Quantitative analysis of redox proteome reveals oxidation-sensitive protein thiols acting in fundamental processes of developmental hematopoiesis

. 2022 Jul ; 53 () : 102343. [epub] 20220523

Jazyk angličtina Země Nizozemsko Médium print-electronic

Typ dokumentu časopisecké články, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/pmid35640380
Odkazy

PubMed 35640380
PubMed Central PMC9157258
DOI 10.1016/j.redox.2022.102343
PII: S2213-2317(22)00115-X
Knihovny.cz E-zdroje

Fetal and adult hematopoietic stem and progenitor cells (HSPCs) are characterized by distinct redox homeostasis that may influence their differential cellular behavior in normal and malignant hematopoiesis. In this work, we have applied a quantitative mass spectrometry-based redox proteomic approach to comprehensively describe reversible cysteine modifications in primary mouse fetal and adult HSPCs. We defined the redox state of 4,438 cysteines in fetal and adult HSPCs and demonstrated a higher susceptibility to oxidation of protein thiols in fetal HSPCs. Our data identified ontogenic changes to oxidation state of thiols in proteins with a pronounced role in metabolism and protein homeostasis. Additional redox proteomic analysis identified oxidation changes to thiols acting in mitochondrial respiration as well as protein homeostasis to be triggered during onset of MLL-ENL leukemogenesis in fetal HSPCs. Our data has demonstrated that redox signaling contributes to the regulation of fundamental processes of developmental hematopoiesis and has pinpointed potential targetable redox-sensitive proteins in in utero-initiated MLL-rearranged leukemia.

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Weissman I.L., Shizuru J.A. The origins of the identification and isolation of hematopoietic stem cells, and their capability to induce donor-specific transplantation tolerance and treat autoimmune diseases. Blood. 2008;112(9):3543–3553. PubMed PMC

Jassinskaja M., et al. Comprehensive proteomic characterization of ontogenic changes in hematopoietic stem and progenitor cells. Cell Rep. 2017;21(11):3285–3297. PubMed

Mikkola H.K., Orkin S.H. vol. 133. 2006. pp. 3733–3744. (The Journey of Developing Hematopoietic Stem Cells. Development). 19. PubMed

Babovic S., Eaves C.J. Hierarchical organization of fetal and adult hematopoietic stem cells. Exp. Cell Res. 2014;329(2):185–191. PubMed

Pietras E.M., Passegue E. Linking HSCs to their youth. Nat. Cell Biol. 2013;15(8):885–887. PubMed

Ema H., Nakauchi H. Expansion of hematopoietic stem cells in the developing liver of a mouse embryo. Blood. 2000;95(7):2284–2288. PubMed

Morrison S.J., et al. The purification and characterization of fetal liver hematopoietic stem cells. Proc. Natl. Acad. Sci. U. S. A. 1995;92(22):10302–10306. PubMed PMC

Bowie M.B., et al. Hematopoietic stem cells proliferate until after birth and show a reversible phase-specific engraftment defect. J. Clin. Invest. 2006;116(10):2808–2816. PubMed PMC

Pietras E.M., Warr M.R., Passegue E. Cell cycle regulation in hematopoietic stem cells. J. Cell Biol. 2011;195(5):709–720. PubMed PMC

Manesia J.K., et al. Highly proliferative primitive fetal liver hematopoietic stem cells are fueled by oxidative metabolic pathways. Stem Cell Res. 2015;15(3):715–721. PubMed

Sattler M., et al. Hematopoietic growth factors signal through the formation of reactive oxygen species. Blood. 1999;93(9):2928–2935. PubMed

Carlos-Wallace F.M., et al. Parental, in utero, and early-life exposure to benzene and the risk of childhood leukemia: a meta-analysis. Am. J. Epidemiol. 2016;183(1):1–14. PubMed PMC

Kantner H.P., et al. ETV6/RUNX1 induces reactive oxygen species and drives the accumulation of DNA damage in B cells. Neoplasia. 2013;15(11):1292–1300. PubMed PMC

Schieber M., Chandel N.S. ROS function in redox signaling and oxidative stress. Curr. Biol. 2014;24(10):R453–R462. PubMed PMC

Paulsen C.E., Carroll K.S. Cysteine-mediated redox signaling: chemistry, biology, and tools for discovery. Chem. Rev. 2013;113(7):4633–4679. PubMed PMC

Ludin A., et al. Reactive oxygen species regulate hematopoietic stem cell self-renewal, migration and development, as well as their bone marrow microenvironment. Antioxidants Redox Signal. 2014;21(11):1605–1619. PubMed PMC

Prieto-Bermejo R., et al. Reactive oxygen species in haematopoiesis: leukaemic cells take a walk on the wild side. J. Exp. Clin. Cancer Res. 2018;37(1):125. PubMed PMC

Alcock L.J., Perkins M.V., Chalker J.M. Chemical methods for mapping cysteine oxidation. Chem. Soc. Rev. 2018;47(1):231–268. PubMed

Topf U., et al. Quantitative proteomics identifies redox switches for global translation modulation by mitochondrially produced reactive oxygen species. Nat. Commun. 2018;9(1):324. PubMed PMC

Vajrychova M., et al. Quantification of cellular protein and redox imbalance using SILAC-iodoTMT methodology. Redox Biol. 2019;24 PubMed PMC

van der Reest J., et al. Proteome-wide analysis of cysteine oxidation reveals metabolic sensitivity to redox stress. Nat. Commun. 2018;9(1):1581. PubMed PMC

Xiao H., et al. A quantitative tissue-specific landscape of protein redox regulation during aging. Cell. 2020;180(5):968–983 e24. PubMed PMC

Guo J., et al. Resin-assisted enrichment of thiols as a general strategy for proteomic profiling of cysteine-based reversible modifications. Nat. Protoc. 2014;9(1):64–75. PubMed PMC

Duan J., et al. Stochiometric quantification of the thiol redox proteome of macrophages reveals subcellular compartmentalization and susceptibility to oxidative perturbations. Redox Biol. 2020;36 PubMed PMC

Walasek M.A., van Os R., de Haan G. Hematopoietic stem cell expansion: challenges and opportunities. Ann. N. Y. Acad. Sci. 2012;1266:138–150. PubMed

Ito K., Suda T. Metabolic requirements for the maintenance of self-renewing stem cells. Nat. Rev. Mol. Cell Biol. 2014;15(4):243–256. PubMed PMC

Jang Y.Y., Sharkis S.J. A low level of reactive oxygen species selects for primitive hematopoietic stem cells that may reside in the low-oxygenic niche. Blood. 2007;110(8):3056–3063. PubMed PMC

Pajares M., et al. Redox control of protein degradation. Redox Biol. 2015;6:409–420. PubMed PMC

Bindea G., et al. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics. 2009;25(8):1091–1093. PubMed PMC

Shirwany N.A., Zou M.H. AMPK: a cellular metabolic and redox sensor. A minireview. Front Biosci (Landmark Ed) 2014;19:447–474. PubMed PMC

Almeida A., Moncada S., Bolanos J.P. Nitric oxide switches on glycolysis through the AMP protein kinase and 6-phosphofructo-2-kinase pathway. Nat. Cell Biol. 2004;6(1):45–51. PubMed

Zmijewski J.W., et al. Exposure to hydrogen peroxide induces oxidation and activation of AMP-activated protein kinase. J. Biol. Chem. 2010;285(43):33154–33164. PubMed PMC

Martinez-Ruiz A., et al. S-nitrosylation of Hsp90 promotes the inhibition of its ATPase and endothelial nitric oxide synthase regulatory activities. Proc. Natl. Acad. Sci. U. S. A. 2005;102(24):8525–8530. PubMed PMC

Yi W., et al. Protein S-nitrosylation regulates proteostasis and viability of hematopoietic stem cell during regeneration. Cell Rep. 2021;34(13) PubMed PMC

Yang U., et al. The functional role of UBA1 cysteine-278 in ubiquitination. Biochem. Biophys. Res. Commun. 2012;427(3):587–592. PubMed

Yoshimura S.H., et al. Intermolecular disulfide bonds between nucleoporins regulate karyopherin-dependent nuclear transport. J. Cell Sci. 2013;126(Pt 14):3141–3150. PubMed

Zhang X., et al. Mutation in nuclear pore component NUP155 leads to atrial fibrillation and early sudden cardiac death. Cell. 2008;135(6):1017–1027. PubMed

Valasek L.S., et al. Embraced by eIF3: structural and functional insights into the roles of eIF3 across the translation cycle. Nucleic Acids Res. 2017;45(19):10948–10968. PubMed PMC

Hinnebusch A.G. eIF3: a versatile scaffold for translation initiation complexes. Trends Biochem. Sci. 2006;31(10):553–562. PubMed

Lee A.S., Kranzusch P.J., Cate J.H. eIF3 targets cell-proliferation messenger RNAs for translational activation or repression. Nature. 2015;522(7554):111–114. PubMed PMC

Shah M., et al. A transcript-specific eIF3 complex mediates global translational control of energy metabolism. Cell Rep. 2016;16(7):1891–1902. PubMed PMC

Smith T.F., et al. The WD repeat: a common architecture for diverse functions. Trends Biochem. Sci. 1999;24(5):181–185. PubMed

Brina D., et al. Translational control by 80S formation and 60S availability: the central role of eIF6, a rate limiting factor in cell cycle progression and tumorigenesis. Cell Cycle. 2011;10(20):3441–3446. PubMed

Gandin V., et al. Eukaryotic initiation factor 6 is rate-limiting in translation, growth and transformation. Nature. 2008;455(7213):684–688. PubMed PMC

Pulos-Holmes M.C., et al. Repression of ferritin light chain translation by human eIF3. Elife. 2019;8 PubMed PMC

Wilker P.R., et al. Transcription factor Mef2c is required for B cell proliferation and survival after antigen receptor stimulation. Nat. Immunol. 2008;9(6):603–612. PubMed PMC

Schleich S., et al. DENR-MCT-1 promotes translation re-initiation downstream of uORFs to control tissue growth. Nature. 2014;512(7513):208–212. PubMed PMC

Ahmed Y.L., et al. DENR-MCTS1 heterodimerization and tRNA recruitment are required for translation reinitiation. PLoS Biol. 2018;16(6) PubMed PMC

Ceroni A., et al. DISULFIND: a disulfide bonding state and cysteine connectivity prediction server. Nucleic Acids Res. 2006;34:W177–W181. (Web Server issue) PubMed PMC

Ferre F., Clote P. Disulfide connectivity prediction using secondary structure information and diresidue frequencies. Bioinformatics. 2005;21(10):2336–2346. PubMed

Schleich S., et al. Identification of transcripts with short stuORFs as targets for DENR*MCTS1-dependent translation in human cells. Sci. Rep. 2017;7(1):3722. PubMed PMC

Okada T., et al. BCAP: the tyrosine kinase substrate that connects B cell receptor to phosphoinositide 3-kinase activation. Immunity. 2000;13(6):817–827. PubMed

Lawson H., et al. JMJD6 promotes self-renewal and regenerative capacity of hematopoietic stem cells. Blood Adv. 2021;5(3):889–899. PubMed PMC

Zhu Y.X., et al. The SH3-SAM adaptor HACS1 is up-regulated in B cell activation signaling cascades. J. Exp. Med. 2004;200(6):737–747. PubMed PMC

Ford A.M., et al. In utero rearrangements in the trithorax-related oncogene in infant leukaemias. Nature. 1993;363(6427):358–360. PubMed

Greaves M.F., et al. Leukemia in twins: lessons in natural history. Blood. 2003;102(7):2321–2333. PubMed

Hole P.S., Darley R.L., Tonks A. Do reactive oxygen species play a role in myeloid leukemias? Blood. 2011;117(22):5816–5826. PubMed

Hasaart K.A.L., et al. Mutation accumulation and developmental lineages in normal and Down syndrome human fetal haematopoiesis. Sci. Rep. 2020;10(1):12991. PubMed PMC

Ugale A., et al. Hematopoietic stem cells are intrinsically protected against MLL-ENL-mediated transformation. Cell Rep. 2014;9(4):1246–1255. PubMed

Pan S., Berk B.C. Glutathiolation regulates tumor necrosis factor-alpha-induced caspase-3 cleavage and apoptosis: key role for glutaredoxin in the death pathway. Circ. Res. 2007;100(2):213–219. PubMed

Guardia C.M., et al. Structural basis of redox-dependent modulation of galectin-1 dynamics and function. Glycobiology. 2014;24(5):428–441. PubMed PMC

Araki K., et al. Redox sensitivities of global cellular cysteine residues under reductive and oxidative stress. J. Proteome Res. 2016;15(8):2548–2559. PubMed

Garcia-Santamarina S., et al. Monitoring in vivo reversible cysteine oxidation in proteins using ICAT and mass spectrometry. Nat. Protoc. 2014;9(5):1131–1145. PubMed

Sigurdsson V., et al. Bile acids protect expanding hematopoietic stem cells from unfolded protein stress in fetal liver. Cell Stem Cell. 2016;18(4):522–532. PubMed

Filomeni G., De Zio D., Cecconi F. Oxidative stress and autophagy: the clash between damage and metabolic needs. Cell Death Differ. 2015;22(3):377–388. PubMed PMC

Handy D.E., Loscalzo J. Redox regulation of mitochondrial function. Antioxidants Redox Signal. 2012;16(11):1323–1367. PubMed PMC

Hou T., et al. NDUFAB1 confers cardio-protection by enhancing mitochondrial bioenergetics through coordination of respiratory complex and supercomplex assembly. Cell Res. 2019;29(9):754–766. PubMed PMC

D'Autreaux B., Toledano M.B. ROS as signalling molecules: mechanisms that generate specificity in ROS homeostasis. Nat. Rev. Mol. Cell Biol. 2007;8(10):813–824. PubMed

Balaban R.S., Nemoto S., Finkel T. Mitochondria, oxidants, and aging. Cell. 2005;120(4):483–495. PubMed

Hoeller D., Dikic I. Targeting the ubiquitin system in cancer therapy. Nature. 2009;458(7237):438–444. PubMed

Barghout S.H., et al. Preclinical evaluation of the selective small-molecule UBA1 inhibitor, TAK-243, in acute myeloid leukemia. Leukemia. 2019;33(1):37–51. PubMed

Kriegenburg F., et al. Redox control of the ubiquitin-proteasome system: from molecular mechanisms to functional significance. Antioxidants Redox Signal. 2011;15(8):2265–2299. PubMed

Silva G.M., et al. Redox control of 20S proteasome gating. Antioxidants Redox Signal. 2012;16(11):1183–1194. PubMed PMC

Tariq M., et al. Trithorax requires Hsp90 for maintenance of active chromatin at sites of gene expression. Proc. Natl. Acad. Sci. U. S. A. 2009;106(4):1157–1162. PubMed PMC

Pollyea D.A., et al. Venetoclax with azacitidine disrupts energy metabolism and targets leukemia stem cells in patients with acute myeloid leukemia. Nat. Med. 2018;24(12):1859–1866. PubMed PMC

Kohli L., Passegue E. Surviving change: the metabolic journey of hematopoietic stem cells. Trends Cell Biol. 2014;24(8):479–487. PubMed PMC

Jones C.L., et al. Cysteine depletion targets leukemia stem cells through inhibition of electron transport complex II. Blood. 2019;134(4):389–394. PubMed PMC

Hagner P.R., et al. Ribosomal protein S6 is highly expressed in non-Hodgkin lymphoma and associates with mRNA containing a 5' terminal oligopyrimidine tract. Oncogene. 2011;30(13):1531–1541. PubMed PMC

Khajuria R.K., et al. Ribosome levels selectively regulate translation and lineage commitment in human hematopoiesis. Cell. 2018;173(1):90–103 e19. PubMed PMC

Lynch J.R., Wang J.Y. G protein-coupled receptor signaling in stem cells and cancer. Int. J. Mol. Sci. 2016;17(5) PubMed PMC

Zhang P., et al. G protein-coupled receptor 183 facilitates endothelial-to-hematopoietic transition via Notch1 inhibition. Cell Res. 2015;25(10):1093–1107. PubMed PMC

Meyer C., et al. The MLL recombinome of acute leukemias in 2017. Leukemia. 2018;32(2):273–284. PubMed PMC

Gunisova S., et al. Please do not recycle! Translation reinitiation in microbes and higher eukaryotes. FEMS Microbiol. Rev. 2018;42(2):165–192. PubMed PMC

Jassinskaja M., et al. Ontogenic shifts in cellular fate are linked to proteotype changes in lineage-biased hematopoietic progenitor cells. Cell Rep. 2021;34(12) PubMed

Attema J.L., et al. Hematopoietic stem cell ageing is uncoupled from p16 INK4A-mediated senescence. Oncogene. 2009;28(22):2238–2243. PubMed

Wagner S., et al. Functional and biochemical characterization of human eukaryotic translation initiation factor 3 in living cells. Mol. Cell Biol. 2014;34(16):3041–3052. PubMed PMC

Mohammed H., et al. Rapid immunoprecipitation mass spectrometry of endogenous proteins (RIME) for analysis of chromatin complexes. Nat. Protoc. 2016;11(2):316–326. PubMed

Cox J., Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 2008;26(12):1367–1372. PubMed

Tyanova S., et al. The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat. Methods. 2016;13(9):731–740. PubMed

Mi H., et al. Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0) Nat. Protoc. 2019;14(3):703–721. PubMed PMC

Sherman B.T., et al. DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis. BMC Bioinf. 2007;8:426. PubMed PMC

Supek F., et al. REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS One. 2011;6(7) PubMed PMC

Shannon P., et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498–2504. PubMed PMC

Sun M.A., et al. RedoxDB--a curated database for experimentally verified protein oxidative modification. Bioinformatics. 2012;28(19):2551–2552. PubMed

Perez-Riverol Y., et al. The PRIDE database and related tools and resources in 2019: improving support for quantification data. Nucleic Acids Res. 2019;47(D1):D442–D450. PubMed PMC

Gentleman R.C., et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004;5(10):R80. PubMed PMC

Sagliocco F.A., Moore P.A., Brown A.J. Polysome analysis. Methods Mol. Biol. 1996;53:297–311. PubMed

Guzzi N., et al. Pseudouridylation of tRNA-derived fragments steers translational control in stem cells. Cell. 2018;173(5):1204–1216 e26. PubMed

Langmead B., et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25. PubMed PMC

Dobin A., et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15–21. PubMed PMC

Anders S., Pyl P.T., Huber W. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31(2):166–169. PubMed PMC

Love M.I., Huber W., Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550. PubMed PMC

Chothani S., et al. deltaTE: detection of translationally regulated genes by integrative analysis of ribo-seq and RNA-seq data. Curr. Protoc. Mol. Biol. 2019;129(1):e108. PubMed PMC

Subramanian A., et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. U. S. A. 2005;102(43):15545–15550. PubMed PMC

Doudna J.A., Charpentier E. Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science. 2014;346(6213) PubMed

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