Biology subjects

Paszkowski-Rogacz, M.

Publications and source records attributed to Paszkowski-Rogacz, M..

4 recordsLinked to original sources

bioRxiv2026

Loss of UBP1 drives oxaliplatin resistance through a targetable dependency on translation initiation

Oxaliplatin is a common component of various chemotherapeutic regimens for the treatment of gastrointestinal cancers. However, the majority of patients exhibit resistance to oxaliplatin-based therapy. Here, we integrated knockout and transcription-activation CRISPR screens in patient-derived gastric cancer organoids (GC PDOs) to comprehensively profile major genetic and transcriptomic changes observed over the course of resistance acquisition. Our screens identified UBP1, a transcription factor frequently lost in GC, as a critical determinant of oxaliplatin resistance development. Leveraging a large GC organoid biobank from a co-clinical trial and primary tumor omics data, we reveal that downregulation of specifically MYC-driven ribosome biogenesis drives oxaliplatin resistance, highlighting the drugs role as a ribosome biogenesis stressor. Mechanistically, UBP1 loss reduced expression of its direct target, MAX, a MYC cofactor, leading to downregulation of ribosome biogenesis and protection against nucleolar stress. Crucially, we discover that such downregulation is inevitably followed by a compensatory reliance on translation initiation, making it a therapeutic vulnerability in oxaliplatin-resistant tumors. Consequently, the resistance could be overcome by a synergistic action of the translation initiation repressor 4EGI, and the effect was also maintained in PDO that acquired resistance in vivo under clinically relevant conditions. Our data uncover a common marker of oxaliplatin resistance and identify a novel therapeutic strategy to reverse resistance to one of the most frequently used anticancer drugs.

cancer biology↗

bioRxiv2022

Prediction of designer-recombinases for DNA editing with generative deep learning

Site-specific tyrosine-type recombinases are effective tools for genome engineering, with the first engineered variants having demonstrated therapeutic potential. So far, adaptation to new DNA target site selectivity of designer-recombinases has been achieved mostly through iterative cycles of directed molecular evolution. While effective, directed molecular evolution methods are laborious and time consuming. Here we present RecGen (Recombinase Generator), an algorithm for the intelligent generation of designer-recombinases. We gathered the sequence information of over two million Cre-like recombinase sequences evolved for 89 different target sites with which we trained Conditional Variational Autoencoders for recombinase generation. Experimental validation demonstrated that the algorithm can predict recombinase sequences with activity on novel target-sites, indicating that RecGen is useful to accelerate the development of future designer-recombinases. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=137 SRC="FIGDIR/small/486669v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@c08326org.highwire.dtl.DTLVardef@e26984org.highwire.dtl.DTLVardef@7d7542org.highwire.dtl.DTLVardef@9d6642_HPS_FORMAT_FIGEXP M_FIG C_FIG Teaser Figure: Recombinase prediction generates active recombinases for a desired target site, while existing libraries with a similar target site need to go through directed evolution to achieve activity on the new site. While evolution takes weeks, prediction and synthesis of recombinases can be done in days.

bioinformatics↗

bioRxiv2020

Correction of a Factor VIII genomic inversion with designer-recombinases

Despite advances in nuclease-based genome editing technologies, correcting human disease-causing genomic inversions remains a challenge. Here, we describe the potential use of a recombinase-based system to correct a 140 kb genomic inversion of the F8 gene, which is frequently found in patients diagnosed with severe Hemophilia A. Employing substrate-linked directed molecular evolution, we developed a fused heterodimeric recombinase system (RecF8) achieving 30% inversion of the target sequence in human tissue culture cells. Transient RecF8 treatment of endothelial cells, differentiated from patient derived induced pluripotent stem cells (iPSCs) of a hemophilic donor, resulted in prominent correction of the inversion and restored Factor VIII mRNA expression. Our data suggests that designer-recombinases may represent efficient and specific means towards treatment of monogenic diseases caused by large gene inversions.

molecular biology↗

bioRxiv2018

Comparative RNAi Screens in Isogenic Human Stem Cells Reveal SMARCA4 as a Differential Regulator

Large-scale RNAi screens are a powerful approach to identify functions of genes in a cell-type specific manner. For model organisms, genetically identical (isogenic) cells from different cell-types are readily available, making comparative studies meaningful. For humans, however, screening isogenic cells is not straightforward. Here, we show that RNAi screens are possible in genetically identical human stem cells, employing induced pluripotent stem cell as intermediates. The screens revealed SMARCA4 (SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4) as a stemness regulator, while balancing differentiation distinctively for each cell type. SMARCA4 knockdown in hematopoietic stem progenitor cells (HSPC) caused impaired self-renewal in-vitro and in-vivo with skewed myeloid differentiation; whereas in neural stem cells (NSC), it impaired selfrenewal while biasing differentiation towards neural lineage, through combinatorial SWI/SNF subunit assembly. Our findings pose a powerful approach for deciphering human stem cell biology and attribute distinct roles to SMARCA4 in stem cell maintenance.

molecular biology↗