Biology subjects

Dean, M. N.

Publications and source records attributed to Dean, M. N..

4 recordsLinked to original sources

bioRxiv2026

Elucidating the dysbiotic features of gut microbiome, interaction with the human genome, and utility as a biomarker for treatment of Parkinson disease.

Parkinsons disease (PD) is the fastest-growing neurologic disease and a leading cause of disability worldwide. PD affects the body and mind, is progressive, and there is no prevention or cure. Gut microbiome, a recently recognized contributing factor in PD, offers new leads for understanding the underlying pathobiology and devising new treatments. Here, we present the most comprehensive study of the PD gut microbiome to date, comprising three large datasets with a sample size of 1,006 PD and 544 neurologically healthy controls, generated with uniform methodology from subject recruitment to data analysis, and characterized using deep shotgun metagenome sequencing, genome-wide genotypes, and metadata. We begin by describing the gut dysbiosis at the species, gene, pathway, and functional level. Next, we find that PD-associated genetic variants at the SNCA gene region are associated with increased abundance of opportunistic pathogens and depletion of fiber degraders in the PD gut. We show that the presence of opportunistic pathogens at high levels in the gut increases the penetrance of SNCA variants for PD risk, raising the GWAS-derived odds ratio from less than 1.5 to over 8. The genetic variants identified here control splicing of the SNCA transcripts into alpha-synuclein isoforms with varying affinity for pathological aggregation. These data suggest pathogens are triggers for disease in the setting of genetic susceptibility, and the link to the genome implicates the microbes in the causation of PD. Finally, shifting focus to translation, we show that not all PD patients have the same dysbiotic features, and propose a conceptual framework to identify microbiome-based biomarkers to select appropriate patients for targeted microbiome-based clinical trials and personalized treatment.

molecular biology↗

bioRxiv2026

Cartilage canals in sharks and rays show that blood vessels can exist in mature cartilage without triggering endochondral bone formation

Although cartilage in tetrapod skeletons is typically said to lack blood vessels, this is only true for adult cartilage. In young bird and mammal cartilage, a dense network of vasculature-containing tunnels --cartilage canals-- perforate the growing skeleton, helping nourish the cartilage and develop the ossification centers that will later form the skeletons epiphyseal bone. As the canals and their rich vascular network typically recede as animals age, the healthy cartilage of adult animals is typically known to be avascular. Here, however, we use a range of tissue characterization and visualization techniques --including light/electron microscopy and microCT-- to show that the skeletons of rays and sharks (elasmobranch fishes) not only possess cartilage canals, but that these structures persist in the adult skeleton. The morphology and tissue composition of elasmobranch cartilage canals argues homology with mammalian cartilage canals and an ancient invasion of the vascular system into cartilage. However, the anatomical location of canals --extending away from mineralized tissue not toward it-- and the lack of endochondral ossification in ray and shark cartilage suggest that cartilage canals developed early in vertebrates as a transport system for nutrients and mesenchymal cells into the growing skeleton. We describe distinctive features and variation in elasmobranch cartilage canals, discuss their possible roles and their potential for tissue mineralization, and the biomedical implications for their presence in a clade of animals with continuously growing cartilaginous skeletons.

evolutionary biology↗

bioRxiv2022

Metagenomics of Parkinson's disease implicates the gut microbiome in multiple disease mechanisms

Parkinsons disease (PD) may start in the gut and spread to the brain. To investigate the role of gut microbiome, we enrolled 490 PD and 234 control individuals, conducted deep shotgun sequencing of fecal DNA, followed by metagenome-wide association studies requiring significance by two methods (ANCOM-BC and MaAsLin2) to declare disease association. Thirty-percent of species and pathways tested had altered abundances in PD, depicting a widespread dysbiosis. Network analysis showed PD-associated species form polymicrobial clusters that grow or shrink together, and some compete. Metagenomic profile of PD indicates a disease permissive microbiome, evidenced by overabundance of pathogens and immunogenic components, dysregulated neuroactive signaling, preponderance of molecules that induce alpha-synuclein pathology, and over-production of toxicants; with the reduction in anti-inflammatory and neuroprotective factors limiting the capacity to recover. These data provide a broad foundation with a wealth of concrete testable hypotheses to discern the role of the gut microbiome in PD.

genomics↗

bioRxiv2020

Characterizing dysbiosis of gut microbiome in PD: Evidence for overabundance of opportunistic pathogens

In Parkinsons disease (PD), gastrointestinal features are common and often precede the motor signs. Braak and colleagues proposed that PD may start in the gut, triggered by a pathogen, and spread to the brain. Numerous studies have examined the gut microbiome in PD, all found it to be altered, but found inconsistent results on associated microorganisms. Studies to date have been small (N=20 to 306) and are difficult to compare or combine due to varied methodology. We conducted a microbiome-wide association study (MWAS) with two large datasets for internal replication (N=333 and 507). We used uniform methodology when possible, interrogated confounders, and applied two statistical tests for concordance, followed by correlation network analysis to infer interactions. Fifteen genera were associated with PD at a microbiome-wide significance level, in both datasets, with both methods, with or without covariate adjustment. The associations were not independent, rather represented 3 clusters of co-occurring microorganisms. Cluster 1 was composed of opportunistic pathogens; all were elevated in PD. Cluster 2 were short-chain-fatty-acid producing bacteria; all were reduced in PD. Cluster 3 were carbohydrate-metabolizing probiotics; elevated in PD. Depletion of anti-inflammatory short-chain-fatty-acid producing bacteria and elevated levels of probiotics are confirmatory. Overabundance of opportunistic pathogens is a novel finding and their identity provides a lead to experimentally test their role in PD.

genomics↗