Biology subjects

Beltran, M.

Publications and source records attributed to Beltran, M..

7 recordsLinked to original sources

bioRxiv2025

Cultivation and genomic characterization of human gut-associated Bdellovibrio reveals natural predatory bacteria with specialized prey interactions

Predatory bacteria from the Bdellovibrio and Like Organisms (BALOs) group represent promising alternatives to conventional antibiotics, yet their presence in the human microbiome has remained unconfirmed through cultivation. While molecular detection methods have identified Bdellovibrionaceae DNA in human-associated environments, viable predatory bacteria had never been successfully isolated from human samples, limiting our understanding of their ecology and therapeutic potential. Here, we report the first successful isolation and characterization of viable Bdellovibrio strains from human fecal samples. Despite extremely low natural abundance requiring enrichment protocols for detection, two of five pooled samples yielded viable predators with characteristic lytic activity. Whole-genome sequencing of two isolates revealed >99% average nucleotide identity to the reference strain HD100 with only 26 total single nucleotide polymorphisms, indicating minimal genomic divergence between human-associated and environmental strains. Comparative genomic analysis of 163 publicly available Bdellovibrio genomes demonstrated that only 10.4% represented true B. bacteriovorus sensu stricto, highlighting substantial cryptic diversity within this genus. Pangenome analysis across 41 genomes revealed a highly conserved core genome ([~]2,500-2,650 genes) contrasting with an expanding accessory genome, reflecting functional constraints of obligate predation alongside ecological adaptation. Notably, human-associated isolates exhibited narrower prey ranges, including some multidrug-resistant isolates. These findings establish that predatory bacteria are naturally associated with the human intestinal environment without acquiring novel virulence factors, support their biosafety profile for therapeutic development, and reveal prey specialization that may reflect adaptation to human microbiome ecology. IMPORTANCEThis work demonstrates that bacterial predation operates as an active ecological process within the human microbiota. The successful isolation of viable Bdellovibrio establishes that predatory bacteria are viable microbiota members maintaining their predatory phenotype. Genomic conservation (>99% ANI to environmental strains) indicates that predation imposes stringent functional constraints superseding niche-specific adaptations. Our findings reframe microbiome understanding by revealing that predation (a top-down regulatory mechanism) operates in human-associated communities, potentially functioning as a keystone ecological process maintaining diversity through predator-prey dynamics. For microbiome research, this establishes a novel framework for host-microbe-microbe interactions where rare predators may exert disproportionate impacts on community assembly and dysbiosis pathogenesis. This work opens unprecedented opportunities for developing ecologically-informed therapeutics that harness natural predation to simultaneously combat multidrug-resistant infections while restoring microbiota homeostasis, positioning predatory bacteria as a cornerstone strategy for antimicrobial resistance management through ecological microbiota restoration.

microbiology↗

bioRxiv2025

ASD mutations in the ciliary gene CEP41 impact development of projection neurons and interneurons in a human cortical organoid model

Primary cilia control cell-cell signalling and their dysfunction has been implicated in Autism Spectrum Disorders (ASD) but their roles in the ASD aetiology remain largely unexplored. Here, we analysed the impact of ASD mutations in CEP41 using human corticogenesis. CEP41 encodes a centrosomal protein located at the basal body and the ciliary axoneme and is mutated in ASD individuals and in Joubert syndrome, a ciliopathy with high incidence of ASD. To gain insights into CEP41s role in ASD aetiology, we characterised human cortical organoids carrying the CEP41 R242H point mutations found in ASD individuals. This mutation did not interfere with CEP41s ciliary localisation but cilia were shorter and had lower levels of tubulin polyglutamylation, which is indicative of altered cilia stability and signalling. Moreover, scRNAseq analyses revealed that the expression of several transcription factors with critical roles in interneuron development was altered in mutant interneurons and their progenitors. The CEP41 mutation also caused decreased cortical progenitor proliferation and an augmented formation of upper layer cortical neurons. Taken together, these findings indicate that CEP41 controls excitatory and inhibitory neuron differentiation, alterations in which might lead to an excitation/inhibition imbalance that is widely recognized as a convergent mechanism underlying neurodevelopmental disorders.

developmental biology↗

bioRxiv2024

MAGE: Monte Carlo method for Aberrant Gene Expression

Identifying genes that are aberrantly expressed is an important first step in the diagnosis and treatment of many diseases. Conventionally, differential expression (DE) analysis is used to screen gene expression profiles to identify functionally associated genes. DE often relies on the variance and fold change in expression from individual genes, which does not consider the expression of all other genes within the profile. When the overall gene expression is skewed, DE does not capture outliers in gene expression. To address this, we have developed a non-parametric DE method based on the probability density for an entire expression profile to select genes that deviate from the global distribution between two gene expression profiles with multiple replicates. Rather than assuming a particular distribution of expression per gene, our method assumes that aberrantly expressed genes (AEGs) will exhibit expression patterns distinguishable from non-AGEs which make up the majority of the profile. Here we introduce our nonparametric method (MAGE: Monte Carlo method for aberrant gene expression) and demonstrate that MAGE can identify AEGs that are not found by conventional DE analyses. The main feature of MAGE is (1) identifying outliers based on the expression profile of all genes rather than performing DE analyses on a per-gene basis and (2) consideration of the variance in expression between two different conditions. We also compared our results with traditional DE analysis as well as density-based clustering methods. MAGE produces consistent results in a variety of conditions and performs conservatively with the addition of noise. We also applied MAGE to single-cell RNA-seq samples and demonstrated that the analysis is robust with subsampling.

bioinformatics↗

bioRxiv2023

Oncogenic RAS drives rapid onset cellular plasticity and elicits a tumour-promoting neutrophil response at the inception of preneoplastic development

Oncogenic driver mutations are frequently found in normal tissues, suggesting that additional non-genetic factors are required for tumourigenesis. Phenotypic plasticity is an important gateway to malignancy and inflammation can fuel tumourigenesis, however, little is known about when and how these hallmarks first arise. Using single-cell transcriptomics and in vivo live imaging we have characterised the immediate cell intrinsic and innate immune responses during the first 24 hours following oncogenic Ras activation, in an inducible zebrafish model of HRASG12V-mediated skin tumour initiation. We found that only a subset of basal keratinocytes, but not superficial keratinocytes, are susceptible to RAS-driven phenotypic plasticity. These preneoplastic cells undergo dedifferentiation and partial EMT, resembling malignant cells observed in human squamous cell carcinoma (SCC). Strikingly, the same subset instigates the development of tumour-promoting neutrophils, which in turn enhance preneoplastic cell proliferation. Our findings demonstrate that the effects of oncogenic Ras are primarily determined by the cell of origin and reveal an association between the unlocking of phenotypic plasticity and the onset of tumour-promoting inflammation.

cancer biology↗

bioRxiv2023

Loss of PAX6 alters the excitatory/inhibitory neuronal ratio in human cerebral organoids

The transcription factor PAX6 is a crucial regulator of multiple aspects of embryonic forebrain development. It has well-established roles in the regulation of excitatory and inhibitory neuron development in the embryonic cortex in mice but PAX6s roles during human forebrain development are less well understood. Using human cerebral organoids, we investigated PAX6s roles in human neurodevelopment. Homozygous PAX6 mutant (PAX6-/-) organoids were larger than controls and contained increased inhibitory cell types. Excitatory neurons were still generated in PAX6-/- organoids but they were less mature, and a subset showed dysregulated expression of inhibitory identity genes compared to PAX6+/+ controls. The inhibitory cells found in PAX6-/- organoids physically segregated from excitatory neurons and presented a distinct transcriptomic profile when compared to in vivo cortical inhibitory neurons. PAX6-/- organoids showed a dysregulated cellular response to PTN-PTPRZ1 signalling, which contributed to the observed increase in inhibitory neurons and the consequent altered excitatory to inhibitory neuronal ratio. Summary StatementHuman cerebral organoids lacking PAX6 expression show an altered excitatory to inhibitory neuronal ratio, concomitant with altered responses to intercellular PTN-PTPRZ1 signalling.

developmental biology↗

bioRxiv2021

JAZF1-SUZ12 dysregulates PRC2 function and gene expression during cell differentiation

Polycomb repressive complex 2 (PRC2) methylates histone H3 lysine 27 (H3K27me3) to maintain repression of genes specific for other cell types and is essential for cell differentiation. In endometrial stromal sarcoma, the PRC2 subunit SUZ12 is often fused with the NuA4/TIP60 subunit JAZF1. Here, we show that JAZF1-SUZ12 dysregulates PRC2 composition, recruitment, histone modification, gene expression and cell differentiation. The loss of the SUZ12 N-terminus in the fusion protein disrupted interaction with the PRC2 accessory factors JARID2, EPOP and PALI1 and prevented recruitment of PRC2 from RNA to chromatin. In undifferentiated cells, JAZF1-SUZ12 occupied PRC2 target genes but gained a JAZF1-like binding profile during cell differentiation. JAZF1-SUZ12 reduced H3K27me3 and increased H4Kac at PRC2 target genes, and this was associated with disruption in gene expression and cell differentiation programs. These results reveal the defects in chromatin regulation caused by JAZF1-SUZ12, which may underlie its role in oncogenesis.

molecular biology↗

bioRxiv2021

STAG proteins promote cohesin ring loading at R-loops.

Most studies of cohesin function consider the Stromalin Antigen (STAG/SA) proteins as core complex members given their ubiquitous interaction with the cohesin ring. Here, we provide functional data to support the notion that the SA subunit is not a mere passenger in this structure, but instead plays a key role in the localization of cohesin to diverse biological processes and promotes loading of the complex at these sites. We show that in cells acutely depleted for RAD21, SA proteins remain bound to chromatin, cluster in 3D and interact with CTCF, as well as with a wide range of RNA binding proteins involved in multiple RNA processing mechanisms. Accordingly, SA proteins interact with RNA and are localised to R-loops where they contribute to R-loop regulation. Our results place SA1 within R-loop domains upstream of the cohesin complex and reveal a role for SA1 in cohesin loading which is independent of NIPBL, the canonical cohesin loader. We propose that SA1 takes advantage of structural R-loop platforms to link cohesin loading and chromatin structure with diverse functions. Since SA proteins are pan-cancer targets, and R-loops play an increasingly prevalent role in cancer biology, our results have important implications for the mechanistic understanding of SA proteins in cancer and disease.

cell biology↗