Anuja Lipsa

Gliomas with mutant isocitrate dehydrogenase (IDH) are malignant brain tumours that typically arise in early to mid-adulthood and nearly always recur following treatment ^1,2 . However, the genetic and cellular-state changes that drive IDH-mutant glioma progression under treatment remain incompletely understood. Here we integrated single-nucleus transcriptomic profiles, chromatin accessibility profiles and bulk DNA and RNA sequencing from 75 temporally separated gliomas across 35 patients comprising both the oligodendroglioma and astrocytoma IDH-mutant glioma tumour types. We show that malignant cell states transcriptionally resemble stages of normal glial–neuronal lineage development or a reactive mesenchymal-like state, mirroring states previously described in IDH wild-type glioblastoma ^3,4 . Malignant cell states displayed distinct chromatin accessibility profiles that were comparable between both IDH-mutant glioma types. The abundance of less differentiated malignant cells increased with grade and with genetic alterations such as PDGFRA amplification. Longitudinal analysis highlighted two major malignant cell-state transition patterns. First, reduced lineage differentiation and increased proliferative malignant cells at recurrence were enriched in gliomas that acquired recurrence-associated genetic events. These included treatment-associated hypermutation, increased copy number changes and cell cycle alterations. Second, increased mesenchymal-like-state abundance occurred independently of acquired genetic alterations and instead coincided with elevated macrophage expression. Overall, our findings provide an integrative model that traces the cell intrinsic and extrinsic factors that shape cellular states during IDH-mutant glioma disease progression.

Background: Precision medicine has transformed cancer treatment by tailoring therapies to specific molecular aberrations. Integrating high-resolution multi-omics with high-throughput functional profiling in patient-derived organoids of-fers a powerful strategy to further refine patient stratification. While (epi)genetic profiling has drastically improved the classification in diffuse adult gliomas, these advances have not yet translated into effective therapeutic interventions and precision medicine approaches remain to be established. Material and Methods: We investigated a panel of 48 patient-derived organoid and orthotopic xenograft models of adult high-grade gliomas, comprehensively characterized at genomic, epigenomic and transcriptomic levels. A functional drug screen was performed on 27 organoid models using a 202-compound library targeting cancer-related pathways and epigenetic regulators. Unsupervised multi-omics factor analysis was employed to identify patient-specific therapeutic vulnerabilities. Validation included dose-dependent drug efficacy assessments, as well as biomarker assessment in patient tumors across molecular subgroups. Results: Multi-omics analysis revealed a broad spectrum of molecular profiles capturing the genetic, epigenetic, and transcriptomic diversity of high-grade gliomas. Multi-omics factor analysis, integrating multi-omics and drug response profiles, identified distinct subgroups associated with IDH1 mutation and MYCN amplification. IDH1 mutant grade 4 astrocytomas showed selective sensitivity to histone deacetylase 3 inhibitors, while a MYCN -amplified glioblastoma responded preferentially to histone methyltransferase inhibitors. The differential drug responses were linked to specific (epi)genetic and transcriptomic biomarkers. While other glioblastomas exhibited heterogeneous treatment responses, no robust biomarker-defined responder subgroups were identified. Conclusion: Our findings highlight the value of integrating multi-omics and functional profiling to inform precision medicine strategies. This approach enables the stratification of distinct patient subgroups in preclinical models, paving the way for tailored therapeutic interventions. While we observed distinct pharmacogenomic profiles in IDH1 mutant grade 4 astrocytomas and a MYCN -amplified glioblastoma, implementing precision medicine in other glioblastoma subtypes remains a substantial challenge. Key points: Integrating drug screening in a panel of patient-derived organoids with multi-omics enables pharmacogenomic profiling in adult diffuse high-grade gliomas IDH1 mutant grade 4 astrocytomas are sensitive to histone deacetylase 3 inhibitors MYCN -amplified glioblastoma exhibits distinct DNA methylation pattern and drug responses Study importance: To date, attempts to develop effective precision medicine in adult high-grade gliomas failed. Here, we provide a preclinical framework for identifying personalized therapeutic by integrating multi-omics profiling with functional drug screening in patient-derived organoids. We show that IDH1 mutant high-grade astrocytomas present distinct therapeutic vulnerabilities compared to glioblastomas, linked to sensitivity to histone deacetylase 3 inhibitors. Within glioblastomas, we identified a distinct MYCN -amplified tumor, sensitive to histone methyltransferase inhibitors. Applying pharmacogenomic approaches using novel drug libraries holds promise for uncovering additional clinically relevant patient subgroups in the future. Graphical

The evolution of isocitrate dehydrogenase (IDH)-wildtype glioblastoma (GBM) after standard-of-care therapy remains poorly understood. Here we analyzed matched primary and recurrent GBMs from 59 patients using single-nucleus RNA sequencing and bulk DNA sequencing, assessing the longitudinal evolution of the GBM ecosystem across layers of cellular and molecular heterogeneity. The most consistent change was a lower malignant cell fraction at recurrence and a reciprocal increase in glial and neuronal cell types in the tumor microenvironment (TME). The predominant malignant cell state differed between most matched pairs, but no states were exclusive or highly enriched in either time point, nor was there a consistent longitudinal trajectory across the cohort. Nevertheless, specific trajectories were enriched in subsets of patients. Changes in malignant state abundances mirrored changes in TME composition and baseline profiles, reflecting the co-evolution of the GBM ecosystem. Our study provides a blueprint of GBM’s diverse longitudinal trajectories and highlights the treatment and TME modifiers that shape them.

In isocitrate dehydrogenase wildtype glioblastoma (GBM), cellular heterogeneity across and within tumors may drive therapeutic resistance. Here we analyzed 121 primary and recurrent GBM samples from 59 patients using single-nucleus RNA sequencing and bulk tumor DNA sequencing to characterize GBM transcriptional heterogeneity. First, GBMs can be classified by their broad cellular composition, encompassing malignant and nonmalignant cell types. Second, in each cell type we describe the diversity of cellular states and their pathway activation, particularly an expanded set of malignant cell states, including glial progenitor cell-like, neuronal-like and cilia-like. Third, the remaining variation between GBMs highlights three baseline gene expression programs. These three layers of heterogeneity are interrelated and partially associated with specific genetic aberrations, thereby defining three stereotypic GBM ecosystems. This work provides an unparalleled view of the multilayered transcriptional architecture of GBM. How this architecture evolves during disease progression is addressed in the companion manuscript by Spitzer et al.

To understand the role of extrachromosomal DNA (ecDNA) amplifications in cancer progression, we detected and classified focal amplifications in 8,060 newly diagnosed primary cancers, untreated metastases and heavily pretreated tumors. The ecDNAs were detected at significantly higher frequency in untreated metastatic and pretreated tumors compared to newly diagnosed cancers. Tumors from chemotherapy-pretreated patients showed significantly higher ecDNA frequency compared to untreated cancers. In particular, tubulin inhibition associated with ecDNA increases, suggesting a role for ecDNA in treatment response. In longitudinally matched tumor samples, ecDNAs were more likely to be retained compared to chromosomal amplifications. EcDNAs shared between time points, and ecDNAs in advanced cancers were more likely to harbor localized hypermutation events compared to private ecDNAs and ecDNAs in newly diagnosed tumors. Relatively high variant allele fractions of ecDNA localized hypermutations implicated early ecDNA mutagenesis. Our findings nominate ecDNAs to provide tumors with competitive advantages during cancer progression and metastasis.

Background Glioblastoma (GBM) evades the immune system by creating an immune-suppressive tumor microenvironment (TME), where GBM-associated myeloid cells are geared towards tumor-supportive roles. However, it is unclear whether recruited myeloid cells are phenotypically and functionally identical. Here, we aim to understand the TME heterogeneity in GBM patients recapitulated in patient-derived orthotopic xenografts (PDOXs) and systematically characterize myeloid cell type identities at the molecular and functional level. Methods We applied single-cell RNA-sequencing and spatial transcriptomics, multicolor flow cytometry, immunohistochemistry and functional assays to examine the heterogeneity of the TME in GBM. Various GBM PDOXs representing different tumor phenotypes were analyzed and compared to the patient tumors, normal brain and mouse GL261 glioma model. Results PDOX models recapitulate the major components of the TME detected in human GBM, where tumor cells reciprocally interact with host cells to create a GBM-specific TME. We detect the most prominent transcriptomic adaptations in myeloid cells, which are largely of microglial origin. We reveal intra-tumoral heterogeneity of microglia and identify diverse phenotypic states across distinct GBM landscapes and tumor niches. GBM-educated microglia acquire dendritic cell-like features, displaying increased migration and phagocytosis. We further find novel microglial states expressing astrocytic and endothelial markers. Lastly, we show that temozolomide (TMZ) treatment leads to transcriptomic plasticity of both GBM tumor cells and adjacent TME components. Conclusions Our data provide insight into the phenotypic adaptation of the heterogeneous TME instructed by GBM. We uncover that GBM-educated microglia are represented by various concomitant states, both in patients and recapitulated in PDOXs, displaying different pro- or anti-tumoral properties that are modulated by anti-neoplastic treatments, such as TMZ. KEY POINTS GBM-educated tumor microenvironment is faithfully recapitulated and modulated in PDOX models Microglia represent an essential myeloid cell population in the GBM microenvironment GBM-educated microglia acquire heterogeneous transcriptomic states across distinct tumor niches GBM-educated microglia subsets display phagocytic and dendritic cell-like gene expression programs, which are modulated upon TMZ treatment IMPORTANCE OF THE STUDY This manuscript addresses tumor-immune interactions in GBM, focusing on the molecular changes of the myeloid compartment. We find that myeloid cells, the most abundant immune cell population in brain tumors, undergo the most prominent transcriptional adaptation in the TME. Resident microglia represent the main myeloid cell population in the cellular tumor, while peripheral-derived myeloid cells appear to infiltrate the brain at sites of blood-brain barrier disruption. We identify reactive dendritic cell-like gene expression programs associated with enhanced phagocytic and antigen-presentation features in GBM-educated microglia subsets that might be harnessed for novel immunotherapeutic approaches. Overall, PDOX models faithfully recapitulate the major components of the GBM-educated TME and allow assessment of phenotypic changes in the GBM ecosystem upon treatment.

Management of familial adenomatous polyposis (FAP) is guided by the cumulative risk of colorectal cancer (CRC) and aggressive fibromatosis/desmoid (AF/D). The first non-Caucasian FAP cohort with cumulative risk estimates for CRC and AF/D shows distinct differences with the Caucasian and other Asian cohorts. The strong correlation between the adenomatous polyposis coli (APC) mutation location with the FAP phenotype and the geoethnic differences in APC mutation spectrum, genetic constitution, lifestyle and sporadic CRC rates, mandates the use of population-specific cumulative risk estimates for CRC and desmoid for counselling and risk management. On genotype–phenotype correlation in 83 individuals with classical FAP and a confirmed pathogenic/likely Pathogenic (P/LP) APC variant (n=76) or obligate carrier of the family variant (n=7), we observed a high cumulative CRC risk of 40% and 85% by 40 and 60 years, respectively. The observed 30% cumulative risk by 50 years for desmoids was higher than previous European and Asian cohorts and was significantly associated with prophylactic surgery (OR: 4.58, 95% CI 1.06 to 19.78) and APC mutation 3′ of codon 1309 (OR: 13.07, 95% CI 3.58 to 47.56) and also 3′ of codon 1444 (OR: 8.0, 95% CI 1.83 to 34.94). Global cooperation is required to establish FAP genotype–phenotype associations and population-specific risk estimates to guide genetic counselling and risk management.