Multiplexed miRNA and Protein Analysis Using Digital Quantitative PCR in Microwell Arrays

Area of Science:

• Biochemistry
• Molecular Biology
• Biotechnology

Background:

• Proteins and microRNAs (miRNAs) are crucial regulators of cellular functions, and their dysregulation is linked to various diseases.
• Simultaneous analysis of both miRNAs and proteins is essential for understanding complex molecular pathways in pathogenesis.
• Existing analytical techniques often struggle to measure both biomolecules in parallel from a single sample.

Purpose of the Study:

• To develop a novel microfluidic digital quantitative PCR (dqPCR) assay for simultaneous quantification of miRNA and protein targets.
• To integrate base-stacking PCR (BS-PCR) and immuno-PCR (IPCR) for a streamlined, single-detection chemistry multiplexed assay.
• To demonstrate the sensitivity, dynamic range, and applicability of the developed assay in biological samples.

Main Methods:

• Development of a microfluidic dqPCR platform integrating BS-PCR and IPCR.
• Optimization of separate and multiplexed analyses for let-7a (miRNA) and IL-6 (protein).
• Validation of the assay using standard PCR reagents and subsequent application to HEK293 cell lysate.

Main Results:

• Singleplex dqPCR assays successfully demonstrated digital signals and quantification cycles for both let-7a and IL-6.
• Multiplexed analyses achieved high sensitivity (LODs ~3 fM) and a broad dynamic range (5-5000 fM).
• The assay successfully quantified endogenous let-7a and IL-6 in HEK293 cell lysate without prior sample purification.

Conclusions:

• The integrated BS-PCR and IPCR approach provides a sensitive and streamlined method for multiplexed miRNA and protein analysis.
• This novel dqPCR assay facilitates simultaneous measurement of miRNAs and proteins from a single sample.
• The developed technique holds promise for advancing research into disease pathogenesis by enabling comprehensive molecular profiling.