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Shoulders, M. D.

Publications and source records attributed to Shoulders, M. D..

6 recordsLinked to original sources

Chondrodysplasia-inducing COL2A1 p.Gly1170Ser causes an ER storage defect without associated unfolded protein response in a human cartilage model

Mutations in the COL2A1 gene, encoding procollagen-II, cause various chondrodysplasias, including precocious osteoarthritis with mild spondyloepiphyseal dysplasia engendered by the p.Arg719Cys substitution. The molecular mechanisms underlying these disorders remain incompletely understood, largely owing to the absence of models faithfully recapitulating the human disease. Here, we developed an in vitro human cartilage model using isogenic induced pluripotent stem cell (iPSC) lines carrying either wild-type or Arg719Cys COL2A1. Directed differentiation into chondrocytes yielded cartilage tissues that were analyzed by immunohistochemistry, electron microscopy, SDS-PAGE, and RNA-sequencing. Tissues derived from Arg719Cys heterozygotes displayed a deficient matrix, closely reflecting the human disease phenotype. Arg719Cys procollagen-II was excessively post-translationally modified and partially retained within the endoplasmic reticulum (ER), leading to ER distention. Notably, despite introduction of an aberrant cysteine residue--expected to engage redox-sensitive folding and quality control pathways--Arg719Cys procollagen-II was not detectably recognized by the ER proteostasis network. The resulting inability to mount a quality control response, including activation of the unfolded protein response, indicates a failure in cellular surveillance. As a result, malformed procollagen-II both accumulates intracellularly and is secreted, contributing to the deposition of a structurally compromised extracellular matrix that drives disease pathology. The iPSC-derived cartilage model presented here provides a genetically defined and expandable, human-based system for dissecting the mechanisms of failed proteostasis in collagenopathies. These findings shed light on the types of substitutions in procollagen that cells can or cannot recognize, and underscore the therapeutic potential of targeting cellular surveillance and collagen quality control pathways in COL2A1-related disorders and beyond. SIGNIFICANCEThe p.Arg719Cys substitution in COL2A1 is known to cause dominantly inherited precocious osteoarthritis with mild spondyloepiphyseal dysplasia, but its molecular pathogenesis remains poorly understood. Prior work suggests disrupted fibrillogenesis as the molecular etiology, yet phenotypically relevant human models are lacking. Here, we use human iPSC-derived cartilage to uncover how the Arg719Cys substitution alters procollagen-II folding, modification, trafficking, and matrix deposition. We observe hallmark disease phenotypes, including a sparse collagen-II matrix and distended endoplasmic reticulum (ER), consistent with intracellular accumulation of procollagen-II. Surprisingly, the mutant procollagen-II does not appear to be differentially engaged by the ER proteostasis network, despite the incorporation of an aberrant and apparently non-disulfide bond-forming Cys residue, suggesting a fundamental failure of cellular surveillance. This unrecognized misfolding leads to secretion of defective collagen culminating in matrix dysfunction. These findings establish a mechanistic basis for disease etiology and highlight collagen quality control as a potentially tractable therapeutic target. The iPSC-based model provides a scalable, human-relevant platform for dissecting disease mechanisms and developing therapies for COL2A1-related disorders and other collagenopathies.

genetics↗

The Immune-Evasive Proline 283 Substitution in Influenza Nucleoprotein Increases Aggregation Propensity Without Altering the Native Structure

Nucleoprotein (NP) is a key structural protein of influenza ribonucleoprotein complexes and is central to viral RNA packing and trafficking. In human cells, the interferon induced Myxovirus resistance protein 1 (MxA) binds to NP and restricts influenza replication. This selection pressure has caused NP to evolve a few critical MxA-resistant mutations, particularly the highly conserved Pro283 substitution. Previous work showed that this essential Pro283 substitution impairs influenza growth, and the fitness defect becomes particularly prominent at febrile temperature (39 {degrees}C) when host chaperones are depleted. Here, we biophysically characterize Pro283 NP and Ser283 NP to test if the fitness defect is owing to Pro283 substitution introducing folding defects. We show that the Pro283 substitution changes the folding pathway of NP without altering the native structure, making NP more aggregation prone during folding. These findings suggest that influenza has evolved to hijack host chaperones to promote the folding of otherwise biophysically incompetent viral proteins that enable innate immune system escape. TeaserPro283 substitution in flu nucleoprotein introduces folding defects, and makes influenza uniquely dependent on host chaperones.

biophysics↗

Epistasis meets pleiotropy in shaping biophysical protein subspaces associated with antimicrobial resistance

Protein space is a rich analogy for genotype-phenotype maps, where amino acid sequence is organized into a high-dimensional space that highlights the connectivity between protein variants. It is a useful abstraction for understanding the process of evolution, and for efforts to engineer proteins towards desirable phenotypes. Few framings of protein space consider how higher-level protein phenotypes can be described in terms of their biophysical dimensions, nor do they rigorously interrogate how forces like epistasis--describing the nonlinear interaction between mutations and their phenotypic consequences--manifest across these dimensions. In this study, we deconstruct a low-dimensional protein space of a bacterial enzyme (dihydrofolate reductase; DHFR) into "subspaces" corresponding to a set of kinetic and thermodynamic traits [(kcat, KM, Ki, and Tm (melting temperature)]. We then examine how three mutations (eight alleles in total) display pleiotropy in their interactions across these subspaces. We extend this approach to examine protein spaces across three orthologous DHFR enzymes (Escherichia coli, Listeria grayi, and Chlamydia muridarum), adding a genotypic context dimension through which epistasis occurs across subspaces. In doing so, we reveal that protein space is a deceptively complex notion, and that the process of protein evolution and engineering should consider how interactions between amino acid substitutions manifest across different phenotypic subspaces.

systems biology↗

Evolutionary druggability: leveraging low-dimensional fitness landscapes towards new metrics for antimicrobial applications

The term "druggability" describes the molecular properties of drugs or targets in pharmacological interventions and is commonly used in work involving drug development for clinical applications. There are no current analogues for this notion that quantify the drug-target interaction with respect to a given target variants sensitivity across a breadth of drugs in a panel, or a given drugs range of effectiveness across alleles of a target protein. Using data from low-dimensional empirical fitness landscapes composed of 16 {beta}-lactamase alleles and seven {beta}-lactam drugs, we introduce two metrics that capture (i) the average susceptibility of an allelic variant of a drug target to any available drug in a given panel ("variant vulnerability"), and (ii) the average applicability of a drug (or mixture) across allelic variants of a drug target ("drug applicability"). Finally, we (iii) disentangle the quality and magnitude of interactions between loci in the drug target and the seven drug environments in terms of their mutation by mutation by environment (G x G x E) interactions, offering mechanistic insight into the variant variability and drug applicability metrics. Summarizing, we propose that our framework can be applied to other datasets and pathogen-drug systems to understand which pathogen variants in a clinical setting are the most concerning (low variant vulnerability), and which drugs in a panel are most likely to be effective in an infection defined by standing genetic variation in the pathogen drug target (high drug applicability).

systems biology↗

The Host Cell's Endoplasmic Reticulum Proteostasis Network Profoundly Shapes the Protein Sequence Space Accessible to HIV Envelope

The sequence space accessible to evolving proteins can be enhanced by cellular chaperones that assist biophysically defective clients in navigating complex folding landscapes. It is also possible, however, for proteostasis mechanisms that promote strict quality control to greatly constrain accessible protein sequence space. Unfortunately, most efforts to understand how proteostasis mechanisms influence evolution rely on artificial inhibition or genetic knockdown of specific chaperones. The few experiments that perturb quality control pathways also generally modulate the levels of only individual quality control factors. Here, we use chemical genetic strategies to tune proteostasis networks via natural stress response pathways that regulate levels of entire suites of chaperones and quality control mechanisms. Specifically, we upregulate the unfolded protein response (UPR) to test the hypothesis that the host endoplasmic reticulum (ER) proteostasis network shapes the sequence space accessible to human immunodeficiency virus-1 (HIV) envelope (Env) protein. Elucidating factors that enhance or constrain Env sequence space is critical because Env evolves extremely rapidly, yielding HIV strains with antibody and drug escape mutations. We find that UPR-mediated upregulation of ER proteostasis factors, particularly those controlled by the IRE1-XBP1s UPR arm, globally reduces Env mutational tolerance. Conserved, functionally important Env regions exhibit the largest decreases in mutational tolerance upon XBP1s activation. This phenomenon likely reflects strict quality control endowed by XBP1s-mediated remodeling of the ER proteostasis environment. Intriguingly and in contrast, specific regions of Env, including regions targeted by broadly neutralizing antibodies, display enhanced mutational tolerance when XBP1s is activated, hinting at a role for host proteostasis network hijacking in potentiating antibody escape. These observations reveal a key function for proteostasis networks in decreasing instead of expanding the sequence space accessible to client proteins, while also demonstrating that the host ER proteostasis network profoundly shapes the mutational tolerance of Env in ways that could have important consequences for HIV adaptation.

biochemistry↗

XBP1s-Mediated Endoplasmic Reticulum Proteostasis Network Enhancement Can Selectively Improve Folding and Secretion of an Osteogenesis Imperfecta-Causing Collagen-I Variant

Osteogenesis imperfecta (OI) is typically caused by autosomal dominant mutations in genes encoding collagen type-I, most commonly resulting in Gly[->]Ser triple-helical domain substitutions that disrupt collagen folding and/or stability. Here, we test the hypothesis that upregulating the endoplasmic reticulum (ER) proteo-stasis network via the unfolded protein response (UPR) can improve the folding and secretion of the clinically severe, prototypical OI-causing COL1A1 p.G425S collagen-1(I) variant. We first show that small molecules that activate the entire UPR by causing global ER protein misfolding stress severely ablate collagen-I secretion from both G425S Col1(I)- and wild-type (WT) Col1(I)-expressing primary fibroblasts. In contrast, stress-independent, specific induction of just the UPRs XBP1s transcriptional response can enhance collagen-I secretion from G425S Col1(I) patient primary fibroblasts up to ~300% of basal levels. Notably, the effect is selective - collagen-I secretion from WT Col1(I)-expressing healthy donor primary fibroblasts is unaltered by XBP1s. XBP1s pathway activation appears to post-translationally enhance the folding/assembly and secretion of G425S Col1(I), as only modest impacts on collagen-I transcription or synthesis are observed. Consistent with this notion, we find that the stable, triple-helical collagen-I secreted by XBP1s-activated G425S 1(I) patient fibroblasts includes a higher proportion of the mutant 1(I) polypeptide than the collagen-I secreted under basal ER proteostasis conditions. We note that consistent reproducibility of these results is dependent on as yet unascertained experimental variables. Still, these promising observations suggest the potential for ER proteo-stasis network modulation to improve mutant collagen proteostasis in the collagenopathies, motivating further investigation of the effects generality, underlying mechanism, and potential therapeutic benefits.

cell biology↗