Floris P. Barthel

Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma

Therapy development for adult diffuse glioma is hindered by incomplete knowledge of somatic glioma driving alterations and suboptimal disease classification. We defined the complete set of genes associated with 1,122 diffuse grade II-III-IV gliomas from The Cancer Genome Atlas and used molecular profiles to improve disease classification, identify molecular correlations, and provide insights into the progression from low- to high-grade disease. Whole-genome sequencing data analysis determined that ATRX but not TERT promoter mutations are associated with increased telomere length. Recent advances in glioma classification based on IDH mutation and 1p/19q co-deletion status were recapitulated through analysis of DNA methylation profiles, which identified clinically relevant molecular subsets. A subtype of IDH mutant glioma was associated with DNA demethylation and poor outcome; a group of IDH-wild-type diffuse glioma showed molecular similarity to pilocytic astrocytoma and relatively favorable survival. Understanding of cohesive disease groups may aid improved clinical outcomes.

Systematic analysis of telomere length and somatic alterations in 31 cancer types

Cancer cells survive cellular crisis through telomere maintenance mechanisms. We report telomere lengths in 18,430 samples, including tumors and non-neoplastic samples, across 31 cancer types. Telomeres were shorter in tumors than in normal tissues and longer in sarcomas and gliomas than in other cancers. Among 6,835 cancers, 73% expressed telomerase reverse transcriptase (TERT), which was associated with TERT point mutations, rearrangements, DNA amplifications and transcript fusions and predictive of telomerase activity. TERT promoter methylation provided an additional deregulatory TERT expression mechanism. Five percent of cases, characterized by undetectable TERT expression and alterations in ATRX or DAXX, demonstrated elongated telomeres and increased telomeric repeat–containing RNA (TERRA). The remaining 22% of tumors neither expressed TERT nor harbored alterations in ATRX or DAXX. In this group, telomere length positively correlated with TP53 and RB1 mutations. Our analysis integrates TERT abnormalities, telomerase activity and genomic alterations with telomere length in cancer.

TumorFusions: An integrative resource for cancer-associated transcript fusions

Abstract Gene fusion represents a class of molecular aberrations in cancer and has been exploited for therapeutic purposes. In this paper we describe TumorFusions, a data portal that catalogues 20 731 gene fusions detected in 9966 well characterized cancer samples and 648 normal specimens from The Cancer Genome Atlas (TCGA). The portal spans 33 cancer types in TCGA. Fusion transcripts were identified via a uniform pipeline, including filtering against a list of 3838 transcript fusions detected in a panel of 648 non-neoplastic samples. Fusions were mapped to somatic DNA rearrangements identified using whole genome sequencing data from 561 cancer samples as a means of validation. We observed that 65% of transcript fusions were associated with a chromosomal alteration, which is annotated in the portal. Other features of the portal include links to SNP array-based copy number levels and mutational patterns, exon and transcript level expressions of the partner genes, and a network-based centrality score for prioritizing functional fusions. Our portal aims to be a broadly applicable and user friendly resource for cancer gene annotation and is publicly available at http://www.tumorfusions.org.

Multigene signature for predicting prognosis of patients with 1p19q co-deletion diffuse glioma

Background Co-deletion of 1p and 19q marks a diffuse glioma subtype associated with relatively favorable overall survival; however, heterogeneous clinical outcomes are observed within this category. Methods We assembled gene expression profiles and sample annotation of 374 glioma patients carrying the 1p/19q co-deletion. We predicted 1p/19q status using gene expression when annotation was missing. A first cohort was randomly split into training (n = 170) and a validation dataset (n = 163). A second validation set consisted of 41 expression profiles. An elastic-net penalized Cox proportional hazards model was applied to build a classifier model through cross-validation within the training dataset. Results The selected 35-gene signature was used to identify high-risk and low-risk groups in the validation set, which showed significantly different overall survival (P = .00058, log-rank test). For time-to-death events, the high-risk group predicted by the gene signature yielded a hazard ratio of 1.78 (95% confidence interval, 1.02-3.11). The signature was also significantly associated with clinical outcome in the The Cancer Genome Atlas (CGA) IDH-mutant 1p/19q wild-type and IDH-wild-type glioma cohorts. Pathway analysis suggested that high risk was associated with increased acetylation activity and inflammatory response. Tumor purity was found to be significantly decreased in high-risk IDH-mutant with 1p/19q co-deletion gliomas and IDH-wild-type glioblastomas but not in IDH-wild-type lower grade or IDH-mutant, non-co-deleted gliomas. Conclusion We identified a 35-gene signature that identifies high-risk and low-risk categories of 1p/19q positive glioma patients. We have demonstrated heterogeneity amongst a relatively new glioma subtype and provided a stepping stone towards risk stratification.

Erratum: Tumor Evolution of Glioma-Intrinsic Gene Expression Subtypes Associates with Immunological Changes in the Microenvironment (Cancer Cell (2017) 32(1) (42–56.e6)(S1535610817302532)(10.1016/j.ccell.2017.06.003))

Department of Genomic Medicine, Department of Radiation Oncology, Department of 8 Bioinformatics and Computational Biology, Department of Cancer Systems Imaging, 9 Department of Pathology, Department of Cancer Biology, Department of Neurosurgery, The 10 University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; University of 11 Texas-Houston Graduate School in Biomedical Sciences, Houston, TX 77030, USA; Cancer 12 Cell Biology Programme, Seve Ballesteros Foundation Brain Tumor Group, Centro Nacional de 13 Investigaciones Oncológicas, CNIO, 28029 Madrid, Spain; Departments of Neurology and 14 Neurosurgery, Henry Ford Hospital, Detroit, MI 48202, USA; Oncology Graduate School 15 Amsterdam, VU University Medical Center, 1081 HV Amsterdam, The Netherlands; Institute 16 for Refractory Cancer Research, Samsung Medical Center, Seoul 06351, Korea; Department 17 of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and 18 Technology, Sungkyunkwan University, Seoul 06351, Korea; Department of Neurosurgery 19 Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 135-710, Korea. 20 21 * These authors contributed equally 22 †Co-senior authors 23 24 Correspondence: rverhaak@mdanderson.org 25 26

The Tandem Duplicator Phenotype Is a Prevalent Genome-Wide Cancer Configuration Driven by Distinct Gene Mutations.

SUMMARY The tandem duplicator phenotype (TDP) is a genome-wide instability configuration primarily observed in breast, ovarian, and endometrial carcinomas. Here, we stratify TDP tumors by classifying their tandem duplications (TDs) into three span intervals, with modal values of 11 kb, 231 kb, and 1.7 Mb, respectively. TDPs with ~11 kb TDs feature loss of TP53 and BRCA1. TDPs with ~231 kb and ~1.7 Mb TDs associate with CCNE1 pathway activation and CDK12 disruptions, respectively. We demonstrate that p53 and BRCA1 conjoint abrogation drives TDP induction by generating short-span TDP mammary tumors in genetically modified mice lacking them. Lastly, we show how TDs in TDP tumors disrupt heterogeneous combinations of tumor suppressors and chromatin topologically associating domains while duplicating oncogenes and super-enhancers.

TumorFusions: an integrative resource for reporting cancer-associated transcript fusions in 33 tumor types

Fusion genes, particularly those involving kinases, have been demonstrated as drivers and are frequent therapeutic targets in cancer1. Here, we describe our results on detecting transcript fusions across 33 cancer types from The Cancer Genome Atlas (TCGA), totaling 9,966 cancer samples and 648 normal samples2. Preprocessing, including read alignment to both genome and transcriptome, and fusion detection were carried out using a uniform pipeline3. To validate the resultant fusions, we also called somatic structural variations for 561 cancers from whole genome sequencing data. A summary of the data used in this study is provided in Table S1. Our results can be accessed per our portal at http://www.tumorfusions.org.

PO-390 Image-guided stereotactic molecular profiling of samples taken in- and outside conventional tumour boundaries highlight extensive infiltration of tumour cells in diffuse gliomas

Introduction Diffuse gliomas are highly infiltrative tumours of the central nervous system that lack effective treatment options and suffer from poor survival. We and others have used DNA methylation and gene expression profiling to stratify these tumours into clinically relevant subtypes. Nevertheless, diffuse gliomas are notoriously heterogeneous and a single biopsy is unlikely to reflect all tumour cell populations. Advanced sampling schemes guided by imaging are needed for accurate delineation of heterogeneity. Material and methods We obtained 74 stereotactic image-guided biopsies in eight patients with glioma prior to craniotomy in addition to 102 multi-sector glioma samples from 25 patients from outside sources. Patients underwent extensive imaging including standard magnetic resonance imaging and various advanced modalities. For each patient, multiple biopsies were taken from the tumour core, tumour margin and outside of visible imaging abnormalities and each sample was histologically assessed by two board-certified pathologists. We performed methylation profiling on all samples. We used supervised machine learning to determine methylation subtype composition and predict transcriptional subtypes in each sample. Genome wide DNA copy number was inferred. Results and discussions Principal component analysis of DNA methylation separated samples based on IDH status and tumour cell content. Tumour signal could be detected in samples far outside tumour margins on standard MRI, despite demonstrating lower tumour purity and inconclusive tumour subtypes. Samples taken from inside imaging abnormalities demonstrated concordant methylation subtypes, suggesting that this classifier is reliable and not subject to heterogeneity due to microenvironment cell populations as often the case with gene expression subtyping. Despite uniformity in classification, IDH mutant tumours demonstrated a higher degree of epigenetic heterogeneity compared to wild-type tumours, reflecting hypermethylation established by IDH oncometabolites. Although still imperfect, advanced imaging substantially improved tumour delineation. While samples from inside imaging abnormalities are optimal for diagnostic use, tumour cells infiltrate well beyond these boundaries and treatment of these regions should be considered when safe and feasible. Conclusion These data show methylation profiling is stable across multiple biopsies and could serve as a powerful diagnostic biomarker. Moreover, advanced imaging can more accurately delineate tumour margins and could help direct treatment.

Abstract 3468: Comprehensive analysis of telomere length and telomere maintenance mechanisms across 31 human cancer types

Telomeres cap chromosome ends and prevent chromosomal fusions. In the majority of somatic cells telomere shortens with each cell division. Cancer cells, on the other hand, maintain telomere length (TL) through reactivation of telomerase or alternative lengthening of telomere (ALT). Though closely related to cancer hallmarks such as chromosomal instability, telomere length has not been systematically analyzed in cancer. We used DNA sequencing to infer TL in 18,430 samples across 31 cancer types. Tumor TL was shorter compared to normal TL but tended to be longer in testicular germ cell tumors, sarcomas and gliomas. TL in non-neoplastic leukocyte and solid tissue samples was negatively correlated with patient age and varied between lineages, with kidney samples showing the longest TL and leukocytes the shortest. Amongst tumors, 73% expressed telomerase reverse transcriptase (TERT), which was associated with mutations of the TERT promoter (23%), focal amplifications (6%), gene fusions (1%) and structural variants of the promoter (4%) and gene body (3%). Isoform analysis revealed that the full-length TERT transcript was dominantly expressed compared to the enzymatically inactive minus beta variant in all cancer types. TERT expression was positively associated with predicted telomerase activity, inferred from comparison of known ALT and non-ALT tumor samples. Distal breakpoint positions involved in TERT promoter structural variants demonstrated increased levels of H3K27ac and H3K4me1, suggesting displaced enhancer elements. We additionally detected hypermethylation of the TERT promoter in 69%, and found an unexpected association with TERT expression. Combined, 95% of TERT expressing tumors was found positive for at least one potential genomic or epigenetic regulatory event. Six percent of tumors did not express TERT and harbored somatic mutations, deletions, gene fusions or structural variants in ATRX or DAXX, both of which have been shown to be tightly associated with ALT. These tumors demonstrated decreased of ATRX expression in combination with significantly longer TL and expression of telomeric repeat containing RNA (TERRA). Interestingly, 21% of the cohort did not express TERT and was ATRX wild-type. In this double wild-type group, unsupervised analysis identified positive correlations between telomere length, TP53 and RB1 alterations. Predicted telomerase activity in the double wild type and ATRX or DAXX altered groups was significantly lower compared to TERT expressing tumors. Gene expression was found to be TL dependent, with genes nearby telomeres showing a negative correlation (increased expression with shorter TL) whereas genes far away from telomeres showed a positive correlation and (increased expression with longer TL). Our analysis provides insights into the various modalities associated with TERT expression and provides a landscape of determinants of telomere length in cancer. Citation Format: Floris P. Barthel, Siyuan Zheng, Roel G. Verhaak. Comprehensive analysis of telomere length and telomere maintenance mechanisms across 31 human cancer types [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3468. doi:10.1158/1538-7445.AM2017-3468