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James, J.P.; Riis, L.B.; Malham, M.; Høgdall, E.; Langholz, E.; Nielsen, B.S.; James, J. MicroRNA Biomarkers in IBD. Encyclopedia. Available online: (accessed on 23 June 2024).
James JP, Riis LB, Malham M, Høgdall E, Langholz E, Nielsen BS, et al. MicroRNA Biomarkers in IBD. Encyclopedia. Available at: Accessed June 23, 2024.
James, Jaslin P., Lene Buhl Riis, Mikkel Malham, Estrid Høgdall, Ebbe Langholz, Boye S Nielsen, Jaslin James. "MicroRNA Biomarkers in IBD" Encyclopedia, (accessed June 23, 2024).
James, J.P., Riis, L.B., Malham, M., Høgdall, E., Langholz, E., Nielsen, B.S., & James, J. (2020, November 09). MicroRNA Biomarkers in IBD. In Encyclopedia.
James, Jaslin P., et al. "MicroRNA Biomarkers in IBD." Encyclopedia. Web. 09 November, 2020.
MicroRNA Biomarkers in IBD

Inflammatory bowel disease (IBD) includes Crohn’s disease (CD) and ulcerative colitis (UC). These are chronic autoimmune diseases of unknown etiology affecting the gastrointestinal tract. The IBD population includes a heterogeneous group of patients with varying disease courses requiring personalized treatment protocols. The complexity of the disease often delays the diagnosis and the initiation of appropriate treatments. In a subset of patients, IBD leads to colitis-associated cancer (CAC). MicroRNAs are single-stranded regulatory noncoding RNAs of 18 to 22 nucleotides with putative roles in the pathogenesis of IBD and colorectal cancer. They have been explored as biomarkers and therapeutic targets. Both tissue-derived and circulating microRNAs have emerged as promising biomarkers in the differential diagnosis and in the prognosis of disease severity of IBD as well as predictive biomarkers in drug resistance. In addition, knowledge of the cellular localization of differentially expressed microRNAs is a prerequisite for deciphering the biological role of these important epigenetic regulators and the cellular localization may even contribute to an alternative repertoire of biomarkers.

biomarkers circulating miRNA colitis-associated cancer (CAC) Crohn’s disease (CD) inflammatory bowel disease (IBD) microRNA (miRNA) ulcerative colitis (UC)

1. Introduction

Inflammatory bowel disease (IBD) refers to Crohn’s disease (CD) and ulcerative colitis (UC). In UC, inflammation generally includes the rectum and extends towards the coecum and remains confined to the colon. In contrast, in CD, inflammation can involve any part of the gastrointestinal tract (GI) from the oral cavity to the anus. Both CD and UC are associated with multiple pathogenic factors such as environmental changes, the array of susceptibility gene variants, qualitatively and quantitatively abnormal gut microbiota and broadly dysregulated immune response [1]. Although CD and UC have some common pathological and clinical characteristics, they have several different attributes that imply that they are two distinct disease subtypes. In CD, fissuring ulceration and sub-mucosal fibrosis can be observed along with granulomatous inflammation. In UC, the inflammatory process always involves the rectum [2] and general histological findings include crypt distortion, infiltration of lymphocytes and granulocytes and chronic inflammation, usually confined to the lamina propria [3]. The diagnosis of IBD is usually established by a collective assessment of clinical presentation and endoscopic, histopathological, radiographic and laboratory findings. A definitive diagnosis of IBD cannot be made without detailed endoscopic and histologic assessment [4]. However, a subset of IBD cases cannot be classified as either CD or UC but are categorized as IBD unclassified (IBDU). Molecular biomarkers may support differential diagnosis of IBDU cases into CD or UC, or even be helpful in determining if IBDU represents a unique IBD diagnostic entity.

IBD starts developing at a younger age, including in infants [5], and is often characterized by a considerable diagnostic and therapeutic challenge because of the disease’s clinical features and associated complications. The prevalence of IBD in the Western world is projected to be up to 0.5% of the overall population [6]. In Denmark, where one of the highest annual incidence rates of IBD in Europe is seen, the incidence has been increasing over the last three decades [7]. In 2013, the incidence was 9.1 per 100,000 persons and 18.6 per 100,000 persons for CD and UC, respectively [8]. Since the turn of the 21st century, IBD has become a global disease with accelerating incidence rates also in developing countries whose societies have adopted a western diet and lifestyle. Although the incidence rate has become steady in western countries, the burden remains high, as prevalence exceeds 0.3%. The chronical inflammatory condition in the affected colon of IBD patients has been linked to development of neoplastic lesions in the colon. Several studies have shown a higher incidence of colorectal cancer (CRC) in IBD patients [9][10][11]. No biomarkers exist for the identification of IBD patients at risk of developing colitis-associated cancer (CAC), strongly advocating for more translational research in this field.

In this review, we give an overview of microRNAs (miRNAs) as candidate biomarkers in the IBD diagnostic assessment. Changes in miRNA levels are associated with disease development and can be measured both within the diseased tissue and in the circulation by a variety of molecular methods. MiRNAs have been found to be well conserved in archived tissue specimens, enabling retrospective analyses of clinical sample cohorts.

2. MicroRNA—An Introduction

MiRNAs play a central role in the regulation of several immune-mediated disorders including IBD [12][13][14]. MiRNAs are a group of small noncoding RNAs, approximately 18–22 nucleotides [15] which are found conserved across species. Their discovery was first described first in 1993 in Caenorhabditis elegans [16]. MiRNAs are transcribed as primary transcripts by RNA polymerase, processed into a precursor miRNA by the RNase III enzyme, Drosha, and exported from the nucleus to the cytoplasm. The precursor miRNA is cleaved by the RNase III enzyme, Dicer, into its mature form, which becomes stably incorporated into an RNA induced silencing complex (RISC). The miRNA guides the binding of the RNA-induced silencing complex to complementary sequences in the 3′-untranslated regions (UTR) of target mRNA molecules, resulting in either mRNA degradation or translational inhibition [17]. During stages of miRNA biogenesis, several factors can influence the development of the mature miRNA. These include regulation of transcription, cleavage of the stem loop structures by Drosha and Dicer enzymes, and editing as well as regulation of miRNA turnover. Each of these mechanisms acts as part of a signaling network that modulates gene expression in response to cellular or environmental changes.

MiRNA expression has been shown to be of importance in a wide variety of human diseases such as cancer, autoimmune, cardiovascular, and neurodegenerative diseases [18][19][20][21][22][23][24]. The miRNAs not only circulate in the human peripheral blood in a stable form, they are also present in other body fluids such as urine, saliva, milk, cerebrospinal fluid, and feces [25][26][27][28]. The miRNAs are engaged in disease origin and development, and some are pathology-specific [29], thus, changes in miRNA expression profiles have been addressed for applications in early detection as well as prognostics, diagnostic classification and drug response prediction.

3. MiRNAs in IBD

In IBD, miRNAs have been found to be involved in pathogenesis and have been identified as both  diagnostic biomarkers and therapeutic targets [30]. Most of the recent research in the IBD field has measured levels of circulating miRNAs in body fluids such as blood or feces, and in homogenized tissue biopsies using techniques like microarray profiling, RT-qPCR, and NGS [31][32][33][34]. Studies have also performed tissue miRNA expression analysis using in situ hybridization (ISH) methods [35][36][37]. ISH methods for expression analyses of miRNAs can determine the cellular origin of miRNA expression and can offer insight into the biology of the disease mechanisms involved. Local expression levels of miRNAs can greatly vary from those of circulating miRNAs, e.g., due to contribution of miRNAs from circulating cells. Esquela-Kerscher and Slack [38] proposed that tumor cells release miRNAs into the neighboring microenvironment and enter circulation during angiogenesis. Some studies suggest that this likely occurs through exosomal release from cells [39][40]. Changes in the levels of circulating miRNA may occur due to other inflammatory reactions or the host immune response rather than only due to the intrinsic changes within the lesion [41]. Thus, as discussed further below, it is not surprising that miRNAs analyzed in tissue biopsies poorly correlate with those found in the circulation [42]

There is an increasing interest in exploring epigenetic mechanisms in common diseases, with notable progress in characterizing the contribution of miRNAs [43]. In their 2008 study, Wu et al. found that miRNAs regulate colonic epithelial cell-derived chemokine expression and were the first to relate miRNAs to IBD [44]. The field of miRNA research has grown rapidly after their discovery in human disease biology including in IBD [43]. We have listed a series of IBD-related miRNA studies from recent years in Table 1, with a focus on sample type and quantitative method. MiR-21, miR-155, and miR-31 have repeatedly been identified and seem to be the most studied miRNAs related to IBD [45][46][47][48]. MiR-21 is possibly the most intriguing miRNA involved in IBD, with associations between miR-21 and IBD being replicated in several studies, as well as functional relevance reported in mouse models of IBD [49][50]. Each miRNA can potentially target hundreds of mRNAs resulting in mRNA destabilization and/or inhibition of translation, however, restricted to a specific cellular context, the number of relevant targetable transcripts is probably quite low.

MiRNAs regulate important cellular functions such as cell differentiation and proliferation and signal transduction and apoptosis and exhibit highly specific regulated patterns of gene expression [15]. In autoimmune diseases, miRNAs can act through interference with inflammatory signaling pathways, such as the nuclear transcription factor kappa B (NF-κB) pathway, IL23/IL23R pathway, and IL-6/STAT3 pathway[51][52][53][54][55]. Studying the RhoB pathway of cell adhesion in UC mucosa and cultured colon cancer cells, Yang et al. [36] examined the role of miR-21 in regulation of intestinal epithelial barrier function and found that miR-21 induced the degradation of RhoB mRNA, reduction in RhoB protein, causing loss of tight junctions in intestinal epithelial cells. Tian et al. showed miR-31 to be highly expressed in tissues from IBD patients, and miR-31 reduced the inflammatory response in the Dextran Sodium Sulphate (DSS)-induced colitis mouse model (see below), by preventing the expression of inflammatory cytokine receptors such as IL7R and IL17RA and signaling proteins such as GP130 [56]. Another study based on the DSS model showed that miR-155 directly binds to SHIP-1 mRNA and causes a significant decrease in SHIP-1 levels, which regulate cell membrane trafficking, and thereby contribute to the pathogenesis of colitis [57]. Taken together, these examples indicate the complexity of how miRNAs may act through signaling pathways in the biological settings of IBD.

Studies of circulating miRNAs have shown that miRNAs are potential candidates as biomarkers for diagnosing IBD and various other diseases [58][59][60][61][62]. The high stability of miRNAs in the body fluids and the ability to obtain rapid and accurate quantitative estimates are some merits of using circulating miRNAs as biomarkers in IBD [28]. MiRNAs are not only interesting tools for diagnosis, but also for potential future therapeutic applications by miRNA mimics or miRNA antagonists [63][64].

Table 1. A summary of studies on microRNA research in inflammatory bowel disease (IBD). CD: Crohn’s disease, UC: Ulcerative colitis, HC: Healthy controls, RT-qPCR: Quantitative real time polymerase chain reaction, Biopsy: colon tissue biopsy, ISH: In situ hybridization, QISH: Quantitative in-situ hybridization, PBMC: Peripheral blood mononuclear cells, DSS: Dextran sodium sulphate, AOM: Azoxymethane, TNF: Tumor necrosis factor alpha.



Disease Subtype

Sample Type

Techniques Used




miR-16, miR-29a, miR-199a-5p, miR-363-3p, miR-340, miR-532-3p, miRplus-1271, miR-140-3p, miR-127-3p, miR-196b, miR-877, miR-150


Serum, Biopsy

RT-qPCR, Microarray

Mixed outcomes



miR-223-3p, miR-31-5p



Nano string

Mir-223-3p expression showed age and sex effects and miR-31-5p expression was driven by location







MCL-1 is modulated in CD fibrosis by miR-29b via IL-6 and IL-8



miR-141, miR-200a, miR-200b, miR-200c




All investigated miRNAs were significantly down regulated in CD, and 3 of them were downregulated in UC in comparison to the normal or the least affected mucosa.






Microarray, RT-qPCR

MiR-141 plays a role in the bowel inflammation of individuals with active UC via down regulation of CXCL5 expression.







MiR-124 regulates the expression of STAT3. Reduced levels of miR-124 in colon tissues of children with active UC appear to increase expression and activity of STAT3.





Biopsy, Cell culture


MiR-19b suppresses the inflammation and prevents the pathogenesis of CD.





Human and mice tissues


Decreased miR-590-5p levels in CD.






RT-qPCR, Sequencing

Significant increase of miR-122 expression in cells treated with 5′-AZA.







Dendritic cell activation and Th1/Th17 cell immune responses were inhibited via miR-10a in IBD.






RT-qPCR, Microarray, ISH

MiR-192 with decreased expression in active UC.





Biopsy, Cell cultures


MiR-15a negatively regulates epithelial junctions through Cdc42 in Caco-2 cells



miR-146a, miR-155




MiR-146a and -155 shows increased duodenal expression in pediatric CD.







Higher expression of serum miR-146b-5p in patients with CD and UC than in HC.





Biopsy, PBMC


Increased expression of miR-425 in IBD.





PBMC, Biopsy


MiR-301a promotes intestinal mucosal inflammation via induction of IL-17a and TNF in IBD.



miR-125b, miR-155, miR-223 and miR-138



RT-qPCR, Microarray

Differential expression of miR-223, miR-125b, miR-138, and miR-155 in the inflamed mucosa compared to non-inflamed mucosa and controls.



miR-16, miR-21, miR-155, and miR-223


Serum, Feces


Differential expression of miR-16, miR-155, miR-21, and miR-223 in IBD.







Over expression of miR-21 in UC.





Mice Tissue


MiR-133a-UCP2 pathway participates in IBD by altering downstream inflammation, oxidative stress, and markers of energy metabolism.



miR-20b, miR-98, miR-125b-1, let-7e



RT-qPCR, Microarray

MiR-20b, miR-98, miR-125b-1, and let-7e are deregulated in patients with UC.






RT-qPCR, Transfection

MiR-155 regulates IL-10-producing CD24 CD27+ B Cells.



miR-21, miR-126




Endothelial expression of miR-126 are increased in UC. MiR-21 is expressed in subsets of monocytes/macrophages and T cells.





Cell culture, Biopsy

RT-qPCR, ISH, Transfection

Expression of miR-31-3p in human colonic epithelial cells.



miR-21, miR-155




MiR-21 and miR-155 was highly expressed in UC.







MiR-15 activates NF-κB Pathway in UC.



miR-143, miR-145




MiR-143 and miR-145 are down regulated in UC.





Cell culture, Biopsy


MiR-206 as a biomarker for response to mesalamine treatment in UC.





Cell culture, Biopsy


MiR-193a-3p reduces intestinal inflammation in response to microbiota.





Biopsy, mice tissue


Reduced expression of miR-19a in human colon tissue with UC and in DSS-treated mice colitis.





Sera, rat tissue

RT-qPCR, Transfection

MiR-21-5p was down regulated in the sera and colon tissue of UC compared with healthy people and the control group.





Biopsy, Serum. Cell culture


MiR-200b is involved in intestinal fibrosis of CD.





Mice tissue, cell culture

RT-qPCR, Transfection

MiR-155 promotes the pathogenesis of experimental colitis by repressing SHIP-1 expression.






RT-qPCR, Microarray, Transfection

MiR-31 expression levels as a marker for disease progression and to discriminate distinct pathological entities that co-exist in IBD.





murine model


MiR-150 was elevated and c-Myb were down regulated in human colon with active UC compared to HC.





Cell culture

RT-qPCR, Transfection

MiR-122 reduces the expression of pro-inflammatory cytokines (TNF and IFN-γ) and promotes the release of anti-inflammatory cytokines (IL-4 and IL-10).





Murine models, Biopsy

Microarray, RT-qPCR

MiR-141 regulates colonic leukocytic trafficking by targeting CXCL12β during murine colitis and human CD.





Cell culture, Biopsy

Transfection, RT-qPCR

MiR-7 modulates CD98 expression during intestinal epithelial cell differentiation.





IL-10 deficient mouse

Microarray, Transfection, DSS induced colitis in vivo

MiR-146b improves intestinal injury in mouse colitis.





IL-10 deficient mouse, Biopsy

DSS-induced Experimental Colitis, RT-qPCR, ISH

MiR-21 is overexpressed in intestinal inflammation and tissue injury.






Nano string

MiR-215 discriminates patients who progressed to neoplasia as early as 5 years prior to the diagnosis of neoplasia





DSS animal model biopsy


MiR-449a expression decreased gradually during the progression of CAC





DSS mouse model biopsy


MiR-135a in colonic cells were suppressed and up-regulating miR-135a inhibited apoptosis and inflammation of colonic epithelial cells



miR-146a, miR-155, miR-122




Altered expression of all three miRNAs in colonic mucosa of children with IBD



miR-146a, miR-335, miR-26b and miR-124


Genome-wide expression profiles


MiR-146a, miR-335, miR-26b and miR-124 were identified in CD, UC, and CRC samples





AOM and DSS mouse model biopsy

Microarray, RT-qPCR

MiR-155 is upregulated in and relates to CAC



To study the pathogenesis and intricacy of IBD, the advancement of a variety of animal models has provided important information. The most extensively used mouse model of colitis utilizes DSS, a so-called chemical colitogen with anticoagulant properties, to stimulate epithelial damage. The DSS colitis model is simple and easy to administer. Acute and persistent colitis is achieved by altering the concentration of DSS and the frequency of administration [102]. A genetically engineered in vivo model that has been widely used to examine IBD etiology is the interleukin-10 (IL-10)-deficient mouse model [103]. IL-10 is an anti-inflammatory cytokine. Mutated IL-10 signaling systems shows early and aggressive expansion of systemic inflammation in IBD. IL-10 knockout mice develop spontaneous colitis and CAC [104]. Nata et al. [95] performed miRNA microarray profiling on IL-10-deficient mice and identified that several miRNAs were upregulated, including miR-146b that, through further studies, was found to contribute to increased intestinal inflammation by upregulating NF-κB. Shi et al. [96] showed that knockout of miR-21 in mice improved the survival rate in DSS-induced fatal colitis via protecting against inflammation and tissue injury. Hence, it was suggested that impaired expression of miR-21 in gut may block the onset or progression of IBD. Other animal models used in IBD research include genetically engineered mice, congenic mouse strains, chemically induced models, and cell-transfer models [105]. Most of the studies investigating miRNA expression in IBD have used high-throughput methods such as a microarray combined with RT-qPCR as a validation method for prioritized miRNAs.


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