Supplementary Figures and Tables

Figure S1: Optimal peptide length analysis (related to Figure 1). The isothermal titration curves of NprR(∆HTH) with different length of NprX peptide are shown with their corresponding Kd values.


Figure S3
of the receiver operating characteristics (ROC) plot. The AUC was determined when examining the entire dataset or monotherapy patients only. In addition, the response prediction was evaluated based on the complete signature or only on the two proteins that are in the signature. B. Response prediction of the signature in a cohort following random exclusion of 12 patients. The histogram indicates the response prediction of 1000 such iterations. The AUC of combination therapy patient exclusion is indicated with a red dashed line (AUC = 0.7). C. Association between sex, age and smoking. D. Two-way ANNOVA test for determining the association between sex, age and smoking Figure S6: Consensus clusters in T0 and T1 proteomic data. A. Cumulative distribution function (CDF) plot for T1 data. The plot displays the CDF of the consensus matrix for each k, indicated by different colors, as estimated by a histogram of 100 bins. B. Delta area plot for T1 data. The plot displays the relative change in area under the CDF curve, comparing k and k-1. C. CDF plot for T0 data. D. Delta area plot for T0 data. E. Unsupervised analysis using consensus clustering algorithm identified 3 consensus clusters based on T0 data. CC, consensus cluster. F. Voronoi plots displaying the functional groups of the proteins that are present at higher levels in each consensus cluster at T0. Each polygon represents a protein. Polygon size correlates with the difference between responders and non-responders. Proteins with similar functions are grouped together.
BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) Figure S7: Exploration of the ten T1 differentially expressed proteins. A. Expression levels of the ten differentially expressed proteins at T1 in responders and non-responders. B. Survival curves demonstrating association between overall survival and T1 expression levels of each of the ten differentially expressed proteins. Patients were divided into two groups based on the expression level of the examined proteins. The analysis was done using log rank test. C-E. Expression levels of the differentially expressed proteins in healthy tissues (C) tumors (D) and blood cells (E). The data were obtained from the Human Protein Atlas. proteins present at significantly higher levels at T0 and/or T1. The Y-axis designates the log2 average difference between non-responders and responders. B. Venn diagram summarizing the number of neutrophil related proteins at higher levels in non-responders at T0 (blue) or T1 (light blue). C-E. The number of neutrophils at T0 and T1 in the entire cohort (C), in non-responders (D) and in responders (E). F-G. Neutrophil levels in non-responders and responders at T0 (F) and T1 12   Table S1. Clinical data Table S2. Proteomics data.
Source tables 1 and 2 are considered as Table S1 and S2.
BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s)   Table S4: Results of ANOVA test between the patient clusters (T1). The proteins higher in each cluster are indicated under the "Cluster" column, followed by -log10 p-value and the q-value (FDR). The identifiers are then indicated as target name (RayBiotech definition), Uniprot ID and gene name.      Table S7A: Student's t-test results of T0 data. The "p-value < 0.05" column indicates whether the protein passed the t-test with p-value below 0.05. The "FDR<0.1" column indicates whether the protein was significantly different between responders and nonresponders, with FDR < 0.1. The column "direction" indicates whether the protein was higher in responders or non-responders. The p-value (-log10 scale) and the q-value (FDR)   Table S7C: Student's t-test results of T1 data in monotherapy patients. The "p-value < 0.05" column indicates whether the protein passed the t-test with p-value below 0.05.
The "FDR<0.1" column indicates whether the protein was significantly different between responders and non-responders, with FDR < 0.1. "Direction" column indicates whether the protein was higher in responders or non-responders. The p-value (-log10 scale) and the q-value (FDR) are indicated, followed by the average difference between nonresponders and responders (log2 scale) and the T-test statistics. The protein identifiers are indicated as Uniprot IDs and gene name.   Table S8B. Significantly enriched biological pathways at T1 following p-value < 0.05 ttest. Enrichment was evaluated using Fisher exact test, while the enrichment factor is indicated in the table. All categories were significantly enriched (Benjamini Hochberg FDR < 0.1). Enrichment factor above and below 1 indicates enrichment or de-enrichment, respectively. Benj. Hoch. FDR, Benjamini Hochberg false discovery rate.