DOI: 10.5061/dryad.r4xgxd2rr
title: Data from: Ligand-receptor interactions induce and mediate regulatory functions of BATF3+ B cells

description: 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.
description: # Data from: Ligand-receptor interactions induce and mediate regulatory
 functions of BATF3+ B cells Dataset DOI:
 [10.5061/dryad.r4xgxd2rr](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 &lt; -0.5 and –lg10(padj)
 &gt; 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&lt;0.05, Log2 fold
 &gt;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