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

Systematische Analyse der anti-apoptotischen Aktivität der KSHV Proteine mittels Chipbasierter Hochdurchsatz Transfektionstechnik

Kaposi’s sarcoma-associated herpesvirus (KSHV) is the causative agent for Kaposi’s sarcoma (KS), a multi-focal tumor of the endothelium, as well as for two aggressive lymphoproliferative diseases, primary effusion lymphoma (PEL) and multi-centric Castleman’s disease (MCD). The tumour suppressor p53 is a central regulatory molecule of apoptosis and commonly mutated in tumours. KSHV-related malignancies express wild-type p53. Accordingly KSHV encodes proteins that counteract the cell death-inducing effects of p53. Here, the effects of all KSHV genes on the p53 signaling pathway were systematically analyzed using the reversely transfected cell microarray (RTCM) technology. With this approach we detected eight KSHV-encoded genes with potent p53 inhibiting activity in addition to the previously described inhibitory effects of the KSHV genes ORF50, K10 and K10.5. Interestingly, the three most potent newly identified inhibitors were KSHV structural proteins, namely ORF22 (glycoprotein H), ORF25 (major capsid protein) and ORF64 (tegument protein). Validation of these results with a classical transfection approach showed that these proteins inhibited p53 signaling in a dose-dependent manner and that this effect could be reversed by siRNA-mediated knockdown of the respective viral gene. All three genes inhibited p53-mediated apoptosis in response to Nutlin-3 treatment in non-infected and KSHV-infected cells. Addressing putative mechanisms we could show that these proteins inhibit the transactivation of the promoters of apoptotic mediators of p53 such as BAX and PIG3. Altogether, this thesis work demonstrates for the first time that structural proteins of KSHV can counteract p53-induced apoptosis. These proteins are expressed in the late lytic phase of the viral life cycle and are incorporated into the KSHV virion. Accordingly these proteins may inhibit cell death in the productive, as well as in the early entrance phase of KSHV infection.Das Kaposi-Sarkom-assoziierte Herpesvirus (KSHV) ist das kausale Agens sowohl des Kaposi-Sarkoms (KS), eines multifokalen Tumors des Endothels, als auch aggressiver lymphoproliferativer Erkrankungen, wie dem primären Effusionslymphom (PEL) und der multizentrischen Castleman Erkrankung (MCD). Das Tumorsuppressorprotein p53 ist ein zentraler Regulator des programmierten Zelltods (Apoptose), der häufig in Tumoren mutiert ist. In KSHV-assoziierten Erkrankungen konnte bisher keine Mutation von p53 nachgewiesen werden. Folglich könnte KSHV für Proteine kodieren, die der Apoptose-induzierenden Funktion von p53 entgegenwirken. In dieser Arbeit wurde die Methode der reversen Transfektion benutzt, um systematisch die Effekte aller KSHV-Gene auf den p53- Signaltransduktionsweg zu untersuchen. Neben der Bestätigung bereits bekannter p53- Inhibitoren (ORF50, K10 und K10.5), konnten mit diesem Ansatz acht neue KSHV-kodierte Gene gefunden werden, die eine p53-Aktivierung hemmen. Die drei stärksten Inhibitoren ORF22 (Glykoprotein H), ORF25 (Hauptkapsidprotein) und ORF64 (Tegumentprotein) waren interessanterweise Strukturproteine von KSHV. Die Bestätigung mittels klassischer Transfektion zeigte, dass die identifizierten Proteine dosisabhängig den p53-Signalweg hemmen konnten und dass dieser Effekt durch siRNA-vermittelte Herunterregulation der einzelnen KSHV-Gene wieder aufgehoben werden konnte. Alle drei Gene konnten die p53- vermittelte Apoptose, ausgelöst durch Stimulation mit Nutlin-3, sowohl in uninfizierten wie auch in KSHV-infizierten Zellen hemmen. Um die zugrundeliegenden Mechanismen näher zu charakterisieren, wurden die Effekte der KSHV Proteine auf die Transaktivierung der Promotoren der Gene Bax und PIG3 untersucht, die die Induktion der Apoptose durch p53 vermitteln. Die drei KSHV Proteine konnten die Transaktivierung sowohl von BAX, als auch von PIG3 hemmen. Insgesamt zeigt diese Doktorarbeit erstmalig, dass strukturelle Proteine von KSHV der p53- vermittelten Apoptose entgegenwirken können. Die drei Proteine werden während der späten lytischen Phase des viralen Lebenszyklus exprimiert und werden in das KSHV-Virion eingebaut. Dementsprechend könnten diese Proteine den Zelltod sowohl in der produktiven Phase, als auch in der frühen Phase einer KSHV Infektion, und zwar beim Viruseintritt in die Zelle, hemmen

Defective homologous recombination DNA repair as therapeutic target in advanced chordoma

Chordomas are rare bone tumors with limited therapeutic options. Here, the authors identify molecular alterations associated with defective homologous recombination DNA repair in advanced chordomas and report prolonged response in a patient treated with a PARP inhibitor, which later acquired resistance due to a newly gained PARP1 mutation

Integrative genomic and transcriptomic analysis of leiomyosarcoma

The molecular genetic landscape of leiomyosarcoma (LMS) is largely unknown. Here, the authors identify frequent DNA copy number alterations, whole-genome duplication, TP53 and RB1 inactivation, alternative telomere lengthening, and genomic imprints of defective DNA repair via homologous recombination as a potential therapeutic target in LMS patients

Thermal Image Super-Resolution Challenge - PBVS 2020

This paper summarizes the top contributions to the first challenge on thermal image super-resolution (TISR), which was organized as part of the Perception Beyond the Visible Spectrum (PBVS) 2020 workshop. In this challenge, a novel thermal image dataset is considered together with state- of-the-art approaches evaluated under a common framework. The dataset used in the challenge consists of 1021 thermal images, obtained from three distinct thermal cameras at different resolutions (low-resolution, mid-resolution, and high-resolution), resulting in a total of 3063 thermal images. From each resolution, 951 images are used for training and 50 for testing while the 20 remaining images are used for two proposed evaluations. The first evaluation consists of downsampling the low-resolution, mid-resolution, and high-resolution thermal images by ×2, ×3 and ×4 respectively, and comparing their super-resolution results with the corresponding ground truth images. The second evaluation is comprised of obtaining the ×2 super-resolution from a given mid-resolution thermal image and comparing it with the corresponding semi-registered high- resolution thermal image. Out of 51 registered participants, 6 teams reached the final validation phase.info:eu-repo/semantics/publishe

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. (C)2016 AACR

Defective homologous recombination DNA repair as therapeutic target in advanced chordoma

Chordomas are rare bone tumors with few therapeutic options. Here we show, using whole-exome and genome sequencing within a precision oncology program, that advanced chordomas (n = 11) may be characterized by genomic patterns indicative of defective homologous recombination (HR) DNA repair and alterations affecting HR-related genes, including, for example, deletions and pathogenic germline variants of BRCA2, NBN, and CHEK2. A mutational signature associated with HR deficiency was significantly enriched in 72.7% of samples and co-occurred with genomic instability. The poly(ADP-ribose) polymerase (PARP) inhibitor olaparib, which is preferentially toxic to HR-incompetent cells, led to prolonged clinical benefit in a patient with refractory chordoma, and whole-genome analysis at progression revealed a PARP1 p.T910A mutation predicted to disrupt the autoinhibitory PARP1 helical domain. These findings uncover a therapeutic opportunity in chordoma that warrants further exploration, and provide insight into the mechanisms underlying PARP inhibitor resistance