Biology subjects

Sobral, D.

Publications and source records attributed to Sobral, D..

6 recordsLinked to original sources

bioRxiv2026

Widespread cryptic RAG-mediated recombination in developing T lymphocytes

V(D)J recombination generates antigen receptor diversity through the targeted activity of the RAG1/2 recombinase, but the extent to which RAG also engages cryptic genomic targets during normal lymphocyte development remains poorly defined. Here, we developed a targeted PCR-sequencing approach to detect and quantify rare RAG-mediated rearrangements in mouse thymocytes. We first examined the TCRb locus and found that four of its twelve pseudogenes undergo detectable rearrangement in vivo, despite being considered non-functional components of the repertoire. Extending this analysis across the locus revealed 33 previously uncharacterized cryptic recombination sites involved in non-functional rearrangements with DJb segments. These events occurred across both the Vb region and the largely inaccessible Vb30-Db1 intergenic region, with individual cryptic sites spanning a broad range of recombination frequencies. Cryptic sites were highly heterogeneous in sequence and chromatin context: neither RSS resemblance, predicted Z-DNA formation, local epigenetic features, nor chromosomal interactions reliably distinguished sites with detectable recombination from those at which recombination was not detected. We further identified additional cryptic RAG-mediated rearrangements at the Bcl11b locus, demonstrating that such events are not restricted to antigen receptor loci. Together, these findings reveal an unexpectedly broad landscape of low-frequency RAG-mediated DNA rearrangement in developing T lymphocytes and suggest that cryptic target selection cannot be explained solely by the local genetic and epigenetic features examined here.

immunology↗

bioRxiv2025

Dissection of the microRNA transcriptomes of CD4+ T cell subsets in autoimmune inflammation identifies novel regulators of disease pathogenesis

MicroRNAs (miRNAs) are key regulators of CD4+ T cell differentiation, but how they contribute to the course of an autoimmune disease in vivo remains poorly studied. Given the known roles in autoimmunity of pro-inflammatory T helper 1 (Th)1 and Th17 cells, and anti-inflammatory Foxp3+ regulatory cells, we established a triple reporter mouse for Ifng, Il17 and Foxp3, and subjected it to experimental autoimmune encephalomyelitis (EAE) to characterize the miRNomes of the corresponding CD4+ T cell subsets. We identified 110 miRNAs differentially expressed between the pro-inflammatory (Th1 and Th17 cells) and the Treg cell subsets. Among these, we found novel functions for miR-122-5p and miR-1247 as regulators of Th17 cell proliferation and Th1 cell differentiation, thus impacting the course or severity of EAE, respectively. Importantly, their expression patterns suggest miR-122-5p and miR-1247 act as peripheral brakes to CD4+ T cell pathogenicity that are subverted in the inflamed central nervous system.

immunology↗

bioRxiv2024

Optimistic and pessimistic cognitive judgement bias modulates the stress response and cancer progression in zebrafish

Cognitive judgement bias in decision-making under ambiguity occurs both in animals and humans, with some individuals interpreting ambiguous stimulus as positive (optimism) and others as negative (pessimism). We hypothesize that judgement bias is a personality trait and that individuals with a pessimistic bias would be more reactive to stressors and therefore more susceptible to stress-related diseases than optimistic ones. Here, we show that zebrafish judgment bias is a consistent behavioral trait over time, and that pessimistic and optimistic fish express phenotype-specific neurogenomic responses to stress. Furthermore, both phenotypes show differential activation of the hypothalamic-pituitary-interrenal axis in response to chronic stress, suggesting that optimists have a lower stress reactivity. Accordingly, optimists seem to be more resilient to disease than pessimists, as shown by a lower tumorigenesis in a zebrafish melanoma line [Tg(mtifa:HRAS-GFP)]. Together these results indicate that judgement bias is paralleled by differences in the stress response with implications for disease resilience.

animal behavior and cognition↗

bioRxiv2022

The conserved transcriptional program of metazoan male germ cells uncovers ancient origins of human infertility

Male germ cells share a common origin across animal species, therefore they likely retain a conserved genetic program that defines their cellular identity. However, the unique evolutionary dynamics of male germ cells coupled with their widespread leaky transcription pose significant obstacles to the identification of the core spermatogenic program. Through network analysis of the spermatocyte transcriptome of vertebrate and invertebrate species, we describe the conserved evolutionary origin of metazoan male germ cells at the molecular level. We estimate the average functional requirement of a metazoan male germ cell to correspond to the expression of approximately 10,000 protein-coding genes, a third of which defines a genetic scaffold of deeply conserved genes that has been retained throughout evolution. Such scaffold contains a set of 79 functional associations between 104 gene expression regulators that represent a core component of the conserved genetic program of metazoan spermatogenesis. By genetically interfering with the acquisition and maintenance of male germ cell identity, we uncover 161 previously unknown spermatogenesis genes and three new potential genetic causes of human infertility. These findings emphasize the importance of evolutionary history on human reproductive disease and establish a cross-species analytical pipeline that can be repurposed to other cell types and pathologies.

systems biology↗

bioRxiv2021

Glycan-Based Shaping Of The Microbiota During Primate Evolution

Genes encoding certain glycosyltransferases are thought to be under relatively high selection pressure, due to the involvement of the glycans that they synthesize in host-microbe interactions. Here we used a mouse model to investigate whether the loss of -1,3-galactosyltransferase (GGTA1) function and Gal1-3Gal{beta}1-4GlcNAc{beta}1-R (Gal) expression during primate evolution might have affected host-microbiota interactions. We found that Ggta1 deletion in mice shaped the composition of the gut microbiota in relation to the bacterial species present. This occurred via an immunoglobulin (Ig)-dependent mechanism, associated with IgA targeting of Gal-expressing bacteria. Systemic infection by the Ig-shaped microbiota elicited a less severe form of sepsis than infection with the non-Ig-shaped microbiota. This suggests that in the absence of host Gal, the microbiota is shaped towards lower pathogenicity, likely providing a fitness gain to the host. We infer that high selection pressure exerted by bacterial sepsis may have contributed to increase frequency of GGTA1 loss-of-function mutations in ancestral primates that gave rise to humans.

evolutionary biology↗

bioRxiv2020

A TgfβRI/Snai1-dependent developmental module at the core of vertebrate axial elongation

Formation of the vertebrate postcranial body axis follows two sequential but distinct phases. The first phase generates pre-sacral structures (the so-called primary body) through the activity of the primitive streak (PS) on axial progenitors within the epiblast. The embryo then switches to generate the secondary body (post-sacral structures), which depends on axial progenitors in the tail bud. Here we show that the mammalian tail bud is generated through an independent developmental module, concurrent but functionally different to that generating the primary body. This module is triggered by convergent Tgf{beta}RI and Snai1 activities that promote an incomplete epithelial to mesenchymal transition (EMT) on a subset of epiblast axial progenitors. This EMT is functionally different to that coordinated by the PS, as it does not lead to mesodermal differentiation but brings axial progenitors into a transitory state, keeping their progenitor activity to drive further axial body extension.

developmental biology↗