Biology subjects

Ambrogio, C.

Publications and source records attributed to Ambrogio, C..

5 recordsLinked to original sources

bioRxiv2026

An integrated biomaterials-centred approach of the ageing thymic microenvironment reveals design principles for regenerative biomaterials

Thymic involution is commonly addressed as a loss of epithelial and lymphoid tissue, yet the accompanying remodelling of the microenvironment remains poorly defined. This work applied a biomaterials-centered approach to compare young and aged bovine thymus by integrating histology, oscillatory rheology, untargeted lipidomics, ICP-MS and AP-MALDI mass spectrometry imaging. This holistic approach connects the mechanical, compositional, and spatial features of the native thymus with the development of thymus-inspired biomaterials. Ageing increased both storage and loss moduli by more than one order of magnitude and reduced the linear viscoelastic region approximately fivefold, defining a markedly stiffer and more strain-sensitive material state. This mechanical transition was accompanied by lipid remodelling, with double realtive contribution of triacylglycerols to the lipid pool doubled and loss of membrane-associated phospholipids. The elemental profile also contracted, with total metal content decreasing by one-third and zinc showing a reduction of 70%. At the architectural level, the corticomedullary ratio was more than halved, while AP-MALDI imaging revealed an approximately 40% reduction in the annotated molecular repertoire and a shift from homogeneous to fragmented distributions of choline and representative phosphatidylcholine species. These results show that thymic ageing emerges from the concomitant variations of viscoelastic behaviour, chemical composition, and molecular organization. By defining these interconnected alterations, this study establishes a materials-based foundation for the design of bioinspired systems aimed at reproducing features of the young thymic niche and supporting future thymic repair. HighlightsO_LIAgeing increased viscoelastic moduli and reduced deformation tolerance. C_LIO_LIThe lipid profile shifted from membrane lipids towards triacylglycerols. C_LIO_LIThe elemental pool contracted, with zinc showing the strongest depletion. C_LIO_LIHistology and AP-MALDI-MSI revealed loss of spatial organization. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=165 SRC="FIGDIR/small/740917v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@1baa8cdorg.highwire.dtl.DTLVardef@1a04649org.highwire.dtl.DTLVardef@1669ce6org.highwire.dtl.DTLVardef@1c6e9ca_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2024

Targeted KRAS(G12V) degradation elicits efficient and durable lung adenocarcinoma regression in vivo

Recent drug discovery breakthroughs led to the approval of KRASG12C inhibitors in lung adenocarcinoma (LUAD). Unfortunately, clinical responses remain limited due to rapid resistance onset. Proteolysis-targeting chimeras (PROTACs) have emerged as promising alternatives to traditional inhibition. However, there is limited mechanistic understanding of KRAS degradation in vivo. Here, we developed a preclinical LUAD mouse model and demonstrated that targeted oncogenic KRAS degradation induces rapid tumor regression. Transcriptional, histological, and immunophenotypic analyses revealed a substantial remodeling of the tumor microenvironment. Notably, disease relapse observed during long-term degrader treatment stems from proteolysis machinery dysregulation, indicating resistance mechanisms distinct from those reported upon KRAS inhibition. Our findings highlight the therapeutic potential of KRAS degradation in LUAD, offering insights into cell-intrinsic and extrinsic mechanisms driving durable antitumor responses and supporting further clinical exploration. SIGNIFICANCEGiven the short duration of the clinical responses to KRAS inhibitors, complementary therapies are a dire medical need. Our preclinical findings endorse KRAS degradation as a therapeutic alternative in LUAD, where cell-intrinsic and extrinsic mechanisms drive tumor regression and durable therapeutic responses.

cancer biology↗

bioRxiv2024

Pharmacological SOS1 inhibitor BI-3406 demonstrates in vivo anti-tumor activity comparable to SOS1 genetic ablation in KRAS mutant tumors

Resistance to KRASmut inhibitors frequently arises, warranting further searches for anti-RAS cancer therapies. We evaluated the tolerability and efficacy of SOS1 pharmacological inhibition in comparison to genetic ablation in different KRAS-dependent tumor settings. Contrary to the rapid lethality caused by SOS1 genetic ablation in SOS2KO mice, SOS1 pharmacological inhibition by its specific inhibitor BI-3406 did not significantly affect animal weight/viability nor cause noteworthy systemic toxicity. In BI-3406-treated KRASmut MEFs, we observed significantly reduced RAS-GTP levels and RAS downstream signaling, as well as decreased tumor burden and slower disease progression resulting from tumor-intrinsic and extrinsic therapeutic drug effects. In vivo analyses of KRASG12D allografts in immunocompromised mice and KRASG12D-driven lung adenocarcinomas in immunocompetent mice showed that systemic BI-3406 treatment impaired tumor growth and downmodulated components of the tumor microenvironment comparably to the KRASG12D inhibitor MRTX1133. Markedly stronger synergistic antitumor effects were observed upon concomitant BI-3406+MRTX113 treatment, confirming SOS1 as an actionable therapy target in RAS-dependent cancers.

cancer biology↗

bioRxiv2023

scPharm: identifying pharmacological subpopulations of single cells for precision medicine in cancers

Intratumour heterogeneity is a major challenge that limits the effectiveness of anticancer therapies, thus compromising treatment outcomes. Single-cell RNA sequencing (scRNA-seq) technology offers a means to capture gene expression profiles at a single-cell resolution, while drug perturbation experiments yield valuable pharmacological data at the bulk cell level. Here, we introduce "scPharm", a computational framework to integrate large-scale pharmacogenomics profiles with scRNA-seq data, for identifying pharmacological subpopulations within a tumour and prioritizing tailored drugs. scPharm assesses the distribution of the identity genes of single cell (Cell-ID) within drug response-determined gene list, which is accomplished using the normalized enrichment score (NES) obtained from Gene Set Enrichment Analysis (GSEA) as the statistic. One key strength of scPharm is rooted in the robust positive correlation between NES statistics and drug response values at single-cell resolution. scPharm successfully identifies sensitive subpopulations in ER-positive and HER2-positive human breast cancer tissues, discovers dynamic changes in resistant subpopulation of human PC9 cells treated with Erlotinib, and expands its prediction capabilities to a mouse model. By a thoroughly comparative evaluation with other single-cell prediction tools, scPharm presents the superior predictive performance and computational efficiency. Furthermore, scPharm offers a unique feature by predicting combination strategies, gauging compensation effects or booster effects between two drugs through the Set covering method, as well as evaluating drug toxicity on healthy cells within the tumour microenvironment. Together, scPharm provides a novel approach to uncover therapeutic heterogeneity within tumours at single-cell resolution and facilitates precision medicine in cancers.

bioinformatics↗

bioRxiv2020

A structural model of a Ras-Raf signalosome

The protein K-Ras functions as a molecular switch in signaling pathways regulating cell growth. In the MAPK pathway, which is implicated in many cancers, multiple K-Ras proteins are thought to assemble at the cell membrane with Ras-effector proteins from the Raf family. Here we propose an atomistic structural model for such an assembly. Our starting point was an asymmetric, GTP-mediated K-Ras dimer model, which we generated using unbiased molecular dynamics simulations and verified with mutagenesis experiments. Adding further K-Ras monomers in a head-to-tail fashion led to a compact helical assembly, a model we validated using electron microscopy and cell-based experiments. This assembly stabilizes K-Ras in its active state and presents composite interfaces to facilitate Raf binding. Guided by existing experimental data, we then positioned C-Raf, the downstream kinase MEK1, and accessory proteins (Galectin-3 and 14-3-3{sigma}) on the helical assembly. The resulting Ras-Raf signalosome model offers an explanation for a large body of data on MAPK signaling.

molecular biology↗