Biology subjects

Perry, N.

Publications and source records attributed to Perry, N..

5 recordsLinked to original sources

bioRxiv2026

Prokaryotic homologs of the major vault protein form engineerable vault nanocapsules

Vaults are the largest ribonucleoprotein particles in eukaryotic cells, built from 78 copies of the major vault protein (MVP), yet their function remains unknown four decades after their discovery. MVP homologs occur in prokaryotes and bacteriophages, but whether they form vaults is unknown. Here, we show that prokaryotic and bacteriophage MVP homologs assemble into vault particles. We surveyed approximately 15 billion proteins, found MVP homologs in 29 bacterial and 4 archaeal phyla, and used size-exclusion chromatography to rapidly screen and isolate vault particles of eight homologs expressed in Escherichia coli. Cryo-electron microscopy structures of the phage homolog L05 at high resolution reveal a shell of 96 MVP chains enclosing a volume ~25% larger than human vaults, among the largest protein shells of defined size outside virus capsids. Prokaryotic MVPs typically carry seven wall repeats and eukaryotic MVPs nine, and adding wall repeats to L05 yields larger vaults. Prokaryotic vaults expand the known diversity of vault architecture and offer a tractable system for studying vault assembly and a size-tunable scaffold for cargo encapsulation.

molecular biology↗

bioRxiv2026

Sex-Specific Regulation of Endothelial-to-Mesenchymal Transition (EndMT) During Atherosclerosis

Sex differences in atherosclerotic plaque biology underlie clinically distinct manifestations of acute coronary syndromes, yet the molecular mechanisms driving these differences remain incompletely understood. Endothelial-to-mesenchymal transition (EndMT) is increasingly recognized as a contributor to plaque remodeling, but whether EndMT is regulated in a sex-specific and stage-dependent manner across atherosclerosis has not been systematically examined. Here, we integrated bulk RNA sequencing with single-cell transcriptomic analyses in endothelial cells and human atherosclerotic plaques to define sex-specific EndMT regulation across healthy and advanced-stage disease. Using trajectory analyses in endothelial cells undergoing EndMT, we observed pronounced sex-specific regulation in healthy endothelium, with females exhibiting stronger early EndMT activation, whereas endothelial cells derived from atherosclerotic plaques displayed markedly attenuated sex differences with disease progression. Consistent sex-divergent pseudotime trajectories were observed in human carotid plaque endothelial single-cell RNA-seq data, with females showing greater EndMT activation at earlier stages and males at later stages. Together, these findings support a stage-dependent model of sex-specific EndMT regulation, indicating that the functional consequences of EndMT are highly context dependent and may differ across early and late disease stages. Integration of these datasets prioritized high-confidence sex-specific EndMT regulators, including COL4A1, PECAM1, CD151, JAG1, FN1, NEDD9, PODXL, MAFB, PROCR, and CDH13, providing a mechanistic framework to explain clinically observed sex differences in plaque biology and to guide targeted functional interrogation.

genomics↗

bioRxiv2023

Multi-input drug-controlled switches of mammalian gene expression based on engineered nuclear hormone receptors

Protein-based switches that respond to different inputs to regulate cellular outputs, such as gene expression, are central to synthetic biology. For increased controllability, multi-input switches that integrate several cooperating and competing signals for the regulation of a shared output are of particular interest. The nuclear hormone receptor (NHR) superfamily offers promising starting points for engineering multi-input-controlled responses to clinically approved drugs. Starting from the VgEcR/RXR pair, we demonstrate that novel (multi-)drug regulation can be achieved by exchange of the ecdysone receptor (EcR) ligand binding domain (LBD) for other human NHR-derived LBDs. For responses activated to saturation by an agonist for the first LBD, we show that outputs can be boosted by an agonist targeting the second LBD. In combination with an antagonist, output levels are tunable by up to three simultaneously present small-molecule drugs. Such high-level control validates NHRs as a versatile, engineerable platform for programming multi-drug-controlled responses.

synthetic biology↗

bioRxiv2021

Arabidopsis ROOT UV-B SENSITIVE 1 and 2 Interact with Aminotransferases to Regulate Vitamin B6 Homeostasis

Pyridoxal-5-phosphate (PLP), the enzymatic cofactor form of Vitamin B6 (vitB6), is a versatile compound that has essential roles in metabolism. Cellular PLP homeostasic regulation is currently not well understood. Here we report that in Arabidopsis, biosynthesized PLP is sequestered by specific aminotransferases (ATs), and that the proteins ROOT UV-B SENSITIVE 1 (RUS1) and RUS2 function with ATs to regulate PLP homeostasis. The stunted growth phenotypes of rus1 and rus2 mutants were previously shown to be rescuable by exogenously supplied vitB6. Specific residue changes near the PLP-binding pocket in ASPARTATE AMINOTRANSFERASE2 (ASP2) also rescued rus1 and rus2 phenotypes. In this study, saturated suppressor screens identified 14 additional suppressor of rus (sor) alleles in four aminotransferase genes (ASP1, ASP2, ASP3, or ALANIN AMINOTRANSFERASE1 (AAT1)), which suppressed the rus phenotypes to varying degrees. Each of the sor mutations altered an amino acid in the PLP-binding pocket of the protein, and sor proteins were found to have reduced levels of PLP conjugation. Genetic data revealed that the availability of PLP normally requires both RUS1 and RUS2, and that increasing the number of sor mutants additively enhanced the suppression of rus phenotypes. Biochemical results showed that RUS1 and RUS2 physically interacted with ATs. Our studies suggest a mechanism in which RUS1, RUS2 and specific ATs work together to regulate PLP homeostasis in Arabidopsis.

genetics↗

bioRxiv2021

Enhanced Solid Tumor Recognition and T cell Stemness with SynNotch CAR Circuits

The lack of highly tumor-specific antigens limits the development of engineered T cell therapeutics because of life-threatening "on-target/off-tumor" toxicities. Here we identify ALPPL2 as a tumor-specific antigen expressed in a spectrum of solid tumors, including mesothelioma. ALPPL2 can act as a sole target for chimeric antigen receptor (CAR) therapy or be combined with tumor-associated antigens such as MCAM or mesothelin in synthetic Notch (synNotch) CAR combinatorial antigen circuits. SynNotch CAR T cells display superior tumor control when compared to CAR T cells to the same antigens by prevention of CAR-mediated tonic signaling allowing T cells to maintain a long-lived memory and non-exhausted phenotype. Collectively, we establish ALPPL2 as a clinically viable target for multiple solid tumors and demonstrate the multi-faceted therapeutic benefits of synNotch CAR T cells. ONE SENTENCE SUMMARYSynNotch CAR circuits targeting novel solid tumor antigens enhance specificity and improve therapeutic efficacy by regulating T cell exhaustion.

immunology↗