Biology subjects

Verbeke, C. S.

Publications and source records attributed to Verbeke, C. S..

3 recordsLinked to original sources

bioRxiv2026

NFATC2 in pancreatic cancer-associated fibroblasts predicts treatment response and facilitates ERBB-targeted therapies

Pancreatic ductal adenocarcinoma (PDAC) remains a lethal malignancy, with therapeutic resistance influenced by a dense desmoplastic stroma dominated by cancer-associated fibroblasts (CAF). Using single-cell RNA-sequencing and gene regulatory network modeling of 42 PDAC tumors, we identified a CAF subpopulation characterized by elevated NFATC2 expression that is enriched in patients with improved therapeutic response and survival. NFATC2+ CAFs exhibited tumor-suppressive features, including enhanced apoptotic signaling and suppression of ERBB pathway activity. Co-culture experiments demonstrated that NFATC2+ CAFs restrain pancreatic cancer cell growth and enhance chemotherapy-induced apoptosis, increasing sensitivity to standard-of-care chemotherapy regimens and synergizing with ERBB-targeted therapies. The favorable effect of NFATC2+ CAFs on chemotherapy response was validated in two other PDAC cohorts and in rectal cancer. Together, these findings identify NFATC2+ CAFs as a therapy-conditioned stromal state linked to improved treatment response and uncover a context-dependent vulnerability within the tumor microenvironment that may be exploited to rationally optimize combination therapies.

cancer biology↗

bioRxiv2025

Knowledge Discovery in Datasets of Proteomics by Systems Modeling in Translational Research on Pancreatic Cancer

Knowledge discovery in databases (KDD) can contribute to translational research, also known as translational medicine, by bridging the gap between in vitro and in vivo studies and clinical applications. Here, we propose a systems modeling workflow for KDD. This framework includes data collection of composition model (various research models) and processing model (proteomics) and analytical model (bioinformatics, artificial intelligence/machine leaning and pattern evaluation), knowledge presentation, and feedback loops for hypothesis generation and validation. We applied this workflow to study pancreatic ductal adenocarcinoma (PDAC). Through this approach, we identified the common proteins between human PDAC and various research models in vitro (cells, spheroids and organoids) and in vivo (mouse mice). Accordingly, we hypothesized potential translational targets on hub proteins and the related signaling pathways, PDAC specific proteins and signature pathways, and high topological proteins. Thus, we suggest that this systems modeling workflow can be a valuable method for KDD, facilitating knowledge discovery in translational targets in general and in particular to PADA in this case.

systems biology↗

bioRxiv2020

Single-shot Mesoporous Silica Rods Scaffold for Induction of Humoral Responses Against Small Antigens

Vaccines have shown significant promise in eliciting protective and therapeutic responses. However, most effective vaccines require several booster shots, and it is challenging to generate potent responses against small molecules and synthetic peptide antigens often used to increase target specificity and improve vaccine stability. As continuous antigen uptake and processing by APCs and persistent toll-like receptor (TLR) priming have been shown to amplify antigen specific humoral immunity, we explored whether a single injection of a mesoporous silica micro-rod (MSR) vaccine containing synthetic molecules and peptides can effectively generate potent and durable antigen-specific humoral immunity. A single injection of the MSR vaccine against a gonadotropin-releasing hormone (GnRH) decapeptide elicited highly potent anti-GnRH response that lasted for over 12 months. The MSR vaccine generated higher titers than bolus or alhydrogel alum vaccine formulations. Moreover, a MSR vaccine directed against a Her2/neu peptide within the Trastuzumab binding domain showed immunoreactivity to native Her2 protein on tumor cell surface and, when directed against nicotine, generated long-term anti-nicotine antibodies. Mechanistically, we found that the MSR vaccine induced persistent germinal center (GC) B-cell activity for more than 3 weeks after a single injection, generation of memory B cells, and that at least 7 days of immunostimulation by the vaccine was required to generate an effective humoral response. Together, these data suggest that the MSR vaccine represents a promising technology for synthetic antigen vaccines to bypass the need for multiple immunizations and enhance long-term production of antibodies against endogenous antigens in the context of reproductive biology, cancer, and chronic addiction.

bioengineering↗