Biology subjects

Crespo, M.

Publications and source records attributed to Crespo, M..

13 recordsLinked to original sources

bioRxiv2026

ADAM17 Deletion Protects Against Type1 Diabetes-Associated Kidney Injury by Modulating Inflammatory and Fibrotic Pathways

0BackgroundA Disintegrin and Metalloprotease 17 (ADAM17) is a key sheddase regulating multiple inflammatory and growth factor-related pathways implicated in diabetic kidney disease (DKD). While cell-specific deletion of ADAM17 has shown renoprotective effects, the impact of global ADAM17 ablation in the context of diabetes remains incompletely understood. MethodsWe investigated the effects of tamoxifen-induced global Adam17 deletion in a murine model of type 1 diabetes induced by streptozotocin. Renal function, structural injury, inflammatory responses, stress-related signalling pathways, and fibrotic remodelling were comprehensively assessed and compared between diabetic Adam17 knockout and control mice. ResultsDespite persistent hyperglycaemia and albuminuria, diabetic Adam17 knockout mice exhibited preservation of glomerular filtration rate and marked attenuation of diabetes-associated renal injury. Global Adam17 deletion reduced mesangial expansion and structural damage, limited macrophage infiltration and chemokine expression, and significantly attenuated fibrotic remodelling. At the molecular level, Adam17 deficiency was associated with selective modulation of stress-related signalling pathways, including reduced activation of the PI3K/Akt axis and partial preservation of mitochondrial stress regulators, without evidence of a generalized suppression of cellular stress responses. ConclusionsOur findings demonstrate that global deletion of ADAM17 confers robust protection against diabetes-induced kidney injury through coordinated attenuation of inflammatory activation, stress-related signalling, and fibrotic progression. These results highlight the context-dependent role of ADAM17 in diabetic kidney disease and support the concept that therapeutic strategies targeting ADAM17-related pathways may require tissue- and disease-specific modulation to achieve renoprotective effects.

pathology↗

bioRxiv2025

A novel attention mechanism for noise-adaptive and robust segmentation of microtubules in microscopy images

BackgroundSegmenting cytoskeletal filaments in microscopy images is essential for studying their roles in cellular processes such as cell division and intracellular transport. However, this task is highly challenging due to the fine, densely packed, and intertwined nature of these structures. Imaging limitations--noise, low contrast, and uneven fluorescence--further complicate analysis. While deep learning has advanced segmentation of large, well-defined biological structures, its performance often degrades under such adverse conditions. Additional challenges include obtaining precise annotations for curvilinear structures and managing severe class imbalance during training. ResultsWe introduce a novel noise-adaptive attention mechanism that extends the Squeeze-and-Excitation (SE) module to dynamically adjust to varying noise levels. Integrated into a U-Net decoder with residual encoder blocks, this yields ASE_Res_UNet, a lightweight yet high-performance model. To address annotation challenges, we developed a synthetic dataset generation strategy that ensures accurate annotations of fine filaments in noisy images, producing a synthetic dataset with two difficulty levels for segmentation benchmarking. We systematically evaluated loss functions and metrics to mitigate class imbalance, ensuring robust performance assessment. ASE_Res_UNet effectively segmented microtubules in noisy synthetic images, outperforming its ablated variants. It also demonstrated superior segmentation compared to models with alternative attention mechanisms or distinct architectures, while requiring fewer parameters, making it efficient for resource-constrained environments. Evaluation on a newly curated real microscopy dataset and a recently reannotated dataset highlighted ASE_Res_UNets effectiveness in segmenting microtubules beyond synthetic images. For these datasets, ASE_Res_UNet was competitive with a recent synthetic data-driven approach that shares two cytoskeleton pretrained models. Importantly, ASE_Res_UNet showed strong transferability to other curvilinear structures (blood vessels and nerves) across diverse imaging conditions. ConclusionsThis work advances microtubule segmentation through three key contributions: (1) Providing two benchmark datasets (synthetic and real), addressing a critical gap in standardised evaluation resources for this task; (2) Introducing ASE_Res_UNet, a lightweight yet robust model combining noise-adaptive attention with residual learning; (3) Validating competitive performance across synthetic and real microscopy data. Additionally, we demonstrated the robustness and versatility of the proposed architecture across diverse curvilinear segmentation tasks, showcasing potential for broader applications in biological research and medical diagnosis.

bioinformatics↗

bioRxiv2024

The assessment of therapeutic autophagy inhibition in NF1 mutated tumor cells

MAPK pathway activation is found across central nervous system tumors. Neurofibromin 1 (NF1) protein is a GTPase-activating protein and tumor suppressor that negatively regulates RAS protein activity. A NF1 loss of function mutation results in MAPK pathway upregulation and is associated with pediatric gliomas. We previously demonstrated autophagy inhibition improves tumor response to BRAF inhibition. Here we investigate the role of autophagy in NF1 cells in the presence or absence of MEK inhibition (MEKi). NF1 wild type (WT) and NF1 knockout (KO) (HSC1{lambda}, immortalized human Schwann) cells were evaluated. NF1 loss was confirmed, and cell growth was monitored by Incucyte. MAPK/ERK pathway upregulation and autophagy were evaluated via Western blot analysis and RAS pull-down. Effects of MEKi, autophagy inhibition (pharmacologic and genetic), and combination therapy were evaluated via short- and long-term growth assays. NF1 KO cells exhibited MAPK pathway upregulation and increased growth. Additionally, NF KO cells demonstrated increased autophagic activity. Loss of NF1 resulted in increased sensitivity to MEKi and autophagy inhibition alone and in combination. We also demonstrate that the autophagy inhibitor chloroquine (CQ) can improve MEKi sensitivity in a patient harboring a somatic mutation of NF1. This combination is currently being evaluated in clinical trial (NCT04201457).

cancer biology↗

bioRxiv2024

Unbiased discovery of antibody therapies that stimulate macrophage-mediated destruction of B-cell lymphoma

Macrophages are critical effectors of antibody therapies for lymphoma, but the best targets for this purpose remain unknown. Here, we sought to define a comprehensive repertoire of cell surface antigens that can be targeted to stimulate macrophage-mediated destruction of B-cell lymphoma. We developed a high-throughput assay to screen hundreds of antibodies for their ability to provoke macrophages to attack B-cell lymphoma cells. Across both mouse and human systems, we identified multiple unappreciated targets of opsonization as well as putative immune checkpoints. We used this information to engineer a compendium of 156 bispecific antibodies, and we identified dozens of bispecifics that dramatically stimulate macrophage-mediated cytotoxicity of lymphoma cells. Among these, a bispecific comprising a SIRP decoy domain and a CD38-targeting arm (WTa2d1xCD38) exhibited maximal efficacy while minimizing the risk of hematologic toxicity. This bispecific stimulated robust anti-tumor responses in multiple xenograft models of aggressive B-cell lymphoma. Our approach can be directly applied to other cancers to rapidly discover bispecific antibodies that leverage anti-tumor responses by macrophages or other innate immune cells.

immunology↗

bioRxiv2024

Targeting of a STING Agonist to Perivascular Macrophages in Prostate Tumors Delays Resistance to Androgen Deprivation Therapy

BackgroundAndrogen deprivation therapy (ADT) is a frontline treatment for prostate cancer but often leads to the development of castration resistant prostate cancer (CRPC). This causes tumors to regrow and metastasize, despite ongoing treatment, and impacts negatively on patient survival. ADT is known to stimulate the accumulation of immunosuppressive cells like protumoral tumor-associated macrophages (TAMs), myeloid-derived suppressor cells and regulatory T cells in prostate tumors, as well as hypofunctional T cells. Protumoral TAMs have been shown to accumulate around tumor blood vessels during chemotherapy and radiotherapy, where they drive tumor relapse. Our aim was to see if such perivascular (PV) TAMs accumulated in ADT-treated prostate tumors prior to CRPC, and, if so, to selectively target these PV cells with a potent immunostimulant, interferon beta (IFN{beta}), an attempt to stimulate anti-tumor immunity and delay CRPC. MethodsWe first used quantitative, multiplex immunofluorescence to assess the effects of ADT on distribution and activation status of TAMs, CD4+ T cells, CD8+ T cells and NK cells in mouse and human prostate tumors. We then used antibody-coated, lipid nanoparticles to selectively target a STING agonist, 2'3'-cGAMP (cGAMP), to PV TAMs in mouse prostate tumors during ADT. ResultsTAMs accumulated at high density around blood vessels in ADT-treated primary mouse and human prostate tumors prior to CRPC, where they expressed markers of a protumoral phenotype, folate receptor beta (FR{beta}), MRC1 (CD206), SIGLEC1 (CD169) and VISTA. Additionally, higher numbers of inactive (PD-1-) CD8+ T cells and reduced numbers of active (CD69+) NK cells were also present in PV tumor areas after ADT. LNPs coated with antibody to FR{beta} selectively delivered cGAMP to PV TAMs in ADT-treated tumors where they activated STING and expression of IFN{beta} by these cells. This resulted in a marked increase in the density of active CD4+ T cells, CD8+T cells and NK cells in PV tumor areas, and significantly delayed in the onset of CRPC. ConclusionTogether, our data indicate that targeting a STING agonist to PV TAMs could be used to extend the treatment window for ADT in prostate cancer. KEY MESSAGESO_ST_ABSWhat is already known about the topicC_ST_ABSAndrogen deprivation therapy (ADT) is a frontline treatment for prostate cancer. However, tumors often develop resistance and start to regrow and metastasize - a condition called castration resistance prostate cancer (CRPC). Prostate cancer is considered to be an immunologically cold tumor type and while ADT stimulates tumor infiltration by cytotoxic (CD8+) T cells, they are largely hypofunctional, possibly due to the immunosuppressive tumor microenvironment. What this study addsThis study is the first to demonstrate that FR{beta}+ macrophages with a immunosuppressive phenotype accumulate around blood vessels in mouse and human prostate tumors during ADT, prior to the onset of CRPC. Lipid nanoparticles coated with an antibody to FR{beta}+ were then used to deliver a STING agonist selectively to these perivascular (PV) cells during ADT. This triggered STING signalling and the release of the potent immunostimulant, interferon beta, by PV macrophages, which then activated tumour-infiltrating CD4+ and CD8+ T cells, and delayed the onset of CRPC. How this study might affect research, practice or policyThe delivery of an immunostimulant specifically to PV regions of tumors represents a new, more targeted form of immunotherapy that ensures the activation of T cells as soon as they cross the vasculature into tumors. This new approach could be used to extend the treatment window for neoadjuvant ADT in men with localised prostate tumors. In doing so, it would delay/circumvent the need for additional treatments like radiotherapy and/or or prostatectomy.

cancer biology↗

bioRxiv2024

Multi-pronged analysis of pediatric low-grade glioma reveals a unique tumor microenvironment associated with BRAF alterations

Pediatric low-grade gliomas (pLGG) comprise 35% of all brain tumors. Despite favorable survival, patients experience significant morbidity from disease and treatments. A deeper understanding of pLGG biology is essential to identify novel, more effective, and less toxic therapies. We utilized single cell RNA sequencing (scRNA-seq), spatial transcriptomics, and cytokine analyses to characterize and understand tumor and immune cell heterogeneity across pLGG. scRNA-seq revealed tumor and immune cells within the tumor microenvironment (TME). Tumor cell subsets revealed a developmental hierarchy with progenitor and mature cell populations. Immune cells included myeloid and lymphocytic cells. There was a significant difference between the prevalence of two major myeloid subclusters between pilocytic astrocytoma (PA) and ganglioglioma (GG). Bulk and single-cell cytokine analyses evaluated the immune cell signaling cascade with distinct immune phenotypes among tumor samples. KIAA1549-BRAF tumors appeared more immunogenic, secreting higher levels of immune cell activators and chemokines, compared to BRAF V600E tumors. Spatial transcriptomics revealed the differential gene expression of these chemokines and their location within the TME. A multi-pronged analysis of pLGG demonstrated the complexity of the pLGG TME and differences between genetic drivers that may influence their response to immunotherapy. Further investigation of immune cell infiltration and tumor-immune interactions is warranted. Key pointsO_LIThere is a developmental hierarchy in neoplastic population comprising of both progenitor-like and mature cell types in both PA and GG. C_LIO_LIA more immunogenic, immune activating myeloid population is present in PA compared to GG. C_LIO_LIFunctional analysis and spatial transcriptomics show higher levels of immune mobilizing chemokines in KIAA1549-BRAF fusion PA tumor samples compared to BRAF V600E GG samples. C_LI Importance of the StudyWhile scRNA seq provides information on cellular heterogeneity within the tumor microenvironment (TME), it does not provide a complete picture of how these cells are interacting or where they are located. To expand on this, we used a three-pronged approach to better understand the biology of pediatric low-grade glioma (pLGG). By analyzing scRNA-seq, secreted cytokines and spatial orientation of cells within the TME, we strove to gain a more complete picture of the complex interplay between tumor and immune cells within pLGG. Our data revealed a complex heterogeneity in tumor and immune populations and identified an interesting difference in the immune phenotype among different subtypes.

cancer biology↗

bioRxiv2023

Lack of p38 activation in T cells increases IL-35 production and protects against obesity by promoting thermogenesis

Obesity is characterized with low grade inflammation, energy imbalance and impaired thermogenesis. The role of regulatory T cells (Treg) in inflammation-mediated maladaptive thermogenesis has not been well established. We discovered that p38 pathway is a key regulator of T cell-mediated adipose tissue (AT) inflammation and browning. Mice with T cells specific deletion of the p38 activators, MKK3/6, were protected against diet-induced obesity and AT inflammation improving their metabolic profile, higher browning and thermogenesis. We identified IL-35 as a driver of adipocyte thermogenic program through ATF2/UCP1/FGF21 pathway. IL-35 limits CD8+ T cell infiltration and inflammation in AT. Interestingly, we found that IL35 was reduced in visceral fat from obese patients. Mechanistically we showed that p38 controls the expression of IL-35 in human and mouse Treg cells through mTOR pathway activation. Our findings highlight p38 signaling as a molecular orchestrator of AT T cell accumulation and function and identify p38 and IL-35 as promising targets for metabolic diseases.

immunology↗

bioRxiv2022

Targeting the BAG-1 family of co-chaperones in lethal prostate cancer.

Therapies that abrogate persistent androgen receptor (AR) signaling in castration resistant prostate cancer (CRPC) remain an unmet clinical need. The N-terminal domain (NTD) of the AR drives transcriptional activity in CRPC but is intrinsically disordered and remains a challenging therapeutic target. Therefore, inhibiting critical co-chaperones, such as BAG-1L, is an attractive alternative strategy. We performed druggability analyses demonstrating the BAG domain to be a challenging drug target. Thio-2, a tool compound, has been reported to bind the BAG domain of BAG-1L and inhibit BAG-1L-mediated AR transactivation. However, despite these data, the mechanism of action of Thio-2 is poorly understood and the BAG domain which is present in all BAG-1 isoforms has not been validated as a therapeutic target. Herein, we demonstrate growth inhibiting activity of Thio-2 in CRPC cell lines and patient derived models with decreased AR genomic binding and AR signaling independent of BAG-1 isoform function. Furthermore, genomic abrogation of BAG-1 isoforms did not recapitulate the described Thio-2 phenotype, and NMR studies suggest that Thio-2 may bind the AR NTD, uncovering a potential alternative mechanism of action, although in the context of low compound solubility. Furthermore, BAG-1 isoform knockout mice are viable and fertile, in contrast to previous studies, and when crossed with prostate cancer mouse models, BAG-1 deletion does not significantly impact prostate cancer development and growth. Overall, these data demonstrate that Thio-2 inhibits AR signaling and growth in CRPC independent of BAG-1 isoforms, and unlike previous studies of the activated AR, therapeutic targeting of the BAG domain requires further validation before being considered a therapeutic strategy for the treatment of CRPC.

molecular biology↗

bioRxiv2022

The histone methyltransferase DOT1L regulates chromatin reorganization and gene expression during the postmeiotic differentiation of male germ cells

Spermatozoa have a unique genome organization: their chromatin is almost completely devoid of histones and is formed instead of protamines which confer a high level of compaction and preserve paternal genome integrity until fertilization. Histone-to-protamine transition takes place in spermatids and is indispensable for the production of functional sperm. Here we show that the H3K79-methyltransferase DOT1L controls spermatid chromatin remodelling and subsequent reorganization and compaction of spermatozoon genome. Using a mouse model in which Dot1l is knocked-out (KO) in postnatal male germ cells, we found that Dot1l-KO sperm chromatin is less compact and has an abnormal content, characterized by the presence of transition proteins, immature protamine 2 forms and a higher level of histones. Proteomics and transcriptomics analyses performed on spermatids reveal that Dot1l-KO modifies the chromatin prior to histone removal, and leads to the deregulation of genes involved in flagellum formation and apoptosis during spermatid differentiation. As a consequence of these chromatin and gene expression defects, Dot1l-KO spermatozoa have less compact heads and are less motile which results in impaired fertility.

molecular biology↗

bioRxiv2021

Elevated anti-SARS-CoV-2 antibodies and IL-6, IL-8, MIP-1β, early predictors of severe COVID-19.

BackgroundViral and host immune kinetics during acute COVID-19 and after remission of acute symptoms need better characterization. MethodsSARS-CoV-2 RNA, anti-SARS-CoV-2 IgA, IgM, and IgG antibodies, and pro-inflammatory cytokines were measured in sequential samples among hospitalized COVID-19 patients during acute infection and 6 months following diagnosis. Results24 laboratory-confirmed COVID-19 patients with mild/moderate and severe COVID-19 were included. Most were males 83%, median age of 61 years. 21% were admitted to the ICU and 8 of them (33.3%) met criteria for severe COVID-19 disease. A delay in SARS-CoV-2 levels decline during the first 6 days of follow-up and viral load persistence until month 3 were related with severe COVID-19, but not viral load levels at the diagnosis. Higher levels of anti-SARS-CoV-2 IgA, IgM, IgG and the cytokines IL-6, IL-8 and MIP-1{beta} at the diagnosis time were related with severe COVID-19 outcome. Higher levels of MIP-1{beta}, IL-1{beta}, MIP-1 and IFN-{gamma} were observed at month 1/3 during mild/moderate disease compared to severe COVID-19. IgG persisted at low levels after 6 months of diagnosis. ConclusionsHigher concentrations of IgA, IgM, and IgG, and IL-6, IL-8 and MIP-1{beta} are identified as early predictors of COVID-19 severity, but not SARS-CoV-2 RNA levels at diagnosis.

microbiology↗

bioRxiv2020

SARS-CoV-2 infection suppresses ACE2 function and antiviral immune response in the upper respiratory tract of infected patients

There is an urgent need to elucidate the molecular mechanisms underlying the transmissibility and pathogenesis of SARS-CoV-2. ACE2 is a host ectopeptidase with well-described anti-inflammatory and tissue protective functions and the receptor for the virus. Understanding SARS-CoV-2-ACE2 interaction and the expression of antiviral host genes in early infection phase is crucial for fighting the pandemic. We tested the significance of soluble ACE2 enzymatic activity longitudinally in positive nasopharyngeal swabs at two time points after symptom consultation, along with gene expression profiles of ACE2, its proteases, ADAM17 and TMPRRS2, and interferon-stimulated genes (ISGs), DDX58, CXCL10 and IL-6. Soluble ACE2 activity decreased during infection course, in parallel to ACE2 gene expression. On the contrary, SARS-CoV-2 infection induced expression of the ISG genes in positive SARS-CoV-2 samples at baseline compared to negative control subjects, although this increase wanes with time. These changes positively correlated with viral load. Our results demonstrate the existence of mechanisms by which SARS-CoV-2 suppress ACE2 expression and function casting doubt on the IFN-induced upregulation of the receptor. Moreover, we show that initial intracellular viral sensing and subsequent ISG induction is also rapidly downregulated. Overall, our results offer new insights into ACE2 dynamics and inflammatory response in the human upper respiratory tract that may contribute to understand the early antiviral host response to SARS-CoV-2 infection.

immunology↗

bioRxiv2018

Proof of concept: Malaria rapid diagnostic tests and massively parallel sequencing for surveillance of molecular markers of antimalarial resistance in Bissau, Guinea-Bissau during 2014-2017

Real-time and large-scale surveillance of molecular markers of antimalarial drug resistance is a potential method of resistance monitoring, to complement therapeutic efficacy studies in settings where the latter are logistically challenging. This study investigates whether routinely used malaria rapid diagnostic tests (RDTs) can be used for massive parallel amplicon sequencing. RDTs used for malaria diagnosis were routinely collected together with patient age and sex between 2014 and 2017, from two health centres in Bissau, Guinea-Bissau. A subset of positive RDTs (n=2,184) were tested for Plasmodium DNA content. Those containing sufficient Plasmodium DNA (n=1,390) were used for library preparation, consisting of amplification of gene fragments from pfcrt, pfmdr1, pfdhfr, pfdhps and pfK13. A total of 5532 gene fragments were successfully analysed on a single Illumina Miseq flow cell. Pre-screening of samples for Plasmodium DNA content proved necessary and the nested PCR protocol applied for library preparation varied notably in PCR-positivity from 13-87%. We found a high frequency of the pfmdr1 codon 86N at 88%-97%, a significant decrease of the pfcrt wildtype CVMNK haplotype and elevated levels of the pfdhfr/pfdhps quadruple mutant ranging from 33%-51% between 2014-2017. No polymorphisms indicating artemisinin tolerance were discovered. Lastly, the demographic data indicate a large proportion of young adults (66%, interquartile range 11-28 years) presenting with P. falciparum infections. With some caution, our findings suggest that routine collection of RDTs could facilitate large-scale molecular surveillance of antimalarial resistance.\n\nImportance (word count: 147)Continuous spread and repeated emergence of Plasmodium falciparum parasites resistant towards one or more antimalarials represents an enormous threat to current treatment efficacy levels, especially in sub-Saharan Africa, where 90% of malaria infections occur. In order to prevent substantial treatment failure, it is therefore recommended to monitor treatment efficacy every 2-3 years. Therapeutic efficacy studies, however, can present insurmountable logistical and financial challenges in some settings in sub-Saharan Africa. Molecular surveillance of antimalarial resistance is therefore an important proxy for treatment efficacy. However, the scale by which such studies can be performed depends on the development of high-throughput protocols and the accessibility of samples. If RDTs can be used in the high-throughput protocols available with Next Generation Sequencing (NGS)-technology, surveillance can be performed efficiently for any setting in which RDTs are already used for malaria diagnosis. The majority of settings in sub-Saharan Africa have access to RDTs.

molecular biology↗

bioRxiv2018

Host genetic associations with the gut microbiota in HIV-1-infected subjects: a pilot exploratory study

The impact of host genetics on gut microbial dynamics is debated. No study to date has investigated the possible role of host genetics in shaping the gut microbiota in HIV-1 infected subjects. With the aim of generating preliminary data to inform future host genetic studies, we performed an exploratory host exome analysis of 147 subjects either infected or at risk of becoming infected with HIV-1 from the MetaHIV cohort in Barcelona. Using a DNA microarray chip, we sought to identify host genetic variants associated to three specific microbial features with a potentially inheritable component, and which were previously found to be associated with gut dysbiosis in HIV infection, i.e.: gut enterotype, presence of methanogenic archaea and microbial gene richness. After correction for multiple comparisons, we did not observe any statistically significant association between the hosts genetic landscape and the explored gut microbiome traits. These findings will help design future, adequately-powered studies to assess the influence of host genetics in the microbiome of HIV-1-infected subjects.

genomics↗