Overexpression of DDIT4 and TPTEP1 are associated with metastasis and advanced stages in colorectal cancer patients: a study utilizing bioinformatics prediction and experimental validation

Abstract

Background Various diagnostic and prognostic tools exist in colorectal cancer (CRC) due to multiple genetic and epigenetic alterations causing the disease. Today, the expression of RNAs is being used as prognostic markers for cancer. Methods In the current study, various dysregulated RNAs in CRC were identified via bioinformatics prediction. Expression of several of these RNAs were measured by RT-qPCR in 48 tissues from CRC patients as well as in colorectal cancer stem cell-enriched spheroids derived from the HT-29 cell line. The relationships between the expression levels of these RNAs and clinicopathological features were analyzed. Results Our bioinformatics analysis determined 11 key mRNAs, 9 hub miRNAs, and 18 lncRNAs which among them 2 coding RNA genes including DDIT4 and SULF1 as well as 3 non-coding RNA genes including TPTEP1, miR-181d-5p, and miR-148b-3p were selected for the further investigations. Expression of DDIT4, TPTEP1, and miR-181d-5p showed significantly increased levels while SULF1 and miR-148b-3p showed decreased levels in CRC tissues compared to the adjacent normal tissues. Positive relationships between DDIT4, SULF1, and TPTEP1 expression and metastasis and advanced stages of CRC were observed. Additionally, our results showed significant correlations between expression of TPTEP1 with DDIT4 and SULF1. Conclusions Our findings demonstrated increased expression levels of DDIT4 and TPTEP1 in CRC were associated with more aggressive tumor behavior and more advanced stages of the disease. The positive correlations between TPTEP1 as non-coding RNA and both DDIT4 and SULF1 suggest a regulatory effect of TPTEP1 on these genes.

An integrative transcriptome analysis reveals potential predictive, prognostic biomarkers and therapeutic targets in colorectal cancer

“…In this respect, eight mRNAs (SLC4A4, MMP1, MMP3, GCG, CXCL1, CXCL3, CLCA1, and CLCA4), three lncRNAs (UCA1, LINC00449, TPT3P1) and four miRNAs (has-miR-1301, has-miR-132, has-miR-339, has-miR-497) were found to be significantly (p < 0.01) related with poor OS of CRC patients. A majority of these hub genes were recently investigated as potential prognostic biomarkers, bioinformatically and experimentally [62][63][64][65]. Moreover, in our multivariate Cox model, our results suggested that out of four final lncRNAs, LINC00974 was the only lncRNA shown as a novel and potential predictor of DFS in patients with CRC, which is also reported by Gao et al in gastric carcinoma [66].…”

MicroRNA-642a-5p Targets DNA Damage-Inducible Transcript 4 to Suppress Hepatitis B Virus Hepatoma Carcinoma Cell

“…The relative quantity was calculated by the 2 -△ △ Ct method. The results for miRNA were normalized to U6 snRNA, and the results for DDIT4 were normalized to GAPDH (22). The primers are listed in Table 1 (14,22).…”

LncRNAs, the Molecules Involved in Communications With Colorectal Cancer Stem Cells

“…The expression levels of DDIT4 and SULF1 were significantly positively correlated with TPTEP1, and significantly negatively correlated with miR-148b-3p. According to the predicted binding site, these correlations may be explained by mRNA-miRNA network ( 70 ).…”