Gene expression profiling of acidic cell compartments from HCT116 spheroids.

We deciphered specific traits of acidic cancer cells by comparing gene expression profiles in acidic (negative K-pHLIP and positive pHLIP cells) and buffered (negative pHLIP cells) cell compartments from HCT116 colorectal cancer 3D spheroids. HCT116 3D spheroids were labeled with AlexaFluor 568 pHLIP (pH low insertion peptide) and AlexaFluor 594 K-pHLIP (pH-independent control peptide) conjugated peptides, and sorted by FACS to isolate negative K-pHLIP and positive pHLIP cells (acidic) from pHLIP-negative cell population (buffered). We then subjected both cell populations to RNA-seq analysis to compare the transcriptomes acidic vs. buffered cancer cells.