New insight in treating autoimmune diseases by targeting autophagy

Abstract

Autophagy is a highly conserved biological process in eukaryotes, which degrades cellular misfolded proteins, damaged organelles and invasive pathogens in the lysosome-dependent manner. Autoimmune diseases caused by genetic elements, environments and aberrant immune responses severely impact patients’ living quality and even threaten life. Recently, numerous studies have reported autophagy can regulate immune responses, and play an important role in autoimmune diseases. In this review, we summarised the features of autophagy and autophagy-related genes, enumerated some autophagy-related genes involved in autoimmune diseases, and further overviewed how to treat autoimmune diseases through targeting autophagy. Finally, we outlooked the prospect of relieving and curing autoimmune diseases by targeting autophagy pathway.

Keywords:

• Autoimmune diseases
• autophagy
• ATGs
• treatments strategies

1. Overview of autophagy

Autophagy is a self-eating process which was defined by Christian de Duve in 1967 [1]. Autophagy is highly conserved in eukaryotes and essential to maintain homeostasis and supply nutrition to host cell under starvation. Autophagy degrades cargo molecules like aggregated proteins, damaged organelles and invasive pathogens through the lysosome-dependent manner [2–4]. According to specific degradation mechanisms, autophagy is classified into three sections: macroautophagy, chaperone-mediated autophagy (CMA) and microautophagy.

1.1. Macroautophagy

Macroautophagy (also referred as autophagy) is well-studied. The remarkable feature of autophagy is that the substrates are sequestered within cytosolic double-membrane vesicles termed autophagosomes. This process includes phagophore formation, autophagosome formation, and autolysosome formation [5]. Phagophore is double-membrane structure originating from endoplasmic reticulum (ER) or mitochondria. Phagophore recruits cytoplasmic components, further prolongs or expands membrane and ultimately closes to form complete autophagosome. Outer membrane of autophagosomes can fuse with lysosomes to form autolysosomes where various hydrolytic enzymes hydrolyse macromolecules, then the degradation products would recycle into the cytoplasm (Figure 1).

Figure 1. Illustration of the three types of autophagy. (a) In the macroautophagy process, abnormally aggregated protein and microbes are recruited to phagophore, and then phagophore can prolong and enclose to form autophagosomes, and finally the autophagosomes fuse with lysosomes for degradation. (b) In chaperone-mediated autophagy (CMA), proteins containing KFERQ motif keep unfolding with the help of chaperone, and bind to LAMP2A on lysosomes. Proteins translocate from cytosol through LAMP2A into lysosomes lumen one by one. (c) In microautophagy, invagination of lysosome membranes directly engulfs cargoes for degradation.

Previously, autophagy was considered a non-selective process. However, a lot of recent studies have reported that autophagy could selectively degrade cargos such as damaged mitochondria (mitophagy), ER (ER-phagy) and aggregated ubiquitinated-protein (aggrephagy) [6]. Similar to ubiquitin proteasome system (UPS), ubiquitin is important for selective autophagy pathway. Selective autophagy adaptor proteins (SQSTM1/p62, NBR1, NDP52/CALCOCO2, OPTN) can interact with ubiquitinated protein and damaged organelles via their ubiquitin binding domain (UBD), mediating phagophore to isolate cargos through LC3 interacting region (LIR), then promoting phagophore to close for autophagosome formation [6]. p62 is a critical aggrephagy receptor, whose LIR domain can recognise LC3 located on autophagosome membrane. Importantly, p62 recruits ULK1 complex to ubiquitylated proteins through a direct interaction between p62 and FIP200 that is a component of ULK1 complex, which results in autophagosome formation directly on protein aggregates to mediate specific clearance [7]. Moreover, in our previous study, we reported that UXT, a small chaperone-like protein, interacting with p62, synergistically mediates the selective autophagic degradation of STING1 which is an important response element of IFN-I signalling to prevent excessive IFN-I responses [8],which is meaningful to treat diseases caused by hyperactivation of IFN-I responses. NDP52 and OPTN are two essential receptors for selective degradation of mitochondria, which recruit ubiquitinated mitochondria through UBD. And both NDP52 and OPTN are phosphorylated by their substrates TANK-Binding kinase1 (TBK1) to stabilise the combination of damaged mitochondria via affecting them to bind ubiquitin chains [6,9].

1.2. Chaperone-mediated autophagy

Chaperone-mediated autophagy (CMA) [10] selectively degrades single protein in lysosomes. Cytosolic chaperone heat-shock cognate 71 kDa (HSC70) recognises substrate proteins containing a pentapeptide (KFERQ-like motif), and other cochaperones such as carboxyl terminus of HSC70-interacting protein (CHIP), heat shock protein 40 (HSP40; also known as DNABJ1) and HSP70–HSP90 organising protein (HOP) to help substrate proteins keep unfolding which is necessary to access lysosome membrane one by one. Then, the 12-amino-acid cytosolic tail of lysosome-associated membrane protein type 2 A (LAMP2A) can bind HSC70 and substrate proteins at the same time to mediate substrates enter the lysosome lumen (Figure 1). LAMP2A is the rate-limiting component of CMA, some conditions such as mild oxidative stress, genotoxic damage or hypoxia that impact the level of LAMP2A would interfere CMA pathway [10].

CMA regulates numerous cellular processes. CMA dampens NLRP3 inflammasome activation through degradation of NLRP3 to inhibit the progression of atherosclerosis [11]. Another study reported that CMA upregulation ameliorates both systemic metabolic parameters, and vascular cell function based on transgenic mouse models [12]. Therefore, CMA is a potential therapeutic target against cardiovascular disease. CMA regulates adipogenesis at different steps via timely degradation of key proteins and transcription factors that involve in proliferation, energetic adaptation and signal changes for adipogenesis [13]. CMA also maintains neuronal proteostasis through degrading neurodegeneration-related proteins [14]. Moreover, CMA is required for protein quality control in stem cells, which plays a role in sustaining haematopoietic stem-cell function [15]. Remarkably, aberrant CMA process is associated with tumorigenesis. TPD52, a prostate-specific and androgen-responsive gene, can activate CMA via interaction with HSPA8/HSC70 to enhance prostate cancer cell proliferation and stress resistance [16].

1.3. Microautophagy

So far, most autophagy-related studies have focused on macroautophagy and CMA, but studies about microautophagy are scarce. Not similar to mentioned autophagy types, microautophagy needs neither double-membrane vesicles nor chaperones, but instead that cytosolic substrates are directly encapsulated into lysosomal lumen [17], and then degraded by various hydrolases (Figure 1).

One study reported that microautophagy regulates cGAS-STING signalling to prevent IFN-I hyperactivation. ESCRT-driven microautophagy is required for degradation of STING vesicles, and knockdown TSG101 and VPS4, belonging to ESCRT complex, leads to accumulation of the vesicles in the cytoplasm [18].

1.4. Some important autophagy-related genes

Autophagy is an intracellular degradation process regulated strictly by autophagy-related genes (ATGs). Autophagosome formation are divided into five steps: initiation, nucleation, membrane expansion, closure, and fusion [5]. For the first step, ULK complex, ATG9/Atg9-containing vesicles and the class III phosphatidylinositol 3-phosphate kinase complex 1 (PI3KC3-C1) mediates cup-structure isolated membrane (also called phagophore) formation. And then, phagophore clusters together. When phagophore accumulates enough cytoplasmic substrates, the phagophore elongates and encloses to form double-membrane autophagosome dependent on a number of conserved ATGs respectively. Ultimately, autophagosome fuses with lysosome to form autolysosome for degrading substrates.

The core components of autophagy are classified into five functional sections [5]: the ULK protein kinase complex with ULK1/2, ATG13, ATG101 and FIP200 (also called RB1CC1); the class III phosphoinositide 3-kinase complex I (also called VPS34 complex) with VPS34, VPS15, Beclin1 and ATG14; the phosphatidylinositol-3-phosphate (PI3P)-binding ATG2A or -B and WIPI1-4 complex; the two ubiquitin-like (UBL) conjugation systems with ATG5-ATG12 and mammalian ATG8 proteins conjugated with phosphatidylethanolamine (PE).

ULK complex is vital for autophagy initiation and autophagosome formation. In this complex, ATG13 is responsible to activate ULK kinase [19]. During mitosis, the key cell cycle regulator CDK1-CCNB/cyclin B phosphorylates ULK1 and ATG13, then promotes mitotic autophagy and cell cycle progression. ULK1 and ATG13 double-knockout efficiently inhibits cell cycle progression and tumour proliferation [20]. Moreover, ATG13 was also proved to inhibit virus replication independently on its canonical function, but other components of ULK complex like ATG7 have no such effect [21].

Besides, ULK complex has huge relevance with diverse diseases. For example, phospho-defective mutants of ATG13 in renal cells can block glucose starvation-induced autophagy, then render cells more susceptible to hypoglycemia-induced cell death [22]. And ATG13-mediated ULK complex positively regulates autophagy and inflammation in epithelial cells with PM2.5 treatment to aggravate pulmonary fibrosis, and the process can be inhibited by ALKBH5 mediating m6A modification of ATG13 mRNA at site 767 [23]. Ubiquitylated ULK1 by TRIM27 cooperating with STK38L can inhibit autophagy and then promote tumorigenesis like breast cancer [24]. ULK1 can interact with TIR NADase SARM1 to regulate axonal degeneration [25]. ULK1 can ameliorate diabetic kidney disease through miR-214 negative regulation [26]. And ULK1 mediated-autophagy can inhibit gastric cancer, which is phosphorylated at Ser556 by DAPK3 to increase the activity of ULK1 for ULK1 complex formation [27].

ATG9 is the only transmembrane protein of the core autophagy mechanism [28]. ATG9 vesicle originating from Golgi apparatus can be recruited to phagophore assembly site (PAS) under starvation and function as initial membrane source [29,30]. ATG2 can transfer phospholipids from ER to the cytoplasmic leaflet of phagophore via its lipid transfer activity [31,32]. ATG9 as a lipid scramblase can translocate superfluous phospholipids from the cytoplasmic leaflet to the luminal leaflet, which cooperates with ATG2 to promote phagophore expansion [33]. ATG9 vesicles also serve as nucleators to establish membrane contact sites with a donor compartment such as ER. ATG2-mediated lipid transfer in conjunction with energy-consuming reactions such as VPS34-dependent PI3P production and ATG8 lipidation on the ATG9 vesicles drive net flow of lipids into the vesicles, resulting in their expansion for autophagosome formation [34].

VPS34 complex is critical for autophagosome formation, which products phosphatidylinositol 3-phosphate (PI3P). PI3P recruits special autophagy effectors such as DFCP1 (double FYVE-containing protein 1) and the WIPI proteins (WD-repeat protein interacting with PI) to initial autophagosome formation [35]. And other study reported that autophagosome formation is also dependent on noncanonical VPS34-independent pathways in mammalian cells. PI5P, which is synthesised by phosphatidylinositol 5-kinase PIKfyve, can recruit PI3P effectors like DFCP1 and WIPI2 to regulate autophagy when PI3P is inactivated [36]. Conditional Vps34-deficient animals fail to mount autoreactive T cell responses and are resistant to experimental autoimmune encephalomyelitis (EAE) which is an animal model of multiple sclerosis (MS) [37,38]. The interaction between Beclin1 and VPS34 can be disrupted by SRSF1 to inhibit the activation of autophagy inducing lung cancer [39].

In the UBL conjugation systems, ATG7 acts as E1 in the both pathways, ATG10 as E2 in the ATG5-ATG12 pathway and ATG3 as E2 in the ATG8-PE pathway where the ATG5-ATG12-ATG16L1 complex (also called ATG16L complex) acts as an E3 ligase [40,41]. ATG5-ATG12 pathway functions in autophagosome formation. ATG16L1 is bound with a covalent ATG5-ATG12 conjugation that is generated by the action of ATG7. The E3-like complex promotes elongation and closure of autophagosome via generation of lipidated forms of LC3 (microtubule-associated protein 1 light chain 3, ATG8 ortholog) family proteins and promoting it to locate to the autophagosome membrane [42]. There are two forms of LC3, LC3-I that is free in the cytoplasm, and LC3-II that is lipidated and inserted in the membrane, both of them are post-translationally produced. LC3-II is considered as a biomarker of autophagy, which is identified as autophagosome membrane-related mammalian protein firstly. LC3-II locates inside and outside autophagosome membrane, involves in elongation of the phagophore membrane. The conversion between LC3-I and LC3-II is an essential step in phagophore closure to generate autophagosome [43] and controlled by ATG4 prominently. On the one hand, ATG4B can cleave C-terminus of LC3 pre-protein for conjugation with PE to form LC3-II; on the other hand, ATG4B delipidates LC3-II to keep balance of LC3-I and LC3-II [41,44]. ATG5-ATG12 conjugation, a key regulator of the autophagic process, also plays an important role in innate antiviral immune. ATG5 or ATG7-deficient mouse embryonic fibroblasts (MEFs) infected by vesicular stomatitis virus (VSV), can hyperactivate IFN responses. When overexpressing ATG5 and ATG12, ATG5-ATG12 conjugation can negatively regulate IFN pathway by directly targeting pattern recognition receptor retinoic acid-inducible gene I (RIG-I) and downstream mitochondrial antiviral signalling protein (MAVS) via caspase recruitment domains (CARDs) [45]. ATG5-mediated autophagy suppresses NF-κB signalling to limit epithelial inflammatory response to attenuate the kidney injury [46]. ATG5 is required for proper antigen phagocytosis and presentation to MHC class II via modulation of CD36 in dendritic cells to achieve anti-tumour therapy broadly [47]. MiR-30c-5p/ATG5 axis regulates the progression of Parkinson’s Disease [48].

ATG8 can conjugate with phosphatidylserine (PS) during noncanonical autophagy process, such as phagocytosis, on single-membrane compartments. ATG8-PE and ATG8-PS would undergo different cellular dynamics that are controlled by ATG4 isoforms [49]. Furthermore, lipidated ATG8 can activate ATG1/ULK1, a serine/threonine kinase, which downregulates ATG8 lipidation as negative feedback process in turn. And phosphorylated ATG13 can dissociate ATG1 complex to regulate ATG1 complex dynamics at PAS [50].

Various ATGs cooperate synergistically to regulate autophagy process to ensure cellular homeostasis. Aberrant signalling mediated by ATGs can induce various pathology symptoms and cause multiple diseases that involved in tumorigenesis, neurodegeneration, autoimmune diseases, apoptosis, and senescence progresses [3]. As mentioned above, we have already concluded some core proteins including ULK1/ATG1, ATG12, ATG5, ATG13, VPS34, ATG2, which induce disease processes or serve as potential therapeutic targets, published within the last five years (Figure 2).

Figure 2. ATGs involve different diseases. ATGs are significant to regulate autophagy process, while they also involve in the occurrence and progression of various diseases, such as breast cancer, Parkison’s disease, lung cancer and so on.

2. Autophagy in human autoimmune diseases

Approximately 5% of the whole world people are affected by autoimmune diseases, which reduce patients’ living quality severely, impose a huge burden to patients, and are hardly cured. Autoimmune diseases are a diverse group of conditions characterised by aberrant B cell and T cell responses to the host. Autoimmune diseases are caused by various complex and interactional factors, such as genetic predisposition and environmental factors, whose most remarkable biomarker is production of autoantibodies [51,52]. And it is also reported that epigenetic modifications contribute to the initiation and perpetuation of autoimmune diseases [53]. Increasing studies have elucidated that autophagy and autoimmunity have a tight association [54]. We talked about how autophagy regulates autoimmune diseases subsequently (Table 1).

Table 1. Macroautophagy and CMA in autoimmune diseases.

The forms of autophagy	Diseases	Mechanism	References
Macroautophagy (referred as autophagy)	SLE	LRRK2 has a strongly positive correlation with disease severity. LRRK2 deficiency attenuates pristane-induced lupus-like pathology in mice possibly through regulating B cell terminal differentiation and subsequent antibody production.	[55]
		Blocking the activation of mTOR signalling induces autophagy and corrects the functions of T cells to improve SLE.	[56]
	RA	Aberrant autophagy induces the hyperactivation of T cells and the resistance of apoptosis aggravating RA.	[57]
		OPTN plays a protective role in RA upregulated in the presence of proinflammatory cytokines in FLS.	[58]
	MS	Autophagy failure affects OL functions inducing MS under the prolong stress.	[59]
		ATG7 deficiency in microglia leads to an increase in intracellular accumulation of phagocytosed myelin and progressive MS-like disease.	[60]
	IBD	IRGM can block inflammasome assembly and mediate the autophagic degradation of NLRP3. It means that IRGM is protective from inflammatory disorders.	[61]
		Autophagy can enhance TJ barrier to maintain the integrity of barrier.	[62]
	Psoriasis	Autophagic degradation of innate immune sensors like cGAS, RIG-I and TLR3 inhibits synthesis of proinflammation cytokines to relieve psoriasis.	[63]
		PSORI-CM02 induces autophagy and then inhibits the proliferation of HaCaT cells to alleviate psoriasis in vivo and in vitro via suppression of the PI3K/Akt/mTOR pathway.	[64,65]
	Vitiligo	Autophagy-related TNFSF10/ hsa-let-7a-5p axis regulates the development of vitiligo by autophagy and apoptosis.	[66]
		HSF1-ATG5/12 axis can prevent oxidative stress-induced melanocyte death.	[67]
CMA	SLE	It is found that CMA is upregulated in MRL/lpr lupus-prone mice. And using P140 phosphopeptide to inhibit CMA can lower activation of autoreactive T cells and relieve lupus symptoms.	[68]
	Sjögren’s syndrome	Using P140, which acts on CMA, can rescue MRL/lpr mice from cellular infiltration and autophagy defects occurring in salivary glands. It is suggested that targeting CMA might therapy Sjögren’s syndrome.	[69]
	Type 1 diabetes	PFK-2 can be degraded by UPS and CMA. The loss of PFK-2 impaired the capacity to dynamically regulate glycolysis and elevates the levels of early glycolytic intermediates. It means a pathological impairment in type 1 diabetes.	[70]

2.1. Autophagy in Systemic lupus erythematosus

Systemic lupus erythematosus (SLE) is a multisystem autoimmune disease characterised by multiple organs inflammation and injury resulting from the immune system attack. Dysregulation of immune responses and breakdown of self-tolerance play critical roles in the occurrence and development of SLE [71]. The common symptoms of SLE include fever, rash, arthritis, nephritis, and other systematic clinical manifestations. Various factors like environmental, demographic and genetic factors can cause abnormal immune responses. For example, particulate exposure induces apoptosis and the release of intracellular antigens that contribute to SLE. The difference of gender, age and ethnicity affects the incidence of SLE, and specific genetic backgrounds are related to the development of SLE. And the level of various cytokines like Th1, Th2 and Th17 cytokines are significantly increased in the SLE patients, which is associated with disease severity [72]. However, these factors are intricate, and the specific mechanisms still need to be found out [73–75]. More genes linked to SLE and their mechanisms have been discovered in the recent years. Recently, an increasing number of genetic studies have suggested that defect in autophagy pathway is a significant driver of SLE. With the progress of genome-wide association studies and further follow-up studies, some autophagy-related genes have been identified to be susceptible loci for SLE, including ATG5, ATG7, ATG16L2, IRGM, CDKN1B, DRAM1, CLEC16A, LRRK2, MAP1LC3B, MTMR3, and APOL1 [76,77].

Mutations of ATG5 are assumed to be associated with susceptibility to SLE. As reported previously, carriage of ATG5 rs573775 single nucleotide polymorphism leads to IL-10 upregulation and reduces the production of IFNα and TNFα, which contribute to high SLE risk [78]. There are gene interactions between ATG5, ATG7 and IRGM associated with SLE observed in the Chinese population [79]. ATG5 and ATG7 also play important roles in B cell autophagy, which is necessary to the initiation of SLE [80,81]. ATG16L2, an isoform of ATG16L1, can form a heterodimer with ATG16L1 and competitively inhibit formation of ATG12-ATG5-ATG16L1 complex [82] that is required for autophagy [83]. Therefore, ATG16L2 may function as a potential competitive inhibitor of ATG16L1 and downregulate the occurrence of SLE by inhibiting autophagy [84].

CDKN1B rs34330 risk allele (C) was reported to be potentially associated with SLE by influencing the presence of histone markers, RNA Pol II, and IRF-1 transcription factor to regulate expressions of several target genes linked to cell proliferation and apoptosis [85]. It is reported that LRRK2 is upregulated in B cells from SLE patients that has a strongly positive correlation with disease severity. LRRK2 deficiency attenuates pristane-induced lupus-like pathology in mice possibly through regulating B cell terminal differentiation and subsequent antibody production [55]. MAP1LC3B encodes microtubule-associated protein (LC3B), a biomarker of autophagy flux, which was reported to have a likely genetic association with susceptibility to SLE [69]. APOL1 risk variants associate with high prevalence of renal and hypertensive disease in SLE patients of African ancestry [86]. The upregulation of APOL1 may have further implications in SLE through accelerating cell death and organ damage [87].

Among all the immune cells, B cells play the most central role in adaptive immune response of SLE. Autophagy indispensably functions in B cell activation, differentiation and maintenance of memory B cells and plasma cells [88]. B cell autophagy comes up before disease onset in a SLE mouse model, and progressively increases with age, and the similar increase has been seen in SLE patients [81]. Absence of autophagy can eliminate inflammation response and autoantibodies production such as antinuclear antibody to cure the symptoms in lupus mice model [89]. T cells in SLE exhibits aberrant signal transduction and excessive activation leading to disturbances in metabolic and organelle homeostasis [90]. Endocytic control of mitophagy regulated through HRES-1/Rab4 is an important therapeutic target of SLE [91]. CD38 is upregulated and impacts natural cell functions in SLE CD8⁺ T cell. Inhibition of CD38 represents a way to resist viral infection through correcting multiple steps of mitophagy in CD8⁺ T cells of SLE patients [92]. Another therapeutic target of SLE is the mechanistic target of rapamycin (mTOR). One study demonstrated that increased mTOR activation leads to diminished autophagy in SLE regulatory T cells. Blocking activation of mTOR signalling through rapamycin treatment induces autophagy and corrects the functions of T cells [56]. As for innate immune, neutrophils contribute to organs inflammation and injury by forming extracellular chromatin traps in SLE. A study suggested that REDD1-autophagy-NET axis is a promising target to alleviate neutrophil-mediated inflammation and injury for SLE therapy [93].

Furthermore, long noncoding RNA (lncRNA) also plays a nonnegligible role in regulating development and process of autoimmune diseases by targeting autophagy related-pathways. SNHG16, a lncRNA, can regulate TLR4-mediated autophagy and NETosis formation in the human and mouse alveolar haemorrhage (AH) lungs, and intra-pulmonary delivery of shRNA targeting SNHG16 might be a potential therapy approach in this SLE-related AH [94]. LincRNA-Cox2 knockdown inhibits NLRP3 inflammasome activation which suppresses caspase-1 activation and reduces the cleavage of TRIF, resulting in derepressing TRIF-mediated ATG5-dependent autophagy [95]. And LncSIK1 can regulate the development of acute myeloid leukaemia (AML) via regulating the E2F1-autophagy signalling pathway. On the one hand, LncSIK1 can recruit E2F1 protein to the promotor of LC3 and DRAM and induce the autophagic degradation of oncoprotein PML-RARa in NB4 cells. On the other hand, LncSIK1 can also reverse the high autophagy process in Molm13 cells through blocking E2F1 expression and the E2F1-mediated transcription of LC3 and DRAM [96].

Moreover, in our previous study, we found that a small chaperone-like protein UXT plays a positive role in SLE treatment. UXT can promote p62 mediated-selective autophagy to degrade STING, which effectively inhibits overexpression of IFN-I induced by cGAS-STING signaling [8]. It is indicated that UXT might a potential target for SLE treatment. And CSNK1A1/CK1α as a serine/threonine protein kinase, is identified as a negative regulator for cGAS-STING signalling through mediating STING autophagy degradation by enhancing the phosphorylation of SQSTM1/p62 at serine 351 (serine 349 in human). Additionally, we also found that SSTC3, a selective agonist of CSNK1A1/CK1α, can be recognised as a valuable compound to treat autoimmune diseases like SLE [97].

2.2. Autophagy in rheumatoid arthritis

Rheumatoid arthritis (RA) is a chronic and systemic inflammatory disease, which has multiple clinical symptoms that contain the joints of cartilage and bone damage, fibroblast-like synoviocytes (FLS) infiltration into cartilage and bone surfaces, and subchondral bone erosion. And other organs are also affected, such as lungs, eyes and muscles. Autoantibodies which can recognise Fc portion of IgG is called rheumatoid factor (RF), and antibodies against citrullinated protein antigens (ACPAs) are biomarkers of RA [98]. It is demonstrated that RF and ACPAs have already existed before clinical symptoms onset [99], when immune tolerance to specific self-antigen is broken. Additionally, some genetic factors also contribute to development of RA like human leukocyte antigen (HLA) [100].

Autophagy has a tight connection with RA progress. It is found that some core autophagy related-proteins like ATG5, LC3 and Beclin1 obviously increase in synovial tissues of RA patients [101,102]. Importantly, autophagy connects with antigenic peptide presentation and participates in carbamylation that belongs to a nonenzymatic posttranslational modification and accumulates in various diseases [103]. Autophagy induced by tunicamycin or rapamycin promotes protein carbamylation in FLS from RA patients [104]. Lots of studies demonstrated that insufficient apoptosis of inflammatory cells in the RA joint might contribute to pathogenesis, recognised as a therapeutic strategy of RA [105]. In synovial tissues of RA patients, autophagy related proteins were significantly enhanced while apoptosis of synovial tissues was reduced, suggesting a negative correlation between autophagy and apoptosis [106]. IL-17 secreted by the Th17 cells can induce mitochondrial dysfunction and autophagy in FLS via activating STAT3 to antagonise apoptosis in FLS [107]. In the HLA class II-associated autoimmune syndrome RA, CD4 T cells are critical drivers of pathogenic immunity, which is the primary cellular component in the synovitis to promote autoantibodies production. And CD4 T cells of RA are in the state of energy deprivation because of inadequate aerobic glycolysis that could not alleviate the challenge through autophagy. One study expounded that increasing the expression of PFKFB3 in RA T cells can repair the glycolytic insufficiency and the autophagic activity [108]. More, increasing autophagy in CD4 T cell from RA patients induces T cell hyperactivation and apoptosis resistance [57].

Cathepsin K (Ctsk) is a lysosome cysteine protease that is primarily expressed in osteoclasts and plays a key role in bone resorption. Inhibition of Ctsk can modulate autophagy via TLR9, then in turn affect the progression of RA-aggravated periodontitis [109]. Optineurin (OPTN), an autophagy adaptor receptor, plays a protective role in RA that is upregulated in the presence of proinflammatory cytokines in FLS [58]. However, the concrete mechanism needs to further explore.

TNFα is a vital cytokine driving numerous inflammation diseases including RA. TNFα can activate NF-κB signalling in FLS and enhance autophagy, which in turn enhances the resistance of FLS to anti-TNFα therapy for RA [101]. Prolonged TNF treatment can induce cGAS-STING-dependent interferon response, and also alter mitochondrial function to cause the release of mtDNA which can activate cGAS-STING signalling. Furthermore, cGAS deficiency blocks interferon responses and reduces inflammatory cells infiltration and joint swelling in cGAS knockout mouse model [110]. Escape of genes from transcriptional repression in FLS is as a novel mechanism potentially contributing to the chronic unremitting synovitis in RA through genome-wide analysis. Further, TNF induces sustained chromatin activation by regulating elements of the genes escaping transcriptional repression in RA, which is indicated that modulation of chromatin states may be as a potential therapeutic strategy for RA [111].

Celastrol inhibits RA by increasing autophagosome levels and LC3B protein expression to induce autophagy in TNFα-treated FLSs via inhibition of the PI3K/AKT/mTOR signalling pathway [112]. Oridonin can combinate with chloroquine (CQ) to suppress autophagy and FLS proliferation and induce apoptosis, thus it is a potential agent to treat RA [113]. And resveratrol can relieve experimental RA by activating autophagy [114].

Bioinformation analysis identified and validated 52 potential autophagy-related genes in RA. CASP8, CTSB, TNFSF10, FADD, BAX, MYC, FOS, CDKN1A, GABARAPL1, and BNIP3 are ten hub genes, which could be recognised as valuable prognostic markers and new potential therapeutic targets for RA [115]. Furthermore, CXCR4 and SERPINA1 that belong to ATGs are identified as biomarkers to improve differential diagnosis of RA and osteoarthritis (OA) which show statistical difference in the autophagy level and pathogenesis via bioinformatic technology [116]. Derlin-1 which participates in autophagosome formation is identified as a potential early predictive biomarker for nonresponse of infliximab treatment in RA based on GSE58795 and GSE78068 datasets [117].

2.3. Autophagy in multiple sclerosis

Multiple sclerosis (MS) is a neuroinflammatory and neurodegenerative autoimmune disease of the central nervous system (CNS), characterised by demyelination and neuronal loss. MS typically presents in young adults aged 20–30 with female preference and affects estimated 2.8 million people worldwide [118,119]. The pathogenesis of MS is very complex and still opaque, although the interactions between genetic and environmental factors undoubtedly play important roles [120]. MS was previously considered to be principally T-cell driven, but more recent researches have highlighted the roles of other cell types like myeloid cells and B cells in MS [120]. During MS pathology, the immune system directs to CNS autoantigens inducing inflammation and the loss of myelin, thus mediates axonal and neuronal damage, resulting in physical disability and cognitive impairment [120]. Autophagy has an important function in this process. For neurons, autophagy is indispensable for their survival and maintenance of homeostasis and functional stability, therefore autophagy defection can lead to the development of MS. Autophagy has intimate and complicated relationship with both innate and adaptive immunity, affecting the functional metabolism of immune cells, regulating inflammatory responses and influencing the occurrence of MS [121].

A study analysed the expression levels of 78 genes involved in the autophagy pathway, and found out that the expression of 29 genes were significantly altered in MS patients [122]. Another study showed that transcriptional levels of ATGs were decreased and autophagy process was inhibited by regulating mTORC1 depending on the disease stage in EAE mouse model, the same phenomenon was also observed in post-mortem human MS brain tissues [123]. These studies suggested that autophagy involves in MS pathogenesis.

Oligodendrocyte (OL) injury and loss are the characteristics of MS, which functions as wrapping axons in CNS with specialised cell membrane layers, forming insulating myelin sheaths which assist in the efficient transfer of bioelectrical signals and support the normal function of neurons. One study found that autophagy failure affects OL functions under the prolong stress [59].

Microglial cells are the resident immune cells of CNS, heavily participating in promoting brain development, maintaining CNS homeostasis and mediating immune response and neuroinflammation. The ability of microglia to clear tissue debris has been found out to be essential for the recovery from CNS inflammation in EAE mouse model. Specific deletion of ATG7 in microglia leads to an increase in intracellular accumulation of phagocytosed myelin and progressive MS-like disease [60]. This process of relieving neuroinflammation depends on a noncanonical autophagy, with no requirement for ULK1 or ATG5 [60,124]. In addition, the deficiency of Mir223, a kind of miRNAs, was reported to be able to increase autophagy in brain microglia and significantly ameliorate demyelination and CNS inflammation by targeting at ATG16L1 [125].

Mitochondria dysfunction has been found to be associated with MS. The level of Parkin, an E3 ligase of mitophagy, was reported to have a significant increase in serum and cerebrospinal fluid of patients with MS [126]. A recent study identified a natural variant of autophagic receptor NDP52/CALCOCO2 plays a protective role in MS via mediating B cell mitophagy and reducing the production of pro-inflammatory cytokines [127].

2.4. Autophagy in inflammatory bowel disease

Inflammatory bowel disease (IBD) is an inflammation disorder of gastrointestinal trac mainly containing Crohn’s disease (CD) and ulcerative colitis (UC). Both of them are lethal, and the normal symptoms are related to gut inflammation, such as abdominal pain, fever, vomit, diarrhoea, rectal bleeding, anaemia and weight loss [128]. Actually, CD primarily involves in the terminal ileum or the perianal region, while UC is limited to the colon: it begins in the rectum, spreads proximally in a continuous fashion and frequently involves the periappendiceal region.

Autophagy resists infection and removes the intracellular microbes. It is confirmed that ATG16L1 and IRGM involve in IBD pathogenesis through genetic analysis [128]. ATG16L1 promotes formation of autophagosome activated by NOD2 which recognises the peptidoglycan product muramyl dipeptide (MDP) and subsequently activates immune responses [129] when infecting microbes, and also inhibits inflammation cytokines responses [130]. Moreover, ATG16L1 orchestrates IL-22 signalling via cGAS-STING pathway. IL-22 stimulation physiologically leads to transient ER stress, releasing of dsDNA to cytoplasm and subsequent activation of STING-dependent IFN-I signalling to increase production of TNFα leading to necroptotic cell death [131]. But ATG16L1T300A variant affects autophagy-mediated clearance of intracellular microbes and increases pro-inflammatory cytokine production [132]. ATG16L2, the paralog of ATG16L1, is found that highly expresses in colorectal, gastric, and prostate carcinomas [84]. ATG16L2 participates in balancing multiple inflammation pathways in IBD. Therefore, it is considered as a potential treatment target for IBD. NRBF2, the PI3KC3 complex subunit, is essential for apoptotic cell clearance to restrict intestinal inflammation. NRBF2 is indispensable for formation of active form of RAB7 to promote fusion between phagosomes containing engulfed apoptotic cells and lysosomes. And upregulating expression of NRBF2 is detected from biopsies of UC patient colon [133].

Intestinal epithelium is an important defensive barrier to maintain gut homeostasis and minimise intestinal inflammatory responses separating the luminal content from the mucosal immune system [134]. ESRRA, which is critical in mitochondrial biogenesis and autophagy function, plays an important role in regulating intestinal homeostasis by mitigating colonic inflammation through activation of autophagic flux and control of host gut microbiota. Esrra-deficient mice upregulate intestinal inflammatory induced by DSS, and show prominently higher microbial diversity than WT mice [135]. Hypoxia regulates autophagy and NLRP3 signalling to alleviate CD. Hypoxia can reduce expression of TNFα, IL-6 and NLRP3 and increase the turnover of p62 in colon biopsies of CD patients. And it was demonstrated that NLRP3 is a binding partner of mTOR. Hypoxia relieves inflammation through downregulating the binding of mTOR and NLRP3 and activating autophagy [136]. IRGM interacts with NLRP3 and ASC and hinders inflammasome assembly by blocking their oligomerisation. Further, IRGM mediates selective autophagic degradation of NLRP3 and ASC. This study also demonstrated that IRGM is protective from inflammatory disorders for the first time [61].

Starvation-induced autophagy enhances the intestinal epithelial tight junctions (TJs) barrier by degrading pore-forming CLDN2 [62]. Moreover, autophagy promotes the intestinal TJ barrier by increasing occludin levels in an ERK1/2 mitogen-activated protein kinase-dependent mechanism [137]. AP2M1 knockout, a subunit of clathrin and adaptor protein AP2, prevents autophagy-induced CLDN2 degradation via reducing CLDN2-LC3 interaction [138]. This mechanism which links CLDN2, AP2M1, and LC3 could provide a novel approach against intestinal inflammation like IBD. BRG1, an ATPase subunit of the SWI/SNF chromatin remodelling complex, directly governs the transcription of ATG16L1, ATG7, AMBRA1 and WIPI2 that are required for autophagosome biogenesis. Defective autophagy causes excessive ROS leading to barrier damage in BRG1-deficient intestinal epithelial cells (IECs). In other words, BRG1 can alleviate colonic inflammation through autophagy-mediated ROS sequestration [139].

2.5. Autophagy in psoriasis

Psoriasis is recognised as a “chronic, non-communicable, painful, disfiguring, and disabling disease for which there is no cure” by WHO in 2014. And the clinical symptoms of psoriasis include chronic plaque, psoriasis vulgaris, guttate, erythrodermic, and pustular psoriasis. IL-23 and TH17 responses are the essential drivers for psoriasis through hyperactivation of a series of immune cells based on various genome-widely studies and abundant clinical data [140,141].

Additionally, autophagy plays a role in pathogenesis of psoriasis. One study found an increasing autophagy flux which presents highly expression of ATG5, ATG7 and ATG8 in psoriasis patients. Short-term treatment of human primary keratinocytes (KCs) with TNFα which is a proinflammation cytokines regulating psoriasis can enhance autophagy process. While long-term treatment cause accumulation of p62 that means autophagy inhibition. It also demonstrated that TNFα can block lysosome fusion inhibiting to degrade cargos mediated by autophagy [142]. And it is demonstrated that some autophagy related-biomarkers including ATG5, SQSTM1, EGFR, MAPK8, MAPK3, MYC, and PIK3C3 could be involved in the pathogenesis of psoriasis based on bioinformation analysis [143]. Autophagic degradation of innate immune sensers like cGAS, RIG-I and TLR3 inhibits synthesis of proinflammation cytokines to relieve psoriasis [63]. Furthermore, autophagy can negatively regulate inflammation responses via p62, which can activate proinflammatory transcription factors, including NF-κB and NRF2 [144]. When lacking AP1S3, an autophagy regulator, it causes defective autophagy and p62 accumulation, and increases inflammation responses in KCs [145]. Aryl hydrocarbon receptor (AHR) negatively regulates autophagy leading to skin inflammation in KCs through the NF-κB/MAPK signalling pathways, which suggests AHR and autophagy could participate in pathogenesis of psoriasis [146].

IL-17A stimulation activates the PI3K/Akt/mTOR pathway in KCs to inhibit autophagosome formation, meanwhile enhances cellular cholesterol levels which in turn regulates autophagy flux. It suggests regulation of autophagy and/or cholesterol levels may be potential targets for psoriasis [147]. PSORI-CM02 induces autophagy and then inhibits the proliferation of HaCaT cells to alleviate psoriasis in vivo and vitro via suppression of the PI3K/Akt/mTOR pathway [64,65]. Jueyin granules, a traditional Chinese medicine (TCM), can induce autophagy by upregulating ApoA1 and inhibit the infiltration of CD4⁺ T cells and macrophages to alleviate imiquimod-induced psoriatic inflammation in a mouse model [148]. Thus, it provides a strategy to relieve psoriasis through Jueyin granules and other potential TCMs.

2.6. Autophagy in vitiligo

Vitiligo is an acquired chronic depigmenting disorder of the skin resulting from selective destruction of melanocytes [149], which is classified into two classes: non-segmental vitiligo, and segmental vitiligo. Due to vitiligo causes an uneven distribution of depigmentation in the skin, the patients bear a huge psychological burden, and their quality of life is severely impacted. Vitiligo is an autoimmune disease. Autoreactive cytotoxic CD8+ T cells recognise melanocytes and secret IFN-γ to prompt the disease progression. And there is a positive feedback loop, the secretion of IFN-γ induces surrounding keratinocytes to secret chemokines to recruit T cells to the skin aggravating the infiltration of T cells [150]. Thus, blocking IFN-γ signalling transduction is an effective and current therapy, but disease relapse is general when stopping IFN-γ therapy.

Autophagy is relative to vitiligo process. It is found that autophagy plays a protective role in vitiligo. Autophagy occurs in melanocytes and fibroblasts from non-lesional skin of vitiligo patients to antagonise degenerative processes in normal appearing vitiligo skin and resist the metabolic stress [151]. Importantly, the expression levels of LC3 and p62 are discrepant between vitiligo and health people. The decreased ratio of LC3II/LC3 and elevated level of p62 in the vitiligo lesions were detected via western blot [152]. Autophagy-related TNFSF10/hsa-let-7a-5p axis regulates the development of vitiligo by autophagy and apoptosis based on a bioinformatics analysis [66]. HSF1-ATG5/12 axis can prevent oxidative stress-induced melanocyte death based on the results of RNA sequencing. It is indicated that targeting HSF1-ATG5/12 axis might treat vitiligo [67]. TRMP2 inhibits autophagy to promote the secretion of CXCL16 that recruits CD8+ T cells to kill melanocytes inducing vitiligo via ATG5-ATG12-IRF3 signalling [153]. Therefore, blocking TRMP2 is a potential strategy to treat vitiligo.

2.7. Autophagy in other autoimmune diseases

Autophagy also involves in other autoimmune diseases. Autoimmune hepatitis (AIH) is a necroinflammatory disease, featuring various immune cells invade interface to periportal parenchyma. Conventional dendritic cells (cDCs) contribute to the pathogenesis of AIH through excessive maturation which can be blocked by autophagy inhibitors [154]. In other words, tolerogenic cDCs via inhibiting autophagy flux could be a new therapeutic strategy for AIH.

Type 1 diabetes (T1D) is an insulin-dependent autoimmune disease that the pancreatic β cells are destroyed resulting in hyperglycaemia, but the concrete disease mechanism could not be understood clearly. Recent studies demonstrated that autophagy of pancreatic β cells is correlative with T1D [155,156]. Neuregulin-4 that is an adipokine and protects from metabolic disorders, and insulin resistance can attenuate diabetic cardiomyopathy which is a complication of diabetic by regulating autophagy via the AMPK/mTOR signalling pathway in the T1D mouse model [157]. CLEC16A, an autoimmune-associated gene, is associated with numerous autoimmune diseases, such as T1D, SLE, RA, Addison’s disease, primary biliary cirrhosis, alopecia areata and so on. CLEC16A silencing protects from autoimmunity, which is attributable to T cell hyperactivity because of CLEC16A’s role in thymic epithelial cell autophagy in the nonobese diabetic (NOD) model for type 1 diabetes [158].

3. Autophagy, autoimmune diseases and carcinogenesis

Autophagy plays an indispensable role in cellular homeostasis. As mentioned above, autoimmune diseases are caused by aberrant B cell and T cell responses to the host, and autophagy signalling can regulate the occurrence and development of autoimmune diseases, which provides some valuable therapeutic strategies against autoimmune diseases. More, autophagy also impacts carcinogenesis. Autophagy can improve tumorigenesis through numerous mechanisms, including inhibition of p53 activation, maintenance of energy homeostasis for biosynthesis and tumour growth, prevention from genome instability, remission of oxidative stress and suppression of antitumor immune responses [159]. For instance, the fusion between autophagosome and lysosome could be inhibited in the liver when suffering from inflammation or virus infection. And then p62 gradually accumulates, which leads to the activation of NF-κB signalling, and promotes NRF2 to translocate into nuclear to regulate transcription of anti-oxidative genes that allows hepatocellular carcinoma (HCC) survival under oxidative stress. This process causes genomic instability and creates an inflammatory microenvironment for HCC development [160]. Moreover, when infecting HBV, the expression of ARRB1 is upregulated, and it is demonstrated that ARRB1 plays a critical role in HBV-related HCC via modulating autophagy and the CDKN1B-CDK2-CCNE1-E2F1 axis. It is indicated that ARRB1 might be a hopeful target for HCC treatment [161]. TRIM27 can cooperate with STK38L to negatively regulate ULK1-mediated autophagy, and then promote breast tumorigenesis [24]. Knockdown of Atg5 in pancreatic cancer cell lines increases their migratory and invasive capabilities, and formation of metastases following injection into mice [162]. ATG12 deficiency results in intracellular glutamine depletion, abrogation of tumour hypoxia and a favourable prognosis in cancer [163].

Intriguingly, it is notable that heritable factors can affect carcinogenesis and autoimmune diseases. Hereditary defects and genome instability lead to the development and transformation of tumour, and also might prompt to deregulate T cell, which is important for self-tolerance. Besides, environmental factors such as ultraviolet (UV) radiation, microbe infection and drugs, can also induce tumorigenesis, and possibly interfere the recognition of self-antigen leading to aberrant B or T cell activation. Thus, we think it is an estimable therapeutic approach via targeting autophagy to treatment of autoimmune diseases or cancers. But unfortunately, there is an unclear relation among autoimmune diseases, carcinogenesis and autophagy. It is necessary to profoundly explore the mysteries about these [164].

4. Treatment strategies of autoimmune diseases by targeting autophagy

Increasing studies have shown that autophagy is tightly associated with autoimmune diseases [54,63,165,166]. Autoimmune diseases are caused by many different factors, such as genetic factor and environmental factors. Moreover, they affect patients’ life quality, aggravate life burden, are hardly cured and even threat to life. But unfortunately, how treat autoimmune diseases is also a huge challenge. Next, we listed the strategies against autoimmune diseases from a perspective of autophagy (Table 2).

Table 2. Treatment strategies against autoimmune diseases by modulating autophagy.

Treatment strategies	Autoimmune diseases	Targets	References
HCQ and CQ	SLE; RA	HCQ and CQ interfere the presentation of self-antigen, and inhibit the degradation of autophagic cargoes.	[167,168]
	MS	CQ blocks the integration of autophagosome and lysosome.	[169]
ISD017	SLE	ISD170 blocks STING trafficking through STIM1.	[170]
Tocilizumab	SLE	Tocilizumab restores autophagy process, and reverses the accumulation of p62 in the SLE patients’ macrophages.	[171]
Empagliflozin	SLE	Empagliflozin reduces the activity of mTORC1, and relieve the symptoms of lupus nephritis.	[172]
SSTC3	SLE	SSTC3 activates CSNK1A1/CK1α to increase p62-mediated STING degradation.	[97]
P140	SLE	P140 affects refolding properties of HCS70, and increases the accumulation of p62 and LC3 to impact presentation of self-antigens and the activation of T cells.	[173,174]
	IBD	P140 can correct autophagy defects in IBD mice model.	[175]
Quercetin	RA	Quercetin inhibits neutrophil extracellular traps (NET) formation that is associated with the pathogenesis of RA by suppressing autophagy.	[176]
Chelerythrine	RA	Chelerythrine increases the intracellular level of ROS and the apoptotic rate of HFLS-RA by activating the AMPK/mTOR/ULK-1 signalling pathways.	[177]
Celastrol	RA	Celastrol increases the level of autophagosome and the expression of LC3B via inhibiting PI3K/AKT/mTOR signalling pathway.	[112]
Resveratrol	RA	Resveratrol can relieve experimental RA by activating autophagy.	[114]
Anti-TNFα therapy (such as infliximab, adalimumab and golimumab)	RA; IBD	Anti-TNFα antibodies induce regulatory macrophages transform into a phenotype similar to M2, and this progress is tightly related to autophagy.	[178]
Dimethyl fumarate	MS	Dimethyl fumarate treatment increases the expression of LC3 and ATG7 to suppress proinflammatory responses and protect neurons in microglia.	[179]
Haloperidol; clozapine	MS	Haloperidol and clozapine inhibit autophagy, prevent demylinization, induce remyelination, and revert MS behavioural deficits.	[180]
Sildenafil	MS	Sildenafil alleviates EAE by activating autophagy in the spinal cord, by means of the eNOS-NO-AMPK-mTOR-LC3-beclin1-ATG5 and eNOS-NO-AMPK-mTOR-CREB BDNF pathways.	[181]
Nicotinamide adenine dinucleotide	MS	Nicotinamide adenine dinucleotide alleviates EAE through the activation of autophagy and the suppression of NLRP3 inflammasome.	[182]
Dapagliflozin	IBD	Dapagliflozin activates autophagy and suppresses apoptosis to attenuate experimental inflammatory bowel disease in rats through AMPK/mTOR, HMGB1/RAGE and Nrf2/HO-1 pathways.	[183]
Andrographolide	IBD	Andrographolide can prevent colitis-associated cancer via mitophagy-mediated NLRP3 inflammasome inhibition.	[184]
Agonist of cannabinoid receptor 2	IBD	Agonist of cannabinoid receptor 2 inhibits NLRP3 inflammasome activation and alleviates DSS-induced colitis in mice through promoting autophagy process.	[185]
AC-73	IBD	AC-73 inhibits CD147/ERK1/2 and STAT3 signalling pathway activation and induces autophagy.	[186]
Atrial Natriuretic Peptide (ANP)	IBD	ANP can repair the gut barrier and inhibit ER stress-induced autophagy via the STING pathway.	[187]
Cis-khellactone	Psoriasis	Cis-khellactone suppresses proinflammatory phenotypic macrophages by promoting autophagy.	[188]
Jueyin granules	Psoriasis	Jueyin granules induce autophagy by upregulating ApoA1 and inhibit the infiltration of CD4+ T cells and macrophages to alleviate imiquimod-induced psoriatic inflammation in a mouse model.	[148,189]
PSORI-CM02	Psoriasis	PSORI-CM02 induces autophagy and then inhibits the proliferation of HaCaT cells to alleviate psoriasis in vivo and in vitro via suppression of the PI3K/Akt/mTOR pathway.	[64]
Fenofibrate	Psoriasis	Fenofibrate blocks IL-17A signalling and enhance autophagy process inducing anti-inflammatory effects.	[190]
Epigallocatechin-3-gallate (EGCG)	Vitiligo	EGCG induces autophagy and apoptosis to treat vitiligo via targeting TNFSF10.	[66]
Itaconate	AIH	Itaconate can decrease DCs autophagy and maturation to ameliorates liver inflammation through regulating the PI3K/AKT/mTOR pathway.	[191]
Methylprednisolone	AIH	Methylprednisolone ameliorated mitochondria-mediated apoptosis and autophagy dysfunction through the Akt/mTOR signalling pathway.	[192]
Astaxanthin	AIH	Astaxanthin reduced immune liver injury through downregulation of JNK/p-JNK-mediated apoptosis and autophagy.	[193]
Neuregulin-4	T1D	Neuregulin-4 can promote autophagy in T1D mice via the AMPK/mTOR signalling pathway.	[157]
Allicin	T1D	Allicin can activate AMPK/mTOR mediated autophagy pathway to suppress T1D.	[194]
Vitamin D	T1D	Vitamin D can increase autophagy process to prevent T1D.	[195]

4.1. Treating SLE through targeting autophagy

It is demonstrated that HCQ and CQ can effectively block autophagy process to therapy autoimmune diseases, including SLE, RA, MS, Sjögren’s syndrome. HCQ can inhibit the activity of hydrolases of lysosome, which can accumulate in the lysosome along PH gradient, and then interfere the degradation of autophagic cargoes and the presentation of self-antigens. Furthermore, HCQ suppresses the transduction of TLR4 and cGAS-STING signalling to relieve excessive inflammation response [167]. HCQ and CQ also inhibit autophagy to prevent immune activation and cytokine production and regulate the expression of CD154 on T cells [168]. And ISD017 as a selective STING inhibitor, can block STING trafficking from ER to Golgi dependent on the STING ER retention factor STIM1. ISD017 treatment blocks pathological cytokine responses in the cells from lupus patients with higher IFN-I levels [170]. Tocilizumab, a humanised anti-IL-6R monoclonal antibody, can restore autophagic degradation and reverse the accumulation of p62 in a paracrine manner in SLE patients’ macrophages [171]. The SGLT2 inhibitor empagliflozin could alleviate podocyte injury by attenuating inflammation and enhance autophagy via reducing mTORC1 activity and relieve the symptoms of lupus nephritis effectively [172]. SSTC3 can selectively activate CSNK1A1/CK1α to mediate p62-induced STING autophagy degradation to attenuate autoimmune disease symptoms in trex1-/- mouse model and decrease the levels of IFN and ISGs in PBMCs of SLE patients [97]. P140 affects refolding propertied of HSC70, and increases the accumulation of p62 and LC3 with a downregulation of autophagic flux in the MRL/lpr B cells [173]. And P140 treatment also represses B cell differentiation by reducing HLA Class II molecule overexpression [174]. Thus, it is indicated that P140 can impact autophagy process to suppress activation and transduction of B and T cell.

Besides, there are also some potential targets against SLE.REDD1/autophagy/NET axis in end-organ injury and fibrosis in SLE may be used to screen existing drugs for SLE therapy [93]. CD36 promotes podocyte injury by activating NLRP3 inflammasome and inhibiting autophagy leading to SLE aggravation [196]. It implies that CD36 antagonist may be a promising treatment strategy for SLE. Histone deacetylases (HDACs) abundance is lower in the PBMCs from SLE compared to health donors. In uninfected cells, HDACs interacts with IRF3 to inhibit the phosphorylation of IRF3 at Ser396 by TBK1, but suffered infecting, HDACs are degraded through autophagy pathway by interacting with LC3-II to promote IRF3 phosphorylation enhancing IFN-I production. Targeting HADCs may be an approach to treating SLE via reducing the production of IFN-I [197]. It is also demonstrated that antioxidant treatment and metabolic rescue of autolysosome degradation emerges as drug targets in SLE based on the relationship between IFN and mitochondrial functions [198]. Moreover, UXT is also a potential target in SLE patients because of its positive regulation function in the STING degradation [8].

4.2. Treating RA through targeting autophagy

Quercetin inhibits neutrophil extracellular traps (NET) formation that is associated with the pathogenesis of RA by suppressing autophagy [176]. Chelerythrine increases the intracellular level of ROS and the apoptotic rate of HFLS-RA by activating the AMPK/mTOR/ULK-1 signalling pathways [177]. Celastrol inhibits rheumatoid arthritis by increasing autophagosome levels and LC3B protein expression to induce autophagy in TNFα-treated FLSs via inhibition of the PI3K/AKT/mTOR signalling pathway [112]. Resveratrol can relieve experimental RA by activating autophagy [114]. Anti-TNFα antibody, such as infliximab, adalimumab and golimumab, can be used to treat RA and IBD. It can induce regulatory macrophages to a phenotype similar to M2, which participates in suppressing inflammation. And autophagy levels are closely related to phenotypic changes [178].

4.3. Treating MS through targeting autophagy

CQ delays disease onset or severity at different stages of EAE through blocking the integration of autophagosomes and lysosomes [169]. Dimethyl fumarate treatment induces autophagy in microglia to suppress proinflammatory responses and protect neurons with the expression of LC3 and ATG7 increasing [179]. It is found that autophagy is activated in MS or experimental models, but increasing autophagy causes demylinization. Haloperidol and clozapine inhibit autophagy, prevent demylinization, induce remyelination, and revert MS behavioural deficits [180]. Sildenafil alleviates EAE by activating autophagy in the spinal cord, by means of the eNOS-NO-AMPK-mTOR-LC3-beclin1-ATG5 and eNOS-NO-AMPK-mTOR-CREB BDNF pathways [181]. Nicotinamide adenine dinucleotide alleviates EAE through the activation of autophagy and the suppression of NLRP3 inflammasome [182].

4.4. Treating IBD through targeting autophagy

P140 is a pretty worthwhile phosphopeptide for treatment of autoimmune diseases. It can correct autophagy defects in IBD mice model [175]. Dapagliflozin activates autophagy and suppresses apoptosis to attenuate experimental inflammatory bowel disease in rats through AMPK/mTOR, HMGB1/RAGE and Nrf2/HO-1 pathways [183]. Andrographolide (Andro) induces mitophagy in macrophages, leading to a reversed mitochondrial membrane potential collapse, which in turn inactivates the NLRP3 inflammasome. So Andro can prevent colitis-associated cancer via mitophagy-mediated NLRP3 inflammasome inhibition [184]. Agonist of cannabinoid receptor 2 inhibits NLRP3 inflammasome activation and alleviates DSS-induced colitis in mice through increasing autophagy process [185]. AC-73 inhibits CD147/ERK1/2 and STAT3 signalling pathway activation and induces autophagy. It may be a novel anti-fibrotic therapeutic option in IBD [186]. It is reported that the levels of ANP and its receptor decreases and the STING pathway is activated statistically in the UC patients and the mouse model of colitis. And using ANP treatment can reduce the phosphorylation level of STING. Therefore, ANP repairs the gut barrier and inhibits ER stress-induced autophagy via the STING pathway [187].

An increase in LRRK2 suppresses autophagy and enhances Dectin-1-induced immunity in a mouse model of colitis, which means inhibition of LRRK2 may be a potential treatment target for IBD [199]. RNF186 acts as an E3 ubiquitin-protein ligase for EPHB2 and regulates the ubiquitination of EPHB2. And the results showed that rnf186 and ephb2 knockdown mice have a more severe colitis phenotype compared to wild type, which suggests autophagy defection leads to IBD aggravation. Importantly, treating with ephrin-B1-Fc recombinant protein effectively relieves DSS-induced mouse colitis [200]. And as is described above [139], BRG1 can alleviate colonic inflammation through autophagy-mediated ROS sequestration. Thus, BGR1 agonist may be a novel target for IBD treatment. Further, circGMCL1 is identified as the candidate circRNA to treat IBD, which can protect intestinal barrier function through alleviating NLRP3 inflammasome-mediated epithelial pyroptosis by promoting autophagy through regulating ANXA7 via sponging miR-124-3p [201].

4.5. Treating psoriasis through targeting autophagy

Cis-khellactone suppresses proinflammatory phenotypic macrophages by promoting autophagy [188]. Jueyin granules induce autophagy by upregulating ApoA1 and inhibit the infiltration of CD4+ T cells and macrophages to alleviate imiquimod-induced psoriatic inflammation in a mouse model [148,189]. PSORI-CM02 induces autophagy and then inhibits the proliferation of HaCaT cells to alleviate psoriasis in vivo and vitro via suppression of the PI3K/Akt/mTOR pathway [64]. Fenofibrate blocks IL-17A signalling including MAPK and NF-κB signalling pathways. And the enhancement of autophagy by fenofibrate exerts anti-inflammatory effects [190].

4.6. Other treatment strategies through targeting autophagy

Additionally, epigallocatechin-3-gallate (EGCG) induces autophagy and apoptosis to treat vitiligo via targeting TNFSF10 [66]. Itaconate can decrease DCs autophagy and maturation to ameliorates liver inflammation in S100-induced AIH mice through regulating the PI3K/AKT/mTOR pathway [191]. And methylprednisolone can improve ConA-induced hepatocyte injury via regulating mitochondria-mediated apoptosis and autophagy dysfunction through the Akt/mTOR signalling pathway [192]. Astaxanthin reduced immune liver injury in ConA-induced AIH through downregulation of JNK/p-JNK-mediated apoptosis and autophagy [193]. Neuregulin-4 can promote autophagy in T1D mice via the AMPK/mTOR signalling pathway [157]. Allicin treatment suppresses STZ-induced T1D progression via activating AMPK/mTOR mediated autophagy pathway [194]. And vitamin D can increase the mRNA expression of LC3 and Beclin1 to induce autophagy, and promote the expression of Bcl-2 to decrease the rate of apoptosis. It is suggested that vitamin D might be a potential drug to treat T1D via autophagy process [195].

5. Discussion

In this review, we overviewed autophagy pathway, discussed the relation between autophagy and autoimmune diseases, and listed the treatment strategies from a perspective of autophagy.

Autophagy is evolutionarily conserved and regarded as a self-eating process. Autophagy can supply nutrition for cell survivals via degrading some cargoes under starvation, and maintain cellular homeostasis when suffering from virus or microbe infection and stimuli like ROS, ultraviolet radiation and drugs. Autophagy is divided into three classes based on different degradation mechanisms: macroautophagy, CMA and microautophagy. Besides, we talked about the three types of autophagy and essential ATGs respectively. And then we discussed autophagy how participates in regulating autoimmune diseases, including SLE, RA, MS, IBD, psoriasis, vitiligo, AIH and T1D. Autophagy has a tight relation with autoimmune diseases. Autophagy and core proteins involve in regulating occurrence and development of diseases. For instance, ATG5, a core autophagic protein, involves in B cell autophagy to initiate the development of SLE [80,81], and highly expresses in RA patients’ tissues [101,102]. ATG7 defect leads to an increase in intracellular accumulation of phagocytosed myelin and progressive MS-like disease [60]. And ULK1 and ATG5 is necessary to ameliorate neuroinflammation [60,124]. Defective AP1S3 that is an autophagic modulator impacts autophagy process, and increases the accumulation of p62 and inflammation responses in KCs [145]. Furthermore, it is demonstrated that autophagy plays a protective role in vitiligo. Autophagy occurs in melanocytes and fibroblasts from non-lesional skin of vitiligo patients to antagonise degenerative processes in normal appearing vitiligo skin and resist the metabolic stress [151].

Additionally, autophagy has different mechanisms for regulating autoimmune diseases. CK1α can regulate STING degradation via phosphorylating p62 [97]. UXT synergistically promotes p62-mediated STING autophagic degradation [8]. These findings are demonstrated that autophagy negatively regulate IFN-I responses to relieve hyperactivation of inflammation responses in the SLE patients. TNFα is a critical pathogenic factor for RA. Targeting autophagy for inhibition inflammation responses through blocking TNFα response is researched broadly [101]. And OPTN is upregulated in the presence of proinflammatory cytokines in FLS [58]. NDP52 mediates B cell mitophagy and reduces the production of pro-inflammatory cytokines in MS [127]. ATG16L1 mutant could impact the process of autophagy and prompt the production of pro-inflammatory cytokines aggravating IBD [132]. IRGM mediates selective autophagic degradation of NLRP3 and ASC to suppress inflammation responses and the symptoms of IBD [61]. Autophagic degradation of innate immune sensers like cGAS, RIG-I and TLR3 inhibits synthesis of proinflammation cytokines to relieve psoriasis [63]. TRMP2 promotes the secretion of CXCL16 via inhibiting autophagy [153]. Thus, blocking TRMP2 is a potential strategy to treat vitiligo. cDCs excessive maturity contributes to the development of AIH. Increasing tolerogenic cDCs and decreasing inflammation responses via inhibiting autophagy flux could be a new therapeutic strategy for AIH, which indicates autophagy is proinflammatory [154].

Ultimately, we concluded the treatment strategies against autoimmune diseases via targeting autophagy. Nowadays, the ways to treat autoimmune diseases are including but not limited to anti-TNFα therapy and oral chemical agents. Infliximab, adalimumab and golimumab play critical roles in specific inhibition of TNFα to decrease inflammation responses to alleviate autoimmune diseases [84]. Oral chemical agents like HCQ and CQ can effectively inhibit lysosome degradation process and block the fusion of autophagosome and lysosome in the EAE used to treat various autoimmune diseases [167,169]. P140 is a phosphopeptide, which can treat SLE and IBD through preventing hyperactivation of immune cells and restoring immune homeostasis [173–175]. And some traditional Chinese medicines like Jueyin granules [148,189] might relieve autoimmune symptoms.

Recently, numerous researches have reported that autophagy and ATGs can regulate the developments of various autoimmune diseases. Therefore, it is significant to further explore the treatment strategies of autoimmune diseases via targeting autophagy. Canonical oral chemical agents like HCQ and CQ are used broadly, and then whether develop more efficient and lower toxicant drugs. And some traditional Chinese medicines is found to relieve the symptoms of autoimmune diseases. Next, screening out more valuable TCMs is pregnant for treatment. Moreover, it is crucial to exploit more potential treatment targets based on existing researches. Besides, personalised medicine could be applied to treat autoimmune diseases from a perspective of autophagy.

Authors’ contributions

J. Lyu, H.Z. and C.W. wrote the manuscript and prepared figures. Tables were created by J. Lyu. M.P. edited and revised the manuscript. All authors read and approved the final manuscript.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

This work was supported by the National Natural Science Foundation of China (82202008), the Natural Science Foundation of Jiangsu Province (BK20221029).