Biology subjects

Henry, A. G.

Publications and source records attributed to Henry, A. G..

12 recordsLinked to original sources

bioRxiv2025

A Common PD-Risk GBA1 Variant Disrupts LIMP2 Interaction, Impairs Glucocerebrosidase Function, and Drives Lysosomal and Mitochondrial Dysfunction

Variants in GBA1 cause Gaucher disease (GD), a lysosomal storage disorder, and represent the most common genetic risk factor for Parkinsons disease (PD). While some GBA1 variants are associated with both GD and PD, several coding mutations, including E326K, specifically confer risk for developing PD. It is established that GD-linked variants in {beta}-glucocerebrosidase (GCase), the enzyme encoded by GBA1, are loss-of-function, but it remains unclear whether variants solely associated with PD similarly reduce GCase activity. The mechanisms by which some of these variants impact GCase activity and PD-associated pathways, including lysosomal and mitochondrial function, are also poorly defined. Here, we show that the PD-linked E326K variant significantly reduces lysosomal GCase activity by impairing its delivery to lysosomes via altered interactions with its receptor, LIMP2. Biophysical and structural characterization of this variant, both alone and in complex with LIMP2, reveals a dimeric organization that appears to result from the loss of a key salt bridge between E326 and R329. Restoration of this salt bridge through the introduction of a negatively charged side chain at position 329 promotes monomeric organization and interaction with LIMP2 in cells. GBA1-p.E326K cell models show greater deficits in PD-linked pathways compared to more severe loss of GCase function, including secondary lysosomal lipid storage and mitochondrial dysfunction. We confirm the E326K variant impacts GCase pathway activity in relevant CNS cell types, including iPSC-derived microglia, and in biofluids from heterozygous GBA1-p.E326K variant carriers. Together, our data provide key insights into the nature of GCase dysfunction in GBA1-PD and can inform the development of GCase-targeted therapeutic strategies to treat PD.

cell biology↗

bioRxiv2024

Consumption of only wild foods induces large-scale, partially-persistent alterations to the gut microbiome

The composition of the gut microbiome (GM) affects human health and varies among lifestyles. Adopting more "traditional" diets could lead to substantive and health-associated changes in the GM. However, research has focused on diets including domesticated foods. For most of our evolutionary history, humans consumed only wild foods. We explored the impact of a wild-food-only (WF) diet on the GM composition. One participant collected daily fecal samples and recorded daily food consumption over an eight-week period, the middle four weeks of which he consumed only wild foods (nuts, fruits and leafy greens, wild deer, and fish). Samples were profiled through 16S rRNA amplicon sequencing and the species identified by oligotyping. The WF diet altered the GM composition, and the magnitude of the changes is larger than in other diet interventions. However, no new GM taxa, including "old friends" appeared; instead, the relative proportions of already-present taxa shifted. There is a clear successional shift from the pre-, during- and post-WF diet. The GM is very sensitive to the change from a "Western" diet to a WF diet, likely reflecting the different macro- and micronutrient properties of the consumed foods.

microbiology↗

bioRxiv2023

Assessing the validity of a calcifying oral biofilm model as a suitable proxy for dental calculus

AO_SCPLOWBSTRACTC_SCPLOWDental calculus is increasingly used by researchers to study dietary patterns in past populations. The benefits of using dental calculus for this purpose have been clearly demonstrated in previous studies, with dental calculus harbouring a wealth of microremains and biomarkers for health and diet within its mineral matrix. Previous studies have demonstrated some of the limitations and biases of how methods of processing may overlook, or even remove, some of the important information contained within the mineralised matrix. However, there are many factors that are impossible to account for in vivo and in archaeological material, such as exact dietary intake, and individual factors such as pH and enzyme activity, leaving some limitations that may not be addressed through these types of studies and will require a different approach. We present a protocol for creating a calcifying oral biofilm model that can be used to explore the biases and limitations of dental calculus as a medium for paleodietary reconstructions. We report the microbial and mineral composition of our model in an effort to validate the model calculus as an appropriate proxy to natural dental calculus. The microbial profile and species diversity of our model was determined using metagenomic classification with the nf-core/eager pipeline and Kraken2, and compared to various reference samples from oral sites, including saliva, plaque, and dental calculus. We then assessed whether our model calculus mineralises in a manner similar to natural dental calculus using Fourier transform infrared (FTIR) spectroscopy. The metagenomic classification showed a microbial profile predominantly made up of (facultative) anaerobes, with a community structure that was somewhat distinct from other oral reference samples. The core genera of the model consisted of oral species, but clustered separately from oral reference samples, with a higher abundance of anaerobes. Mineral and organic components of our model mimic that of the modern and archaeological reference calculus that was used as a comparison. There was an overall increase in the inorganic component relative to organic over the course of the experiment, with carbonated hydroxyapatite as the principal compound, consistent with natural human-derived calculus. We conclude that oral biofilm models, such as the one presented in this study, have great potential to validate current methods used in the analysis of archaeological dental calculus, and should be used to complement, rather than replace current in vivo studies.

microbiology↗

bioRxiv2023

Rab12 regulates LRRK2 activity by promoting its localization to lysosomes

Leucine-rich repeat kinase 2 (LRRK2) variants associated with Parkinsons disease (PD) and Crohns disease lead to increased phosphorylation of its Rab substrates. While it has been recently shown that perturbations in cellular homeostasis including lysosomal damage and stress can increase LRRK2 activity and localization to lysosomes, the molecular mechanisms by which LRRK2 activity is regulated have remained poorly defined. We performed a targeted siRNA screen to identify regulators of LRRK2 activity and identified Rab12 as a novel modulator of LRRK2-dependent phosphorylation of one of its substrates, Rab10. Using a combination of imaging and immunopurification methods to isolate lysosomes, we demonstrated that Rab12 is actively recruited to damaged lysosomes and leads to a local and LRRK2-dependent increase in Rab10 phosphorylation. PD-linked variants, including LRRK2 R1441G and VPS35 D620N, lead to increased recruitment of LRRK2 to the lysosome and a local elevation in lysosomal levels of pT73 Rab10. Together, these data suggest a conserved mechanism by which Rab12, in response to damage or expression of PD-associated variants, promotes the recruitment of LRRK2 and phosphorylation of its Rab substrate(s) at the lysosome.

cell biology↗

bioRxiv2022

LRRK2 Kinase Activity Regulates Parkinson's Disease-Relevant Lipids at the Lysosome

Lysosomal dysfunction is a hallmark of Parkinsons disease (PD), and variants in several PD-associated genes, including LRRK2, perturb lysosomal homeostasis. Based on this, LRRK2 kinase inhibition is being explored as a therapeutic approach for the treatment of PD. LRRK2 inhibitors reduce levels of BMP, an endolysosomal lipid involved in glycosphingolipid (GSL) catabolism, in urine from preclinical models and clinical subjects, however, the mechanisms by which LRRK2 regulates BMP and the functional significance of this change to disease are undefined. We establish that LRRK2 regulates secretion of BMP- and GSL-containing vesicles from kidney into urine and modulates BMP and GSL levels in the brain. BMP accumulates within lysosomes as a secondary response to LRRK2s effects on the activity of glucocerebrosidase (GCase), a PD-linked enzyme involved in GSL catabolism. Alterations in BMP and GCase substrate turnover are observed in CSF from LRRK2-PD patients, highlighting the relevance of LRRK2-dependent lysosomal dysfunction in disease.

neuroscience↗

bioRxiv2022

High conservation of the dental plaque microbiome community across populations with differing subsistence strategies and levels of market integration

Industrialization - including urbanization, participation in the global food chain, and consumption of heavily processed foods - is thought to drive substantial shifts in the human microbiome. While diet strongly influences stool microbiome composition, the influence of diet on the oral microbiome, and particularly dental plaque, is largely speculative. Here we investigated whether dental plaque microbial communities are distinctly different across populations with dissimilar subsistence strategies and degree of industrialized market integration. Using a metagenomic approach, we compared the dental plaque microbiomes of Baka foragers and Nzime subsistence agriculturalists in Cameroon (n = 46) with the dental plaque and calculus microbiomes of highly industrialized populations in North America and Europe. We found that differences in microbial taxonomic composition between populations were minimal, with high conservation of abundant microbial taxa and no significant differences in microbial diversity related to dietary practices. Instead, we find that the major source of variation in dental plaque microbial species composition is related to tooth location and oxygen availability, and may be influenced by toothbrushing or other dental hygiene measures. Our results support that dental plaque, in contrast to the stool microbiome, maintains an inherent stability against ecological perturbations in the oral environment.

microbiology↗

bioRxiv2021

Investigating Biases Associated with Dietary Starch Incorporation and Retention with an Oral Biofilm Model

Dental calculus has proven to contain a wealth of information on the dietary habits of past populations. These insights have, to a large extent, been obtained by the extraction and identification of starch granules contained within the mineralised dental plaque from a wide range of regions and time periods. The scope of previous studies have been limited to microfossil extraction and identification to reconstruct dietary preferences from the archaeological record, and few studies have attempted to address the biases of starch retention in dental calculus. Those that have considered this problem have been limited to in vivo studies on modern humans and non-human primates. Here, we present a multispecies oral biofilm model, which allows experimental research on starch incorporation and retention to be conducted on in vitro dental calculus in a controlled laboratory setting. The biofilms were exposed to treatment solutions with known quantities of dietary starches (wheat and potato) during the 25-day growth period. After this, the starch granules were extracted from the mature biofilm (by dissolution in EDTA), and counted. We show that the granule counts extracted from the model dental calculus represented a low proportion (ranging from 0.06% to 0.16%) of the total number of granules exposed to the biofilms throughout the experiment. Additionally, we found that the ratios of granule sizes from the extracted starch granules differed from the original treatment solutions, with large granules (>20 m) consistently being under-represented. We also found a correlation between the absolute granule counts and dry-weight of the biofilm (r = 0.66, 90%CI[0.46,0.79]), as well as between the concentration (count per mg) of granules and dry-weight (r = 0.30, 90%CI[0.06,0.51]). Our results reinforce previous in vivo studies suggesting that dental calculus presents a very small, and partly biased picture of the original dietary intake of starches, with an over-representation of plants producing granules smaller than 20 m in size. The experimental model presented here is well-suited to address the need for further validation of methods and biases associated with dietary research on dental calculus.

microbiology↗

bioRxiv2021

Molecular architecture determines brain delivery of a transferrin-receptor targeted lysosomal enzyme

Delivery of biotherapeutics across the blood-brain barrier (BBB) is a challenge. Many approaches fuse biotherapeutics to platforms that bind the transferrin receptor (TfR), a brain endothelial cell target, to facilitate receptor-mediated transcytosis across the BBB. Here, we characterized the pharmacological behavior of two distinct TfR-targeted platforms fused to iduronate 2-sulfatase (IDS), a lysosomal enzyme deficient in mucopolysaccharidosis type II (MPS II), and compared the relative brain exposures and functional activities of both approaches in mouse models. IDS fused to a moderate-affinity, monovalent TfR binding enzyme transport vehicle (ETV:IDS) resulted in widespread brain exposure, internalization by parenchymal cells, and significant substrate reduction in the CNS of an MPS II mouse model. In contrast, IDS fused to a standard high-affinity bivalent antibody (IgG:IDS) resulted in lower brain uptake, limited biodistribution beyond brain endothelial cells, and reduced brain substrate reduction. These results highlight important features likely to impact the clinical development of TfR-targeting platforms in MPS II and potentially other CNS diseases. SummaryBrain delivery, biodistribution and pharmacodynamics of a lysosomal enzyme fused to a moderate-affinity transferrin receptor-directed blood-brain barrier enzyme transport vehicle are superior to a traditional high-affinity anti-TfR monoclonal antibody fusion.

neuroscience↗

bioRxiv2021

Understanding LRRK2 kinase activity in preclinical models and human subjects through quantitative analysis of LRRK2 and pRab10

Variants in the leucine-rich repeat kinase 2 (LRRK2) gene are associated with increased risk for familial and sporadic Parkinsons disease (PD). Pathogenic variants in LRRK2, including the common variant G2019S, result in increased LRRK2 kinase activity, supporting the therapeutic potential of LRRK2 kinase inhibitors for PD. To better understand the role of LRRK2 in disease and to support the clinical development of LRRK2 inhibitors, quantitative and high-throughput assays to measure LRRK2 levels and activity are needed. We developed and applied such assays to measure the levels of LRRK2 as well as the phosphorylation of LRRK2 itself or one of its substrates, Rab10 (pT73 Rab10). We observed increased LRRK2 activity in various cellular models of disease, including iPSC-derived microglia, as well as in human subjects carrying disease-linked variant in LRRK2 (G2019S). Capitalizing on the high-throughput and sensitive nature of these assays, we detected a significant reduction in LRRK2 activity in subjects carrying missense variants in LRRK2 associated with reduced disease risk. Finally, we optimized these assays to enable analysis of LRRK2 activity following inhibition in human peripheral blood mononuclear cells (PBMCs) and whole blood, demonstrating their potential utility as biomarkers to assess changes in LRRK2 expression and activity in the clinic.

neuroscience↗

bioRxiv2020

Multi-contrast Anatomical Subcortical Structures Parcellation

The human subcortex is comprised of more than 450 individual nuclei which lie deep in the brain. Due to their small size and close proximity, up until now only 7% have been depicted in standard MRI atlases. Thus, the human subcortex can largely be considered as terra incognita. Here we present a new open source parcellation algorithm to automatically map the subcortex. The new algorithm has been tested on 17 prominent subcortical structures based on a large quantitative MRI dataset at 7 Tesla. It has been carefully validated against expert human raters and previous methods, and can easily be extended to other subcortical structures and applied to any quantitative MRI dataset. In sum, we hope this novel parcellation algorithm will facilitate functional and structural neuroimaging research into small subcortical nuclei and help to chart terra incognita.

neuroscience↗

bioRxiv2020

Methodological priorities in assessing wild edible plant knowledge and use: a case study among the Baka in Cameroon.

Freelisting and dietary recalls are frequently used methods in ethnobotany to assess wild edible plant (WEP) knowledge and use. Though these ex-situ interviewing methods are practical to perform and may yield large datasets in a short time, they are known to be limited by the informants memory and cognitive bias. Alternatively, the much more laborious walk-in-the-woods method may be used, in which informants point out edible plants in-situ. Few studies, however, examine quantitatively how these different methods influence results. In this study, we assessed how these methods capture the diversity of wild edible plant knowledge and use among the Baka, a group of forager-horticulturalists from southeastern Cameroon. We show that within a single population, and when data on consumption frequency are collected simultaneously, the walk-in-the-woods method results in more detailed information of WEP knowledge and use than do freelisting or dietary recalls. Our in-situ method yielded 91 species of WEP, much more than the ex-situ methods of freelisting (34 spp.) and dietary recalls (12 spp.). Our results imply that previous studies based only on ex situ surveys may have underestimated the importance of WEP for local communities. We propose that future studies on WEP knowledge and use frequency should rely on mixed methods, taking an in-situ method as the starting point of their approach.

plant biology↗

bioRxiv2018

Comment on \"Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania\"

In a recent paper, Smits et al. (Science, 25 August 2017, p. 802) report on seasonal changes in the gut microbiome of Hadza hunter-gatherers. They argue that seasonal volatility of some bacterial taxa corresponds to seasonal dietary changes. We address the authors insufficient reporting of relevant data and problematic areas in their assumptions about Hadza diet that yield inconsistencies in their results and interpretations.

ecology↗