Biology subjects

Barbosa, D.

Publications and source records attributed to Barbosa, D..

11 recordsLinked to original sources

bioRxiv2026

Oligodendrocyte ER-phagy Restricts Excessive Myelination by Degrading Sphingolipid Synthases

Myelination is critical for nervous system function. Numerous signaling pathways have been identified that promote myelin sheath growth, disruption of which can lead to hypomyelination, characterized by a reduction in myelin sheath thickness. However, the negative regulators of myelin sheath expansion remain poorly defined. Here, we identify a cellular brake on central nervous system myelination that restricts myelin sheath thickness during brain development. This brake is mediated by a selective form of autophagy, known as endoplasmic reticulum (ER)-phagy, which degrades the ER and its resident sphingolipid synthases. ER-phagy is highly active in oligodendrocytes during myelin membrane expansion, and its impairment leads to ER accumulation, elevated sphingolipid production, and excessive myelin thickening. Genetic reduction of de novo sphingolipid biosynthesis in the ER rescues the hypermyelination phenotype caused by ER-phagy disruption. In summary, our findings establish ER-phagy as a key regulator of sphingolipid metabolism and reveal a mechanistic link between ER homeostasis and myelin production by oligodendrocytes, providing insight into mechanisms underlying pathological hypermyelination.

neuroscience↗

bioRxiv2025

Transcriptome profiling reveals differential expression of virulence genes in Xylella fastidiosa under nutrient-rich and xylem-like conditions

Xylella fastidiosa is a xylem-limited, insect-vectored pathogen. To capture the metabolic changes that underlie its adaptation to both nutrient-rich and xylem-like environments, we performed transcriptome analyses on two reference strains, Temecula1 and 9a5c, sampled at early and late exponential phases in a complex laboratory medium (PWG) and a defined, xylem-mimicking medium (PIM6). Across eight conditions (24 transcriptomes), over 90% of annotated coding sequences were expressed, although 40-80% of transcripts exhibited low abundance (TPM < 100). In contrast, a core set of highly abundant transcripts was seen in both strains and media, including the non-coding RNAs 6S and RNase P, as well as multiple colicin- and microcin-like toxins, proteases, lipases, and stress-response factors. Comprehensive pathway reconstruction confirmed the activity of all essential metabolic pathways, while revealing conditional enrichment of stress-related and defense modules under nutrient limitation. We annotated 5' and 3' untranslated regions for thousands of transcripts and defined over 900 operons across both genomes. Differential expression analysis demonstrated that PIM6 medium confers a far greater transcriptional reprogramming between early and late phases than PWG. Strain-to-strain comparisons revealed that up to 12.6% of orthologous genes were differentially regulated, emphasizing divergent regulatory networks even under identical growth conditions. This multi-dimensional transcriptome atlas not only refines X. fastidiosa genome annotation but also pinpoints candidate regulators, non-coding RNAs, and operon variants for functional validation. By illuminating the dynamic gene expression landscapes that enable xylem colonization and environmental resilience, our study lays a foundation for targeted disruption of key pathways in this important plant pathogen.

genetics↗

bioRxiv2025

Actionable biological programs to enhance EGFR-targeted therapy response unveiled by single-cell lineage tracing in clinically relevant lung cancer models

Developing high-resolution approaches to capture both tumor architectural clonality and transcriptional state(s) in individual cells within heterogeneous tumor cell populations could shed light on the evolution of pre-existing and newly emergent tumor subclones and their phenotypes, elucidating their trajectories in response to selective pressures such as drug treatment. Reports to date have focused primarily on analyzing the drug-induced evolution of lung cancer cells in in vitro preclinical models with limited complexity and a relative lack of characterization of actionable biological programs to induce durable responses. Here, we challenged this paradigm and employed a lineage tracing single-cell RNAseq method to track the evolution of primary non-small cell lung cancer (NSCLC) patient-derived organoids (PDOs) and tumor xenografts in response to the standard-of-care EGFR inhibitor osimertinib, with a focus on understanding drug persistence and resistance. Our single-cell lineage tracing-RNAseq system revealed the presence of a discrete set of lineages with distinct transcriptional phenotypes over the course of the treatment. We identified two lineage populations that became predominant during drug treatment and resisted therapy in the PDOs and tumor xenografts. These lineages were present before treatment and harbored Hedgehog pathway and FOXD1 transcriptional programs, respectively. These specific transcriptomic lineages were otherwise undetectable by lower-resolution profiling. Functional studies confirmed the protective role that the baseline expression of the Hedgehog pathway and FOXD1 programs in the lineage tumor cell sub-populations exerts upon targeted therapy. The potential clinical relevance of these regulatory programs was validated by cross-analysis of single-cell transcriptomic data obtained from human NSCLC specimens. Overall, our approach identified pre-existing seeds of resistance before therapy and convergent, adaptive mechanisms supporting tumor residual disease and resistant states. This study highlights the utility of high-resolution tracing of tumor clonal heterogeneity with matched single-cell profiling to reveal occult cell states and molecular mechanisms of therapy resistance and develop counteracting strategies.

cancer biology↗

bioRxiv2025

Tracking White Matter Changes After Stereotaxic Radiosurgery inMiniature Pigs Using structural MRI, DTI, and FDG-PET

Stereotaxic radiosurgery (SRS) non-invasively and precisely ablates brain tumors or glioma located in the location where is surgically inaccessible with the aid of three- dimensional coordination system. This technique can also treat functional or psychiatric disorders, yet its dosimetry and curative mechanism remain to be elucidated. In this study, a miniature pig model was utilized to verify the effect of stereotaxic radiosurgery on a white matter tract with various doses delivered by CyberKnife. As porcine brain bears high resemblance to that of human in size and structure, the potential irradiation- induced change in structures and metabolism was monitored by conventional tools in clinical, including anatomical magnetic resonance image (MRI), diffusion tensor image (DTI) and 18F-Fluoro-D-Glucose positron emission tomography (FDG-PET). The right internal capsule was selected as the surgical target, and a one-year longitudinal study was conducted with whole brain images obtained once per three months. The results indicate that a dose equal to or higher than 60 Gy led to a late-onset radionecrosis which took a period close to 180 d to develop edema and breakage in the blood-brain barrier. In the meanwhile, DTI indices and differential tractography further illustrate a dose- and distance-dependent white matter injury along the tract of internal capsule. In contrast, doses of 40 Gy and below did not result in any discernible harm to the brain structure, but a sustained local inhibition in brain metabolism was observed in some pigs. The modulatory effect of low dose radiation awaits a comprehensive assessment throughout the whole brain in combination with behavioral or cognitive tasks built on pigs. This study showing the dose- and time-dependent changes will improve the understanding of the SRS dosimetry on the white matter and help investigators to decide an optimal window for brain imaging or behavioral assessment to take place on patients.

neuroscience↗

bioRxiv2024

Genetically Labeled Premyelinating Oligodendrocytes: Bridging Oligodendrogenesis and Neuronal Activity

To myelinate axons, oligodendrocyte precursor cells (OPCs) must stop dividing and differentiate into premyelinating oligodendrocytes (preOLs). PreOLs are thought to survey and begin ensheathing nearby axons, and their maturation is often stalled at human demyelinating lesions. Lack of genetic tools to visualize and manipulate preOLs has left this critical differentiation stage woefully understudied. Here, we generated a knock-in mouse line that specifically labels preOLs across the central nervous system. Genetically labeled preOLs exhibit distinct morphology, unique transcriptomic and electrophysiological features, and do not overlap with OPCs. PreOL lineage tracing revealed that subsets of them undergo prolonged maturation and that different brain regions initiate oligodendrogenesis with the spatiotemporal specificity. Lastly, by fate mapping preOLs under sensory deprivation, we find that neuronal activity functions within a narrow time window of preOL maturation to promote their survival and successful integration. Our work provides a new tool to probe this critical cell stage during axon ensheathment, allowing for fine dissection of axon-oligodendrocyte interactions.

neuroscience↗

bioRxiv2024

CDK4 and CDK6 upregulation promotes DNA replication stress, genomic instability and resistance to EGFR targeted therapy in lung cancer

Epidermal growth factor receptor (EGFR) mutant lung adenocarcinomas (LUAD) harbor a complex landscape of genetic co-alterations and potential oncogenic interactions. Among them are recurrent amplifications of the cell cycle regulatory genes CDK4 and CDK6, which have been clinically implicated in resistance to EGFR tyrosine kinase inhibitors (TKIs). However, the mechanisms by which CDK4/6 upregulation promotes therapy resistance remain poorly defined. Here, we demonstrate that CDK4 or CDK6 overexpression limits EGFR inhibitor-induced proliferative arrest, promoting continued cell cycle progression. This is accompanied by elevated replication stress, increased TPX2 expression, DNA damage leading to ATM activation, and ultimately genomic instability. Integrative transcriptomic and copy number analyses of EGFR-mutant LUAD tumors from both patients and preclinical models revealed that CDK4 or CDK6 amplification is associated with the upregulation of genes linked to tumor progression, including AGR2, ASNS, and STEAP1. CDK4 amplification was also highly correlated with gene expression changes associated with epithelial-to-mesenchymal transition (EMT) in a single-cell RNA sequencing dataset from patient biopsies. In preclinical models, co-treatment with CDK4/6 and EGFR inhibitors restored proliferative arrest, induced tumor cell apoptosis, and reduced replication stress, DNA damage, and genomic instability. Our findings uncover a mechanistic basis for EGFR inhibitor resistance of CDK4 and CDK6 amplified EGFR-mutant LUAD. They also provide a rationale for the biomarker-driven clinical development of combination EGFR and CDK4/6-targeted therapies for the treatment of a subset of EGFR-mutant LUAD patients.

cancer biology↗

bioRxiv2023

Autophagy collaborates with apoptosis pathways to control myelination specificity and function

Oligodendrocytes are the sole myelin producing cells in the central nervous system. Oligodendrocyte numbers are tightly controlled across diverse brain regions to match local axon type and number, but the underlying mechanisms and functional significance remain unclear. Here, we show that autophagy, an evolutionarily conserved cellular process that promotes cell survival under canonical settings, elicits premyelinating oligodendrocyte apoptosis during development and regulates critical aspects of nerve pulse propagation. Autophagy flux is increased in premyelinating oligodendrocytes, and its genetic blockage causes ectopic oligodendrocyte survival throughout the entire brain. Autophagy acts in the TFEB-Bax/Bak pathway and elevates PUMA mRNA levels to trigger premyelinating oligodendrocyte apoptosis cell-autonomously. Autophagy continuously functions in the myelinating oligodendrocytes to limit myelin sheath numbers and fine-tune nerve pulse propagation. Our results provide in vivo evidence showing that autophagy promotes apoptosis in mammalian cells under physiological conditions and reveal key intrinsic mechanisms governing oligodendrocyte number. HIGHLIGHTSO_LIAutophagy flux increases in the premyelinating and myelinating oligodendrocytes C_LIO_LIAutophagy promotes premyelinating oligodendrocyte (pre-OL) apoptosis to control myelination location and timing C_LIO_LIAutophagy acts in the TFEB-PUMA-Bax/Bak pathway and elevates PUMA mRNA levels to determine pre-OL fate C_LIO_LIAutophagy continuously functions in the myelinating oligodendrocytes to limit myelin sheath thickness and finetune nerve pulse propagation C_LI

neuroscience↗

bioRxiv2021

Comparative genomics of Xylella fastidiosa suggests determinants of host-specificity and expands its mobile genetic elements repertoire

The Gram-negative bacterium Xylella fastidiosa colonizes plant xylem vessels and is obligately vectored by xylem sap-feeding hemipteran insects. X. fastidiosa causes diseases in many plant species but in a variety of its plant hosts this bacterium behaves as a commensal endophyte. Originally confined to the Americas, infecting mainly grapevine, citrus and coffee plants, X. fastidiosa has spread to several plant species in Europe, causing devastating crop diseases. Although many pathogenicity and virulence factors have been identified in X. fastidiosa which enable the bacterium to successfully establish in the xylem tissue, the mechanisms by which distinct X. fastidiosa strains colonize and cause disease in specific plant hosts have not been fully elucidated. Here we present comparative analyses of 94 publicly available whole-genome sequences of X. fastidiosa strains with the goal of providing insights into plant host specificity determinants for this phytopathogen as well as of expanding the knowledge of its mobile genetic elements (MGE) content, mainly prophages. Our results revealed a pangenome of 4,549 protein coding sequences (CDSs) which is still open. The core- and accessory genomes comprise 954 and 2,219 CDSs, respectively. Phylogenetic tree construction using all core genome CDSs grouped the strains in three major clades of subspecies fastidiosa, multiplex and pauca, with subclades related to the strains sequence type (ST) obtained from multi-locus sequence typing (MLST). The geographic region where the strains were collected showed stronger association with the clades of X. fastidiosa strains rather than the plant species from which they were isolated. Among the CDS related to virulence and pathogenicity found in the core genome, those related to lipopolysaccharide (LPS) synthesis and trimeric autotransporter adhesins (TAA) are somewhat related with the plant host of a given strain according to phylogenetic inference. The X. fastidiosa accessory genome is represented by an abundant and heterogeneous mobilome, which includes a diversity of prophage regions. In summary, the genome comparisons reported here will enable a better understanding of the diversity of phylogenetically close genomes and warrant further investigation of LPS and TAAs as potential X. fastidiosa host-specificity determinants. Impact statementThe bacterium Xylella fastidiosa is a pathogen that infects many plant species and has caused devastating diseases in grapevine, citrus, coffee, and olive plants. This phytopathogen X. fastidiosa is original from the Americas and has emerged in Europe where it is causing severe economic losses for olive producers, mainly in Italy. Although many pathogenicity and virulence factors have been identified in X. fastidiosa, which enable this bacterium to successfully establish in the xylem vessels network, the mechanisms by which distinct X. fastidiosa strains colonize and cause disease in the different plant host species have not been fully elucidated. The comparative analyses of 94 whole-genome sequences from X. fastidiosa strains from diverse hosts and geographic regions provide insights into host specificity determinants for this phytopathogen as well as expand the knowledge of its mobile genetic elements (MGE) content, mainly prophages. Our results contribute for a better understanding of the diversity of phylogenetically close genomes and warrant further experimental investigation of lipopolysaccharide and trimeric autotransporter adhesins as potential host-specificity determinants for X. fastidiosa. Data summaryAll genomic sequences were accessed from publicly available GenBank RefSeq database at NCBI (National Center for Biotechnology Information). A full listing of NCBI accession numbers for X. fastidiosa strains described in this paper is available in Table S1 (available in the online version of this article).

genomics↗

bioRxiv2021

Plasmodium falciparum Acetyl-CoA Synthetase is essential for parasite intraerythrocytic development and chromatin modification

The malaria parasite Plasmodium falciparum possesses a unique Acetyl-CoA Synthetase (PfACS) which provides acetyl moieties for different metabolic and regulatory cellular pathways. We characterized PfACS and studied its role focusing on epigenetic modifications using the var gene family as reporter genes. For this, mutant lines to modulate plasmodial ACS expression by degron-mediated protein degradation or ribozyme induced transcript decay were created. Additionally, an ACS inhibitor was tested for its effectiveness and specificity in interfering with PfACS. The knockdown of PfACS or its inhibition led to impaired parasite growth. Decreased levels of PfACS also led to differential histone acetylation patterns, altered variant gene expression and concomitantly decreased cytoadherence of infected red blood cells containing knocked-down parasites. Further, ChIP analysis revealed the presence of PfACS in many loci in ring stage parasites, underscoring its involvement in the regulation of chromatin. Due to its significant differences to human ACS, PfACS seems an interesting target for drug development.

microbiology↗

bioRxiv2020

Dynein-dynactin segregate meiotic chromosomes in C. elegans spermatocytes

The dynactin complex is an essential co-factor of the microtubule-based motor dynein. Dynein-dynactin have well-documented roles in spindle assembly and positioning during C. elegans female meiosis and embryonic mitosis, while dynein-dynactins contribution to male meiosis has not been investigated. Here, we characterize the G33S mutation in DNC-1s N-terminal microtubule binding domain, which corresponds to G59S in the human dynactin subunit p150/Glued that causes motor neuron disease. In spermatocytes, dnc-1(G33S) delays spindle assembly and penetrantly inhibits anaphase spindle elongation in meiosis I, which prevents homologous chromosome segregation and generates aneuploid sperm with an extra centrosome. Consequently, embryos produced by dnc-1(G33S) hermaphrodites exhibit a high incidence of tetrapolar mitotic spindles, yet dnc-1(G33S) embryos with bipolar spindles proceed through early mitotic divisions without errors in chromosome segregation. Deletion of the DNC-1 N-terminus shows that defective meiosis in dnc-1(G33S) spermatocytes is not due to DNC-1s inability to interact with microtubules. Rather, our results suggest that the DNC-1(G33S) protein, which is aggregation-prone in vitro, is less stable in spermatocytes than the early embryo, resulting in different phenotypic severity in the two dividing tissues. Thus, the unusual hypomorphic nature of the dnc-1(G33S) mutant reveals that dynein-dynactin drive meiotic chromosome segregation in spermatocytes and illustrates that the extent to which protein misfolding leads to loss of function can vary significantly between cell types.

cell biology↗

bioRxiv2018

Early Life Trauma Predicts Affective Phenomenology and the Effects are Partly Mediated by Staging Coupled with Lowered Lipid-Associated Antioxidant Defences.

BackgroundEarly life trauma (ELT) may drive mood disorder phenomenology, neuro-oxidative and neuro-immune pathways and impairments in semantic memory. Nevertheless, there are no data regarding the impact of ELT on affective phenomenology and whether these pathways are mediated by staging or lowered lipid-associated antioxidant defences.\n\nMethodsThis study examined healthy controls (n=54) and patients with affective disorders including major depression, bipolar disorder and anxiety disorders (n=118). ELT was assessed using the Child Trauma Questionnaire. In addition, we measured affective phenomenology and assayed advanced oxidation protein products; malondialdehyde, paraoxonase 1 (CMPAase) activity, high-sensitivity C-reactive protein (hsCRP), and high-density lipoprotein (HDL) cholesterol.\n\nResultsELT was associated with increased risk for mood and comorbid anxiety disorders and a more severe phenomenology, including staging characteristics (number of mood episodes), severity of depression and anxiety, suicide attempts, suicidal ideation, type of treatments received, disabilities, body mass index, smoking behaviour and hsCRP, as well as lowered health-related quality of life, socio-economic status, antioxidant defences and semantic memory. The number of mood episodes and CMPAase/HDL-cholesterol levels could be reliably combined into a new vulnerability staging-biomarker index, which mediates in part the effects of ELT on affective phenomenology, while lowered antioxidant defences are associated with increased oxidative stress. Moreover, the effects of female sex on mood disorders and affective phenomenology are mediated by ELT.\n\nDiscussionThe cumulative effects of different types of ELT drive many aspects of affective phenomenology either directly or indirectly through effects of staging and/or lipid-associated antioxidant defences. The results show that children, especially girls, with ELT are at great risk to develop mood disorders and more severe phenotypes of affective disorders.

neuroscience↗