Single-Cell RNA Sequencing of Peripheral Blood Mononuclear Cells From Pediatric Coeliac Disease Patients Suggests Potential Pre-Seroconversion Markers

Abstract

Celiac Disease (CeD) is a complex immune disorder involving villous atrophy in the small intestine that is triggered by gluten intake. Current CeD diagnosis is based on late-stage pathophysiological parameters such as detection of specific antibodies in blood and histochemical detection of villus atrophy and lymphocyte infiltration in intestinal biopsies. To date, no early onset biomarkers are available that would help prevent widespread villous atrophy and severe symptoms and co-morbidities. To search for novel CeD biomarkers, we used single-cell RNA sequencing (scRNAseq) to investigate PBMC samples from 11 children before and after seroconversion for CeD and 10 control individuals matched for age, sex and HLA-genotype. We generated scRNAseq profiles of 9559 cells and identified the expected major cellular lineages. Cell proportions remained stable across the different timepoints and health conditions, but we observed differences in gene expression profiles in specific cell types when comparing patient samples before and after disease development and comparing patients with controls. Based on the time when transcripts were differentially expressed, we could classify the deregulated genes as biomarkers for active CeD or as potential pre-diagnostic markers. Pathway analysis showed that active CeD biomarkers display a transcriptional profile associated with antigen activation in CD4+ T cells, whereas NK cells express a subset of biomarker genes even before CeD diagnosis. Intersection of biomarker genes with CeD-associated genetic risk loci pinpointed genetic factors that might play a role in CeD onset. Investigation of potential cellular interaction pathways of PBMC cell subpopulations highlighted the importance of TNF pathways in CeD. Altogether, our results pinpoint genes and pathways that are altered prior to and during CeD onset, thereby identifying novel potential biomarkers for CeD diagnosis in blood.

Single-cell transcriptome landscape of circulating CD4+ T cell populations in autoimmune diseases

“…To extend CD4 + T cell profiling to various autoimmune and infectious diseases, we performed a meta-analysis using publicly available single-cell data. 6 , 8 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 We integrated publicly available datasets with two strategies: (1) quantitative evaluation of cell frequencies by mapping to our reference and (2) evaluation of qualitative changes per cell type using NMFproj. We extracted CD4 + T cells from peripheral blood mononuclear cells (PBMCs) using Azimuth 62 and then mapped them to our reference using Symphony 14 ( Figure 3 A, the pipeline is available at https://github.com/yyoshiaki/screfmapping ).…”

“…We collected scRNA-seq data from PBMC generated by 10x platforms, Seq-Well or SPLiT-seq (Parse Biosciences WT Mega) 6 , 8 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 ( Table S6 ). If the count matrix was available, we used the quantified matrix.…”

Single-Cell Meta-Analysis of Neutrophil Activation in Kawasaki Disease and Multisystem Inflammatory Syndrome in Children Reveals Potential Shared Immunological Drivers

“…All studies were approved by the National Yang Ming Chiao Tung University institutional review board under NCTU-REC-109-036F. All the scRNA-seq PBMC data used in this study are publicly available: GSE168732, 15 GSE167029, 17 GSE183716, 25 GSE152450, 16 GSE166489, 19 GSE184330, 20 GSE205095, 26 GSE154386, 27 Ramirez-Sanchez et al, 28 GSE200743, 29 GSE217370, 30 GSE198616, 31 and GSE198891 32 (Tables S1–S3). In brief, we integrated and harmonized 9 cohorts with healthy control (HC), KD, MIS-C, dengue virus infection (DNV), juvenile idiopathic arthritis (JIA), and pediatric celiac disease (PCD) pediatric data.…”

Trends in biological and genetic markers of gluten-related disorders research

“…Despite the association between CD and the presence of HLA class II haplotypes (HLA-DQ2 and HLA-DQ8) is well established, CD results from the combination of effects of different gene products, including other HLA and non-HLA genes, which are also important in the development of the disease. To date, 40 genes have been genetically associated with CD, but it is not known how these pathways transform a predisposed individual into an affected person (Ramirez-Sanchez et al, 2022;Rodríguez-Martín, Vaquero, & Vivas, 2020). Besides, although HLA-DQ2 and HLA-DQ8 haplotypes are found in approximately 50% of patients with NCGS, HLA typing cannot be used for diagnosing NCGS as is the case in biopsy-confirmed celiac patients (Cabanillas, 2020).…”