Biology subjects

Cecconi, F.

Publications and source records attributed to Cecconi, F..

5 recordsLinked to original sources

bioRxiv2026

Selective autophagy of whole micronuclei suppresses chromosomal instability

Chromosomal instability (CIN) arising from mitotic errors generates pervasive structural and numerical chromosome alterations fueling cancer evolution1-3. Entrapment of missegregated chromosomes within micronuclei exacerbates CIN by fostering repeated rounds of aberrant mitotic segregation4-6 and, following micronucleus rupture, promoting catastrophic chromosomal rearrangement processes such as chromothripsis5-9. Whether cellular mechanisms exist to restrain micronucleus-driven CIN has remained unclear. Developing a live-cell chromatin acidification sensor, we tracked micronuclei from genesis through subsequent cell cycles and observed frequent whole-micronucleus capture and acidification via the autophagy pathway. Autophagic targeting is selective for micronuclei with nuclear envelope defects seeded at mitotic exit. Our data indicate that these defects drive progressive loss of chromatin-nuclear envelope tethering, producing a mechanically altered state that is recognised by the autophagic machinery. Autophagy and rupture represent distinct micronuclear fates with opposing genomic consequences. Single-cell sequencing of fate-matched cells demonstrates complete digestion of the chromosomal contents of autophagy-targeted micronuclei, a process we term chromophagy (chromosome-autophagy). By eliminating micronuclei, chromophagy promotes chromosomal loss and arrests the intergenerational transmission of missegregated chromosomal material. This constrains the mutational consequences of micronucleation and suppresses micronucleus-mediated CIN.

cell biology↗

bioRxiv2025

Ubiquitin-dependent degradation of p21Waf1/Cip1 is mediated by AMBRA1 to limit DNA replication stress

The cell cycle is a fundamental process that orchestrates the events that lead to cell replication and division. AMBRA1 is a scaffold factor that interacts with the E3 ubiquitin ligase CRL4-DDB1 complex to regulate the stability of cyclin D-type proteins, key regulators of the G1/S phase transition. However, how cells complete S-phase and coordinate the speed of DNA synthesis is still to be fully elucidated. Here we demonstrate that AMBRA1 affects the turnover of p21Waf1/Cip1 and p27Kip1, by coupling the CRL4-DDB1 complex directly to these proteins. In the absence of AMBRA1, the increased stability of p21Waf1/Cip1, rather than p27Kip1, resulted in the accumulation of replication stress by leaving under-replicated DNA during the S phase. We also found that AMBRA1-depleted cells with consequent high p21Waf1/Cip1 are sensitive to the inhibition of lagging-strand DNA synthesis. Of clinical relevance, low levels of AMBRA1 in Sonic-Hedgehog medulloblastoma correlate with a worse prognosis, suggesting that AMBRA1 expression levels could be an informative criterion for patient stratification and treatment.

molecular biology↗

bioRxiv2025

Active Gaussian Network Model: a non-equilibrium description of protein fluctuations and allosteric behavior

Understanding the link between structure and function in proteins is fundamental in molecular biology and proteomics. A central question in this context is whether allostery -- where the binding of a molecule at one site affects the activity of a distant site -- emerges as a further manifestation of the intricate interplay between structure, function, and intrinsic dynamics. This study explores how allosteric regulation is modified when intrinsic protein dynamics operate under out-of-equilibrium conditions. To this purpose, we introduce a simple nonequilibrium model of protein dynamics, inspired by active matter systems, by generalizing the widely employed Gaussian Network Model (GNM) to incorporate non-thermal effects. Our approach underscores the advantage of framing allostery as a causal process by using, as a benchmark system, the second PDZ domain of the human phosphatase hPTP1E that mediates protein-protein interactions. We employ causal indicators, such as response functions and transfer entropy, to identify the network of PDZ2 residues through which the allosteric signal propagates across the protein structure. These indicators reveal specific regions that align well with experimental observations. Furthermore, our results suggest that deviations from purely thermal fluctuations can significantly influence allosteric communication by introducing distinct timescales and memory effects. This influence is particularly relevant when the allosteric response unfolds on timescales incompatible with relaxation to equilibrium. Accordingly, non-thermal fluctuations may become essential for accurately describing protein responses to ligand binding and developing a comprehensive understanding of allosteric regulation.

biophysics↗

bioRxiv2022

The Cancermuts software package for the prioritization of missense cancer variants: a case study of AMBRA1 in melanoma

Cancer genomics and cancer mutation databases have made a wealth of information about missense mutations found in cancer patient samples. Contextualizing by means of annotation and predicting the effect of amino acid change help identify which ones are more likely to have a pathogenic impact. Those can be validated by means of experimental approaches that assess the impact of protein mutations on the cellular functions or their tumorigenic potential. Here, we propose the integrative bioinformatic approach Cancermuts, implemented as a Python package. Cancermuts is able to gather known missense cancer mutations from databases such as cBioPortal and COSMIC, and annotate them with the pathogenicity score REVEL as well as information on their source. It is also able to add annotations about the protein context these mutations are found in, such as post-translational modification sites, structured/ustructured regions, presence of short linear motifs and more. We applied Cancermuts to the intrinsically disordered protein AMBRA1, a key regulator of many cellular processes tightly (de)regulated in cancer. By these means, we classified mutations of AMBRA1 in melanoma, where AMBRA1 is highly mutated and displays a tumor-suppressive role. Next, based on REVEL score, position along the sequence and their local context, we applied cellular and molecular approaches to validate the predicted pathogenicity of a subset of mutations in an in vitro melanoma model. By doing so, we have identified two AMBRA1 mutations which show enhanced tumorigenic potential and are worth further investigation, highlighting the usefulness of the tool. Cancermuts can be used on any protein targets starting from minimal information, and it is available at https://www.github.com/ELELAB/cancermuts as free software.

bioinformatics↗

bioRxiv2020

The intraflagellar transport protein IFT20 recruits ATG16L1 to early endosomes to promote autophagosome formation in T cells

Lymphocyte homeostasis, activation and differentiation crucially rely on basal autophagy. The fine-tuning of this process depends on autophagy-related (ATG) proteins and their interaction with the trafficking machinery that orchestrates the membrane rearrangements leading to autophagosome biogenesis. The underlying mechanisms are as yet not fully understood. The intraflagellar transport (IFT) system, known for its role in cargo transport along the axonemal microtubules of the primary cilium, has emerged as a regulator of autophagy in ciliated cells. Growing evidence indicates that ciliogenesis proteins participate in cilia-independent processes, including autophagy, in the non-ciliated T cell. Here we investigate the mechanism by which IFT20, an integral component of the IFT system, regulates basal T cell autophagy. We show that IFT20 interacts with the core autophagy protein ATG16L1 through its CC domain, which is also essential for its pro-autophagic activity. We demonstrate that IFT20 is required for the association of ATG16L1 with the Golgi complex and early endosomes, both of which have been identified as membrane sources for phagophore elongation. This involves the ability of IFT20 to interact with proteins that are resident at these subcellular localizations, namely the golgin GMAP210 at the Golgi apparatus and Rab5 at early endosomes. GMAP210 depletion, while leading to a dispersion of ATG16L1 from the Golgi, did not affect basal autophagy. Conversely, IFT20 was found to recruit ATG16L1 to early endosomes tagged for autophagosome formation by the BECLIN 1/VPS34/Rab5 complex, which resulted in the local accumulation of LC3. Hence IFT20 participates in autophagosome biogenesis under basal conditions by regulating the localization of ATG16L1 at early endosomes to promote autophagosome biogenesis. These data identify IFT20 as a new regulator of an early step of basal autophagy in T cells.

immunology↗