Biology subjects

Bergamaschi, L.

Publications and source records attributed to Bergamaschi, L..

4 recordsLinked to original sources

bioRxiv2026

Active Surveillance Reveals a Systemic Pro-Resolving Th2 Immune Program Linked to 1 Desmoid Tumor Regression

Desmoid fibromatosis (DF) is a rare mesenchymal neoplasm with an unpredictable clinical course, where spontaneous regression or progression occurs in a significant subset of patients through largely undefined mechanisms. The use of active surveillance (AS) offers the opportunity to investigate whether tumor- or host-driven systemic and local immune features may explain these divergent outcomes, improving patient management. A prospective observational study enrolled 55 patients with primary sporadic DF managed with AS. Clinical evolution was categorized as progression, regression, or stable disease according to RECIST 1.1. Immunomonitoring with multicolor flow cytometry identified distinct systemic T-helper polarization states stratifying clinical trajectories: regressors showed a Th2-skewed profile, while progressors displayed activated T-helper cells and Th1/Th9/Th17 subsets. Higher baseline Th2 levels associated with regression and longer progression-free survival. Plasma proteomic and whole-blood transcriptomic analyses confirmed coordinated IL-4/IL-13-linked pro-resolving programs in regressors and inflammatory, early T-cell activation signatures in progressors. Tumor transcriptomics revealed adaptive, antigen-presentation and restrained immune programs in regressing lesions versus innate inflammatory, interferon and TGF-{beta}-driven fibrotic pathways in progressing tumors. These findings identify systemic T-helper polarization as a biomarker of DF behavior and highlight coordinated systemic-tumoral immune programs underlying clinical outcomes, supporting more precise clinical management.

immunology↗

bioRxiv2025

Structural basis for synergistic antibody protection against the essential malaria invasion complex protein RIPR

Plasmodium falciparum RH5-interacting protein (RIPR) is central to the essential PTRAMP-CSS-RIPR-CyRPA-RH5 (PCRCR)-complex; a leading target of blood-stage malaria vaccines. However, mechanisms whereby anti-RIPR antibodies inhibit parasite invasion are poorly understood. Here, we characterise 83 human IgG mAbs from RIPR-vaccinated Kymouse platform mice. Single mAbs have minimal neutralising activity, however, high-level synergistic inhibition is observed with pools of mAbs targeting the RIPR-Tail region. Structural characterisation and molecular dynamics simulations of RIPR-Tail show that mAbs targeting EGF-like domains 6-8 (RIPREGF (6-8)), but not EGF-like domains 9-10 or the C-terminal domain (RIPREGF (9-10)-CTD), synergise to constrain the RIPR-Tail conformation. The same antibodies dissociate PTRAMP-CSS from RIPR, thereby enabling anti-RIPREGF (9-10)-CTD mAbs or anti-CSS sdAbs to bind and potentiate anti-RIPREGF (6-8) IgG. Addition of these mAbs to IgG from humans immunised with the R78C (RIPREGF (7-8)-CyRPA) candidate vaccine enhances malaria growth inhibition. These data provide a framework to guide next-generation blood-stage malaria vaccine design.

immunology↗

bioRxiv2025

Stochastic Emergence of Irregular Infection Fronts in Motile Bacteria-Phage Populations

Interactions between bacteriophages and motile bacteria can produce irregular spatial patterns. Here we show that these irregularities arise from stochastic infection dynamics at the single-cell level. We develop a discrete, stochastic model of phage-bacteria co-propagation, which represents bacteria and phage numbers as non-negative integers on a two-dimensional lattice, while nutrients and attractants are treated as real-valued fields. Stochastic rules govern bacterial growth, chemotactic movement, infection, and lysis, allowing spatial heterogeneity to emerge in agreement with experimentally observed asymmetric patterns. Simulations reveal that rare events, in which an infected bacterium migrates ahead of the front before lysis, locally seed new infection centers. The resulting front roughness is controlled by the product of burst size and adsorption rate, and is suppressed when the effective population size per lattice site increases or the variability of latent period decreases. These results link microscopic stochasticity to emergent spatial structure in phage-bacteria populations.

ecology↗

bioRxiv2020

A thermostable, closed, SARS-CoV-2 spike protein trimer.

The spike (S) protein of SARS-CoV-2 mediates receptor binding and cell entry and is the dominant target of the immune system. S exhibits substantial conformational flexibility. It transitions from closed to open conformations to expose its receptor binding site, and subsequently from prefusion to postfusion conformations to mediate fusion of viral and cellular membranes. S protein derivatives are components of vaccine candidates and diagnostic assays, as well as tools for research into the biology and immunology of SARS-CoV-2. Here we have designed mutations in S which allow production of thermostable, crosslinked, S protein trimers that are trapped in the closed, pre-fusion, state. We have determined the structures of crosslinked and non-crosslinked proteins, identifying two distinct closed conformations of the S trimer. We demonstrate that the designed, thermostable, closed S trimer can be used in serological assays. This protein has potential applications as a reagent for serology, virology and as an immunogen.

biochemistry↗