DOI: 10.5061/dryad.gmsbcc30j
title: Supplementary data for: Ligand-specific tuning of CLEC10A signalling strength and dendritic cell responses through engagement of different GalNAc-containing glycan structures

description: C-type lectin receptors on dendritic cells shape immune responses to
 pathogens and tumour cells through the specific recognition of glycans.
 C-type lectin domain family 10 member A [CLEC10A; also known as macrophage
 galactose-type lectin (MGL)] binds terminal N-Acetylgalactosamine (GalNAc)
 residues, which are often highly exposed on tumours. Signalling through
 this receptor increases interleukin-10 (IL-10) and tumour necrosis factor
 alpha production by monocyte-derived dendritic cells (moDCs), which
 promotes a T helper 2 (Th2) or type 1 regulatory T cell (Tr1) response.
 Recently, several CLEC10A glycan ligands were identified that induce
 distinct conformational changes in the CLEC10A carbohydrate-recognition
 domain, but their ability to alter moDC function has not been thoroughly
 explored. Here, we used CLEC10A ligand glycodendrimers to investigate the
 transcriptional responses induced by the CLEC10A ligands previously
 modelled, and determined how these transcriptional programs were
 associated with the cellular moDC responses. The CLEC10A ligand dendrimers
 varied in their affinity for CLEC10A and their capacity to increase IL-10
 produced by moDCs. Although all glycodendrimers induced differential gene
 expression, this was strongest for the Forssman antigen dendrimer. The
 volcano plots and gene lists from this analysis are included in the
 supporting data provided here. The gene ontology (GO) terms
 associated with genes detected across ligands related to mitogen-activated
 protein kinase (MAPK) signalling, chemotaxis, apoptosis, angiogenesis,
 cytokine production and CD4+ T cell differentiation, as seen in the
 supporting table 2. The CLEC10A ligand dendrimers also altered
 the chemokine profile secreted by moDCs. Furthermore, these
 glycodendrimers increased the percentage of C-C chemokine receptor type 7
 (CCR7)-expressing moDCs, which was prevented by inhibiting CLEC10A
 signalling. Overall, there was limited evidence for glycan-specific
 signalling via CLEC10A, but the glycans did alter the magnitude of the
 CLEC10A-mediated responses.
description: # Supplementary data for: Ligand-specific tuning of CLEC10A signalling
 strength and dendritic cell responses through engagement of different
 GalNAc-containing glycan structures Dataset DOI:
 [10.5061/dryad.gmsbcc30j](10.5061/dryad.gmsbcc30j) ## Description of the
 data and file structure Supplementary data associated with the paper
 "**Ligand-specific tuning of CLEC10A signalling strength and
 dendritic cell responses through engagement of different GalNAc-containing
 glycan structures". ** ### Files and variables ``` File:
 Supporting_information_v3.pdf ``` **Description:** Combined PDF containing
 1 supporting figure and supporting tables 3 & 4. The descriptions of
 supporting tables 1&2 are included as well.  In supporting table 4,
 the aGM2 dendrimer was not included for the detection of chemokines
 (second part of the table) because this dendrimer had no biological effect
 in any of the previous analyses. These cells were therefore left empty in
 the table.  #### #### File:
 Table_S1_DESeq2_Differential_Expression_Tables.xlsx
 **Description:** Significant differentially expressed genes on mRNA level
 for moDCs stimulated with CLEC10A ligand glycodendrimers compared to a
 control dendrimer. Each CLEC10A dendrimer is compared to the control
 dendrimer in a separate tab labeled Control_"Dendrimer in
 analysis".  ##### Variables * ENSEMBL: ENSEMBL number of each gene in
 the analysis. * BaseMean: displays the mean normalized gene expression for
 the control dendrimer. * Log2FoldChange: displays the log-transformed
 change in expression of the control dendrimer minus the specific
 glycodendrimer. * lfcSE: the standard error of the Log2FoldChange. * stat:
 the test statistic. The Log2FoldChange and lfcSE are used to create this
 test statistic.  * pvalue: the p-value corresponding to the test
 statistic. * padj: column contained the pvalues adjusted for multiple
 comparisons. Genes with padj &lt; 0.05 were considered as significantly
 differentially expressed. The padj column has the value #N/B if no padj
 could be calculated.  * GeneName: the HGNC symbols of the genes in the
 analysis. These are the commonly used biological names of the genes. The
 GeneName column was given the value n/a if no HGNC symbol is associated
 with the ENSEMBL number.  
 
 #### File: Table_S2_GO_term_analysis.xlsx **Description:** Gene ontology
 terms that are associated with the significant differentially expressed
 genes for each glycodendrimer. The upregulated and downregulated genes for
 the Forssman antigen, GalNAc, blood group A antigen and GM2 dendrimer are
 in seperate tabs, named for the specific dendrimer and up/down. The
 CLEC10A core genes, overlapping genes between the GalNAc and Forssman
 antigen (Forss & GalNAc) and Forssman specific (Forss specific) DEGs
 were also included. The overview page displays the GO terms displayed in
 figure 3C of the paper and the associated -log10 p-values. The p-values
 were not significant (-Log(10) Pvalue &lt; 5) for the cells labelled n/s. 
 ##### Variables For the overview tab: * ID: GO number from the GO
 database.  * Term: name associated with the GO number * -Log(10) Pvalue
 Forssman: the -log10 p-value for the GO term for the Forssman dendrimer
 specifically. n/s means not significant.  * -Log(10) Pvalue GalNAc: the
 -log10 p-value for the GO term for the GalNAc dendrimer specifically. n/s
 means not significant.  * -Log(10) Pvalue BGA: the -log10 p-value for the
 GO term for the blood group A antigen dendrimer specifically. n/s means
 not significant.  * -Log(10) Pvalue GM2: the -log10 p-value for the GO
 term for the GM2 dendrimer specifically. n/s means not significant.  For
 the remaining tabs: * ID: GO number from the GO database.  * GOGroups: the
 umbrella group in which the GO term was placed during the analysis.  *
 Term: name associated with the GO number * Term PValue: p-value for each
 GO term. P&lt;0.05 was used as cut-off for significant GO terms. * Term
 PValue Corrected with Benjamini-Hochberg: the p-values with
 Benjamini-Hochberg correction. P&lt;0.05 was used as cut-off for
 significant GO terms. * -Log(10) PValue: the -log10- transformed values of
 the corrected p-values from column E, the p-values with Benjamini-Hochberg
 correction. * % Associated Genes: Each term has a list of genes associated
 with it prepared beforehand. The % Associated Genes displays the
 percentage of genes from this list that were found in the current analysis
 of differentially expressed genes.  * Nr. Genes: the number of genes from
 the associated gene list that were found in the current analysis of
 differentially expressed genes.  * Associated Genes Found: the HGNC
 symbols of the genes, associated with the GO term, that were found in the
 differentially expressed genes from the current analysis.