Up-regulation of miR-1290 in tumor tissues and serum of CRC patients.
Our early research confirmed that miR-1290 expression is highly increased in tumor tissues of CRC patients, and up-regulation of miR-1290 impairs cytokinesis and affects the reprogramming of colon cancer cells. Therefore, miR-1290 plays an important role in CRC progression. To further verify the expression level of miR-1290 in CRC, we collected 10 pairs of tumor tissues and adjacent tissues, and found that miR-1290 was significantly overexpressed in tumor tissues (Figure 1A).
In order to evaluate circulating miR-1290 expression levels, three pairs of CRC and control serum specimens matched for clinical characteristics, such as age, gender, and past history, were selected for miRNA sequencing analysis. The data suggested that compared to healthy controls, there were 656 differentially expressed miRNAs in CRC serum, of which 261 miRNAs were up-regulated and 395 miRNAs down-regulated (p < 0.01). miRNAs with very low expression levels were excluded, and volcano graph analysis was performed. Compared with the control group, 94 miRNAs were up-regulated and 104 miRNAs were down-regulated in CRC (|log2FC| > 1, p < 0.01) (Figure 1B). Based on the miRNA expression profiles, differentially expressed miRNAs with high expression levels were chosen for cluster analysis. As shown in the heatmap, hsa-miR-1290 was significantly overexpressed in CRC serum (Figure 1C), suggesting that miR-1290 might be a potential biomarker for gastrointestinal tumors.
Establishment and evaluation of circulating miRNA detection technologies for clinical identification.
A reliable methodology was needed to analyze circulating miR-1290 expression levels in clinical samples. First, we used different methods of circulating miRNA extraction, including three extraction kits from QIAGEN and two TRIzol reagents from Invitrogen, each following different extraction principles, as shown in Table S1. We examined the serum miR-1290 expression levels of 20 healthy individuals using cel-miR-39 or miR-16-5p as reference miRNAs (Table S2). We obtained different results when choosing different reference miRNAs, indicating the importance of an appropriate control. The extraction efficiencies of the miRNeasy Serum/Plasma Kit, miRNeasy Serum/Plasma Advanced Kit and TRIzol LS were better than the other two methods. Considering that the miRNeasy Serum/Plasma Advanced Kit and miRNeasy Serum/Plasma Advanced Kit belong to QIAGEN and miRNeasy Serum/Plasma Advanced Kit was an improvement over the miRNeasy Serum/Plasma Kit, we further compared the extraction efficiency of the miRNeasy Serum/Plasma Advanced Kit and TRIzol LS for cell-free miRNA.
The influence of reference miRNA was eliminated by adding the same amount of cel-miR-39 (10μM, 5μl) to the same volume of serum. The results showed that for the same amount of circulating cel-miR-39, the extraction efficiency of the miRNeasy Serum/Plasma Advanced Kit was apparently higher than that of TRIzol LS (figure 2A, p < 0.0001). Therefore, the miRNeasy Serum/Plasma Advanced Kit was chosen as the main method for subsequent experiments.
To further evaluate the recovery efficiency of the entire circulating miRNA detection system, we tested miR-1290 standards with different concentrations (100 nM, 10 nM, 1 nM, 10 pM, 1 pM, 0.1 pM) and drew a standard curve (y = -4.173x + 58.96, R2 = 0.9998) (Figure 2B). Then, standard solutions of low, middle, and high concentrations were added to the sample solutions and analyzed in the same way. miRNA concentration in the sample was calculated according to the standard curve, and the recovery rate was evaluated. The recoveries of the three groups with low, middle, and high concentration standards were 103%, 116%, and 87.8%, respectively (Table S3), which were within the acceptable range. The influence of interference factors in the serum was also evaluated. We collected three samples with high bilirubin, triglyceride or rheumatoid factor, and analyzed the recovery efficiency as described above. The results showed that the recovery efficiencies of the three groups were 119%, 93.0%, and 107%, respectively (Table S3), which were within the acceptable range of error. Therefore, serum bilirubin, triglycerides and rheumatoid factor levels did not interfere with the miRNA detection method.
miR-16-5p is a commonly used internal control for circulating miRNA detection. Previous studies have shown that miR-16-5p is overexpressed in breast cancer, chronic lymphocytic leukemia, rheumatoid arthritis, and other diseases. In order to verify the reliability of miR-16-5p as an internal control, we collected serum samples from patients with breast cancer and rheumatoid arthritis and evaluated the miR-16-5p expression in different diseases using cel-miR-39 as the exogenous control (Figure 2C). The expression levels of miR-16-5p in the serum of breast cancer patients and rheumatoid arthritis patients were significantly higher than in healthy controls (p < 0.001). We also analyzed the Cq values of miR-16-5p and cel-miR-39 in PC patients, GC patients and healthy controls. The results were shown in Figure 2D, Cq values of miR-16-5p in patients with PC and GC patients were much higher than those in healthy controls, while there were no significant differences in Cq values of cel-miR-39, indicating that miR-16-5p expression fluctuates in gastrointestinal tumors and is not suitable as an internal control.
In the final part of the methodological evaluation, we collected plasma and serum samples from 20 healthy individuals to evaluate the differences between miR-1290 expression in serum and plasma sample from the same individual (Figure 2E-F). We found that miR-1290 expression levels in plasma were higher than those in serum when cel-miR-39 was used as a reference miRNA. In contrast, in some individuals, the expression levels of miR-1290 were higher in the serum than in plasma when miR-16-5p was used as a reference miRNA, which also indicated that miR-16-5p is not a reliable internal control.
Human gastrointestinal tumor cells express and secret miR-1290.
To clarify the source of circulating miR-1290, we examined expression levels of miR-1290 in human gastrointestinal tumor cell lines. As shown in Figure 3A, five CRC cell lines including HT29, HCT116, P4, SW480, and SW620 cells, three PC cell lines including ASPC-1, BXPC-3, and SW1990 cells, and two GC cell lines including SGC7901 and BGC823 cells were analyzed. The expression levels of miR-1290 in GC cell lines were lower than in CRC and PC cell lines. miR-1290 expression was the lowest in BGC823 cells, while miR-1290 expression in HT29, HCT116, P4, ASPC-1, and BXPC-3 cells was relatively high. We further examined miR-1290 expression levels in cellular supernatants of five cell lines (HT-29, HCT116, ASPC-1, BXPC-3 and SGC7901 cells) when cultured at different cell densities for 24 h, 48 h, and 72 h. As shown in Figure 3B-F, gastrointestinal tumor cells expressed and secreted miR-1290 into the cell supernatant, and miR-1290 expression levels in the cell supernatant increased with cell amounts and culture time. Therefore, circulating miR-1290 might derive from tumor cell secretion as a potential tumor biomarker.
Circulating miR-1290 serves as a diagnostic biomarker in gastrointestinal tumors.
In the subsequent validation phase, circulating miR-1290 expression levels were detected in 46 PC patients, 50 CRC patients, 50 GC patients, and 50 healthy controls. The clinical characteristics of participants are summarized in Table 1. There was no statistical difference in gender, BMI, smoking history, or alcohol consumption between the PC group and control group. Patients in the PC group had a higher average age (p < 0.05) and a higher proportion of hypertension (p < 0.05) and diabetes (p < 0.05). Furthermore, the CEA (p < 0.001), CA199 (p < 0.001), CA125 (p < 0.001), CA242 (p < 0.001), and CA211 (p <0.01) levels in the PC group were significantly higher than those in the control group. There was no significant variation in age, gender, BMI, alcohol consumption or diabetes history between the CRC group and the control group, but the ratio of smoking (p < 0.05) and hypertension (p < 0.05) was much higher in the CRC group than in the control group. The CEA level (p < 0.001) in the CRC group was apparently higher than that in the control group, while expression levels of the other biomarkers were similar to the controls. In addition, there were no statistical differences in age, gender, BMI, smoking history, alcohol consumption, hypertension history, or diabetes history between the GC group and control group. The CEA expression level was higher in the GC group (p < 0.01) while the remaining biomarkers were not significantly different from the control group.
As shown in Figure 4A-C, the expression level of circulating miR-1290 was considerably increased in PC (p < 0.01), CRC (p < 0.05), and GC (p < 0.01). Correlations between serum miR-1290 expression levels and clinicopathological features in gastrointestinal cancer patients were explored. In PC patients (Table 2), there was no statistical correlation between circulating miR-1290 expression and age, gender, BMI, smoking history, alcohol consumption, hypertension history, diabetes history, or tumor site. High expression levels of miR-1290 were associated with tumor size (p < 0.01), lymphatic invasion (p < 0.01), vascular invasion (p < 0.05), distant metastasis (p < 0.05), tumor differentiation (p < 0.05), and tumor AJCC stage (p < 0.05). However, there was no significant relationship between circulating miR-1290 expression level and the other tumor biomarkers including CEA, CA199, CA125, CA242, and CA211. In CRC patients (Table 3), there was no clear association between circulating miR-1290 expression levels and age, gender, BMI, smoking history, alcohol consumption, hypertension history, diabetes history, or tumor site. Circulating miR-1290 expression was significantly higher in CRC patients with larger tumor size (p < 0.05), lymphatic invasion (p < 0.05), vascular invasion (p < 0.05), distant metastasis (p < 0.05), poorer tumor differentiation (p < 0.05), and more advanced AJCC stage (p < 0.05). miR-1290 expression levels were related with CEA (p < 0.05), while there was no statistical correlation with levels of CA199, CA125, CA242, or CA211. As for GC patients (Table 4), there was no significant relationship between circulating miR-1290 expression level and age, gender, BMI, smoking, drinking, diabetes, or tumor location. The size of tumor, lymphoid invasion, vascular invasion, distant metastasis, tumor differentiation degree, and AJCC stage, as well as common tumor markers, also showed no remarkable correlation with circulating miR-1290 expression.
To evaluate the potential diagnostic value of circulating miR-1290, receiver operating characteristic (ROC) curve analysis was performed. The area under the curve (AUC) was 0.8857 (p < 0.0001) in PC, with 60.9% sensitivity and 90.0% specificity. The AUC was 0.7852 (p < 0.0001) for circulating miR-1290 in CRC, with a sensitivity of 42.0% and specificity of 90.0%. In GC, the AUC of miR-1290 was 0.6576 (p < 0.01), with a sensitivity of 26.0%, and specificity of 90.0%. Moreover, as shown in Figure 4G-I, combination of circulating miR-1290 and traditional biomarkers had higher diagnostic value. In PC patients, sensitivity and specificity of miR-1290 combined with CA199 were 80.4% and 90.0%, with the AUC value of 0.9626 (p < 0.0001). In CRC patients, sensitivity and specificity of miR-1290 combined with CEA were 58.0% and 90.0%, with the AUC value of 0.8348 (p < 0.0001). Sensitivity and specificity of miR-1290 combined with CA211 were 38.0% and 90.0% in GC patients, with the AUC value of 0.7788 (p < 0.0001). As a result, miR-1290 may serve as a potential diagnostic biomarker for gastrointestinal cancers, with different diagnostic efficiency in different tumors.
miR-1290 is a potential biomarker for gastrointestinal tumor surveillance.
To assess the monitoring value of circulating miR-1290, we explored the changes of miR-1290 expression levels after surgery in 10 CRC patients. As shown in Figure 5A, miR-1290 expression decreased greatly after surgery (p < 0.05). Meanwhile, a subcutaneous xenograft model of CRC in nude mice was constructed to evaluate the fluctuation of circulating miR-1290 during disease progression and drug treatment. Circulating miR-1290 significantly increased after tumor formation (Figure 5B). After treatment with 5-Fu, the tumor tissue structure was destroyed, and tumor cells were largely necrotic, with a remarkable reduction of circulating miR-1290 (Figure 5B). Therefore, miR-1290 is a promising biomarker for gastrointestinal tumor surveillance.