The immune system has an invaluable role in the resistance to pathogenic infections and the maintenance of homeostasis. An adequate immune response to an encountered danger is an eligible and a deliberate balance-saving mechanism (1–4). However, an amplified and out-of-control immune response can act as a self-driving positive feedback loop and can have severe implications and is tightly connected to the development of a wide range of diseases (5, 6). Some of them have their source in the chronic inflammatory process, while others result from the buildup of an abnormal immune response against particular cells, thus leading to the development of autoimmune diseases. There is no doubt that the progression of inflammation conduces to disease aggravation and deterioration of patient status. It is legitimate to externally attenuate the immune response because an increasing number of evidence indicates that chronic inflammation, manifested, i.e., by an increase in the levels of proinflammatory cytokines, is involved in the pathogenesis of many diseases including asthma, rheumatoid arthritis, hepatitis, heart disease, and even some of the most prevalent disorders of the central nervous system (CNS) such as Alzheimer’s disease, epilepsy, depression, and schizophrenia. Immunomodulation is a potent branch, with a steady progress in pharmacokinetics and pharmacodynamics. There are many difficulties that need to be faced such as attenuation of the side effects in pharmacological treatment (7, 8) or toxicity in the newest interventions (9). However, so far, immunomodulation is successfully applied in the clinic (10, 11).

The immune system is a multiscale system that involves genes, molecules, cells, and organs, organized in complex networks of synergistic interactions and aimed at combating various types of threats to the organism (12). Our systematically expanding knowledge about this complex network has enabled us to more selectively influence its individual components, allowing a more effective treatment of many diseases. For example, in oncology, it is possible to enhance the natural ability of human T cells to recognize tumor cells (11, 13). The paracrine anti-inflammatory properties of mesenchymal stem cells (MSCs) are used in the treatment of some diseases (described further in a subsection in this article). Another possibility is to inactivate specific proinflammatory factors (i.e., TNF-α, IL-6) using monoclonal antibodies (14, 15). This clinical branch also benefits from novel methods of antibody design and production (16, 17). Monoclonal antibodies can be also used as agonists to imitate immunomodulatory signaling on antigen-presenting cells. We also can inhibit proinflammatory factors by blocking their release (18–20). There is also a wide range of pharmaceuticals modulating inflammasome functioning (21, 22). Also, well-established immunomodulatory therapies, such as corticosteroids, non-steroidal anti-inflammatory drugs, histamine antagonists, and interferons, have a new face in the context of research aiming to improve their efficiency. In brief, there are various potential targets in immunomodulatory intervention which efficiently modulate the immune response at its many stages. Immunomodulation, based on our knowledge about immunity, has not yet been fully explored but constitutes a perfect tool or an adjunct to regulate some disease progression.

In this review, we introduce the mechanisms of immunity and immunomodulation strategies used in basic science and in the clinic. Immunomodulation strategies are described cross-sectionally starting from well-established pharmaceutical interventions, through biological strategies, to the most recent scientific achievements as genome editing and regenerative medicine tools.

Innate immunity is the first line of defense against pathogens. This kind of immune response is not selective and does not result in immune memory; however, it is rapid in reaction. It involves epithelial barriers and phagocytes, which are a group of myeloid cells, composed of neutrophils, dendritic cells, blood monocytes, and tissue macrophages. The innate immune response involves also the complement system, natural killer (NK) cells, and tissue-resident immune cells (23). An example of the regulation of this type of immunity is paracrine secretion of residual MSCs, which can modulate the functions of tissue macrophages, which is discussed further in this article.

In case of the presence of signals, which indicate infections or death of neighboring cells, phagocytes can intercept pathogen-associated molecular patterns (PAMPs) or damage/danger-associated molecular patterns (DAMPs) by pattern recognition receptors (PRRs) on their surface (24–26). The pathogen is internalized by the phagocyte and digested down into component proteins, which are afterward exposed to the cells of the adaptive immune system via major histocompatibility complex II (MHCII) on the surface of the phagocyte. Simultaneously, to multiply the immune response, at the initial moment of PRR activation, nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) is activated (27, 28) and initiates the transcription of pro-IL-1β and pro-IL-18 and the inactive form of inflammasomes such as inflammasome NLRP3. This multimeric protein is involved in the activation of caspase-1 enzyme, which in turn converts proinflammatory cytokines to their active form. However, only in case of additional stimuli, which indicate a potential threat to homeostasis, i.e., potassium efflux, calcium influx, mitochondrial damage, or the presence of reactive oxygen species (ROS), cathepsins, or extracellular ATP, the dimerization of caspase-1 occurs, and pro-IL-1β and pro-IL-18 can be activated via proteolytic cleavage. Mature cytokines are secreted and activate the subsequent inflammatory pathways. A group of monoclonal antibodies is used as interleukin inhibitors in the clinic in diseases such as atopic dermatitis (dupilumab), plaque psoriasis (ustekinumab, ixekizumab), and COVID-19 infections (tocilizumab). In a phase 2 clinical trial, the IL-6 receptor inhibitor sarilumab was used in combination with other monoclonal antibodies in patients with melanoma (NCT05428007). Interestingly, the NLRP3-mediated inflammatory pathway is the potential target of the beneficial and anti-inflammatory effects of some antidepressants, i.e., tianeptine, venlafaxine, fluoxetine, or reboxetine (29). Fingolimod (FTY-720), a modulator of sphingosine-1-phosphate (S1P) receptor used in the therapy of multiple sclerosis, is known to block NLRP3 inflammasome assembly by downregulating NLRP3, apoptosis-associated speck-like protein (ASC), and caspase-1, thus reducing the levels of TNF-α, IL-6, and IL-1β and promoting microglia polarization into the M2 phenotype (22, 30). Aside from the activation of proinflammatory cytokines, caspase-1 is also responsible for cleaving pro-gasdermin D proteins. The products of this cleavage are involved in a specific cell death—pyroptosis (31, 32).

Cellular innate immunity is also composed of NK cells, which have the ability to release factors to induce cell apoptosis. They do not require activation by specific antigens and are able to respond immediately when exposed to a pathogen. Their action is inhibited by major histocompatibility complex I (MHCI) which is expressed on the surface of all nucleated cells of the body and protects them from destructive NK-cell action. During some viral infections or carcinogenesis, body cells could suppress MHCI expression which leads them to be recognized as non-self and to be eliminated by NK cells (33, 34). The action of NK cells can be modulated by IL-22 secreted by T lymphocytes which indirectly suppress the function of NK cells against cancer cells by modulating CD155 expression on the cancer cells’ surface (35).

The innate immune system is not specific and creates a first line of barrier against pathogens. However, in case of an escalated infection caused by a specific pathogen, a proper, more specific immune response mechanism needs to be activated. This is done via antigen presentation to the adaptive immune system by antigen-presenting cells (APCs), i.e., dendritic cells, B cells, and macrophages. Dendritic cells with digested pathogens travel via circulation to the lymph nodes and present their antigens to the T-cell receptor (TCR) of naive T helper cells (Th0) within MHCII complexes on their surfaces. To become fully activated, Th0 cells also require co-stimulation from APCs, in the form of B7 proteins (CD80 or CD86) expressed on the dendritic cell surface, which binds to the T cell CD28. This promotes Th0 cell differentiation either into Th1 cells, which promote cytotoxic T cells and cell-mediated immunity, or Th2 cells, which promote B cells and humoral immunity (36, 37).

Activation of the innate immune system promotes induction of adaptive immunity because cellular innate immune system components, such as dendritic cells and also cytokines, are able to stimulate the proliferation, differentiation, and survival of lymphocytes.

Adaptive immunity involves mostly lymphocytes, namely, T cells and B cells. It provides long-lasting immunity with highly specific clonal responses to a large diversity of antigens. The adaptive immune response is self-limiting and quickly declines as the infection is eliminated as it generates immune memory and self-reactivity.

The development and progression of the inflammatory process is tightly connected with the innate immune system action. The main initial features of inflammation include vasodilation and increased blood flow. This leads to erythema and an increase in the temperature of the inflammation-affected area. Increased vascular permeability allows the inflammatory cells to infiltrate from the blood flow to the tissue, causing tissue edema and swelling. Inflammatory mediators such as bradykinins and prostaglandins increase pain sensitivity and cause hyperalgesia (63). Cleaning up of the infected area is possible because of the chemotaxis ability of neutrophils triggered by a gradient of chemokines released by the damaged tissue (64) ( Figure 3 ). Fever and “flu-like” symptoms like hot flushes, sweats, chills, rigors, headache, and fatigue force an infected organism to save energy to fight with the pathogen and are induced by an increase in inflammatory markers like CRP and ferritin. During an innate inflammatory response, upregulation of co-stimulatory molecules such as MHCII and B7 occurs to encourage activation of the adaptive immune system. An overactive or chronic inflammatory response lies at the core of numerous pathological conditions, and thus, many of the immunomodulatory drugs used today are aimed specifically at suppressing inflammation.

Immunosuppressants can modulate multiple sites of the immune response, starting with the influence on the transcription rate of genes encoding proteins necessary for lymphocyte action and then with the regulation of the final stages of the humoral response, e.g., regulation of the antibody titer and the degree of their affinity. They are applied in different clinical branches, including the treatment of autoimmune diseases and transplantations, using, i.e., corticosteroids, non-steroidal anti-inflammatory drugs (NSAIDs), histamine antagonists (HAs), and also a wide range of cellular signaling inhibitors.

Current biologic strategies to modulate the action of the immune system rely on the application of either the naturally occurring or modified components of the innate and adaptive immune response, like interferons or monoclonal antibodies.

MSCs were discovered in 1970 (152), and they are multipotent adult cells with self-renewing properties. These cells have immunomodulatory features; therefore, MSCs are potential tools in treating inflammation-related diseases. The common sources of MSCs are the bone marrow (BMMSCs), adipose tissue (ATMSCs), and perinatal tissues, such as Wharton’s jelly (WJMSCs) and amniotic fluid (AFMSCs). The features of MSCs are high, multilineage proliferative potential; low immunogenicity; specific migration to the sites of tissue injury; and immunomodulatory potential. Paracrine secretion triggers anti-apoptotic activity, angiogenesis, and anti-fibrosis and reverses remodeling (153).

The Mesenchymal and Tissue Stem Cell Committee of the International Society for Cellular Therapy determines that MSCs could be differentiated by their phenotypic features, like the expression of CD105, CD73, and CD90 and the lack of CD34, CD45, CD14 or CD11b, CD79a or CD19, and HLA-DR expression. MSCs could be also separated by their morphological properties, i.e., adherent, fibroblast-like morphology in standard culture conditions, and they are able to cluster into fibroblast colonies, potent to multidirectional differentiation at least into osteoblasts, adipocytes, and chondrocytes (154). The biological role of MSCs is supportive: derivates of MSCs (osteoblasts and fibroblasts) co-create marrow niches for hematopoietic cells. Stromal cells take part in hematopoietic regulation; they secrete growth factors, chemokines, and cytokines (GM-CSF, LIF, SCF, thrombopoietin, IL-8, IL-10, IL-11, IL-14, IL-15). MSCs are involved in tissue regeneration and immunomodulation. They enable the settlement of the marrow environment by transplanted hematopoietic stem cells.

In a low concentration of environmental INF-γ or TNF-α, MSCs are polarized into the M1 phenotype. They express a high level of TLR4 to which LPS can be ligated. Then, MSCs M1 secrete low levels of IDO, NO, and PGE2 but high levels of CXCL9, CXCL10, MIP-1a/β, and Regulated upon Activation, Normal T Cell Expressed and Secreted (RANTES) (155, 156). This activates T0 cells to become T cytotoxic cells with a high expression of CCR5 and CXCR3. Within the negative feedback loop, activated T cytotoxic cell secretes a high level of IFN-γ and TNF-α to initiate an anti-inflammatory pathway of MSCs. Collaterally, MSCs M1 stimulate monocytes into the M1 phenotype (CD86 positive) (157), which secretes a high level of IFN-γ and TNF-α to the environment.

MSCs exhibit infinitesimal immunogenicity. They have a low expression of HLA-I, which increases after exposition to INF-γ, and they also have a low expression of HLA-II. MSCs exhibit a lack of antigen-specific response because of the lack of the co-stimulant molecules CD80 and CD86. MSCs express non-specific HLA-I antigens, which are involved in the tolerogenic process occurring in the fetal–maternal interface: HLA-G, HLA-G5 (induction of regulator T cells and suppression of INF-γ production from natural killer cells), HLA-E, and HLA-F (158). WJMSCs exhibit a higher expression of HLA-G antigens in comparison to other types of MSCs. MSCs have a high and multidirectional proliferation potential in vitro. They spontaneously migrate to the area of injury (159). MSCs produce components of the extracellular matrix: collagen types I, III, IV, and VI; fibronectin; laminin; hyaluronan; and proteoglycans. They suppress the proliferation of alloT lymphocytes after transplantation. There are no antibody anti-surface proteins of MSCs. In the presence of MSCs, mitogen-stimulated lymphocytes do not proliferate. Transplantation of MSCs does not cause tolerance induction for HLA antigens of given stem cells (160, 161).

MSCs have a wide range of impacts on T cells. They inhibit the proliferation of T cells in response to mitogens, anti-CD3, anti-CD28, or alloantigens. MSCs induce anergy of naive T cells, induce T regulator cell expansion, and inhibit the expression of CD25 and CD69 (inhibition of activation). They also inhibit the alloreactivation of cytotoxic T cells. The immunomodulatory action of MSCs is conditioned by the environment of the cells. In a high concentration of environmental INF-γ or TNF-α, MSCs are polarized into the M2 phenotype. They express a high level of TLR3 to which dsRNA can be ligated (162). Then, MSCs M2 secrete high levels of IDO, NO, PGE2, HGF, and TGF-β. TGF-β, PGE2, and sHLA-G factors evoke T0 cells to become T regulator cells (CD4, CD25, FoxP3 positive). Additionally, IDO and PGE2 secreted by MSCs M2 stimulate monocytes into the M2 phenotype (CD206 and CD163 positive), which in turn secrete anti-inflammatory cytokines (Il-6, IL-10, and CCL-18) (157).

MSCs are applied in clinical settings. By May 2022, there were 1,022 registered clinical trials worldwide involving over 10,000 patients investigating the therapeutic potential of MSCs. Their differentiation into osteoblasts is used in osteonecrosis and osteogenesis imperfecta treatment. MSCs can be used in the reconstruction of the cartilage, e.g., nose, ears, or trachea. MSCs after transplantation accelerate hematopoietic reconstitution in hematopoietic cancers. They also accelerate hematopoietic reconstitution in non-hematopoietic cancers, like breast cancer. MSCs are widely used in orthopedics: implantation of an endoprosthesis along with MSCs and hydroxyapatite accelerates bone regeneration.

The trophic factors secreted by MSCs have beneficial effects on the central nervous system, thus making MSC-based therapies suitable candidates for the treatment of CNS injuries and neurodegenerative diseases. In light of the current scientific data, the MSC secretome was shown to display both direct and indirect influences on neuronal and glial survival and differentiation (163), peripheral nerve regeneration (164), and potency to induce neurite growth (165). On one hand, the MSC exosomes possess immunomodulatory properties and can have an impact on M2-type macrophages in the injured spinal cord (166).

In lower limb ischemia, MSC transplantation can result in the improvement of vascularity (167). MSCs when used on hard-to-heal wounds can result in skin reconstruction and closing of the wound.

MSCs are also used to treat cardiomyopathy or myocardial infarction. The mechanism of action of MSCs in cardiovascular diseases is proposed to be direct cell–cell contact (respiratory chain salvage and stimulation of differentiation). They directly differentiate into cardiomyocytes and smooth muscle cells. It is speculated that they can also differentiate into endothelial cells. The efficacy of MSCs in cardiac diseases was proven by many preclinical and clinical trials (168–176).

MSCs also inhibit inflammation by anti-graft-versus-host disease action (153, 177). They could be widely used in the treatment of steroid-resistant acute graft-versus-host disease (GvHD) by their immunosuppressive properties (178) and also by healing damaged intestinal epithelium (179); however, in the case of antigen-mismatched bone marrow transplantation, donor MSCs can induce chronic GvHD by interacting with residual host T cells. Prochymal was first approved by the Food and Drug Administration against GvHD and is composed of BM-MSCs (180); it is mostly used in patients non-responsive to steroids and other immunosuppressive agents (181). Another drug based on MSCs—Alofisel—is based on expanded adipose-derived stem cells (182) and has been approved by the European Medicines Agency as therapy for complex perianal fistulas. Both of these drugs are allogeneic and derived from healthy adult individuals (183) (Table 2).

The regenerative potential of MSCs is still intensively explored. There is a wide MSC secretome spectrum to explore in order to broaden its application in regenerative medicine. There are many challenges and translational considerations in the clinical usage of MSCs, which include the following: MSC donor (age, gender, health status), tissue source (umbilical cord, adipose tissue, bone marrow), MSC manufacturing variables (isolation and expansion methods, culture conditions, cryopreservation, banking approach), MSC administration (patient population, route of delivery, dosage, frequency of dosage, dosing interval, using of biomaterials), and recipients (patient variability, disease severity, immune factors, host cytotoxicity, and responses). All the above variables need to be considered in the context of cell-based therapy applications in the clinic.

A broad spectrum of diseases is related to an amplified immune response. The immune system is complex and multifactorial, providing footholds for possible immunomodulatory intervention. In this review, we outlined immunomodulators, such as the widely used corticosteroids, non-steroidal anti-inflammatory drugs, histamine antagonists, cellular signaling inhibitors, monoclonal antibodies, and interferons, and also explored the immunomodulatory properties of hMSCs or novel strategies with great potential to be implemented as future immune-related disease therapeutics, i.e., genomic strategies in immunomodulation (CRISPR–Cas9 and RNA interference).

The classic pharmacological approach, using drug classes such as corticosteroids, NSAIDs, and histamine antagonists, is the oldest known immunomodulatory intervention from all those described in our review, and over the years, these drugs have proven successful in the suppression of inflammatory processes in patients. However, it does not mean that are the best established and best known, since their action is not tissue- or cell-selective and thus can result in a plethora of side effects, especially after their long-term usage. The design of new compounds from these drug classes is currently aimed mostly at the improvement of their selectivity as well as pharmacodynamic and pharmacokinetic properties in comparison with currently used molecules. An interesting branch of small molecule immunomodulatory drugs is compounds that act on intracellular pathways, as inhibitors of selected protein kinases, thus allowing a more specific and targeted therapeutic approach.

Even greater selectivity toward targeting particular cellular and molecular components of the immune system has been achieved with antibody therapies and the introduction of mAb-based drugs in the 1990s, which are used in patients suffering from autoimmune diseases, such as Crohn’s disease, rheumatoid arthritis, lupus, psoriasis, and MS (110). Currently, the greatest challenge in mAb therapeutics is mainly their immunogenicity and the formation of antidrug antibodies which decrease their clinical efficacy; however, more refined methods of mAb production and the development of bispecific mAbs, which would also influence endogenous B-cell action (112), appear to be promising strategies of improving their action. It is, however, also worth pointing out that the therapeutic potential of mAbs is limited to extracellular targets, such as cytokines or receptors and other transmembrane proteins, and thus, they cannot directly target intracellular proteins.

Genomic strategies, which include RNAi using siRNAs or miRNAs and CRISPR–Cas9 on the other hand, allow for the selective targeting of every cellular protein, including transcription factors. Additionally, CRISPR–Cas9 gene editing also enables a stable replacement of particular DNA sequences within the genome. The modification of T cells by CRISPR–Cas9 in cancer has refreshed and augmented our existing therapeutic strategies (184). In 2018, the US Food and Drug Administration approved the first therapeutic agent which implements the mechanism of RNAi. However, in the case of both interventions, there are some heavy limitations, which need to be challenged, before they could be widely used in the treatment of immune-related disorders, such as their effective and specific transfer to a selected cell type in a complex eukaryotic organism and the prevention of off-target effects. On the other hand, the CRISPR–Cas9 system may offer a significant advantage also in basic preclinical research, aimed at expanding our knowledge about different autoimmune diseases, since it constitutes a convenient tool for identifying new targets related to their pathogenesis (185).

Last but not least, hMSCs constitute a promising tool in the modulation of the immune status of injured tissue. The undisputed advantage of MSCs is their low immunogenicity: MSCs constitute an inexhaustible source of the immunomodulatory secretome. Researchers and clinicians, however, need to face many challenges to unify outcomes arising from both basal research and clinical trials in terms of the gender, age, and health of the MSC donor; tissue source; MSC manufacturing conditions; MSC route of delivery; dosage and pattern of administration; and recipients (patient variability, disease severity, immune factors, host cytotoxicity, and responses) (186). All the above variables need to be considered in the context of cell-based therapy application in the clinic.

Immunomodulation is a challenging branch of medical science, and with the steady improvements in drug design, immunomodulators have become more selective and attenuate the side effects of novel pharmacological treatments (7–9). There are limitations in improving manufacturing capabilities: chemical formulation and delivery mechanisms of recently designed highly selective molecules to be safer and more efficacious therapeutic compounds (14, 18, 19). As in the case of treating diseases in general, these substantive advances need to be combined with a more judicious selection of disease indications and better-validated intervention pathways (148). In summary, introducing new therapeutic approaches to treating inflammatory and autoimmune diseases requires ongoing collaboration between clinics and basic research to better understand the complex interactions between individual components of the immune system to identify potentially new targets for more specific therapeutic interventions.

MSt and MM: conceptualization and design. MSt, JD, and MM: data collection and analysis. MSt, JD, PM, and MSo: preparation of the original draft. MSt, JD, PM, MSo, and MM: revision and approval of the subsequent drafts of the manuscript. All authors contributed to the article and approved the submitted version.