Platform for combined analysis of functional and biomolecular phenotypes of the same cell

L Kelbauskas,T Paulson,D Derkach,S Ashili,Y Tian,Deirdre R Meldrum,D Smith,W Gao,J Zeng,A Rezaie,H Wang,B Ueberroth,K Lee,B Reid

doi:10.1038/srep44636

Abstract

Functional and molecular cell-to-cell variability is pivotal at the cellular, tissue and whole-organism levels. Yet, the ultimate goal of directly correlating the function of the individual cell with its biomolecular profile remains elusive. We present a platform for integrated analysis of functional and transcriptional phenotypes in the same single cells. We investigated changes in the cellular respiration and gene expression diversity resulting from adaptation to repeated episodes of acute hypoxia in a premalignant progression model. We find differential, progression stage-specific alterations in phenotypic heterogeneity and identify cells with aberrant phenotypes. To our knowledge, this study is the first demonstration of an integrated approach to elucidate how heterogeneity at the transcriptional level manifests in the physiologic profile of individual cells in the context of disease progression.

Highlights

Functional and molecular cell-to-cell variability is pivotal at the cellular, tissue and whole-organism levels
We used a panel of four immortalized human esophageal epithelial cell lines representing the metaplastic (CP-A) and dysplastic (CP-B, CP-C, and CP-D) stages in premalignant progression in Barrett’s esophagus (BE) (Supplementary Table 1)[37,38]
Cells were repeatedly exposed to low oxygen levels (

Summary

Introduction

Functional and molecular cell-to-cell variability is pivotal at the cellular, tissue and whole-organism levels. This study is the first demonstration of an integrated approach to elucidate how heterogeneity at the transcriptional level manifests in the physiologic profile of individual cells in the context of disease progression. While several groundbreaking technologies for genotyping, gene transcription, protein expression level, and metabolic profiling at the single cell level exist[16,17,18,19,20,21,22,23], each of them provides only one type of molecular information limiting the ability to link differences at the genome or transcriptome level and their phenotypic manifestation in individual cells. We created a novel integrated platform and approach that combines a technology for respiration rate determination of single cells with a method for harvesting the same cells[26,27], followed by gene expression level analysis on the same individual cells. It is hypothesized that the interplay between these changes in esophageal www.nature.com/scientificreports/

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