Fig 2: Identification of specific mutations of SMARCA4 in CRC patients.a Oncoprint plot showing the genomic profiles of SMARCA4, SMARCA2, SMARCB1, SMARCC1, SMARCC2, SMARCE1, ARID1A, ARID1B, and other CRC relevant genes, data compiled from the cBioPortal based on original data from TCGA CRC project. b Detection of the SMARCA4 gene showing the c. 3721C>T (p. Arg1157Trp) mutation in tumor samples of CRC patients using DNA sequencing.

Fig 3: HINT1 contributes to age-related Tfam downregulation in heart. (A) Relative expression of Hint1 and Tfam in P19.CL6 cells transfected with negative control siRNA (siControl) or Hint1 siRNAs (siHint1-A and siHint1-B) (n = 6 per group). Values in control group were set to 1. (B) Schematic diagram showing IP coupled to mass spectrometry (IP-MS) analysis and Venn diagram showing the number of identified HINT1-interacting protein candidates in P19.CL6 cells and heart tissue of aged mice (24-months-old), or candidate proteins overlapping between P19.CL6 cells and heart tissue. (C) Gene ontology (GO) enrichment analysis of cellular compartment of the 508 overlapping HINT1-interacting protein candidates. Shown is a bubble plot representing top 20 enriched terms sorted by the average of their ranks based on both false discovery rate (FDR) and fold-enrichment. (D) IP of HINT1 protein in P19.CL6 cells. Shown is representative immunoblotting for ARID1A, SMARCE1, BRG1, and HINT1. (E) Representative immunofluorescence staining for HINT1 (red) and ARID1A (green) in P19.CL6 cells. Nuclei were counterstained with DAPI (blue). Scale bar, 20 μm. (F) IP of HINT1 protein in heart tissues of young (3-months-old) and aged (24–26-months-old) mice. Shown is representative immunoblotting for ARID1A, SMARCE1, BRG1, and HINT1 (left). Hsc70 served as loading control. Levels of indicated proteins co-IP'd with HINT1 in hearts of aged relative to young mice (right, n = 6). (G) CUT&RUN analysis of SMARCE1 and H3K27Ac in heart tissues of young (3-months-old) and aged (24–26-months-old) mice (n = 4). (H) IP of ARID1A protein in heart tissues of young (3-months-old) and aged (24–26-months-old) mice. Shown is representative immunoblotting for ARID1A, SMARCE1, and BRG1 (left). Hsc70 served as loading control. Levels of indicated proteins co-IP'd with ARID1A in hearts of aged relative to young mice (right, n = 6). Statistical significance was determined by a two-sided unpaired Student's t-test (F, H) or one-way ANOVA followed by Sidak's post hoc test (A, G). n.s, not significant, between groups. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article).

Fig 4: Nuclear accumulation of ARID1B results in a reduction of ARID1A‐bound BAF complexes. A) Immunoblot analysis of ARID1A and SMARCE1 levels in WT (Parental), empty vector control (pHAGE), and ARID1B OE breast cell lines. The levels of ARID1A and SMARCE1 were analyzed in MDA‐MB‐231, MDA‐MB‐468, MDA‐MB‐436, and HCC1954 cell lines. GAPDH was used as a loading control. B) mRNA levels of ARID1A in empty vector control and ARID1B OE MDA‐MB‐231 and ‐468 cell lines. The data are presented as mean ± SD; n = 3 independent experiments, two‐tailed t‐tests. C) Immunoblot analysis of total cell lysate protein input and immunoprecipitates (IP) by SMARCE1, SMARCA2, and SMARCA4‐specific antibodies from MDA‐MB‐231 and MDA‐MB‐468 empty vector control (pHAGE) and ARID1B OE cells. Immunoglobulin G (IgG) IPs were used as negative control. D) Comparison of the complex formed by the BAF core with ARID1A (left) and ARID1B (right). E) Results from docking simulations of the ARID of ARID1A (left) and ARID1B (right) onto the nucleosome within the BAF complex. The three most energetically favorable poses are shown in each case, along with their corresponding binding energies. The HTH motifs near AT‐rich motifs are shown in salmon and brown ( poses 1 and 2 ), and the HTH motif in the binding of ARID to solvent‐accessible DNA is shown in red. F) Schematic description of the mechanisms by which ARID1B OE suppresses ARID1A expression and reduces the formation of the ARID1A‐bound BAF complexes, leading to tumor growth and progression. Created with BioRender.com.Nuclear accumulation of ARID1B results in a reduction of ARID1A‐bound BAF complexes. A) Immunoblot analysis of ARID1A and SMARCE1 levels in WT (Parental), empty vector control (pHAGE), and ARID1B OE breast cell lines. The levels of ARID1A and SMARCE1 were analyzed in MDA‐MB‐231, MDA‐MB‐468, MDA‐MB‐436, and HCC1954 cell lines. GAPDH was used as a loading control. B) mRNA levels of ARID1A in empty vector control and ARID1B OE MDA‐MB‐231 and ‐468 cell lines. The data are presented as mean ± SD; n = 3 independent experiments, two‐tailed t‐tests. C) Immunoblot analysis of total cell lysate protein input and immunoprecipitates (IP) by SMARCE1, SMARCA2, and SMARCA4‐specific antibodies from MDA‐MB‐231 and MDA‐MB‐468 empty vector control (pHAGE) and ARID1B OE cells. Immunoglobulin G (IgG) IPs were used as negative control. D) Comparison of the complex formed by the BAF core with ARID1A (left) and ARID1B (right). E) Results from docking simulations of the ARID of ARID1A (left) and ARID1B (right) onto the nucleosome within the BAF complex. The three most energetically favorable poses are shown in each case, along with their corresponding binding energies. The HTH motifs near AT‐rich motifs are shown in salmon and brown ( poses 1 and 2 ), and the HTH motif in the binding of ARID to solvent‐accessible DNA is shown in red. F) Schematic description of the mechanisms by which ARID1B OE suppresses ARID1A expression and reduces the formation of the ARID1A‐bound BAF complexes, leading to tumor growth and progression. Created with BioRender.com.

Fig 5: Disruption of KPNA2–KPNB1–RANBP2‐facilitated ARID1B nuclear translocation alters gene expression and suppresses tumor growth. A) 20X IHC of ARID1B, KPNA2, and Ki67 in breast cancer and normal tissues. B) Correlation of Ki67 and KPNA2 in breast cancer. C) Comparison of KPNA2 protein expression between normal tissue samples (n = 18) and tumor tissue samples from Luminal (n = 64), HER2+ (n = 10), and TNBC (n = 16) patients. Analysis of KPNA2 protein levels using CPTAC database and UALCAN data analysis portal showed significant accumulation of KPNA2 in HER2+ (p = 0.0097), and TNBC (p ≤ 0.0001), and no significant difference in Luminal (ns) compared to normal tissues.[ 79 , 80 ] P‐values are summarized with asterisks: *** – p ≤ 0.0001, ** – p ≤ 0.01, * – p ≤ 0.05. D) Correlation of ARID1B and KPNA2 in breast cancer. E) Immunofluorescence assay was conducted to detect levels of ARID1B (green) in MDA‐MB‐231 cells in response to IPZ treatment. Cells were treated with IPZ (40 µm) for 2 h. Nuclei were stained with DAPI (blue). The scale bars indicate 5 µm. F) Quantification of relative ARID1B fluorescence intensity in the nuclei of MDA‐MB‐231 cells after 2‐h IPZ treatment. G) Immunoblot analysis of cytosolic and nuclear fractions of MDA‐MB‐231 cells in response to IPZ treatment. MDA‐MB‐231 cells were treated with 40 µM IPZ or DMSO for 2 h. The protein levels of ARID1B, ARID1A, SMARCE1, and KPNB1 in the cytosolic and nuclear fractions were examined. Lamin A/C and Histone H3 were used as nuclear marker proteins. GAPDH was used as a cytoplasmic marker protein. Each lane was loaded with 30 µg of cytoplasmic or nuclear extract. H) Colony formation assay in response to continuous IPZ treatment in MDA‐MB‐231 cells. I) Survival rate of MDA‐MB‐231 cells under continuous IPZ treatment. Cell viability was determined using the CCK‐8 assay. The data is presented as the mean±SD of three independent experiments. Statistical significance was determined by two‐way ANOVA followed by the Bonferroni test. P‐values are summarized with asterisks: *** – p ≤ 0.0001 J) Immunoblot analysis of ARID1B following 2‐h IPZ (40 µM) treatment in MDA‐MB‐231 cells. Two‐hour IPZ treatment didnot affect total ARID1B levels. K) Differential gene expression in IPZ‐ or BRMi‐treated groups versus the control group. L) Immunoblot analysis of cytosolic and nuclear fractions of control and RANBP2 KO MDA‐MB‐468 cells. The protein levels of RANBP2, ARID1B, SMARCA4, SMARCA2, ARID1A, SMARCE1, KPNB1, and KPNA2 in the cytosolic and nuclear fractions were examined. Lamin A/C and Histone H3 were used as nuclear marker proteins. GAPDH was used as a cytoplasmic marker protein. Each lane was loaded with 30 µg of cytoplasmic or nuclear extract. M) Immunofluorescence assay was conducted to detect levels of ARID1B (green) and RANBP2 (red) in empty vector control (CRISPRv2) and RANBP2 KO breast cancer cell lines. Nuclei were stained with DAPI (blue). The scale bars indicate 5 µm. N,O) Immunoblot analysis of ARID1B in RANBP2 KO and empty vector control (Control) TNBC cells. RANBP2 KO resulted in a significant reduction of ARID1B in MDA‐MB‐231 N) and MDA‐MB‐468 O) cells.Disruption of KPNA2–KPNB1–RANBP2‐facilitated ARID1B nuclear translocation alters gene expression and suppresses tumor growth. A) 20X IHC of ARID1B, KPNA2, and Ki67 in breast cancer and normal tissues. B) Correlation of Ki67 and KPNA2 in breast cancer. C) Comparison of KPNA2 protein expression between normal tissue samples (n = 18) and tumor tissue samples from Luminal (n = 64), HER2+ (n = 10), and TNBC (n = 16) patients. Analysis of KPNA2 protein levels using CPTAC database and UALCAN data analysis portal showed significant accumulation of KPNA2 in HER2+ (p = 0.0097), and TNBC (p ≤ 0.0001), and no significant difference in Luminal (ns) compared to normal tissues.[ 79 , 80 ] P‐values are summarized with asterisks: *** – p ≤ 0.0001, ** – p ≤ 0.01, * – p ≤ 0.05. D) Correlation of ARID1B and KPNA2 in breast cancer. E) Immunofluorescence assay was conducted to detect levels of ARID1B (green) in MDA‐MB‐231 cells in response to IPZ treatment. Cells were treated with IPZ (40 µm) for 2 h. Nuclei were stained with DAPI (blue). The scale bars indicate 5 µm. F) Quantification of relative ARID1B fluorescence intensity in the nuclei of MDA‐MB‐231 cells after 2‐h IPZ treatment. G) Immunoblot analysis of cytosolic and nuclear fractions of MDA‐MB‐231 cells in response to IPZ treatment. MDA‐MB‐231 cells were treated with 40 µM IPZ or DMSO for 2 h. The protein levels of ARID1B, ARID1A, SMARCE1, and KPNB1 in the cytosolic and nuclear fractions were examined. Lamin A/C and Histone H3 were used as nuclear marker proteins. GAPDH was used as a cytoplasmic marker protein. Each lane was loaded with 30 µg of cytoplasmic or nuclear extract. H) Colony formation assay in response to continuous IPZ treatment in MDA‐MB‐231 cells. I) Survival rate of MDA‐MB‐231 cells under continuous IPZ treatment. Cell viability was determined using the CCK‐8 assay. The data is presented as the mean±SD of three independent experiments. Statistical significance was determined by two‐way ANOVA followed by the Bonferroni test. P‐values are summarized with asterisks: *** – p ≤ 0.0001 J) Immunoblot analysis of ARID1B following 2‐h IPZ (40 µM) treatment in MDA‐MB‐231 cells. Two‐hour IPZ treatment didnot affect total ARID1B levels. K) Differential gene expression in IPZ‐ or BRMi‐treated groups versus the control group. L) Immunoblot analysis of cytosolic and nuclear fractions of control and RANBP2 KO MDA‐MB‐468 cells. The protein levels of RANBP2, ARID1B, SMARCA4, SMARCA2, ARID1A, SMARCE1, KPNB1, and KPNA2 in the cytosolic and nuclear fractions were examined. Lamin A/C and Histone H3 were used as nuclear marker proteins. GAPDH was used as a cytoplasmic marker protein. Each lane was loaded with 30 µg of cytoplasmic or nuclear extract. M) Immunofluorescence assay was conducted to detect levels of ARID1B (green) and RANBP2 (red) in empty vector control (CRISPRv2) and RANBP2 KO breast cancer cell lines. Nuclei were stained with DAPI (blue). The scale bars indicate 5 µm. N,O) Immunoblot analysis of ARID1B in RANBP2 KO and empty vector control (Control) TNBC cells. RANBP2 KO resulted in a significant reduction of ARID1B in MDA‐MB‐231 N) and MDA‐MB‐468 O) cells.