Fig 1.
Consort diagram of patient recruitment.
Fig 2.
Increased expression of genes associated with the innate immune response and inflammation, and reduced expression of genes associated with T and NK cell functions in patients on intensive phase treatment.
(a) Principal component analysis (PCA) of gene expression data derived from RNA-sequencing. Principal component (PC1) and PC2 accounts for 26% and 19%, respectively, variance of dataset. Each dot represents one patient from the study; different colours represent different phases of MABC-PD treatment and disease progression. (b) Differential expression analysis was conducted using Deseq2, imposing a threshold of adjusted p-value <0.05 and fold change of >1.3 and <-1.3. The number of differentially expressed genes (DEGs) in different phases of MABC-PD treatment and disease progression relative to healthy controls is presented. (c-d) Enrichr geneset pathway enrichment analysis (GSEA) using the BTM-plus module was conducted for identified DEGs. Pathways (c) positively and (d) negatively enriched in MABC-PD patients on intensive phase treatment compared to healthy controls. (e-f) Unsupervised clustering of leading-edge genes (LEGs) from the top two (e) positively and (f) negatively enriched genesets in MABC-PD patients on intensive phase treatment compared to healthy controls. Z-score of VST normalized gene counts are presented.
Fig 3.
Elevated plasma concentrations of TNFSF10, IFN
γ, IL17F, and IL17C in MABC-PD patients on intensive phase treatment compared to healthy controls. (a) Unsupervised clustering of plasma concentration of proteins in different treatment phases of MABC-PD. Z-scores of plasma concentrations are presented. (b-e) Box and whiskers plot comparing plasma concentration of (b) TNFSF10, (c) IFNγ, (d) IL17F, and (e) IL17C between patients on intensive phase treatment and healthy controls. Student’s t-test was used to test the difference in mean between the two groups. (e-f) Pearson’s correlation between (f) IFNγ, (g) IL17F, and (h) IL17C plasma concentration and average VST-transformed counts of T cell associated genes. n = 3 (intensive phase); n = 8 (healthy controls).
Fig 4.
Immune profiling discriminates MABC-PD patients on treatment from healthy controls.
Receiver operating characteristic (ROC) analysis was conducted with treatment group classified as MABC-PD patients on intensive and continuation phase treatment; no treatment group included healthy controls. (a-c) ROC curve of (a) IFNγ, (b) IL17F, and (c) IL17C. (e-f) Dotplot of plasma concentration of (e) IFNγ and (f) IL17F in patients at different phases of MABC-PD treatment, patients on watchful waiting, and healthy controls. The red horizontal line depicts cutoff values as defined by ROC analysis. Darker shades of pink and grey points depict relapsed MABC-PD patients who have previously received multiple treatment courses; lighter shades of pink and grey points depict MABC-PD patients in their first treatment course.