Discovery of potent and selective HER2 inhibitors with efficacy against HER2 exon 20 insertion-driven tumors, which preserve wild-type EGFR signaling

Oncogenic alterations in human epidermal growth factor receptor 2 (HER2) occur in approximately 2% of patients with non-small cell lung cancer and predominantly affect the tyrosine kinase domain and cluster in exon 20 of the ERBB2 gene. Most clinical-grade tyrosine kinase inhibitors are limited by either insufficient selectivity against wild-type (WT) epidermal growth factor receptor (EGFR), which is a major cause of dose-limiting toxicity or by potency against HER2 exon 20 mutant variants. Here we report the discovery of covalent tyrosine kinase inhibitors that potently inhibit HER2 exon 20 mutants while sparing WT EGFR, which reduce tumor cell survival and proliferation in vitro and result in regressions in preclinical xenograft models of HER2 exon 20 mutant non-small cell lung cancer, concomitant with inhibition of downstream HER2 signaling. Our results suggest that HER2 exon 20 insertion-driven tumors can be effectively treated by a potent and highly selective HER2 inhibitor while sparing WT EGFR, paving the way for clinical translation.

Abstract 4004: Interrogation of cancer gene dependencies reveals novel paralog interactions of autosome and sex chromosome encoded genes

Genetic networks are characterized by extensive buffering. During tumor evolution, disruption of these functional redundancies can create de novo vulnerabilities that are specific to cancer cells. In this regard, paralog genes are of particular interest, as the loss of one paralog gene can render tumor cells dependent on a remaining paralog. To systematically identify cancer-relevant paralog dependencies, we searched for candidate dependencies using CRISPR screens and publicly available loss-of-function datasets. Our analysis revealed >2,000 potential candidate dependencies, several of which were subsequently experimentally validated. We provide evidence that DNAJC15-DNAJC19, FAM50A-FAM50B and RPP25-RPP25L are novel cancer relevant paralog dependencies. Importantly, our analysis also revealed unexpected redundancies between sex chromosome genes. We show that chrX- and chrY- encoded paralogs, as exemplified by ZFX-ZFY, DDX3X-DDX3Y and EIF1AX-EIF1AY, are functionally linked so that tumor cell lines from male patients with Y-chromosome loss become exquisitely dependent on the chrX-encoded gene. We therefore propose genetic redundancies between chrX- and chrY- encoded paralogs as a general therapeutic strategy for human tumors that have lost the Y-chromosome.

Citation Format: Anna Köferle, Andreas Schlattl, Alexandra Hörmann, Fiona Spreitzer, Alexandra Popa, Venu Thatikonda, Teresa Puchner, Verena Supper, Madhwesh C. Ravichandran, Sarah Oberndorfer, Corinna Wieshofer, Maja Corcokovic, Christoph Reiser, Simon Wöhrle, Johannes Popow, Mark Pearson, Barbara Mair, Ralph A. Neumüller. Interrogation of cancer gene dependencies reveals novel paralog interactions of autosome and sex chromosome encoded genes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4004.

Abstract 3623: Targetable cofactor landscape of transcription factors in human cancers

Transcription factors (TF) are proteins that bind to DNA to regulate target gene expression and play a crucial role in maintaining tumor initiating and maintenance programs. However, except for a small fraction, it is difficult to directly target TF proteins due to lack of defined pockets and inherent protein-DNA, protein-protein interactions. In many cases, TF activity is tuned via cofactors, which e.g. dimerize to bind DNA (MYC/MAX) or maintain active TF protein turnover (HIF1A/EGLN1, MYC/HDAC2). Identifying such targetable cofactors of TFs will open new opportunities to target oncogenic TFs in cancers. Genome-scale CRISPR knock-out screens have been proven to be a valuable resource for identifying targets and biomarkers in cancers. In this work, we developed a framework called CONTEXT (COfactor depeNdencies in high Transcription factor EXpression phenoType) utilizing functional genomic screens and matched TF expression data. In CONTEXT, we aim to identify cofactor dependencies associated with TF activities using 859 cell lines spanning 28 cancer types. We further utilized patient cancer gene expression data from the TCGA project, to prioritize clinically relevant TF-cofactor associations. In total, we identified 1,003 TF-cofactor associations which involve 196 and 503 unique TFs and cofactors, respectively. Our approach reliably identified previously known TF-cofactor associations e.g. HIF1A/EGLN1, HIF1A/VHL, TEAD1/JUN but also previously unknown associations such as TEAD1/RAC1 or TEAD1/PTK2. Our analysis and validations provide a framework for the identification of potential cofactors of TFs which are crucial for the development and progression of cancer. We anticipate the cofactor dependencies from this resource to guide early stage drug development and inform on potential combination therapies in resistant phenotypes.

Citation Format: Venu Thatikonda, Jesse Lipp, Andreas Schlattl, Daniel Gerlach, Alexandra Popa. Targetable cofactor landscape of transcription factors in human cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3623.

Interrogation of cancer gene dependencies reveals paralog interactions of autosome and sex chromosome-encoded genes

Genetic networks are characterized by extensive buffering. During tumor evolution, disruption of functional redundancies can create de novo vulnerabilities that are specific to cancer cells. Here, we systematically search for cancer-relevant paralog interactions using CRISPR screens and publicly available loss-of-function datasets. Our analysis reveals >2,000 candidate dependencies, several of which we validate experimentally, including CSTF2-CSTF2T, DNAJC15-DNAJC19, FAM50A-FAM50B, and RPP25-RPP25L. We provide evidence that RPP25L can physically and functionally compensate for the absence of RPP25 as a member of the RNase P/MRP complexes in tRNA processing. Our analysis also reveals unexpected redundancies between sex chromosome genes. We show that chrX- and chrY-encoded paralogs, such as ZFX-ZFY, DDX3X-DDX3Y, and EIF1AX-EIF1AY, are functionally linked. Tumor cell lines from male patients with loss of chromosome Y become dependent on the chrX-encoded gene. We propose targeting of chrX-encoded paralogs as a general therapeutic strategy for human tumors that have lost the Y chromosome.

QTc-time-prolongating drugs and additional risk factors for long-QT-syndrome at hospital admission of surgical patients - risk assessment by pharmacists

Drugs can cause long-QTc-syndrome (LQTS), thereby elevating the risk for palpitations, syncopes, and sudden cardiac death. Additional risk factors such as the intake of more than one QTc-prolongating drug (QTPD) and surgery (cardiac and non-cardiac) increase the risk considerably. Therefore, a good knowledge of patientś perioperative risk is important. Data concerning this issue in surgical patients is, however, scarce. We aimed to determine the number of surgical patients taking QTPD at hospital admission and to assess the presence of additional risk factors for LQTS. In addition, we determined the LQTS-risk at hospital admission by calculating the Tisdale Risk Score, enabling early detection of patients at risk. In a retrospective study, the pre-hospital medication of a 4-month cohort of surgical patients admitted to a tertiary teaching hospital was evaluated for QTPD-intake. For these patients, additional risk factors for LQTS were assessed and the Tisdale Risk Score was calculated. Of 837 surgical patients, 419 (50%) took at least one QTPD. In total, 3,376 drugs were taken and 723 (21%) classified as QTPD with a median number of 2 (range 1-8) per patient. The median number of LQTS-risk factors for these patients at hospital admission was 2 (range 0-5). The Tisdale Risk Score classified 23 patients (5%) as high, 187 (45%) as moderate, and 209 (50%) as low risk. These findings indicate a high number of surgical patients with QTPD and additional risk factors. The Tisdale Risk Score can be used as a screening instrument for patients at risk for QTc-prolongation during medication reconciliation by pharmacists at hospital admission. Patients identified as high and moderate risk should be evaluated for adjustable risk factors and monitored adequately. Medical treatment needs to be chosen carefully in view of in-hospital patient safety.

Abstract 6221: Targeting IAP in cancer: BI 891065 a potent small molecule SMAC mimetic that synergizes with immune checkpoint inhibition

Background: Engagement of Tumor Necrosis Factor-α (TNF-α) with its receptor can lead to dramatically different cellular outcomes ranging from regulating cell survival and inflammation to induction of programmed forms of cell death. A critical proximal checkpoint determining the nature of TNF-α signaling is put in place by the cellular inhibitor of apoptosis proteins (cIAPs). In the context of cancer therapy these constitute an attractive target as they (1) block the TNF-α induced activation of apoptotic/necroptotic cues and (2) are negatively regulated by a highly selective endogenous ligand (i.e. SMAC), which served as a blueprint for the development of small molecule inhibitors of IAP (so called SMAC mimetics).

Methods: Here we investigated the efficacy of SMAC mimetic BI891065 in enhancing targeted and chemotherapeutic approaches in preclinical mouse cancer models and describe immune-modulatory effects in syngeneic settings. To identify responding indications, a large pan-cancer cell line panel screening comprising 246 cell lines was performed (Eurofins). Proliferation of cells treated with increasing concentrations of BI 891065 combined with a fixed concentration of TNF-α was assessed by high-content screening. Furthermore, to gain a better understanding of the molecular determinants associated with sensitivity to SMAC mimetic treatment, genome-wide CRISPR/Cas9 drug modifier screens were performed.

Results: Here we present key data demonstrating antitumor activity of BI891065 in preclinical models, our efforts towards understanding of genetic determinants of SMAC sensitivity and of potential responsive indications. By using genome-wide CRISPR/Cas9 drug modifier screens we not only demonstrated the feasibility of such unbiased approaches, as we identified many known (e.g. TNF Receptor 1, RIPK1, Caspase 8 and members of the NFκB signaling pathways) - but also potentially novel - regulators of TNF-α/SMAC mimetic induced cell death. In addition, to identify potential responsive indications to BI891065, extensive profiling of in vitro drug sensitivity across a large set of cancer cell types was performed. As a result of this, colorectal cancer (n=56) was identified as a promising indication: 5% of cell lines were found to be sensitive to BI 891065 single treatment. This could be further extended by the exogenous supply of TNF-α to BI 891065, increasing the number of sensitive cells to 21%.

Conclusion: The presented data demonstrate the potential of BI 891065 to facilitate tumor cell death and to enhance anti-tumor immune responses, and nominate the compound as an attractive combination partner in cancer therapy. Our results led to the identification of potentially novel modulators of SMAC mimetic sensitivity via genome-wide CRISPR/Cas9 drug sensitizer screens and suggest colorectal cancer as a promising indication for clinical positioning.

Citation Format: Martin Aichinger, Valeria Santoro, Ksenija Slavic-Obradovic, Stefanie Ruhland, Andreas Wernitznig, Andrea Neudolt, Markus Schaefer, Sabine Kallenda, Daniel Zach, Sabine Olt, Carina Salomon, Sarah Rieser, Martina Weissenboeck, Florian Ebner, Andreas Schlattl, Melanie Talata De Almeida, Rebecca Langlois, Martina Sykora, Markus Reschke, Thomas Zichner, Daniel Gerlach, Julian Jude, Michaela Fellner, Dirk Scharn, Norbert Kraut, Juergen Moll, Johannes Zuber, Sebastian Carotta, Maria Antonietta Impagnatiello, Ulrike Tontsch-Grunt. Targeting IAP in cancer: BI 891065 a potent small molecule SMAC mimetic that synergizes with immune checkpoint inhibition [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6221.

Abstract 3227: CLIFF, a bioinformatics software tool to explore molecular differences between two sets of cancer cell lines

Cancer cell lines are important models for drug tests and viability screens. For the evaluation and understanding of differences between two groups of cell lines, we created a research software application called CLIFF (cell line differences). CLIFF finds differences in mutational pattern or DNA copy number, lists and visualizes the significantly differentially expressed genes or proteins or performs Gene Set Enrichment Analysis (GSEA) to name a few.

Today we have data from large panels of cancer cell lines consisting of gene-, protein- and microRNA expression, DNA copy number, DNA mutations, methylation, histone H3 modification, and concentration of metabolites, in addition to annotations of the tumor of origin. A number of cell line properties have been derived from these data, like microsatellite-(in)stability (MSS/MSI), mutation pattern classifications, or mutational burden. Many drugs have been tested and genes have been knocked in and out to study changes in molecular processes and proliferation. Even though cell lines in vitro do not represent the growth-properties and -conditions in a multi-cell-type tumor environment very well, they are indispensable cancer models in research and drug discovery.

After testing or evaluating various properties of cell lines, like e.g. the viability dependency on short hairpin RNA (shRNA) knockdown or CRISPR-Cas9 knockout, as well as the expression of a specific gene, the presence or absence of a DNA mutation, or any other of the above-mentioned annotations, cell lines can be classified into two classes. In addition, users can upload cell line classifications based on external data, e.g. sensitivity or resistance to drug treatments or growth media formulations.

Here are two examples of the application of CLIFF: (1) the association of knockdown or knockout of WRN in colorectal cell lines with microsatellite instability (MSI) could be confirmed. (2) The growth media has an important impact on the dependency on certain gene knockouts. It could be verified, that low concentrations of L-asparagine in the growth medium is associated with increased dependency on the asparagine producing enzyme asparagine synthetase (ASNS).

In summary, we integrated various cell line data into CLIFF to provide sophisticated statistical analysis to researchers without deeper bioinformatics knowledge. This supports the understanding of molecular mechanisms of tumor growth, helps defining drug targets for treating cancer within defined patient populations, and accelerates our understanding of the molecular drivers of cancer.

Citation Format: Andreas Wernitznig, Jesse J. Lipp, Thomas Zichner, Daniel Gerlach, Markus J. Bauer, Tilman Voss, Andreas Schlattl, Christian Haslinger, Philip G. Montgomery, Mahdi Zamanighomi, William R. Sellers, Norbert Kraut. CLIFF, a bioinformatics software tool to explore molecular differences between two sets of cancer cell lines [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3227.

SMARCA2-deficiency confers sensitivity to targeted inhibition of SMARCA4 in esophageal squamous cell carcinoma cell lines

SMARCA4/BRG1 and SMARCA2/BRM, the two mutually exclusive catalytic subunits of the BAF complex, display a well-established synthetic lethal relationship in SMARCA4-deficient cancers. Using CRISPR-Cas9 screening, we identify SMARCA4 as a novel dependency in SMARCA2-deficient esophageal squamous cell carcinoma (ESCC) models, reciprocal to the known synthetic lethal interaction. Restoration of SMARCA2 expression alleviates the dependency on SMARCA4, while engineered loss of SMARCA2 renders ESCC models vulnerable to concomitant depletion of SMARCA4. Dependency on SMARCA4 is linked to its ATPase activity, but not to bromodomain function. We highlight the relevance of SMARCA4 as a drug target in esophageal cancer using an engineered ESCC cell model harboring a SMARCA4 allele amenable to targeted proteolysis and identify SMARCA4-dependent cell models with low or absent SMARCA2 expression from additional tumor types. These findings expand the concept of SMARCA2/SMARCA4 paralog dependency and suggest that pharmacological inhibition of SMARCA4 represents a novel therapeutic opportunity for SMARCA2-deficient cancers.

Abstract 397: SMARCA4 is a selective vulnerability in SMARCA2-deficient esophageal squamous cell carcinoma cell lines

Esophageal squamous cell carcinoma (ESCC) is a highly prevalent tumor type with poor prognosis and limited treatment options. In this study, we aimed to discover potential novel drug targets using a pooled epigenome sgRNA viability screen in a panel of ESCC cell models. We identify the BAF chromatin remodeling helicase subunit SMARCA4/BRG1 as a novel dependency in a subset of ESCC cell lines. In line with the established synthetic lethal interaction of SMARCA4 and SMARCA2/BRM, the two mutual exclusive catalytic subunits of the BAF complex, SMARCA4-dependent cell lines display low or absent expression of SMARCA2. In rescue studies using SMARCA4 variants, we demonstrate that SMARCA4-dependency is linked to its ATPase/helicase activity, but not to bromodomain function. Similarly, ectopic expression of wild-type and bromodomain-mutant SMARCA2, but not a helicase-dead variant, rescues from loss of SMARCA4 in SMARCA2-low ESCC cells. SMARCA2-proficient ESCC cell models are rendered SMARCA4-dependent upon CRISPR/Cas9-mediated knock-out of SMARCA2. We further identify SMARCA4-dependent cell models from additional tumor types (colon, ovarian and pancreas carcinoma) with low or absent SMARCA2 expression. These findings expand the concept of SMARCA2/SMARCA4 paralog dependency and indicate pharmacological inhibition of SMARCA4 as a novel opportunity for targeted therapy of SMARCA2-deficient cancers.

Citation Format: Katharina Ehrenhöfer-Wölfer, Teresa Puchner, Silvia Blaha-Ostermann, Alexandra Hörmann, Wolfgang Sommergruber, Norbert Schweifer, Thomas Zichner, Andreas Schlattl, Ralph A. Neumüller, Manfred Koegl, Mark P. Petronczki, Mark Pearson, Simon Wöhrle. SMARCA4 is a selective vulnerability in SMARCA2-deficient esophageal squamous cell carcinoma cell lines [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 397.

Werner syndrome helicase is a selective vulnerability of microsatellite instability-high tumor cells

Targeted cancer therapy is based on exploiting selective dependencies of tumor cells. By leveraging recent functional screening data of cancer cell lines we identify Werner syndrome helicase (WRN) as a novel specific vulnerability of microsatellite instability-high (MSI-H) cancer cells. MSI, caused by defective mismatch repair (MMR), occurs frequently in colorectal, endometrial and gastric cancers. We demonstrate that WRN inactivation selectively impairs the viability of MSI-H but not microsatellite stable (MSS) colorectal and endometrial cancer cell lines. In MSI-H cells, WRN loss results in severe genome integrity defects. ATP-binding deficient variants of WRN fail to rescue the viability phenotype of WRN-depleted MSI-H cancer cells. Reconstitution and depletion studies indicate that WRN dependence is not attributable to acute loss of MMR gene function but might arise during sustained MMR-deficiency. Our study suggests that pharmacological inhibition of WRN helicase function represents an opportunity to develop a novel targeted therapy for MSI-H cancers.

Abstract 4449: Synthetic lethality between CSTF2 and CSTF2T in lung adenocarcinoma and melanoma cell lines

Genomic instability is a hallmark of cancer and can result in the deletion of genes with no apparent or as yet unknown relevance to tumor survival and proliferation. Although the deletion of such genes may be tolerated due to functional compensation it, however, entails a cancer cell specific vulnerability as the tumor cell relies on the function of compensating redundant genes. Recurrent deletions of cleavage stimulation factor subunit 2 Tau (CSTF2T) have been observed in several tumor samples (TCGA). During meiosis CSTF2, a paralogue of CSTF2T, which resides on the X-chromosome, is transcriptionally silenced and the zygote depends on the activity of CSTF2T. As a result, CSTF2T knockout mice exhibit male sterility which corroborates that CSTF2 and CSTF2T form a functionally redundant pair of genes with an essential function (Dass et al. 2007). With the aim to apply these findings to tumor biology, we therefore tested whether tumor cells with homozygous CSTF2T deletions depend on CSTF2 using CRISPR-based growth competition assays and confirmed this concept in lung adenocarcinoma and melanoma cell line models. Our data establish synthetic lethality between CSTF2 and CSTF2T and suggest inhibition of CSTF2 in CSTF2T deficient tumors as a new therapeutic concept.

Citation Format: Johannes Popow, Corinna Wieshofer, Andreas Schlattl, Simon Woehrle, Ralph Neumüller, Mark P. Petronczki, Jark Boettcher, Manfred Koegl, Mark Pearson. Synthetic lethality between CSTF2 and CSTF2T in lung adenocarcinoma and melanoma cell lines [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 4449.

Expansion of DUB functionality generated by alternative isoforms - USP35, a case study

Protein ubiquitylation is a dynamic post-translational modification that can be reversed by deubiquitylating enzymes (DUBs). It is unclear how the small number (∼100) of DUBs present in mammalian cells regulate the thousands of different ubiquitylation events. Here, we analysed annotated transcripts of human DUBs and found ∼300 ribosome-associated transcripts annotated as protein coding, which thus increases the total number of DUBs. By using USP35, a poorly studied DUB, as a case study, we provide evidence that alternative isoforms contribute to the functional expansion of DUBs. We show that there are two different USP35 isoforms that localise to different intracellular compartments and have distinct functions. Our results reveal that isoform 1 is an anti-apoptotic factor that inhibits staurosporine- and TNF-related apoptosis-inducing ligand (TRAIL; also known as TNFSF10)-induced apoptosis. In contrast, USP35 isoform 2 is an integral membrane protein of the endoplasmic reticulum (ER) that is also present at lipid droplets. Manipulations of isoform 2 levels cause rapid ER stress, likely through deregulation of lipid homeostasis, and lead to cell death. Our work highlights how alternative isoforms provide functional expansion of DUBs and sets directions for future research.This article has an associated First Person interview with the first author of the paper.

Synthetic lethality between the cohesin subunits STAG1 and STAG2 in diverse cancer contexts

Recent genome analyses have identified recurrent mutations in the cohesin complex in a wide range of human cancers. Here we demonstrate that the most frequently mutated subunit of the cohesin complex, STAG2, displays a strong synthetic lethal interaction with its paralog STAG1. Mechanistically, STAG1 loss abrogates sister chromatid cohesion in STAG2 mutated but not in wild-type cells leading to mitotic catastrophe, defective cell division and apoptosis. STAG1 inactivation inhibits the proliferation of STAG2 mutated but not wild-type bladder cancer and Ewing sarcoma cell lines. Restoration of STAG2 expression in a mutated bladder cancer model alleviates the dependency on STAG1. Thus, STAG1 and STAG2 support sister chromatid cohesion to redundantly ensure cell survival. STAG1 represents a vulnerability of cancer cells carrying mutations in the major emerging tumor suppressor STAG2 across different cancer contexts. Exploiting synthetic lethal interactions to target recurrent cohesin mutations in cancer, e.g. by inhibiting STAG1, holds the promise for the development of selective therapeutics.

Novel non-canonical role of STAT1 in Natural Killer cell cytotoxicity

STAT1 is an important regulator of NK cell maturation and cytotoxicity. Although the consequences of Stat1-deficiency have been described in detail the underlying molecular functions of STAT1 in NK cells are only partially understood. Here, we describe a novel non-canonical role of STAT1 that was unmasked in NK cells expressing a Stat1-Y701F mutant. This mutation prevents JAK-dependent phosphorylation, subsequent nuclear translocation and cytokine-induced transcriptional activity as verified by RNA-seq analysis. As expected Stat1-Y701F mice displayed impaired NK cell maturation comparable to Stat1^−/− animals. In contrast Stat1-Y701F NK cells exerted a significantly enhanced cytotoxicity in vitro and in vivo compared to Stat1^−/− NK cells in the absence of detectable transcriptional activity. We thus investigated the STAT1 interactome using primary NK cells derived from Stat1^ind mice that inducibly express a FLAG-tagged STAT1. Mass spectrometry revealed that STAT1 directly binds proteins involved in cell junction formation and proteins associated to membrane or membrane-bound vesicles. In line, immunofluorescence studies uncovered the recruitment of STAT1 to the target-cell interphase during NK cell killing. This led us to propose a novel function for STAT1 at the immunological synapse in NK cells regulating tumor surveillance and cytotoxicity.

A Novel RAF Kinase Inhibitor with DFG-Out-Binding Mode: High Efficacy in BRAF-Mutant Tumor Xenograft Models in the Absence of Normal Tissue Hyperproliferation

BI 882370 is a highly potent and selective RAF inhibitor that binds to the DFG-out (inactive) conformation of the BRAF kinase. The compound inhibited proliferation of human BRAF-mutant melanoma cells with 100× higher potency (1-10 nmol/L) than vemurafenib, whereas wild-type cells were not affected at 1,000 nmol/L. BI 882370 administered orally was efficacious in multiple mouse models of BRAF-mutant melanomas and colorectal carcinomas, and at 25 mg/kg twice daily showed superior efficacy compared with vemurafenib, dabrafenib, or trametinib (dosed to provide exposures reached in patients). To model drug resistance, A375 melanoma-bearing mice were initially treated with vemurafenib; all tumors responded with regression, but the majority subsequently resumed growth. Trametinib did not show any efficacy in this progressing population. BI 882370 induced tumor regression; however, resistance developed within 3 weeks. BI 882370 in combination with trametinib resulted in more pronounced regressions, and resistance was not observed during 5 weeks of second-line therapy. Importantly, mice treated with BI 882370 did not show any body weight loss or clinical signs of intolerability, and no pathologic changes were observed in several major organs investigated, including skin. Furthermore, a pilot study in rats (up to 60 mg/kg daily for 2 weeks) indicated lack of toxicity in terms of clinical chemistry, hematology, pathology, and toxicogenomics. Our results indicate the feasibility of developing novel compounds that provide an improved therapeutic window compared with first-generation BRAF inhibitors, resulting in more pronounced and long-lasting pathway suppression and thus improved efficacy.

An integrated map of structural variation in 2,504 human genomes

Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which we constructed using short-read DNA sequencing data and statistically phased onto haplotype blocks in 26 human populations. Analysing this set, we identify numerous gene-intersecting structural variants exhibiting population stratification and describe naturally occurring homozygous gene knockouts that suggest the dispensability of a variety of human genes. We demonstrate that structural variants are enriched on haplotypes identified by genome-wide association studies and exhibit enrichment for expression quantitative trait loci. Additionally, we uncover appreciable levels of structural variant complexity at different scales, including genic loci subject to clusters of repeated rearrangement and complex structural variants with multiple breakpoints likely to have formed through individual mutational events. Our catalogue will enhance future studies into structural variant demography, functional impact and disease association.

A common microdeletion affecting a hippocampus- and amygdala-specific isoform of tryptophan hydroxylase 2 is not associated with affective disorders

OBJECTIVES

Copy number variants (CNVs) have been shown to affect susceptibility for neuropsychiatric disorders. To date, studies implicating the serotonergic system in complex conditions have just focused on single nucleotide polymorphisms (SNPs). We therefore sought to identify novel common genetic copy number polymorphisms affecting genes of the serotonergic system, and to assess their putative role in bipolar affective disorder (BPAD) and major depressive disorder (MDD).

METHODS

A selection of 41 genes of the serotonergic system encoding receptors, the serotonin transporter, metabolic enzymes and chaperones were investigated using a paired-end mapping (PEM) approach on next-generation sequencing data from the pilot project of the 1000 Genomes Project. For association testing, 593 patients with MDD, 1,145 patients with BPAD, and 1,738 healthy controls were included in the study.

RESULTS

PEM led to the identification of a microdeletion in the gene encoding tryptophan hydroxylase 2 (TPH2), affecting an amygdala- and hippocampus-specific isoform. It was not associated with BPAD or MDD using a case-control association approach.

CONCLUSIONS

We did not find evidence for a role of the TPH2 microdeletion in the pathoetiology of affective disorders. Further studies examining its putative role in behavioral traits regulated by the limbic system are warranted.

DELLY: structural variant discovery by integrated paired-end and split-read analysis

MOTIVATION

The discovery of genomic structural variants (SVs) at high sensitivity and specificity is an essential requirement for characterizing naturally occurring variation and for understanding pathological somatic rearrangements in personal genome sequencing data. Of particular interest are integrated methods that accurately identify simple and complex rearrangements in heterogeneous sequencing datasets at single-nucleotide resolution, as an optimal basis for investigating the formation mechanisms and functional consequences of SVs.

RESULTS

We have developed an SV discovery method, called DELLY, that integrates short insert paired-ends, long-range mate-pairs and split-read alignments to accurately delineate genomic rearrangements at single-nucleotide resolution. DELLY is suitable for detecting copy-number variable deletion and tandem duplication events as well as balanced rearrangements such as inversions or reciprocal translocations. DELLY, thus, enables to ascertain the full spectrum of genomic rearrangements, including complex events. On simulated data, DELLY compares favorably to other SV prediction methods across a wide range of sequencing parameters. On real data, DELLY reliably uncovers SVs from the 1000 Genomes Project and cancer genomes, and validation experiments of randomly selected deletion loci show a high specificity.

AVAILABILITY

DELLY is available at www.korbel.embl.de/software.html

CONTACT

tobias.rausch@embl.de.

Relating CNVs to transcriptome data at fine resolution: assessment of the effect of variant size, type, and overlap with functional regions

Copy-number variants (CNVs) form an abundant class of genetic variation with a presumed widespread impact on individual traits. While recent advances, such as the population-scale sequencing of human genomes, facilitated the fine-scale mapping of CNVs, the phenotypic impact of most of these CNVs remains unclear. By relating copy-number genotypes to transcriptome sequencing data, we have evaluated the impact of CNVs, mapped at fine scale, on gene expression. Based on data from 129 individuals with ancestry from two populations, we identified CNVs associated with the expression of 110 genes, with 13% of the associations involving complex, multiallelic CNVs. Categorization of CNVs according to variant type, size, and gene overlap enabled us to examine the impact of different CNV classes on expression variation. While many small (<4 kb) CNVs were associated with expression variation, overall we observed an enrichment of large duplications and deletions, including large intergenic CNVs, relative to the entire set of expression-associated CNVs. Furthermore, the copy number of genes intersecting with CNVs typically correlated positively with the genes' expression, and also was more strongly correlated with expression than nearby single nucleotide polymorphisms, suggesting a frequent causal role of CNVs in expression quantitative trait loci (eQTLs). We also elucidated unexpected cases of negative correlations between copy number and expression by assessing the CNVs' effects on the structure and regulation of genes. Finally, we examined dosage compensation of transcript levels. Our results suggest that association studies can gain in resolution and power by including fine-scale CNV information, such as those obtained from population-scale sequencing.

Systematic inference of copy-number genotypes from personal genome sequencing data reveals extensive olfactory receptor gene content diversity

Copy-number variations (CNVs) are widespread in the human genome, but comprehensive assignments of integer locus copy-numbers (i.e., copy-number genotypes) that, for example, enable discrimination of homozygous from heterozygous CNVs, have remained challenging. Here we present CopySeq, a novel computational approach with an underlying statistical framework that analyzes the depth-of-coverage of high-throughput DNA sequencing reads, and can incorporate paired-end and breakpoint junction analysis based CNV-analysis approaches, to infer locus copy-number genotypes. We benchmarked CopySeq by genotyping 500 chromosome 1 CNV regions in 150 personal genomes sequenced at low-coverage. The assessed copy-number genotypes were highly concordant with our performed qPCR experiments (Pearson correlation coefficient 0.94), and with the published results of two microarray platforms (95–99% concordance). We further demonstrated the utility of CopySeq for analyzing gene regions enriched for segmental duplications by comprehensively inferring copy-number genotypes in the CNV-enriched >800 olfactory receptor (OR) human gene and pseudogene loci. CopySeq revealed that OR loci display an extensive range of locus copy-numbers across individuals, with zero to two copies in some OR loci, and two to nine copies in others. Among genetic variants affecting OR loci we identified deleterious variants including CNVs and SNPs affecting ∼15% and ∼20% of the human OR gene repertoire, respectively, implying that genetic variants with a possible impact on smell perception are widespread. Finally, we found that for several OR loci the reference genome appears to represent a minor-frequency variant, implying a necessary revision of the OR repertoire for future functional studies. CopySeq can ascertain genomic structural variation in specific gene families as well as at a genome-wide scale, where it may enable the quantitative evaluation of CNVs in genome-wide association studies involving high-throughput sequencing.

Human individual genome sequencing has recently become affordable, enabling highly detailed genetic sequence comparisons. While the identification and genotyping of single-nucleotide polymorphisms has already been successfully established for different sequencing platforms, the detection, quantification and genotyping of large-scale copy-number variants (CNVs), i.e., losses or gains of long genomic segments, has remained challenging. We present a computational approach that enables detecting CNVs in sequencing data and accurately identifies the actual copy-number at which DNA segments of interest occur in an individual genome. This approach enabled us to obtain novel insights into the largest human gene family – the olfactory receptors (ORs) – involved in smell perception. While previous studies reported an abundance of CNVs in ORs, our approach enabled us to globally identify absolute differences in OR gene counts that exist between humans. While several OR genes have very high gene counts, other ORs are found only once or are missing entirely in some individuals. The latter have a particularly high probability of influencing individual differences in the perception of smell, a question that future experimental efforts can now address. Furthermore, we observed differences in OR gene counts between populations, pointing at ORs that might contribute to population-specific differences in smell.

The baker's yeast diploid genome is remarkably stable in vegetative growth and meiosis

Accurate estimates of mutation rates provide critical information to analyze genome evolution and organism fitness. We used whole-genome DNA sequencing, pulse-field gel electrophoresis, and comparative genome hybridization to determine mutation rates in diploid vegetative and meiotic mutation accumulation lines of Saccharomyces cerevisiae. The vegetative lines underwent only mitotic divisions while the meiotic lines underwent a meiotic cycle every ∼20 vegetative divisions. Similar base substitution rates were estimated for both lines. Given our experimental design, these measures indicated that the meiotic mutation rate is within the range of being equal to zero to being 55-fold higher than the vegetative rate. Mutations detected in vegetative lines were all heterozygous while those in meiotic lines were homozygous. A quantitative analysis of intra-tetrad mating events in the meiotic lines showed that inter-spore mating is primarily responsible for rapidly fixing mutations to homozygosity as well as for removing mutations. We did not observe 1-2 nt insertion/deletion (in-del) mutations in any of the sequenced lines and only one structural variant in a non-telomeric location was found. However, a large number of structural variations in subtelomeric sequences were seen in both vegetative and meiotic lines that did not affect viability. Our results indicate that the diploid yeast nuclear genome is remarkably stable during the vegetative and meiotic cell cycles and support the hypothesis that peripheral regions of chromosomes are more dynamic than gene-rich central sections where structural rearrangements could be deleterious. This work also provides an improved estimate for the mutational load carried by diploid organisms.