Biology subjects

Gryder, B.

Publications and source records attributed to Gryder, B..

8 recordsLinked to original sources

bioRxiv2026

Synergistic targeting of EP300/CBP and EYA co-activators collapses the rhabdomyosarcoma core regulatory circuit

Rhabdomyosarcoma (RMS) is a multi-subtype, high-risk pediatric sarcoma with a low mutational burden. The mutations found in RMS often alter genes involved in transcriptional control. Approaches to target dysregulated RMS transcription have remained elusive. Here, we develop a novel approach to target RMS transcription comprising simultaneous targeting of two distinctly acting transcriptional co-activators. We discover a common identity-controlling pan-RMS core regulatory circuit (CRC) composed of oncogenic and lineage-specific myogenic master transcription factors (mTFs). Using a super-enhancer-based reporter screen, we identify the EP300/CBP inhibitor A485 as a potent inhibitor of the pan-RMS CRC, though with efficacy-limiting toxicities. To enhance efficacy, we identify the mTF-binding co-activator EYA2 as a co-factor of this pan-RMS CRC and exploit a new second-generation EYA1/2 inhibitor, LG1-34, to disrupt its function. Combined co-activator inhibition inactivates the CRC and synergistically reduces RMS growth. This strategy dually targets CRC-associated co-activators to cooperatively suppress the RMS transcriptome and enforce cell death.

cancer biology↗

bioRxiv2026

Selection for targeted therapy resistance leads to an indirect selection for higher phenotypic plasticity and enhanced evolvability to orthogonal stressors

Acquired resistance to targeted therapies is a primary barrier to durable cancer control. Resistance frequently coincides with stem-like features and EMT-associated cell-state changes (partial EMT), yet whether these programs directly cause resistance or instead enable escape by increasing phenotypic plasticity remains debated. Integrating computational modeling, functional experimental assays, and lineage tracing, we investigated how cell-state plasticity shapes acquired resistance to ALK inhibition in ALK+ lung cancer models. Our results support a model in which drug exposure selects for cells with higher phenotypic plasticity, progressively increasing their representation as resistance emerges. Consequently, resistant populations show enhanced capacity to adapt to orthogonal therapeutic and environmental stressors and exhibit heightened metastatic potential. Bulk ATAC-seq showed that highly plastic cells have increased chromatin accessibility at regulators of EMT and stemness. Consistent with this, boosting plasticity via Yamanaka-factor induction or EMT-factor expression reduced ALKi sensitivity over time. In contrast, constraining plasticity (SOX2 knockdown or epigenetic inhibition) reduced long-term resistance outgrowth and prolonged ALKi response. Together, our results indicate that targeted therapy indirectly selects for cells with increased phenotypic plasticity, providing the substrate from which multifactorial resistance and metastatic competence evolve. Further, it suggests that constraining plasticity could delay resistance and extend response durability.

cancer biology↗

bioRxiv2025

In Vivo Multiplexed Modeling Reveals Diverse Roles of the TBX2 Subfamily and Egr1 in Ras-Driven Lung Adenocarcinoma

The TBX2 subfamily of T-box transcription factors (including Tbx2, Tbx3, Tbx4, Tbx5) plays an essential role in lung development. Downregulation of these genes in human Lung adenocarcinoma (LUAD) suggests that these genes may be tumor suppressive, however because downregulation appears to occur primarily via epigenetic change, it remains unclear if these changes causally drive tumor progression or are merely the consequence of upstream events. Herein, we developed the first multiplexed mouse model to study the impact of TBX2 subfamily loss, alongside associated signaling genes Egr1, Chd2, Tnfaip3a, and Atf3, in Ras-driven lung cancer. Using TuBa-seq, a high-throughput tumor-barcoding system, we quantified the growth effects of these knockouts during early and late tumorigenesis. Chd2 loss consistently suppressed tumor progression, while Tbx2 loss exhibited stage-dependent effects. Notably, Egr1 emerged as a potent tumor suppressor, with its knockout increasing tumor size ([~]5x) at 20 weeks, surpassing Rb1 loss. Transcriptomic analyses of Egr1-deficient tumors suggested immune dysregulation, including heightened inflammation and potential markers of T cell exhaustion in the tumor microenvironment. These findings indicate that Egr1 may play a role in suppressing tumor growth through modulating immune dynamics, offering new insights into the interplay between tumor progression and immune regulation in LUAD.

cancer biology↗

bioRxiv2025

Dynamic activity of Erg promotes aging of the hematopoietic system

Hematopoiesis changes to adapt to the physiology of development and aging. Temporal changes in hematopoiesis parallel age-dependent incidences of blood diseases. Several heterochronic regulators of hematopoiesis have been identified, but how the master transcription factor (TF) circuitry of definitive hematopoietic stem cells (HSCs) adapts over the lifespan is unknown. Here, we show that expression of the ETS family TF Erg is adult-biased, and that programmed upregulation of Erg expression during juvenile to adult aging is evolutionarily conserved and required for complete implementation of adult patterns of HSC self-renewal and myeloid, erythroid, and lymphoid differentiation. Erg deficiency maintains fetal transcriptional and epigenetic programs, and persistent juvenile phenotypes in Erg haploinsufficient mice are dependent on deregulation of the fetal-biased TF Hmga2. Finally, Erg haploinsufficiency in the adult results in fetal-like resistance to leukemogenesis. Overall, we identify a mechanism whereby HSC TF networks are rewired to specify stage-specific hematopoiesis, a finding directly relevant to age-biased blood diseases. SUMMARYThe hematopoietic system undergoes a process of coordinated aging from the juvenile to adult states. Here, we find that expression of ETS family transcription factor Erg is temporally regulated. Impaired upregulation of Erg during the hematopoietic maturation results in persistence of juvenile phenotypes.

developmental biology↗

bioRxiv2023

Oncogenic reactivation of young L1s is a hallmark of colon cancer

Transposable elements become increasingly active in both cancerous and aging cells, driven by loss of DNA methylation as cells divide. Here we leverage the epigenomes of colon cancers with matched adjacent tissue, in addition to non-cancerous normals and cell line models, to assess the role of transposable elements as drivers or passengers in cancer development. Using the baseline of activity from normal and adjacent tissue, we show that the youngest subfamilies of the LINE1 (L1) family exhibit a degree of activity and recurrence across patients that goes beyond what is expected from hypomethylation and cell division, suggesting an additional mechanism of oncogenic reactivation. We characterize this mechanism and find that the loss of the tumor suppressor PLZF drives young L1 reactivation in a cell-division-independent manner. PLZF de-repression exposes abundant motifs for tumor core factors in the L1 5UTR. Active young L1s act as oncogenic enhancers, interacting with oncogenes via gained chromatin loops. We uncover oncogenic L1 reactivation as a hallmark of colon cancer, where young L1s activate universally in our cohort at high levels of recurrence, act as enhancers to oncogenes, and become wired into the core regulatory circuitry of colon cancer.

genomics↗

bioRxiv2021

SNAI2-mediated direct repression of BIM protects rhabdomyosarcoma from ionizing radiation

Ionizing radiation (IR) and chemotherapy are the mainstays of treatment for patients with rhabdomyosarcoma (RMS). Yet, the molecular mechanisms that underlie the success or failure of radiotherapy remain unclear. The transcriptional repressor SNAI2 was previously identified as a key regulator of IR sensitivity in normal and malignant stem cells through its repression of the proapoptotic BH3-only gene PUMA. Here, we demonstrate a clear correlation between SNAI2 expression levels and radiosensitivity across multiple RMS cell lines. Moreover, modulating SNAI2 levels in RMS cells through its overexpression or knockdown can alter radiosensitivity in vitro and in vivo. SNAI2 expression reliably promotes overall cell growth and inhibits mitochondrial apoptosis following exposure to IR, with either variable or minimal effects on differentiation and senescence, respectively. Importantly, SNAI2 knockdown results in a striking increase in expression of the proapoptotic BH3-only gene BIM, and ChIP-seq experiments establish that SNAI2 is a direct repressor of BIM. Since the P53 pathway is nonfunctional in the RMS cells used in this study, we have identified a new, P53-independent SNAI2/BIM axis that could potentially predict clinical responses to IR treatment and be exploited to improve RMS therapy. HighlightsO_LISNAI2 expression levels are directly correlated with protection from radiation in rhabdomyosarcoma. C_LIO_LILoss of SNAI2 primes rhabdomyosarcomas for IR-induced apoptosis. C_LIO_LISNAI2 directly represses the expression of the proapoptotic BH3-only gene BIM. C_LI

cancer biology↗

bioRxiv2020

Lineage specific transcription factor waves reprogram neuroblastoma from self-renewal to differentiation

Temporal regulation of super-enhancer (SE) driven lineage specific transcription factors (TFs) underlies normal developmental programs. Neuroblastoma (NB) arises from an inability of sympathoadrenal progenitors to exit a self-renewal program and terminally differentiate. To identify critical SEs driving TF regulators of NB, we utilized NB cells in which all-trans retinoic acid (ATRA) induces growth arrest and differentiation. H3K27ac ChIP-seq paired with RNA-seq over a time course of ATRA treatment revealed SEs moving in a coordinated manner with four distinct temporal patterns (clusters). SEs that decreased with ATRA linked to 24 TFs involved in stem cell development/specialization (MYCN, GATA3, SOX11) along with LMO1, a transcriptional coregulator and oncogene identified via a genome-wide association study (GWAS) of NB. H3K27ac levels and GATA3 binding at the NB-associated rs2168101 site of the LMO1 SE were reduced with ATRA treatment, resulting in 1.46 fold decreased LMO1 expression. The SOX11 SE was lost coincident with a 50% decrease in mRNA after 8 days of ATRA treatment. CRISPR-Cas9 screening and siRNA inhibition showed a dependency on SOX11 for cell growth in NB cell lines. Silencing of the SOX11 SE using dCAS9-KRAB targeted guides caused a 40% decrease in SOX11 mRNA and inhibited cell growth. Three other TF SE clusters had sequential waves of activation at 2, 4 and 8 days of ATRA treatment and involved TFs regulating neural development (GATA2 and SOX4). Silencing of the gained SOX4 SE using dCAS9-KRAB targeting, caused a 50% decrease in SOX4 expression and attenuated expression of ATRA-induced differentiation genes. Our study has identified candidate oncogenic lineage drivers of NB self-renewal and TFs critical for implementing a differentiation program.

cancer biology↗

bioRxiv2019

Targeting the PI3K/AKT pathway overcomes enzalutamide resistance by inhibiting induction of the glucocorticoid receptor

The PI3K-AKT pathway has pleiotropic effects, and its inhibition has long been of interest in the management of prostate cancer, where a compensatory increase in PI3K signaling has been reported following Androgen Receptor (AR) blockade. Prostate cancer cells can also bypass AR blockade through induction of other hormone receptors, in particular the glucocorticoid receptor (GR). Here we demonstrate that AKT inhibition significantly decreases cell proliferation through both cytostatic and cytotoxic effects. The cytotoxic effect is enhanced by AR inhibition and is most pronounced in models that induce compensatory GR expression. AKT inhibition increases canonical AR activity and remodels the chromatin landscape, decreasing enhancer interaction at the GR gene (NR3C1) locus. Importantly, it blocks induction of GR expression and activity following AR blockade. This is confirmed in multiple in vivo models, where AKT inhibition of established xenografts leads to increased canonical AR activity, decreased GR expression, and marked anti-tumor activity. Overall, our results demonstrate that inhibition of the PI3K/AKT pathway can block GR activity and overcome GR-mediated resistance to AR-targeted therapy. Ipatasertib is currently in clinical development, and GR induction may be a biomarker to identify responsive patients or a responsive disease state.\n\nSIGNIFICANCEInduced GR expression is compensatory for AR blockade and confers resistance to AR-targeted therapy. Here we show that inhibition of the PI3K/AKT pathway remodels the chromatin landscape, blocks the induction of GR expression and overrides enzalutamide resistance.

cancer biology↗