Biology subjects

Blanco, C.

Publications and source records attributed to Blanco, C..

11 recordsLinked to original sources

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↗

bioRxiv2025

BUB1B MITOTIC KINASE DRIVES THERAPY RESISTANT PROSTATE CANCER

Castration-resistant prostate cancer (CRPC) that progresses despite treatment with potent AR antagonists such as enzalutamide is a major clinical problem. Through an unbiased systems biology approach, we previously identified a therapeutically relevant seven gene set that drives CRPC. The mitotic checkpoint kinase, BUB1B (BUBR1) is a key member of this gene set, and we report here that BUB1B is a tractable and promising new therapeutic target in aggressive, treatment-resistant PC. We found that high BUB1B expression is correlated with PC progression and aggressiveness. In established CRPC cells, BUB1B depletion blocked cell proliferation through cell cycle arrest and mitosis delay. Ectopic expression of BUB1B, at levels found in CRPC, conferred castration-resistant growth of androgen-dependent PC cells in vitro and in vivo. We showed that BUB1B kinase activity was essential for CRPC progression, as only wild type (wt) BUB1B and neither of two kinase-dead mutants promoted castration-resistant growth of androgen-dependent PC cells. Rescue experiments with wt or kinase-dead mutants showed further that BUB1B kinase activity was also required to maintain proliferation of established CRPC cells. While persistent androgen receptor (AR) signaling is a mechanism of CRPC progression, BUB1B promotion of CRPC was not dependent on AR as assessed through AR knockdown. Consistent with an AR-bypass mechanism, ectopic expression of BUB1B rendered PC cells resistant to enzalutamide in vitro and in vivo. Our data points to BUB1B as a key driver of CRPC progression and enzalutamide resistance and suggests that targeting BUB1B kinase is a promising therapeutic approach for lethal, treatment-resistant disease. Statement of significanceWe document a novel role for BUB1B kinase as a critical driver of castration- and enzalutamide-resistant prostate cancer, highlighting the therapeutic potential of BUB1B kinase inhibition to overcome lethal treatment-resistant disease.

cancer biology↗

bioRxiv2025

Conserved architecture of a functional lncRNA-protein interaction in the DNA damage response pathway

LncRNAs are typically poorly conserved at the sequence level, which complicates the use of sequence-based approaches to identify conserved functions. The stress-associated lincRNA-p21 is a paradigm for a sequence-divergent lncRNA. In mice, the interaction between lincRNA-p21 and the hnRNP K protein activates the Cdkn1a gene in cis, encoding the cell-cycle regulator p21, a key effector of the cellular stress response to DNA damage. However, the molecular details of this interaction, and its conservation in other species, remained unknown. To address this, we applied an integrated structural and functional approach, combining in silico, in vitro, ex cellulo, and in cellulo assays. We identified a structural element in mouse and human lincRNA-p21 containing a tetranucleotide motif conserved across more than 100 mammals. This element directly mediates weak binding to the hnRNP K protein in both species, which may enable rapid and reversible modulation of Cdkn1a and timely resolution of the DNA damage response. Conserved hnRNP K binding in humans suggests that the mechanism of Cdkn1a activation may also occur in this species. Our findings establish a shared RNA-protein contact between two syntenic but sequence-divergent transcripts, offering a general strategy for identifying functional RNA elements in other lncRNAs with limited sequence conservation.

molecular biology↗

bioRxiv2025

Microbial metabolism of food allergens determines the severity of IgE-mediated anaphylaxis

Anaphylaxis is an acute, potentially life-threatening reaction, often triggered by foods and largely mediated by IgE. Critically important to anaphylaxis are the factors that modulate its severity. The human microbiota is known to influence oral tolerance, but the microbial mechanisms directly involved in IgE-mediated anaphylaxis remain unknown. Here, we demonstrate that human saliva and jejunum harbor peanut-degrading bacteria that metabolize immunodominant allergens (Ara h 1 and 2) and alter IgE-binding. Additionally, we provide in vivo evidence that oral bacteria metabolize peanut allergens, influencing systemic allergen exposure and anaphylaxis severity. Finally, in clinical studies, we observe that common peanut-degrading bacteria, such as Rothia, from the oral cavity, are more abundant in peanut-allergic patients who exhibit better tolerance to allergen exposure. Altogether, these results demonstrate that human microbiota modulates IgE-mediated reactions through allergen metabolism. We reveal a novel microbial mechanism with potential to prevent, or reduce, the severity of IgE-mediated anaphylaxis.

immunology↗

bioRxiv2024

Circadian PERIOD proteins sculpt themammalian alternative splicing landscape

Mammalian circadian oscillators are driven by a transcription-translation feedback loop where CLOCK:BMAL1 activity is repressed by the PER:CRY complex. While transcriptional regulation by PER is well established, the role of circadian feedback in co- and post- transcriptional processes remains unclear. Here, we used Nanopore long-read direct RNA sequencing (dRNAseq) and quantitative mass spectrometry (qMS) to uncover a critical function of PERs in alternative splicing (AS) regulation in the liver. Our expanded long-read transcriptome revealed significant changes in rhythmic expression of annotated transcripts, novel isoforms of known genes, and previously unannotated genes, with widespread perturbations in Per1-/-;Per2-/- (PerKO) livers. Rhythmic AS events were restricted to a distinct subset of transcripts, and splicing entropy - a metric of AS complexity - displayed oscillations in only a limited number of pathways, primarily those associated with glucose homeostasis and cellular responses to insulin. In PerKO livers, however, we detected increased isoform complexity and altered splicing entropy across a broad range of pathways linked to cell growth, morphogenesis, ER-associated degradation (ERAD), insulin response and histone methylation. Biochemical analyses and qMS data indicate that these changes are not due to mis-expression of splicing factors, but rather stem from altered nuclear abundance and chromatin retention of a few Serine-Arginine-rich splicing factors (SRSFs). In particular, SRSF3 acts proximal to the core-clock by defining both the period and amplitude of cellular rhythms. Our findings highlight a critical role for PER proteins in shaping the circadian liver proteome by integrating rhythmic transcription with the regulation of a complex and dynamic splicing landscape.

physiology↗

bioRxiv2024

Synergistic DNA and RNA binding of the Hox transcription factor Ultrabithorax coordinates splicing and shapes in vivo homeotic functions

The dual interaction of many transcription factors (TFs) with both DNA and RNA is an underexplored issue that could fundamentally reshape our understanding of gene regulation. We address this central issue by investigating the RNA binding activity of the Drosophila Hox TF Ultrabithorax (Ubx) in alternative splicing and morphogenesis. Relying on molecular and genetic interactions, we uncover a homodimerization-dependent mechanism by which Ubx regulates splicing. Notably, this mechanism enables the decoupling of Ubx-DNA and -RNA binding activity in splicing. We identify a critical residue for Ubx-RNA binding and demonstrate the essential role of Ubx-RNA binding ability for its homeotic functions. Overall, we uncover a unique mechanism for Ubx-mediated splicing and underscore the critical contribution of synergistic DNA/RNA binding for its morphogenetic functions. These findings advance our understanding of co-transcriptional regulation and highlight the significance of TF-DNA/RNA synergistic function in shaping gene regulatory networks in living organisms. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/612310v1_ufig1.gif" ALT="Figure 1"> View larger version (65K): org.highwire.dtl.DTLVardef@6b3f84org.highwire.dtl.DTLVardef@116f353org.highwire.dtl.DTLVardef@1c0ceb4org.highwire.dtl.DTLVardef@142906c_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIUbx homodimerization enables decoupling of DNA- and RNA-dependent splicing regulation C_LIO_LIThe homeodomain K58 amino acid is critical for Ubx-RNA binding ability C_LIO_LIUbx-RNA binding ability is essential for splicing regulation C_LIO_LIDual DNA/RNA binding activities shape Ubx homeotic functions C_LI

molecular biology↗

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↗

bioRxiv2022

Endoglin, a novel biomarker and therapeutical target to prevent malignant peripheral nerve sheath tumor growth and metastasis

PurposeMalignant peripheral nerve sheath tumors (MPNSTs) are highly aggressive softtissue sarcomas that lack effective treatments, underscoring the urgent need to uncover novel mediators of MPNST pathogenesis that may serve as potential therapeutic targets. Tumor angiogenesis is considered a critical event in MPNST transformation and progression. Here, we have investigated whether endoglin (ENG), a TGF-{beta} coreceptor with a crucial role in angiogenesis, could be a novel therapeutic target in MPNSTs. Experimental DesignENG expression was evaluated in human peripheral nerve sheath tumor tissues and plasma samples. Effects of tumor cell-specific ENG expression on gene expression, signaling pathways and in vivo MPNST growth and metastasis were investigated. The efficacy of ENG targeting in monotherapy or in combination with MEK inhibition was analyzed in xenograft models. ResultsENG expression was found to be upregulated in both human MPNST tumor tissues and plasma circulating small extracellular vesicles. We demonstrated that ENG modulates Smad1/5 and MAPK/ERK pathway activation and pro-angiogenic and pro-metastatic gene expression in MPNST cells and plays an active role in tumor growth and metastasis in vivo. Targeting with ENG-neutralizing antibodies (TRC105/M1043) decreased MPNST tumor growth and metastasis in xenograft models by reducing tumor cell proliferation and angiogenesis. Importantly, combination of anti-ENG therapy with MEK inhibition reduced more effectively tumor cell growth and angiogenesis. ConclusionsOur data unveil a tumor-promoting function of ENG in MPNSTs and support the combined use of anti-ENG antibodies and MEK inhibitors as a novel potential combination to control MPNSTs growth and metastasis. Statement of translational relevanceMalignant peripheral nerve sheath tumors (MPNSTs) present a poor clinical outcome due to tumor aggressiveness and the absence of effective treatments that underline the need for identifying novel therapeutic approaches. Here, we show that ENG is upregulated in human MPNSTs and we uncover an important role for this coreceptor in MPNST. ENG-neutralizing antibodies (TRC105/M1043) decreased MPNST tumor growth and metastasis in xenograft models, supporting a novel use of anti-ENG therapies for MPNST treatment. Currently, MEK inhibitors are used in the clinic to shrink peripheral nerve sheath tumors (e.g. plexiform neurofibromas). Importantly, we demonstrate that combination of anti ENG antibodies with MEK inhibitors efficiently blocked MPNST growth and metastasis. Our findings provide a rationale for combining anti-ENG and MEK inhibitors as a new strategy for MPNST management.

cancer biology↗

bioRxiv2021

Error minimization and specificity could emerge in a genetic code as by-products ofprebiotic evolution

The emergence of the genetic code was a major transition in the evolution from a prebiotic RNA world to the earliest modern cells1. A prominent feature of the standard genetic code is error minimization, or the tendency of mutations to be unusually conservative in preserving biophysical features of the amino acid2-6. While error minimization is often assumed to result from natural selection, it has also been speculated that error minimization may be a by-product of emergence of the genetic code3. During establishment of the genetic code in an RNA world, self-aminoacylating ribozymes would enforce the mapping of amino acids to anticodons. Here we show that expansion of the genetic code, through co-option of ribozymes for new substrates, could result in error minimization as an emergent property. Using self-aminoacylating ribozymes previously identified during an exhaustive search of sequence space7, we measured the activity of thousands of candidate ribozymes on alternative substrates (activated analogs for tryptophan, phenylalanine, leucine, isoleucine, valine, and methionine). Related ribozymes exhibited preferences for biophysically similar substrates, indicating that co-option of existing ribozymes to adopt additional amino acids into the genetic code would itself lead to error minimization. Furthermore, ribozyme activity was positively correlated with specificity, indicating that selection for increased activity would also lead to increased specificity. These results demonstrate that by-products of the evolution and functional expansion of a ribozyme system could lead to adaptive properties of a genetic code. Such spandrels could thus underlie significant prebiotic developments.

biochemistry↗

bioRxiv2020

Structural refinement of the auditory brainstem neurons in baboons during perinatal development

Children born prematurely suffer from learning disabilities and exhibit reading, speech, and cognitive difficulties, which are associated with an auditory processing disorder. However, it is unknown whether gestational age at delivery and the unnatural auditory environment in neonatal intensive care units (NICU) collectively affect proper auditory development and neuronal circuitry in premature newborns. We morphologically characterized fetal development of the medial superior olivary nucleus (MSO), an area important for binaural hearing and sound localization, in the auditory brainstem of baboon neonates at different gestational ages. Axonal and synaptic structures and the tonotopic differentiation of ion channels in the MSO underwent profound refinements after hearing onset in the uterus. In preterm baboon neonates, these developmental refinements of the MSO were significantly altered by limited maternal sound inputs from the isolated and unnatural environment in the NICU. Thus, the maternal environment, including auditory stimuli in uterus, is essential for auditory nervous system development during the last trimester of pregnancy and critically affects the anatomic and functional formation of synapses and neural circuitry in the preterm newborn brain.

developmental biology↗

bioRxiv2020

PyEcoLib: a python library for simulating E. coli stochastic size dynamics

Recent studies describe bacterial division as a jump process triggered when it reaches a fixed number of stochastic discrete events at a rate depending on the cell-size. This theoretical approach enabled the computation of stochastic cell-size transient dynamics with arbitrary precision, with the possibility of being coupled to other continuous processes as gene expression. Here we synthesize most of this theory in the tool PyEcoLib, a python-based library to estimate bacterial cell size stochastic dynamics including continuous growth and division events. In this library, we include examples predicting statistical properties seen in experiments.

systems biology↗