NPJ Precision Oncology最新文献

We report a child with an antenatally detected brain tumor that progressed over three years' time despite surgery, chemo- and proton therapy. Retrospective whole-genome and transcriptome sequencing with methylation analysis of primary tumor tissue led to the molecular diagnosis infant-type hemispheric glioma, and identified a novel SNRNP70::ALK fusion, providing a therapeutic target for compassionate-use precision treatment with the ALK tyrosine kinase inhibitor lorlatinib. Functional studies confirmed the fusion protein to be expressed and active in the patient's tumor. After two years of therapy, the child has sustained partial tumor regression on MRI and no new neurological symptoms. We conclude that comprehensive multi-omics analyses are required for correct molecular diagnosis in childhood CNS tumors and can radically impact patient outcome by identifying molecular targets for precision treatment.

Unique disease characteristics of younger patients warrants investigation of tumor genomics in young-onset metastatic breast cancer (MBC). Targeted DNA sequencing was completed for tumors of MBC patients diagnosed between 2009-2020. Multivariable logistic regression tested associations between single nucleotide variants (SNVs) and copy number variants and age at MBC diagnosis. Multivariable Cox regression estimated hazard ratios for overall survival (OS) by somatic alterations. Among 2,357 MBC patients, tumors of those ≤40 years at diagnosis (vs. >55) were more likely to harbor amplifications in ERBB2 and MYC (p < 0.01) and mutations in TP53 (odds ratio [OR] = 1.83, p < 0.001), and less likely to harbor mutations in CDH1 and PIK3CA (p < 0.001). OS was shorter among younger recurrent MBC patients [median: 2.8 (≤ 40) vs. 3.6 years ( > 55), p = 0.04], with SNVs in TP53 and PTEN associated with shorter OS. Distinct tumor genomics of young-onset MBC patients suggest differences in tumor biology that should guide investigation of targetable pathways.

Acute myeloid leukemia (AML) is sustained by oncogenic signaling and stress-adaptive networks that enable proliferative sustenance and therapeutic resistance. Transcriptomic profiling of AML blasts revealed upregulation of FLT3, SYK, HOXA9/10, and CTNNB1 with elevated oxidative phosphorylation (OXPHOS). Proteasome inhibition induced phosphorylation-dependent ubiquitination and nuclear export of β-catenin, triggering stress signaling (p62/SQSTM1/c-JUN/NRF2) and apoptosis in FLT3^ITD mutant AML blasts. Dual targeting of FLT3/SYK (TAK-659) and the proteasome (Ixazomib) showed strong synergy across genetically defined AML subsets, irrespective of FLT3 mutant status. In Tet2^-/-;Flt3^ITD AML-transplanted mice models, combination therapy markedly reduced leukemic burden, restored CD45.1⁺ normal hematopoiesis, corrected disease-associated cytopenias, and normalized hematopoietic stem and progenitor composition. In our phase I/II clinical trial, this combination therapy induced rapid leukemic clearance, early transcriptional silencing of HOXA/FLT3/NRF2 programs, and durable hematologic responses in refractory AML patients. These findings define a therapeutically targetable axis linking FLT3/SYK/β-catenin signaling to stress adaptation, provide a mechanistic basis for combinatorial targeting in high-risk AML. Trial registration: NCT04079738, Date of registration 03 September 2019.

Class II and III BRAF mutations are uncommon events, with limited data on their clinical and biological characteristics. We investigated clinical and molecular features of BRAF mutation classes in a total of 24,402 patients with mismatch repair proficient CRC (MMRp). Samples collected between 2006 and 2023 were profiled using next-generation sequencing and whole-transcriptome sequencing. We identified 1268 (5.2%), 132 (0.54%), and 323 (1.3%) patients with class I, II, and III BRAF-mutated CRC. Patients with class III mutations had significantly better median overall survival (OS) than those with class I mutations (23.6 vs 17.4 months; HR = 1.26, CI: 1.08-1.47, p = 0.004). Transcriptomic analyses revealed that the MAPK pathway score was significantly lower for class II and III BRAF mutations without concurrent RAS mutations than for those with RAS co-mutations. The cetuximab score, an RNA expression-based predictor of EGFR therapy response, was significantly better for class II and III BRAF mutations than for class I. The cetuximab score significantly improved for only class III BRAF mutations when those with concurrent RAS mutations were excluded. The results of this large multi-institutional analysis of BRAF mutation classes reveal the prognostic value of class II and III BRAF mutations, and their distinct clinical and molecular features.

Poly (ADP-ribose) polymerase (PARP) inhibitors provide clinical benefit for patients with metastatic castration-resistant prostate cancer (mCRPC) harboring BRCA1/2 pathogenic variants. This study aimed to investigate the genomic landscape of mCRPC and evaluate the prognostic and therapeutic impact of pathogenic BRCA1/2 variants. We conducted a retrospective cohort study of 5893 patients with mCRPC registered in Japan. Overall survival (OS) was compared according to homologous recombination repair (HRR) gene alteration status and specific BRCA1/2 pathogenic variants. Of 5893 patients, 2203 carried at least one pathogenic variant in HRR genes, and 792 had BRCA1/2 pathogenic variants. Olaparib was recommended for all patients with BRCA1/2 pathogenic variants, of whom 389 received the treatment. Patients with HRR gene alterations had significantly shorter OS than those without (P = 0.023). Among olaparib-treated patients, BRCA1 pathogenic variants were significantly associated with worse OS compared with BRCA2 pathogenic variants (P = 0.008). Within BRCA2-altered cases, BRCA2 loss was associated with the most favorable OS (P < 0.001). Multivariate analysis confirmed BRCA1 pathogenic variants as an independent adverse prognostic factor and BRCA2 loss as an independent favorable factor in patients treated with olaparib. These findings highlight the clinical importance of detailed genomic annotation for precision oncology in mCRPC.

Aberrant cellular signaling underlies cancer development and progression. Identifying alterations in these pathways yields critical insights for personalized oncology. Clinically, assessing the activation status of signaling proteins complements genetic and histopathological analyses, improving therapeutic evaluation and accuracy. In this study, we employed the high-throughput Western blot system DigiWest for the characterization of gastrointestinal tumors, both retrospectively and in a proof-of-concept direct clinical application. Retrospective analyses of pancreatic and colorectal carcinomas (n = 20) compared with matched normal tissues revealed distinct protein expression and activation patterns differentiating tumor subtypes and defining clinically relevant subgroups. By resolving individualized, treatment-relevant signaling signatures we demonstrate the feasibility of molecular-level personalization in samples with high clinical heterogeneity. In the clinical proof-of-concept, single core needle biopsies from 14 patients with gastrointestinal tumors who underwent Molecular Tumor Board presentation were analyzed. The resulting proteomic profiles uncovered patient-specific, targetable pathway activation patterns and showed concordance with mutational data and therapy recommendations. Collectively, these findings establish DigiWest as a valuable, robust complementary tool to sequencing-based approaches for personalized diagnostics and treatment evaluation in precision oncology.

The effective application of precision oncology in solid tumors remains challenging due to genetic heterogeneity and the absence of actionable alterations in some cancers. In this review, we discuss the integration of liquid biopsy and mutational signatures as a potential framework to address these limitations by enabling longitudinal detection of mutational processes that arise during tumor development and evolution. Together, these complementary approaches hold substantial promise for enhancing cancer screening, refining diagnosis, and guiding personalized therapeutic strategies, thereby advancing the field of precision oncology.

Chemoresistance remains a critical challenge in breast cancer (BC) treatment. By integrating multi-omics (single-cell, spatial, and bulk transcriptomics) with clinical validation, we identified a specific COL3A^high CAF subset that drives BC chemoresistance. Mechanistically, these CAFs undergo lipid metabolic reprogramming, secreting excess oleic acid via SCD. This oleic acid binds to ENO1 on tumor cells, activating the PI3K/Akt pathway and inhibiting chemotherapy-induced apoptosis. Simultaneously, COL3A^high CAFs orchestrate an immunosuppressive niche by recruiting regulatory T cells and impairing cytotoxic CD8⁺ T cells. Our findings establish COL3A^high CAFs as key mediators of resistance through metabolic symbiosis and immune evasion. The strong correlation between COL3A^high CAF abundance and clinical poor response highlights their potential as both predictive biomarkers and therapeutic targets to overcome chemoresistance in BC patients.

Genetic interactions (GIs) drive carcinogenesis and treatment resistance via non-additive phenotypic effects between genes. Traditional bulk-based methods fail to capture cell-type-specific interactions in heterogeneous tumors like lung adenocarcinoma (LUAD), limiting precision oncology. Resolving cell-type-specific GIs at single-cell resolution persists as a major hurdle, hindered by limited analytical methodologies. Here, we develop scPGI-finder, a computational framework that identifies gene pairs whose coordinated high expression is associated with higher proliferation-related fitness at single-cell resolution, which we refer to operationally as single-cell positive genetic interactions (scPGIs). Using scPGI-finder, we identify 49,808 and 15,896 scPGIs spanning epithelial cells and T cells in LUAD, respectively. The predicted scPGIs display tighter junctions in the protein interaction network compared to non-scPGIs. Furthermore, we demonstrate the predictive power of scPGIs for malignancy and immunotherapy response through multi-omics validation across diverse cohorts. Notably, with a mean area under the ROC curve (AUROC) of 0.974 in bulk tissue validation, the epithelial-derived scPGI classifier enables concordant malignancy identification across scales ranging from epithelial single cells and lung cancer cell lines, through spatial transcriptomic maps, to bulk LUAD tissue profiles. Additionally, a six-scPGI T cell signature reliably forecasts immunotherapy efficacy, with AUROC values exceeding 0.80 across multiple datasets. Together, our research advances the understanding of underlying cancer-positive GIs at the single-cell level. scPGIs of epithelial and T cells serve as robust biomarkers for malignancy evaluation and treatment response, offering a translational framework for precision oncology.

Sex differences in cancer susceptibility and prognosis are partially driven by sex chromosomes and sex hormones. However, the molecular mechanisms underlying the higher incidence and mortality of multiple myeloma (MM) in males remain poorly defined. In this study, we identify the Y-linked gene EIF1AY as a tumor-suppressive regulator in male MM. Clinical analysis reveals that partial deletions of EIF1AY in male MM patients are significantly associated with disease progression, reduced treatment responsiveness, and shorter overall survival. Functionally, loss of EIF1AY promotes M2 macrophage polarization and recruitment, thereby enhancing MM cell proliferation. Mechanistically, EIF1AY forms a protein complex with RPS4Y1 that directly binds to and stabilizes CD134 mRNA, thereby promoting CD134 expression in MM cells. The RPS4Y1-EIF1AY-CD134 axis suppresses IL-4 and IL-13 secretion from MM cells, which in turn downregulates the membrane receptor DDR1 on co-cultured macrophages, thereby inhibiting M2 macrophage polarization and recruitment, and ultimately restraining MM cell proliferation. These findings uncover a feed-forward loop in which the RPS4Y1-EIF1AY-CD134 axis suppresses IL-4/IL-13-DDR1 signaling, thereby suppressing M2 macrophage polarization and recruitment, and sustaining tumor growth through reciprocal crosstalk between tumor cells and macrophages. Collectively, our study elucidates a novel immune regulatory pathway driving sex differences in MM and highlights EIF1AY as a promising target for precision immunotherapy in male patients.