Biology subjects

Duncan, E.

Publications and source records attributed to Duncan, E..

10 recordsLinked to original sources

bioRxiv2026

Synaptic microRNA dysregulation orchestrates aberrant glutamatergic transmission in a human neuronal model of 22q11.2 deletion syndrome

22q11.2 Deletion Syndrome (22q11DS), the most prevalent chromosomal microdeletion disorder in humans (incidence ~1 in 4,000 live births), arises from hemizygous deletions of a 1.5-3.0 Mb region on chromosome 22. Notably, 20-30% of individuals with 22q11DS develop schizophrenia (SCZ) by early adulthood, making 22q11DS one of the strongest genetic risk factors for SCZ. However, the mechanisms by which the 22q11.2 deletion perturbs neuronal function and drive psychotic manifestations in 22q11DS remain poorly defined. In this study, we generated human 2D cortical neurons and 3D cortical organoids from induced pluripotent stem cells (iPSCs) derived from clinically well-characterized individuals with 22q11DS. Cellular and electrophysiological analyses revealed that 22q11DS neurons exhibit hyperexcitability, reduced glutamatergic synaptic transmission, and impaired homeostatic synaptic plasticity, which are pathophysiological hallmarks that may be relevant to the clinical, cognitive, and psychophysiological profiles of patients. Transcriptomic profiling of neurons and synaptosomes from 22q11DS cortical organoids uncovered dysregulated immune pathways and synaptic gene networks. Integrative mRNA-microRNA network analysis identified synergistic downregulation of hsa-miR-185-5p and hsa-miR-128-3p at synapses, driving aberrant regulation of immune and synaptic transcripts. Experimental knockdown of these microRNAs in control neurons recapitulated the molecular and functional phenotypes of 22q11DS neurons, thereby establishing a mechanistic link to synaptic dysfunction and impaired plasticity. Collectively, these findings delineate a multimodal mechanistic framework that bridges genetic vulnerability, synaptic pathology, and psychosis penetrance in 22q11DS, positioning dysregulated synaptic microRNAs as nodal regulators of neurodevelopmental networks and potential therapeutic targets.

neuroscience↗

bioRxiv2026

Phosphoproteomics identifies the DYRK1B protein kinase as a regulator of processing bodies

Dual-specificity tyrosine-phosphorylation-regulated kinase 1B (DYRK1B) modulates the cell cycle, cell fate during development, and is deregulated in cancer and metabolic syndrome. However, only a few DYRK1B substrates have been defined, so we undertook a phosphoproteomics screen in cells that exhibit inducible DYRK1B expression. Motif analysis revealed enrichment for proline-directed serine or threonine phosphorylation sites (pSer/pThr-Pro), consistent with the consensus motif of class I DYRKs. Gene ontology analysis revealed enrichment of proteins involved in mRNA binding, mRNA processing and ribonucleoprotein complexes. Several processing body (PB) components, including DCP1A, PATL1(PAT1B), EDC3 and 4E-T, were identified as DYRK1B-inducible phosphoproteins. DYRK1B also co-immunoprecipitated with DCP1A, PAT1B, EDC3, EDC4, DDX6 and XRN1. Super-resolution microscopy demonstrated that DYRK1B co-localised with DCP1A, DCP1B and DDX6 in PBs. Activation of DYRK1B increased PB abundance, whereas inhibition, depletion or knockout of DYRK1B reduced phosphorylation of DCP1A and 4E-T and decreased PB number. Re-expression of wild type, but not kinase-dead, DYRK1B restored PB numbers in knockout cells. These findings reveal novel DYRK1B targets and establish DYRK1B as a regulator of processing body abundance. HighlightsO_LIDYRK1B induces phosphorylation of a cluster of RNA binding and processing body associated proteins. C_LIO_LIDYRK1B localises to PBs and associates with multiple PB components. C_LIO_LIDYRK1B controls P-body abundance in a kinase-dependent manner. C_LI

cell biology↗

bioRxiv2026

Convergent effects of neurodevelopmental disorder-associated variants at mitochondria

Investigations into the molecular pathogenesis of clinically defined neurodevelopmental disorders (NDDs) including autism spectrum disorders (ASD) and schizophrenia (SCZ) have produced evidence implicating dysfunctional mitochondrial metabolism. However, the functional connection between risk variants and mitochondrial proteins largely remains unclear. We tested the hypothesis that proteins encoded by NDD-associated copy number variants (CNVs) and SCZ risk genes are enriched within the mitochondrial interactome. We found that NDD- and SCZ-associated genes exhibit mitochondrial association comparable to their overlap with synaptic proteins, with interaction networks converging most strongly on mitochondrial translation. Two high-risk CNVs, the 3q29 deletion (3q29Del) and the 22q11.2 deletion (22q11Del), confer similar risks for ASD and SCZ and have independently been linked to mitochondrial phenotypes. To test whether these CNVs produce convergent effects on mitochondrial proteins in developing human neural tissue, we generated an isogenic series of 3q29Del and 22q11Del induced-pluripotent stem cells (iPSCs) and differentiated them into forebrain cortical organoids. Quantitative proteomic analysis showed high similarity in the profiles of dysregulated proteins in 3q29Del and 22q11Del compared to isogenic controls. Enrichment analysis of proteins altered in both variants revealed significant convergence on the mitochondrial ribosome and translation machinery. Furthermore, manipulation of mitochondrial translation elicited similar proteomic and functional responses in organoids and neural progenitor cells across both CNVs. These findings indicate that NDD-associated genes have rich interactions with mitochondrial proteins and that two of the strongest risk factors for NDDs may similarly disrupt neural mitochondrial metabolism through impaired mitochondrial translation.

neuroscience↗

bioRxiv2024

Injury-induced transcription in the planarian outer epithelium is critical for tissue regeneration

Planarian flatworms have an extraordinary regenerative capacity; even a small, asymmetrical fragment of amputated planarian tissue can recreate an entirely new animal. The planarian field has made significant progress in identifying specific genes and cell types required for this complex process, but substantially less is known about the molecular mechanisms that convert a significant physical injury (e.g., head amputation) into the expression of specific genes in particular cell types. One tissue in which this question is particularly relevant is the planarian epidermis, a single-layer, mucociliary epithelium with similarities to the epithelia of mammalian airways. This epithelium plays an essential, early role in planarian regeneration as the cells surrounding the wound site must quickly stretch and extend to cover the wound area after injury. We hypothesized that these injury-induced morphological changes activate the transcription of genes with essential functions in the regenerative process. To best detect these transcriptional changes, we developed a rapid method for isolating the planarian outer epithelium and prepared ribodepleted RNA-sequencing libraries from samples isolated at multiple time points after tissue amputation. One gene we both identified using these methods and found to be functionally important for regeneration is a putative planarian homolog of vertebrate Shoc2. SHOC2 is an essential scaffolding protein that mediates specific, context-dependent activation of the ERK1/2 signaling pathway (J O_SCPLOWANGC_SCPLOW O_SCPLOWANDC_SCPLOWG O_SCPLOWALPERINC_SCPLOW2016). Notably, the ERK1/2 pathway is known to be activated after injury and required for regeneration in multiple species (M O_SCPLOWANUELC_SCPLOW et al. 2006; O O_SCPLOWWLARNC_SCPLOWet al. 2017; T O_SCPLOWOMASSOC_SCPLOWet al. 2023). These findings suggest that these epithelial datasets have the potential to uncover many functionally relevant and possibly highly conserved genes that play fundamental roles in animal regeneration.

developmental biology↗

bioRxiv2024

RNaseH-based ribodepletion of total planarian RNA improves detection of longer and non-polyadenylated transcripts

The overwhelming majority of RNA species isolated from cells or tissues using organic extraction are ribosomal RNAs (rRNA), whereas a relatively small percentage are messenger RNAs (mRNA). For studies that seek to detect mRNA transcripts and measure changes in their expression, this lopsided ratio of desired transcripts to undesired transcripts creates a significant challenge to obtaining sensitive and reproducible results. One method for improving mRNA detection is to selectively amplify polyadenylated (polyA) mRNA molecules when generating RNA-seq libraries, a strategy that is generally very successful in many species. However, this strategy is less effective when starting with total RNA from some species e.g., the planarian species Schmidtea mediterranea (S.med), as it generates libraries that still contain significant and variable amounts of rRNA reads. Further, commercially available ribodepletion kits do not efficiently deplete rRNAs from these samples because their sequences are divergent from mammalian rRNAs. Here we report a customized, optimized, and economical ribodepletion strategy than allows the generation of comprehensive RNA-seq libraries with less than one percent rRNA contamination. We show that this method improves transcript detection, particularly for those without polyA tails (e.g., core histones) and those that are relatively long (e.g., microtubule motor proteins). Using this custom ribodepletion approach, we also detected many transcripts that are not represented in the most recent set of S.med gene annotations, including a subset that are likely expressed transposable elements (TEs). To facilitate future differential expression analyses of these newly identified loci, we created both an annotation file of the new loci we identified and a bioinformatic pipeline for generating additional annotations from future libraries. As significant recent research shows that TE activation is regulated and functionally important, the resources provided here will provide a starting point for investigating such mechanisms in planarians and other species with less conserved rRNA sequences.

molecular biology↗

bioRxiv2024

DNA methylation machinery is involved in development and reproduction in the viviparous pea aphid (Acyrthosiphon pisum).

The pea aphid (Acyrthosiphon pisum) like the majority of extant aphids displays cyclical parthenogenesis - the ability of mothers to switch the reproductive mode of their offspring from reproducing parthenogenetically to sexually in response to environmental cues. The pea aphid genome encodes two paralogs of the de novo DNA methyltransferase gene, dnmt3a and dnmt3x. Here we show, using phylogenetic analysis, that this gene duplication event occurred at least 106 million years ago, likely after the divergence of the lineage leading to the Aphidomorpha (aphids, phylloxera and adelgids) from that leading to the scale insects (Coccoidea) and that the two paralogs are maintained in the genomes of all aphids examined. We also show that the mRNA of both dnmt3 paralogs are maternally expressed in the viviparous aphid ovary. During development both paralogs are expressed in the germ cells of embryos beginning at stage 5 and persisting throughout development. Chemical inhibition of the DNA methylation machinery leads to defects of oocytes and early stage embryos, and causes a proportion of later stage embryos to be born dead or die soon after birth. These phenotypes suggest a role for DNA methyltransferases in reproduction, consistent with that seen in other insects. Taking the vast evolutionary history of the dnmt3 paralogs, and the localization of their mRNAs in the ovary, we suggest there is a role for dnmt3a and/or dnmt3x in early development, and a role for DNA methylation machinery in reproduction and development of the viviparous pea aphid.

developmental biology↗

bioRxiv2021

Rab40/Cullin5 complex regulates EPLIN and actin cytoskeleton dynamics during cell migration and invasion

Rab40b is a SOCS box containing protein that regulates the secretion of MMPs to facilitate extracellular matrix remodeling during cell migration. Here we show that Rab40b interacts with Cullin5 via the Rab40b SOCS domain. We demonstrate that loss of Rab40b/Cullin5 binding decreases cell motility and invasive potential, and show that defective cell migration and invasion stem from alteration to the actin cytoskeleton, leading to decreased invadopodia formation, decreased actin dynamics at the leading edge, and an increase in stress fibers. We also show that these stress fibers anchor at less dynamic, more stable focal adhesions. Mechanistically, changes in the cytoskeleton and focal adhesion dynamics are mediated in part by EPLIN, which we demonstrate to be a binding partner of Rab40b and a target for Rab40b/Cullin5 dependent localized ubiquitylation and degradation. Thus, we propose a model where the Rab40b/Cullin5 dependent ubiquitylation regulates EPLIN localization to promote cell migration and invasion by altering focal adhesion and cytoskeletal dynamics.

cell biology↗

bioRxiv2020

A novel mutation in KCNK16 causing a gain-of-function in the TALK-1 potassium channel: a new cause of maturity onset diabetes of the young.

BackgroundMaturity-onset diabetes of the young (MODY) is a heterogeneous group of monogenic disorders of impaired glucose-stimulated insulin secretion (GSIS). Mechanisms include {beta}-cell KATP channel dysfunction (e.g., KCNJ11 (MODY13) or ABCC8 (MODY12) mutations); however, no other {beta}-cell channelopathies have been identified in MODY. MethodsA four-generation family with autosomal dominant non-obese, non-ketotic antibody-negative diabetes, without mutations in known MODY genes, underwent exome sequencing. Whole-cell and single-channel K+ currents, Ca2+ handling, and GSIS were determined in cells expressing either mutated or wild-type (WT) protein. ResultsWe identified a novel non-synonymous genetic mutation in KCNK16 (NM_001135105: c.341T>C, p.Leu114Pro) segregating with MODY. KCNK16 is the most abundant and {beta}-cell-restricted K+ channel transcript and encodes the two-pore-domain K+ channel TALK-1. Whole-cell K+ currents in transfected HEK293 cells demonstrated drastic (312-fold increase) gain-of-function with TALK-1 Leu144Pro vs. WT, due to greater single channel activity. Glucose-stimulated cytosolic Ca2+ influx was inhibited in mouse islets expressing TALK-1 Leu114Pro (area under the curve [AUC] at 20mM glucose: Leu114Pro 60.1 vs. WT 89.1; P=0.030) and less endoplasmic reticulum calcium storage (cyclopiazonic acid-induced release AUC: Leu114Pro 17.5 vs. WT 46.8; P=0.008). TALK-1 Leu114Pro significantly blunted GSIS compared to TALK-1 WT in both mouse (52% decrease, P=0.039) and human (38% decrease, P=0.019) islets. ConclusionsOur data identify a novel MODY-associated gene, KCNK16; with a gain-of-function mutation limiting Ca2+ influx and GSIS. A gain-of-function common polymorphism in KCNK16 is associated with type 2 diabetes (T2DM); thus, our findings have therapeutic implications not only for KCNK16-associated MODY but also for T2DM.

genetics↗

bioRxiv2019

Reliability of Mismatch Negativity Event-Related Potentials in a Multisite, Traveling Subjects Study

ObjectiveMismatch negativity (MMN) is an auditory event-related potential (ERP) used to study schizophrenia and psychosis risk. MMN reliability from a multisite, traveling subjects study was compared using different ERP referencing, averaging, and scoring techniques.\n\nMethodsReliability of frequency, duration, and double (frequency+duration) MMN was determined from eight traveling subjects, tested on two occasions at eight EEG laboratory sites. Deviant-specific variance components were estimated for MMN peak amplitude and latency measures using different ERP processing methods. Generalizability (G) coefficients were calculated using two-facet (site, occasion), fully-crossed models and single-facet (occasion) models within each laboratory to assess MMN reliability.\n\nResultsG-coefficients calculated from two-facet models indicated fair (0.4 0.5). Reliability of MMN amplitude was greater than latency, and reliability with mastoid referencing significantly outperformed nose-referencing.\n\nConclusionsEEG preprocessing methods have a significant impact on the reliability of MMN amplitude. Within site MMN reliability can be excellent, consistent with prior single site studies.\n\nSignificanceWith standardized data collection and ERP processing, MMN can be reliably obtained in multisite studies, providing larger samples sizes within rare patient groups.

neuroscience↗

bioRxiv2018

The genome of the water strider Gerris buenoi reveals expansions of gene repertoires associated with adaptations to life on the water

The semi-aquatic bugs conquered water surfaces worldwide and occupy ponds, streams, lakes, mangroves, and even open oceans. As such, they inspired a range of scientific studies from ecology and evolution to developmental genetics and hydrodynamics of fluid locomotion. However, the lack of a representative water strider genome hinders thorough investigations of the mechanisms underlying the processes of adaptation and diversification in this group. Here we report the sequencing and manual annotation of the Gerris buenoi (G. buenoi) genome, the first water strider genome to be sequenced so far. G. buenoi genome is about 1 000Mb and the sequencing effort recovered 20 949 predicted protein-coding genes. Manual annotation uncovered a number of local (tandem and proximal) gene duplications and expansions of gene families known for their importance in a variety of processes associated with morphological and physiological adaptations to water surface lifestyle. These expansions affect key processes such as growth, vision, desiccation resistance, detoxification, olfaction and epigenetic components. Strikingly, the G. buenoi genome contains three Insulin Receptors, a unique case among metazoans, suggesting key changes in the rewiring and function of the insulin pathway. Other genomic changes include wavelength sensitivity shifts in opsin proteins likely in association with the requirements of vision in water habitats. Our findings suggest that local gene duplications might have had an important role during the evolution of water striders. These findings along with the G. buenoi genome open exciting research opportunities to understand adaptation and genome evolution of this unique hemimetabolous insect.

genomics↗