Additional file 1 of Localized microglia dysregulation impairs central nervous system myelination in development
Creators: name: Holloway, Rebecca K.
name: Zhang, Liang
name: Molina-Gonzalez, Irene
name: Ton, Kathy
name: Nicoll, James A. R.
name: Boardman, James P.
name: Liang, Yan
name: Williams, Anna
name: Miron, Veronique E.
Publisher: name: figshare
Year: 2024
Subjects: subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Pharmacology
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: Cancer
subject: Mental Health

description: Additional file 1: Table S1. Neuropathological and Clinical information of human infant brain samples used for digital spatial profiling and immunofluorescent assessment. Table S2. Clinical information of human infant cerebrospinal fluid samples used for SPP1 assessment. Fig. S1. Digital Spatial Transcriptomic profiling of human infant brain. A Overview images of ROI selection in injured infant cerebellum, stained for myelin (MBP; green), microglia/macrophages (CD68; red), and counterstained with Hoechst. B PCA plot of ROIs from female (orange) versus male (blue) human infant cerebellar white matter. C PCA plot of ROIs from human infant cerebellar white matter from cases with a neuropathological diagnosis of periventricular leukomalacia (PVL; purple) or hypoxic ischemic encephalopathy (HIE) or hypoxia (blue). Control infants are indicated in grey. D PCA plot of ROIs from human infant cerebellar white matter with age indicated. Individual infants indicated in different colours (injured are pink, control are green). E Volcano plot of control infants comparing those who died from Sudden Unexpected Death in Infancy (SUDI) versus other causes of death. Differentially expressed genes shown in grey, and interferon-related genes indicated in pink. Fig. S2. Oligodendrocyte lineage cell responses in human infant brain injury. A Mean proportion of IRF8+ cells that are OLIG2+ ± s.e.m. in cROI (n = 6 infants), iROI-M+ (n = 4 infants) and iROI-M− (n = 6 infants). B Mean proportion of IRF8+ cells that are CD68+ ± s.e.m. in cROI (n+6 infants), iROI-M+ (n = 4 infants) and iROI-M− (n = 6 infants).**P = 0.0039, Unpaired 2-tailed Student’s t-test. C Mean SOX10 normalized RNA counts ± s.e.m. for control and injured infants. Unpaired 2-tailed Student’s t-test, **P = 0.0080, n = 6 infants per group. D Mean OLIG2+ cells per mm2 ± s.e.m. in iROI-M+ and iROI-M−. n = 5 infants. Unpaired 2-tailed Student’s t-test, P &gt; 0.05. E Mean OLIG2+ CC1- cells per mm2 ± s.e.m. in cROI (n = 6 infants), iROI-M+ (n = 4 infants) and iROI-M− (n = 6 infants). *P = 0.0108, Mann-Whitney test. F Sphericity (based on CNPase) versus percent CNPase area per respective ROI, in iROI-M+ (grey) and iROI-M− (pink). G Sphericity (based on CNPase) versus number of CNPase+ cells per respective ROI, in iROI-M+ (grey) and iROI-M− (pink). H Sphericity (based on MBP) versus MBP area in myelinating cultures exposed to conditioned media (CM) from microglia treated with PBS vehicle (grey) or IFNγ and LPS (pink). I Average fraction of total spectral counts (SC) in conditioned media (CM) from microglia treated with IFNγ and LPS, where proteins enriched in this condition are indicated in pink (e.g. TNF, IL1B) whereas proteins enriched in vehicle (Veh) control are indicated in grey (E.g. SPP1). Fig. S3. Analysis of sex and Osteopontin regulation in human infant brain injury. A Volcano plot of control infants, comparing female versus male gene expression. Differentially significantly regulated genes shown in grey. SPP1 indicated in pink. B Volcano plot of iROI-M+, comparing female versus male gene expression. Differentially significantly regulated genes shown in grey. SPP1 indicated in pink. C Volcano plot of iROI-M−, comparing female versus male gene expression. Differentially significantly regulated genes shown in grey. SPP1 indicated in pink. D SPP1 protein levels in CSF of term versus preterm infants, with females indicated in pink and males indicated in grey. Mann-Whitney test, **P = 0.0031, n = 20 term infants and 17 pre-term infants.