GRB2 stabilizes RAD51 at reversed replication forks suppressing genomic instability and innate immunity against cancer

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: March 8, 2024

Abstract Growth factor receptor-bound protein 2 (GRB2) is a cytoplasmic adapter for tyrosine kinase signaling and nuclear homology-directed-DNA repair. Here we find GRB2 protects DNA at stalled replication forks from MRE11-mediated degradation in the BRCA2 fork protection axis. Mechanistically, binds inhibits RAD51 ATPase activity to stabilize on forks. In GRB2-depleted cells, PARP inhibitor (PARPi) treatment releases fragments into cytoplasm that activate cGAS–STING pathway trigger pro-inflammatory cytokine production. Moreover syngeneic mouse metastatic ovarian cancer model, depletion context of PARPi reduced tumor burden enabled high survival consistent with immune suppression growth. Collective findings unveil function mechanism BRCA2-RAD51-MRE11 axis suggest as potential therapeutic target an enabling predictive biomarker patient selection immunotherapy combination.

Language: Английский

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Automating data analysis for hydrogen/deuterium exchange mass spectrometry using data-independent acquisition methodology

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: March 11, 2024

Abstract We present a hydrogen/deuterium exchange workflow coupled to tandem mass spectrometry (HX-MS 2 ) that supports the acquisition of peptide fragment ions alongside their precursors. The approach enables true auto-curation HX data by mining rich set deuterated fragments, generated collisional-induced dissociation (CID), simultaneously confirm ID and authenticate MS 1 -based deuteration calculations. high redundancy provided fragments confidence assessment deuterium calculations using combinatorial strategy. requires data-independent (DIA) methods are available on most platforms, making switch HX-MS straightforward. Importantly, we find HX-DIA proteomics-grade wide-spread applications. Considerable time is saved through complex samples can now be characterized at higher throughput. illustrate these advantages in drug binding analysis ultra-large protein kinase DNA-PKcs, isolated directly from mammalian cells.

Language: Английский

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Discovery and Proof of Concept of Potent Dual Polθ/PARP Inhibitors for Efficient Treatment of Homologous Recombination-Deficient Tumors

Journal of Medicinal Chemistry, Journal Year: 2024, Volume and Issue: 67(5), P. 3606 - 3625

Published: Feb. 20, 2024

DNA polymerase theta (Polθ) has recently emerged as a new attractive synthetic lethal target involved in damage repair. Inactivating Polθ alone or combination with PARP inhibitors demonstrated substantial therapeutic potential against tumors homologous recombination (HR) defects such alternation of BRCA genes. Herein, we report the design and proof concept highly potent dual Polθ/PARP inhibitor 25d, which exhibited low nanomolar inhibitory activities both PARP1. Compared to treatment, 25d superior antitumor efficacy MDA-MB-436 cells xenografts by inducing more apoptosis. Importantly, retained sensitivity inhibitor-resistant 53BP1 defect. Altogether, these findings illustrate advantages first-in-class inhibitor, over monotherapy treating HR-deficient tumors, including those acquired resistance.

Language: Английский

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Marine-Derived Leads as Anticancer Candidates by Disrupting Hypoxic Signaling through Hypoxia-Inducible Factors Inhibition

Marine Drugs, Journal Year: 2024, Volume and Issue: 22(4), P. 143 - 143

Published: March 23, 2024

The inadequate vascularization seen in fast-growing solid tumors gives rise to hypoxic areas, fostering specific changes gene expression that bolster tumor cell survival and metastasis, ultimately leading unfavorable clinical prognoses across different cancer types. Hypoxia-inducible factors (HIF-1 HIF-2) emerge as druggable pivotal players orchestrating metastasis angiogenesis, thus positioning them prime targets for treatment. A range of HIF inhibitors, notably natural compounds originating from marine organisms, exhibit encouraging anticancer properties, underscoring their significance promising therapeutic options. Bioprospection the environment is now a well-settled approach discovery development agents might have medicinal chemistry developed into candidates. However, despite massive increase number products classified ‘anticancer leads,’ most which correspond general cytotoxic agents, only few been characterized regarding molecular mechanisms action. current review presents critical analysis inhibitors HIF-1 HIF-2 hypoxia-selective sourced organisms act new chemotherapeutic candidates or serve templates structurally similar derivatives with improved efficacy.

Language: Английский

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Polymerase Ѳ Inhibitors Combinations with Approved and Investigational Agents in Patient-Derived Tumor Multi-Cell Type (Mct) Spheroids

Published: Jan. 1, 2025

Language: Английский

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Ligand-receptor interactions combined with histopathology for improved prognostic modeling in HPV-negative head and neck squamous cell carcinoma

npj Precision Oncology, Journal Year: 2025, Volume and Issue: 9(1)

Published: Feb. 28, 2025

Abstract Head and neck squamous cell carcinoma (HNSC) is a prevalent malignancy, with HPV-negative tumors exhibiting aggressive behavior poor prognosis. Understanding the intricate interactions within tumor microenvironment (TME) crucial for improving prognostic models identifying therapeutic targets. Using BulkSignalR, we identified ligand-receptor in TCGA-HNSC cohort ( n = 395). A model incorporating 14 pairs was developed using random forest survival analysis LASSO-penalized Cox regression based on overall progression-free interval of from TCGA-HNSC. Multi-omics revealed distinct molecular features between risk groups, including differences extracellular matrix remodeling, angiogenesis, immune infiltration, APOBEC enzyme activity. Deep learning-based tissue morphology HE-stained whole slide images further improved stratification, region selection via Silicon enhancing accuracy. The integration routine histopathology deep learning multi-omics data offers clinically accessible tool precise facilitating personalized treatment strategies HNSC.

Language: Английский

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Harnessing transcriptional regulation of alternative end-joining to predict cancer treatment

NAR Cancer, Journal Year: 2025, Volume and Issue: 7(1)

Published: Jan. 15, 2025

Abstract Alternative end-joining (alt-EJ) is an error-prone DNA repair pathway that cancer cells deficient in homologous recombination rely on, making them vulnerable to synthetic lethality via inhibition of poly(ADP-ribose) polymerase (PARP). Targeting alt-EJ effector theta (POLθ), which synergizes with PARP inhibitors and can overcome resistance, significant preclinical clinical interest. However, the transcriptional regulation its interactions processes driving progression remain poorly understood. Here, we show suppressed by hypoxia while positively associated MYC (myelocytomatosis oncogene) activity. Hypoxia reduces PARP1 POLQ expression, decreases binding at their promoters, lowers PARylation alt-EJ-mediated cells. Tumors HIF1A mutations overexpress gene signature. Inhibition hypoxia-inducible factor 1α or expression depletion, combined POLθ inhibition, synergistically colony-forming capacity Deep learning reveals anticorrelation between across regions tumor images, predictions for these activity achieve area under curve values 0.70 0.86. These findings further highlight critical role modulating present a strategy predicting improving outcomes centered on targeting alt-EJ.

Language: Английский

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Examining Instrumental Factors Influencing the Performance of Data-Independent Acquisition Methods in Hydrogen/Deuterium Exchange Mass Spectrometry

Analytical Chemistry, Journal Year: 2025, Volume and Issue: unknown

Published: March 31, 2025

Hydrogen/deuterium exchange mass spectrometry (HX-MS) is a method used to study solution-phase protein structure and dynamics. Despite its many applications, HX-MS limited in throughput because manual data analysis still the norm. We previously developed HX-MS2 technology add second dimension of deuteration promote automated processing. Data-independent acquisition (DIA) techniques enable this approach, but we require optimized methods for best performance. Using an Orbitrap Eclipse illustration, show that ion optics collision energy settings typical proteomics DIA experiment generate maximal peptide retrieval from library. As few as three MS2 sequence ions are sufficient measurement with precision exceeds what possible traditional HX-MS. window sizes based on chromatographic resolution method. An inter-scan offset recommended default configuration most HX-DIA applications butan intra-scan overlap can be tuned highest performance when maximum desired. demonstrate robustness one (consisting Trajan HDX automation technology, spectrometer AutoHX software) extensive time-course phosphorylase B epitope single-domain antibodies (VHHs, nanobodies) specific receptor binding domain SARS-CoV-2 spike protein.

Language: Английский

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ASCC1 structures and bioinformatics reveal a novel Helix-Clasp-Helix RNA-binding motif linked to a two-histidine phosphodiesterase

Journal of Biological Chemistry, Journal Year: 2024, Volume and Issue: 300(6), P. 107368 - 107368

Published: May 14, 2024

Activating signal co-integrator complex 1 (ASCC1) acts with ASCC-ALKBH3 in alkylation damage responses. ASCC1 uniquely combines two evolutionarily ancient domains: nucleotide-binding K-Homology (KH) (associated regulating splicing, transcriptional, and translation) two-histidine phosphodiesterase (PDE) hydrolysis of cyclic nucleotide phosphate bonds). Germline mutations link loss function to spinal muscular atrophy congenital bone fractures 2 (SMABF2). Herein analysis The Cancer Genome Atlas (TCGA) suggests RNA overexpression certain tumors correlates poor survival, Signatures 29 3 mutations, genetic instability markers. We determined crystal structures Alvinella pompejana (Ap) Human (Hs) PDE domain revealing high resolution details features conserved over 500 million years evolution. Extending understanding the KH Gly-X-X-Gly sequence motif, we define a novel structural Helix-Clasp-Helix (HCH) binding motif show sequence–specific CGCG-containing RNA. V-shaped channel has His-Φ-Ser/Thr-Φ (HXT) motifs (Φ being hydrophobic) positioned initiate bond hydrolysis. A atypical active-site histidine torsion angle implies substrate. Flexible active site loop arginine-rich linker appear regulatory. Small X-ray scattering (SAXS) revealed aligned KH-PDE sites limited flexibility solution. Quantitative evolutionary bioinformatic analyses disease cancer-associated support implied functional roles for binding, activity, regulation. Collective results inform transactivation responses, its targeting by structure-based inhibitors, how may impact inherited cancer.

Language: Английский

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Structural basis for a Polθ helicase small-molecule inhibitor revealed by cryo-EM

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Aug. 14, 2024

DNA polymerase theta (Polθ) is a helicase-polymerase protein that facilitates repair and synthetic lethal with homology-directed (HDR) factors. Thus, Polθ promising precision oncology drug-target in HDR-deficient cancers. Here, we characterize the binding mechanism of action helicase (Polθ-hel) small-molecule inhibitor (AB25583) using cryo-EM. AB25583 exhibits 6 nM IC50 against Polθ-hel, selectively kills BRCA1/2-deficient cells, acts synergistically olaparib cancer cells harboring pathogenic BRCA1/2 mutations. Cryo-EM uncovers predominantly dimeric Polθ-hel:AB25583 complex structures at 3.0-3.2 Å. The reveal binding-pocket deep inside central-channel, which underscores high specificity potency AB25583. cryo-EM conjunction biochemical data indicate inhibits ATPase activity Polθ-hel via an allosteric mechanism. These detailed structural insights about inhibition pave way for accelerating drug development targeting crucial target medicine therapy. authors AB25583, show its selective killing BRCA1/2– synergy olaparib.

Language: Английский

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