Extended Data Fig. 8: Analyses of MIRAS patient brain autopsy samples.
From: Ancestral allele of DNA polymerase gamma modifies antiviral tolerance
(a) mtDNA replisome and mtDNA amount in patient cerebellum. Western blot and quantification (loading control ATP5A) and native POLG replisome complex amount (loading control HSP60 complex) from isolated mitochondria; qPCR for mtDNA amount (mtDNA, MTCO1 relative to nuclear gene, B2M). N = 2 patient cerebellar samples and 6 (or 5 for native complex analysis) controls, all females. Mean ± SEM; two-tailed unpaired student’s t test. (b) Immune-related gene expression in MIRAS patients’ cerebral cortex. qPCR of cDNA, reference gene ACTB. N = 3 patients and 6 controls, all females; box plot: minimum-25th-50th(median)-75th percentile-maximum (whiskers extend to the smallest and largest value); + symbol indicates the mean expression value; two-tailed unpaired student’s t test. (c-g) Pathway enrichment analyses of MIRAS patient cerebral cortex transcriptome. RNA-seq; N = 3 patients compared to 5 controls, all females. (c) Ingenuity pathway analysis using genes with p-value < 0.05 in MIRAS patient/control transcriptome. The most significantly affected (based on p-value; Fisher’s exact test) canonical pathways with their predicted activation or inactivation status are tabulated. Red: predicted activation (z-score≥2); blue: predicted inactivation (z-score ≤ −2); grey: pathway with no predicted significant activation/inhibition. (d) Inhibition of Interferon (IFN) signalling. Heatmap: fold change of IFN signalling gene expressions in MIRAS patients compared to the controls, and gene mapping onto the IFN-signalling pathway (generated by Ingenuity Pathway Analysis). (e) KEGG pathway enrichment analysis of downregulated genes (p-value < 0.05; Fold change > −1.5) in MIRAS patients compared to controls; generated using gProfiler server; Fisher’s one-tailed test with multiple testing correction using the server default algorithm g:SCS. (f, g) Integrated network summary of canonical pathways, upstream regulators, diseases and biological functions associated with patient/control cerebral cortex transcriptome (genes with p-value < 0.05). Generated using Ingenuity Pathway Analysis knowledgebase. The network in g shows also predicted relationships to transcripts with levels altered in the dataset.
