Extended Data Fig. 4: Enrichment analysis for patient subgroups stratified by the protein abundance of either NDUFB8 or CEMIP2.

(a) Protein-protein interaction (PPI) network (left) centered on NDUFB8 and functional enrichment (right) for NDUFB8. PPI data was obtained from the STRING database, and functional enrichment analysis was performed using DAVID. P-values were calculated from the STRING database. Two-sided P-values were calculated. (b) Violin plots displaying the protein abundance of NDUFB8 and CEMIP2 between tumors and TATs. P-values were calculated using the Mann-Whitney U test. In the boxplot, a black line within the box marks the median. The bottom and top of the box are located at the 25^th and 75^th percentiles, respectively. The bars represent values that are more than 1.5 times the interquartile range from the border of each box. N = 281 biologically independent samples including 191 tumors and 90 TATs. Two-sided P-values were calculated. (c-d) Kaplan-Meier survival curves comparing OS between patient subgroups stratified by gemcitabine-included (Gem), non-gemcitabine-included (non-Gem), and without adjuvant therapy (No) according to the high/low abundance (median cutoff) of NDUFB8 (c) and CEMIP2 (d). P-values were calculated using the log-rank test, and the hazard ratios calculated using the univariable Cox regression analysis. (e-f) Kaplan-Meier survival curves comparing OS between patient subgroups stratified by adjuvant chemotherapy and the high/low expression of NDUFB8 in patients with LASSO score-low (e) or -high (f) in ‘RJ-cohort 1’. P-values were calculated using the log-rank test. (g) Associations of NDUFB8 and CEMIP2 abundance with proteomic profiles. Significantly enriched pathways were calculated using GSEA. (h) The fold changes of NDUFB8 and CEMIP2 in three pancreatic cell lines (HPNE, 8988 and CFPAC) and two PDOs (T1030411 and T983610). HPNE was used as an internal control, and β-actin used as a loading control. Error bars represent the means ± SD (n = 3 biologically independent experiments). Two-sided P-values were calculated. (i) The fold change of NDUFB8 and CEMIP2 in two PDAC cells (8988 and CFPAC) and two PDOs (T1030411 and T983610) upon gene silencing. Control plasmid-transfected cells were used as an internal control, and β-actin used as a loading control. Error bars represent the means ± SD (n = 3 biologically independent experiments). Two-sided P-values were calculated.