Biology subjects

Lomberk, G.

Publications and source records attributed to Lomberk, G..

4 recordsLinked to original sources

bioRxiv2026

STRUCTURAL AND MOLECULAR DYNAMICS ANALYSIS OF HUMAN β-DEFENSIN 1 VARIANTS REVEALS DISTINCT PERTURBATION SIGNATURES

Human {beta}-defensin 1 (hBD-1) is a small, disulfide-constrained antimicrobial peptide produced predominantly in the kidney and urogenital tract, where it contributes to epithelial innate defense. Genetic variation in the gene encoding hBD-1 has been associated with altered expression levels and susceptibility to infections, including infection following solid organ transplantation, yet the molecular consequences of coding substitutions in the active, mature form remain largely undefined. Here, we integrate conventional genomics, protein bioinformatics, structural modeling, and molecular dynamics to investigate the molecular consequences of 93 human-observed hBD-1 missense variants. Evaluation of hBD-1 missense variants across sequence-, structure-, and dynamics-based dimensions reveals variant-specific molecular perturbation signatures that complement conventional and static biophysical predictions. By treating naturally occurring substitutions as a perturbation series across a compact defensin scaffold, this study identifies multiple molecular routes through which sequence variation can remodel an endogenous antimicrobial peptide and prioritizes variants for direct structure-function testing. These findings provide a mechanistic framework for investigating how naturally occurring hBD-1 variation may influence peptide behavior and, ultimately, antimicrobial function.

biophysics↗

bioRxiv2025

KRAS Inhibition Reverses Chemotherapy Resistance Promoted by Therapy-Induced Senescence-like in Pancreatic Ductal Adenocarcinoma

BackgroundEmerging evidence suggests that chemotherapy can accumulate senescent-like cells within tumor tissues, a phenomenon linked to therapy resistance. The aim of this study is to analyze the senescence-like state of after-treatment persistent cells associated with KRAS mutational status to offer a therapeutic strategy to target these cells in pancreatic ductal adenocarcinoma (PDAC). Experimental DesignThree commercial cell lines and five patient-derived primary cell cultures with different KRAS statuses were studied following gemcitabine treatment. Senescence-like status was assessed using SA-{beta}-gal, together with cell cycle regulators such as p21. Additionally, KRAS mutations were modulated using MRTX1133 and AMG-510, and the signaling pathways ERK and AKT were analyzed and modulated in vitro. Finally, p21 expression, associated with the senescence-like state, on patient outcomes and treatment response was analyzed in publicly available bulk RNA-seq and single-nucleus datasets. ResultsWe observed an overexpression of p21 alongside an increase in SA-{beta}-gal signal in response to gemcitabine treatment, indicating the induction of a senescence-like state. Specific inhibition of KRAS G12D or G12C mutations reduced SA-{beta}-gal signal and sensitized PDAC cells to gemcitabine. Moreover, ERK inhibition but not AKT inhibition decreased SA-{beta}-gal signal. Additionally, we characterized p21 expression levels in relation to patient outcomes and found that they are modulated by treatment. ConclusionsThis dual-targeted therapeutic strategy holds promises for overcoming the challenges posed by KRAS-driven cancers, particularly in addressing the formidable obstacle of pancreatic cancer. Highlights The accumulation of senescent-like cells in tumor tissues because of chemotherapy is linked to treatment resistance, specifically in pancreatic ductal adenocarcinoma (PDAC). Therapy-induced senescence-like in PDAC is influenced by the mutational status of KRAS, affecting the response to chemotherapeutic agents. The expression of the p21 is activated in response to therapy-induced senescence-like, particularly after gemcitabine treatment and is associated with patients outcome. Specifically inhibiting the mutated form of KRAS with small compounds can sensitize PDAC cells to gemcitabine and reduce SA-{beta}-gal signal, acting through the ERK pathway but not the AKT pathway. The study presents a dual-targeted therapeutic strategy that combines KRAS inhibition with cytotoxic agents, potentially improving treatment efficacy and overcoming resistance in KRAS-driven cancers, such as PDAC.

cancer biology↗

bioRxiv2023

EZH2 deletion does not impact acinar cell regeneration but restricts progression to pancreatic cancer in mice

Enhancer of Zeste Homologue 2 (EZH2) is part of the Polycomb Repressor Complex 2, which induces trimethylation of lysine 27 on histone 3 (H3K27me3) and promotes genes repression. EZH2 is overexpressed in many cancers including pancreatic ductal adenocarcinoma (PDAC). Previous studies in mice attributed both pro-oncogenic and tumor suppressive functions to EZH2. Deletion of the EZH2 enhances de novo KRAS-driven neoplasia following pancreatic injury by preventing acinar cell regeneration, while increased EZH2 expression in PDAC is correlated to poor prognosis, suggesting a context-dependant effect for EZH2 in PDAC progression. In this study, we examined EZH2 function in pre-and early neoplastic stages of PDAC. Using an inducible model to generate deletion of EZH2 only in adult acinar cells (EZH2{Delta}SET), we showed loss of EZH2 activity did not prevent acinar cell regeneration in the absence of oncogenic KRAS (KRASG12D), nor lead to increased PanIN formation in the presence of KRASG12D in adult mice. However, loss of EZH2 did reduce recruitment of inflammatory cells and, when combined with a PDAC model, promoted widespread PDAC progression. Loss of EZH2 function also correlated to remodeling of the tumor microenvironment, which favors cancer cell progression. This study suggests expression of EZH2 in adult acinar cells restricts PDAC initiation and progression by affecting both the tumour microenvironment and acinar cell differentiation.

cancer biology↗

bioRxiv2019

Discovery, Expression, Cellular Localization, and Molecular Properties of a Novel, Alternative Spliced HP1g Isoform, Lacking the Chromoshadow Domain

By reading the H3K9Me3 mark through their N-terminal chromodomain (CD), HP1 proteins play a significant role in cancer-associated processes, including cell proliferation, differentiation, chromosomal stability, and DNA repair. Here, we used a combination of bioinformatics-based methodologies, as well as experimentally-derived datasets, that reveal the existence of a novel short HP1{gamma} (CBX3) isoform, named here sHP1{gamma}, generated by alternative splicing of the CBX3 locus. The sHP1{gamma} mRNA encodes a protein composed of 101 residues and lacks the C-terminal chromoshadow domain (CSD) that is required for dimerization and heterodimerization in the previously described 183 a. a HP1{gamma} protein. Fold recognition, order-to-disorder calculations, threading, homology-based molecular modeling, docking, and molecular dynamic simulations show that the sHP1{gamma} is comprised of a CD flanked by intrinsically disordered regions (IDRs) with an IDR-CD-IDR domain organization and likely retains the ability to bind to the H3K9Me3. Both qPCR analyses and mRNA-seq data derived from large-scale studies confirmed that sHP1{gamma} mRNA is expressed in the majority of human tissues at approximately constant ratios with the chromoshadow domain containing isoform. However, sHP1{gamma} mRNA levels appear to be dysregulated in different cancer types. Thus, our data supports the notion that, due to the existence of functionally different isoforms, the regulation of HP1{gamma}-mediated functions is more complex than previously anticipated.

molecular biology↗