Biology subjects

Bucklan, M.

Publications and source records attributed to Bucklan, M..

2 recordsLinked to original sources

bioRxiv2026

Loss of cBAF Complex Confers Sorafenib Resistance in Liver Cancer

Sorafenib resistance limits the clinical benefit of first-line therapy in hepatocellular carcinoma (HCC), yet the epigenetic mechanisms underlying this resistance remain poorly understood. Using a chromatin-focused CRISPR/Cas9 dropout screen in HepG2 cells, we identified subunits of the canonical BAF (cBAF) complex -- ARID1A, ARID1B, and SMARCC1 -- as functional drivers of sorafenib resistance, while loss of the PBAF-specific subunit ARID2 had no effect, implicating cBAF specifically rather than SWI/SNF broadly. ARID1A and ARID1B mutations are associated with significantly worse overall survival in TCGA hepatocellular carcinoma cohorts. To define the underlying mechanism, we performed CUT&RUN profiling and RNA-seq in ARID1B-knockout HepG2 cells under sorafenib treatment. ARID1B loss triggered selective depletion of H3K4me3 and H3K27ac at 74 cBAF-dependent regulatory elements, 72% of which were directly occupied by ARID1B in wild-type cells. These sites were enriched for FOXA1 and HNF4 motifs, consistent with disruption of hepatocyte lineage regulatory chromatin. Direct profiling in HLF hepatocellular carcinoma cells confirmed that 179 FOXA1 binding sites were lost specifically under the combined perturbation of ARID1B loss and sorafenib treatment, with neither condition alone sufficient to drive this effect. Transcriptionally, ARID1B loss induced epithelial-mesenchymal transition programs and suppressed MYC targets, E2F targets, and mTORC1 signaling. These findings define a cBAF-FOXA1 regulatory axis that maintains hepatocyte lineage identity under kinase inhibitor stress, and whose disruption drives epigenetic reprogramming toward a mesenchymal drug-tolerant state. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=92 SRC="FIGDIR/small/731725v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@1ce2352org.highwire.dtl.DTLVardef@70f2f5org.highwire.dtl.DTLVardef@15ee96borg.highwire.dtl.DTLVardef@2e7edd_HPS_FORMAT_FIGEXP M_FIG C_FIG

Cancer Biology↗

bioRxiv2025

BAP1 deletion in hepatocytes primes an inflammatory transcriptional response

BackgroundBRCA1-associated protein 1 (BAP1) is a deubiquitinase, frequently altered in cancers including hepatocellular carcinoma and cholangiocarcinoma. While Bap1 has been shown to play key roles in metabolism, maintenance of tissue homeostasis, and immune cell development, little is known about its normal functions in the liver in vivo. This study aims to identify Bap1 specific effects on the livers immune microenvironment and biological functions. MethodsUsing AAV8-mediated CRISPR/CAS9 genome editing we generated a mouse hepatocyte-specific model of Bap1 knockout to define the changes that occur in liver biology in an in vivo system and characterize how loss of Bap1 alters the livers response to injury. Single-cell resolution spatial transcriptomics were performed in conjunction with immunohistochemistry to analyze cell-type composition and immune cell recruitment changes. Bulk RNA-sequencing was performed for further assessment of the impact of Bap1 loss on transcription. ResultsHepatocyte-specific depletion of Bap1 induced transcriptional changes shared with acute injury. We observed a strong dysregulation of inflammatory pathways associated with BAP1 loss. Moreover, the transcriptional response of Bap1 depletion in hepatocytes to damage was markedly different than in control liver, with Bap1-deleted livers showing a decreased hepatocyte identity based on gene expression. Spatial transcriptomics and quantitative texture analysis of immunohistochemistry revealed an altered immune environment prior to damage and an impaired recruitment of immune cells in Bap1 depleted livers after damage. ConclusionsUsing a hepatocyte-specific Bap1 deletion we identified Bap1 as a critical modulator in the livers immune cell response. We show that Bap1 loss leads to an inflammatory environment prior to damage and disrupts the recruitment immune cells. Our quantitative spatial analysis highlights the power of such approaches to characterize the spatial distribution of different cell types in a tissue.

genetics↗