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Table 2. Key miRNAs in EoE, their predicted targets and anticipated phenotypic changes as a result
microRNA Esophageal expression mRNA target Phenotype
(EoE vs. healthy)
miR-375 Decreased expression CXCL12; JAK2; MMD Increased lymphocyte chemotaxis; increased JAK/stat-mediat-
ed cytokine signaling; increased macrophage differentiation
miR-21 Increased expression IL-12 Promotes Th2 type inflammation in the esophagus
miR-223 Increased expression SPINK7 Destruction and impairment of the epithelial barrier

Online bioinformatics database, miRWalk 2.0, was used to predict biologic targets of miRNAs that have yet to be validated in vitro or in
vivo [34] . Relevant targets involved in inflammatory, immune and barrier function are listed

tients. High levels of miR-21 in the esophagus of EoE patients correlated with decreased IL-12p35, suggesting
a tendency towards Th2 or allergic inflammation in EoE tissue.

Unlike miR-21, which has been actively investigated in numerous types of inflammatory and immune medi-
ated diseases, miR-223 action and targets are not known. Although targets of miR-223 have not be identified
in vitro or in vivo, mRNAs that may be bound by miR-223 were predicted by our group through bioinfor-
matic software miRWalk 2.0 [Table 2]. Serine protease inhibitor, SPINK7, was predicted as a direct target of
miR-223. Interestingly, a recent study led by Marc Rothenberg discovered that individuals with active EoE
[35]
lack SPINK7 in their esophageal epithelium . In vitro experiments in esophageal epithelial cell lines dem-
onstrated that knockdown and knockout of SPINK7 disrupted barrier function and increased inflammatory
cytokine production, suggesting that SPINK7 deficiency may contribute to EoE pathogenesis. Independent
of this study, miR-223 has been shown to be upregulated in esophageal biopsies of EoE patients and our bio-
informatics modeling predicts miR-223 can bind SPINK7. Taken together, these observations suggest a po-
tential uninvestigated mechanism by which miR-223 exerts pathogenic effects in EoE [Figure 5]. Increased
miR-223 in the epithelium may bind to the 3’ UTR of SPINK7, depleting this key protective protein in the
esophagus. SPINK7 deficiency ultimately leads to impaired barrier integrity and inflammation.

MIRNA REPLACEMENT THERAPY WITH MIR-375
[31]
In vitro experiments conducted by Lu et al. in 2012 showed relevance of miR-375 in the pathogenesis and
treatment of EoE beyond biomarker capacity. Overexpression of miR-375 in esophageal epithelium down-
regulated a panel of IL-13 associated inflammatory genes pathogenic in eosinophilic esophagitis, includ-
ing Th2 cytokines, and proteins involved in mast cell activation and eosinophil chemoattraction . Taken
[31]
together, transfection or “add back” of mir-375 into esophageal epithelium had anti-inflammatory function
that inhibited allergic responses associated with EoE. This work suggests that miR-375 may be protective
against EoE. In many fields like oncology, pharmaceutical and drug development efforts have trialed miRNA
replacement therapy. This therapeutic strategy employs delivery of synthetic, double-stranded miRNA mim-
[36]
ics, encased in lipid-based vectors to diseased tissue . EoE esophageal tissue has been shown to be depleted
of natural or endogenous miR-375, so oral administration of artificial miR-375 could be effective at restoring
anti-inflammatory function missing in EoE patients.

miRNA-based immunotherapies are already under investigation for other inflammatory diseases of the gas-
trointestinal tract, so they may not be out of reach for EoE. Research in the inflammatory bowel disease field
has begun to address potential limitations for RNA delivery to gastrointestinal tissue, accounting for the sta-
bility and protection of RNA in nanoparticles to successfully avoid degradation by ribonucleases, bile salts,
pancreatic lipases and extreme pH. Preliminary miRNA therapeutic work done in murine models of colitis
show efficacy for delivering miRNAs to diseased tissue and exerting appreciable anti-inflammatory effects,
[37]
decreasing cytokine expression and reducing disease scores on histology . This encouraging work points
towards future investigations of therapeutic oral administration of miR-375 for EoE.