Medical Discovery Institute
Over the past several years, my lab was focused on mechanism of neural stem cell self-renewal and neuronal differentiation. Primary cilium is a key structure mediating the function of
Shh in hippocampal neurogenesis. To get insights into this pathway we established a physiological model of deficient hippocampal neurogenesis by ablating primary cilia in radial glial
stem cells of the adult dentate gyrus (Amador-Arjona et al., 2011). Sox2 is a master regulator of neural stem cells biology. We discovered novel epigenetic mechanisms of Sox2 function
in neural stem cell self-renewal and neuronal differentiation. In neural stem cells Sox2 supports the recruitment of the adaptor protein TRRAP and histone acetyl transferases (such as
GCN5) to maintain the levels of H3K9me3 at the proximal promoters of genes critical for neural stem cell proliferation (Cimadamore et al., 2013). On the other hand, we found that Sox2
function is required for the appropriate activation of neurogenic genes (Cimadamore et al., 2011). Sox2 binds to the regulatory elements of poised neurogenic genes and regulates the and
identified hits with improved activity compared to etoposide providing additional proof of continuity of our drug activity PRC2 complex and the levels of H3K27me3, thus enabling a robust
activation of these genes upon neurogenic stimuli (Amador-Arjona et al., 2015).
Over the past decade we developed a unique phenotypic screening approach: Microscopic Imaging of Epigenetic Landscapes (MIEL) captures patterns of nuclear staining of epigenetic marks from
which derived texture features are used to compare different populations of cells or different cell treatments to generate discernable signatures of such states and to provide the accuracy of
the result - Farhy et al., 2018, BioRxiv 348888 (preprint) available from: https://doi.org/10.1101/348888. MIEL enabled discrimination between cell types with high accuracy and derivation of
image-based signatures of drug-induced perturbations. Based single cell imaging of epigenetic landscapes, we have successfully identified multiparametric signature of GBM differentiation induced
by biologicals such as serum and BMP. Using such controls, we performed a pilot screening of the focused Prestwick chemical library validating the utility of MIEL approach in 384-well format. Critically,
our preliminary results suggest that MIEL-based screening of compounds inducing GBM differentiation correlates well with hit prioritization based on the whole genome expression profiling, thus validating
MIEL for screening large small molecule libraries to identify novel scaffolds and functions.
As an alternative approach, we generated a small library of shape mimetics of etoposide (our best hit identified in Prestwick library) and identified a number of hits with the improved activity thus documenting
our ability to march through the improvement and optimization steps using MIEL platform. More recently, we have documented MIEL’s power to derive epigenetic signatures for over 200 drug-induced perturbations in
primary glioblastoma and provide functional information such as attribution to particular drug class or the mechanism of action, Farhy et al., 2019 - BioRxiv 541151 (preprint) available from:
In the present application, joining efforts with the Lukyanov’s laboratory, we propose to advance arguably the most important direction for MIEL development – live imaging of epigenetic landscape in space and time (Live-MIEL). Rooted in the single cell analysis such approach will enable, for the first time, to get insights into the dynamics of epigenetic changes in single cells. By analogy, this will be equivalent to moving from bulk sequencing to single cell sequencing, with the huge advantage that we will actually gain in resolution and not lose (due to the loss of small amounts of RNA in single cells).