Biology subjects

Eacker, S. M.

Publications and source records attributed to Eacker, S. M..

3 recordsLinked to original sources

bioRxiv2025

Spatially Organized IGF1 mTOR Signaling Controls Human Forebrain Progenitor Fate Through Coordinated Transcriptional and Translational Programs

The specification and maintenance of human forebrain neural progenitor cells (NPCs) depend on both intrinsic gene networks and spatially localized niche signals, but the interplay between these cues remains incompletely understood. Here, we identify a spatially organized, paracrine IGF1 signaling architecture that regulates human FOXG1 NPCs through multilayered transcriptional and translational control. Using a pluripotent stem cell-derived forebrain model, we show that FOXG1 NPCs express IGF1 receptors but lack endogenous IGF1, instead depending on neighboring epithelial-like domains that secrete IGF1. IGF1 promotes progenitor proliferation, clonal expansion, and vertical tissue growth by activating PI3K-AKT-mTOR and MEK-ERK pathways. Ribosome profiling and 5'UTR reporter assays reveal that mTOR signaling selectively enhances translation of neurodevelopmental and biosynthetic transcripts-- including GSX1, a ventral fate determinant implicated in interneuron specification and autism. These findings uncover a human-specific regulatory mechanism in which spatially restricted IGF1-mTOR signaling integrates niche signals with translational output to support progenitor identity, biosynthetic capacity, and developmental resilience.

neuroscience↗

bioRxiv2021

Accurate viral genome reconstruction and host assignment with proximity-ligation sequencing

Viruses play crucial roles in the ecology of microbial communities, yet they remain relatively understudied in their native environments. Despite many advancements in high-throughput whole-genome sequencing (WGS), sequence assembly, and annotation of viruses, the reconstruction of full-length viral genomes directly from metagenomic sequencing is possible only for the most abundant phages and requires long-read sequencing technologies. Additionally, the prediction of their cellular hosts remains difficult from conventional metagenomic sequencing alone. To address these gaps in the field and to accelerate the study of viruses directly in their native microbiomes, we developed an end-to-end bioinformatics platform for viral genome reconstruction and host attribution from metagenomic data using proximity-ligation sequencing (i.e., Hi-C). We demonstrate the capabilities of the platform by recovering and characterizing the metavirome of a variety of metagenomes, including a fecal microbiome that has also been sequenced with accurate long reads, allowing for the assessment and benchmarking of the new methods. The platform can accurately extract numerous near-complete viral genomes even from highly fragmented short-read assemblies and can reliably predict their cellular hosts with minimal false positives. To our knowledge, this is the first software for performing these tasks. Being significantly cheaper than long-read sequencing of comparable depth, the incorporation of proximity-ligation sequencing in microbiome research shows promise to greatly accelerate future advancements in the field.

genomics↗

bioRxiv2017

Experience-dependent translational state defined by cell type-specific ribosome profiling

Experience-dependent neuronal activity regulates the translation of mRNA, supporting memory formation. We have developed a new method termed translating ribosome affinity purification and ribosome profiling (TRiP) which allows us to determine cell type-specific ribosome occupancy of mRNA with nucleotide resolution. Using TRiP we show that a memory-inducing experience creates a distinct translational state in mouse CA1 pyramidal cells. The experience-dependent translation state is characterized by enhanced translation of protein-coding open reading frames (ORFs) including numerous components of the actin cytoskeleton and calcium/calmodulin binding proteins, and by decreased translation of a defined subset of genes containing upstream ORFs (uORFs). Using animals heterozygous for an unphosphorylatable allele of the eukaryotic translation initiation factor 2 (eIF2), we show that dephosphorylation of eIF2 contributes significantly to the experience-dependent translation state. These observations demonstrate that TRiP is a valuable methodology for studying physiologically relevant changes in translational state in genetically defined cell types.

genomics↗