Project description:To determine whether the microRNA content of CSF vesicles changes throughout life we performed experiments including miRNA microarrays. Hierarchical clustering analysis indicated that the miRNA content of CSF vesicles changes when patients less than 2 years are compared to those older than 70 years of age. CSF vesicles were fractionated and isolated from patients of different ages, total RNA extracted, and subjected to miRNA microarray analysis
Project description:To determine whether the microRNA content of CSF vesicles changes throughout life we performed experiments including miRNA microarrays. Hierarchical clustering analysis indicated that the miRNA content of CSF vesicles changes when patients less than 2 years are compared to those older than 70 years of age.
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.
Project description:Patients suffering from Coronavirus disease 2019 (COVID-19) can develop neurological sequelae, such as headache, neuroinflammatory or cerebrovascular disease. These conditions - here termed Neuro-COVID - are more frequent in patients with severe COVID-19. To understand the etiology of these neurological sequelae, we utilized single-cell sequencing and examined the immune cell profiles from the cerebrospinal fluid (CSF) of Neuro-COVID patients compared to patients with non-inflammatory and autoimmune neurological diseases or with viral encephalitis. The CSF of Neuro-COVID patients exhibited an expansion of dedifferentiated monocytes and of exhausted CD4+ T cells. Neuro-COVID CSF leukocytes featured an enriched interferon signature; however, this was less pronounced than in viral encephalitis. Repertoire analysis revealed broad clonal T cell expansion and curtailed interferon response in severe compared to mild Neuro-COVID patients. Collectively, our findings document the CSF immune compartment in Neuro-COVID patients and suggest compromised antiviral responses in this setting.
Project description:Purpose: Leptomeningeal metastasis (LM) is a dismal terminal stage disease of solid cancer without definitive treatment. Both the limitation of cerebrospinal fluid (CSF) sample volume and a paucity of floating cancer cells are difficulties to study the genomic profiling of LM. As the profiling of microRNAs reflect the strategy and behavior of cancer cells to survive, and CSF is carrying micro-molecules from central nervous system (CNS), we evaluated the extracellular microRNA profiles of CSF from different CNS tumor status including LM. Materials and Methods: We prospectively collected CSF from 65 patients of five groups of cancer control (CC), healthy control (HC), LM, brain metastasis (BM); and brain tumor (BT). Extracellular RNA was extracted from 2 mL of CSF after proper cell down, and preceded to small RNA microarray with Affymetrix miRNA 4.0 microarray chips. Results: The mean RNA yield of LM patients was significantly higher compared to that of other patients groups (9.28 vs. 6.30 ㎍, p = 0.003). The small RNA (< 70 nucleotides) percentage was the highest in controls than that of other groups (53% vs. 26%, p < 0.001). Among 6,599 small RNA probes, mature microRNAs showed higher expression than that of pre-microRNAs and small nucleolar RNAs. The number of probes with the Present call in all samples is 22 mature microRNAs, 18 pre-mature microRNAs, and 27 small nucleolar RNAs. Expression value of mature microRNAs regarding their direction of 5 prime (5p) and 3 prime (3p), the expression of 3p microRNA is higher than those of 5p microRNA in both LM and BM samples (p < 0.001). Both supervised and unsupervised hierarchical clustering of 263 microRNAs, which showed more than 2 fold change at a significance level of p < 0.05, can differentiate LM from other CNS tumor patient groups. Prediction analysis of microarray (PAM) identified 13 microRNAs differentiate LM group from others including hsa-miR-335-5p and hsa-miR-466. MicroRNA profiling using significance of analysis of microarrays (SAM) analysis did not differentiate HC and CC. Whereas CSF samples from patients with LM showed the most number of 108 differentially expressed (more than 2 fold change) microRNAs compared to control group and also revealed 36 differentially expressed microRNAs between LM and BM including hsa-miR-466, hsa-miR-190a-3p, hsa-miR-98-3p, hsa-miR-34b-3p and so on. Representative discriminative microRNAs from microarray data were confirmed their expression level by digital droplet PCR in available CSF samples among the microarray samples. Gene Set Enrichment Analysis was performed using both 10 highly expressed and 6 suppressed microRNAs between LM and BM after normalization and 13 microRNAs from PAM analysis. The most targeted pathway was ‘positive-/ negative-transcription from RNA polymerase II promoter followed by ‘positive regulation of transcription, DNA-templated’ by discriminative microRNAs. When pathways were denoted by microRNAs from PAM, the most enriched pathway was inflammatory response and transcription relative to immune response. Conclusion: We performed extracellular small RNA microarray successfully with small volume of CSF. Analysis of profiles of microRNA according to patients with various CNS tumor status suggested the unique profiles might responsible for leptomeningeal metastasis.
Project description:The development of the human brain starts in the first weeks of embryo differentiation. However, there are many relevant neurodevelopmental processes that take place after birth and during lifespan. Such a fine and changing scenario requires the coordinated expression of thousands of genes to achieve the proper specialization and inter-connectivity. In this context, microRNAs (miRNAs), which can modulate mRNA stability and translation, are gaining recognition for their involvement in both brain development and neurodevelopmental disorders. Therefore, cerebrospinal fluid (CSF) miRNAs should be perfectly differentiated in relevant age periods. In this study, we aimed to highlight the biological variability of miRNA expression in the CSF throughout life, which is also crucial for biomarker discovery in CNS pathologies, especially in children, where they are desperately needed. We analyzed the CSF microRNAome of 14 healthy children (aged 0–7.4 years) by smallRNA-Seq and compared it with previously published data in adults (N = 7) and elders (N = 11). miR-423-5p and miR-22-3p were overexpressed in the < 1 and > 3 years groups, respectively. Additionally, we detected 18 miRNAs that reached their highest peak of expression at different time-points during the lifespan and sets of miRNAs that were exclusively expressed in a specific age group. On the contrary, miR-191-5p showed stable expression in CSF from the first year of life. Our results remark the complex differential miRNA expression profile that can be observed through life, which underlines the need for including appropriate age-matched controls when the expression of CSF miRNAs is analyzed in different pathological contexts.
Project description:Lipids comprise 70% of the myelin sheath, and autoantibodies against lipids may contribute to the demyelination that characterizes multiple sclerosis (MS). We used lipid antigen microarrays and lipid mass spectrometry to identify bona fide lipid targets of the autoimmune response in MS brain and an animal model of MS to explore the role of the identified lipids in autoimmune demyelination. We found that autoantibodies in MS target a phosphate group in phosphatidylserine and oxidized phosphatidylcholine derivatives. Administration of these lipids ameliorated experimental autoimmune encephalomyelitis by suppressing activation and inducing apoptosis of autoreactive T cells, effects mediated by the lipids' saturated fatty-acid side chains. Thus, phospholipids represent a natural anti-inflammatory class of compounds that have potential as novel therapeutics for MS. Fig. 2A. Mini-Array I: IgG antibody reactivity to various glycero-3-phosphocholine lipids in CSF samples from patients with relapsing remitting MS and from control patients with other neurological disease. Lipid hits with the lowest FDR (q=0.029) were clustered according to their reactivity profiles. 47 different lipids were custom-spotted in duplicate using the CAMAG Automatic TLC Sampler (ATS4) robot to spray 200 nl of 10 to 100 pmol of lipids onto PVDF membranes affixed to the surface of microscope slides. The slides were probed with cerebrospinal fluid (CSF) from 24 human patient samples. 25 slides total: 13 relapsing-remitting MS, 11 other neurological disease, and 1 secondary Ab alone (not included in this submission). CSF diluted 1/20. HRP-conjugated secondary Ab (goat anti-human IgM/IgG) diluted 1/175. ECL for 3 minutes.
Project description:This study aimed to identify specific CSF miRNAs for diagnosing and monitoring leptomeningeal metastasis with lung adenocarcinoma. In discovery phase, we performed miRNA microarray analysis in CSF samples from leptomeningeal metastasis patients and non-leptomeningeal metastasis controls.