Cracking the code: lncRNA-miRNA-mRNA integrated network analysis unveiling lncRNAs as promising non-invasive NAFLD biomarkers toward precision diagnosis

Nouran Yonis; Ahmed Mousa; Mohamed H Yousef; Ahmed M Ghouneimy; Areeg M Dabbish; Hana Abdelzaher; Mohamed Ali Hussein; Shahd Ezzeldin; Abdelmoneim A Adel; Yosra H Mahmoud; Nashwa El-Khazragy; Anwar Abdelnaser

doi:10.1016/j.compbiolchem.2024.108325

Cracking the code: lncRNA-miRNA-mRNA integrated network analysis unveiling lncRNAs as promising non-invasive NAFLD biomarkers toward precision diagnosis

Comput Biol Chem. 2025 Jan 9:115:108325. doi: 10.1016/j.compbiolchem.2024.108325. Online ahead of print.

Affiliations

¹ Institute of Global Health and Human Ecology (IGHHE), School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt.
² University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt.
³ Biotechnology Graduate Program, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt.
⁴ Department of Biology, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt.
⁵ Basic Research Department, Proteomics and Metabolomics Research Program, Children's Cancer Hospital 57357 (CCHE-57357), Cairo, Egypt.
⁶ Hematology and Gastroenterology Department, National Hepatology and Tropical Medicine Research Institute (NHTMRI), Egypt.
⁷ Clinical Pathology and Hematology Department, Faculty of Medicine, Ain Shams University Biomedical Research Department, Cairo 11381, Egypt.
⁸ Institute of Global Health and Human Ecology (IGHHE), School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt. Electronic address: [email protected].

PMID: 39832417
DOI: 10.1016/j.compbiolchem.2024.108325

Abstract

Background: Non-alcoholic fatty liver disease (NAFLD) involves abnormal fat accumulation in the liver, mainly as triglycerides. It ranges from steatosis to non-alcoholic steatohepatitis (NASH), which can lead to inflammation, cellular damage, liver fibrosis, cirrhosis, or hepatocellular carcinoma (HCC). Long non-coding RNAs (lncRNAs) are crucial for regulating gene expression across various conditions. LncRNAs are emerging as potential putative diagnostic markers for NAFLD-associated HCC.

Methods: We used two human and two mouse datasets from the Gene Expression Omnibus to analyze the expression profiles of mRNAs and lncRNAs. We created a network linking lncRNAs, miRNAs, and mRNAs to investigate the relationships among these RNA types. Additionally, we identified NAFLD-related lncRNAs from existing literature. We then quantified the expression levels of four specific lncRNAs, including PVT1, DUBR, SNHG17, and SNHG14, in the serum of 92 Egyptian participants using qPCR. Finally, we performed a Receiver Operating Characteristic analysis to evaluate the diagnostic potential of the candidate lncRNAs.

Results: Our data suggests that maternally expressed gene 3 (MEG3), H19, and DPPA2 Upstream Binding RNA (DUBR) were significantly upregulated, and plasmacytoma variant translocation 1 (PVT1) was markedly downregulated. PVT1 showed the highest diagnostic accuracy for both NAFLD and NASH. The combined panels of PVT1 +H19 for NAFLD and PVT1 +H19 +DUBR for NASH demonstrated high diagnostic potential. Uniquely, PVT1 can distinguish between NAFLD and NASH. PVT1 exhibited strong diagnostic potential for NAFLD and NASH, individually and in combination with other lncRNAs.

Conclusion: Our study identifies four lncRNAs as putative biomarkers with high specificity and accuracy, individually or combined, for differentiating between NAFLD and NASH. Healthy volunteers with PVT1 possess the highest diagnostic accuracy and significantly discriminate between NAFLD and NASH.

Keywords: LncRNAs; PVT1; non-alcoholic fatty liver disease; non-alcoholic steatohepatitis.