LncRNA-mediated posttranslational modifications and reprogramming of energy metabolism in cancer

2.1 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 (PFKFB3)

In aerobic glycolysis, PFKFB3 converts fructose 6-phosphate (F6P) into fructose-2,6-bisphosphate (F-2,6-BP), which can act as an allosteric activator of the rate-limiting enzyme phosphofructokinase-1 (PFK1) [25]. Studies have identified that lncRNA-mediated reprogramming of energy metabolism is closely related to the PFKFB3 ubiquitination and phosphorylation in cancer [25, 32]. Moreover, our recent study revealed that the lncRNA actin gamma 1 pseudogene (AGPG) specifically bound to the C-terminal domain of PFKFB3, which stimulated the stable expression of PFKFB3 and activated the glycolytic flux by inhibiting the ubiquitination of PFKFB3 at Lys302 and its subsequent proteasome-dependent degradation, leading to metabolic reprogramming in esophageal squamous cell carcinoma cells [25]. In addition, PFKFB3 could also be phosphorylated by the lncRNA YIYA (LINC00538), which was associated with cyclin-dependent kinase 6 (CDK6) and facilitated its binding to cyclin D3. Thus, YIYA regulated the CDK6-dependent phosphorylation of PFKFB3 in a cell cycle-independent manner, which led to the enhanced conversion of F6P to F-2,6-BP and promoted the reprogramming of glucose metabolism and the growth of breast cancer [32].

2.2 Phosphoglycerate kinase 1 (PGK1)

PGK1 is the first crucial metabolic enzyme mediating adenosine-triphosphate (ATP) production via glycolysis and catalysing the conversion of 1,3-bisphosphoglycerate (1,3-BPG) to 3-phosphoglycerate (3-PG) [33]. The activity of PGK1 is mediated by different posttranslational modifications. For example, PGK1 can frequently be phosphorylated, ubiquitinated, and acetylated at multiple sites to regulate tumor metabolism and cancer progression [34-37]. A recent study showed that MetaLnc9 (LINC00963) played a dominant role in the posttranslational activity of PGK1 and stabilized PGK1 by blocking its ubiquitin-mediated degradation, allowing it to exert its carcinogenic activity and accelerate the metastasis of non-small cell lung cancer (NSCLC) cells via the phosphoinositide-3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) signalling [36]. Similarly, gallbladder cancer drug resistance-associated lncRNA1 (GBCDRlnc1), which served as a “decoy molecule”, posttranslationally regulated the level of PGK1 by directly preventing its ubiquitin-mediated degradation in gallbladder cancer. Expression of the autophagy initiator autophagy-related gene 5 (ATG5)-ATG12 conjugate was ultimately up-regulated through the formation of the GBCDRlnc1/PGK1/ATG5-ATG12 complex, which induced autophagy and drug resistance in gallbladder cancer cells [37].

2.3 Pyruvate kinase muscle isozyme M2 (PKM2)

PKM2 catalyses the conversion of phosphoenolpyruvate to pyruvate and generates ATP in the rate-limiting step in glycolysis, which switches glucose metabolism from the normal respiratory chain to lactate production in tumor cells [38, 39]. Coincidentally, PKM2 activity is also regulated by posttranslational modifications, including O-GlcNAcylation, acetylation, phosphorylation, ubiquitination, etc [40-45]. The lncRNAs AC020978, Fez family zinc finger protein 1 antisense ribonucleic acid 1 (FEZF1-AS1), and LINC01554 can reprogram tumor metabolism by regulating the stability of PKM2 via the ubiquitin-mediated proteasome pathway. In detail, AC020978 specifically modulated the stability of the PKM2/hypoxia-inducible factor-1α (HIF-1α) complex, furthered the action of HIF-1α on its target genes, thus forming a positive feedback loop related to tumor-specific metabolism and endowing NSCLC cells with an aggressive phenotype [40]. Additionally, FEZF1-AS1 bound to and increased the stability of PKM2, increasing cytoplasmic and nuclear PKM2 levels. Thus, FEZF1-AS1 promoted the aerobic glycolysis and accelerated the proliferation and metastasis of colorectal cancer (CRC) cells [41]. In contrast, the lncRNA LINC01554 accelerated ubiquitin-mediated degradation of PKM2 to inhibit aerobic glycolysis in hepatocellular carcinoma (HCC) cells via the AKT/mTOR signalling pathway [42]. Moreover, the lncRNA highly up-regulated in liver cancer (HULC) functioned as an adaptor molecule and enhanced the interactions of lactate dehydrogenase A (LDHA) and PKM2 with the intracellular domain of the upstream kinase fibroblast growth factor receptor type 1 (FGFR1), leading to the elevated phosphorylation of LDHA and PKM2, which consequently enhanced glycolysis and increased the proliferation of liver cancer cells [46].

3.1 HIF-1α

HIF-1α plays a key role in the reprogramming of cancer metabolism by activating the transcription of genes that encode glucose transporters and glycolytic enzymes [48, 49]. Accumulating evidence suggests that lncRNAs play important functional roles in regulating HIF-1α activity and stability. For example, Su et al. [50] found that the lncRNA cancer susceptibility candidate 9 (CASC9) reprogramed glycolytic metabolism and stimulated the tumorigenic behaviour of nasopharyngeal cancer cells by interacting with HIF-1α and increasing the abundance of HIF-1α. Chen et al. [51] found that HIF-1α-stabilizing lncRNA (HISLA) inhibited the hydroxylation and degradation of HIF-1α and promoted the aerobic glycolysis in breast cancer cells by blocking the interaction between proline hydroxylase domain 2 (PHD2) and HIF-1α. More interestingly, by activating breast tumor kinase (BRK) phosphorylation at Tyr351, long intergenic noncoding RNA for kinase activation (LINK-A) mediated HIF-1α phosphorylation at Tyr565, which prevented the degradation of HIF-1α under normoxic conditions; moreover, leucine-rich repeat kinase 2 (LRRK2) recruited by LINK-A could also phosphorylate HIF-1α at Ser797, which led to the activation of HIF-1α target genes. The above series of LINK-A-mediated posttranslational modifications promoted glycolytic reprogramming and tumorigenesis in triple-negative breast cancer [52].

Under normoxic conditions, HIF-1α is hydroxylated by PHD at Pro402 and/or Pro564 [53]. After hydroxylation, HIF-1α binds to von Hippel-Lindau (VHL) and undergoes VHL-mediated ubiquitination and degradation via the proteasome pathway. However, the activity of PHD is suppressed under hypoxic conditions. A recent study reported that accumulation of HIF-1α resulted in high expression of PHD, which rapidly induced transcription of long intergenic noncoding RNA (lincRNA)-p21 [54]. Interestingly, highly expressed lincRNA-p21 removed the polyubiquitin chain at Hyp564 installed by VHL and decreased HIF-1α degradation via competitively binding with HIF-1α. As discussed above, the formation of a positive HIF-1α-lincRNA-p21-HIF-1α feedback loop ensured that HIF-1α was highly induced in hypoxia, activating glucose transporter isoform 1 (GLUT1) and LDHA and enhancing the anaerobic glycolysis pathway, which promoted tumor growth [54]. Similarly, the lncRNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) increased the expression of core glycolytic enzymes, including hexokinase 2 (HK2), enolase 1 (ENO1), and GLUT4, by reducing the VHL-mediated ubiquitination and subsequent degradation of HIF-1α [20, 55].

3.2 c-Myc

The c-Myc protein acts as a “master regulator” of cellular metabolism and cancer progression by stimulating many metabolic changes that result in malignant transformation [56]. Additionally, lncRNAs have been reported to be involved in the regulation of cancer energy metabolism via the posttranslational modification of c-Myc. Several lncRNAs are significantly overexpressed and function as oncogenes in CRC or pancreatic cancer, including glycolysis-associated lncRNA of colorectal cancer 1 (GLCC1), long intergenic noncoding RNA for insulin-like growth factor 2 mRNA-binding protein 2 stability (LINRIS), and lncRNA XLOC_006390. Mechanistically, the lncRNA GLCC1 protected c-Myc from ubiquitination by directly interacting with the chaperone heat shock protein 90 (HSP90) and further specified the transcriptional modification pattern of c-Myc target genes such as LDHA, consequently reprogramming glycolytic metabolism for CRC cell proliferation [57]. The lncRNA LINRIS bound to insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2), repressed its ubiquitination and prevented its degradation via the autophagy-lysosome pathway. The LINRIS-IGF2BP2 axis promoted the translation of its target gene c-Myc and accelerated the malignant proliferation of CRC cells by up-regulating aerobic glycolysis [26]. The lncRNA XLOC_006390 stablized c-Myc by preventing its ubiquitination, increasing the expression of glutamate dehydrogenase 1 (GDH1), and subsequently stimulating the production of alpha-ketoglutarate (α-KG). Excess α-KG supplied the tricarboxylic acid (TCA) cycle and facilitated glutamate metabolism, promoting pancreatic cancer growth [58].

In contrast, the lncRNA maternally expressed gene 3 (MEG3) and the lncRNA antisense lncRNA of glutaminase (GLS-AS) were down-regulated and functioned as tumor suppressors in cancer. Mechanistically, MEG3 overexpression enhanced ubiquitin-dependent degradation of c-Myc and repressed c-Myc target genes involved in the glycolytic pathway, including LDHA, PKM2, and HK2 [59]. Similarly, the lncRNA GLS-AS restricts glutaminase expression at the posttranscriptional level by binding with the glutaminase pre-mRNA, resulting in the formation of a double-stranded RNA. Furthermore, GLS-AS reduce Myc expression by disrupting the glutaminase-mediated stabilization of Myc. Conversely, in pancreatic cancer, Myc up-regulated the expression of GLS-AS under nutritional stress, thus forming a mutual feedback loop to inhibit metabolic reprogramming [60].

3.3 NF-κB

NF-κB is an inducible transcription factor that plays a core role in diverse biological processes, including cellular metabolism, epithelial-to-mesenchymal transition, invasion, angiogenesis, metastasis, therapeutic resistance, and other processes [61]. Aberrant NF-κB signalling has been verified to be involved in the pathogenesis of most human cancers [62]. Direct regulation of cell metabolism via the NF-κB pathway has been addressed by several recent studies [63, 64]. In particular, our recent study validated that lncRNA for calcium-dependent kinase activation (CamK-A) regulated Ca²⁺ signalling-mediated remodelling of tumor microenvironment and reprogramming of energy metabolism through posttranslational modification and NF-κB activation [27]. Mechanistically, CamK-A bound both the calmodulin-dependent kinase pregnancy up-regulated non-ubiquitous calmodulin kinase (PNCK) and the C-terminal SH3-like region of inhibitor kappa B alpha (IκBα). Thus, CamK-A promotes PNCK-induce phosphorylation of IκBα at Ser32 under hypoxic conditions, which further induce IκBα degradation and NF-κB activation. In contrast, several NF-κB-related lncRNAs are down-regulated and function as tumor suppressors during cancer progression. For example, Saha et al. [65] reported that the downregulated RNA in cancer (DRAIC) interacted with the subunits of the IκB kinase (IKK) complex and subsequently inhibited prostate cancer progression by repressing IκBα phosphorylation and NF-κB activation. Additionally, the lncRNA keratin 19 pseudogene 3 (KRT19P3) inhibited gastric cancer cell growth and metastasis by modulating IκBα deubiquitination and inactivating NF-κB signalling [66].

4.1 AMPK signalling pathway

AMPK is a critical cellular energy sensor that mainly functions as a metabolic checkpoint to restore energy balance in response to different types of metabolic stress [68]. AMPK is activated by phosphorylation, which maintains energy balance, redox homeostasis and cell survival by regulating glycolysis, fatty acid metabolism, antioxidant reactions, and other processes [69, 70]. Recent studies have showed that AMPK phosphorylation is epigenetically regulated by different signalling pathways involving different lncRNAs, including metastasis-associated in colon cancer-1 (MACC1)-AS1, antisense noncoding RNA in the INK4 locus (ANRIL), lncRNA in nonhomologous end joining pathway 1 (LINP1) and neighbour of BRCA1 gene 2 (NBR2). MACC1-AS1 is the antisense lncRNA transcript of the transcriptional regulator MACC1, which is recognized as an oncogene in cancer. MACC1-AS1 mediated metabolic plasticity by up-regulating MACC1 and subsequently enhanced glycolysis and antioxidative capabilities via the phosphorylation of AMPK and the translocation of Lin28 (an evolutionarily conserved RNA-binding protein), ultimately accelerating the growth of gastric cancer [71]. In addition, the lncRNA ANRIL promoted the survival of malignant cells and cellular glucose metabolism, accelerating acute myeloid leukaemia (AML) progression through AMPK phosphorylation and forming the AdipoR1/AMPK/Sirtuin 1 (SIRT1) pathway [72]. In addition, the lncRNA LINP1 regulated AML progression via increasing AMPK phosphorylation mediated through the hepatocyte nuclear factor 4 alpha (HNF4α)/AMPK/WNT5A signalling pathway [73]. In contrast, Liu et al. [74] proposed a feed-forward model of NBR2-AMPK regulation, in which the lncRNA NBR2 was induced by the liver kinase B1 (LKB1)-AMPK pathway under energy stress, and in turn NBR2 interacted with AMPK and promoted its phosphorylation.

4.2 PI3K/AKT signalling pathway

PI3K/AKT plays a key role in diverse cellular processes in cancer, including cell survival, proliferation, angiogenesis, and energy metabolism [75, 76]. Evidence has revealed that numerous positive regulators, including growth factors, regulatory proteins, and microRNAs (miRNAs), promote the overactivation of AKT signalling [77]. Some lncRNAs, such as LOC572558, LINC00184, LINC00470 (also known as C18orf2) and AK023948, have been associated with AKT phosphorylation and energy metabolic reprogramming in diseases, especially in cancer. One study showed that LINC00184 modulated glycolysis and mitochondrial oxidative phosphorylation in oesophageal cancer cells through inducing AKT phosphorylation [78]. In addition, Liu et al. [79] demonstrated that LINC00470 was a positive regulator of AKT activation in glioblastoma cells. Mechanistically, LINC00470 bound to the RNA-binding protein fused in sarcoma (FUS) and AKT, forming a ternary complex that anchors FUS in the cytoplasm and increases AKT phosphorylation. AKT activation by LINC00470 inhibited HK1 ubiquitination and promoted aerobic glycolysis and glioblastoma tumorigenesis. AK023948 is also reported to function as a positive regulator of AKT. AK023948 was required for the interaction between DEAH (Asp-Glu-Ala- His) box helicase proteins 9 (DHX9) and p85 to enhance p85 stability and promote AKT activity, which may contribute to breast tumor progression [80]. Overexpression of LOC572558, however, resulted in the dephosphorylation of AKT and murine double minute 2 (MDM2) while the phosphorylation of p53, which inhibited cell proliferation and tumor growth in bladder cancer through the AKT-MDM2-p53 axis [81].

4.3 p53 signalling pathway

In addition to the functions of the above basic metabolic pathways, the functions of p53-related signalling pathways in metabolism cannot be ignored [82, 83]. Kruiswijk et al. [84] proposed that cell metabolism was a noncanonical p53-controlled process, and this idea had attracted considerable attention. Importantly, activation of p53 reprograms tumor glucose metabolism by reversing the Warburg effect, which negatively affected the carcinogenic metabolism of cancer cells and prevented the development of aggressive tumor phenotypes [84, 85]. Recently, the importance of lncRNAs and p53 in cancer metabolic reprogramming has been confirmed [29, 86]. Mao et al. [87] confirmed that the interaction between the lncRNA P53RRA and Ras-GTPase-activating protein-binding protein 1 (G3BP1) prevented p53 from forming the G3BP1 complex, which repressed the transcription of several metabolism-related genes. In addition, various lncRNAs, such as LOC572558, p53 regulation-associated lncRNA (PRAL), LINK-A and MALAT1, also regulated p53 through the posttranslational modifications. In terms of ubiquitination, PRAL enhanced the stability of p53 by competitively binding with it and blocking its MDM2-dependent degradation. The three stem-loop motifs at the 5' end of PRAL promoted the interaction between p53 and HSP90 [88]. However, LINK-A enhanced the K48-polyubiquitination-mediated degradation of p53 [89]. In addition, Chen et al. [90] suggested that MALAT1 suppressed cell apoptosis and promoted cell proliferation by enhancing the SIRT1-mediated deacetylation of p53 and then down-regulating its downstream target genes. Together, the above findings indicate that lncRNA-mediated posttranslational modifications are crucial to the p53-related metabolic pathways.