Biology subjects

Dykhuizen, E.

Publications and source records attributed to Dykhuizen, E..

6 recordsLinked to original sources

bioRxiv2026

cBAF drives AR-V7 expression through regulation of transcriptional termination in castration-resistant prostate cancer

The androgen receptor splice variant AR-V7 drives resistance to androgen receptor-targeted therapies in castration-resistant prostate cancer (CRPC), but the mechanisms governing its expression remain incompletely understood. Here, we identify the canonical BAF (cBAF) chromatin remodeling complex as a selective regulator of AR-V7 expression. Pharmacologic and genetic disruption of cBAF reduced AR-V7 levels, suppressed AR-V7-dependent transcriptional programs, and impaired CRPC cell proliferation. Mechanistically, cBAF binds an intronic regulatory element downstream of AR cryptic exon 3, where it maintains chromatin accessibility, enhancer activity, and promoter-enhancer looping. cBAF loss decreases recruitment of transcription termination machinery, reduces RNA polymerase II Thr4 phosphorylation, and promotes transcriptional readthrough beyond the AR-V7 polyadenylation site. POINT-seq revealed that cBAF-dependent transcriptional termination is required for AR-V7 biogenesis and regulates termination at a subset of genes genome-wide. Together, these findings uncover a role for cBAF in chromatin-mediated control of transcriptional termination and establish this mechanism as a critical determinant of AR-V7 expression.

molecular biology↗

bioRxiv2026

PBRM1-VHL cooperation rewires lipid and iron metabolism to promote ferroptosis resistance in clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) is initiated by biallelic loss of the tumor suppressor VHL followed by additional genomic alterations, including loss of tumor suppressors PBRM1, BAP1 or SETD2. Although ccRCC is known to be intrinsically sensitive to ferroptosis, the contribution of PBRM1 to this vulnerability, and how it interfaces with VHL loss, has remained unexplored. Using isogenic ccRCC and non-transformed cell models, we show that re-expression of PBRM1 and/or VHL attenuates GPX4-inhibitor-induced ferroptosis, and that the two tumor suppressors act cooperatively: dual reconstitution confers the greatest protection, suppresses lipid peroxidation, and preserves redox homeostasis. Time-resolved RNA-seq reveals that PBRM1 and VHL establish additive, largely non-overlapping "ground-state" transcriptional programs. Integrated pharmacogenomic, CRISPR dependency, and lipidomic analyses converge on two protective axes: restricted labile iron and MUFA-biased membrane remodeling. These findings identify PBRM1 as a previously unrecognized modulator of ferroptosis and define a cooperative chromatin-metabolic axis that buffers ferroptotic cell death in ccRCC.

cell biology↗

bioRxiv2024

Loss of Bicra/Gltscr1 leads to a defect in fetal liver macrophages responsible for erythrocyte maturation in mice.

Key pointsBicra/Gltscr1 homozygous knockout mice are perinatal lethal with aberrant liver resident macrophage gene expression and function. Dysfunctional macrophages result in accumulation of immature nucleated red blood cells in peripheral blood and liver of the knockout mice. GLTSCR1, a protein encoded by the Bicra gene, is a defining subunit of the SWI/SNF (also called mammalian BAF) chromatin remodeling subcomplex called GBAF/ncBAF. To determine the role of GLTSCR1 during mouse development, we generated a Bicra germline knockout mouse using CRISPR/Cas9. Mice with homozygous loss of Bicra were born at Mendelian ratios but were small, pale and died within 24 hours after birth. Histology indicated blood-related defects including defective erythroblastic islands and irregularly sized red blood cells. Gene expression profiling of fetal livers pinpointed a defect in liver resident macrophages involved in the last stage of erythrocyte maturation, resulting in accumulation of nucleated erythrocytes in Bicra-/- pups. Together, these results demonstrate that Bicra is critical for fetal liver macrophage function during development. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/618940v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@150ac36org.highwire.dtl.DTLVardef@15a4758org.highwire.dtl.DTLVardef@2176aorg.highwire.dtl.DTLVardef@14f5d49_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOVisual AbstractC_FLOATNO C_FIG

developmental biology↗

bioRxiv2023

KRAS-mediated upregulation of CIP2A promotes suppression of PP2A-B56α to initiate pancreatic cancer development

Oncogenic mutations in KRAS are present in approximately 95% of patients diagnosed with pancreatic ductal adenocarcinoma (PDAC) and are considered the initiating event of pancreatic intraepithelial neoplasia (PanIN) precursor lesions. While it is well established that KRAS mutations drive the activation of oncogenic kinase cascades during pancreatic oncogenesis, the effects of oncogenic KRAS signaling on regulation of phosphatases during this process is not fully appreciated. Protein Phosphatase 2A (PP2A) has been implicated in suppressing KRAS-driven cellular transformation. However, low PP2A activity is observed in PDAC cells compared to non-transformed cells, suggesting that suppression of PP2A activity is an important step in the overall development of PDAC. In the current study, we demonstrate that KRASG12D induces the expression of both an endogenous inhibitor of PP2A activity, Cancerous Inhibitor of PP2A (CIP2A), and the PP2A substrate, c-MYC. Consistent with these findings, KRASG12D sequestered the specific PP2A subunit responsible for c-MYC degradation, B56, away from the active PP2A holoenzyme in a CIP2A-dependent manner. During PDAC initiation in vivo, knockout of B56 promoted KRASG12D tumorigenesis by accelerating acinar-to-ductal metaplasia (ADM) and the formation of PanIN lesions. The process of ADM was attenuated ex vivo in response to pharmacological re-activation of PP2A utilizing direct small molecule activators of PP2A (SMAPs). Together, our results suggest that suppression of PP2A-B56 through KRAS signaling can promote the MYC-driven initiation of pancreatic tumorigenesis.

cancer biology↗

bioRxiv2022

PBRM1 BD2 and BD4 associate with RNA to facilitate chromatin association

PBRM1 is a subunit of the PBAF chromatin remodeling complex, which is mutated in 40-50% of clear cell renal cell carcinoma patients. It is thought to largely function as a chromatin binding subunit of the PBAF complex, but the molecular mechanism underlying this activity is not fully known. PBRM1 contains six tandem bromodomains which are known to cooperate in binding of nucleosomes acetylated at histone H3 lysine 14 (H3K14ac). Here we demonstrate that the second and fourth bromodomains from PBRM1 also bind nucleic acids, selectively associating with double stranded RNA elements. Disruption of the RNA binding pocket is found to compromise PBRM1 chromatin binding and inhibit PBRM1-mediated cellular growth effects.

biochemistry↗

bioRxiv2018

PBRM1 regulates stress response in epithelial cells

Polybromo1 (PBRM1) is a chromatin remodeler subunit highly mutated in cancer, particularly renal clear cell carcinoma. PBRM1 is a member of the SWI/SNF subcomplex, PBAF (PBRM1-Brg1/Brm Associated Factors) and is characterized by six tandem bromodomains. Here we establish a role for PBRM1 in epithelial cell maintenance through the expression of genes involved in cell adhesion, metabolism, stress response, and apoptosis. In support of a general role for PBRM1 in stress response and apoptosis, we observe that loss of PBRM1 results in an increase in reactive oxygen species generation and a decrease in cellular viability under stress conditions. We find that loss of PBRM1 promotes cell growth under favorable conditions but is required for cell survival under conditions of cellular stress.

cell biology↗