Biology subjects

Meffert, M. K.

Publications and source records attributed to Meffert, M. K..

3 recordsLinked to original sources

bioRxiv2026

A human model of the neurodevelopmental metabolic shift

The neurodevelopmental metabolic shift transitions the energy sources and metabolic pathways used by neurons to critically support survival, growth, and the timing of functional maturation. To better understand metabolic regulation during human neuronal development, and to facilitate the study of early neurodevelopmental disorders impacting this time window, establishing a combination of effective human model systems will be required. We report that a streamlined strategy using genetic induction of neuronal differentiation by NGN2 expression recapitulates hallmarks of metabolic reprogramming associated with neuronal maturation. The approach is refined to increase the uniformity of differentiation, allowing reproducible high-throughput assessments. We validate appropriate readouts of metabolic function, including gene expression, cellular respiration, and mitochondrial imaging which can be combined to present a cohesive assessment of metabolic status and reliance on oxidative phosphorylation relative to glycolysis. Collectively, the strategy presented will enhance the ability of investigators to gather foundational and disease-related insights into regulatory mechanisms of the metabolic shift critical to successful neuronal differentiation.

neuroscience↗

bioRxiv2022

PACeR: a bioinformatic pipeline for the analysis of chimeric RNA-seq data

MicroRNAs (miRNAs) are small non-coding RNAs that function in post-transcriptional gene regulation through imperfect base pairing with mRNA targets which results in inhibition of translation and often destabilization of bound transcripts. Sequence-based algorithms historically used to predict miRNA targets face inherent challenges in reliably reflecting in vivo interactions. Recent strategies have directly profiled miRNA-target interactions by cross-linking and ligation of miRNAs to their targets within the RNA-induced silencing complex (RISC), followed by high throughput sequencing of the chimeric RNAs. Despite the strength of these direct chimeric miRNA:target profiling approaches, standardized pipelines for analyzing the resulting chimeric RNA sequencing data are not readily available. Here we present PACeR, a robust bioinformatic pipeline for the analysis of chimeric RNA sequencing data. PACeR consists of two parts, each of which are optimized for the distinctive characteristics of chimeric RNA sequencing reads: first, read processing and alignment and second, peak calling and motif analysis. We apply PACeR to chimeric RNA sequencing data generated in our lab as well as a published benchmark dataset. PACeR has minimal computational power requirements and contains extensive annotation to broaden accessibility for processing chimeric RNA sequencing data and enable insights to be gained about the targets of small non-coding RNAs in regulating diverse biological systems.

bioinformatics↗

bioRxiv2018

Targeting of NF-κB to Dendritic Spines is Required for Synaptic Signaling and Spine Development

Long-term forms of brain plasticity share a requirement for changes in gene expression induced by neuronal activity. Mechanisms that determine how the distinct and overlapping functions of multiple activity-responsive transcription factors, including nuclear factor kappa B (NF-{kappa}B), give rise to stimulus-appropriate neuronal responses remain unclear. We report that the p65/RelA subunit of NF-{kappa}B confers subcellular enrichment at neuronal dendritic spines and engineer a p65 mutant that lacks spine-enrichment ({Delta}SEp65) but retains inherent transcriptional activity equivalent to wild-type p65. Wild-type p65 or {Delta}SEp65 both rescue NF-{kappa}B-dependent gene expression in p65-deficient murine hippocampal neurons responding to diffuse (PMA/ionomycin) stimulation. In contrast, neurons lacking spine-enriched NF-{kappa}B are selectively impaired in NF-{kappa}B-dependent gene expression induced by elevated excitatory synaptic stimulation (bicuculline or glycine). We used the setting of excitatory synaptic activity during development that produces NF-{kappa}B-dependent growth of dendritic spines to test physiological function of spine-enriched NF-{kappa}B in an activity-dependent response. Expression of wild-type p65, but not {Delta}SEp65, is capable of rescuing spine density to normal levels in p65-deficient pyramidal neurons. Collectively, these data reveal that spatial localization in dendritic spines contributes unique capacities to the NF-{kappa}B transcription factor in synaptic activity-dependent responses.\n\nSIGNIFICANCE STATEMENTExtensive research has established a model in which the regulation of neuronal gene expression enables enduring forms of plasticity and learning. However, mechanisms imparting stimulus-specificity to gene regulation, insuring biologically appropriate responses, remain incompletely understood. NF-{kappa}B is a potent transcription factor with evolutionarily-conserved functions in learning and the growth of excitatory synaptic contacts. Neuronal NF-{kappa}B is localized in both synapse and somatic compartments, but whether the synaptic pool of NF-{kappa}B has discrete functions is unknown. This study reveals that NF-{kappa}B enriched in dendritic spines (the postsynaptic sites of excitatory contacts) is selectively required for NF-{kappa}B activation by synaptic stimulation and normal dendritic spine development. These results support spatial localization at synapses as a key variable mediating selective stimulus-response coupling.

neuroscience↗