Biology subjects

Botto, M.

Publications and source records attributed to Botto, M..

6 recordsLinked to original sources

bioRxiv2026

Single-cell multi-ancestry regulatory map of systemic lupus erythematosus

Integrating genomic and single-cell transcriptomic profiles from patient cohorts can uncover regulatory effects underlying genetic associations with disease. Here we present SLEmap, a multi-ancestry single-cell expression quantitative trait locus (sc-eQTL) map generated from peripheral blood mononuclear cells from 281 patients with systemic lupus erythematosus (SLE). We identified 18,608 independent eQTLs in 5,656 genes, of which 149 signals in 66 genes colocalized with SLE GWAS loci. Nearly half of these colocalizations were detected exclusively through cell type-level analyses, highlighting the importance of cellular context for interpreting disease-associated genetic variation. Multi-ancestry data identified regulatory signals robust across diverse ancestral backgrounds and improved signal resolution. Most colocalizations were undetectable in sc-eQTLs from a healthy cohort (OneK1K), with novel SLE colocalizations highlighting disease-relevant regulatory mechanisms across distinct cell types, including the NF-{kappa}B pathway. These findings demonstrate the value of disease-specific, multi-ancestry single-cell regulatory maps for resolving the genes and cellular mechanisms underlying disease-associated genetic variation.

genetics↗

bioRxiv2025

Vaccine-induced antibodies are sufficient to limit Salmonella infection in the absence of complement or macrophages.

Antibodies to Salmonella Typhimurium (STm) can protect against infection. Understanding better how antibodies, complement, and leukocytes interplay can support vaccine development. We used an Outer Membrane Vesicle (OMV) vaccine against STm to study the in vivo function of anti-STm antibodies. Using intravital microscopy, we found that upon challenge, OMV-specific antibodies promote STm uptake by spleen and liver macrophages, with neutrophils rarely capturing the bacteria. Clodronate-liposome depletion of monocytic cells reveals that these cells help prevent antigen dissemination. After vaccination and challenge of C1q, C3, C4, and C5-deficient mice, all mice except C3-deficient were protected by OMV immunization. C3-deficient mice failed to mount significant germinal center and plasma cell responses; however, after the adoptive transfer of immune sera, they had lower bacterial burdens than controls. In vitro, we showed that antibodies enhance bacterial capture in macrophages. Thus, antibodies alone are sufficient to reduce bacterial burdens, but they cooperate with complement and macrophages to maximize their functions in vivo.

immunology↗

bioRxiv2025

Substrate recognition by human separase

The protein complex cohesin encircles the sister chromatids in early mitosis1. At anaphase onset, sister separation is triggered by cleavage of the cohesin subunit SCC1/RAD21 by the cysteine protease separase2-5. SCC1 contains two cleavage sites, where cleavage is stimulated by SCC1 phosphorylation5,6. The molecular mechanisms of substrate recognition and cleavage are only partly understood7. Here, we determined a series of cryoEM structures of human separase in apo-or substrate-bound forms that, together with biochemical analysis, provide novel insights into the regulation of separase cleavage activity. We verify the first SCC1 cleavage site and reassign the second site. We show that multiple substrates, including separase autocleavage sites8,9 and the two SCC1 cleavage sites, interact with several docking sites in separase, including four phosphate-binding sites. We also describe the structural basis of the interaction between the cohesin subunit SA1/A2 and separase, which promotes cleavage at the second site in SCC1. Finally, using cross-linking mass spectrometry and cryoEM, we propose a model of how cohesin is targeted by human separase. Our work provides an extensive functional and structural framework that explains one of the most fundamental events in cell division.

biochemistry↗

bioRxiv2023

TLR7 activation at epithelial barriers promotes emergency myelopoiesis and lung anti-viral immunity

Monocytes are heterogeneous innate effector leukocytes generated in the bone marrow and released into circulation in a CCR2-dependent manner. During infection or inflammation myelopoiesis is modulated to rapidly meet demand for more effector cells. Danger signals from peripheral tissues can influence this process. Herein we demonstrate that repetitive TLR7 stimulation via the epithelial barriers drove a potent emergency bone marrow monocyte response. This process was unique to TLR7 activation and occurred independently of the canonical CCR2 and CX3CR1 axes or prototypical cytokines. The monocytes egressing the bone marrow had an immature Ly6C-high profile and differentiated into vascular Ly6C-low monocytes and tissue macrophages in multiple organs. They displayed a blunted cytokine response to further TLR7 stimulation and reduced lung viral load after RSV and influenza virus infection. These data provide insights into the emergency myelopoiesis likely to occur in response to the encounter of single-stranded RNA viruses at barrier sites.

immunology↗

bioRxiv2022

A high-throughput exonuclease assay based on the fluorescent base analog 2-aminopurine

Exonucleases are essential enzymes that remove nucleotides from free DNA ends during DNA replication, DNA repair and telomere maintenance. Due to their essential role, they are potential targets for novel anticancer and antimicrobial drugs but have so far have been little exploited. Here we present a simple and versatile real-time exonuclease assay based on 2-aminopurine, an intrinsically fluorescent nucleotide that is quenched by neighboring bases when embedded in DNA. We show that our assay is applicable to different eukaryotic and bacterial exonucleases acting on both 3 and 5 DNA ends, over a wide range of protein activities and suitable for a high throughput inhibitor screening campaign. Using our assay, we discover a novel inhibitor of the Mycobacterium tuberculosis PHP-exonuclease that is part of the replicative DNA polymerase DnaE1. Hence, our novel assay will be a useful tool for high throughput screening for novel exonuclease inhibitors that may interfere with DNA replication or DNA maintenance.

biochemistry↗

bioRxiv2022

A four-point molecular handover during Okazaki maturation

DNA replication introduces thousands of RNA primers into the lagging strand that need to be removed for replication to be completed. In Escherichia coli when the replicative DNA polymerase Pol III terminates at a previously synthesized RNA primer, DNA Pol I takes over and continues DNA synthesis while displacing the downstream RNA primer. The displaced primer is subsequently excised by an endonuclease, followed by the sealing of the nick by a DNA ligase. Yet how the sequential actions of Pol III, Pol I, endonuclease and ligase are coordinated is poorly defined. Here we show that each enzymatic activity prepares the DNA substrate for the next activity, creating an efficient four-point molecular handover. The cryo-EM structure of Pol I bound to a DNA substrate with both an upstream and downstream primer reveals how it displaces the primer in a manner analogous to the monomeric helicases. Moreover, we find that in addition to its flap-directed nuclease activity, the endonuclease domain of Pol I also specifically cuts at the RNA/DNA junction, thus marking the end of the RNA primer and creating an 5 end that is a suitable substrate for the ligase activity of LigA once all RNA has been removed.

biochemistry↗