Mass is the key. Maartje van den Biggelaar. British Society for Proteome Research meeting CIDA September 29 th Sanquin Plasma Proteins

Transcription

1 Mass is the key Maartje van den Biggelaar British Society for Proteome Research meeting 2013 CIDA September 29 th 2016 Maartje van den Biggelaar Sanquin Plasma Proteins

2 Mass spectrometry approaches to unravel the key to life

3 Blood cell proteomics

4 Blood cell proteomics

5 The central dogma of life Proteomics in the postgenomic era Banks et al. The Lancet 2000

6 mrna and protein levels correlate poorly Wilhelm et al. Nature 2014

7 Label-free analysis of CD8+ T cell subset proteomes supports a progressive differentiation model of virus-specific T cells in humans Michiel van Aalderen Esther Remmerswaal Ineke ten Berge René van Lier

8 Several human CD8+ T-cell subsets have been described Naïve CD27 CCR7 CD45RA Hamann et al. J Exp Med 1997 Sallusto et al. Nature 1999 Appay et al. Nat Med 2002 Romero et al. J Immunol 2007 CD28 CCR7 Central-memory CD27 CD28 Effector-memory CD27 CD27 CD28 CD28 RA + effector-type (T EM RA) CD45RA

9 Several human CD8+ T-cell subsets have been described Naïve CD27 CCR7 CD45RA Hamann et al. J Exp Med 1997 Sallusto et al. Nature 1999 Appay et al. Nat Med 2002 Romero et al. J Immunol 2007 CD28 CCR7 Central-memory CD27 CD28 Effector-memory CD27 CD27 CD28 CD28 Early differentiated Early like Intermediate RAˉ effector type RA + effector-type (T EM RA) CD45RA van Aalderen et al. J Virol 2015

10 Different virus-specific populations have distinct surface marker and transcription factor phenotypes CD45RA CCR7 CD28 CD naïve central-memory early early-like intermediate effector-type effector-type RSV EBV bmlf T-Bet Eomes lo lo int lo lo hi int hi hi hi hi lo FLU HIV GAG van Aalderen et al. J Virol 2015

11 Proteomics workflow

12 Proteomics workflow > peptides identified 6114 proteins identified 4816 proteins quantified

13 CD8+ T cell subsets show a similar wide range of expression and cumulative protein abundance

14 CD8+ effector type cells gain expression of proteins involved in adherens junction and regulation of actin cytoskeleton naïve RA+ effector type

15 Top20 proteins include histones, and cytoskeleton components including profilin, vimentin and cofilin naïve CD8+ T cells Highly similar to murine CD8+ T cells Hukelmann et al. Nature Immunology 2016 cyclophilin, target of cyclosporin rank protein name gene names copy number % cum % 1 Histone H4 HIST1H4A 2.41E Profilin 1 PFN1 3.17E Cofilin 1 CFL1 2.62E Vimentin VIM 2.30E Triosephosphate isomerase TPI1 2.30E L lactate dehydrogenase B chain LDHB 2.02E Thymosin beta 4 TMSB4X 1.88E protein zeta/delta YWHAZ 1.67E Rho GDP dissociation inhibitor 2 ARHGDIB 1.63E Plastin 2 LCP1 1.49E Phosphoglycerate kinase 1 PGK1 1.36E S acidic ribosomal protein P2 RPLP2 1.16E Histone H3;Histone H3.3 H3F3B;H3F3A 1.11E Peptidyl prolyl cis trans isomerase A PPIA 1.10E Heterogeneousnuclear ribonucleoproteinsa2/b1 HNRNPA2B1 1.05E Elongation factor 1 alpha 1 EEF1A1;EEF1A1P5 1.04E Histone H3 HIST2H3PS2 1.02E Fructose bisphosphate aldolase A ALDOA 1.00E Calmodulin CALM2;CALM1;CALM3 9.90E+06 < Histone H2A H2AFV;H2AFZ 9.90E+06 <1 27

16 Subsets of CD8+ T cells can be distinguished based on their proteomic profile 286 proteins differentially expressed

17 Enrichment analysis of differentially expressed proteins in CD8+ subsets

18 Distinct clusters of up- and downregulated proteins in CD8+ T cell subsets

19

20 Combined analysis of CX3CR1/CD62L sorted CD8+ T-cells supports a progressive differentiation model

21 Combined analysis of CX3CR1/CD62L sorted CD8+ T-cells supports a progressive differentiation model

22 Proteome changes occur mostly gradually between the antigen-experienced CD8+ T cell subsets GRZK cluster

23 Proteome changes occur mostly gradually between the antigen-experienced CD8+ T cell subsets GRZA/M cluster

24 Proteome changes occur mostly gradually between the antigen-experienced CD8+ T cell subsets GRZH/B cluster

25 Proteome changes occur mostly gradually between the antigen-experienced CD8+ T cell subsets PRKCA cluster

26 A small proportion of proteins display non-linear transitions between the different CD8+ T-cell subsets top cluster

27 A small proportion of proteins display non-linear transitions between the different CD8+ T-cell subsets dip cluster

28 Physical and functional interactions of the differentially expressed proteins in CD8+ T cells

29 Distinct metabolic regulation of the different CD8+ T-cell subsets

30 Distinct expression patterns of adhesion-related proteins per CD8+ T-cell subset

31 Proteotranscriptomics reveals a multipronged program to prevent production of inflammatory cytokines by human regulatory CD4+ T-cells Eloy Cuadrado Derk Amsen Jannie Borst René van Lier

32 Subsets of CD4+ T cells can be distinguished based on their proteomic profile

33 CD4+ T-cells abundantly express proteins related to ribosomes, proteasome, spliceosome and metabolism

34 Top20 proteins include histones, and cytoskeleton components including profilin, vimentin and cofilin

35 In all CD4+ T-cell subsets there is a poor correlation between mrna and protein expression

36 Distinct clusters of up- and downregulated proteins in CD4+ T cell subsets

37 Core proteome of regulatory CD4+ T cells

38 Stoichiometry of FoxP3-transcription factor complexes is drastically different in regulatory T cells Hori et al. Nature Immunology 2012

39 Limited differences in proteomic profiles between naïve CD4+ and CD8+ T cells naïve CD8+ naïve CD4+

40 Limited differences in proteomic profiles between naïve CD4+ and CD8+ T cells naïve CD8+ naïve CD4+ ZBTB7B, aka Th POK Taniuchi, Immunological Reviews 2016

41 Comparison of all CD4+ and CD8+ T-cell subsets T EM RA T EM 4 T EM 3 T EM 2 T EM 1 T CM T N ntconv ntregs P3 mtconv etreg

42 Comparison of all CD4+ and CD8+ T-cell subsets T EM RA T EM 4 T EM 3 T EM 2 T EM 1 T CM T N ntconv ntregs P3 mtconv etreg CD8+ > CD4+ up in CD8+ effector up in both CD4+ and CD8+ effector dip in T EM 2 4 CD8+ subsets down in both CD4+ and CD8+ effector CD4+ > CD8+

43 Comparison of all CD4+ and CD8+ T-cell subsets

44 CD8+ > CD4+ up in CD8+ effector up in both CD4+ and CD8+ effector down in both CD4+ and CD8+ effector CD4+ > CD8+ fibrinogen complex platelet alpha granule platelet alpha granule lumen secretory granule lumen cytoplasmic membrane-bounded vesicle lumen vesicle lumen platelet degranulation external side of plasma membrane receptor complex exocytosis secretion by cell mitochondrial matrix extracellular space organelle lumen membrane-enclosed lumen sulfuric ester hydrolase activity Glycosaminoglycan degradation keratan sulfate catabolic process keratan sulfate metabolic process Glycosphingolipid biosynthesis - globo series cytolysis glycosaminoglycan catabolic process glycolipid catabolic process hexosaminidase activity sulfur compound catabolic process aminoglycan catabolic process membrane lipid catabolic process ribonucleoside catabolic process sphingolipid catabolic process lysosomal lumen glycolipid metabolic process Other glycan degradation vacuolar lumen glycosphingolipid metabolic process Sphingolipid metabolism glycosaminoglycan metabolic process Lysosome aminoglycan metabolic process ceramide metabolic process nucleoside catabolic process sphingoid metabolic process regulation of blood coagulation polysaccharide catabolic process serine-type endopeptidase activity membrane lipid metabolic process sphingolipid metabolic process lysosome lytic vacuole vacuole hydrolase activity, hydrolyzing O-glycosyl compounds vacuolar part hydrolase activity, acting on glycosyl bonds cellular lipid catabolic process polysaccharide metabolic process carbohydrate catabolic process cell projection membrane lipid catabolic process extracellular region lysosomal membrane vacuolar membrane lipid metabolic process intracellular organelle lumen cellular lipid metabolic process plasma membrane part carbohydrate metabolic process multicellular organismal process extracellular membrane-bounded organelle extracellular organelle extracellular vesicular exosome hydrolase activity extracellular region part vesicle membrane-bounded vesicle plasma membrane membrane part membrane sarcolemma cell surface response to endoplasmic reticulum stress positive regulation of protein phosphorylation positive regulation of phosphorylation calcium ion binding regulation of protein phosphorylation cellular response to stimulus response to stimulus cellular aromatic compound metabolic process MCM complex intrinsic to plasma membrane integral to plasma membrane immune response

45 Summary branched vs linear differentiation/specialization define core proteome of specialized T cells biological processes, protein complexes and individual proteins stoichiometry of cooperating or antagonizing proteins define new markers for T cell subsets new targets for functional follow up Mass is the key?

46 Acknowledgements Carmen van der Zwaan Floris van Alphen Alexander Meijer