VPS34-dependent control of apical membrane function of proximal tubule cells and nutrient recovery by the kidney

Abstract

The lipid kinase VPS34 orchestrates autophagy, endocytosis, and metabolism and is implicated in cancer and metabolic disease. The proximal tubule in the kidney is a key metabolic organ that controls reabsorption of nutrients such as fatty acids, amino acids, sugars, and proteins. Here, by combining metabolomics, proteomics, and phosphoproteomics analyses with functional and superresolution imaging assays of mice with an inducible deficiency in proximal tubular cells, we revealed that VPS34 controlled the metabolome of the proximal tubule. In addition to inhibiting pinocytosis and autophagy, VPS34 depletion induced membrane exocytosis and reduced the abundance of the retromer complex necessary for proper membrane recycling and lipid retention, leading to a loss of fuel and biomass. Integration of omics data into a kidney cell metabolomic model demonstrated that VPS34 deficiency increased β-oxidation, reduced gluconeogenesis, and enhanced the use of glutamine for energy consumption. Furthermore, the omics datasets revealed that VPS34 depletion triggered an antiviral response that included a decrease in the abundance of apically localized virus receptors such as ACE2. VPS34 inhibition abrogated SARS-CoV-2 infection in human kidney organoids and cultured proximal tubule cells in a glutamine-dependent manner. Thus, our results demonstrate that VPS34 adjusts endocytosis, nutrient transport, autophagy, and antiviral responses in proximal tubule cells in the kidney.

WHAMM functions in kidney reabsorption and polymerizes actin to promote autophagosomal membrane closure and cargo sequestration

“…However, the irregular distribution of ACE2 staining in WHAMM knockout tissue is suggestive of defects in proximal tubule organization, polarity, or membrane trafficking. Interestingly, alterations in the urinary proteome, proximal tubule reabsorption, and ACE2 localization have also been observed upon disruption of Vps34, a PI-3 kinase with critical roles in autophagosome biogenesis and endocytic trafficking (Grieco et al ., 2018; Rinschen et al ., 2022).…”

“…The lipidation status of the autophagosomal protein LC3 is altered in WHAMM KO kidneys Cellular proteostasis systems are important for maintaining the integrity of proximal tubules (Cybulsky, 2017;Tang et al, 2020), and conditional deletions of Vps34, a key initiator of autophagic membrane biogenesis, alter the urinary proteome and perturb the apical localization of several membrane transport proteins including ACE2 in mice (Grieco et al, 2018;Rinschen et al, 2022). Because WHAMM plays a role in multiple steps of autophagy (Kast et al, 2015;Mathiowetz et al, 2017;Dai et al, 2019;Wu et al, 2021), we next sought to determine whether some aspect of autophagy might be altered in WHAMM KO kidney tissue.…”

Isocitrate dehydrogenase 1 upregulation in urinary extracellular vesicles from proximal tubules of type 2 diabetic rats

“…Most glomerular‐filtered substances, such as nutrients and ions in primary urine, are reabsorbed into the proximal tubular cells. The metabolic function of the proximal tubular cells is strongly associated with renal, cardiovascular, and metabolic diseases 37 . Reportedly, at the early stage of DN, proximal tubular damage is more closely linked to kidney dysfunction than glomerular defects, challenging the long‐standing belief that DN is primarily characterized by glomerular issues 38 .…”

“…The metabolic function of the proximal tubular cells is strongly associated with renal, cardiovascular, and metabolic diseases. 37 Reportedly, at the early stage of DN, proximal tubular damage is more closely linked to kidney dysfunction than glomerular defects, challenging the long-standing belief that DN is primarily characterized by glomerular issues. 38 This report supports our finding that IDH1, a protein that increases in uEVs in the early stages of DN, originates from proximal tubular cells.…”

Octyl itaconate enhances VSVΔ51 oncolytic virotherapy by multitarget inhibition of antiviral and inflammatory pathways

“…Targeted metabolomic analysis was performed on a triple quadrupole (QQQ) mass spectrometer (Agilent Triple Quadrupole 6495C, San Diego, CA), coupled to an ultra-high pressure liquid chromatography system (UPLC) system (1290 Infinity, Agilent Technologies) as previously described 81 . Data were acquired with Agilent MassHunter Workstation Data Acquisition (version 10.1).…”