A High-Throughput, Multi-Omic Assay of Tumor Biomarkers from Single-Cells

SUMMARY Although solid tumors oftentimes arise from the uninhibited growth of a single aberrant cellthe population of cells within a tumor are genetically and molecularly heterogenousThis makes it very difficult to evaluate a therapy s efficacy when using bulk population measurementsFurthermorerecent research has implicated microRNAsmiRNAsas drivers of progression and malignancy in many tumor typesMiRNAssmall noncoding RNAs that are typically aboutnucleotides longcan modulate target gene expression by binding to mRNAsignaling for its degradation or inactivationThe relationship between miRNA and target genes becomes even more complex since miRNAs can target multiple mRNAsand most of what is known about miRNA targets is theoretical and based on sequence based predication algorithmsIt is the correlation between miRNAs and target protein that therapy developers need to be able to monitor to tell if their therapy is going to be effective for a certain tumor typeThe only way to quickly discover accurate correlations between RNA and proteinsis to monitor the transcriptome and proteome on a single cell levelThis will tell drug developersexactly what the relationship is between a specific miRNA and protein of intertestand in what cell types these correlations are most prevalentThe IsoPlexis Single Cell BarcodeSCBCis the only technology that currently exists that can obtain this correlation data from single cellsmeasuring up tosecreted or intracellular proteins along with up tophenotypic surface markers from a single cell making our technology able to measurefold more proteins per cell than our competitors and requires only a few thousand cells to provide significantand importantly quantitativeresultsOur platform has recently been further developed to lyse cells on chip in a cell specific mannerallowing for the capture of circulating RNA speciesincluding miRNA and mRNAHereinwe propose to use this phase I grant to develop a new toolusing the IsoPlexis SCBC platformfor multi omic analysis that canimake highly multiplexed measurements from a single celliiwhile being able to gather both proteomic and transcriptomic data from the same celliiiin a manner that is high throughout and capable of being fully automatedWe propose the following specific aimsAimDevelop and optimize SCBC flow cell for dual capture of protein and RNA on chipAimDeliver validation for ability to monitor multi omic GBM biomarkers from a single cell usingpatient samples in collaboration with UCLA and Caltech NARRATIVE MicroRNAs are small non coding RNAs that bind target transcriptsmarking them either for inactivation or degradationThe relationship between microRNAs and their targets is a complex onewhere a single microRNA may have tensor even hundredsof potential protein targetsBeing able to elucidate the correlations between miRNAs and protein at a single cell levelmay allow us to uncover network interactions that contribute to therapeutic resistance and that are not predicted by analyzing pathways in isolationFurther development of the IsoPlexis platform would allow us toimake highly multiplexed measurements from a single celliiwhile being able to gather both proteomic and transcriptomic data from the same celliiiin a manner that is high throughout and capable of being fully automated