The lncRNAs/miR-30e/CHI3L1 Axis Is Dysregulated in Systemic Sclerosis - PubMed (original) (raw)

The lncRNAs/miR-30e/CHI3L1 Axis Is Dysregulated in Systemic Sclerosis

Valentin Dichev et al. Biomedicines. 2022.

Abstract

Systemic sclerosis (SSc) is an autoimmune disease with completely undefined etiology and treatment difficulties. The expression of both protein coding and non-coding RNAs is dysregulated during disease development. We aimed to examine a possible regulatory axis implemented in the control of chitinase-3 like protein 1 (CHI3L1) or YKL-40, an inflammation-associated glycoprotein, shown to be elevated in SSc. A panel of seven miRNAs and three lncRNAs potentially involved in the control of CHI3L1 were selected on the basis of in silico analysis. TagMan assay was used to evaluate the expression levels of miRNAs and RT-qPCR for lncRNAs in white blood cells (WBCs) and plasma from SSc patients and healthy controls. Among the eight screened miRNAs, miR-30e-5p (p = 0.04) and miR-30a-5p (p = 0.01) were significantly downregulated in WBCs and plasma of SSc patients, respectively. On the contrary, the expression of the metastasis associated lung adenocarcinoma transcript 1 (MALAT1) (p = 0.044) and the Nuclear enriched abundant transcript 1 (NEAT1) (p = 0.008) in WBCs was upregulated compared to the controls. Increased levels of MALAT1 and NEAT1 could be associated with the downregulation of miR-30e-5p and miR-30a-5p expression in WBCs and plasma. We present novel data on the involvement of a possible regulatory axis lncRNAs/miR-30e/CHI3L1 in SSc and hypothesize that MALAT1 and NEAT1 could act as miR-30e-5p and miR-30a-5p decoys. This may be a reason for the increased serum levels of CHI3L1 in SSc patients.

Keywords: CHI3L1; MALAT1; NEAT1; miR-30e; systemic sclerosis.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1

Figure 1

miR-30a-5p and miR-30e-5p are downregulated in SSc. Box plot of (A) miR-24-3p, (C) miR-30a-5p, (D) miR-30b-5p, (E) miR-30c-5p, (G) miR-30e-5p, (F) miR-30d-5p and (B) miR-125a-3p measured in both WBC and plasma of SSc (WBC, n = 31; plasma, n = 30) and healthy controls (WBC, n = 12; plasma, n = 9). Expression levels were determined by TagMan assay after total RNA extraction and presented as fold difference. snoRNA U48 and U6 were used as miRNA normalizers. The data are summarized from two technical replicates for each examined individual. p > 0.05 was marked with *.

Figure 2

Figure 2

miR-30e-5p and miR-30a-5p are differentially expressed in SSc subgroups. Box plot of miR-30e-5p (A) in WBCs of lcSSc patients (n = 12) and miR-30a-5p (B) in plasma of dcSSc patients (n = 14), compared to healthy controls (WBC, n = 12; plasma, n = 9). Expression levels were determined by TagMan assay after total RNA extraction and presented as fold difference. snoRNA U48 and U6 were used as miRNA normalizers. The data are summarized from two technical replicates for each examined individual. p > 0.05 was marked with *; p > 0.01 was marked with **.

Figure 3

Figure 3

Binding sites of miR-30e-5p (A) and miR-30a-5p (B) in CHI3L1mRNA and MALAT1. DIANA-LncBase v3 and Starbas bioinformatical tools were applied to predict the binding sequence of the two down regulated miRNAs: miR-30e-5p and miR-30a-5p in the 3’UTR of CHI3L1mRNA and lncRNA MALAT1. The in silico analysis revealed that both have a conserved seed region by which they could bind to the complementary sites in CHI3L1mRNA and lncRNA MALAT1 molecules.

Figure 4

Figure 4

MALAT1 and NEAT1 are upregulated in SSc WBCs. MALAT1 and NEAT1 are induced in WBCs of SSc patients, compared with the control subjects. Expression levels of MALAT1, NEAT1 and UCA1 were evaluated in WBCs of patients (n = 31) and controls (n = 12) by RT-qPCR after total RNA extraction and presented as fold difference. GAPDH, ACTINβ and hUBC were used as RNA normalizers. The data are summarized from two technical replicates for each examined individual. p > 0.05 was marked with *; p > 0.01 was marked with **.

Figure 5

Figure 5

Discriminatory potential of plasma miR-30a-5p levels. ROC analysis was performed to access the discriminatory power of miR-30a-5p in plasma. The AUC values show that miR-30a-5p has the potential as a biomarker for distinguishing SSc from healthy subjects.

Figure 6

Figure 6

Possible lncRNAs/miR30e/CHI3L1regulatory axis in SSc. In SSc, the expression of MALAT1 and NEAT1 in WBCs is upregulated. MALAT1 and NEAT1 can act as competitive endogenous RNAs for miR-30e. Interaction between MALAT1/NEAT1 and miR-30e-5p would abolish the suppressive effect of miR-30e-5p over CHI3L1production, leading to increased serum levels of the glycoprotein in patients with SSc. ↑ indicates induction, whereas ↓ shows downregulation.

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