Stem cells, which represent a fundamental pillar of modern regenerative medicine, require specific conditions for successful differentiation. They include the presence of growth factors, cytokines, enzymes, and components of the ECM (e.g., collagen), ions, as well as mechanical stimuli. This encompasses physical parameters such as stiffness, which is considered a critical determinant, and viscosity (Pennings et al., 2018; Zhou et al., 2019; Lim et al., 2022). Blood and lymphatic vessels, nerves, and elements of the immune system further complement this framework, collectively forming the stem cell niche. These cells are extremely sensitive to their surrounding environment; therefore, any alteration—even those associated with physiological aging—can directly impact their behavior. Communication between stem cells and their niches determines their ability to maintain homeostasis and respond to tissue demands (Fuchs and Blau, 2020; Farahzadi et al., 2023). This reciprocal interaction is exemplified in MSCs, which modulate macrophage activity through the secretion of soluble mediators. These signals shift macrophage polarization from the pro-inflammatory M1 phenotype to the anti-inflammatory M2 subtype. Furthermore, interleukin 17 (IL-17), whose production is stimulated by MSC, enhances the phagocytic capacity and effector functions of neutrophils (Hsu et al., 2013). Depending on external stimuli—such as insulin-like growth factor 1 (IGF-1) — MSC can be directed towards specific differentiation pathways. It has been demonstrated, for example, that IGF-1 induces osteogenic differentiation and delays the commitment of placental mesenchymal stem cells (PMSCs) towards the myogenic lineage, in contrast to IGF-2, which promotes the development of myoblast cells (Aboalola and Han, 2017; Liu et al., 2022). Recent reports have demonstrated that bone marrow-derived stem cells (BMSCs) placed within a neuronal niche can undergo transdifferentiation into neuronal cells. This plasticity, driven by the surrounding niche, is also being leveraged in vitro to alter culture conditions—such as those used for hepatic cells—to enable their transdifferentiation into insulin-producing pancreatic islet-like cells (Elsayed Azab et al., 2021). We draw attention to recent reports that have confirmed the existence of a reprogramming process through which the endothelium of major embryonic arteries contributes to the formation of HSCs. This finding has revolutionized the previously accepted yolk sac–based model of hematopoietic origin (Dzierzak and Bigas, 2024). The newly generated HSCs remain highly responsive to niche-derived signals, and an improved understanding of these interactions paves the way for the refinement of ex vivo cell culture protocols (Cain et al., 2024). Furthermore, these discoveries hold the potential to inform novel strategies in regenerative medicine. There is now evidence supporting the role of the human placenta as an extraembryonic niche facilitating the development of HSC. The presence of CD34⁺ HSCs has been detected throughout the entire duration of pregnancy. Expression of CD117 and CD41 is observed during the first and second trimesters, with a peak occurring in the second trimester. Stromal cells present within the placental microenvironment exhibit the capacity to support hematopoiesis and maintain the stem cell population. This makes the placental stroma a promising tool for therapies targeting bone marrow damage and related hematological deficiencies (Gao et al., 2018; Jovicic et al., 2025). Despite the promising proliferative potential and satisfactory availability of placental cells, obtaining pure cultures devoid of maternal cell contamination remains challenging. A key obstacle is the overgrowth of maternal-derived MSC in the established cell cultures (Sardesai et al., 2017). Although stem cell niches across different organs share common structural and functional components, they exhibit significant heterogeneity depending on their tissue-specific localization. These differences manifest in the way they generate signaling pathways and respond to physical and biological stimuli, thereby influencing the functional state of the resident stem cells (Singh et al., 2019). Given these abilities, stem cells have been implemented in sophisticated therapeutic techniques. For instance, HSCs are utilized in bone marrow transplantation to regenerate blood cells in patients with hematological malignancies. Similarly, stem cells derived from the skin are employed in regenerative therapies for patients suffering from extensive burns (Cable et al., 2020). For example, blood and intestinal epithelium are characterized by high rates of proliferative activity, in contrast to the relatively quiescent nervous tissue. Positioned between these extremes, skeletal muscle tissue exhibits substantial regenerative potential, which, however, is activated only under specific conditions (Mannino et al., 2022). Throughout the lifespan of a niche, its architecture undergoes modifications not only in response to pathological conditions but also as part of natural maturation processes (Hicks and Pyle, 2023).

Proper functioning of the niche is associated with the desirable regulation of stem cells and maintenance of homeostasis. Its aging is linked to the disruption of normal stem cell processes, which consequently contributes to the development of various diseases (Farahzadi et al., 2023). Changes in molecular-level determinants play a crucial role in this context. The affected stem cells include, among others, hematopoietic, mesenchymal, and NSCs, which will be the focus of our attention (Pérez et al., 2018).

The embryonic period marks the beginning of niche formation. During this time, NSCs within the ventricular zone of the neural tube initiate the formation of all central nervous system structures, including neurons and glial cells. Interestingly, certain populations of these stem cells can remain quiescent from embryogenesis and only become activated in adulthood. Notable adult neurogenic niches such as the subventricular zone adjacent to the lateral ventricles and the subgranular zone of the dentate gyrus are enriched in regulatory factors—such as doublecortin—and their dysfunction has been implicated in neurodegenerative diseases like Parkinson’s and Alzheimer’s (Llorente et al., 2022). Damage to these niches often results in the depletion of resident NSCs. Importantly, biological sex influences neurogenic niche dynamics; for instance, menopause in females is associated with a reduction in stem cell populations, which may contribute to gender differences in disease susceptibility (Velikic et al., 2024). The stem cell niche plays a crucial role also in the context of the progression of cancer cell processes (Wagers, 2012). Certain pediatric leukemias have been linked to the persistence of fetal-like niches, with origins traced back to prenatal development. This supports the theory that abnormal niche formation and maturation could underlie developmental origins of disease (Hicks and Pyle, 2023). In the context of cancer, niches also serve as sanctuaries for CSCs, protecting them from immune surveillance. Metastatic colonization, such as in the liver, often involves niche remodeling by CSCs, for instance via inhibition of proteases and upregulation of Tissue Inhibitor of Metalloproteinases 1 (TIMP-1), which aids in the establishment of pre-metastatic niches. Given the dependence of CSCs on supportive niches, niche-targeted strategies—such as oxidative modulation—represent promising therapeutic avenues that can be tailored to tumor type and stage (Plaks et al., 2015; Oshimori et al., 2021; Ju et al., 2022).

Therapeutic potential continues to expand rapidly, reinforcing optimism for future breakthroughs. The ability of niches to condition stem cell responses—for instance in injury—provides a foundation for controlled repair processes. Leveraging this knowledge, advanced technologies now enable the development of in vitro niche models and the genetic editing of both stem cells and their niches (Chacón-Martínez et al., 2018). In replacement therapies, human PSCs, especially ESCs, are of particular relevance due to their relatively easy maintenance in culture and capacity to differentiate into mesoderm, endoderm, and ectoderm lineages (Martinez et al., 2022; Tian et al., 2023). Their responsiveness to hormetic stimuli further underscores the influence of the niche (Calabrese, 2022). Nevertheless, challenges remain in optimizing the delivery of regulatory molecules and components into niches to promote targeted stem cell differentiation and function (Subramanian et al., 2024). Strategies to overcome transplantation barriers include the use of biomaterials that mimic the microenvironment. Depending on their physical properties, such scaffolds not only provide structural support but also emit biochemical signals that influence cellular differentiation (Zhao et al., 2021). Modifying the surrounding conditions of stem cells—such as ionic signals released from engineered inorganic crystalline materials—can trigger niche-specific responses, although clinical outcomes of such approaches are still under investigation (Zhou et al., 2019). There are reports describing composites of bioceramics and hydrogels that, through the release of lithium, magnesium, and silicon ions, contribute to the specialization of bone marrow-derived cells. In contrast, strontium and silicon ions have been associated with the promotion of angiogenesis, particularly in relation to human umbilical vein endothelial cells (Zhang et al., 2025). Recent scientific advances have enabled the reconstruction of stem cell niche environments, allowing precise in situ assessments. Laboratory modeling requires not only the presence of stromal cells and structural protection but also a balanced scaffold that supports the desired microenvironment (Abdul-Al et al., 2021). These scaffolds can be integrated with biological materials that transduce exogenous signals (e.g., light, electric fields, ultrasound, or magnetic forces) into cellular instructions, simulating the dynamic interactions found in living tissues (Gelmi and Schutt, 2021). Hydrogels—polymer networks with a three-dimensional structure—are widely used biomaterials, applied, for example, in the treatment of osteoarthritis. A notable example is the study by Park Yong-Beom et al., which involved seven patients treated with allogeneic human umbilical cord blood-derived mesenchymal stem cells (hUCB-MSCs) suspended in a hyaluronic acid hydrogel. The study demonstrated the presence of repair tissue after 12 weeks, with its maturation and durability confirmed by magnetic resonance imaging after 3 years. There is growing evidence that preconditioning of MSCs prior to transplantation enhances their clinical potential by supporting large-scale expansion and functional optimization. These cells can be modulated to preserve their phenotype or directed towards specific cell lineages (Park et al., 2017; Madl and Heilshorn, 2018; Sun et al., 2023). 3D bioprinting is gaining traction as an alternative to hydrogel-based methods, enabling scaffold fabrication followed by cell seeding. In this context, porosity and biocompatibility are critical parameters. These technologies have been applied in cartilage repair and other regenerative models (Huang J. et al., 2021; Su et al., 2021). More recently, the development of three-dimensional bacterial cellulose–graphene foam has been shown to support neuronal stem cell growth and differentiation, offering a promising approach for neurodegenerative diseases (Guo et al., 2021). To mitigate immune responses, scaffold-free strategies such as cell sheets and spheroids are being explored. Cell sheets can be harvested using stimuli such as temperature, light, or magnetic fields in combination with titanium dioxide, while spheroids are formed through cellular aggregation. Despite their promise, challenges remain, particularly regarding efficacy and the need for standardized protocols in stem cell manipulation (Liu et al., 2024).

Organoids allow researchers to study disease modelling, offering a hopeful, ethical alternative to animal models (Ho et al., 2018). For instance, brain organoids hold significant promise for studying neurodegenerative diseases including, Alzheimer’s and Parkinson’s diseases (Urrestizala-Arenaza et al., 2024). Research demonstrates that brain organoids can replicate pathological hallmarks of Alzheimer’s disease, such as the presence of phosphorylated tau protein, the aggregation of beta-amyloid, and the role of nitric oxide release in neuronal damage (Papaspyropoulos et al., 2020). Studies conducted on chimeric human cerebral organoids (chCOs) have shown that the presence of the apolipoprotein E4 (APOE4) genotype correlates with increased cholesterol accumulation in neurons and elevated levels of phosphorylated tau protein (Huang et al., 2022).

The ability of retinal organoids to replicate the structure and function of the retina allows for a more physiological studies of disease mechanisms and drug effectiveness compared to conventional 2D models (Mousavi et al., 2025). Similarly, midbrain organoids are valuable for modeling Parkinson’s disease. Midbrain organoids contain dopaminergic neurons and other cell types found in the human midbrain, such as astrocytes (Solana-Manrique et al., 2025).

After analysing the use of organoids in scientific research, we will now focus on their application in personalized medicine. The role of tumour organoids in personalized medicine presents considerable potential. Samples collected from tumour biopsies can be used to develop patient-derived organoids (PDOs). These organoids enable clinicians to test drug efficacy and select optimal therapies for individual patients (Chen et al., 2024). Cancer organoids are also used to evaluate radiotherapy responses. However, organoids require further investigation to establish their role as reliable components of personalized anticancer treatment strategies (Kretzschmar, 2021). Another example of the application of organoids are the treatment of cystic fibrosis (CF), a genetic disorder caused by mutations in the CFTR (CF transmembrane conductance regulator) gene. These mutations impair the function of chloride channels, leading to the accumulation of viscous mucus in multiple organ systems, including the respiratory and digestive tracts (Dickinson and Collaco, 2021; Jia and Taylor-Cousar, 2022). Current CF treatment strategies rely on symptomatic management and CFTR modulator therapy, which increase the number of functional channels and restore their activity. However, patients with rare CFTR mutations cannot benefit from this approach due to the inability to conduct clinical trials for such a limited population (Conti et al., 2025). The capability of patient-derived intestinal organoids to identify genetic variants of CFTR mutations allow the potential application of modulators. These modulators could be used for rare variants that were previously untreated with these substances. This capability enables personalized evaluation of therapeutic efficacy and the determination of optimal treatment (Conti et al., 2022).

After discussing how organoids contribute to the development of personalized therapies, we will now proceed to consider their application in regenerative medicine. Organoids offer new opportunities in regenerative medicine. For instance, liver organoids could provide an alternative to liver transplantation. Transplantation is currently the only effective treatment for liver failure, but requiring lifelong immunosuppression (Olgasi et al., 2020). Studies in animal models demonstrate that transplanted hepatocellular organoids successfully engraft and demonstrate functionality. This is evidenced by the detection of human liver markers, such as human albumin, in recipient models (Jalan-Sakrikar et al., 2022). The ability of organoids to generate safe, functional biological structures positions them as a transformative tools for regenerative therapies (Gu et al., 2023). Another notable example is research focused on generating insulin-secreting islet organoids from stem cells, which may represent an advancement in diabetes therapy (Yu et al., 2024). Despite the morphological and functional similarities between pancreatic organoids and native pancreatic beta cells, these structures have limitations. They exhibit impaired responsiveness to elevated blood sugar level and lack of some signature biomarkers characteristic of mature pancreatic beta cells (Yang et al., 2024). The various organoids and their uses are illustrated in Figure 2.

After discussing the various organoid types, we will now proceed to a detailed analysis of brain organoids. Over the past few years, brain organoids have become more important in neurological research. In brain organoid development, dual inhibition of SMAD signalling (Suppressor of Mothers against Decapentaplegic) is essential for inducing stem cells to differentiate into neuroectodermal tissue (Mulder et al., 2023). Creating organoids specific to different brain regions requires modulating signalling pathways such as WNT, SHH, FGF and BMP. This approach enables the modelling of diseases in various brain areas (Susaimanickam et al., 2022). To evaluate brain organoids, it is necessary to apply various techniques to assess the function and structure of the neuronal cells. Techniques like immunohistochemistry allow for the identification of markers and analysis of cellular organization within the organoid (Bell et al., 2025) Another example involves employing Transmission Electron Microscopy (TEM), which reveals neuronal connections and other neuronal structures (Noh et al., 2025). A key limitation in the development of brain organoids is their inability to replicate the human brain’s complexity due to the absence of critical cell types (e.g., immune cells) and the inability to mimic intricate microenvironmental signals (Harati and Wang, 2024).

Despite their potential, organoids face significant limitations. Currently, the size and proportions of organoids pose challenges for their future application in regenerative medicine. One of the main factors inhibiting their growth is the lack of vascularization. This limitation restricts gas exchange, the removal of metabolic waste products, and the delivery of essential nutrients. (Huang et al., 2021). As a result, the cultured tissues gradually undergo necrosis before reaching several hundred micrometres in size (Zhang et al., 2021b; Andrews and Kriegstein, 2022). Moreover, cultured organoids differ from original tissues. For example, analyses of kidney organoids revealed that up to 20% of cells are unrelated to kidneys (Romero-Guevara et al., 2020). Another challenge for scientists is finding an alternative to Matrigel, which is currently widely used. Matrigel is characterized by its high cost and variability between batches, which hinders the development of organoids (Sulaksono et al., 2024). Studies highlight key limitations that require further research to advance this technology. Overcoming these obstacles will pave the way for new era in patient care.

In response to these limitations, new solutions are emerging. One of these solutions uses microfluidic perfusion to monitor the microenvironment through precise regulation of fluid and nutrient supply (Saorin et al., 2023). Studies shows that certain perfusion systems incorporating microvessel printing reduce the risk of necrosis in large tissue models (Grebenyuk et al., 2023). To solve vascularization problems, organoids can be co-cultured with endothelial cells, which leads to the formation of vascular networks and improves oxygen and nutrient delivery (Zhao and Haddad, 2024).

Organoid research represents a breakthrough in regenerative medicine and disease modeling. However, researchers face many challenges. One of the foremost challenges in organoid development is standardizing culture conditions and ensuring reproducibility.

The heterogeneity of tissue sources, processing methods, and culture-medium components leads to differences in organoid culture outcomes (Guo et al., 2024). A prime example is the use of Matrigel, which is derived from mouse sarcoma. This leads to batch-to-batch variability that negatively impacts culture reproducibility. Finding an alternative organoid matrix that offers stable physical parameters for organoid cultivation is crucial (Huang et al., 2025). Researchers are currently developing synthetic alternatives to ECM such as nanomaterial hydrogels. It is important to guarantee their functionality, stability, and safety (Kim and Cha, 2025). The implementation of standardized guidelines is expected to promote the further practical development of organoids (Lee et al., 2024). To ensure comparability of organoid research results, new initiatives have been introduced. One of the initiatives is the Human Endoderm-Derived Organoid Cell Atlas (HEOCA), an atlas compiling data from organoid cultures that contains approximately one million cells. This resource will enable researchers to more easily compare organoids and develop new culture protocols in the future (Xu et al., 2025). Another project is the Organoid Cell Atlas, part of the Human Cell Atlas initiative. This effort is focused on standardizing cultivation methods, analysing data, and accelerating organoid research to advance this technology (Bock et al., 2020). In conclusion, key priorities include harmonizing tissue origins, standardizing growth media, establishing alternative organoid matrices, and improving global collaboration on research outcomes.

Stem cell therapy is one of the most promising and forward-looking fields in medicine. This therapy offers a vast array of possibilities for patients suffering from severe medical conditions. Regenerative medicine is likely the future of treating numerous diseases. It is only a matter of time before many of these techniques are applied in clinical practice. These techniques provide prospects not only for repairing and modifying diseased cells but extend further to organs such as the kidneys, lungs, heart, and liver.

Nevertheless, multiple factors must be considered before administering such therapy to a potential patient. Primarily, the sex of both the donor and recipient, their age, and hormonal status should be taken into account to optimize the clinical outcome. Clinical studies on cardiac cell therapy have revealed significant sex-based differences in therapeutic responses. Meta-analyses of trials utilizing autologous BMSCs have shown that therapy in postmenopausal women resulted in significantly better outcomes compared to age-matched men. The mechanisms underlying this differential response are likely associated with epigenetic regulation (Thej et al., 2024). The aging process of stem cells also plays a critical role in therapeutic efficacy. Aged stem cells exhibit reduced proliferative and regenerative capacities. Clinical trials have demonstrated that advanced age of both the donor and the recipient is associated with decreased treatment efficacy (Fan et al., 2010; Ahmed et al., 2017; Chen et al., 2021). In experimental models, younger MSCs demonstrated superior therapeutic effects in infarcted rats, as evidenced by improved left ventricular (LV) ejection fraction and reduced LV volume, compared to older MSCs (Fan et al., 2010). In another study focused on bone regeneration, younger mice showed a more favorable response to MSC therapy than older animals. Another crucial factor is the influence of sex hormones, which play a vital role in modulating stem cell function. Research has demonstrated that estrogens exert a beneficial effect on the migration and proliferation of endothelial progenitor cells toward dysfunctional or ischemic tissues, including cardiac muscle (Ray et al., 2008).

To date, numerous scientific studies verified in clinical trials have demonstrated the potential for treating various diseases, including diabetes, liver cirrhosis, and heart or kidney failure (Aly, 2020; Petrosyan et al., 2022).

Hundreds of millions of people worldwide suffer from diabetes. This disease is associated with problems such as diabetic nephropathy, retinopathy, and neuropathy (Sneddon et al., 2018). There are two main types of diabetes: type 1 (T1D) and type 2 (T2D). T1D is characterized by the destruction of beta cells through autoimmune processes, leading to a complete deficiency of insulin, whereas T2D is characterized by insulin resistance, resulting in a relative deficiency of insulin supply (Memon and Abdelalim, 2020; Bourgeois et al., 2021). Patients with T1D require exogenous insulin to survive. However, injecting appropriate amounts at the right time is highly complex due to a wide range of factors that must be considered, highlighting the need for new therapeutic approaches (Hogrebe et al., 2023). Beta cells can develop from human ESCs and iPSCs (Verhoeff et al., 2021). A Phase 1 clinical trial involving a single patient yielded promising results: the patient with T1D achieved insulin independence 75 days after iPSC transplantation, and no abnormalities were observed after 1 year (Wang S. et al., 2024). MSCs are also being explored for T1D therapy (de Klerk and Hebrok, 2021). These cells possess remarkable properties. It is hypothesized that, apart from differentiating into islet cells, they can also protect them by secreting various cytokines and growth factors. Moreover, MSCs exhibit immunomodulatory effects, which appear to be the primary anti-diabetic mechanism (Cho et al., 2018). A study involving seven newly diagnosed T1D patients used MSC therapy derived from adipose tissue in combination with vitamin D supplementation for 6 months. The study demonstrated that this treatment was safe and beneficial for beta cell functionality and maintenance (Dantas et al., 2021). While these treatment methods hold promise, significantly more research is needed to determine their potential risks and long-term effects conclusively.

Heart failure (HF) is typically defined as a syndrome characterized by clinical features that include both structural and functional cardiac abnormalities, usually associated with reduced cardiac output and/or increased intracardiac pressure (Chandramouli et al., 2022). Approximately 64 million people worldwide suffer from HF (Shahim et al., 2023). It is evident that research into new therapeutic options is of paramount importance. Various categories of stem cells can be used in HF therapy (Müller et al., 2018). A clinical study conducted on female Wistar rats compared the therapeutic properties of MSCs and human ESCs. Although no definitive superiority of one therapy over the other was determined, co-transplantation of both cell types led to better LV functionality preservation compared to single-cell treatment. This result confirms that using multiple stem cell types may be more beneficial than a single type, though further clinical studies are required to validate this hypothesis (Puymirat et al., 2008). Another study involving patients suffering from severe ischemic heart failure with depressed LV systolic function demonstrated that BMSCs could play a crucial role in treating this condition. Among the thirty-two patients who completed the study, after two intracoronary infusions of BMSCs, there was an improvement in LV filling and an enhancement in NYHA functional class. However, no significant improvement was observed in LV ejection fraction (Diederichsen et al., 2010).

Liver cirrhosis is a disease that may result from multiple factors, including obesity, alcoholism, viral hepatitis B and C, autoimmune disorders, or excessive accumulation of certain elements such as iron or copper (Ginès et al., 2021). This chronic condition is characterized by fibrosis and regeneration of liver nodules, leading to portal hypertension and liver failure (Geong et al., 2019). Liver cirrhosis ranks 14th among the most common causes of death worldwide. It cannot be classified as a single disease entity due to the existence of multiple clinical stages (Tsochatzis et al., 2014). Common therapeutic approaches include eliminating etiological factors, administering anti-inflammatory and immunosuppressive pharmacotherapy, inhibiting activation and promoting apoptosis of hepatic stellate cells, and using hepatoprotective drugs, among others (Zhou et al., 2014). However, over time, some patients require liver transplantation, which is often challenging due to the limited availability of donors (Schuppan and Afdhal, 2008; Tsuchiya et al., 2019). A promising alternative is the use of MSCs, which possess anti-inflammatory and hepatoprotective properties, prevent hepatic stellate cell activation, and polarize macrophages into an anti-inflammatory phenotype, ultimately improving liver function (Tsuchiya et al., 2019). A study involving eight patients with liver cirrhosis (caused by different factors) demonstrated that MSCs injection into the peripheral or portal vein was well tolerated and led to improved liver functionality (Kharaziha et al., 2009). Another study applying autologous MSC therapy to a group of 25 patients with HCV-induced liver cirrhosis (12 of whom completed the study) reaffirmed its safety and efficacy. However, the authors emphasized that MSCs did not reach the liver in satisfactory quantities, suggesting that the observed clinical improvements were due to the immunomodulatory functions of MSCs, which facilitated the clearance of HCV RNA (Kantarcioʇlu et al., 2015).

Acute kidney injury (AKI) is characterized by a sudden decline in glomerular filtration rate, resulting in the accumulation of metabolic waste products and ion homeostasis disturbances, often accompanied by increased serum creatinine levels (Hoste et al., 2018; Mercado et al., 2019; Ronco et al., 2019). AKI is associated with progressive renal dysfunction or continuous kidney impairment, which leads to irreversible nephron loss and may culminate in chronic kidney disease (CKD) (Kellum et al., 2021). AKI etiology can be classified as prerenal, renal, or postrenal (Mercado et al., 2019).

Complete renal function restoration is rarely achieved, making patients susceptible to complications that may result in mortality (Hoste et al., 2018). Thus, expanding medical knowledge on therapeutic options and their potential applications is crucial for improving the prognosis and quality of life of AKI patients. The use of human ESCs and iPSCs is being considered as a potential treatment due to their extraordinary regenerative potential, including for kidney tissues (Rota et al., 2019). However, there are currently insufficient studies to determine their utility in AKI treatment definitively. Studies conducted on mice have shown that MSCs can differentiate into renal tubular epithelium, demonstrating potential for kidney tissue regeneration. Moreover, MSCs exhibit the ability to secrete various cytokines, chemokines, and growth factors, further enhancing tissue regeneration and inducing cell proliferation (Yun and Lee, 2019). Unfortunately, human clinical studies using these treatment options remain scarce. Table 2 illustrates key findings.

Gene therapy represents a rapidly evolving branch of regenerative medicine. It is an advanced method that modifies the genome by introducing genetic material via a vector, with the aim of replacing a defective gene (Gonçalves and Paiva, 2017). Two main approaches are distinguished: in vivo, where the vector is directly administered into the patient’s body, and ex vivo, where cells are harvested from the patient, genetically modified outside the body, and then reintroduced (Arabi et al., 2022). The development of gene-editing technologies such as the CRISPR/Cas9 system has enabled precise modification of genetic material within stem cells (Razavi et al., 2024). The ability to alter DNA in human embryos represents a promising future in preventing congenital genetic disorders at the earliest stages of cellular development (Alnasser, 2021). One of the key achievements in gene therapy is the clinical use of Onasemnogene Abeparvovec, commercially known as Zolgensma, for the treatment of spinal muscular atrophy. In this disorder, a mutation in the SMN1 gene leads to the loss of alpha motor neurons, which control muscle function, resulting in progressive atrophy. The therapy involves the delivery of a functional copy of the SMN1 gene directly into the body, enabling production of essential proteins required for the survival and proper functioning of motor neurons (Ogbonmide et al., 2023; Shchaslyvyi et al., 2023). Another emerging application of gene therapy is in oncology, where genes can be introduced into tumors, immune cells are genetically modified to enhance anti-tumor responses, and cancer vaccines are being developed (Akbulut, 2020; Sayed et al., 2022). Notably, the integration of artificial intelligence (AI) in gene therapy could significantly enhance therapeutic outcomes. Through machine learning (ML), genome analysis can be optimized to select the most appropriate gene-editing tools (Asadi Sarabi et al., 2024). One example of ML application is the CRISPR-GEM algorithm. It enables prediction of optimal gene-editing targets, permitting precise selection of genes to achieve the intended therapeutic effect (Graham et al., 2024). A critical aspect of regeneration is the regulation of gene expression, as regenerative processes often recapitulate patterns observed during embryogenesis (Goldman and Poss, 2020). Numerous studies highlight the importance of understanding signaling pathways involved in gene expression related to organogenesis and tissue repair. Stem cells, with their unique capacity for self-renewal and differentiation into specialized cell types, play a fundamental role in regenerative medicine. The use of stem cells for the cultivation of organoids opens new possibilities for organ development studies, disease modeling, and the design of personalized therapies. Organoids, miniature structures allow for drug testing without the need for animal models (Margiana et al., 2022; Silva-Pedrosa et al., 2023; Park et al., 2024). One example of AI application in organoid culture is its ability to streamline the development of this technology. AI customizes personalized culture conditions, performs quality control, and carries out a detailed analysis of the collected data (Bai et al., 2023). Cell therapy is another widely employed technique in regenerative medicine. It involves the transplantation of autologous or allogeneic cells to enhance the regenerative potential of tissues with limited repair capacity. A notable example is the use of autologous chondrocytes for knee cartilage repair, where healthy cartilage cells are harvested from the patient, expanded in vitro, and reintroduced into the damaged site (El-Kadiry et al., 2021; Makarczyk, 2023). 3D bioprinting, a key innovation in tissue engineering, offers an alternative to traditional transplants. This technology enables the creation of biologically functional tissue structures by layering bio-ink composed of biomaterials compatible with the human body (Kantaros, 2022). Owing to its precision in cell placement, it is possible to produce tissues that mimic native human tissues in both form and function (Zhang et al., 2021). Bioprinting also holds great potential in bone tissue regeneration, facilitating fracture healing through the creation of scaffolds that accelerate the repair process and promote functional recovery (Maresca et al., 2023). Thanks to FRESH technology (Freeform Reversible Embedding of Suspended Hydrogels), an in vitro full-scale model of the human heart was successfully printed. This model reproduces the anatomical structure but exhibits no biological activity (Mirdamadi et al., 2020). Scientists studying in vivo bioprinting obtained tissue resembling an ear, in which histopathological examination revealed the presence of chondrocytes. This represents a significant step toward a novel technique for auricular reconstruction (Chen et al., 2020).

Now we will examine the differences in regulations concerning stem cells and ATMPs (advanced therapy medicinal products) To regulate clinical trials involving ATMPs, the EU introduced Regulation 1,394/2007, which streamlined the marketing-authorization procedure. ATMPs were defined as gene therapy products, somatic-cell therapy products, and tissue-engineered products (Priesner and Hildebrandt, 2022; Schuessler-Lenz et al., 2023). In the European Union, the law rigorously addresses safety and ethical matters in human-embryo research. In contrast, the United States generally adopts a more liberal approach to stem-cell research (Song S. J. et al., 2024) In 2017 in the United States, the FDA introduced the Regenerative Medicine Advanced Therapy (RMAT) designation, aimed at streamlining drug development and potentially accelerating the approval of these therapies (Vaggelas and Seimetz, 2019). Other programs in the United States include Fast Track and Breakthrough Therapy, which facilitate the implementation of new drugs (Iglesias-Lopez et al., 2020). An analysis of regulatory pathways in highly developed countries such as the United States, Japan, South Korea, and EU nations revealed the existence of accelerated pathways that enable more efficient approval of new therapies (Qiu et al., 2020). Between 2010 and 2020, only 15 ATMPs were approved in the EU, and 14 in the United States of America. Despite these advances, regulatory barriers obstruct the availability of these products. Collaboration among centres worldwide is essential to streamline ATMP regulation and approval (Warreth and Harris, 2020). In low- and middle-income countries, regulatory frameworks are the least developed. In most of these nations, there is a lack of guidelines aligned with their economic circumstances. Many may be unable to afford the development of advanced technologies such as gene therapies (Olayemi et al., 2017; Cornetta et al., 2022). As a result of legal gaps worldwide, the concept of cell tourism has emerged. In low-income countries, clinics offering stem-cell therapies of questionable efficacy have arisen. These clinics attract travellers from across the globe (Lyons et al., 2022). Legal oversight of these therapies and the introduction of regulations to limit this precedent are essential.

Despite significant technological advances, several technical limitations persist. In the case of cell-based therapies, one major challenge is cellular heterogeneity, which hampers the standardization of treatments across patient populations. Research has demonstrated that the application of such therapies may increase the risk of oncogenic transformation, for example, into hepatocellular carcinoma, highlighting the necessity for further safety evaluations (Petrosyan et al., 2022). Another concern is the elevated risk of rejection of transplanted stem cells due to the limited expression of tissue-specific antigens, which leads the recipient’s immune system to recognize these cells as foreign (Wang J. et al., 2024). The bioprinting of large organs, such as the heart, remains a considerable challenge due to the limited oxygen diffusion capacity through bioprinted tissue. The current resolution of 3D printing technologies does not allow for the fabrication of capillary networks, which are essential for the effective delivery of oxygen and nutrients to cells (Ramadan and Zourob, 2020). Additionally, the high costs associated with acquiring, maintaining, and operating 3D printers present a significant barrier to the clinical implementation of this technique (Saini et al., 2021). Another ongoing challenge is the development of suitable bioinks used in 3D bioprinting. These materials must be biodegradable, non-toxic, and compatible with the recipient’s cellular matrix (Thakur et al., 2023). Addressing issues such as host immune response, lack of vascularization, and ensuring the long-term stability of applied solutions is critical for the advancement of regenerative technologies (Yuan et al., 2025). Although gene therapy holds enormous therapeutic potential, numerous barriers hinder its widespread application, particularly those related to treatment costs. One example is the single-dose therapy for spinal muscular atrophy, which currently costs approximately two million euros per dose—a price inaccessible to many patients globally (Nuijten, 2022).

In conclusion, the synergy between medical embryology and regenerative medicine offers promising avenues for the treatment of various diseases. Continued interdisciplinary collaboration, alongside the advancement of current technologies, is essential for revolutionizing regenerative medicine and improving patient care. Future research should prioritize reducing production costs, increasing accessibility, and addressing immunological challenges and the durability of therapeutic approaches. Figure 3 shows challenges and limitations in this topic.