Biology subjects

Sher, F.

Publications and source records attributed to Sher, F..

5 recordsLinked to original sources

bioRxiv2026

Dense CRISPR Mapping of the WAVE Complex Identifies Pharmacological Modulators of AD-Linked Myeloid Migration

Although genetic risk for Alzheimers disease (AD) strongly converges on microglial pathways, the druggable functional protein regions that control disease-relevant microglial behaviors remain largely unknown. Here, we applied dense CRISPR-Cas9 mutagenesis and CRISPRtile-based functional mapping to the WAVE regulatory complex (WRC), a central regulator of actin remodeling and cell migration. In a pooled CCL2-directed migration assay in human THP-1 myeloid cells, perturbation of NCKAP1L, CYFIP1, and BRK1 impaired migration and revealed divergent effects among WRC paralogs. Residue-level analysis mapped discrete migration-associated functional regions within CYFIP1 and NCKAP1L, including a CYFIP1 regulatory hotspot and a prioritized NCKAP1L region nominated for pharmacological targeting. Human single-nucleus datasets identified NCKAP1L as a microglia-enriched WRC component expressed across diverse microglial states. Machine-learning-guided compound prediction nominated Montelukast sodium and Piperacetazine, which we experimentally validated as negative and positive modulators of chemokine-directed migration, respectively. These findings establish WRC-dependent migration as a pharmacologically tunable myeloid process relevant to AD.

neuroscience↗

bioRxiv2026

AI platform for CRISPR functional mapping and function-based drug design

Conventional structure-based drug design has high clinical failure rates due to the disconnect where binding affinity does not guarantee safe functional modulation. To bridge this gap, we present CRISPRtile, a cloud-based platform for function-based drug design. By deriving library coverage optimization equations and leveraging AI to correct CRISPR guide biases, we generated toxicity and functional landscapes with over threefold error reduction compared to conventional methods. These maps bypass error and orders of magnitude higher computational cost in structure-based pipelines by enabling AI prediction of drug interaction directly from nontoxic functional sequences, while predicting brain penetration with benchmark leading performance. We demonstrate CRISPRtile by mapping the NLRP3 inflammasome and identifying FDA approved drugs with previously unrecognized ability to modulate it, revealing strategies to amplify or inhibit our immune response to homeostatic perturbations. These advances establish a generalizable strategy for the systematic discovery of safe functional modulators.

genetics↗

bioRxiv2025

A proteogenomic tool uncovers protein markers for human microglial states

Human microglial heterogeneity has been largely described using transcriptomic data. Here, we introduce a microglial proteomic data resource and a Cellular Indexing of Transcriptomes and Epitopes by Sequencing panel enhanced with antibodies targeting 17 microglial cell surface proteins (mCITE-Seq). We evaluated mCITE-Seq on HMC3 microglia-like cells, induced-pluripotent stem cell-derived microglia (iMG), and freshly isolated primary human microglia. We identified novel protein microglial markers such as CD51 and relate expression of 101 cell surface proteins to transcriptional programs. This results in the identification and validation of three protein marker combinations with which to purify microglia enriched with each of 23 transcriptional programs; for example, CD49D, HLA-DR and CD32 enrich for GPNMBhigh ("disease associated") microglia. Further, we identify and validate proteins - SIRPA, PDPN and CD162 - that differentiate microglia from infiltrating macrophages. The mCITE-Seq panel enables the transition from RNA-based classification and facilitates the functional characterization and harmonization of model systems.

neuroscience↗

bioRxiv2018

CRISPR-SURF: Discovering regulatory elements by deconvolution of CRISPR tiling screen data

Tiling screens using CRISPR-Cas technologies provide a powerful approach to map regulatory elements to phenotypes of interest, but computational methods that effectively model these experimental approaches for different CRISPR technologies are not readily available. Here we present CRISPR-SURF, a deconvolution framework to identify functional regulatory regions in the genome from data generated by CRISPR-Cas nuclease, CRISPR interference (CRISPRi), or CRISPR activation (CRISPRa) tiling screens. We validated CRISPR-SURF on previously published and new data, identifying both experimentally validated and new potential regulatory elements. With CRISPR tiling screens now being increasingly used to elucidate the regulatory architecture of the non-coding genome, CRISPRSURF provides a generalizable and accessible solution for the discovery of regulatory elements.

bioinformatics↗

bioRxiv2018

CRISPRO Identifies Functional Protein Coding Sequences Based on Genome Editing Dense Mutagenesis

CRISPR/Cas9 pooled screening permits parallel evaluation of comprehensive guide RNA libraries to systematically perturb protein coding sequences in situ and correlate with functional readouts. For the analysis and visualization of the resulting datasets we have developed CRISPRO, a computational pipeline that maps functional scores associated with guide RNAs to genome, transcript, and protein coordinates and structure. No available tool has similar functionality. The ensuing genotype-phenotype linear and 3D maps raise hypotheses about structure-function relationships at discrete protein regions. Machine learning based on CRISPRO features improves prediction of guide RNA efficacy. The CRISPRO tool is freely available at gitlab.com/bauerlab/crispro.

bioinformatics↗