Transcriptional profiling of canine osteosarcoma identifies prognostic gene expression signatures with translational value for humans

Canine osteosarcoma is increasingly recognized as an informative model for human osteosarcoma. Here we show in one of the largest clinically annotated canine osteosarcoma transcriptional datasets that two previously reported, as well as de novo gene signatures devised through single sample Gene Set Enrichment Analysis (ssGSEA), have prognostic utility in both human and canine patients. Shared molecular pathway alterations are seen in immune cell signaling and activation including TH1 and TH2 signaling, interferon signaling, and inflammatory responses. Virtual cell sorting to estimate immune cell populations within canine and human tumors showed similar trends, predominantly for macrophages and CD8+ T cells. Immunohistochemical staining verified the increased presence of immune cells in tumors exhibiting immune gene enrichment. Collectively these findings further validate naturally occurring osteosarcoma of the pet dog as a translationally relevant patient model for humans and improve our understanding of the immunologic and genomic landscape of the disease in both species.

Highly Multiplexed Spatially Resolved Proteomic and Transcriptional Profiling of the Glioblastoma Microenvironment Using Archived Formalin-Fixed Paraffin-Embedded Specimens

Glioblastoma is a heterogeneous tumor for which effective treatment options are limited and often insufficient. Few studies have examined the intratumoral transcriptional and proteomic heterogeneity of the glioblastoma microenvironment to characterize the spatial distribution of potential molecular and cellular therapeutic immunooncology targets. We applied an integrated multimodal approach comprised of NanoString GeoMx Digital Spatial Profiling, single-cell RNA-seq (scRNA-seq), and expert neuropathologic assessment to characterize archival formalin-fixed paraffin-embedded glioblastoma specimens. Clustering analysis and spatial cluster maps highlighted the intratumoral heterogeneity of each specimen. Mixed cell deconvolution analysis revealed that neoplastic and vascular cells were the prominent cell types throughout each specimen, with macrophages, oligodendrocyte precursors, neurons, astrocytes, and oligodendrocytes present in lower abundance and illustrated the regional distribution of the respective cellular enrichment scores. The spatial resolution of the actionable immunotherapeutic landscape showed that robust B7H3 gene and protein expression was broadly distributed throughout each specimen and identified STING and VISTA as potential targets. Lastly, we uncovered remarkable variability in VEGFA expression and discovered unanticipated associations between VEGFA, endothelial cell markers, hypoxia, and the expression of immunoregulatory genes, indicative of regionally distinct immunosuppressive microdomains. This work provides an early demonstration of the ability of an integrated panel-based spatial biology approach to characterize and quantify the intrinsic molecular heterogeneity of the glioblastoma microenvironment.

Recent Advances in Pediatric Cancer Research

Over the past few years, the field of pediatric cancer has experienced a shift in momentum, and this has led to new and exciting findings that have relevance beyond pediatric malignancies. Here we present the current status of key aspects of pediatric cancer research. We have focused on genetic and epigenetic drivers of disease, cellular origins of different pediatric cancers, disease models, the tumor microenvironment, and cellular immunotherapies.

Immunohistochemical analysis of glassy cell carcinoma of the cervix reveals robust lymphocyte infiltrate and the expression of targetable inhibitory immune checkpoints

OBJECTIVE

To validate our previous findings of high-level EGFR expression in GCCC using an expanded cohort of specimens and to further examine the molecular and cellular features of this aggressive malignancy to identify potentially actionable therapeutic targets.

METHODS

The SEER database was queried to obtain the epidemiological data regarding the current national survival trends for GCCC. Immunohistochemistry (IHC) was used to examine the expression of EGFR, PD-1, and PD-L1. CiberSort analysis was used to analyze a previously published RNA-sequencing dataset obtained from a single patient diagnosed with GCCC.

RESULTS

In comparison to squamous cell carcinomas and adenocarcinoma/adenosquamous carcinomas, GCCC was observed in younger patients (p < 0.001) and demonstrated inferior survival (p < 0.001). All (100%) of the specimens (8/8) exhibited immunoreactivity when stained for CD3ε (T-cell marker), EGFR, PD-1, and PD-L1 whereas CTLA4 expression was not detected. Analysis of RNA-sequencing data revealed that cetuximab and erlotinib altered the chemokine profile, lymphocyte abundance, and expression of inhibitory immune checkpoints in a single patient when combined with cytotoxic chemotherapy in a single patient.

CONCLUSIONS

The data from this descriptive study suggests that immune checkpoint blockade, whether single agent or in combination, may be a suitable therapeutic option for a disease for which targeted approaches do not currently exist.

Applicability of spatial transcriptional profiling to cancer research

Spatial transcriptional profiling provides gene expression information within the important anatomical context of tissue architecture. This approach is well suited to characterizing solid tumors, which develop within a complex landscape of malignant cells, immune cells, and stroma. In a single assay, spatial transcriptional profiling can interrogate the role of spatial relationships among these cell populations as well as reveal spatial patterns of relevant oncogenic genetic events. The broad utility of this approach is reflected in the array of strategies that have been developed for its implementation as well as in the recent commercial development of several profiling platforms. The flexibility to apply these technologies to both hypothesis-driven and discovery-driven studies allows widespread applicability in research settings. This review discusses available technologies for spatial transcriptional profiling and several applications for their use in cancer research.

Transcriptome analysis of desmoplastic small round cell tumors identifies actionable therapeutic targets: a report from the Children's Oncology Group

To further understand the molecular pathogenesis of desmoplastic small round cell tumor (DSRCT), a fatal malignancy occurring primarily in adolescent/young adult males, we used next-generation RNA sequencing to investigate the gene expression profiles intrinsic to this disease. RNA from DSRCT specimens obtained from the Children's Oncology Group was sequenced using the Illumina HiSeq 2000 system and subjected to bioinformatic analyses. Validation and functional studies included WT1 ChIP-seq, EWS-WT1 knockdown using JN-DSRCT-1 cells and immunohistochemistry. A panel of immune signature genes was also evaluated to identify possible immune therapeutic targets. Twelve of 14 tumor samples demonstrated presence of the diagnostic EWSR1-WT1 translocation and these 12 samples were used for the remainder of the analysis. RNA sequencing confirmed the lack of full-length WT1 in all fusion positive samples as well as the JN-DSRCT-1 cell line. ChIP-seq for WT1 showed significant overlap with genes found to be highly expressed, including IGF2 and FGFR4, which were both highly expressed and targets of the EWS-WT1 fusion protein. In addition, we identified CD200 and CD276 as potentially targetable immune checkpoints whose expression is independent of the EWS-WT1 fusion gene in cultured DSCRT cells. In conclusion, we identified IGF2, FGFR4, CD200, and CD276 as potential therapeutic targets with clinical relevance for patients with DSRCT.

Abstract 208: Transcriptional profiling of the microenvironment in pediatric osteosarcoma

Osteosarcoma (OS) is the most common bone tumor in pediatric and adolescent/young adult patients. Over the past three decades, significant improvements in the survival rates or therapeutic approaches for these patients have not been made, especially in the context of metastatic disease. While immune checkpoint blockade has revolutionized the therapeutic landscape in various adult malignancies, its impact in OS has been largely underwhelming. Currently, it is unknown whether the lack of therapeutic benefit of immune checkpoint inhibition observed in patients with OS is truly due to treatment inefficacy rather than a limited understanding of the tumor microenvironment that supports this aggressive disease. To address this knowledge gap, we have performed targeted gene expression profiling of metastatic and non-metastatic osteosarcoma specimens. Our profiling experiments have revealed that metastatic OS specimens are immunologically “colder” than non-metastatic OS specimens. Our data also demonstrates that T cells are largely excluded from the metastatic specimens and that this exclusion significantly correlates with markers of vascular instability. In a pathological setting, such as that of cancer, VEGF and ANG2 signaling promote vascular instability which limits leukocyte extravasation and subsequent tumor infiltration. Our data suggests that vascular destabilization mediated by VEGF/ANG2 signaling impedes T cell infiltration specifically in metastatic OS and identifies these molecules as potential targets for therapeutic intervention.

Citation Format: Laurie Sorenson, Troy A. McEachron. Transcriptional profiling of the microenvironment in pediatric osteosarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 208.

Targeted transcriptional profiling of the tumor microenvironment reveals lymphocyte exclusion and vascular dysfunction in metastatic osteosarcoma

Osteosarcoma (OS) is the most common bone tumor in pediatric and adolescent/young adult patients yet little is known about the microenvironment that supports this aggressive disease. We have used targeted gene expression profiling and immunohistochemistry to characterize the microenvironment of metastatic and non-metastatic OS specimens from pediatric patients exhibiting poor histologic response to chemotherapy. Our results indicate that metastatic specimens exhibit lymphocyte exclusion as T cells are confined to the periphery of the pulmonary lesions. Furthermore, our data provides evidence of vascular dysfunction in metastatic OS indicated by increased expression of VEGFA, an increased ANGPT2:ANGPT1 gene expression ratio, and decreased expression of SELE, the gene encoding the adhesion molecule E-selectin. Moreover, correlation analyses show an inverse relationship between lymphocyte abundance and markers of vascular dysfunction exclusively in the metastatic specimens. Together, our data shows that the non-metastatic OS specimens demonstrate increased expression of various immunotherapeutic targets in comparison metastatic specimens and identifies vascular dysfunction and lymphocyte exclusion as important processes for therapeutic intervention in metastatic disease.

Profiling targetable immune checkpoints in osteosarcoma

Osteosarcomas are aggressive bone tumors for which therapeutic advances have not improved over several decades. Unlike most pediatric tumors, the osteosarcoma genome is remarkably unstable, characterized by numerous copy number alterations and chromosomal structural aberrations. In this study, we asked if the targetable immune checkpoints CD274 (PD-L1), PDCD1LG2 (PD-L2), CD276 (B7-H3) and IDO1 are impacted by copy number alterations in osteosarcoma. Of the 215 osteosarcoma samples investigated, PD-L1/PD-L2, B7-H3 and IDO1 were independently gained at frequencies of approximately 8-9%, with a cumulative frequency of approximately 24%. RNA sequencing data from two independent cohorts revealed that B7-H3 is the most highly expressed immune checkpoint gene among the four investigated. We also show that IDO1 is preferentially expressed in pediatric solid tumors and that increased protein expression of B7-H3 and IDO1 are significantly associated with inferior survival in patient samples. Using human osteosarcoma cell lines, we demonstrate that IDO1 is gained in MG63 and G292 cells and that the IDO1 inhibitor, epacadostat, inhibits the enzymatic activity of IDO1 in a dose-dependent manner in these cells. Together, these data reveal the genomic and transcriptomic profiles of PD-L1, PD-L2, B7-H3 and IDO1 in osteosarcoma and identifies a potential context for targeted immunotherapeutic intervention in a subset of patients.

Abstract P1-03-13: Immunohistochemistry cannot be used to detect PD-L1/JAK-2 amplification

Introduction: We have previously identified a 9p24.1 amplicon targeting PD-L1/JAK2 (PDJ) in subset (26.7%) of triple negative breast cancer (TNBC) patients. The PDJ amplicon is common in newly diagnosed and chemotherapy treated TNBCs and is associated with a worse prognosis. Our goal in this study was to determine whether immunohistochemistry (IHC) evaluation could identify those patients who harbor the PDJ amplicon.

Methods: TNBC patients from 1999 to 2015 whose tumors were flow-sorted and evaluated by array-based comparative genomic hybridization (CGH) were identified; paraffin slides were obtained for IHC staining evaluation of JAK-2, phosphorylated STAT3 (pSTAT3), and PD-L1. Pathologic analysis consisted of scoring the stains for intensity (0-3+) and the relative percent of tumor cells with positive staining; positive score was defined as 3+ for any percent staining. Statistical analysis of IHC staining was performed to determine association with the PDJ amplicon defined by focal 9p24.1 copy number gain with CGH log2ratios of &gt;1.0 for each sorted TNBC sample.

Results: Eleven of 43 TNBC patients evaluable by IHC had the PDJ amplicon. There was no association between PDJ amplification and IHC staining for JAK-2, pSTAT3, or PD-L1 regardless of staining intensity or percentage tumor cells positive. Table 1 describes PDJ amplicon status and positivity for JAK2, pSTAT3 and PD-L1. Of PDJ-positive samples, 64%, stained positive for JAK2, 27% positive for pSTAT3, but 0% for PD-L1 in tumor cells. However, in the PDJ-negative group, 69% still stained positive for JAK2, 19% positive for pSTAT3, and 9% for PD-L1.

Table 1: PDJ amplicon status and IHC staining JAK2 (3+) (n;%)pSTAT3 (3+) (n;%)PD-L1 (3+) (n;%)PDJ - (n=32)22;69%6;19%3;9%PDJ + (n=11)7;64%3;27%0;0%

JAK2: Most PDJ-positive samples (10/11, 91%) showed some JAK-2 staining. Although one had only 1+ staining at 5% of the cells, the majority (7/11, 64%) had staining of 3+ and &gt;10% of the cells with 2 patients demonstrating 3+ staining of 75% and 90% of the cells. However, those patients without the PDJ amplicon also exhibited JAK2 staining, with 66% (n= 22) of PDJ-negative cases staining strongly for JAK-2 (3+) and &gt; 10% of cells.

pSTAT3: All but one PDJ-positive case demonstrated some staining (1+ or greater) for pSTAT3; the staining intensity and percent positivity were much less than the JAK-2 staining with only 2 cases (18%) having 3+ staining of &gt; 10%. Similar staining was seen in the PDJ-negative cohort; 75% of PDJ-negative patients had some pSTAT3 staining (1+ or greater) and 1 patient (5%) exhibited 3+ staining &gt; 10%.

PD-L1: Finally, the PD-L1 staining was low overall with only 18% of PDJ-positive cases demonstrating some staining for PD-L1. Notably, only one case stained 3+ with 20% positivity while the majority of the samples had a 2+ intensity encompassing 5-50% of the cells.

Conclusions: IHC staining for JAK2, pSTAT3, or PD-L1 was not associated with the presence of the PDJ amplicon. Notably positive IHC staining for JAK2 was observed for both PDJ-positive and PDJ-negative tumor cells, thereby nullifying its application as a screening tool for PDJ amplification. Alternative methods, such as fluorescence in situ hybridization, are needed to identify PDJ-positive patients for further study.

Citation Format: Linnaus ME, Kosiorek H, Ocal IT, Dixon L, Barrett MT, Gawryletz CD, Anderson KS, McCullough AE, McEachron TA, Pockaj BA. Immunohistochemistry cannot be used to detect PD-L1/JAK-2 amplification [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-03-13.

Abstract IA36: Caught in the middle: Viewing adolescent/young adult oncology patients as the medically underserved

Traditionally cancer has been thought to arise in two distinct age groups, pediatrics and adults. In the United States, pediatric patients range in age from newborn up to 21 years old while adult patients are considered to be older than 21. Recently a new patient population has begun to emerge, collectively known as the adolescent-young adult (AYA) population. In the United States, AYA patients span the age range from 15-39 years old. Much is known about a variety of “adult” cancers and our understanding of “pediatric” cancers is steadily growing. Despite these advances, there is very little data regarding AYA-specific cancers. Furthermore, the differences in normal human development and/or maturation that are encompassed within the AYA age range is extremely dynamic thus leading to the hypothesis that the molecular and clinical characteristics of malignancies in AYA patients may be inherently different than those which are observed in patients outside of this age range. This talk will highlight some of the unique challenges faced by this medically underserved population as it pertains to cancer care, treatment, and outcome. This talk will also focus on the importance of the AYA oncology population to cancer research and our biological understanding of different malignancies as it pertains to precision medicine and subsequent therapeutic strategies.

Citation Format: Troy A. McEachron. Caught in the middle: Viewing adolescent/young adult oncology patients as the medically underserved. [abstract]. In: Proceedings of the Ninth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2016 Sep 25-28; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2017;26(2 Suppl):Abstract nr IA36.

Successful Treatment of Genetically Profiled Pediatric Extranodal NK/T-Cell Lymphoma Targeting Oncogenic STAT3 Mutation

Extranodal natural killer (NK)/T-cell lymphoma (ENKTCL) is a distinct type of non-Hodgkin lymphoma predominantly observed in Asian and Latin American adult males. A 12-year-old Hispanic female diagnosed with ENKTCL was enrolled in our genomic profiling research protocol. We identified specific somatic alterations consistent with diagnosis of ENKTCL as well as oncogenic mutations in MAP2K1 and STAT3. To our knowledge, this is the first report of an immunophenotypically confirmed and genetically profiled case of ENKTCL in a female pediatric patient in the United States, including its unique treatment and favorable outcome.

Molecular Genetic Profiling of Adolescent Glassy Cell Carcinoma of the Cervix Reveals Targetable EGFR Amplification with Potential Therapeutic Implications

Glassy cell carcinoma of the cervix (GCCC) is a very rare and aggressive form of cervical cancer. An adolescent female with advanced metastatic disease was enrolled in our genomic profiling research protocol. We identified high-level amplification of epidermal growth factor receptor (EGFR) and Yes-associated protein-1 (YAP1), which led to the addition of EGFR inhibitors to the chemotherapy regimen. Here, we report the first genetically profiled case of GCCC with potential therapeutic implications.

Abstract A42: Precision medicine for pediatric, adolescent, and young adult patients with newly diagnosed or refractory/recurrent cancer: Lessons learned from N=1 studies on rare tumors

Next-generation sequencing has rapidly emerged as the preferred method for unbiased genomic interrogation and is increasingly being integrated into clinical practice. Utilizing this technology, we have developed a precision medicine clinical research protocol focused on pediatric, adolescent, and young adult (AYA) patients with cancer. Our objectives are two-fold: 1) To arrive at genome informed treatment recommendations for individual patients suffering from aggressive and/or worsening disease in a clinically relevant time-frame; 2) To survey the genomic landscape of patients with newly diagnosed and/or recurrent/refractory disease. To accomplish this, we have employed an interdisciplinary workflow including a customized bioinformatic analysis pipeline, contextual biological interpretation of the data, and case reviews during regularly scheduled molecular tumor board meetings. To date we have sequenced over 50 patients. Here, we present the data from those patients diagnosed with rare malignancies. Factors affecting the successful identification of actionable targets and subsequent intervention are varied. Furthermore, we highlight the realistic opportunities, challenges, and insight gained from an ongoing single institution experience.

Citation Format: Troy A. McEachron, Keri B. Zabokrtsky, Aaron Sassoon, Zarko Manoljvic, David W. Craig, John D. Carpten, Leonard S. Sender. Precision medicine for pediatric, adolescent, and young adult patients with newly diagnosed or refractory/recurrent cancer: Lessons learned from N=1 studies on rare tumors. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; 2015 Nov 9-12; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(5 Suppl):Abstract nr A42.

Abstract PR06: Precision medicine for newly diagnosed and refractory/recurrent pediatric cancer patients: Lessons learned from “N=1” studies

Whole genome sequencing has rapidly emerged as the preferred method for unbiased genomic interrogation. Leveraging this technology, we have developed a precision medicine clinical research protocol for pediatric, adolescent, and young adult cancer patients. The primary objective of this study is to arrive at genome informed treatment recommendations for individual patients suffering from aggressive and/or worsening disease in a clinically relevant time frame. The second objective is to survey the genomic landscape of newly diagnosed and recurrent/refractory patients. To accomplish this, we have employed an interdisciplinary workflow including a customized bioinformatic analysis pipeline, contextual biological interpretation of the data, and case reviews during weekly molecular tumor board meetings. Here we report the results of having sequenced over 50 patients diagnosed with both common and rare malignancies. Factors affecting the successful identification of therapeutically actionable targets and subsequent intervention are varied. The most consistent findings are the increased mutation burden in patients who have received chemotherapy and/or radiation prior to tissue collection. Lastly, we highlight the realistic opportunities, challenges, and insight gained from an ongoing single institution experience.

This abstract is also presented as Poster 27.

Citation Format: Troy A. McEachron, Keri B. Zabokrtsky, Aaron F. Sassoon, Sara Nasser, Tyler Izatt, Chad P. Garner, David W. Craig, John D. Carpten, Leonard S. Sender. Precision medicine for newly diagnosed and refractory/recurrent pediatric cancer patients: Lessons learned from “N=1” studies. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Integrating Clinical Genomics and Cancer Therapy; Jun 13-16, 2015; Salt Lake City, UT. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(1_Suppl):Abstract nr PR06.

Abstract POSTER-BIOL-1327: Small cell carcinoma of the ovary, hypercalcemic type displays frequent inactivating germline and somatic mutations in SMARCA4

Introduction: Small cell carcinoma of the ovary of hypercalcemic type (SCCOHT) is arguably the most aggressive ovarian cancer. Most patients are diagnosed at an advanced stage, do not respond to chemotherapy, and die of disease within 1-2 years. It affects children and young women and is reported to occur in families. The cause of the disease is poorly understood. Therefore, we used next generation sequencing technology to identify the genetic basis of the disease.

Method: We performed whole genome, whole exome sequencing or targeted sequencing on tumours and germline samples from 17 SCCOHT patients and on the SCCOHT cell line BIN-67 and SCCOHT-1. Immunohistochemistry (IHC) was performed on formalin-fixed, paraffin-embedded tumors from 23 patients and on a tissue microarray of 485 primary ovarian tumours of other subtypes. BIN-67 cells harbouring biallelic inactivation of SMARCA4 were transduced with a lentivirus expressing wild type SMARCA4.

Result: We identified inactivating germline and somatic mutations in the SWI/SNF chromatin-remodeling gene SMARCA4 in 79% (11/14) of SCCOHT patients, 2 of whom bore germline mutations, and in both cell lines. SMARCA4 protein was lost in 87% (20/23) of SCCOHT tumours but in only 0.4% (2/485) of other primary ovarian tumours. Reintroduction of wild-type SMARCA4 into BIN-67 cells resulted in altered cell morphology and growth arrest.

Conclusions: The mutation spectrum, IHC profile and cell culture phenotype implicate SMARCA4 as a critical tumour suppressor in SCCOHT pathogenesis.

Citation Format: Pilar Ramos, Anthony N. Karnezis, David W. Craig, Aleksandar Sekulic, Megan L. Russell, William P.D. Hendricks, Jason J. Corneveaux, Michael T. Barrett, Karey Shumansky, Yidong Yang, Sohrab P. Shah, Leah M. Prentice, Marco A. Marra, Jeffrey Kiefer, Victoria L. Zismann, Troy A. McEachron, Bodour Salhia, Jaime Prat, Blaise A. Clarke, Joseph G. Pressey, John H. Farley, Stephen P. Anthony, Richard B.S. Roden, Heather E. Cunliffe, David G. Huntsman, Jeffrey M. Trent. Small cell carcinoma of the ovary, hypercalcemic type displays frequent inactivating germline and somatic mutations in SMARCA4 [abstract]. In: Proceedings of the 10th Biennial Ovarian Cancer Research Symposium; Sep 8-9, 2014; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(16 Suppl):Abstract nr POSTER-BIOL-1327.

Histone H3 mutations in pediatric brain tumors

Until recently, mutations in histones had not been described in any human disease. However, genome-wide sequencing of pediatric high-grade gliomas revealed somatic heterozygous mutations in the genes encoding histones H3.1 and H3.3, as well as mutations in the chromatin modifiers ATRX and DAXX. The functional significance and mechanistic details of how these mutations affect the tumors is currently under intensive investigation. The information gained from these studies will shed new light on normal brain development as well as increase our understanding of the tumorigenic processes that drive pediatric high-grade gliomas.

Abstract A15: Variant histone H3 mutations associate with histone modification, DNA methylation, and gene expression changes in pediatric high-grade gliomas

High-grade gliomas (HGG) account for twenty percent of primary brain tumors in children and have a devastating outcome with a 2-year survival rate of less than 30%. While adult HGG arise frequently in the cerebral cortex, pediatric HGG can form in cerebral cortex as well as midline regions including thalamus and brainstem, and are genetically distinct from adult tumors. Brainstem HGGs, referred to as diffuse intrinsic pontine glioma (DIPG), are mostly exclusive to children and confer a dismal less than 10% 2-year survival rate. Recent genome-wide sequence analysis of pediatric DIPG and non-brainstem HGG revealed a predominance of mutually exclusive somatic heterozygous H3F3A or HIST1H3B mutations encoding a K27M variant of histone H3.3 or H3.1, respectively. These mutations were found in 78% of DIPG patients and 22% of non-brainstem pediatric HGG. An additional mutually exclusive somatic heterozygous H3F3A mutation encoding histone H3.3 G34R was identified in 14% of non-brainstem HGG. We established xenografts from human non-brainstem HGGs carrying wild-type H3 or the H3.3 G34R mutant, and DIPGs with H3.3 or H3.1 K27M mutations. H3 K27M mutant xenografts showed a marked reduction in H3K27 trimethylation (H3K27me3), while tumors with wild-type or H3.3 G34R mutations retain H3K27me3 as demonstrated by immunohistochemistry and Western blot analyses. To determine if this was a dominant effect of K27M mutation or a developmental signature of DIPG we transduced primary astrocyte cultures derived from p53-deficient neonatal mouse cortex or brainstem with retrovirus expressing wild-type, K27M, K27A or G34R H3 mutant variants. Low-level expression of exogenous H3.3 K27M compared to endogenous H3 was sufficient to recapitulate prominent H3K27me3 reduction observed in the xenografts. Furthermore, we evaluated correlation between H3 mutation and H3K27me3 status in a large cohort of primary pediatric HGG including DIPG. From this we identified a significant relationship between H3 K27M mutation and H3K27me3 loss in DIPG. However, we also observed rare wild-type H3 DIPG cases exhibiting reduced H3K27me3 indicating a potential alternative mechanism for this methylation state. In addition, we evaluated the association of H3K27me3 and K27M mutations with genome-wide DNA methylation patterns, and gene expression signatures. Together, these results implicate histone H3 K27M and G34R mutations as unique, dominant genetic drivers in distinct subtypes of pediatric HGG. Current efforts focus on delineating the divergent pathological roles of H3 K27M and G34R mutations during DIPG and non-brainstem HGG tumorigenesis.

Citation Format: Jon D. Larson, Troy A. McEachron, Chunxu Qu, Xiaoyan Zhu, Alexander K. Diaz, David W. Ellison, Brent A. Orr, Suzanne J. Baker. Variant histone H3 mutations associate with histone modification, DNA methylation, and gene expression changes in pediatric high-grade gliomas. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr A15.