Biology subjects

Ramos, Y.

Publications and source records attributed to Ramos, Y..

13 recordsLinked to original sources

bioRxiv2026

Spatial transcriptomics defines the mechanisms of hiPSC derived stem cell mediated repair in human articular cartilage

We here determined therapeutic efficacy and mode-of-action of human induced pluripotent-derived therapeutic stem cells (hiMSCs) across in vivo mouse and ex vivo human osteoarthritis models. hiMSC treatment in DMM-mice significantly reduced OARSI damage scores, which was affirmed by a decrease in the catabolic marker Mmp13 and an increase in the anabolic marker Col2. These treatment effects appeared, irrespective of modifying factors such as xeno-free media or thermosensitive hydrogel carrier. Subsequently treatment of hiMSC+gel in human osteoarthritic cartilage explants showed a transcriptome-wide significant activation of the cholesterol and sterol synthesis pathways marked by genes such as MVD, DHCR7, MSMO1, FABP3. Additionally, we showed that these changes alleviated OA-associated imbalances of the cellular Zinc-ion homeostasis pathways, represented by genes such as MT1F, MT1G, MT1H and SLC30A1. Spatial transcriptomics then sensitively captured that hiMSC+gel treatment evoked, specifically at the superficial cartilage layer, a consistent upregulation of healthy chondrocyte markers such as CHAD, ACAN, FRZB, and SOX9, alongside a suppression of catabolic and inflammatory mediators such as SERPINE1, SPP1, MMP13, ADAMTS5. Our findings link therapeutic outcomes of hiMSC treatment to precise spatially resolved molecular changes in human tissue, that would otherwise be obscured by heterogeneous cell populations. Collectively our study highlighted that hiPSC-derived stem cell therapy (hiMSCs) could provide a scalable off-the-shelf solution to treat osteoarthritis, with strong prospects for clinical applications in the near future.

developmental biology↗

bioRxiv2026

Dynamic suspension culture enhances scalable maturation of hiPSC-derived cartilage organoids for regenerative medicine

BackgroundCartilage tissue engineering requires scalable culture strategies to produce high-quality organoids. Human induced pluripotent stem cells (hiPSCs) provide a renewable source of chondrogenic cells. However, conventional static 3D culture limits tissue maturation, reproducibility, and scalability. Dynamic culture systems may help overcome these limitations, although their application for hiPSC-derived cartilage maturation remains poorly explored. MethodsIn this study, we established and validated a dynamic suspension bioreactor culture platform (CERO, OLS) for scalable maturation of hiPSC-derived chondroprogenitor cells (hiCPCs) into cartilage organoids populated by biomimetic human induced chondrocytes (hiCHOs). Key culture parameters, including aggregate preparation strategy, agitation speed, and maturation duration, were systematically evaluated. Cartilage maturation under dynamic and conventional static culture conditions was assessed by histology and immunohistochemistry, biochemical assays, organoid size measurements, and gene expression (RT-qPCR). In addition, the functional integration of optimized organoids was evaluated in a human osteochondral explant model. ResultsPre-formed manually picked hiCPC aggregates showed improved cartilage formation compared with single-cell seeding or pelleted aggregates in the bioreactor. Dynamic suspension culture promoted increased construct growth, enhanced ECM deposition, and a more favourable cartilage-associated molecular phenotype compared with static culture. HiCHO organoids matured under dynamic suspension conditions displayed increased sulphated glycosaminoglycan and proteoglycan deposition together with higher expression of cartilage-associated genes ACAN, COMP, MGP, and COL2A1. Although prolonged static maturation alone supported continued cartilage development, introducing dynamic suspension culture during later maturation stages further reinforced favourable molecular and matrix-associated features. Importantly, hiCHO organoids generated under optimized dynamic culture conditions successfully filled human cartilage defects and established matrix continuity with surrounding native tissue in a human osteochondral ex vivo explant model. ConclusionsThis study shows that dynamic suspension culture is an effective and scalable strategy for maturation of hiPSC-derived cartilage organoids. Consequently, this approach supports reproducible neo-cartilage production and allows functional testing in human tissue models. These findings support the use of dynamic culture systems for cartilage repair and in vitro/ex vivo cartilage research.

Cell Biology↗

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

Nuclear Factor I genes drive chondrogenic cell-fate commitment

Human induced pluripotent stem cells (hiPSCs) offer a powerful platform to model chondrogenesis and enable regenerative strategies, yet regulation of cell-fate commitment remains elusive. Here, we systematically mapped cell-fate trajectories from 7 time points during a 49-day chondrogenic hiPSC differentiation protocol using single-nucleus multimodal transcriptomic and chromatin accessibility profiling (scRNA-seq and scATAC-seq). Integrative analysis of dynamics revealed branching differentiation trajectories with clear bifurcation points and distinct cell-fates. Notably, the chondrogenic trajectory originated at day 6 as a neurogenic development and branched off at day 21 to a chondrogenic cell-fate. Through transcription factor activity analysis (TFAA) and cis-co-accessibility networks, we found that NFIA and NFIB drove chondrogenic distinction, exhibited in both modalities as directly targeting chondrogenic genes such as COMP, FIBIN, VIM. This was then confirmed by experimental validation as modulation of NFIA expression at this point further enhanced chondrocyte formation. Together, our study provides a high-resolution multimodal atlas of chondrogenic differentiation and identified critical transcriptional regulators that can now be leveraged to implement regenerative cartilage therapies from hiPSCs.

cell biology↗

bioRxiv2024

Structural and Functional Glycosylation of the Abdala COVID-19 Vaccine

Abdala is a COVID-19 vaccine produced in Pichia pastoris and is based on the receptor-binding domain (RBD) of the SARS-CoV-2 spike. Abdala is currently approved for use in multiple countries with clinical trials confirming its safety and efficacy in preventing severe illness and death. Although P. pastoris is used as an expression system for protein-based vaccines, yeast glycosylation remains largely uncharacterised across immunogens. Here, we characterise N-glycan structures and their site of attachment on Abdala and show how yeast-specific glycosylation decreases binding to the ACE2 receptor and a receptor-binding motif (RBM) targeting antibody compared to the equivalent mammalian-derived RBD. Reduced receptor and antibody binding is attributed to changes in conformational dynamics resulting from N-glycosylation. These data highlight the critical importance of glycosylation in vaccine design and demonstrate how individual glycans can influence host interactions and immune recognition via protein structural dynamics.

biochemistry↗

bioRxiv2022

Proteomics and phosphoproteomics profiling of the co-formulation of type I and II interferons, HeberFERON, in the glioblastoma-derived cell line U-87 MG

HeberFERON is a co-formulation of Interferon (IFN)-2b and IFN-{gamma} in synergic proportions, with a demonstrated effect on skin cancer and other solid tumors. It has antiproliferative effects over glioblastoma multiform (GBM) clones and cell lines in culture, including U-87 MG. Omics studies in U-87 MG showed distinctive expression patterns compared to individual IFNs. Kinase signaling pathways dysregulation can also contribute to HeberFERON effects. Here, we report the first label-free quantitative proteomic and phosphoproteomic analyses to evaluate changes induced by HeberFERON after 72h incubation of U-87 MG cell line. LC-MS/MS analysis identified 7627 proteins with a fold change >2 (p<0.05); 122 and 211 were down- and up-regulated by HeberFERON, respectively. We identified 23549 peptides (5692 proteins) and 8900 phosphopeptides, 412 of these phosphopeptides (359 proteins) were differentially modified with fold change >2 (p<0.05). Proteomic enrichment analysis showed IFN signaling and its control, together to direct and indirect antiviral mechanisms were the main modulated processes. Enrichment analysis of phosphoproteome pointed to the cell cycle, cytoskeleton organization, translation and RNA splicing, autophagy, and DNA repair as biological processes represented. There is a high interconnection of phosphoproteins in a molecular network, where mTOR occupies a centric hub. HeberFERON regulates many phosphosites newly reported or with no clear association to kinases. Of interest is phosphosites increasing phosphorylation were mainly modified by CDK and ERK kinases, thus new cascades regulations can be determining the antiproliferation outcome. Our results contribute to a better mechanistic understanding of HeberFERON in the context of GBM. Significance of the StudyHeberFERON is a co-formulation of IFN-2b and -{gamma} in synergic proportion, registered for skin basal cell carcinoma treatment, also demonstrating clinical effect over solid tumors, including GBM. GBM is a very lethal tumor, protected by the blood-brain barrier (BBB), highly mutated in proliferative signaling pathways with little treatment success. Interferons have been widely used in cancer; they pass BBB and act at JAK/STAT, PI3K/AKT/mTOR, and MAPKs cascades. We observed antiproliferative effects over GBM clones and cell lines in culture. U-87 MG is used as a model to understand the HeberFERON mechanism of action in GBM. We completed the first proteomic and label-free quantitative phosphoproteomic analysis after incubation of U-87 MG cell line with HeberFERON for 72h. The main contribution of this article is the description of phosphosites regulated in proteins participating in cell cycle, cytoskeleton organization, translation, autophagy, and DNA repair in a highly interconnected molecular network, where mTOR occupies a centric hub. Together with reported phosphosites, we described new ones and others with no associated kinases. Increased phosphorylation is mainly accounted by CDK and ERK kinases pointing to possibly new cascades regulations. This knowledge will contribute to the functional understanding of HeberFERON in GBM joined to general regulatory mechanisms in cancer cells.

cancer biology↗

bioRxiv2021

Targeting of Protein Kinase CK2 Elicits Antiviral Activity on Bovine Coronavirus Infection

Coronaviruses constitute a global threat to human population since three highly pathogenic coronaviruses (SARS-CoV, MERS-CoV and SARS-CoV-2) have crossed species to cause severe human respiratory disease. Considering the worldwide emergency status due to the current COVID-19 pandemic, effective pan-coronavirus antiviral drugs are required to tackle the ongoing as well as future (re)emerging virus outbreaks. Protein kinase CK2 has been deemed a promising therapeutic target in COVID-19 supported by its in vitro pharmacologic inhibition and molecular studies on SARS-CoV-2 infected cells. CIGB-325 is a first-in-class synthetic peptide impairing the CK2-mediated signaling whose safety and clinical benefit have been evidenced in Covid-19 and cancer patients after intravenous administration. Here, we explored the putative antiviral effect of CIGB-325 over MDBK cells infected by bovine coronavirus (BCoV) Mebus. Importantly, CIGB-325 inhibited both the cytopathic effect and the number of plaques forming units with a half-inhibitory concentrations IC50 = 3.5 M and 17.7 M, respectively. Accordingly, viral protein accumulation at the cytoplasm was clearly reduced by treating BCoV-infected cells with CIGB-325 over time, as determined by immunocytochemistry. Of note, data from pull-down assay followed by western blot and/or mass spectrometry identification revealed physical interaction of CIGB-325 with nucleocapsid (N) protein and a bona fide cellular CK2 substrates. Functional enrichment and network analysis from the CIGB-325 interacting proteins indicated cytoskeleton reorganization and protein folding as the most represented biological processes disturbed by this anti-CK2 peptide. Altogether, our findings not only unveil the direct antiviral activity of CIGB-325 on coronavirus infection but also provide molecular clues underlying such effect. Also, our data reinforce the scientific rationality behind the pharmacologic inhibition of CK2 to treat coronavirus infections.

pharmacology and toxicology↗

bioRxiv2021

Targeting of Protein Kinase CK2 in Acute Myeloid Leukemia Cells Using the Clinical-Grade Synthetic-Peptide CIGB-300

Protein kinase CK2 has emerged as an attractive therapeutic target in acute myeloid leukemia (AML), advent that becomes particularly relevant since the treatment of this hematological neoplasia remains challenging. Here we explored for the first time the effect of the clinical-grade peptide-based CK2 inhibitor CIGB-300 on AML cells proliferation and viability. CIGB-300 internalization and subcellular distribution were also studied, and the role of B23/nucleophosmin 1 (NPM1), a major target for the peptide in solid tumors, was addressed by knock-down in model cell lines. Finally, pull-down experiments and phosphoproteomic analysis were performed to study CIGB-interacting proteins and identify the array of CK2 substrates differentially modulated after treatment with the peptide. Importantly, CIGB-300 elicited a potent anti-proliferative and proapoptotic effect in AML cells, with more than 80% of peptide transduced cells within three minutes. Unlike solid tumor cells, NPM1 did not appear to be a major target for CIGB-300 in AML cells. However, in vivo pull-down experiments and phosphoproteomic analysis evidenced that CIGB-300 targeted the CK2 catalytic subunit, different ribosomal proteins, and inhibited the phosphorylation of a common CK2 substrates array among both AML backgrounds. Remarkably, our results not only provide cellular and molecular insights unveiling the complexity of the CIGB-300 anti-leukemic effect in AML cells, but also reinforce the rationale behind the pharmacologic blockade of protein kinase CK2 for AML targeted therapy.

cancer biology↗

bioRxiv2021

In-solution buffer-free digestion for the analysis of SARS-CoV-2 RBD proteins allows a full sequence coverage and detection of post-translational modifications in a single ESI-MS spectrum

Subunit vaccines based on the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2, are among the most promising strategies to fight the COVID-19 pandemic. The detailed characterization of the protein primary structure by mass spectrometry (MS) is mandatory, as described in ICHQ6B guidelines. In this work, several recombinant RBD proteins produced in five expression systems were characterized using a non-conventional protocol known as in-solution buffer-free digestion (BFD). In a single ESI-MS spectrum, BFD allowed very high sequence coverage ([≥] 99 %) and the detection of highly hydrophilic regions, including very short and hydrophilic peptides (2-8 amino acids), the His6-tagged C-terminal peptide carrying several post-translational modifications at Cys538 such as cysteinylation, glutathionylation, cyanilation, among others. The analysis using the conventional digestion protocol allowed lower sequence coverage (80-90 %) and did not detect peptides carrying some of the above-mentioned post-translational modifications. The two C-terminal peptides of a dimer [RBD(319-541)-(His)6]2 linked by an intermolecular disulfide bond (Cys538-Cys538) with twelve histidine residues were only detected by BFD. This protocol allows the detection of the four disulfide bonds present in the native RBD and the low-abundance scrambling variants, free cysteine residues, O-glycoforms and incomplete processing of the N-terminal end, if present. Artifacts that might be generated by the in-solution BFD protocol were also characterized. BFD can be easily implemented and we foresee that it can be also helpful to the characterization of mutated RBD.

biochemistry↗

bioRxiv2021

Gel Electrophoresis/Electroelution Sorting Fractionator combined with Filter Aided Sample preparation (FASP) for deep proteomic analysis.

Sample preparation and protein fractionation are important issues in proteomic studies in spite of the technological achievements on protein mass spectrometry. Protein extraction procedures strongly affect the performance of fractionation methods by provoking protein dispersion in several fractions. The most notable exception is SDS-PAGE-based protein fractionation due to its extraordinary resolution and the effectiveness of SDS as a solubilizing agent. Its main limitation lies in the poor recovery of the gel-trapped proteins, where protein electro-elution is the most successful approach to overcome this drawback. We created a device to separate complex mixture of proteins and peptides (named "GEES fractionator") that is based on the continuous Gel Electrophoresis/Electro-elution Sorting of these molecules. In an unsupervised process, complex mixtures of proteins or peptides are fractionated into the gel while separated fractions are simultaneously and sequentially electro-eluted to the solution containing wells. The performance of the device was studied for SDS-PAGE-based protein fractionation in terms of reproducibility, protein recovery and loading capacity. In the SDS-free PAGE setup, complex peptide mixtures can also be fractionated. More than 11 700 proteins were identified in the whole-cell lysate of the CaSki cell line by using the GEES fractionator combined with the Filter Aided Sample Preparation (FASP) method and mass spectrometry analysis. GEES-based proteome characterization shows a 1.7 fold increase in the number of identified proteins compared to the unfractionated sample analysis. Proteins involved in the co-regulated transcription activity, as well as cancer related pathways such as apoptosis signaling, P53 and RAS pathways are more represented in the protein identification output of GEES-based fractionation approaches.

bioengineering↗

bioRxiv2021

SARS-CoV-2 RBD-Tetanus toxoid conjugate vaccine induces a strong neutralizing immunity in preclinical studies

Controlling the global COVID-19 pandemic depends, among other measures, on developing preventive vaccines at an unprecedented pace. Vaccines approved for use and those in development intend to use neutralizing antibodies to block viral sites binding to the hosts cellular receptors. Virus infection is mediated by the spike glycoprotein trimer on the virion surface via its receptor binding domain (RBD). Antibody response to this domain is an important outcome of the immunization and correlates well with viral neutralization. Here we show that macromolecular constructs with recombinant RBD conjugated to tetanus toxoid induce a potent immune response in laboratory animals. Some advantages of the immunization with the viral antigen coupled to tetanus toxoid have become evident such as predominant IgG immune response due to affinity maturation and long-term specific B-memory cells. This paper demonstrates that subunit conjugate vaccines can be an alternative for COVID-19, paving the way for other viral conjugate vaccines based on the use of small viral proteins involved in the infection process.

immunology↗

bioRxiv2021

Phosphoproteomic Landscape of AML Cells Treated with the ATP-Competitive CK2 Inhibitor CX-4945

Casein kinase 2 (CK2) regulates a plethora of proteins with pivotal roles in solid and hematological neoplasia. Particularly, in acute myeloid leukemia (AML) CK2 has been pointed as an attractive therapeutic target and prognostic marker. Here, we explored the impact of CK2 inhibition over the phosphoproteome of two cell lines representing major AML subtypes. Quantitative phosphoproteomic analysis was conducted to evaluate changes in phosphorylation levels after incubation with the ATP-competitive CK2 inhibitor CX-4945. Functional enrichment, network analysis, and database mining were performed to identify biological processes, signaling pathways, and CK2 substrates that are responsive to CX-4945. A total of 273 and 1310 phosphopeptides were found differentially modulated in HL-60 and OCI-AML3 cells, respectively. Despite regulated phosphopeptides belong to proteins involved in multiple biological processes and signaling pathways, most of these perturbations can be explain by direct CK2 inhibition rather than off-target effects. Furthermore, CK2 substrates regulated by CX-4945 are mainly related to mRNA processing, translation, DNA repair, and cell cycle. Overall, we evidenced that CK2 inhibitor CX-4945 impinge on mediators of signaling pathways and biological processes essential for primary AML cells survival and chemosensitivity, reinforcing the rationale behind the pharmacologic blockade of protein kinase CK2 for AML targeted therapy.

cancer biology↗

bioRxiv2020

The low-density lipoprotein receptor-related protein-1 is essential for Dengue virus infection

Dengue virus (DENV) causes the most prevalent and rapidly spreading arboviral disease of humans. It enters human cells by receptor-mediated endocytosis. Numerous cell surface proteins have been proposed as DENV entry factors. Among these, the phosphatidylserine receptor TIM-1 is the only one known to mediate virus internalization. However, several cellular models lacking TIM-1 are permissive to DENV infection, suggesting that other receptors exist. Here we show that the Low-density lipoprotein receptor-related protein-1 (LRP1) binds DENV virions by interacting with the DIII of the viral envelope glycoprotein. DENV infection is effectively inhibited by the purified receptor at 5x10-8 mol/L and the interaction of the envelope protein with LRP1 is also blocked by a natural ligand of LRP1. Depletion of LRP1 causes 100-fold lower production of infectious virus than controls. Our results indicate that LRP1 is another DENV receptor thus, becoming an attractive target to evaluate for the development of effective antiviral drugs against DENV. Author summaryDengue virus (DENV) is a complex of four related viruses, recognized as serotypes, designated as DENV1-4. Any of the four DENV serotypes can cause a self-limited disease of mild flu-like symptoms known as dengue or its life threatening form, severe dengue, with hemorrhagic manifestations, organ impairment and shock. This disease is widely spread in tropical and sub-tropical areas worldwide, where the incidence of severe dengue has been increasing steadily. So far, efforts that target components of the viral replication machinery in order to develop a specific antiviral drug for dengue disease patients have failed. Thus, identifying the cell surface receptors used by DENV to enter host cells would provide a new molecular target to develop inhibitory drugs. Here, we evaluate the Low density lipoprotein receptor-related protein-1 (LRP1) as a putative DENV receptor. We present evidence demonstrating that LRP1 binds DENV through the viral envelope protein. We show that the production of infective virus is impaired on cells lacking LRP1, and that purified LRP1 is a potent blocker of DENV infection. These results are consistent with LRP1 playing an important role on DENV entry, making this receptor a molecule of interest on the investigation for medical treatments of dengue/severe dengue disease.

biochemistry↗