Systematic Identification of Metabolite-Protein Interactions in Human Cells

Damon Runyon - Mark Foundation Postdoctoral Fellow (2019-Present)

Jonathan Van Vranken, PhD, Harvard Medical School

Jonathan Van Vranken, PhD

Dr. Van Vranken is focusing on the metabolic alterations associated with human cancers. In order to support normal physiology, all cells must obtain nutrients from the environment and allocate them toward both the production of energy and synthesis of cellular building blocks. Cancer cells often reprogram their metabolism to support the uncontrolled growth associated with tumors. Dr. Van Vranken is using mass spectrometry-based approaches to investigate the mechanisms underlying the changes in cellular metabolism. His research will shed light on how metabolites interact with the proteome (all the proteins in a cell) to support cell growth and proliferation.

Content courtesy of Damon Runyon Cancer Research Foundation


Li J, Van Vranken JG, Vaites LP, Schweppe DK, Huttlin EL, Etienne C, Nandhikonda P, Viner R, Robitaille AM, Thompson AH, Kuhn K, Pike I, Bomgarden RD, Rogers JC, Gygi SP, Paulo JA. TMTpro Reagents: A Set of Isobaric Labeling Mass Tags Enables Simultaneous Proteome-Wide Measurements Across 16 Samples. Nat Methods. 2020.

Li J, Van Vranken JG, Paulo JA, Huttlin EL, Gygi SP. Selection of Heating Temperatures Improves the Sensitivity of the Proteome Integral Solubility Alteration Assay. J Proteome Res. 2020.

Navarrete-Perea J, Guerra-Moreno A, Van Vranken J, Isasa M, Paulo JA, Gygi SP. Iron Deficiency and Recovery in Yeast: A Quantitative Proteomics Approach. J Proteome Res. 2021.

Van Vranken JG, Li J, Mitchell DC, Navarrete-Perea J, Gygi SP. Assessing target engagement using proteome-wide solvent shift assays. Elife. 2021.

Kam TI, Park H, Chou SC, Van Vranken JG, Mittenbühler MJ, Kim H, A M, Choi YR, Biswas D, Wang J, Shin Y, Loder A, Karuppagounder SS, Wrann CD, Dawson VL, Spiegelman BM, Dawson TM. Amelioration of pathologic α-synuclein-induced Parkinson’s disease by irisin. Proc Natl Acad Sci U S A. 2022.

Mitchell DC, Kuljanin M, Li J, Van Vranken JG, Bulloch N, Schweppe DK, Huttlin EL, Gygi SP. A proteome-wide atlas of drug mechanism of action. Nat Biotechnol. 2023.

Mittenbühler MJ, Jedrychowski MP, Van Vranken JG, Sprenger HG, Wilensky S, Dumesic PA, Sun Y, Tartaglia A, Bogoslavski D, A M, Xiao H, Blackmore KA, Reddy A, Gygi SP, Chouchani ET, Spiegelman BM. Isolation of extracellular fluids reveals novel secreted bioactive proteins from muscle and fat tissues. Cell Metab. 2023.

Yin TC, Van Vranken JG, Srivastava D, Mittal A, Buscaglia P, Moore AE, Verdinez JA, Graham AE, Walsh SA, Acevedo MA, Kerns RJ, Artemyev NO, Gygi SP, Sebag JA. Insulin sensitization by small molecules enhancing GLUT4 translocation. Cell Chem Biol. 2023.

Ouyang Y, Jeong MY, Cunningham CN, Berg JA, Toshniwal AG, Hughes CE, Seiler K, Van Vranken JG, Cluntun AA, Lam G, Winter JM, Akdogan E, Dove KK, Nowinski SM, West M, Odorizzi G, Gygi SP, Dunn CD, Winge DR, Rutter J. Phosphate starvation signaling increases mitochondrial membrane potential through respiration-independent mechanisms. Elife. 2024.