The landscape of liver disease nomenclature has recently undergone a significant transformation, igniting curiosity and discussion among healthcare professionals and researchers alike. The shift from non-alcoholic fatty liver disease (NAFLD) to metabolic dysfunction-associated steatotic liver disease (MASLD), along with the transition from non-alcoholic steatohepatitis (NASH) to metabolic dysfunction-associated steatohepatitis (MASH), reflects an evolving scientific understanding that emphasises the metabolic dysfunction underlying these conditions. This rebranding highlights that the “M” in MASLD and MASH signifies metabolic dysfunction, inherently linking these diseases to prevalent metabolic disorders such as obesity and type 2 diabetes, which are critical contributors to liver injury [1, 2]. The reformulation of these terms was guided by a comprehensive Delphi consensus process involving multiple stakeholders in hepatology, aimed at establishing a more accurate and clinically relevant framework for diagnosis and treatment [3, 4]. Currently, the global prevalence of MASLD is estimated at approximately 32%, with projections suggesting it could rise to 55.4% by 2040 due to increasing rates of obesity and type 2 diabetes [5–7]. In India, the prevalence stands at around 38% among adults, indicating a significant public health concern as the nation faces rising obesity rates and associated metabolic disorders [6, 8–10]. Regions such as Latin America report even higher prevalence rates, reaching 44.4%, underscoring the urgent need for targeted interventions globally [6, 11–13].

Despite advancements in nomenclature and understanding, the pathogenesis of MASLD remains incompletely elucidated, with steatosis defined as the presence of triglycerides (TGs) in hepatocytes serving as the primary precursor for the disease [14–17]. The development of hepatic steatosis arises from an imbalance between lipid intake and lipid removal, which is regulated by four key mechanisms: fatty acid uptake, de novo lipogenesis (DNL), fatty acid oxidation, and lipid export. These mechanisms play a crucial role in both the physiological and pathological progression of MASLD [11, 18–20].

Targeting farnesoid X receptor (FXR) presents a promising therapeutic strategy for managing MASLD because FXR is integral in regulating these four key mechanisms of hepatic lipid metabolism [21]. By selectively modulating FXR activity through agonist ligands, it can effectively control lipid acquisition (fatty acid acquisition) and lipid removal to mitigate hepatic steatosis and its progression to more severe liver conditions [22, 23]. Furthermore, FXR agonists have demonstrated significant histological improvements in clinical trials for liver diseases, indicating their potential to enhance treatment outcomes for patients with MASLD [24–29]. This approach not only targets the underlying metabolic dysfunction but also opens avenues for combination therapies that may improve efficacy while minimising side effects associated with current treatments [30].

As research progresses, exploring FXR’s role in MASLD will be crucial for developing innovative therapeutic strategies to effectively manage this complex disease and its associated metabolic disorders [31]. This review explores the role of FXR in liver physiology and the progression of MASLD. We begin by examining FXR’s normal functions and how its dysregulation contributes to disease pathology. We then identify specific lipid classes that alter during the shift from health to disease, highlighting their significance as diagnostic markers and potential biomarkers. Following this, we discuss treatment strategies using FXR agonists and ongoing clinical trials evaluating their effectiveness in managing MASLD. Additionally, we emphasize the crucial roles of fatty acids and lipid classes in the pathogenesis of MASLD and present lipid analyses conducted with hyphenated techniques to reinforce our findings on relevant biomarkers. To ensure clarity and consistency, we will refer to the disease as MASLD and MASH, regardless of whether the underlying populations in the referenced studies were originally classified as patients with NAFLD or NASH.

MASLD condition is characterized by fat deposition in the liver, which can lead to inflammation and fibrosis, ultimately resulting in more severe liver disease, MASH [32–34]. The relationship between MASLD and metabolic syndrome is mutual and bi-directional, highlighting the complexity of these interconnected conditions [35, 36].

FXR is a key nuclear receptor that acts as a bile acid sensor, playing a significant role in maintaining metabolic homeostasis [77–79]. Predominantly found in the liver and intestine, FXR integrates metabolic signals and is activated by bile acids such as, which are crucial for cholesterol and lipid metabolism [77, 80, 81]. Upon activation, FXR heterodimerizes with retinoid X receptor (RXR) and binds to FXR response elements (FXREs) to regulate genes involved in bile acid synthesis and metabolism [82, 83]. It’s essential for coordinating metabolic processes and acts as a therapeutic target for metabolic disorders [31, 84–86]. FXR is an essential modulator of lipid metabolism [87, 88]. Exerting its effects by modulating the activity of several transcription factors, including sterol regulatory element-binding protein-1c (SREBP-1c) and carbohydrate response element-binding protein (ChREBP). SREBP-1c is crucial for the regulation of genes involved in fatty acid and TG synthesis, and FXR activation leads to the repression of SREBP-1c expression. This inhibition is significant as it reduces hepatic TG levels and helps prevent hepatic steatosis, particularly in MASLD [89, 90]. Additionally, FXR interacts with ChREBP to fine-tune lipogenesis based on glucose availability, ensuring lipid synthesis is aligned with the body’s energy status [91, 92]. The activation of FXR decreases the expression of fatty acid synthase (FASN), an enzyme essential for fatty acid biosynthesis, and regulates other pathways critical for lipid homeostasis [93, 94]. The small heterodimer partner (SHP) is another important component in this regulatory network. Upon activation by bile acids, FXR induces SHP expression, which acts as a transcriptional repressor of various target genes involved in lipogenesis and bile acid synthesis [95]. This mechanism helps to prevent excessive TG accumulation and maintain normal lipid profiles within hepatocytes [96, 97]. Furthermore, the FXR-SHP pathway interacts with other nuclear receptors such as peroxisome proliferator-activated receptor alpha (PPARα), enhancing its regulatory capacity on lipid metabolism [90, 98]. Comprehensive, through the modulation of SREBP-1c and ChREBP, along with the involvement of SHP, FXR plays a pivotal role in coordinating lipid metabolism [99, 100]. Xu et al. [101] studied the impact of the activation of the FXR by obeticholic acid (OCA) significantly inhibits hepatic cholesterol 7α-hydroxylase (CYP7A1) and sterol 12α-hydroxylase (Cyp8b1), partly through the induction of SHP. This inhibition leads to a reduced bile acid pool size and altered bile acid composition, which contributes to decreased intestinal cholesterol absorption and enhanced macrophage reverse cholesterol transport (RCT). The reduction in hepatic microsomal cholesterol content triggers an elevation in the expression and functionality of low-density lipoprotein receptors (LDL-R) within the liver [102]. Consequently, this cascade of events leads to a decrease in plasma LDL-cholesterol (LDL-C) levels [103]. In addition to inhibiting CYP7A1, enhanced excretion into bile occurs via the cholesterol transporters known as adenosine triphosphate-binding cassette transporters (ABCG5/8), which can elevate blood cholesterol levels in knockout (KO) mice [104]. Reduction in intestinal bile acids and promotion of transintestinal cholesterol excretion serve as mechanisms to lower cholesterol levels in the intestine [105]. While FXR induces an anti-atherogenic effect in mice, the scenario differs in humans. This was possible in mice due to the presence of enzymes Cyp2c70 (cytochrome P450 2C70) and Cyp2a12 (cytochrome P450 2A12) [106–108].

FXR-induced lipoprotein metabolism is complex and differs mainly in ligands and species. FXR is known to reduce high-density lipoprotein (HDL) cholesterol, resulting in a pro-atherogenic profile. The proatherogenic effect is due to the stimulating effects of cholesterol ester transfer protein (CETP), which increases LDL and decreases HDL cholesterol [109]. In addition, the transformation of very low-density lipoprotein (VLDL) rich in TG is converted to cholesterol-rich LDL particles [110]. The major difference between the normal liver and disease progression.

The mechanism behind MASLD primarily involves insulin resistance and lipotoxicity. Insulin resistance leads to increased FFA release from adipose tissue, which accumulates in the liver, causing hepatic steatosis as mentioned in Figure 1 [34, 51]. This accumulation triggers oxidative stress and inflammation, further exacerbated by elevated levels of reactive oxygen species (ROS) that activate pro-inflammatory pathways [111]. Increased ROS levels stimulate kinases such as c-Jun N-terminal kinase (JNK) and p38 mitogen-activated protein kinases (MAPK), promoting inflammation and disrupting insulin signalling. This results in a vicious cycle where inflammation worsens insulin resistance [112]. Additionally, dietary factors like high fructose and saturated fat intake enhance DNL and contribute to the progression from simple steatosis to steatohepatitis. The interplay between gut microbiota dysbiosis and metabolic perturbations also fuels hepatic inflammation and injury [113]. Understanding these specific mechanisms is crucial for developing targeted therapies for MASLD [114], as illustrated by the alterations in disease identifiers depicted in Figure 2.

FXR has emerged as a potential therapeutic target for the management of metabolic syndrome and liver disorders, particularly MASLD. The therapeutic potential of FXR agonists is being explored to mitigate the adverse effects associated with MASLD, MASH, and other metabolic disorders, as clearly discussed in Figure 3 [135]. The ligands for the FXR receptor can be classified based on their chemical nature: natural agonists [chenodeoxy cholic acid (CDCA), cholic acid, ursodeoxycholic acid (UDCA)], semisynthetic bile acids (OCA), and synthetic non-steroidal agonists (GW-4064 and WAY 362450) [136]. FXR agonists, such as OCA, have proven effective in reducing hepatic steatosis, enhancing insulin sensitivity, and providing anti-inflammatory effects in clinical trials. FXR agonists, such as OCA, have proven effective in reducing hepatic steatosis, enhancing insulin sensitivity, and providing anti-inflammatory effects in clinical trials. These agents work by restoring normal FXR signalling pathways that regulate lipid metabolism and inflammation [123]. Deoxycholic acid (DCA) and lithocholic acid (LCA) can activate FXR, albeit with lower efficiency. UDCA is a partial agonist inhibiting CDCA activity [137, 138]. FXR agonists have been used recently for the improvement of ailments like MASH, diabetes mellitus, and primary biliary cholangitis (PBC) [139]. OCA, developed by Intercept Pharmaceuticals, is one of the earlier FXR agonists, and its regenerate phase III trial demonstrated reproducibility with phase II data. However, the FDA denied approval for its use in MASH and has currently banned it from phase III clinical trials due to severe side effects, including pruritus; aside from pruritus, OCA was generally well-tolerated [140]. Notably, there was a reduction in HDL cholesterol levels. The U.S. FDA approved OCA for second-line treatment of PBC in 2016 [123, 141].

Clinical data of patients and rodent studies using UDCA showed that the benefits were more effective than clofibrate ones. Small trials showed elevated levels of enzymes, which generally show an increase during liver diseases (alanine aminotransferase, aspartate aminotransferase, gamma-glutamyl transferase, and alkaline phosphatases). These are reduced in the treatment [142]. However, norUDCA, a shortened UDCA derivative, gave promising results in phase II dosing trials in mice models [143]. MET-409, a non-steroidal FXR agonist currently in phase IIa clinical trial, is different in structure from bile acids and has an entirely different chemical nature from other FXR agonists (tropifexor and cilofexor) [144]. The agonist showed potent liver fat reduction, but a transient increase in alanine aminotransferase and FGF-19 was observed [145]. The regulation of fatty acid influx into the hepatic plasma membrane is governed by specialized transporters such as FATP, CD36, and caveolins [146, 147]. Depletion of FATP2, a specific isoform of FATP, has been demonstrated to ameliorate hepatic steatosis and diminish the uptake of fatty acids, suggesting a potential therapeutic avenue for mitigating excessive lipid accumulation in the liver [148]. The transportation of elongated fatty acids is facilitated by CD36, a mechanism regulated by PPAR-gamma [149]. There exists a clear association between the expression of CD36 and the concentration of TGs within hepatic tissue [150]. Investigations carried out in obese murine models propose that administration of GW4064 induces a subsequent decline in the expression of CD36 at a molecular scale, thereby reducing circulating lipid levels [151]. Caveolin functions in the formation of lipid droplets by associating fatty acids with binding proteins (FABP) [152]. Vitamin D receptor-interacting protein 205 (DRIP205), coactivator-associated arginine methyltransferase-1 (CARM-1), and protein arginine methyltransferase 1 (PRMT-1) are some of the secondary coactivators that play a role in FXR-mediated transcription [153]. CARM-1 acts by its protein methylase activity, known to interact indirectly with nuclear receptors of the p160 family. Steroid receptor coactivator 1 (SRC-1), one of the nuclear receptors of the p160 family, acts on RXR-FXR heterodimers. Peroxisome proliferator-activated receptor-gamma coactivator-1 alpha (PGC-1 alpha), a well-known coactivator of PPAR-gamma, shows more FXR coactivating properties than SRC-1. FXR activates PGC-1 alpha by binding to the NH₂ position [154–156].

Lipidomics is an emerging field that provides a comprehensive analysis of lipid compositions in biological samples, offering valuable insights into MASLD [159]. Studies of liver biopsies from MASLD patients have revealed significant alterations in lipid profiles, particularly in glycerophospholipids and sphingolipids. Notably, an increased n-6/n-3 fatty acid ratio and decreased levels of essential long-chain PUFAs, such as arachidonic and EPA, have been observed, indicating a shift in lipid metabolism that contributes to disease progression [53, 160]. In addition to liver tissue analysis, lipidomic studies of plasma samples have identified specific lipid changes that may serve as non-invasive biomarkers for disease progression. For example, significant alterations in phosphatidylcholine (PC), phosphatidylethanolamine (PE), and sphingomyelin levels have been documented between healthy individuals and those with varying stages of MASLD, including MASH as detailed described in Table 3 [161, 162]. These lipid changes highlight the critical role of lipid metabolism in the development and progression of MASLD. The accumulation of lipids within hepatocytes leads to increased metabolic demands, resulting in the production of ROS and oxidative stress [163]. This process is exacerbated by obesity-related expansion of adipose tissue and insulin resistance, which promote the release of FFAs and activate inflammatory pathways. Elevated levels of ceramides a class of sphingolipids have been linked to lipotoxicity and hepatic inflammation, further contributing to the pathogenesis of MASLD [34].

To analyse these complex lipid profiles, researchers utilize hyphenated techniques such as liquid chromatography-mass spectrometry (LC-MS) and gas chromatography-mass spectrometry (GC-MS) as represented in Figure 4. These methodologies enable the identification and quantification of thousands of lipid species, enhancing our understanding of their roles in liver disease [164–166]. Lipidomic profiling is crucial for uncovering the specific lipid alterations associated with MASLD [60, 167]. By identifying potential biomarkers for distinguishing between MASLD and MASH, lipidomics offers promising avenues for early diagnosis and targeted therapeutic strategies aimed at restoring lipid homeostasis and improving patient outcomes [168].

In this review, we have clearly articulated the renaming of NAFLD to MASLD and NASH to MASH. We explored the association of MASLD with features of metabolic syndrome, emphasizing the central role of fatty acids in disease development and progression. Additionally, we examined the role of FXR in both physiological and pathological conditions, detailing how hepatic steatosis can progress to severe outcomes like fibrosis and CKD. The therapeutic potential of FXR agonists in treating MASLD and other metabolic diseases was discussed, alongside a review of clinical trial drugs targeting the FXR receptor. Furthermore, we highlighted the importance of lipidomic studies for quantifying fatty acids responsible for MASLD and MASH pathogenesis using advanced analytical techniques.

Despite these insights, significant research gaps remain due to the complex pathology of MASLD. Over 30% of the global population is affected by MAFLD, highlighting this silent epidemic’s growing prevalence. Current diagnostic techniques are limited, necessitating improvements in lipidomics through advanced methods like LC-MS/MS and GC-MS/MS to accurately assess disease severity. Optimizing sample preparation protocols and minimizing matrix effects are essential steps forward. Currently, only one drug, resmetirom, has been approved by the FDA for MASLD treatment. While FXR agonists show promise in mitigating disease pathology, side effects have hindered others, such as OCA, from progressing to phase III trials. There is a pressing need for early-stage identification of MASLD and further advancements in lipidomic studies, alongside the development of new therapeutic options to address this widespread health issue. By pursuing these avenues, we can enhance our understanding and management of MASLD, ultimately improving patient outcomes in this prevalent liver disease.