Biology subjects

Siegfried, Z.

Publications and source records attributed to Siegfried, Z..

3 recordsLinked to original sources

bioRxiv2026

Targeting the 3 splice site by a decoy oligonucleotide attenuates U2AF1 splicing activity and inhibits leukemia

Recurrent mutations in spliceosomal genes are a hallmark of myeloid malignancies, with SF3B1, SRSF2, U2AF1 and ZRSR2 among the most frequently affected. These alterations are typically heterozygous, mutually exclusive missense mutations targeting highly conserved residues, reflecting a selective pressure to maintain a dysregulated yet essential splicing machinery. This constraint suggests that leukemic cells remain dependent on residual splicing activity, exposing a potential therapeutic vulnerability that extends beyond genetically defined subsets. For example, a previously developed therapeutic, Pladienolide B, is a potent cancer cell growth inhibitor targeting the SF3B1 subunit of the spliceosome1,2. Here we present an RNA decoy-based strategy to disrupt 3' splice site recognition by competitively engaging components of the spliceosomal machinery. We engineered a chemically stabilized RNA decoy that mimics the 3 splice site (3'SS decoy), thereby sequestering proteins involved in 3 splice site recognition from endogenous pre-mRNA targets. Although the decoy is expected to engage multiple components of the 3' splice site recognition complex, U2AF1 was used as the primary molecular readout to assess target engagement and downstream effects. To enable intracellular delivery, decoys were encapsulated in lipid nanoparticles (LNPs), facilitating efficient uptake in leukemic systems. We show that LNP-encapsulated decoys are efficiently delivered into leukemic cells, including established cell lines and patient-derived blasts, and directly engage components of the splicing machinery. Decoy treatment induces widespread alterations in RNA splicing programs and impairs leukemic cell fitness in vitro. Importantly, systemic administration of the 3SS decoy significantly reduces leukemia burden in an in vivo xenograft model. Notably, these effects are observed independently of spliceosomal mutational status, supporting a broader dependency of leukemic cells on intact splicing factor function. Together, our findings establish decoy-mediated disruption of splicing factor activity as a mechanistically targeted therapeutic strategy and identify LNPs as an effective platform for the delivery of RNA-based modulators of essential RNA-protein interactions in myeloid malignancies.

molecular biology↗

bioRxiv2026

Molecular characterization of the heterozygous loss of function mutations in the X-linked PCDH19 gene causing PCDH19-Cluster Epilepsy

PCDH19-Cluster Epilepsy (PCDH19-CE) is a rare neurological disorder caused by mutations in the PCDH19 (Protocadherin-19) gene and is characterized by early-onset seizures and cognitive impairment. In contrast to most X-linked disorders, PCDH19 mutations predominantly affect heterozygous females, while hemizygous males are largely spared. Although advances have been made to understand the pathological mechanism underlying PCDH19-CE, key downstream targets and compensatory pathways are yet to be elucidated. Using CRISPR/Cas9 technology, we generated both a mouse model of PCDH19-CE and a human embryonic stem cell (ESC) model. Transcriptomic analysis identified genes that were differentially expressed in the brains of heterozygous (Pcdh19WT/mut) female mice compared with wildtype (WT) and homozygous (Pcdh19mut/mut) female mice. Pathway analysis of these differentially expressed genes (DEGs) revealed enrichment in pathways involved in neuronal development, ion channel activity, synaptic development and neuronal signalling. Neurons differentiated from human ESCs carrying a PCDH19 mutation exhibited similar gene expression patterns, with heterozygous neurons displaying a distinct expression pattern compared to both WT and homozygous mutant neurons. In contrast to the molecular phenotype, neurons derived from homozygous mutant cells showed highly elongated neurites while neurons from heterozygous cells showed intermediate neurite elongation. This suggests that neurite morphology correlates directly with levels of WT PCDH19. Overall, our findings indicate that heterozygous PCDH19 mutations are associated with defects in the expression of genes involved in developmental, signalling, and neuronal pathways in both mouse and human disease models, while certain morphological phenotypes appear to depend on the levels of WT PCDH19.

genetics↗

bioRxiv2022

S6K1 phosphorylates Cdk1 and MSH6 to regulate DNA repair.

The mTORC1 substrate, S6 Kinase 1 (S6K1), is involved in the regulation of cell growth, ribosome biogenesis, glucose homeostasis and adipogenesis. Accumulating evidence has suggested a role for mTORC1 signaling in the DNA damage response. This is mostly based on the findings that mTORC1 inhibitors sensitized cells to DNA damage. However, a direct role of the mTORC1-S6K1 signaling pathway in DNA repair and the mechanism by which this signaling pathway regulates DNA repair is unknown. In this study, we discovered a novel role for S6K1 in regulating DNA repair through the coordinated regulation of the cell cycle, homologous recombination (HR) DNA repair (HRR) and mismatch DNA repair (MMR) mechanisms. Here we show that S6K1 orchestrates DNA repair by phosphorylation of Cdk1 at serine 39, causing G2/M cell cycle arrest enabling homologous recombination and by phosphorylation of MSH6 at serine 309, enhancing MMR. Moreover, breast cancer cells harboring RPS6KB1 gene amplification show increased resistance to several DNA damaging agents and S6K1 expression is associated with poor survival of breast cancer patients treated with chemotherapy. Our findings reveal an unexpected function of S6K1 in the DNA repair pathway, serving as a tumorigenic barrier by safeguarding genomic stability.

cancer biology↗