PDK3 drives colorectal carcinogenesis and immune evasion and is a therapeutic target for boosting immunotherapy.

Pyruvate Dehydrogenase Kinase 3 (PDK3) has emerged as a significant player in various cancer types, yet its specific impact on cancers including colon cancer remains ambiguous. Through pan-cancer analysis using TCGA data, we found that the expression of PDK3 and the composition of the immune microenvironment for different tumors were highly heterogeneous across tumors. PDK3 is highly expressed in colorectal cancer and may promote tumor proliferation by activating PI3K-AKT signaling. In addition, we found that PDK3 was able to inhibit tumor antigen presentation signals to suppress immune killing. High PDK3 expression predicts less CD8+ T cell infiltration and effector function. Moreover, inhibition of PDK3 expression bolstered CD8+ T cell-mediated cytotoxicity CD8+ T cell infiltration and activation in vivo. Notably, PDK3 was found to facilitate STAT1 activation and elevate programmed death-ligand 1 (PD-L1) expression in colon cancer cells. Importantly, PDK3 inhibition combination with PD-1 blockade significantly activates the infiltrated CD8+ T cells to suppress tumor growth and improves the survival benefit in several murine tumor models. In summary, these findings underscore PDK3's role in fueling colon cancer growth by orchestrating PI3K-AKT signaling and PD-L1 expression and dampening CD8+ T cell function.

Overexpression of Pyruvate Dehydrogenase Kinase-3 Predicts Poor Prognosis in Urothelial Carcinoma.

BACKGROUND: The mitochondrial pyruvate dehydrogenase complex (PDC) link glycolysis to the tricarboxylic acid cycle by decarboxylating pyruvate to acetyl coenzyme A irreversibly. Cancer cells are characterized by a shift in cellular metabolism from mitochondrial respiration to glycolysis. PDC activity inhibition mediated by phosphorylation via pyruvate dehydrogenase kinase (PDK) has been linked to cancer. However, the clinical significance of PDKs in urothelial cancer prognosis is not clear. We investigated the role and prognostic value of PDK3 expression in patients with upper urinary tract urothelial carcinoma (UTUC) and urinary bladder urothelial carcinoma (UBUC). PATIENTS AND METHODS: We retrospectively analyzed clinical data and pathological features. Formalin-fixed urothelial carcinoma (UC) tissues were collected and embedded in paraffin. The correlation of PDK3 expression with clinical characteristics, pathological findings and patient outcomes, including metastasis-free survival (MFS) and disease-specific survival (DSS) were analyzed by Pearson's chi-square test, Kaplan-Meier analysis, and the multivariate Cox proportional hazards model. RESULTS: Data from 295 patients with UBUC and 340 patients with UTUC were evaluated. High PDK3 expression significantly correlated with several pathologic variables such as high T stage, lymph node metastases, high tumor grade, vascular invasion, and high mitotic rate (all P < 0.001). High PDK3 expression was associated with poor disease-specific survival (DSS) (P < 0.0001) and metastatic free survival (MFS) (P < 0.0001) in a Kaplan-Meier analysis. Additionally, multivariate analysis demonstrated increased PDK3 expression is a significant predictive risk factor for DSS [hazard ratio (HR) in UBUC, 2.79, P = 0.009; in UTUC, 2.561, P = 0.03] and MFS (HR in UBUC, 1.907, P = 0.024; in UTUC, 1.793, P = 0.044). The gene co-expression analysis showed abundant PDK3 co-upregulated genes were involved in the processes of DNA replication and repair through the Gene Ontology classification system. CONCLUSION: High PDK3 expression has been linked to negative pathologic characteristics and poor oncological outcomes, suggesting that it could be used as a predictive biomarker for UC. PDK3 mRNA levels and its co-upregulated genes were strongly associated with DNA replication and repair. These results suggest that PDK3 may play a key role in tumor proliferation and development.

LncRNA POT1-AS1 accelerates the progression of gastric cancer by serving as a competing endogenous RNA of microRNA-497-5p to increase PDK3 expression.

BACKGROUND: Gastric cancer (GC) is the most common malignant tumor of the digestive system. Although progress has been reported in terms of treatment, it is still the second leading cause of cancer-related death. Long non-coding RNAs have been shown to play a key role in human cancers in recent investigations. However, the role of POT1-AS1 in GC is still unclear. METHODS: The relative POT1-AS1 level in GC tissues and paracancerous tissues was detected by quantitative Real Time-Polymerase Chain Reaction (qRT-PCR). The biological function of POT1-AS1 was studied by CCK8 and Transwell assays in vitro experiments. Moreover, the downstream target genes of POT1-AS1 were predicted by bioinformatics. RESULTS: In this study, high POT1-AS1 expression in GC cells was confirmed, and its elevated expression was linked to patients' negative clinicopathological characteristics, as well as shorter disease-free survival (DFS) and overall survival (OS). POT1-AS1 was shown to serve as a competing endogenous RNA (ceRNA) by sponging miR-497-5p to increase PDK3 expression. The impact of POT1-AS1 silencing on GC malignant phenotypes could be reversed by suppressing miR-497-5p or restoring PDK3, according to rescue experiments. CONCLUSIONS: In brief, POT1-AS1 acted as an oncogenic lncRNA in GC, facilitating GC development by affecting the miR-497-5p/PDK3 axis, implying that the POT1-AS1/miR-497-5p/PDK3 axis is a useful target in anticancer therapy.

Identification of high-affinity inhibitors of pyruvate dehydrogenase kinase-3: towards therapeutic management of cancer.

Pyruvate dehydrogenase kinase 3 (PDK3) is a multifunctional enzyme that plays a central role in the cancer metabolic switch by blocking pyruvate catabolism in the TCA cycle. PDK3 plays a significant role in the TCA cycle and cancer cell progression, thus, considered as a novel drug target for developing effective therapeutics against varying types of cancer. Here, we employed a structure-based virtual high-throughput screening of natural compounds from the ZINC database to identify potential inhibitors of PDK3. First, the resulted hits were selected on the basis of their physicochemical and ADMET properties. Further, PAINS filter, binding affinities based on the docking analysis and interaction analysis was carried out to find safe and better hits against PDK3. Finally, we identified four natural compounds bearing admirable affinity towards PDK3. Selected compounds showed appreciable drug-like properties and preferentially interact to the residues of the ATP-binding pocket of PDK3. Binding and structural annotations made in docking analysis were supplemented by all-atom molecular dynamics simulations to evaluate the conformational dynamics, stability and interaction mechanism of PDK3 in complex with one of the identified compounds ZINC08764476. PDK3 and ZINC08764476 forming a stable complex throughout the simulation trajectory. We suggest that compound ZINC08764476 may be exploited as a promising scaffold for the development of potential inhibitors of PDK3 to combat cancer and associated diseases.Communicated by Ramaswamy H. Sarma.

VHL Dependent Expression of REDD1 and PDK3 Proteins in Clear-cell Renal Cell Carcinoma.

BACKGROUND: Sporadic clear-cell renal cell carcinoma (ccRCC) is associated with mutations in the VHL gene, upregulated mammalian target of rapamycin (mTOR) activity and glycolytic metabolism. Here, we analyze the effect of VHL mutational status on the expression level of mTOR, eIF4E-BP1, AMPK, REDD1, and PDK3 proteins. METHODS: Total proteins were isolated from 21 tumorous samples with biallelic inactivation, 10 with monoallelic inactivation and 6 tumors with a wild-type VHL (wtVHL) gene obtained from patients who underwent total nephrectomy. The expressions of target proteins were assessed using Western blot. RESULTS: Expressions of mTOR, eIF4EBP1 and AMPK were VHL independent. Tumors with monoallelic inactivation of VHL underexpressed REDD1 in comparison to wtVHL tumors (P = 0.042), tumors with biallelic VHL inactivation (P < 0.005) and control tissue (P = 0.004). Additionally, REDD1 expression was higher in tumors with VHL biallelic inactivation than in control tissue (P = 0.008). Only in wt tumor samples PDK3 was overexpressed in comparison to tumors with biallelic inactivation of VHL gene (P = 0.012) and controls (P = 0.016). In wtVHL ccRCC, multivariate linear regression analysis revealed that 97.4% of variability in PDK3 expression can be explained by variations in AMPK amount. CONCLUSION: Expressions of mTOR, eIF4EBP1 and AMPK were VHL independent. We have shown for the first time VHL dependent expression of PDK3 and we provide additional evidence that VHL mutational status affects REDD1 expression in sporadic ccRCC.

Pathogenic mechanisms underlying X-linked Charcot-Marie-Tooth neuropathy (CMTX6) in patients with a pyruvate dehydrogenase kinase 3 mutation.

Charcot-Marie-Tooth disease (CMT) is the most common inherited peripheral neuropathy. An X-linked form of CMT (CMTX6) is caused by a missense mutation (R158H) in the pyruvate dehydrogenase kinase isoenzyme 3 (PDK3) gene. PDK3 is one of 4 isoenzymes that negatively regulate the activity of the pyruvate dehydrogenase complex (PDC) by reversible phosphorylation of its first catalytic component pyruvate dehydrogenase (designated as E1). Mitochondrial PDC catalyses the oxidative decarboxylation of pyruvate to acetyl CoA and links glycolysis to the energy-producing Krebs cycle. We have previously shown the R158H mutation confers PDK3 enzyme hyperactivity. In this study we demonstrate that the increased PDK3 activity in patient fibroblasts (PDK3(R158H)) leads to the attenuation of PDC through hyper-phosphorylation of E1 at selected serine residues. This hyper-phosphorylation can be reversed by treating the PDK3(R158H) fibroblasts with the PDK inhibitor dichloroacetate (DCA). In the patient cells, down-regulation of PDC leads to increased lactate, decreased ATP and alteration of the mitochondrial network. Our findings highlight the potential to develop specific drug targeting of the mutant PDK3 as a therapeutic approach to treating CMTX6.