Single-cell profiling reveals periventricular CD56bright NK cell accumulation in multiple sclerosis
- MS Center Amsterdam, Department of Molecular Cell Biology and Immunology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Netherlands
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, Amsterdam Infection and Immunity Institute, Netherlands
Figures
Figure 1 with 5 supplements
Immune phenotyping of the septum using mass cytometry reveals inflammation in multiple sclerosis involving T cells and natural killer cells.
(a) Schematic overview of the study design. Immune cells were isolated from septum, choroid plexus and blood samples. Cells were then fixed, barcoded, stained and acquired on a CyTOF Helios system …
Figure 1—figure supplement 1
Demographic and clinical information.
Clinical parameters of the septum samples. Age and PMD (postmortem delay): pairwise comparisons using Wilcoxon rank-sum test with continuity correction; p-values adjusted with Benjamini-Hochberg …
Figure 1—figure supplement 2
Staining intensity between the different barcoded CyTOF runs displayed using a reference sample.
(a) UMAP plots based on the arcsinh-transformed expression of all markers in the reference sample that were stained together with barcoded runs of septum, choroid plexus and blood samples. A total …
Figure 1—figure supplement 3
Immune phenotyping of the septum using mass cytometry reveals inflammation in multiple sclerosis involving T cells and natural killer cells.
(a) Bar plot showing the number of cells used for clustering from each septum sample. A threshold was set at the 75th percentile to avoid over-representation of certain samples in the analysis. (b) …
Figure 1—figure supplement 4
Myeloid subclustering in the septum.
(a) UMAPs displaying pre-gated myeloid subpopulation in the septum. The cells are colored according to PARC-guided clustering. (b) Median marker intensities of pre-selected markers across myeloid …
Figure 1—figure supplement 5
Correlations between the percentage of immune cells from the septum and clinical parameters.
Dot plots show the significant correlations (p<0.05) between the percentage of the septum-derived immune cells and sample parameters. Non-normally distributed data: Spearman’s rank correlation rho; …
Figure 2 with 2 supplements
Phenotyping the T cell populations in the septum using mass cytometry.
(a) Median scaled intensities of the ‘type’ markers across T cell subpopulations in the septum. The horizontal gray bars show the percentage of each cluster out of the total investigated cells. The …
Figure 2—figure supplement 1
Phenotyping the T cell populations in the septum using mass cytometry.
(a) Delta area (‘elbow’) plot indicating the relative increase in cluster stability when clustering into k groups the 100 SOM clusters generated by FlowSOM. CDF: Consensus Cumulative Distribution …
Figure 2—figure supplement 2
Correlations between the percentage of T cells and different clinical parameters.
Dot plots show the significant correlations (p<0.05) found between the percentage of the T cell subsets of the septum and clinical sample parameters. Spearman’s rank correlation rho is shown for …
Figure 3 with 4 supplements
Activated CD56bright NK cells and antibody-secreting cells accumulate in the MS septum.
(a) Median scaled intensities of the ‘state’ markers in NK cells across all septum samples. Column annotation shows disease groups; row annotation shows adjusted p-values of comparing MS vs dementia …
Figure 3—figure supplement 1
Subclustering of NK and B cell populations in the septum.
(a) Delta area (‘elbow’) plot indicating the relative increase in cluster stability when clustering into k groups the 100 SOM clusters generated by FlowSOM in the NK and B cell populations. CDF: …
Figure 3—figure supplement 2
NK cell subclustering in the septum.
(a) UMAPs displaying pre-gated CD56bright NK subpopulation in the septum. The cells are colored according to PARC-guided clustering. (b) Median marker intensities of pre-selected markers across …
Figure 3—figure supplement 3
Marker expression in T-bet- B cells from the septum.
Boxplots display the median marker expression of CD25 and CD49d in T-bet- B cells from the septum. *adjusted p<0.1. Con: controls; Dem: dementia; MS: multiple sclerosis. Source data is listed in Sour…
Figure 3—figure supplement 4
Correlation plots between the percentage of NK and B cell subsets and clinical parameters.
Dot plots show the significant correlations (p<0.05) found between the percentage of the septum NK and B cell subsets and clinical sample parameters. ** p<0.01. Spearman’s rank correlation rho is …
Figure 4 with 2 supplements
Immune phenotyping of the choroid plexus using mass cytometry.
(a) UMAP plot based on the arcsinh-transformed expression of the ‘type’ (lineage) markers in the choroid plexus-derived immune cells. A subset of 1000 randomly selected cells per sample is shown, …
Figure 4—figure supplement 1
Demographic and clinical information.
Clinical parameters of the choroid plexus samples. Age and PMD (postmortem delay): pairwise comparisons using Wilcoxon rank-sum test with continuity correction; p-values adjusted with …
Figure 4—figure supplement 2
Immune phenotyping of the choroid plexus using mass cytometry.
(a) Bar plot of the number of cells used for clustering from each choroid plexus sample. A threshold was set at the 75th percentile to avoid over-representation of certain samples. (b) Delta area …
Figure 5 with 1 supplement
The choroid plexus in MS presents alterations in the NK cell populations.
(a) Median scaled intensities of the ‘type’ markers across T cell subsets in the choroid plexus. The table shows tentative biological names of the T cell subpopulations. (b) Median scaled …
Figure 5—figure supplement 1
Immune phenotyping of the T cell, NK and B cell subsets in choroid plexus.
(a) Median scaled intensities of the ‘type’ markers across T cell clusters of the choroid plexus obtained with FlowSOM and ConsensusClusterPlus. (b) Percentage of each annotated cell population out …
Figure 6 with 2 supplements
Immune phenotyping reveals an accumulation of B cells in postmortem MS blood.
(a) UMAP plot based on the arcsinh-transformed expression of all markers in the immune cells of the septum, choroid plexus, and blood. A total of 100,000 randomly selected cells were selected per …
Figure 6—figure supplement 1
Demographic and clinical information.
Clinical parameters of the blood samples. Age and PMD (post-mortem delay): pairwise comparisons using Wilcoxon rank-sum test with continuity correction; p-values adjusted with Benjamini-Hochberg …
Figure 6—figure supplement 2
Immune phenotyping of the main immune cell populations in blood and their correlations with those in septum and choroid plexus.
(a) Bar plot of the number of cells used for clustering from each blood sample. A threshold was set at the 75th percentile to avoid over-representation of certain samples. (b) Delta area (‘elbow’) …
Figure 7 with 2 supplements
Circulating Tbet+ B cells in MS express higher levels of T-bet.
(a) Median scaled intensities of the ‘type’ markers across T cell subpopulations in blood. Table shows tentative biological names of the T cell subpopulations. (b) Median scaled intensities of the …
Figure 7—figure supplement 1
Immune phenotyping of the T cell, NK and B cell subsets in blood and their correlations with those in septum and choroid plexus.
(a) Median scaled intensities of the ‘type’ markers across T cell clusters in the blood obtained with FlowSOM and ConsensusClusterPlus. (b) Percentage of each annotated cell population out of the …
Figure 7—figure supplement 2
Median intensity of NK and B cell subsets in blood and correlations of their proportions with those in septum and choroid plexus.
(a) Median scaled intensities of the ‘type’ markers across NK and B cell lineage populations in the blood obtained with FlowSOM and ConsensusClusterPlus. (b) Spearman correlation matrix of the …
Figure 8
Granzyme K+ NK cells accumulate in periventricular lesions and choroid plexus.
(a) Representative immunohistochemical staining of myelin with proteolipid protein (PLP) and presence of immune cells with HLA-DR. The overview shows the location of the normal-appearing white …
Author response image 1
Absolute live immune cell numbers per mg of septum.
Author response image 2
CD56bright NK cells and myeloid cells subpopulations in septum.
(a) UMAPs displaying pre-gated CD56bright NK subpopulation in the septum. The cells are coloured according to PARC-guided clustering. (b) Median marker intensities of pre-selected markers across …
Author response image 3
Spearman correlation matrix of the proportion of the main immune cell populations among the studied tissues in the control and MS samples, separately.
Positive correlations are displayed in red and negative correlations in blue. The size of the circle is proportional to the correlation coefficients. P-values adjusted with Benjamini-Hochberg …
Tables
Author response table 1
Yield of isolated live immune cells per mg of septal tissue.
| Donor | Yield (cells/mg) | Condition |
|---|---|---|
| 2018-120 | 4782.3 | Control |
| 2018-123 | 1666.2 | Control |
| 2019-054 | 3231.4 | Control |
| 2019-079 | 3596.2 | Control |
| 2020-003 | 4861.1 | Control |
| 2020-028 | 1110.4 | Control |
| 2019-030 | 3286.3 | Dementia |
| 2020-013 | 3607.5 | Dementia |
| 2019-016 | 3052.9 | MS |
| 2019-027 | 2183.0 | MS |
| 2019-031 | 6232.0 | MS |
| 2019-069 | 3175.9 | MS |
| 2019-107 | 2288.9 | MS |
| 2019-109 | 1345.3 | MS |
| 2019-110 | 2846.6 | MS |
Additional files
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Transparent reporting form
- https://cdn.elifesciences.org/articles/73849/elife-73849-transrepform1-v2.docx
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Supplementary file 1
Information of the donors used in this study.
- https://cdn.elifesciences.org/articles/73849/elife-73849-supp1-v2.xlsx
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Supplementary file 2
Antibody panel used for CyTOF.
- https://cdn.elifesciences.org/articles/73849/elife-73849-supp2-v2.xlsx
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Supplementary file 3
Details of antibodies used for multiplex immunohistochemistry.
- https://cdn.elifesciences.org/articles/73849/elife-73849-supp3-v2.xlsx
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Source data 1
Percentage of each annotated cell population out of the total CD45+ cells from the choroid plexus of controls (Con), dementia (AD) and multiple sclerosis (MS) donors.
Median scaled intensities of the “state” (phenotype) markers for each cell population.
- https://cdn.elifesciences.org/articles/73849/elife-73849-data1-v2.xlsx
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Source data 2
Percentage of each annotated cell population out of the total CD45+ cells from the choroid plexus of controls (Con), dementia (AD) and multiple sclerosis (MS) donors.
Median scaled intensities of the “state” (phenotype) markers for each cell population.
- https://cdn.elifesciences.org/articles/73849/elife-73849-data2-v2.xlsx
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Source data 3
Percentage of each annotated cell population out of the total CD45+ cells from the blood of controls (Con), dementia (AD) and multiple sclerosis (MS) donors.
Median scaled intensities of the “state” (phenotype) markers for each cell population.
- https://cdn.elifesciences.org/articles/73849/elife-73849-data3-v2.xlsx
