Abstract Background Although targeted therapies for paediatric low-grade gliomas (pLGG) have shown efficacy, comparisons of alteration-specific long-term outcomes between targeted therapies and conventional chemotherapy are lacking. Methods We performed a population-based study of BRAF-altered pLGG treated at relapse with trametinib (for BRAF fused pLGG) or dabrafenib +/- trametinib (BRAF V600E), compared with chemotherapy-treated pLGG. Imaging responses (RAPNO) were assessed by neuroradiologists. Results The initial cohort comprised 267 BRAF fused and 161 BRAF V600E pLGG. Across alterations and lines of therapy, imaging responses for chemotherapy-treated pLGG were similar. Clinician-determined progression-free survival (PFS) was poor and, importantly, equivalent between first/second-line chemotherapy. For BRAF fused pLGG treated with chemotherapy or trametinib, there was a higher objective response rate (>25% reduction) with trametinib – 60% (18/30) versus 36% (8/22) [second-line] versus 39% (22/56) [first-line]. Trametinib yielded significantly more partial responses. Moreover, 56% of tumours refractory/non-responsive to first-line chemotherapy responded to trametinib. These responses translated to superior disease control with 18-month PFS of 91% (n = 34) versus 52% for second-line chemotherapy (n = 27) (p < 0.001). At 3.5 years, PFS for patients who remained on therapy was 82% versus 19% for chemotherapy. These differences narrowed for patients who discontinued trametinib, with 49% progressing within 2 years. Interestingly, disseminated tumours were more likely to progress on therapy – 67% probability at 5 years (p = 0.001). BRAF V600E pLGG treated with targeted therapy (n = 19) also showed superior disease control with 5-year PFS of 82% versus 33% for second-line chemotherapy (n = 9) (p = 0.02). With prolonged treatment times (median 5.5 years [1-10.9]), tumour control persisted – only 16% of patients progressed on therapy. Review of V600E imaging responses is ongoing. Conclusion Acknowledging variation in treatment courses and follow-up, targeted therapy for relapsed BRAF-altered pLGG yields superior tumour control relative to chemotherapy. Ongoing work will help elucidate optimal treatment schedules and long-term functional outcomes.

Purpose:To characterize the clinical, radiological, and molecular characteristics of CNS tumors associated with Noonan syndrome (NS) and other non-Neurofibromatosis type 1 RASopathies. Methods:Twenty-four patients with concern for NS underwent clinical and central radiological review in this multi-institutional study. Whole-exome sequencing, RNA sequencing, and methylation analyses of peripheral blood and/or tumor specimens were performed. Results:Nineteen (79%) of 24 participants had NS, 17/19 (89%) of which had a germline PTPN11 variant; Nineteen of 24 participants (79%) were male. Seventeen (89%) patients with NS developed CNS cancers, including low-grade glioma, (LGG; pure pilocytic/pilomyxoid astrocytoma; n=9) and mixed dysembryoplastic neuroepithelial tumor (DNET; n=6). Five patients incidentally diagnosed did not undergo histological confirmation. Radiological review showed multifocal parenchymal tumors in 9 patients with NS, including histologically confirmed neoplasm (n=2), radiologic progression (n=6), or typical tumoral imaging (n=1). All LGGs in patients with NS and germline PTPN11 variants except one (14/15; 93%) harbored somatic FGFR1 abnormalities. RNA sequencing of 12 tumors detected FGFR1 internal tandem duplication in one patient. Comparison with published data showed a statistically significant association between brain tumor occurrence and PTPN11-related NS, driven by two genotypes: NM_002834.5(PTPN11):c.182A>G (p.Asp61Gly) and c.417G>T (p.Glu139Asp). Ten patients with LGGs, including 7 (41%) with NS, required chemotherapy. After median follow-up of 7.5 years, one patient died of CNS cancer. Conclusion:PTPN11-related NS predisposes to multifocal pure and mixed LGGs confirmed by radiological, histological, and molecular characteristics. Targeting FGFR1-related pathways may provide new treatment approaches for patients with NS and LGGs.

Abstract Background In the era of molecular characterization and targeted therapies for paediatric low-grade gliomas (pLGG), it is essential to understand the role of driver alterations in determining responses and long-term outcomes for upfront chemotherapy. Methods We performed a population-based study of pLGG treated with upfront chemotherapy. Chemotherapy responses (RAPNO) were assessed by expert neuroradiologists. Results We analyzed 247 BRAF fused, 139 BRAF V600E, and 188 NF1 pLGG (median follow-up 8.2 years). Incompletely resected BRAF-altered pLGG could be stratified into 3 groups based on location and need for chemotherapy/radiation: hemispheric/cerebellar (25% BRAF fused and 10% BRAF V600E treated by 5 years), midline (59% & 56%), and optic pathway (92% & 79%) (p < 0.002). All disseminated pLGG required treatment. The objective response rates (>25% reduction) to chemotherapy were 39% (22/56) for BRAF fused, 20% (3/15) for V600E, and 32% (12/38) for NF1. Interestingly, BRAF fused responders had superior clinician-determined progression-free survival (PFS) relative to initially stable tumours (p = 0.0041). Dismal long-term control was observed for BRAF fused (n = 73) and V600E (n = 22) pLGG with 15-year PFS of 16% and 22% (p = 0.5953), contrasting 49% for NF1 (n = 51) (p < 0.0001). Strikingly, all V600E pLGG in patients <7 y.o. progressed within 3 years (p = 0.0063). V600E optic pathway gliomas also fared poorly with 4-year PFS of 8%, versus 34% for BRAF fused (p = 0.0721) versus 73% for NF1 (p < 0.0001). Despite superior PFS for NF1 optic pathway glioma patients, 49% had profound or worse visual impairment at last follow-up, versus 23% for BRAF fused (p = 0.0441). Imaging review revealed further >25% shrinkage beyond the chemotherapy period in 16% of BRAF fused and 27% of NF1 tumours, with 91% showing best response at > 5 years. Conclusion This study provides important driver alteration-specific information on long-term pLGG tumour control and patient outcomes. Insights from these observations can inform trial design and comparison with targeted therapies.

BACKGROUND:Due to the novelty and rarity of infant-type hemispheric glioma (IHG), optimal treatment and factors determining clinical outcomes are yet to be established. METHODS:We curated a series of 164 patients with IHG; 155 identified by methodical literature search and nine additional patients contributed by collaborators. RESULTS:All tumors were hemispheric, diagnosed at a median age of 3.4 (0-52) months, and frequently (95%) non-metastatic. One hundred forty-two (86.5%) tumors harbored fusions involving receptor tyrosine kinase (RTK) genes (ALK [67/142, 47%], NTRK1/2/3 [32/142, 22.5%], ROS1 [29/142, 20.4%], MET [13/142, 9.2%], and ABL2 [1/142, 0.7%]). Sixty-four percentage, 20%, and 8% of patients were treated with surgery and adjuvant chemotherapy, surgery-only, and surgery plus targeted therapy, respectively. Five patients received radiation. Three-year event-free survival (EFS) and overall survival (OS) was 49.5% [40.7-60.2] and 79.6% [72.1-87.9], respectively. Twenty-two patients succumbed to disease, of which tumor progression (8/22, 36%) and intra-cranial hemorrhage (5/22, 23%) were the most common causes. Multivariate analysis showed that the factors most associated with an increased risk of death were no treatment except for surgery and presence of residual tumor after definitive surgery. These findings present a challenging dichotomy where surgery is both a serious risk factor for early death and, when successful, a benefit. CONCLUSIONS:Together, these findings show that IHG is a fusion driven tumor of the very young that is survivable even after progression. While optimal primary therapy for patients with IHG has yet to be established, the findings of this meta-analysis suggest treatment should focus on lowering surgical morbidity and improving its success.

Chromosome-arm copy number alterations (CNAs) are an important component of cancer molecular classifiers. CNAs are often translated into binary chromosome arm calls (arm gain/loss) using an arm call threshold before integration into classification schemes. However, substantial variability exists in thresholds used to define arm calls from CNA data. Here, we analyze 1042 meningiomas with whole-genome microarray data and 13 meningiomas with multifocal sampling to characterize how CNA thresholds influence molecular classification and prognostication. Changing arm call thresholds shifts the association of chromosomal arm calls with meningioma recurrence in an arm-dependent manner and upgrades 21.5% of cases from low-grade to high-grade in a molecularly Integrated Grade (IG) scheme. The impact of threshold differences in IG prediction of recurrence is most evident amongst intermediate grade (IG-2) tumors and CNA call thresholds approaching whole-chromosome arm length (>95%). The designation of chromosome loss or gain remains stable across a majority of thresholds, although this varies in a chromosome-dependent manner. CNAs fluctuate among paired primary-recurrent tumors, mostly growing on recurrence, but cluster in discrete sizes within a tumor. Appreciation of the impact of chromosome arm call thresholds can help ensure robustness of molecular classification paradigms.

Gliomas are a major cause of cancer-related deaths in adolescents and young adults (AYAs; ages 15-39 years). Different molecular alterations drive gliomas in children and adults, leading to distinct biology and clinical consequences, but the implications of pediatric- versus adult-type alterations in AYAs are unknown. Our population-based analysis of 1,456 clinically and molecularly characterized gliomas in patients aged 0-39 years addresses this gap. Pediatric-type alterations were found in 31% of AYA gliomas and conferred superior outcomes compared to adult-type alterations. AYA low-grade gliomas with specific RAS-MAPK alterations exhibited senescence, tended to arise in different locations and were associated with superior outcomes compared to gliomas in children, suggesting different cellular origins. Hemispheric IDH-mutant, BRAF p.V600E and FGFR-altered gliomas were associated with the risk of malignant transformation, having worse outcomes with increased age. These insights into gliomagenesis may provide a rationale for earlier intervention for certain tumors to disrupt the typical behavior, leading to improved outcomes.

Diffuse Midline Glioma (DMG) is a incurable tumor affecting children. Recent genomic investigations have identified a recurrent H3K27M mutation which induces global alterations in histone methylation patterns and DNA methylation. These epigenetic modifications hint at pivotal roles in DMG pathogenesis, yet effective therapeutic strategies remain elusive, with median survival rates stagnant at approximately one year. This shortfall stems from two main factors: 1) Inadequate multiomics studies hindering our understanding of DMG evolution and tumor progression, and 2) Limited comprehension of the tumor microenvironment in DMG. To elucidate DMG’s clonal evolution, we adopted a comprehensive multi-region sampling approach, acquiring 33 specimens from seven patients. Whole-exome and transcriptome sequencing, alongside DNA methylation profiling, were performed. Additionally, we generated one of the most extensive single-cell multiomics datasets (>300,000 cells from 21 additional samples), with a focus on pre- and post-treatment, and dissemination effects in DMG. Our analysis delineated a tumor-promoting microenvironment characterized by hypoxia and pro-inflammatory conditions, nurturing genomic alterations and specialized biological processes such as proliferation and epithelial-mesenchymal transition. Notably, a majority of immune cells exhibited M1-like polarization, bolstering pro-inflammatory programs within the tumor milieu. Subclones within the DMG cohort demonstrated dissemination potential, often exhibiting up-regulation of NOTCH, P53, and WNT beta-catenin signaling pathways. These findings suggest that DMG clones harboring dissemination capabilities outside the pons acquire additional phenotypic features, possibly mediated by epigenetic or transcriptional alterations, contributing to enhanced migratory and aggressive behaviors. Our study unveils the parallel evolution of DMG at genetic, epigenetic, and transcriptional levels, unveiling novel subclonal phenotypes governing tumor behavior. Crucially, we identify critical environmental shifts such as hypoxia and inflammatory changes, coupled with specialized signaling programs, driving dissemination and resistance phenotypes. These insights may pave the way for generating accurate genetically mouse models and targeted therapeutic interventions to combat this challenging malignancy.

Abstract BACKGROUND Infant-type hemispheric gliomas (IHG) are epigenetically distinct pediatric high-grade gliomas characterized by fusions in receptor tyrosine kinase (RTK) genes. METHODS We performed a methodical literature search, including 30 publications (22 case reports), to identify patients who met the diagnostic criteria of IHG based on the 2021 WHO Classification of CNS Tumors. Individual patient data were obtained from published literature and/or via the authors of the publications. Survival analysis was conducted using the Kaplan-Meier method, and multivariate analysis was performed to investigate the effect of clinical and molecular variables on outcomes. RESULTS Hundred-fifty-five previously reported and one unpublished IHG were identified: 131 (84%) had fusions in RTK genes, of which ALK was most prevalent (62/131), followed by NTRK1/2/3 (30/131), ROS1 (30/131), and MET (9/131). Twenty-five patients, with either no identified RTK fusion (6/156) or not assessable fusion (19/156), had methylation scores ≥ 0.9 for IHG (using the Molecular Neuropathology brain tumor classifier versions ≥ 11b4). Surgery followed by adjuvant chemotherapy in 69% (67/97) was the most common primary treatment used in our cohort. The 3-year EFS and OS were 55% (95%CI: 45-67) and 81 % (95%CI: 73-89). 41 patients with relapsed or progressive tumors received various second-line treatments including surgery, chemotherapy, radiotherapy, and targeted therapy. Based on multivariate analysis, complete resection resulted in better EFS (p = 0.05) and OS (p = 0.009), and the presence and type of RTK gene fusion were not associated with clinical outcomes. CONCLUSION Our results show that despite favorable OS, patients with IHG often show early progression, indicating that the primary optimal treatment for IHG is yet to be established. Our analysis further indicates that achieving a safe, complete resection may play an important role in treating these patients. A comprehensive analysis of the salvage regimen is required to understand their role in OS.

Abstract BACKGROUND Gliomas are a heterogenous and common cancer in children, adolescents and young adults (CAYA, ages 0-39 years). Little is known about the biologic and clinical implications of gliomas in AYA limiting our ability to appropriately manage these patients. METHODS We compiled a population-based cohort of patients with glioma aged 0-39 years diagnosed between 2000-2020, performed molecular characterization of the tumors and collected clinical data including therapy and long-term outcome. RESULTS A total of 1456 patients, including 873 AYA patients were included. A pathogenic molecular alteration was found in 98% of AYA samples available. Strikingly, pediatric-type mutations were found in 31% of AYA glioma of which 37% were BRAF V600E and 23% FGFR alterations. Important differences were observed between gliomas in children versus AYAs. First, hemispheric tumors were enriched in AYAs compared to midline tumors in children, especially for RAS/MAPK alterations. Second, increased incidence of high grade tumors in AYA compared to children were observed for BRAF V600E and FGFR mutations (p<0.0001). In contrast, if these alterations were identified in AYA and the tumor was low grade, outcome was improved for BRAF V600E and FGFR mutant tumors in AYAs compared to pediatrics (for BRAF V600E 5 year PFS 55.6% <10 years, 78.1% for 10-20 years and 87.1% for 10-20 years of age, p=0.0002). Third, a specific time window for transformation was observed for each alteration (BRAF, FGFR, IDH). This correlated with different methylation profiles and transcriptional patterns between early midline and late hemispheric tumors. Increased senescence signatures were observed in older patients with low grade RAS/MAPK driven tumors with superior outcome. CONCLUSIONS Different cell of origin and secondary mutations shape tumor behavior and lead to either transformation or senescence during gliomagenesis in CAYA. These can affect early interventions and tailored approaches for gliomas by age and molecular alteration.

With the success of immunotherapy in cancer, understanding the tumor immune microenvironment (TIME) has become increasingly important; however in pediatric brain tumors this remains poorly characterized. Accordingly, we developed a clinical immune-oncology gene expression assay and used it to profile a diverse range of 1382 samples with detailed clinical and molecular annotation. In low-grade gliomas we identify distinct patterns of immune activation with prognostic significance in BRAF V600E-mutant tumors. In high-grade gliomas, we observe immune activation and T-cell infiltrates in tumors that have historically been considered immune cold, as well as genomic correlates of inflammation levels. In mismatch repair deficient high-grade gliomas, we find that high tumor inflammation signature is a significant predictor of response to immune checkpoint inhibition, and demonstrate the potential for multimodal biomarkers to improve treatment stratification. Importantly, while overall patterns of immune activation are observed for histologically and genetically defined tumor types, there is significant variability within each entity, indicating that the TIME must be evaluated as an independent feature from diagnosis. In sum, in addition to the histology and molecular profile, this work underscores the importance of reporting on the TIME as an essential axis of cancer diagnosis in the era of personalized medicine.

Accurate diagnosis and risk stratification of hematological malignancies require disease-specific laboratory testing procedures involving the use of hematopathology, flow cytometry, molecular and cytogenetic testing. While individual laboratories develop unique workflows to accommodate volume, clinical needs and staffing, cytogenetic laboratories generally require a multitude of targeted and genome-wide tests that detect clinically relevant aberrations in hematologic malignancies. Specifically, the frequent use of multiple FISH panels coupled with concurrent chromosome analysis, can be both labor, and resource intensive.. Optical Genome Mapping (OGM) is a comprehensive cytogenetic solution for detecting structural variants with high resolution and increased accuracy for hematological malignancy subtypes at the DNA level without need of any cell culture regimens. A new software tool for analysis of OGM data called VIA (for Variant Intelligence Applications), provides an integrative analysis, interpretation and reporting solution for OGM and other datatypes. In this pilot study, we performed retrospective review of 56 datasets, representing 10 unique myeloid cases to assess multi-user (technologist and laboratory director) analyses and classification. Interpretation and reporting of OGM results were 100% concordant between reviewers for four cases with negative results by standard of care (SOC) testing. For the other six cases, five pathognomonic gene fusions identified by SOC assays were unanimously reported as Tier 1A variants. relevance not found by SOC methods in five of the six positive cases. Leveraging automatic pre-classification of variants and custom decision tree, the VIA software enabled to complete analysis with a mean technologist review time (variant analysis and initial tier determination) of 30.7 minutes. The analysis, interpretation, and reporting workflow described in this pilot study provides a framework for standardized and streamlined reporting of clinically significant variant in myeloid malignancies using VIA.### Competing Interest StatementTS is employed by Bionano Labs, a wholly owned subsidiary of Bionano Genomics RK has received honoraria, and/or travel funding, and/or research support from Illumina, Cepheid, ALDA, OCDdx, Roche, Agena, Bionano, PGDx (LabCorp), Novartis, AbbVie, AstraZeneca and Lilly. ### Funding StatementThis study was funded in part by Bionano Genomics, inc. ### Author DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesThe details of the IRB/oversight body that provided approval or exemption for the research described are given below:IRB and consent IRB-20212956 Bionano Genomics Inc., San Diego, CA, USA IRB 00007527 University of Rochester Medical Center Office for Human Subject Protection IRB A #00000150 (HAC IRB # 611298) Medical College of Georgia, Augusta University, Augusta, GA, USA I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).YesI have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable.YesData will be made available upon reasonable request and in accordance with IRB protocols.

PURPOSE:Molecular characterization is key to optimally diagnose and manage cancer. The complexity and cost of routine genomic analysis have unfortunately limited its use and denied many patients access to precision medicine. A possible solution is to rationalize use-creating a tiered approach to testing which uses inexpensive techniques for most patients and limits expensive testing to patients with the highest needs. Here, we tested the utility of this approach to molecularly characterize pediatric glioma in a cost- and time-sensitive manner. METHODS:We used a tiered testing pipeline of immunohistochemistry (IHC), customized fusion panels or fluorescence in situ hybridization (FISH), and targeted RNA sequencing in pediatric gliomas. Two distinct diagnostic algorithms were used for low- and high-grade gliomas (LGGs and HGGs). The percentage of driver alterations identified, associated testing costs, and turnaround time (TAT) are reported. RESULTS:The tiered approach successfully characterized 96% (95 of 99) of gliomas. For 82 LGGs, IHC, targeted fusion panel or FISH, and targeted RNA sequencing solved 35% (29 of 82), 29% (24 of 82), and 30% (25 of 82) of cases, respectively. A total of 64% (53 of 82) of samples were characterized without targeted RNA sequencing. Of 17 HGG samples, 13 were characterized by IHC and four were characterized by targeted RNA sequencing. The average cost per sample was more affordable when using the tiered approach as compared with up-front targeted RNA sequencing in LGG ($405 US dollars [USD] v $745 USD) and HGGs ($282 USD v $745 USD). The average TAT per sample was also shorter using the tiered approach (10 days for LGG, 5 days for HGG v 14 days for targeted RNA sequencing). CONCLUSION:Our tiered approach molecularly characterized 96% of samples in a cost- and time-sensitive manner. Such an approach may be feasible in neuro-oncology centers worldwide, particularly in resource-limited settings.

High-grade diffuse glioma (HGG) is the leading cause of brain tumour death. While the genetic drivers of HGG have been well described, targeting these has thus far had little impact on survival suggesting other mechanisms are at play. Here we interrogate the alternative splicing landscape of pediatric and adult HGG through multi-omic analyses, uncovering an increased splicing burden compared with normal brain. The rate of recurrent alternative splicing in cancer drivers exceeds their mutation rate, a pattern that is recapitulated in pan-cancer analyses, and is associated with worse prognosis in HGG. We investigate potential oncogenicity by interrogating cancer pathways affected by alternative splicing in HGG; spliced cancer drivers include members of the RAS/MAPK pathway. RAS suppressor neurofibromin 1 is differentially spliced to a less active isoform in >80% of HGG downstream from REST upregulation, activating the RAS/MAPK pathway and reducing glioblastoma patient survival. Overall, our results identify non-mutagenic mechanisms by which cancers activate oncogenic pathways which need to accounted for in personalized medicine approaches.

Abstract Immunotherapy, predominantly through immune checkpoint inhibition (ICI), has had incredible success in treating some metastatic cancers, however, outside of rare cases of mismatch repair deficient (MMRD) gliomas, brain tumors have not had consistent responses to ICI. This can be attributed to a variety of factors including a low tumor mutation burden, lack of T cell infiltrates, and the CNS immune privilege. There are numerous strategies to target the tumor immune microenvironment (TIME) beyond ICI, include CAR-T cells, tumor vaccines, and myeloid cell modulation. The investigation of these depends critically on detailed characterization of the cell populations and interactions in the CNS TIME. We developed a 103 gene NanoString immune-oncology gene expression panel that includes markers reflecting selected cell types, therapeutic targets, and cellular pathways, as well as the 18-gene Tumor Inflammation Signature, a well validate biomarker for ICI response. We have used this to characterize over 500 brain tumors, including a diverse set of 227 pediatric low-grade gliomas (LGG), 86 MMRD gliomas, 47 diffuse intrinsic pontine gliomas (DIPG), 26 ependymomas, 36 medulloblastomas, 70 adult gliomas, and 35 non-tumor brain samples. Our results demonstrate a broad range of immunologic states, including within groups of tumors with the same genetic driver alteration. In pediatric LGG with BRAF V600E, there was clear histologic correlation with immune status, as glioneuronal tumors had substantial upregulation of T cell markers and regulatory genes, while diffuse astrocytomas had a near normal immune profile. In DIPG there was strong upregulation of macrophage markers, contradicting prior reports that have characterized these tumors as immunologically neutral. In a set of MMRD gliomas treated with ICI we identified several differentially expressed genes correlating with therapeutic response, including CCL4, CXCL9, and HGPD. In sum, this provides a characterization of diverse immune activation states across pediatric gliomas and other brain tumors.

Diffuse intrinsic pontine glioma (DIPG) is an infiltrative incurable tumor affecting children. DIPG tumors often harbor a recurrent H3K27M mutation which leads to a global loss of H3K27me2/3 and overall DNA hypomethylation, suggesting an important role of the epigenome, and consequent transcriptome in DIPG pathogenesis. To thoroughly characterize the clonal evolution of DIPG, we collected 33 samples from 7 DIPG patients using a multi-region sampling strategy and generated whole-exome and transcriptome sequencing, and DNA methylation profiling data. Using our novel bioinformatics approach, 28 distinct tumor sub-clones were identified and characterized in our cohort of DIPG patients whilst simultaneously interrogating the tumor’s ability to migrate and disseminate. When present, initiating tumor clone (Clone 1) exclusively contained H3K27M with significant DNA methylation changes whereas the divergent clones that arise later in DIPG evolutionary trees were typically driven by the copy number aberrations. Further characterization of DIPG sub-clones identified unique gene expression profiles (i.e. cell migration and angiogenesis programs) that support and enable DIPG dissemination. In this study, we uncovered how DIPG evolves at the genetic, epigenetic, and transcriptional levels in parallel and in doing so, reveal novel evolutionary phenotypes at the sub-clonal level related to the tumor’s behavior. We are further validating these results in single-cell RNA sequencing experiments and gaining further insights into the underlying molecular mechanisms responsible for invasive and aggressive DIPG phenotypes.