Biology subjects

McBride, J. L.

Publications and source records attributed to McBride, J. L..

6 recordsLinked to original sources

bioRxiv2026

Hybrid transcriptome assembly and annotation of Japanese macaque prefrontal cortex

Japanese macaque (Macaca fuscata) is used in biomedical and neurobiology research, yet transcriptomic resources for the brain are limited. We present a hybrid RNA sequencing dataset and a prefrontal cortex transcriptome assembly from two healthy 6-year-old animals. Short-read Illumina ({approx}70 million paired-end reads per sample) and long-read Oxford Nanopore direct RNA sequencing ({approx}2.5 million reads per sample) were combined. Reads were quality controlled, aligned to the macFus_1.0 reference genome, and assembled with StringTie2. Transcripts were annotated using Trinotate and eggNOG-mapper, and open reading frames were predicted with TransDecoder. The released data package includes raw reads (NCBI SRA BioProject PRJNA1295993), transcript sequences and structural annotation files, predicted coding sequences and proteins, functional annotation tables, and transcript abundance estimates (TPM). Technical validation includes read-level QC and protein-level comparisons to expressed gene sets from human, rhesus macaque and chimpanzee prefrontal cortex. These resources enable reuse for transcript-level expression studies, isoform characterization and comparative primate neurogenomics.

neuroscience↗

bioRxiv2025

Prodromal pathogenesis of CLN7 Batten Disease revealed by multimodal biomarkers in macaques

Neuronal ceroid lipofuscinosis type 7 (CLN7) is a devastating paediatric neurodegenerative disorder with no cure and limited natural history data to guide therapeutic development. Here, we present the first multimodal characterization of prodromal and early-stage CLN7 disease in Japanese macaques carrying a spontaneous CLN7-/- mutation. Using structural T2-weighted MRI for volumetry, [18F]FDG PET for glucose metabolism, and [11C]PBR28 PET for neuroinflammation, we observed region-dependent patterns in volumetric, molecular, and metabolic alterations. MRI confirmed the presence of disease-associated atrophy in many cortical and subcortical brain regions, consistent with human pathology, [18F]FDG PET revealed early cortical and subcortical widespread hypometabolism, and [11C]PBR28 PET imaging detected progressive neuroinflammation in the same brain areas. CSF analyses further showed age-dependent increases in neurofilament light (NfL), providing convergent evidence for neurodegeneration. Together, these results define a prodromal trajectory in CLN7 disease, establish sensitive imaging and fluid biomarkers, and validate the macaque model as a powerful platform for testing interventions.

neuroscience↗

bioRxiv2025

Longitudinal Investigation of Structural and Resting-State Effective Connectivity Alterations in a Non-Human Primate Model of Huntington's Disease

Huntingtons disease (HD) is a genetic neurodegenerative disorder caused by expanded CAG repeats in the huntingtin gene which produce a mutant huntingtin (mHTT) protein that contributes to progressive striatal, cortical, and white-matter atrophy, resulting in motor dysfunction and cognitive decline. Recently, a non-human primate (NHP) model of HD was developed via stereotaxic delivery of an adeno-associated viral vector expressing 85 CAG repeats (85Q) into the striatum. This model recapitulates several neuropathological changes and symptoms observed in people with HD (PwHD) including chorea and mild cognitive impairment. A previous longitudinal, multimodal MRI investigation in this model revealed volumetric and resting-state functional connectivity (rs-FC) changes compared to controls, in key regions involved in HD, over the course of 30 months. We aimed to study longitudinal changes in structural connectivity (SC), obtained from diffusion MRI scans from the same animals, comparing the 85Q animals to the control (Buffer) group. Additionally, going beyond the correlative rs-FC analyses, we investigated changes in causal, inter-regional functional interactions by estimating effective connectivity (EC) from rs functional MRI scans, constrained to strong structural connections. We found that the SC between basal ganglia regions and the cortex was reduced in the 85Q primates compared to the Buffer group at 14-months post virus injection, aligning with the pathological process observed in PwHD at later stages of the disease. EC from the caudate and putamen to the motor cortex was significantly reduced in the 85Q animals as early as 3-months post-injection providing novel insights into early alterations in causal functional interactions.

neuroscience↗

bioRxiv2025

Administration of barcoded AAV capsid library to the putamen of non-human primates identifies variants with efficient retrograde transport

Adeno-associated viral vectors have become a leading choice for gene therapy in the central nervous system due to their safety profile, efficient neuronal transduction, and capacity for sustained transgene expression. We previously reported that AAV2-derived capsids developed using the BRAVE (Barcoded Rational AAV Vector Evolution) approach have enhanced retrograde transport properties in the rodent brain, compared to parental AAV2. Retrograde transport enables broader coverage of connected brain regions after a single focal intraparenchymal brain injection and is therefore a powerful tool for delivery of vectors to distant sites with potentially higher specificity, transduction efficacy and safety. Because transport properties can vary among species, we further characterized a barcoded library of 25 BRAVE-derived AAV2 capsid variants, along with the parental AAV2 serotype and benchmark AAV capsids, in brains of adult cynomolgus monkeys after intraputaminal dosing. Based on RNA and DNA amplicon sequencing, single-nucleus RNA sequencing, and histological assessment, we report here capsid variants with enhanced retrograde transport and expression compared to the parental AAV2 capsid. These properties make them potentially useful for disease indications in which broader brain coverage is desirable beyond the injection site.

neuroscience↗

bioRxiv2022

A novel rhesus macaque model of Huntington's disease recapitulates key neuropathological changes along with progressive motor and cognitive decline

We created a new nonhuman primate model of the genetic neurodegenerative disorder, Huntingtons disease (HD), by injecting a mixture of recombinant adeno-associated viral vectors, serotypes AAV2 and AAV2.retro, each expressing a fragment of human mutant HTT (mHTT) into the caudate and putamen of adult rhesus macaques. This novel modeling strategy results in robust expression of mutant huntingtin protein (mHTT) in the injected brain regions, as well as dozens of other cortical and subcortical brain regions that are also affected in human HD patients. We queried the disruption of cortico-basal ganglia circuitry for 20-months post-surgery using a variety of behavioral and imaging readouts. Compared to controls, mHTT-treated macaques developed progressive working memory decline and motor impairment. Multimodal imaging revealed circuit-wide white and gray matter degenerative processes in several key brain regions affected in HD. This novel model will aid in the development of disease biomarkers and therapeutic strategies for this devastating disorder.

neuroscience↗

bioRxiv2020

Intra-striatal AAV2.retro administration leads to extensive retrograde transport in the rhesus macaque brain: implications for disease modeling and therapeutic development

Recently, AAV2.retro, a new capsid variant capable of efficient retrograde transport in brain, was generated in mice using a directed evolution approach. However, it remains unclear to what degree transport will be recapitulated in the substantially larger and more complex nonhuman primate (NHP) brain. Here, we compared the biodistribution of AAV2.retro with its parent serotype, AAV2, in adult macaques following delivery into the caudate and putamen, brain regions which comprise the striatum. While AAV2 transduction was primarily limited to the injected brain regions, AAV2.retro transduced cells in the striatum and in dozens of cortical and subcortical regions with known striatal afferents. We then evaluated the capability of AAV2.retro to deliver disease-related gene cargo to biologically-relevant NHP brain circuits by packaging a fragment of human mutant HTT, the causative gene mutation in Huntingtons disease. Following intra-striatal delivery, pathological mHTT-positive protein aggregates were distributed widely among cognitive, motor, and limbic cortico-basal ganglia circuits. Together, these studies demonstrate strong retrograde transport of AAV2.retro in NHP brain, highlight its utility in developing novel NHP models of brain disease and suggest its potential for querying circuit function and delivering therapeutic genes in the brain, particularly where treating dysfunctional circuits, versus single brain regions, is warranted.

neuroscience↗