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Furudate, K.

Publications and source records attributed to Furudate, K..

5 recordsLinked to original sources

LLM-PathwayCurator transforms enrichment terms into audit-gated decision-grade claims

Pathway enrichment of omics data requires careful interpretation, and LLM-PathwayCurator transforms enrichment outputs into auditable, evidence-linked claims with redundancy-highlighting module mapping. Across seven cohorts from The Cancer Genome Atlas (TCGA), it achieved qualified coverage of 0.66 to 0.80 but fell to a range of 0.20 to 0.42 under context swap and 0.20 to 0.30 after supporting-gene dropout due to contract violations or weak gene support. LLM-PathwayCurator generates decision-grade claims with audit-gated abstention to establish a reproducible quality-assurance layer for omics interpretation.

bioinformatics↗

LLM-scCurator: Data-centric feature distillation for zero-shot cell-type annotation

Zero-shot cell-type annotation with language models degrades when marker lists are dominated by biological-noise programs (e.g., ribosomal/cell-cycle/stress). We present LLM-scCurator, a data-centric, backend-agnostic framework using pre-prompt noise masking and Gini-informed distillation to recover identity markers. Across benchmarks, LLM-scCurator improves ontology-aware hierarchical accuracy from 78.4% to 86.1% (52 clusters) over naive prompting, approaching supervised/reference-transfer performance without training data. LLM-scCurator extends to spatial transcriptomics (Visium, Xenium) for reference-free discovery of fine-grained niches.

bioinformatics↗

Exploring the immune environment of glioblastoma through single-cell RNA sequencing in humanized mouse models

BackgroundGlioblastoma (GBM) is the deadliest primary brain tumor in adults, where current therapies fail to meaningfully extend survival. Available animal GBM tumor models, especially therapy-resistant and recurrent ones with unique immunological aspects, are restricted, impeding innovative treatment research. To confront this critical obstacle we established a unique GBM mouse model that utilizes patient-derived xenografts (PDXs) within humanized mice. MethodsWe selected two immune-deficient mouse models to facilitate the reconstitution of myeloid lineage cells. After undergoing myeloablation, mice received CD34+ hematopoietic stem progenitor cells derived from human umbilical cord blood for humanization. Upon confirming the reconstitution of human blood cells, mice were xenografted with PDXs resistant to radiation. Tumor profiles and immune cell infiltration were analyzed via flow cytometry, immunohistochemistry, and single-cell RNA sequencing (scRNA-seq). The findings were evaluated against scRNA-seq data from recurrent human GBM. ResultsA diverse range of human immune cells, including T, NK, and myeloid lineage cells, infiltrated PDX tumors in humanized mice. Notably, gene expression profiles in these immune cells resembled that of recurrent human GBM. Unlike conventional xenograft models, this model highlighted enhanced tumor diversity, particularly a high fraction of neural progenitor-like cells. ConclusionsOur humanized GBM mouse model displayed an immune cell signature similar to recurrent GBM. This model is a valuable resource for analyzing the tumor immune landscape and assessing new therapies, particularly immunotherapies. By enabling effective evaluation of novel treatments, our model has the potential to significantly advance GBM research. Key PointsO_LIA wide array of human immune cells infiltrates GBM-PDX tumors in humanized mice. C_LIO_LIThe tumor heterogeneity of GBM-PDX is more evident in humanized mouse xenografts. C_LI Importance of the studyCurrent GBM treatment development is primarily constrained by the absence of appropriate animal models that can enhance our understanding of human GBM biology and its immune dynamics. We created a specialized GBM mouse model using humanized mice with patient-derived xenografts resistant to radiation. Detailed immune cell analysis showed various human blood cells in the GBM-PDX derived from humanized mice. Single-cell RNA sequencing uncovered crucial T-cell subgroups, notably regulatory and exhausted T cells, which matched those observed in recurrent GBM patient tumors. Moreover, the model outperformed standard xenograft approaches in tumor heterogeneity, resembling the intricate diversity observed in recurrent GBM samples. Our humanized GBM mouse model provides a powerful platform to study the interactions between human tumors and immune cells. This tool will facilitate the discovery of immunosuppressive mechanisms and accelerate the assessment of immunotherapies applicable to various brain tumors.

immunology↗

Clonal evolution of hematopoietic stem cells after cancer chemotherapy

Normal hematopoietic stem and progenitor cells (HSPCs) inherently accumulate somatic mutations and lose clonal diversity with age, processes implicated in the development of myeloid malignancies1. The impact of exogenous stressors, such as cancer chemotherapies, on the genomic integrity and clonal dynamics of normal HSPCs is not well defined. We conducted whole-genome sequencing on 1,032 single-cell-derived HSPC colonies from 10 patients with multiple myeloma (MM), who had undergone various chemotherapy regimens. Our findings reveal that melphalan treatment distinctly increases mutational burden with a unique mutation signature, whereas other MM chemotherapies do not significantly affect the normal mutation rate of HSPCs. Among these therapy-induced mutations were several oncogenic drivers such as TET2 and PPM1D. Phylogenetic analysis showed a clonal architecture in post-treatment HSPCs characterized by extensive convergent evolution of mutations in genes such as TP53 and PPM1D. Consequently, the clonal diversity and structure of post-treatment HSPCs mirror those observed in normal elderly individuals, suggesting an accelerated clonal aging due to chemotherapy. Furthermore, analysis of matched therapy-related myeloid neoplasm (t-MN) samples, which occurred 1-8 years later, enabled us to trace the clonal origin of t-MNs to a single HSPC clone among a group of clones with competing malignant potential, indicating the critical role of secondary mutations in dictating clonal dominance and malignant transformation. Our findings suggest that cancer chemotherapy promotes an oligoclonal architecture with multiple HSPC clones possessing competing leukemic potentials, setting the stage for the selective emergence of a singular clone that evolves into t-MNs after acquiring secondary mutations. These results underscore the importance of further systematic research to elucidate the long-term hematological consequences of cancer chemotherapy.

cancer biology↗

Leukemia stemness and co-occurring mutations drive resistance to IDH inhibitors in acute myeloid leukemia

Allosteric inhibitors of mutant IDH1 or IDH2 induce terminal differentiation of the mutant leukemic blasts and provide durable clinical responses in approximately 40% of acute myeloid leukemia (AML) patients with the mutations. However, primary resistance and acquired resistance to the drugs are major clinical issues. To understand the molecular underpinnings of clinical resistance to IDH inhibitors (IDHi), we performed multipronged genomic analyses (DNA sequencing, RNA sequencing and cytosine methylation profiling) in longitudinally collected specimens from 68 IDH1- or IDH2-mutant AML patients treated with the inhibitors. The analysis revealed that leukemia stemness is a major driver of primary resistance to IDHi, whereas selection of mutations in RUNX1/CEBPA or RAS-RTK pathway genes was the main driver of acquired resistance to IDHi, along with BCOR, homologous IDH gene, and TET2. These data suggest that targeting stemness and certain high-risk co-occurring mutations may overcome resistance to IDHi in AML.

cancer biology↗