Global Profiling of Remodeled Subcellular Structures Due to Drug Treatment and Disease

Victor, R. A.; Altemus, J. J.; Lay, M. A.; Shepherd, S. N.; Padilla-Rodriguez, M.; Lipinski, A. A.; Mouneimne, G.; Langlais, P. R.; Schwartz, J. C.

doi:10.1101/2025.08.27.672480

bioRxiv · 10.1101/2025.08.27.672480

Global Profiling of Remodeled Subcellular Structures Due to Drug Treatment and Disease

Victor, R. A.·Altemus, J. J.·Lay, M. A.·Shepherd, S. N.·Padilla-Rodriguez, M.·Lipinski, A. A.·Mouneimne, G.·Langlais, P. R.·Schwartz, J. C.

View original source ↗Export metadata ↓

Abstract

Cellular biochemistry arises from various interactions between macromolecules, including proteins, nucleic acids, and lipids. These make up membrane-bound organelles, membrane-less compartments, and molecular assemblies and scaffolds. Changes due to stimuli or disease can significantly impact cell fate and metabolism. We recently reported our protocol combining crosslinking and size exclusion chromatography with mass spectrometry (SEC-MS). In this study, we explore global changes to subcellular structure in Ewing sarcoma cell lines or in response to drug treatment. Crosslinking-dependent differential enrichment across four human cell lines is seen for proteins involved in splicing, mitochondria function, and cell division. We confirmed changes to nucleoli structure. We also examine structures affected by a transcription inhibitor, flavopiridol. Following flavopiridol treatment, we observed changes to the levels of transcription and mRNA processing machinery present in large subcellular structures. Unexpected effects were also found, including structural changes to a cytoplasmic organelle, the peroxisome. Along with a reduction in peroxisome function, dissociation of peroxisome pore proteins PEX13 and PEX14 was detected by STORM microscopy. We conclude that SEC-MS combined with crosslinking is a valuable method to detect and quantify drug or disease effects on subcellular structures and may shed light on new aspects to mechanisms underlying their biologic outcomes. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=71 SRC="FIGDIR/small/672480v2_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@1f01b55org.highwire.dtl.DTLVardef@9279d4org.highwire.dtl.DTLVardef@7c7492org.highwire.dtl.DTLVardef@c92ff4_HPS_FORMAT_FIGEXP M_FIG C_FIG Key PointsO_LICrosslinking plus SEC-MS shows global effects on subcellular structure in disease and treatment. C_LIO_LIEwing sarcoma cell lines tested present distinct molecular composition in splicing, mitochondria, and nucleoli. C_LIO_LIA transcription inhibitor flavopiridol disrupts peroxisome function and protein import pores C_LI

Source connections

Published article ↗

Explore related subjects

biochemistry Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Victor, R. A., Altemus, J. J., Lay, M. A., Shepherd, S. N., Padilla-Rodriguez, M., Lipinski, A. A., Mouneimne, G., Langlais, P. R., Schwartz, J. C.. 2025-08-31. Global Profiling of Remodeled Subcellular Structures Due to Drug Treatment and Disease. https://doi.org/10.1101/2025.08.27.672480

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Conjunctive Targeting Links Drug Synergy to Emergent Proteome Structural States

Combinatorial therapies are widely used in the treatment of acute myeloid leukemia (AML) to address disease heterogeneity, adaptive resistance, and rewired signaling and metabolic states. Yet drug prioritization remains largely guided by clinical or phenotypic evidence, while the molecular mechanisms underlying effective drug combinations remain incompletely defined. To narrow this gap, we developed Combinatorial high-ratio Partial proteolysis with reference PRoteome Analysis (CoPPRA), a structural proteomics workflow based on limited proteolysis of cell lysates that profiles drug-associated changes in regional protein accessibility at peptide-level resolution. Here, we applied CoPPRA to ruxolitinib and ulixertinib, individually and in combination, in AML-related cell lysates. Our findings extend conjunctive targeting (CT), a recently proposed mechanism of combinatorial drug action in which combined exposure produces protein targeting patterns not observed with either drug alone. Previously identified through combination-associated changes in protein solubility/stability, CT is examined here at peptide-level resolution through regional differences in proteolytic accessibility. The ruxolitinib-ulixertinib combination produced broad peptide-level accessibility changes, including a subset meeting the predefined criteria for CT. CT candidates predominantly exhibited regional accessibility changes, with altered peptide regions occurring against comparatively small changes across the remaining quantified peptides from the same proteins. MAP2K1 and ATP6V1G1 showed pronounced differences between overlapping peptide sequences, highlighting localized variation in combination-associated accessibility, including an ATP6V1G1 peptide mapping to an annotated helical region. Combination-associated increases in peptide signals were also observed in PIK3R1, BRD4, and PTPN11, linking regional accessibility changes to signaling and transcriptional regulators relevant to AML. Functional enrichment and network analyses further implicated nucleotide and glucose metabolism, ficolin-1-rich granules, ribosome-associated processes, and phagocytic vesicles. These results extend conjunctive targeting from protein-level solubility/stability changes to regional differences in proteolytic accessibility, showing that combination-associated effects can be concentrated within specific peptide regions rather than distributed uniformly across proteins. More broadly, CoPPRA provides a peptide-resolved approach for investigating the molecular features of combinatorial drug action and prioritizing protein regions for subsequent mechanistic validation.

biochemistry↗

bioRxiv2026

Structural and biochemical characterisation of an iterative GCN5-related N-acetyltransferase required for fungal siderophore tailoring

Siderophore-mediated iron acquisition is essential for fungal survival, particularly under iron-limiting conditions. In Aspergillus fumigatus, SidG, a member of the GCN5-related N-acetyltransferase (GNAT) superfamily, catalyses the final step in the biosynthesis of the extracellular siderophore triacetylfusarinine C (TAFC) through sequential acetylation of the precursor fusarinine C (FsC). However, the timing, catalytic mechanism, and functional significance of this modification are not fully understood. Here, we reconstituted SidG activity in vitro and combined native mass spectrometry, X-ray crystallography, molecular dynamics simulations, and site-directed mutagenesis to investigate its catalytic properties. Our analyses demonstrate that SidG selectively binds acetyl-CoA from the cellular milieu and iteratively acetylates the FsC scaffold prior to iron chelation. Structural, biochemical, and molecular dynamics analyses support a direct transfer mechanism, identify key catalytic residues, and demonstrate the strict selectivity of SidG for short-chain acyl-CoA donors. Together, these findings establish the molecular basis for SidG-dependent siderophore tailoring and expand our understanding of GNAT-catalysed transformations in fungal natural product biosynthesis.

biochemistry↗

bioRxiv2026

Reconstitution of +1 nucleosome transcription reveals coordinated functions of SAGA, Mediator, and TFIIH

The +1 nucleosome has emerged as a key regulator of eukaryotic transcription, but how it controls transcription initiation remains poorly understood. Here we reconstitute transcription through the +1 nucleosome using eleven purified yeast factors: RNA polymerase II (Pol II), the six general transcription factors (GTFs), TFIIS, the activator Pho4, and the SAGA and Mediator complexes. The system recapitulates key features of regulation observed in vivo. SAGA, acting with Pho4, directs pre-initiation complex (PIC) assembly to the correct position through its TBP-loading activity. Mediator stimulates transcription when the +1 nucleosome imposes a barrier to PIC formation, consistent with stabilization of productive TFIIH-DNA engagement. Contrary to the prevailing model, SAGA remains bound to the PIC after TBP loading and acetylates the +1 nucleosome within the assembled complex. The isolated PIC-Mediator-SAGA-nucleosome complex is transcriptionally active, and the repressive effect of the nucleosome is relieved by the DNA translocase activity of Ssl2, the TFIIH subunit that opens promoter DNA. TFIIH thus couples promoter melting to remodeling of the +1 nucleosome.

biochemistry↗