Biology subjects

Ferguson, K. M.

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

4 recordsLinked to original sources

bioRxiv2026

Dual recognition of negative charge by pleckstrin homology (PH) domains

Pleckstrin homology (PH) domains are typically assumed to be phosphoinositide-binding modules, although most lack strong lipid specificity and their broader ligand repertoire remains poorly defined. We find that many yeast PH domains bind Nsr1p, the ortholog of nucleolin, also identified as a PH domain ligand, suggesting widespread recognition of negatively charged protein regions. The phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2)-binding PLC{delta}1 PH domain also binds a highly phosphorylated region of IRBIT through the same site that recognizes PtdIns(4,5)P2. Using high-throughput integrated phosphopeptide (Hi-P) screening, we surveyed 38,624 mammalian sequences containing three documented phosphoserines. PLC{delta}1-PH bound numerous phosphorylated and unphosphorylated acidic peptides, and phosphorylation generally strengthened pre-existing interactions rather than conferring strict specificity, without requiring a fixed phosphoserine spacing. Instead, favored phosphopeptides combined a key phosphoserine with upstream acidic residues. Structural modeling suggests that this phosphoserine occupies the canonical inositol phosphate binding pocket, while adjacent acidic residues make delocalized electrostatic contacts. Thus, PH domains can recognize various patterns of protein negative charge, expanding their potential regulatory roles beyond membrane targeting.

biochemistry↗

bioRxiv2025

ProteoForge: An Imputation-Aware Framework for Differential Proteoform Discovery in Bottom-Up Proteomics

The human genome contains approximately 20,000 protein-coding genes. However, millions of diverse protein variants, called proteoforms, exist. Despite originating from the same gene, proteoforms often have distinct biological roles. In bottom-up proteomics, the aggregation of peptide measurements into protein-level quantities often obscures this information. Existing methods for proteoform deconvolution are limited by their handling of missing data, which can introduce significant bias. To address this we developed ProteoForge, which builds on an imputation-aware statistical model to identify and group co-varying peptides into quantitatively differential proteoforms (dPFs). Benchmarking against existing deconvolution methods demonstrated that ProteoForge provides high accuracy and stability in datasets with high rates of missing values, complex experimental designs, or varying signal strengths. Application of ProteoForge to proteomics data from lung cancer cells under hypoxia revealed extensive proteoform-level regulation hidden by standard protein-level analysis.

bioinformatics↗

bioRxiv2022

Elevated FOXG1 supports exit from quiescence in neural stem cells through FoxO6

The molecular mechanisms controlling the balance of quiescence and proliferation in adult neural stem cells (NSCs) are often deregulated in brain cancers such as glioblastoma (GBM). Previously, we reported that FOXG1, a forebrain-restricted neurodevelopmental transcription factor, is frequently upregulated in glioblastoma stem cells (GSCs) and limits the effects of cytostatic pathways, in part by repression of the tumour suppressor Foxo3. Here, we show that increased FOXG1 upregulates FoxO6, a more recently discovered FoxO family member with potential oncogenic functions. Although genetic ablation of FoxO6 in proliferating NSCs has no effect on the cell cycle or entry into quiescence, we find that FoxO6-null NSCs can no longer efficiently exit quiescence following FOXG1 elevation. Increased FoxO6 results in the formation of large acidic vacuoles, reminiscent of Pak1-regulated macropinocytosis. Consistently, Pak1 expression is upregulated by FOXG1 overexpression and downregulated upon FoxO6 loss in proliferative NSCs. These data suggest a pro-oncogenic role for FoxO6 in controlling the exit from quiescence in NSCs, and shed light on the functions of this underexplored FoxO family member. Research highlightsO_LIFoxO6 is a downstream effector of elevated FOXG1 in mouse NSCs and GSCs. C_LIO_LIUpregulation of FoxO6 is necessary for FOXG1 to drive efficient quiescence exit of NSCs. C_LIO_LIFoxO6 overexpression stimulates macropinocytosis, a process regulated by the actin cytoskeleton regulator Pak1. C_LIO_LIPak1 is upregulated by FOXG1 overexpression and downregulated upon FoxO6 loss. C_LI

cancer biology↗

bioRxiv2021

Glioblastoma mutations impair ligand discrimination by EGFR

The epidermal growth factor receptor (EGFR) is frequently mutated in human cancer, and is an important therapeutic target. EGFR inhibitors have been successful in lung cancer, where the intracellular tyrosine kinase domain is mutated, but not in glioblastoma multiforme (GBM) - where mutations (or deletions) occur exclusively in the EGFR extracellular region. Wild-type EGFR is known to elicit distinct signals in response to different growth factor ligands, exhibiting biased agonism. We recently showed that individual ligands stabilize distinct receptor dimer structures, which signal with different kinetics to specify outcome. EGF induces strong symmetric dimers that signal transiently to promote proliferation. Epiregulin (EREG) induces weak asymmetric dimers that generate sustained signaling and differentiation. Intriguingly, several GBM mutation hotspots coincide with residues that define the asymmetric and symmetric dimer structures. Here, we show that common extracellular GBM mutations prevent EGFR from distinguishing between EGF and EREG based on dimer structure and stability - allowing strong dimers to form with both ligands. Crystal structures show that the R84K mutation symmetrizes EREG-driven dimers, whereas the A265V mutation remodels key dimerization sites. Our results suggest that modulating EGFRs biased agonism plays an important role in GBM, and suggest new approaches for correcting aberrant EGFR signaling in cancer.

biochemistry↗