Single Cell Transcriptomics of Myeloid Cells in Black Americans with Multiple Sclerosis
Jeremy Bingen1, Lindsay Clark2, Chris Wright2, Fangxiu Xu2, Michael Carrithers3
1University of Illinois at Chicago, 2University of Illinois Urbana-Champaign, 3University of Illinois College of Medicine
Objective:

Identify myeloid cell subsets from peripheral blood and monocyte-derived macrophages associated with MS in Black Americans.

Background:

Prior work in a cohort of patients composed primarily of underrepresented minority populations suggested an association between MS susceptibility and differential DNA methylation of genes that regulate cellular differentiation, proliferation, and invasion.

Design/Methods:

Peripheral blood mononuclear cells (PBMC) were obtained from Black American patients with MS and controls with non-inflammatory neurologic conditions under an IRB-approved protocol (UIC Neuroimmunology Biobank). Single cell libraries for RNAseq were constructed from PBMC (n=9) and monocyte-derived macrophages (MDM, n=6) using the Chromium Next GEM Single Cell 3' Kit v3.1 and Chromium Next GEM Chip G (10x Genomics). Libraries were sequenced on an Illumina NovaSeq 6000. Expression data was analyzed in R software using the Seurat package (Butler et al., 2018). The SingleR and celldex packages (Aran et al., 2019) were used for identification of human peripheral immune cell types.

 

Results:

Peripheral blood monocytes from MS patients demonstrated an increase in relative numbers of transitional macrophages. These cells included those from classical CD163+ and non-classical CD16+ monocyte populations. Transcriptomic analysis showed an increase in the expression of a lncRNA (long non-coding RNA), KCNQ1OT1, in these cells. Analysis of MDM revealed expansion of a subset of C1Q1+ macrophages in MS. These cells express high levels of a pattern recognition receptor, FCN1 (ficolin 1). Global transcriptomic analysis revealed increased expression of SNHG5, a small nucleolar RNA host gene, in MS in all macrophage subtypes.

Conclusions:

These results suggest an association between expansion of specific monocyte-macrophage populations in our patient cohort. Increased expression of KCNQ1OT1 in transitional macrophages and SNHG5 in MDM is also consistent with our prior study of epigenetic biomarkers because these non-coding RNA’s are associated with cellular differentiation and proliferation in neoplastic diseases.

 

10.1212/WNL.0000000000202689