Code for integrated multi-cohort analysis of the Parkinson’s disease gut metagenome
By onDetailed scripts to reproduce all analysis and data visualization for the paper "Integrated multi-cohort analysis of the Parkinson's disease gut metagenome."
Transcriptional analysis of peripheral memory T cells reveals Parkinson’s disease-specific gene signatures–Gene Validation FCS
By onFCS files corresponding to the gene validation experiment described in "Transcriptional analysis of peripheral memory T cells reveals Parkinson’s disease-specific gene signatures"
Transcriptional analysis of peripheral memory T cells reveals Parkinson’s disease-specific gene signatures–Cell Surface FCS
By onFCS files corresponding to the cell surface experiment described in "Transcriptional analysis of peripheral memory T cells reveals Parkinson’s disease-specific gene signatures"
Border-associated macrophages mediate the neuroinflammatory response in an alpha-synuclein model of Parkinson disease
By onBorder-associated macrophages (BAMs) are crucial in Parkinson's disease pathogenesis by initiating neuroinflammation, highlighting a potential target for therapeutic intervention.
Unaltered T cell responses to common antigens in individuals with Parkinson’s disease
By onT cells have been shown to be overactive in individuals with PD. The authors tested a wide variety of commonly encountered immune targets on PD and non-PD control derived T cells and observed no differences between their immune responses.
Mitochondrial Antigen Presentation in RAW macrophages
By onThis protocol details methods for 3-day Mitochondrial Antigen Presentation Assay in a murine macrophage cell line (RAW) that expresses a glycoprotein B (gB) of herpes simplex virus 1 (HSV1) targeted to the mitochondrial matrix (mito-gB). A gB-specific CD8+ T cell hybridoma recognizing the gB498–505peptide loaded on MHC class I molecules is also used to monitor antigen presentation through a beta-galactosidase assay kit.
Glucocerebrosidase 1 and leucine-rich repeat kinase 2 in Parkinson disease and interplay between the two genes
By onReview: This review focuses on the endolysosomal pathway roles of GBA and LRRK2, highlighting the role and activity of Rab GTPases as LRRK2 substrates.
(x6) GBA heterozygous and homozygous mutant fibroblast lines available to share
By onCell lines deposited at ATCC used in a publication (10.1093/hmg/ddac233) include UCL-CTRL001, UCL-CTRL002, UCL-CTRL003, UCL-YCTRL001, UCL-E001K, UCL-N001S, and UCL-N002S, each with specific RRIDs.
Fecal metagenomic sequencing data for PD patients and controls from the BioCollective
By onFecal metagenomic sequencing data associated with Boktor et al. (2023). This dataset includes samples from the BioCollective cohort.
Bile acids and neurological disease
By onThis review will focus on how bile acids are being used in clinical trials to treat neurological diseases due to their central involvement with the gut-liver-brain axis and their physiological and pathophysiological roles in both normal brain function and multiple neurological diseases. The synthesis of primary and secondary bile acids species and how the regulation of the bile acid pool may differ between the gut and brain is discussed. The expression of several bile acid receptors in brain and their currently known functions along with the tools available to manipulate them pharmacologically are examined, together with discussion of the interaction of bile acids with the gut microbiome and their lesser-known effects upon brain glucose and lipid metabolism. How dysregulation of the gut microbiome, aging and sex differences may lead to disruption of bile acid signalling and possible causal roles in a number of neurological disorders are also considered. Finally, we discuss how pharmacological treatments targeting bile acid receptors are currently being tested in an array of clinical trials for several different neurodegenerative diseases
Measurement of GLP-1 release in cell supernatant from Hutu-80 enteroendocrine cells via ELISA
By onMeasurement of GLP-1 release in cell supernatant from Hutu-80 enteroendocrine cells via ELISA
Protocols for “Characterizing the diversity of enteric neurons using Dopamine Transporter (DAT)-Cre reporter mice”.
By onThis is a collection of protocols associated to the manuscript "Characterizing the diversity of enteric neurons using Dopamine Transporter (DAT)-Cre reporter mice".
Western blot – alpha-synuclein
By onThis protocol describes how to detect alpha-synuclein in protein derived from STC-1 cells by western blot using DAB/peroxidase or ECL to visualize the bands.
Alpha-synuclein immunochemistry on STC-1 cells using DAB
By onThis protocol describes how to visualise alpha-synuclein in STC-1 cells by DAB immunohistochemistry. It also works for other antibodies (e.g. 5-HT, CCK, GLP).
Oncogenic BRAF V600E induces glial proliferation through ERK and neuronal death through JNK
By onActivating V600E in v-Raf murine sarcoma viral oncogene homolog B (BRAF) is a common driver mutation in cancers of multiple tissue origins, including melanoma and glioma. BRAFV600E has also been implicated in neurodegeneration. The present study aims to characterize BRAFV600E during cell death and proliferation of three major cell types of the central nervous system: neurons, astrocytes, and microglia. Multiple primary cultures (primary cortical mixed culture) and cell lines of glial cells (BV2) and neurons (SH-SY5Y) were employed. BRAFV600E and BRAFWT expression was mediated by lentivirus or retrovirus. Blockage of downstream effectors (extracellular signal-regulated kinase 1/2 and JNK1/2) were achieved by siRNA. In astrocytes and microglia, BRAFV600E induces cell proliferation, and the proliferative effect in microglia is mediated by activated extracellular signal-regulated kinase, but not c-Jun N-terminal kinase. Conditioned medium from BRAFV600E-expressing microglia induced neuronal death. In neuronal cells, BRAFV600E directly induces neuronal death, through c-Jun N-terminal kinase but not extracellular signal-regulated kinase. We further show that BRAF-related genes are enriched in pathways in patients with Parkinson's disease. Our study identifies distinct consequences mediated by distinct downstream effectors in dividing glial cells and in neurons following the same BRAF mutational activation and a causal link between BRAF-activated microglia and neuronal cell death that does not require physical proximity. It provides insight into a possibly important role of BRAF in neurodegeneration as a result of either dysregulated BRAF in neurons or its impact on glial cells.
Cell viability assessment
By onThis is the protocol for assessing cell viability using a MTS cell proliferation assay kit.
Midbrain-like Organoids generation from hiPSCs
By onProtocol for generating midbrain organoids from human iPSCs.
Single-cell transcriptomic and proteomic analysis of Parkinson’s disease Brains
By onThis article established a single-nucleus transcriptomic profile of the prefrontal cortex from postmortem human brains of six patients with PD and six age-matched controls.
Isolation of NeuN+ cells from brain tissue (for CUT and RUN)
By onThis protocol describes the steps to isolate NeuN+ cells from brain tissue in preparation for CUT and RUN.
Data set of the manuscript “Neuronal hyperactivity-induced oxidant stress promotes in vivo a-synuclein brain spreading”
By onData set of the manuscript "Neuronal hyperactivity-induced oxidant stress promotes in vivo a-synuclein brain spreading."