Additional file 1 of Prognostic biomarkers for the response to the radiosensitizer nimorazole combined with RCTx: a pre-clinical trial in HNSCC xenografts
Creators: name: Koi, Lydia
name: Bitto, Verena
name: Weise, Corina
name: Möbius, Lisa
name: Linge, Annett
name: Löck, Steffen
name: Yaromina, Ala
name: Besso, María José
name: Valentini, Chiara
name: Pfeifer, Manuel
name: Overgaard, Jens
name: Zips, Daniel
name: Kurth, Ina
name: Krause, Mechthild
name: Baumann, Michael
Publisher: name: figshare
Year: 2023
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Mathematical Sciences not elsewhere classified
subject: Marine Biology
subject: Cancer

description: Additional file 1: Figure S1. Rolling mean relative body weight of all tumor models over time of experiment, starting from the first treatment (day = 0). Vertical line represents approximate time point at which treatments were finished and follow-up measurements were carried out. Figure S2. Pseudo-colored images of representative sections from SAS (responder to nimorazole addition) and CAL33 (non-responder to nimorazole addition) tumors untreated and after 10fx RCTx treated with nimorazole. Green: hypoxia, pimonidazole; blue: perfusion, Hoechst 33342; red: vascular endothelium, CD31; grey necrotic area. Nimorazole abbreviated as nimo. Figure S3. Histological evaluation of (A) tumor volume (B) pimonidazole hypoxic fraction (pHF), (C) perfused fraction (PF), (D) relative vascular area (RVA) and (E) necrotic fraction (NF) and for seven different tumor models, untreated (leftmost bars) and after RCTx with 10 fractions in 2 weeks and cisplatin in combination with carrier (middle bars) or nimorazole (rightmost bars). The box plots displayed adhere to the Tukey style (see Methods). P value cutpoints: **** &lt; 1e-04, *** &lt; 0.001, ** &lt; 0.01, * &lt; 0.05. Figure S4. Hypoxia estimation using previously published gene signatures. (A) Expression values of hypoxia 15-gene signature. Only two genes (ADM, FAM162A) emerged in differential gene expression (DGE) analysis to be significantly different between responding (FaDu, SAS) and non-responding (UT45, CAL33, SAT) models to nimorazole. Of note, Lox is expressed inversely to other genes among responders and non-responders to nimorazole addition. Shown are only RCTx + nimorazole samples. The box plots displayed adhere to the Tukey style (see Methods). (B) Heatmap analysis of hypoxia 15 and hypoxia 26 gene signature on all treatment arms for individual tumor models. No clear expression pattern among responding, low-responding and non-responding models to nimorazole addition emerged for hypoxia-related genes. Only UT8 (low-responder to nimorazole addition) expressed a clear downregulation of genes from the two hypoxia gene signatures for both, RCTx + nimorazole and RCTx + carrier arm. Data is z-transformed, yellow: high expression, grey: low expression. Figure S5. Kaplan–Meier estimates of loco-regional control on retrospective HNSCC cohort of the DKTK-ROG that received primary RCTx. Patients are split according to their gene expression into one of two groups. Patients with gene expression higher than gene’s mean expression are categorized into”high”, patients with gene expression lower or equal to gene’s mean expression are categorized into”low”. Individual genes belong to differentially expressed genes (DEG), p values corresponds to log-rank test and were not adjusted for multiple testing. Table S1. Start mean tumor volume and corresponding 95% confidence intervals for the seven different tumor models and their assigned treatment group. Mean tumor volumes were calculated before animals received the first treatment. Table S2. Follow-up information for the seven different tumor models irradiated with fractionated irradiation within 6 weeks in combination with cisplatin and nimorazole or carrier. Table S3. Results of differential gene expression (DGE) analysis between nimorazole-responding and non-responding tumor models to nimorazole addition in RCTx + nimorazole treated samples. Shown are estimates of the log2-fold-changes per contrast. Genes are ranked in descending order according to their adjusted p value (all p. adj. &lt; 0.001).