Biology subjects

Kitaygorodsky, J.

Publications and source records attributed to Kitaygorodsky, J..

3 recordsLinked to original sources

bioRxiv2026

Spatiotemporal remodeling of cytoskeletal and junction networks during somatic cell reprogramming

Summary/AbstractReprogramming somatic cells into induced pluripotent stem cells involves a dramatic reorganization of the cytoskeleton and junctions during the critical mesenchymal-to-epithelial transition stage. While protein abundance changes have been profiled, the spatiotemporal dynamics of protein-protein associations involving these structural components remain poorly resolved. Here, we present a time-resolved proximity proteomics resource that maps cytoskeletal and junctional remodeling across 27 baits during the early stages of reprogramming. We identified over 1100 high-confidence interactions, including many not previously reported, capturing the dynamic reorganization of cell architecture. By integrating proximity-dependent biotinylation with quantitative proteomics, we distinguished spatial relocalizations from abundance-driven effects. Dynamic redistributions of actin regulators and desmosomal proteins were observed, and a targeted short interfering RNA screen uncovered early acting structural proteins essential for colony formation. Our findings reveal adhesion and cytoskeletal maturation as structural bottlenecks in reprogramming and provide a broadly applicable framework for mapping subcellular remodeling during dynamic cell fate transitions.

systems biology↗

bioRxiv2025

Benchmarking of proximity-dependent biotinylation enzymes across cellular compartments and time windows

Proximity-dependent biotinylation has become a powerful approach for mapping protein interactions and subcellular organization in living cells. Although a growing number of engineered biotin ligases have been introduced, their performance has not been systematically evaluated across diverse cellular contexts. Here, we benchmark ten proximity ligases spanning three bacterial lineages using standardized proteomic workflows across multiple labeling durations, subcellular compartments, and two human cell types. While all enzymes efficiently detect proximal associations, they differ in labeling kinetics, background activity, and spatial specificity. TurboID exhibits the highest overall activity but generates substantial background in standard media. miniTurbo and ultraID support rapid, biotin-dependent labeling with low background, making them better suited for dynamic and time-resolved applications. However, miniTurbo showed aberrant mitochondrial localization with two cytoskeletal baits (VASP and PFN1). Across 15 diverse baits, ultraID consistently provides an excellent combination of specificity, efficiency, and spatial compatibility--including unique recovery of Golgi-resident glycosyltransferases. This study serves as a comparative resource, offering guidance for enzyme selection and experimental design in proximity proteomics.

systems biology↗

bioRxiv2018

A proactive genotype-to-patient-phenotype map for cystathionine beta-synthase

Success in precision medicine depends on our ability to determine which rare human genetic variants have functional effects. Classical homocystinuria--characterized by elevated homocyst(e)ine in plasma and urine--is caused by primarily-rare variants in the cystathionine beta-synthase (CBS) gene. About half of patients respond to vitamin B6 therapy. With early detection in newborns, existing therapies are highly effective. Functional CBS variants, especially those that respond to vitamin B6, can be detected based on their ability to restore growth in yeast cells lacking CYS4 (the yeast ortholog of CBS). This assay has previously been carried out only reactively after first observation of a variant in patients. Here we describe a proactive comprehensive missense variant effect map for human CBS. Together, saturation codon-replacement mutagenesis, en masse growth selection at different vitamin B6 levels, and sequencing yielded a look-up table for CBS missense variant function and vitamin B6-remediability in yeast. The CBS variant effect map identified disease variants and predicted both disease severity (r = 0.82) and human clinical response to vitamin B6 (r = 0.89). Thus, highly-multiplexed cell-based assays can yield proactive maps of variant function and patient response to therapy, even for rare variants not previously seen in the clinic.

genetics↗