RNA-Seq Profiling of Serum Exosomal Circular RNAs Reveals Circ-PNN as a Potential Biomarker for Human Colorectal Cancer

Abstract Chemo-resistance is associated with poor prognosis in colorectal cancer (CRC), with the absence of early biomarker. Exosomes are microvesicles released by body cells for intercellular communication. Circular RNAs (circRNAs) are non-coding RNAs with covalently closed loops and enriched in exosomes. Crosstalk between circRNAs in exosomes and chemo-resistance in CRC remains unknown. This research aims to identify exosomal circRNAs associated with FOLFOX-resistance in CRC. FOLFOX-resistant HCT116 CRC cells (HCT116-R) were generated from parental HCT116 cells (HCT116-P) using periodic drug induction. Exosomes were characterized using transmission electron microscopy (TEM), Zetasizer and Western blot. Our exosomes were translucent cup-shaped structures under TEM with differential expression of TSG101, CD9, and CD63. We performed circRNAs microarray using exosomal RNAs from HCT116-R and HCT116-P cells. We validated our microarray data using serum samples. We performed drug sensitivity assay and cell cycle analysis to characterize selected circRNA after siRNA-knockdown. Using fold change >2 and p < 0.05, we identified 105 significantly upregulated and 34 downregulated circRNAs in HCT116-R exosomes. Knockdown of circ_0000338 improved the chemo-resistance of CRC cells. We have proposed that circ_0000338 may have dual regulatory roles in chemo-resistant CRC. Exosomal circ_0000338 could be a potential biomarker for further validation in CRC.

Download Full-text

Identification of differentially expressed circular RNAs in human colorectal cancer

Tumor Biology ◽

10.1177/1010428317694546 ◽

2017 ◽

Vol 39 (3) ◽

pp. 101042831769454 ◽

Cited By ~ 31

Author(s):

Peili Zhang ◽

Zhigui Zuo ◽

Wenjing Shang ◽

Aihua Wu ◽

Ruichun Bi ◽

...

Keyword(s):

Colorectal Cancer ◽

Receiver Operating Characteristic ◽

Operating Characteristic ◽

Circular Rna ◽

Expression Level ◽

Circular Rnas ◽

Human Colorectal Cancer ◽

Expression Levels ◽

Normal Tissues ◽

Node Metastasis

Circular RNA, a class of non-coding RNA, is a new group of RNAs and is related to tumorigenesis. Circular RNAs are suggested to be ideal candidate biomarkers with potential diagnostic and therapeutic implications. However, little is known about their expression in human colorectal cancer. In our study, differentially expressed circular RNAs were detected using circular RNA array in paired tumor and adjacent non-tumorous tissues from six colorectal cancer patients. Expression levels of selected circular RNAs (hsa_circRNA_103809 and hsa_circRNA_104700) were measured by real-time polymerase chain reaction in 170 paired colorectal cancer samples for validation. Statistical analyses were conducted to investigate the association between hsa_circRNA_103809 and hsa_circRNA_104700 expression levels and respective patient clinicopathological features. Receiver operating characteristic curve was constructed to evaluate the diagnostic values. Our results indicated that there were 125 downregulated and 76 upregulated circular RNAs in colorectal cancer tissues compared with normal tissues. We also first demonstrated that the expression levels of hsa_circRNA_103809 ( p < 0.0001) and hsa_circRNA_104700 ( p = 0.0003) were significantly lower in colorectal cancer than in normal tissues. The expression level of hsa_circRNA_103809 was significantly correlated with lymph node metastasis ( p = 0.021) and tumor-node-metastasis stage ( p = 0.011), and the expression level of hsa_circRNA_104700 was significantly correlated with distal metastasis ( p = 0.036). The area under receiver operating characteristic curves of hsa_circRNA_103809 and hsa_circRNA_104700 were 0.699 ( p < 0.0001) and 0.616 ( p < 0.0001), respectively. In conclusion, these results suggest that hsa_circRNA_103809 and hsa_circRNA_104700 may be potentially involved in the development of colorectal cancer and serve as potential biomarkers for the diagnosis of colorectal cancer.

Download Full-text

Prognostic and diagnostic value of circRNA expression in colorectal carcinoma: a meta-analysis

10.21203/rs.2.16194/v2 ◽

2020 ◽

Author(s):

Jinpeng Yuan ◽

Dongming Guo ◽

Xinxin Li ◽

Juntian Chen

Keyword(s):

Colorectal Cancer ◽

Meta Analysis ◽

Area Under The Curve ◽

Diagnostic Value ◽

Cochrane Library ◽

Circular Rnas ◽

Control Factors ◽

Potential Biomarker ◽

Negative Effect ◽

Newcastle Ottawa Scale

Abstract Background: Circular RNAs (circRNAs) are new stars in the network of noncoding RNAs and are regarded as key control factors in numerous tumours. The purpose of our study was to evaluate the clinical, prognostic and diagnostic role of circRNAs in colorectal cancer. The quality of all the articles were assessed by the Newcastle‐Ottawa Scale. Methods: An online search in electronic databases, including the PubMed, Cochrane Library and Web of Science online databases, was conducted to identify as many relevant papers as possible. Nineteen relevant studies were enrolled in this meta-analysis, with seven on diagnosis, eight on prognosis and 11 on clinicopathological features. Results: For the diagnostic value of circRNAs, the pooled results showed that the area under the curve (AUC) was 0.82 for identifying patients with colorectal cancer, with a sensitivity of 83% and a specificity of 72%. In terms of prognosis, carcinogenic circRNAs have a negative effect on overall survival (OS: HR = 2.29, 95% CI: 1.50-3.52), and increases in tumour suppressor circRNA expression are associated with longer survival (OS: HR = 0.37, 95% CI: 0.22-0.64). And the elevated expression of oncogenic circRNAs is associated with poor clinical features while tumor suppressor circRNAs are the complete opposite. Conclusions: These results suggest that circRNAs may be a potential biomarker for the diagnosis and prognosis of colorectal cancer.

Download Full-text

Discovery of a potential predictive marker for eribulin treatment and novel target genes in BRAF V600E mutant metastatic colorectal cancer using an AI-driven RNA-seq analysis platform: Translational research of the BRAVERY study (EPOC1701).

Journal of Clinical Oncology ◽

10.1200/jco.2021.39.15_suppl.e15532 ◽

2021 ◽

Vol 39 (15_suppl) ◽

pp. e15532-e15532

Author(s):

Toshiki Masuishi ◽

Hiroya Taniguchi ◽

Daisuke Kotani ◽

Hideaki Bando ◽

Taroh Satoh ◽

...

Keyword(s):

Gene Expression ◽

Colorectal Cancer ◽

Cell Cycle ◽

Metastatic Colorectal Cancer ◽

Predictive Marker ◽

Braf V600e ◽

Rna Seq ◽

The Poor ◽

Potential Biomarker ◽

Poor Group

e15532 Background: Patients (pts) with BRAF V600E mutant (mt) metastatic colorectal cancer (mCRC) still have a poor prognosis even when treated with encorafenib plus cetuximab. We reported that eribulin that inhibits G2-M cell cycle had limited activity for these pts in the phase II BRAVERY study (Masuishi T, et al. WCGC 2020). Barras D, et al. (2017) reported that BRAF V600E mt mCRCs were classified into BM1 and BM2 characterized by KRAS/AKT pathway activation and deregulation of the cell cycle with G2-M phase activation, respectively, based on gene expression. Methods: Whole transcriptome RNA-seq of FFPE pre-treatment tumor samples was performed using NovaSeq 6000 in the BRAVERY study. Molecular features were extracted using the Txome.ai platform (Ocean Genomics Inc., PA, USA) which included transcript- and gene-level expression quantification, expression-based clustering, and structural variant calling. Efficacy of eribulin was classified as “good” if pts had a tumor reduction and/or progression-free survival (PFS) of more than 6 months, and “poor” otherwise. The differential gene expression analysis was performed between pts with “good” and “poor” using Txome.ai. In addition, BM and consensus molecular subtype (CMS) classification were performed using the model developed by Barras D, et al. (2017) and Guinney J, et al. (2015), respectively. Results: Among 27 pts, 26 tumor samples were available to perform RNA-seq and analyze gene expression despite low mapping rates. Patient characteristics were as follows: median age of 58.5 (range, 33–71) years; ECOG PS of 0/1 (16/10); primary tumor location of right/left (11/15); and all 26 pts had MSS/pMMR. Four and 22 pts were classified into “good” and “poor” groups, respectively. Among 52 differentially expressed genes (GENCODE v31) with false discovery rate-adjusted P- value < 0.05, the top 5 genes with the lowest P-values are provided in the table. All 4 pts in the “good” group were classified into BM2 and pts in the “poor” group were classified into BM1 (8/22) and BM2 (14/22) (p = 0.07). In addition, all but 2 pts were classified into CMS4. These two pts belong to the “poor” group with one of them classified into CMS1 and the other into CMS2. Conclusions: These gene expression analyses suggest that BM2 subtype could be a predictive marker for the efficacy of eribulin and some genes could be novel targets with the goal to improve prognosis of pts with BRAF V600E mt mCRC. This is the first finding for a potential biomarker in this subgroup using RNA-seq analysis tools. These findings will require additional validation. Clinical trial information: UMIN000031552. [Table: see text]

Download Full-text

Exploration of small RNA-seq data for small non-coding RNAs in Human Colorectal Cancer

Journal of Genomics ◽

10.7150/jgen.18856 ◽

2017 ◽

Vol 5 ◽

pp. 16-31 ◽

Cited By ~ 16

Author(s):

Srinivas V Koduru ◽

Amit K Tiwari ◽

Sprague W Hazard ◽

Milind Mahajan ◽

Dino J Ravnic

Keyword(s):

Colorectal Cancer ◽

Small Rna ◽

Rna Seq ◽

Human Colorectal Cancer ◽

Non Coding Rnas

Download Full-text

The hsa_circ_0000523/miR-let-7b/METLL3 Axis Regulates the Proliferation, Apoptosis and Metastasis of Human Colorectal Cancer Cell Line HCT116

10.21203/rs.3.rs-142499/v1 ◽

2021 ◽

Author(s):

Yansheng Wang ◽

Baolei Zhang ◽

Yun Zhu ◽

Yong Zhang ◽

Li Li ◽

...

Keyword(s):

Colorectal Cancer ◽

Cell Proliferation ◽

Cell Line ◽

Quantitative Polymerase Chain Reaction ◽

Negative Control ◽

Colorectal Cancer Cell Line ◽

Circular Rnas ◽

Human Colorectal Cancer ◽

Reaction Cell ◽

Hct116 Cells

Abstract Background: Circular RNAs (circRNAs) have gained wide attention as a class of potential biomarkers for the early detection of multiple cancers. However, the functions and mechanisms of circRNAs in the oncogenesis of human colorectal cancer (CRC) remain to be elucidated. This study aimed to investigate the roles of hsa_circ_0000523 and its parental gene METTL3 in regulating cell proliferation, apoptosis and metastasis in a human CRC cell line (HCT116).Methods: HCT116 cells were left untreated, transfected with hsa_circ_0000523- or METTL3-expressing plasmid, transfected with siRNA oligo against hsa_circ_0000523 or METTL3, or transfected with negative control vector or siRNA oligo. All transfections were performed with Lipofectamine 2000. Transcriptional levels of hsa_circ_0000523, miR-let-7b, and METTL3 were measured by real-time quantitative polymerase chain reaction. Cell proliferation was assessed by CCK-8 assay. Apoptosis was evaluated by flow cytometry after staining for annexin V and propidium iodide. Cellular potential for migration was detected by transwell assay. Results: In HCT116 cells, hsa_circ-0000523 indirectly regulated METTL3 expression by suppressing the transcription of miR-let-7b. The expression of METTL3 promoted cell proliferation and suppressed apoptosis. Higher levels of METTL3 expression were associated with more aggressive tumor invasion.Conclusion: The hsa_circ_0000523/miR-let-7b/METLL3 axis functions in the tumorigenesis and pathogenesis of human CRC. Our results suggest that circRNAs and METTL3 may be used for the highly sensitive diagnosis of CRC and predicting prognosis in patients who have undergone therapy.

Download Full-text