Biology subjects

Armirotti, A.

Publications and source records attributed to Armirotti, A..

16 recordsLinked to original sources

bioRxiv2026

Controlled Blood-Brain Barrier Modulation by a High-Affinity Claudin-5 Peptide Binder

The blood-brain barrier (BBB) is a specialized interface that tightly regulates the exchange of molecules between the bloodstream and the brain. Its barrier function relies on a monolayer of brain endothelial cells sealed by tight junctions (TJs) that restrict paracellular flux through claudin-5 (CLDN5) multimeric complexes. To improve the delivery of nutrients and drugs to the brain, CLDN5-competitive peptides are promising carriers for creating size-controlled, temporary openings in the paracellular pathway. Here, we combine generative protein design and atomistic simulations to design ST9, a peptide with high nanomolar affinity for CLDN5. Compared with f1-C5C2, a CLDN5-binding peptide that we previously reported, ST9 induces a rapid, transient, size-controlled, and fully reversible increase in paracellular permeability, without altering CLDN5 expression or the proteomic profile of brain endothelial cells, indicating distinct mechanisms of TJ destabilization. This work provides a promising approach for developing next-generation BBB-opening agents to effectively treat neurological diseases.

neuroscience↗

bioRxiv2026

Human ASPDH is a 2-aminomuconate reductase that produces L-2-aminohex-3-enedioic acid in tryptophan catabolism

Most tryptophan catabolism in animals occurs through the kynurenine pathway, which generates the essential NAD cofactor and multiple bioactive metabolites. Knowledge of this pathway in eukaryotes ends at the unstable intermediate 2-aminomuconate (2-AM). Here, by leveraging evolutionary information from more than 5,000 eukaryotes, we identify two distinct genes acting downstream of 2-AM in fungi and metazoa. The fungal gene is homologous to bacterial 2-AM deaminase, whereas the metazoan gene is homologous to aspartate dehydrogenase (ASPDH), which in prokaryotes catalyses the first reaction of NAD biosynthesis. Biochemical and structural analyses show that human ASPDH has evolved an unprecedented function as an NAD(P)H-dependent 2-AM reductase (AMR) in tryptophan catabolism. The reaction forms L-2-aminohex-3-enedioic acid, an unsaturated -amino acid absent from current biological databases. Isotope-labeling NMR experiments and structural modelling support a mechanism in which hydride transfer is coupled to double-bond rearrangement of the conjugated system. These findings reveal a previously unknown metazoan branch of the kynurenine pathway, expand the repertoire of endogenous amino acids, and illustrate how comparative genomics can uncover hidden reactions in human metabolism.

biochemistry↗

bioRxiv2026

A NAPE-LRRK2 metabolic axis controls lysosomal homeostasis in Parkinson's disease

N-acylphosphatidylethanolamines (NAPEs) are atypical glycerophospholipids that accumulate in response to cellular stress, yet their roles beyond serving as precursors of fatty-acid ethanolamines (FAEs) remain largely unexplored. Here, we identify NAPEs as endogenous regulators of leucine-rich repeat kinase 2 (LRRK2), a master controller of lysosomal homeostasis and a genetic driver of Parkinsons disease. We show that increasing NAPE synthesis or blocking their hydrolysis inhibits LRRK2 kinase activity, enhances lysosomal function, and promotes the clearance of -synuclein aggregates. Conversely, cells in which NAPE hydrolysis is enhanced display increased LRRK2 activation and lysosomal dysfunction. Importantly, in induced pluripotent stem cell-derived dopaminergic neurons carrying the LRRK2-G2019S variant, pharmacological inhibition of NAPE-PLD - the enzyme that degrades NAPEs - restores lysosomal activity and favors the clearance of preformed -synuclein fibrils. Together, our findings identify NAPEs as previously unrecognized lipid regulators of LRRK2 signaling and lysosomal function, revealing a metabolic axis with therapeutic potential in Parkinsons disease. TeaserBoosting neuronal NAPEs silences LRRK2 hyperactivity and clears -synuclein: a lipid-based strategy for Parkinsons disease.

cell biology↗

bioRxiv2025

REST/NRSF phosphorylation by CaMKIV regulates its transcriptional repressor activity and half-life

REST is a repressor of a large cluster of neural genes that homeostatically regulates neural activity. However, whether REST can be regulated by Ca2+ and Ca2+-activated kinases is unknown. We investigated Ca2+/calmodulin-dependent protein kinases (CaMKs) as upstream regulators of REST fate and activity. We show that REST is phosphorylated by CaMKIV at Ser-322 site located within the linker between the 5th-6th Zn-finger domains. Phosphomimic REST mutant in Serine-322 decreased REST repressor activity and caused its transition from nucleus to cytosol, followed by degradation. Molecular dynamics simulations of the phosphomimic N-terminal REST and the DNA RE1 sequence revealed a sharp decrease in the stability of the REST-RE1 binding interface. Moreover, the homeostatic effects of CaMKIV on the amplitude of excitatory synaptic currents were inhibited by the genetic deletion of REST. The results demonstrate that CaMKIV phosphorylation has a crucial role in the homeostatic regulation of REST levels and repressor activity. TeaserCaMKIV phosphorylation homeostatically regulates the repressor activity of REST on neural genes and its half-life.

neuroscience↗

bioRxiv2025

A microRNA-based Therapy against Human Medulloblastoma Validated in a Xenotransplant Model using Wild-Type Mouse Embryos

Medulloblastoma (MB) is the most prevalent malignant pediatric brain tumor. Its poor prognosis is driven by therapy-resistant cancer stem-like cells (CSCs), which are challenging to study in traditional preclinical models. MicroRNAs (miRNAs) modulate tumor-related pathways by repressing oncogenic gene expression, a function lost in cancer. We assessed the therapeutic potential of miRNA restoration in human MB from distinct subgroups, validated in a xenotransplant model using wild-type (WT) mouse embryos. Multi-omics, imaging, and in silico analyses were employed to identify underlying mechanisms and therapeutic targets. Human MB cells formed tumors in embryonic mouse brains that mirrored key MB features, including vascularized CSC niches and metastases. Restoration of underexpressed miRNAs reduced tumor growth and invasiveness in vitro and in vivo. These miRNAs synergistically repressed gene networks related to cell adhesion and RNA metabolism, shared oncogenic pathways across MB subgroups. Our embryonic xenotransplant model provides a clinically relevant platform for evaluating next-generation gene therapies in pediatric brain cancer.

cancer biology↗

bioRxiv2025

Synergic microRNAs suppress human glioblastoma progression by modulating clinically relevant targets

Glioblastoma (GBM) is a highly aggressive brain tumor characterized by therapy-resistant glioma stem-like cells (GSCs) and extensive infiltration into surrounding brain tissue. MicroRNAs (miRNAs) are post-transcriptional regulators of oncogenic pathways, but their tumor-suppressive function is frequently lost in GBM. This study explores a multimodal therapeutic approach by restoring a combination of miRNAs to exploit their synergistic effects against GBM. Using patient-derived GBM cells cultured under stem cell-permissive conditions, we demonstrate that miRNA restoration reduces tumor growth, limits invasiveness, stemness and enhances sensitivity to temozolomide. In vivo studies in an orthotopic xenograft mouse model of GBM confirm the therapeutic efficacy and low toxicity of the nanoformulated miRNAs, following local injection. Multi-omics and computational analyses on different GBM subtypes reveal that these miRNAs synergistically suppress tumor-promoting extracellular matrix interactions, particularly through the collagen pathway, and downregulate genes associated with GBM progression. The identified miRNA targets correlate with glioma grade and poor patient prognosis, further underscoring their therapeutic potential. These findings highlight the promise of combinatorial miRNA therapy as a novel strategy for GBM treatment and suggest new molecular targets for theragnostic development.

cancer biology↗

bioRxiv2024

A claudin5-binding peptide enhances the permeability of the blood-brain-barrier

The blood-brain barrier (BBB) is essential to maintain brain homeostasis and healthy conditions but it also prevents drugs from reaching brain cells. In the BBB, tight junctions (TJs) are multi-protein complexes located at the interface between adjacent brain endothelial cells that regulate paracellular diffusion and claudin-5 (CLDN5) is the major component of the TJ portfolio, playing a pivotal role in restricting the paracellular traffic. In view of obtaining fine control over the transport across the BBB, the use of competing peptides able to bind CLDN5 to induce transient and regulated permeabilization of the paracellular passage is emerging as a potentially translatable strategy for clinical applications. In this work, we designed and tested short peptides with improved solubility and biocompatibility using a combined approach that involved structural modeling techniques and in vitro validation, generating a robust workflow for the design, screening, and optimization of peptides for the modulation of the BBB paracellular permeability. We designed a selection of 11- to 16-mer compounds derived from the first CLDN5 extracellular domain and from the CLDN5-binding domain of Clostridium perfringens enterotoxin and determined their efficiency in enhancing BBB permeability. The computational analysis classified all tested peptides based on solubility and affinity to CLDN5, and provided atom-level details of the binding process. From our screening, we identified a novel CLDN5-derived peptide, here called f1-C5C2, which demonstrated good solubility in biological media, efficient binding to CLDN5 subunits, and capability to increase permeability at low concentrations. The peptidomimetic in silico/in vitro strategy described here can achieve a transient and reversible permeabilization of the BBB with potential applications in the pharmacological treatment of brain diseases. HIGHLIGHTSO_LIWater-soluble peptidomimetics are used to competitively bind claudin-5 tight junction proteins and increase the permeability of the blood-brain barrier; C_LIO_LITrans-endothelial electrical resistance and dissociation constant measurements demonstrate the binding affinity of the peptide f1-C5C2 for claudin-5; C_LIO_LIUnbinding free energy calculations correlated with experimental results and provided information on the protein-peptide binding interface. C_LIO_LIIncubation with the peptide f1-C5C2 allows paracellular transport of 4K, but not 70K, dextran. C_LI GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=88 SRC="FIGDIR/small/591687v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@70fe54org.highwire.dtl.DTLVardef@496a28org.highwire.dtl.DTLVardef@1d89a81org.highwire.dtl.DTLVardef@187acec_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2024

CDC42 Inhibitors Alter Patterns of Vessel Arborization in Skin and Tumors in vivo

Tumors that arise in the epidermis must develop a vascular supply to grow beyond a millimeter in depth. This process requires CDC42 GTPases such as CDC42, RhoJ and RhoQ. Despite this dependence on angiogenesis for growth, melanoma tumors are minimally responsive to current anti-angiogenesis agents, highlighting the need for more effective drugs in this class. Here we integrate antibody infusion, optical tissue clearing, multiphoton imaging, and three-dimensional semi-automated tracing to develop a quantitative approach to measure changes in vascular architecture in skin and skin tumors. This new approach uncovered differences in vessel arborization in the skin of RhoJ KO mice as compared to wild-type mice. Furthermore, novel small molecules that inhibit CDC42 GTPases inhibited both tumor growth and vessel branching within tumors to a similar degree as Braf inhibitors, which are commonly used to treat melanoma. In contrast to Braf inhibitors, however, which only affected tumor vasculature, CDC42 inhibitors affected vascularization in both tumor and normal skin without apparent toxicity to endothelial or stromal cells. These novel CDC42 inhibitors similarly blocked vessel branching in human cell-based micro-physiological models of normal and tumor vessels. RNA sequencing revealed reduced expression of multiple angiogenesis-related genes in drug-treated skin. Taken together, these studies identify a new class of pharmacologic agents that inhibit vessel branching in both normal skin and tumors with potential utility for treating skin cancer and skin diseases characterized by pathologic angiogenesis.

cancer biology↗

bioRxiv2024

Monitoring myelin lipid composition and structure of myelinated fibers reveals a maturation delay in CMT1A

1.Findings accumulated over time show that neurophysiological, neuropathological, and molecular alterations are present in CMT1A and support the dysmyelinating rather than demyelinating nature of this neuropathy. Moreover, uniform slowing of nerve conduction velocity is already manifest in CMT1A children and does not improve throughout their life. This evidence and our previous studies displaying aberrant myelin composition and structure in adult CMT1A rats prompt us to hypothesize a myelin and axon developmental defect in the CMT1A peripheral nervous system. Peripheral myelination begins during the early stages of development in mammals and, during this process, chemical and structural features of myelinated fibers (MFs) evolve towards a mature phenotype; deficiencies within this self-modulating circuit can cause its blockage. Therefore, to shed light on pathophysiological mechanisms that occur during development, and to investigate the relationship among axonal, myelin, and lipidome deficiencies in CMT1A, we extensively analyzed the evolution of both myelin lipid profile and MF structure in WT and CMT1A rats. Lipidomic analysis revealed a delayed maturation of CMT1A myelin already detectable at P10 characterized by deprivation of sphingolipid species such as hexosylceramides and long-chain sphingomyelins, whose concentration physiologically increases in WT, and an increase in lipids typical of unspecialized plasma membranes, including phosphatidylcholines and phosphatidylethanolamines. Consistently, advanced morphometric analysis on more than 130.000 MFs revealed a delay in the evolution of CMT1A axon and myelin geometric parameters, appearing concomitantly with lipid impairment. We here demonstrate that, during normal development, MFs undergo a continuous maturation process in both chemical composition and physical structure, but these processes are delayed in CMT1A.

neuroscience↗

bioRxiv2024

Connectomic and behavioral alterations in creatine transporter deficiency are partially normalized by gene therapy

Creatine Transporter Deficiency (CTD) is an X-linked disorder due to the loss of SLC6A8 gene and presenting with low brain creatine, intellectual disability, autistic-like behavior and seizures. No treatments are available yet for CTD, and little is known about the brain circuit alterations underlying its pathological endophenotypes. Here, we tracked brain network and behavioral dysfunction in a murine model of CTD at two stages of disease progression. fMRI mapping revealed widespread disruption of brain connectivity in Slc6a8-KO mice, with robust somatomotor hypoconnectivity in juvenile animals, and weaker and more focal alterations of cortical and subcortical connectivity in adulthood. Notably, perinatal AAV-mediated expression of human SLC6A8 in Slc6a8- KO mice robustly prevented juvenile fMRI hypoconnectivity, an effect accompanied by the regression of multiple translationally relevant phenotypes, including reduced stereotyped movements, improved declarative memory and increased body weight, all of which persisted into adulthood. However, early cognitive deficits, impairments in working memory and residual fMRI hypoconnectivity in adult mice were not ameliorated by gene therapy. Furthermore, significant cognitive impairments were observed in WT mice receiving gene therapy, highlighting a potential detrimental effect of ectopic expression of SLC6A8 in healthy brain circuits. Finally, multivariate modeling in adult mice revealed a basal forebrain network whose activity was associated with behavioral performance and modulated by brain creatine levels. This brain-behavior relationship was disrupted in Slc6a8-KO mice. Our results document robust network disruption in CTD and demonstrate that CTD pathology can be partially alleviated by perinatal genetic expression of SLC6A8, providing a foundation for the future development of experimental therapies for this genetic disorder.

neuroscience↗

bioRxiv2023

ALS-associated FUS mutation reshapes the RNA and protein composition and dynamic of Stress Granules.

Stress Granules (SG) formation is a cellular protection mechanism, constituting a storage for untranslated mRNAs and RNA-binding proteins (RBPs); however, these condensates can turn into pathological aggregates, related to the onset of neurodegenerative diseases like Amyotrophic Lateral Sclerosis (ALS). This transition towards cytotoxic inclusions is triggered by ALS-causative mutations in the RBP FUS, which lead to its cytoplasmic mis-localization and accumulation in SG. Here, we describe the SG transcriptome in a neural context and describe several features for RNA recruitment in SG. We demonstrate that SG dynamics and RNA content are strongly modified by the incorporation of mutant FUS, switching to a more unstructured, AU-rich SG transcriptome. Moreover, we show that mutant FUS, together with its protein interactors and their target RNAs, are responsible for the reshaping of the mutant SG transcriptome with alterations that can be linked to neurodegeneration. Therefore, our data give a comprehensive view of the molecular differences between physiological and pathological SG in ALS conditions, showing how FUS mutations impact the RNA and protein population of these condensates.

molecular biology↗

bioRxiv2023

Internal Ribosome Entry Sites act as Effector Domain in linear and circular antisense long non-coding SINEUP RNAs

SINEUPs are antisense long non-coding RNAs that enhance translation of overlapping sense mRNAs through the activity of two domains: a SINEB2 sequence UP-regulating translation (Effector Domain, ED) and an antisense region providing target specificity (Binding Domain, BD). In this study, we demonstrate that the invSINEB2 sequence from the natural SINEUP AS Uchl1 RNA is an Internal Ribosomal Entry Site (IRES) when acting in cis and that known viral and cellular IRES sequences can act as Effector Domain in synthetic SINEUPs. To identify natural IRES-containing, non-coding RNAs with SINEUP-like activity, we focused on circular RNAs showing that the non-coding circ5533, transcribed from the c-myc locus, enhances endogenous protein expression of its target PX Domain Containing Serine/Threonine Kinase Like (Pxk) by increasing mRNA association to polysomes. In summary, this study shows that natural and synthetic SINEUPs include linear and circular transcripts with an embedded IRES sequence as ED.

molecular biology↗

bioRxiv2021

Structure-based Design of CDC42 Effector Interaction Inhibitors For the Treatment of Cancer

CDC42 family GTPases (RHOJ, RHOQ, CDC42) are upregulated but rarely mutated in cancer and control both the ability of tumor cells to invade surrounding tissues and the ability of endothelial cells to vascularize tumors. Here we use computer-aided drug design to discover a new chemical entity (ARN22089) that targets CDC42 GTPases and blocks CDC42 effector interactions without affecting the binding between closely related GTPases (RAC1, RAS, RAL) and their downstream effectors. Our lead compound has broad activity against a panel of cancer cell lines, inhibits S6 phosphorylation and MAPK activation, activates pro-inflammatory and apoptotic signaling, and blocks tumor growth and angiogenesis in three-dimensional vascularized microtumor models (VMT) in vitro. In addition, ARN22089 has a favorable pharmacokinetic profile and can inhibit the growth of BRAF mutant mouse melanomas and patient-derived xenografts in vivo. Taken together, this work identifies a promising new class of therapeutic agents that influence tumor growth by modulating CDC42 signaling in both the tumor cell and its microenvironment.

molecular biology↗

bioRxiv2021

RAD51 nuclear recruitment and inhibition towards innovative strategies against pancreatic cancer

RAD51, a key player in the homologous recombination (HR) mechanism, is a critical protein to preserve genomic stability. BRCA2, upon DNA damage, promotes RAD51 fibrils disassembly and its nuclear recruitment. Here, we use BRC4, a peptide derived from the fourth BRC repeat of BRCA2; BRC4 induces RAD51 defibrillation through a domino effect, eroding fibrils from their termini, and yielding monomeric RAD51. The congruence among several techniques (static and dynamic light scattering, negative staining transmission electron microscopy (TEM), and microscale thermophoresis) allows an accurate estimation of the kinetic and thermodynamic parameters of this process. BRC4 lacks, however, a nuclear localization sequence; therefore, it cannot transport RAD51 into the nucleus, thus behaving as a RAD51 inhibitor. Cellular assays (BxPC-3, pancreatic cancer cells) indeed show that BRC4 efficiently inhibits HR and enhances the cytotoxic effect of cisplatin, a DNA-damaging drug. The present study sheds further light on the complexity of the HR pathway, paving the way for designing peptide and small organic molecule inhibitors of RAD51 as innovative anticancer and chemo/radiosensitizer compounds.

biophysics↗

bioRxiv2019

The paternally imprinted gene Snord116 regulates cortical neuronal activity

Prader-Willi syndrome (PWS) is a neurodevelopmental disorder that is characterized by rapid eye movement (REM) sleep abnormalities. The disease is caused by genomic imprinting defects that are inherited through the paternal line. Among the genes located in the PWS region on chromosome 15 (15q11-q13), small nucleolar RNA 116 (Snord116) has been previously associated with intrusions of REM sleep into wakefulness in both humans and mice.\n\nHere, we further explore the processes of sleep regulation by studying the PWScrm+/p- mouse line, which carries a paternal deletion of Snord116. We focused on microstructural electrophysiological components of sleep, such as REM sleep features and sleep spindles within NREM sleep. While the former are thought to contribute to neuronal network formation early in brain development, the latter are markers of thalamocortical processes. Both signals are often compromised in neurodevelopmental disorders and influence functional properties of cortical neurons. Thus, we isolated and characterized the intrinsic activity of cortical neurons using in vitro microelectrode array (MEA) studies.\n\nOur results indicate that the Snord116 gene in mice selectively influences REM sleep properties, such as theta rhythms and the organization of REM episodes throughout sleep-wake cycles. Moreover, sleep spindles present specific abnormalities in PWS model systems, indicating that these features of sleep may translate as potential biomarkers in human PWS. We observed abnormalities in the synchronization of cortical neuronal activity that are accounted for by high levels of norepinephrine.\n\nIn conclusion, our results provide support for an important role of Snord116 in regulating brain activity during sleep and, in particular, cortical neuronal properties, thereby opening new avenues for developing interventions in PWS.\n\nSignificance StatementWe found that the Snord116 gene, a major player in Prader-Willi syndrome (PWS), significantly impacts REM sleep and its regulation. Additionally, we found that sleep spindles, a subtle electroencephalography (EEG) marker that occurs during NREM sleep, are dysregulated in PWS mice that carry a paternal deletion of the Snord116 gene. Using a combination of in vivo and in vitro experiments, we identified sleep features at the network and molecular level that suggest that Snord116 is fundamental in the synchronization of neuronal networks. Our study also provides a new pre-clinical tool to investigate the pathophysiology of sleep in PWS.

neuroscience↗

bioRxiv2018

Elevated plasma ceramide levels in post-menopausal women

Circulating ceramide levels are abnormally elevated in age-dependent pathologies such as cardiovascular diseases, obesity and Alzheimers disease. Nevertheless, the potential impact of age on plasma ceramide levels has not yet been systematically examined. In the present study, we quantified a focused panel of plasma ceramides and dihydroceramides in a cohort of 164 subjects (84 women) 19 to 80 years of age. After adjusting for potential confounders, multivariable linear regression analysis revealed a positive association between age and ceramide (d18:1/24:0) ({beta} (SE) = 5.67 (2.38); p = .0198) and ceramide (d18:1/24:1) ({beta} (SE) = 2.88 (.61); p < .001) in women, and between age and ceramide (d18:1/24:1) in men ({beta} (SE) = 1.86 (.77); p = .0179). In women of all ages, but not men, plasma ceramide (d18:1/24:1) was negatively correlated with plasma estradiol (r = -0.294; p = .007). Finally, in vitro experiments in human cancer cells expressing estrogen receptors showed that incubation with estradiol (10 nM, 24 h) significantly decreased ceramide accumulation. Together, the results suggest that aging is associated with an increase in circulating ceramide levels, which in post-menopausal women may be at least partially dependent on lower estradiol levels.

biochemistry↗