Biology subjects

Thompson, P. A.

Publications and source records attributed to Thompson, P. A..

5 recordsLinked to original sources

bioRxiv2025

Discovery of a VHL molecular glue degrader of GEMIN3 by Picowell RNA-seq

Targeted protein degradation (TPD) is an emerging therapeutic modality in which small molecules are used to recruit targets to the natural protein degradation machinery of the cell. Molecular glue degraders (MGD) are monovalent small molecules that accomplish this by redirecting E3 ubiquitin ligases to target proteins, offering the potential to degrade previously unliganded and "undruggable" proteins in cancer, neurodegenerative, and other diseases. While attractive due to their drug-like properties, MGDs are exceptionally hard to discover and have largely been identified serendipitously. The Von Hippel-Lindau (VHL) E3 ligase is the second most widely used effector for TPD, though current VHL-based degraders are primarily large heterobifunctional PROTACs (proteolysis-targeting chimeras) designed using target-based ligands. Here, we have instead pursued target-agnostic discovery of VHL MGDs leveraging proprietary ultra-miniaturized microfluidics devices (Picowells) to facilitate unbiased RNA-seq screening of a biased E3-focused library. This resulted in dGEM3, a novel VHL molecular glue that targets the survival of motor neuron (SMN) complex member GEMIN3 for degradation. Through a combination of cellular, biochemical, and biophysical assays, we have characterized the GEMIN3 degron within its helicase ATP-binding domain, and how the kinetics of ternary complex formation impact degradation. These findings provide insights on the re-programmability of VHL for novel targets using drug-like molecular glues.

biochemistry↗

bioRxiv2024

eIF4A controls translation of estrogen receptor alpha and is a therapeutic target in advanced breast cancer

The majority of human breast cancers are dependent on hormone-stimulated estrogen receptor alpha (ER) and are sensitive to its inhibition. Treatment resistance arises in most advanced cancers due to genetic alterations that promote ligand independent activation of ER itself or ER target genes. Whereas re-targeting of the ER ligand binding domain (LBD) with newer ER antagonists can work in some cases, these drugs are largely ineffective in many genetic backgrounds including ER fusions that lose the LBD or in cancers that hyperactivate ER targets. By identifying the mechanism of ER translation, we herein present an alternative strategy to target ER and difficult to treat ER variants. We find that ER translation is cap-independent and mTOR inhibitor insensitive, but dependent on 5 UTR elements and sensitive to pharmacologic inhibition of the translation initiation factor eIF4A, an mRNA helicase. EIF4A inhibition rapidly reduces expression of ER and short-lived targets of ER such as cyclin D1 and other components of the cyclin D-CDK complex in breast cancer cells. These effects translate into suppression of growth of a variety of ligand-independent breast cancer models including those driven by ER fusion proteins that lack the ligand binding site. The efficacy of eIF4A inhibition is enhanced when it is combined with fulvestrant--an ER degrader. Concomitant inhibition of ER synthesis and induction of its degradation causes synergistic and durable inhibition of ER expression and tumor growth. The clinical importance of these findings is confirmed by results of an early clinical trial (NCT04092673) of the selective eIF4A inhibitor zotatifin in patients with estrogen receptor positive metastatic breast cancer. Multiple clinical responses have been observed on combination therapy including durable regressions. These data suggest that eIF4A inhibition could be a useful new strategy for treating advanced ER+ breast cancer.

cancer biology↗

bioRxiv2022

A new method for a priori practical identifiability

Background and objectivePractical identifiability analysis - to determine whether a model property can be determined from given data - is central to model-based data analysis in biomedicine. The main approaches used today all require that the coverage of the parameter space be exhaustive, which is usually not possible. An attractive alternative could be to use structural identifiability methods, since they do not need such a parameter coverage. However, current structural methods are unsuited for practical identifiability analysis, since they assume that all higher-order derivatives of the measured variables are available, and we do not know the implications of this assumption. Herein, we provide new definitions and methods that allow for this assumption to be relaxed. MethodsThe new methods and definitions are valid for ordinary differential equations, and use a combination of differential algebra and modulus calculus, implemented in Maple. ResultsWe introduce the concept of ({nu}1, ..., {nu}m)-identifiability, which differs from previous definitions in that it assumes that only the first {nu}i derivatives of the measurement signal yi are available. This new type of identifiability can be determined using our new algorithm, as is demonstrated by applications to various published biomedical models. Our methods allow for identifiability of not only parameters, but of any model property, i.e. observability. These new results provide further strengthening of conclusions made in previous analysis of these models. Importantly, our analysis can for the first time quantify the impact of the assumption that all derivatives are available in specific examples. If one e.g. assumes that only up to third order derivatives, instead of all derivatives, are available, the number of identifiable parameters drops from 17 to 1 for a Drosophila model, and from 21 to 6 for an NF-{kappa}B model. In both these models, the previously obtained identifiability is present only if at least 20 derivatives of all measurement signals are available. ConclusionsOur results demonstrate that the assumption regarding availability of derivatives done in traditional structural identifiability analysis causes a big overestimation regarding the number of parameters that can be estimated. Our new methods and algorithms allow for this assumption to be relaxed, which moves structural identifiability methodology one step closer to practical identifiability analysis.

bioengineering↗

bioRxiv2018

Testing the unitary theory of language lateralisation using functional transcranial Doppler sonography study in adults

Cerebral lateralisation for language can vary from task to task, but it is unclear if this reflects error of measurement or independent lateralisation of different language systems. We used functional transcranial Doppler sonography to assess language lateralisation in 37 adults (7 left-handers) on six tasks, each given on two occasions. Tasks taxed different aspects of language function. A preregistered structural equation analysis was used to compare models of means and covariances. For most people, a single lateralised factor explained most of the covariance between tasks. A minority, however, showed dissociation of asymmetry, giving a second factor. This was mostly derived from a receptive task, which was highly reliable but not lateralised. The results suggest that variation in strength of language lateralisation reflects true individual differences and not just error of measurement. Inclusion of several tasks in a laterality battery makes it easier to detect cases of atypical asymmetry.

neuroscience↗

bioRxiv2017

Lack of Evidence that Ursodeoxycholic Acid’s Effects on the Gut Microbiome Influence Colorectal Adenoma Risk

ObjectiveWe previously reported that Ursodeoxycholic acid (UDCA), a therapeutic bile acid, reduces risk for advanced colorectal adenoma in men but not women. Interactions between the gut microbiome and fecal bile acid composition as a factor in colon cancer neoplasia have been postulated but evidence is limited to small cohorts and animal studies.\n\nDesignUsing banked stool samples collected as part of a phase III randomized clinical trial of UDCA for the prevention of colorectal neoplasia, we compared change in the microbiome composition after 3 years intervention in a subset of participants randomized to 8-10 mg/kg of body weight UDCA (n=198) to placebo (n=203). UDCA effects on the microbiome, sex and adenoma outcome were investigated.\n\nResultsStudy participants randomized to UDCA experienced compositional changes in their microbiome that were statistically more similar to other individuals in the UDCA arm than to those in the placebo arm. This change reflected an UDCA-associated shift in microbial community distance metrics (P <0.001), independent of sex, with no evidence of UDCA effect on microbial richness (P > 0.05). These UDCA-associated shifts in microbial community distance metrics from baseline to end-of-study were not associated with risk of any or advanced adenoma (all P> 0.05) in men or women.\n\nConclusionDespite a large sampling of randomized clinical trial participants, daily UDCA use only modestly influenced the relative abundance of microbial species in stool with no evidence for effects of UDCA on stool microbial community composition as a modifier of colorectal adenoma risk.\n\nSUMMARYO_ST_ABSWhat is already known about this subject?C_ST_ABSO_LIUrsodeoxycholic acid (UDCA) is a therapeutic bile acid used in the treatment of primary biliary cirrhosis (PBC) and investigated for anti-cancer activity in the colon\nC_LIO_LIIn humans, UDCA is produced in the colon from the conjugation of primary bile acids by intestinal bacteria\nC_LIO_LIIntestinal bacteria play a critical role in human intestinal health and disease including a hypothesized role in the development of colorectal cancer.\nC_LIO_LIUDCA was found to reduce the risk of more advanced colorectal adenoma with effects present in men but not women.\nC_LIO_LITherapeutic UDCA was recently shown to reduce the extent of bacterial dysbiosis in patients with PBC\nC_LI\n\nWhat are the new findings?O_LIAmong a population of patients with colorectal adenoma, low dose oral UDCA taken daily produced modest changes in fecal bacterial composition\nC_LIO_LIUDCA associated changes in the gut microbiome were similar in men and women.\nC_LIO_LIUDCA associated changes in the gut micobiome were not associated with risk of any or advanced colorectal adenoma in the patient population.\nC_LI\n\nHow might it impact on clinical practice in the foreseeable future?O_LIThese findings confirm effects of oral UDCA on the microbiome that may be beneficial for patients with PBC.\nC_LIO_LIThese findings suggest that the anti-cancer effects of UDCA for colorectal adenoma prevention are not due to major effects of UDCA on the gut microbiome.\nC_LI

cancer biology↗