Biology subjects

Nucci, A.

Publications and source records attributed to Nucci, A..

7 recordsLinked to original sources

bioRxiv2026

Nanoparticle size governs engagement with myeloid cells and hitchhiking to hematopoietic organs in myeloproliferative neoplasms

Nanoparticle design principles contribute to desirable in vivo performance, including prolonged circulation, desirable biodistribution profiles, and tuned interactions with the immune system. The importance of these variables, although well-established in solid tumors, remains elusive in the context of hematological malignancies. Here, we investigated the influence of liposome size on biodistribution and cellular uptake within hematopoietic compartments - bone marrow (BM) and spleen - in JAK2V617F myeloproliferative neoplasms (MPN). A milli-fluidic manufacturing platform combined with a Design-of-Experiments (DoE) approach was used to generate small, medium, and large liposomes. Liposome uptake was assessed ex vivo using blood samples from healthy donors and MPN patients, followed by in vivo biodistribution studies in a transgenic JAK2V617F MPN mouse model. Organ-level accumulation was quantified using hybrid fluorescence / computed tomography (FLT/CT) imaging, while cellular uptake was evaluated via flow cytometry. Whole-body imaging revealed that increasing liposome size enhanced delivery to both the spleen and BM, with larger liposomes exhibiting the highest accumulation in both organs. Cellular analysis corroborated the in vivo observations, demonstrating that large liposomes are taken up to a greater extent by monocytes and granulocytes, in both spleen and BM. At late time-points post-injection, the liposomal accumulation was twice as high in the BM in comparison to the spleen and peripheral blood, highlighting the progressively elevated accumulation and retention in the BM, as opposed to the elimination phase nanoparticles undergo in clearance organs and circulation at these time-points. Of note, among BM mature myeloid cells, neutrophils were associated with a higher nanoparticle uptake than monocytes, highlighting their capability to phagocytose material in circulation and hitchhike it to malignant or inflamed regions. These findings demonstrate that continuous flow manufacturing procedures can swiftly produce nanoparticles with desirable characteristics that are essential for tuning the biodistribution towards hematopoietic organs and myeloid immune cells. By providing mechanistic insights into nanoparticle behavior within hematopoietic compartments, this work advances our understanding of nanomedicine in vivo performance and highlights particle size as a critical quality attribute that can be optimized and controlled to improve targeted delivery to myeloid cells in the treatment of hematological malignancies.

cancer biology↗

bioRxiv2026

Genomic Islands as minimal hitchers of conjugative elements

Bacterial chromosomes contain Genomic Islands carrying genes involved in virulence, mutualism, and resistance to antibiotics that are transferred horizontally. Some of them conjugate autonomously (Integrative Conjugative Elements, ICEs), while others use relaxases to hitch on the formers conjugation machinery (Integrative Mobilizable Elements, IMEs). Yet, the mobility mechanism of most Genomic Islands remains elusive. Here, we explore the hypothesis that many carry origins of transfer (oriTs) by conjugation. Since very few known oriTs were found in ICEs and IMEs, we identified 52 novel families of oriTs that cover most integrative elements in 6 major nosocomial species. Most of these oriTs are specific to integrative elements, suggesting a clear split in the targets of hitchers of conjugative elements between plasmids and integrative elements. Among 7,363 Genomic Islands, we discovered more than 1,500 IMEs carrying an oriT and lacking relaxases and MPF systems. These elements, coined iOriTs, form diverse large ancient families that can be found in different species. These hitchers are genetically unrelated to the putative helpers, beyond the similarity at the oriT sequence, and often outnumber them. They include well-known pathogenicity islands, for which the mechanisms of mobility remained unknown. Unlike plasmids, iOriTs have few antibiotic resistance genes, but high density of virulence factors. Like plasmids, the vicinity of oriTs concentrates defense and counter-defense systems potentially favoring Genomic Islands dissemination. Hence, iOriTs are frequent integrative mobile genetic elements that evolved to transfer horizontally by hitching on other elements while contributing to bacterial genetic adaptation.

microbiology↗

bioRxiv2024

From North to South: Transmission Dynamics of H1N1pdm09 Swine Influenza A Viruses in Italy

The influenza A H1N1pdm09 virus continues to be a significant pathogen, posing potential risks to both animal and human health due to its zoonotic potential. Italy, which has one of the largest swine populations in Europe, plays a crucial role in monitoring the evolution of influenza viruses in livestock. This study aims to address the existing knowledge gaps regarding the genetic diversity and transmission dynamics of H1N1pdm09 circulating in Italian swine populations. Utilizing whole genome sequencing and dynamic modeling, we conducted a comprehensive analysis of virus samples collected from swine farms across Italy. Our results reveal that multiple independent viral introductions have occurred into the country, with most cases resulting in self-limited infections and limited onward transmission. However, six distinct transmission clusters were identified, suggesting instances of sustained viral spread. These clusters were found across multiple regions of Italy, highlighting the broad geographic distribution of virus lineages. Our findings indicate that while many introductions led to localized containment, certain virus lineages were able to spread within specific regions of Italy. Through a detailed examination of selective pressures, we observed that most viral genes are under strong purifying selection in both swine and human hosts, as reflected by dN/dS ratios well below 1. The hemagglutinin (HA) gene exhibited a notably higher dN/dS ratio in swine ([~]0.28) compared to humans ([~]0.22), indicating slightly relaxed selection in swine. In contrast, other genes, such as neuraminidase (NA) and non-structural protein (NS), showed similarly strong purifying selection across both hosts. These results reflect a general trend of selective pressures affecting multiple viral components, rather than emphasizing specific genes. Our study emphasizes the importance of ongoing genomic surveillance in detecting viral circulation and mitigating risks to both animal and public health. Italys efforts contribute significantly to global influenza monitoring and highlight the importance of a One Health approach that integrates human, animal, and environmental health. These findings provide essential data to inform public health policies and enhance preparedness against future zoonotic influenza outbreaks.

microbiology↗

bioRxiv2024

Identification of novel origins of transfer across bacterial plasmids

Conjugative plasmids are important drivers of bacterial evolution, but most plasmids lack genes for conjugation. It is currently not known if the latter can transfer because origins of transfer by conjugation (oriT), which would allow their mobilization by conjugative plasmids, are poorly known. Here, we identify and characterize occurrences of known oriT families across thousands of plasmids confirming that most conjugative and mobilizable plasmids still lack identifiable families of oriTs. They reveal clear patterns in terms of intergenic position, distance to the relaxases, and MOB-type association. This allowed to develop a computational method to discover novel oriTs. As a proof of concept, we identify 21 novel oriTs from the nosocomial pathogens Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii, some of them responsible for the mobility of critical antimicrobial resistance genes. These 21 oriT families share key characteristics of the others and fill most of the missing diversity of oriTs in relaxase-encoding plasmids both in terms of frequency and phylogeny. We confirmed experimentally the function of six of them. The ability to identify novel oriTs paves the way to explore conjugation across bacterial plasmids, notably among the majority lacking conjugation-related genes.

microbiology↗

bioRxiv2023

Emergence of novel non-aggregative variants under negative frequency-dependent selection in Klebsiella variicola

Klebsiella variicola is an emergent human pathogen causing diverse infections, including in the urinary tract. However, little is known about the evolution and maintenance of genetic diversity in this species, the molecular mechanisms and their population dynamics. Here, we characterized the emergence of a novel rdar-like morphotype which is contingent both on the genetic background and the environment. We show that mutations in either the nitrogen assimilation control gene (nac) or the type III fimbriae regulator, mrkH, suffice to generate rdar-like colonies. These morphotypes are primarily selected for the reduced inter-cellular aggregation as a result of loss-of-function yielding reduced fimbriae expression. Additionally, these clones also display increased growth rate and reduced biofilm formation. Direct competitions between rdar and wild type clone show that mutations in mrkH provide large fitness advantages. In artificial urine, the morphotype is under strong negative frequency-dependent selection and is able to socially exploit wild type strains. An exhaustive search for mrkH mutants in public databases revealed that ca 8% of natural isolates analysed had truncated MrkH proteins many of which were due to insertions of IS elements, including a reported clinical isolate with rdar morphology. These strains were all isolated from human, mostly from urine. The decreased aggregation of these mutants could have important clinical implications as such clones could better disperse within the host allowing colonisation of other body sites and leading to systemic infections. One-sentence SummaryReport of the emergence of a novel non-aggregative colony morphology in K. variicola and the first example of social exploitation in the Klebsiella genus.

microbiology↗

bioRxiv2023

Capsules and their traits shape phage susceptibility and plasmid conjugation efficiency

Bacterial evolution is affected by mobile genetic elements such as phages and conjugative plasmids, which may provide novel adaptive traits but also incur in fitness costs. Infection by these elements is affected by the bacterial capsule. Yet, its importance has been difficult to quantify and characterise because of the high diversity of bacterial genomes regarding confounding mechanisms such as anti-viral systems. We swapped capsule loci between Klebsiella pneumoniae strains to quantify their effect on transfer of conjugative plasmids and phages independently of the genetic background. Capsule swaps systematically invert phage susceptibility, demonstrating that serotypes are key determinants of phage infection. Capsule types also affect conjugation efficiency in both donor and recipient cells depending on the serotype, a mechanism shaped by the capsule volume and depending on the structure of the conjugative pilus. Comparative genomics confirmed that more permissive serotypes in the lab correspond to the strains acquiring more conjugative plasmids in nature. The pili least sensitive to capsules (F-like) are also the most frequent in the species plasmids, and are the only ones associated with both antibiotic resistance and virulence factors, driving the convergence between virulence and antibiotics resistance in the population. These results show how the traits of cellular envelopes define slow and fast lanes of infection by mobile genetic elements, with implications for population dynamics and horizontal gene transfer. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/536574v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@157bc4eorg.highwire.dtl.DTLVardef@10bc979org.highwire.dtl.DTLVardef@d85080org.highwire.dtl.DTLVardef@18d331e_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2023

Latent evolution of biofilm formation depends on life-history and genetic background

Adaptation to one environment can often generate phenotypic and genotypic changes which impact the future ability of an organism to thrive in other environmental conditions. In the context of host-microbe interactions, biofilm formation can increase survival rates in vivo upon exposure to stresses, like the hosts immune system or antibiotic therapy. However, how the generic process of adaptation impacts the ability to form biofilm and how it may change through time has seldomly been studied. To do so, we used a previous evolution experiment with three strains of the Klebsiella pneumoniae species complex, in which we did not specifically select for biofilm formation. We observed that changes in the ability to form biofilm happened very fast at first and afterwards reverted to ancestral levels in many populations. Biofilm changes were associated to phenotypic changes in population yield and surface polysaccharide production. Genotypically, mutational targets in the tip adhesin of type III fimbriae (mrkD) or the fim switch of type I fimbriae were driven by nutrient availability during evolution, and their impact on biofilm formation was dependent on capsule production. Analyses of natural isolates revealed similar mutations in mrkD, suggesting that they also play an important role in adaptation outside the laboratory. Our work reveals that the latent evolution of biofilm formation, and its evolutionary dynamics, depend on nutrient availability, the genetic background and other intertwined phenotypic and genotypic changes. Ultimately, it suggests that small differences in the environment can alter an organisms fate in more complex niches like the host.

microbiology↗