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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 chronic intratumoral hypoxia. Experimental Design: A DNA-methylome–based tumor hypoxia classifier (Hypoxia-M) was trained in the TCGA (The Cancer Genome Atlas)-HNSCC cohort based on matched assignments using gene expression–based signatures of hypoxia (Hypoxia-GES). Hypoxia-M was validated in a multicenter DKTK-ROG trial consisting of human papillomavirus (HPV)–negative patients with HNSCC treated with primary radiochemotherapy (RCHT). Results: Although hypoxia-GES failed to stratify patients in the DKTK-ROG, Hypoxia-M was independently prognostic for local recurrence (HR, 4.3; P = 0.001) and overall survival (HR, 2.34; P = 0.03) but not distant metastasis after RCHT in both cohorts. Hypoxia-M status was inversely associated with CD8 T-cell infiltration in both cohorts. Hypoxia-M was further prognostic in the TCGA-PanCancer cohort (HR, 1.83; P = 0.04), underscoring the breadth of this classifier for predicting tumor hypoxia status. Conclusions: Our findings highlight an unexplored avenue for DNA methylation–based classifiers as biomarkers of tumoral hypoxia for identifying high-risk features in patients with HNSCC tumors.

Purpose Radiolucent anterior and posterior implants by carbon fiber–reinforced polyetheretherketone (CFR PEEK) aim to improve treatment of primary and secondary tumors of the spine during the last years. The aim of this study was to evaluate clinical and radiological outcomes after dorsoventral instrumentation using a CFR PEEK implant in a cohort of patients representing clinical reality. Methods A total of 25 patients with tumor manifestation of the thoracic and lumbar spine underwent vertebral body replacement (VBR) using an expandable CFR PEEK implant between January 2021 and January 2022. Patient outcome, complications, and radiographic follow-up were analyzed. Results A consecutive series aged 65.8 ± 14.7 (27.6–91.2) years were treated at 37 vertebrae of tumor manifestation, including two cases (8.0%) of primary tumor as well as 23 cases (92.0%) of spinal metastases. Overall, 26 cages covering a median of 1 level (1–4) were implanted. Duration of surgery was 134 ± 104 (65–576) min, with a blood loss of 792 ± 785 (100–4000) ml. No intraoperative cage revision was required. Surgical complications were reported in three (12.0%) cases including hemothorax in two cases (one intraoperative, one postoperative) and atrophic wound healing disorder in one case. In two cases (8.0%), revision surgery was performed (fracture of the adjacent tumorous vertebrae, progressive construct failure regarding cage subsidence). No implant failure was observed. Conclusion VBR using CFR PEEK cages represents a legitimate surgical strategy which opens a variety of improvements—especially in patients in need of postoperative radiotherapy of the spine and MRI-based follow-up examinations.

Purpose To review existing scientific literature on mobile applications (apps) in the field of radiation oncology and to evaluate characteristics of commercially available apps across different platforms. Methods A systematic review of the literature for publications presenting apps in the field of radiation oncology was carried out using the PubMed database, Cochrane library, Google Scholar, and annual meetings of major radiation oncology societies. Additionally, the two major marketplaces for apps, App Store and Play Store, were searched for available radiation oncology apps for patients and health care professionals (HCP). Results A total of 38 original publications which met the inclusion criteria were identified. Within those publications, 32 apps were developed for patients and 6 for HCP. The vast majority of patient apps focused on documenting electronic patient-reported outcomes (ePROs). In the two major marketplaces, 26 apps were found, mainly supporting HCP with dose calculations. Conclusion Apps used in (and for) scientific research in radiation oncology are rarely available for patients and HCP in common marketplaces.

Multi-view classification with limited sample size and data augmentation is a very common machine learning (ML) problem in medicine. With limited data, a triplet network approach for two-stage representation learning has been proposed. However, effective training and verifying the features from the representation network for their suitability in subsequent classifiers are still unsolved problems. Although typical distance-based metrics for the training capture the overall class separability of the features, the performance according to these metrics does not always lead to an optimal classification. Consequently, an exhaustive tuning with all feature-classifier combinations is required to search for the best end result. To overcome this challenge, we developed a novel nearest-neighbor (NN) validation strategy based on the triplet metric. This strategy is supported by a theoretical foundation to provide the best selection of the features with a lower bound of the highest end performance. The proposed strategy is a transparent approach to identify whether to improve the features or the classifier. This avoids the need for repeated tuning. Our evaluations on real-world medical imaging tasks (i.e., radiation therapy delivery error prediction and sarcoma survival prediction) show that our strategy is superior to other common deep representation learning baselines [i.e., autoencoder (AE) and softmax]. The strategy addresses the issue of feature's interpretability which enables more holistic feature creation such that the medical experts can focus on specifying relevant data as opposed to tedious feature engineering.

Immune checkpoint inhibitors (ICIs) have revolutionized cancer therapy. However, structured knowledge to mitigate a patient's specific risk of developing adverse events are limited. Nevertheless, there is an exponential growth of clinical studies combining conventional therapies such as radiation therapy (RT) with ICIs. Cutaneous reactions are among the most common adverse events after monotherapy with either ICIs or RT. So far, little is known about interindividual differences for the risk of developing severe tissue toxicity after the combination of RT with ICIs, and the underlying biological mechanisms are ill defined. We used experimental models of RT-induced skin injury to analyze skin toxicity after simultaneous application of ICIs. We compared different RT regimens such as fractionated or stereotactic RT with varying dose intensity. Strikingly, we found that simultaneous application of RT and ICIs did not significantly aggravate acute skin injury in two different mouse strains. Detailed examination of long-term tissue damage of the skin revealed similar signs of epidermal hyperplasia, dermal fibrosis, and adnexal atrophy. In summary, we here present the first experimental study demonstrating the excellent safety profiles of concurrent treatment with RT and ICIs. These findings will help to interpret the development of adverse events of the skin after radioimmunotherapy and guide the design of new clinical trials and clinical decision-making in individual cases. © 2022 The Authors. The Journal of Pathology published by John Wileyamp; Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

To analyze long-term results of two multicenter prospective single-arm trials (ARO-2010-01 and ARO-2013-04) investigating adjuvant hypofractionated radiotherapy (HF) with simultaneous integrated boost (SIB) after breast-conserving surgery (BCS).Eligible patients had histopathologically confirmed unifocal breast cancer planned for whole breast irradiation plus boost radiotherapy to the tumor bed. In both studies, a total dose of 40 Gy was applied to the whole breast and of 48 Gy to the tumor bed in 16 fractions of 2.5 and 3.0 Gy. Radiotherapy could be given either as three-dimensional conformal radiotherapy (3D-CRT) or as intensity-modulated radiotherapy (IMRT). The primary study objectives were feasibility and security within an observation period of six months. The current investigation focuses on long-term efficacy and toxicities.Between 2011 and 2014, both trials enrolled 300 patients in total. Data from 274 of these patients could be used for the current analysis. The median follow-up time was 60 months and the 5-year disease-free survival 92.1%. Three patients suffered a local recurrence (after 36-72 months) while a regional recurrence occurred in one patient (after 17 months). The 5-year local control rate in the breast was 99.6%. 63.5% of all patients did not report any late radiation-related toxicity, 28.5% reported grade 1 and 7.3% grade 2 toxicities. The highest late toxicity was grade 3 in 2 women (0.7%, telangiectasia and lymphedema of the breast).Our analysis demonstrates favorable efficacy and low rates of long-term side effects of HF with SIB after BCS. Randomized controlled phase III trials are ongoing.

In the field of preclinical radiotherapy, many new developments were driven by technical innovations. To make research of different groups comparable in that context and reliable, high quality has to be maintained. Therefore, standardized protocols and programs should be used. Here we present a guideline for a comprehensive and efficient quality assurance program for an image-guided small animal irradiation system, which is meant to test all the involved subsystems (imaging, treatment planning, and the irradiation system in terms of geometric accuracy and dosimetric aspects) as well as the complete procedure (end-to-end test) in a time efficient way. The suggestions are developed on a Small Animal Radiation Research Platform (SARRP) from Xstrahl (Xstrahl Ltd., Camberley, UK) and are presented together with proposed frequencies (from monthly to yearly) and experiences on the duration of each test. All output and energy related measurements showed stable results within small variation. Also, the motorized parts (couch, gantry) and other geometrical alignments were very stable. For the checks of the imaging system, the results are highly dependent on the chosen protocol and differ according to the settings. We received nevertheless stable and comparably good results for our mainly used protocol. All investigated aspects of treatment planning were exactly fulfilled and also the end-to-end test showed satisfying values. The mean overall time we needed for our checks to have a well monitored machine is less than two hours per month.

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).

Type I interferons, particularly IFNα-2b, play essential roles in eliciting adaptive and innate immune responses, being implicated in the pathogenesis of various diseases, including cancer, and autoimmune and infectious diseases. Therefore, the development of a highly sensitive platform for analysis of either IFNα-2b or anti-IFNα-2b antibodies is of high importance to improve the diagnosis of various pathologies associated with the IFNα-2b disbalance. For evaluation of the anti-IFNα-2b antibody level, we have synthesized superparamagnetic iron oxide nanoparticles (SPIONs) coupled with the recombinant human IFNα-2b protein (SPIONs@IFNα-2b). Employing a magnetic relaxation switching assay (MRSw)-based nanosensor, we detected picomolar concentrations (0.36 pg/mL) of anti-INFα-2b antibodies. The high sensitivity of the real-time antibodies’ detection was ensured by the specificity of immune responses and the maintenance of resonance conditions for water spins by choosing a high-frequency filling of short radio-frequency pulses of the generator. The formation of a complex of the SPIONs@IFNα-2b nanoparticles with the anti-INFα-2b antibodies led to a cascade process of the formation of nanoparticle clusters, which was further enhanced by exposure to a strong (7.1 T) homogenous magnetic field. Obtained magnetic conjugates exhibited high negative MR contrast-enhancing properties (as shown by NMR studies) that were also preserved when particles were administered in vivo. Thus, we observed a 1.2-fold decrease of the T2 relaxation time in the liver following administration of magnetic conjugates as compared to the control. In conclusion, the developed MRSw assay based on SPIONs@IFNα-2b nanoparticles represents an alternative immunological probe for the estimation of anti-IFNα-2b antibodies that could be further employed in clinical studies.

Introduction Historical reservations regarding radiosurgery (SRS) for small-cell-lung-cancer (SCLC) brain metastases (BrM) include concerns for short-interval/diffuse CNS-progression, poor prognoses, and increased neurological mortality specific to SCLC histology. We compared SRS outcomes for SCLC and non-small-cell-lung-cancer (NSCLC) where SRS is well established. Methods Multicenter first-line SRS outcomes for SCLC and NSCLC from 2000-2022 were retrospectively collected (N=892-SCLC/N=4,785-NSCLC). Data from the prospective JLGK0901 SRS trial were analyzed as a comparison cohort (N=98-SCLC/N=794-NSCLC). OS and CNS-progression were analyzed using Cox-Proportional-Hazard and Fine-Gray models, respectively, with multivariable (MV) adjustment (including age/sex/performance-status/year/extracranial disease/BrM-number/BrM-volume). Mutation-stratified analyses were performed in propensity score-matched (PSM) retrospective cohorts of EGFR/ALK-positive-NSCLC, mutation-negative-NSCLC, and SCLC. Results OS was superior with NSCLC over SCLC in the retrospective dataset (median-OS, 10.5 vs 8.6 months, MV-p Conclusion After SRS, SCLC was associated with shorter OS compared to NSCLC. CNS progression occurred earlier in SCLC overall but was similar in patients matched on baseline characteristics. Neurological mortality, lesions at CNS-progression, and leptomeningeal-progression were comparable. These findings may better inform clinical decision-making for SCLC patients.

Supplementary Figure S2. (Top) Hypoxia-M V2 is prognostic in the DKTK-ROG cohort. Patients predicted to have higher tumor hypoxia by Hypoxia-M V2 had higher rates of death (p=0.0097), local recurrence (p=0.0037), distant metastasis (p=0.027) and disease progression (p=0.00096). (Bottom) Hypoxia-M V2 remains an independent prognosticator of OS, LR and disease progression after adjusting for age, smoking status, GTV and anatomical site. Additionally, there is a trend towards higher rates of distant metastasis (HR=2.33, p=0.13)

Supplementary Methods, Results, Table of Contents

Supplementary Table S2. Treatment Information for the validation cohort (n=88, DKTK-ROG)

Supplementary Figure 4 (Top). CD8 T cell enrichment is prognostic for Overall Survival (OS), local recurrence (LR) and disease progression but not for distant metastasis (DM) in HPV negative HNSCC in the DKTK-ROG cohort (n=88). (Bottom) After adjusting for Immune cell Infiltration, Hypoxia-M remained an independent prognosticator for local recurrence (HR=3.06, p

Supplementary Table S3. Distribution of clinical and biomarker-related characteristics between Methylation Hypoxia High vs Low in the training cohort (TCGA-HNSCC)

Supplementary Table S7. Distribution of clinical and biomarker-related characteristics between Methylation Hypoxia High vs Low in the TCGA-pancancer cohort

Supplementary Table S6. Contingency Table of Hypoxia-M and CD8-immunohistochemistry (IHC) staining for CD8-T cells

Statistical Output

Supplementary Table S5. Distribution of clinical and biomarker-related characteristics between Methylation Hypoxia High vs Low in the validation cohort (DKTK-ROG)

Supplementary Figure S3. (Top) Hypoxia-M V2 is associated with decreased OS in the TCGApancancer cohort (p

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 chronic intratumoral hypoxia.Experimental Design:A DNA-methylome–based tumor hypoxia classifier (Hypoxia-M) was trained in the TCGA (The Cancer Genome Atlas)-HNSCC cohort based on matched assignments using gene expression–based signatures of hypoxia (Hypoxia-GES). Hypoxia-M was validated in a multicenter DKTK-ROG trial consisting of human papillomavirus (HPV)–negative patients with HNSCC treated with primary radiochemotherapy (RCHT).Results:Although hypoxia-GES failed to stratify patients in the DKTK-ROG, Hypoxia-M was independently prognostic for local recurrence (HR, 4.3; P = 0.001) and overall survival (HR, 2.34; P = 0.03) but not distant metastasis after RCHT in both cohorts. Hypoxia-M status was inversely associated with CD8 T-cell infiltration in both cohorts. Hypoxia-M was further prognostic in the TCGA-PanCancer cohort (HR, 1.83; P = 0.04), underscoring the breadth of this classifier for predicting tumor hypoxia status.Conclusions:Our findings highlight an unexplored avenue for DNA methylation–based classifiers as biomarkers of tumoral hypoxia for identifying high-risk features in patients with HNSCC tumors.

BackgroundMany automatic approaches to brain tumor segmentation employ multiple magnetic resonance imaging (MRI) sequences. The goal of this project was to compare different combinations of input sequences to determine which MRI sequences are needed for effective automated brain metastasis (BM) segmentation.MethodsWe analyzed preoperative imaging (T1-weighted sequence ± contrast-enhancement (T1/T1-CE), T2-weighted sequence (T2), and T2 fluid-attenuated inversion recovery (T2-FLAIR) sequence) from 333 patients with BMs from six centers. A baseline 3D U-Net with all four sequences and six U-Nets with plausible sequence combinations (T1-CE, T1, T2-FLAIR, T1-CE+T2-FLAIR, T1-CE+T1+T2-FLAIR, T1-CE+T1) were trained on 239 patients from two centers and subsequently tested on an external cohort of 94 patients from four centers.ResultsThe model based on T1-CE alone achieved the best segmentation performance for BM segmentation with a median Dice similarity coefficient (DSC) of 0.96. Models trained without T1-CE performed worse (T1-only: DSC = 0.70 and T2-FLAIR-only: DSC = 0.72). For edema segmentation, models that included both T1-CE and T2-FLAIR performed best (DSC = 0.93), while the remaining four models without simultaneous inclusion of these both sequences reached a median DSC of 0.81-0.89.ConclusionsA T1-CE-only protocol suffices for the segmentation of BMs. The combination of T1-CE and T2-FLAIR is important for edema segmentation. Missing either T1-CE or T2-FLAIR decreases performance. These findings may improve imaging routines by omitting unnecessary sequences, thus allowing for faster procedures in daily clinical practice while enabling optimal neural network-based target definitions.

Supplementary Table S1. Multivariate Analysis for the Hypoxia-M and Brooks signature.

Background and purposeIn breast cancer patients, the increasing de-escalation of axillary surgery and the improving resolution of diagnostic imaging results in a more frequent detection of residual, radiographically suspect lymph nodes (sLN) after surgery. If resection of the remaining suspect lymph nodes is not feasible, a simultaneous boost to the lymph node metastases (LN-SIB) can be applied. However, literature lacks data regarding the outcome and safety of this technique.Materials and methodsWe included 48 patients with breast cancer and sLN in this retrospective study. All patients received a LN-SIB. The median dose to the breast or chest wall and the lymph node system was 50.4 Gy in 28 fractions. The median dose of the LN-SIB was 58.8 Gy / 2.1 Gy (56-63 Gy / 2-2.25 Gy). The brachial plexus was contoured in every case and the dose within the plexus PRV (+0.3-0.5mm) was limited to an EQD2 of 59 Gy. All patients received structured radiooncological and gynecological follow-up by clinically experienced physicians. Radiooncological follow-ups were at baseline, 6 weeks, 3 months, 6 months and subsequent annually after irradiation.ResultsThe median follow-up time was 557 days and ranged from 41 to 3373 days. Overall, 28 patients developed I°, 18 patients II° and 2 patients III° acute toxicity. There were no severe late side effects (≥ III°) observed during the follow-up period. The most frequent chronic side effect was fatigue. One patient (2.1 %) developed pain and mild paresthesia in the ipsilateral arm after radiotherapy. After a follow-up of 557 days (41 to 3373 days), in 8 patients a recurrence was observed (16.7%). In 4 patients the recurrence involved the regional lymph node system. Hence, local control in the lymph node drainage system after a median follow-up of 557 days was 91.6 %.ConclusionIf surgical re-dissection of residual lymph nodes is not feasible or refused by the patient, LN-SIB-irradiation can be considered as a potential treatment option. However, patients need to be informed about a higher risk of regional recurrence compared to surgery and an additional risk of acute and late toxicity compared to adjuvant radiotherapy without regional dose escalation.

Background: The aim of this study was to develop and validate radiogenomic models to predict the MDM2 gene amplification status and differentiate between ALTs and lipomas on preoperative MR images. Methods: MR images were obtained in 257 patients diagnosed with ALTs (n = 65) or lipomas (n = 192) using histology and the MDM2 gene analysis as a reference standard. The protocols included T2-, T1-, and fat-suppressed contrast-enhanced T1-weighted sequences. Additionally, 50 patients were obtained from a different hospital for external testing. Radiomic features were selected using mRMR. Using repeated nested cross-validation, the machine-learning models were trained on radiomic features and demographic information. For comparison, the external test set was evaluated by three radiology residents and one attending radiologist. Results: A LASSO classifier trained on radiomic features from all sequences performed best, with an AUC of 0.88, 70% sensitivity, 81% specificity, and 76% accuracy. In comparison, the radiology residents achieved 60–70% accuracy, 55–80% sensitivity, and 63–77% specificity, while the attending radiologist achieved 90% accuracy, 96% sensitivity, and 87% specificity. Conclusion: A radiogenomic model combining features from multiple MR sequences showed the best performance in predicting the MDM2 gene amplification status. The model showed a higher accuracy compared to the radiology residents, though lower compared to the attending radiologist.

Background The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has changed the lives of most humans worldwide. The aim of this study was to evaluate the impact of the SARS-CoV‑2 pandemic on health care professionals (HCPs) in radiation oncology facilities. Methods We distributed an online survey to HCPs in radiation oncology (physicians, medical physics experts, radiology assistants/radiation therapists, nurses, and administrative personnel). The survey was completed by 334 participants between May 23 and June 9, 2020. Results In 66.2% of the cases, HCPs reported a shortage of protective clothing. The protective measures were regarded as very reasonable by 47.4%, while 0.8% regarded them as not reasonable (rather reasonable: 44.0%; less reasonable 7.8%). 29.0% of the participants had children who needed care. The most frequently used care options were public emergency childcare (36.1%) and private childcare (e.g. relatives/friends). HCPs reported about additional work burden (fully agreed: 27.2%, rather agreed: 34.4%, less agreed: 28.2%, not agreed: 10.2%), and reduced work satisfaction (fully agreed: 11.7%, rather agreed: 29.6%, less agreed: 39.8%, not agreed: 18.9%). 12.9% and 29.0% of the participants were fully or rather mentally strained (less mentally strained: 44.0%, not mentally strained: 14.1%). Conclusion We must learn from this pandemic how to prepare for further outbreaks and similar conditions. This includes the vast availability of protective clothing and efficient tracing of infection chains among the HCPs, but also secured childcare programs and experienced mental health support are crucial. Further, work satisfaction and appreciation by employers is essential.

State-of-the-art deep survival prediction approaches expand network parameters to accommodate performance over a fine discretization of output time. For medical applications where data are limited, the regression-based Deepsurv approach is more advantageous because its continuous output design limits unnecessary network parameters. Despite the practical advantage, the typical network lacks control over the feature distribution causing the network to be more prone to noisy information and occasional poor prediction performance. We propose a novel projection loss as a regularizing objective to improve the time-to-event Deepsurv model. The loss formulation maximizes the lower bound of the multiple-correlation coefficient between the network’s features and the desired hazard value. Reducing the loss also theoretically lowers the upper bound on the likelihood of discordant pair and improves C-index performance. We observe superior performances and robustness of regularized Deepsurv over many state-of-the-art approaches in our experiments with five public medical datasets and two cross-cohort validation tasks.

Purpose:Human papillomavirus (HPV)–negative head and neck squamous cell carcinoma (HNSCC) is associated with unfavorable prognosis, while independent prognostic markers remain to be defined.Experimental Design:We retrospectively performed miRNA expression profiling. Patients were operated for locally advanced HPV-negative HNSCC and had received radiochemotherapy in eight different hospitals (DKTK-ROG; n = 85). Selection fulfilled comparable demographic, treatment, and follow-up characteristics. Findings were validated in an independent single-center patient sample (LMU-KKG; n = 77). A prognostic miRNA signature was developed for freedom from recurrence and tested for other endpoints. Recursive-partitioning analysis was performed on the miRNA signature, tumor and nodal stage, and extracapsular nodal spread. Technical validation used qRT-PCR. An miRNA–mRNA target network was generated and analyzed.Results:For DKTK-ROG and LMU-KKG patients, the median follow-up was 5.1 and 5.3 years, and the 5-year freedom from recurrence rate was 63.5% and 75.3%, respectively. A five-miRNA signature (hsa-let-7g-3p, hsa-miR-6508-5p, hsa-miR-210-5p, hsa-miR-4306, and hsa-miR-7161-3p) predicted freedom from recurrence in DKTK-ROG [hazard ratio (HR) 4.42; 95% confidence interval (CI), 1.98−9.88, P < 0.001], which was confirmed in LMU-KKG (HR 4.24; 95% CI, 1.40−12.81, P = 0.005). The signature also predicted overall survival (HR 3.03; 95% CI, 1.50−6.12, P = 0.001), recurrence-free survival (HR 3.16; 95% CI, 1.65−6.04, P < 0.001), and disease-specific survival (HR 5.12; 95% CI, 1.88−13.92, P < 0.001), all confirmed in LMU-KKG data. Adjustment for relevant covariates maintained the miRNA signature predicting all endpoints. Recursive-partitioning analysis of both samples combined classified patients into low (n = 17), low-intermediate (n = 80), high-intermediate (n = 48), or high risk (n = 17) for recurrence (P < 0.001).Conclusions:The five-miRNA signature is a strong and independent prognostic factor for disease recurrence and survival of patients with HPV-negative HNSCC.See related commentary by Clump et al., p. 1441

A. Correlation of CSC marker expressions. B. Multivariate analyses of stem cell markers and additional prognostic factors for all patients. HR = hazard ratio; 95% CI = 95 percent confidence interval ; ECE = extracapsular extension. C. Correlation of CSC marker expression and HPV16 DNA.

Correlation of tumor hypoxia using nanoString vs PCR.

Multivariate analyses of hypoxia-gene signatures and additional prognostic factors assessed for all patients. HR = hazard ratio; 95% CI = 95 percent confidence interval; ECE = extracapsular extension.

Purpose: Preclinical data indicate anti-invasive activity of APG101, a CD95 ligand (CD95L)–binding fusion protein, in glioblastoma.Experimental Design: Patients (N = 91) with glioblastoma at first or second progression were randomized 1:2 between second radiotherapy (rRT; 36 Gy; five times 2 Gy per week) or rRT+APG101 (400 mg weekly i.v.). Patient characteristics [N = 84 (26 patients rRT, 58 patients rRT+APG101)] were balanced.Results: Progression-free survival at 6 months (PFS-6) rates were 3.8% [95% confidence interval (CI), 0.1–19.6] for rRT and 20.7% (95% CI, 11.2–33.4) for rRT+APG101 (P = 0.048). Median PFS was 2.5 (95% CI, 2.3–3.8) months and 4.5 (95% CI, 3.7–5.4) months with a hazard ratio (HR) of 0.49 (95% CI, 0.27–0.88; P = 0.0162) adjusted for tumor size. Cox regression analysis adjusted for tumor size revealed a HR of 0.60 (95% CI, 0.36–1.01; P = 0.0559) for rRT+APG101 for death of any cause. Lower methylation levels at CpG2 in the CD95L promoter in the tumor conferred a stronger risk reduction (HR, 0.19; 95% CI, 0.06–0.58) for treatment with APG101, suggesting a potential biomarker.Conclusions: CD95 pathway inhibition in combination with rRT is an innovative concept with clinical efficacy. It warrants further clinical development. CD95L promoter methylation in the tumor may be developed as a biomarker. Clin Cancer Res; 20(24); 6304–13. ©2014 AACR.

Purpose: The aim of this study was to identify and independently validate a novel gene signature predicting locoregional tumor control (LRC) for treatment individualization of patients with locally advanced HPV-negative head and neck squamous cell carcinomas (HNSCC) who are treated with postoperative radio(chemo)therapy (PORT-C).Experimental Design: Gene expression analyses were performed using NanoString technology on a multicenter training cohort of 130 patients and an independent validation cohort of 121 patients. The analyzed gene set was composed of genes with a previously reported association with radio(chemo)sensitivity or resistance to radio(chemo)therapy. Gene selection and model building were performed comparing several machine-learning algorithms.Results: We identified a 7-gene signature consisting of the three individual genes HILPDA, CD24, TCF3, and one metagene combining the highly correlated genes SERPINE1, INHBA, P4HA2, and ACTN1. The 7-gene signature was used, in combination with clinical parameters, to fit a multivariable Cox model to the training data (concordance index, ci = 0.82), which was successfully validated (ci = 0.71). The signature showed improved performance compared with clinical parameters alone (ci = 0.66) and with a previously published model including hypoxia-associated genes and cancer stem cell markers (ci = 0.65). It was used to stratify patients into groups with low and high risk of recurrence, leading to significant differences in LRC in training and validation (P < 0.001).Conclusions: We have identified and validated the first hypothesis-based gene signature for HPV-negative HNSCC treated by PORT-C including genes related to several radiobiological aspects. A prospective validation is planned in an ongoing prospective clinical trial before potential application in clinical trials for patient stratification. Clin Cancer Res; 24(6); 1364–74. ©2018 AACR.

Univariate analyses of both hypoxia gene signatures using nanoString or RT-PCR analyses. HR = hazard ratio; 95% CI = 95 percent confidence interval.

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.

Univariate analyses of CSC markers. HR = hazard ratio; 95% CI = 95 percent confidence interval.

Combined multivariate analyses of HPV16 DNA, cancer stem cell markers, hypoxia and additional prognostic factors for all patients (endpoint loco-regional control). HR = hazard ratio; 95% CI = 95 percent confidence interval; ECE = extracapsular extension.

Supplemetary Tables 1-3

A. Correlation of hypoxia gene-signatures and HPV16 DNA. B. Correlation of CSC marker expression and HPV16 DNA.

Supplementary Figures 1-20

Acknowledgement. List of investigators and other study stuff at the individual sites.

CONSORT Statement

Table S1 Analyzed genes of the hypothesis-driven gene set. Table S2 Programs and packages used for evaluation. Figure S1 Results of repeated 3-fold cross validation for LRC. Figure S2 Mean oob ci depending of the signature size for LRC. Figure S3 Importance score for genes associated with LRC. Table S3 Increasing robustness by including highly correlated genes. Figure S4 Patient stratification by the 7-gene signature for LRC. Figure S5 Patient stratification by the 7-gene signature and clinical parameters for LRC. Table S4 Multivariable Cox regression of OS. Figure S6 Patient stratification by the 7-gene signature and clinical parameters for OS. Table S5 Multivariable Cox regression of DM. Figure S7 Patient stratification by the 7-gene signature and clinical parameters for DM. Table S6 Means and standard deviations of the 7-gene signature gene expressions. Table S7 Comparison of gene expressions between patient groups. Table S8 Hyper-parameters for feature selection algorithms and predictive models. Table S9 Patient characteristics of all patients. Figure S8 Identification of the final gene signature.

Suppl Figures S1-S4. S1: Genomic Localization of the CpG2 in the CD95 L promoter. S2: Survival probability according to CpG2 methylation status. S3: Survival probability according to CD95L expression as detected by IHC. S4 a and b: Cox regression data for CpG1 and 2 in the CD95L promoter.

Supplementary Data from Differentiation Therapy Exerts Antitumor Effects on Stem-like Glioma Cells

Supplementary Tables 1-4