Biology subjects

Ortega, M. A.

Publications and source records attributed to Ortega, M. A..

6 recordsLinked to original sources

bioRxiv2026

A comparative transcriptomic framework across kidney organoid, assembloid, and transplantation models

Human kidney organoids recapitulate key aspects of renal development and have emerged as valuable platforms for disease modeling, nephrotoxicity screening, and therapeutic development. The field now includes a wide range of emerging protocols with distinct cellular compositions and maturation states, which complicates systematic comparison and model selection. Here, we integrated single-cell and single-nucleus transcriptomes from 11 studies spanning kidney organoid and assembloids, both in vitro and following transplantation, benchmarked against fetal and adult kidney references. Transcriptional maturation toward adult identity is compartment specific and does not correlate with protocol complexity. Assembloid protocols show the most adult-like podocyte and distal nephron signatures, transplantation is associated with enhanced tubular oxidative metabolic features, only protocols incorporating ureteric progenitors reliably generate collecting-duct lineages, and no protocol achieves mature adult proximal tubule identity. Annotating against either fetal or adult kidney reference alone leads to misassignment, because early fetal nephron epithelium transcriptionally resembles injury-dedifferentiated adult proximal tubule cells. Assembloid and transplantation models share elevated mechanosensing pathway expression independently of vascularization. Together, these findings provide a framework for kidney organoid model selection.

bioinformatics↗

bioRxiv2026

The exocyst is an insulin-sensitive regulator of amyloid precursor protein trafficking and amyloid-beta generation in neurons

Intracellular trafficking of amyloid precursor protein (APP) critically influences amyloidogenic processing, yet the mechanisms regulating this pathway remain incompletely defined. The exocyst is a highly conserved, insulin-responsive, eight-protein Rab effector complex that directs intracellular transport vesicle targeting and docking. We identified APP in a proteomics screen of neuronal cell surface proteins altered after chemical inhibition of exocyst activity. In SH-SY5Y cells expressing a mutant APP that enhances amyloidogenic processing, RNAi-mediated silencing of exocyst subunits significantly decreased sAPP and A{beta} secretion, leading to significant intracellular APP accumulation. We found high-resolution co-localization of APP with exocyst subunits in soma and neurites of differentiated human SH-SY5Y neurons and mouse primary hippocampal neurons, and live-cell TIRF microscopy identified highly coordinated movement between fluorescently-tagged exocyst and APP proteins. These interactions were confirmed in these cells and in mouse brain histological sections by proximity ligation assays (PLAs) demonstrating close (<40nm) APP-EXOC5 association. To examine if exocyst activity in neurons is regulated by insulin, as it is in adipocytes and muscle, we generated a SH-SY5Y cell line with pHluorin-tagged GLUT4. Inhibition of the exocyst prevented exocytosis of GLUT4 to the plasma membrane in response to insulin. Additionally, using PLAs in mouse primary hippocampal neurons and SH-SY5Y neurons, we found that GLUT4-EXOC5 associations were increased by insulin signaling, but APP-EXOC5 associations were markedly reduced, indicating insulin-dependent retargeting of the exocyst complex away from APP+ vesicles towards GLUT+ vesicles. All together, these data identify the exocyst as a novel insulin-regulated mediator of neuronal APP trafficking and A{beta} secretion. In BriefWe show that the insulin-responsive exocyst regulates amyloidogenic processing of APP in neurons and that insulin signaling shifts the exocyst away from APP trafficking to promote the translocation of GLUT4-containing vesicles to the plasma membrane of neurons.

neuroscience↗

bioRxiv2025

Loss of flavonol 3-O-glucosyltransferase activity confers soybean resistance to leaf-chewing insects

Caterpillars and beetles are among the most economically damaging defoliating insects, and their economic damage is predicted to increase in the coming decades. Hence the use of genetically derived resistance to supplement other pest control strategies is warranted. In soybean (Glycine max (L.) Merr.), a major determinant for resistance is the quantitative trait locus, QTL-M. Glyma07g14530, the gene underlying QTL-M, encodes a feeding-inducible flavonol 3-O-glycosyltransferase (F3GlcT or UGT78D2) that glucosylates kaempferol, as well as quercetin, myricetin, and isorhamnetin. The resistant allele has a premature stop codon in it, thus preventing the glucosylation and sequestration of flavonols in the vacuole, leading to a concomitant accumulation of proanthocyanidins and manifestation of resistance. Expressing the dominant (susceptible) allele in resistant plants restores susceptibility and silencing the susceptible allele results in resistance. The discovery and characterization of GmF3GlcT helps clarify the role of flavonoids in resistance to leaf-chewing insects and facilitates the development of insect-resistant cultivars that ultimately can lower production costs and reduce insecticide applications. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=131 SRC="FIGDIR/small/679769v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@10e2e77org.highwire.dtl.DTLVardef@ca905org.highwire.dtl.DTLVardef@12cb46corg.highwire.dtl.DTLVardef@1f9328b_HPS_FORMAT_FIGEXP M_FIG C_FIG The loss of flavonol 3-O-glucosyltransferase in soybean reduces feeding damage from defoliating insects and is accompanied by a concomitant increase in proanthocyanidins (red arrowhead). SignificanceUnraveling the biochemical and genetic basis of soybean resistance to leaf-chewing insects facilitates the development of new, naturally insect resistant varieties. Such varieties contribute to on-farm profitability and reduced concerns over pesticide residues in the field.

plant biology↗

bioRxiv2024

A compendium of nonredundant short Polymerase III promoters for CRISPR applications

Multiplex genome editing via CRISPR enables simultaneous gene knockout, activation, and repression, but current toolkits often rely on repetitive and lengthy Pol III promoters, limiting construct diversity and genetic stability. Here, we present a diverse collection of minimal U6 and U3 Pol III promoters that support efficient guide RNA (gRNA) expression in dicots. Using CRISPR-Cas9 editing of mEGFP in Nicotiana benthamiana and Populus tremula x alba, we demonstrate that minimal promoters can match the performance of their longer counterparts. A systematic evaluation of 14 short promoters revealed that most are functional across species, with exceptions linked to sequence variations in the upstream sequence element (USE) and TATA box. Mutagenesis confirmed the causal role of specific nucleotide changes in promoter activity. Furthermore, we show that regions outside these conserved motifs can be modified to create new-to-nature, functional promoters. This work refines the consensus for functional Pol III promoter elements and expands the toolkit for efficient, stable, and scalable CRISPR editing in dicots, with implications for synthetic promoter design.

plant biology↗

bioRxiv2022

In vitro floral development in poplar: Insights into seed trichome and trimonoecy regulation

Woody perennials including Populus spp. (poplars) have a juvenile phase that ranges from several years to decades in length. This and the year-long floral development process are major impediments to breeding and to fundamental research of reproductive traits. Here we report a CRISPR-empowered in vitro flowering system and demonstrate its application using three reproductive traits: sex, seed trichomes, and a previously undescribed potential for trimonoecy in poplar.

plant biology↗

bioRxiv2021

Exocyst Inactivation in Urothelial Cells Disrupts Autophagy and Activates non-canonical NF-κB

Ureter obstruction is a highly prevalent event during embryonic development and is a major cause of pediatric kidney disease. We have reported that ureteric bud-specific ablation of the exocyst Exoc5 subunit in late-murine gestation results in failure of urothelial stratification, cell death, and complete ureter obstruction. However, the mechanistic connection between disrupted exocyst activity, urothelial cell death, and subsequent ureter obstruction was unclear. Here, we report that inhibited urothelial stratification does not drive cell death during ureter development. Instead, we demonstrate that the exocyst plays a critical role in autophagy in urothelial cells, and that disruption of autophagy activates a urothelial NF-{kappa}B stress response. Impaired autophagy first provokes canonical NF-{kappa}B activity which is progressively followed by increasing non-canonical NF-{kappa}B activity and cell death if the stress remains unresolved. Furthermore, we demonstrate that ureter obstructions can be completely rescued in Exoc5 conditional knockout mice by administering a single dose of pan-caspase inhibitor z-VAD-FMK at E16.5 prior to urothelial cell death. Taken together, ablation of Exoc5 disrupts autophagic stress response and activates progressive NF-{kappa}B signaling which promotes obstructive uropathy.

developmental biology↗