Biology subjects

Bilbao, D.

Publications and source records attributed to Bilbao, D..

6 recordsLinked to original sources

bioRxiv2025

RHOA Loss of Function Impairs the IFNγ Response and Promotes CD19 Antigen Escape to Drive CAR-T Resistance in Diffuse Large B-cell Lymphoma

CD19-directed chimeric antigen receptor (CAR)-T cells are breakthrough therapies for aggressive B-cell lymphomas, but less than half of patients achieve durable responses. We previously showed through whole-genome sequencing of tumors from CAR-T-treated patients that deletions of RHOA (3p21.31) are enriched in cases progressing after treatment. RHOAs roles in resistance and pathogenesis are poorly defined, despite loss-of-function alterations that occur in [~]20% of newly diagnosed large B-cell lymphoma (LBCL) cases. We created RHOA-deficient LBCL systems and confirmed cell-intrinsic loss of response to CAR-19 in vitro and in vivo driven by CD19 downregulation. Impact on CD19, however, was variable and would not explain selection for RHOA deletion in newly diagnosed cases. We therefore created RHOA-deficient tumors in immunocompetent mice and found remarkable correlation with dysfunctional lymphoma microenvironment (LME) signatures in CAR-19 resistant patients. These LMEs are marked by a type 1-like immune infiltrate with terminally exhausted CD8 T cells, Th1-like CD4 cytotoxic lymphocytes (CTLs), and increased production of interferon gamma (IFN{gamma}). RHOA-deficient tumor cells themselves have significantly impaired IFN{gamma} responses, providing resistance to CD8 T cell clearance by way of diminished induction of major histocompatibility complex class I (MHC-I). These findings support a model that depletion of healthy effector populations by RHOA-deficient lymphoma is a key driver of immune dysfunction thwarting CAR-19 clinical responses. Overall, we describe for the first time how a single-gene alteration found recurrently in CAR-19-resistant LBCL contributes to treatment failures.

cancer biology↗

bioRxiv2024

Higher-Order Interaction Analysis via Hypergraph Models for Studying Multidimensional Neuroscience Data.

Higher-Order Interaction (HOI) theory offers a powerful framework for capturing complex, non-linear relationships within multidimensional systems, moving beyond traditional pairwise graph methods to encompass multi-way interactions. This study applies HOI analysis, specifically using hypergraph theory, to explore intricate connectivity patterns in electrophysiological signals from neuroscience. Hypergraphs were constructed from connectivity data across various frequency bands, characterized through metrics such as spectral entropy, hyperedge centrality, and vertex centrality, and compared using spectral and centrality distance measures. Three distinct neurophysiological datasets were analyzed: intracranial EEG signals from rats during different sleep stages, scalp EEG data to distinguish between epilepsy types, and MEG recordings of seizure dynamics. The findings highlight the effectiveness of hypergraph-based HOI analysis in mapping neural dynamics across normal and pathological brain states. In sleep studies, it reveals distinct connectivity patterns between REM and NREM stages, while in epilepsy, it differentiates seizure types and stages, identifying spectral entropy as a potential marker for seizure onset. Notably, HOI analysis captures differences between primary and secondary generalized epilepsy, suggesting enhanced diagnostic accuracy. This approach provides a powerful tool for understanding complex neural interactions in high-dimensional data.

neuroscience↗

bioRxiv2024

The cyclin-G associated kinase (GAK) is a novel mitotic kinase and therapeutic target in diffuse large B-cell lymphoma

New drug targets are needed for diffuse large B-cell lymphoma (DLBCL), the most common lymphoma subtype, to enable enable development better treatments for patients not cured by standard care. We conducted a phenotypic screen of kinase inhibitors and identified the cyclin G-associated kinase (GAK) as a tumor-selective target. Though GAK is previously described primarily as a participant in membrane trafficking, we found its kinase activity is a key mitotic regulator in DLBCL. Inhibition caused G2/M-phase arrest, chromosome misalignment, and spindle distortion, effects absent in non-malignant controls. Transcriptomics data from clinical samples showed increased GAK expression associates with RB1 deficiency in DLBCL cases, suggesting dependency on GAK linked to retinoblastoma associated protein (RB) loss of function, a common DLBCL driver. RB-deficient DLBCL cells treated with a selective GAK tool compound showed complete arrest at G2/M, pronounced distortion of mitotic spindles, and widespread chromosomal damage. High-content live-cell imaging revealed onset of mitotic catastrophe in response to GAK inhibition, which was more rapid and severe in isogenic cells with RB1 deletion. No GAK-selective inhibitors suitable for clinical development are currently available, but several drugs approved or under development inhibit GAK activity even more potently than thier intended clinical targets. For instance, OTS167, developed against MELK for use in solid tumors, has particularly potent anti-GAK potency and has achieved single-agent tumor-burden reduction in vivo against a DLBCL patient-derived xenograft. GAK is therefore a novel mitotic kinase in DLBCL, linked to the common, undruggable RB loss of function biomarker, and suitable for rapid clinical translation through drug repurposing. SignificanceWe identify cyclin-G associated kinase (GAK) as a novel therapeutic vulnerability in diffuse large B-cell lymphoma. Clinical kinase inhibitors with GAK activity create an opportunity for rapid therapeutic translation through drug repurposing.

cancer biology↗

bioRxiv2024

Identification of targetable epigenetic vulnerabilities in uveal melanoma

Uveal melanoma (UM) is the most common primary intraocular malignancy in adults, with a strong predilection for hepatic metastasis, occurring in approximately 50% of cases. Metastatic UM remains highly resistant to therapy and is almost invariably fatal. The strongest genetic drivers of UM metastasis are loss-of-function mutations in tumor suppressor BAP1, an epigenetic regulator that serves as the ubiquitin hydrolase subunit of the polycomb repressive deubiquitinase (PR-DUB) complex, and a key player in global epigenetic regulation. Inactivation of BRCA Associated Protein 1 (BAP1) has been shown to induce widespread epigenetic alterations across multiple model systems. To identify novel therapeutic strategies, we investigated whether targeting the epigenome could reveal new vulnerabilities in UM. We performed high-throughput compound screening using a curated epigenetic inhibitor library and identified BET (bromodomain and extra-terminal domain) inhibition as a particularly promising approach. Interestingly, we observed significant heterogeneity in the efficacy of different BET inhibitors in UM. While previous clinical trials with two BET inhibitors have failed to show efficacy in UM, our findings highlight substantial differences in the potency of specific BET inhibitors for this malignancy. Notably, the BET inhibitor mivebresib (ABBV-075) significantly improved survival rates by 50% in a metastatic UM xenograft mouse model and completely prevented detectable metastases in the bones, spinal cord, and brain. Unexpectedly, RNA sequencing revealed a strong transcriptional overlap between BET inhibition and histone deacetylase (HDAC) inhibition--an approach currently under clinical evaluation for UM treatment. Both BET and HDAC inhibitors reversed gene expression signatures associated with high metastatic risk and induced a neuronal differentiation-like phenotype in UM cells. Together, our findings demonstrate that UM cells exhibit a distinct vulnerability to BET inhibition and establish BET inhibitors as promising candidates for further clinical evaluation for metastatic UM.

cancer biology↗

bioRxiv2024

NRF2 translation block by inhibition of cap-dependent initiation sensitizes lymphoma cells to ferroptosis and CAR-T immunotherapy

Cancers coopt stress-response pathways to drive oncogenesis, dodge immune surveillance, and resist cytotoxic therapies. Several of these provide protection from ferroptosis, iron-mediated oxidative cell death. Here, we found dramatic sensitization to ferroptosis upon disruption of cap-dependent translation in diffuse large B-cell lymphoma (DLBCL). Specifically, rocaglate inhibitors of the eIF4A1 RNA helicase synergized with pharmacologic ferroptosis inducers, driven by a collapse of glutathione production that protects polyunsaturated fatty acids from ferroptotic oxidation. These effects occur despite initial up-regulation of specific protective factors. We find lost translation of NRF2, oncogenic master regulator of antioxidant gene-expression, is a key consequence of eIF4A1 inhibition. In vivo, combination of the clinical rocaglate zotatifin with a pharmacologically optimized ferroptosis inducer eradicated DLBCL patient derived xenografts. Moreover, we found zotatifin pre-exposure sensitized DLBCL to CD19-directed chimeric antigen receptor (CAR-19) T cells. Translational disruption therefore provides new opportunities to leverage therapeutic impacts of ferroptosis inducers including cytotoxic immunotherapies. SignificanceWe find translational disruption sensitizes lymphomas to ferroptosis, enhancing efficacy of CAR-T cells and multiple drugs. NRF2 loss mediates these effects, informing promising new therapeutic combinations. Multiple cancers exploit NRF2 to resist a wide variety treatments. These results expand therapeutic implications from its loss downstream of eIF4A1 inhibition.

cancer biology↗

bioRxiv2023

Methylation of histone H3 lysine 36 is a barrier for therapeutic interventions of head and neck squamous cell carcinoma.

Approximately 20% of head and neck squamous cell carcinomas (HNSCC) exhibit reduced methylation on lysine 36 of histone H3 (H3K36me) due to mutations in histone methylase NSD1 or a lysine-to-methionine mutation in histone H3 (H3K36M). Whether such alterations of H3K36me can be exploited for therapeutic interventions is still unknown. Here, we show that HNSCC models expressing H3K36M can be divided into two groups: those that display aberrant accumulation of H3K27me3 and those that maintain steady levels of H3K27me3. The first group shows decreased proliferation, genome instability, and increased sensitivity to genotoxic agents, such as PARP1/2 inhibitors. In contrast, the H3K36M HNSCC models with steady H3K27me3 levels do not exhibit these characteristics unless H3K27me3 levels are elevated, either by DNA hypomethylating agents or by inhibiting the H3K27me3 demethylases KDM6A/B. Mechanistically, we found that H3K36M reduces H3K36me by directly impeding the activities of the histone methyltransferase NSD3 and the histone demethylase LSD2. Notably, we found that aberrant H3K27me3 levels induced by H3K36M expression is not a bona fide epigenetic mark in HNSCC since it requires continuous expression of H3K36M to be inherited. Moreover, increased sensitivity of H3K36M HNSCC models to PARP1/2 inhibitors solely depends on the increased H3K27me3 levels. Indeed, aberrantly high H3K27me3 levels decrease BRCA1 and FANCD2-dependent DNA repair, resulting in higher sensitivity to DNA breaks and replication stress. Finally, in support of our in vitro findings, a PARP1/2 inhibitor alone reduce tumor burden in a H3K36M HNSCC xenograft model with elevated H3K27me3, whereas in a H3K36M HNSCC xenograft model with consistent H3K27me3 levels, a combination of PARP1/2 inhibitors and agents that upregulate H3K27me3 proves to be successful. In conclusion, our findings underscore a delicate balance between H3K36 and H3K27 methylation, essential for maintaining genome stability. This equilibrium presents promising therapeutic opportunities for patients with H3K36me-deficient tumors.

cancer biology↗