Fig. 1: Overview of the study workflow.
From: The responses of HNSCC patients to immunotherapy are shown by two novel co-expression patterns
A Secretome data were collected from patient-derived fresh tumor explants, and RNAseq was obtained from two large HNSCC cohort studies. Multi-parameter immunofluorescence (mIF) of patient-derived explants was used to validate the results experimentally. B Surprisal analysis (SA) was carried out on the secretomes of explant supernatant and the RNA sequencing of the two large cohorts (Methods). In brief, proteins/genes whose expression levels deviate from the reference state in the same or opposing manners (upper right panel) are computed via the covariance matrix of the natural logarithms of the expression levels as dictated by the theory (middle panels and “Methods”). Transcripts/proteins that deviate from the steady state in a coordinated manner are grouped into unbalanced processes (lower panel). Several different protein–protein (mRNA-mRNA) unbalanced processes can be found in the entire population of cancer samples. C Patient-derived explants and available datasets of HNSCC patients were used to confirm the relationship between unbalanced processes associated with T-cell function and response to immunotherapies (IM) and patient survival.
