Journal: Clinical Epigenetics

Article Title: Abnormal DNA methylation analysis of leucine-rich glioma-inactivated 1 antibody encephalitis reveals novel methylation-driven genes related to prognostic and clinical features

doi: 10.1186/s13148-023-01550-5

Figure Lengend Snippet: A A cluster heatmap showing methylation changes in promoter of 13 microRNAs between LGI1 encephalitis cohort and normal donors. B Morphological characteristics of apoptotic body, microvesicles, and exosome isolated from serum of one LGI1 encephalitis patient by TEM. C Particle size of microvesicles and exosome using NTA. D Protein markers of apoptotic body (C3B, C1QC), microvesicles (ARF6), exosome (CD63, TSG101) and serum supernatant by western blot. E Volcano plot of differentially expressive exosome-microRNAs between LGI1 encephalitis and healthy control. F A scatter plot assessing the expression variation of exosome microRNAs between LGI1 encephalitis patients and healthy donors. G Venn diagram showing the overlap of 71 differential exosome microRNAs and 13 methylated-driven microRNAs. H The methylation changes in promoter of hsa-miR-2467-5p between LGI1 encephalitis cases and healthy donors. I PCR analysis of miR-2467-5p expression in PBMCs between LGI1 encephalitis patients and healthy donors. J PCR analysis of miR-2467-5p expression in apoptotic bodies isolated from LGI1 encephalitis patients and healthy donors. K PCR analysis of miR-2467-5p in microvesicles isolated from LGI1 encephalitis patients and healthy donors. L PCR analysis of miR-2467-5p in exosomes isolated from LGI1 encephalitis patients and healthy donors. M Schematic representation of the complementary binding sites of CSF3 and PDCD1 with miR-2467-5p. Relative luciferase activity of wild-type and 3`UTR mutant constructs of CSF3 N and PDCD1 O cotransfected with miR-2467-5p mimics and miRNA-NC. PCR analysis of PDCD1 P , CSF3 Q and CCL15 R expression in PBMCs after transfection of miR-2467-5p mimics, inhibitor or scramble control into PBMCs. ELISA analysis of PDCD1 S , CSF3 T, and CCL15 U expression in cell supernatants after transfection of miR-2467-5p mimics, inhibitor or scramble control into PBMCs. Scatterplots showing the association of miR-2467-5p in PBMCs with the expression of PDCD1 V , CSF3 W , and CCL15 X in serum in LGI1 encephalitis patients ( n = 6) and healthy donors ( n = 4). LGI1-E LGI1 encephalitis; ND normal donor; AE autoimmune encephalitis; MV microvesicles; ABs apoptotic bodies; Sup supernatant; NC negative control. Data are means ± SD of three experiments. * p < 0.05, ** p < 0.01, *** p < 0.001

Article Snippet: ELISA kits were used to measure CSF3, PDCD1, and CCL15 according to the manufacturer's instructions (Boster, Wuhan, China).

Techniques: Methylation, Isolation, Western Blot, Control, Expressing, Binding Assay, Luciferase, Activity Assay, Mutagenesis, Construct, Transfection, Enzyme-linked Immunosorbent Assay, Negative Control

Journal: Clinical Epigenetics

Article Title: Abnormal DNA methylation analysis of leucine-rich glioma-inactivated 1 antibody encephalitis reveals novel methylation-driven genes related to prognostic and clinical features

doi: 10.1186/s13148-023-01550-5

Figure Lengend Snippet: PDCD1 and CSF3 expression level in thymoma. A and B PDCD1 and CSF3 expression were compared between thymoma and normal tissues. C and D PDCD1 and CSF3 expression in thymoma were indicated in Masaoka stage I–IV. E and F PDCD1 and CSF3 expression in histological type A–C of thymoma. G and H PDCD1 and CSF3 expression in different tumor sites. All expression value (TPM value) were acquired using the TCGA dataset on the Xiantao platform. ns no significant. * p < 0.05, ** p < 0.01, *** p < 0.001

Article Snippet: ELISA kits were used to measure CSF3, PDCD1, and CCL15 according to the manufacturer's instructions (Boster, Wuhan, China).

Techniques: Expressing

Journal: Clinical Epigenetics

Article Title: Abnormal DNA methylation analysis of leucine-rich glioma-inactivated 1 antibody encephalitis reveals novel methylation-driven genes related to prognostic and clinical features

doi: 10.1186/s13148-023-01550-5

Figure Lengend Snippet: The association of PDCD1 and CSF3 expression with thymoma immune infiltration. A The expression of IFNγ, ICAM1, TNF and CCL2 were compared between thymoma and normal tissues using the TCGA dataset on the Xiantao platform. B Spearman correlation were shown between PDCD1 and CSF3 expression in thymoma. C and D The correlations of PDCD1 and CSF3 with all 24 immune cell types. iDC immature DC; Tem T effector memory; TFH T follicular helper; Tgd T gamma delta; pDC plasmacytoid DC; aDC activated DC; Tcm T central memory. * p < 0.05, ** p < 0.01, *** p < 0.001

Article Snippet: ELISA kits were used to measure CSF3, PDCD1, and CCL15 according to the manufacturer's instructions (Boster, Wuhan, China).

Techniques: Expressing