Biology subjects

Hopkins, M.

Publications and source records attributed to Hopkins, M..

8 recordsLinked to original sources

bioRxiv2026

Massively scaled variant effect mapping across the MAPK pathway reveals the importance of molecular and cellular context

Variation alters inherent protein properties like thermodynamic stability and catalytic activity, and these intrinsic effects are shaped by the complex cellular environment. Signaling cascades typify this complexity, with tens or hundreds of proteins acting in concert through regulated states and interactions to transduce signals. Here, we measure the effect of 186,676 variants across 17 proteins in the RAS-MAPK pathway on protein abundance and pathway activity in human cells under diverse conditions, for a total of 503,099 variant effect measurements. We discovered 14,412 dominant negative variants across 12 proteins, nearly all previously unknown, that disrupt specific domains or interaction interfaces while leaving other functions intact and that are depleted from the human population. Measuring the abundance of 106,642 variants across 10 proteins under HSP90 inhibition showed that HSP90 shapes the effect of 67% of missense variants across the pathway, buffering destabilizing variants in both strong and weak clients. Our variant effect data, collected in the context of an intact proteome, enabled us to assess the functional importance of 395 experimentally and computationally modeled MAPK protein interactions. Using additional mutational scans, we resolved how the promiscuous switch II helix binding surface of KRAS accommodates overlapping interactions with LZTR1 and SOS1, revealing distinct allosteric networks that support each interaction. Thus, we establish a framework for measuring variant effects at unprecedented scale in human cells, illuminating fundamental MAPK pathway signaling mechanisms and demonstrating that cellular context profoundly shapes the effect of most variants.

genomics↗

bioRxiv2026

Spatially resolved gene expression and tumour-microenvironment interactions across malignant transformation in IDH-mutant glioma

Isocitrate dehydrogenase (IDH)-mutant gliomas represent most lower-grade diffuse gliomas in young adults. Although IDH-mutant gliomas initially behave indolently relative to IDH-wildtype counterparts, they undergo inevitable malignant transformation. The mechanisms driving this progression remain poorly defined. We analyzed a unique longitudinal cohort of two patients with IDH-mutant diffuse gliomas, each with matched WHO grade 2, 3, and 4 tumours. Spatial transcriptomics (NanoString GeoMx and 10X Visium), combined with differential expression, spatially variable gene analysis, and gene ontology enrichment, were used to define transcriptional programs underlying progression. Unexpectedly, across both patients, higher-grade tumours demonstrated reduced proliferation at the infiltrative margin as measured by Ki67. Spatial transcriptomic analysis identified an enrichment of invasion-associated genes associated with increasing tumour grade. In an independent bulk RNA-seq cohort, expression of this spatially derived program did not outperform grade-only PFS or OS analysis. These observations underscore the need to develop new metrics that account for spatial evolution that occurs across progression, but escapes detection in bulk analyses and provide the rationale for prioritizing migration-, cytoskeletal- and stress-associated programs for further investigation.

cancer biology↗

bioRxiv2026

Complex interplay of biomechanics and ecology influenced crab claw morphology evolution

True crabs (Brachyura) are among the most iconic marine arthropods, representing noteworthy examples of morphological and ecological disparity. A striking feature of brachyurans are their anterior pincer-like appendages: chelipeds. These structures showcase a large diversity of morphologies that reflect ecology and overall multifunctionality. Yet, a comprehensive assessment of appendage functional morphology within phylogenetic and ecological trait contexts has never been attempted. By combining 3D geometric morphometrics, finite element analyses, multilocus molecular phylogeny, and ecological trait data for 80 crab species, including three fossil forms, we unveil a complex evolutionary history for crab chelipeds. Despite extreme shape diversity amongst chelipeds, stress distributions are very similar across taxa and hint a many-to-one pattern. High concentrations of chelipeds within constrained morphospace regions associated with peak pinch forces illustrates that brachyuran morphologies optimised for shell crushing may have arisen in the Cretaceous. Deviations from this morphospace highlight the diversification of non-shell-crushing life modes and the influence of sexual selection on appendages. Neither cheliped shape nor pinch force show phylogenetic signal. Together these results indicate that the evolution of cheliped shape is closely associated with, and inferred to have been strongly influenced by, crab ecology, biomechanical needs and sexual selection. SIGNIFICANCE STATEMENTChelipeds, the pincer-like claws of crabs, are among the most morphologically diverse appendages within Arthropoda, yet the evolutionary forces driving this diversity remain poorly understood. By integrating 3D geometric morphometrics, biomechanical modelling, molecular phylogeny, and ecological data across 80 crab species including fossil forms, we demonstrate that cheliped morphology is driven by ecology, biomechanical demands, and sexual selection rather than phylogenetic relatedness. The multifunctionality of these structures produces strong evidence for many-to-one mapping of form to function. Morphologies optimised for durophagy appear to have originated in the Cretaceous, with subsequent diversification into manipulative and sexually selected forms from a morphologically flexible foundation. These findings demonstrate that cheliped diversity reflects a complex interplay between ecological specialisation, biomechanical optimisation, and sexual selection across Brachyura.

ecology↗

bioRxiv2024

Using state space models to understand trait evolution in fossil lineages

Linear state space models provide a useful framework for investigating phenotypic evolution in fossil lineages in a wide variety of models including Brownian motion, Ornstein-Uhlenbeck processes, and models that incorporate potentially explanatory environmental covariates. A state space framework also provides access to residuals for the predicted and observed values at each time point as well as improved numerical stability. We illustrate the value of the state space approach by re-analyzing a classic dataset of diatom evolution in Yellowstone Lake. We find that number of spines is best explained by adaptation to changing solar insolation as an exogenous environmental covariate.

evolutionary biology↗

bioRxiv2024

The contribution of neutrophils to bacteriophage clearance and pharmacokinetics in vivo

With the increasing prevalence of antimicrobial-resistant bacterial infections, there is great interest in using lytic bacteriophages (phages) to treat such infections. However, the factors that govern bacteriophage pharmacokinetics in vivo remain poorly understood. Here, we have examined the contribution of neutrophils, the most abundant phagocytes in the body, to the pharmacokinetics of intravenously administered bacteriophage in uninfected mice. A single dose of LPS-5, an antipseudomonal bacteriophage recently used in human clinical trials, was administered intravenously to both wild-type BALB/c and neutropenic ICR mice. Phage concentrations were assessed in peripheral blood and spleen at 0.5, 1, 2, 4, 8, 12, and 24 hours after administration by plaque assay and qPCR. We observed that the phage clearance is only minimally affected by neutropenia. Indeed, the half-life of phages in blood in BALB/c and ICR mice is 3.45 and 3.66 hours, respectively. These data suggest that neutrophil-mediated phagocytosis is not a major determinant of phage clearance. Conversely, we observed a substantial discrepancy in circulating phage levels over time when measured by qPCR versus plaque assay, suggesting that substantial functional inactivation of circulating phages occurs over time. These data indicate that circulating factors, but not neutrophils, inactivate intravenously administered phages.

pharmacology and toxicology↗

bioRxiv2023

Rational development of a small-molecule activator of CK1γ2 that decreases C99 and beta-amyloid levels

Alzheimers disease (AD) is a debilitating neurodegenerative disorder characterized by the accumulation of beta-amyloid (A{beta}), C99, and Tau in vulnerable areas of the brain. Despite extensive research, current strategies to lower A{beta} levels have shown limited efficacy in slowing the cognitive decline associated with AD. Recent findings suggest that C99 may also play a crucial role in the pathogenesis of AD. Our laboratory has discovered that CK1{gamma}2 phosphorylates Presenilin 1 at the {gamma}-secretase complex, leading to decreased C99 and A{beta} levels. Thus, CK1{gamma}2 activation appears as a promising therapeutic target to lower both C99 and A{beta} levels. In this study, we demonstrate that CK1{gamma}2 is inhibited by intramolecular autophosphorylation and describe a high-throughput screen designed to identify inhibitors of CK1{gamma}2 autophosphorylation. We hypothesize that these inhibitors could lead to CK1{gamma}2 activation and increased PS1-Ser367 phosphorylation, ultimately reducing C99 and A{beta} levels. Using cultured cells, we investigated the impact of these compounds on C99 and A{beta} concentrations and confirmed that CK1{gamma}2 activation effectively reduces their levels. Our results provide proof of concept that CK1{gamma}2 is an attractive therapeutic target for AD. Future studies should focus on the identification of specific compounds that can inhibit CK1{gamma}2 autophosphorylation and evaluate their efficacy in preclinical models of AD. These studies will pave the way for the development of novel therapeutics for the treatment of AD.

pharmacology and toxicology↗

bioRxiv2020

Transforming the Language of Life: Transformer Neural Networks for Protein Prediction Tasks

AO_SCPLOWBSTRACTC_SCPLOWThe scientific community is rapidly generating protein sequence information, but only a fraction of these proteins can be experimentally characterized. While promising deep learning approaches for protein prediction tasks have emerged, they have computational limitations or are designed to solve a specific task. We present a Transformer neural network that pre-trains task-agnostic sequence representations. This model is fine-tuned to solve two different protein prediction tasks: protein family classification and protein interaction prediction. Our method is comparable to existing state-of-the art approaches for protein family classification, while being much more general than other architectures. Further, our method outperforms all other approaches for protein interaction prediction. These results offer a promising framework for fine-tuning the pre-trained sequence representations for other protein prediction tasks.

bioinformatics↗

bioRxiv2019

C99, not beta-amyloid, is associated with selective death of vulnerable neurons in Alzheimer's disease.

IntroductionThe levels and distribution of amyloid deposits in the brain does not correlate well with Alzheimers disease (AD) progression. Therefore, it is likely that Amyloid-precursor-protein proteolytic fragments other than beta-amyloid contribute to the onset of AD.\n\nMethodsWe developed a sensitive assay adapted to the detection of C99, the direct precursor of beta-amyloid. Three postmortem groups were studied: control with normal and stable cognition; subjects with moderate AD, and individuals with severe AD. The amount of C99 and beta-amyloid was quantified and correlated with the severity of AD.\n\nResultsC99 accumulates in vulnerable neurons, and its levels correlate with the degree of cognitive impairment in patients suffering from AD. In contrast, beta-amyloid levels are increased in both vulnerable and resistant brain areas.\n\nDiscussionThese results raise the possibility that C99, rather than beta-amyloid plaques, is responsible for the death of nerve cells in Alzheimers disease.

neuroscience↗