Biology subjects

Vandenberghe, A.

Publications and source records attributed to Vandenberghe, A..

11 recordsLinked to original sources

bioRxiv2026

Experimental and mathematical models reveal that AMPK modulates circadian clock gene expression and period through NAD+-dependent regulation of Bmal1

The circadian clock allows living systems to anticipate environmental daily variations by scheduling cellular mechanisms according to the time of the day. The reciprocal interplay between metabolism and circadian clock is essential for energy homeostasis, and the disruption of metabolic clock inputs contributes to dysfunction of clocks in peripheral tissues. However, the molecular mechanisms through which the feeding/fasting cycle entrains peripheral clocks remain incompletely understood. Here, we investigate experimentally and theoretically the role of AMP-dependent kinase (AMPK), a key fasting sensor, in metabolic regulation of the circadian clock. Using a luciferase reporter driven by the Bmal1 promoter to monitor molecular clock activity in human U2OS cells, and thanks to a signal processing method based on the Hilbert transform to retrieve the instantaneous phase and period of circadian signals, we show that pharmacological activation of AMPK by AICAR significantly elevates Bmal1 promoter activity and markedly lengthens the clock period in a dose-dependent manner. Conversely, the clock period is shortened by the pharmacological inhibition by SR18292 of Peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1-alpha). Importantly, the action of AICAR is abolished by FK866, a nicotinamide phosphoribosyltransferase (NAMPT) inhibitor, demonstrating that AMPK-dependent modulation of Bmal1 promoter activity requires NAD+ availability. These experimental results are recapitulated by numerical simulations of our previously published mathematical model, where PGC-1-alpha plays a key role in mediating AMPK activity to the clock. Moreover, the comparison of experimentally measured and theoretically predicted phase response curves, following AMPK activation at different circadian phases, provides an additional validation of the model. By integrating biological experiments with mathematical modeling, our results identify a key mechanism through which metabolic factors can entrain and regulate the circadian clock via NAD+-dependent AMPK-mediated regulation of Bmal1 promoter activity.

cell biology↗

bioRxiv2026

Variant-specific spike conformational dynamics shape memory B cell selection during recall

Immune imprinting profoundly shapes antibody responses to breakthrough infections and vaccination against evolving endemic viruses. Current vaccine design primarily focuses on antigen sequence and variant mutations but rarely consider the structural context in which these antigens are being recognized. In this study, we make use of the longitudinal analysis of memory B cell (MBC) responses in boosted individuals enrolled in the COVIBOOST clinical trial to provide a proof of principle that variant-specific conformational dynamics can impact MBC recruitment and protective antibody responses, independently of epitope conservation. Combining functional characterization of MBC-derived monoclonal antibodies, repertoire analysis, epitope mapping and in silico structural modeling of epitope accessibility, we found that the adjuvanted B.1.351 spike vaccine preferentially recalled MBCs targeting exposed receptor-binding domain neutralizing epitopes. This preferential recruitment arises from the more restricted conformational dynamics of the B.1.351 spike compared to the ancestral Hu-1 spike, leading to increased masking of class 4 and 5 cryptic RBD epitopes. These findings demonstrate that antigen conformational dynamics can be leveraged to redirect pre-existing immunity toward neutralizing epitopes upon boost immunization.

immunology↗

bioRxiv2025

L-asparaginase treatment induces a tumor metabolic plasticity and reveals a vulnerability to PARP1/2 inhibitor Olaparib, in B-cell lymphomas.

Intrinsic mechanisms driving secondary resistance to L-asparaginase (ASNase) treatment remain poorly understood. Using a preclinical model of B-cell lymphomas (BCL), sensitive to ASNase, we observed tumor relapse during ASNase treatment despite an initial antineoplastic response. Through in vivo metabolic profiling of BCL and stable isotope resolved metabolomics in vitro and in vivo, we show that ASNase induces a flexible metabolic reprogramming marked by increased de novo serine biosynthesis. This adaptive response is driven in part by phosphoglycerate dehydrogenase (PHGDH), which mitigates ASNase-induced reactive oxygen species (ROS) and ROS-mediated DNA damage, enabling tumor cell survival under therapeutic pressure. ASNase-treated malignant B cells exhibit features of replication stress, with activation of the ATR-dependent DNA damage response and increased poly(ADP-ribose) polymerase 1/2 (PARP) activity. Targeting initiation of DNA repair mechanism using the PARP inhibitor Olaparib, enhances the antineoplastic effect of each individual mono-chemotherapy, both in vitro and in vivo. Importantly, we showed that this therapeutic combination was also effective in homologous recombination (HR)-proficient colorectal cancer cells, supporting its broader therapeutic relevance beyond lymphoid malignancies. Altogether, our findings reveal redox- and DNA repair-dependent metabolic vulnerabilities in ASNase-treated B-cell lymphomas and provide proof-of-concept for a rational combination therapy using clinically approved agents, ASNase and Olaparib.

cancer biology↗

bioRxiv2025

Body movement perception is shaped by both generic and actor-specific models of human bodies

Body movement perception is shaped by knowledge of the human body biomechanics. Apparent motion elicited by rapidly alternating pictures follows the shortest path between two body postures only if it is biomechanically plausible. And although we tend to perceive the location of a moving body part as slightly shifted forward along its trajectory, this perceptual extrapolation is absent (or reduced) if the movement would have been unlikely to continue along the same trajectory because of the body biomechanical constraints. The received view is that perception is shaped by a model of the observers own body. Here, we report three lines of evidence suggesting otherwise. First, we report the typical influence of knowledge of the upper limb biomechanics on apparent movement perception and perceptual extrapolation in two individuals born completely without (upper and lower) limbs (Experiments 1 and 2). Second, we report that we failed to find evidence that observers own biomechanics influence perceptual extrapolation of body movements (Experiment 3). Third, we show that participants perception is influenced by their knowledge of actor-specific biomechanics (Experiments 4- 8). We conclude that body movement perception is shaped by visually acquired models of both generic and actor-specific body biomechanics. Public significance statementAlthough information about others body movements reaches our visual system with a considerable delay, we can interact with them in real-time. Although we often blink, we perceive uninterrupted body movements. To solve the problems posed by informational lag and intermittence, the visual system appears to rely on knowledge of the human body biomechanics to extrapolate the most likely future (or unseen) position of observed limb movements. For the last 20 years, the received view has been that perceptual "filling-in" and extrapolation of others body movements are underpinned by a model of the observers own body, acquired through motor experience and proprioceptive feedback. Here, we report three lines of evidence indicating that body movement perception is rather shaped by visually acquired models of both generic and actor-specific body biomechanics. These findings provide new insight into how the human visual system extrapolates future body positions.

neuroscience↗

bioRxiv2023

Omicron BA.1 breakthrough infection drives long-term remodeling of the memory B cell repertoire in vaccinated individuals.

How infection by a viral variant showing antigenic drift impacts a preformed mature human memory B cell (MBC) repertoire remains an open question. Here, we studied the MBC response up to 6 months after Omicron BA.1 breakthrough infection in individuals previously vaccinated with three doses of mRNA vaccine. Longitudinal analysis, using single-cell multi-omics and functional analysis of monoclonal antibodies from RBD-specific MBCs, revealed that a BA.1 breakthrough infection mostly recruited pre-existing cross-reactive MBCs with limited de novo response against BA.1-restricted epitopes. Reorganization of clonal hierarchy and new rounds of germinal center reaction, however, combined to maintain diversity and induce progressive maturation of the MBC repertoire against common Hu-1 and BA.1, but not BA.5-restricted, SARS-CoV-2 Spike RBD epitopes. Such remodeling was further associated with marked improvement in overall neutralizing breadth and potency. These findings have fundamental implications for the design of future vaccination booster strategies.

immunology↗

bioRxiv2021

Immune escape of SARS-CoV-2 Omicron variant from mRNA vaccination-elicited RBD-specific memory B cells.

Memory B cells (MBCs) represent a second layer of immune protection against SARS-CoV-2. Whether MBCs elicited by mRNA vaccines can recognize the Omicron variant is of major concern. We used bio-layer interferometry to assess the affinity against the receptor-binding-domain (RBD) of Omicron spike of 313 naturally expressed monoclonal IgG that were previously tested for affinity and neutralization against VOC prior to Omicron. We report here that Omicron evades recognition from a larger fraction of these antibodies than any of the previous VOCs. Additionally, whereas 30% of these antibodies retained high affinity against Omicron-RBD, our analysis suggest that Omicron specifically evades antibodies displaying potent neutralizing activity against the D614G and Beta variant viruses. Further studies are warranted to understand the consequences of a lower memory B cell potency on the overall protection associated with current vaccines.

immunology↗

bioRxiv2021

Single-cell analyses of immune thrombocytopenic patients reveal multiorgan dissemination of high-affinity autoreactive plasma cells

The major therapeutic goal for immune thrombocytopenia (ITP) is to restore normal platelet counts using drugs to promote platelet production or by interfering with mechanisms responsible for platelet destruction. 80% of patients possess anti-integrin IIb{beta}3 (GPIIbIIIa) IgG autoantibodies causing platelet opsonization and phagocytosis. The spleen is considered the primary site of autoantibody production by autoreactive B cells and platelet destruction. The immediate failure in ~50% of patients to recover a normal platelet count after anti-CD20 Rituximab-mediated B cell depletion and splenectomy suggest that autoreactive, rituximab-resistant, IgG-secreting B cells (IgG-SC) reside in other anatomical compartments. We analyzed >3,300 single IgG-SC from spleen, bone marrow and/or blood of 27 patients with ITP revealing high inter-individual variability in affinity for GPIIbIIIa with variations over 3 logs. IgG-SC dissemination and range of affinities were however similar per patient. Longitudinal analysis of autoreactive IgG-SC upon treatment with anti-CD38 mAb daratumumab demonstrated variable outcomes, from complete remission to failure with persistence of high-affinity anti-GPIIbIIIa IgG-SC in the bone marrow. This study demonstrates the existence and dissemination of high-affinity autoreactive plasma cells in multiple anatomical compartments of patients with ITP that may cause the failure of current therapies.

immunology↗

bioRxiv2021

Memory B cells control SARS-CoV-2 variants upon mRNA vaccination of naive and COVID-19 recovered individuals.

How a previous SARS-CoV-2 infection may amplify and model the memory B cell (MBC) response elicited by mRNA vaccines was addressed by a comparative longitudinal study of two cohorts, naive individuals and disease-recovered patients, up to 2 months after vaccination. The quality of the memory response was assessed by analysis of the VDJ repertoire, affinity and neutralization against variants of concerns (VOC), using unbiased cultures of 2452 MBCs. Upon boost, the MBC pool of recovered patients selectively expanded, further matured and harbored potent neutralizers against VOC. Maturation of the MBC response in naive individuals was much less pronounced. Nevertheless, and as opposed to their weaker neutralizing serum response, half of their RBD-specific MBCs displayed high affinity towards multiple VOC and one-third retained neutralizing potency against B.1.351. Thus, repeated vaccine challenges could reduce these differences by recall of affinity-matured MBCs and allow naive vaccinees to cope efficiently with VOC.

immunology↗

bioRxiv2020

Maturation and persistence of the anti-SARS-CoV-2 memory B cell response.

Memory B cells play a fundamental role in host defenses against viruses, but to date, their role have been relatively unsettled in the context of SARS-CoV-2. We report here a longitudinal single-cell and repertoire profiling of the B cell response up to 6 months in mild and severe COVID-19 patients. Distinct SARS-CoV-2 Spike-specific activated B cell clones fueled an early antibody-secreting cell burst as well as a durable synchronous germinal center response. While highly mutated memory B cells, including preexisting cross-reactive seasonal Betacoronavirus-specific clones, were recruited early in the response, neutralizing SARS-CoV-2 RBD-specific clones accumulated with time and largely contributed to the late remarkably stable memory B-cell pool. Highlighting germinal center maturation, these cells displayed clear accumulation of somatic mutations in their variable region genes over time. Overall, these findings demonstrate that an antigen-driven activation persisted and matured up to 6 months after SARS-CoV-2 infection and may provide long-term protection.

immunology↗

bioRxiv2020

The antiangiogenic compound axitinib demonstrates low toxicity and anti-tumoral effects against medulloblastoma

Evolution of medulloblastoma (MB) treatments has increased the 5-year overall survival of to more than 70%. However, an increasing number of survivors face severe long-term adverse effects and associated morbidity due to multimodal treatments particularly harsh for the younger patients. Chemotherapeutic compounds inducing less adverse effects are key to improving the care of MB patients. The preclinical relevance of last generation anti-angiogenic compounds deserves to be fully assessed. Among these, axitinib showed the highest selectivity index for MB cells, efficiently reduced the growth rate of experimental tumors and led to less toxicity towards normal cells than did a reference treatment. In vivo, axitinib did not lead to acute toxicity in very young rats and was able to cross the blood brain barrier. Analysis of public databases shows that high expression of axitinib targets are of poor prognosis. Altogether, our results suggest that axitinib is a compelling candidate for MB treatment.

cancer biology↗

bioRxiv2019

A reservoir of rituximab-resistant splenic memory B cells contributes to relapses after B-cell depletion therapy

Immune thrombocytopenia (ITP) is an autoimmune disease mediated by pathogenic antibodies directed against platelet antigens, including GPIIbIIIa. Taking advantage of spleen samples obtained from ITP patients, we characterized by multiples approaches the onset of disease relapses occurring after an initial complete response to rituximab. Analysis of splenic B cell immunoglobulin heavy chain gene repertoire at bulk level and from single anti-GPIIbIIIa B cells revealed that germinal centers were fueled by B cells originating from the ongoing lymphopoiesis, but also by rituximab-resistant memory B cells, both giving rise to anti-GPIIbIIIa plasma cells. We identified a population of splenic memory B cells that resisted rituximab through acquisition of a unique phenotype and contributed to relapses, providing a new target in B cell mediated autoimmune diseases.

immunology↗