Barbara C. Worst

Selective repression of MEF2 activity by PKA-dependent proteolysis of HDAC4

PKA and CaM kinase II both target the histone deacetylase HDAC4 such that the former antagonizes MEF2 activity and the latter promotes it.

Active medulloblastoma enhancers reveal subgroup-specific cellular origins

Medulloblastoma is a highly malignant paediatric brain tumour, often inflicting devastating consequences on the developing child. Genomic studies have revealed four distinct molecular subgroups with divergent biology and clinical behaviour. An understanding of the regulatory circuitry governing the transcriptional landscapes of medulloblastoma subgroups, and how this relates to their respective developmental origins, is lacking. Here, using H3K27ac and BRD4 chromatin immunoprecipitation followed by sequencing (ChIP-seq) coupled with tissue-matched DNA methylation and transcriptome data, we describe the active cis-regulatory landscape across 28 primary medulloblastoma specimens. Analysis of differentially regulated enhancers and super-enhancers reinforced inter-subgroup heterogeneity and revealed novel, clinically relevant insights into medulloblastoma biology. Computational reconstruction of core regulatory circuitry identified a master set of transcription factors, validated by ChIP-seq, that is responsible for subgroup divergence, and implicates candidate cells of origin for Group 4. Our integrated analysis of enhancer elements in a large series of primary tumour samples reveals insights into cis-regulatory architecture, unrecognized dependencies, and cellular origins.

The whole-genome landscape of medulloblastoma subtypes

Current therapies for medulloblastoma, a highly malignant childhood brain tumour, impose debilitating effects on the developing child, and highlight the need for molecularly targeted treatments with reduced toxicity. Previous studies have been unable to identify the full spectrum of driver genes and molecular processes that operate in medulloblastoma subgroups. Here we analyse the somatic landscape across 491 sequenced medulloblastoma samples and the molecular heterogeneity among 1,256 epigenetically analysed cases, and identify subgroup-specific driver alterations that include previously undiscovered actionable targets. Driver mutations were confidently assigned to most patients belonging to Group 3 and Group 4 medulloblastoma subgroups, greatly enhancing previous knowledge. New molecular subtypes were differentially enriched for specific driver events, including hotspot in-frame insertions that target KBTBD4 and ‘enhancer hijacking’ events that activate PRDM6. Thus, the application of integrative genomics to an extensive cohort of clinical samples derived from a single childhood cancer entity revealed a series of cancer genes and biologically relevant subtype diversity that represent attractive therapeutic targets for the treatment of patients with medulloblastoma.

Recurrent MET fusion genes represent a drug target in pediatric glioblastoma

Pediatric glioblastoma is one of the most common and most deadly brain tumors in childhood. Using an integrative genetic analysis of 53 pediatric glioblastomas and five in vitro model systems, we identified previously unidentified gene fusions involving the MET oncogene in ∼10% of cases. These MET fusions activated mitogen-activated protein kinase (MAPK) signaling and, in cooperation with lesions compromising cell cycle regulation, induced aggressive glial tumors in vivo. MET inhibitors suppressed MET tumor growth in xenograft models. Finally, we treated a pediatric patient bearing a MET-fusion-expressing glioblastoma with the targeted inhibitor crizotinib. This therapy led to substantial tumor shrinkage and associated relief of symptoms, but new treatment-resistant lesions appeared, indicating that combination therapies are likely necessary to achieve a durable clinical response.

Histone deacetylase signaling in cardioprotection

Abstract Cardiovascular disease (CVD) represents a major challenge for health care systems, both in terms of the high mortality associated with it and the huge economic burden of its treatment. Although CVD represents a diverse range of disorders, they share common compensatory changes in the heart at the structural, cellular, and molecular level that, in the long term, can become maladaptive and lead to heart failure. Treatment of adverse cardiac remodeling is therefore an important step in preventing this fatal progression. Although previous efforts have been primarily focused on inhibition of deleterious signaling cascades, the stimulation of endogenous cardioprotective mechanisms offers a potent therapeutic tool. In this review, we discuss class I and class II histone deacetylases, a subset of chromatin-modifying enzymes known to have critical roles in the regulation of cardiac remodeling. In particular, we discuss their molecular modes of action and go on to consider how their inhibition or the stimulation of their intrinsic cardioprotective properties may provide a potential therapeutic route for the clinical treatment of CVD.

Molecular mechanisms and therapeutic targets in pediatric brain tumors

Molecular signatures hint at new opportunities for targeted and selective therapies for children with brain tumors. Gloss Brain tumors are the leading cause of cancer-related deaths in children, and therapies are few and cause devastating long-term side effects. Genomics and epigenomics have revealed that these tumors are molecularly diverse and appear to be driven by mutations in various signaling pathways, which may present new opportunities for a more targeted therapeutic intervention. In this Review, which contains three figures and 224 references, we discuss our current understanding of the molecular basis of the three most common malignant pediatric brain tumors (medulloblastoma, ependymoma, and high-grade glioma) and the prospects for developing safer and more effective therapies. Brain tumors are among the leading causes of cancer-related deaths in children. Although surgery, aggressive radiation, and chemotherapy have improved outcomes, many patients still die of their disease. Moreover, those who survive often suffer devastating long-term side effects from the therapies. A greater understanding of the molecular underpinnings of these diseases will drive the development of new therapeutic approaches. Advances in genomics and epigenomics have provided unprecedented insight into the molecular diversity of these diseases and, in several cases, have revealed key genes and signaling pathways that drive tumor growth. These not only serve as potential therapeutic targets but also have facilitated the creation of animal models that faithfully recapitulate the human disease for preclinical studies. In this Review, we discuss recent progress in understanding the molecular basis of the three most common malignant pediatric brain tumors—medulloblastoma, ependymoma, and high-grade glioma—and the implications for development of safer and more effective therapies.

Genomic profiling of Acute lymphoblastic leukemia in ataxia telangiectasia patients reveals tight link between ATM mutations and chromothripsis

Recent developments in sequencing technologies led to the discovery of a novel form of genomic instability, termed chromothripsis. This catastrophic genomic event, involved in tumorigenesis, is characterized by tens to hundreds of simultaneously acquired locally clustered rearrangements on one chromosome. We hypothesized that leukemias developing in individuals with Ataxia Telangiectasia, who are born with two mutated copies of the ATM gene, an essential guardian of genome stability, would show a higher prevalence of chromothripsis due to the associated defect in DNA double-strand break repair. Using whole-genome sequencing, fluorescence in situ hybridization and RNA sequencing, we characterized the genomic landscape of Acute Lymphoblastic Leukemia (ALL) arising in patients with Ataxia Telangiectasia. We detected a high frequency of chromothriptic events in these tumors, specifically on acrocentric chromosomes, as compared with tumors from individuals with other types of DNA repair syndromes (27 cases total, 10 with Ataxia Telangiectasia). Our data suggest that the genomic landscape of Ataxia Telangiectasia ALL is clearly distinct from that of sporadic ALL. Mechanistically, short telomeres and compromised DNA damage response in cells of Ataxia Telangiectasia patients may be linked with frequent chromothripsis. Furthermore, we show that ATM loss is associated with increased chromothripsis prevalence in additional tumor entities.

Abstract LB-B23: Medulloblastoma regulatory circuitries reveal subgroup-specific cellular origins

Medulloblastoma is a highly malignant paediatric brain tumour, often inflicting devastating consequences on the developing child. Genomic studies have revealed four distinct molecular subgroups with divergent biology and clinical behaviour. An understanding of the regulatory circuitry governing the transcriptional landscapes of medulloblastoma subgroups, and how this relates to their respective developmental origins, is currently lacking. Using H3K27ac and BRD4 ChIP-Seq, coupled with tissue-matched DNA methylation and transcriptome data, we describe the active cis-regulatory landscape across 28 primary medulloblastoma specimens. Analysis of differentially regulated enhancers and super-enhancers reinforced inter-subgroup heterogeneity and revealed novel, clinically relevant insights into medulloblastoma biology. Computational reconstruction of core regulatory circuitry identified a master set of transcription factors responsible for subgroup divergence that validated by ChIP-Seq and implicated candidate cells-of-origin for Group 4. Our integrated analysis of cis-regulatory elements in a large series of primary tumour samples reveals insights into cis-regulatory architecture, unrecognized dependencies, and cellular origins. Citation Format: Charles Y. Lin, Serap Erkek, Yiai Tong, Linlin Yang, Alexander J. Federation, Marc Zapatka, Parthiv Haldipur, Daisuke Kawauchi, Thomas Risch, Hans-Jorg Warnatz, Barbara Worst, Bensheng Ju, Brent A. Orr, Rhamy Zeid, Donald R. Polaski, Maia Segura-Wang, Sebastian M. Waszak, David TW Jones, Marcel Kool, Volker Hovestadt, Ivo Buchhalter, Laura Sieber, Pascal Johann, Stefan Groschel, Marina Ryzhova, Andrey Korshunov, Wenbiao Chen, Victor V. Chizhikov, Kathleen J. Millen, Vyacheslav Amstislavskiy, Hans Lehrach, Marie-Laure Yaspo, Roland Eils, Peter Lichter, Jan O. Korbel, Stefan Pfister, James E. Bradner, Paul A. Northcott. Medulloblastoma regulatory circuitries reveal subgroup-specific cellular origins. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr LB-B23.

Abstract LB-114: The INFORM personalized medicine study for high-risk pediatric cancer patients

Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA Background: Despite substantial progress in treating primary childhood malignancies, relapses from high-risk entities remain a major clinical challenge. The German INFORM study (INdividualized therapy FOr Relapsed Malignancies) is attempting to address this problem using an integrated next-generation sequencing analysis to rapidly generate personalized tumor profiles and identify therapeutic targets. Methods: The INFORM pilot phase assessed the feasibility of integrating rapid molecular profiling into the clinical management of progressive or relapsed high-risk pediatric cancer patients. Whole-exome and low-coverage whole-genome sequencing of tumor and normal DNA was complemented with tumor RNA sequencing (Illumina HiSeq2500, ‘rapid’ mode). This allowed reliable detection of copy-number changes, point mutations, InDels, fusion genes and deregulated gene expression. Identified alterations were prioritized according to tumor biological relevance and potential as an actionable drug target, with results discussed in a weekly molecular tumor board. Results: From Oct 2013 to Jan 2015, 57 patients (average age 13 years) were enrolled from 20 centers throughout Germany. Entities included: high-grade glioma (n = 12), Ewings sarcoma (n = 11), rhabdomyosarcoma/DSRCT (n = 7), medulloblastoma (n = 5), ependymoma (n = 5), osteosarcoma (n = 4), neuroblastoma (n = 4), and others (n = 9). Tumor tissue was sufficient for analysis of 52 cases. Average turnaround time from tissue arrival to molecular results was 25 days. Actionable targets with at least ‘borderline’ evidence (according to a prioritization score harmonized with other pediatric precision oncology programs across Europe) were identified in 28 patients (49%). The most commonly affected targets included: tyrosine kinases (ALK, n = 5; FGFR, n = 4; MET, n = 4; others, n = 4), the PI3K/mTOR-pathway (PIK3CA, n = 4; PIK3R1, n = 1; TSC2, n = 1), the MAPK pathway (BRAF, n = 1; KRAS, n = 1), the SHH-pathway (PTCH1, n = 3) and cell-cycle control (CCND1/2, n = 4; CDK4, n = 4; CDKN2A/B, n = 3). Based on these findings, targeted therapeutics were incorporated into the therapy regime of several patients (as single experimental treatments or in clinical trials), with anecdotal reports of marked responses. For example, one patient with a previously inoperable myofibroblastic sarcoma is now in complete remission more than 12 months after entering an ALK-inhibitor trial on the basis of our identification of an ALK fusion. Conclusion: A nationwide individualized diagnostic and treatment approach for pediatric cancer patients based on rapid next-generation sequencing is feasible. Our pilot phase results show that actionable targets can be identified in roughly half of the patients. The INFORM registry study has now opened ([www.dkfz.de/en/inform/][1]), to collect molecular and clinical data and establish the infrastructure for prospective clinical trials on personalized pediatric oncology. Citation Format: Barbara C. Worst, Cornelis M. van Tilburg, Gnana P. Balasubramanian, Petra Fiesel, David Capper, Miream Boudalil, Stephan Wolf, Sabine Schmidt, Melanie Bewerunge-Hudler, Matthias Schick, Angelika Freitag, Ruth Witt, Lenka Taylor, Andreas von Deimling, Matthias Schlesner, Angelika Eggert, Peter Lichter, David TW Jones, Olaf Witt, Stefan M. Pfister. The INFORM personalized medicine study for high-risk pediatric cancer patients. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-114. doi:10.1158/1538-7445.AM2015-LB-114 [1]: http://www.dkfz.de/en/inform/