Biology subjects

Runnebohm, A. M.

Publications and source records attributed to Runnebohm, A. M..

7 recordsLinked to original sources

bioRxiv2026

EXOSC3 G191 Variants Trigger System-Wide Recalibration of RNA Processing Machinery

Pathogenic variants in EXOSC3, a noncatalytic subunit of the RNA exosome, cause pontocerebellar hypoplasia type 1B (PCH1B), yet substantial variability in disease severity is observed among individuals carrying different EXOSC3 alleles. The molecular mechanisms of RNA exosome dysfunction in individuals carrying EXOSC3 p.G191 variants remains unresolved. To address this, we generated CRISPR/Cas9-engineered human cell models harboring EXOSC3 p.G191 variants and performed integrated transcriptomic, proteomic, and computational structural analyses. EXOSC3 p.G191 variants produced extensive, allele- and dosage-dependent alterations in gene expression and splicing, with heterozygous variants causing broad but attenuated disruption relative to homozygous EXOSC3 G191D/G191D cells. All EXOSC3 G191 variants promoted increased skipping of exon 3 in EXOSC3 transcripts, generating a short isoform predicted to encode an unstable proteoform. Molecular dynamics and {lambda}-dynamics simulations predicted substantial thermodynamic destabilization of all EXOSC3 G191 variant proteoforms, consistent with reduced protein abundance and thermal stability measured by global proteomics and PISA. At the protein complex level, EXOSC3 p.G191 variants were associated with coordinated decreases in all RNA exosome core subunits and the exonuclease EXOSC10, consistent with destabilization of RNA exosome assembly and orphan protein decay. In contrast, the catalytic exonuclease DIS3 and multiple independent RNA processing pathways were upregulated, indicating compensatory recalibration of RNA metabolism. Together, these findings link variant-induced alternative splicing, RNA exosome complex destabilization, and adaptive network responses to phenotypic variability in EXOSC3 p.G191-associated disease.

systems biology↗

bioRxiv2025

Quantifying the Structural and Energetic Consequences of EXOSC3 S1 Domain Variants from a Comparative Assessment of {lambda}-Dynamics with Two Charge-Changing Perturbation Strategies

Charge-changing perturbations are notoriously dificult to investigate with alchemical free energy calculations. The routine use of periodic boundary conditions and electrostatic approximations, such as particle-mesh Ewald (PME), may produce finite-size efect errors that become non-negligible as a perturbation changes a simulation cells net charge away from zero. Two prevalent strategies exist to correct for these errors: the analytic correction (AC) and co-alchemical ion (CI) methods. Both correction schemes have been found to produce comparable relative free energy results for small molecule perturbations, but these methods have not been compared using {lambda}-dynamics ({lambda}D) free energy calculations or for protein side chain mutations. Recently, we investigated relative folding and binding free energies ({Delta}{Delta}Gs) of a series of EXOSC3 variants involved in a rare neurodegenerative disorder, including D132A, G135R, and G191D charge-change perturbations, with a simplified AC scheme in {lambda}D. In this study, these perturbations are reevaluated with the CI scheme for comparison with AC to identify the best correction strategy for {lambda}D. The collected AC- and CI-corrected {Delta}{Delta}Gs show excellent agreement with a mean unsigned error of 0.4 kcal/mol. However, reduced sampling proficiency and increased dificulties of evaluating multisite perturbations with the CI method suggest that a simplified AC approach may be more generalizable for future {lambda}D calculations. Previously, the use of the CI approach with {lambda}D has been limited due to a lack of infrastructure available to users to simplify its more involved setup procedure. This study introduces an automated workflow for implementation of the CI approach with {lambda}D, laying the foundation for future comparisons between charge-change correction schemes. These studies facilitated analysis of the {lambda}D trajectories to identify structural changes within EXOSC3 and the RNA exosome complex that clearly rationalize the calculated {Delta}{Delta}Gs for the D132A, G135R, G191C, and G191D EXOSC3 variants, providing insight into potential disease-causing mechanisms of EXOSC3 modifications.

biophysics↗

bioRxiv2025

EXOSC3 S1-domain variants implicated in PCH1b alter RNA exosome cap subunit abundance and thermal stability disrupting rRNA processing and targeting of AU-rich mRNA

Missense variants in EXOSC3, an RNA exosome subunit, have been identified in patients with PCH1b. We investigated three missense variants in the S1 domain of EXOSC3, including one variant of uncertain significance (VUS) and two pathogenic variants (hence S1 variants). EXOSC3 S1 variant cell lines were generated using CRISPR-Cas9 resulting in widespread proteome changes including decreases in some RNA exosome subunits paired with increases in the catalytic subunit DIS3. Thermal stability, analyzed by PISA, revealed extensive destabilization of RNA exosome cap subunits and the cap-associated exonuclease EXOSC10. Functionally, S1 variants altered rRNA processing with corresponding protein compensation observed in rRNA processing proteins outside the RNA exosome. Exogenous overexpression of EXOSC3 rescues many molecular defects caused by S1 variants suggesting that protein destabilization and turnover strongly contribute to molecular defects. Overall, our findings define the mechanisms through which cells respond to EXOSC3 S1 variant disruption of RNA processing homeostasis.

systems biology↗

bioRxiv2025

Application of Whole Proteome Thermal Shift Assays to Define PERK-dependent Changes in Protein Homeostasis during the Unfolded Protein Response

The Unfolded Protein Response (UPR) is a cellular pathway activated by sensory proteins, including the protein kinase PERK (EIF2AK3), that monitors perturbations in the endoplasmic reticulum (ER). Using tunicamycin, which induces ER stress by thwarting N-glycosylation, we monitored system-wide changes in the proteome using PISA (Proteome Integral Solubility Alteration) and abundance analysis. Global proteomics revealed precise changes in membrane- and ER-associated proteins through widespread induction of ER-associated degradation (ERAD) while normalized PISA (nPISA) analyses selectively identified pathway changes associated with drug mechanism of action. nPISA analysis following tunicamycin treatment in cells, in combination with genetic disruption of PERK, facilitated identification of novel proteins involved in PERK-dependent and -independent processes and how those changes intersect with PERK function specifically during the ER stress response. Overall, protein-centered multiomics analyses defined the precise proteome alterations in tunicamycin-induced ER stress, highlighting the consequences of PERK disruption on ER-mitochondrial homeostasis.

systems biology↗

bioRxiv2024

IB-DNQ and Rucaparib dual treatment alters cell cycle regulation and DNA repair in triple negative breast cancer cells

Triple negative breast cancer (TNBC) is a highly aggressive breast cancer that is unresponsive to hormonal therapies. One potential TNBC-specific therapeutic target is NQO1, as it is highly expressed in many TNBC patients and lowly expressed in non-cancer tissues. Here we use a derivative of DNQ, isobutyl-deoxynyboquinone (IB-DNQ) that is more potent and specific in killing TNBC cells than NQO1-activator {beta}-lapachone while displaying strong NQO1-dependence. We evaluated the cellular signaling changes that occur following 4-hour treatment of TNBC cells with either single agent or combination IB-DNQ and / or PARP inhibitor (Rucaparib). Short treatments (4 hours) with IB-DNQ alone or combined with the PARP inhibitor Rucaparib revealed few changes in protein abundance but significant rapid alterations in protein phosphorylation and thermal stability, with clear synergy in the combination treatment. Key phosphorylated targets linked to RNA Polymerase II inhibition and DNA damage response were altered during our short time treatment. Thermal proteome profiling (TPP) identified novel, combination-specific changes in protein biophysical state suggesting new therapeutic vulnerabilities in TNBC cells. Our findings highlight how even brief treatments can uncover distinct biophysical protein changes via TPP, offering a resource for mechanistic studies of IB-DNQ mechanism of action and the development of NQO1-activated therapeutics for TNBC treatment.

cancer biology↗

bioRxiv2022

Obtaining Increased Functional Proteomics Insights from Thermal Proteome Profiling through Optimized Melt Shift Calculation and Statistical Analysis

Thermal Proteome Profiling (TPP) is an invaluable tool for functional proteomics studies that has been shown to discover changes associated with protein-ligand, protein- protein, and protein-RNA interaction dynamics along with changes in protein stability resulting from cellular signaling. The increasing number of reports employing this assay has not been met concomitantly with advancements and improvements in the quality and sensitivity of the corresponding data analysis. The gap between data acquisition and data analysis tools is even more apparent as TPP findings have reported more subtle melt shift changes related to protein post-translational modifications. In this study, we have improved the Inflect data analysis pipeline (now referred to as InflectSSP, available at https://CRAN.R-project.org/package=InflectSSP) to increase the sensitivity of detection for both large and subtle changes in the proteome as measured by TPP. Specifically, InflectSSP now has integrated statistical and bioinformatic functions to improve objective functional proteomics findings from the quantitative results obtained from TPP studies through increasing both the sensitivity and specificity of the data analysis pipeline. To benchmark InflectSSP, we have reanalyzed two publicly available datasets to demonstrate the performance of this publicly available R based program for TPP data analysis. Additionally, we report new findings following temporal treatment of human cells with the small molecule Thapsigargin which induces the unfolded protein response (UPR). InflectSSP analysis of our UPR study revealed highly reproducible target engagement over time while simultaneously providing new insights into the dynamics of UPR induction.

biophysics↗

bioRxiv2022

Lipid Biosynthesis Perturbation Impairs Endoplasmic Reticulum-Associated Degradation

The relationship between lipid homeostasis and protein homeostasis (proteostasis) is complex and remains incompletely understood. We conducted a screen for genes required for efficient degradation of Deg1-Sec62, a model aberrant translocon-associated substrate of the endoplasmic reticulum (ER) ubiquitin ligase Hrd1, in Saccharomyces cerevisiae. This screen revealed that INO4 is required for efficient Deg1-Sec62 degradation. INO4 encodes one subunit of the Ino2/Ino4 heterodimeric transcription factor, which regulates expression of genes required for lipid biosynthesis. Deg1-Sec62 degradation was also impaired by mutation of genes encoding several enzymes mediating phospholipid and sterol biosynthesis. The degradation defect in ino4{Delta} yeast was rescued by supplementation with metabolites whose synthesis and uptake are mediated by Ino2/Ino4 targets. Stabilization of a panel of substrates of the Hrd1 and Doa10 ER ubiquitin ligases by INO4 deletion indicates ER protein quality control is generally sensitive to perturbed lipid homeostasis. Further, loss of INO4 sensitized yeast to proteotoxic stress, suggesting a broad requirement for lipid homeostasis in maintaining proteostasis. Abundance of the ER ubiquitin-conjugating enzyme Ubc7 was reduced in the absence of INO4, consistent with a model whereby perturbed lipid biosynthesis alters the abundance of critical protein quality control mediators, with broad consequences for ER proteostasis. A better understanding of the dynamic relationship between lipid homeostasis and proteostasis may lead to improved understanding and treatment of several human diseases associated with altered lipid biosynthesis.

cell biology↗