Biology subjects

Gomez, E.

Publications and source records attributed to Gomez, E..

14 recordsLinked to original sources

bioRxiv2026

Distinct Rab11-associated membrane trafficking pathways bidirectionally control neuronal extracellular vesicle cargo traffic

Neuronal extracellular vesicles (EVs) are released from synapses, and play roles in cellular communication, proteostasis, and the spread of toxic proteins in disease. The small GTPase Rab11 is required to maintain a reservoir of EV cargoes at presynaptic terminals, but how its diverse effector proteins contribute to this function and where Rab11 acts in neurons remains unclear. Using Drosophila motor neurons as a model, we show that EV cargoes redistribute from synapses to axons and cell bodies in rab11 mutants, concomitant with reduced release from synapses. We conducted a directed genetic screen of Rab11-associated factors and found that they have distinct roles in EV trafficking. Tethering and sorting factors are required to maintain levels of presynaptic EV precursors, supporting the hypothesis that Rab11 regulates EV cargo pools through recycling flux rather than by directly mediating EV release. Unexpectedly, we found that different classes of Rab11-associated proteins have opposite functions: the motor protein MyoV and the PI4KIII component Rbo sustain cargo levels at synapses, while the motor adaptor Nuf/Rab11FIP4 and the PI4KIII{beta} homolog Fwd restrict cargo levels. Together, these results indicate that Rab11 regulates multiple distinct organelle transport trajectories and PI(4)P populations to direct EV cargoes toward different cellular fates.

cell biology↗

bioRxiv2025

Dietary α-Ketoglutarate delays lung adenocarcinoma in females and modulates TBX5-associated transcriptional programs and the immune microenvironment

Lung adenocarcinoma (LUAD) is the most common form of lung cancer and a leading cause of cancer-related mortality, underscoring the need for new chemopreventive strategies. -Ketoglutarate (-KG), a tricarboxylic acid cycle metabolite and dioxygenase cofactor, links cellular metabolism to chromatin regulation. Here, we show that dietary -KG remodels LUAD in a sex-dependent manner. In female mice, -KG reduced tumor area, decreased repressive histone marks (H3K27me3, H3K9me3), and upregulated TBX5 and myogenesis-associated genes. In male mice, -KG-treated male mice exhibited increased tumor area, elevated H3K27me3, and immune remodeling characterized by CD8 T cell expansion and transcriptomic signatures of T cell exhaustion. Analysis of human LUAD revealed that TBX5 expression is enriched in female tumors and associated with improved survival, suggesting it may serve as a marker of favorable outcome. Together, these findings support -KG as an epigenetic modulator with potential chemopreventive activity in lung cancer and highlight the importance of incorporating sex as a biological variable in preclinical studies. SummaryOral -Ketoglutarate (-KG) has a known anti-aging effect and has been suggested to inhibit cancer development. However, the role of -KG in lung cancer is not known. Here, we investigated the effect of oral -KG on the development of lung adenocarcinoma in a KrasG12D-driven murine model. In females, -KG reduced lung tumor growth, accompanied by TBX5 induction, activation of a myogenesis transcriptional program, and loss of repressive histone methylation. In males, -KG increased tumor growth, coinciding with TBX5 repression, suppression of myogenesis programs, and accumulation of repressive histone methylation. -Ketoglutarate also remodeled the tumor immune microenvironment in a sex-dependent manner, with divergent effects on T cell infiltration. HIGHLIGHTSO_LIOral -Ketoglutarate reduces lung adenocarcinoma development in a genetically engineered murine model in a sex-dependent manner C_LIO_LIIn females, -Ketoglutarate reduces repressive histone marks and induces TBX5/myogenesis C_LIO_LIIn males, -Ketoglutarate increases repressive histone marks and suppresses TBX5/myogenesis C_LIO_LI-Ketoglutarate remodels the tumor immune microenvironment with sex-specific effects C_LIO_LITBX5 is enriched in female LUAD patients and predicts improved survival in human datasets C_LI CONTEXT AND SIGNIFICANCELung adenocarcinoma (LUAD) is the most common form of lung cancer and a leading cause of cancer mortality worldwide. Preventive strategies are limited, highlighting the need for safe approaches that can intercept tumor progression. Metabolic cofactors are increasingly recognized as modulators of the cancer epigenome. Among these, -Ketoglutarate (-KG), a central metabolite of the tricarboxylic acid cycle, functions as a cofactor for chromatin-modifying enzymes. Here, we demonstrate that dietary -KG supplementation limits LUAD progression in female mice, reduces repressive histone methylation, and activates TBX5-associated transcriptional programs. These effects are sex dependent, underscoring the importance of biological context in shaping metabolic responses. In human LUAD, TBX5 is enriched in females and predicts improved survival, suggesting that it may serve as a marker of favorable outcome and help guide future studies of -KG. Together, this work identifies -KG as an epigenetically active metabolite with translational promise for lung cancer chemoprevention. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=154 SRC="FIGDIR/small/677388v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@1615a31org.highwire.dtl.DTLVardef@68884corg.highwire.dtl.DTLVardef@cc5ed1org.highwire.dtl.DTLVardef@1652c60_HPS_FORMAT_FIGEXP M_FIG C_FIG One-sentence summary-Ketoglutarate remodels lung adenocarcinoma through sex-dependent epigenetic, transcriptional, and immune reprogramming.

cancer biology↗

bioRxiv2025

Investigation of CD36 interactome provides insights into multimolecular complexes necessary for anti-angiogenic signalling

Signal transduction is a fundamental process that enables cells to adapt to external cues and organize adequate responses including survival, death, growth, and homeostasis. A key mechanism modulating signal transduction relies on the formation of multimolecular complexes optimized for specificity, modularity and signal amplification. The scavenger receptor CD36, which binds diverse ligands in different cellular contexts, illustrates this principle. To uncover the nature of CD36 multimolecular complexes, we employed a proximity biotinylation labeling approach on human endothelial cells, where CD36 binds to thrombospondin-1 (TSP-1) to initiate a signaling cascade promoting programmed cell death. Using biotin capture and mass spectrometry protein identification, we uncovered a list of proteins in the vicinity of CD36. This list of candidates was refined by proximity ligation assays. The relationship between key CD36 interacting molecules, in particular active integrin beta-1 (ITGB1) and CD9, was further decoded by conditional colocalization analysis, providing support for their association within a tri-molecular complex. The implication of selected candidates in the signaling function of CD36 was further evaluated using shRNA knockdown, revealing that active ITGB1 is essential for Fyn activation downstream of CD36, with the tetraspanin playing a connecting role between CD36 and active ITGB1. Our approach to investigating CD36 complexes emphasizes the complexity and fundamental role of protein-protein interactions and coordination in the context of transmembrane signal transduction.

cell biology↗

bioRxiv2025

Root exudation facilitate water infiltration and rewetting of dry soil

The way plant roots facilitate water infiltration in soil may be just as important as the efficiency with which the root system in turn extracts it from the soil. Here we studied the mechanisms through which the root system facilitates water infiltration through a dry soil layer. Dye tracing experiments were conducted in model soil microcosms to characterise how root growth and exudation affects the permeability of dry layers of the model soil. Results showed that dissolved root exudates may be the primary facilitator of water infiltration, which may be linked to water surface tension. We conclude that in dry soil, root architecture and root exudation may combine to facilitate the infiltration of water and decrease the water lost by evaporation. These findings could enhance our understanding of the traits that provide drought resistance in crops.

plant biology↗

bioRxiv2025

Diclofenac stress responses and biotransformation pathways in the marine diatom Phaeodactylum tricornutum

Effects of organic contaminants (OCs) on phytoplankton physiology were extensively studied in the last years while a knowledge gap exists regarding the ability of phytoplankton to transform OCs. Knowledge about biotransformation pathways in these organisms lag far behind that of other microorganisms. A better understanding of biotransformation pathways would help identify biomarkers of contaminants exposure, improve microalgae-based water remediation strategies and help better assess contaminants persistence and trophic transfer in natural aquatic environments. The present study investigated diclofenac (DCF) physiological effects, transcriptional responses and metabolism in the marine diatom Phaeodactylum tricornutum with the aim of getting an insight on detoxifications pathways. P. tricornutum did not result in significant removal capacity of DCF from the exposure medium. Bioconcentration factors varied depending on the exposure concentration (3.9 and 2.7 for 1.5 mg L-1 and 10 mg L-1 DCF respectively) but remained relatively low. DCF resulted in mild physiological effects on P. tricornutum but gene expression analysis indicated that multiple molecular functions and biological processes were altered by DCF exposure. Transcriptomic analysis suggested increased nutrients and energy requirements possibly associated with the contaminant stress and detoxification metabolism. CYP gene expression was not significantly regulated upon DCF exposure but 4-Hydroxy Diclofenac (OH-DCF), a metabolite generally associated with CYP enzymatic activity, was detected. However, CYP gene expression was not significantly regulated upon DCF exposure. Five additional DCF metabolites with high molecular weight were detected. These metabolites were not previously described in the literature and were suggested to be generated via amino acid (or peptides) conjugation. Gene ontology analysis indicated that amino acid and peptide biosynthetic pathways were regulated upon DCF exposure supporting a possible correlation between organic contaminants detoxification responses and amino acid and protein content in phytoplankton cells. Our findings contribute to highlighting the diversity of biotransformation pathways in phytoplankton and provide mechanistic information about contaminants detoxification.

microbiology↗

bioRxiv2025

p16.1 and p16.2, new HSPC markers, play redundant roles in zebrafish T-cell lymphopoiesis

In the recent years, the zebrafish model has become a first-choice animal model in the field of hematopoiesis, due to extra-uterine development and optical transparency that allow an easy observation of early stages of hematopoietic stem and progenitor cells (HSPCs) development. Here, we characterized the function of two undescribed genes, si:ch211-214p16.1 and si:ch211-214p16.2 (shortened p16.1 and p16.2) that are expressed by HSPCs, as early as their emergence. By combining different strategies, we have demonstrated that p16.1 and p16.2 play redundant roles in embryonic thymopoiesis. Knocking-down both genes at the same time - or one gene in the mutant background for the other gene - impaired HSPCs commitment towards lymphoid fate and homing to the thymus. However double mutant embryos did not show any phenotype. As these double-mutant animals were viable, their thymocytes were compared to their wild-type counterparts by RNA sequencing, revealing that double mutant thymocytes compensated the lack of p16.1 and p16.2 by upregulating genes involved in chemotaxis and cell migration. One of these transcripts, ccr9b, was indeed validated as an important regulator of thymic homing in double mutant embryos, only. In summary, we found two new markers of embryonic HSPCs, functionally linked to lymphoid fate. The description of such markers will be important for our understanding of heterogeneity among emerging HSPCs in the embryo.

developmental biology↗

bioRxiv2023

Alzheimer's disease associated isoforms of human CD33 distinctively modulate microglial cell responses in 5XFAD mice

Microglia play diverse pathophysiological roles in Alzheimers disease (AD), with genetic susceptibility factors skewing microglial cell function to influence AD risk. CD33 is an immunomodulatory receptor associated with AD susceptibility through a single nucleotide polymorphism that modulates mRNA splicing, skewing protein expression from a long protein isoform (CD33M) to a short isoform (CD33m). Understanding how human CD33 isoforms differentially impact microglial cell function in vivo has been challenging due to functional divergence of CD33 between mice and humans. We address this challenge by studying transgenic mice expressing either of the human CD33 isoforms crossed with the 5XFAD mouse model of amyloidosis and find that human CD33 isoforms have opposing effects on the response of microglia to amyloid-{beta} (A{beta}) deposition. Mice expressing CD33M have increased A{beta} levels, mo7re diffuse plaques, fewer disease-associated microglia, and more dystrophic neurites compared to control 5XFAD mice. Conversely, CD33m promotes plaque compaction and microglia-plaque contacts, and minimizes neuritic plaque pathology, highlighting an AD protective role for this isoform. Protective phenotypes driven by CD33m are detected at an earlier timepoint compared to the more aggressive pathology in CD33M mice that appears at a later timepoint, suggesting that CD33m has a more prominent impact on microglia cell function at earlier stages of disease progression. In addition to divergent roles in modulating phagocytosis, scRNAseq and proteomics analyses demonstrate that CD33m+ microglia upregulate nestin, an intermediate filament involved in cell migration, at plaque contact sites. Overall, our work provides new functional insights into how CD33, as a top genetic susceptibility factor for AD, modulates microglial cell function.

neuroscience↗

bioRxiv2022

Molecular dynamics simulations reveal the impact of NUTD15 variants in structural conformation and dynamics

NUDT15 or MTH2 is a member of NUDIX protein family that catalyze the hydrolysis of nucleotides and deoxynucleotides, including thioguanine analogues. NUTD15 has been reported as a DNA sanitizer in humans, and more recent studies have proved that genomic variants are related to a poor prognosis in inmoplastic and immunologic diseases with thioguanines. Despite of this, the role of NUTD15 in physiology and molecular biology is quite unclear, as well as the mechanism of action of this enzyme. The existence of clinically relevant variants has prompted the study of this enzymes, whose capacity to bound and hydrolyze thioguanine nucleotides is still poor understood. By using a combination of biomolecular modelling techniques together with molecular dynamics we have studied the monomeric wild type NUTD15, as well as two important variants R139C and R139H. Our findings reveal not only how nucleotide binding stabilizes the enzyme, but also how two loops are responsible for keeping the enzyme in a packed close conformation. Mutations in 2 helix affect a network of hydrophobic and {pi}-interactions that are responsible of active site enclosing.

biophysics↗

bioRxiv2022

Functional entry of Members of Venezuelan Equine Encephalitis Complex into host cells is dependent on clathrin-mediated endocytosis, in a pH-Dependent Manner

Pixuna virus (PIXV) and Rio Negro virus (RNV) are mosquito-borne alphaviruses belonging to the Venezuelan Equine Encephalitis (VEE) complex, which includes pathogenic epizootic and enzootic subtypes responsible for life-threatening diseases in equines. Considering that the first steps in viral infection are crucial for the efficient production of new progeny, the aim of this study was to elucidate the early events of the replication cycle of these two viruses. To this end, we used chemical inhibitors and the expression of dominant-negative constructs to study the dependence of clathrin and endosomal pH on PIXV and RNV internalization mechanisms. We demonstrated that both viruses are internalized primarily via clathrin-mediated endocytosis, where the low pH in endosomes is crucial for viral replication. Contributing knowledge regarding the entry route of VEE complex members is important to understand the pathogenesis of these viruses and also to develop new antiviral strategies.

microbiology↗

bioRxiv2021

Generation of iPSC lines with high cytogenetic stability from peripheral blood mononuclear cells (PBMCs)

The utility of human induced pluripotent stem cells (hiPSCs) is contingent upon genomic integrity and stability. Recurrent genomic aberrations have been observed in human iPSC lines upon long-term culture, [~]10-25% demonstrate karyotype abnormalities. We describe a new and reliable non-integrating episomal plasmid reprogramming method for fresh (unexpanded) peripheral blood mononuclear cells (PBMC) into iPSCs (PBMC-iPSCs). PBMC-iPSCs produced using this method have a superior chromosome-level karyotype stability rate ([~]5% abnormality rate for all chromosomes; 2.8% for autosomes). After extended culture PBMC-iPSCs maintain a low rate of abnormalities (2% for autosomes). Deep coverage whole genome sequencing in a subset of PBMC-iPSC lines showed no shared single nucleotide polymorphisms (SNPs) or structural variants are introduced during reprogramming and maintenance of PBMC-iPSCs. iPSCs reprogrammed from unexpanded PBMCs have consistently high cytogenetic stability and minimal genomic aberrations, suggesting this method is highly suited for iPSCs in research and therapeutic clinical applications.

cell biology↗

bioRxiv2020

An integrated multi-omic analysis of iPSC-derived motor neurons from C9ORF72 ALS patients

Neurodegenerative diseases present a challenge for systems biology, due to the lack of reliable animal models and the difficulties in obtaining samples from patients at early stages of disease, when interventions might be most effective. Studying induced pluripotent stem cell (iPSC)-derived neurons could overcome these challenges and dramatically accelerate and broaden therapeutic strategies. Here we undertook a network-based multi-omic characterization of iPSC-derived motor neurons from ALS patients carrying genetically dominant hexanucleotide expansions in C9orf72 to gain a deeper understanding of the relationship between DNA, RNA, epigenetics and protein in the same pool of tissue. ALS motor neurons showed the expected C9orf72-related alterations to specific nucleoporins and production of dipeptide repeats. RNA-seq, ATAC-seq and data-independent acquisition mass-spectrometry (DIA-MS) proteomics were then performed on the same motor neuron cultures. Using integrative computational methods that combined all of the omics, we discovered a number of novel dysregulated pathways including biological adhesion and extracellular matrix organization and disruption in other expected pathways such as RNA splicing and nuclear transport. We tested the relevance of these pathways in vivo in a C9orf72 Drosophila model, analyzing the data to determine which pathways were causing disease phenotypes and which were compensatory. We also confirmed that some pathways are altered in late-stage neurodegeneration by analyzing human postmortem C9 cervical spine data. To validate that these key pathways were integral to the C9 signature, we prepared a separate set of C9orf72 and control motor neuron cultures using a different differentiation protocol and applied the same methods. As expected, there were major overall differences between the differentiation protocols, especially at the level of in individual omics data. However, a number of the core dysregulated pathways remained significant using the integrated multiomic analysis. This new method of analyzing patient specific neural cultures allows the generation of disease-related hypotheses with a small number of patient lines which can be tested in larger cohorts of patients.

neuroscience↗

bioRxiv2020

Generation of twenty four induced pluripotent stem cell lines from twenty four members of the Lothian Birth Cohort 1936

Cognitive decline is among the most feared aspects of ageing. We have generated induced pluripotent stem cells (iPSCs) from 24 people from the Lothian Birth Cohort 1936, whose cognitive ability was tested in childhood and in older age. Peripheral blood mononuclear cells (PBMCs) were reprogrammed using non-integrating oriP/EBNA1 backbone plasmids expressing six iPSC reprogramming factors (OCT3/4 (POU5F1), SOX2, KLF4, L-Myc, shp53, Lin28, SV40LT). All lines demonstrated STR matched karyotype and pluripotency was validated by multiple methods. These iPSC lines are a valuable resource to study molecular mechanisms underlying individual differences in cognitive ageing and resilience to age-related neurodegenerative diseases.

cell biology↗

bioRxiv2019

The macrophage-expressed gene (mpeg) 1 identifies a subpopulation of B cells in the adult zebrafish

The mononuclear phagocytic system (MPS) consists of many cells, in particular macrophages, scattered throughout the body. However, there is increasing evidence for the heterogeneity of tissue-resident macrophages, leading to a pressing need for new tools to discriminate MPS subsets from other hematopoietic lineages. Mpeg1.1 is an evolutionary conserved gene encoding perforin-2, a pore-forming protein associated with host defense against pathogens. Zebrafish mpeg1.1:GFP and mpeg1.1:mCherry reporters were originally established to specifically label macrophages. Since, more than 100 peer-reviewed publications have made use of mpeg1.1-driven transgenics for in vivo studies, providing new insights into key aspects of macrophage ontogeny, activation and function. However, while the macrophage-specific expression pattern of the mpeg1.1 promoter has been firmly established in the zebrafish embryo, it is currently not known whether this specificity is maintained through adulthood. Here we report direct evidence that beside macrophages, a subpopulation of B-lymphocytes is marked by mpeg1.1 reporters in most adult zebrafish organs. These mpeg1.1+ lymphoid cells endogenously express mpeg1.1 and can be separated from mpeg1.1+ macrophages by virtue of their light-scatter characteristics using FACS. Remarkably, our analyses also revealed that B-lymphocytes, rather than mononuclear phagocytes, constitute the main mpeg1.1-positive population in irf8null myeloid-defective mutants, which were previously reported to recover tissue-resident macrophages in adulthood. One notable exception are skin macrophages, whose development and maintenance appear to be independent from irf8, similar to mammals. Collectively, our findings demonstrate that irf8 functions in myelopoiesis are evolutionary conserved and highlight the need for alternative macrophage-specific markers to study the MPS in adult zebrafish. SUMMARY SENTENCEMpeg1 is not a restricted macrophage marker, but also labels B cells in the adult zebrafish. Therefore, previously identified irf8-independent macrophages likely consist of B lymphocytes. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=183 SRC="FIGDIR/small/836098v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@128a738org.highwire.dtl.DTLVardef@1fa6097org.highwire.dtl.DTLVardef@db61b2org.highwire.dtl.DTLVardef@eb2e2e_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2017

A Comparison of mRNA Sequencing with Random Primed and 3’-Directed Libraries

Deep mRNA sequencing (mRNAseq) is the state-of-the-art for whole transcriptome measurements. A key step is creating a library of cDNA sequencing fragments from RNA. This is generally done by random priming, creating multiple sequencing fragments along the length of each transcript. A 3 end-focused library approach cannot detect differential splicing, but has potentially higher throughput at lower cost (~10-fold lower), along with the ability to improve quantification by using transcript molecule counting with unique molecular identifiers (UMI) to correct for PCR bias. Here, we compare implementation of such a 3-digital gene expression (3-DGE) approach with \"conventional\" random primed mRNAseq, which has not yet been done. We find that while conventional mRNAseq detects ~15% more genes, the resulting lists of differentially expressed genes and therefore biological conclusions and gene signatures are highly concordant between the two techniques. We also find good quantitative agreement on the level of individual genes between the two techniques in terms of both read counts and fold change between two conditions. We conclude that for high-throughput applications, the potential cost savings associated with the 3-DGE approach are a very reasonable tradeoff for modest reduction in sensitivity and inability to observe alternative splicing, and should enable much larger scale studies focused on not only differential expression analysis, but also quantitative transcriptome profiling. The computational scripts and programs, along with experimental standard operating procedures used in our pipeline presented here, are freely available on our website (www.dtoxs.org).

genomics↗