Cancer stem cells and niches: challenges in immunotherapy resistance

Immune checkpoints

Immune checkpoints expressed on tumor cell surfaces interact with ligands on immune cells, suppressing their activity and fostering an immunosuppressive TME. Herein, we provide an overview of immune checkpoints regulation involved in CSCs immune evasion (Fig. 1). A prominent example is PD-L1, which binds to programmed cell death protein-1 (PD-1) on CD8⁺ T cells, thereby inhibiting T-cell activation and facilitating immune evasion [28]. This mechanism is particularly prominent in CSCs. For instance, the stemness-related transcription factor MYC directly binds to the promoter region of PD-L1 in hepatocellular carcinoma (HCC), driving its transcription and enhancing the immunosuppressive microenvironment. Conversely, the inactivation of MYC leads to a downregulation of PD-L1 expression and strengthens anti-tumor immunity [29]. Similarly, quiescin sulfhydryl oxidase 1 (QSOX1) has been shown to promote the expression of PD-L1 in dormant esophageal cancer stem cells by increasing the levels of reactive oxygen species, thereby facilitating the exclusion of CD8⁺ T cells [24]. PD-L1 itself also forms a positive feedback loop with the β-catenin signaling pathway, promoting cancer progression by maintaining and expanding tumor stem cells [30]. This interaction underscores the dual role of PD-L1 in both immune evasion and the maintenance of CSC characteristics. In bladder cancer, the stem cell marker aldehyde dehydrogenase 1A1 (ALDH1A1) is positively correlated with PD-L1 expression, linking stemness with immune evasion in this context [31]. Elevated PD-L1 levels have also been reported in CSCs from breast cancer, colon cancer, and human neck squamous cell carcinoma (HNSCC), further highlighting its pivotal role in immune escape [32–36].

Beyond PD-L1, other immune checkpoints play pivotal roles in CSC-mediated immune evasion. For instance, B7-H4, another immune checkpoint, has also been found to exhibit elevated expression levels in CD133⁺ glioblastoma stem cells compared to non-CSCs [37]. B7-H4 suppresses T-cell proliferation and cytokine production, further impairing anti-tumor immunity. Similarly, B7-H4 and B7-H3 are utilized to evade immune surveillance during the progression and metastasis of breast CSCs and SCC stem cells, respectively [38, 39]. CD80, a ligand for the cytotoxic T-lymphocyte antigen 4 (CTLA-4), is expressed in stem cells of HNSCC in response to transforming growth factor beta (TGF-β), thereby weakening CTLs toxicity and promoting tumor immune resistance and relapse [40]. Emerging immune checkpoint molecules, such as CD155, have also been implicated in CSC-mediated immune evasion. CD155 interacts with the inhibitory receptor T cell immunoreceptor with Ig and immunoreceptor tyrosine-based inhibitory domains (TIGIT) on T cells, mediates immune escape driven by CD49f-high tumor-initiating cells (TICs) [41, 42]. Similarly, CD24, widely recognized as a CSC marker, functions as an immune checkpoint by directly binding to Siglec-10 on tumor-associated macrophages (TAMs), thereby inhibiting phagocytosis [43, 44]. CD47, as a classic “don’t eat me” signal molecule, is upregulated in circulating hematopoietic stem cells and leukemia cells, protecting them from phagocytosis by macrophages [45, 46]. Notably, recent studies have demonstrated that targeting CD47 in combination with PD-L1 blockade can synergistically enhance anti-tumor immunity, highlighting the potential for dual immune checkpoint inhibition in CSC-targeted therapies [47, 48]. In conclusion, CSCs exploit a diverse array of immune checkpoint pathways as a strategy to evade immune surveillance, thereby promoting tumor progression and immune resistance. Elucidating the mechanisms of immune escape in CSCs is essential for developing more effective therapies to overcome their immunosuppressive effects, improve treatment outcomes and overcoming immune resistance.

Antigen processing and presentation

For T cells to recognize tumor cells and generate an immune response, the binding of MHC-I antigens to T cell receptor (TCR) on CTLs is essential [49]. However, prior to this recognition, a series of intricate processes must take place for the successful presentation of tumor antigens. First, tumor antigens are degraded in the proteasome, followed by transport to the endoplasmic reticulum via transporter proteins, where they are loaded onto MHC-I molecules. These MHC-I molecules then travel to the cell surface, where they present the tumor-derived peptides to T cells [50, 51]. Without this precise mechanism of antigen processing and presentation, T cells would lack the necessary cues for identifying and targeting tumor cells. CSCs regulate tumor antigens both by controlling the production of the antigens themselves and by modulating MHC molecules (Fig. 1). Similar to tissue-resident stem cells, which downregulate MHC class I and transporter associated with antigen processing (TAP) proteins to maintain tissue homeostasis, CSCs employ analogous mechanisms to evade immune surveillance [52]. For instance, polycomb repressive complex 2 (PRC2) has been shown to suppresses MHC-I expression at the transcriptional level through epigenetic mechanisms, affecting antigen processing in small cell lung cancer and neuroblastoma [53]. Moreover, in squamous cell carcinoma (SCC), a subset of CSCs responding to TGFβ signaling shows further suppression of antigen presentation, thereby promoting immune escape [40]. Furthermore, tumor spheres cultured from 12 human solid tumor cell lines have demonstrated that the downregulation or loss of human leukocyte antigen class I/II (HLA-I/-II) molecules in CSCs, combined with an absence of response to interferon-gamma (IFN-γ) stimulation, results in impaired antigen presentation. This suggests that impaired antigen presentation due to the downregulation of HLA surface expression may be one of the reasons for CSC immune evasion [54]. A similar pattern of MHC-I downregulation is observed in glioblastoma (GBM) CSCs, where although MHC-I molecules are expressed at lower levels compared to non-CSCs, their upregulation upon stimulation with IFN-α and IFN-γ is limited. Moreover, upon stimulation with IFN-α and IFN-γ, the increase in MHC class I molecules and their heavy chains (i.e., A-HC) as well as β2-microglobulin was greater in non-CSCs than in CSCs [55]. In both colorectal cancer and glioblastoma, the reduced expression of MHC class I molecules on CSCs makes them more susceptible to NK cell-mediated killing compared to their differentiated counterparts, emphasizing the altered immune evasion strategies of CSCs [56–59]. CSCs in other malignancies, including lung cancer, HCC, and melanoma, also exhibit similar immune evasion tactics by downregulating MHC-I molecules, thereby impeding the presentation of neoantigens to T cells [60–62]. A similar phenomenon can be observed in head and HNSCC. CD44⁺ HNSCC cells exhibit CSC characteristics, along with downregulated expression of HLA-A2, HLA class II molecules, MHC-I and TAP2, indicating impaired antigen presentation and processing functions in these CSCs [63, 64]. These alterations further reinforce the immune-resistant properties of CSCs and their ability to thrive in an immune-suppressive environment. Additionally, melanoma CSCs not only downregulate MHC-related molecules but also reduce the expression of tumor-associated antigens, providing an additional layer of immune evasion [60, 65]. In breast cancer, CSCs exhibit low expression of LCOR, and through a mechanism independent of the IFN signaling pathway, interact with the IFN-stimulated response element, leading to the suppression of genes involved in the antigen processing/presentation machinery, thereby promoting immune evasion and resistance to ICB [66]. In summary, CSCs adopt sophisticated strategies to evade immune detection by disrupting antigen presentation and modulating MHC-related pathways. These adaptations not only hinder T cell recognition but also foster the overall immunosuppressive environment, where CSCs persist and contribute to tumor progression. Therefore, understanding and targeting these immune evasion mechanisms are pivotal for the development of novel therapeutic strategies aimed at overcoming CSC-mediated immune resistance.

Regulation of secretome

Intercellular communication mediated by cytokines and extracellular vesicles (EVs) plays a crucial role in enabling tumors to interact with their microenvironment. The secretome of CSCs is crucial for immune evasion, invasive progression, and drug resistance [67]. Next, we will primarily outline the regulation of the secretome of CSCs on the niche (Fig. 1). Interleukin-33 (IL-33), under normal physiological conditions, is primarily localized in the nucleus of CSCs. However, in TGF-β-responsive TICs of SCC, IL-33 is released into the extracellular space through nuclear factor erythroid 2-related factor 2 (NRF2)-mediated antioxidant mechanisms. IL-33 derived from TICs induces the differentiation of immature bone marrow cells into FcεRIα⁺ macrophages, which contribute to the formation of an immunosuppressive microenvironment [68]. Whereas in HCC-CSCs, the inactivation of P53 leads to the aberrant high-level secretion of IL-34, which induces a population of CD36⁺ foam-like pro-tumor macrophages, thereby promoting tumor immune escape [69]. In cholangiocarcinoma-CSCs, IL-13, IL-34, and osteoactivin are secreted into the microenvironment to promote macrophage differentiation, promoting immune suppression and tumor progression [20]. In ovarian cancer, CSCs have been shown to increase the secretion of pro-tumor cytokines such as IL-10 and WNT, which in turn promote the activation of M2 macrophages, supporting immune evasion [70]. Upregulated phosphorylation of signal transducer and activator of transcription 3 (STAT3) in glioma CSCs promotes the production of IL-6, IL-10, colony-stimulating factor (CSF)-1, TGF-β1, and MΦ inhibitory cytokine-1, which are cytokines that can recruit and polarize macrophages/microglia phagocytosis to form an immunosuppressive microenvironment, thereby promoting immune evasion [37, 71]. In colorectal cancer (CRC), CD133⁺ CSCs protect themselves from chemotherapy-induced cell death by secreting IL-4 [72]. Meanwhile, IL-4 induces the formation of M2 macrophages in CRC, contributing to the establishment of an immunosuppressive microenvironment [73]. Membrane-anchored IL-30 expressed by CRC-CSCs has been shown to be associated with lymphocyte infiltration and survival in CRC patients [74]. Additionally, in breast CSCs, the autocrine IL-30 shapes the immune landscape by regulating the expression of IL-23 and CXCL10, which are crucial for immune response modulation [75]. The secretion of macrophage colony-stimulating factor by CSCs, under the regulation of the transcription factor IFN regulatory factor 5 (IRF5), promotes the generation of pro-tumor M2 macrophages, further supporting tumor growth and immune evasion [76]. In non-small cell lung cancer (NSCLC) -CSCs, upregulation of ubiquitin-specific protease 17 (USP17) enhances the production of cytokines TNF-α, IL-1β, and IL-6, promoting macrophage infiltration [77]. Similarly, in bladder cancer-CSCs, mutations causing the loss of lysine demethylase 6 A (KDM6A) function promote the secretion of IL-6 and CCL2, driving macrophage recruitment and contributing to tumor progression [78].

Vascular endothelial growth factor (VEGF) plays a key role in promoting vascular permeability and angiogenesis and binds to VEGF receptors on endothelial cells, thereby stimulating angiogenesis [79]. CSCs can also regulate the immune microenvironment by secreting VEGF, contributing to tumor vascularization and immunotherapy resistance [80–82]. Chemokines, another major class of secreted proteins, are integral in connecting tumor cells to their surrounding microenvironment [83]. For example, CD49f has been identified as a marker of HCC-CSCs, which secrete CXCL2 to recruit neutrophils and acquire immune privilege, evading immune surveillance [41]. Similarly, CXCL1, as an autocrine chemokine of breast CSCs, primarily triggers tumor progression and immune evasion-related pathways by regulating tumor-promoting and immunosuppressive factors [84]. Treg cells, as the main subset of suppressive T cells, play a central role in tumor immunobiology. Meanwhile, CSCs secrete chemokines CCL1, CCL2, and CCL5 to actively recruit Treg cells [26, 85–88]. In glioblastoma, histamine, a metabolite preferentially secreted by glioma stem cells (GSCs), regulates endothelial cell activity, thereby promoting angiogenesis in the GSC microenvironment [89]. Moreover, the Wnt/β-catenin signaling pathway plays multiple roles in stem cells and CSCs, including promoting the secretion of chemokines [90]. In lymphoma, overactivation of the Wnt/β-catenin signaling pathway promotes the chemotaxis of lymphoma cells toward endothelial cells, enhancing adhesion and promoting tumor progression [91]. In melanoma, lung cancer, and colon cancer, activation of the Wnt/β-catenin signaling inhibits T cell infiltration and promotes tumor growth and therapeutic resistance by regulating the secretion of CCL4 and CCL5 [92, 93]. In breast cancer, CSCs secrete higher levels of IL-6, IL-8, CSF2, and CCL2, which activate their own NF-κB and Wnt/β-catenin pathways, forming an autocrine inflammatory feedback loop that further enriches drug-resistant cancer cells and CSCs [94]. In GBM-CSCs, Wnt-induced signaling protein 1, activated by Wnt/β-catenin signaling, is a secreted protein that can promote tumor progression by recruiting tumor-supportive TAMs [95].

Additionally, CSCs also release another significant type of membrane-bound EVs into the TME [96]. These EVs efficiently transfer signaling molecules from the originating cells to neighboring cells, thereby influencing their characteristics, such as promoting metastasis, stimulating angiogenesis, and modulating immune responses [27, 97]. Exosomes, a subset of EVs secreted by GBM tumor stem cells, are enriched with proteins from the STAT3 signaling pathway and can activate PD-L1 expression in CD14⁺ monocytes, promoting their differentiation into M2 macrophages [98]. Tumor-derived exosomes, rich in PD-L1, also contribute to the systemic exhaustion of CD8⁺ T cells, further promoting immune evasion [99]. In summary, CSCs utilize a variety of secreted factors, including cytokines, chemokines, and EVs, to shape the TME and facilitate immune evasion. Through autocrine and paracrine signaling, CSCs not only promote immune suppression but also enhance tumor progression, metastasis, and resistance to treatment. The interplay between these secreted molecules and the immune cells, is crucial for the establishment of an immunosuppressive microenvironment that supports tumor survival and recurrence.

Epigenetic reprogramming and chromatin architecture

Epigenetic reprogramming is one of the fundamental characteristics of tumors, particularly in the context of their plasticity, which involves alterations in DNA methylation, histone modifications, and chromatin architecture [100–103]. These modifications are essential not only for tumor initiation and progression but also for the immune evasion mechanisms orchestrated by CSCs, which contribute to the creation of an immunosuppressive TME (Fig. 2A).

Cancer-testis antigen and oncofetal protein

The process of immune evasion mediated by tumor cells shares similarities with immune tolerance mediated by organs such as the embryo and testes (Fig. 2B). CSCs often hijack characteristics associated with the testes and embryo to evade attacks by the immune system. CTAs are a class of multifunctional proteins that exhibit unique expression patterns in germline cells and various types of cancer cells. These CTAs are involved in regulating cellular processes related to development, stem cell differentiation, and tumor initiation [134]. In addition, CTAs are also considered unique stem cell markers. The CTA score generated from 201 CTA genes, has been shown to have a strong positive correlation with the stemness score within tumors. Furthermore, this CTA score displays a negative correlation with immune infiltration characteristics, a relationship that holds true across all eight major tumor types [135]. For example, one specific cancer-testis antigen, KK-LC-1, demonstrates a negative correlation with CD4⁺ T cells, macrophages, and dendritic cells in lung adenocarcinoma (LUAD) [136]. Macrophages and dendritic cells, crucial for antigen presentation, are often suppressed in the presence of high levels of such antigens. In breast cancer, the expression of cancer-testis antigen PRAME is associated with poorer survival prognosis, particularly in immune-unfavorable tumors. Silencing preferentially expressed antigen in melanoma (PRAME) reduces the expression of immune checkpoints and ligands, such as PD-1, lymphocyte activation gene 3 (LAG3), PD-L1, CD86, galectin-9 (Gal-9), and V-domain immunoglobulin suppressor of T-cell activation (VISTA) [137]. Interestingly, many embryonic genes and developmental signaling pathways that regulate the characteristics of embryonic stem cells (ESCs) are reactivated in CSCs. These are referred to as “oncofetal drivers,” linking tumors to ESCs [138]. For instance, OCT4, a key transcription factor, is highly expressed in liver tumors, breast cancer, and lung cancer [139–141]. Similarly, SOX2 is overexpressed in osteosarcoma, glioblastoma, and SCC [142–144], while NANOG is highly expressed in brain tumors, colon cancer, and liver tumors. These oncofetal proteins are pivotal stemness-associated transcription factors [145–147]. These classic oncofetal protein have all been proven to be associated with an immunosuppressive microenvironment. In glioblastoma, for instance, OCT4 and SOX2 function as transcription factors that regulate multiple immunosuppressive checkpoints, cytokines, and chemokines, thereby promoting the establishment of an immunosuppressive microenvironment [148]. Furthermore, recent studies have identified additional oncofetal proteins that further regulate the positive correlation between cancer stemness and immune evasion. For instance, heterogeneous nuclear ribonucleoprotein M (HNRNPM) influences β-catenin through the alternative splicing of methyl-CpG-binding domain (MBD2) in HCC-CSCs, thereby modulating immune evasion [149]. In summary, CSCs employ these mechanisms to evade immune detection, and this ability to “revert” to an embryonic-like state is one of the defining features of CSCs, known as their plasticity. This plasticity enables CSCs to persist and thrive despite immune surveillance and treatment pressures, ultimately contributing to tumor progression, metastasis, and therapy resistance.

Immune cells in the CSC niche

The interaction between immune cells within the CSC niche and CSCs plays a crucial role in promoting immune evasion and tumor progression [152]. Various immune cells, including macrophages, T cells, and MDSCs, contribute to maintaining CSC properties and facilitating immune escape, thereby enhancing tumor aggressiveness and treatment resistance (Fig. 3). For instance, FcεRIα⁺ macrophages secrete TGF-β, which acts on SCC-CSCs to promote the invasive progression and drug resistance of SCC [68]. Furthermore, using single-cell spatial transcriptomics technology, it was discovered that in residual lesions of HCC, PD-L1⁺ M2-like macrophages interact with stem-like tumor cells and release TGFβ1, which mediates the persistence of stem-like tumor cells and the exhaustion of CD8⁺ T cells, ultimately leading to HCC recurrence [14]. TAMs are also crucial in sustaining CSC populations in various cancers. For example, in breast cancer, TAMs support CSC survival through direct interaction between Ephrin and the EPH receptor A4. This triggers CSCs to secrete inflammatory cytokines such as IL-1, IL-8, and IL-6, which further support tumor growth and immune resistance [22, 153]. Similarly, MDSCs provide a supportive niche for CSCs by inhibiting immune cell activity in the TME. In ovarian cancer, MDSCs has been shown to enhance CSC-like traits by upregulating microRNA-101, which drives the expression of genes linked to stemness, thus promoting immune evasion and tumor progression [154]. Within the niche, MDSCs further promote tumor immune evasion by inducing STAT3 phosphorylation through IL6 and activating NOTCH via nitric oxide, which enhances the stem cell-like properties of breast cancer cells and inhibits T cell activation [155]. Similarly, in CRC-CSCs, MDSCs promote stemness by secreting exosomal S100A9. This mechanism is primarily achieved through the activation of the STAT and NF-kB pathways in CSCs [156]. Spatial transcriptomics analysis in HCC has demonstrated that CSCs co-localize with SPP1⁺ macrophages, with the SPP1-CD44 and SPP1-ITGA/ITGB ligand-receptor pairs identified as key mediators of this interaction. Interestingly, this communication leads to the exclusion of CD8⁺ T cells from tumor regions, further exacerbating the immune-exhaustive environment [157].

IFNγ, a key cytokine produced by T cells during immunotherapy, can directly convert non-CSCs into CSCs and sustain their stemness [8]. This process has been linked to branched-chain aminotransferase 1 (BCAT1), which serves as an intermediary molecule in the IFNγ-induced polyoma middle T plasticity transformation. A similar phenomenon has also been observed in NSCLC, where low-dose IFNγ can maintain stemness through the PI3K/AKT/NOTCH1 pathway, thereby enhancing tumor malignancy [158]. Furthermore, IL-17 from Th17 cells or CD4⁺ T cells can also promote the stemness of ovarian cancer, pancreatic cancer, and gastric cancer CSCs by activating the NF-kβ, p38 MAPK, and STAT3 pathways [159–161]. Beyond secreting cytokines, T cells regulate CSC stemness through direct cell-to-cell contact mechanisms in breast cancer. Among them, the cognate non-lytic interactions between CD8⁺ T cells and cancer cells can promote the stemness of cancer cells [162]. In preclinical models, such as in a mouse SCC model driven by HRAS^G12V, single-cell transcriptomics and lineage tracing have shown that abnormal crosstalk between CSCs and their niche promotes the elevation of leptin receptor levels, mediated by stromal TGF-β and vascularly-mediated tissue leptin. This leads to the activation of the LEPR-leptin signaling pathway, which in turn triggers the PI3K-AKT-mTOR pathway in CSCs, driving malignant invasion and metastasis [163]. CAFs represent a highly heterogeneous cellular component within the TME, characterized by remarkable plasticity. They play a crucial role in maintaining CSC stemness and facilitating immune evasion [164]. In bladder cancer, CAF subpopulations characterized by the overexpression of SLC14A1 can induce and maintain stemness through type I IFN signaling, leading to treatment resistance and recurrence [165]. Additionally, CD10⁺GPR77⁺ CAFs sustain cancer stemness and chemoresistance by secreting IL-6 and IL-8 [166]. These complex interactions within the CSC niche establish an immunosuppressive microenvironment that supports CSC survival, immune evasion, and tumor recurrence, highlighting the need to unravel these mechanisms to develop targeted therapies that overcome treatment resistance and enhance therapeutic outcomes.

Mechanotransduction signaling in the CSC niche contributes to immune evasion of cancer

Abnormal tumor biomechanics represents a pivotal physical characteristic of tumors, and its influence on maintaining tumor stemness is increasingly recognized [167–170]. The ECM, a complex network composed of proteins and glycosaminoglycans, plays a critical role in all physiological processes of multicellular organisms. Its mechanical properties, such as stiffness and elasticity, can significantly impact cellular behaviors, including proliferation, differentiation, invasion, and migration, through mechanotransduction signaling [171, 172]. These mechanical signals are vital in regulating the TME and the behavior of CSCs (Fig. 3). SMYD3 mediates the trimethylation of H3K4 at the CSDE1 locus, thereby influencing the immunogenicity of TICs and promoting their immune evasion. This process is regulated by mechanotransduction through the ECM and cell-to-cell contact [129]. Discoidin domain receptor 1 (DDR1), a collagen receptor with tyrosine kinase activity, contributes to immune exclusion by promoting the alignment and remodeling of ECM [173]. DDR1 signaling is particularly relevant in HCC-CSCs, where the co-receptor CD44 enhances type I collagen-induced DDR1 activation, facilitating the recruitment of PP2A. This, in turn, dephosphorylates MST1/2, leading to the activation of YAP and its translocation to the nucleus, where it maintains the stem cell phenotype [174]. YAP and TAZ, two key downstream effectors of the Hippo signaling pathway, are highly responsive to mechanical cues from the ECM and function as mechanosensors, detecting forces such as shear stress, cell shape, and matrix stiffness, and transduce these signals into specific transcriptional profiles that regulate stem cell behavior and tissue regeneration [175]. In the TME, increased ECM stiffness inhibits T cell cytotoxicity and proliferative capacity through YAP signaling [176]. However, some studies have shown that softer ECM can attenuate T-cell cytotoxicity, as cell softness may prevent pore formation induced by CTLs, thereby enabling them to evade CTL-mediated cell killing [177]. Hardening soft cancer cells and stem cell-like cancer cells can achieve effective killing induced by CTLs [169]. This duality highlights the heterogeneity of the TME and suggests that ECM properties can be tailored to either promote or hinder immune responses. In addition to the YAP/TAZ signaling pathway, deregulated integrin signaling in tumors is also closely associated with mechanotransduction, stemness, epithelial plasticity, and therapeutic resistance [178]. Ligand-bound integrins (primarily the αLβ2 subtype, LFA-1) serve as spatial signals to attract lytic granules containing perforin and granzymes and induce their fusion with the plasma membrane to release their contents. Thus, lymphocytes utilize an integrin-dependent mechanical inspection mechanism to enhance their cytotoxic capacity and precision [179]. Although this phenomenon has not been studied in CSCs, it has been reported that integrins can regulate tumor stemness and chemoresistance via the FAK/TAZ pathway [180]. In summary, it is reasonable to speculate that integrin-mediated mechanical forces may influence the tumor stem cell niche by regulating stemness and immune evasion. The PIEZO signaling pathway can also sense mechanical signals to determine stem cell fate and lineage differentiation, a process primarily dependent on the influx of Ca2⁺ signals [181]. The latest studies using transgenic mice combined with single-cell sequencing have revealed that PIEZO channels play a decisive role in the intestinal stem cell niche [182]. Notably, Piezo1 in macrophages can also sense changes in stiffness, enhancing CD11b expression and Ca²⁺ influx, thereby regulating macrophage morphology and function [183, 184]. This mechanism may be involved in modulating tumor immunity.

In summary, tumor biomechanics—through mechanotransduction pathways like YAP/TAZ, integrin signaling, and PIEZO—plays a critical role in shaping the TME and regulating CSC behavior. The mechanical properties of the CSC niche not only influence stem cell maintenance and tissue regeneration but also modulate immune cell function. The dynamic interplay between biomechanical forces and immune responses presents an exciting avenue for future research, with the potential to develop innovative approaches that target both the mechanical and immunological aspects of tumor biology.

CSC niche-driven metabolic reprogramming contributes to immune evasion of cancer

Tumors commonly exhibit increased glycolytic flux under aerobic conditions, a phenomenon known as the Warburg effect, which is crucial for sustaining their malignant phenotype and promoting uncontrolled proliferation [185]. However, CSCs display distinct metabolic characteristics compared to non-CSCs, not only in terms of their phenotype and function but also at the metabolic level. Unlike their non-CSC counterparts, which predominantly rely on glycolysis, CSCs exhibit a preference for mitochondrial oxidative phosphorylation (OXPHOS), a key metabolic pathway for ATP production in normal cells [186, 187]. This shift toward OXPHOS is believed to confer certain advantages, such as increased resistance to glycolysis inhibitors, and the ability to utilize mitochondrial fatty acid oxidation (FAO) for energy production, thereby promoting cellular survival and metabolic flexibility [187–189]. Consequently, CSCs with OXPHOS characteristics may gain an evolutionary advantage in the TME due to their more efficient utilization of limited nutrients. This metabolic adaptation allows CSCs to thrive even under nutrient-limited conditions, providing them with an evolutionary advantage. Interestingly, lactate, which is produced by more differentiated non-CSCs relying on glycolysis, can serve as valuable fuel for OXPHOS in CSCs, establishing a metabolic symbiosis system [187, 190]. This interdependence creates a metabolic microenvironment that enhances the survival and stemness properties of CSCs, ultimately contributing to tumor progression. However, similar to the plasticity inherent in stem cells, the metabolic characteristics of CSCs are not fixed. Glycolytic and OXPHOS traits can coexist within CSCs, with the balance between the two pathways likely influenced by the cellular state and external cues from the TME [191–195]. For instance, in the quiescent state of CSCs, glycolysis plays a crucial role in sustaining their antioxidative capacity, maintaining stemness, and supporting self-renewal [196, 197]. Moreover, tumors consume glucose in large amounts through glycolysis, competitively limiting T cell effector function, thereby promoting tumor progression [198, 199]. Although direct evidence linking this competitive metabolic mechanism to the CSC niche remains elusive, it is an area of ongoing investigation. Notably, factors such as PPARγ, HIF-1α, and mTOR, which are known to regulate metabolic pathways in immune cells, have also been implicated in the regulation of Treg differentiation, suggesting a complex interplay between CSCs, immune cells, and metabolic regulation [200–203]. Tregs, which are key modulators of immune responses, could potentially influence the immune landscape within the CSC niche, contributing to immune evasion and tumor progression [204]. Next, we will primarily outline the effects of energy sources and metabolites within the niche on CSCs’ immune evasion (Fig. 4).

A fascinating example of metabolic reprogramming occurs in pancreatic ductal adenocarcinoma (PDAC), when the exogenous carbon source is switched from glucose to galactose, PDAC cells rely more on OXPHOS for energy production. This metabolic shift promotes the enrichment of CSCs, as evidenced by increased expression of CSC markers and pluripotency genes, enhanced invasiveness, and upregulation of immune evasion factors such as PDL1, CD206, and CD47 [205]. Additionally, mitochondrial FAO has been identified as a major source of bioenergy and, similar to other metabolic pathways implicated in cancer, its dysregulation supports various cancer hallmarks, including proliferation, survival, stemness, drug resistance, and metastasis [206]. Furthermore, FAO is reprogrammed in cancer-associated immune and host cells, potentially contributing to the creation of an immunosuppressive, tumor-promoting microenvironment [207]. For instance, Leptin derived from adipocytes maintains the self-renewal and therapeutic resistance of breast cancer stem cells (BCSCs) by activating the JAK/STAT3 pathway, which subsequently upregulates the expression of carnitine palmitoyltransferase 1B (CPT1B), a key enzyme in FAO [208]. Additionally, the FAO metabolite acetyl-CoA enhances the acetylation level of H3K27Ac in the stemness gene (NANOG, SOX2, and OCT4) promoters, thereby increasing stemness and lymph node metastasis in the lipid-rich lymph node environment [209].

Other metabolites in the CSC niche have also been shown to influence immune evasion. For example, kynurenine, catalyzed by indoleamine 2,3 dioxygenase 1 (IDO1) and tryptophan 2,3 dioxygenase 2 (TDO2), can promote cancer progression by impairing host immune surveillance [210, 211]. Mechanistically, TDO2-mediated immune evasion and the maintenance of stem cell characteristics promote liver metastasis of colorectal cancer through the regulation of PD-L1 by mediating aryl hydrocarbon receptor (AHR) activity [211]. Neurotransmitter 5-hydroxytryptamine (5-HT), a metabolite of tryptophan, regulates the Wnt/β-catenin signaling pathway and drives the self-renewal of CSCs in CRC by binding to 5-HT receptors HTR1B, HTR1D, and HTR1F on CSCs [212]. Previous studies have also demonstrated the significant role of 5-HT in regulating tumor immunity [213]. The abnormal metabolic reprogramming of vitamin B3 can promote the secretion of pro-stemness and immunosuppressive factors from CAFs, thereby increasing the abundance of CSCs and immunosuppressive cells while reducing the infiltration of CTLs [214]. Mechanistically, the abnormal metabolism of vitamin B3 leads to an increase in NNMT and a decrease in SAM, which in turn promotes the upregulation of IL6, IL8, CXCL1, CCL2, CCL5, and CXCL12 through epigenetic reprogramming. In conclusion, CSCs adopt distinct metabolic adaptations, including metabolic plasticity and niche metabolite interactions, which not only sustain their survival in the TME but also enhance their stemness and immune evasion, distinguishing them from non-CSCs.