Biology subjects

Miranda, J.

Publications and source records attributed to Miranda, J..

8 recordsLinked to original sources

bioRxiv2026

Integrated Analysis of HeberFERON-Driven Comparative Proteomic regulation in Glioblastoma Cells U-87MG

Glioblastoma is a very aggressive brain tumor with few therapeutics options. Type I and II Interferons (IFNs) co-formulation HeberFERON has been used in cancer treatment, with promising results in high grade brain tumors. High throughput techniques in easy-to-handle models have been important to interrogate biomolecules changes, describe mechanisms and find pharmacodynamic biomarkers. This study aims to elucidate the effect of HeberFERON over the cell proteome in comparison to its individual IFNs components. Proteomic changes with HeberFERON in the glioblastoma-derived cell line U-87MG, in comparison with individual IFN-2b and IFN-{gamma}, were studied using a nanoLC instrument EasyLC coupled to Velos Pro mass spectrometer; Maxquant and Perseus were also used. Several enrichment tools, networking analysis and canSAR for drug targets were employed. Translation, RNA processing, mitotic cell cycle, cytoskeleton and chromosome organization, apoptosis, autophagy, DNA repair are enriched to limit cellular growing together with changes in immune response components, supporting HeberFERON as a multitarget treatment. This co-formulation is distinguished at modulating RNA splicing with SMN complex, cytoskeleton organization and microtubule-based movement, nuclear envelope breakdown, DNA conformational changes, and oxidative phosphorylation, with a better drawing of effects over a variety of systems inside the tumoral cell. Together with previous microarray experiment, informative genes and proteins as pharmacodynamic biomarkers for antiproliferative effects showed up (ex. STAT1/2, CENPE, ATRIP, MAP1B, LIMA1, VCP, several ribosomal, spliceosome and proteasomal complexes proteins). This study complements transcriptomic and phosphoproteomic previous experiments in this model and underscore HeberFERON as a glioblastoma therapeutic.

cancer biology↗

bioRxiv2026

TMEM174 Deficiency Reduces Longevity by Promoting Phosphate-Driven Vascular Calcification

BackgroundDysregulation of phosphate homeostasis contributes to reduced longevity and vascular complications in chronic kidney disease and aging. This study investigates the role of TMEM174, a proximal tubule-specific protein, in regulating the phosphate co-transporter NPT2A and its subsequent impact on lifespan and vascular health. MethodsTMEM174 knockout (KO) mice (C57BL6/J and DBA/2J) were fed diets with varying phosphate concentrations (0.6% vs. 1.2%). In OKP cells, TIRF and FRET microscopy, alongside immunoprecipitation, were used to identify the TMEM174 protein regions essential for NPT2A binding and endocytosis. ResultsTMEM174 KO mice exhibited significantly shorter lifespans than wild-type controls. High phosphate diets exacerbated vascular calcification, stiffness, and mortality, while low phosphate diets rescued these phenotypes. In vitro, TMEM174 siRNA blocked PTH-induced NPT2A endocytosis, increasing its apical membrane retention. FRET and biochemical assays revealed that the C-terminal region of TMEM174 is essential for its association with NPT2A. While intact TMEM174 and N-terminal mutants (TMEM174{Delta}N) facilitated NPT2A degradation, C-terminal deletions (TMEM174{Delta}C) failed to associate with or degrade NPT2A. ConclusionsTMEM174 is a critical regulator of phosphate homeostasis and longevity. The C-terminal region of TMEM174 is specifically required for NPT2A endocytosis and degradation, identifying it as a potential therapeutic target for managing phosphate-related vascular complications.

physiology↗

bioRxiv2026

The Protein Tyrosine Phosphatase CD45 promotes PMN Transepithelial Migration, Antimicrobial Function and Colonic Mucosal Repair

Polymorphonuclear neutrophils (PMNs) serve as frontline defenders against injury and infection, eliminating pathogens and initiating mucosal tissue repair. However, excessive PMN transepithelial migration (TEpM) contributes to chronic mucosal inflammatory disorders, including inflammatory bowel disease. PMN pro-inflammatory and pro-repair functions are regulated by incompletely defined signaling cascades involving kinases and phosphatases. Here, we determined how the protein tyrosine phosphatase CD45/PTPRC regulates PMN trafficking and effector functions in the gut. Pharmacologic inhibition of CD45 significantly reduced PMN colonic TEpM in vitro and in vivo and decreased intestinal PMN trafficking was observed in transgenic mice with PMN-specific deletion of CD45 (MRP8-Cre;Cd45fl/fl). Beyond limiting TEpM, CD45 depletion impaired key antimicrobial functions, including degranulation and phagocytosis, indicating broader effects on PMN effector activity. Importantly, recovery from dextran sodium sulfate (DSS)-induced colitis and biopsy-induced colonic wounding was delayed in MRP8-Cre;Cd45fl/fl mice, linking altered PMN function to defective mucosal healing. Mechanistically, CD45 depletion reduced surface expression of the {beta}2 integrin CD11b/CD18 and inactivated the Src family kinase member Lyn. Together, data highlight a novel CD45-CD11b-Lyn signaling axis that regulates PMN trafficking and effector functions in the intestine and identify CD45 as a promising target for modulating PMN function to promote mucosal tissue repair.

immunology↗

bioRxiv2025

RUNX2 promotes epigenetic WNT signaling in inflamed intestinal epithelial cells

Ulcerative colitis (UC) is characterized by chronic mucosal inflammation, recurrent epithelial injury, and impaired colonic mucosal wound healing. While WNT/{beta}-catenin dysregulation has been reported in UC, the mechanisms of such abnormalities remain unclear. To investigate epithelial intrinsic alterations associated with UC, we performed single-nucleus RNA-seq (snRNA-seq) and ATAC-seq (snATAC-seq) multiomics on human primary colonic epithelial cells (colonoids) from healthy donors and patients with inactive or active UC. Colonoids were cultured in a 3D matrix recapitulating crypt base cells or grown as 2D monolayers in differentiation medium to recapitulate luminal epithelial cells. Colonoids from active UC had a unique cell population with elevated CTNNB1 and reduced APC expression. Chromatin profiling identified enrichment of RUNX2 motifs in this UC-associated cell population. Active UC colonoids exhibited reduced OLFM4 expression in 3D and the differentiation marker VIL1 in 2D, suggesting impaired self-renewal and maturation. RUNX2 inhibition using CADD522 reduced {beta}-catenin levels in 3D colonoids and restored VIL1 expression and junctional {beta}-catenin localization in 2D cultures. These findings reveal an intrinsic defect in epithelial renewal in UC, driven in part by RUNX2-dependent WNT dysregulation. Our study identifies RUNX2 as a transcriptional regulator of epithelial stem cell function and WNT signaling in the inflamed human colon. Graphical Abstract summarySingle-nucleus RNA and ATAC sequencing of UC patient-derived colonoids reveals a RUNX2-associated WNT signature in active inflammation. Elevated {beta}-catenin and reduced OLFM4 and VIL1 expression indicate impaired self-renewal and differentiation. Pharmacologic inhibition of RUNX2 restores epithelial maturation, identifying RUNX2 as a key regulator of epithelial dysfunction in UC. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/688458v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@14c0093org.highwire.dtl.DTLVardef@b9b6a3org.highwire.dtl.DTLVardef@858ee2org.highwire.dtl.DTLVardef@67b98c_HPS_FORMAT_FIGEXP M_FIG C_FIG

pathology↗

bioRxiv2025

Cost of altered translation accuracy shapes adaptation to antibiotics in E. coli

Protein synthesis, while central to cellular function, is error-prone. The resulting mistranslation is generally costly, but we do not know how these costs compare or interact with the costs imposed by external selection pressures such as antibiotics. We also do not know whether and how these costs are compensated during evolution. It is important to answer these questions, since mistranslation is ubiquitous and antibiotic exposure, widespread. We quantified the growth cost of genetically increasing and decreasing mistranslation rates, and exposure to low antibiotic concentrations, in Escherichia coli. Mistranslation costs were generally lower than the cost imposed by antibiotics, and exacerbated in a strain-specific manner under antibiotic exposure. All strains quickly compensated the antibiotic cost during experimental evolution, via antibiotic- and genotype-specific mutations. In contrast, mistranslation costs were significantly reduced only in some cases, without clear causal mutations. Control populations that evolved without antibiotics consistently compensated the cost of accuracy, and evolved increased antibiotic resistance as a by-product. Our work demonstrates that even when the cost of mistranslation is weak, altered translation accuracy can shape adaptive outcomes and underlying genetic mechanisms, with strong collateral fitness effects for apparently unrelated phenotypes such as antibiotic resistance.

evolutionary biology↗

bioRxiv2024

Local control of cellular proliferation underlies neuromast regeneration in zebrafish

Biological systems are never in equilibrium but maintain stability despite continuous external disturbances. A prime example of this is organ regeneration, where, despite intrinsically stochastic damage, organs are rebuilt through controlled cellular proliferation. In this study, we employ a cell- based computational modelling approach to investigate the proliferative response to injury. We developed a minimal two-dimensional Cellular Potts Model (CPM) using empirical data from regenerating neuromasts in larval zebrafish. Remarkably, the CPM both qualitatively and quantitatively recapitulates the regenerative response of neuromasts following laser-mediated cell ablation. Assuming that cell proliferation is locally regulated by a delayed switch, mitotic activity ceases once the type-dependent number of neighbouring cells exceeds a deterministic critical threshold. An intriguing corollary of our findings is that a local negative feedback loop among identical cells may represent a general mechanism underlying organ-level proportional homeostasis.

developmental biology↗

bioRxiv2022

HeberFERON distinctively targets Cell Cycle in the glioblastoma-derived cell line U-87MG.

BackgroundHeberFERON is a co-formulation of 2b and {gamma} interferons, based on their synergism, that have shown its clinical superiority over individual interferons in basal cell carcinomas. In Glioblastoma (GBM), HeberFERON has shown promising preclinical and clinical results. This motivated us to design a microarray experiment aimed to identify the molecular mechanisms involved into the distinctive effect of HeberFERON compared with individual interferons. MethodsTranscriptional expression profiling including a control (untreated) and three groups receiving 2b-interferon, {gamma}-interferon and HeberFERON was performed using an Illumina HT-12 microarray platform. Unsupervised methods for gene and sample grouping, identification of differentially expressed genes, functional enrichment and network analysis computational biology methods were applied to identify distinctive patterns of HeberFERON action. Validation of most distinctive genes was performed by qPCR. Cell Cycle analysis of cell treated by HeberFERON for 24h, 48h and 72h was carried out by flow cytometry. ResultsThe three treatments show different behavior based on the gene expression profiles. Enrichment analysis identified several Mitotic Cell Cycle related events, in particular from Prometaphase to Anaphase, that are exclusively targeted by HeberFERON. FOXM1 transcription factor network which is involved in several Cell Cycle phases and is highly expressed in GBMs is significantly down regulated by HeberFERON. Flow cytometry experiments corroborated the action of HeberFERON over Cell Cycle in a dose and time dependent manner with a clear cellular arrest since 24h post-treatment. Despite the fact that p53 was not down-regulated by HeberFERON several genes involved in its regulatory activity were functionally enriched. Network analysis also revealed a strong relation of p53 with genes targeted by HeberFERON. We propose a mechanistic model to explain HeberFERON distinctive action, based on the simultaneous activation of PKR and ATF3, p53 phosphorylation changes as well as its reduced MDM2 mediated ubiquitination and export from nucleus to cytoplasm. PLK1, AURKB, BIRC5 and CCNB1 genes, all regulated by FOXM1, also play central roles in this model. These and other interactions could explain a G2/M arrest and the effect of HeberFERON over the proliferation of U-87MG. ConclusionsWe proposed molecular mechanisms underlying the distinctive behavior of HeberFERON compared to individual interferon treatments, where Cell Cycle related events showed the highest relevance.

cancer biology↗

bioRxiv2021

CIGB-300 synthetic peptide, an antagonist of CK2 kinase activity, as a treatment for Covid-19. A computational biology approach

Drug repositioning became the first choice for treating Covid-19 patients due to the urgent need to deal with the pandemic. Similarities in the hijacking mechanisms used by SARS-CoV-2 and several type of cancer, suggest the repurposing of cancer drugs to treat Covid-19. CK2 kinase antagonists have been proposed for the treatment of cancer. A recent study in cells infected with SARS-CoV-2 virus found a significant CK2 kinase activity, and the use of a CK2 inhibitor showed antiviral responses. CIGB-300, originally designed as an anticancer peptide, is an antagonist of CK2 kinase activity that binds to CK2 phospho-acceptor sites. Recent preliminary results show an antiviral activity of CIGB-300 versus a surrogate model of coronavirus. Here we present a computational biology study that provides evidences at the molecular level of how CIGB-300 might interfere with SARS-CoV-2 life cycle inside infected human cells. First, from SARS-CoV studies, we infer the potential incidence of CIGB-300 in SARS-CoV-2 interference on immune response. Next, from the analysis of multiple Omics data, we propose the action of CIGB-300 since early stage of viral infections perturbing the virus hijacking of RNA splicing machinery. It was also predicted the interference of CIGB-300 in virus-host interactions responsible for the high infectivity and the particular immune response to SARS-CoV-2 infection. Further, we provide evidences of CIGB-300 attenuation of phenotypes related to muscle, bleeding, coagulation and respiratory disorders.

bioinformatics↗