Biology subjects

Soriano, M.

Publications and source records attributed to Soriano, M..

11 recordsLinked to original sources

bioRxiv2026

Machine learning guided design of strong transcriptional activation domains

Artificial intelligence has accelerated the design of structured proteins, but it remains difficult to design functional intrinsically disordered proteins because of weak structural constraints and poorly defined sequence-to-function relationships1. Activation domains (ADs), transcription factor regions that recruit coactivators, are an excellent test case for the de novo design of intrinsically disordered sequences. ADs are one of the oldest groups of functional intrinsically disordered sequences2 and designed ADs have applications in synthetic biology, biotechnology, and agriculture. We computationally generated 500,000 candidate sequences that resembled known ADs and predicted AD function with extant machine learning models, including three neural networks. From high-scoring sequences, we selected 18,750 for experimental validation in yeast. Surprisingly, >90% of the 16,770 well-measured sequences function as ADs. Sequences predicted to be active by multiple models were stronger, motivating development of a fast and accurate consensus AD predictor, MADRIGAL. A number of our designed ADs retain functionality across fungi, plants, and human cells. This work illustrates a generalizable paradigm for incorporating sequence-to-function models into the design loop to efficiently generate functional intrinsically disordered sequences.

synthetic biology↗

bioRxiv2026

Plastin-3 membrane recruitment drives cell-in-cell invasion during entosis

Entosis is a cell-in-cell (CIC) invasion process in which one living cell actively invades into another, with important implications for tumor evolution, cell competition, and responses to cellular stress. Both the initiation and progression of entosis require extensive actin cytoskeletal remodeling, as one cell must physically accommodate the complete internalization of another viable cell, which can subsequently migrate, divide, undergo degradation, or escape. Nearly two decades after its discovery, mechanistic insight into how cytoskeleton organization is regulated during entosis remains poorly understood. The most consistent observation is that inhibition of Rho-ROCK signaling blocks entosis, indicating a central role for actomyosin contractility. Consistently, increased phosphorylation of myosin light chain and cortical actomyosin accumulation have been reported in invading cells, yet the underlying mechanisms remain largely unknown. Here, we systematically interrogated ROCK activation as a driver of the entotic internalization program. Constitutively active mutant ROCK1 or pharmacological ROCK1 activation using narciclasine rapidly triggered canonical entosis pathway through MLC2 phosphorylation. Mass spectrometry identified Plastin-3 (PLS3, T-plastin), a crucial calcium-sensitive actin-bundling protein, which was recruited to the plasma membrane to trigger entosis upon ROCK1 activation. Our study uncovers a key cytoskeletal remodeling step which may support cortical tension required for CIC invasion during entosis.

cancer biology↗

bioRxiv2026

Preferential vulnerability of cortical GABAergic interneurons to Nalcn deficiency

Neuronal resting membrane potential (RMP) reflects the balance of leak conductances and varies systematically across cortical cell types. Many GABAergic interneurons exhibit more depolarized RMPs than neighbouring excitatory neurons, but the molecular mechanisms underlying these systematic differences in intrinsic excitability remain incompletely defined. The sodium leak channel non-selective (NALCN) mediates a major fraction of basal sodium conductance and cause neurodevelopmental syndromes characterized by developmental delay and cognitive impairment. Here we define NALCN contribution to cortical circuit development and function with cell-type precision. Using Nalcn-GFP reporter line, we map Nalcn expression across cortical types revealing enrichment in GABAergic hippocampal interneurons relative to hippocampal pyramidal neurons. Using conditional mouse models, we selectively deleted Nalcn in cortical glutamatergic lineages or forebrain GABAergic cells from early embryogenesis. Electrophysiological analysis show that developmental loss of Nalcn preferentially reduces intrinsic excitability across GABAergic interneuron subtypes while sparing pyramidal neurons. To understand the impact of a depolarized GABAergic RMP on brain function, we assessed the behavioral performance of Nalcn-deficient mice that revealed persistent deficits in contextual adaptation and spatial short-term memory. These findings reveal a neuron type-specific function of NALCN in the cerebral cortex and position NALCN as a crucial ion channel regulating basal excitability of GABAergic inhibitory circuits and cortical circuit function.

neuroscience↗

bioRxiv2024

Conservation of function without conservation of amino acid sequence in intrinsically disordered transcriptional activation domains

Protein function is canonically believed to be more conserved than amino acid sequence, but this idea is only well supported in folded domains, where highly diverged sequences can fold into equivalent 3D structures with identical function. Intrinsically disordered protein regions (IDRs) often experience rapid amino acid sequence divergence, but because they do not fold into stable 3D structures, it remains unknown when and how function is conserved. As a model system for studying the evolution of IDRs, we examined transcriptional activation domains, the regions of transcription factors that bind to coactivator complexes. We systematically identified activation domains on 502 homologs of the transcriptional activator Gcn4 spanning 600 MY of fungal evolution in the Ascomycota. We find that the central activation domain shows strong conservation of function without conservation of sequence. We identify the molecular mechanism for this conservation of function without conservation of sequence: evolutionary turnover (gain and loss) of acidic and aromatic residues that are important for function. We further see turnover of complete N-terminal activation domains. This turnover at two length scales confounds multiple sequence alignments, explaining why traditional comparative genomics cannot detect functional conservation of activation domains. Evolutionary turnover of key residues is likely a general mechanism for conservation of function without conservation of sequence in IDRs.

systems biology↗

bioRxiv2024

Resveratrol targets G-quadruplexes to exert its pharmacological effects

Resveratrol (RSV) is one of the most studied and used biomolecules, for which many pharmacological effects targeting multiple tissues have been described. However, a common underlying mechanism driving its full pharmacological activity has not been elucidated to date. G-quadruplexes (G4s) are non-canonical nucleic acid structures found in promoters and involved in controlling gene transcription. This study demonstrates a G4-dependent mode of action for RSV, explaining its multi-target traits. RSV was shown to stabilise cellular G4s, which accumulate around double strand breaks (DSBs) in the promoters of differentially expressed genes (DEGs). G4 targeting triggers DNA damage and controls gene expression. Unravelling the main mode of action of RSV will be helpful to improve its therapeutic potential in a wide variety of health scenarios.

physiology↗

bioRxiv2023

Molecular pharmacology of selective NaV1.6 and dual NaV1.6 and NaV1.2 channel inhibitors that suppress excitatory neuronal activity ex vivo

Sodium channel inhibitors are used to treat neurological disorders of hyperexcitability. However, all currently available sodium channel targeting anti-seizure medications are non-selective among the NaV isoforms which potentially limits efficacy and therapeutic safety margins. XPC-7724 and XPC-5462 represent a new class of small molecule compounds. These compounds target inhibition of the NaV1.6 and NaV1.2 channels in excitatory pyramidal neurons and possess a molecular selectivity of >100 fold against NaV1.1 channels that are dominant in inhibitory cells. This profile will enable pharmacological dissection of the physiological roles of NaV1.2 and NaV1.6 and help to define the role of each channel in disease states. These compounds bind to and stabilize the inactivated-state of the channels, demonstrate higher potency with longer residency times, and slower off-rates than carbamazepine and phenytoin. These compounds possess cellular selectivity ex vivo in inhibiting action potential firing in cortical excitatory pyramidal neurons, whilst sparing fast spiking inhibitory interneurons. XPC-5462 also suppresses epileptiform activity in an ex vivo brain slice seizure model. This class of compounds provides a unique approach for treating neuronal excitability disorders by selectively down-regulating excitatory circuits. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=194 HEIGHT=200 SRC="FIGDIR/small/551643v2_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@70750corg.highwire.dtl.DTLVardef@114756aorg.highwire.dtl.DTLVardef@289009org.highwire.dtl.DTLVardef@1086e23_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2023

Comprehensive insight into the alterations in the gut microbiome and the intestinal barrier as a consequence of iron deficiency anaemia

BackgroundIron is an essential micronutrient for all living organisms, and as such, iron deficiency is the top leading cause of anaemia. Iron supplements have been shown to be detrimental to the gut microbiome and the intestinal epithelium, triggering dysbiosis and an impaired gut barrier. However, a comprehensive analysis of these two aspects have not been performed during IDA. This study aims to delve further into the analysis of the gut microbiome in an animal model of IDA and to relate microbial changes to the biological processes occurring in the colonic epithelium, with a special focus on the gut barrier. This in-depth analysis might mean a step forward minimising the negative impact of iron supplements on intestinal health during IDA. MethodsIDA was experimentally induced in an animal model through the use of an iron deficient diet. Shotgun sequencing was used to gain insight into alterations of the gut microbiome in the most affected intestinal region during IDA, the colon. Histological analyses, mRNA sequencing (RNA-Seq), qPCR and immunofluorescence were used to study transcriptionally deregulated processes in the colonic epithelium. Determinations of lipopolysaccharide and bacteria-specific immunoglobulins were performed to assess microbial translocation. ResultsMicrobial metabolism in the colon shifted towards an increased production of certain amino acids, short chain fatty acids and nucleotides, with Clostridium species being enriched during IDA. Structural alterations of the colonic epithelium were shown by histological analysis. RNA-Seq revealed a downregulation of extracellular matrix-associated genes and proteins and an overall underdeveloped epithelium. Increased levels of serum LPS in the anaemic animals and an increased immune response against IDA dysbiotic bacteria support an impairment in the integrity of the gut barrier. ConclusionsIDA negatively impacts the gut microbiome and the intestinal barrier, triggering an increased microbial translocation. This study emphasizes the deterioration of gut health during IDA and the fact that it should be addressed when treating the disease.

pathology↗

bioRxiv2022

Distinct GSDMB protein isoforms and protease cleavage processes differentially control pyroptotic cell death and mitochondrial damage in cancer cells.

The formation of Gasdermin (GSDM) pores, leading to pyroptosis or other context-dependent consequences, is directly involved in multiple diseases. Gasdermin-B (GSDMB) plays complex and controversial roles in pathologies, with pyroptosis-dependent and independent functions. GSDMB is promising oncologic therapeutic target since it exhibits either antitumor function, when immunocyte-mediated Granzyme-A (GZMA) cleaves GSDMB releasing its cytotoxic N-terminal domain, or pro-tumoral activities (invasion, metastasis, and drug resistance). However, it is still unknown the precise regulatory mechanisms of GSDMB pyroptosis as well as the differential effects of the four translated GSDMB variants (GSDMB1-4, that differ in the alternative usage of exons 6-7) in this process. Here, we first prove that exon 6 translation (in the interdomain protein linker) is essential for pyroptosis, and therefore, GSDMB isoforms lacking this exon (GSDMB1-2) cannot provoke cancer cell death. Consistently, in large series of breast cancer samples GSDMB2 expression, and not of exon6-containing variants (GSDMB3-4), associates with unfavourable clinical-pathological parameters. Moreover, cellular, and biochemical analyses combined with confocal, live cell imaging, and electron microscopy studies, demonstrated that diverse GSDMB N-terminal constructs containing exon-6 induce mitochondrial damage (increased mitochondrial ROS, membrane potential loss and mitochondrial DNA release) together with pyroptotic membrane cell lysis. While exon-6 residues are not required for membrane or mitochondrial localization, we also identified other key residues for N-terminal domain cytotoxicity. Additionally, we demonstrated that all GSDMB variants share the cleavage sites for GZMA, Neutrophil Elastase (identified in this study) and caspases. Interestingly, whereas Neutrophil Elastase and caspases produce N-terminal fragments in all GSDMB isoforms with no pyroptotic activity, thus acting as a potential inhibitory mechanism, GZMA cleavage activates pyroptosis in an isoform-dependent way. Summarizing, our results have important implications for understanding the complex roles of GSDMB isoforms in cancer and other pathologies and for the future design of GSDMB-targeted therapies.

molecular biology↗

bioRxiv2022

Pharmacological determination of the fractional block of Nav channels required to impair neuronal excitability and ex vivo seizures

Voltage-gated sodium channels (Nav) are essential for the initiation and propagation of action potentials in neurons. Of the different channel subtypes, Nav1.1, Nav1.2 and Nav1.6 are prominently expressed in the adult central nervous system (CNS). All three of these sodium channel subtypes are sensitive to block by the neurotoxin tetrodotoxin (TTX), with TTX being almost equipotent on all three subtypes. In the present study we have used TTX to determine the fractional block of Nav channels required to impair action potential firing in pyramidal neurons and reduce network seizure-like activity. Using automated patch-clamp electrophysiology, we first determined the IC50s of TTX on mouse Nav1.1, Nav1.2 and Nav1.6 channels expressed in HEK cells, demonstrating this to be consistent with previously published data on human Nav channels. We then compared this data to the potency of block of Nav current measured in pyramidal neurons from neocortical brain slices. Interestingly, we found that it requires nearly 10-fold greater concentration of TTX over the IC50 to induce significant block of action potentials using a current-step protocol. In contrast, concentrations near the IC50 resulted in a significant reduction in AP firing and increase in rheobase using a ramp protocol. Surprisingly, a 20% reduction in action potential generation observed with 3 nM TTX resulted in significant block of seizure-like activity in the 0 Mg2+ model of epilepsy. Additionally, we found that approximately 50% block in pyramidal cell intrinsic excitability is sufficient to completely block all seizure-like events. These data serve as a critical starting point in understanding how fractional block of Nav channels affect intrinsic neuronal excitability and seizure-like activity. It further suggests that seizures can be controlled without significantly compromising intrinsic neuronal activity and determines the required fold over IC50 for novel and clinically relevant Nav channel blockers to produce efficacy and limit side effects.

neuroscience↗

bioRxiv2020

Transient disruption of the inferior parietal lobule impairs the ability to attribute intention to action

Although it is well established that fronto-parietal regions are active during action observation, whether they play a causal role in the ability to infer others intentions from visual kinematics remains undetermined. In experiments reported here, we combined offline continuous theta-burst stimulation (cTBS) with computational modeling to reveal single-trial computations in the inferior parietal lobule (IPL) and inferior frontal gyrus (IFG). Participants received cTBS over the left anterior IPL and the left IFG pars orbitalis, in separate sessions, before completing an intention discrimination task (discriminate intention of observed reach-to-grasp acts) or a kinematic discrimination task (discriminate peak wrist height of the same acts) unrelated to intention. We targeted intentions-sensitive regions whose fMRI-measured activity accurately discriminated intention from the same action stimuli. We found that transient disruption of activity of the left IPL, but not the IFG, impaired the observers ability to judge intention from movement kinematics. Kinematic discrimination unrelated to intention, in contrast, was largely unaffected. Computational analyses revealed that IPL cTBS did not impair the ability to see changes in movement kinematics, nor did it alter the weight given to informative versus non-informative kinematic features. Rather, it selectively impaired the ability to link variations in informative features to the correct intention. These results provide the first causal evidence that left anterior IPL maps kinematics to intentions.

neuroscience↗

bioRxiv2019

Transient disruption of the inferior parietal lobule impairs action mindreading

Although it is well established that fronto-parietal regions are active during action observation, whether they play a causal role in the ability to "mindread" others actions remains controversial. In experiments reported here, we combined offline continuous theta-burst stimulation (cTBS) with computational modeling to reveal single-trial computations in the inferior parietal lobule (IPL) and inferior frontal gyrus (IFG). Participants received cTBS over the left IPL and IFG, in separate sessions, before completing an intention discrimination task or a kinematic discrimination task unrelated to intention. We found that transient disruption of activity of the IPL, but not the IFG, specifically impaired the observers ability to judge intention from movement kinematics. Kinematic discrimination unrelated to intention, in contrast, was largely unaffected. Computational analyses revealed that IPL cTBS did not impair the ability to see changes in movement kinematics, nor did it alter the weight given to informative versus non-informative kinematic features. Rather, it selectively impaired the ability to link variations in informative features to the correct intention. These results provide the first causal evidence that IPL maps kinematics to intentions.

neuroscience↗