PRKAB2 as a tumor suppressor in renal cell carcinoma: inhibiting mitophagy via the LRPPRC-PRKN/parkin interaction and cardiolipin biosynthesis

Renal cell carcinoma (RCC) is characterized by dysregulated lipid metabolism and a high propensity for developing resistance to targeted therapies. Mitophagy is a key process involved in the progression of various cancers, including RCC. Here, using in vivo genome-wide CRISPR screening, we identified PRKAB2 as a crucial tumor suppressor in RCC. Reduced PRKAB2 expression correlated with poor prognosis and aggressive clinical features, whereas overexpression of PRKAB2 markedly inhibited RCC cell proliferation, migration, invasion, tumor growth, and metastasis both in vitro and in vivo. Mechanistically, PRKAB2 overexpression inhibited mitophagy primarily through two distinct mechanisms. First, PRKAB2 enhanced the binding between LRPPRC and PRKN/parkin, competitively reducing PRKN’s interaction with PINK1 and thus suppressing ubiquitin-dependent mitophagy. Second, PRKAB2 promoted AMPK phosphorylation, which in turn suppressed SREBF1/SREBP1-mediated transcriptional activation of CRLS1, leading to decreased CRLS1 expression and reduced synthesis of cardiolipin, a lipid essential for mitophagy. Importantly, PRKAB2 overexpression significantly restored sensitivity to tyrosine kinase inhibitors (TKIs) in sunitinib-resistant RCC cells. Conversely, forced PRKN expression promoted resistance to these drugs, further implicating mitophagy as a key mechanism underlying TKI resistance. Depmap analysis confirmed the association between increased mitophagy and TKI resistance. Overall, our findings identify PRKAB2 as a critical tumor suppressor in RCC, regulating both protein-protein interactions and lipid metabolism to suppress mitophagy. Targeting PRKAB2-associated pathways may provide a promising therapeutic strategy to enhance treatment efficacy and overcome drug resistance in RCC. Abbreviations: ACACA/ACC1: acetyl-CoA carboxylase alpha; AMPK: AMP-activated protein kinase; ATCC: American Type Culture Collection; ATP5F1A: ATP synthase F1 subunit alpha; BNIP3: BCL2 interacting protein 3; BNIP3L/NIX: BCL2 interacting protein 3 like; BRCA1: BRCA1 DNA repair associated; Cas: CRISPR-associated; CCCP: carbonyl cyanide m-chlorophenyl hydrazone; ccRCC: clear cell renal cell carcinoma; ChIP: chromatin immunoprecipitation; Co-IP: co-immunoprecipitation; COX4I1: cytochrome c oxidase subunit 4I1; CRISPR: clustered regularly interspaced short palindromic repeats; CRLS1: cardiolipin synthase 1; DNM1L/DRP1: dynamin 1 like; DOX: doxorubicin; FUNDC1: FUN14 domain containing 1; HSPA8: heat shock protein family A (Hsp70) member 8; HSPD1: heat shock protein family D (Hsp60) member 1; GO: gene ontology; IHC: immunohistochemistry; IMM: inner mitochondrial membrane; LDLR: low density lipoprotein receptor; m-SREBF1: mature sterol regulatory element binding transcriptional factor 1; LRPPRC: leucine rich pentatricopeptide repeat containing; MAP1LC3B: microtubule associated protein 1 light chain 3 beta; MFN1, mitofusin 1; MFN2: mitofusin 2; MTOR: mechanistic target of rapamycin kinase; OMM: outer mitochondrial membrane; OS: overall survival; PA: phosphatidic acid; PG: phosphatidylglycerol; PGS1: phosphatidylglycerophosphate synthase 1; PINK1: PTEN induced kinase1; PRKAA1/AMPKα1: protein kinase AMP-activated catalytic subunit alpha 1; PRKAA2/AMPKα2: protein kinase AMP-activated catalytic subunit alpha 2; PRKAB1/AMPKβ1: protein kinase AMP-activated catalytic subunit beta 1; PRKAB2/AMPKβ2: protein kinase AMP-activated non-catalytic subunit beta 2; PRKAG1/AMPKγ1: protein kinase AMP-activated non-catalytic subunit gamma 1; PRKN: parkin RBR E3 ubiquitin protein ligase; RCC: renal cell carcinoma; SASA: solvent-accessible surface areas; SUCLG1: succinate-CoA ligase GDP/ADP-forming subunit alpha; TCGA: The Cancer Genome Atlas; TKI: tyrosine kinase inhibitors; UCP1: uncoupling protein 1; ULK1: unc-51 like autophagy activating kinase 1; WCL: whole-cell lysate.