Single-cell division tracing and transcriptomics reveal cell types and differentiation paths in the regenerating lung

Understanding the molecular and cellular processes involved in lung epithelial regeneration may fuel the development of therapeutic approaches for lung diseases. We combine mouse models allowing diphtheria toxin-mediated damage of specific epithelial cell types and parallel GFP-labeling of functionally dividing cells with single-cell transcriptomics to characterize the regeneration of the distal lung. We uncover cell types, including Krt13+ basal and Krt15+ club cells, detect an intermediate cell state between basal and goblet cells, reveal goblet cells as actively dividing progenitor cells, and provide evidence that adventitial fibroblasts act as supporting cells in epithelial regeneration. We also show that diphtheria toxin-expressing cells can persist in the lung, express specific inflammatory factors, and transcriptionally resemble a previously undescribed population in the lungs of COVID-19 patients. Our study provides a comprehensive single-cell atlas of the distal lung that characterizes early transcriptional and cellular responses to concise epithelial injury, encompassing proliferation, differentiation, and cell-to-cell interactions.

Multi-omic and functional analysis for classification and treatment of sarcomas with FUS-TFCP2 or EWSR1-TFCP2 fusions

Linking clinical multi-omics with mechanistic studies may improve the understanding of rare cancers. We leverage two precision oncology programs to investigate rhabdomyosarcoma with FUS/EWSR1-TFCP2 fusions, an orphan malignancy without effective therapies. All tumors exhibit outlier ALK expression, partly accompanied by intragenic deletions and aberrant splicing resulting in ALK variants that are oncogenic and sensitive to ALK inhibitors. Additionally, recurrent CKDN2A/MTAP co-deletions provide a rationale for PRMT5-targeted therapies. Functional studies show that FUS-TFCP2 blocks myogenic differentiation, induces transcription of ALK and truncated TERT, and inhibits DNA repair. Unlike other fusion-driven sarcomas, TFCP2-rearranged tumors exhibit genomic instability and signs of defective homologous recombination. DNA methylation profiling demonstrates a close relationship with undifferentiated sarcomas. In two patients, sarcoma was preceded by benign lesions carrying FUS-TFCP2, indicating stepwise sarcomagenesis. This study illustrates the potential of linking precision oncology with preclinical research to gain insight into the classification, pathogenesis, and therapeutic vulnerabilities of rare cancers.

Single-cell RNA sequencing of mouse lower respiratory tract epithelial cells: A meta-analysis

The respiratory system is a vital component of our body, essential for both oxygen uptake and immune defense. Knowledge of cellular composition and function in different parts of the respiratory tract provides the basis for a better understanding of the pathological processes involved in various diseases such as chronic respiratory diseases and cancer. Single-cell RNA sequencing (scRNA-seq) is a proficient approach for the identification and transcriptional characterization of cellular phenotypes. Although the mouse is an essential tool for the study of lung development, regeneration, and disease, a scRNA-seq mouse atlas of the lung in which all epithelial cell types are included and annotated systematically is lacking. Here, we established a single-cell transcriptome landscape of the mouse lower respiratory tract by performing a meta-analysis of seven different studies in which mouse lungs and trachea were analyzed by droplet and/or plate-based scRNA-seq technologies. We provide information on the best markers for each epithelial cell type, propose surface markers for the isolation of viable cells, harmonized the annotation of cell types, and compare the mouse single-cell transcriptomes with human scRNA-seq data of the lung.

Abstract 4544: Genomic, transcriptomic, functional, and mechanistic characterization of rhabdomyosarcoma with FUS-TFCP2 or EWSR1-TFCP2 fusions

Rhabdomyosarcoma (RMS) is a soft-tissue sarcoma subtype composed of malignant immature precursor cells with myogenic differentiation defined by aberrant expression of the transcription factors MYOD1 and MYOG. Four subtypes are distinguished, characterized by considerable clinical, histologic, and genetic heterogeneity. RMS with fusions of the transcription factor TFCP2 to either FUS or EWSR1 has only recently been observed, but its classification and pathogenesis are unclear. We studied the clinical course, histopathology, and molecular landscape of 12 cases of this new RMS type and determined the functional properties of tumor-specific genetic alterations. Unusually for gene fusion-driven sarcomas, most tumors had highly rearranged genomes, including chromothripsis, and signs of defective homologous recombination DNA repair. All tumors were characterized by extremely high expression of a truncated TERT variant and the receptor tyrosine kinase ALK. The latter was additionally affected by intragenic deletions (33%), which resulted, together with aberrant splicing events, in the expression of shortened ALK variants (58%). Three ALK variants were oncogenic in immortalized cells in vitro and after xenotransplantation in mice and responded variably to different ALK inhibitors. Additional recurrent alterations included CDKN2A/MTAP co-deletions (67%) and mutations in PAPPA2 (25%) encoding an IGFBP5-specific proteinase. DNA methylation analysis of FUS/EWSR1-TFCP2 RMS, along with 19 other soft-tissue sarcoma types, revealed a close relationship with undifferentiated sarcoma but not with other RMS subtypes, suggesting that FUS/EWSR1-TFCP2 RMS is a distinct sarcoma entity possibly arising from a different cell of origin than other RMS types. Transduction of TFCP2 fusions into immortalized human cells conferred anchorage-independent growth and blocked late myogenic differentiation. Genes significantly induced in these cells were also highly expressed in patient tumors, including ALK, TERT, and two known regulators of skeletal muscle cells, IGFBP5 and PTH1R. ACT-seq demonstrated direct binding of FUS-TFCP2 to the ALK and TERT gene loci outside their regular promoters, which correlated with the expression of alternative transcript variants. Finally, FUS-TFCP2 appeared to induce a defect in DNA double-strand repair in immortalized cells, rendering them sensitive to treatment with cisplatin. Together, our study gives insights into the pathogenesis of a new RMS subtype defined by FUS-TFCP2 or EWSR1-TFCP2 fusions and suggests entry points for therapeutic intervention with DNA-damaging agents, ALK inhibitors, and, in the case of additional CDKN2A/MTAP co-deletion, drugs targeting PRMT5.

Citation Format: Julia Schoepf, Sebastian Uhrig, Christoph E. Heilig, Kwang-Seok Lee, Tatjana Walther, Alexander Carazzato, Anna Maria Dobberkau, Dieter Weichenhan, Christoph Plass, Mark Hartmann, Gaurav Diwan, Zunamys Carrero, Claudia R. Ball, Tobias Hohl, Thomas Kindler, Patricia Rudolph-Hähnel, Anna Nilsson, Ingrid Øra, Roland Imle, Ana Banito, Robert Russell, Barbara C. Jones, Daniel B. Lipka, Hanno Glimm, Daniel Hübschmann, Wolfgang Hartmann, Stefan Fröhling, Claudia Scholl. Genomic, transcriptomic, functional, and mechanistic characterization of rhabdomyosarcoma with FUS-TFCP2 or EWSR1-TFCP2 fusions. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4544.

Abstract A027: Characterization of WEE1 kinase activity in myxoid liposarcoma

Introduction: Myxoid liposarcomas (MLS), malignant soft tissue tumors of adipocyte origin, are genetically characterized by a chromosomal t(12;16)(q13;p11) translocation encoding the chimeric FUS-DDIT3 fusion gene. The resulting fusion protein drives MLS pathogenesis via (dys-)regulation of oncogenic signaling pathways. Since FUS-DDIT3 is not selectively antagonizable, counteracting the oncogenic effects of FUS-DDIT3 fusion protein represents the most promising strategy to target MLS cells. In this study, we identified cell cycle checkpoint kinase WEE1 as FUS-DDIT3 depending effector and investigated the functional requirement for WEE1 kinase activity in MLS pathogenesis. Experimental Procedures: Characterization of WEE1 expression and kinase activity was performed in multiple MLS cell lines, cell lines derived from other liposarcoma subtypes and a mesenchymal stem cell system. Modulation of WEE1 signaling was carried out by means of small-molecule inhibitor Adavosertib (MK-1775) and RNA interference (RNAi)-mediated depletion, and effects were analyzed in immunoblots, cell proliferation assays and caspase 3/7 activity-based apoptosis assays in vitro. Results: Functional genomic RNAi screening uncovered dependence of FUS-DDIT3-expressing mesenchymal stem cells and MLS cell lines on WEE1 kinase activity. Additional expression analysis revealed increased WEE1 protein levels in MLS cell lines. Moreover, pharmacologic inhibition of WEE1 demonstrated significant reduction of MLS cell viability. Accordingly, functional loss of WEE1 by inhibition or RNAi-mediated depletion was found to induce DNA damage accompanied by unscheduled mitotic entry and cell death via activation of the apoptotic program in MLS cells. Conclusions: Our results identify WEE1 kinase activity as functional liability of FUS-DDIT3 expressing MLS cells and provide first evidence that overactive WEE1 signaling represents a promising target for therapeutic intervention in MLS.

Citation Format: Lorena Heinst, Ruth Berthold, Ilka Isfort, Svenja Wosnig, Thomas Kindler, Pierre Åman, Eva Wardelmann, Claudia Scholl, Stefan Fröhling, Wolfgang Hartmann, Marcel Trautmann. Characterization of WEE1 kinase activity in myxoid liposarcoma [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr A027.

Abstract PR004: Fusion protein-driven IGF-IR signals deregulate hippo pathway promoting oncogenic cooperation of YAP1 and FUS-DDIT3

Introduction: Myxoid liposarcoma (MLS) is molecularly characterized by a recurrent chromosomal translocation which generates a chimeric FUS-DDIT3 fusion gene. The FUS-DDIT3 oncoprotein, acting as a transcriptional dysregulator, has been shown to be essential in MLS pathogenesis, among others through deregulation of IGF-IR/PI3K/AKT signaling, but its exact mode of function remains incompletely understood. Recently, a particular reliance on the Hippo pathway effector and transcriptional co-regulator YAP1 was found in MLS; however, the molecular mechanism of FUS-DDIT3-dependent YAP1 activation and its contribution to MLS pathogenesis remain unclear. Experimental Procedures: The expression of IGF-IR and YAP1 was analyzed in a large cohort of MLS specimens by immunohistochemistry. In vitro analyses were performed employing a human mesenchymal stem cell system stably expressing FUS-DDIT3 and human MLS cell lines. RNA interference-based approaches, experiments with small-molecule kinase inhibitors, co-immunoprecipitation, proximity ligation assays, transcriptome sequencing and adipogenic differentiation assays were performed to determine the interplay of FUS-DDIT3, IGF-IR-dependent signals, and YAP1 in MLS cells. Results: Immunohistochemically, a significant subset of MLS samples showed concurrent expression of IGF-IR and nuclear YAP1. In vitro, FUS-DDIT3-driven IGF-IR signaling was found to promote stability and nuclear accumulation of YAP1 via deregulation of the Hippo pathway. Co-immunoprecipitation and proximity ligation assays revealed nuclear co-localization of FUS-DDIT3 and YAP1 in FUS-DDIT3-expressing mesenchymal stem cells and MLS cell lines. Transcriptome sequencing of MLS cells demonstrated that FUS-DDIT3 and YAP1 co-regulate specific oncogenic gene signatures related to proliferation, cell cycle progression, apoptosis, and adipogenesis. In differentiation assays, FUS-DDIT3 and YAP1 were found to cooperate in adipogenic differentiation arrest. Conclusions: Our study provides molecular insights into a complex FUS-DDIT3-driven network involving IGF-IR signals acting on Hippo/YAP1, and uncovers cooperative effects of YAP1 and FUS-DDIT3 in the pathogenesis of MLS.

Citation Format: Ruth Berthold, Ilka Isfort, Cihan Erkut, Lorena Heinst, Inga Grünewald, Eva Wardelmann, Thomas Kindler, Pierre Åman, Thomas G.P. Grünewald, Florencia Cidre-Aranaz, Marcel Trautmann, Stefan Fröhling, Claudia Scholl, Wolfgang Hartmann. Fusion protein-driven IGF-IR signals deregulate hippo pathway promoting oncogenic cooperation of YAP1 and FUS-DDIT3 [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr PR004.

BTBBCL6 dimers as building blocks for reversible drug-induced protein oligomerization

Here, we characterize the BTB domain of the transcription factor BCL6 (BTBBCL6) as a small-molecule-controlled, reversible oligomerization switch, which oligomerizes upon BI-3802 treatment and de-oligomerizes upon addition of BI-3812. We show that the magnitude of oligomerization can be controlled in vitro by BI-3802 concentration and exposure time. In cellular models, exposure to BI-3802/BI-3812 can drive multiple cycles of foci formation consisting of BTBBCL6 fused to EGFP, which are not degraded due to the lack of a degron. We generated an epidermal growth factor receptor (EGFR)-BTBBCL6 fusion. Treatment with BI-3802, as an ON switch, induced EGFR-BTBBCL6 phosphorylation and activation of downstream effectors, which could in part be reversed by the addition of BI-3812, as an OFF switch. Finally, BI-3802-induced oligomerization of the EGFR-BTBBCL6 fusion enhanced proliferation of an EGF-dependent cell line in absence of EGF. These results demonstrate the successful application of small-molecule-induced, reversible oligomerization as a switch for synthetic biology.

Abstract 2003: Oncogenic interplay of FUS-DDIT3 and YAP1 in myxoid liposarcoma

Introduction: Myxoid liposarcoma (MLS) represents the second most common subtype of liposarcoma. MLS is characterized by a chromosomal translocation t(12;16)(q13;p11) encoding a chimeric FUS-DDIT3 fusion gene. The resulting FUS-DDIT3 oncoprotein acts as a transcriptional dysregulator that was recently shown to mediate (i) IGF-IR/PI3K/AKT signaling and (ii) aberrant activation of the Hippo pathway effector YAP1 in MLS. This study was performed to analyze the functional interplay between IGF-IR/PI3K/AKT signals and aberrant YAP1 activity in MLS, aiming at a better functional understanding of MLS and the identification of specific molecular vulnerabilities.

Experimental procedures: Immunohistochemical stainings of IGF-IR, IGF-II and YAP1 were performed in a cohort of MLS specimens (n=45). To study FUS-DDIT3-dependency in vitro, SCP-1 mesenchymal stem cells stably expressing FUS-DDIT3, and MLS cell lines expressing a doxycycline-inducible shRNA against FUS-DDIT3 were employed. Interactions between the IGF-IR/PI3K/AKT and Hippo/YAP1 pathways were investigated using RNAi approaches as well as the small molecule compounds BMS-754807 and BKM120; effects were analyzed by immunoblotting and TEAD luciferase reporter assays. To determine the impact of YAP1 in FUS-DDIT3-mediated oncogenic effects, qPCR analysis and adipogenic differentiation assays were performed.

Results: Immunohistochemical analysis of human MLS tissue specimens demonstrated that expression of IGF-II and IGF-IR is associated with concomitant nuclear expression of YAP1 in a significant subset of MLS. Both, IGF-IR-dependent signals and YAP1 expression were shown to be functionally dependent on FUS-DDIT3. In MLS cell lines, inhibition of the IGF-IR/PI3K/AKT signaling cascade promoted downregulation of YAP1, accompanied by reduced TEAD transcriptional activity. Employing qPCR analyses, YAP1 was shown to co-regulate FUS-DDIT3 transcriptional targets and to be functionally involved in FUS-DDIT3-driven disruption of normal adipocytic differentiation.

Conclusions: Our study provides evidence of a complex regulatory interplay in MLS with FUS-DDIT3-driven IGF-IR/PI3K/AKT signals acting as activators of nuclear YAP1 expression. Conversely, YAP1 contributes to shape FUS-DDIT3 effects on the MLS transcriptional landscape and functionally adds to an immature non-lipogenic phenotype. Our data contribute to the understanding of MLS biology and reveal specific molecular liabilities to be considered in therapeutic approaches of MLS.

Citation Format: Ruth Berthold, Ilka Isfort, Jonas Breuer, Lorena Heinst, Thomas Kindler, Pierre Åman, Inga Grünewald, Eva Wardelmann, Thomas G. Grünewald, Florencia Cidre-Aranaz, Claudia Scholl, Stefan Fröhling, Marcel Trautmann, Wolfgang Hartmann. Oncogenic interplay of FUS-DDIT3 and YAP1 in myxoid liposarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2003.

Accurate and efficient detection of gene fusions from RNA sequencing data

The identification of gene fusions from RNA sequencing data is a routine task in cancer research and precision oncology. However, despite the availability of many computational tools, fusion detection remains challenging. Existing methods suffer from poor prediction accuracy and are computationally demanding. We developed Arriba, a novel fusion detection algorithm with high sensitivity and short runtime. When applied to a large collection of published pancreatic cancer samples (n = 803), Arriba identified a variety of driver fusions, many of which affected druggable proteins, including ALK, BRAF, FGFR2, NRG1, NTRK1, NTRK3, RET, and ROS1. The fusions were significantly associated with KRAS wild-type tumors and involved proteins stimulating the MAPK signaling pathway, suggesting that they substitute for activating mutations in KRAS In addition, we confirmed the transforming potential of two novel fusions, RRBP1-RAF1 and RASGRP1-ATP1A1, in cellular assays. These results show Arriba's utility in both basic cancer research and clinical translation.

The CDK inhibitor CR8 acts as a molecular glue degrader that depletes cyclin K

Molecular glue compounds induce protein-protein interactions that, in the context of a ubiquitin ligase, lead to protein degradation1. Unlike traditional enzyme inhibitors, these molecular glue degraders act substoichiometrically to catalyse the rapid depletion of previously inaccessible targets2. They are clinically effective and highly sought-after, but have thus far only been discovered serendipitously. Here, through systematically mining databases for correlations between the cytotoxicity of 4,518 clinical and preclinical small molecules and the expression levels of E3 ligase components across hundreds of human cancer cell lines3-5, we identify CR8-a cyclin-dependent kinase (CDK) inhibitor6-as a compound that acts as a molecular glue degrader. The CDK-bound form of CR8 has a solvent-exposed pyridyl moiety that induces the formation of a complex between CDK12-cyclin K and the CUL4 adaptor protein DDB1, bypassing the requirement for a substrate receptor and presenting cyclin K for ubiquitination and degradation. Our studies demonstrate that chemical alteration of surface-exposed moieties can confer gain-of-function glue properties to an inhibitor, and we propose this as a broader strategy through which target-binding molecules could be converted into molecular glues.

Requirement for LIM kinases in acute myeloid leukemia

Acute myeloid leukemia (AML) is an aggressive disease for which only few targeted therapies are available. Using high-throughput RNA interference (RNAi) screening in AML cell lines, we identified LIM kinase 1 (LIMK1) as a potential novel target for AML treatment. High LIMK1 expression was significantly correlated with shorter survival of AML patients and coincided with FLT3 mutations, KMT2A rearrangements, and elevated HOX gene expression. RNAi- and CRISPR-Cas9-mediated suppression as well as pharmacologic inhibition of LIMK1 and its close homolog LIMK2 reduced colony formation and decreased proliferation due to slowed cell-cycle progression of KMT2A-rearranged AML cell lines and patient-derived xenograft (PDX) samples. This was accompanied by morphologic changes indicative of myeloid differentiation. Transcriptome analysis showed upregulation of several tumor suppressor genes as well as downregulation of HOXA9 targets and mitosis-associated genes in response to LIMK1 suppression, providing a potential mechanistic basis for the anti-leukemic phenotype. Finally, we observed a reciprocal regulation between LIM kinases (LIMK) and CDK6, a kinase known to be involved in the differentiation block of KMT2A-rearranged AML, and addition of the CDK6 inhibitor palbociclib further enhanced the anti-proliferative effect of LIMK inhibition. Together, these data suggest that LIMK are promising targets for AML therapy.

Abstract B27: A DARPin-based toolbox to understand and treat RAS-addicted cancers

The repeating failure of small molecules as specific inhibitors of KRAS has drawn the attention to macromolecular structures, which can recognize their target with high affinity and specificity. Designed Ankyrin Repeat Proteins (DARPins) are multipurpose alternative affinity reagents that have proved to recognize targets with exceptional specificities and selectivity that often surpass those of antibodies. Due to their additional outstanding ability to act intracellularly within living cells and their recognition of structural rather than linear epitopes, DARPins have enabled a multitude of more advanced projects. In-house selections against GTP- or GDP-loaded KRAS were performed, and several hundred different DARPins could be identified. In subsequent validations, we not only analyzed their affinities, but also focused on the essential features of cross-reactivities, the recognition of various epitopes and their biologic functionalities. A number of candidates directly interfere with the RAS-Raf interaction and SOS-mediated nucleotide exchange by binding to the identical epitope on RAS as proved by crystal structures. One of these lead candidates with an affinity of 10 nM was used to elucidate whether anti-KRAS DARPins can mediate a biologic effect in model systems of human cancers. For this purpose, we chose cell lines categorized as KRAS dependent to generate stable cell lines expressing a highly active anti-KRAS DARPin under an inducible promotor, and it revealed potent antitumor activity, reducing the proliferation, colony formation and anchorage-independent growth. We could furthermore show that the observed effect resulted from reduced signaling of KRAS through its downstream MEK-ERK and PI3K-AKT pathways and the induction of apoptosis. Importantly, this anti-KRAS DARPin was shown to have no effects in the immortalized cell line HEK293T. In addition to traditional knockdown approaches, this model could be used to assess RAS dependency of human cancers. Combined with various suitable intracellular delivery techniques currently under development in our laboratory, the potential of this model will be further investigated for its potential in the treatment of solid tumors in a mouse model. In our broad effort many additional DARPins were identified that recognize different, nonoverlapping epitopes and most likely will interfere with other essential functions, such as the nanoclustering of RAS. This toolbox also allows the development of various biosensors in living cells. This large set of binders has the potential not just to help the community to gain detailed insights into the various functions and of RAS, but also might highlight novel vulnerabilities and innovative ways to finally make these key players druggable.

Citation Format: Jonas N. Kapp, Jonas V. Schaefer, Wouter Verdurmen, Gabriela Nagy, Ralph Degen, Patrick Ernst, Claudia Scholl, Andreas Plückthun. A DARPin-based toolbox to understand and treat RAS-addicted cancers [abstract]. In: Proceedings of the AACR Special Conference on Targeting RAS-Driven Cancers; 2018 Dec 9-12; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(5_Suppl):Abstract nr B27.

Abstract 2723: Defective homologous recombination DNA repair as therapeutic target in advanced chordoma

Chordomas are rare tumors of the axial skeleton and skull base with few therapeutic options and no clinically validated molecular drug targets. The value of comprehensive genomic analyses for guiding medical therapy of patients with advanced-stage chordoma is unknown. We performed whole-exome and genome sequencing of tumor and matched germline control samples from 11 patients with locally advanced or metastatic chordoma within the MASTER program, a prospective clinical sequencing program of the German Cancer Consortium. All patients were pretreated and had progressive disease prior to molecular analysis. Genomic profiling showed that advanced chordomas are frequently characterized by genomic patterns indicative of defective homologous recombination (HR) DNA repair. First, DNA copy number profiles showed high numbers of structural variants greater than 10 million base pairs in size in the majority of cases. Second, all patients harbored somatic aberrations of at least 2 genes known to be involved in HR, and 10/11 cases harbored somatic alterations in 3 or more HR pathway genes. For example, 8 patients showed heterozygous BRCA2 deletions, which were associated with heterozygous deletions of ERCC6 in 6 patients and RAD54L in 7 patients, as well as PTEN alterations (heterozygous deletion, heterozygous mutation and deletion of the wildtype allele or loss of heterozygosity). Other recurrently altered HR genes included ATR, CHEK2, FANCC, FANCD2, FANCG, RAD18, RAD51B, and XRCC3. Third, pathogenic germline alterations were detected in 3 patients. A heterozygous BRCA2 frameshift mutation (p.T3085fs*26; ACMG Class 5), a heterozygous NBN frameshift mutation (p.K219Nfs*16; ACMG Class 5), and a heterozygous CHEK2 missense mutation (p.R145W; ACMG Class 4) were accompanied by somatic deletion of the respective wildtype alleles. Fourth, a mutational signature associated with HR deficiency was significantly enriched in 72.7% of samples and coincided with genomic instability. The high prevalence of an HR deficiency “footprint” in chordoma patients prompted us to explore the clinical efficacy of the poly(ADP-ribose) polymerase(PARP) inhibitor olaparib, which is preferentially toxic to HR-incompetent cells. Olaparib treatment of a patient whose tumor showed a prominent exposure to an HR deficiency-associated mutational signature, a high degree of genomic instability, and 13 heterozygous HR gene alterations halted tumor growth for 10 months. Whole-genome analysis at progression revealed a PARP1 p.T910A mutation predicted to disrupt the autoinhibitory PARP1 helical domain, providing novel insight into the mechanisms of PARP inhibitor resistance. In summary, our study has uncovered a key biological feature of advanced chordoma that represents an immediately actionable therapeutic target and provides a rationale for genomics-guided clinical trials of PARP inhibition in this intractable tumor entity.

Citation Format: Stefan Gröschel, Daniel Hübschmann, Francesco Raimondi, Peter Horak, Gregor Warsow, Martina Fröhlich, Barbara Klink, Laura Gieldon, Barbara Hutter, Kortine Kleinhenz, David Bonekamp, Oliver Marschal, Priya Chudasama, Jagoda Mika, Marie Groth, Sebastian Uhrig, Stephen Krämer, Christoph Heining, Christoph Heilig, Daniela Richter, Eva Reisinger, Katrin Pfütze, Roland Eils, Stephan Wolf, Christof von Kalle, Christian Brandts, Claudia Scholl, Wilko Weichert, Stephan Richter, Sebastian Bauer, Roland Penzel, Evelin Schröck, Albrecht Stenzinger, Richard Schlenk, Benedikt Brors, Robert Russell, Hanno Glimm, Matthias Schlesner, Stefan Fröhling. Defective homologous recombination DNA repair as therapeutic target in advanced chordoma [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 2723.

Abstract 2126: Development of a precision chordoma research program

Chordomas are malignant tumors of the axial skeleton that originate from remnants of the embryonic notochord. With an incidence of one per million per year, chordoma is a rare disease that accounts for 1-4% of all bone tumors and approximately 20% of primary spinal tumors. As first-line treatment, patients undergo surgical resection followed by adjuvant radiotherapy, whereas most chordomas are resistant to conventional cytotoxic drugs and there are no clinically validated molecular drug targets.

To overcome the lack of effective medical treatment and to better understand chordoma biology, we have established a chordoma precision research program. Here, whole-exome or genome and transcriptome sequencing are used to determine mutational landscapes, DNA copy number profiles, and transcriptome changes in chordoma cell lines and patient samples. Additionally, large-scale functional genomic screens and (phospho-)proteomic analyses have been performed in multiple chordoma cell lines to identify new chordoma-specific vulnerabilities. Based on these multilayered datasets, we selected a panel of previously unrecognized candidate chordoma driver genes, which are currently being validated as novel therapeutic targets using genetic and pharmacologic approaches.

In addition to this unbiased approach, we seek to inhibit the embryonic transcription factor brachyury, an established driver of chordomagenesis. Although brachyury represents, in principle, a promising therapeutic target, inhibition of transcription factors remains difficult. To circumvent this challenge, we are developing Designed Ankyrin Repeat Proteins (DARPins) that specifically prevent the binding of brachyury to DNA. These DARPins are not only a valuable tool for studying chordomagenesis, but also represent a new class of molecularly targeted agents that might be used for the treatment of chordoma patients.

In summary, using multi-omics data, functional genetics, and inhibition of an established chordoma driver, we are working towards a better understanding of chordoma biology and the development of new therapeutic approaches. Updated results of the precision chordoma research program will be presented.

Citation Format: Marie Groth, Jana Kress, Matea Hajnic, Joana Marinho, Kevin Mellert, Thomas F. Barth, Peter Möller, Birgit Dreier, Andreas Plückthun, Claudia Scholl, Stefan Fröhling. Development of a precision chordoma research program [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 2126.

Abstract 3437: Requirement for YAP1 signaling in myxoid liposarcoma

Myxoid liposarcomas (MLS) account for 20% of malignant adipocytic tumors and are characterized by a high rate of local recurrence and development of distant metastases in approximately 40% of patients. Most MLS are driven by the FUS-DDIT3 fusion gene encoding an aberrant transcription factor. The mechanisms whereby FUS-DDIT3 mediates sarcomagenesis are incompletely understood, and strategies to selectively target MLS cells remain elusive. In this study, we employed genome-scale RNA interference (RNAi) screening to uncover that human mesenchymal stem cells engineered to express FUS-DDIT3 and MLS cell lines are dependent on YAP1, a transcriptional co-activator and central effector of the Hippo pathway involved in tissue growth and tumorigenesis. Analysis of a large cohort of primary MLS specimens (n=223) revealed that nuclear YAP1 expression was significantly more prevalent in MLS compared to other liposarcoma subtypes. In support of the concept that increased YAP1-mediated transcriptional activity represents an essential feature of MLS development, RNAi-based YAP1 depletion in cultured MLS cells resulted in suppression of cell viability, cell cycle arrest, cellular senescence, and induction of apoptosis accompanied by decreased YAP1 target gene expression, and YAP1-positive primary MLS tumors showed strong expression of YAP1 downstream effectors such as FOXM1 and PLK1. Mechanistically, FUS-DDIT3 promotes YAP1 transcription, nuclear localization, and transcriptional activity and physically associates with YAP1 in the nucleus of MLS cells, pointing to the coordinate establishment of gene expression programs that promote MLS tumorigenesis. Consistent with the hypothesis that a YAP1-directed therapeutic approach could represent a rational strategy to selectively target FUS-DDIT3-expressing MLS cells, pharmacologic inhibition of YAP1 activity with verteporfin suppressed cell viability and YAP1 target gene expression in MLS cell lines, and the growth-inhibitory effects of YAP1 knockdown or verteporfin treatment could be recapitulated in MLS cell line-based xenograft models. Collectively, our data identify dependence on aberrant YAP1 activity as specific liability of FUS-DDIT3-expressing MLS cells, and provide preclinical evidence that YAP1-mediated signal transduction represents a candidate target for therapeutic intervention that warrants further investigation.

Citation Format: Marcel Trautmann, Ya-Yun Cheng, Patrizia Jensen, Ninel Azoitei, Ines Brunner, Jennifer Hüllein, Mikolaj Slabicki, Ilka Isfort, Magdalene Cyra, Eva Wardelmann, Sebastian Huss, Bianca Altvater, Claudia Rossig, Susanne Hafner, Thomas Simmet, Anders Ståhlberg, Pierre Åman, Thorsten Zenz, Undine Lange, Thomas Kindler, Claudia Scholl, Wolfgang Hartmann, Stefan Fröhling. Requirement for YAP1 signaling in myxoid liposarcoma [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 3437.

TelomereHunter - in silico estimation of telomere content and composition from cancer genomes

BACKGROUND

Establishment of telomere maintenance mechanisms is a universal step in tumor development to achieve replicative immortality. These processes leave molecular footprints in cancer genomes in the form of altered telomere content and aberrations in telomere composition. To retrieve these telomere characteristics from high-throughput sequencing data the available computational approaches need to be extended and optimized to fully exploit the information provided by large scale cancer genome data sets.

RESULTS

We here present TelomereHunter, a software for the detailed characterization of telomere maintenance mechanism footprints in the genome. The tool is implemented for the analysis of large cancer genome cohorts and provides a variety of diagnostic diagrams as well as machine-readable output for subsequent analysis. A novel key feature is the extraction of singleton telomere variant repeats, which improves the identification and subclassification of the alternative lengthening of telomeres phenotype. We find that whole genome sequencing-derived telomere content estimates strongly correlate with telomere qPCR measurements (r = 0.94). For the first time, we determine the correlation of in silico telomere content quantification from whole genome sequencing and whole genome bisulfite sequencing data derived from the same tumor sample (r = 0.78). An analogous comparison of whole exome sequencing data and whole genome sequencing data measured slightly lower correlation (r = 0.79). However, this is considerably improved by normalization with matched controls (r = 0.91).

CONCLUSIONS

TelomereHunter provides new functionality for the analysis of the footprints of telomere maintenance mechanisms in cancer genomes. Besides whole genome sequencing, whole exome sequencing and whole genome bisulfite sequencing are suited for in silico telomere content quantification, especially if matched control samples are available. The software runs under a GPL license and is available at https://www.dkfz.de/en/applied-bioinformatics/telomerehunter/telomerehunter.html .

Requirement for YAP1 signaling in myxoid liposarcoma

Myxoid liposarcomas (MLS), malignant tumors of adipocyte origin, are driven by the FUS-DDIT3 fusion gene encoding an aberrant transcription factor. The mechanisms whereby FUS-DDIT3 mediates sarcomagenesis are incompletely understood, and strategies to selectively target MLS cells remain elusive. Here we show, using an unbiased functional genomic approach, that FUS-DDIT3-expressing mesenchymal stem cells and MLS cell lines are dependent on YAP1, a transcriptional co-activator and central effector of the Hippo pathway involved in tissue growth and tumorigenesis, and that increased YAP1 activity is a hallmark of human MLS Mechanistically, FUS-DDIT3 promotes YAP1 expression, nuclear localization, and transcriptional activity and physically associates with YAP1 in the nucleus of MLS cells. Pharmacologic inhibition of YAP1 activity impairs the growth of MLS cells in vitro and in vivo These findings identify overactive YAP1 signaling as unifying feature of MLS development that could represent a novel target for therapeutic intervention.

Exploiting rare driver mutations for precision cancer medicine

Catalyzed by the ability to develop precision therapies targeting the unique genetic changes that drive individual tumors, sequencing patients' tumor genomes is an increasingly common practice in oncology. In most cancer types, however, a limited number of common mutations are accompanied by a plethora of low-frequency variants whose functional consequences and clinical actionability are often unknown. We here illustrate that this 'long tail' of infrequent molecular alterations includes oncogenic drivers of biological significance that can be the genetic basis of extraordinary responses to systemic cancer therapies. Furthermore, we review current strategies to identify, prioritize, and experimentally validate novel long-tail driver mutations, efforts that will likely provide new insights into the clinically actionable genome and improve outcomes for patients.

Author Correction: BCAT1 restricts αKG levels in AML stem cells leading to IDHmut-like DNA hypermethylation

In Extended Data Fig. 1a of this Letter, the flow cytometry plot depicting the surface phenotype of AML sample DD08 was a duplicate of the plot for AML sample DD06. Supplementary Data 4 has been added to the Supplementary Information of the original Letter to clarify the proteome data acquisition and presentation. The original Letter has been corrected online.

Abstract 4336: Integrative genomic and transcriptomic analysis of leiomyosarcoma

Leiomyosarcomas (LMS) are malignant tumors of smooth-muscle origin that occur across age groups. The mechanisms underlying LMS development, including clinically actionable genetic vulnerabilities, are largely unknown, and few therapeutic options exist for LMS patients. To detect somatic mutations, copy number alterations, and structural rearrangements, we performed whole-exome and transcriptome sequencing of 49 and 37 LMS tumors, respectively, and performed integrative analysis. Recurrence analysis identified TP53, RB1, and ATRX as significantly mutated genes and various other cancer-associated genes mutated at low frequency, indicating substantial mutational heterogeneity. Copy number analysis revealed widespread chromosomal gains and losses and highly rearranged genomes in all tumors. Additionally, chromothripsis and whole-genome duplication were detected in 35% and 51% of cases, respectively. Principle component analysis and unsupervised hierarchical clustering of transcriptome data revealed three distinct subgroups of patients. Furthermore, we detected multiple non-recurrent fusion transcripts resulting from chromosomal rearrangements, many of which were predicted to result in loss of TP53 and RB1 function. In-depth analysis of these loci revealed protein-damaging microdeletions, intragenic or distal inversions, and exon skipping events as additional, previously unrecognized mechanisms of TP53 and RB1 disruption. Integration of whole-exome and transcriptome data demonstrated biallelic disruption of TP53 and RB1 in 92% and 94% of cases, respectively, and tumors with wildtype RB1 displayed loss of CDKN2A expression, overexpression of CCND1, or mutation of MAX resulting in CDK4 and CCND2 overexpression as alternative mechanisms of RB1 suppression. We also detected alternative lengthening of telomeres (ALT) in 78% of cases, and identified recurrent alterations in telomere maintenance genes such as ATRX, RBL2, and SP100, providing novel insight into the genetic basis of this mechanism. Finally, most tumors displayed hallmarks of “BRCAness”, including alterations in homologous recombination DNA repair genes and enrichment of specific mutational signatures, and cultured LMS cells were sensitive towards olaparib and cisplatin. This comprehensive genomic and transcriptomic analysis has unveiled that LMS is characterized by mutational heterogeneity, genomic instability, near-universal inactivation of TP53 and RB1, and frequent whole-genome duplication. Furthermore, we have established that most LMS tumors rely on ALT to escape replicative senescence, and identified recurrent alterations in a broad spectrum of telomere maintenance genes. Finally, our findings uncover “BRCAness” as potentially actionable feature of LMS tumors, and provide a rich resource for guiding future investigations into the mechanisms underlying LMS development and the design of novel therapeutic strategies.

Citation Format: Priya Chudasama, Sadaf Mughal, Mathijs Sanders, Daniel Hübschmann, Inn Chung, Aurélie Ernst, Bernd Kasper, Hans-Georg Kopp, Sebastian Bauer, Karsten Rippe, Benedikt Brors, Marcus Renner, Peter Hohenberger, Claudia Scholl, Stefan Fröhling. Integrative genomic and transcriptomic analysis of leiomyosarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4336.

NRG1 Fusions in KRAS Wild-Type Pancreatic Cancer

We used whole-genome and transcriptome sequencing to identify clinically actionable genomic alterations in young adults with pancreatic ductal adenocarcinoma (PDAC). Molecular characterization of 17 patients with PDAC enrolled in a precision oncology program revealed gene fusions amenable to pharmacologic inhibition by small-molecule tyrosine kinase inhibitors in all patients with KRAS wild-type (KRAS^WT) tumors (4 of 17). These alterations included recurrent NRG1 rearrangements predicted to drive PDAC development through aberrant ERBB receptor-mediated signaling, and pharmacologic ERBB inhibition resulted in clinical improvement and remission of liver metastases in 2 patients with NRG1-rearranged tumors that had proved resistant to standard treatment. Our findings demonstrate that systematic screening of KRAS^WT tumors for oncogenic fusion genes will substantially improve the therapeutic prospects for a sizeable fraction of patients with PDAC.Significance: Advanced PDAC is a malignancy with few treatment options that lacks molecular mechanism-based therapies. Our study uncovers recurrent gene rearrangements such as NRG1 fusions as disease-driving events in KRAS^wt tumors, thereby providing novel insights into oncogenic signaling and new therapeutic options in this entity. Cancer Discov; 8(9); 1087-95. ©2018 AACR.This article is highlighted in the In This Issue feature, p. 1047.

Succession of transiently active tumor-initiating cell clones in human pancreatic cancer xenografts

Although tumor-initiating cell (TIC) self-renewal has been postulated to be essential in progression and metastasis formation of human pancreatic adenocarcinoma (PDAC), clonal dynamics of TICs within PDAC tumors are yet unknown. Here, we show that long-term progression of PDAC in serial xenotransplantation is driven by a succession of transiently active TICs producing tumor cells in temporally restricted bursts. Clonal tracking of individual, genetically marked TICs revealed that individual tumors are generated by distinct sets of TICs with very little overlap between subsequent xenograft generations. An unexpected functional and phenotypic plasticity of pancreatic TICs in vivo underlies the recruitment of inactive TIC clones in serial xenografts. The observed clonal succession of TIC activity in serial xenotransplantation is in stark contrast to the continuous activity of limited numbers of self-renewing TICs within a fixed cellular hierarchy observed in other epithelial cancers and emphasizes the need to target TIC activation, rather than a fixed TIC population, in PDAC.

Prospective identification of resistance mechanisms to HSP90 inhibition in KRAS mutant cancer cells

Inhibition of the HSP90 chaperone results in depletion of many signaling proteins that drive tumorigenesis, such as downstream effectors of KRAS, the most commonly mutated human oncogene. As a consequence, several small-molecule HSP90 inhibitors are being evaluated in clinical trials as anticancer agents. To prospectively identify mechanisms through which HSP90-dependent cancer cells evade pharmacologic HSP90 blockade, we generated multiple mutant KRAS-driven cancer cell lines with acquired resistance to the purine-scaffold HSP90 inhibitor PU-H71. All cell lines retained dependence on HSP90 function, as evidenced by sensitivity to short hairpin RNA-mediated suppression of HSP90AA1 or HSP90AB1 (also called HSP90α and HSP90β, respectively), and exhibited two types of genomic alterations that interfere with the effects of PU-H71 on cell viability and proliferation: (i) a Y142N missense mutation in the ATP-binding domain of HSP90α that co-occurred with amplification of the HSP90AA1 locus, (ii) genomic amplification and overexpression of the ABCB1 gene encoding the MDR1 drug efflux pump. In support of a functional role for these alterations, exogenous expression of HSP90α Y142N conferred PU-H71 resistance to HSP90-dependent cells, and pharmacologic MDR1 inhibition with tariquidar or lowering ABCB1 expression restored sensitivity to PU-H71 in ABCB1-amplified cells. Finally, comparison with structurally distinct HSP90 inhibitors currently in clinical development revealed that PU-H71 resistance could be overcome, in part, by ganetespib (also known as STA9090) but not tanespimycin (also known as 17-AAG). Together, these data identify potential mechanisms of acquired resistance to small molecules targeting HSP90 that may warrant proactive screening for additional HSP90 inhibitors or rational combination therapies.

Protein Kinase C Epsilon Is a Key Regulator of Mitochondrial Redox Homeostasis in Acute Myeloid Leukemia

Purpose: The intracellular redox environment of acute myeloid leukemia (AML) cells is often highly oxidized compared to healthy hematopoietic progenitors and this is purported to contribute to disease pathogenesis. However, the redox regulators that allow AML cell survival in this oxidized environment remain largely unknown.Experimental Design: Utilizing several chemical and genetically-encoded redox sensing probes across multiple human and mouse models of AML, we evaluated the role of the serine/threonine kinase PKC-epsilon (PKCε) in intracellular redox biology, cell survival and disease progression.Results: We show that RNA interference-mediated inhibition of PKCε significantly reduces patient-derived AML cell survival as well as disease onset in a genetically engineered mouse model (GEMM) of AML driven by MLL-AF9. We also show that PKCε inhibition induces multiple reactive oxygen species (ROS) and that neutralization of mitochondrial ROS with chemical antioxidants or co-expression of the mitochondrial ROS-buffering enzymes SOD2 and CAT, mitigates the anti-leukemia effects of PKCε inhibition. Moreover, direct inhibition of SOD2 increases mitochondrial ROS and significantly impedes AML progression in vivo Furthermore, we report that PKCε over-expression protects AML cells from otherwise-lethal doses of mitochondrial ROS-inducing agents. Proteomic analysis reveals that PKCε may control mitochondrial ROS by controlling the expression of regulatory proteins of redox homeostasis, electron transport chain flux, as well as outer mitochondrial membrane potential and transport.Conclusions: This study uncovers a previously unrecognized role for PKCε in supporting AML cell survival and disease progression by regulating mitochondrial ROS biology and positions mitochondrial redox regulators as potential therapeutic targets in AML. Clin Cancer Res; 24(3); 608-18. ©2017 AACR.

BCAT1 restricts αKG levels in AML stem cells leading to IDHmut-like DNA hypermethylation

The branched-chain amino acid (BCAA) pathway and high levels of BCAA transaminase 1 (BCAT1) have recently been associated with aggressiveness in several cancer entities. However, the mechanistic role of BCAT1 in this process remains largely uncertain. Here, by performing high-resolution proteomic analysis of human acute myeloid leukaemia (AML) stem-cell and non-stem-cell populations, we find the BCAA pathway enriched and BCAT1 protein and transcripts overexpressed in leukaemia stem cells. We show that BCAT1, which transfers α-amino groups from BCAAs to α-ketoglutarate (αKG), is a critical regulator of intracellular αKG homeostasis. Further to its role in the tricarboxylic acid cycle, αKG is an essential cofactor for αKG-dependent dioxygenases such as Egl-9 family hypoxia inducible factor 1 (EGLN1) and the ten-eleven translocation (TET) family of DNA demethylases. Knockdown of BCAT1 in leukaemia cells caused accumulation of αKG, leading to EGLN1-mediated HIF1α protein degradation. This resulted in a growth and survival defect and abrogated leukaemia-initiating potential. By contrast, overexpression of BCAT1 in leukaemia cells decreased intracellular αKG levels and caused DNA hypermethylation through altered TET activity. AML with high levels of BCAT1 (BCAT1^high) displayed a DNA hypermethylation phenotype similar to cases carrying a mutant isocitrate dehydrogenase (IDH^mut), in which TET2 is inhibited by the oncometabolite 2-hydroxyglutarate. High levels of BCAT1 strongly correlate with shorter overall survival in IDH^WTTET2^WT, but not IDH^mut or TET2^mut AML. Gene sets characteristic for IDH^mut AML were enriched in samples from patients with an IDH^WTTET2^WTBCAT1^high status. BCAT1^high AML showed robust enrichment for leukaemia stem-cell signatures, and paired sample analysis showed a significant increase in BCAT1 levels upon disease relapse. In summary, by limiting intracellular αKG, BCAT1 links BCAA catabolism to HIF1α stability and regulation of the epigenomic landscape, mimicking the effects of IDH mutations. Our results suggest the BCAA-BCAT1-αKG pathway as a therapeutic target to compromise leukaemia stem-cell function in patients with IDH^WTTET2^WT AML.

Abstract 5766: High-content microscopy-based screening of colorectal organoids

High-content screening of cells has become a widespread approach for cellular assays due to its capacity to capture complex biological processes. However, conventional cell culture is limited with respect to cell and tissue architecture. Organoids are a unique model system for the intact and diseased intestinal epithelium. The 3D model can be used for the functional study of cancer development and, potentially, prospective therapeutic testing of drugs in patient derived tumor organoids. Here, we present a high-content microscopy based screening workflow to study organoid self-organization and growth with up to single cell resolution. After seeding of organoid fragments in a basal membrane extract, screening plates are incubated to allow for organoid formation. Subsequent treatment and incubation is followed by staining and imaging on a high-throughput microscopy platform followed by automated image analysis using open-source software. Profiling of both complete organoids and their individual architecture enables the quantitative description of population and tissue heterogeneity in the context of various perturbations. We generated four distinct colon organoid lines from mice carrying mutations of APC and KRAS in different combinations. These are profiled for differential phenotypic responses to a library of >1000 drug-like compounds. Also, this methodology is used to screen for clinically relevant differential treatment responses in patient derived tumor and normal colon organoids. Hence, based on this work we are able to analyze gene-drug interactions in early colon cancer development and drug response of patient derived colorectal cancer organoids.

Citation Format: Niklas T. Rindtorff, Johannes Betge, Jan Sauer, Thilo Miersch, Tianzuo Zhan, Florian Heigwer, Claudia Scholl, Matthias Ebert, Bernd Fischer, Michael Boutros. High-content microscopy-based screening of colorectal organoids [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 5766. doi:10.1158/1538-7445.AM2017-5766

Genetic subclone architecture of tumor clone-initiating cells in colorectal cancer

Combining high-coverage whole-genome sequencing with functional analyses, Giessler et al. demonstrate that tumor initiation and long-term tumor formation in human colorectal cancer are driven by multiple genomic subclones and that the functional heterogeneity of colorectal cancer tumor clone–initiating cells is not based on genomic architecture.

A hierarchically organized cell compartment drives colorectal cancer (CRC) progression. Genetic barcoding allows monitoring of the clonal output of tumorigenic cells without prospective isolation. In this study, we asked whether tumor clone-initiating cells (TcICs) were genetically heterogeneous and whether differences in self-renewal and activation reflected differential kinetics among individual subclones or functional hierarchies within subclones. Monitoring genomic subclone kinetics in three patient tumors and corresponding serial xenografts and spheroids by high-coverage whole-genome sequencing, clustering of genetic aberrations, subclone combinatorics, and mutational signature analysis revealed at least two to four genetic subclones per sample. Long-term growth in serial xenografts and spheroids was driven by multiple genomic subclones with profoundly differing growth dynamics and hence different quantitative contributions over time. Strikingly, genetic barcoding demonstrated stable functional heterogeneity of CRC TcICs during serial xenografting despite near-complete changes in genomic subclone contribution. This demonstrates that functional heterogeneity is, at least frequently, present within genomic subclones and independent of mutational subclone differences.

Gene expression and proliferation biomarkers for antidepressant treatment resistance

The neurotrophic hypothesis of depression suggests an association between effects on neuroplasticity and clinical response to antidepressant drug therapy. We studied individual variability in antidepressant drug effects on cell proliferation in lymphoblastoid cell lines (LCLs) from n=25 therapy-resistant patients versus n=25 first-line therapy responders from the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study. Furthermore, the variability in gene expression of genes associated with cell proliferation was analyzed for tentative candidate genes for prediction of individual LCL donor's treatment response. Cell proliferation was quantified by EdU (5-ethynyl-2'-deoxyuridine) assays after 21-day incubation of LCLs with fluoxetine (0.5 ng μl^-1) and citalopram (0.3 ng μl^-1) as developed and described earlier. Gene expression of a panel of candidate genes derived from genome-wide expression analyses of antidepressant effects on cell proliferation of LCLs from the Munich Antidepressant Response Signature (MARS) study was analyzed by real-time PCR. Significant differences in in vitro cell proliferation effects were detected between the group of LCLs from first-line therapy responders and LCLs from treatment-resistant patients. Gene expression analysis of the candidate gene panel revealed and confirmed influence of the candidate genes ABCB1, FZD7 and WNT2B on antidepressant drug resistance. The potential of these genes as tentative biomarkers for antidepressant drug resistance was confirmed. In vitro cell proliferation testing may serve as functional biomarker for individual neuroplasticity effects of antidepressants.

Targeting Fibroblast Growth Factor Receptor 1 for Treatment of Soft-Tissue Sarcoma

Purpose: Altered FGFR1 signaling has emerged as a therapeutic target in epithelial malignancies. In contrast, the role of FGFR1 in soft-tissue sarcoma (STS) has not been established. Prompted by the detection and subsequent therapeutic inhibition of amplified FGFR1 in a patient with metastatic leiomyosarcoma, we investigated the oncogenic properties of FGFR1 and its potential as a drug target in patients with STS.Experimental Design: The frequency of FGFR1 amplification and overexpression, as assessed by FISH, microarray-based comparative genomic hybridization and mRNA expression profiling, SNP array profiling, and RNA sequencing, was determined in three patient cohorts. The sensitivity of STS cell lines with or without FGFR1 alterations to genetic and pharmacologic FGFR1 inhibition and the signaling pathways engaged by FGFR1 were investigated using viability assays, colony formation assays, and biochemical analysis.Results: Increased FGFR1 copy number was detected in 74 of 190 (38.9%; cohort 1), 13 of 79 (16.5%; cohort 2), and 80 of 254 (31.5%; cohort 3) patients. FGFR1 overexpression occurred in 16 of 79 (20.2%, cohort 2) and 39 of 254 (15.4%; cohort 3) patients. Targeting of FGFR1 by RNA interference and small-molecule inhibitors (PD173074, AZD4547, BGJ398) revealed that the requirement for FGFR1 signaling in STS cells is dictated by FGFR1 expression levels, and identified the MAPK-ERK1/2 axis as critical FGFR1 effector pathway.Conclusions: These data identify FGFR1 as a driver gene in multiple STS subtypes and support FGFR1 inhibition, guided by patient selection according to the FGFR1 expression and monitoring of MAPK-ERK1/2 signaling, as a therapeutic option in this challenging group of diseases. Clin Cancer Res; 23(4); 962-73. ©2016 AACR.

[Personalized drug therapy based on genetics. Possibilities and examples from clinical practice]

BACKGROUND

Pharmacogenetics are an important component in the individualization of treatment; however, pharmacogenetic diagnostics have so far not been used to any great extent in clinical practice. A consistent consideration of individual patient factors, such as pharmacogenetics may help to improve drug therapy and increase individual safety and efficacy aspects.

OBJECTIVE

A brief summary of structures and effects of genetic variations on drug efficacy is presented. Some frequently prescribed pharmaceuticals are specified. Furthermore, the feasibility of pharmacogenetic diagnostics and dose recommendations in the clinical practice are described.

CURRENT DATA

The European Medicines Agency (EMA) as the European approval authority has already extended the drug labels of more than 70 pharmaceuticals by information on pharmacogenetic biomarkers and the U.S. Food and Drug Administration (FDA) more than 150. This is a crucial step towards targeted medicine. Guidelines on dose and therapy adjustments are provided by the Clinical Pharmacogenetics Implementation Consortium of the Pharmacogenomics Research Network.

CONCLUSION

It is fundamental to consider individual patient factors for successful drug therapy. Dose and therapy recommendations based on pharmacogenetic diagnostics are highly important for individualization as well as improvement of safety and efficiency of drug therapy.

Proliferation rates and gene expression profiles in human lymphoblastoid cell lines from patients with depression characterized in response to antidepressant drug therapy

The current therapy success of depressive disorders remains in need of improvement due to low response rates and a delay in symptomatic improvement. Reliable functional biomarkers would be necessary to predict the individual treatment outcome. On the basis of the neurotrophic hypothesis of antidepressant's action, effects of antidepressant drugs on proliferation may serve as tentative individual markers for treatment efficacy. We studied individual differences in antidepressant drug effects on cell proliferation and gene expression in lymphoblastoid cell lines (LCLs) derived from patients treated for depression with documented clinical treatment outcome. Cell proliferation was characterized by EdU (5-ethynyl-2'-deoxyuridine) incorporation assays following a 3-week incubation with therapeutic concentrations of fluoxetine. Genome-wide expression profiling was conducted by microarrays, and candidate genes such as betacellulin-a gene involved in neuronal stem cell regeneration-were validated by quantitative real-time PCR. Ex vivo assessment of proliferation revealed large differences in fluoxetine-induced proliferation inhibition between donor LCLs, but no association with clinical response was observed. Genome-wide expression analyses followed by pathway and gene ontology analyses identified genes with different expression before vs after 21-day incubation with fluoxetine. Significant correlations between proliferation and gene expression of WNT2B, FZD7, TCF7L2, SULT4A1 and ABCB1 (all involved in neurogenesis or brain protection) were also found. Basal gene expression of SULT4A1 (P=0.029), and gene expression fold changes of WNT2B by ex vivo fluoxetine (P=0.025) correlated with clinical response and clinical remission, respectively. Thus, we identified potential gene expression biomarkers eventually being useful as baseline predictors or as longitudinal targets in antidepressant therapy.

LESSONS LEARNED FROM THE EURADOS SURVEY ON INDIVIDUAL MONITORING DATA AND INTERNAL DOSE ASSESSMENTS OF FOREIGNERS EXPOSED IN JAPAN FOLLOWING THE FUKUSHIMA DAIICHI NPP ACCIDENT

European Radiation Dosimetry Group e.V. (EURADOS) survey on individual monitoring data and dose assessment has been carried out for 550 foreigners returning home after being exposed in Japan to intakes of radionuclides (mainly (131)I, (132)I, (132)Te, (134)Cs and (137)Cs) as a consequence of the Fukushima Daiichi NPP accident. In vivo and in vitro measurements were performed in their respective countries at an early stage after that accident. Intakes of radionuclides were detected in 208 persons from Europe and Canada, but the committed effective dose E(50) was below the annual dose limit for the public (<1 mSv) in all the cases. Lessons learned from this EURADOS survey are presented here regarding not only internal dosimetry issues, but also the management of the emergency situation, the perception of the risk of health effects due to radiation and the communication with exposed persons who showed anxiety and lack of trust in monitoring data and dose assessments.

Abstract 457: FGFR1 overexpression is frequent in adult soft tissue sarcoma and predicts sensitivity to FGFR inhibitors

Purpose: Soft-tissue sarcomas (STS) are highly diverse, devastating and clinically challenging malignancies. In advanced-stage STS, conventional chemotherapy provides symptom palliation but not prolonged survival, which typically ranges from 11-15 months after development of distant metastases. Thus, there is an urgent need for more effective, well-tolerated and targeted STS therapies. Alterations of the FGFR1 receptor tyrosine kinase are under investigation as biomarker of FGFR inhibitor sensitivity in several epithelial cancers. Prompted by the detection of high-level FGFR1 amplification in a patient with metastatic leiomyosarcoma through clinical exome sequencing, we investigated the role of FGFR1 as oncogenic driver and potential drug target in STS. Specific aims were to (i) determine the frequency of FGFR1 amplification and overexpression in adult STS, (ii) evaluate the sensitivity of FGFR1-altered STS cells to genetic and pharmacologic FGFR1 inhibition, and (iii) delineate the signaling pathways engaged by FGFR1 in these cells.

Experimental design: The frequency of FGFR1 amplification and overexpression was established in a cohort of patients with treatment-näive high-grade STS using array-based comparative genomic hybridization and mRNA expression profiling, respectively, and results were validated using data from The Cancer Genome Atlas (TCGA). FGFR1 dependence was assessed in STS cell lines with and without FGFR1 alteration through RNA interference (RNAi)-mediated knockdown and selective small-molecule FGFR inhibitors. FGFR ligand and pharmacologic inhibitors were employed to dissect FGFR signaling in FGFR1-altered STS cells.

Results: FGFR1 amplification and overexpression were present in 31% and 34% of cases in the untreated high-grade STS cohort (n = 176) and in 16% and 15% of cases in the TCGA cohort (n = 256). Interestingly, FGFR1 overexpression was detected in a substantial proportion of cases

with no amplification (high-grade sarcoma cohort, 26%; TCGA cohort, 6.6%) comprising seven STS subtypes. Functional studies employing RNAi and different FGFR inhibitors (PD173074, AZD4547, BGJ398) demonstrated that the degree of dependence on FGFR1 for proliferation, survival, and anchorage-independent growth was primarily determined by FGFR1 expression levels. Furthermore, we identified the MAPK-ERK1/2 signaling axis as critical FGFR1 effector pathway whose suppression dictates the sensitivity of FGFR1-driven STS cells to FGFR-targeted therapy.

Conclusions: FGFR1 amplification and overexpression are frequent events in multiple STS subtypes, and high FGFR1-expressing STS cells are sensitive to FGFR inhibition. These findings support FGFR1 as novel therapeutic target in STS and point to FGFR1 overexpression as a more reliable biomarker of sensitivity to FGFR pathway inhibition than genomic amplification, which might be of value for enrichment of future clinical trial populations.

Citation Format: Priya Chudasama, Marcus Renner, Katja Specht, Sadaf Mughal, Barbara Hutter, Ingo Alldinger, Simon Schimmack, Dirk Jäger, Christof von Kalle, Stefan Gröschel, Stephan Wolf, Benedikt Brors, Wilko Weichert, Hanno Glimm, Gunhild Mechtersheimer, Claudia Scholl, Stefan Fröhling. FGFR1 overexpression is frequent in adult soft tissue sarcoma and predicts sensitivity to FGFR inhibitors. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 457.

Phenotypic differentiation does not affect tumorigenicity of primary human colon cancer initiating cells

Within primary colorectal cancer (CRC) a subfraction of all tumor-initiating cells (TIC) drives long-term progression in serial xenotransplantation. It has been postulated that efficient maintenance of TIC activity in vitro requires serum-free spheroid culture conditions that support a stem-like state of CRC cells. To address whether tumorigenicity is indeed tightly linked to such a stem-like state in spheroids, we transferred TIC-enriched spheroid cultures to serum-containing adherent conditions that should favor their differentiation. Under these conditions, primary CRC cells did no longer grow as spheroids but formed an adherent cell layer, up-regulated colon epithelial differentiation markers, and down-regulated TIC-associated markers. Strikingly, upon xenotransplantation cells cultured under either condition equally efficient formed serially transplantable tumors. Clonal analyses of individual lentivirally marked TIC clones cultured under either culture condition revealed no systematic differences in contributing clone numbers, indicating that phenotypic differentiation does not select for few individual clones adapted to unfavorable culture conditions. Our results reveal that CRC TIC can be propagated under conditions previously thought to induce their elimination. This phenotypic plasticity allows addressing primary human CRC TIC properties in experimental settings based on adherent cell growth.

Cooperation of BRAF(F595L) and mutant HRAS in histiocytic sarcoma provides new insights into oncogenic BRAF signaling

Activating BRAF mutations, in particular V600E/K, drive many cancers and are considered mutually exclusive with mutant RAS, whereas inactivating BRAF mutations in the D(594)F(595)G(596) motif cooperate with RAS via paradoxical MEK/ERK activation. Due to the increasing use of comprehensive tumor genomic profiling, many non-V600 BRAF mutations are being detected whose functional consequences and therapeutic actionability are often unknown. We investigated an atypical BRAF mutation, F595L, which was identified along with mutant HRAS in histiocytic sarcoma and also occurs in epithelial cancers, melanoma and neuroblastoma, and determined its interaction with mutant RAS. Unlike other DFG motif mutants, BRAF(F595L) is a gain-of-function variant with intermediate activity that does not act paradoxically, but nevertheless cooperates with mutant RAS to promote oncogenic signaling, which is efficiently blocked by pan-RAF and MEK inhibitors. Mutation data from patients and cell lines show that BRAF(F595L), as well as other intermediate-activity BRAF mutations, frequently coincide with mutant RAS in various cancers. These data define a distinct class of activating BRAF mutations, extend the spectrum of patients with systemic histiocytoses and other malignancies who are candidates for therapeutic blockade of the RAF-MEK-ERK pathway and underscore the value of comprehensive genomic testing for uncovering the vulnerabilities of individual tumors.

Abstract 1435: Role of PRKD2 in HSP90- and hypoxia-mediated epithelial-to-mesenchymal transition

The protein kinase D (PRKD) family of serine/threonine kinases belongs to the calcium/calmodulin-dependent protein kinase superfamily and comprises three isoforms, PRKD1, PRKD2 and PRKD3. We have recently identified PRKD2 as a novel client of HSP90 chaperone in several cancer cell lines. Depletion of PRKD2 protein following pharmacologic inhibition of HSP90 was associated with tumor cell death in vitro and in vivo. Furthermore, abrogation of PRKD2 in cancer cells prevented hypoxia-induced accumulation and promoter activity of HIF-1a, an oxygen sensor also shown to be regulated by HSP90. Since, both HSP90 and hypoxia/HIF-1a regulate epithelial-to-mesenchymal transition (EMT), we sought to investigate the role played by PRKD2 in this process.

Here we report that ectopic expression of PRKD2 was associated with a change in morphology, from epithelial polarized to a spindle-like phenotype, in lung and pancreatic cancer cells. This observation was associated with impaired E-cadherin and augmented vimentin protein levels. Pharmacologic inhibition of HSP90 was associated not only with PRKD2 degradation but also with decreased vimentin expression. However, the higher remaining PRKD2 levels after HSP90 inhibition of tumor cells expressing ectopic PRKD2 partially restored the vimentin expression suggesting a contribution of kinase to the chaperone-supported EMT. Incubation of cancer cells under low oxygen atmosphere showed decreased epithelial marker proteins and elevated vimentin levels, which was further enhanced by overexpressing PRKD2 suggesting that PRKD2 is involved in hypoxia-triggered EMT process. The fact that PRKD2 is able to interact with hypoxia-stabilized HIF-1a, which regulates EMT by controlling expression of Twist, a basic helix-loop-helix transcription factor reported to repress E-cadherin, suggests that PRKD2 may influence crucial EMT molecules via HIF-1a. Altogether, these findings 1) suggest PRKD2 as a crucial modulator of HSP90- and hypoxia-mediated EMT process, 2) suggest PRKD2 ablation through HSP90 inhibition as a potential therapeutic strategy in cancer with immediate implementation since several chaperone inhibitors are in clinical trials and 3) promote the intensification of designing specific PRKD2 inhibitors and their implementation in targeted therapy in human cancer.

Citation Format: Ninel Azoitei, Alexander Becher, Kristina Diepold, Susanne Bobrovich, Cornelia Brunner, Gabriela Chiosis, Stefan Fröhling, van Lint Johan, Claudia Scholl, Thomas Seufferlein. Role of PRKD2 in HSP90- and hypoxia-mediated epithelial-to-mesenchymal transition. [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 1435. doi:10.1158/1538-7445.AM2015-1435

PRKD2: A two-pronged kinase crucial for the tumor-supporting activity of HSP90

PRKD2 plays an important role in tumor cell survival, proliferation, migration, and angiogenesis. We recently reported that cell death and impaired blood vessel formation evoked by inhibition of the HSP90 chaperone in human cancer cells of various tissue origins is mediated by destabilization of PRKD2.

HOX Gene Regulation in Acute Myeloid Leukemia: CDX Marks the Spot?

Gene targeting and overexpression studies have demonstrated the importance of the clustered homeobox (HOX) genes in hematopoesis. In addition, global HOX gene dysregulation is found in the majority of cases of acute myeloid leukemia (AML) and many cases of acute lymphoblastic leukemia (ALL), and substantial evidence exists to suggest that aberrant expression of HOX genes contributes to the pathogenesis of leukemia. However, although individual HOX genes are rearranged in rare cases of AML and HOX genes are known transcriptional targets of certain leukemia-associated fusion proteins, such as those involving the mixed lineage leukemia (MLL) gene, in the majority of cases, the upstream regulators of HOX genes are unknown. The CDX family of non-clustered homeobox genes are known developmental regulators of HOX gene expression. We have recently demonstrated that Cdx4 is expressed in adult murine bone marrow where its expression pattern follows that of Hox genes. We also demonstrated that CDX2 is expressed in the majority, and that CDX4 is expressed in almost a quarter, of AML patient samples. For CDX2, this expression was predominantly monoallelic but was not associated with coding sequence or promoter mutations, gene amplification, or aberrant promoter methylation. In addition, stable knockdown of CDX2 resulted in a loss of proliferation and clonogenicity in AML cell lines, and bone marrow retrovirally engineered to express either Cdx2 or Cdx4 generated AML in transplant recipients. Cdx4 was shown to cooperate with the known Hox cofactor Meis1a, and structure-function experiments confirmed that the transcription factor function of Cdx4 was required for transformation. Finally, expression of either Cdx2 or Cdx4 generated a dysregulated Hox gene program in normal hematopoietic progenitors and in leukemic tissue. Taken together, these studies implicate CDX proteins as master regulators of HOX gene regulation in AML.

HSP90 supports tumor growth and angiogenesis through PRKD2 protein stabilization

The kinase PRKD2 (protein kinase D) is a crucial regulator of tumor cell-endothelial cell communication in gastrointestinal tumors and glioblastomas, but its mechanistic contributions to malignant development are not understood. Here, we report that the oncogenic chaperone HSP90 binds to and stabilizes PRKD2 in human cancer cells. Pharmacologic inhibition of HSP90 with structurally divergent small molecules currently in clinical development triggered proteasome-dependent degradation of PRKD2, augmenting apoptosis in human cancer cells of various tissue origins. Conversely, ectopic expression of PRKD2 protected cancer cells from the apoptotic effects of HSP90 abrogation, restoring blood vessel formation in two preclinical models of solid tumors. Mechanistic studies revealed that PRKD2 is essential for hypoxia-induced accumulation of hypoxia-inducible factor-1α (HIF1α) and activation of NF-κB in tumor cells. Notably, ectopic expression of PRKD2 was able to partially restore HIF1α and secreted VEGF-A levels in hypoxic cancer cells treated with HSP90 inhibitors. Taken together, our findings indicate that signals from hypoxia and HSP90 pathways are interconnected and funneled by PRKD2 into the NF-κB/VEGF-A signaling axis to promote tumor angiogenesis and tumor growth.

Abstract 5129: Role of PRKD2 in HSP90 inhibition-mediated suppression of cancer growth

In various types of malignancies, conventional forms of therapy such as surgery, radiation and chemotherapy are often ineffective. In the past decade, a convergence of scientific and technological advances has enabled the identification of molecular targets and signaling pathways specific to cancer cells, resulting in therapies with enhanced selectivity and efficacy and reduced toxicity. Protein kinases represent such molecular targets. We have recently shown that PRKD2 is a crucial regulator of tumor cell - endothelial cell communication in gastrointestinal tumors and demonstrated the kinase to be a novel regulator of glioblastoma growth. Here we report that HSP90/Cdc37 chaperone complex binds to and stabilizes PRKD2 in human cancer cells. RNAi-mediated ablation of HSP90 expression but also the pharmacological inhibition of the chaperone with two independent inhibitors induced degradation of PRKD2 in a broad range of human cancer cell lines and in vivo. Treatment of various cancer cell lines with proteasome inhibitors such as MG-132 or Bortezomib, followed by incubation with HSP90 inhibitors rescued the PRKD2 levels to the detergent-insoluble fraction suggesting that degradation of the kinase follows the proteasomal pathway. Kinetic experiments conducted with chaperone inhibitors demonstrated that PRKD2 was degraded in a time- and dose-dependent manner and this degradation was associated with the activation of the apoptotic programme both in vitro and in vivo. Furthermore, ectopic expression of the kinase protected cancer cells from the apoptotic effects of HSP90 abrogation suggesting PRKD2 as a protein whose depletion mediates the sensitivity of tumor cells to chaperone inhibition. Altogether, these findings 1) propose PRKD2 ablation through HSP90 inhibition as a potential therapeutic strategy with immediate implementation, 2) reveal the kinase as a crucial modulator of HSP90-mediated apoptotic effects and 3) promote the intensification of designing specific PRKD2 inhibitors and their implementation in targeted therapy in human cancer.

Citation Format: Ninel Azoitei, Kristina Diepold, Felicitas Genze, Arefeh Rouhi, Susanne Brobovich, Stefan Froehling, Gabriela Chiosis, Cornelia Brunner, Johan van Lint, Marcus Cronauer, Claudia Scholl, Thomas Seufferlein. Role of PRKD2 in HSP90 inhibition-mediated suppression of cancer growth. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5129. doi:10.1158/1538-7445.AM2014-5129

Observation of low- and high-energy Gamow-Teller phonon excitations in nuclei

Gamow-Teller (GT) transitions in atomic nuclei are sensitive to both nuclear shell structure and effective residual interactions. The nuclear GT excitations were studied for the mass number A = 42, 46, 50, and 54 "f-shell" nuclei in ((3)He, t) charge-exchange reactions. In the (42)Ca → (42)Sc reaction, most of the GT strength is concentrated in the lowest excited state at 0.6 MeV, suggesting the existence of a low-energy GT phonon excitation. As A increases, a high-energy GT phonon excitation develops in the 6-11 MeV region. In the (54)Fe → (54)Co reaction, the high-energy GT phonon excitation mainly carries the GT strength. The existence of these two GT phonon excitations are attributed to the 2 fermionic degrees of freedom in nuclei.