Autophagy/Mitophagy Regulated by Ubiquitination: A Promising Pathway in Cancer Therapeutics

Simple Summary Autophagy and mitophagy are important processes in the regulation of cancer progression. Although autophagy and mitophagy have dual roles in cancer, targeting their regulation has potential for developing an effective cancer treatment strategy. Thus, it is important to understand how ubiquitination and deubiquitination of autophagy-related proteins are regulated to exploit autophagy and mitophagy during cancer development. Abstract Autophagy is essential for organismal development, maintenance of energy homeostasis, and quality control of organelles and proteins. As a selective form of autophagy, mitophagy is necessary for effectively eliminating dysfunctional mitochondria. Both autophagy and mitophagy are linked with tumor progression and inhibition. The regulation of mitophagy and autophagy depend upon tumor type and stage. In tumors, mitophagy has dual roles: it removes damaged mitochondria to maintain healthy mitochondria and energy production, which are necessary for tumor growth. In contrast, mitophagy has been shown to inhibit tumor growth by mitigating excessive ROS production, thus preventing mutation and chromosomal instability. Ubiquitination and deubiquitination are important modifications that regulate autophagy. Multiple E3 ubiquitin ligases and DUBs modulate the activity of the autophagy and mitophagy machinery, thereby influencing cancer progression. In this review, we summarize the mechanistic association between cancer development and autophagy/mitophagy activities regulated by the ubiquitin modification of autophagic proteins. In addition, we discuss the function of multiple proteins involved in autophagy/mitophagy in tumors that may represent potential therapeutic targets.


Introduction
The ubiquitin-proteasome system (UPS) and autophagy are important for the maintenance of cellular homeostasis. A variety of stimuli such as oxidative stress, heat stress, and DNA damage induces the accumulation of abnormal proteins in the ER [1]. Moreover, in normal cells, approximately 30% of newly synthesized proteins are misfolded [2]. These abnormal proteins are eliminated through UPS and autophagy, which contributes to the maintenance of cellular proteostasis.
Ubiquitination is important for the degradation of proteins, thereby regulating their function. The inhibition of ubiquitination is responsible for the development of certain diseases and cancers [3]. In particular, the regulation of metabolic signaling pathways and transcription factors, such as oncogenes or tumor suppressors, is closely associated with cancer metabolism through ubiquitination [4]. Deubiquitination maintains homeostasis, and deubiquitinating enzymes (DUBs) regulate many cellular processes. Studies have shown that the activation of DUBs is also dysregulated in cancer [5].
Recent reports have suggested that UPS is interconnected with autophagy, and many studies have focused on the relationship between autophagy and the ubiquitination process. Autophagy is known for its pathophysiological role in cancer and is involved in the or lysosomes. Recent studies have suggested that the SNARE complex is important for autophagosome-lysosome fusion. There are four types of SNARE-mediated fusion: Q a , Q b , Q c , and R of SNARE motifs [39]. STX17 and SNAP29, a major autophagosomal Q-SNARE protein, are involved in autophagosome maturation. STX17 and SNAP29 form the autophagosome Q abc bundle, which subsequently forms a complex with a lysosomelocalized R-SNARE, such as VAMP7, VAMP8, and YKT6, during autophagosome-lysosome fusion [40].
Understanding the processes of molecular regulation occurring at each step of autophagy will provide insight for effective targeting of autophagy given its involvement in the development of diseases such as cancer. Table 1. Specific roles of ATG proteins in autophagy.

The Relationship between Autophagy and Cancer
Autophagy is vital in organismal development, assisting in the regulation of the adaptive immune system, the maintenance of energy homeostasis, and quality control of organelles and proteins [69,70]. Accordingly, autophagy is considered an important biological process and is closely linked to various diseases. Moreover, autophagy plays a complex role in cancer, which is not fully understood [71].
Autophagy exhibits both tumor-suppressing and tumor-promoting functions depending on the cellular context of tumors, such as cancer stage, primary type, and the tumor microenvironment. The functional complexities of autophagy have been reported because of its association with multiple oncogenes or tumor suppressors. The tumorsuppressing role of autophagy was initially identified in a study of the BECN1 gene, which is monoallelically deleted in dominant portions of human breast, ovarian, and prostate tumors [72]. Homozygous BECN1 knockout mice are embryonically lethal, whereas heterozygous BECN1 expression in mice results in spontaneous tumorigenesis. Mice with heterozygotic BECN1 develop lymphoma, hepatocellular carcinoma, and lung adenocarcinomas [73].
Deletion of ATG5 results in a tumor-suppressive phenotype, similar to abnormal BECN1 in cancer models, but only benign hepatomas in a mouse liver model [74]. ATG2B and ATG5 suppress cancer stemness by inducing autophagy in TNBC [75]. These results suggest that deficient autophagy enhances tumor initiation at the early stages of liver cancer but does not contribute to further progression of malignant tumors. In colorectal and gastric cancer patients, a reduction in autophagy because of a mutation in ATG2, ATG5, ATG9, and ATG12 was observed [76]. Moreover, ATG12 inhibits anti-apoptotic BCL-2 expression, which inhibits tumor cell survival [77]. These results indicate that autophagy has a tumor-suppressive role in cancer.
The autophagy substrate protein p62/SQSM1 is positively associated with tumor progression. Studies have shown that abnormal p62 accumulation is associated with various cancers [78][79][80][81][82]. Autophagy deficient cells accumulate p62 and induce metabolic stress, which results in oxidative stress and damaged mitochondria [83]. When exposed to metabolic stress, autophagy contributes to survival. Other studies have provided evidence that autophagy induces tumor cell survival and progression [84,85]. Moreover, autophagyrelated genes, such as LC3, GABARAP, and ATG8, are induced in tumors compared with normal tissues and are associated with a poor diagnosis [86]. One study suggested that EI24 (etoposide-induced gene 2.4 kb; PIG8, p53-induced gene 8) is a key component of autophagy and promotes the proliferation of pancreatic tumor cells [87].
Autophagy has a dual role in cancer depending on tumor stage and type [88]. Autophagy can regulate genome stability and prevent cell damage at early stages of cancer progression and inhibit the accumulation of p62 aggregates, thereby preventing tumor progression [89]. However, at later stages, autophagy acts as a defense mechanism, maintains mitochondrial function, and attenuates DNA damage, resulting in cancer cell survival through resistance to various stimuli such as nutrient deprivation, DNA damage, hypoxia, and chemotherapy [90]. Multiple studies using genetically engineered mouse models of cancer have suggested support for the cancer-promoting roles of autophagy, despite the fact that induction of tumor initiation by autophagy depletion and genetic deletion of ATG5 and ATG7 in mice ultimately decreases malignant tumor progression in tissue-specific tumor models that are spontaneously derived from known oncogenes [91][92][93]. Consequently, autophagy is interconnected with tumor metabolic alteration and supports tumor progression [94,95]. These results indicate that autophagy is clearly involved in cancer progression; however, its roles in different cancers varu depending on the cancer type, stage, and tumor microenvironment (TME).

Machinery for Ubiquitination and Deubiquitination of Autophagy in Cancer
Recently, numerous reports have suggested a role for ubiquitination/deubiquitination in modulating autophagy [96,97]. In this part of the review, we discuss how certain autophagy-related proteins are regulated by various molecular modes of ubiquitin modification [98,99]. As previously discussed, ubiquitination, and deubiquitination are important for cell function and homeostasis. The modulating systems of ubiquitin are important for proteostasis in cells, which is regulated by autophagy and UPS. Autophagy is regulated by ubiquitination through at least two pathways. First, the stability of upstream autophagy regulators and autophagy machinery are controlled through ubiquitination. Second, protein proximity, or interactions between autophagy components and ubiquitinated proteins are facilitated by the recruitment of autophagy adaptors, such as histone deacetylase 6 (HDAC6), ubiquitin receptor nuclear dot protein 52kd (NDP52), and p62, thereby promoting autolysosome formation [100].
As a key factor in autophagy initiation, ULK1 levels are regulated through ubiquitination and deubiquitination by E3 ubiquitin ligases and DUBs. TRAF6 induces polyubiquitination of ULK1 via Lys63-linked ubiquitin and promotes autophagy [101]. TRAF6-ULK1-dependent activation of autophagy plays a role in chronic myeloid leukemia drug resistance [102]. Conversely, TMEM189 (transmembrane protein 189) disrupts the interaction between TRAF6 and ULK1 and inhibits K63-linked polyubiquitination of ULK1, resulting in reduction of autophagy and induction of tumorigenesis [103]. Moreover, we and another group reported that NEDD4L, an E3 ubiquitin ligase, interacts with ULK1, which results in its ubiquitination, with a subsequent reduction in ULK1 levels and autophagy [104,105]. These phenotypes attenuate cancer cell survival and in vivo tumorigenesis in pancreatic cancer model [104]. Modulation of DUBs affects ULK1 ubiquitination, thereby regulating ULK1 kinase activity and protein stability [106]. Ubiquitin-specific protease 20 (USP20) induces deubiquitination of ULK1, which maintains basal ULK1 levels by preventing ULK1 degradation, and it directly affects autophagy initiation [107]. Finally, USP20 interacts with ULK1 and suppresses autophagy termination under starvation conditions. These studies demonstrate that the balance of ubiquitination and deubiquitination of ULK1 is important for regulating the process of autophagy, and modulating ULK1 stability is a potential strategy for the treatment of cancer.
As a subunit of PI3KC3, AMBRA1 also acts a downstream substrate of ULK1 kinase. Because of the spatial closeness of AMBRA1 to ULK1 and Beclin1, AMBRA1 is required for the recruitment of ULK1 to TRAF6 and is also involved in Beclin-1 ubiquitination by TRAF6 and CUL4 [101,117]. CUL4-mediated AMBRA1 regulation is associated with cell proliferation, migration, and invasion [117]. AMBRA1 is highly expressed in cancers and associated with poor patient prognosis [118]. However, recent studies showed that AMBRA1 functions as a tumor suppressor by ubiquitinating and degrading cyclin D, a substrate receptor of the CUL4 complex [119].
The mammalian ATG8 homologs GABARAPs and LC3s are required for autophagosome membrane formation and are associated with autophagy induction and autophagosome-lysosome fusion. Members of the GABARAP and LC3 family have dual roles in cancer depending on the tumor type [120]. GABARAP upregulation is associated with a favorable prognosis in pancreatic cancer but poor prognosis in liver cancer [121,122]. Normally, LC3 expression levels are induced in multiple cancers; however, high LC3A and LC3B expression in pancreatic and renal cancer are associated with prolonged survival [121]. These GABARPs and LC3s are regulated by several ubiquitin ligases such as BIRC6 and UBA6 [123]. To address these functional differences in LC3 on cancer, in a recent study focused on LB3B mutation, P32Q mutation of LC3B reduces the stability of LC3B and its ability to interact with p62, resulting in autophagy dysfunction in cancer [124].
These studies suggest that autophagy plays a tumor-suppressive or oncogenic role based on the ubiquitin-mediated regulation of autophagy-related proteins. UVRAG (ultraviolet radiation resistance-associated gene), a beclin1-binding autophagy regulator, induces nonsense mutations in gastric cancers [128]. UVRAG is ubiquitinated by SMURF1, which promotes autophagosome maturation. The DUB ZRANB1 deubiquitinates UVRAG of attached ubiquitin chains, thereby inhibiting autophagy through increasing interactions with RUBCN, an autophagy inhibiting factor, to form UVRAG-RUBCN. Moreover, UVRAG ubiquitination, associated with phosphorylation status, results in a significant blockade of hepatocellular carcinoma (HCC) growth in vitro and in vivo [129].
Additional examples of enzymes that regulate other autophagy components, including ATG3, ATG4, ATG13, ATG14, and ATG16L, are summarized in Figure 1 and Table 2. Overall, the role of autophagy in different cancer types and stages of progression may be determined by the specific modifications, such as ubiquitination, of the individual autophagy components; however, it remains unknown which ubiquitin-modulating factors and how E3/DUBs regulate autophagy-mediated cancerous phenotypes during specific oncogenic stages.

Mitophagy
Mitochondria are intracellular organelles that produce ATP by utilizing substrates, such as glucose, amino acids, and fatty acids, to control cellular metabolic activities. These organelles also participate in programmed cell death by regulating intracellular calcium signaling, hormone synthesis, and inflammatory responses. To meet the increased bioenergetics and biosynthetic needs of cancer cells and manage oxidative stress, mitochondrial metabolic activities tend to be rewired, and their numbers must be precisely controlled.
Autophagy has been traditionally considered a nonselective bulk-degradation system that ultimately serves as a eukaryotic survival strategy; however, Terje Johansen group proposed a selective degradation mechanism for ubiquitinated proteins by autophagy [141,142]. Selective autophagy is classified according to the type of cargo, which can be protein aggregates, lysosomes, or mitochondria, and is referred to as aggrephagy, lysophagy, or mitophagy, respectively. Mitophagy is one of the mechanisms that controls mitochondrial quality (selective degradation of mitochondria).
Mitophagy is required for mitochondrial mass control as well as the removal of damaged, dysfunctional, and obsolete mitochondria. Mitochondria that are dysfunctional are unable to efficiently carry out oxidative phosphorylation (OXPHOS), which results in increased oxidative stress and accelerates mitochondria-mediated cell death. Because mitochondria are highly dynamic networks rather than isolated organelles, dysfunctional mitochondria must be removed from the healthy network and subjected to fission, fusion, and mitophagy machinery [143,144]. Mitophagy receptors recognize damaged mitochondria and induce mitochondrial clearance. Numerous studies have demonstrated that dysregulated mitophagy is linked to pathological and physiological processes [145,146]. Moreover, because of the close relationship between cell death susceptibility and mitochondrial homeostasis, mitophagy, as a mitochondrial quality control process, is important for the anticancer therapeutic response. These finely controlled processes are regulated through ubiquitin-dependent and -independent pathways, which may also be categorized based on the types of mitochondrial cargo receptors present during various cellular stresses.

Ubiquitin-Dependent-Mitophagy
As a ubiquitin-dependent pathway, PTEN-induced kinase 1 (PINK1)-Parkin-mediated mitophagy was the first identified and most studied in neurodegenerative disease. PINK1, a serine/threonine protein kinase that initiates the PINK1-Parkin pathway, is encoded by the PARK6 locus. PINK1 is translocated into the inner and outer membrane, where it is cleaved by proteases including presenilin-associated rhomboid-like (PARL) and degraded by the proteasome, resulting in low basal levels [147]. Parkin, a component of the E3 ubiquitin ligase complex, is phosphorylated by PINK1 and translocated into the mitochondria [148], where it ubiquitinates several mitochondrial proteins in the outer membrane, such as Miro1, voltage-dependent anion channel-1 (VDAC-1), Mitofusin-1 (MFN1), and MFN2, thereby recruiting mitophagy receptor/adaptors including sequestosome-1-like receptors, SQSTM1/p62, NBR1, NDP52, TAX1BP1, and OPTN and providing signals for Parkinmediated mitochondrial degradation [149]. The selective autophagy receptor/adaptors interact with the ubiquitinated outer membrane mitochondrial proteins for cargo recognition and subsequently bind to autophagosome-associated proteins, such as LC3 and GABARAP, resulting in the autophagosomal sequestration of damaged mitochondria. Finally, the engulfed mitochondria are eliminated by autolysosomes.
Activated Parkin is negatively regulated by three DUBs: USP15, USP30, and USP35. USP15 inhibits Parkin-mediated mitochondrial ubiquitination and mitophagy [150]. USP30 is a major DUB that inhibits mitophagy by deubiquitinating Parkin substrates, such as TOM20 [151]. This study showed that depletion of USP30 induces the degradation of mitochondria in HeLa and neuronal cells. Although it can process K11, K48, and K63 chains, USP30 proteolytic activity on K6-linked ubiquitin chains is more efficient [152,153]. In addition, the short form of USP35 impairs mitophagy through Parkin deubiquitination [154]. Unlike other DUBs, however, USP8 positively regulates mitophagy by removing K6-linked ubiquitin chains from Parkin [155]. These processes are important for maintaining mitochondrial quality.
FUNDC1 is found in OMM which binds LC3 directly and acts as autophagy receptor for mitophagy under hypoxic conditions [162,163]. FUNDC1 activity is regulated by phosphorylation or dephosphorylation, which modulates the interaction with mitophagy related genes such as OPA1, DRP1, and ULK1. Previous studies have demonstrated that FUNDC1 regulates mitochondrial dynamics and mitophagy by interacting with OPA1 and DRP1/DNM1L [164]. In addition, ULK1 regulates FUNDC1 through phosphorylation, which is essential for recruitment into damaged mitochondria and mitophagy [165,166]. FUNDC1 phosphorylated by CK2 is dephosphorylated by phosphoglycerate mutase 5 (PGAM5) under hypoxic conditions, which reduces pFUNDC1-OPA1 levels and promotes the interaction with DRP1 and MAP1LC3, thereby forming autophagosomes to eliminate damaged mitochondria [166]. Moreover, the cytosolic molecular chaperone heat shock protein family A (hsp70) member 8 (HSPA8) interacts with FUNDC1 and regulates FUNDC1 stability and mitophagy [167].
Overall, these findings indicate that mitophagy is regulated by both ubiquitinindependent and -dependent pathways, both of which are important in regulating mitochondrial dynamics and mitophagy. Several additional mitophagy-modulating proteins are summarized in Figure 2 and Table 3.
FUNDC1 is found in OMM which binds LC3 directly and acts as autophagy receptor for mitophagy under hypoxic conditions [162,163]. FUNDC1 activity is regulated by phosphorylation or dephosphorylation, which modulates the interaction with mitophagy related genes such as OPA1, DRP1, and ULK1. Previous studies have demonstrated that FUNDC1 regulates mitochondrial dynamics and mitophagy by interacting with OPA1 and DRP1/DNM1L [164]. In addition, ULK1 regulates FUNDC1 through phosphorylation, which is essential for recruitment into damaged mitochondria and mitophagy [165,166]. FUNDC1 phosphorylated by CK2 is dephosphorylated by phosphoglycerate mutase 5 (PGAM5) under hypoxic conditions, which reduces pFUNDC1-OPA1 levels and promotes the interaction with DRP1 and MAP1LC3, thereby forming autophagosomes to eliminate damaged mitochondria [166]. Moreover, the cytosolic molecular chaperone heat shock protein family A (hsp70) member 8 (HSPA8) interacts with FUNDC1 and regulates FUNDC1 stability and mitophagy [167].
Overall, these findings indicate that mitophagy is regulated by both ubiquitin-independent and -dependent pathways, both of which are important in regulating mitochondrial dynamics and mitophagy. Several additional mitophagy-modulating proteins are summarized in Figure 2 and Table 3.

Relationship between Mitophagy and Cancer
Although multiple reports have suggested that autophagy is elevated in several cancers and is important for cancer cell growth and survival, the precise role of mitophagy as a type of selective autophagy during cancer progression remains controversial. The roles of mitophagy in cancer are complicated and influenced by the type and stage of the disease. Similar to autophagy, mitophagy is normally associated with tumor suppression at early stages of tumor development by removing excess ROS derived from damaged mitochondria and reducing genome instability, which further activates the immune response. However, mitophagy supports tumor growth at later stages, which may be used by cancer cells during to meet their metabolic demands and to resist apoptosis during tumor growth, thereby promoting tumor development. Most mitophagy receptors or regulators involved in cancer patients are dysregulated; however, whether they function as tumor promoters or suppressors appears to be highly dependent on the cancer subtype and the TME [188]. Mitophagy may be divided into two types: ubiquitin-dependent and -independent pathways. Some mitophagy receptors/adaptors have not revealed their precise regulation mechanisms yet. The relationship of both mitophagy pathways and cancer development have been reported in various of cancers, but the phenotypic results are quite varied despite the same genetic background of tumor models.

Ubiquitination of Mitophagy in Cancers
PINK1-Parkin is one of the main ubiquitin-dependent signaling pathways of mitophagy and is known to be involved in neurodegenerative diseases and cancer [189]. Dysfunction of PINK/Parkin disrupts mitochondrial quality control and has been observed in a variety of human cancers [190]. Previous studies have shown that PINK1 deficiency promotes the Warburg effect and cancer progression by regulating mitophagy, cancer metabolic reprogramming, and tumor-associated macrophage polarization in gastric cancer [163]. In addition, upregulation of STMOL2 induces mitophagy and tumor metastasis by interacting with PINK1 in HCC, and depletion of PINK1 induces mutant Kras-mediated pancreatic tumorigenesis [164,191]. Parkin and PINK1 suppress HIF-1α stabilization through HIF1 ubiquitination. These features support the link of Parkin and PINK1 to a tumor-suppressing mechanism in multiple cancers, including breast and pancreatic cancer [191,192]. A more recent study suggested that Parkin has an important tumor-suppressing role through metabolic reprogramming, which further inhibits cell migration, exacerbates oxidative stress, and ultimately suppresses tumor progression. Interestingly, Parkin-mediated mitophagy is dispensable for Parkin-driven tumor suppression [193].
As discussed above, however, although PINK1-Parkin is the primary ubiquitindependent pathway, other E3 ligases can substitute for Parkin. One study showed that MUL1 is an E3 ubiquitin ligase that can compensate for Parkin deficiency in Drosophila [194]. Moreover, MUL1 regulates mitochondrial dynamics and mitophagy through various substrates, including mitochondrial fission proteins and autophagy-related proteins. Furthermore, this ubiquitin mediated regulation is associated with several cancer types and neurological diseases [195,196]. SIAH1, a RING-type E3-ubiquitin ligase, is involved in mitophagy by forming a PINK1 and SNCAIP/synphilin-1 complex, which recruits LC3, and initiates mitophagy. Mutation of PINK1 impairs the recruitment of SNCAIP in Parkinson's disease [197]. ARIH1 E3 ubiquitin ligase is recruited to mitochondria by PINK1 to eliminate mitophagy of polyubiquitinated, damaged mitochondria in response to chemotherapeutic drug-induced death, thereby protecting cancer cells [198]. Several recent studies have shown that mitophagy is regulated in a Pink1-dependent but not Parkin-dependent manner. Vps13D regulates mitophagy via a core machinery dependent pathway by modulating ubiquitin and ATG8a localization that is dependent upon Pink1 but not Parkin [199]. In addition, Parkin is regulated by PINK1 in normal cells, but it is not involved in Pink1-dependent mitophagy in pancreatic cancer cells [200].
Multiple PINK1/Parkin-independent as well as -dependent mitophagy receptors/ adaptors have been reported for their cancer-associated roles and functional regulation by ubiquitination in cancer ( Table 4). As well-studied PINK1/Parkin-independent mitophagy receptor/adaptors, BNIP3 and BNIP3L/NIX have dual roles in cancer progression. Depletion of BNIP3 in multiple cancers inhibits mitochondrial function and promotes tumor progression through various cell death resistance mechanisms [201][202][203][204][205]. Upregulation of BNIP3L reduces apoptosis and oxidative damage, thereby inducing breast cancer and glioblastoma cell survival [206,207]. On the other hand, suppression of BNIP3L/NIX results in maintenance of mitochondrial functionality and decreases tumor growth in a pancreatic cancer model, thus showing its oncogenic feature [208].
The role of another PINK1/Parkin-independent mitophagy adaptor, FUNDC1, in mitophagy has been demonstrated, in which it is regulated by MARCH5-mediated ubiquitination [182] as well as ULK1-, CK2-, or SRC-mediated phosphorylation [164][165][166]. In cancer, FUNDC1 has dual roles in tumor progression at the initial stage of hepatocellular carcinoma (HCC) and suppresses tumorigenesis by inhibiting the inflammation response. It also induces HCC development at a late stage in a chemical-induced HCC mouse model [209]. However, in breast cancer, FUNDC1 likely functions as a tumor promoter through different mechanisms, in which depletion of FUNDC1 blocks TNBC cell proliferation by deregulating Ca2+ release from the ER and through NFATC1 activation, which are reversed by overexpression of BMI1 [210]. Moreover, downregulation of FUNDC1 and lnc049808 were observed following melatonin treatment in TNBC, and knockdown of FUNDC1 and lnc049808 inhibits TNBC progression by deregulating the interaction of oncogenic microRNA [211].
In addition to mitophagy cargo receptors, multiple proteins involved in mitochondrial dynamics and morphology are also associated with the development of various cancers. A mitochondrial fission factor, Drp1, has an oncogenic role in multiple cancers by promoting autophagy, altering energy metabolism pathways, and promoting cancer cell survival [212][213][214][215]. In contrast to mitochondrial fusion molecules, MFN1 and MFN2 exhibit tumor-suppressing roles in cancer, and deletion of MFN1/2 promotes tumor growth and malignancy, whereas overexpression of MFN2 results in significant tumor reduction in vitro and in vivo [215][216][217].
Finally, the selective autophagy receptor/adaptors, including p62/SQSTM1, contain ubiquitin binding domains and/or are ubiquitinated to regulate their activity. These molecules are closely linked to various tumorigenic processes (Table 4).  [198] • MUC1 degrades ATAD3A by inducing ubiquitination and promotes mitophagy in a Pink1-dependent manner, thereby inducing breast cancer progression. [218] Gastric cancer • Deficiency of PINK1 promotes the Warburg effect and cancer progression by regulating mitophagy, metabolic reprogramming, and tumor-associated macrophagy (TAM) polarization. [219] Hepatocellular carcinoma • Upregulation of STMOL2 induces mitophagy and tumor metastasis via interaction with PINK1 in HCC. [192] Pancreatic ductal adenocarcinoma • Depletion of PINK1 induces mutant KRas-driven pancreatic tumorigenesis. [191] Parkin Breast cancer • Parkin inhibits breast tumor progression through degradation of HIF-1a by inducing ubiquitination. [220] • Parkin was identified as a key tumor suppressor through metabolic alteration by cancer ubiquinone analysis. [193] BNIP3 Breast cancer • Knockout of BNIP3 disrupts mitochondrial function and induces tumor progression. [201] Hepatocellular carcinoma • Inhibition of CDK9 disrupts mitochondrial homeostasis and cell death in HCC through the SIRT1-FOXO3-BNIP3 axis and PINK1-PRKN pathway. [202] Lung cancer • Cyclovirobuxine D (CVB-D)-induced mitophagy is regulated via p65/BNIP3/LC3 axis in lung cancer. [203] Pancreatic cancer • BNIP3 is downregulated and hypermethylated in pancreatic cancer in resistance against cell death. [204] • Low levels of BNIP3 at a late stage of pancreatic cancer promote chemoresistance and are associated with poor prognosis.

DRP1
Breast cancer • Notch induces DRP1-mediated mitochondrial fission, thereby inducing survivin expression and cancer cell survival. [212] Colorectal cancer • RAGE induces ERK1/2 activation and DRP1 phosphorylation, which promotes autophagy and then supports cancer cell survival. [213] Pancreatic cancer • Drp1 supports KRas-driven cancer growth through glycolysis induction. [214] •  • p62 is required for hepatocellular carcinoma (HCC) induction in mice by activating NRF2 and mTORC1 and protecting against oxidative stress-induced cell death. [224,225] Breast cancer • p62 is ubiquitinated by TRIM21, which blocks p62 oligomerization and sequestration of proteins to maintain the redox balance. [226] • p62 expression is elevated in breast cancer stem cells by MYC mRNA stabilization.

Autophagy/Mitophagy as Potential Therapeutic Target
Side effects and resistance to chemotherapeutic drugs are major obstacles to cancer treatment. To circumvent drug resistance, numerous studies have examined multitarget combination treatment, since autophagy and mitophagy are induced by numerous conventional cancer therapeutics that block growth factor signaling (e.g., TKI) and/or induce multiple cytotoxic reactions (e.g., proteasome, and anti-apoptosis inhibitors). Autophagy/mitophagy have been considered part of the drug-resistant process for maintaining cancer cell survival and dormancy. Therefore, inhibition of autophagy in combination with conventional anticancer drugs has been tested in clinical trials for a variety of human cancers.
For example, treatment with the autophagy inhibitor and MEK inhibitor trametinib reduces tumor growth in Kras-driven PDAC [232]. In addition, treatment with chloroquine and temozolomide increases patient survival in multiple cancers, including glioma [233]. However, the regulation of autophagy and/or mitophagy results in several unexpected side effects, such as drug resistance and reduced apoptosis [234]. Recent studies have focused on mitochondria as a major source of ROS. Induction of ROS induces cell death during chemotherapy; however, mitophagy reduces ROS formation by degrading damaged mitochondria.
As a result, it is thought that regulating mitophagy-mediated pathways during cancer treatment can overcome tumor cell resistance [235]. Inhibition of mitophagy induces cell death; however, it also promotes cancer cell metastasis. Moreover, the induction of mitophagy promotes drug sensitivity [205].
These unique resistance mechanisms may be the main reason for the failure in anticancer drug development. Although regulating autophagy and/or mitophagy has unexpected effects, numerous studies have attempted to treat cancers in combination with other regimens, such as radiotherapy, chemotherapy, and immunotherapy, which have been shown to inhibit tumor progression. A recent study suggested that the upregulation of mitophagy induces immunogenic cell death and reduces tumor growth by activating cytotoxic T lymphocytes [236].
Concurrent mitophagy modulation during radio-, chemo-, and immuno-therapeutic treatment may overcome the autophagy/mitophagy side effects induced by conventional therapies, and markers of mitophagy related genes may represent novel targets for cancer treatment.
Dysregulation of the ubiquitin-mediated autophagy process has been implicated in various diseases including cancer. In particular, we addressed the impact of ubiquitination in autophagy/mitophagy related proteins on cancer progression. Based on the essential role of autophagy in maintaining cellular homeostasis, ubiquitination of the autophagy components in multiple diseases, particularly cancer, may be closely related to one another. Taken together, ubiquitination of autophagy/mitophagy pathways has great potential for disease treatment, including cancer.

Conclusions
A specific type of selective autophagy, mitophagy, is essential for mitochondrial quality control in cells, which is involved in tumor progression through energy production and the regulation of cell death. Multiple mitophagy pathways are linked to tumor progression. The roles of mitophagy and autophagy are regulated depending on the type and stage of the tumor. Mitophagy has dual functions in tumor progression: it eliminates damaged mitochondria, maintains mitochondrial integrity, and maintains metabolic homeostasis in cancer cells, which promotes tumor growth and survival. In contrast, mitophagy inhibits tumor growth by reducing ROS production and thus prevents mutation and chromosomal instability.
In this review, previously identified autophagy/mitophagy related receptors and adaptors have been suggested as the basis for determining the functional complexity of cancer through E3 ubiquitin ligases and DUB-mediated regulation. Additionally, the regulation of autophagy/mitophagy related receptors and adaptors by E3 ubiquitin ligases or DUBs has different functions in various cancer types. Although multiple studies support the concept that autophagy/mitophagy-related proteins induce or reduce cancer progression, it is still largely unknown how these individual proteins are interconnected with the oncogenic and tumor-suppressing signal cascades. Furthermore, more research should be needed for explaining how cancer-related ubiquitin-regulating enzymes (e.g., E3s and DUBs) directly modulate the autophagy/mitophagy-related proteins during tumor progression. Therefore, understanding the molecular mechanism of ubiquitination of autophagy/mitophagy related proteins, such as mitophagy adaptors/receptors, will provide insight for the development of anticancer therapeutics.