Nutritional research has successfully incorporated animal models to gain new insights into topics like the effects of nutrients on physiological functions and the associations between nutrient intake and disease development. However, these approaches have some limitations. The exposure of specific tissues to particular nutrients is difficult to predict because it is dependent on many processes, including absorption, distribution, metabolism, and excretion, which are regulated by complex pathways [1,2]. In addition, various confounding factors prevent us from clearly determining the role of specific nutrients on tissues, such as dietary consistency, circulating hormone levels, intestinal flora, and physical activity [3], [4], [5]. To account for these challenges, immortalized cell lines (e.g., HepG2) have been used for nutritional research. However, they are often limited by abnormal liver-specific genomes and function [6]. In addition, traditional two-dimensional (2D) cell culture systems often lack cell–cell interactions and exhibit different tissue-specific properties and functions when compared to three-dimensional (3D) tissue. Therefore, the development of more precise in vitro models to increase our understanding of the mechanisms of nutrient action is crucial.

Organoids, known as in vitro “mini-organs”, are 3D cell culture systems [7]. Since organoids can mimic physiological architecture and recapitulate the key in vivo functions of tissues, they have been increasingly utilized in biomedical studies to better understand physiological and pathological phenomena [8,9]. Organoids have great potential for biomedical applications, such as disease modeling, regenerative medicine and drug delivery [10], [11], [12]; however, limited number of studies have investigated the utility of organoid culture systems in nutritional research [13]. Organoids allow us to easily manipulate the type, concentration, and duration of nutrient exposure to the organ. In fact, a previous study examined the relationship between six common dietary nutrients and the growth of intestinal organoids to identify nutrients that promote or inhibit intestinal epithelial health and growth rate [13]. As they are in vitro systems, they can easily differentiate between the effects of specific nutrients and relevant confounding factors, while compensating for the limitations of animal models and cell culture methods. Therefore, organoids may be a major technological breakthrough for nutritional research.

High fructose-containing sugar intake (e.g., sucrose and high-fructose corn syrup; HFCS) has been attributed to an increased risk of metabolic disorders [14,15]. There is strong evidence that sugar-sweetened beverages (SSBs), a primary source of fructose in the American diet [16], are associated with an increased risk of metabolic syndrome, type 2 diabetes, myocardial infarction, and stroke [17], [18], [19]. Specifically, fructose (a monosaccharide) has been identified as a key component contributing to their epidemics [20], [21], [22], [23]. Therefore, fructose consumption has become a global hot topic as a factor of negative health outcomes. Despite these findings, the pathogenic mechanisms underlying fructose-induced metabolic disease have not yet been fully elucidated. This is due to the methodological limitations in understanding the underlying biologic mechanisms mediating the effects of nutrients.

Hepatokines are diverse proteins produced by the liver, which participate in a range of biological processes [24]. Associations have been reported between hepatokines and various diseases, including diabetes, non-alcoholic fatty liver disease (NAFLD), and atherosclerosis [24]. Furthermore, it is well established that both nutritional status and specific nutrients impact hepatic metabolic functions, thereby influencing hepatokines secretion. For example, high-fat diets have been shown to increase the production of hepatokines [25]. Excessive consumption of simple sugars, especially fructose, can disrupt the balance of hepatokines, potentially increasing the risk of NAFLD, insulin resistance and dyslipidemia [26,27]. Selenoprotein P (SEPP1), classified as a hepatokine, has garnered attention due to its emerging roles in metabolic regulation. Recent studies indicate that SEPP1 interferes with insulin sensitivity, glucose, and lipid metabolism [28,29]. Dysregulation of SEPP1 expression has also been implicated in the onset of metabolic diseases such as type 2 diabetes and NAFLD [30,31]. Therefore, SEPP1 may be an important molecule linked to metabolic homeostasis and the pathophysiology of metabolic disorders.

In this study, we aim to demonstrate the utility of organoids in nutritional research by further investigating the molecular mechanisms responsible for the negative effects of fructose intake using liver organoids. We next investigated the gene expression and DNA methylation response patterns to fructose in liver organoids. Moreover, we verified if the changes in gene expression and epigenetic modifications in fructose-treated organoids were mirrored in the liver tissues of fructose-fed rats. Our findings suggest a novel strategy for nutritional research to comprehend the mechanisms of nutrient action using an organoid model.