BCL7B, a SWI/SNF complex subunit, orchestrates cancer immunity and stemness

Cancer is one of the main causes of human death. Here, we focus on the B-cell lymphoma 7 protein family member B (BCL7B) gene, an accessory subunit of the SWI/SNF chromatin-remodelling complex. To characterize the function of BCL7B, heterozygous BCL7B-deficient stomach cancer cell lines were generated with the CRISPR/Cas9 genome editing system. The comprehensive gene expression patterns were compared between parental cells and each ΔBCL7B cell line by RNA-seq. The results showed marked downregulation of immune-related genes and upregulation of stemness-related genes in the ΔBCL7B cell lines. Moreover, by ChIP-seq analysis with H3K27me3 antibody, the changes of epigenetic modification sequences were compared between parental cells and each ΔBCL7B cell line. After machine learning, we detected the centroid sequence changes, which exerted an impact on antigen presentation. The regulation of BCL7B expression in cancer cells gives rise to cancer stem cell-like characteristics and the acquisition of an immune evasion phenotype. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-023-11321-3.

Extended Data Table 1 The list of genes indicates the downregulated mRNAs in all three BCL7B-deficient cell lines compared to the control Kato III cell line, as shown in ascending order of the average ratio.Gene short name Gene short name Gene short name Gene short name  3 The list of genes indicates the commonly upregulated mRNAs in all three BCL7B-deficient cell lines compared to control Kato III cells.Average ratios and chromosomal locations are shown.

Extended Data Figure 5
Comparison between control siRNA and bcl-7 siRNA in several C. elegans mutants related to epigenetic markers.

Extended Data Figure 1 (
a) Schematic representation of the BCL7B gene.The yellow columns indicate the exon regions, and black lines indicate intron regions.The brown lines indicate the first methionine (M).The green columns under the first (I) and the second (II) exons indicate the conserved Nterminal region in BCL family genes.The dotted lines indicate the two target sites of singleguide RNAs used with the CRISPR/Cas9 editing system (C1 and C2).(b) Schematic representation showing BCL7B genome editing by the CRISPR/Cas9 system.The yellow columns indicate the first exon, and the grey columns indicate the 5' UTR and the intron regions.The brown line indicates the first methionine (M).The dotted lines indicate the two target sites of single guide RNAs used in the CRISPR/Cas9 editing system (C1 and C2).The two CRISPR/Cas9 vectors, including each gRNA sequence, were transfected with a concatenated regions obtained by PCR before and after gRNA (i and ii) for homology-directed repair (HDR).(c) The deleted portions of sequences in each cell line are shown.The dotted columns (C1 and C2) indicate the two reference sequences used for the single-guide RNAs.The yellow sequences indicate exon sequences, and the first methionine codon is shown in orange.The black sequences indicate introns.
The comparison of gene expression levels between KatoIII and BCL7B deficient cells by qPCR.(a) The expression levels of BCL7B were determined by qPCR and were reported relative to that in control cells.(b) Simplified diagram showing the relationships of antigen presentation molecules.(c-h) The expression levels of the antigen-presentation related genes were determined by qPCR and were reported relative to that in control cells.(a, c-h) SE (n = 3).The symbols show the statistical significance (*p < 0.005).(*p < 0.005, #p < 0.05, §p < The expression levels of the BCL7 family genes (BCL7A, BCL7B and BCL7C) in the several cell lines shown under the bars, as determined by qPCR.The BCL7A abundance in H4 cells was set to be equal to 1. SE (n = 2).The BCL7B expression levels were high in Kato III and U937 cells.Error bars represent the SEMs.(b-e) Establishment of BCL7B-deficient U937 cell lines and the expression levels of the BCL7B, NLRC5 and CIITA genes.(b) Phase contrast images of cultured cells.Scale bar, 200 μm.(c) The expression levels of the BCL7B gene were determined by qPCR and are reported relative to that in control cells.SE (n = 3).The symbols show the statistical significance (*p < 0.005).(d) The expression levels of the NLRC5 gene were determined by qPCR and are reported relative to that in control cells.SE (n = 3).The symbols show the statistical significance (*p < 0.005).(e) The expression levels of the CIITA gene were determined by qPCR and are reported relative to those in the control cells.SE (n = 3).The symbols show the statistical significance (*p < 0.005).(f) Comparison of cell sizes by flow cytometry.Abbreviations, S; small, L; large.(g) The relative population of small, middle and large cells.Each coloured column indicates the following information: blue bars, small cells; red bars, medium-sized cells; right green bars, large cells.SE (n = 3).The symbols show the statistical significance (*p < 0.005, #p < 0.05, §p < 0.01).Abbreviations, NS; no significance.
Comparison of gene expression profiles between chronic myeloblastic leukaemia (K562) cells and acute leukaemia (HL-60, MOLT-4, CCRF-CEM, SR, RPMI-8226) cells and between the Kato III cell line and BCL7B-deficient Kato III cell lines.(a) Gene set enrichment analysis (GSEA).The heatmap colour scale is shown at the bottom.The expression of the majority of the genes in the blue cluster was downregulated.Each sample is listed in two lines: the left line indicates downregulated genes, and the right line indicates upregulated genes.(b) The Gene Ontology (GO) terms in the blue cluster shown in (a) were related mainly to immunity.
(a) List of C. elegans mutants.(b) Comparison between control siRNA and bcl-7 siRNA in the MES-2::GFP-carrying C. elegans mutant.Images of MES-2::GFP (top) and image showing the contrast between different levels of interference (middle and bottom) of oocyte cells.Arrows indicate nuclei (top and middle).Dotted lines indicate the edges of cells.(c) The total fluorescence (px) in the nucleolus was measured by ImageJ.Error bars, SEs (control siRNA, n=63, bcl-7 siRNA, n=63).The asterisk shows the statistical significance (****p<0.0001).