Multi-Omics Analysis Revealed a Significant Alteration of Critical Metabolic Pathways Due to Sorafenib-Resistance in Hep3B Cell Lines

Abstract

Hepatocellular carcinoma (HCC) is the second prominent cause of cancer-associated death worldwide. Usually, HCC is diagnosed in advanced stages, wherein sorafenib, a multiple target tyrosine kinase inhibitor, is used as the first line of treatment. Unfortunately, resistance to sorafenib is usually encountered within six months of treatment. Therefore, there is a critical need to identify the underlying reasons for drug resistance. In the present study, we investigated the proteomic and metabolomics alterations accompanying sorafenib resistance in hepatocellular carcinoma Hep3B cells by employing ultra-high-performance liquid chromatography quadrupole time of flight mass spectrometry (UHPLC-QTOF-MS). The Bruker Human Metabolome Database (HMDB) library was used to identify the differentially abundant metabolites through MetaboScape 4.0 software (Bruker). For protein annotation and identification, the Uniprot proteome for Homo sapiens (Human) database was utilized through MaxQuant. The results revealed that 27 metabolites and 18 proteins were significantly dysregulated due to sorafenib resistance in Hep3B cells compared to the parental phenotype. D-alanine, L-proline, o-tyrosine, succinic acid and phosphatidylcholine (PC, 16:0/16:0) were among the significantly altered metabolites. Ubiquitin carboxyl-terminal hydrolase isozyme L1, mitochondrial superoxide dismutase, UDP-glucose-6-dehydrogenase, sorbitol dehydrogenase and calpain small subunit 1 were among the significantly altered proteins. The findings revealed that resistant Hep3B cells demonstrated significant alterations in amino acid and nucleotide metabolic pathways, energy production pathways and other pathways related to cancer aggressiveness, such as migration, proliferation and drug-resistance. Joint pathway enrichment analysis unveiled unique pathways, including the antifolate resistance pathway and other important pathways that maintain cancer cells' survival, growth, and proliferation. Collectively, the results identified potential biomarkers for sorafenib-resistant HCC and gave insights into their role in chemotherapeutic drug resistance, cancer initiation, progression and aggressiveness, which may contribute to better prognosis and chemotherapeutic outcomes.

Reproducible generation of human liver organoids (HLOs) on a pillar plate platform via microarray 3D bioprinting

“…Notably, the IC 50 values of sorafenib obtained from HLOs on the pillar plate closely aligned with previously reported IC 50 values from 2D- and 3D spheroid-cultured human hepatocellular carcinoma cell lines: 5.3–8.5 μM from HepG2 cells, 4.7–17.1 μM from Huh7 cells, and 3.3–4.7 μM from Hep3B cells. 42–47 In addition, the IC50 values obtained from HLOs on the pillar plate were comparable with those obtained from HLOs in the 24-well plate (Fig. 7).…”

Metabolomics in hepatocellular carcinoma: From biomarker discovery to precision medicine

“…The enrichment analysis revealed several dysregulated pathways involved in sorafenib-resistance, including the antifolate resistance pathway, amino acid metabolic pathway, pathways related to the protein synthesis, and other energy production metabolism. Together, this work identified potential biomarkers and therapeutic targets for sorafenib-resistant HCC ( 120 ).…”

Potential of CDC25 phosphatases in cancer research and treatment: key to precision medicine

“…Furthermore, precision medicine promotes the development of biomarker-driven clinical trials, which aim to test the efficacy of new medicines on patient subgroups with similar genetic or molecular traits. This approach enables researchers to find novel therapeutic targets and hasten the development of innovative medications that are more effective and less hazardous (Abushawish et al, 2022;Ahmed et al, 2023).…”