Biology subjects

Murchison, C. F.

Publications and source records attributed to Murchison, C. F..

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↗

bioRxiv2024

Carboxy-terminal blockade of sortilin binding enhances progranulin gene therapy, a potential treatment for frontotemporal dementia

Frontotemporal dementia is commonly caused by loss-of-function mutations in the progranulin gene. Potential therapies for this disorder have entered clinical trials, including progranulin gene therapy and drugs that reduce progranulin interactions with sortilin. Both approaches ameliorate functional and pathological abnormalities in mouse models of progranulin insufficiency. Here we investigated whether modifying the progranulin carboxy terminus to block sortilin interactions would improve the efficacy of progranulin gene therapy. We compared the effects of treating progranulin-deficient mice with gene therapy vectors expressing progranulin with intact sortilin interactions, progranulin with the carboxy terminus blocked to reduce sortilin interactions, or GFP control. We found that expressing carboxy-terminally blocked progranulin generated higher levels of progranulin both at the injection site and in more distant regions. Carboxy-terminally blocked progranulin was also more effective at ameliorating microgliosis, microglial lipofuscinosis, and lipid abnormalities including ganglioside accumulation and loss of bis(monoacylglycero)phosphate lipids. Finally, only carboxy-terminally blocked progranulin reduced plasma neurofilament light chain, a biomarker of neurodegeneration, in progranulin-deficient mice. These results demonstrate that modifying the progranulin cargo to block sortilin interactions may be important for increasing the effectiveness of progranulin gene therapy. One-sentence SummaryThe effectiveness of progranulin gene therapy in models of FTD is improved by blocking the proteins carboxy terminus, which prevents sortilin binding

neuroscience↗

bioRxiv2021

Sleep Dependent Changes of Lactate Concentration in Human Brain

Lactate is an important cellular metabolite that is present at high concentrations in the brain, both within cells and in the extracellular space between cells. Small animal studies demonstrated high extracellular concentrations of lactate during wakefulness with reductions during sleep and/or anesthesia with a recent study suggesting the glymphatic activity as the mechanism for the reduction of lactate concentrations. We have recently developed a rigorous non-invasive imaging approach combining simultaneous magnetic resonance spectroscopy (MRS) and polysomnography (PSG) measurements, and here, we present the first in-vivo evaluation of brain lactate levels during sleep-wake cycles in young healthy humans. First, we collected single voxel proton MRS (1H-MRS) data at the posterior cingulate with high temporal resolution (every 7.5 sec), and simultaneously recorded PSG data while temporally registering with 1H-MRS time-series. Second, we evaluated PSG data in 30 s epochs, and classified into four stages Wake (W), Non-REM sleep stage 1 (N1), Non-REM sleep stage 2 (N2), and Non-REM sleep stage 3 (N3). Third, we determined lactate signal intensity from each 7.5-s spectrum, normalized to corresponding water signal, and averaged over 30-s for each PSG epoch. In examinations of nine healthy participants (four females, five males; mean age 24.2 ({+/-}2; SD) years; age range: 21-27 years) undergoing up to 3-hour simultaneous MRS/PSG recordings, we observed a group mean reduction of [4.9 {+/-} 4.9] % in N1, [10.4 {+/-} 5.2] % in N2, and [24.0 {+/-} 5.8] % in N3 when compared to W. Our finding is consistent with more than 70 years of invasive lactate measurements from small animal studies. In addition, reduced brain lactate was accompanied by a significant reduction the apparent diffusion coefficient of brain lactate. Taken together, these findings are consistent with the loss of lactate from the extracellular space during sleep while suggesting lactate metabolism is altered and/or lactate clearance via glymphatic exchange is increased during sleep. Significance StatementThis study describes a non-invasive magnetic resonance spectroscopy/polysomnography technique that allows rigorous measurement of brain metabolite levels together with simultaneous characterization of brain arousal state as either wakeful or one of the several sleep states. The results provide the first in-vivo demonstration of reductions in brain lactate concentration and diffusivity during sleep versus wakefulness in young healthy human brain. These findings are consistent with invasive small-animal studies showing the loss of extracellular lactate during sleep, and support the notion of altered lactate metabolism and/or increased glymphatic activity in sleeping human brain.

neuroscience↗

bioRxiv2019

Biomarker Localization, Analysis, Visualization, Extraction, and Registration (BLAzER) Workflow for Research and Clinical Brain PET Applications

ObjectiveThere is a need for tools enabling efficient evaluation of amyloid- and tau-PET images suited for both clinical and research settings. The purpose of this study was to assess and validate a semi-automated imaging workflow, called Biomarker Localization, Analysis, Visualization, Extraction, and Registration (BLAzER). We tested BLAzER using two different segmentation platforms, FreeSurfer (FS) and Neuroreader (NR), for regional brain PET quantification in images from participants in the Alzheimers Disease Neuroimaging Initiative (ADNI) dataset.\n\nMethods127 amyloid-PET and 55 tau-PET studies along with corresponding volumetric MRI were obtained from ADNI. The BLAzER workflow utilizes segmentation of MR images by FS or NR, then visualizes and quantifies regional brain PET data using FDA-cleared software (MIM), enabling quality control to ensure optimal registration and detect segmentation errors.\n\nResultsBLAzER analysis required only [~]5 min plus segmentation time. BLAzER using FS segmentation showed strong agreement with ADNI for global amyloid-PET standardized uptake value ratios (SUVRs) (r = 0.9922, p < 0.001) and regional tau-PET SUVRs across all Braak staging regions (r > 0.97, p < 0.001) with high inter-operator reproducibility for both (ICC > 0.97) and nearly identical dichotomization as amyloid-positive or -negative (2 discrepant cases out of 127). Comparing FS vs. NR segmentation with BLAzER, the global SUVRs were strongly correlated for global amyloid-PET (r = 0.9841, p < 0.001), but were systematically higher (4% on average) with NR, likely due to more inclusion of white matter, which has high florbetapir binding.\n\nConclusionsBLAzER provides an efficient workflow for regional brain PET quantification. FDA-cleared components and the ability to visualize registration reduce barriers between research and clinical applications.

neuroscience↗