Profling of breast cancer cells using single-cell triomics analysis of DNA, RNA, and proteins with Tapestri chemistry

Cancer displays large heterogeneity both between and within tumors where intratumor heterogeneity can occur at genetical, transcriptional and translational level. The variability results in tumor cell subpopulations with distinct molecular and cellular characteristics, some of which can have therapy-resistant properties. To date it has been experimentally challenging to study tumor cell heterogeneity. Here, we present a single-cell triomics approach to assess DNA, RNA and protein simultaneously in thousands of single cells using microfluidics. First, we profiled two breast cancer cell lines, MCF7 and T-47D, cultured in monolayer with and without 5-fluorouracil treatment. Next, we generated cell-free patient-derived scaffolds (PDS) that we repopulated with MCF7 cells for 21 days. This experimental model system mimics in vivo tumor cell growth and is suitable for drug testing, such as chemotherapies. We profiled individual MCF7 cells cultured in different PDSs with and without 5-fluorouracil treatment using triomics. Our approach and data demonstrate that single-cell triomics is feasible, which opens up new means to decipher tumor heterogeneity at different layers. Overall design: Single-cell triomics using Tapestri chemistry (MissionBio) assessing DNA, RNA and protein in MCF7 and T-47D breast cancer cells grown in monolayer culture and MCF7 cells grown in patient-derived scaffold, with or without 5-fluorouracil.