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(1) Background: Patients with locally advanced head and neck squamous cell carcinoma (HNSCC) who are at biologically high risk for the development of loco-regional recurrences af-ter postoperative radiotherapy (PORT) but at intermediate risk according to clinical risk factors may benefit from additional concurrent chemotherapy. In this matched-pair study, we aimed to identify a corresponding predictive gene signature. (2) Methods: Gene expression analysis was performed on a multicentre retrospective cohort of 221 patients that were treated with postoper-ative radiochemotherapy (PORT-C) and 283 patients that were treated with PORT alone. Propen-sity score analysis was used to identify matched patient pairs from both cohorts. From differen-tial gene expression analysis and Cox regression, a predictive gene signature was identified. (3) Results: 108 patient matched patient pairs were selected. We identified a 2-metagene signature that stratified patients into risk groups in both cohorts. The comparison of the high-risk patients between the two types of treatment showed higher LRC after treatment with PORT-C (p<0.001), which was confirmed by a significant interaction term in Cox regression (p=0.027), i.e. the 2-metagene signature was indicative for the type of treatment. (4) Conclusion: We have identi-fied a novel gene signature that may be helpful to identify patients with high-risk HNSCC amongst those at intermediate clinical risk treated with PORT, who may benefit from additional concurrent chemotherapy.

Purpose To assess the relation of the previously reported classification of molecular subtypes to the outcome of patients with HNSCC treated with postoperative radio(chemo)therapy (PORT-C), and to assess the association of these subtypes with gene expressions reflecting known mechanisms of radioresistance. Material and methods Gene expression analyses were performed using the GeneChip Human Transcriptome Array 2.0 on a multicentre retrospective patient cohort (N = 128) of the German Cancer Consortium Radiation Oncology Group (DKTK-ROG) with locally advanced HNSCC treated with PORT-C. Tumours were assigned to four molecular subtypes, and correlation analyses between subtypes and clinical risk factors were performed. In addition, the classifications of eight genes or gene signatures related to mechanisms of radioresistance, which have previously shown an association with outcome of patients with HNSCC, were compared between the molecular subtypes. The endpoints loco-regional control (LRC) and overall survival (OS) were evaluated by log-rank tests and Cox regression. Results Tumours were classified into the four subtypes basal (19.5%), mesenchymal (18.8%), atypical (15.6%) and classical (14.1%). The remaining tumours could not be classified (32.0%). Tumours of the mesenchymal subtype showed a lower LRC compared to the other subtypes (p = 0.012). These tumours were associated with increased epithelial-mesenchymal transition (EMT) and overexpression of a gene signature enriched in DNA repair genes. The majority of the eight considered gene classifiers were significantly associated to LRC or OS in the whole cohort. Conclusion Molecular subtypes, previously identified on HNSCC patients treated with primary radio(chemo)therapy or surgery, were related to LRC for patients treated with PORT-C, where mesenchymal tumours presented with worse prognosis. After prospective validation, subtype-based patient stratification, potentially in combination with other molecular classifiers

Purpose: To develop prognostic biomarker signatures for patients with locally advanced head and neck squamous cell carcinoma (HNSCC) treated by primary radiochemotherapy (RCTx) based on previously published molecular analyses of the retrospective biomarker study of the German Cancer Consortium – Radiation Oncology Group (DKTK-ROG).

Purpose: The aim of this study was to develop and validate a novel gene signature from full-transcriptome data using machine-learning approaches to predict loco-regional control (LRC) of patients with human papilloma virus (HPV)-negative locally advanced head and neck squamous cell carcinoma (HNSCC), who received postoperative radio(chemo)therapy (PORT-C). Materials and methods: Gene expression analysis was performed using Affymetrix GeneChip Human Transcriptome Array 2.0 on a multicentre retrospective training cohort of 128 patients and an independent validation cohort of 114 patients from the German Cancer Consortium - Radiation Oncology Group (DKTK-ROG). Genes were filtered based on differential gene expression analyses and Cox regression. The identified gene signature was combined with clinical parameters and with previously identified genes related to stem cells and hypoxia. Technical validation was performed using nanoString technology. Results: We identified a 6-gene signature consisting of four individual genes CAV1, GPX8, IGLV3-25, TGFBI, and one metagene combining the highly correlated genes INHBA and SERPINE1. This signature was prognostic for LRC on the training data (ci = 0.84) and in validation (ci = 0.63) with a significant patient stratification into two risk groups (p = 0.005). Combining the 6-gene signature with the clinical parameters T stage and tumour localisation as well as the cancer stem cell marker CD44 and the 15-gene hypoxia-associated signature improved the validation performance (ci = 0.69, p = 0.001). Conclusion: We have developed and validated a novel prognostic 6-gene signature for LRC of HNSCC patients with HPV-negative tumours treated by PORT-C. After successful prospective validation the signature can be part of clinical trials on the individualization of radiotherapy.

This article compares the expression and applicability of biomarkers, from single genes and gene signatures, identified in patients with locally advanced head and neck squamous cell carcinoma using the GeneChip Human Transcriptome Array 2.0, nCounter, and real-time PCR analyses. Two multicenter, retrospective cohorts of patients with head and neck squamous cell carcinoma from the German Cancer Consortium Radiation Oncology Group who received postoperative radiochemotherapy or primary radiochemotherapy were considered. Real-time PCR was performed for a limited number of 38 genes of the cohort who received postoperative radiochemotherapy only. Correlations between the methods were evaluated by the Spearman rank correlation coefficient. Patients were stratified based on the expression of putative cancer stem cell markers, hypoxia-associated gene signatures, and a previously developed seven-gene signature. Locoregional tumor control was compared between these patient subgroups using log-rank tests. Gene expressions obtained from nCounter analyses were moderately correlated to GeneChip analyses (median r Z approximately 0.68). A higher correlation was obtained between nCounter analyses and real-time PCR (median r Z 0.84). Significant associations with locoregional tumor control were observed for most of the considered biomarkers evaluated by GeneChip and nCounter analyses. In general, all applied biomarkers (single genes and gene signatures) classified approximately 70% to 85% of the patients similarly. Overall, gene signatures seem to be more robust and had a better transferability among different measurement methods.

In search of new biomarkers suitable for the diagnosis and treatment of prostate cancer, genome-wide transcriptome sequencing was carried out with tissue specimens from 40 prostate cancer (PCa) and 8 benign prostate hyperplasia patients. We identified two intergenic long non-coding transcripts, located in close genomic proximity, which are highly expressed in PCa. Microarray studies on a larger cohort comprising 155 patients showed a profound diagnostic potential of these transcripts (AUC~0.94), which we designated as tumor associated prostate cancer increased lncRNA (TAPIR-1 and -2). To test their therapeutic potential, knockdown experiments with siRNA were carried out. The knockdown caused an increase in the p53/TP53 tumor suppressor protein level followed by downregulation of a large number of cell cycle- and DNA-damage repair key regulators. Furthermore, in radiation therapy resistant tumor cells, the knockdown leads to a renewed sensitization of these cells to radiation treatment. Accordingly, in a preclinical PCa xenograft model in mice, the systemic application of nanoparticles loaded with siRNA targeting TAPIR-1 significantly reduced tumor growth. These findings point to a crucial role of TAPIR-1 and -2 in PCa.

Purpose or Objective: To personalize radiotherapy of locally advanced head and neck squamous cell carcinoma (HNSCC), gene signatures have been developed that are related to processes involved in radioresistance of HNSCC. To date, most of these signatures were developed for patients who have received primary radiotherapy (pRCTx). The aim of our study was (I) to apply existing gene signatures related to different radio-biological processes for patients treated with postoperative radiochemotherapy (PORT-C) and (II) to validate these signatures in xenograft models. Material and Methods: This study is based on two cohorts: (i) 128 patients with locally advanced HVP16 DNA-negative HNSCC who received PORT-C in a multicentre retrospective study of the German Cancer Consortium Radiation Oncology Group (DKTK-ROG) between 2005 and 2011 and (ii) 60 mice bearing xenografts of 10 cell lines of human squamous cell carcinoma. Gene signatures related to cancer stem cell (CSC) markers [1], DNA repair [2], hypoxia [3], radiosensitivity [4] and epithelial mesenchymal transition (EMT) [5] were selected. Whole transcriptome analysis was performed using the HTA 2.0 Array (Affymetrix). Based on the gene signatures, risk groups were generated as described in the original publications (i) for the PORT-C cohort and (ii) for the xenograft data. The primary endpoint for the PORT-C cohort was loco-regional control (LRC), while the endpoint for the xenograft data was the dose to control 50% of the tumours (TCD50). The endpoints were evaluated byCox regression and the Mann-Whitney-U test, respectively. Results: All signatures were able to stratify patients treated with PORT-C into risk groups with a significant difference in LRC (figure A) or showed a statistical trend (radiosensitivity signature). This was confirmed in multivariable Cox regression including age and T stage. In the xenograft models, the gene signatures based on cancer stem cell markers, hypoxia and radiosensitivity showed a signif

The aim of this study was to identify and independently validate a novel gene signature predicting loco-regional tumor control (LRC) for treatment individualization of patients with locally advanced head and neck squamous cell carcinomas (HNSCC) who are treated with postoperative radio(chemo)therapy (PORT-C). Gene expression analyses were performed using nanoString technology on a multicenter training cohort of 195 patients and an independent validation cohort of 142 patients. The analyzed gene set was composed hypothesis-driven and included genes with previously reported association to radio(chemo)sensitivity or resistance to radio(chemo)therapy. Gene selection and model building were performed within a specifically developed statistical framework comparing several machine-learning algorithms. This procedure identified a 7-gene signature for HPV16 DNA negative tumors consisting of the genes: SERPINE1, INHBA, P4HA2, ACTN1, HILPDA, CD24 and TCF3. The 7-gene signature was used to fit a multivariable Cox model to the training data (concordance index, ci=0.84), which was successfully validated (ci=0.71). Thus, the signature showed improved performance compared to a clinical model (ci=0.66) and to a previously published model including hypoxia-associated genes and cancer stem cell markers (ci=0.65). Furthermore, the signature was used to stratify patients into groups with low and high risk of recurrence. Significant differences in LRC between these groups were found in training and validation (p<0.001). A prospective validation is planned in an ongoing prospective clinical trial of the DKTK-ROG before potential application in clinical trials for patient stratification.

Purpose: Tumour hypoxia is well known to increase radio-resistance of tumours. In a recent prospective biomarker imaging trial, hypoxia has been measured by [18F]fluoromisonidazole positron emission tomography (FMISO-PET) scans [1,2]. Here, we compared hypoxia imaging with the expression of hypoxia-associated gene signatures for patients with locally advanced head and neck squamous cell carcinoma (HNSCC) treated by primary radiochemotherapy (RCHT). Material and methods: FMISO-PET imaging and gene expression analyses were performed on the cohort of 50 HNSCC patients [1,2]. For this study, the FMISO-PET parameters tumour-to-background ratio (TBPpeak) and hypoxic tumour volume (HV1.6) analysed before RCHT were considered. Expressions of 15-, 26- and 30-gene hypoxia-associated signatures [3-5] were analysed from formalin-fixed paraffin-embedded (FFPE) tumour biopsies obtained before RCHT using the GeneChip® Human Transcriptome Array 2.0 (Affymetrix) and nanoString analysis. Gene expressions were compared between the two methods using the Pearson correlation coefficient. Linear regression was applied to relate TBRpeak and HV1.6 to the mean expression of the gene signatures, including the interaction with tumour volume which was assessed on the planning CT by an experienced radiation oncologist. The association of FMISO-PET parameters and gene expressions to loco-regional control (LRC) and progression-free survival (PFS) was assessed by Cox regression. Results: The mean expressions of all hypoxia-associated gene signatures were highly correlated between Affymetrix and nanoString analyses (R>0.5). While TBRpeak and HV1.6 were weakly correlated with the expression of hypoxia-associated genes alone, significant correlations were observed if the interaction term of gene expression and tumour volume was included (R>0.5). Both FMISO-PET parameters were significantly correlated with LRC and PFS (p<0.01), while the combination of hypoxia-associated gene expressions and their inte

PO-0616: HPV, CSC marker expression and tumor hypoxia as prognosticators for LRC in patients with HNSCC

A gene signature predicting loco-regional control (LRC) of locally advanced head and neck squamous cell carcinoma (HNSCC) after postoperative radiochemotherapy (PORTC) will be evaluated using nanoString and RNA microarray data. The prognostic power of the signature as well as the correlation between both methods is evaluated to underline the robustness of the proposed signature.

Valid HER2 testing is essential for optimal therapy of patients with HER2 positive gastric cancer and the correct use of first-line treatment. While each breast cancer is routinely being tested for the HER2 status, HER2 testing in gastric cancer has still not become part of the routine and is often only done upon request by the therapist. An interdisciplinary German expert group took the challenges of HER2 testing in gastric cancer as an opportunity to address essential aspects and questions for the practical use of HER2 testing in this indication from the perspective of pathologists and therapists. The recommendations made in this manuscript reflect the consensus of all participants and correspond to their opinions and long-term experience.

OBJECTIVE: To investigate the impact of the tumour volume, HPV status, cancer stem cell (CSC) marker expression and hypoxia gene signatures, as potential markers of radiobiological mechanisms of radioresistance, in a contemporary cohort of patients with locally advanced head and neck squamous cell carcinoma (HNSCC), who received primary radiochemotherapy (RCTx). MATERIALS AND METHODS: For 158 patients with locally advanced HNSCC of the oral cavity, oropharynx or hypopharynx who were treated at six DKTK partner sites, the impact of tumour volume, HPV DNA, p16 overexpression, p53 expression, CSC marker expression and hypoxia-associated gene signatures on outcome of primary RCTx was retrospectively analyzed. The primary endpoint of this study was loco-regional control (LRC). RESULTS: Univariate Cox regression revealed a significant impact of tumour volume, p16 overexpression, and SLC3A2 and CD44 protein expression on LRC. The tumour hypoxia classification showed a significant impact only for small tumours. In multivariate analyses an independent correlation of tumour volume, SLC3A2 expression, and the 15-gene hypoxia signature with LRC was identified (CD44 protein n/a because of no event in the CD44-negative group). Logistic modelling showed that inclusion of CD44 protein expression and p16 overexpression significantly improved the performance to predict LRC at 2years compared to the model with tumour volume alone. CONCLUSIONS: Tumour volume, HPV status, CSC marker expression and hypoxia gene signatures are potential prognostic biomarkers for patients with locally advanced HNSCC, who were treated by primary RCTx. The study also supports that the individual tumour volumes should generally be included in biomarker studies and that panels of biomarkers are superior to individual parameters.

Objective To validate the impact of HPV status, cancer stem cell (CSC) marker expression and tumour hypoxia status in patients with locally advanced head and neck squamous cell carcinoma (HNSCC), who received postoperative radiotherapy. The results of the exploration cohort have previously been reported by the German Cancer Consortium Radiation Oncology Group (DKTK-ROG; Lohaus et al., 2014; Linge et al., 2016). Materials and methods For 152 patients with locally advanced HNSCC the impact of HPV16 DNA status, CSC marker expression and hypoxia-associated gene signatures on outcome of postoperative radiotherapy were retrospectively analysed. Out of them, 40 patients received postoperative radiochemotherapy. Cox models presented in a previous study were validated using the concordance index as a performance measure. The primary endpoint of this study was loco-regional control. Results were compared to those previously reported by DKTK-ROG. Results Loco-regional control, freedom from distant metastases and overall survival were inferior to the previously reported cohort. Despite of this, the prognostic value of the combination of HPV infection status, CSC marker expression (SLC3A2) and tumour hypoxia status could be validated in univariate analyses using an independent validation cohort. For multivariate models, the concordance index was between 0.58 and 0.69 in validation, indicating a good prognostic performance of the models. The inclusion of CD44 and the 15-gene hypoxia signature moderately improved the performance compared to a baseline model without CSC markers or hypoxia classifiers. Conclusions The HPV status, CSC marker expression of CD44 and SLC3A2 as well as hypoxia status are potential prognostic biomarkers for patients with locally advanced HNSCC treated by postoperative radiotherapy.

PURPOSE: To investigate the impact of hypoxia-induced gene expression and cancer stem cell (CSC) marker expression on outcome of postoperative cisplatin-based radiochemotherapy (PORT-C) in patients with locally advanced head and neck squamous cell carcinoma (HNSCC). EXPERIMENTAL DESIGN: Expression of the CSC markers CD44, MET, and SLC3A2, and hypoxia gene signatures were analyzed in the resected primary tumors using RT-PCR and nanoString technology in a multicenter retrospective cohort of 195 patients. CD44 protein expression was further analyzed in tissue microarrays. Primary endpoint was locoregional tumor control. RESULTS: Univariate analysis showed that hypoxia-induced gene expression was significantly associated with a high risk of locoregional recurrence using the 15-gene signature (P = 0.010) or the 26-gene signature (P = 0.002). In multivariate analyses, in patients with HPV16 DNA-negative but not with HPV16 DNA-positive tumors the effect of hypoxia-induced genes on locoregional control was apparent (15-gene signature: HR 4.54, P = 0.006; 26-gene signature: HR 10.27, P = 0.024). Furthermore, MET, SLC3A2, CD44, and CD44 protein showed an association with locoregional tumor control in multivariate analyses (MET: HR 3.71, P = 0.016; SLC3A2: HR 8.54, P = 0.037; CD44: HR 3.36, P = 0.054; CD44 protein n/a because of no event in the CD44-negative group) in the HPV16 DNA-negative subgroup. CONCLUSIONS: We have shown for the first time that high hypoxia-induced gene expression and high CSC marker expression levels correlate with tumor recurrence after PORT-C in patients with HPV16 DNA-negative HNSCC. After validation in a currently ongoing prospective trial, these parameters may help to further stratify patients for individualized treatment de-escalation or intensification strategies. Clin Cancer Res; 22(11); 2639-49. ©2016 AACR.