The SOX9 promoter resides upstream of the gene, in the DNA sequence preceding the transcription start site. Certain members of the protein family, cytokines, and fibroblast growth factors (TGF) may be involved in SOX9 gene regulation mechanisms. Previous research has shown that fibroblast growth factors increase Sox9 mRNA expression in mesenchymal C3H10T1/2 cell line and mice primary chondrocytes via MAP kinase-mediated pathway (Murakami et al., 2000). Furthermore, by chromatin immunoprecipitation and Dual-Luciferase reporter assay technology, through binding to the promoter of SOX9, the FOXO4 protein transcriptionally increases SOX9 expression, while IL-1β has the opposite effect (Ma et al., 2021). Recent research indicates that transcription factors CREB1 and CEBPB, which are attracted to the proximal promoter area, regulate the SOX9 promoter in TM4 Sertoli cells (Diawara et al., 2023).

Numerous SOX9 enhancers have been found. In mice, the Testis-specific Enhancer of Sox9 (TES) is a 3.2 kilobase (kb) enhancer, featuring a 1.4 kb core element (TESCO). This enhancer is situated 13 kb upstream of the Sox9 gene, which could drive the expression of Sertoli cell-specific. In vivo, steroidogenic factor 1(Sf1) and SRY bind to TES, enhancing Sox9 expression, and SOX9’s interaction with TESCO suggests a feed-forward regulation loop, maintaining its expression after SRY expression ceases (Sekido and Lovell-Badge, 2008). According to a different study, Sf1 binding to the SOX9 gene enhancer is prevented by β-catenin activation during ovarian development, which suppresses SOX9 expression and Sertoli cell differentiation (Bernard et al., 2012). SOM, an enhancer 70 kb upstream of mouse Sox9, works in tandem with Sox9 dimers to activate Sox9 expression, ensuring sufficient SOX9 molecules for SOM activation (Mead et al., 2013).

Three serine residues on SOX9 are phosphorylated: S64, S181, and S211. The phosphorylation of SOX9 at the S64 and S181 PKA sites occurs as a result of the activation of cAMP-dependent protein kinase A (PKA) during the development of gonadal development. This phosphorylation event enhances the binding of SOX9 to importin b, a protein involved in nucleocytoplasmic transport, resulting in nuclear localization (Malki et al., 2005). Extracellular signal-regulated kinases 1 and 2 (ERK1/2) are activated by sublytic C5b-9, which phosphorylates S64 and S181 in SOX9, plays an essential role in its proproliferative as well as profibrotic functions (Wu Z. et al., 2024). Another study showed that in chick neural tubes, extracellular signals induce the phosphorylation of S64 and S181 in SOX9, along with Snail2, leading to neural crest cell delamination (Liu et al., 2013). The phosphorylation site in S211 of SOX9 was identified in the research by Wendong Huang et al. Immunohistochemistry analysis of mouse embryo hind legs revealed the presence of phosphorylated SOX9 at S211 within the prehypertrophic region of the growth plate, a key site for parathyroid hormone-related peptide receptor expression (Huang et al., 2000).

The lysine residues at positions K61, K253, and K398 on SOX9 are subject to acetylation. Acetylation and deacetylation of SOX9 significantly affect the activation of genes that are specific to cartilage tissue. The presence of nuclear export signal (NES) and nuclear localization signal (NLS) promotes SOX9 localization to both the nucleus and the cytoplasm (Gasca et al., 2002; Südbeck and Scherer, 1997). According to a research, phosphorylation and acetylation of Sox9 are necessary for the sublytic C5b-9-induced proliferation of glomerular mesangial cells (GMCs) in rat Thy-1 nephritis (Thy-1N), which enhances Cyclin D1 gene transcription (Xie et al., 2021). The levels of SOX9 acetylation are closely linked to osteoarthritis development, as they diminish nuclear entry capability and impact transactivation of the ACAN gene (Bar et al., 2016). Deacetylase SIRT1 can remove acetyl groups from SOX9, facilitating its nuclear entry and activation. This suggests that regulating SOX9 acetylation levels and SIRT1 activity could be a potential treatment strategy for osteoarthritis (Bar et al., 2016).

The ubiquitin proteasome system is the primary pathway for cells to degrade and eliminate unwanted proteins. Both in vivo and in vitro, E6-AP ubiquitinates SOX9 by attaching to it and acting as a ubiquitin ligase to bind ubiquitin to SOX9 (30). This ubiquitination leads to the degradation of SOX9, thus regulating its protein levels (Hattori et al., 2013). Additional research has been conducted on tumors. Cullin 3-based ubiquitin ligase KEAP1 regulates SOX9 protein stability via proteasome-mediated degradation (Shao et al., 2020). Loss-of-function mutations in KEAP1 impair its interaction with SOX9, inhibiting SOX9 ubiquitination, which results in elevated protein levels and promotes tumorigenesis (Shao et al., 2020). FBW7, an E3 ubiquitin ligase, is responsible for ubiquitinating and degrading specific target proteins. Rhabdomyosarcoma 2-associated transcript, a type of long-chain non-coding RNA, is shown in another tumor study to inhibit the development and dissemination of lung adenocarcinoma cells by mediating the ubiquitination and degradation of SOX9 (Pei et al., 2022). RMST directly binds to the SOX9 protein, enhancing its interaction with the ubiquitin ligase FBW7 (Pei et al., 2022).

SUMOylation, a post-translational protein modification, involves covalently attaching a small ubiquitin-like modifier (SUMO) to the substrate protein. SUMOylation can alter a protein’s structure, location, or stability. In human cells, the 61st, 253rd, and 398th lysines of SOX9 could be SUMOylated (Hattori et al., 2006). A study revealed that protein inhibitors of activated STAT (PIAS) contribute to the SUMOylation of SOX9, altering its function and stability. PIAS, functioning as a SUMO-binding enzyme, can conjugate SUMO proteins to SOX9, thereby increasing the stability of SOX9 by preventing its degradation (Hattori et al., 2006). Conversely, another study indicates that SUMOylation diminishes the synergistic activity of SOX9 with other co-factors, thus inhibiting its transcriptional activity (Oh et al., 2007). To measure SOX9-SUMOylation levels in live cells, researchers have developed a novel reporter gene, aiding in understanding SOX9’s regulatory dynamics during chondrogenesis (Saotome et al., 2020).

However, there is a paucity of studies concerning PTM in fibrosis. Fortunately, in other diseases, some authors have successfully achieved therapeutic effects by investigating the regulation of PTM of the SOX9 protein. In medulloblastoma, authors demonstrated that the phosphorylation of SOX9 could be degraded by FBW7. Ultimately, they demonstrate that pharmacological suppression of the PI3K/AKT/mTOR pathway destabilizes SOX9 in a GSK3/FBW7-dependent manner, enabling medulloblastoma cells susceptible to cytostatic therapy (Suryo Rahmanto et al., 2016). Jih-Yang Ko et al. have shown that in a model of transgenic mice that overexpressed human heat shock proteins 60 (TgHPS60), the overexpression level of HSP60 alleviated the pathological conditions of collagenase-induced osteoarthritis knees. Furthermore, the overexpression of HSP60 can sustain SOX9 levels and reduce the hyperubiquitination of SOX9 in the suffering joints (Ko et al., 2016). In another study about osteoarthritis, it shows that the PARylation (poly (ADP-ribosyl)ation), which promotes the ubiquitination and degradation of SOX9, is modified by tankyrase. They discovered that suppressing Tankyrase diminishes SOX9’s PTM (PARylation) and degradation, consequently augmenting its stability and boosting its transcriptional activity to stimulate the expression of cartilage matrix gene (Kim et al., 2019). Maybe in the future, research on fibrosis may yield advancements in disease therapy by concentrating on the PTM of SOX9.

The human heart consists of cardiomyocytes, non-cardiomyocytes (for instance fibroblasts, endothelial cells and vascular smooth muscle, and the extracellular matrix (Dostal et al., 2015). Due to the non-regenerative nature of cardiac myocytes, the replacement of dead cardiomyocytes following damage, such as a cardiac infarction, is crucial (Frangogiannis, 2012). Damaged areas trigger the inflammatory reaction, which clears matrix debris and dead cells and then activates the repaired procedures crucial for cardiac fibrosis (Frangogiannis, 2012). Cardiac fibrosis is characterized by the buildup of the extracellular matrix, particularly collagen I and III (Chikungunya Virus Infections, 2015). Various diseases (such as atrial fibrillation (AF), hypertension, heart failure, and myocardial infarction (MI)) can lead to cardiac fibrosis through different pathophysiological mechanisms, yet the process involves several cell types and similar cytokines (Kong et al., 2014).

In the fibrotic response, myofibroblasts (MFs) play a significant role. They can be differentiated from endothelial cells by the endothelium-mesenchymal transition (EndMT) and from cardiac fibroblasts (CFs), bone marrow-derived progenitors, and epicardial cells by the epithelial-mesenchymal transition (EMT) (Haudek et al., 2006; Zeisberg et al., 2007). Typically, CFs are inactive and do not synthesize proteins of the extracellular matrix (ECM). However, following cardiac injury, cytokines and growth factors mediate their transformation into MFs, which produce α-smooth muscle actin (α-SMA) (Hinz et al., 2007) indicating myofibroblast maturity (Shinde et al., 2017). MFs originating from bone marrow-derived precursors can produce collagen I, contributing to tensile strength (van Amerongen et al., 2008; Weber, 1989). EMT (Blom and Feng, 2018) and EndMT (Cheng W. et al., 2021) are regulated by numerous signaling pathways, including transforming growth factor β(TGF-β), wingless int (Wnt), Notch, and others, which are essential in heart fibrosis.

Immune cells are involved in the development of heart fibrosis. Tissue-resident macrophages are one of the initial immune cells that respond to indications of damage (Rurik et al., 2021). Due to their phagocytic properties, They can remove matrix debris, dead cells, and apoptotic MFs from the wound (Kong et al., 2014). Additionally, macrophages produce pro-inflammatory cytokines and chemokines, including CC-chemokine ligand 2 (CCL2), interleukin-6 (IL-6), and tumor necrosis factor (TNF) (Swirski and Nahrendorf, 2018). Mast cells can also secrete fibrogenic mediators, including histamine, cytokines, and growth factors (Levi-Schaffer and Rubinchik, 1994). Meanwhile, necrotizing cardiomyocytes release damage-related molecular motifs identified by neutrophils, dendritic cells, macrophages, and various other immune cells (Silvis et al., 2020). Those processes cause neutrophils and monocytes to migrate to the necrotic area, where they release proteolytic enzymes, MMPs, and factors such as IL-6 and TNF (Daseke et al., 2019). B lymphocytes produce inflammatory factors similar to those associated with fibrosis in neutrophils and monocytes (Cordero-Reyes et al., 2016). Additionally, neutrophils synthesize CCL, stimulating the expression of CCL and vascular cellular adhesion molecule (VCAM) in endothelial cells (Saparov et al., 2017). Endothelial cells are capable of generating pro-inflammatory chemokines and cytokines, which help attract lymphocytes and macrophages (Kong et al., 2014). These changes can further amplify inflammation (Saparov et al., 2017).

Cardiac fibrosis progresses due to a variety of cell types and signaling pathways. Numerous studies have identified the WNT and TGF-β signaling pathways as crucial in cardiac fibrosis. Researchers have found that these two signaling pathways can regulate the transformation of CFs (Yousefi et al., 2020).

Recent research has shown a connection between cardiac fibrosis and SOX9. Cardiac fibrosis can be involved in various cardiovascular diseases, including hypertension, heart failure, AF, and MI. Studies suggest that SOX9 is involved in the pathogenic mechanisms associated with fibrosis.

As previously stated, EndMT is a major contributor to fibrosis. EndMT is crucial in the progression of cardiac fibrosis. This process involves transforming endothelial cells from their original state to mesenchymal-like phenotypes. Deleting Sox9 in endothelial cells greatly inhibits EndMT as well as decreases scar formation during wound healing (Zhao et al., 2021). EJilai Zhao and colleagues, through mouse experiments, concluded that inhibition of Notch signaling upregulates Sox9 gene expression in cells undergoing pathological EndMT, contributing to excess fibrosis (Zhao et al., 2021). Christopher L. Smith et al. reported that blood vessel formation and matrix organization require noncardiomyocytes (Smith et al., 2011). They identified SOX9 as the downstream transcription factor target in platelet-derived growth factor (PDGF)–stimulated EMT (70). Another study focused on endocardial fibroelastosis (EFE). Fibroblasts are mainly Fibroblasts primarily originate from epicardium-derived mesenchymal cells (MCs) (Zhang et al., 2017). Researchers discovered that in an EFE model, cells marked by SOX9 predominantly contribute to fibroblast formation (Zhang et al., 2017). In the EFE-like model, blocking TGF-β signaling could diminish tissue fibrosis and fibroblast accumulation (Zhang et al., 2017).

Following MI, cardiac fibrosis plays a role in myocardial remodeling. Recent studies have shown that reducing SOX9 expression effectively ameliorates fibrosis. Grégory P.A. Lacraz and colleagues employed tomo-seq and lineage-tracing experiments to identify genes co-regulated with cardiac fibrosis. Their findings revealed that most fibroblasts expressing COL1 originate from cells expressing SOX9 (Lacraz et al., 2017). And the fibrotic response of heart to ischemia damage was diminished when SOX9 was absent (Lacraz et al., 2017). In Sox9 deficiency mice model, it confirmed that SOX9 is a common transcriptional regulator involved in ECM deposition and cardiac fibrosis mediation (Lacraz et al., 2017). Another team reached similar conclusions in a mouse model of MI, reporting that reducing SOX9 lessened the deposition of ECM and SOX9 also inhibited the activation of migrating fibroblasts in vitro (Scharf et al., 2019). Additionally, in fibroblasts, downregulating SOX9 expression can suppress severe inflammation in the infarct area, protect the heart from dilation, and improve cardiac function post-MI (Scharf et al., 2019). Adrián Ruiz-Villalba and colleagues found that SOX9 overexpression induces fibrosis-related gene expression in CFs, similar to the outcomes seen with TGF-β incubation (Ruiz-Villalba et al., 2020).

Myocardial fibrosis often occurs in the enlarged left ventricle in cases of arterial hypertension. Antje Schauer and colleagues showed that both control and Sox9-KO group developed high blood pressure, with the control group exhibiting fibrosis and left ventricular remodeling, while the conditional Sox9-KO group displayed delayed fibrosis and slight hypertrophy (Schauer et al., 2019). Interestingly, Sox9 loss does not preserve cardiac function; instead, it slows down the development and remodeling of the heart.

Atrial fibrosis is crucial in the development of AF. A new research used cellular studies to demonstrate the function of SOX9 in human right atrial tissue. They isolated and cultured rat atrial fibroblasts, treating them with adenovirus to overexpress the Sox9 gene or with siRNA to decrease SOX9 expression (Wang H. et al., 2021). Ultimately, they discovered that TGF-β1 increases SOX9 expression at the cellular level, and SOX9 overexpression may enhance cell migration, collagen deposition, and fibroblast differentiation (Wang H. et al., 2021). In patient atrial tissues, following RT-qPCR, Masson’s trichrome staining, and some other experimental methods, it was concluded that high expression level of SOX9 and α-SMA aggravates cardiac fibrosis (Wang H. et al., 2021).

Under conditions of cardiac pressure overload, SOX9 mediates hypertrophy and early fibrosis through cardiomyocytes and fibroblasts, ultimately leading to left ventricular remodeling. CHIA-FENG LIU and colleagues analyzed RNA levels in cardiac tissue samples from heart failure patients using whole-transcriptome sequencing, finding significant upregulation of SOX9 RNA in patients with dilated cardiomyopathy and hypertrophic cardiomyopathy (Liu et al., 2022). They noted a significant association between SOX9 RNA levels and the level of expression of fibrosis-related genes (Liu et al., 2022).

To sum up, overexpression of SOX9 gene could induce cardiac fibrosis, several cell types are significant for tissue repair. However, excessive early inflammation can lead to severe degradation of the ECM, potentially causing heart rupture. Prolonged inflammation can diminish cardiac tensile strength and result in ventricular dilation. It is crucial to identify a balance that not only repairs damaged cardiac tissue but also preserves as much of the heart chamber’s function as possible.

The liver is composed of two main kinds of cells: parenchymal cells and non-parenchymal cells (NPLCs). Hepatocytes, a parenchymal cell type constituting the majority of liver cells, comprising about 60% of the overall cell count and around 80% of the volume of liver. Sinusoidal endothelial cells, Kupffer cells (a type of macrophage), and hepatic stellate cells (HSCs) are involved in NPLCs. Hepatic fibrosis, involving the aforementioned cells, can arise from various liver diseases. Hepatotoxic and cholestatic injuries represent the two prevalent forms of chronic liver damage leading to hepatic fibrosis. Hepatotoxic injury refers to long-term damage to liver cells, for instance, alcohol, metabolic syndrome including metabolic syndrome inducing hepatitis C virus (HCV) or hepatitis B virus (HBV) infections, non-alcoholic steatohepatitis (NASH). Cholestatic injury, caused by bile flow obstruction, can occur in conditions like primary sclerosing cholangitis (PSC), biliary atresia (BA), and primary or secondary biliary cholangitis (PBC).

Liver fibrosis results from repeated, persistent damage, starting with hepatocyte injury, leading to inflammation and the subsequent activation and recruitment of immune cells, resulting in the activation of HSCs. In response to injury or external stimuli, hepatocytes modify their gene expression and secretion profiles. When factors like TGF-β, Hedgehog, and Notch are expressed, they may activate HSCs. These cells then elevate α-smooth muscle actin levels, migrate to the damage site, and synthesize the ECM, forming a dense fibrous scar (Xu et al., 2016; Xie et al., 2013; Hu et al., 2022). In fibrotic livers, MFs which are absent in healthy livers, are the primary ECM source and become activated following liver injury (Kisseleva and Brenner, 2008). MFs, primarily responsible for collagen production and extracellular matrix accumulation, could originate from various sources. Inflammation also is essential to the pathogenesis of hepatic fibrosis, characterized by the recruitment of various inflammatory cells, including early activated proinflammatory macrophages, neutrophils, natural killer (NK) cells and monocytes. As initial responders, neutrophils are capable of chemotaxis and rapid migration to the site of inflammation, where they eliminate apoptotic hepatocytes. Experimental evidence indicates that neutrophil elimination exacerbates liver fibrosis, whereas their presence aids in fibrosis resolution (Calvente et al., 2019). The presence of various macrophage types is well-documented. Research has indicated that these cells may contribute to fibrosis by secreting substances including monocyte chemoattractant protein-1 and TGF-β (Kishore and Petrek, 2021). However, some studies have shown that macrophages may impede the fibrosis process. In the late stages of hepatic fibrosis, MMPs release can significantly influence fibrosis regression by affecting macrophages (Feng et al., 2018). NK cells, another type of immune cell, possess antifibrotic characteristics in liver fibrosis through the inhibition of HSC populations. NK cells have the ability to impact the fibrosis process through modulating the activity and cytokine secretion of other immune cells, such as macrophages and dendritic cells. NK cells directly kill activated HSCs by releasing cytotoxic molecules and inducing cell apoptosis, thereby reducing the progression of fibrosis (Tao et al., 2022). Maybe that was the difference between the liver fibrosis and the cardiac fibrosis. Liver regeneration typically occurs in cases of acute liver injury, such as liver resection and recovery from hepatitis (Campana et al., 2021). When the liver is acutely injured, hepatocytes undergo proliferation and differentiation to restore the damaged tissue. This regeneration process usually spans several days to weeks, allowing the liver to return to its normal size and restore functionality (Ben-Moshe et al., 2022). It is significant to note that the capacity of the liver to regenerate is restricted. In severe hepatic diseases, such as advanced cirrhosis, the regenerative ability of the liver may be impaired, leading to incomplete restoration. Another important phenomenon in liver fibrosis is the ductular response (DR), which is characterized by a proliferation of reactive bile ducts as a result of liver damage. Pathologically characteristic of biliary disorders such as BA, PSC, and PBC, DR is observed histologically in liver samples (Zhang Z. et al., 2022).

In activated HSCs, SOX9 was identified as an upregulated gene linked to liver fibrosis (Lin et al., 2020). There is a study concluded that SOX9 and β-catenin interactions may enhance HSC activation. The study revealed that SOX9 might bind to the TGF-β1 promoter, enhancing TGF-β1 transcription activity and thereby promoting HSC activation (Wang Q. et al., 2021). In the study by Varinder S. Athwal et al., it was found that over 30% of the genes (Osteopontin (OPN), et al.) regulated by SOX9 are involved in extracellular matrix production. Furthermore, RosaCreER: Sox9 ^fl/fl mutant mice with the Sox9 gene knocked down exhibited reduced fibrosis (Athwal et al., 2018). Another study shows that the PTM of histone H3 on the 18th lysine (H3K18) residue may regulate liver fibrosis. Later experiments demonstrated that the suppression of lactate dehydrogenase A (LDHA) obstructed H3K18 lactylation and positively regulated liver fibrosis by inhibiting HSC proliferation, motility, and ECM deposition (Wu S. et al., 2024). Furthermore, the overexpression of SOX9 significantly alleviated the effects of LDHA silencing on activated HSCs, suggesting that SOX9 operates downstream of H3K18 lactylation in the promotion of liver fibrosis (Wu S. et al., 2024).

Nonalcoholic fatty liver disease (NAFLD) is becoming increasingly prevalent. NAFLD advances from non-alcoholic fatty liver (NAFL) to NASH and might potentially result in liver cirrhosis and liver cancer. Z. Wang et al. used bioinformatics analysis on databases (GSE135251 and GSE162694) and concluded that SOX9 genes are associated with liver fibrosis (Wang Z. et al., 2022). Another research group, analyzing databases (GSE89377 and GSE139602), found that elevated SOX9 expression is associated with heightened immune infiltration, suggesting its potential as a biomarker for cirrhosis diagnosis or therapeutic targeting (Du et al., 2023). Yue Li et al.'s research, utilizing the GEO database (GSE14323, GSE36411, and GSE89377), found a positive correlation between the degree of liver fibrosis and the levels of SOX9 expression (Li et al., 2022). Additionally, the higher expression level of SOX9 was found in hepatic fibrosis in mice (Li et al., 2022). Moreover, they demonstrated that patients with HCC had a considerably poorer 5-year survival rate than those without the disease by Kaplan-Meier curves (Li et al., 2022).

By using knockout technology, Zhu and colleagues were able to demonstrate how HSCs were stimulated by secreted phosphoprotein 1 (Spp1), which ultimately results in the generation of fibrogenic factors like Opn (Zhu et al., 2018). They noted that SOX9, a crucial transcriptional mediator in the signaling pathway, might enhance Spp1 expression during liver fibrosis progression (Zhu et al., 2018). Another fascinating study shows that c-Jun, an independent transcription factor, has cell-type-specific functions in mice. c-Jun helps protect hepatocytes from the regenerative DR of SOX9/Opn co-expressing NPLCs (Schulien et al., 2019). However, it regulates the expression of Opn and CD44 in NPLCs, which results in the promotion of fibrogenesis and DR (97). A high-fat diet (HFD) was shown to promote severe cholangitis in the research conducted by Shin Maeda and colleagues. This was attributed to the deletion of the E-cadherin gene (CDH1), which resulted in the absence of E-cadherin expression (Maeda et al., 2021). In these gene knockout models, the number of CD44 and SOX9-positive stem cell-like cells was vitally increased, which is associated with fibrosis (Maeda et al., 2021). The Cirrhosis Risk Score (CRS) gene includes SOX9, which acts as an indicator for liver progenitor cells. The Cirrhosis Risk Score (CRS) gene includes SOX9, which acts as an indicator for liver progenitor cells (Sanchez et al., 2023). SOX9 expression levels were significant predictors of hepatic fibrosis progression (Sanchez et al., 2023). In the choline-deficient diet supplemented with ethionine (CDE) injury model, SOX9-positive liver progenitor cells are significant in the fibrosis process (Li et al., 2024). Following CDE injury, there is a notable rise in the percentage of liver progenitor cells which exhibit SOX9 positivity inside the DR (100). Additionally, the expression of GITRL, a cytokine, is notably elevated in SOX9-positive hepatic progenitor cells, which are important in liver fibrosis (Li et al., 2024).

There are 9 genes (ADAMTS2, ARHGEF5, CCT8, ERG, LBH, FRMD6, INMT, RASGRF2 and DHRS4) are related to SOX9 (Cai et al., 2025). All those 9 factors, except for DHRS4, which is protective, are considered deleterious and are recognized as risk factors in the progression of early-stage fibrosis generated by the HCV (Cai et al., 2025). Nourdine Hamdane et al. have been discribing that functional deletion of SOX9, which means selectively deleting or turning off a gene or gene segment in the genome, slows the growth of liver cancer cells. It was also found that SOX9 is overexpressed in liver tissues during chronic HCV infection, and this overexpression persists even after antiviral treatment (Hamdane et al., 2019). However, a different study revealed an alternate mechanism, concluding that HBV activates the promoter of SOX9, leading to the expression of SOX9 (103). Conversely, SOX9 inhibits the replication of HBV in human hepatoma cells by binding to and blocking HBV Enhll/Cp via HMG domain of SOX9 gene (Yang H. et al., 2020). Fibrosis is associated not only with viral infections but also with aging. In E. G. Skurikhin et al.'s study, fibrosis induced by CCL4 or 5% ethanol may be associated with SOX9-positive cells (Skurikhin et al., 2021). In young rats, higher levels of SOX9-positive cells and MSCs activity lead to more severe liver fibrosis (Skurikhin et al., 2021).

Fibrosis is a reaction to liver damage, and cirrhosis represents the ultimate phase of fibrosis. Progression to cirrhosis result in increased mortality as well as an increased prevalence of hepatocellular carcinoma. Additionally, the SOX9/INHBB axis mediates the activation of HSCs, which produce collagen and the extracellular matrix, inducing liver fibrosis (Chen et al., 2021). Prolonged parasite infection, such as Clonorchis sinensis, can result in hepatic impairment, inflammation, and fibrotic responses. Without timely treatment, fibrosis can progress to more severe conditions, such as cirrhosis and liver cancer. According to immunohistochemistry and RT-PCR data, CK19, SOX9, and EpCAM, hepatic progenitor cell markers, were significantly upregulated in the experimental group (Qi et al., 2022).

Despite differing pathological mechanisms in the early stages of Alagille syndrome, BA, and cholestatic liver disease (CLD), these three diseases exhibit similar clinical symptoms. Numerous research has demonstrated the vital role of SOX9 in all three diseases. Manar M. Esmail and colleagues demonstrated that in a rat model of bile duct ligation, niclosamide may lessen liver fibrosis (Esmail et al., 2021). Furthermore, it has been shown that niclosamide lowers SOX9 expression in the NOTCH signaling pathway (Esmail et al., 2021). In CLD, the expression level of Hes1 could regulated by SOX9, and it could also associated with trans-differentiation of hepatocytes (Tharehalli et al., 2018). Duplication of the Rbpj gene can upregulate SOX9, which is associated with fibrosis (Tharehalli et al., 2018). In Dino Šisl et al.'s research, mice treated with treated with tamoxifen showed a much lower degree of liver fibrosis compared to those given a vehicle (corn oil) (Šisl et al., 2022). This conclusion was further supported by qPCR results showing low SOX9 expression, indicating inhibited activation of HSCs, biliary duct proliferation and collagen production (Šisl et al., 2022). Another study showed that reversine prevented liver fibrosis in vitro by causing HSC death, limiting cell proliferation, reducing HSC activation, and degrading the extracellular matrix (Huang et al., 2023). And they concluded that reversine inhibited cholestatic DR and liver fibrosis in rats, and decreased bile duct formation through the Dlk1/Notch/SOX9 signaling pathway (Huang et al., 2023).

BA leads to progressive scarring and damage of both extrahepatic and intrahepatic biliary ducts, resulting in obliterative cholangiopathy (Shamir et al., 2017). Giulia Jannone’s study showed that administering human allogeneic hepatogenic progenitor cells (HALPC) in biliary ligated mice successfully repaired biliary tract damage and reduced SOX9 expression levels (Jannone et al., 2023). In BA, numerous studies involving SOX9 have drawn conclusions from clinical patient biopsies. According to a study by Jenny E. Arboleda-Bustan et al. study, SOX9 was found to be highly expressed in the nuclei of reactive epithelium, fibrotic bridges and proliferating ductules in portal spaces (Arboleda-Bustan et al., 2022). In cholestatic liver injury, SOX9-positive liver progenitor-like cells (LPLCs) transform into cells with characteristics of bile duct cells, expressing markers like SOX9 (Lin et al., 2022). They also concluded that LPLCs can transform into reactive ductular cells (RDCs), which are associated with liver fibrosis, potentially leading to liver fibrosis when the liver is injured (Lin et al., 2022). However, another study demonstrated that SOX9-positive hepatocytes were identified in a bile duct ligation (BDL) mouse model. DR progression was quicker in wild-type BDL mice compared to liver epithelium-specific SOX9-knockout BDL mice (Yoshii et al., 2022). In other words, SOX9 facilitates the advancement of ductular responses to safeguard against chronic liver injury (Yoshii et al., 2022). An additional investigation, which examined liver specimens obtained from individuals diagnosed with BA, concluded that an important correlation among hepatic progenitor cells (HPCs) proliferation, aberrant SOX9 expression, and fibrosis in patients (El-Araby et al., 2021). Alagille syndrome is a genetic disorder causing severe liver disease. However, SOX9 levels are negatively correlated with severity, with lower levels in severe cases and higher levels in mild cases (Adams et al., 2020). A single Sox9 copy conditionally deleted in Jag1 ^+/− liver tissue reduces cholangiocyte biliary commitment and exacerbates liver fibrosis in Alagille syndrome (Adams et al., 2020).

Multiple mechanisms implicated in the regulation of hepatic fibrosis have been identified through the research mentioned above. These identified mechanisms have the potential to be therapeutic targets in the treatment of fibrosis. While there are no papers explicitly indicating that SOX9 is crucial for early healing in liver damage, continued expression in the later stages may lead to fibrosis. Nonetheless, we might hypothesize that the advantage of SOX9’s expression is dependent upon the timing of its expression.

The similar fibrotic process also occurs in the kidney. Renal fibrogenesis is often viewed as a failed wound healing process following initial damage from various injuries (Wynn, 2008). Crucial pathophysiological elements of both chronic kidney disease (CKD) and acute kidney injury (AKI) include renal inflammation and fibrosis.

The development of renal fibrosis requires the buildup of ECM components. MFs, originating from local fibroblasts exposed to fibrosis-promoting stimuli, are the primary contributors to ECM deposition in renal fibrosis. Other resident or infiltrating cells, including fibroblasts, tubular epithelial cells, mesangial cells, endothelial cells, podocytes, and macrophages, also contribute to matrix development. Fibroblasts are primarily residual in the kidney’s interstitium and are present in the normal cortex of a healthy kidney. In pathological conditions, pre-existing fibroblasts become activated and transdifferentiate into MFs. Similar to other organs, the kidneys also have multiple origins for MFs. Tubular epithelial cells and endothelial cells could differentiate into MFs through EndMT or EMT (Huang and Ogawa, 2020). However, there is considerable disagreement or debate surrounding this topic specifically in relation to the kidneys. The pericytes, also named perivascular fibroblasts, are described as the alternative origin for myofibroblast precursors (LeBleu et al., 2013). At the same time, both mesangial cells and podocytes can produce excessive pro-inflammatory and pro-fibrotic factors during renal fibrosis, stimulating the response of surrounding cells and matrix, and promoting the process of fibrosis (Song et al., 2023; Zhong et al., 2022).

The immune system is also involved in kidney fibrosis. Following an injury, chemotactic proteins create concentration gradients that attract inflammatory cells to the damaged site. Macrophages are usually the first immune cells to reach the site of inflammation. Macrophages have a dual function in renal fibrosis, as they contribute to both the progression of fibrosis and the inflammation reduction (Huen and Cantley, 2017). The chemokines as well as inflammatory mediators released by macrophages can attract other immune cells to the damaged tissues for participating in immune responses and repair processes.

Renal fibrosis is a characteristic feature of CKD and commonly occurs in final stage of kidney disease, related to various types of renal damage and diminished kidney function. Numerous animal experiments have demonstrated a correlation between the expression of SOX9 and the development of fibrosis.

The high expression level of SOX9 has been found during renal fibrosis. Several potential genes including SOX9 have been found to be biomarkers for renal fibrosis by using datasets (GSE76882, GSE22459), and this was also confirmed in cell experiments by RT-qPCR (Guo et al., 2023). In both mouse models and biopsy tissues from CKD patients, increased expression level of SOX9 was also observed (Abe et al., 2015).

SOX9 is involved in multiple signaling pathways that regulate fibrosis. Sayyid Raza et al. have linked the transcription factor SOX9 to kidney fibrosis, suggesting it may regulate fibrosis via the SOX9-NAV3-YAP1 axis (Raza et al., 2021). Another signaling pathway indicates that SOX9 could enhance ECM synthesis and fibroblast activation. In Martina Feger et al.’s research, they found that during fibrosis, SOX9 expression is regulated by TGF-β1 as well as TGF-β-activated kinase 1 (Tak1) (Feger et al., 2015). TGF-β1 induces fibrotic effects by activating Smad-independent pathways (Feger et al., 2015). Tak1 is regarded as a key non-canonical signaling molecule in fibrosis which is regulated by TGF-β(127). Haixia Mao and colleagues found that serum levels of PIIINP, TGF-β1, and SOX9 were considerably elevated in a rat model of chronic kidney disease compared to the control group (Mao et al., 2023). SOX9 serum is anticipated to emerge as a novel diagnostic biomarker for renal fibrosis (Mao et al., 2023). Markus Tölle et al. demonstrated that uremic mice elevated levels of SOX9 expression in comparison to the control group (Tölle et al., 2022).

AKI is a life-threatening condition that can lead to CKD in survivors without specific treatment. In AKI, SOX9 expression has dual effects: promoting repair and exacerbating fibrosis. Different views have been demonstrated in the following articles. Kohei Matsushita and colleagues developed a rat model of AKI and investigated the immunohistochemistry markers of renal tubules throughout both adaptive and maladaptive restoration procedures (Matsushita et al., 2020). Following ischemia/reperfusion (I/R), both regenerating and dilated tubules could be observed in the AKI model, while regions of renal fibrosis demonstrate either tubular dilation or atrophy (Matsushita et al., 2020). Regenerative tubules progressively redifferentiated following I/R, while dilated tubules showed little capacity for redifferentiation (Matsushita et al., 2020). Immunohistochemical investigations revealed that regenerating tubules expressed survivin and SOX9, while fibrotic renal tubules also contained SOX9 (130). Therefore, SOX9 as well as survivin contribute to renal tubular regeneration, but persistent expression of SOX9 might be related to fibrosis (Matsushita et al., 2020). In other words, whether fibrosis occurs or whether severe fibrosis occurs is depend on the time-dependent expression of SOX9.

However, in the following studies, there is a disagreement on whether SOX9 will exacerbate fibrosis. Lu Yu et al. found that embryonic stem cell-derived extracellular vesicles (ESC-EVs), which could provide a therapeutic impact by stimulating SOX9⁺ cells in the kidney, notably enhanced the rebuilding of both the structure and function of the impaired kidney (Yu et al., 2021). They concluded that following kidney injury, Sox9 activation can promote the proliferation and regeneration of renal tubular epithelial cells (Yu et al., 2021). Whereas, Hyun Mi Kang et al. concluded that SOX9 has the ability to control the expression of genes related to fibrosis, which affects the development and deposition of fibrous tissue (Yu et al., 2021). Shang Chen and their colleagues established an AKI model utilizing prostaglandin E2 (PGE2) medication in a SOX9 lineage tracing mouse model (Chen et al., 2024a). Their findings underscore the potential for activating endogenous renal SOX9⁺ stem cells by PGE2 for the regenerative treatment of AKI (Chen et al., 2024a). In models of AKI, the expression of microRNA (miR-1247) could downregulate the SOX9. In this article, authors suggest that the significant reduction in SOX9, an essential regeneration regulator, greatly exacerbates the severity of AKI and impairs cellular and molecular repair mechanisms following renal damage (Dreval et al., 2017). As AKI progresses, injury- and repair-regulated markers like SOX9, VCAM1, and EGR1 are upregulated in three new subtypes of proximal tubule cells (Zhang M. et al., 2022).

AKI damages kidney structures, leading to chronic inflammation, fibrosis, and damage to glomeruli and tubules, resulting in persistent renal tissue changes and ultimately CKD. A study showed that in a rat model of obstructive nephropathy, the expression levels of SOX9 were elevated in tubular epithelial cells (Zhang et al., 2020). EMT refers to the process whereby damaged renal tubular epithelial cells undergo a phenotypic transformation, adopting mesenchymal features and differentiating into fibroblasts. Additionally, it was shown that renal tubular EMT and ECM accumulation were enhanced by SOX9 overexpression in NRK-52E cells (Zhang et al., 2020). Furthermore, The research revealed that SOX9-mediated renal tubular EMT and ECM deposition may be regulated by the PI3K/AKT as well as TGFβ1 signaling pathway (Zhang et al., 2020). Xiao Wang et al. found that SOX9 is upregulated in the models of kidney injury. SOX9 exacerbates kidney injury development and progression by inhibiting miR-96-5p expression, which subsequently upregulates Trib3 expression (Wang et al., 2023). Additionally, SOX9 overexpression triggers the IL-6 signaling pathway, escalating the degree of kidney damage and the inflammatory response (Wang et al., 2023).

Within other various types of kidney diseases, a relationship between SOX9 and fibrosis persists. The study reveals that sublytic C5b-9 activates Sox9 in GMCs, increasing the expression of fibroblast growth factor 1, PDGFα, and TGF-β1 (23). Overexpression of S64 and S181 in SOX9 significantly increases these genes, with phosphorylation modifications playing a crucial role (Wu Z. et al., 2024). In cultured mesangial cells, JQ1 can inhibit Sox9 activation, regulating type IV collagen production associated with kidney fibrosis. Additionally, in the mouse model, JQ1 inhibits SOX9 nuclear translocation and interstitial fibrosis (Morgado-Pascual et al., 2022).

For many years, people have held differing opinions on whether SOX9 promotes fibrosis. Recently, Science magazine revealed the relationship between the SOX9 switch and fibrosis. They discovered a dynamic SOX9 switch in the healing of epithelial tissues. In models of AKI caused by ischemia-reperfusion injury and rhabdomyolysis resulting in CKD, there exist SOX9^on-off and SOX9^on-on lineages (Aggarwal et al., 2024). The SOX9^on-off lineage can inhibit SOX9 during regeneration, preventing fibrosis during healing, while the SOX9^on-on lineage sustains SOX9 activity throughout ongoing regeneration, which is intimately linked to myofibroblasts and results in fibrosis (Aggarwal et al., 2024). This study conducted in this article on the kidneys indicates that SOX9 is crucial for epithelial tissue repair; nevertheless, persistent expression may induce or worsen fibrosis.

In summary, the prolonged issue has now been resolved: SOX9 facilitates regeneration during the initial phases of kidney injury; however, persistent expression in later stages leads to fibrosis.

Pulmonary fibrosis, a clinical endpoint in various chronic lung disorders, including interstitial lung disease (ILD), idiopathic pulmonary fibrosis (IPF), and systemic sclerosis (SSc). It is characterized by persistent collagen deposition and recurrent lung damage (Noble et al., 2012; Kolb and Vašáková, 2019). Pulmonary fibrosis often develops following acute lung inflammation, triggered by factors like viral or bacterial infections, ionizing radiation, chemotherapy, and exposure to air irritants and pollutants (Kligerman, 2022). Alveolar macrophages, the first cells to encounter external pathogens and irritants, initiate and later resolve the immune response in the lungs. Proinflammatory cytokines and chemokines secreted by macrophages can increase chemotaxis and progressively enrich alveolar spaces with monocytes and neutrophils (Kligerman, 2022). MFs actively produce ECM components during lung tissue repair. In a healthy organism, MFs undergo apoptosis once a sufficient amount of ECM is formed. However, in the context of persistent inflammation, MFs evade programmed cell death, resulting in abnormal tissue repair, excessive ECM production, and ultimately pulmonary fibrosis. This process is similar to fibrosis in other organs.

Additionally, systemic sclerosis, an autoimmune disease, causes fibrosis and vascular abnormalities in multiple organs. The lungs are among the organs most commonly affected by systemic sclerosis. About 50%–65% of systemic sclerosis patients show interstitial lung abnormalities on HRCT. ILD is the primary cause of mortality among SSc patients (Volkmann et al., 2023). Owing to the shared characteristics of systemic sclerosis and pulmonary fibrosis, they are being addressed collectively.

In tracheal injury, SOX9 expression was elevated in rat tracheal fibroblast cells under TGF-β1 treatment. SOX9 overexpression stimulated fibroblasts and enhanced ECM(143). Inhibition of SOX9 suppressed cell proliferation, migration, and ECM deposition and heightened apoptosis in rat tracheal fibroblast cells (Gu et al., 2024). Maybe there is a similar way related to kidney (the regeneration of SOX9 temporal switch triggers), but this article does not discover the specific mechanisms. Another group of people revealed the contrasting functions of interleukin-4 (IL-4) cytokine signaling in interstitial macrophages and type II alveolar epithelial cells (ATIIs) (Cai et al., 2024). IL-4Rα signaling in macrophages facilitates alveolar epithelial regeneration following bleomycin-induced lung damage (Cai et al., 2024). Through organ and murine models, they established that IL-4 directly influences the ATII subset, prompting the production of the transcription factor SOX9 and reprogramming it into a progenitor-like state with potential for alveolar lineages and airway (Cai et al., 2024). Kevin Y. Huang and colleagues showed that SOX9, PT63 et al. become activated during the differentiation of transitional from type 2 pneumocyte (AT2) cells to KRT5^-/KRT17⁺ positive cells, closely associated with molecular phenotypes like fibrosis (Huang and Petretto, 2021). Prathibha R. Gajjala’s research shown that specifically deleting Sox9 in fibroblasts during TGF-α-induced pulmonary fibrosis reduces collagen deposition and enhances lung function (Gajjala et al., 2021). Furthermore, in bleomycin-induced pulmonary fibrosis mouse model, they found that overexpressing SOX9 in MFs increases the activation of fibroblast as well as lead to lung fibrosis (Gajjala et al., 2021). In the silica-treated mouse model of silicosis, researchers found that SOX9 and SOX2 are markers of embryonic lung stem/progenitor cells (Zhou H. et al., 2024). During the early inflammatory phase of silicosis, SOX9 and SOX2 were re-expressed in the distal lung and exhibited abnormal distribution (Zhou H. et al., 2024). However, in the later stages of silicosis, SOX9’s expression level decreased and was unrelated to the progression of fibrosis, indicating that SOX9 could be important in regulating fibrosis during the development of silicosis (Zhou H. et al., 2024). In SSc, researchers have found that SOX9 is overexpressed in the lungs. Kristy M. Waldrep et al. demonstrated that insulin-like growth factor-II (IGF-II) induces SOX9 expression (Waldrep et al., 2023). In SSc lung tissues compared to healthy controls, there is an overexpression of SOX9 at both mRNA and protein levels (Waldrep et al., 2023). Through the IGF1R/IR hybrid receptor, IGF-II activates SOX9 in lung fibroblasts, and SOX9’s downstream effects include COL3A1, P4HA2, TGF-β2, and TGF-β3 (148). In Elisha D. O. Roberson et al.'s research, the SOX9 locus is identified as a hub gene with significant connectivity in the systemic sclerosis skin gene network (Roberson et al., 2022).

Fibrosis can be a result of various other pulmonary disorders. The Wnt/β-catenin-SOX9 axis is activated in tracheal injury and fibrosis, and inhibiting SOX9 may ameliorate tracheal fibrosis (Gu et al., 2022). Milena Paw et al. suggested that overexpressing SOX9 activates human bronchial fibroblasts (HBFs) and enhances the transcription of genes associated with fibrosis in vitro (Paw et al., 2023). Additionally, SOX9 expression are increased by TGF-β1 stimulation and decreased by inhibition of TGF-β1 signaling pathway (Paw et al., 2023).