| Literature DB >> 31346335 |
Chang-Li Zhu1, Xiaofeng Sha2, Yuan Wang1, Jin Li1, Men-Yan Zhang1, Zhong-Ying Guo3, Su-An Sun3, Jing-Dong He1.
Abstract
Circular RNAs (circRNAs) are a large class of endogenous noncoding RNAs that regulate gene expression and mainly function as microRNA sponges. This study aimed to explore the aberrant expression of circRNAs in colorectal cancer (CRC). Using a circRNA microarray, we identified 892 differentially expressed circRNAs between six pairs of CRC and adjacent paracancerous tissues. Among them, hsa_circ_0007142 was significantly upregulated. Further analysis in 50 CRC clinical samples revealed that hsa_circ_0007142 upregulation was associated with poor differentiation and lymphatic metastasis of CRC. Bioinformatic analysis and luciferase reporter assay showed that hsa_circ_0007142 targeted miR-103a-2-5p in CRC cells. Moreover, the silencing of hsa_circ_0007142 by siRNAs decreased the proliferation, migration, and invasion of HT-29 and HCT-116 cells. Taken together, these findings suggest that hsa_circ_0007142 is upregulated in CRC and targets miR-103a-2-5p to promote CRC.Entities:
Year: 2019 PMID: 31346335 PMCID: PMC6617873 DOI: 10.1155/2019/9836819
Source DB: PubMed Journal: J Oncol ISSN: 1687-8450 Impact factor: 4.375
The sequences for primers and siRNAs.
| Primers used for qRT-PCR | ||
| GAPDH F | GGGAGCCAAAAGGGTCAT | |
| GAPDH R | GAGTCCTTCCACGATACCAA | |
| hsa_circ_0007142 F | GAACTCTGCCTCAGGATGAA | |
| hsa_circ_0007142 R | AACGTGTAACCTCGGTACCA | |
| U6 | F | CTCGCTTCGGCAGCACA |
| U6 | R | AACGCTTCACGAATTTGCGT |
| U6 | RT | GTCGTATCCAGTGCAGGGTCCGAGGTAT |
| TCGCACTGGATACGACCAAATATGGAAC | ||
| miR-103a-2-5p | F | GCGCGAGCTTCTTTACAGTGCT |
| miR-103a-2-5p | R | ATCCAGTGCAGGGTCCGAGG |
| miR-103a-2-5p | RT | GTCGTATCCAGTGCAGGGTCCGA |
| GGTATTCGCACTGGATACGACCA AGGC | ||
| siRNAs oligonucleotides | ||
| si-circ_0007142 | GGAAACAGCTTTTTATAAC | |
Figure 1Comparison of circRNA expression profiles between CRC and paired pericancerous tissues. (a) Scatter plots for assessing the difference in the expression of circRNAs among samples (T for CRC and B for adjacent tissues). The values of each group were plotted on the X and Y axes (log2 scaled). The middle green line represented no difference between two groups, while the flank green lines indicated 2-fold changes. The circRNAs beyond the lines referred to > 2-fold changes between two groups. (b) Volcano plots for differential circRNA expression between two groups. The vertical lines indicated 2 folds (log2 scaled), and the horizontal line represented P of 0.05 (log10 scaled). The red dots represented differentially expressed circRNAs with statistical significance.
The top ten upregulated and downregulated circRNAs in CRC ranked by fold changes in microarray data.
| CircRNA ID | CircRNA type | Chrom | Gene symbol | Fold change | Regulation | P value |
|---|---|---|---|---|---|---|
| hsa_circ_0000072 | exonic | chr1 | OMA1 | 43.4572991 | up | 0.005985797 |
| hsa_circ_0007142 | exonic | chr10 | DOCK1 | 34.9353568 | up | 2.71168E-05 |
| hsa_circ_0008812 | exonic | chr9 | RAD23B | 32.0813361 | up | 0.00009244 |
| hsa_circ_0050514 | exonic | chr19 | UBA2 | 27.7446201 | up | 2.68425E-05 |
| hsa_circ_0085923 | exonic | chr8 | PLEC | 23.5020249 | up | 0.004162563 |
| hsa_circ_0087855 | exonic | chr9 | RAD23B | 23.161069 | up | 0.000133271 |
| hsa_circ_0005954 | exonic | chr6 | AMD1 | 22.1403464 | up | 0.00069505 |
| hsa_circ_0005050 | exonic | chr2 | XPO1 | 22.0953662 | up | 0.000244329 |
| hsa_circ_0005281 | exonic | chr17 | TBCD | 21.7534364 | up | 1.32686E-06 |
| hsa_circ_0000994 | exonic | chr2 | SLC8A1 | 21.3375077 | up | 0.000346993 |
| hsa_circ_0072279 | exonic | chr5 | NUP1 | 13.3423298 | down | 0.000659178 |
| hsa_circ_0001704 | intragenic | chr7 | - | 12.7785132 | down | 0.000891495 |
| hsa_circ_0035626 | exonic | chr15 | RPS27L | 11.6798313 | down | 0.029341895 |
| hsa_circ_0001525 | intronic | chr5 | - | 10.49926 | down | 0.000123931 |
| hsa_circ_0005904 | exonic | chr2 | DCAF17 | 10.3297308 | down | 1.74038E-06 |
| hsa_circ_0008367 | exonic | chr9 | IARS | 10.183079 | down | 0.00136856 |
| hsa_circ_0047303 | exonic | chr18 | ZNF521 | 9.2977975 | down | 0.006717343 |
| hsa_circ_0087565 | exonic | chr9 | ZNF169 | 8.7255455 | down | 0.018358601 |
| hsa_circ_0000488 | intronic | chr13 | - | 8.4844294 | down | 0.000260793 |
| hsa_circ_0031569 | exonic | chr14 | HEATR5A | 8.432469 | down | 0.00854826 |
CircRNA ID: The circRNA ID can be found in circBase (http://www.circbase.org/). Gene symbol represents the liner RNA where
circRNAs generated from. “-” indicates that circRNA microarray did not provide the gene symbol of circRNA derived from intragenic or intronic types.
Fold Change: calculated from the ratio of the two groups (normal tissues versus CRC tissues). P-value: computed from paired t-test.
Five target miRNAs of differentially expressed circRNAs in microarray data.
| CircRNA ID | Regulation | MRE |
|---|---|---|
| hsa_circ_0000072 | up | hsa-miR-136-5p, hsa-miR-606, hsa-miR-145-5p, hsa-miR-153-5p, hsa-miR-302d-5p |
| hsa_circ_0007142 | up | hsa-miR-651-3p,hsa-miR-103a-2-5p,hsa-miR-744-3p,hsa-miR-96-3p,hsa-miR-128-3p |
| hsa_circ_0008812 | up | hsa-miR-138-5p,hsa-miR-325,hsa-miR-593-3p,hsa-miR-512-3p,hsa-miR-766-5p |
| hsa_circ_0050514 | up | hsa-miR-433-3p,hsa-miR-215-3p,hsa-miR-34b-5p,hsa-miR-23b-3p,hsa-miR-891a-5p |
| hsa_circ_0085923 | up | hsa-miR-580-5p,hsa-miR-198,hsa-miR-656-5p,hsa-miR-219a-5p,hsa-miR-758-5p |
| hsa_circ_0087855 | up | hsa-miR-138-5p,hsa-miR-325,hsa-miR-593-3p,hsa-miR-512-3p,hsa-miR-766-5p |
| hsa_circ_0005954 | up | hsa-miR-520f-3p,hsa-miR-618,hsa-miR-223-3p,hsa-miR-875-3p,hsa-miR-495-3p |
| hsa_circ_0005050 | up | hsa-miR-452-5p,hsa-miR-146b-5p,hsa-miR-146a-5p,hsa-miR-597-3p,hsa-miR-578 |
| hsa_circ_0005281 | up | hsa-miR-576-3p,hsa-miR-646,hsa-miR-219a-2-3p,hsa-miR-181b-2-3p,hsa-miR-181b-3p |
| hsa_circ_0000994 | up | hsa-miR-27b-3p,hsa-miR-27a-3p,hsa-miR-373-5p,hsa-miR-335-3p,hsa-miR-628-5p |
| hsa_circ_0072279 | down | hsa-miR-665,hsa-miR-874-5p,hsa-miR-188-3p,hsa-miR-29b-2-5p,hsa-miR-1271-3p |
| hsa_circ_0001704 | down | hsa-miR-20b-3p,hsa-miR-641,hsa-miR-766-3p,hsa-miR-661,hsa-miR-625-5p |
| hsa_circ_0035626 | down | hsa-miR-619-3p,hsa-miR-653-5p,hsa-miR-660-3p,hsa-miR-548d-5p,hsa-miR-200a-3p |
| hsa_circ_0001525 | down | hsa-let-7i-5p,hsa-let-7g-5p,hsa-miR-619-5p,hsa-let-7f-5p,hsa-miR-98-5p |
| hsa_circ_0005904 | down | hsa-let-7g-5p,hsa-let-7i-5p,hsa-miR-98-5p,hsa-miR-141-3p,hsa-miR-545-3p |
| hsa_circ_0008367 | down | hsa-miR-330-5p,hsa-miR-216a-3p,hsa-miR-342-5p,hsa-miR-891a-3p,hsa-miR-326 |
| hsa_circ_0047303 | down | hsa-miR-149-3p,hsa-miR-17-3p,hsa-miR-1301-3p,hsa-miR-509-5p,hsa-miR-516b-5p |
| hsa_circ_0087565 | down | hsa-miR-766-3p,hsa-miR-612,hsa-miR-338-3p,hsa-let-7g-3p,hsa-let-7a-2-3p |
| hsa_circ_0000488 | down | hsa-miR-519a-3p,hsa-miR-519b-3p,hsa-miR-28-5p,hsa-miR-130b-3p,hsa-miR-708-5p |
| hsa_circ_0031569 | down | hsa-miR-128-3p,hsa-miR-30c-2-3p,hsa-miR-216a-3p,hsa-miR-585-5p,hsa-miR-140-3p |
MRE: miRNA response element.
Figure 2hsa_circ_0007142 expression is elevated in CRC tissues and cells. (a) hsa_circ_0007142 expression in CRC tissues (n=50) and paired pericancerous tissues (n=50) was determined by PCR and normalized to GAPDH. Sequencing results confirmed PCR products, especially the junction part. (b) The tissues were divided into two groups. Positive –ΔΔcT indicated high hsa_circ_0007142 expression, while negative -ΔΔCT indicated low hsa_circ_0007142 expression. (c) Relative hsa_circ_0007142 expression in HT-29, HCT116, LoVo, and HCO cells. (d) Relative hsa_circ_0007142 expression level in HT-29 and HCT-116 cells transfected with circ_0007142 (si-circ_0007142) or control siRNA (si-NC). (e) Relative DOCK1 mRNA expression in HT-29 and HCT116 cells transfected with si-circ_0007142 or si-NC. Error bars represented mean ± standard deviation (SD). ∗P<0.05 and ∗∗P<0.01. ΔCT is the difference between the CT value of hsa_circ_0007142 and CT value of GAPDH. ΔΔCT is the difference between the ΔCT of CRC tissues and the ΔCT of adjacent normal tissues.
Correlation between hsa_circ_0007142 expression and clinicopathological characteristics of CRC.
| Clinical Parameter | Hsa_circ_0007142 (2−ΔΔCT) | Chi-squared test | |
|---|---|---|---|
| High group | Low group | P value | |
| (≥1, n=33) | (<1, n=17) | ||
| Gender | 0.623 | ||
| Male | 21 | 12 | |
| Female | 12 | 5 | |
| Age (years) | 0.209 | ||
| ≤50 | 6 | 7 | |
| 50–70 | 15 | 6 | |
| > 70 | 12 | 4 | |
| Tumor size | 0.577 | ||
| ≤3 cm | 8 | 5 | |
| 3–5 cm | 17 | 10 | |
| >5 cm | 8 | 2 | |
| Differentiation | 0.008 | ||
| Poor | 2 | 6 | |
| Moderate | 24 | 11 | |
| Well | 7 | 0 | |
| Lymphatic metastasis | 0.037 | ||
| Nx&N0 | 13 | 12 | |
| N1&N2 | 20 | 5 | |
| Tumor stage | 0.136 | ||
| I–II | 19 | 6 | |
| III–IV | 14 | 11 | |
| Distant metastasis | 0.11 | ||
| No | 33 | 15 | |
| Yes | 0 | 2 | |
∗P<0.05, ∗∗P<0.01. ΔCT is the difference between the CT value of hsa_circ_0007142 and of GAPDH.
ΔΔCT is the difference between the ΔCT of CRC tissues and the ΔCT of adjacent normal tissues.
Figure 3hsa_circ_0007142 knockdown inhibited CRC cell proliferation. (a) CCK8 assay of the viability of HT-29 and HCT116 cells transfected with circ_0007142 (si-circ_0007142) or control siRNA (si-NC). (b) Colony-forming assay of HT-29 and HCT-116 cells transfected with si-circ_0007142 or si-NC. Data were presented as the mean ± SD of three independent experiments. ∗P<0.05, ∗∗P<0.01.
Figure 4hsa_circ_0007142 knockdown inhibited CRC cell migration and invasion. Transwell assays on the migration (a) and invasion (b) of HT-29 and HCT-116 cells transfected with si-circ_0007142 or si-NC. ∗∗P<0.01; magnification ×100.
Figure 5MiR-103a-2-5p is a target of hsa_circ_0007142. (a) The binding site of miR-103a-2-5p for hsa_circ_0007142 was predicted by circRNA microarray. (b) miR-103a-2-5p expression was determined by RT-qPCR in HT-29 and HCT-116 cells transfected with si-circ_0007142 or si-NC. (c) PCR analysis of hsa_circ_0007142 and miR-103a-2-5p expression in CRC tissues (n=30) and paired pericancerous tissues (PT, n=30). (d) The correlation of the expression of miR-103a-2-5p and hsa_circ_0007142 in CRC tissues (n=30) and paired pericancerous tissues (n=30). (e) The luciferase activity in HT-29 cells cotransfected with the plasmids of wild-type hsa_circ_0007142 and miR-103a-2-5p mimics. (f) The luciferase activity in HT-29 cells cotransfected with plasmids of mutant hsa_circ_0007142 and miR-103a-2-5p mimics. ∗P<0.05, ∗∗P<0.01.