Kevin C. Johnson

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: Treatment decisions in IDH-mutant oligodendrogliomas are shaped by tumor aggressiveness, underscoring the need for objective grading of these malignant brain tumors. Material and Methods: We collected 302 primary and recurrent resections from oligodendrogliomas and performed Ki-67 staining, proteomics and DNA methylation profiling. Results & conclusion: During tumor progression, DNA methylation of oligodendrogliomas changed along a continuum. This continuum is linked to increased epigenetic aging, methylation of transcription factors and Ki-67+ cell density, and to large scale DNA demethylation. Demethylation was correlated with CpGs flanking sequences preferred by TET enzymes. We confirmed these findings in previously profiled astrocytomas, indicating IDH-mutant gliomas progress along a shared epigenetic axis. We developed an objective DNA methylation based prognostic continuous grading coefficient (CGC ^ψ ) that captured these changes and outperformed WHO grading for oligodendrogliomas. Our findings underscore the potential of DNA methylation-based grading to more accurately reflect tumor biology and inform clinical decision-making in IDH-mutant gliomas.

Next-generation sequencing has transformed cancer care by providing essential insights for diagnosis, prognosis, and treatment. However, variability in testing timing, reporting practices, and interpretation challenges limits its clinical impact. This article highlights key opportunities to optimize somatic reporting, emphasizing the importance of timely testing throughout the cancer care continuum to maximize the diagnostic and therapeutic relevance of findings. Technical factors such as test design, sequencing depth, and the use of liquid biopsy substantially influence result accuracy and interpretation, underscoring the need for careful integration with clinical history. Standardized reporting practices that clearly delineate diagnostic, prognostic, and therapeutic findings can enhance the clinical utility of next-generation sequencing results. Streamlined formats and curated clinical trial data further support actionable decision making. Additionally, direct patient engagement and education are essential for empowering patients to navigate genomic testing and make informed decisions about their care. By leveraging multidisciplinary tumor boards, decision-support tools, and emerging artificial intelligence technologies, clinicians can better navigate the complexities of somatic reports. Standardization and clarity in reporting are critical to advancing precision oncology, empowering providers and patients to make informed treatment decisions and improve outcomes.

Background: Engaging patients, care partners, and others in research planning and conduct is increasingly valued. However, identifying the most effective ways to do so remains a challenge. Objective: This study aimed to evaluate participation and participant experience using 3 engagement methods with the Low-Grade Glioma (LGG) Registry’s Optimizing Engagement in Discovery of Molecular Evolution of Low-Grade Glioma (OPTIMUM) project, part of the National Cancer Institute’s Participant Engagement and Cancer Genome Sequencing Network. Methods: We evaluated LGG Registry research advisory council (RAC) meetings, Twitter (now known as X), and Facebook discussions across 4 engagement activities with each group. Researchers recorded discussions and performed qualitative content analysis to evaluate differences in the nature of interactions and recommendations for promoting trust and participation in LGG Registry research. Participants completed experience surveys after engagements 1 and 4 (Public and Patient Engagement Evaluation Tool, Research Engagement Survey Tool, Trust in Medical Researchers Scale, and Patient Engagement in Research Scale). Results: RAC engagements involved 25 unique participants representing diverse backgrounds; tweet chats and Facebook discussions had 197 and 133 participants, respectively. Qualitative findings highlighted differences in the nature of interactions (eg, communication styles and types of information shared) across groups, but there was general agreement around recommendations for promoting participation in genomic research. Postengagement surveys (n=52 in ipostengagement activity 1; n=40 in postengagement activity 4) showed patterns suggesting a more positive experience overall for the RAC. Conclusions: Advisory councils and social media engagement methods have advantages and disadvantages. Advisory councils provide consistent interactions with the same individuals and clear procedures. Despite theoretically broader reach, social media engagement may yield less diverse perspectives. The LGG Registry aims to use RAC and social media engagement methods to promote diverse perspectives and maintain consistent interactions.

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.

BACKGROUND Engaging patients, care partners, and others in research planning and conduct is increasingly valued. However, identifying the most effective ways to do so remains a challenge. OBJECTIVE This study aimed to evaluate participation and participant experience using 3 engagement methods with the Low-Grade Glioma (LGG) Registry’s Optimizing Engagement in Discovery of Molecular Evolution of Low-Grade Glioma (OPTIMUM) project, part of the National Cancer Institute’s Participant Engagement and Cancer Genome Sequencing Network. METHODS We evaluated LGG Registry research advisory council (RAC) meetings, Twitter (now known as X), and Facebook discussions across 4 engagement activities with each group. Researchers recorded discussions and performed qualitative content analysis to evaluate differences in the nature of interactions and recommendations for promoting trust and participation in LGG Registry research. Participants completed experience surveys after engagements 1 and 4 (Public and Patient Engagement Evaluation Tool, Research Engagement Survey Tool, Trust in Medical Researchers Scale, and Patient Engagement in Research Scale). RESULTS RAC engagements involved 25 unique participants representing diverse backgrounds; tweet chats and Facebook discussions had 197 and 133 participants, respectively. Qualitative findings highlighted differences in the nature of interactions (eg, communication styles and types of information shared) across groups, but there was general agreement around recommendations for promoting participation in genomic research. Postengagement surveys (n=52 in ipostengagement activity 1; n=40 in postengagement activity 4) showed patterns suggesting a more positive experience overall for the RAC. CONCLUSIONS Advisory councils and social media engagement methods have advantages and disadvantages. Advisory councils provide consistent interactions with the same individuals and clear procedures. Despite theoretically broader reach, social media engagement may yield less diverse perspectives. The LGG Registry aims to use RAC and social media engagement methods to promote diverse perspectives and maintain consistent interactions.

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.