Authors While the current gold standard for drug metabolism and toxicology studies is the use of primary human liver cells (PHHs) [
21], their short lifespan, high cost, limited availability and the observed inter-donor variability severely restrict their use in high throughput in vitro drug screening. Therefore, the immortalised hepatic lines HepG2 and HepaRG were used in this study. While HepG2 cells have many limitations in 2D culture, including loss of liver-specific structure and functionality [
21], the ease of handling compared to PHH, coupled with a stable phenotype and lack of donor variability [
21,
22], offers many advantages for standard operating procedures (SOPs) development in preclinical drug screening. On the other hand, culturing HepG2 cells in a 3D environment has been shown to restore some of the characteristics lost when cultured in a 2D environment. In addition, 3D cultured HepG2 cells has a reduced proliferation rate, self-organise and differentiate into 3D spheroids that restore lost liver structure and function [
23,
24]. HepaRG cells are a hepatocellular carcinoma-derived human cell line expressing functional liver markers such as several cytochrome P450 (CYP) and phase II enzymes, nuclear receptors and membrane transporters. HepaRG cells have been shown to be an excellent surrogate for primary human hepatocytes in cytochrome P450 3A4 (CYP3A4) induction studies. Therefore, we cultured cells in 2D and 3D cell culture type using HepG2 and HepaRG cells, which are most commonly used for hepatotoxicity studies. We also compared the response to drug treatment by each cell and culture type. Cell viability was measured for both 2D and 3D spheroid viability using CellTiter-Glo® ATP quantification. In parallel with the assessment of viability by quantification of ATP, the LDH assay was used to determine the cytotoxicity induced by ADR and AAP. The LDH assay avoids the problems of having to dissociate the spheroid structure as required by other methods of assessing membrane integrity, such as neutral red or trypan blue, because it is supernatant based, with the cytosolic enzyme LDH being released into the culture supernatant by compromised plasma membranes. When evaluated using these assays, we observed decreased viability or increased cytotoxicity induction after treatment with ADR and AAP in both culture types. When comparing the responsiveness to the drugs in each cell type, HepG2 cells were more sensitive to ADR treatment, while HepaRG cells were more sensitive to AAP treatment. Changes in cell viability based on cell culture type were also observed. For both HepG2 and HepaRG cells, it was observed that 2D cultures were more sensitive to drugs than 3D cultures. These results were also observed as a result of cytotoxicity induction. The expression of LDH increased in a drug concentration-dependent manner, with 2D cultures being more sensitive than 3D cultures. AST and ALT are markers of liver injury that increase when cells are damaged [
25]. Two well-known markers of liver function are albumin and urea. Albumin is a major protein synthesized in the liver and plays an important role in maintaining tumor pressure, transporting various molecules and regulating pH balance. Urea is a waste product formed in the liver during protein metabolism. The liver's ability to metabolize ammonia into urea is crucial for maintaining nitrogen balance in the body [
26,
27]. HepG2 and HepaRG cells were cultured in 2D and 3D forms and each cell was treated with ADR and AAP to determine the extent of liver damage. Similar to cell viability and toxicity tests, the expression of AST and ALT increased in a drug concentration-dependent manner. Similar results were observed for the secretion of ALB and Urea. Secretion decreased in a concentration-dependent manner and expression was significantly reduced in 2D cultures. In addition, HepaRG cells had higher basal expression compared to HepG2 cells when tested under the same conditions. In the same cells, expression of ALB and urea was higher in cells cultured in a 3D cultures. The hepatotoxicants ADR and AAP cause mitochondrial dysfunction [
28] and liver failure [
29]. ADR and AAP has been reported to cause hepatotoxicity and decrease cell viability in HepG2 [
30,
31] and HepaRG [
32,
33] cells. These findings are consistent with our results which showed decreased cell viability, increased expression of liver injury markers, and decreased liver function after drug treatment. The evaluation of DILI using hepatocytes relies on an accurate understanding of the characteristics of the cells and drugs, which is difficult to achieve. There are studies that show different liver cells have different responses to the same drug [
34]. Alternatively, studies have shown that when a single cell is treated with different drugs and shows varying sensitivity to each drug [
17]. Therefore, it is important to study liver toxicity using a variety of cells and drugs, as we have done in our study
. A number of critical enzymes play an important role in cellular metabolism under disease conditions or in the metabolism of drugs. Cytochrome P450 enzymes have been extensively studied since their identification because of their involvement in the metabolism of various substrates, including therapeutic agents and components of biological processes, in humans [
31,
35]. In particular, over 95% of oxidative and reductive reactions are reported to be catalysed by CYPs [
31]. They mediate the activation/inactivation of exogenous substrates, including drugs, xenobiotics, food additives or endogenous compounds such as steroids, eicosanoids or fatty acids [
37,
38]. In particular, CYP1A2, CYP2C9 and CYP3A4 enzymes are known to be the most involved in drug metabolism in human hepatocytes. CYP1A2 is a member of the cytochrome P450 enzyme family primarily found in the liver, although it is also present in other tissues. This enzyme is responsible for the metabolism of various substrates, including caffeine, theophylline, certain drugs, and environmental toxins like polycyclic aromatic hydrocarbons found in cigarette smoke. CYP1A2 has been extensively studied due to its role in drug metabolism and its potential impact on drug efficacy and toxicity [
39]. CYP2C9 is another important cytochrome P450 enzyme predominantly expressed in the liver, although it is also found in other tissues. CYP2C9 substrate specificity and catalytic properties have been extensively studied to understand its role in drug metabolism and pharmacokinetics [
40]. CYP3A4 is one of the most abundant cytochrome P450 enzymes in the liver and intestine, playing a pivotal role in the metabolism of a wide range of drugs. It metabolizes approximately 50% of clinically used drugs, including statins, immunosuppressants, antivirals, and many others. Due to its broad substrate specificity and significant contribution to drug metabolism, CYP3A4 is a major determinant of drug clearance and efficacy [
41]. In this study, we compared the mRNA expression of CYP enzymes in HepG2 and HepaRG cells in 2D and 3D cultures. The expression of each enzyme was induced by treating the cells with known standard inducers. HepG2 cells showed no expression of CYP1A2 and CYP2C9 enzymes in both 2D and 3D cultures. On the other hand, the expression of CYP3A4 was increased by inducer treatment. It also showed higher expression in 3D culture. As demonstrated in various studies, HepG2 cells normally express CYP1A2 [
42]. However, there is evidence that while caffeine induces CYP1A2 expression in rat hepatocytes, it may not have the same effect in human HepG2 cells [
43]. HepG2 cells generally express CYP1A2, but the expression level and regulatory factors can vary depending on the experimental conditions and stimuli. There is also evidence that HepG2 cells have low expression of CYP2C9, an important enzyme involved in drug metabolism [
44,
45,
46]. This low expression affects their suitability as a model for studying hepatotoxicity and drug metabolism[
47,
48]. It is important to consider this limitation when using HepG2 cells as a model system for drug metabolism research. In contrast to HepG2 cells, HepaRG cells showed expression of CYP1A2, CYP2C9 and CYP3A4 enzymes in both 2D and 3D cultures. Furthermore, we found that all three enzymes were more highly expressed in 3D cultures than in 2D cultures. Interestingly, the expression of all enzymes was much higher than in HepG2 cells. HepaRG cells are a widely used model for drug metabolism studies due to their ability to express a variety of cytochrome P450 enzymes [
49]. They respond to typical inducers by inducing a variety of cytochrome P450 enzymes, including CYP1A2, CYP2C9, and CYP3A4 enzymes, which are essentially involved in human drug metabolism [
50]. HepaRG cells are known to be metabolically similar to human adult hepatocytes, making them useful for drug metabolism and toxicity studies [
51]. These findings corroborate our results that HepaRG cells have a higher capacity to induce CYP enzymes compared to HepG2 cells. Furthermore, our results are consistent with studies showing increased mRNA levels of CYP1A2, CYP3A4 [
52,
53] and increased expression of drug metabolising enzymes including CYP2C9 in HepaRG 3D cultures [
54]. In conclusion, the development of in vitro models that can predict DILI at the preclinical stage for drug development is becoming increasingly important. Therefore, the selection of in vitro models that can study a clearer and more diverse range of drug responses is important. In this study, HepG2 cells and HepaRG cells, which are often used in drug screening were compared, and each cell was cultured in 2D and 3D forms to evaluate them as in vitro models for drug development. The results of the study showed that the sensitivity of the cells varied depending on the type of cell, culture type and type of drug. In addition, HepaRG cells with higher expression of CYP enzymes involved in human drug metabolism are more suitable for drug metabolism evaluation, and 3D culture is more suitable as a model for drug metabolism evaluation than 2D culture. However, the results of CYP enzymes need to be validated by further experiments on metabolic mechanisms through enzyme activity measurement or LC-MS/MS metabolite.