Data from: Ligand-receptor interactions induce and mediate regulatory functions of BATF3+ B cells
Data files
Sep 10, 2025 version files 88.27 MB
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Data_Table_S1.xlsx
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Data_Table_S10.xlsx
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README.md
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Supplemental_Table_2.xlsx
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Abstract
B cells express protein ligands, whose potential regulatory functions remain incompletely understood. Here, we profiled the ligand expression in murine B sub-lineage cells, including those activated by defined receptor signals, and assessed their regulatory capacities and specificities by analyzing ligand-receptor interactions in silico. We identified a B subset for their specific expression of cytokine IL-27 and chemokine CXCL10. Through the IL-27-IL-27 receptor interaction, IL-27/CXCL10-producing B cells targeted CD40-activated B cells in vitro and, upon induction by immunization and viral infection, optimized antibody responses and anti-viral immunity in vivo. Also present in breast cancer tumors and retained there through CXCL10-CXCR3 interaction-mediated self-targeting, they promoted B-cell PD-L1 expression and immune evasion. Mechanistically, Il27 and Cxcl10 transcription was induced by synergizing TLR and CD40 signals and mediated by co-induced transcription factor (TF) BATF3, which directly targeted these genes. By utilizing a framework focusing on discovering regulatory cells and their hallmark TFs, our findings have broadened the scope of B cell regulatory functions.
Dataset DOI: 10.5061/dryad.r4xgxd2rr
Description of the data
This study has generated multiple datasets, including bulk RNA-Seq of in vitro stimulated B cells, bulk RNA-Seq B cells sorted from virus infected mice in vivo, CUT&Tag and ChIP-Seq of BATF3 and NF-kappaB (RELA subunit) binding of genomic DNA, CUT&Tag to analyze histone modifications, and Tandem mass spectrometry of protein expression in in vitro stimulated B cells. The study has also performed an integrated analysis by normalizing bulk RNA-Seq of B cells (in vitro and in vivo) and that from the ImmGen dataset, yielding total 225 samples representing 46 immune cell lineages/sub-lineages. Using the normalized data, the study has calculated the gene expression specific score in each cell type and quantified the ligand-receptor interactions in each cell-cell communications.
Files and variables
File: Data_Table_S1.xlsx
Description: RNA-Seq of B cells stimulated in vitro.
Page 1. All genes in the genome
Page 2. Genes encoding communication factors
Page 3. Genes encoding ligands or receptors
Page 4. Genes encoding ligands
Page 5. IgH VDJ and IgL VJ genes
Page 6. Genes encoding transcription factors
Sample names are described as Treatment_Batch_SampleNumber. Nil: non-treated; LPS: LPS treated; CD154: CD154 treated; LC: LPS and CD154 treated; LC21: LPS, CD154 and IL-21 treated. A: Batch A; B: Batch B. 1: sample number 1; 2: sample number 2.
Genes are described as Group 0-3. Group 0: genes with no expression in all B cells; Group 1: genes with no expression in Nil B cells but inducible in any of the stimulation conditions (Inducible); Group 2: genes with constitutive expression in all B cells (Constitutively active); Group 3: genes with low but detectable expression in all B cells (Constitutively inactive).
File: Data_Table_S2.xlsx
Description: ATAC-Seq of B cells stimulated in vitro.
Sample names are described as Treatment_ReplicateNumber.
File: Data_Table_S3.xlsx
Description: Induction of transcript expression and accessibility of B cells stimulated in vitro.
Cons. Active: Constitutively active; Cons. Inactive: Constitutively inactive.
File: Data_Table_S4.xlsx
Description: Signature ligand and receptor-encoding genes of B.Nil, B.LPS, B.CD154 and B.LC cells.
Sample names are shown as B (cell).Treatment. LR_gene: Ligand or receptor gene. Y: yes. N: no
File: Data_Table_S5.xlsx
Description: DEGs of B.LC/21 cells compared to combined B.LPS and B.CD154 cells.
B.LC/21 cells: LPS and CD154 co-stimulated B cells in the absence (B.LC) or presence of IL-21 (B.LC21). Differentially expressed genes (DEGs) of B.LC/21 cells compared with combined B cells stimulated with either LPS (B.LPS) or CD154 (B.CD154) are shown in this datasheet. Genes were defined as upregulated when –log2FoldChange < -0.5 and –lg10(padj) > 1.3. Upregulated genes in B.LC/21 cells are shown in red.
Page 1. Genes encoding ligands
Page 2. Genes encoding ligands or receptors
Page 3. Genes encoding communication factors
Page 4. Ig genes
Page 5. All genes
File: Data_Table_S6.xlsx
Description: Accessibility of the promoter, intragenic and intergenic regions of different genes in B cells.
Page 1. ATAC Hi Induction: ATAC-Seq reads in the promoter, intragenic and intergenic regions of 120 genes whose locus accessibility in B cells stimulated with any of the conditions (B.LPS, B.CD154, B.LC and B.LC21) was induced by over 250-fold as compared to that in B. Nil cells.
Page 2. ATAC Low Induction: ATAC-Seq reads in the promoter, intragenic and intergenic regions of 2299 genes whose locus accessibility in B cells stimulated with all the conditions (B.LPS, B.CD154, B.LC and B.LC21) was induced by less than 250-fold or even slightly decreased as compared to that in B. Nil cells.
File: Data_Table_S7.xlsx
Description: Normalized RNA-Seq reads of B cells stimulated in vitro and isolated in vivo (ImmGen).
IgD_Pos: IgD-positive B cells, this study;
IgD_Neg_GFP_Neg: IgD-negative Il27p28-GFP-negative B cells, this study;
IgD_Neg_GFP_Pos: IgD-negative Il27p28-GFP-positive B cells, this study;
FO: follicular B cells, ImmGen;
CB: centroblasts, ImmGen;
CC: centrocytes, ImmGen;
MZ: marginal zone B cells, ImmGen;
PB/BC: plasmablasts or plasma cells, ImmGen;
B1b: B1b cells, ImmGen.
File: Data_Table_S8.xlsx
Description: Normalized RNA-Seq reads of B cells and other immune cells (ImmGen).
Page 1. 26 samples (column B-AA) from this study, 199 samples (column AB-HR) from ImmGen.
Page 2. first row, sample_name_without_grouping; second row, sample_name_after_grouping: cells with similar properties were assigned into one group, forming 46 groups, and were given new names within each group.
File: Data_Table_S9.xlsx
Description: High-confidence LRIs based on the STRING database.
Page 1. 1248 pairs of ligands and receptors whose interactions have a combined confidence score over 800.
Page 2. String output file of the ligand-receptor interaction score in each category that together form the basis of combined confidence scores.
File: Data_Table_S10.xlsx
Description: Immune cell-pairwise comparison of the expression of each ligand-encoding gene.
In each row, expression of the gene is higher in celltype1 than in celltype2 (p value<0.05, Log2 fold >2).
File: Data_Table_S11.xlsx
Description: Specificity score of a ligand-encoding gene in any given immune cell type.
File: Data_Table_S12.xlsx
Description: Enrichment score of an LRI in any given CCC (Cell_L:Cell_R).
LRI: ligand-receptor interaction; CCC: cell-cell communication.
Cell_L: ligand-expressing cell; Cell_R: receptor-expressing cell.
Page 1. enrichment scores of different LRIs (rows) in different CCCs (columns).
Page 2. enrichment scores of different LRIs (columns) in different CCC pairs (rows).
File: Data_Table_S13.xlsx
Description: Effect of IL-27 and IFNgamma on the transcriptome of B.CD154 cells.
CD154: B cells stimulated with CD154; CD154_Il27: B cells stimulated with CD154 plus IL-27; CD154_IFNg: B cells stimulated with CD154 plus IFNgamma.
File: Data_Table_S14.xlsx
Description: Super-enhancers in B.LA21 and B.LPS cells.
Super-enhancers are marked by “1”; typical enhancers are marked by “0”.
Page 1. Super-enhancers and typical enhancers in B.LA21 cells (B cells stimulated with LPS plus an agonistic anti-CD40 antibody and cytokine IL-21).
Page 2. Super-enhancers and typical enhancers in B.LPS cells.
File: Data_Table_S15.xlsx
Description: Protein expression (peptide counts) in B cells stimulated in vitro.
Page 1. Transcription factor expression (peptide counts) in B.Nil cells and stimulated B cells.
Page 2. Communication factor expression (peptide counts) in B.Nil cells and stimulated B cells.
Page 3. Ligand and receptor expression (peptide counts) in B.Nil cells and stimulated B cells.
Page 4. All detectable protein expression (peptide counts) in B.Nil cells and stimulated B cells.
File: Data_Table_S16.xlsx
Description: Taiji-calculated PageRank of different TFs in B cells stimulated in vitro.
File: Data_Table_S17.xlsx
Description: PageRank and expression differences of different TFs in B cells stimulated in vitro.
Page 1. PageRank and expression differences of different TFs in B.LC21 cells vs B.Nil cells.
Page 2. PageRank and expression differences of different TFs in B.LC21 cells vs B.LPS cells.
Page 3. PageRank and expression differences of different TFs in B.LC21 cells vs B.CD154 cells.
Page 4. PageRank and expression differences of different TFs in B.LC cells vs B.Nil cells.
Page 5. PageRank and expression differences of different TFs in B.LC cells vs B.LPS cells.
Page 6. PageRank and expression differences of different TFs in B.LC cells vs B.CD154 cells.
File: Data_Table_S18.xlsx
Description: DARs in stimulated B cells relative to B.Nil cells and in B.LC/21 cells relative to other B cells. “-“ indicates a region with no “Nearest Unigene” or “Nearest Ensembl”.
Page 1. All_Up.peaks vs B.Nil: ATAC sequencing peaks that are higher in each of the four stimulated B cells (B.LPS, B.CD154, B.LC, B.LC21) than B.Nil cells.
Page 2. LC_21_Up.peaks: ATAC sequencing peaks that are higher in B.LC and B.LC21 cells than in B.Nil, B.LPS and B.CD154 cells.
File: Data_Table_S19.xlsx
Description: Putative BATF3 target gene weight in B cells stimulated in vitro.
Page 1. Putative BATF3 target gene weight in B.Nil cells.
Page 2. Putative BATF3 target gene weight in B.LPS cells.
Page 3. Putative BATF3 target gene weight in B.CD154 cells.
Page 4. Putative BATF3 target gene weight in B.LC cells.
Page 5. Putative BATF3 target gene weight in B.LC21 cells.
File: Data_Table_S20.xlsx
Description: DEGs upregulated or downregulated in Batf3-/- versus Batf3+/+ B.LA21 cells.
DEGs upregulated in Batf3-/- B.LA21 cells, as compared to Batf3+/+ B.LA21 cells, are in red; DEGs downregulated in Batf3-/- B.LA21 cells, as compared to Batf3+/+ B.LA21 cells, are in blue.
Page 1. All DEGs.
Page 2. DEGs that encode communication factors.
Page 3. DEGs that encode ligands or receptors.
Page 4. DEGs that encode ligands.
Page 5. DEGs that are immunoglobin genes
File: Data_Table_S21.xlsx
Description: BATF3 binding DNA in B.LA21 (CUT&Tag).
Anti-Batf3 CUT&Tag signals in Batf3+/+ B.LA21 cells were normalized to those in Batf3-/- B.LA21 cells.
File: Data_Table_S22.xlsx
Description: The probability of a gene to be directly targeted by BATF3, positively or negatively.
Page 1. All genes
Four datasets were integrated: each gene’s expression correlation with Batf3, its Taiji-predicted gene weight for BATF3, its differential expression in Batf3+/+ B.LA21 cells versus Batf3-/- B.LA21 cells (either upregulation or downregulation) and its directly binding by BATF3. The relative values of each of the four parameters (0-100) are used calculate the area of the quadrilateral shape, as the likelihood of this gene being a direct BATF target.
Page 2. Direct targeting
Genes with direct Batf3 binding are marked as “1”; genes without direct Batf3 binding are marked as “0”. Genes downregulated in Batf3-/- B.LA21 cells, as compared to Batf3+/+ B.LA21 cells, have positive area values; genes upregulated in Batf3-/- B.LA21 cells, have negative area values.
File: Data_Table_S23.xlsx
Description: RELA binding DNA in B.LA21 cells (ChIP-Seq).
File: Data_Table_S24.xlsx
Description: BATF3 and RELA binding of super-enhancers and typical enhancers in B.LPS and B.LA21 cells.
Page 1. Super-enhancers and typical enhancers in B.LPS cells, their marking by H3K27ac and H3K27me3 (CUT&Tag), and their binding by BATF3 (CUT&Tag) and RELA (ChIP-Seq).
Page 2. Super-enhancers and typical enhancers in B.LA21 cells, their marking by H3K27ac and H3K27me3 (CUT&Tag), and their binding by BATF3 (CUT&Tag) and RELA (ChIP-Seq).
File: Data_Table_S25.xlsx
Description: BATF3 and RELA binding, H3K27ac and H3K27me3 marks, and Taiji-predicted TF binding in the Il27p28 and Cxcl10 gene promoters. In Taiji-predicted TF binding activity, the value is assigned to only the first nucleotide of the predicted binding site. Empty spaces indicate nucleotides that either show no TF binding or are after the first nucleotide of the binding site.
Page 1. BATF3 and RELA binding, H3K27ac and H3K27me3 marks, and Taiji-predicted TF binding in the Il27p28 promoter.
Page 2. BATF3 and RELA binding, H3K27ac and H3K27me3 marks, and Taiji-predicted TF binding in the Cxcl10 promoter.
File: Data_Table_S26.xlsx
Description: Taiji-calculated activities of selected TFs across the genome.
Page 1. The activity of RELA in regulating different genes in the genome in Batf3+/+ B.LA21 (WT) and Batf3-/- B.LA21 (KO) cells.
Page 2. The activity of JUNB in regulating different genes in the genome in WT and KO B cells.
Page 3. The activity of T-bet in regulating different genes in the genome in WT and KO B cells.
Page 4. The activity of IRF8 in regulating different genes in the genome in WT and KO B cells.
File: Data_Table_S27.xlsx
Description: The list of genes that were direct targets of BATF3 for transcription upregulation, Taiji-calculated RELA target genes at which the RELA activity was enhanced by BATF3, and Taiji-calculated IRF8 target genes at which the RELA activity was enhanced by BATF3.
Page 1. The list of genes that were direct targets of BATF3 for transcription upregulation.
Page 2. Taiji-calculated RELA target genes at which the RELA activity was enhanced by BATF3.
Page 3. Taiji-calculated IRF8 target genes at which the RELA activity was enhanced by BATF3.
Supplemental_Table_2.xlsx
Description: Antibodies, reagents, oligonucleotides and software
Page 1. Antibodies used in flow cytometry.
Page 2. Other antibodies used in other experiments.
Page 3. Oligonucleotides.
Page 4. Software and Algorithms