Biology subjects

Gubicza, K.

Publications and source records attributed to Gubicza, K..

3 recordsLinked to original sources

bioRxiv2026

Cell organization and disturbance-mapping using image activated cell-profiling (CODIAC)

Protein localization and abundance are tightly regulated to maintain cellular homeostasis, and their dysregulation is a hallmark of disease. However, methods that monitor the spatial localization changes of many proteins at once, and at scale, remain limited. Here we introduce CODIAC (Cell Organization and Disturbance-mapping using Image-Activated Cell-profiling), which couples image-enabled cell sorting (ICS) with improved Cas12a-assisted endogenous PCR tagging and machine-learning-guided gating to profile pools of fluorescently tagged proteins. Rather than isolating discrete cell populations, CODIAC reads the "phenotypic fingerprint" of each fluorescently tagged protein, defined by its distribution across a fixed set of image-defined sort bins. The method resolves localization-associated phenotypes, reproducibly profiles complex pools, generalizes to proteins absent from the training set, and detects shifts in protein localization and abundance following chemical perturbation. CODIAC thus extends ICS from outlier screening toward systematic profiling of the spatial proteome and its remodeling under perturbation.

cell biology↗

bioRxiv2025

Improved cloning-free one-step CRISPR-Cas12a-assisted tagging of mammalian genes using PCR generated reagents (PCR tagging)

Precise DNA integration in mammalian genomes using CRISPR/Cas based strategies remains challenging due to competing DNA repair pathways. We present an update for our CRISPR/Cas12a-assisted PCR-tagging method using linear donor cassettes and self-targeting gRNAs for gene tagging. By incorporating 2A-linked selection markers and chemically modifying PCR cassettes with phosphorothioate and biotin, along with the inhibition of NHEJ, we improve precise insertions while reducing unwanted integration products and we devise a variant of the method for seamless gene tagging. To profile integration outcomes, we further developed our integration site sequencing protocol (Tn5-Anchor-Seq, Meurer et al., 2018) to obtain a protocol using long-read (ONT) sequencing coupled with a custom computational pipeline. This enables high-resolution quantification of all integration events with respect to integration by HDR or NHEJ, as well as the presence of concatemers and off-target integrations. Our data reveal gene-specific editing profiles and demonstrate that combining cassette design with DNA repair modulation yields up to 5-fold increases in HDR and suppression of concatemers and indels. Together, our improvements outline an robust strategy for efficient and high-fidelity gene tagging in mammalian cells, facilitating functional genomics and cell engineering applications.

molecular biology↗

bioRxiv2018

CRISPR/Cas12a-assisted PCR tagging of mammalian genes

Here we describe a time-efficient strategy for endogenous C-terminal gene tagging in mammalian tissue culture cells. An online platform is used to design two long gene-specific oligonucleotides for PCR with generic template cassettes to create linear dsDNA donors, termed PCR cassettes. PCR cassettes encode the tag (e.g. GFP), a Cas12a CRISPR RNA for cleavage of the target locus and short homology arms for directed integration via homologous recombination. The integrated tag is coupled to a generic terminator shielding the tagged gene from the co-inserted auxiliary sequences. Co-transfection of PCR cassettes with a Cas12a-encoding plasmid leads to robust endogenous expression of tagged genes, with tagging efficiency of up to 20% without selection, and up to 60% when selection markers are used. We used target-enrichment sequencing to investigate all potential sources of artefacts. Our work outlines a quick strategy particularly suitable for exploratory studies using endogenous expression of fluorescent protein tagged genes

cell biology↗