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Single cell RNA (scRNAseq) and T cell receptor sequencing (scTCRseq) of cerebrospinal fluid (CSF) samples from three patients with spinal cord injury (SCI) [scRNA-seq]

ABSTRACT: Single cell RNA (scRNAseq) and T cell receptor sequencing (scTCRseq) of cerebrospinal fluid (CSF) samples from three patients with spinal cord injury (SCI) [scRNA-seq]

PROVIDER: PRJNA1070003 | ENA |

REPOSITORIES: ENA

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Single cell RNA (scRNAseq) and T cell receptor sequencing (scTCRseq) of cerebrospinal fluid (CSF) samples from three patients with spinal cord injury (SCI) [scRNA-seq]

Project description:The CSF encompasses a highly controlled immune system. However, little is known about the alterations in CSF immune microenvironment after SCI. Here, we performed scRNA and TCRseq on CSF collected from three SCI patients caused by car accidents to analyze the transcriptomic changes of CSF immune cells.

2025-04-03 | GSE254355 | GEO

Single cell RNA (scRNAseq) and T cell receptor sequencing (scTCRseq) of cerebrospinal fluid (CSF) samples from three patients with spinal cord injury (SCI) [TCR-seq]

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Project description:Cerebrospinal fluid (CSF) contains a tightly regulated, specialized immune system. Yet, little is known about how aging influences CSF immunity in cognitively typical versus cognitively impaired individuals. Here, we performed single cell RNA sequencing (scRNAseq) on CSF collected from 45 cognitively typical subjects ranging from 54-82 years old. We then assessed age-related transcriptomic changes using several bioinformatic approaches, including linear and local polynomial regression. We reveal pronounced changes to several CSF immune cell types that occur around age 75, including alterations to clonally expanded T cells and activated monocytes. We then compared CSF immune systems from cognitively typical subjects to 14 subjects with mild cognitive impairment or Alzheimer’s disease. Our results indicate disparate age-related CSF immune system perturbations in cognitively impaired subjects. These results highlight the potential to utilize CSF immune changes to identify age-related neuroinflammation in cognitively impaired individuals.

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Single cell RNA (scRNAseq) and T cell receptor sequencing (scTCRseq) of cerebrospinal fluid (CSF) samples from three patients with spinal cord injury (SCI) [TCR-seq]

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Clonally expanded CD8 T cells patrol Alzheimer's cerebrospinal fluid [CSF]

Project description:Alzheimer’s disease (AD) is an age-related neurodegenerative disorder in which neuroinflammation plays a critical function. Recurring viral infections and loss of immune competence increase risk for developing AD, yet the cellular and molecular mechanisms driving these immune changes are unknown. Here we performed mass cytometry of peripheral blood mononuclear cells and detected an immunologic signature of AD characterized by increased numbers of CD8+ T effector memory CD45RA+ (TEMRA) cells. CD8+ TEMRA cells were negatively associated with cognition and single cell RNA sequencing revealed their cytotoxic effector function. Strikingly, we discovered identical, shared T cell receptors (TCRs) of clonally expanded CD8+ TEMRA cells in cerebrospinal fluid (CSF) of three AD patients. Deep TCR sequencing, machine learning, and peptide screens identified the HLA-B*08:01-restricted Epstein-Barr virus trans-activator protein BZLF1 as the cognate antigen of a novel AD CSF TCR . These results provide the first evidence of clonal, antigen-specific T cells patrolling the intrathecal space of brains affected by age-related neurodegeneration

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Clonally expanded CD8 T cells patrol Alzheimer's cerebrospinal fluid [CSF]

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Project description:Medulloblastoma (MB) is an embryonal tumor of the cerebellum and a highly malignant childhood brain tumor. Cell-free circulating tumor DNA (ctDNA) from the cerebrospinal fluid (CSF) of patients with brain tumors faithfully represent genomic alterations of brain tumors. Distinct epigenetic signatures among subgroups of MB allow us to detect epigenetic alterations in CSF to aid classify and guide therapy of MB tumors. Here, we evaluate DNA methylation of ctDNA derived from small amount of CSF (200 µL) and matched tumor DNA from four subtypes of MB patients. We find highly concordance of DNA methylation between CSF ctDNA and tumor DNA in a subtype manner. Our results show that CSF ctNDA methylation can be a minimal invasive precisely method to assess epigenetic alterations of MB in a subtype manner, which is complementary to current diagnoses of MB tumors.

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