Organ damage and degenerative diseases are caused by cell death through ageing or loss of function and can seriously affect people’s lives. Examples of such conditions include degenerative diseases like Parkinson’s disease, Alzheimer’s disease, cirrhosis of the liver, and hearing loss, as well as injurious diseases such as myocardial infarction and skin burns. Organs such as the liver have high regenerative capacity and can regenerate sufficiently to maintain functional stability under certain circumstances (Michalopoulos and Bhushan, 2021). Mouse liver has demonstrated robust regeneration that supports liver function after partial hepatectomy (Zhang et al., 2021; Duan et al., 2022; Fan et al., 2022). Unfortunately, most tissues and organs do not have such regenerative capacity and cannot repair themselves after injury, eventually leading to loss of function. An example of this would be the hair cells in the cochlea, which do not regenerate once they are damaged, resulting in irreversible hearing loss (Warchol et al., 1993). These patients will require a cochlear implant, whereby an electronic device containing an array of electrodes and a receiver is surgically implanted into the patient’s inner ear to directly stimulate the auditory nerve and recover some of the patient’s hearing (Lenarz, 2017; Carlson, 2020; Weltin et al., 2022). Similarly, patients with damaged heart valves will require replacement with artificial valves made of metal or biological material in order to maintain heart function (Singh et al., 2019; Hofferberth et al., 2020; Dreyfus et al., 2022; Figure 1).

Artificial organ replacement is complex and patients can develop infections or immune rejection after transplantation (Ko et al., 2016; Bakir et al., 2022; Crespo-Leiro et al., 2022). Some inflammatory reactions, such as infectious endocarditis, can be fatal (Berisha et al., 2022). Therefore, there is a need for an immunogenically weak treatment that can effectively repair damaged tissues and organs in patients, aiming to minimize the occurrence of adverse events. Stem cells (SCs), which have great potential to differentiate into a variety of cells and can proliferate indefinitely (Jin, 2017). SCs can be induced to differentiate into specific cell or tissue types in vitro before transplanting into the patient to replace degenerated or necrotic cells (Czajkowski et al., 2019; Selvaraj et al., 2019; Gholamigeravand et al., 2021; Melton, 2021). In addition, SCs can secrete anti-inflammatory factors, cytokines, and exosomes to suppress the inflammatory response and improve the microenvironment of the damaged area, ultimately regulating cell proliferation and differentiation (Vakhshiteh et al., 2019; Veneruso et al., 2019; Lv et al., 2021). This review provides a comprehensive overview of the mechanistic studies and clinical applications of stem cell therapy, while also pointing out pertinent issues in the field.

SCs are cells with multi-directional differentiation potential while retaining the ability to replicate and renew themselves. They can be classified according to the extent of their differentiation capability (Table 1).

Totipotent stem cells (TSCs) are a type of stem cell with the remarkable ability to differentiate into any cell type within an organism, including the placental cells necessary for embryonic development (Malik and Wang, 2022). TSCs exist at the earliest stages of embryonic development, typically at the zygote stage after fertilization when a sperm cell fertilizes an egg cell. At this point, the zygote is formed, which possesses the potential to develop into a complete organism (Baumann, 2017). TSCs often have a number of unique molecular features, including lower DNA methylation (Smith et al., 2014) and activation of endogenous retroviral components (ERVs) (Hurst and Magiorkinis, 2017). The TSC state can be induced by several methods. A mixture of the GSK inhibitor 1-azakenpaullone, the retinoic acid analogue TTNPB, and the kinase blocker WS6 can induce mouse embryonic stem cells (ESCs) to exhibit a phenotype similar to that of TSCs at the fertilized egg and two-cell stages (Hu et al., 2023). Furthermore, heterochromatin remodeling has also been demonstrated to help establish allozygous-specific H3K4me3 structural domains, thus effectively facilitating the transformation of ESCs from pluripotency to allozygosity (Yang et al., 2022). The unique ability of TSCs to differentiate into whole organisms is of great interest to developmental biology and regenerative medicine research. Still, there are specific ethical issues associated with their use and study (Takahashi and Yamanaka, 2006).

Pluripotent stem cells (PSCs) are known for their exceptional ability to differentiate into various specialized cell types across all three germ layers: ectoderm, endoderm, and mesoderm. Specifically, PSCs exhibit a significant capacity for differentiation into ectodermal derivatives (Yilmaz and Benvenisty, 2019). This is evidenced by their ability to generate neurons, glial cells, neural crest cells, and other cell types originating from the ectoderm (Yang et al., 2022). They are typically derived from ESCs at the blastocyst stage (Varzideh et al., 2023), or induced pluripotent stem cells (iPSCs) by reprogramming adult cells with four transcription factors: Oct4, Sox2, Klf4, and c-Myc (Takahashi and Yamanaka, 2006). The most significant advantage of iPSCs is that they are derived from differentiated somatic cells, providing the advantages of SCs while significantly avoiding the ethical issues associated with TSCs and ESCs. The indefinite self-renewal capacity of iPSCs in culture allows the generation of an almost unlimited supply of specialized cells, offering a great potential for the study of early human development, disease modeling and regenerative therapies (Chandy et al., 2022; Cho et al., 2022; Varzideh et al., 2023).

Adult stem cells (ASCs), categorized as multipotent stem cells, demonstrate a more restricted capacity for differentiation compared to pluripotent stem cells. These cells reside in various tissues and organs throughout the body, playing a role in maintaining, repairing, and regenerating tissues within their specific microenvironments (Prentice, 2019). Unlike pluripotent stem cells, which possess a broader potential to differentiate into diverse cell types from multiple germ layers, ASCs are more constrained in their differentiation scope. They typically generate cell types specific to their tissue or organ of origin and are more specialized than pluripotent stem cells. Consequently, ASCs can only generate specific cell lineages corresponding to the exact tissue of their origin, differing from the broader differentiation potential exhibited by their pluripotent stem cell counterparts (Barker et al., 2010). The most common ASCs include hematopoietic stem cells (HSCs; responsible for the production of blood cells in the bone marrow) (Cho et al., 2022), mesenchymal stem cells (MSCs; differentiate into fat, cartilage, and bone cells in various tissues) (Wang et al., 2023), and neural stem cells (NSCs; differentiate into neurons, astrocytes, and oligodendrocytes of the nervous system) (Zholudeva et al., 2021). ASCs are characterized by their relative abundance in adult tissues, their ability to regulate the microenvironment by secreting specific signaling molecules, and their ease of isolation (Ma et al., 2014; Zholudeva et al., 2021). They are, therefore, of great value for tissue and organ repair and cancer therapy (Barker et al., 2010; Liu et al., 2023; Wang et al., 2023).

Unipotent stem cells (USCs) constitute a specialized subset among stem cells, distinguished by their notably restricted differentiation potential. In contrast to pluripotent or multipotent stem cells, which are capable of generating a variety of cell types, USCs are dedicated solely to generating a single specific cell type (Lilja et al., 2018). These cells predominantly reside in specific tissues or organs, fulfilling a crucial function in sustaining, repairing, and rejuvenating the particular tissue they inhabit (Thomson et al., 1998). USCs are commonly found in adult tissues and are able to continuously replenish particular cell populations that are consumed, playing a vital role in tissue maintenance and repair. Examples of USCs include basal cells in the skin (Lin and Lu, 2021) and satellite cells in the skeletal muscle (Mierzejewski et al., 2020). The potential of USCs in the treatment of diseases is limited by their single mode of differentiation.

To employ SCs for therapy, it is essential to first consider the source of the SCs. Considering their differentiation capacity and ethical issues, the most widely used SCs for treatment are currently PSCs and ASCs. ESCs are typically derived from the inner cell mass of a blastocyst (Bacakova et al., 2018). iPSCs are generated as described above and ASCs are derived from a variety of adult tissues, including adipose tissue, bone marrow, neural tissue, blood, skeletal muscle, etc., which provide convenient cell sources (Bacakova et al., 2018).

In order to maintain the multigenerational self-renewal capacity and differentiation ability of SCs, specialized culture systems are required to support this. Different biomaterials in the culture medium can impact the differentiation potential and the amplification capacity of SCs. Media containing oligopeptide-grafted hydrogels have been shown to enhance the proliferation and pluripotency of human ESCs and iPSCs (Chen et al., 2017). The use of culture systems containing human plasma and human embryo extracts maximizes the number of passages while maintaining the self-renewal and differentiation potential of iPSCs (Wang et al., 2012). In addition, compared to 2D cultures, 3D culture systems can better mimic the microenvironment of SCs in vivo and enhance the stemness of different SC species (Al Madhoun et al., 2016; Thakur et al., 2022). For example, a combination of 3D cell culture and natural brain tissue extracts can accelerate the differentiation of SCs into neuronal phenotypes (Azizi et al., 2018).

For SC therapy, the most crucial step is to direct the differentiation of SCs toward the target cell type by regulating culture conditions and signaling molecules. This can be achieved by mimicking the signaling pathways and microenvironment during embryonic development. Studies have shown that inner ear development is closely linked to fibroblast growth factor (FGF) signaling (Alvarez et al., 2003). Stimulating this pathway in human ESCs can induce two types of ear progenitor cells that differentiate into inner ear hair-like cells and auditory neurons, respectively (Chen et al., 2012). Mild activation of Wnt signaling promotes the differentiation of MSCs into chondrogenic cells (Schizas et al., 2021). The adhesion and growth characteristics of cells can also be influenced by culturing them on the surface of nanomaterial composites, which triggers mechanotransduction-induced changes in gene expression through changes in cytoskeletal structure. Mouse kidney-derived SCs have been induced to differentiate into podocytes or proximal tubular cells in this way (MacGregor-Ramiasa et al., 2017). In contrast, in neural differentiation of SCs, chemical inducers or growth factors, including retinoic acid (RA), brain-derived neurotrophic factor (BDNF), and nerve growth factor (NGF), are required (Gupta and Singh, 2022). Finally, the most direct way to induce directed differentiation of SCs is through transcription factor regulation. In addition to the above-mentioned transcription factors that can reprogram fibroblasts to iPSC, different transcription factors are required to induce differentiation of the required cell population (Ng et al., 2021). Overexpression of NR5A1 and RUNNX1 or RUNX2 induces the differentiation of iPSC into human ovarian granulosa cells (Pierson Smela et al., 2023). The combined action of transcription factors, GATA4, Tbx5, MEF2C, and Hand2, reprograms mouse tail-tip and cardiac fibroblasts to cardiomyocyte-like cells with cardiac function in vitro (Song et al., 2012). Overexpression of GFI1, Pou4f3, and ATOH1 directly induces the transformation of human fibroblasts into inner ear hair cell lineages (Duran Alonso et al., 2018).

Following combination and optimization of the above methods, directed differentiation of SCs can be achieved. After ensuring the validity and stability of the differentiation process, cell identification and functional validation, including cell phenotype analysis, gene expression analysis and functional assessment, are required to confirm that the differentiated cell types are as expected, thus ensuring that the resulting cells have the desired properties and functions.

Finally, differentiated and validated SCs are transplanted into patients via different vectors and scaffolds. At this stage, enhancing the retention of SCs in tissues is critical to the efficacy of the therapy. The most commonly used modality is injecting a saline suspension of the SCs directly into the target organ or tissue (Mousaei Ghasroldasht et al., 2022). However, due to the low adhesion of saline, only a small number of cells may remain in the tissue following injection. Therefore, a medium with higher adhesion properties is needed as a vehicle for SCs transplantation, such as a hydrogel (Nayagam et al., 2012; Niu et al., 2019). Nanohybrid hydrogels containing sufated glycosaminoglycan-based polyelectrolyte complex nanoparticles (PCN) are able to mimic extracellular matrices and contain a variety of bioactive factors to improve the implantation rate of neural SCs, while enabling cellular responses after central nervous system injury (Jian et al., 2018). Gelatin methacrylate (GelMA)/sodium alginate (Alg) (GelMA/Alg) hydrogels also contribute to the reduction of cellular damage after the implantation of neural SCs (Chen et al., 2023). Hydrogels of different compositions have played essential roles in cardiac infarction, skin regeneration, liver regeneration, etc., (Mardpour et al., 2019; Ke et al., 2020; Gong et al., 2022).

In summary, a complete SC therapeutic process comprises three significant aspects: SC generation and amplification, targeted differentiation and application, and selection of the optimal technical route to achieve regeneration and functional recovery of damaged tissues and organs is required for different clinical areas (Figure 2).

Cell therapy for organ and tissue regeneration encompasses a range of methods aimed at repairing or regenerating damaged tissues or organs by introducing exogenous cells into the body. Stem cell therapies, among other approaches, constitute a significant aspect of this field, harnessing the regenerative potential of specific cell populations to restore tissue function in conditions ranging from degenerative diseases to injuries.

In the current phase of rapid development in SC-based therapies, it is still important not to overlook some of the problems they pose. The first issue to be considered is the source of SCs as there are ethical and legal considerations (King and Perrin, 2014). The use of ESCs is subjected to ethical debates and legal limits, while the acquisition and amplification of adult SCs are technically tricky and have quality control issues (Chen et al., 2020). Another issue arising from prolonged continuous culture is the loss of cell viability, leading to reduced proliferative and differentiation capabilities. Addressing this necessitates the use of new materials, such as silica nanoparticles, for the long-term preservation of stem cells in a desiccated state (Gallina et al., 2015). Secondly, the efficiency and direction of differentiation of SCs is a major issue as this determines the effectiveness of the treatment. Directed differentiation is a complex process that we do not yet fully understand and many factors, such as cell culture conditions, cytokines, and signaling pathways can influence the process (Kim et al., 2016). Therefore, more research is still required to better control the direction and quality of differentiation of SCs to prevent adverse events such as tumorigenesis (Andrews et al., 2022). Another crucial determinant of stem cell therapy is the capacity to target cellular migration. Prior to assuming their role in differentiation, stem cells must be effectively delivered to the intended site. Currently, most stem cell therapeutic approaches employ intravenous drug delivery, which exhibits limited efficacy in facilitating targeted migration from blood circulation to tissues (Liu et al., 2020). Survival of the transplanted SCs is another major issue facing SC therapy. SC therapy, characterized by its low expression of MHC and HLA, holds the potential to achieve reduced immunogenicity and significantly enhance the suppression of the graft-versus-host response. However, owing to the limitations in pre-expansion technology associated with SC therapy, its immune privilege is progressively compromised. Upon infusion into the human body, the presence of inflammatory factors within the body further escalates the immunogenicity of SCs, thereby elevating the risk of rejection (Barrachina et al., 2017). Cell survival and growth after transplantation are influenced by the host immune system, since the host immune responses to the allogeneic cells directly contributes to graft rejection (Sanz-Ruiz and Fernández-Avilés, 2018). A possible solution for allo-rejection is to knockout immune-related genes by gene editing to generate immune-compatible SCs (Ye et al., 2020). Further research will be required to resolve these and other challenges to successfully translate SCs therapies to the clinics.

Since Ernst Haeckel first identified SCs in 1868, the development of these cells had gone through several critical stages. Initially, SCs were isolated and identified from various tissues, followed by the development of iPSCs and the combination of gene editing with SCs, leading to the progressive refinement of SC therapy. The most direct application for SCs is cell-based therapy, owing to their multi-directional differentiation capabilities. This approach involves the injection of SCs, both allogeneic and genetically modified autologous SCs, into the sites of disease or injury to promote tissue regeneration and functional recovery. The administration of cardiopoietic stem cell injection, induced by a cardiogenic growth factor, effectively enhanced cardiac function in patients with chronic heart failure during a clinical trial. Notably, no adverse effects on the heart or systemic toxicity were observed among the subjects (Bartunek et al., 2013). The deficiency of arylsulfatase A (ARSA), an inherited disorder known as metachromatic leukodystrophy (MLD), can be addressed through in vitro lentiviral transduction of autologous hematopoietic stem cells with cDNA encoding ARSA. This approach leads to enhanced ARSA activity and reduced brain damage (Fumagalli et al., 2022). An alternative application is cell-free therapy, utilizing the secretory ability of SCs, is also a critical approach. SC secreted factors can modulate the target tissue cells and the microenvironment, including the immune microenvironment and angiogenesis. Allogeneic expanded adipose-derived mesenchymal stem cells (Cx601) have been proven to secrete immunomodulators and anti-inflammatory factors, and have certain potential in the treatment of inflammatory bowel disease, especially in the treatment of anal fistula in patients with Crohn’s disease (Panés et al., 2018). The latest therapeutic approach is to use SCs as vehicles for the targeted delivery of effectors, drugs, and genes into damaged tissues or tumors to exert the appropriate regulatory effects. The potential of oncolytic adenovirus as an antitumor therapy is limited in central nervous system tumors due to the presence of the blood–brain barrier. However, a clinical trial demonstrated that delivery via neural stem cells (NSC) facilitated safe and efficient transportation of oncolytic adenovirus to the tumor site (Fares et al., 2021).

However, SC therapy also faces a number of safety issues. Allogeneic SCs can trigger the patient’s immune system, leading to graft rejection, while excessive proliferation and differentiation of transplanted SCs may lead to tumor formation. Ensuring the safety of SC therapy is, therefore, a significant challenge. It is also crucial in SC therapy to ensure that SCs can differentiate directionally into target cell types and maintain their function and stability. Further research and improved differentiation techniques are needed to ensure that differentiated cells have the desired characteristics.

In conclusion, as an essential therapeutic tool in regenerative medicine, SC therapy plays a vital role in a number of ways, both in the cells themselves and in their secreted components. With a better understanding of the properties and functions of SCs, it is expected that more diseases and injuries will be able to benefit from SC therapy.

JW: Writing – original draft. GD: Writing – original draft. SW: Project administration, Supervision, Writing – review & editing. SL: Data curation, Investigation, Writing – review & editing. PS: Formal analysis, Investigation, Writing – review & editing. KL: Data curation, Formal analysis, Writing – review & editing. XX: Funding acquisition, Project administration, Writing – review & editing. ZH: Conceptualization, Funding acquisition, Writing – review & editing.