Biology subjects

Rubio, M.

Publications and source records attributed to Rubio, M..

9 recordsLinked to original sources

bioRxiv2026

Sex influences gliovascular unit assembly and function in the developing mouse brain

The gliovascular unit (GVU), a specialized interface between the brain and the vascular system, assembles and matures after birth and establishes essential homeostatic functions, including blood-brain barrier integrity, metabolic exchanges, fluid drainage, neurovascular coupling, and immune surveillance. Here, we systematically compared the postnatal maturation of the cortical GVU in male vs. female mice. On P15, males exhibited a transiently greater vessel density and a higher level of aquaporin 4 expression in perivascular astrocyte processes. Females exhibited a higher density of perivascular macrophages expressing the lymphatic vessel endothelial hyaluronan receptor 1 (Lyve-1), along with earlier development of arterial vascular smooth muscle cells and greater cerebral blood flow. Transcriptomic profiling during the P5-P120 period revealed sex-specific developmental trajectories within the GVU, with the most prominent differences on P5. Taken as a whole, our results highlight pronounced sex-dependent differences in GVU assembly, GVU maturation, and the development of molecular programs that might influence brain physiology and vulnerability to neurodevelopmental disorders.

neuroscience↗

bioRxiv2026

A dual role for CTCF in development

CTCF is an essential DNA binding protein whose absence leads to embryonic lethality. CTCF is primarily known for its role in 3D genome organization where its N-terminal domain interacts with cohesin to anchor chromatin loops. How CTCF facilitates proper embryonic development remains unclear, necessitating temporal control to resolve its stage-specific functions. By combining gastruloids, an in vitro model of embryonic development, with a degron system to rapidly deplete CTCF at defined timepoints, we show that early CTCF depletion impairs early gastruloid morphogenesis. Surprisingly, ATAC-seq and time-resolved RNA-seq revealed that differentiation was unaffected. CTCF binding is strongly enriched at promoters of downregulated genes. Re-expression of a CTCF variant with an N-terminal truncation, incapable of looping, was sufficient to rescue the expression of CTCF-promoter bound genes and the defects in morphogenesis. However, extended culture (up to 168 hours) of gastruloids reconstituted with N-terminal truncated CTCF led to their collapse. Our work shows that CTCF has a dual function in early mammalian development: at early stages CTCF regulates developmentally important genes through promoter binding, while at later stages its looping function is required for correct development. HighlightsO_LICTCF is essential for gastruloid morphogenesis but dispensable for cell differentiation C_LIO_LICTCF activates genes through promoter binding C_LIO_LICTCF promoter target regulation drives in vitro gastrulation C_LIO_LIPost-gastrulation development in vitro is driven by CTCFs looping function C_LI

genomics↗

bioRxiv2025

PTEN-loss confers dependence on the guanylate synthesis enzyme IMPDH in T-cell acute lymphoblastic leukemia

Loss of the tumor suppressor PTEN is common in T-cell acute lymphoblastic leukemia (T-ALL), and is associated with poor prognosis. PTEN-loss drives robust activation of AKT/mTORC1 signaling to promote leukemic cell growth. We find that PTEN-loss in T-ALL confers dependence on the guanylate nucleotide synthesis enzyme inosine 5-monophosphate dehydrogenase (IMPDH) for cell growth and viability. This metabolic vulnerability is dependent on sustained mTORC1 signaling and can be exploited using clinically approved IMPDH inhibitors to selectively kill PTEN-deficient T-ALL cells, and extend survival in genetic and xenograft T-ALL models in mice. Mechanistically, IMPDH inhibitors cause early DNA replication stress, followed by DNA damage. In contrast to treatment with mTORC1 inhibitors, these events culminate in robust and selective cell death in PTEN-deficient T-ALL cells. These findings reveal a targetable metabolic vulnerability in T-ALL, which could provide rationale for repurposing clinically approved IMPDH inhibitors. Statement of SignificanceWe find that the IMPDH inhibitors mycophenolic acid and mizoribine, which are currently used as well-tolerated immunosuppressants, exert anti-leukemic activity in an aggressive molecular subset of T-ALL cells that are associated with poor prognosis. The use of clinically approved compounds to exploit this vulnerability could lead to rapid drug repurposing.

cancer biology↗

bioRxiv2025

Open RGB Imaging Workflow for Morphological and Morphometric Analysis of Fruits using AI: A Case Study on Almonds.

High-throughput phenotyping is addressing the current bottleneck in phenotyping within breeding programs. Imaging tools are becoming the primary resource for improving the efficiency of phenotyping processes and providing large datasets for genomic selection approaches. The advent of AI brings new advantages by enhancing phenotyping methods using imaging, making them more accessible to breeding programs. In this context, we have developed an open Python workflow for analyzing morphology and heritable morphometric traits using AI, which can be applied to fruits and other plant organs. This workflow has been implemented in almond (Prunus dulcis), a species where efficiency is critical due to its long breeding cycle. Over 25,000 kernels, more than 20,000 nuts, and over 600 individuals have been phenotyped, making this the largest morphological study conducted in almond. As result, new heritable morphometric traits of interest have been identified. These findings pave the way for more efficient breeding strategies, ultimately facilitating the development of improved cultivars with desirable traits.

plant biology↗

bioRxiv2024

Pharmacological inhibition of mTORC1 reduces neural death and damage volume after MCAO by modulating microglial reactivity

Ischemic stroke is a sudden and acute disease characterized by neuronal death, glia activation, and a severe inflammatory process. Neuroinflammation is an early event after cerebral ischemia, with microglia playing a leading role. Microglial activation involves functional and morphological changes that drive a wide variety of phenotypes. In this context, deciphering the molecular mechanisms underlying such microglial activation is essential to devise strategies to protect neurons and maintain certain brain functions affected by early neuroinflammation after ischemia. Here, we studied the role of mammalian target of rapamycin (mTOR) activity in the microglial response using a murine model of cerebral ischemia in the acute phase. We also determined the therapeutic relevance of the pharmacological administration of rapamycin, a mTOR inhibitor, before and after ischemic injury. Our data show that rapamycin, administered before or after brain ischemia induction, reduced the volume of brain damage and neuronal loss by attenuating the microglial response. Therefore, our findings indicate that the pharmacological inhibition of mTORC1 in the acute phase of ischemia may provide an alternative strategy to reduce neuronal damage through attenuation of the associated neuroinflammation.

neuroscience↗

bioRxiv2020

Chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes

Generating chromosome-level, haplotype-resolved assemblies of heterozygous genomes remains challenging. To address this, we developed gamete binning, a method based on single-cell sequencing of haploid gametes enabling separation of the whole-genome sequencing reads into haplotype-specific reads sets. After assembling the reads of each haplotype, the contigs are scaffolded to chromosome-level using a genetic map derived from the gametes. As a proof-of-concept, we assembled the two genomes of a diploid apricot tree based on whole-genome sequencing of 445 individual pollen grains. The two haplotype assemblies (N50: 25.5 and 25.8 Mb) featured a haplotyping precision of >99% and were accurately scaffolded to chromosome-level.

genomics↗

bioRxiv2019

Cross-transmission is not the source of new Mycobacteirum abscessus infections in a multi-centre cohort of cystic fibrosis patients

BackgroundMycobacterium abscessus is an extensively drug resistant pathogen that causes pulmonary disease particularly in cystic fibrosis (CF) patients. Identifying direct patient-to-patient transmission of M. abscessus is critically important in directing infection control policy for the management of risk in CF patients. A variety of clinical labs have used molecular epidemiology to investigate transmission. However there is still conflicting evidence as to how M. abscessus is acquired and whether cross-transmission occurs. Recently labs have applied whole-genome sequencing (WGS) to investigate this further and in this study we investigate whether WGS can reliably identify cross-transmission in M. abscessus.\n\nMethodsWe retrospectively sequenced the whole genomes of 145 M. abscessus isolates from 62 patients seen at four hospitals in two countries over 16 years.\n\nResultsWe have shown that a comparison of a fixed number of core single nucleotide variants (SNVs) alone cannot be used to infer cross-transmission in M. abscessus but does provide enough information to replace multiple existing molecular assays. We detected one episode of possible direct patient-to-patient transmission in a sibling pair. We found that patients acquired unique M. abscessus strains even after spending considerable time on the same wards with other M. abscessus positive patients.\n\nConclusionsThis novel analysis has demonstrated that the majority of patients in this study have not acquired M. abscessus through direct patient-patient transmission or a common reservoir. Tracking transmission using WGS will only realise its full potential with proper environmental screening as well as patient sampling.\n\nKey pointsO_LIWhole genome sequencing should replace current molecular typing used routinely in clinical microbiology laboratories.\nC_LIO_LIPatient-to-patient spread of M. abscessus is not common.\nC_LIO_LIEnvironmental screening may provide a better understanding acquisition of M. abscessus infections.\nC_LI

microbiology↗

bioRxiv2018

Comparative RNA-seq based transcriptomic analysis of Aspergillus nidulans recombinant strains overproducing heterologous glycoside hydrolases

Filamentous fungi are important cellular factories for the production and secretion of homologous and heterologous enzymes such as carbohydrate-active enzymes. However, the regulation of protein secretion in these microorganisms requires more profound studies since the enzyme levels produced are usually below the levels required by industry for profitable processes. Genomic and transcriptomic approaches have been used to understand the overexpression and production of heterologous enzymes and their capacity to induce different cellular biological processes. To investigate this regulation, Aspergillus nidulans recombinant strains were analyzed by transcriptomics. We designed three A. nidulans recombinant strains producing the following heterologous proteins: alpha-arabinofuranosidase (AbfA), beta-glucosidase (BglC) and thermophilic mannanase (Tp-Man5). The heterologous genes abfA and bglC were highly expressed, while tp-man5 mRNA levels were low and similar to those of a reference gene. There was an indirect relationship between mRNA and protein secretion levels, suggesting that transcription is not a bottleneck for target gene expression in this system. Despite the distinct features of the recombinant proteins, 30 differentially expressed genes were common to all the recombinant strains, suggesting that these genes represent a general response to the expression of heterologous genes. We also showed that the early activation of the canonical unfolded protein response (UPR) pathway by hacA alternative splicing was normalized after 8h, except in the strain expressing BglC, suggesting either no accumulation of the BglC misfolded form or the presence of an alternative endoplasmic reticulum (ER) stress and UPR pathway. Finally, to focus our analysis on the secretion pathway, a set of 374 genes was further evaluated. Seventeen genes were common to all the recombinant strains, suggesting again that these genes represent a general response of A. nidulans cells to the overexpression of recombinant genes, even thermophilic genes. Additionally, we reported the possible genetic interactions of these 17 genes based on coexpression network calculations. Interestingly, protein improvements are nongeneric, and improvements in the production of one target protein are not necessarily transferable to another one. Thus, this study may provide genetic and cellular background and targets for genetic manipulation to improve protein secretion by A. nidulans.

microbiology↗

bioRxiv2017

Comparative analysis of neutrophil and monocyte epigenomes

Neutrophils and monocytes provide a first line of defense against infections as part of the innate immune system. Here we report the integrated analysis of transcriptomic and epigenetic landscapes for circulating monocytes and neutrophils with the aim to enable downstream interpretation and functional validation of key regulatory elements in health and disease. We collected RNA-seq data, ChIP-seq of six histone modifications and of DNA methylation by bisulfite sequencing at base pair resolution from up to 6 individuals per cell type. Chromatin segmentation analyses suggested that monocytes have a higher number of cell-specific enhancer regions (4-fold) compared to neutrophils. This highly plastic epigenome is likely indicative of the greater differentiation potential of monocytes into macrophages, dendritic cells and osteoclasts. In contrast, most of the neutrophil-specific features tend to be characterized by repressed chromatin, reflective of their status as terminally differentiated cells. Enhancers were the regions where most of differences in DNA methylation between cells were observed, with monocyte-specific enhancers being generally hypomethylated. Monocytes show a substantially higher gene expression levels than neutrophils, in line with epigenomic analysis revealing that gene more active elements in monocytes. Our analyses suggest that the overexpression of c-Myc in monocytes and its binding to monocyte-specific enhancers could be an important contributor to these differences. Altogether, our study provides a comprehensive epigenetic chart of chromatin states in primary human neutrophils and monocytes, thus providing a valuable resource for studying the regulation of the human innate immune system.

genomics↗