Christian Schwager

• Heidelberg University

Purpose Tumor hypoxia is a paradigmatic negative prognosticator of treatment resistance in head and neck squamous cell carcinoma (HNSCC). The lack of robust and reliable hypoxia classifiers limits the adaptation of stratified therapies. We hypothesized that the tumor DNA methylation landscape might indicate epigenetic reprogramming induced by chron...

Background and purpose: Glioblastoma multiforme (GBM) is a stroma rich immune cold tumor with still dismal prognosis of despite multimodal therapy consisting of postoperative surgery and radiochemotherapy. Consequently, all randomized Phase III clinical GBM trials attempting to integrate immune checkpoint blockade (ICB) have failed to demonstrate e...

Background Selective uptake of (18)F-fluoro-ethyl-tyrosine (¹⁸F-FET) is used in high-grade glioma (HGG) to assess tumor metabolic activity via positron emission tomography (PET). We aim to investigate its value for target volume definition, as a prognosticator, and associations with whole-blood transcriptome liquid biopsy (WBT lbx) for which we rec...

Purpose: To assess the value of whole blood transcriptome data from liquid biopsy (lbx) in recurrent high-grade glioma (rHGG) patients for longitudinal molecular monitoring of tumor evolution under carbon ion irradiation (CIR). Methods: Whole blood transcriptome (WBT) analysis (Illumina HumanHT-12 Expression BeadChips) was performed in 14 patien...

Purpose: To develop a model to accurately segment mouse lungs with varying levels of fibrosis and investigate its applicability to mouse images with different resolutions. Materials and methods: In this experimental retrospective study, a U-Net was trained to automatically segment lungs on mouse CT images. The model was trained (n = 1200), valid...

It is elusive whether clonal selection of tumor cells in response to ionizing radiation (IR) is a deterministic or stochastic process. With high resolution clonal barcoding and tracking of over 400 000 HNSCC patient‐derived tumor cells the clonal dynamics of tumor cells in response to IR was analyzed. Fractionated IR induced a strong selective pres...

Biomarkers with relevance for loco‐regional therapy are needed in human papillomavirus negative aka HPV(−) head and neck squamous cell carcinoma (HNSCC). Based on the premise that DNA methylation pattern is highly conserved, we sought to develop a reliable and robust methylome‐based classifier identifying HPV(−) HNSCC patients at risk for loco‐regi...

Localized radiotherapy (RT) induces an immunogenic antitumor response that is in part counterbalanced by activation of immune evasive and tissue remodeling processes, e.g., via upregulation of programmed cell death-ligand 1 (PD-L1) and transforming growth factor β (TGF-β). We report that a bifunctional fusion protein that simultaneously inhibits TG...

Purpose: Infiltrative growth pattern is a hallmark of glioblastoma (GBM). Radiotherapy aims to eradicate microscopic residual GBM cells post-surgical removal of the visible tumor bulk. However, in field recurrences remain the major pattern of therapy failure. We hypothesized that the radiosensitivity of peripheral invasive tumor cells (peri) may d...

Radiotherapy is one of the curative treatment options for localized prostate cancer (PCa). The curative potential of radiotherapy is mediated by irradiation-induced oxidative stress and DNA damage in tumor cells. However, PCa radiocurability can be impeded by tumor resistance mechanisms and normal tissue toxicity. Metabolic reprogramming is one of...

MicroRNAs (miRs) are non-coding master regulators of transcriptome that could act as tumor suppressors (TSs) or oncogenes (oncomiRs). We aimed to systematically investigate the relevance of miRs as prognostic biomarkers in primary glioblastoma multiforme (GBM) treated with postoperative radio(chemo)therapy (PORT). For hypothesis generation, tumor m...

Radiotherapy is one of the curative treatment options for localized prostate cancer (PCa). The curative potential of radiotherapy is mediated by irradiation-induced oxidative stress and DNA damage in tumor cells. However, PCa radiocurability can be impeded by tumor resistance mechanisms and normal tissue toxicity. Metabolic reprogramming is one of...

Purpose/Objectives: We aimed to evaluate the impact of a novel highly potent and selective serine-threonine DNA-dependent Protein Kinase inhibitor (DI, M3814) on high-precision particle therapy of non-small cell lung cancer (NSCLC) with carbon ions (CI) and to study the effect of this combination therapy on tumor microenvironment (TME). Material/m...

The impact of functional heterogeneity in response to radiation therapy is poorly understood to the present. It remains elusive whether clonal selection of tumor cells in response to ionizing radiation (IR) is a deterministic or stochastic process. We applied high-resolution lentiviral cellular barcoding for quantitative clonal tracking and deconvo...

Radiation-induced normal tissue toxicity often limits the curative treatment of cancer. Moreover, normal tissue relative biological effectiveness data for high-linear energy transfer particles are urgently needed. We propose a strategy based on transcriptome analysis of patient-derived human intestinal organoids (HIO) to determine molecular surroga...

Purpose/Objective(s): CIRT is a promising treatment for thoracic malignancies and the precise knowledge of RBE is of utmost importance for translational research in this area. Current planning systems and modelling algorithms for RBE determination mainly rely on in-vitro clonogenic survival or empirical normal tissue tolerance information derived f...

6050 Background: CTGF plays a central role in tissue remodeling and has emerged as an attractive novel therapeutic target. We sought to investigate the impact of CTGF methylation status (CTGF-M) in predicting outcome of HNSCC patients undergoing RCHT. Methods: CTGF-M was discovered by applying Illumina 450K/850K arrays to DNA extracted from FFPE ma...

8543 Background: A better understanding of molecular mechanisms governing clonal tumor evolution under RCHT is of utmost importance for development of novel biomarker and targeted therapies. We report here the first attempt to decipher RCHT induced cellular and molecular perturbation in NSCLC on an integrative multiscale level. Methods: Patients wi...

Purpose The heavy chain of the CD98 protein (CD98hc) is encoded by the SLC3A2 gene. Together with the light subunit LAT1, CD98hc constitutes a heterodimeric transmembrane amino acid transporter. High SLC3A2 mRNA expression levels are associated with poor prognosis in patients with head and neck squamous cell carcinoma (HNSCC) treated with radiochem...

Pulmonary fibrosis represents a leading cause of morbidity and mortality worldwide. Therapy induced lung fibrosis constitutes a pivotal dose‐limiting side effect of radiotherapy and other anticancer agents. We aimed to develop objective criteria for assessment of fibrosis and discover pathophysiological and molecular correlates of lung fibrosis as...

Micro RNAs (miR) are master regulators of cellular transcriptome. We aimed to investigate the role of miR regulation on tumor radiosensitivity and development of local tumor recurrence by a novel large‐scale in vivo loss of function screen. For stable miR silencing, human A431 tumor cells were transduced with lentiviral constructs against 170 valid...

Background and purposes: Carbon ion radiotherapy (CIRT) with raster scanning technology is a promising treatment for lung cancer and thoracic malignancies. Determining normal tissue tolerance of organs at risk is of utmost importance for the success of CIRT. Here we report the relative biological effectiveness (RBE) of CIRT as a function of dose a...

External beam radiotherapy (EBRT) with carbon ions and endoradiotherapy using radiolabeled tumor targeting agents are emerging concepts in precision cancer therapy. We report on combination effects of these two promising strategies. Tumor targeting ¹³¹I-labelled anti-EGFR-antibody (Cetuximab) was used in the prototypic EGFR-expressing A431 human sq...

Local recurrence and distant metastasis constitutes a major obstacle in the curative treatment of cancer. The clonal evolution and molecular mechanisms governing these processes remain elusive. We utilized the CRISPR/Cas9 based genome-wide GeCKO library stably transduced in head and neck cancer (HNSCC) cells (FaDu) and orthotopically transplanted i...

Background Patients with Echinoderm microtubule-associated protein-like 4 (EML4)-anaplastic lymphoma kinase (ALK) positive lung cancer are sensitive to ALK-kinase inhibitors. TAE684 is a potent second generation ALK inhibitor that overcomes Crizotinib resistance. Radiotherapy is an integral therapeutic component of locally advanced lung cancer. The...

Inhibiting angiogenesis, which is a shared characteristic of all solid tumors, is a promising approach for treating cancer. However, emerging resistance after initial response is still a drawback. We sought to decipher the molecular landscape of tumor resistance to continuous treatment with VEGF-receptor tyrosine kinase inhibitor (RTKi) sunitinib (...

Background Normal lung tissue tolerance constitutes a limiting factor in delivering the required dose of radiotherapy to cure thoracic and chest wall malignancies. Radiation-induced lung fibrosis (RILF) is considered a critical determinant for late normal tissue complications. While RILF mouse models are frequently approached e.g., as a single high...

The hybrid technology cell-fluorescent ion track hybrid detector (Cell-Fit-HD) enables the investigation of radiation-related cellular events along single ion tracks on the subcellular scale in clinical ion beams. The Cell-Fit-HD comprises a fluorescent nuclear track detector (FNTD, the physical compartment), a device for individual particle detect...

Acquired tumor resistance to vascular endothelial growth factor (VEGF) receptor tyrosine kinase inhibitors (RTKi) constitutes a major obstacle for sustained efficacy of antiangiogenic cancer therapy. We sought to decipher the molecular landscape of tumor resistance to continuous VEGF-RTKi sunitinib (SU11248, SU) treatment via serial transplantation...

Mutational activation of K-Ras is an initiating event of pancreatic ductal adenocarcinomas (PDAC) that may develop either from pancreatic intraepithelial neoplasia (PanIN) or intraductal papillary mucinous neoplasms (IPMN). Cyclooxygenase-2 (COX-2)-derived prostaglandin E2 (PGE2) is causally related to pancreatic carcinogenesis. Here, we deciphered...

MGMT promoter methylation status is currently the only established molecular prognosticator in IDH wild-type glioblastoma multiforme (GBM). Therefore, we aimed to discover novel therapy-associated epigenetic biomarkers. After enrichment for hypermethylated fractions using Methyl-CpG-Immunoprecipitation (MCIp), we performed global DNA methylation pr...

Background and purpose: Hypoxia renders tumors resistant to radiotherapy. However, the paucity of sensitive and reliable methods for detection of tumor hypoxia limits the translation of novel therapy strategies targeting this well-known resistance factor. We sought to investigate the ability of three previously discovered transcriptomics based hyp...

Background & aims: Cancer cells with high metastatic potential and stem cell-like characteristics express the cell surface marker CD44. CD44 isoforms that include the v6 exon are co-receptors for the receptor tyrosine kinases MET and VEGFR2. We studied CD44v6 signaling in several pancreatic cancer cell lines, and its role in tumor growth and metas...

Glioblastoma (GBM) is a devastating tumor and few patients survive beyond 3 years. Defining the molecular determinants underlying long-term survival is essential for insights into tumor biology and biomarker identification. We therefore investigated homogeneously treated, IDH wt long-term (LTS, n = 10) and short-term survivors (STS, n = 6) by micro...

Background and purpose: Non-small cell lung cancer (NSCLC) patients with chromosomal rearrangements of the anaplastic lymphoma kinase gene (ALK) are sensitive to the tyrosine kinase inhibitor crizotinib. We aimed to investigate the effects of combined radiotherapy and crizotinib in ALK-positive vs. wild type NSCLC models. Material and methods: C...

The mTOR signaling plays an integral role in cellular homeostasis controlling the transition between the catabolic and anabolic states. Originally approved as immunosuppressive agents preventing allograft rejection, inhibitors of mTOR signaling have recently entered the arena of cancer therapy. Using rapamycin derivative (RAD001) as a prototype inh...

Tumor dormancy refers to a critical stage in cancer development in which tumor cells remain occult for a prolonged period of time until they eventually progress and become clinically apparent. We previously showed that the switch of dormant tumors to fast-growth is angiogenesis dependent and requires a stable transcriptional reprogramming in tumor...

Figure S1. Confirmation of miR-580 and miR-190 regulation in an independent tumor set. Expression levels of tumor dormancy associated microRNAs were analyzed using real-time qRT-PCR and compared between dormant and fast-growing tumor cells of each cancer type. Figure S2. Over-expression of miR-580, miR-588 and miR-190 in fast-growing angiogenic gli...

Differential expression of all miRs profiled in dormant vs. fast-growing tumors. (DOC)

Real time quantitative reverse transcription-PCR (qRT-PCR) analysis of single microRNA targets. All assays were performed according to Applied Biosystems TaqMan MicroRNA Assays Protocol recommendation. Briefly, 10ng (5ul) of total RNA was taken per 15-ul RT reaction. Reverse transcription was performed using MultiScribe™ Reverse Transcriptase (Appl...

Background: Quantitative analysis of transcriptional regulation of genes is a prerequisite for a better understanding of the molecular mechanisms of action of different radiation qualities such as photon, proton or carbon ion irradiation. Microarrays and real-time quantitative RT-PCR (qRT-PCR) are considered the two cornerstones of gene expression...

List of 32 endogenous control genes used in the study.

Cycle threshold range and coefficient of variation (CV) of 32 ECGs in each cell line. The genes are sorted by the coefficient of variation increasing from top to bottom. Four replicates were used in all the three cell lines.

We have previously reported that over-expression of a panel of 119 genes correlates with the metastatic potential of pancreatic carcinoma cells. We sought to identify and functionally characterize candidate tumour metastasis promoting genes among this library using a secondary phenotype-assisted screen. Here we report the discovery of the metastasi...

Oxygen deficiency in tumor tissue is associated with a malign phenotype, characterized by high invasiveness, increased metastatic potential and poor prognosis. Hypoxia chambers are the established standard model for in vitro studies on tumor hypoxia. An enzymatic hypoxia system (GOX/CAT) based on the use of glucose oxidase (GOX) and catalase (CAT)...

Gene expression of known and validated HIF-1 target genes. Gene expression in HNO97 cells under normoxic and hypoxic (2% O2) conditions using both a hypoxia chamber and the enzymatic GOX/CAT system. Mean values and standard deviation vs. reference normoxia t = 0 RNA.

Cell response to photon irradiation for various cell numbers. Cells were seeded in different confluences and incubated for 24 h under normoxia. Cell number was determined prior to irradiation. The ratio vital treated to vital untreated cells was determined 72 h after photon irradiation. Mean values and standard deviation.

SOM Table S1 (0.87 MB XLS)

(0.03 MB DOC)

Cardiac surgery with cardiopulmonary bypass (CS/CPB) is associated with increased risk for postoperative complications causing substantial morbidity and mortality. To identify the molecular mechanisms underlying CS/CPB-induced pathophysiology we employed an integrative systems biology approach using the whole blood transcriptome as the sentinel org...

e21018 Background: There is an unmet need for molecular predictors of early breast cancer. We hypothesized that gene expression as measured by peripheral blood mRNA profiles might distinguish women with early stage invasive (but nonmetastatic) breast cancer (IBC), ductal carcinoma in situ (DCIS), and healthy volunteers (V). Methods: Sixty-one patie...

Expression profile of stellate cells for typical markers. The purity of the stellate cell population was routinely checked by immunocytochemistry and immunofluorescence analyses at every passage used. Cells were seeded on Teflon covered slides, fixed, permeabilized and immunostained with specific antibodies against α-SMA, collagen type-Ia, fibronec...

Tissue fibrosis is an integral component of chronic inflammatory (liver and pancreas) diseases and pancreatic cancer. Activated pancreatic- (PSC) and hepatic- (HSC) stellate cells play a key role in fibrogenesis. To identify organ- and disease-specific stellate cell transcriptional fingerprints, we employed genome-wide transcriptional analysis of p...

List of miRNAs on the microarrays. The file contains a list of miRNAs (Reporter ID, miRBase Entry and sequence) which were spotted on the microarrays.

Microarray data of let-7 family members from HDMEC. Microarrays were performed of radiation treated (2 Gy) versus untreated cells; t-test was done with 3 biological replicates each. Each 'fold change' value represents the mean of all spot values.

Testing of various transfection conditions for functional assays. HDMEC were transfected with miR-1 (Ambion), then RNA was isolated and the expression of the PTK9 gene was measured by real-time PCR (Roche Light Cycler 480). miR-1 is known to down-regulate the PTK9 mRNA in human cells. Bar chart: Expression ratio of the PTK9 gene versus a reference...

Endothelial cells (EC) in tumor and normal tissue constitute critical radiotherapy targets. MicroRNAs have emerged as master switchers of the cellular transcriptome. Here, we seek to investigate the role of miRNAs in primary human dermal microvascular endothelial cells (HDMEC) after ionizing radiation. The microRNA status in HDMEC after 2 Gy radiat...

To unravel biological mechanisms potentially resulting in the obliteration process after radiosurgery (RS) of human cerebral arteriovenous malformations (AVMs) by investigating molecular signatures on the transcriptomic level in peripheral blood of patients. Venous blood samples were obtained at definite points of time before and after RS. The samp...

With the use of genome-wide cDNA microarrays, we investigated the transcriptome profile of the human osteosarcoma Sa OS and U-2 OS cell lines. In all, 1,098 chip entries were differentially regulated in the two cell lines; of these, 796 entries corresponded to characterized mRNAs. The identified genes are mostly expressed in epithelial tissues and...

The Ras oncogene is known to activate three major MAPK pathways, ERK, JNK, p38 and exert distinct cellular phenotypes, that is, apoptosis and invasion through the Ras-MKK3-p38-signaling cascade. We attempted to identify the molecular targets of this pathway that selectively govern the invasive phenotype. Stable transfection of NIH3T3 fibroblasts wi...

High-throughput "omics" based data analysis play emerging roles in life sciences and molecular diagnostics. This emphasizes the urgent need for user-friendly windows-based software interfaces that could process the diversity of large tab-delimited raw data files generated by these methods. Depending on the study, dozens to hundreds of these data ta...

Testicular germ cell cancers in young adult men derive from a precursor lesion called carcinoma in situ (CIS) of the testis. CIS cells were suggested to arise from primordial germ cells or gonocytes. However, direct studies on purified samples of CIS cells are lacking. To overcome this problem, we performed laser microdissection of CIS cells. Highl...

Perineural invasion, the growth of tumor cells along nerves, is a key feature of pancreatic cancer. The cardinal symptom of pancreatic cancer, abdominal pain often radiating to the back, as well as the high frequency of local tumor recurrence following resection are both attributed to the unique ability of pancreatic tumor cells to invade the neuro...

Tumor dormancy has important implications for early detection and treatment of cancer. Lack of experimental models and limited clinical accessibility constitute major obstacles to the molecular characterization of dormant tumors. We have developed models in which human tumors remain dormant for a prolonged period of time (>120 days) until they swit...

The relative risk for the development of malignancies following solid organ transplantation seems to be decreased in patients treated with the immunosuppressive agent mycophenolic acid (MPA). However, the molecular mechanisms of the antineoplastic effects of MPA are not completely understood. Here, we report that human endothelial cells and fibrobl...

A shift of the angiogenic balance to the proangiogenic state, termed the “angiogenic switch,” is a hallmark of cancer progression. Here we devise a strategy for identifying genetic participants of the angiogenic switch based on inverse regulation of genes in human endothelial cells in response to key endogenous pro- and antiangiogenic proteins. Thi...

Unlabelled: With the production of whole genome microarray chips the ability arises to investigate whether the regulation of particular groups of genes may be influenced by their chromosomal localization. Chromosome Co-Localization probability calculator (ChroCoLoc) is a publicly available web-based tool for the analysis of co-localization of co-e...

Various preparative protocols have been proposed for the acquisition and cultivation of mesenchymal stem cells (MSC). Whereas surface antigen markers have failed to precisely define this population, microarray analysis might provide a better tool for characterization of MSC. In this study, we have analyzed global gene expression profiles of human M...

In this study, we analyzed whether retroviral integration sites in repopulating hematopoietic cells correlate with genes expressed in fractions enriched in hematopoietic stem cells (HSCs). We have previously described microarray studies of two populations enriched in HSCs: CD34+/CD38- and the slow dividing fraction of CD34+/CD38- cells (SDF). Furth...

Cell-cell contact between stem cells and cellular determinants of the microenvironment plays an essential role in controlling cell division. Using human hematopoietic progenitor cells (CD34+/CD38-) and a stroma cell line (AFT024) as a model, we have studied the initial behavioral and molecular sequel of this interaction. Time-lapse microscopy showe...

Unlabelled: BLoader is a client server application for annotating and loading large amounts of Microarray data into a local installation of the MIAMExpress database. A set of nested spreadsheets is used to collect the required MIAME annotation. Controlled vocabularies are downloaded from MIAMExpress and ArrayExpress databases to guarantee MIAME co...

NOVELTY - Determining the presence of precursors of germ cell tumors in a sample comprises determining the expression profile of a group of markers or intensity signal of the proteins encoded by each of the members of the group of markers, in the sample, where the group of markers consists of at least one marker selected independently from the mark...