Biology subjects

Salgado, G.

Publications and source records attributed to Salgado, G..

7 recordsLinked to original sources

bioRxiv2026

Multi-omics links microbial dysbiosis, systemic inflammation and metabolomic disruptions to SNAE risk in treated HIV

Serious non-AIDS events (SNAEs), including non-AIDS malignancies, cardiovascular disease, and hepatic complications, remain major causes of mortality in treated HIV infection. These outcomes are driven by persistent immune activation, systemic inflammation, and metabolic dysfunction despite effective viral suppression with antiretroviral therapy (ART). To investigate mechanisms underlying SNAE pathogenesis, we performed a cross-site multi-omic analysis integrating plasma proteins, plasma metabolites, and mucosal microbiomes (ileum and rectum) in 82 ART-treated people with HIV (PWH) and 10 people without HIV (PWoH) from the United States and Mexico. Geography was the dominant source of variation, particularly across lipid classes. However, individuals at high risk for SNAEs, defined by low CD4 T cell counts and low CD4/CD8 ratios, shared a consistent signature of systemic inflammation, mitochondrial dysfunction, and microbial dysbiosis including elevated plasma IL-6, {omega}-oxidation products (adipic and suberic acids), and depletion of short-chain fatty acid-producing commensals in the gut mucosa, including Akkermansia muciniphila, Bacteroides uniformis, and Ruminococcus. Notably, A. muciniphila abundance correlated with lower IL-6 levels, fewer HIV RNA-producing cells in lymph nodes, and higher CD4/CD8 ratios. Together, these findings identify a shared inflammatory and metabolic phenotype in PWH and implicate A. muciniphila as a potential microbiome-based target to mitigate immune activation and SNAE risk in treated HIV.

immunology↗

bioRxiv2025

Apurinic/apyrimidinic endodeoxyribonuclease 1 contributes to the repair of damaged intercalated-motif of telomeric sequences

Apurinic/apyrimidinic endodeoxyribonuclease 1 (APE1) is a key enzyme in the Base Excision Repair pathway, responsible for processing abasic (AP-) sites. Recent studies revealed that APE1 participates in repairing DNA secondary structures as G-quadruplexes (G4). Telomeres, stabilized by shelterin proteins, are rich in G4, where APE1 binds and repairs AP-sites to maintain their integrity. The complementary cytosine-rich strand forms another structure, the i-motif (iM), essential for telomere maintenance, though its repair mechanism remains unclear. Herein we investigate APE1 binding and processing capabilities toward native and damaged telomeric iM, bearing AP-sites in different positions. Using biochemical and biophysical assays, we found that APE1 binds the telomeric iM-sequence and that its cleavage efficiency depends on AP-site position within iM. Proximity Ligation Assay analysis, in HeLa and U2OS cells, highlighted a novel interaction between APE1 and PCBP1, a well-known iM-folding modulator. PCBP1 binds iM with higher affinity than APE1 and inhibits its cleavage activity on damaged iM. Immunofluorescence and Telomere Restriction Fragment analyses showed that depletion of APE1 or PCBP1 impairs their interaction with the shelterin components, affecting telomere length. These results connect APE1 canonical DNA repair activity with the maintenance of non-canonical DNA secondary structures in telomeres, through its interaction with PCBP1. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/694817v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@1962c63org.highwire.dtl.DTLVardef@3c3f60org.highwire.dtl.DTLVardef@164d78borg.highwire.dtl.DTLVardef@1831aae_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

Selective infection and loss of PRDM1+ LN Tfh cells in uncontrolled HIV infection precludes formation of Tfh reservoirs under ART

The multifaceted and long-lived nature of HIV-1 reservoirs has proven to be a formidable obstacle in the development of a therapeutic cure of HIV-1. One of the major dimensions of the HIV-1 reservoir is its prevalence and persistence in tissue environments, including in lymph nodes (LN). Within LN, T follicular helper (Tfh) cells are widely considered as the dominant sub-reservoir in viremic people with HIV (PWH). However, whether Tfh cells survive to establish a reservoir in PWH undergoing suppressive antiretroviral therapy (ART) has remained controversial. To address these issues, we deeply phenotyped over 500,000 cells and identified over 2,000 HIV-1 infected cells by employing single-cell multiomics on LN from PWH during viremia and suppressed on ART. While we detected HIV-1 infected Tfh cells, the majority of infected cells during viremia and ART had non-follicular phenotypes and were instead heterogeneously distributed between various CD4+ T-cell subsets. Within-subset comparisons of HIV+ and HIV- cells revealed heightened activation signatures and altered cell cycle states during viremia, but largely similar features during ART. Furthermore, the comparison between viremia and ART in PWH highlighted a noncanonical Tfh subset - defined by high locus accessibility and transcription of PRDM1 - that is selectively depleted during viremia, recovers after ART, and is highly susceptible to infection in vitro. Our work suggests a revised direction for the HIV-1 cure field where a mandate of any comprehensive strategy will be to address the high proportional burden of non-follicular cells within the HIV reservoir.

immunology↗

bioRxiv2025

A unified network systems approach uncovers a core novel program underlying T follicular helper cell differentiation

T follicular helper (Tfh) cells are central to the adaptive immune response and exhibit remarkable functional diversity and plasticity. The complex nature of Tfh cell populations, inconsistent findings across experimental systems and potential differences across species have fueled ongoing debate regarding core regulatory pathways that govern Tfh differentiation. Many studies have experimentally investigated individual proteins and circuits involved in Tfh differentiation in limited contexts, each providing only a partial understanding of the process. To address this, we adopted a novel multi-scale network systems approach that incorporates both regulatory and protein-protein interactions. Our approach integrates diverse data types, captures regulation across multiple levels of immune system organization, and recapitulates known drivers. Further, we discover a core Tfh gene set that is conserved across tissue types and disease contexts, and is consistent across data modalities - bulk, single-cell and spatial. While components of this set have been individually reported, a novel aspect of our work lies in the discovery, characterization, and connectivity of this core signature using a single unbiased approach. Using this method, we also uncover a novel function of IL-12, a molecule with reported conflicting functions, in the regulation of Tfh differentiation. Notably, we find that, in both humans and mice, IL-12 is permissive for the differentiation of Tfh precursors, but blocks subsequent differentiation into GC Tfh cells. Overall, this work elucidates novel networks with unexplored roles in governing Tfh cell differentiation across species and tissues, paving the way for novel -therapeutic interventions.

immunology↗

bioRxiv2025

Lysine acetylation plays a role in RNA binding protein-regulated alternative pre-mRNA splicing.

Alternative pre-mRNA splicing allows one gene to encode multiple spliced messenger RNAs and, in turn, multiple proteins from a single gene transcript. This process is tightly regulated by cis elements within the pre-mRNA and trans-acting RNA binding proteins that recognize and bind to these elements, thus influencing the spliceosome assembly at adjacent splice sites. Thus, chemical modifications in either the cis-elements or trans factors or both can significantly alter splicing patterns and, thereby, the cellular proteome. Recent studies highlight that many RNA binding proteins (RBPs) are modified at multiple lysine side chains via acetylation, which neutralizes the formal positive charge and disrupts RPBs ability to participate in RNA recognition, binding and protein-protein interactions. This suggests that lysine acetylation of RPBs may be a novel mode of eukaryotic gene regulation during pre-mRNA processing. To test this, we used the well-characterized polypyrimidine tract binding protein (which is acetylated at several lysine side chains) as a model system to investigate the role of reversible RBP acetylation in regulating alternative-pre mRNA splicing. Using multiple sequence analysis, structure-based electrostatic modeling of RNA-protein interactions, and multi-site glutamine (acetyllysine mimic) and arginine (deacetyllysine mimic) mutants, we show for the first time that for a subset of PTBP1-regulated exons, acetylation at RNA-interacting lysine side chains significantly alters PTBP1 splicing activity.

biochemistry↗

bioRxiv2025

Membrane partition and structural reorganization induced by anti-psychotics with distinct clinical profiles

Antipsychotics (APs) are used in the treatment of severe mental disorders. Their mechanism of action involves interaction with multiple brain targets, notably the dopamine D2 receptors (D2R), where they compete with dopamine. Due to their lipophilic nature, APs also partition and accumulate in lipid membranes, particularly around the D2R and in synaptic vesicles. When intercalated into brain membranes, APs slowly accumulate and act as a reservoir, allowing their rapid release on demand to modulate neurotransmitter signaling. They also modify the physicochemical and mechanical properties of the lipid bilayer. These modifications can subsequently affect the conformational changes of embedded membrane proteins like the D2R. The present study investigated two major APs with different pharmacological and clinical profiles: chlorpromazine, which exerts its clinical activity mainly through a strong antagonistic action at the D2R, and clozapine, the weakest D2R antagonist of all APs. Surprisingly, although D2R antagonism is usually associated with AP potency, clozapine has repeatedly demonstrated clinical superior efficacy to all APs and is therefore recommended for treatment-resistant schizophrenia. The current work aims to extend the classical AP receptor mediated paradigmatic mode of action to their potential and unique membrane remodeling properties by thoroughly comparing their partitioning and impact on the physicochemical properties of the lipid membrane. Lipid model membranes mimicking synaptic vesicles have been investigated using a combination of several biophysical methods. The study aims to determine how the partitioning of the two APs modifies membrane order, phase transition, thickness, elasticity, phase separation, membrane integrity and charge. Differences have been demonstrated between these two compounds, which may further differ both over time as they accumulate as well as depending on their pre- or post-synaptic location.

biophysics↗

bioRxiv2024

The Apurinic/Apyrimidinic Endodeoxyribonuclease 1 is an RNA G-quadruplex binding protein and regulates miR-92b expression in cancer cells

In the last decade, several novel functions of the mammalian Apurinic/Apyrimidinic Endodeoxyribonuclease 1 (APE1) have been discovered, going far beyond its canonical function as a DNA repair enzyme, unveiling its potential roles in cancer development. Indeed, it was shown to be involved in DNA G-quadruplex biology and RNA metabolism, most importantly in the miRNA maturation pathway and the decay of oxidized- or abasic-miRNAs during oxidative stress conditions. Furthermore, in recent years several non-canonical pathways of miRNA biogenesis have been described, with a specific focus on guanosine-rich precursors that can form RNA G-quadruplex (rG4) structures. In this study, we show that several miRNA precursors, dysregulated upon APE1-depletion, contain an rG4 motif and that their corresponding target genes are upregulated after APE1-depletion. We also show, both by in vitro assays and by using a HeLa cell model, that APE1 can bind and regulate the folding of an rG4 structure contained in pre-miR92b, with a mechanism strictly dependent on critical lysine residues present in the N-terminal disordered region. Furthermore, APE1 depletion in HeLa cells alters the maturation process of miR-92b, mainly affecting the shuttling between the nucleus and cytosol. Lastly, bioinformatic analysis of APE1-regulated rG4-containing miRNAs supports the relevance of our findings for cancer biology. Specifically, these miRNAs exhibit high prognostic significance in lung, cervical, and liver cancer, as suggested by their involvement in several cancer-related pathways. Significance StatementWe highlight an undescribed non-canonical role of the mammalian Apurinic/Apyrimidinic Endodeoxyribonuclease 1 (APE1) in the context of RNA G-quadruplexes (rG4), specifically in the alternative pathway of miRNA maturation of guanosine-rich miRNA precursors. Specifically, APE1 binds these structures and modulates their folding, mainly through its N-terminal region and some residues in its catalytic domain. Moreover, we showed an interesting new role of APE1 in regulating the shuttling and accumulation of miR-92b between the nuclear and cytosolic compartments, opening new perspectives on how APE1 may exercise its role in the miRNA maturation pathway and function. Moreover, APE1-depleted dysregulated miRNAs with rG4 motifs in their precursors have significant prognostic value in lung, cervical, and liver tumors, suggesting potential targets for cancer therapy.

molecular biology↗