Biology subjects

Anselmo, A.

Publications and source records attributed to Anselmo, A..

5 recordsLinked to original sources

bioRxiv2025

Evaluation of single-cell RNA profiling technologies using FFPE, fresh, and frozen ccRCC tumor specimens

The application of single-cell transcriptomic approaches has deepened our understanding of tumor heterogeneity, immune dynamics, and molecular programs underlying therapy response. The recent development of fixation-compatible single-cell platforms, such as 10x Genomics Flex, offers the opportunity to profile archived formalin-fixed, paraffin-embedded (FFPE) specimens, expanding access to clinically valuable samples. However, most benchmarking studies of recent single-cell RNA sequencing (scRNA-seq) technologies have relied on peripheral blood mononuclear cells, limiting their relevance to human tissues. Here, we compared three 10x single-cell RNA profiling methods, fresh tumor scRNA-seq, flash-frozen single-nucleus Multiome, and FFPE single-nucleus Flex (snFlex), using clear cell renal cell carcinoma (ccRCC) biopsies. Across methods, we observed broadly consistent cell type-specific transcriptional profiles among major ccRCC cell populations. Despite lower gene and UMI counts, snFlex reliably identified fine-grained states within CD8+ T cells, tumor-associated macrophages, and tumor compartments, comparable to those detected by scRNA-seq. Together, these findings highlight the distinct advantages of each technology depending on sample preservation type and study design, providing practical guidance for single-cell RNA profiling technology selection in translational studies using human tumor biopsies.

cancer biology↗

bioRxiv2025

Fbxl10/Kdm2b is required for Kmt2b/Mll2 binding across thegenome and regulates H3K4 methylation on bivalent promoters

The presence of histone modifications associated with both transcriptional repression (H3K27me3) and activation (H3K4me3) on key developmental promoters in embryonic stem cells results from the co-localization of repressive Polycomb group (PcG) and activating Trithorax group (TrxG) protein complexes. Functional interactions between PcG and TrxG on these promoters are not fully understood. Here we focus on the relationships between Fbxl10/Kdm2b, a component of a PcG complex PRC1, and Kmt2b/Mll2, an essential component of TrxG at bivalent promoters. Computational analysis of previously published data revealed genome-wide correlation between chromatin occupancies of these two proteins, suggesting potential crosstalk between Kdm2b and Mll2 at both active and repressed promoters. We tested this hypothesis experimentally and found that loss of Kdm2b resulted in depletion of Mll2 at promoters genome-wide, suggesting that Kdm2b is required for Mll2 occupancy at both bivalent and active promoters. Loss of Kdm2b or the core PRC1 component Ring1b also resulted in the reduction of H3K4me3 specifically at bivalent promoters. These findings provide a direct pathway for cooperation between PcG and TrxG at bivalent promoters, suggesting an unexpected modification to the current model of bivalency. In addition, these findings reveal genome-wide role of Kdm2b independent of the full PRC1 complex.

molecular biology↗

bioRxiv2024

WNKs regulate mouse behavior and alter central nervous system glucose uptake and insulin signaling

Certain areas of the brain involved in episodic memory and behavior, such as the hippocampus, express high levels of insulin receptors and glucose transporter-4 (GLUT4) and are responsive to insulin. Insulin and neuronal glucose metabolism improve cognitive functions and regulate mood in humans. Insulin-dependent GLUT4 trafficking has been extensively studied in muscle and adipose tissue, but little work has demonstrated either how it is controlled in insulin-responsive brain regions or its mechanistic connection to cognitive functions. In this study, we demonstrate that inhibition of WNK (With-No-lysine (K)) kinases improves learning and memory in mice. Neuronal inhibition of WNK enhances in vivo hippocampal glucose uptake. Inhibition of WNK enhances insulin signaling output and insulin-dependent GLUT4 trafficking to the plasma membrane in mice primary cortical neurons and hippocampal slices. Therefore, we propose that the extent of neuronal WNK kinase activity has an important influence on learning, memory and anxiety-related behaviors, in part, by modulation of neuronal insulin signaling.

animal behavior and cognition↗

bioRxiv2023

Genome analysis of Legionella pneumophila ST901 an Italian endemic strain.

Legionella pneumophila typing, based on SBT analysis, has been allowing to identify sequence types (ST) responsible for many Legionnaires disease cases. ST901 has so far been identified only in a town of the northern Italy, where it caused numerous travel-associated Legionnaires disease cases over a 32-year period. In this study, ST901 were analyzed by whole genome sequencing in looking for both differences and similarities inside this ST and with other unrelated Legionella strains. To this aim core genome multi locus sequence type, single nucleotide polymorphisms and pangenome analyses were performed. ST901 resulted highly similar each other, characterized by I-C CRISPR-cas system, located on the chromosome and by a putative plasmid, highly similar to that found in Lp strain Lens, which contains I-F CRISPR-cas system. Accessory genomic islands, either already described or specifically found in ST901, were also shown. In conclusion ST901 has been quite preserved over the time. The co-occurrence of two phage resistance systems and genomic islands of virulence could have made the ST901 enough virulent to cause such a high number of cases. Summary blurbST901 appears as endemic of the Northern Italy, with virulence traits similar to those in Alcoy and Corby, and with two CRISPR-cas systems which probably preserved them in their environmental niche.

genomics↗

bioRxiv2021

tiRNA signaling via stress-regulated vesicle transfer in the hematopoietic niche

Extracellular vesicles transfer complex biologic material between cells, whose role in in-vivo organismal physiology is poorly defined. Here, we demonstrate that osteoblastic cells in the bone marrow elaborate extracellular vesicles that are taken up by hematopoietic progenitor cells in vivo. Genotoxic or infectious stress rapidly increased stromal-derived extracellular vesicle transfer to granulocyte-monocyte progenitors. Stimulating osteoblastic cells with parathyroid hormone or activating its receptor enhanced extracellular vesicle transfer, myeloid recovery post radiation and improved animal survival from Candida sepsis. The extracellular vesicles contained tiRNAs known to modulate protein translation. 5-ti-Pro-CGG-1 was preferentially abundant in osteoblast-derived extracellular vesicles and when transferred to granulocyte macrophage progenitors, increased protein translation, cell proliferation and myeloid differentiation. Therefore, EV-mediated tiRNA transfer provides a stress modulated signaling axis distinct from conventional cytokine-driven stress responses. One sentence summaryStress regulated tiRNA transfer alters hematopoiesis

cell biology↗