Hallmark microRNA signature in liquid biopsy identifies hepatocellular carcinoma and differentiates it from liver metastasis

Abstract

This study aims to develop a liquid biopsy assay to identify HCC and differentially diagnose hepatocellular carcinoma (HCC) from colorectal carcinoma (CRC) liver metastasis. Methods: Thirty-two microRNAs ("HallMark-32" panel) were designed to target the ten cancer hallmarks in HCC. Quantitative PCR and supervised machine learning models were applied to develop an HCC-specific diagnostic model. One hundred thirty-three plasma samples from intermediate-stage HCC patients, colorectal cancer (CRC) patients with liver metastasis, and healthy individuals were examined. Results: Six differentially expressed microRNAs ("Signature-Six" panel) were identified after comparing HCC and healthy individuals. The microRNA miR-221-3p, miR-223-3p, miR-26a-5p, and miR-30c-5p were significantly down-regulated in the plasma of HCC samples, while miR-365a-3p and miR-423-3p were significantly up-regulated. Machine learning models combined with HallMark-32 and Signature-Six panels demonstrated promising performance with an AUC of 0.85-0.96 (p ≤ 0.018) and 0.84-0.93 (p ≤ 0.021), respectively. Further modeling improvement by adjusting sample quality variation in the HallMark-32 panel boosted the accuracy to 95% ± 0.01 and AUC to 0.991 (95% CI 0.96-1, p = 0.001), respectively. Even in alpha fetoprotein (AFP)-negative (< 20ng/mL) HCC samples, HallMark-32 still achieved 100% sensitivity in identifying HCC. The Cancer Genome Atlas (TCGA, n=372) analysis demonstrated a significant association between HallMark-32 and HCC patient survival. Conclusion: To the best of our knowledge, this is the first report to utilize circulating miRNAs and machine learning to differentiate HCC from CRC liver metastasis. In this setting, HallMark-32 and Signature-Six are promising non-invasive tests for HCC differential diagnosis and distinguishing HCC from healthy individuals.

Salivary miR-30c-5p as Potential Biomarker for Detection of Oral Squamous Cell Carcinoma

“…miR-30c-5p studied here has been shown to be involved in other cancers such as colorectal cancer [ 32 , 33 ], non-small cell lung cancer [ 34 , 35 ], gastric cancer [ 36 ], pancreatic ductal adenocarcinoma [ 37 ], renal cell carcinoma [ 38 , 39 ], hepatocellular carcinoma [ 40 , 41 , 42 , 43 ], breast cancer [ 44 , 45 , 46 , 47 , 48 ], laryngeal cancer [ 49 ], and other malignancies. For example, in gastric cancer, miR-30c-5p suppresses migration, invasion, and epithelial to mesenchymal transition via targeting MTA1 [ 36 ].…”

Effects and prognostic values of miR-30c-5p target genes in gastric cancer via a comprehensive analysis using bioinformatics

“…MiRNA-30c-5p could suppress breast cancer survival by targeting KRAS Proto-Oncogene 38 , or histone deacetylase 9 (HDAC9) gene 39 . A recent study reported that miR-30c-5p was significantly decreased in the blood of HCC patients and could effectively discriminate HCC patients from healthy individuals 40 . There were also several studies on miR-30c-5p in GC.…”

Identification of microRNA hsa-miR-30c-5p as an inhibitory factor in the progression of hepatocellular carcinoma and investigation of its regulatory network via comprehensive analysis

“…In the development and progression of pancreatic cancer, miR-30 c had vital functions by targeting twinfilin 1 (TWF1) [ 28 ] or DNA topoisomerase II alpha gene (TOP2A) [ 29 ]. Because the expression of miR-30 c was significantly down-regulated in the plasma of HCC samples, it might be used as a noninvasive diagnostic marker [ 30 ]. The urinary exosome miR-30 c was also suggested as a biomarker of clear cell renal cell carcinoma [ 31 ].…”