Biology subjects

Alvarez, V.

Publications and source records attributed to Alvarez, V..

16 recordsLinked to original sources

bioRxiv2026

Dual Role of Cx43 in Enhancing CDK4/6 Inhibitor Response and Promoting the Elimination of Therapy-Induced Senescent Tumor Cells

Breast cancer has become the most prevalent malignancy worldwide. A key clinical advance has been the introduction of cyclin-dependent kinase 4/6 inhibitors (CDK4/6i), that in combination with endocrine therapy has been a major advance for the treatment of luminal (ER/HER2-) breast cancer. CDK4/6i induce cell cycle arrest in G1 and cellular senescence improving clinical outputs. However, limited efficacy and therapeutic resistance remain major challenges due to incomplete effects or the failure to eliminate the accumulated tumor senescent cells. Here, we identify connexin 43 (Cx43), a membrane channel protein involved in cell-to-cell communication, identified as a novel target in luminal breast cancer that potentiates the effects of CDK4/6 inhibitors. We found that Cx43 not only reduces tumor cell proliferation by enhancing senescence but also reshapes the Senescence-Associated Secretory Phenotype (SASP) profile. We also demonstrate that, in combination with CDK4/6i, Cx43 reinforces G1 arrest via transcriptional downregulation of E2F targets including CDK4 and CDK6, and through interaction with p21/p27, deepens the senescent state. Importantly, the Cx43-associated senescent phenotype sensitizes tumor cells accumulated under CDK4/6i treatment to the senolytic agent Navitoclax. Our results demonstrate that upregulation of Cx43 in breast cancer reduces proliferation and enhances the clearance of therapy-induced senescent cells. The triple-drug strategy comprising CDK4/6i, Cx43 delivery, and a senolytic drug such as Navitoclax holds great promise for overcoming CDK4/6i resistance and improving clinical outcomes in ER/HER2- breast cancer and may also be applicable to other cancer types that respond to CDK4/6i or other pro-senescence antitumoral drugs.

cancer biology↗

bioRxiv2026

Targeting an RNA Editor to Impede H3K27M+ Pediatric Gliomas

Diffuse midline glioma (DMG) is a lethal pediatric brain tumor with no curative therapies. Immune checkpoint blockade (ICB) has shown limited efficacy in DMG, largely due to poor T cell infiltration, low immune checkpoint (IC) expression, and a low tumor mutational burden. Here, we identify adenosine deaminase acting on RNA (ADAR), an RNA-editing enzyme that suppresses endogenous dsRNA sensing, as a key mediator of immune evasion in H3K27M-mutant DMG. ADAR is significantly overexpressed in H3K27M tumors relative to wild-type high-grade gliomas, and its depletion selectively suppresses proliferation in patient-derived DMG cells. The H3K27M mutation was found to synergize with ADAR loss to increase retroelement expression, activate type I interferon signaling, and induce immune checkpoint expression. We further identify all-trans retinoic acid (ATRA) as a pharmacologic inducer of ADAR degradation. At clinically relevant doses, ATRA phenocopies ADAR depletion, enhancing antiviral and interferon responses while increasing tumor immunogenicity. In orthotopic immunocompetent DMG models, ATRA enhances CD8+ T cell infiltration and synergizes with ICB and irradiation to improve survival.

cancer biology↗

bioRxiv2026

Proteomic Analysis of Human Chronic Traumatic Encephalopathy Brain Implicates Proteasome and Ribosome Dysfunction in Disease Progression

Chronic traumatic encephalopathy (CTE) is a progressive neurodegenerative disease associated with repeated head injuries (RHI) commonly experienced by contact sport athletes, military personnel, and domestic abuse victims. Despite growing recognition of CTE, the molecular mechanisms underlying disease progression remain poorly understood. This study aims to identify proteomic alterations associated with CTE pathology and clinical features to elucidate key biological pathways involved in disease pathogenesis. SomaScan 7k high-throughput proteomics was performed on 204 dorsolateral prefrontal cortex samples from the Boston University CTE Center Brain Bank. We identified differentially expressed proteins associated with CTE, hyperphosphorylated tau (ptau) pathology, duration of contact sports play, dementia status, and Cognitive Difficulty Scale (CDS) scores. Gene set enrichment analysis revealed that proteasome subunit proteins and related pathways were strongly associated with CTE progression and correlated with years of contact sports play. Reduction in ribosomal proteins and pathways was closely associated with ptau burden. Additionally, multiple models demonstrated significant alterations in MAPK-related cell signaling pathways. These findings advance our understanding of CTE progression and identify mechanisms correlated with key pathological features of the disease. Validation of these results could inform the development of diagnostics and treatments for CTE.

molecular biology↗

bioRxiv2025

Early life adversity increases striatal dopamine D1 receptor density and promotes social alcohol drinking in mice, especially males

The brains reward circuitry remains sensitive to experience throughout early life and into adulthood, allowing individuals to adapt to their unique environments. Adverse experiences early in life can increase vulnerability to substance use disorders, likely through alterations to this circuitry. Yet, the precise neurobiological mechanisms by which early life adversity acts are incompletely characterized. In this study, we used a limited bedding and nesting (LBN) paradigm as a translationally relevant model of early life adversity in genetically-identical C57BL/6J mice. After LBN-rearing, we assess the lasting behavioral and neurobiological impacts of this experience in adulthood. In robust sample sizes, our results validated previous findings of increased risk avoidance, enhanced acute response to alcohol, and greater voluntary alcohol drinking in socially-housed LBN-reared mice, especially males. Further, using autoradiography, we found LBN-reared mice had increased striatal D1-like receptor binding, skewing D1-to D2-like receptor balance relative to cross-fostered controls. However, after voluntary alcohol drinking, we found a strong downregulation in D1-like, and some D2-like, receptor binding, negating pre-existing differences in striatal dopamine receptor binding. We posit that via both transcriptional and post-transcriptional mechanisms, LBN-rearing upregulates striatal D1-receptor density and alters risk avoidance and acute alcohol stimulation to promote alcohol drinking among adversity-exposed mice. Together, these findings reveal specific neurobiological mechanisms that promote alcohol consumption following early life adversity and suggest complex interactions between early life adversity, sex-related factors, and dopamine receptor regulation in contributing to alcohol use disorder (AUD) vulnerability.

neuroscience↗

bioRxiv2025

PHD1-dependent hydroxylation of RepoMan (CDCA2) on P604 modulates the control of mitotic progression

Prolyl-hydroxylases (PHDs) are oxygen sensing enzymes that mediate the hydroxylation of proline residues. In mammals, three PHD isoforms (PHD1-3) are responsible for proline hydroxylation of Hypoxia Inducible Factor (HIF) alpha, a key regulator of the hypoxia response. In the accompanying paper (Jiang et. al., 2025) we report development of a mass spectrometry-based method to reliably identify proline hydroxylation (OH-Pro) sites on proteins and use this to identify a PHD-dependent OH-Pro modification at Pro604 on the protein RepoMan (CDCA2), a regulatory subunit for protein phosphatase PP1{gamma}, with important roles in mitotic progression and cell viability. Here, we investigate the functional significance of hydroxylation of RepoMan at P604. During M phase, the PP1-RepoMan complex dephosphorylates Thr3 of Histone H3 (H3T3) on chromosomes arms to ensure the correct localisation of the chromosomal passenger complex (CPC) at centromeres. We show that siRNA depletion of PHD1, but not PHD2, increases H3T3 phosphorylation in prometaphase-arrested cells. In cells depleted of endogenous RepoMan, exogenous expression of wild type RepoMan, but not a RepoMan P604A mutant, restored normal H3T3 phosphorylation localisation in prometaphase arrested cells. RepoMan P604 is located proximal to the Short Linear Motifs (SLiMs) that function as binding sites for the serine/threonine Protein Phosphatase 2A (PP2A). The interaction of RepoMan and PP2A-B56{gamma} is reduced in cells expressing RepoMan P604A. Moreover, analyses in both fixed and live cells released from a prometaphase arrest, show that expression of the RepoMan P604A mutant delays completion of mitosis, results in defects in chromosome alignment and segregation and increases levels of cell death. These data support a role for PHD1-mediated prolyl hydroxylation in controlling progression through mitosis, acting, at least in part, via hydroxylation of RepoMan at P604 regulating the interaction of RepoMan with PP2A during chromosome alignment and thereby controlling the levels of Histone H3 phosphorylation at Thr3.

cell biology↗

bioRxiv2025

Bodily perception links memory and self: a case study of an amnesic patient

Episodic autobiographical memory (EAM) is a building block of self-consciousness, involving recollection and subjective re-experiencing of personal past experiences. Any life episode is originally encoded by a subject within a body. This raises the possibility that memory encoding is shaped by bodily self-consciousness (BSC), a basic form of self-consciousness arising from the multisensory and sensorimotor perceptual signals from the body. Recent studies in healthy subjects showed that embodied encoding improves EAM, with the involvement of the hippocampus. However, there are only few imaging studies to date, hippocampal data are not consistent, and the role of hippocampal damage is not understood. We investigated how different BSC states during encoding, modulate later EAM retrieval, in a patient with severe amnesia caused by rare bilateral hippocampal damage. We performed three separate behavioral experiments using immersive virtual reality. The patient showed consistently more difficulties recollecting information encoded in embodied vs. disembodied states, particularly when asked to recall her perspective experienced at encoding. These results contrasted with the usual beneficial effect of BSC on EAM, and significantly differed from controls. These data provide consistent evidence that BSC impacts encoding and later reliving, and shows that the hippocampus is not just a critical structure for EAM, but also for effects of embodiment on memory. Additional fMRI data extend these findings by revealing that hippocampal-parietal connectivity mediates BSC-EAM coupling. Our findings plead for an important role of BSC in EAM, mediated by the hippocampus and its connectivity, leading to embodied memories that are experienced as belonging to the self. HighlightsO_LIWe studied a patient with memory deficits caused by bilateral hippocampal atrophy C_LIO_LIMultisensory stimulation modulated embodiment during episode encoding C_LIO_LIAcross three studies the patient showed stronger memory deficits for embodied episodes C_LIO_LIMultisensory bodily perception impacts bodily self-consciousness and episodic memory C_LIO_LIOur findings link the bodily self to episodic memory and the hippocampus C_LI

neuroscience↗

bioRxiv2024

Cx43 Enhances Response to BRAF/MEK Inhibitors by Reducing DNA Repair Capacity

BRAF and MEK inhibitors (BRAF/MEKi) have radically changed the treatment landscape of advanced BRAF mutation-positive tumours. However, limited efficacy and emergence of drug resistance are major handicaps for successful treatments. Here, by using relevant preclinical models, we found that Connexin43 (Cx43), a protein that plays a role in cell-to-cell communication, increases effectiveness of BRAF/MEKi by recruiting DNA repair complexes to lamin-associated domains and promoting persistent DNA damage and cellular senescence. The nuclear compartmentalization promoted by Cx43 contributes to genome instability and synthetic lethality caused by excessive DNA damage, which could lead to a novel therapeutic approach for these tumours to overcome drug resistance. Based on these findings, we designed an innovative drug combination using small extracellular vesicles (sEVs) to deliver the full-Cx43 in combination with the BRAF/MEKi. This study reveals Cx43 as a new player on DNA repair and BRAF/MEKi response, underlining the therapeutical potential that this approach could eventually have in the clinic to overcome the limitations of current therapies and improve treatment outcomes for patients with advanced BRAF mutant tumours.

cancer biology↗

bioRxiv2023

De novo design of diverse small molecule binders and sensors using Shape Complementary Pseudocycles

A general method for designing proteins to bind and sense any small molecule of interest would be widely useful. Due to the small number of atoms to interact with, binding to small molecules with high affinity requires highly shape complementary pockets, and transducing binding events into signals is challenging. Here we describe an integrated deep learning and energy based approach for designing high shape complementarity binders to small molecules that are poised for downstream sensing applications. We employ deep learning generated psuedocycles with repeating structural units surrounding central pockets; depending on the geometry of the structural unit and repeat number, these pockets span wide ranges of sizes and shapes. For a small molecule target of interest, we extensively sample high shape complementarity pseudocycles to generate large numbers of customized potential binding pockets; the ligand binding poses and the interacting interfaces are then optimized for high affinity binding. We computationally design binders to four diverse molecules, including for the first time polar flexible molecules such as methotrexate and thyroxine, which are expressed at high levels and have nanomolar affinities straight out of the computer. Co-crystal structures are nearly identical to the design models. Taking advantage of the modular repeating structure of pseudocycles and central location of the binding pockets, we constructed low noise nanopore sensors and chemically induced dimerization systems by splitting the binders into domains which assemble into the original pseudocycle pocket upon target molecule addition. One Sentence SummaryWe use a pseuodocycle-based shape complementarity optimizing approach to design nanomolar binders to diverse ligands, including the flexible and polar methotrexate and thyroxine, that can be directly converted into ligand-gated nanopores and chemically induced dimerization systems.

biochemistry↗

bioRxiv2023

Embodiment in episodic memory through premotor-hippocampal coupling

Episodic memory (EM) allows us to remember and relieve past events and experiences, depending on cortical-hippocampal reinstatement involved during encoding. Although it has been claimed that EM is fundamental to establish a sense of self across time, this has never been shown experimentally. Here we combine immersive virtual reality and fMRI and report stronger hippocampal reinstatement for scenes encoded under preserved sense of self, reflecting later recall performance. We further link the sense of self to EM showing that hippocampal reinstatement is coupled with reinstatement in premotor cortex, a key sense of self region. We extend these findings in a severe amnesic patient (caused by bilateral hippocampal damage), whose memory and re-experiencing lacked the normal dependency on the sense of self. Premotor-hippocampal coupling in EM describes how the self at encoding is neurally reinstated during the retrieval of past episodes, enabling a sense of self across time. TeaserPremotor-hippocampal coupling reveals how the self is reinstated when retrieving past episodes.

neuroscience↗

bioRxiv2023

DONSON is required for CMG helicase assembly in the mammalian cell cycle

DONSON is one of 13 genes mutated in a form of primordial microcephalic dwarfism known as Meier-Gorlin Syndrome. The other 12 encode components of the CDC45-MCM-GINS helicase, around which the eukaryotic replisome forms, or are factors required for helicase assembly during DNA replication initiation. A role for DONSON in CDC45-MCM-GINS assembly was unanticipated, since DNA replication initiation can be reconstituted in vitro with purified proteins from budding yeast, which lacks DONSON. Using mouse embryonic stem cells as a model for the mammalian helicase, we show that DONSON binds directly but transiently to CDC45-MCM-GINS during S-phase and is essential for chromosome duplication. Rapid depletion of DONSON leads to the disappearance of the CDC45-MCM-GINS helicase from S-phase cells and our data indicate that DONSON is dispensable for loading of the MCM2-7 helicase core onto chromatin during G1-phase, but instead is essential for CDC45-MCM-GINS assembly during S-phase. These data identify DONSON as a missing link in our understanding of mammalian chromosome duplication and provide a molecular explanation for why mutations in human DONSON are associated with Meier-Gorlin syndrome.

biochemistry↗

bioRxiv2023

Transcription promotes the restoration of chromatin following DNA replication.

DNA replication results in the transient eviction of nucleosomes, RNAPII and transcription regulators. How chromatin organization is duplicated on the two daughter strands is a central question in epigenetics. In mammals, transcription restarts on newly replicated DNA within a couple of hours, promoting chromatin accessibility. However, the role of transcription in the restoration of other chromatin determinants following DNA replication remains unclear. Here we have monitored protein re-association to newly replicated DNA upon inhibition of transcription using iPOND coupled to quantitative mass spectrometry. We show that nucleosome assembly and the re-establishment of most histone modifications are uncoupled from transcription restart. However, upon transcription inhibition, the re-association of many proteins was altered, including ATP-dependent remodellers, transcription regulators, the histone variant H2A.Z, histone modifiers as well as the restoration of H3.3K36me2. Finally, transcription also provoked the recruitment of several DNA repair proteins, revealing that transcription promotes chromatin reestablishment post-replication but is also a potential source of genotoxic stress.

molecular biology↗

bioRxiv2022

Differential impact of brain network efficiency on post-stroke motor and attentional deficits

BackgroundMost studies on stroke have been designed to examine one deficit in isolation, yet survivors often have multiple deficits in different domains. While the mechanisms underlying multiple-domain deficits remain poorly understood, network-theoretical methods may open new avenues of understanding. Methods50 subacute stroke patients (7{+/-}3days post-stroke) underwent diffusion-weighted magnetic resonance imaging and a battery of clinical tests of motor and cognitive functions. We defined indices of impairment in strength, dexterity, and attention. We also computed imaging-based probabilistic tractography and whole brain connectomes. Overlaying individual lesion masks onto the tractograms enabled us to split the connectomes into their affected and unaffected parts and associate them to impairment. ResultsTo efficiently integrate inputs from different sources, brain networks rely on a "rich-club" of a few hub nodes. Lesions harm efficiency, particularly when they target the rich-club. We computed efficiency of the unaffected connectome, and found it was more strongly correlated to impairment in strength, dexterity and attention than efficiency of the total connectome. The magnitude of the correlation between efficiency and impairment followed the order attention > dexterity {approx} strength. Network weights associated with the rich-club were more strongly correlated to efficiency than non-rich-club weights. ConclusionsAttentional impairment is more sensitive to disruption of coordinated network activity between brain regions than motor impairment, which is sensitive to disruption of localized network activity. Providing more accurate reflections of actually functioning parts of the network enables the incorporation of information about the impact of brain lesions on connectomics contributing to a better understanding of underlying stroke mechanisms.

neuroscience↗

bioRxiv2021

Interferon-gamma and TNF-alpha synergistically enhance the immunomodulatory capacity of Endometrial-Derived Mesenchymal Stromal Cell secretomes by differential microRNA and extracellular vesicle release

Endometrial Mesenchymal Stromal Cells (endMSCs) can be easily isolated from menstrual blood by plastic adherence. These cells have a potent pro-angiogenic and immunomodulatory capacity, and their therapeutic effect is mediated by paracrine mechanisms where secretome have a key role. In this paper, we aimed to evaluate different priming conditions in endMSCs using pro-inflammatory cytokines and Toll-Like Receptor ligands. Our in vitro results revealed a synergistic and additive effect of IFN{gamma} and TNF on endMSCs. The combination of these pro-inflammatory cytokines significantly increased the release of Indoleamine 2,3-dioxygenase (IDO1) in endMSCs. Additionally, this study was focused on the phenotype of IFN{gamma}/TNF-primed endMSCs (endMSCs*). Here we found that immune system-related molecules such as CD49d, CD49e, CD54, CD56, CD58, CD63, CD126, CD152, or CD274 were significantly altered in endMSCs* when compared to control cells. Afterward, our study was completed with the characterization of released miRNAs by Next Generation Sequencing (NGS). Briefly, our system biology approaches demonstrated that endMSCs* showed an increased release of 25 miRNAs whose target genes were involved in immune response and inflammation. Finally, the cellular and molecular characterization was completed with in vitro functional assays. In summary, the relevance of our results lies in the therapeutic potential of endMSCs*. The differences in cell surface molecules involved in migration, adhesion and immunogenicity, allowed us to hypothesize that endMSCs* may have an optimal homing and migration capacity towards inflammatory lesions. Secondly, the analysis of miRNAs, target genes and the subsequent lymphocyte activation assays demonstrated that IFN{gamma}/TNF-primed secretome may exert a potent effect on the regulation of adverse inflammatory reactions.

cell biology↗

bioRxiv2020

FAM111A regulates replication origin activation and cell fitness

FAM111A is a replisome associated protein and dominant mutations within its trypsin-like peptidase domain are linked to severe human developmental syndromes. However, FAM111A functions and its putative substrates remain largely unknown. Here, we showed that FAM111A promotes origin activation and interacts with the putative peptidase FAM111B, and we identified the first potential FAM111A substrate, the suicide enzyme HMCES. Moreover, unrestrained expression of FAM111A wild-type and patient mutants impaired DNA replication and caused cell death only when the peptidase domain remained intact. Altogether our data reveal how FAM111A promotes DNA replication in normal conditions and becomes harmful in a disease context.

molecular biology↗

bioRxiv2020

Autosomal Recessive Alzheimer disease (arAD): homozygosity mapping of genomic regions containing arAD loci

Long runs of homozygosity (ROH) are contiguous stretches of homozygous genotypes, which are a footprint of recent inbreeding and recessive inheritance. The presence of recessive loci is suggested for Alzheimers disease (AD). However, the search for recessive variants has been poorly assessed to date. To investigate homozygosity in AD, we performed a fine-scale ROH analysis including 21,100 individuals from 10 cohorts of European ancestry (11,919 AD cases and 9,181 controls). We detected an increase of homozygosity in AD cases compared to controls [{beta}FROH (CI95%) = 0.051 (0.023 - 0.078); P = 3.25 x 10-4]. ROHs increasing the risk of AD (OR > 1) were significantly overrepresented compared to ROHs increasing protection (p < 2.20 x 10-16). The top associated ROH with AD risk ({beta} (CI95%) = 1.09 (0.48 - 1.48), p value = 9.03 x 10-4) was detected upstream the HS3ST1 locus (chr4:11,189,482-11,305,456), previously related to AD. Next, to construct a homozygosity map of AD cases, we selected ROHs shared by inbred AD cases extracted from an outbred population. We used whole-exome sequencing data from 1,449 individuals from the Knight-ADRC-NIA-LOAD (KANL) cohort to identify potential recessive variants in candidate ROHs. We detected a candidate marker, rs117458494, mapped in the SPON1 locus, which has been previously associated with amyloid metabolism. Here, we provide a research framework to look for recessive variants in AD using outbred populations. Our results showed that AD cases have enriched homozygosity, suggesting that recessive effects may explain a proportion of AD heritability.

genetics↗

bioRxiv2020

cAMP-Fyn signaling in the dorsomedial striatum direct pathway drives excessive alcohol use

Fyn kinase in the dorsomedial striatum (DMS) of rodents plays a central role in mechanisms underlying excessive alcohol intake. The DMS is comprised of medium spiny neurons (MSNs) that project directly (dMSNs) or indirectly (iMSNs) to the substantia nigra. Here, we examined the cell-type specificity of Fyns actions on alcohol use. First, we knocked down Fyn selectively in DMS dMSNs or iMSNs of mice and measured the level of alcohol consumption. We found that downregulation of Fyn in dMSNs, but not in iMSNs, reduces excessive alcohol but not saccharin intake. D1Rs are coupled to Gs/olf, which activate cAMP signaling. To examine whether Fyns actions are mediated through cAMP signaling, DMS dMSNs were infected with GsDREADD, and the activation of Fyn signaling was measured following CNO treatment. We found that remote stimulation of cAMP signaling in DMS dMSNs activates Fyn and promotes the phosphorylation of the Fyn substrate, GluN2B. In contract, remote activation of GsDREADD in DLS dMSNs did not alter Fyn signaling. We then tested whether activation of GsDREADD in DMS dMSNs or iMSNs alters alcohol intake and observed that CNO-dependent activation of GsDREADD in DMS dMSNs but not iMSNs increases alcohol but not saccharin intake. Finally, we examined the contribution of Fyn to GsDREADD-dependent increase in alcohol intake, and found that systemic administration of the Fyn inhibitor, AZD0503 blocks GsDREADD-dependent increase in alcohol consumption. Our results suggest that the cAMP-Fyn axis in the DMS dMSNs is a molecular transducer of mechanisms underlying the development of excessive alcohol consumption.

neuroscience↗