Biology subjects

Dias, J.

Publications and source records attributed to Dias, J..

13 recordsLinked to original sources

bioRxiv2026

ALDH Activity in Monocytes is Associated with Subclinical Coronary Atherosclerosis in Treated People with HIV-1

People living with HIV-1 (PWH) receiving antiretroviral therapy (ART) exhibit an increased cardiovascular disease (CVD) risk. Coronary atherosclerotic plaque formation is linked to chronic immune activation, a process fueled in PWH by additional mechanisms likely including residual HIV-1 production and microbial translocation from the gut during ART. Our previous studies demonstrated that aldehyde dehydrogenase (ALDH), an enzyme converting vitamin A into retinoic acid (RA), is upregulated in myeloid cells upon exposure to viral/bacterial/fungal products and that RA promotes HIV-1 production. To explore the link between ALDH/RA pathway and CVD risk, we used PBMC/plasma from ART-treated PWH (PWH+ART; n=51) and people without HIV-1 (Pw/oH; n=63) from the Canadian HIV/Aging Cohort Study, with/without subclinical coronary atherosclerosis, measured by coronary computed tomography angiography. ALDH expression was analyzed by flow cytometry on monocyte subsets, dendritic cells, and CD4+ T-cells. Unsupervised t-SNE-guided FlowSOM analysis associated top ALDH activity with a monocyte phenotype. The frequency of ALDH+ monocytes and plasma levels of RA and retinol binding protein 4 were increased in PWH+ART versus Pw/oH, with the highest RA levels coinciding with detectable plasma levels of soluble HIV-1 gp120. Multivariate regression models linked ALDH activity in monocytes to subclinical coronary atherosclerosis (i.e., total plaque volume, low attenuated plaque volume, coronary artery calcification score) presence/burden in PWH+ART, independently of Framingham risk score. Finally, ALDH+ monocyte frequency and RA levels positively correlated with pericoronary fat attenuation index, an emerging CVD predictor. Thus, ALDH/RA pathway may represent a new marker of metabolic/immune dysfunction contributing to CVD risk in ART-treated PWH.

immunology↗

bioRxiv2026

REV-ERBα/β Targeting Transcriptionally Reprograms HIV-Infected CD4+ T-Cells for Increased Viral Reactivation but Limited Virion Spread

The circadian clock repressors REV-ERB/{beta} control rhythmic gene expression and inhibit HIV-1 transcription. Whether REV-ERB/{beta} modulate the HIV-1 replication cycle beyond transcription remains unknown. Here, we demonstrate that memory CD4+ T-cells predominantly express the REV-ERB{beta} isoform ex vivo and that T-cell receptor (TCR) triggering downregulates both REV-ERB/{beta} expression, with levels of REV-ERB/{beta} mRNA being lower in ART-treated people with HIV (PWH) receiving antiretroviral therapy (ART) compared to people without HIV (PWoH) before/after TCR triggering. In single-round infection, the REV-ERB/{beta} antagonist SR8278 facilitated HIV-1 reverse transcription, integration, and intracellular HIV-p24 expression, but limited virion release. Moreover, SR8278 downregulated CCR5 mRNA expression, inhibited R5-tropic HIV-1 replication in vitro, and limited viral outgrowth in CD4+ T-cells from ART-treated PWH. Finally, genome-wide RNA-sequencing and functional validations revealed HIV-1 restriction/dependency factors that represent novel putative REV-ERB/{beta} targets. Thus, pharmacological inhibition of REV-ERB/{beta} uniquely combines a latency reversal activity with the inhibition of progeny virion spread.

immunology↗

bioRxiv2026

Identification of the cellular transcription factor KLF16 as a novel repressive epigenetic repressor of HIV-1 transcription

Despite antiretroviral therapy, human immunodeficiency virus type 1 (HIV-1) persists in latently-infected cells through epigenetic and transcriptional mechanisms. Latency-reversing agents have failed clinically, partly due to incomplete understanding of HIV-1 latency reversal. Here, using DNA-affinity capture and mass spectrometry on the HIV-1 5 long terminal repeat (5LTR) enhancer-core promoter, we identify KLF16 (Kruppel-like Factor 16) as a novel regulator of HIV-1 gene expression. KLF16 binds to the HIV-1 5LTR in vivo at Sp1 binding sites, and KLF16 depletion reactivates latent HIV-1 in T-lymphoid and monocytic cell models. Mechanistically, KLF16 represses HIV-1 transcription by competing with Sp1 for promoter binding and by recruiting the Sin3A/HDAC1 and HP1/Suv39H1 repressive epigenetic complexes. KLF16 is also upregulated in CD4+ T cells from ART-treated people with HIV-1 upon T-cell activation. Additionally, All-Trans retinoic acid (ATRA) reactivates latent HIV-1 in myeloid cells, partly by downregulating KLF16. These findings establish KLF16 as a novel transcriptional repressor of HIV-1, identifying it as a potential promising therapeutic target for cure strategies. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=136 SRC="FIGDIR/small/722432v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1611026org.highwire.dtl.DTLVardef@16b5eaforg.highwire.dtl.DTLVardef@153b11org.highwire.dtl.DTLVardef@1d90330_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

Tunable nucleofugality in carbamoyl-bearing covalent cholinesterase inhibitors

A handful of carbamate warheads is utilised in chemical biology to target serine hydrolases. The following case study on cholinesterases is the first comprehensive structure-reactivity exploration of the carbamoyl warhead, rather than one-target-oriented structure-activity study, with in-depth profiling of diverse halogen, chalcogen, and nitrogen-based leaving groups (nucleofuges) that can tune warhead reactivity. With computational tools we correlated the experimentally observed reactivities with steric and electronic factors of the investigated warheads. QM/MM simulations considering the enzymatic environment explained how substitution of carbon for nitrogen in the leaving groups of compounds 26 and 28 through resonance stabilisation, inductive bond polarization, and acidity amplification lowered the reaction barrier and increased the reaction rate >360 million times, making compound 28 a covalent inhibitor. Our findings underline the complexity of covalent inhibition and demonstrate that multiple complementary methods are required to interpret and predict covalent behaviour. Additionally, even though carbamates typically act as slow substrates, we were able to slow down decarbamoylation to a point where inhibition became de facto irreversible. The most interesting O-isoxazol-3-yl carbamate warhead was further profiled against the wider human proteome and showed low off-target reactivity, making it useful in further drug discovery. By establishing structure-reactivity principles for carbamoyl warhead, this study provides a generalisable framework for the development of selective covalent inhibitors and activity-based probes across diverse targets.

pharmacology and toxicology↗

bioRxiv2025

Humanized Bone Marrow-Liver-Thymus Mice for Studying HIV-1 Persistence in Liver and Lung CD4+ T and Myeloid Cell Subsets during Antiretroviral Therapy

BackgroundWhile the role of CD4+ T-cells in HIV-1 reservoir persistence during antiretroviral therapy (ART) is well-established, studies on tissue-resident macrophages (M{Phi}) in people with HIV-1 (PWH) are restricted by difficulties in accessing deep tissue samples. Investigations in myeloid-only humanized mouse models demonstrated the contribution of M{Phi} to viral rebound upon ART interruption. Two distinct M{Phi} subsets exist in mice and humans: one of embryonic origin and self-renewal capacity generating long-lived tissue-resident M{Phi} (LL-TRM), and another one of short-lived M{Phi} (SL-M{Phi}), constantly replenished by bone marrow monocytes. The relative contribution of LL-TRM versus SL-M{Phi} to tissue HIV-1 reservoir persistence during ART remains understudied. Here, we used a humanized BM-liver-thymus (hu-BLT) mouse model to quantify integrative HIV-1 infection in liver/lung M{Phi} versus CD4+ T-cells before/after ART and document their expression of LL-TRM/SL-M{Phi} markers. ResultsLung/liver immune cells were extracted from ART-naive (ART-) and ART-treated (ART+) HIV-infected (HIV+) hu-BLT mice, as well as HIV-uninfected mice (HIV-). M{Phi} were identified as cells expressing the myeloid markers CD33/HLA-DR and/or CD68 and flow-cytometry sorted based on their differential expression of CD14 and/or CCR2. Matched CD3+CD4+ T-cells were sorted in parallel and used as controls. HIV-DNA integration was measured by nested real-time PCR. In contrast to CD4+ T-cells that carried the highest levels of proviral HIV-DNA before and after ART, integrative infection in liver/lung M{Phi} was detected before ART, but was drastically reduced in HIV+ART+ hu-BLT mice, regardless of CD14 or CCR2 expression on M{Phi}. Markers of LL-TRM (CD163/CX3CR1/Ki67/c-Kit) were expressed on a small fraction of liver but not lung M{Phi}, indicative of a deficient LL-TRM development in this hu-BLT model. ConclusionsTogether our results demonstrate that lung/liver M{Phi} in hu-BLT mice support integrative HIV-1 infection in vivo, but their contribution to viral reservoir persistence during ART is minor when compared to CD4+ T-cells. This is consistent with the deficient development of LL-TRM we observed in hu-BLT mice. However, HIV-1 permissive M{Phi} present in this model likely contribute to viral rebound upon ART interruption. Therefore, HIV-1 cure interventions that are tested in such preclinical models should consider targeting HIV-1 replication in both M{Phi} and CD4+ T-cells.

immunology↗

bioRxiv2024

Novel Immunological Markers of Intestinal Impairment Indicative of HIV-1 Status and/or Subclinical Atherosclerosis

Antiretroviral therapy (ART) controls HIV-1 replication in people with HIV-1 (PWH), but immunological restauration is not achieved at mucosal barriers. Intestinal integrity impairment fuels microbial translocation and chronic immune activation, thus heightening the cardiovascular disease (CVD) risk. Here, we sought to identify novel immunological predictors of the HIV and CVD status in the peripheral blood of ART-treated PWH (HIV+; n=42) and uninfected participants (HIV-; n=40) of the Canadian HIV and Aging Cohort Study (CHACS), with/without subclinical coronary atherosclerotic plaques, measured by Coronary Computed Tomography Angiography as total plaque volume (TPV, mm3). PBMCs were analyzed by flow cytometry for the expression of T-cell lineage (CD45, CD3, CD4, CD8, CD8{beta}, TCR{beta}, TCR{gamma}{delta}), epithelial cell (EpCAM/CD326), activation (HLA-DR), and gut-homing/residency markers (CD69, CD196/CCR6, CD199/CCR9, CD49d/Itg4, CD103/ItgE, Itg{beta}7). CellEngine supervised clustering of the flow cytometry data revealed profound alterations in the CD3+ T-cell pool in relationship with the HIV status, with the accumulation of peculiar CD8+TCR{beta}+ and TCR{gamma}{delta}+ cells, to the detriment of CD4+TCR{beta}+ subsets. FlowJo manual gating further identified CD4+ T-cell subsets with peculiar CD326+CD69+CCR6+ItgE+ and CCR6+Itg{beta}7- phenotypes that were increased in frequency in HIV+ versus HIV- participants, together with a decreased frequency of CD8+ T-cells with an intraepithelial lymphocyte (IEL)-like CD3+CD4- TCR{beta}+TCR{gamma}{delta}-CD8+CD8{beta}- phenotype. Finally, multivariate logistic regression revealed the predictive capacity of specific T-cell subsets regarding the HIV/CVD status, and TPV values. Of particular relevance, we identified ItgE+CD8+, ItgE-CD8+, CCR6+CD4+, and CCR6+Itg{beta}7- CD4+ T-cell subsets as strong positive predictors of atherosclerotic plaque volume in crude models or upon adjustment for HIV/CVD confounding factors.

immunology↗

bioRxiv2024

Effect of high-intensity anaerobic exercise on electrocortical activity in athletes and non-athletes

AimThe present study aims to verify the information processing in athletes through electroencephalography, analyze cortical areas responsible for cognitive functions related to attentional processing of visual stimuli, and investigate motor activitys influence on cognitive aspects. Material and MethodsThe sample consisted of 29 subjects, divided into an experimental group (n = 13 modern pentathlon athletes) and a control group (n = 16 non-athletes). We collected the electrocortical activity before and after the Wingate Anaerobic Test. During the electrophysiological measures, the volunteers performed a saccadic eye movement paradigm. They also performed cognitive tasks, resting heart rate, and anthropometric measurements. ResultsA mixed ANOVA was applied to analyze the statistical differences between groups (athletes and control) and moments (before and after exercise) for F3, F4, P3, and P4 electrodes during rest one and task (pre-stimulus GO). There was an interaction for the group vs. moment factors in F3 [F = 17,129; p = 0,000; {eta}{superscript 2} = 0.512], F4 [F = 22,774; p = 0,000; {eta}{superscript 2} = 0.510], P3 [F = 11,429; p = 0,001; {eta}{superscript 2} = 0.405], and P4 electrodes [F = 18,651; p = 0,000; {eta}{superscript 2} = 0.379]. We found the main effect for group factors in the frontal and parietal electrodes of the right hemisphere (F4 and P4) and a main effect of the moment factor on the frontal (F3 and F4) and parietal (P3 and P4) electrodes. There was an interaction between the group vs. moment factors for the reaction time. The groups were different in Peak Power (Watts/kg), Average Power (Watts/kg), Fatigue Index (%), and Maximum Power (ms). ConclusionsWe identified chronic effects of exercise training on the cortical activity of modern pentathlon athletes, read-through differences in absolute alpha power, and acute effects of a high-intensity exercise session for athletes and non-athletes for electrocortical and behavioral responses.

neuroscience↗

bioRxiv2024

Posterior specification of multi-lineage axial assembloids from human pluripotent stem cells.

Elongation of the posterior body axis is driven by multi-potent neuromesodermal progenitors (NMPs), which both self-renew and simultaneously generate neural tube, neural crest, and presomitc mesoderm lineages at successive anterior posterior (A-P) levels. The ensuing diversification of these three NMP lineages is remarkably extensive, and also essential for an immense range of clinically important adult posterior body tissues. Here, we describe a human pluripotent stem cell protocol that successfully specifies authentic NMPs using a cocktail of seven factors (7F). 7F-NMPs express requisite markers, exhibit co-linear HOX activation, and can be purposely specified into each of the three NMP daughter lineages, demonstrating genuine multi-potency. 3D assembly of neural tube, neural crest, and presomitic mesoderm spheroids followed by long-term floating culture derives mature, multi-compartment Posterior Axial Assembloids, or PAXAs. PAXAs constitute a complex heterogeneous tissue containing spinal motor neurons and interneurons, central and peripheral glia, connective tissues, muscle satellite cells and contractile muscle fibres. Together, 7F-NMP and PAXA protocols establish a versatile in vitro platform to model mechanisms of human posterior body axis development, and for the study of a wide range of human diseases.

cell biology↗

bioRxiv2024

Inclusion of Salicornia ramosissima biomass in diets for juvenile whiteleg shrimp (Penaeus vannamei) induces favourable but transient effects in the immune and oxidative status

The whiteleg shrimp, Penaeus vannamei, is a highly valued and globally produced crustacean species. However, the rising cost of shrimp feed, exacerbated by increasing cereal prices, prompts the exploration of cost-effective and sustainable formulations for shrimp farming. This study investigates the potential of Salicornia ramosissima, a non-edible biomass co-product, as a substitute for wheat meal in juvenile whiteleg shrimp diets, aiming to create economically and ecologically sound formulations. The present study aimed to assess the impact of incorporating S. ramosissima into whiteleg shrimp aquafeeds on various aspects of shrimp development, including growth performance, survival, immune status, and oxidative status. A commercial-like diet was formulated and served as control, whereas four other diets contained S. ramosissima stems or a combination of leaves and seeds, both at inclusion levels of 5% and 10%, in addition to the control diet. Whiteleg shrimps were fed the experimental diets for 31 and 55 days, followed by a bacterial bath challenge to gauge their immune response to pathogens. At the end of the feeding period, whiteleg shrimps growth performance and survival rates remained consistent across all diets. However, whiteleg shrimp fed diets with S. ramosissima inclusion consumed more feed to achieve similar weights to those fed on the control diet, particularly in diets containing leaves and seeds at a 10% inclusion level, likely due to lower digestibility of dry matter, lipids, and energy. While S. ramosissima biomass inclusion did not affect shrimp weight, relative growth rate, or survival, it did lead to higher feed conversion ratios and feed intake, suggesting differences in nutrient digestibility and metabolic utilization. Additionally, S. ramosissima inclusion affected whiteleg shrimps overall body composition, particularly moisture and ash content. Dietary S. ramosissima inclusion modulated antioxidant enzyme activity in the shrimps hepatopancreas, indicating potential health improvements. The study also observed gene expression changes related to antioxidant enzymes, indicating an overall down-regulation with the inclusion of S. ramosissima. Despite challenges in feeding efficiency, the inclusion of S. ramosissima, especially stems, shows promise in reducing feed costs by utilizing a by-product. Furthermore, S. ramosissima inclusion led to subtle changes in certain plasma humoral parameters and hepatopancreas gene expression. Although some immune parameters varied, these effects appeared to diminish over time. In conclusion, this study highlights the potential of S. ramosissima as a functional feed ingredient capable of enhancing shrimps antioxidant response, aligning with global resource optimization and sustainability initiatives.

immunology↗

bioRxiv2024

A generative foundation model for antibody sequence understanding

Here we introduce FAbCon, a generative antibody-specific language model comprising 2.4 billion parameters. A commonly accepted wisdom in developing large language models is that increasing model scale will translate to higher performance on downstream tasks. Starting from a 144-million parameter setup, we show that progressively larger models achieve greater accuracy in predicting antigen binding and can also be used to design new antibodies with good predicted developability potential. FAbCon is available on huggingface.co/alchemab.

bioinformatics↗

bioRxiv2024

LSD1 inhibition suppresses ASCL1 and de-represses YAP1 to drive potent activity against neuroendocrine prostate cancer

Progression to lethal metastatic castration-resistant prostate cancer (mCRPC) is driven in part by epigenetic modulators such as LSD1 (KDM1A), a lysine-specific demethylase. Yet, mCRPC is increasingly recognized as a highly heterogeneous disease whose classification into subtypes is defined by the extent of androgen receptor (AR) and/or neuroendocrine (NE) characteristics. Meanwhile, the role of LSD1 in driving the different subtypes of mCRPC has remained unclear. Here, we assess the necessity of LSD1 in driving progression of mCRPC subtypes including AR+/NE- (ARPC), AR-/NE+ (NEPC), AR+/NE+ (amphicrine; AMPC), and AR-/NE- (double-negative; DNPC) through the use of LSD1 inhibitors in clinical development. LSD1 inhibition (LSD1i) was observed to be highly effective in restricting growth of NEPC, and efficacy was associated with TP53 loss-of-function. Mice bearing NEPC patient-derived xenografts treated with the LSD1 inhibitors, bomedemstat (MK-3543) or iadademstat (ORY-1001), exhibited suppression of the NE transcriptional profile, including ASCL1. LSD1i also induced expression and activity of YAP1, a non-NE transcription factor canonically silenced in NEPC (YAPOFF cancer), thereby switching NEPC from a YAPOFF to a YAPON cancer class. Therapeutically-induced YAPON NEPC tumors exhibited cell cycle arrest and repression of proliferative transcriptional programs. Importantly, the LSD1i-mediated YAPON state induced sensitivity to an inhibitor of YAP/TEAD function, IAG933, which extended antitumor efficacy against NEPC. Altogether, these findings indicate that patients diagnosed with NEPC may obtain greater relative benefit from LSD1-targeted therapies compared to those with other mCRPC subtypes and that dual inhibition of LSD1 and YAP/TEAD function demonstrates a promising treatment strategy potentially extending to other YAPOFF cancers. SignificanceAcross prostate cancer subtypes, NEPC is exceptionally responsive to LSD1 inhibition and this response is enhanced in combination with a YAP/TEAD disruptor which may improve patient selection and outcomes. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=171 HEIGHT=200 SRC="FIGDIR/small/576106v2_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@77332eorg.highwire.dtl.DTLVardef@1c127d0org.highwire.dtl.DTLVardef@1cec77org.highwire.dtl.DTLVardef@e87ed7_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2023

Retinoic Acid Boosts HIV-1 Replication in Macrophages via CCR5/SAMHD1-Dependent and mTOR-Modulated Mechanisms

The intestinal environment facilitates HIV-1 infection via mechanisms involving the gut-homing elixir retinoic acid (RA), which transcriptionally reprograms CD4+ T-cells for increased HIV-1 permissiveness. Consistently, colon-infiltrating CD4+ T-cells carry replication-competent viral reservoirs in people living with HIV-1 (PLWH) receiving antiretroviral therapy (ART). Intriguingly, integrative infection in colon macrophages, a pool replenished by circulating monocytes, represents a rare event in ART-treated PLWH, thus questioning on HIV-1 permissiveness in gut-resident macrophages. Here, we demonstrate that RA significantly boosts R5 but not X4 HIV-1 replication in monocyte-derived macrophages (MDMs). RNA-Sequencing, Gene Set Variation Analysis, and HIV interactor NCBI database interrogation, revealed RA- mediated transcriptional reprogramming associated with metabolic/inflammatory processes and HIV-1 resistance/dependency factors. Functional validations pointed to mechanisms of RA action, including CCR5 upregulation and SAMHD1 phosphorylation under the control of mTOR. These results support a model in which intestinal MDM contribute to viral replication/dissemination before ART and upon treatment interruption in mTOR-sensitive manner. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/561142v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@f966a0org.highwire.dtl.DTLVardef@1c0b4baorg.highwire.dtl.DTLVardef@992142org.highwire.dtl.DTLVardef@156a599_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1:C_FLOATNO C_FIG

immunology↗

bioRxiv2020

Deep sequencing of B cell receptor repertoires from COVID-19 patients reveals strong convergent immune signatures

Deep sequencing of B cell receptor (BCR) heavy chains from a cohort of 19 COVID-19 patients from the UK reveals a stereotypical naive immune response to SARS-CoV-2 which is consistent across patients and may be a positive indicator of disease outcome. Clonal expansion of the B cell memory response is also observed and may be the result of memory bystander effects. There was a strong convergent sequence signature across patients, and we identified 777 clonotypes convergent between at least four of the COVID-19 patients, but not present in healthy controls. A subset of the convergent clonotypes were homologous to known SARS and SARS-CoV-2 spike protein neutralising antibodies. Convergence was also demonstrated across wide geographies by comparison of data sets between patients from UK, USA and China, further validating the disease association and consistency of the stereotypical immune response even at the sequence level. These convergent clonotypes provide a resource to identify potential therapeutic and prophylactic antibodies and demonstrate the potential of BCR profiling as a tool to help understand and predict positive patient responses.

immunology↗