Extracellular matrix gene expression profiling using microfluidics for colorectal carcinoma stratification.

Christopher J Hayes,Catriona M Dowling,Shona M Tormey,Mary E Mccumiskey,B Anne Merrigan,John C Coffey,Susan Dwane,Patrick A Kiely,Tara M Dalton

doi:10.1063/1.4966245

Christopher J Hayes, Catriona M Dowling + Show 7 more

Open Access

https://doi.org/10.1063/1.4966245

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Abstract

In cancer, biomarkers have many potential applications including generation of a differential diagnosis, prediction of response to treatment, and monitoring disease progression. Many molecular biomarkers have been put forward for different diseases but most of them do not possess the required specificity and sensitivity. A biomarker with a high sensitivity has a low specificity and vice versa. The inaccuracy of the biomarkers currently in use has led to a compelling need to identify more accurate markers with diagnostic and prognostic significance. The aim of the present study was to use a novel, droplet-based, microfluidic platform to evaluate the prognostic value of a panel of thirty-four genes that regulate the composition of extracellular matrices in colorectal carcinoma. Our method is a novel approach as it uses using continuous-flowing Polymerase Chain Reaction for the sensitive detection and accurate quantitation of gene expression. We identified a panel of relevant extracellular matrix genes whose expression levels were measured by real-time quantitative polymerase chain reaction using Taqman® reagents in twenty-four pairs of matched colorectal cancer tumour and associated normal tissue. Differential expression patterns occurred between the normal and malignant tissue and correlated with histopathological parameters and overall surgical staging. The findings demonstrate that a droplet-based microfluidic quantitative PCR system enables biomarker classification. It was further possible to sub-classify colorectal cancer based on extracellular matrix protein expressing groups which in turn correlated with prognosis.

Highlights

Include microRNAs, single nucleotide polymorphisms, and ribonucleic acid (RNA)-based determination of gene expression
The hypothesis of this study is to use microfluidic droplets acting as distinct miniature reactors to identify differentially expressed extracellular-matrix (ECM) genes in colorectal cancer tissue and matched patient normal tissue to determine if differential expression could be correlated with an increased metastatic potential
RNA expression levels of the panel of thirty-four ECM genes were measured by qPCR in the twenty-four malignant tissue samples and their corresponding normal tissue

Summary

Introduction

Include microRNAs, single nucleotide polymorphisms, and RNA-based determination of gene expression The convergence of these efforts with the development of array-based technologies has led to the development of omics, or high-throughput based, biomarkers. Polyps can be removed but we cannot accurately determine the probability that the tumour will have spread to nodes within the associated mesentery This spread is thought to be a critical step in metastasis development. The hypothesis of this study is to use microfluidic droplets acting as distinct miniature reactors to identify differentially expressed extracellular-matrix (ECM) genes in colorectal cancer tissue and matched patient normal tissue to determine if differential expression could be correlated with an increased metastatic potential. ECM components constantly interact with epithelia as ligands for receptors including integrins In this manner, they instigate intracellular activities related to a vast array of biologic functions, including tissue development and homeostasis.. The identification of prominent ECM tumour markers that derive biological insight into tumour development and progression would be of clinical value

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