Biology subjects

Farhy, C.

Publications and source records attributed to Farhy, C..

5 recordsLinked to original sources

bioRxiv2022

Microscopic Imaging of Epigenetic Age

Biomarkers of biological age that predict the risk of disease and expected lifespan better than chronological age are key to efficient and cost-effective healthcare1-3. To advance a personalized approach to healthcare, such biomarkers must perform on the individual rather than population level, demonstrate single cell resolution, and provide scalable and cost-effective measurements. We developed a novel approach - image-based chromatin and epigenetic age (ImAge), that utilizes image texture features based on the patterns of chromatin and epigenetic marks in single nuclei. We observed the emergence of intrinsic trajectories of ImAge using dimensionality reduction without regression on chronological age. ImAge was correlated with chronological age in all tissues and organs examined and was consistent with the expected acceleration and/or deceleration of biological age in chronologically identical mice treated with chemotherapy or following a caloric restriction regimen, respectively. ImAge from chronologically identical mice inversely correlated with their locomotor activity (greater activity for younger ImAge), consistent with the essential role of locomotion as an aging biomarker. Finally, we demonstrated that ImAge is reduced upon partial reprogramming in vivo following transient expression of OSKM cassette in the liver and skeletal muscles of old mice and validated the power of ImAge to assess the heterogeneity of reprogramming. We propose that ImAge represents the first-in-class individual-level biomarker of aging and rejuvenation with single-cell resolution.

systems biology↗

bioRxiv2022

Canonical BMP2/4 signaling degrades SOX2 in glioblastoma propagating cells.

The effect of Bone Morphogenetic Proteins (BMPs) on glioblastoma propagation cells (GPCs) is being debated [1-5]. We observed that exposure of GPCs to BMP2/4 initiates a rapid proteasomal degradation of the pluripotency factor SOX2 followed by the differentiation of GPCs into glial cells using 5 primary human glioblastoma lines tested. Enforced expression of SOX2 in GPCs antagonized BMP2/4-induced gliogenesis and reduction of proliferation. Both outcomes are consistent with the role of SOX2 in normal neurogenesis [6-8]. Using gene expression analysis, we observed that level of SOX2 in different glioblastoma lines tracks with the levels of oncogenes H/K/N-RAS and OLIG2. Our work provides support for BMP2/4-SOX2 axis in GPCs and points to the proteasome-regulated degradation of SOX2 that initiates glycogenic differentiation similar to that observed during normal development [6, 7]. Our work supports a potential for developing novel therapeutic strategies aimed at differentiation of GPC into non-tumorigenic glia.

cancer biology↗

bioRxiv2020

Activity-Dependent Modulation of Synapse-Regulating Genes in Astrocytes

Astrocytes regulate the formation and function of neuronal synapses via multiple signals, however, what controls regional and temporal expression of these signals during development is unknown. We determined the expression profile of astrocyte synapse-regulating genes in the developing mouse visual cortex, identifying astrocyte signals that show differential temporal and layer-enriched expression. These patterns are not intrinsic to astrocytes, but regulated by visually-evoked neuronal activity, as they are absent in mice lacking glutamate release from thalamocortical terminals. Consequently, synapses remain immature. Expression of synapse-regulating genes and synaptic development are also altered when astrocyte signaling is blunted by diminishing calcium release from astrocyte stores. Single nucleus RNA sequencing identified groups of astrocytic genes regulated by neuronal and astrocyte activity, and a cassette of genes that show layer-specific enrichment. Thus, the development of cortical circuits requires coordinated signaling between astrocytes and neurons, identifying astrocytes as a target to manipulate in neurodevelopmental disorders.

neuroscience↗

bioRxiv2019

Improving drug discovery using image-based multiparametric analysis of epigenetic landscape.

With the advent of automatic cell imaging and machine learning, high-content phenotypic screening has become the approach of choice for drug discovery due to its ability to extract drug specific multilayered data and compare it to known profiles. In the field of epigenetics such screening approaches has suffered from the lack of tools sensitive to selective epigenetic perturbations. Here we describe a novel approach Microscopic Imaging of Epigenetic Landscapes (MIEL) that captures patterns of nuclear staining of epigenetic marks (e.g. acetylated and methylated histones) and employs machine learning to accurately distinguish between such patterns (1). We demonstrated that MIEL has superior resolution compared to conventional intensity thresholding techniques and enables efficient detection of epigenetically active compounds, function-based classification, flagging possible off-target effects and even predict novel drug function. We validated MIEL platform across multiple cells lines and using dose-response curves to insure the robustness of this approach for the high content high throughput drug discovery.

cell biology↗

bioRxiv2018

Multiparametric Signature of Glioblastoma Differentiation Revealed by Imaging of Cellular Epigenetic Landscapes

The resistance of Glioblastoma (GBM) to conventional cytotoxic drugs has prompted novel therapeutic strategies, including differentiating tumor propagating cells (TPCs) into less tumorigenic cells using small molecule inducers of TPC differentiation. However, high-throughput screening for such molecules is hampered by the lack of robust markers of GBM differentiation. To obtain a signature of differentiated TPCs, we developed \"Microscopic Imaging of Epigenetic Landscapes\" (MIEL), which captures patterns of nuclear staining for epigenetic marks to derive feature-fingerprints of individual cells. We confirmed MIELs ability to accurately distinguish multiple cell fates and identified a multiparametric epigenetic signature of differentiated TPCs. Critically, we validated epigenetic imaging-based signature using global gene expression thus providing the proof of principle for the MIELs ability to select and prioritize small molecules, which induce TPC differentiation.

cancer biology↗