Co-sequencing and novel delayed anti-correlation identify function for pancreatic enriched microRNA biomarkers in a rat model of acute pancreatic injury

Zhihua Li,Rodney Rouse

doi:10.1186/s12864-018-4657-2

Abstract

BackgroundCo-sequencing of messenger ribonucleic acid (mRNA) and micro ribonucleic acid (miRNA) across a time series (1, 3, 6, 24, and 48 h post injury) was used to identify potential miRNA-gene interactions during pancreatic injury, associate serum and tissue levels of candidate miRNA biomarkers of pancreatic injury, and functionally link these candidate miRNA biomarkers to observed histopathology. RNAs were derived from pancreatic tissues obtained in experiments characterizing the serum levels of candidate miRNA biomarkers in response to acute pancreatic injury in rats.ResultsNo correlation was discovered between tissue and serum levels of the miRNAs. A combination of differential gene expression, novel delayed anti-correlation analysis and experimental database interrogation was used to identify messenger RNAs and miRNAs that experienced significant expression change across the time series, that were negatively correlated, that were complementary in sequence, and that had experimentally supported relationships. This approach yielded a complex signaling network for future investigation and a link for the specific candidate miRNA biomarkers, miR-216a-5p and miR-217-5p, to cellular processes that were in fact the prominent histopathology observations in the same experimental samples. RNA quality bias by treatment was observed in the study samples and a statistical correction was applied. The relevance and impact of that correction on significant results is discussed.ConclusionThe described approach allowed extraction of miRNA function from genomic data and defined a mechanistic anchor for these miRNAs as biomarkers. Functional and mechanistic conclusions are supported by histopathology findings.

Highlights

Co-sequencing of messenger ribonucleic acid and micro ribonucleic acid across a time series (1, 3, 6, 24, and 48 h post injury) was used to identify potential miRNA-gene interactions during pancreatic injury, associate serum and tissue levels of candidate miRNA biomarkers of pancreatic injury, and functionally link these candidate miRNA biomarkers to observed histopathology
Details of all the animal study methodology that yielded the samples from which the present molecular study were derived and the other findings from the animal study including all histopathology findings, characterization of miRNA levels in serum following acute pancreatic injury, and the relationship of the miRNAs to histopathology, have been previously published [6]
Experimental repeats may have been completed to demonstrate reproducibility, the majority of these studies focused on miRNA and messenger ribonucleic acid (mRNA) differences in treatment groups at single time points or within single time point comparisons. These single time points have been logically chosen to provide the largest opportunity to capture relevant data but do not attempt to identify temporal relationships. Those studies that examine time series data [64, 65] rely upon intra-time point comparisons with the advantage of assessing changes for individual molecules from time point to time point but do not address how a change in one entity at one time point might impact a different entity at a the authors recognize that even delayed anti-correlation analysis across 5 time points would not reliably identify miRNA-mRNA regulatory pairs or modules others have published time series relationships with even fewer time points [11, 12]

Summary

Introduction

Co-sequencing of messenger ribonucleic acid (mRNA) and micro ribonucleic acid (miRNA) across a time series (1, 3, 6, 24, and 48 h post injury) was used to identify potential miRNA-gene interactions during pancreatic injury, associate serum and tissue levels of candidate miRNA biomarkers of pancreatic injury, and functionally link these candidate miRNA biomarkers to observed histopathology. MicroRNAs (miRNAs) are short ribonucleic acid (RNA) sequences that are hypothesized to primarily function as negative regulators of gene expression [1]. They accomplish this regulation largely through suppressing translation or catalyzing degradation of messenger RNAs (mRNAs) that serve as the template for protein synthesis in the cell [2]. Tools are constantly evolving to identify and provide validated interaction information for miRNAs and the mRNAs that they regulate

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Discussion

Conclusion