8/1/13% Stanford University School of Medicine Department of Radiation Oncology Division of Radiation Physics Pushing%PET%Imaging%to%the% Cellular%Level:%Development%of%a% Radioluminescence%Microscope% ! Guillem!Pratx,!PhD! Stanford%University% 432 Fig. 4 A 53-year-old woman with T3 (52 mm) N0 left breast invasive ductal carcinoma, SBR grade 1, ER +++ , PR +++, c-erbB-2−, p53 wild-type. Tumour SUVmax is 2.5 % Eur J Nucl Med Mol Imaging (2011) 38:426–435 AAPM%Annual%MeeFng% Nanotechnology%&%Molecular%Imaging% Thursday,%August%8th,%2013% InterLtumor%heterogeneity% mulation measured by IHC and p53 mutation detected by sequencing has been estimated to be less than 75% [28]. The yeast functional assay that we used is robust and is even more sensitive than direct sequencing [29]. Some explanations can be proposed for the high FDG uptake in tumours with non-functional p53. Mutations of 432 Eur J Nucl Med Mol Imaging (2011) 38:426–435 Fig. 4 A 53-year-old woman with T3 (52 mm) N0 left breast invasive ductal carcinoma, SBR grade 1, ER +++ , PR +++, c-erbB-2−, p53 wild-type. Tumour SUVmax is 2.5 Fig. 5 A 64-year-old woman with T4 (extension to chest wall) N0 invasive ductal carcinoma measuring 52 mm, SBR grade 3, triple-negative, mutated p53. SUVmax of the tumour is 12.9 SUV%=2.5%% p53 were found to impair the repressive effect of p53 on Woman%with%T3%(52%mm)%N0%leV%breast%invasive% GLUT1 and GLUT4 gene promoters [30, 31]. Loss of expression of TIGAR (TP53-induced glycolysis and apoductal%carcinoma,%SBR%grade%1,%ER%+++%,%PR%+++,% ptosis regulator) in non-functional p53 tumours could also cLerbBL2−,%p53%wildLtype.%% explain high FDG uptake [32]. Finally, a recent (in vitro) mulation measured by IHC and p53 mutation detected by sequencing has been estimated to be less than 75% [28]. The yeast functional assay that we used is robust and is even more sensitive than direct sequencing [29]. Some explanations can be proposed for the high FDG uptake in tumours with non-functional p53. Mutations of Fig. 5 A 64-year-old woman with T4 (extension to chest wall) N0 invasive ductal carcinoma measuring 52 mm, SBR grade 3, triple-negative, mutated p53. SUVmax of the tumour is 12.9 p53 were found to impair the repressive effect of p53 on GLUT1 and GLUT4 gene promoters [30, 31]. Loss of expression of TIGAR (TP53-induced glycolysis and apoptosis regulator) in non-functional p53 tumours could also explain high FDG uptake [32]. Finally, a recent (in vitro) study suggests that abrogation of p53 is associated with SUV%=12.9% Woman% with% T4% (extension% to% chest% wall)% N0% invasive% ductal% carcinoma% measuring% 52% mm,% SBR%grade%3,%tripleLnegaFve,%mutated%p53.% study suggests that abrogation of p53 is associated with Eur$J$Nucl$Med$Mol$Imaging$38:426–435%(2011)% 1% 8/1/13% The%Standardized%Uptake%Value% acFvity%in% the%tumor% mass%of% the%tumor% Tumor% acFvity%in% the%paFent% mass%of% the%paFent% Tracer%Compartmental%Analysis% K1$ K4$ FDGL6L% phosphate% FDG% FDG% HK! K3$ HK! K2$ Tumor% 2% R3 (G4) Tamar Danon1, Natalie Perzov1 & Uri Alon1 R5 (G4) R9 Lung metastases M2a Hilum R4 (G1) Chest-wall metastasis M2b 8/1/13% Primary tumor R6 (G1) foun were way migh time popu W indi cell l snap such their beha time ory prot No. of Cells IL12RB2 BCAS2 IFI16 FCAMR PLB1 ALS2CR12 C2orf21 VHL SGOL1 KLHL18 SSR3 CLCN2 WHSC1 ATXN1 DOPEY1 CCR6 INTS1 PTPRZ1 ZC3HC1 EXT1 RALGDS MSRB2 EIF4G2 ANO5 C11orf68 MRPL51 KDM2B X4 NUSAP1 TCF12 ZC3H18 DDX52 ZNF519 AKAP8 CYP4F3 KIAA0355 WDR62 KLK4 IGLON5 NLRP7 MAGEB16 SESN2 CCBL2 SETD2 PLRG1 CASP2 SSNA1 TH PPFIA1 CDKN1B WSCD2 ZNF780A PPP6R2 MTOR UGT2A1 ABHD11 GALNT11 RIMBP2 PSMD7 CENPN SOX9 NPHS1 RBFOX2 KDM5C KDM5C SATL1 FLNA ITGB3 LATS2 DIRAS3 NGEF ZNF493 SPATA21 DDX58 DAPK1 ALKBH8 KL ERCC5 DIO1 PIAS3 MR1 C3orf20 SETD2 TNIK LIAS FBXO1 AKAP9 ITIH5 WDR24 MYH8 TOM1 SBF1 KDM5C USP51 NAP1L3 ADAMTSL4 DUSP12 SLC2A12 RAB27A CIB2 RPS8 FAM129B PHF21B HDAC6 MAP3K6 MAMLD1 RLF DNMT3A HMG20A ZNF521 MMAB DACH2 SLC2A1 TM7SF4 ANKRD26 CD44 RT4 KIAA1267 C3 DAMTS10 IFNAR1 BCL11A PLCL1 SETD2 KIAA1524 NRAP HPS5 DIXDC1 LAMA3 CDH19 SUPT6H WDR7 C2orf85 Protein expression is a stochastic process that leads to phenotypic R7 (G4) R8 (G4) variation amongPerinephric cells1–6. The cell–cell distribution of protein levels metastasis 10 cm M1 in microorganisms has been well characterized7–23 but little is known about such variability in human cells. Here, we studied B Regional Distribution of Mutations Ubiquitous Shared primary Shared metastasis Private the variability of protein levels in human cells, as well as the temporal dynamics of this variability, and addressed whether cells IntraLtumor%Heterogeneity% M2b with higher than average proteinM2a levels eventually have lower than M1 R4 R9 R8 average levels, and if so, over what timescale does this mixing R5 R3 R2 occur. We measured fluctuations over time in the levels of 20 R1 PreM endogenous proteins in living human cells, tagged by the gene Tumor%Microenvironment% PreP GeneFc%Heterogeneity% for yellow fluorescent protein at their chromosomal loci24. We C Phylogenetic Relationships of Tumor Regions D Ploidy Profiling FDG% Ubiquitous R2 R4 found variability with a standard deviation that ranged, for differR1 R2 Shared primary R8 R3 R9 Shared metastasis R5 Tetraploid to 30% of the mean. Mixing between ent proteins, from about 15% KDM5C (missense and frameshift) Private PreP mTOR (missense) high and low levels occurred for all proteins, but the mixing time R4b SETD2 (frameshift) longer than two cell generations (more than 40 h) for many SETD2 (splice was site) M2b R9 Normal tissue ? proteins. We also taggedDI=1.43 pairs of proteins with two colours, and R4a Intr atumor Heterogeneity Revealed by multiregion Sequencing A Biopsy Sites R1 (G3) R2 (G3) R3 (G4) VHL R4 (G1) R9 SETD2 (missense) KDM5C (splice site) Chest-wall metastasis M2b Primary tumor R6 (G1) R7 (G4) DI=1.81 Lung metastases M2a Hilum R5 (G4) R8 (G4) Perinephric metastasis 10 cm M2b PreM M1 M2a Perfusion% M1 Hypoxia% a ProliferaFon% Propidium Iodide Staining Slow mixing long memory No mixing B Regional Distribution of Mutations Shared primary Shared metastasis Private IL12RB2 BCAS2 IFI16 FCAMR PLB1 ALS2CR12 C2orf21 VHL SGOL1 KLHL18 SSR3 CLCN2 WHSC1 ATXN1 DOPEY1 CCR6 INTS1 PTPRZ1 ZC3HC1 EXT1 RALGDS MSRB2 EIF4G2 ANO5 C11orf68 MRPL51 KDM2B X4 NUSAP1 TCF12 ZC3H18 DDX52 ZNF519 AKAP8 CYP4F3 KIAA0355 WDR62 KLK4 IGLON5 NLRP7 MAGEB16 SESN2 CCBL2 SETD2 PLRG1 CASP2 SSNA1 TH PPFIA1 CDKN1B WSCD2 ZNF780A PPP6R2 MTOR UGT2A1 ABHD11 GALNT11 RIMBP2 PSMD7 CENPN SOX9 NPHS1 RBFOX2 KDM5C KDM5C SATL1 FLNA ITGB3 LATS2 DIRAS3 NGEF ZNF493 SPATA21 DDX58 DAPK1 ALKBH8 KL ERCC5 DIO1 PIAS3 MR1 C3orf20 SETD2 TNIK LIAS FBXO1 AKAP9 ITIH5 WDR24 MYH8 TOM1 SBF1 KDM5C USP51 NAP1L3 ADAMTSL4 DUSP12 SLC2A12 RAB27A CIB2 RPS8 FAM129B PHF21B HDAC6 MAP3K6 MAMLD1 RLF DNMT3A HMG20A ZNF521 MMAB DACH2 SLC2A1 TM7SF4 ANKRD26 CD44 RT4 KIAA1267 C3 DAMTS10 IFNAR1 BCL11A PLCL1 SETD2 KIAA1524 NRAP HPS5 DIXDC1 LAMA3 CDH19 SUPT6H WDR7 C2orf85 IJROBP%62:545L553%(2009)% tion through loss of SETD2 methyltransferase function driven by three distinct, regionally separated mutations on a background of ubiquitous loss of the other SETD2 allele on chromosome 3p. Convergent evolution was observed for the X-chromosome–encoded histone H3K4 demethylase KDM5C, harboring disruptive mutations in R1 through R3, R5, and R8 through R9 (missense C Phylogenetic Relationships of Tumor Regions D Ploidy Profiling Ubiquitous R1 R2 Shared primary R8 R3 R9 Shared metastasis R5 KDM5C (missense and frameshift) Private PreP mTOR (missense) R2 R4 No. of Cells Tetraploid R4b SETD2 (frameshift) SETD2 (splice site) Normal tissue ? R4a M2b R9 DI=1.43 DI=1.81 VHL SETD2 (missense) KDM5C (splice site) M2b M2a M1 R4 R9 R8 R5 R3 R2 R1 PreM PreP M2b PreM tion through loss of SETD2 methyltransferase function driven by three distinct, regionally separated mutations on a background of ubiquitous loss of the other SETD2 allele on chromosome 3p. Convergent evolution was observed for the X-chromosome–encoded histone H3K4 demethylase KDM5C, harboring disruptive mutations in R1 through R3, R5, and R8 through R9 (missense M1 M2a Propidium Iodide Staining and frameshift deletion) and a splice-site mutation in the metastases (Fig. 2B and 2C). mTOR Functional Intratumor Heterogeneity The mammalian target of rapamycin (mTOR) kinase carried a kinase-domain missense mutation (L2431P) in all primary tumor regions except R4. All tumor regions harboring mTOR (L2431P) had and frameshift deletion) and a splice-site mutation in the metastases (Fig. 2B and 2C). mTOR n engl j med 366;10 Functional Intratumor Heterogeneity The mammalian target of rapamycin (mTOR) kinase carried a kinase-domain missense mutation (L2431P) in all primary tumor regions except R4. All tumor regions harboring mTOR (L2431P) had Protein level Ubiquitous N$Engl$J$Med$366:883L892%(2012)% nejm.org march 8, 2012 PERSPECTIVES Time b Time 887 The New England Journal of Medicine 887 Downloaded from nejm.org at STANFORD UNIVERSITY on July 8, 2013. For personal use only. No other uses without permission. Copyright © 2012 Massachusetts Medical Society. All rights reserved. n engl j med 366;10 nejm.org march 8, 2012 The New England Journal of Medicine Downloaded from nejm.org at STANFORD UNIVERSITY on July 8, 2013. For personal use only. No other uses without permission. Copyright © 2012 Massachusetts Medical Society. All rights reserved. Role of non-genetic heterogeneity in tumour evolution. Assume that in a tumour cell population, non-genetic heterogeneity spreads the expression level of a protein among the cells so as to consistently produce 1% of cells with a high expression of the encoding gene at a level that confers the ability to survive exposure to a cytotoxic drug, at a given dose (FIG. 2). In a small non-necrotic early tumour that contains ~109 cells, as many as 107 cells would always survive the treatment regardless of the presence of genetic variants. To be conservative, if only 1% of these 107 cells — that is, 105 cells — were capable of expansion (the socalled cancer stem cells), and if these cells maintained their transient advantageous phenotype for just four cell divisions, there would be 1,600,000 surviving cells in the presence of the selective environment. This ‘pre-selection’ of non-genetic variants would property of cell population dynamics that may increase the effectiveness of Darwinian selection by stretching the variability of a trait by up to several orders of magnitude. A role of non-genetic inheritance in evolution in general has been discussed, but it has NonLGeneFc%Heterogeneity% Stable B A B A A B B A B Unstable A B Stable A B d 8 6 4 2 0 20 60 Time (h) 11 h 100 e 2 0.3 CV A Cell%cycle% c State space within the epigenetic landscape Protein level (a.u.) Network states The network Two-gene genome 0h Protein level (norm.) Gene%regulaFon%networks% Box 2 | Basic concepts of network dynamics Potential Mutation-less evolution of malignant traits The varying cellular response to environmental factors by phenotypic outlier cells suggests the following possibility: if slow random fluctuations cause certain genes to be expressed at abnormally high levels over multiple cell generations in an outlier cell, and if they encode proteins that, when expressed at a higher level, confer a growth advantage under some selective conditions, then that cell could be selected for — as though the advantageous trait were caused by a gain-of-function mutation. Even if the non-genetic ‘fitter’ state eventually wanes after several cell divisions, this may temporarily expand a fitter subpopulation of cells capable of surviving the selective environment, which itself may also be of limited duration. Thus, enduring individuality that is due to non-genetic heterogeneity satisfies the conditions for Darwinian evolution for a limited period of time. non-genetic heterogeneity neither supports nor refutes either side of the long-lasting debate about whether genomic instability that increases mutation rate is necessary 47,48 or not 49 for tumour progression. Instead, we have illuminated a neglected but inevitable Expression level bacteria, known as persisters, may exhibit an increased resistance to penicillin that can be inherited, and hence they epitomize the contribution of phenotypic variability to overall population fitness40,42,45,46. Similarly, phenotypic variability in the level of reduced glutathione confers resistance to cadmium in Saccharomyces cerevisiae populations44. 0.2 1 0.1 0 3 2 1 Time (cell generations) Nature%444,%643L646%(2006)%% A B Figure 1 | Protein level dynamics in individual cells. a, Possible mixing High Low dynamics of a protein in a population of cells. b, Cells expressing YFP CDA B tagged topoisomerase 1 (TOP1) at different time-points. All cells are the Networks dynamics Nature Reviews | Genetics Nat.$Rev.$Gen.%10,%336L342%(2009)% A gene regulatory network orchestrates the expression of genes across the genome, generating progeny of the cell shown in the first frame. Scale bar is 25 mm c, TOP1 levels gene expression patterns, or profiles. Thus, each gene expression pattern reflects a state of the as a function of time in a cell lineage. Sharp decreases in protein levels network. Changes of the network states drive biological processes, such as cell differentiation, by controlling the necessary gene expression pattern. Such network dynamics are conveniently indicate cell-division events and lines originating after each division are the represented by the state space of the network, in which each point at a given position of that space Expression level A B Unstable represents a particular network state, hence, a gene expression pattern24. For this conceptual illustration, the state space can be imagined as projected onto 1 a two-dimensional plane in which each position represents a state. Neighbouring points in this plane represent similar gene expression patterns. Changes in gene expression, and hence of the gene expression pattern, then translate into the movement of the network state in the state space. Because of the regulatory interactions, the genes cannot alter their expression independently. Instead, gene expression changes are highly constrained such that a given expression pattern will change as a whole, moving (or flowing) in a particular state space direction along a trajectory that is dictated by the network interactions. If, for instance, gene A and gene B inhibit each other, then all expression patterns in which A and B are equally expressed would be highly unstable. For example, a slight excess of gene A (so that A>B) would suppress gene B, reducing its own inhibition and, hence, promoting its own expression, which further increases the excess of A over B expression. This would continue until the network reaches an equilibrium state at A>>B when the expression of A cannot increase further owing to other limitations. In general, because of the interactions, most network states are unstable. They move in state space seeking to satisfy the regulatory interactions or, equivalently, until they find stable equilibrium states. Such stable steady states are also called attractor states. They correspond to the gene expression patterns that define the biological cell types26,27,71,72 (see the figure). 0 T TOP cell-c by th acros meas (CV Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 76100 Israel. {P Massachusetts 02115, USA. *These authors contributed equally to this work. The epigenetic landscape For better intuitive conceptualization, each network state in the state space plane can be assigned an ‘elevation’ or a quasi-potential energy (that is, the potential), the height of which is inversely ©2006 Nature Publishing G 3% 8/1/13% How%do%QuanFtaFve%PET%Measurements%Relate% to%Individual%Cell%Parameters?% Cancer%cells% +%Stromal%cells% +%Immune%cells% %%%%%%%%%%%%%%%%%%%%%%%%%%%%% 1%SUV%number% Radionuclide%Imaging:%The%UlFmate% Heterogeneity%is%at%the%SingleLCell%Level% One%voxel% =%108%–%109%cells% CPS! One%pixel% =%102%–%103%cells% SingleLcell%imaging% 5%μm% SUV! Autoradiography% 100%μm% 4%mm% PET%scan% Goal% J.$Nucl.$Med.$Technol.$33(2),%2005,%pp.%69L74% Nucl.$Med.$Biol.$31(7),%2004,%pp.%875L882% 4% 8/1/13% SpaFal%ResoluFon%for%Radionuclide%Imaging% Digital%autoradiography% ron %ra ng e% Positron%emission%tomography% po si t 51 1%k ev % 18F% sample% 18F% e+% e+% sample% thickness% stopping% power% water% phosphor%plate% For%high%spaFal%resoluFon:% L Thin%sample% L High%stopping%power% C.S.$Levin,$et$al.$1999$ A%“radioluminescence%microscope”% ScinFllator:%CdWO4% % Imaging%system% Density:%7.9%g/cm3% EffecFve%Z:%64% Light%yield:%15,000% photons%/%MeV% Hygroscopic:%No% AVerglow:%No% % EMLCCD%camera% 1024x1024%pixels% Cooled%@%L70°C% 40X,%1.3%NA%objecFve% Live%cell%imaging% 5% 8/1/13% A%digital%image%acquisiFon%scheme% Track%analysis:% annihilaFon% photon% short%positron% track% Imaging%scheme:% long%positron% track% G.$Pratx$et$al.$JNM$(in$press)$ FDG%uptake%in%single%cells% FDG%(420%μCi/ml)% 2.%Fast%(1%h)%&% incubate%(1%h)%% 1.%Seed%104%4T1% cells% 3.%Wash%out%&% image%(5%min)% 5%min% Brighrield% FDG%(reconstrucFon)% 6% 8/1/13% FDG%uptake%in%single%cells% FDG%(420%μCi/ml)% 3.%Wash%out%&% image%(5%min)% 2.%Fast%(1%h)%&% incubate%(1%h)%% 1.%Seed%104%4T1% cells% 5%min% Overlay% FDG%uptake%in%single%cells% FDG%(420%μCi/ml)% 3.%Wash%out%&% image%(5%min)% 2.%Fast%(1%h)%&% incubate%(1%h)%% 1.%Seed%104%4T1% cells% 5%min% “SUV”%=%% 150 COV%=%46%% cell% weight% acFvity%in% the%media% 100 SUV Cell% acFvity%% volume%of% media% 50 0 0 Cell%weight%≈%3%ng%%(HeLa)% 10 20 Cell # 30 40 hLp://bionumbers.hms.harvard.edu$ 7% 8/1/13% Timelapse%imaging%of%FDG%uptake:%Protocol% Seed%104%MDAL MBL231%cells% (24%h)%&%fast%(1%h)% Timelapse:% 10%images%/%h% +%FDG%(5%μCi)% Influx! 5%min% +%FDG%(400%μCi)% wash%out% Efflux! 5%min% T%=%L1%h% T%=%0%h% T%=%8%h% Uptake%of%FDG%in%live%cells% Note: Video available on PLOS One 8% 8/1/13% Tracer%kineFc%modeling:%Influx% brighrield% radioluminescence%(Fmelapse,%10%images%/%h)% +%5%μCi%FDG% 1 RL signal (A.U.) 0 0 1 Cell avg. Cont. avg. RL signal (A.U.) Cell Control 2 4 Time (hr) 6 8 0 0 single% cell% Data Model Patlak 2 4 Time (hr) 6 8 G.$Pratx$et$al.$PLOS$One$2012$ Efflux%of%FDG%from%live%cells% Note: Video available on PLOS One 9% 8/1/13% Tracer%kineFc%modeling:%Efflux% radioluminescence%(Fmelapse,%10%images%/%h)% 0.5h t = 0h 1 RL signal (A.U.) Cell Control 0 0 8h 2h Cell avg. Cont. avg. 1 RL signal (A.U.) brighrield% single% cell% Data Model Fast comp. Slow comp. 0 2 4 Time (hr) 6 8 0 2 4 Time (hr) 6 8 G.$Pratx$et$al.$PLOS$One$2012$ Piralls%of%Bulk%Cell%Measurements% Bulk% Σ% Compartmental% Analysis% k1% k2% …% ?% Single% cell% Compartmental% Analysis% k1,%k2,%…% k1,%k2,%…% k1,%k2,%…% Σ% k1% k2% …% 10% 8/1/13% Bulk%ProperFes%≠%Average%ProperFes% RL signal (A.U.) 1 1 RL signal (A.U.) 1 RL signal (A.U.) 0 0 2 0 0 single% cells% 4 Time (hr) 2 6 4 Time (hr) 0 0 2 K1% bulk% RL signal (A.U.) 1 8 6 4 Time (hr) 0 0 8 6 2 4 Time (hr) 6 8 8 K2% K3% Tissue%SecFon%Imaging:%Zr89LRituximab%in%the%Spleen% 11% 8/1/13% Tissue%SecFon%Imaging:%Zr89LRituximab%in%the%Spleen% Conclusions% Radioluminescence% microscopy% is% a% new% imaging% technique% that%can%sensiFvely%and%quanFtaFvely%characterize%the%uptake% of% small% molecules% in% heterogeneous% populaFons% of% single% cells.% % We% are% applying% it% to% relate% macroscopic% parameters% measured% by% PET% to% cellular% parameters% that% are% specific% to% cellular%funcFon,%disease%state,%and%response%to%therapy.% 12% 8/1/13% Acknowledgements% Conroy%Sun% Laura%Sasportas% Marian%Axente% Marta%Colomer% Colin%Carpenter% % BCRP W81XWH-11-1-0087 Kai%Chen% Lynn%MarFn% John%Sunwoo% Ted%Graves% Lei%Xing% NIH 5P50CA114747 ICMIC Equipment loan 13%