Biology subjects

Botos, M.

Publications and source records attributed to Botos, M..

5 recordsLinked to original sources

bioRxiv2025

Dendritic-cell diversity in equine blood revealed by single-cell transcriptomics

Unbiased classification of equine dendritic cells (DC) is necessary to address various research questions such as the role of DC subsets in immune-mediated diseases of horses. We applied single-cell RNA sequencing (scRNA-seq) on DC enriched from the blood of two horses. All main DC subsets were detected by key gene expression, including conventional DC type 1 (cDC1; XCR1) and type 2 (cDC2; FCER1A, CD1E) as well as plasmacytoid DC (pDC; TCF4). In addition, we detected a small cluster of hematopoietic progenitors, as well as transitional DC (tDC; FCER1A, TCF4) and putative DC type 3 (DC3; FLT3, CD163). Our data confirms the previously reported phenotype of equine pDC (Flt3+MHC-IIlowCADM1lowCD172aint), cDC1 (Flt3+MHC-IIhighCADM1highCD172alow-int) and cDC2 (Flt3+MHC-IIhighCADM1intCD172ahigh), while also highlighting considerable CD14 expression for cDC2. Two subclusters of equine cDC2 were found to be enriched in FCER1A or CX3CR1 transcripts (cDC2.1 and cDC2.2, respectively), with suggested enhanced extravasation and T-cell stimulatory capacities of the latter. Conservation of DC subsets across species (horse, pig, human, mouse) was illustrated by enrichment analyses with subset-specific gene signatures and by cross-species data integration with publicly available scRNA-seq datasets. Our atlas of equine blood DC is a valuable resource for comparative analyses, and it forms the foundation for understanding the involvement of distinct DC subsets in infections and immune-mediated pathologies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=93 SRC="FIGDIR/small/644174v2_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@bdce22org.highwire.dtl.DTLVardef@1285715org.highwire.dtl.DTLVardef@16d37c8org.highwire.dtl.DTLVardef@1695121_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Unraveling dendritic-cell diversity in blood of pigs: welcome tDC and DC3

Dendritic cells (DC) are professional antigen presenting cells playing a major role in orchestrating adaptative immune responses. To adapt to various immune challenges, such as different classes of pathogens, specialized subsets of DC have evolved across species. To date, DC are classified as conventional DC (cDC1, cDC2) and plasmacytoid DC (pDC), with the more recent addition of DC3 and transitional DC (tDC) that were discovered in human and mouse thanks to high-dimensional phenotyping and single-cell sequencing technologies. Here, by combining flow cytometry and RNA-seq on the bulk- and single-cell level, we identified the porcine equivalent of tDC in blood as CD14-CADM1-CD172a+CD4-cells expressing both Flt3 and CD123 (IL-3RA). This new subset forms a well-defined cluster when mapped onto scRNA-seq data of enriched DC and shares transcriptomic features and abundance with porcine blood cDC2 and pDC. Moreover, we describe putative porcine DC3 as transcriptionally overlapping cells in-between cDC2 and monocytes. With the core functions of tDC and DC3 remaining to be elucidated, our datasets provide a valuable resource for cross-species research on DC heterogeneity in various lymphoid and non-lymphoid tissues.

immunology↗

bioRxiv2025

Deep learning-based 3D spatial transcriptomics with X-Pression

Spatial transcriptomics technologies currently lack scalable and cost-effective options to profile tissues in three dimensions. Technological advances in microcomputed tomography enabled non-destructive volumetric imaging of tissue blocks with sub-micron resolution at a centimetre scale. Here, we present X-Pression, a deep convolutional neural network-based frame-work designed to reconstruct 3D expression signatures of cellular niches from volumetric microcomputed tomography data. By training on a singular 2D section of a paired spatial transcriptomics experiment, X-Pression achieves high accuracy and is capable of generalising to out-of-sample examples. We utilised X-Pression to demonstrate the benefit of 3D examination of tissues on a paired SARS-CoV-2 vaccine efficacy spatial transcriptomics and microcomputed tomography cohort of a recently developed live attenuated SARS-CoV-2 vaccine. By applying X-Pression to the entire mouse lung, we visualised the sites of viral replication at the organ level and the simultaneous collapse of small alveoli in their vicinity. In addition, we assessed the immunological response following vaccination and virus challenge infection. X-Pression offers a valuable and cost-effective addition to infer expression signatures without the need for consecutive 2D sectioning and reconstruction, providing new insights into transcriptomic profiles in three dimensions.

bioinformatics↗

bioRxiv2019

Respiratory supercomplexes provide metabolic efficiency in zebrafish

The oxidative phosphorylation (OXPHOS) system is a dynamic system in which the respiratory complexes coexist with super-assembled quaternary structures called supercomplexes (SCs). The physiological role of SCs is still disputed. Here we used zebrafish to study the relevance of respiratory SCs. We combined immunodetection analysis and deep data-independent proteomics to characterize these structures and found similar SCs to those described in mice, as well as novel SCs including III2+IV2, I+IV and I+III2+IV2. To study the physiological role of SCs, we generated two null allele zebrafish lines for supercomplex assembly factor 1 (SCAF1). SCAF1-/- fish displayed altered OXPHOS activity due to the disrupted interaction of complex III and IV. SCAF1-/- fish were smaller in size, and showed abnormal fat deposition and decreased female fertility. These physiological phenotypes were rescued by doubling the food supply, which correlated with improved bioenergetics and alterations in the metabolic gene expression program. These results reveal that SC assembly by SCAF1 modulates OXPHOS efficiency and allows for the optimization of metabolic resources.

physiology↗

bioRxiv2019

Pre-existent adult sox10+ cardiomyocytes contribute to myocardial regeneration in the zebrafish

During heart regeneration in the zebrafish, fibrotic tissue is replaced by newly formed cardiomyocytes derived from pre-existing ones. It is unclear whether the heart is comprised of several cardiomyocyte populations bearing different capacity to replace lost myocardium. Here, using sox10 genetic fate mapping, we identified a subset of pre-existent cardiomyocytes in the adult zebrafish heart with a distinct gene expression profile that expanded massively after cryoinjury. Genetic ablation of sox10+ cardiomyocytes severely impaired cardiac regeneration revealing that they play a crucial role for heart regeneration.

developmental biology↗