Biology subjects

Bartelt, L. C.

Publications and source records attributed to Bartelt, L. C..

5 recordsLinked to original sources

bioRxiv2025

SMARCA2 is an essential and potent cofactor for a specific subset of the glucocorticoid response in A549 cells

Glucocorticoids are a widely used, potent class of anti-inflammatory drugs that modulate the expression of hundreds of genes across the genome. Although the glucocorticoid response is primarily carried out by the glucocorticoid receptor (NR3C1, a.k.a. GR), there are many glucocorticoid receptor co-factors that are also essential to the downstream effects. To identify novel factors necessary for the glucocorticoid gene expression response, we used a genome-wide CRISPR screen in A549 lung adenocarcinoma cells. In that screen, we knocked out every gene in the human genome, and measured the effect of expression of the glucocorticoid-induced leucine zipper (GILZ), a classic glucocorticoid-response gene. We identified two chromatin remodeling proteins, SMARCA2 and BPTF, that are essential for GILZ expression. We then evaluated the genome-wide effects of SMARCA2 and BPTF on glucocorticoid-mediated gene expression. BPTF had a highly specific role in the glucocorticoid response, affecting the expression of only a handful of genes, and having virtually no effect on dexamethasone-induced changes in chromatin accessibility. However, SMARCA2 was necessary for 27% of dexamethasone-induced transcriptional changes (152 genes), and [~]7% of dexamethasone-induced changes in chromatin accessibility (586 regions of the genome). Genomic regions with SMARCA2-dependent changes in chromatin accessibility were characterized by high dexamethasone-induced regulatory activity in a massively parallel reporter assay, and dexamethasone-induced increases in transcription factor binding and chromatin states. Taken together, these data suggest that SMARCA2 is critical for chromatin remodeling at a specific set of genomic regions with high regulatory activity, which in turn drive changes in expression for many glucocorticoid-responsive genes.

genomics↗

bioRxiv2023

Purkinje-Enriched snRNA-seq in SCA7 Cerebellum Reveals Zebrin Identity Loss as a Central Feature of Polyglutamine Ataxias

Spinocerebellar ataxia type 7 (SCA7) is an inherited neurodegenerative disorder caused by a CAG-polyglutamine repeat expansion. SCA7 patients display a striking loss of Purkinje cell (PC) neurons with disease progression; however, PCs are rare, making them difficult to characterize. We developed a PC nuclei enrichment protocol and applied it to single-nucleus RNA-seq of a SCA7 knock-in mouse model. Our results unify prior observations into a central mechanism of cell identity loss, impacting both glia and PCs, driving accumulation of inhibitory synapses and altered PC spiking. Zebrin-II subtype dysregulation is the predominant signal in PCs, leading to complete loss of zebrin-II striping at motor symptom onset in SCA7 mice. We show this zebrin-II subtype degradation is shared across Polyglutamine Ataxia mouse models and SCA7 patients. It has been speculated that PC subtype organization is critical for cerebellar function, and our results suggest that a breakdown of zebrin-II parasagittal striping is pathological.

genomics↗

bioRxiv2023

Single-nucleus transcriptional profiling of GAD2-positive neurons from mouse lateral habenula reveals distinct expression of neurotransmission- and depression-related genes

Glutamatergic projection neurons of the lateral habenula (LHb) drive behavioral state modulation by regulating the activity of midbrain monoaminergic neurons. Identifying circuit mechanisms that modulate LHb output is of interest for understanding control of motivated behaviors. A small population of neurons within the medial subnucleus of the mouse LHb express the GABAergic synthesizing enzyme GAD2, and they can inhibit nearby LHb projection neurons; however, these neurons lack markers of classic inhibitory interneurons and they co-express the vesicular glutamate transporter VGLUT2. To determine the molecular phenotype of these neurons, we genetically tagged the nuclei of GAD2-positive cells and used fluorescence-activated nuclear sorting to isolate and enrich these nuclei for single nuclear RNA sequencing (FANS-snRNAseq). Our data confirm that GAD2+/VGLUT2+ neurons intrinsic to the LHb co-express markers of both glutamatergic and GABAergic transmission and that they are transcriptionally distinct from either GABAergic interneurons or habenular glutamatergic neurons. We identify gene expression programs within these cells that show sex-specific differences in expression and that are implicated in major depressive disorder (MDD), which has been linked to LHb hyperactivity. Finally, we identify the Ntng2 gene encoding the cell adhesion protein Netrin-G2 as a marker of LHb GAD2+/VGLUT+ neurons and a gene product that may contribute to their target projections. These data show the value of using genetic enrichment of rare cell types for transcriptome studies, and they advance understanding of the molecular composition of a functionally important class of GAD2+ neurons in the LHb.

neuroscience↗

bioRxiv2021

Cell-type specific transcriptional adaptations of nucleus accumbens interneurons to amphetamine

Parvalbumin-expressing (PV+) interneurons of the nucleus accumbens (NAc) play an essential role in the addictive-like behaviors induced by psychostimulant exposure. To identify molecular mechanisms of PV+ neuron plasticity, we isolated interneuron nuclei from the NAc of male and female mice following acute or repeated exposure to amphetamine (AMPH) and sequenced for cell type-specific RNA expression and chromatin accessibility. AMPH regulated the transcription of hundreds of genes in PV+ interneurons, and this program was largely distinct from that regulated in other NAc GABAergic neurons. Chromatin accessibility at enhancers predicted cell-type specific gene regulation, identifying transcriptional mechanisms of differential AMPH responses. Finally, we observed dysregulation of multiple PV-specific, AMPH-regulated genes in an Mecp2 mutant mouse strain that shows heightened behavioral sensitivity to psychostimulants, suggesting the functional importance of this transcriptional program. Together these data provide novel insight into the cell-type specific programs of transcriptional plasticity in NAc neurons that underlie addictive-like behaviors.

neuroscience↗

bioRxiv2021

Cooperative regulation of coupled oncoprotein translation and stability in triple-negative breast cancer by EGFR and CDK12

Evidence has long suggested that epidermal growth factor receptor (EGFR) may play a prominent role in triple-negative breast cancer (TNBC) pathogenesis, but clinical trials of EGFR inhibitors have yielded disappointing results. Using a candidate drug screen, we discovered that inhibition of CDK12 dramatically sensitizes diverse models of TNBC to EGFR blockade. Instead of functioning through CDK12s well-established roles proximal to transcription, this combination therapy drives cell death through the 4E-BP1-dependent suppression of the translation and consequent stability of driver oncoproteins, including MYC. A genome-wide CRISPR/Cas9 screen identified the CCR4-NOT complex as a major determinant of sensitivity to the combination therapy whose loss renders 4E-BP1 unresponsive to drug-induced dephosphorylation, rescuing MYC translational suppression and stability. The central roles of CCR4-NOT and 4E-BP1 in response to the combination therapy were further underscored by the observation of CNOT1 loss and rescue of 4E-BP1 phosphorylation in TNBC cells that naturally evolved therapy resistance. Thus, pharmacological inhibition of CDK12 reveals a long proposed EGFR dependence in TNBC that functions through the cooperative regulation of translation-coupled oncoprotein stability.

cancer biology↗