Biology subjects

Sanchez-Madrid, F.

Publications and source records attributed to Sanchez-Madrid, F..

13 recordsLinked to original sources

bioRxiv2026

Lamin A/C regulates the compartment-specific contributions of immune and stromal cells to intestinal inflammation and colitis-associated colon cancer

Inflammatory bowel disease (IBD) arises from dysregulated crosstalk between innate immune, adaptive immune, and stromal compartments, yet the compartment-specific mechanisms driving tissue injury and tumorigenesis remain incompletely defined. To address this gap, we used conditional knockout and overexpression mouse models together with human IBD biopsy analysis to dissect the compartment-specific roles of lamin A/C in intestinal inflammation and colitis-associated tumorigenesis. Pan-hematopoietic lamin A/C deletion attenuated acute dextran sulfate sodium (DSS)-induced colitis. Myeloid-specific lamin A/C deletion ameliorated chronic colitis and was associated with altered dendritic cell (DC) programs, enhanced regulatory T cell (Treg) responses, and reduced effector T cell activation. Adoptive transfer of lamin A/C-deficient bone marrow-derived DCs recapitulated this reduced-damage phenotype in DSS colitis, while proteomic profiling revealed reduced antigen-processing and inflammatory programs together with enhanced metabolic and mucosal defense pathways. T cell-specific lamin A/C deletion reduced the Th1/Treg ratio and limited tumor development by suppressing chronic inflammation, whereas T cell-specific lamin A/C overexpression promoted severe Th1-skewed pathology, sustained intestinal inflammation, and increased colitis-associated tumor burden. Stromal fibroblast-specific lamin A/C deletion generated a tissue-protective niche characterized by enhanced epithelial barrier gene expression, regulatory cytokine production, and remodeling of the local immune milieu. Human IBD biopsies revealed compartment-specific lamin A/C alterations consistent with the murine findings. In lamina propria CD3 T cells, lamin A/C levels were blunted in IBD and associated with local histological severity rather than IBD diagnosis, whereas epithelial lamin A/C showed a steeper crypt-axis spatial gradient in a Crohns disease-specific pattern. Together, these findings identify lamin A/C as a cell-type- and context-dependent regulator of intestinal inflammation and tumorigenesis.

immunology↗

bioRxiv2026

Therapeutically targetable Th17-derived miR-721 drives autoimmune myocarditis through PPARγ repression

BACKGROUNDMyocarditis is an inflammatory cardiac disease in which Th17-driven immune responses contribute to progression toward dilated cardiomyopathy and heart failure. Current therapies mainly rely on corticosteroids but lack specificity, while the role of miR-721, synthesized by Th17 cells, remains largely unexplored in disease pathogenesis. METHODSWe characterized the presence of mmu-miR-721 and its human homolog hsa-RNA-Chr8:96 in extracellular vesicles (EVs) secreted by Th17 cells from IL-17eGFP mice with experimental autoimmune myocarditis (EAM) and myocarditis patients. MxCre-Ppargfl/fl mice and luciferase reporter assays were used to validate the target genes of miR-721 and hsa-RNA-Chr8:96, respectively. The functional role of miR-721 in EAM was investigated by lentiviral vectors overexpression and inhibition using miRNA sponge molecules. Th17 responses and heart inflammation were assessed and echocardiography was performed after in vivo blockade of mmu-miR-721 in EAM mice. RESULTSBoth mmu-miR-721 and hsa-RNA-Chr8:96 were encapsulated in EVs and secreted by Th17 cells of mice and patients with myocarditis. Overexpression of mmu-miR-721 in draining-lymph node cells from EAM mice inhibited Pparg transcription, leading to increased ROR{gamma}t and IL-17 expression and promoting Th17 differentiation. In contrast, in the absence of Pparg, a target of miR-721, no differences in ROR{gamma}t expression were observed, indicating that miR-721 promotes Th17 responses through repression of Pparg. Human PPARG was validated as a target gene of hsa-RNA-Chr8:96 and its overexpression in peripheral blood leukocytes downregulated PPARG mRNA levels, suggesting similar pathways involved in human pathology. In vivo blockade of mmu-miR-721 increased Pparg expression, reducing ROR{gamma}t and IL-17 activation in T cells and leading to decreased leukocyte infiltration in the heart and improved cardiac function. CONCLUSIONSmiR-721 is released by Th17 cells in EVs and promotes Th17 responses during myocarditis through repression of PPAR{gamma}, identifying this miRNA as both a mechanistic driver of disease and a potential therapeutic target. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=168 SRC="FIGDIR/small/713340v1_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@1a69953org.highwire.dtl.DTLVardef@9c36bdorg.highwire.dtl.DTLVardef@1cdce4dorg.highwire.dtl.DTLVardef@a34715_HPS_FORMAT_FIGEXP M_FIG C_FIG Novelty and significanceO_ST_ABSWhat is known?C_ST_ABSO_LImiR-721 and its human homolog are upregulated in the plasma of mice and humans with myocarditis C_LIO_LITh17 cells synthesize miR-721 C_LIO_LIMmu-miR-721 targets Pparg mRNA C_LI What new information does this article contribute?O_LImiR-721 is sorted into extracellular vesicles in the context of acute myocarditis C_LIO_LImiR-721 enhances Th17 differentiation via the Pparg/Rorc double inhibitory axis. C_LIO_LIHsa-RNA-Chr8:96 targets human PPARG mRNA for degradation, inhibiting its expression C_LIO_LIBlockade of miR-721 dampens acute myocarditis development in vivo C_LI This study reveals a novel miRNA-based therapeutic strategy to inhibit Th17 responses and treat myocarditis. Using the experimental autoimmune myocarditis model, the authors unravel the mechanisms by which mmu-miR-721 can enhance Th17 responses and show how targeting this regulatory molecule could ameliorate the progression of the disease. Remarkably, this regulatory axis is suggested to be present in humans as well, since PPARG gene is validated as a target gene for hsa-RNA-Chr8:96. These findings highlights the potential of miR-721 not only as a diagnostic tool but also as a cell-specific therapeutic target to control Th17 responses in the clinical setting.

immunology↗

bioRxiv2026

Mast cell desensitization induces a distinct IgE-dependent transcriptional program associated with immune regulation

Allergen-driven IgE-mast cell (MC) activation is a central feature of allergic diseases, whose prevalence continues to increase worldwide. Allergen immunotherapy (AIT) is currently the only disease-modifying treatment and induces a state of MC hyporesponsiveness termed desensitization; however, its underlying molecular mechanisms remain incompletely understood and whether this state reflects passive signal attenuation or active cellular reprogramming remains unresolved. Here, we define the molecular landscape of MC desensitization using a human polyclonal platform that captures the physiological diversity of allergen-specific IgE. Desensitization reduced degranulation in an allergen-specific manner and induced progressive internalization of allergen-specific IgE. Although early steps were associated with LAT phosphorylation, subsequent allergen challenge failed to propagate activation to distal IgE/Fc{varepsilon}RI effectors, revealing selective signaling uncoupling. Transcriptomic profiling uncovered a distinct transcriptional program comprising 168 upregulated genes enriched in immunoregulatory pathways and largely non-overlapping with classical activation signatures. This reprogramming occurred despite minimal alterations in mitochondrial respiration and selective impairment of allergen-induced glycolysis. Functionally, desensitized MCs enhanced allergen-driven proliferation of memory CD4 T cells. Together, these findings demonstrate that MC desensitization is not merely passive hyporesponsiveness but involves time-dependent allergen-specific IgE internalization, selective signal propagation, and a unique immunoregulatory transcriptional imprint that may contribute to tolerance during AIT.

immunology↗

bioRxiv2026

IFI16/AIM2 inflammasomes control Gal-9 and PVR in myeloid cells from PWH and their targeting improves immunotherapy against HIV-1

Chronic inflammation in people with HIV-1 (PWH) is associated with low CD4/CD8 T-cell ratios and inflammasome activation, which may impair monocyte (Mo) and monocyte-derived dendritic cell (MDDC) function and limit the efficacy of myeloid-based immunotherapies. Here, we investigated the role of inflammasome sensors in regulating immune ligands for TIM3 and TIGIT immune checkpoints in Mo and MDDC from PWH and their capacity to activate HIV-1-specific CD8+ T cells. Following TLR stimulation, galectin-9 (Gal-9), PVR and IL-1{beta} were preferentially upregulated in cells from PWH with low CD4/CD8 ratios. IFI16 and AIM2 expression was increased basally or inducible in Mo and co-localized with caspase-1 in these myeloid cells present in lymphoid tissues of HIV-1-infected humanized mice. Si-RNA or small molecule-mediated inhibition of IFI16/AIM2 reduced Gal-9 and PVR expression in MDDC and enhanced their ability to activate polyfunctional HIV-1-specific CD8+ T-cells displaying improved elimination of infected CD4+ T cells in vitro and in vivo. These findings identify IFI16 and AIM2 as key regulators of myeloid dysfunction and therapeutic targets to enhance HIV-1 immunotherapies.

immunology↗

bioRxiv2024

Role of Lamin A/C on dendritic cell function in antiviral immunity

Dendritic cells (DCs) play a crucial role in orchestrating immune responses, particularly in promoting IFN{gamma}-producing-CD8 cytotoxic T lymphocytes (CTLs) and IFN{gamma}-producing -CD4 T helper 1 (Th1) cells, which are essential for defending against viral infections. Additionally, the nuclear envelope protein lamin A/C has been implicated in T cell immunity. Nevertheless, the intricate interplay between innate and adaptive immunity in response to viral infections, particularly the role of lamin A/C in DC functions within this context, remains poorly understood. In this study, we demonstrate that mice lacking lamin A/C in myeloid LysM promoter-expressing cells exhibit a reduced capacity to induce Th1 and CD8 CTL responses, leading to impaired clearance of acute primary Vaccinia virus (VACV) infection. Remarkably, in vitro-generated granulocyte macrophage colony-stimulating factor bone marrow-derived DCs (GM-CSF BMDCs) show high levels of lamin A/C. Lamin A/C absence on GM-CSF BMDCs does not affect the expression of costimulatory molecules on the cell membrane but it reduces the cellular ability to form immunological synapses with naive CD4 T cells. Lamin A/C deletion induces alterations in NF{kappa}B nuclear localization, thereby influencing NF{kappa}B-dependent transcription. Furthermore, lamin A/C ablation modifies the epigenetic signature of BMDCs, predisposing these cells to mount a less effective antiviral response upon TLR stimulation. This study highlights the critical role of DCs in interacting with CD4 T cells during antiviral responses and elucidates the molecular mechanisms through which lamin A/C modulates DC function via epigenetic and transcriptional regulation.

immunology↗

bioRxiv2024

In-gel protein digestion using acidic methanol produces a highly selective methylation of glutamic 1 acid residues.

Mass-tolerant open search methods allow the high-throughput analysis of modified peptides by mass spectrometry. These techniques have paved the way to unbiased analysis of post-translational modifications (PTMs) in biological contexts, as well as of chemical modifications produced during the manipulation of protein samples. In this work, we have analyzed in-depth a wide variety of samples of different biological origin, including cells, extracellular vesicles, secretomes, centrosomes and tissue preparations, using Comet-ReCom, a recently improved version of the open search engine Comet-PTM. Our results demonstrate that glutamic acid residues undergo intensive methyl esterification when protein digestion is performed using in-gel techniques, but not using gel-free approaches. This effect was highly specific to Glu and was not found for other methylable residues such as Asp.

systems biology↗

bioRxiv2023

Phosphatases of regenerating liver balance F-actin rearrangements during T cell activation through WD repeat containing protein 1

Phosphatases of regenerating liver (PRLs) have been proposed to regulate actin dynamics in lymphoid cells. However, the mechanism mediating this role remained unknown. Here we showed the interaction of the PRLs with the actin regulator WD repeat containing protein 1 (WDR1). The interaction of the PRLs with WDR1 was dependent on F-actin integrity and the proper recruitment of the PRLs to cell membranes through the CAAX motif. Endogenous PRLs and WDR1 were distributed to the Immunological Synapse (IS) and perturbed expression of PRL-1 or PRL-2 by CRISPR/Cas9 mediated genome editing showed that the PRLs were required for proper distribution of WDR1 to filamentous (F)-actin at the IS. Further, perturbed expression of the PRLs or WDR1 resulted in defective IS assembly with deregulated F-actin rearrangements, altered positioning of LFA-1, and reduced IL-2 production. Interestingly, balanced expression of PRLs was required for accumulation of CD3{varepsilon} at the IS and early activating signalling. We propose that PRLs regulate early T cell signalling and are required for proper F-actin dynamics by regulating the WDR1 access to F-actin networks. As a consequence, PRLs regulate LFA-1 positioning at the IS and proper cytokine secretion.

immunology↗

bioRxiv2023

Allergic inflammation triggers dyslipidemia via IgG signalling

BackgroundAllergic diseases begin early in life and are often chronic, thus creating an inflammatory environment that may precede or exacerbate other pathologies. In this regard, allergy has been associated to metabolic disorders and with a higher risk of cardiovascular disease, but the underlying mechanisms remain incompletely understood. MethodsWe used a murine model of allergy and atherosclerosis, different diets and sensitization methods, and cell-depleting strategies to ascertain the contribution of acute and late phase inflammation to dyslipidemia. Untargeted lipidomic analyses were applied to define the lipid fingerprint of allergic inflammation at different phases of allergic pathology. Expression of genes related to lipid metabolism was assessed in liver and adipose tissue at different times post-allergen challenge. Also, changes in serum triglycerides (TG) were evaluated in a group of 59 patients [≥]14 days after the onset of an allergic reaction. ResultsWe found that allergic inflammation induces a unique lipid signature that is characterized by increased serum TG and changes in the expression of genes related to lipid metabolism in liver and adipose tissue. Alterations in blood TGs following an allergic reaction are independent of T-cell-driven late phase inflammation. On the contrary, the IgG-mediated alternative pathway of anaphylaxis is sufficient to induce a TG increase and a unique lipid profile. Lastly, we demonstrated an increase in serum TG in 59 patients after undergoing an allergic reaction. ConclusionOverall, this study reveals that IgG-mediated allergic inflammation regulates lipid metabolism.

immunology↗

bioRxiv2023

ReCom: A semi-supervised approach to ultra-tolerant database search for improved identification of modified peptides

Open-search methods allow unbiased, high-throughput identification of post-translational modifications in proteins at an unprecedented scale. The performance of current open-search algorithms is diminished by experimental errors in the determination of the precursor peptide mass. In this work we propose a semi-supervised open search approach, called ReCom, that minimizes this effect by taking advantage of a priori known information from a reference database, such as Unimod or a database provided by the user. We present a proof-of-concept study using Comet-ReCom, an improved version of Comet-PTM. Comet-ReCom increased identification performance of Comet-PTM by 68%. This increased performance of Comet-ReCom to score the MS/MS spectrum comes in parallel with a significantly better assignation of the monoisotopic peak of the precursor peptide in the MS spectrum, even in cases of peptide coelution. Our data demonstrate that open searches using ultra-tolerant mass windows can benefit from using a semi-supervised approach that takes advantage from previous knowledge on the nature of protein modifications. For Table of Contents Only O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/535358v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@1069b1borg.highwire.dtl.DTLVardef@b12bfdorg.highwire.dtl.DTLVardef@1bf23b6org.highwire.dtl.DTLVardef@1c1c02b_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2022

ART duration and immunometabolic state determine efficacy of DC-based treatment restoring functional HIV- specific CD8+ T cells in Chronic PLWH.

Dysfunction of CD8+ T cells in people living with HIV-1 (PLWH) receiving anti-retroviral therapy (ART) has restricted the efficacy of dendritic cell (DC)-based immunotherapies against HIV-1. Heterogeneous immune exhaustion and metabolic states of CD8+ T cells might differentially associate with dysfunction. However, specific parameters associated to functional restoration of CD8+ T cells after DC treatment have not been investigated in detail. Here, we studied the association of ART duration with memory subsets, exhaustion and metabolic profiles of CD8+ T cells from PLWH and improvement of polyfunctional and effector HIV-1 specific responses after stimulation with Gag-adjuvant-primed DC. HIV-1-specific CD8+ T cell responses from a larger proportion PLWH on ART for more than 10 years (LT-ARTp) improved polyfunctionality and capacity to eliminate autologous p24+ infected CD4+ T cells in vitro. In contrast, CD8+ T cells from PLWH on ART for less than a decade (ST-ARTp) were less responsive to DC treatment and functional improvement was limited in this group. This was associated with lower frequencies of central memory CD8+ T cells, increased co-expression of PD1 and TIGIT and reduced mitochondrial respiration and glycolytic induction upon TCR activation. In contrast, CD8+ T cells from LT-ARTp showed increased frequencies of TIM3+PD1-cells and preserved induction of glycolysis. Treatment of dysfunctional CD8+ T cells from ST-ARTp with combined anti-PD1 and anti-TIGIT antibodies plus a glycolysis promoting drug restored their ability to eliminate infected CD4+ T cells. Together, our study identifies specific immunometabolic parameters for different PLWH subgroups potentially useful for future personalized DC-based HIV-1 vaccines.

immunology↗

bioRxiv2021

TAILORED DC INDUCE PROTECTIVE HIV-1 SPECIFIC POLYFUNCTIONAL CD8+ T CELLS IN THE LYMPHOID TISSUE FROM HUMANIZED BLT MICE

Effective function of CD8+ T cells and enhanced innate activation of dendritic cells (DC) in response to HIV-1 is linked to protective antiviral immunity in controllers. Manipulation of DC targeting the master regulator TANK-binding Kinase 1 (TBK1) might be useful to acquire controller-like properties. Here, we evaluated the impact of TBK1-primed DC inducing protective CD8+ T cell responses in lymphoid tissue and peripheral blood and their association with reduced HIV-1 disease progression in vivo in the humanized bone marrow, liver and thymus (hBLT) mouse model. A higher proportion of hBLT-mice vaccinated with TBK1-primed DC exhibited less severe CD4+ T cell depletion following HIV-1 infection compared to control groups. This was associated with infiltration of CD8+ T cells in the white pulp from the spleen, reduced spread of infected p24+ cells to secondary lymphoid organs and with preserved abilities of CD8+ T cells from the spleen and blood of vaccinated animals to induce specific polyfunctional responses upon antigen stimulation. Therefore, TBK1-primed DC might be an useful tool for subsequent vaccine studies. Author summaryEmulating protective immunological characteristics from individuals capable of spontaneously controlling HIV-1 infection might be useful for the development of a protective vaccine. Enhanced function of dendritic cells (DC) in these HIV-1 controllers depends on the activation of TANK-binding Kinase 1 (TBK1) and might associate with protective T cells. Our study evaluated the ability of DCs trained through TBK1 activation inducing protective adaptive immune responses against HIV-1 and reducing disease progression in vivo, using a humanized mouse model. Our data indicate that mice vaccinated with tailored DC exhibit delayed disease progression, increased induction of protective CD8+ T lymphocyte subsets in the lymphoid tissue and blood upon antigen recognition. Therefore, trained-DC might be an useful tool for future HIV-1 vaccine designs.

immunology↗

bioRxiv2021

Synthetic Antigen Presenting cells reveal the diversity and functional specialization of extracellular vesicles composing the fourth signal of T cell immunological synapses.

The T cell Immunological Synapse (IS) is a pivotal hub for the regulation of adaptive immunity by endowing the exchange of information between cells engaged in physical contacts. Beyond the integration of antigen (signal one), co-stimulation (signal two), and cytokines (signal three), the IS facilitates the delivery of T-cell effector assemblies including supramolecular attack particles (SMAPs) and extracellular vesicles (EVs). How these particulate outputs differ among T -cell subsets and how subcellular compartments and signals exchanged at the synapse contribute to their composition is not fully understood. Here we harnessed bead-supported lipid bilayers (BSLBs) as a tailorable and versatile technology for the study of synaptic particle biogenesis and composition in different T-cell subsets, including CART. These synthetic antigen-presenting cells (APCs) facilitated the characterisation of trans-synaptic vesicles (tSV) as a heterogeneous population of EVs comprising among others PM-derived synaptic ectosomes and CD63+ exosomes. We harnessed BSLB to unveil the factors influencing the vesicular release of CD40L, as a model effector, identifying CD40 trans presentation, T-cell activation, ESCRT upregulation/recruitment, antigen density/potency, co-repression by PD-1 ligands, and its processing by ADAM10 as major determinants. Further, BSLB made possible the comparison of microRNA (miR) species associated with tSV and steadily released EVs. Altogether, our data provide evidence for a higher specialisation of tSV which are enriched not only in effector immune receptors but also in miR and RNA-binding proteins. Considering the molecular uniqueness and functional complexity of the tSV output, which is also accompanied by SMAPs, we propose their classification as signal four. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=198 HEIGHT=200 SRC="FIGDIR/small/445691v3_ufig1.gif" ALT="Figure 1"> View larger version (67K): org.highwire.dtl.DTLVardef@100f3aorg.highwire.dtl.DTLVardef@57adfforg.highwire.dtl.DTLVardef@6052fcorg.highwire.dtl.DTLVardef@1e85c21_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIBead Supported Lipid Bilayers (BSLB) reconstituting antigen-presenting cells support synapse assembly by T cells and the release of effector particles. C_LIO_LIBSLB facilitate the dissection of the cellular machineries and synapse composition shaping the released tSV. C_LIO_LItSV and their steadily released counterparts have a different composition. TSV show a higher enrichment of effectors including immune receptors, miR, RNA- and other nucleic acid-binding proteins, than EVs. C_LI

immunology↗

bioRxiv2020

Impaired miRNA degradation by post-transcriptional addition of 3' cytosine and adenine in T cell activation

MiRNA repertoire of T cells undergoes extensive changes in response to activation. Whereas global miRNA downregulation occurs few hours after activation, some individual miRNAs are specifically up- or down-regulated. In this study, we have assessed miRNA expression and post-transcriptional modification kinetics in human primary CD4+ T cells upon short-term stimulation with CD3CD28 or IFN I using Next Generation Sequencing. Multiple miRNAs not related before with T cell activation profile have been identified as differentially expressed. Downregulated miRNAs presented higher 3 uridylation. Dis3L2 and Eri1 (3 to 5 exoribonucleases that prefer uridylated RNA as substrates) increased their expression upon TCR stimulation, probably generating an adverse environment for miRNAs. Remarkably, non-templated cytosine additions to 3 end, previously unknown to be a relevant post-transcriptional modification mechanism, were overrepresented in upregulated miRNAs, together with high levels of adenylation. In the midst of an increasing presence of exoribonucleases, miRNAs multiplying their levels may successfully escape degradation due to 3 cytosine and adenine addition. These protective signals open a new avenue to improve miRNA stability for therapy in T cells.

immunology↗