Biology subjects

Sanchez, G.

Publications and source records attributed to Sanchez, G..

17 recordsLinked to original sources

bioRxiv2026

Functional diversification of UBP6 in plant immunity through N-degron pathway regulation

Deubiquitylases are key proteolytic regulators of ubiquitin-dependent cellular processes, catalyzing the removal or remodelling of ubiquitin modifications on substrate proteins, including those targeted for proteasomal degradation. UBIQUITIN PROTEASE (UBP)6 is a deubiquitylase that promotes the abundance of NONEXPRESSOR OF PATHOGENESIS RELATED GENES (NPR)1, a conserved master regulator of plant immunity. Here, we show that the Arabidopsis thaliana protease METACASPASE (MC)9 site-specifically processes UBP6, generating the E157-UBP6 proteoform, whose stability is controlled by the Arginyl-transferase (ATE) N-degron pathway. We observed that pathogen recognition both triggers UBP6 cleavage and leads to conditional stabilisation of E157 UBP6, which is enhanced as the defence response intensifies. Our data suggest that E157 UBP6, which lacks deubiquitylating activity, may induce inhibition of the proteasome, elevating NPR1 levels and enhancing salicylic acid (SA) induced gene activation, all of which collectively contribute to restricting pathogen growth. Thus, UBP6 cleavage and N-degron pathway regulation provide distinct proteoforms of UBP6 with specific effects on the immune processes.

plant biology↗

bioRxiv2026

Environmental Regulation and Gene-by-Environment Interaction Influence RAP1 Activity and its Impact on Gene Expression

Gene-by-environment (GxE) interactions play a major role in shaping both phenotypic and molecular variation, with important implications for human health and disease. In this study, we used the Doxycycline (Dox) regulated, tetracycline-responsive (Tet-Off) promoter system to sequentially reduce or titrate gene expression levels of the essential yeast transcription factor Repressor Activator Protein 1 (RAP1) similar to a hypomorph allele series, across three distinct environments: Yeast Peptone Dextrose (YPD) media, YPD media with Heat Shock (HS), and Yeast Peptone Acetate (YPAC) media. We then performed RNA sequencing (RNA Seq) to assess global transcriptional responses to RAP1 reduction in these different growth environments. Our analysis first focused on the independent effects of varying RAP1 expression levels within and across environments. We then explored GxE interactions, revealing a subset of genes with significant consequences of reduced levels of RAP1 and environment-specific expression patterns. Notably, many genes exhibited opposite effects of RAP1 titration on gene expression when yeast were grown in YPAC media compared to YPD media and/or HS, suggesting environment-dependent regulatory architecture. This design reveals how cells integrate internal transcriptional and regulatory changes with external environmental cues, providing a deeper view of GxE architecture. Using Weighted Gene Co-expression Network Analysis (WGCNA), we identified co-regulated gene modules, and by combining this with transcription factor motif enrichment tests, our study identified candidate regulators driving their dynamics. Our findings demonstrate that gene regulatory networks can vary dramatically depending on the environmental context an organism experiences, which can then influence the specific phenotypes produced by a particular genetic perturbation. This illustrates the complexity of genotype-environment interactions and the importance of studying gene function in multiple environments to gain a truly comprehensive understanding of a genes sometimes numerous and diverse functions.

genomics↗

bioRxiv2025

GABA-induced Ca2+ signaling in the primary cilium of neurons

The complex signaling processing in neurons requires establishment of autonomous compartments. The compartment that is unique for neurons and crucial for neuron-neuron signaling is the synapse. Another compartment, that neurons share with all other cells in the body, is the primary cilium. The primary cilium is a solitary organelle, present in almost every neuronal cell type, that extends into the extracellular space for detection of signals. Several GPCRs have been identified as ciliary receptors, and here we show that the metabotropic GABA receptor subtype 1 localizes to primary cilia of neurons across different regions of the mouse brain and that activation of these receptors initiates Ca2+ signaling that is restricted to this organelle. The excitatory nature of GABAergic signaling in primary cilia is opposite to GABA action in other neuronal domains, indicating distinct modes of action of this universal inhibitory neurotransmitter even within the same neuron.

neuroscience↗

bioRxiv2025

MIR192 Upregulates GLP-1 Receptor and Improves Statin-Induced Impairment of Insulin Secretion

Statins are a commonly prescribed cholesterol lowering drug class that can increase the risk of new-onset diabetes (NOD). To investigate the molecular mechanisms underlying this effect, we generated human induced pluripotent stem cells (iPSCs) from individuals identified from electronic health records of Kaiser Permanente of Northern California who were susceptible to developing NOD after statin initiation or controls who maintained stable fasting glucose on statin treatment. RNA-seq analysis of iPSCs incubated with atorvastatin, simvastatin or mock buffer for 24 hours identified the long non-coding RNA MIR194-2HG as a top candidate gene. Statin-induced increases in its expression were observed in NOD resistant controls, while statin-induced reductions occurred in NOD susceptible cases. MIR194-2HG encompasses two microRNA genes: MIR192 and MIR194-2. The mature microRNA miR-192-5p, derived from the 5 arm of MIR192, was predicted to bind the 3UTR of the glucagon like peptide 1 (GLP-1) receptor (GLP1R) transcript. Transfection of a rat insulinoma cell line INS-1 with a miR-192-5p mimic increased Glp1r transcript (1.41-fold) and protein (1.51-fold) levels compared to a scrambled control. Using a luciferase reporter containing the human GLP1R 3UTR, miR-192-5p overexpression similarly increased luciferase signal (1.44-fold). The miR-192-5p mimic enhanced glucose stimulated insulin secretion (GSIS) in response to GLP1R agonists (1.64-1.81-fold) and rescued simvastatin-induced GSIS impairment in INS-1 cells. Wild-type mice treated with miR-192 AAV8 had improved glucose sensitivity. Islets isolated from these mice exhibited enhanced GLP-1 potentiated GSIS during perifusion ex vivo. These effects were absent in the DIRKO (Glp1r/Gipr double knockout) mouse islets, consistent with the idea that miR-192 promotes GLP-1 mediated GSIS through GLP1R. These findings implicate MIR192 in statin-induced impairment of GSIS by modulating GLP1R, potentially contributing to the susceptibility to NOD in statin users.

cell biology↗

bioRxiv2025

The sperm specific Na+,K+-ATPase α4 shows a highly structured and dynamic distribution at the sperm flagellum

Na+,K+-ATPase 4 is a unique cell plasma membrane Na+ and K+ transporter of spermatozoa, which is essential for male fertility. Previous studies have shown that Na+,K+-ATPase 4 is highly expressed in the sperm flagellum; however, the spatial arrangement of Na+,K+-ATPase 4 at the subcellular level and its relationship to the functional state of the cells are unknown. We studied this here using stimulated emission depletion (STED) super-resolution microscopy. We show that, under non-capacitated conditions, Na+,K+-ATPase 4 is distributed in a trilinear pattern along the midpiece and as a scattered single line along the principal piece segment of the sperm flagellum. Under capacitated conditions, Na+,K+-ATPase 4 pattern undergoes remodelling and its distribution shifts into a single line along the entire length of the flagellum. On the other hand, Na+,K+-ATPase 1 the somatic isoform of Na+,K+-ATPase also present in sperm, exhibits a similar trilaminar localization at the flagellar midpiece but a bilinear pattern in the principal piece. This distribution, unlike that of Na+,K+-ATPase 4, does not change during sperm capacitation. These differences in the localization pattern and spatial dynamics of Na+,K+- ATPase isoform expression highlights the dissimilarities in the roles of both ion transporters. The specific modulation of Na+,K+-ATPase 4 distribution, combined with the unique role that it has in sperm function, stresses the importance of Na+,K+-ATPase 4 for male fertility. Significance statementThis is the first demonstration of the highly structured nature of Na+,K+-ATPase in the plasma membrane of sperm, including the sperm specific Na+,K+-ATPase 4 isoform, which is key for male fertility, and the somatic Na+,K+-ATPase 1, which is present in all cells. Utilizing stimulated emission depletion (STED) super resolution microscopy, we discovered that Na+,K+- ATPase 4 and Na+,K+-ATPase 1 have different distributions along the sperm flagellum. Moreover, only Na+,K+-ATPase 4 undergoes remodelling during sperm capacitation. These specific patterns of localization that are dependent on the sperm functional state in combination with the different function and regulation of Na+,K+-ATPase isoforms highlights the sophisticated mechanisms that cells have evolved to fulfil their unique function.

cell biology↗

bioRxiv2024

Locally released somatostatin triggers cAMP and Ca2+ signaling in primary cilia to modulate pancreatic β-cell function

Somatostatin is produced and released from {delta}-cells within pancreatic islets of Langerhans and constitutes one of the most important negative regulators of islet hormone secretion. Somatostatin receptors (SSTR) are abundantly expressed in the islet cells and coupled to Gi and lowering of intracellular cAMP. We find that both SSTR3 and SSTR5 localize to primary cilia of {beta}-cells, and that activation of these receptors lowers the ciliary cAMP concentration. cAMP produced in the cytosol can enter the cilium through diffusion, but activation of ciliary SSTR3 specifically counteracts the rise of cAMP in the cilium. Moreover, we find that islet {delta}-cells are positioned near primary cilia of the other islet cell types and that somatostatin secretion is directed towards primary cilia. While acute exposure to somatostatin caused a rapid lowering of ciliary cAMP, sustained exposure promoted nuclear entry of the cilia-dependent transcription factor GLI2 through a mechanism that operated in parallel with the canonical Hedgehog pathway and depended on ciliary Ca2+ signaling. We also find that primary cilia length is reduced in islets from human donors with type-2 diabetes, which is associated with a reduction in cilia-{delta}-cell interactions. Our findings show that islet cell primary cilia constitute an important target of somatostatin action that endows it with the ability to regulate islet cell function beyond the acute suppression of hormone release.

cell biology↗

bioRxiv2023

Human organoid modeling of congenital malformations caused by RFX6 mutations reveal an essential role for this transcription factor in establishing and maintaining duodenal identity upstream of PDX1

The gastrointestinal (GI) tract consists of highly specialized organs from the proximal esophagus to the distal colon, each with unique functions. Rare congenital malformations of the GI tract, including organ atresia, agenesis or mis-patterning are linked to gene mutations although the molecular basis of these malformations has been poorly studied due to lack of model systems to study human development. We identified a patient with compound heterozygous mutations in the transcription factor RFX6 with pancreatic agenesis as previously described. In addition, the patient had duodenal mal-rotation and atresia suggesting that establishment of the proximal small intestine was impaired in these patients. To identify the molecular basis of the intestinal malformation we generated induced pluripotent stem cell lines from this patient, and derived human intestinal organoid (HIOs) to identify how mutations in RFX6 impact intestinal patterning and function. We identified that the duodenal identity of HIOs and patient tissues had adopted a more distal small intestinal signature, including expression of SATB2, normally expressed in the ileum and colon. CRISPR-mediated correction of RFX6 restored duodenal identity, including expression of PDX1, which is required for duodenal development. Using transcriptomic approaches in HIOs and Xenopus embryos we identified that PDX1 is a downstream transcriptional target of RFX6 and that PDX1 expression in a RFX6 mutant background was sufficient to rescue duodenal identity. However, RFX6 had a PDX1-independent role in regulating expression of components of WNT, HH, and BMP signaling pathways that are critical for establishing early regional identity in the GI tract. In summary, we have identified that RFX6 is one of the most upstream regulators early intestinal patterning in vertebrates and that it acts by regulating key transcriptional and signaling pathways.

developmental biology↗

bioRxiv2023

ddRAD-seq-derived SNPs reveal novel association signatures for fruit-related traits in peach

Breeding for new peach cultivars with enhanced traits is a prime target in breeding programs. In this study, we used a discovery panel of 90 peach accessions in order to dissect the genetic architecture of 16 fruit-related traits. ddRAD-seq genotyping and the intersection between three variant callers yielded 13,045 high-confidence SNPs. These markers were subjected to an exhaustive association analysis by testing up to seven GWAS models. Blink was selected as the most adjusted, simultaneously balancing false positive and negative associations. Totally, we identified 16 association signals for six traits showing high broad-sense heritability: harvest date, fruit weight, flesh firmness, contents of flavonoids, anthocyanins and sorbitol. By assessing the allelic effect of significant markers on phenotypic attributes, nine SNP alleles were denoted favorable. A promising marker (SNC_034014.1_7012470) was found to be simultaneously associated with harvest date and fruit firmness conferring a positive allelic effect on both traits. We anticipate that this marker could be used to improve firmness in late harvested cultivars. Candidate causal genes were shortlisted when fulfilling the following criteria: i) position within the linkage disequilibrium block, ii) functional annotation and iii) expression pattern. A bibliographic review of previously reported QTLs mapping nearby the associated markers allowed us to benchmark the accuracy of our approach. Despite the moderate germplasm size, ddRAD-seq allowed us to produce an accurate representation of peachs genome resulting in SNP markers suitable for empirical association studies. Together with candidate genes, they lay the foundation for further genetic dissection of peach key traits.

plant biology↗

bioRxiv2022

X chromosome dosage drives statin-induced dysglycemia and mitochondrial dysfunction

Statin drugs lower blood cholesterol levels for cardiovascular disease prevention. Women are more likely than men to experience adverse statin effects, particularly new-onset diabetes (NOD) and muscle weakness. We determined that female mice are more susceptible than males to glucose intolerance, fasting hyperglycemia, and muscle weakness after short-term statin treatment. Lipidomic, transcriptomic, and biochemical analyses identified reduced docosahexaenoic acid (DHA) levels, and impaired redox tone and mitochondrial respiration specifically in statin-treated female mice. Statin adverse effects could be prevented in females by complementation with a source of DHA. Statin adverse effects segregated with XX chromosome complement, and specifically dosage of the Kdm5c gene, which regulates fatty acid gene expression and has differential expression levels in females and males. In humans, we found that women experience more severe reductions than men in DHA levels after short-term statin administration, and that DHA reduction was correlated with increases in fasting glucose levels. Furthermore, induced pluripotent stem cells derived from women, but not men, who developed NOD exhibited impaired mitochondrial function when treated with statin. Overall, our studies identify biochemical mechanisms, biomarkers, and a genetic risk factor for susceptibility to statin adverse effects, and point to DHA supplementation as a preventive co-therapy.

physiology↗

bioRxiv2021

The β-cell primary cilium is an autonomous Ca2+ compartment for paracrine GABA signalling

The primary cilium is an organelle present in most adult mammalian cells and is thought of as an antenna for detection of a variety of signals. Here we use intact mouse pancreatic islets of Langerhans to investigate signalling properties of the primary cilium in {beta}-cells. Using cilia-targeted Ca2+ indicators we find that the resting Ca2+ concentration in the cilium is lower than that of the cytosol, and we uncover a Ca2+ extrusion mechanism in the cilium that effectively insulates the cilium from changes in cytosolic Ca2+. Stimuli that give rise to pronounced cytosolic Ca2+ concentration increases, such as glucose- and depolarization-induced Ca2+ influx, and mobilization of Ca2+ from the ER, was accompanied by minor increases in cilia Ca2+ concentrations that were spatially restricted to a small compartment at the base. Conversely, we observe pronounced Ca2+ concentration changes in the primary cilia of islet {beta}-cells that do not propagate into the cytosol and show that paracrine GABA signalling via cilia-localized GABA-B1-receptors is responsible for this Ca2+ signalling. Finally, we demonstrate that the cilia response to GABA involves ligand-dependent transport of GABA-B1 receptors into the cilium.

cell biology↗

bioRxiv2020

PAF1 facilitates RNA polymerase II ubiquitination by the Elongin A complex through phosphorylation by CDK12

The conserved Polymerase-Associated Factor 1 complex (PAF1C) regulates all stages of the RNA polymerase II (RNAPII) transcription cycle from the promoter to the 3 end formation site of mRNA encoding genes and has been linked to numerous transcription related processes. Here, we show that PAF1 interacts with Elongin A, a transcription elongation factor as well as a component of a cullin-RING ligase that targets stalled RNAPII for ubiquitination and proteasome-dependent degradation in response to DNA damage or other stresses. We show that, in absence of any induced stress, PAF1 physically interacts with the E3 ubiquitin ligase form of the Elongin A complex and facilitates ubiquitination of RNAPII. We demonstrate that this ubiquitination is dependent of the Ser2 phosphorylation of the RNAPII carboxy-terminal domain (CTD) by CDK12. Our findings highlight a novel unexpected role of PAF1-CDK12 in RNAPII transcription cycle, raising the possibility that the Elongin A ubiquitin ligase plays a role in normal transcription process, and suggest a transcription surveillance mechanism ready to degrade RNAPII if needed.

cell biology↗

bioRxiv2020

Piezo1 activation attenuates thrombin-induced blebbing in breast cancer cells

Cancer cells exploit a variety of migration modes to leave primary tumors and establish metastases, including amoeboid cell migration facilitated by bleb formation. Here we demonstrate that thrombin induces dynamic blebbing in the MDA-MB-231 breast cancer cell line, and confirm that PAR2 activation is sufficient to induce this effect. Cell confinement has been implicated as a driving force in bleb-based migration. Unexpectedly, we find that gentle contact compression, exerted using a "Cell Press" to mechanically stimulate cells, attenuated thrombin-induced blebbing with an associated increase in cytosolic calcium. Thrombin-induced blebbing was similarly attenuated using Yoda1, an agonist of the mechanosensitive calcium channel Piezo1, and its capacity to attenuate blebbing was impaired in Piezo1 depleted cells. Additionally, Piezo1 activation suppressed and reversed the thrombin-induced phosphorylation of ERM proteins, which are implicated in the blebbing process, and this activity was in part mediated through activation of the PP1A/PP2A family of serine/threonine phosphatases. Our results provide mechanistic insights into Piezo1 activation as a suppressor of dynamic blebbing, specifically that which is induced by thrombin.

cell biology↗

bioRxiv2020

NF90 Modulates Processing of a Subset of Human Pri-miRNAs

MicroRNAs are predicted to regulate the expression of more than 60% of mammalian genes and play fundamental roles in most biological processes. Deregulation of miRNA expression is a hallmark of most cancers and further investigation of mechanisms controlling miRNA biogenesis is needed. The dsRNA-binding protein, NF90 has been shown to act as a competitor of Microprocessor for a limited number of pri-miRNAs. Here, we show that NF90 has a more widespread effect on pri-miRNA biogenesis than previously thought. Genome-wide approaches revealed that NF90 is associated with the stem region of 38 pri-miRNAs, in a manner that is largely exclusive of Microprocessor. Following loss of NF90, 22 NF90-bound pri-miRNAs showed increased abundance of mature miRNA products. NF90-targeted pri-miRNAs are highly stable, having a lower free energy and fewer mismatches compared to all pri-miRNAs. Mutations leading to less stable structures reduced NF90 binding while increasing pri-miRNA stability led to acquisition of NF90 association, as determined by RNA EMSA. NF90-bound and modulated pri-miRNAs are embedded in introns of host genes and expression of several host genes is concomitantly modulated. These data suggest that NF90 controls the processing of a subset of highly stable, intronic miRNAs.

molecular biology↗

bioRxiv2019

Sporadic ERK pulses drive non-genetic resistance in drug-adapted BRAFV600E melanoma cells

Anti-cancer drugs commonly target signal transduction proteins activated by mutation. In patients with BRAFV600E melanoma, small molecule RAF and MEK kinase inhibitors cause dramatic but often transient tumor regression. Emerging evidence suggests that cancer cells adapting by non-genetic mechanisms constitute a reservoir for the development of drug-resistant tumors. Here, we show that few hours after exposure to RAF/MEK inhibitors, BRAFV600E melanomas undergo adaptive changes involving disruption of negative feedback and sporadic pulsatile reactivation of the MAPK pathway, so that MAPK activity is transiently high enough in some cells to drive proliferation. Quantitative proteomics and computational modeling show that pulsatile MAPK reactivation is possible due to the co-existence in cells of two MAPK cascades: one driven by BRAFV600E that is drug-sensitive and a second driven by receptors that is drug-resistant. Paradoxically, this may account both for the frequent emergence of drug resistance and for the tolerability of RAF/MEK therapy in patients.

cancer biology↗

bioRxiv2019

Head MagnetoMyography (hMMG): a novel approach to monitor face and whole-head muscular activity

Muscular activity recording is of high basic science and clinical relevance and is typically achieved using electromyography (EMG). While providing detailed information about the state of a specific muscle, this technique has limitations such as the need for a-priori assumptions about electrode placement and difficulty with recording muscular activity patterns from extended body areas at once. For head and face muscle activity, the present work aimed to overcome these restrictions by exploiting magnetoencephalography (MEG) as a whole-head myographic recorder (head magnetomyography, hMMG). This is in contrast to common MEG studies, which treat muscular activity as artifact in electromagnetic brain activity. In a first proof-of-concept step, participants imitated emotional facial expressions performed by a model. Exploiting source projection algorithms, we were able to reconstruct muscular activity, showing spatial activation patterns in accord with the hypothesized muscular contractions. Going one step further, participants passively observed affective pictures with negative, neutral, or positive valence. Applying multivariate pattern analysis to the reconstructed hMMG signal, we were able to decode above chance the valence category of the presented pictures. Underlining the potential of hMMG, a searchlight analysis revealed that generally neglected neck muscles exhibit information on stimulus valence. Results confirm the utility of hMMG as a whole-head electromyographic recorder to quantify muscular activation patterns including muscular regions that are typically not recorded with EMG. This key advantage beyond conventional EMG has substantial scientific and clinical potential.

neuroscience↗

bioRxiv2018

Prediction-related neural activity during silent periods is sharply tuned

Prior experience shapes sensory perception by enabling the formation of expectations with regards to the occurrence of upcoming sensory events. Especially in the visual modality, an increasing number of studies show that prediction-related neural signals carry feature-specific information about the stimulus. This is less established in the auditory modality, in particular without bottom-up signals driving neural activity. We studied whether auditory predictions are sharply tuned to even carry tonotopic specific information. For this purpose, we conducted a Magnetoencephalography (MEG) experiment in which participants passively listened to sound sequences that varied in their regularity (i.e. entropy). Sound presentations were temporally predictable (3 Hz rate), but were occasionally omitted. Training classifiers on the random (high entropy) sound sequence and applying them to all conditions in a time-generalized manner, allowed us to assess whether and how carrier frequency specific information in the MEG signal is modulated according to the entropy level. We show that especially in an ordered (most predictable) sensory context neural activity during the anticipatory and omission periods contains carrier-frequency specific information. Overall our results illustrate in the human auditory system that prediction-related neural activity can be tuned in a tonotopically specific manner.

neuroscience↗

bioRxiv2017

Decoding across sensory modalities reveals common supramodal signatures of conscious perception

An increasing number of studies highlight common brain regions and processes in mediating conscious sensory experience. While most studies have been performed in the visual modality, it is implicitly assumed that similar processes are involved in other sensory modalities. However, the existence of supramodal neural processes related to conscious perception has not been convincingly shown so far. Here, we aim to directly address this issue by investigating whether neural correlates of conscious perception in one modality can predict conscious perception in a different modality. In two separate experiments, we presented participants with successive blocks of near-threshold tasks involving tactile, visual or auditory stimuli during the same magnetoencephalography (MEG) acquisition. Using decoding analysis in the post-stimulus period between sensory modalities, our first experiment uncovered supramodal spatio-temporal neural activity patterns predicting conscious perception of the feeble stimulation. Strikingly, these supramodal patterns included activity in primary sensory regions not directly relevant to the task (e.g. neural activity in visual cortex predicting conscious perception of auditory near-threshold stimulation). We carefully replicate our results in a control experiment that furthermore show that the relevant patterns are independent of the type of report (i.e. whether conscious perception was reported by pressing or withholding a button-press). Using standard paradigms for probing neural correlates of conscious perception, our findings reveal a common signature of conscious access across sensory modalities and illustrate the temporally late and widespread broadcasting of neural representations, even into task-unrelated primary sensory processing regions.

neuroscience↗