Supplementary Figure 1. Chromatin signature profiling by mass spectrometry.
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- Stanley George
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1 Supplementary Information Supplementary Figure 1. Chromatin signature profiling by mass spectrometry. 115 cell lines from the CCLE collection were subjected to chromatin signature profiling by mass spectrometry. Each row corresponds to a histone H3 peptide with the specific combination of marks shown on the right. The value in each cell of the heatmap corresponds to the log2-fold change of the mark combination vs. the median for each row. Tissue origin, hematological subtypes and mutation status of EZH2 and NSD2 are indicated. Clusters A-F are marked for reference in the main text.
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3 Supplementary Figure 2. Cell lines containing NSD2 E1099K mutation express both wild type and E1099K mutant NSD2 alleles. cdna from six NSD2 E1099K mutant expressing cell lines and three NSD2 wildtype cell lines was subjected to Sanger Sequencing and sequencing chromatograms are shown; left and right columns are chromatograms using forward and reverse sequencing primers respectively. cdna sequencing of all mutant cell lines showed that both the wild type and mutant NSD2 transcripts are expressed. Mutation caused nucleotide change of Gà A (red) at codon 1099 (underlined and marked by red arrow in the chromatograms) resulting amino acid change of Eà K.
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6 Supplementary Figure 3. Structural model of NSD2 E1099K mutation Structural model of NSD2 sequence mutations, E1099 (magenta stick with black text) to K1099 (white stick with red text) and D1125 (magenta stick with black text) to N1125 (white stick with red text). They are predicted to alter binding between NSD2 (green cartoon) and the histone peptide (blue cartoon). Amino acids K1124 and C1183 are labeled and shown as green sticks. Residues that line the I-SET histone binding groove are labeled with grey text and shown as green sticks (C1102, I1106, M1119, I1127, and T1121). The residues S31 (blue stick) and K36 (blue stick) are shown to identify modeled locations of residues on the H3 peptide. Black dash highlights key interactions.
7 Supplementary Figure 4. Molecular chromatin signatures of KMS11-TKO engineered lines.
8 Supplementary Figure 5. NSD2 variants identified in primary ALL samples promote H3K36 dimethylation and transformation. A) Western blot of KMS11-TKO cells reconstituted with NSD2-wt, NSD2-CDM (catalytic dead mutation), NSD2-E1099K, NSD2-E1099K-CDM (harboring both E1099K and the catalytic inactive mutation), NSD2-D1125N, NSD2-MB4-2 (N-terminal truncation), or the empty vector. NSD2 MB4-2 is a structural variant identified in pediatric tumor sample (see Supplementary information, NSD2 structural variations in pediatric cancer. Cell lysates were blotted with the indicated antibodies. Histone H3 serves as loading control. B) Quantification of soft agar transformation (in presence of 5% serum) of KMS11-TKO cells reconstituted with the indicated NSD2 variants. Error bars indicate the s.d. of triplicate samples. C) Quantification of soft agar transformation of KMS11-TKO cells reconstituted with the indicated NSD2 variants in the presence of 10% serum. Two independent experiments were shown. Error bars indicate the s.d. of triplicate samples. This set of experiments was performed to evaluate if different serum concentration (5% vs 10%) might affect the outcome of soft agar transformation. The actual number of colonies differs under the different serum concentration. Overall, these data showed transforming activity of (NSD2 E1099K ~ NSD2 D1125N ~ MB4-2) > NSD2 wt > (vector control ~ NSD2 CDM ~ NSD2 E1099KCDM).
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10 Supplementary Figure 6. NSD2 E1099K specifically alters H3K36 methylation and not generally affects other histone H3 modifications. a) Immunoblot of blot of H3K4me1/2/3 and H3K9me1/2/3 of KMS11-TKO cells transduced with the lentivirus expressing the indicated NSD2 variants. b) Mass spectrometry profiling of the indicated histone peptides in SEM cells following NSD2 knockdown. C) Immunoblot of H3K27me3 and H3 of the tumor samples as shown in Fig 4f.
11 Supplementary Figure 7. NSD2 E1099K promotes H3K36me2 in NIH3T3. Western blot of NSD2, H3K36me3, total H3 and γ-tubulin in NIH3T3 cells transfected with the indicated NSD2 variants. Results from two independent experiments were shown.
12 Supplementary Figure 8. An example of NSD2 mutant isoform detected by RNA-seq in the three ETV6-RUNX1 ALL cases with intra-genic 5 deletion. A) Junction reads from RNA-seq across the alternative exon 1 and exon 6 confirm a novel isoform resulting from intra-genic genomic deletion in sample ETV086. The junction reads spans the alternative exon 1 (encoded only by isoform 10 of NSD2, accession NM_ ) and exon 6 of NSD2. The alternative ATG is shown in black box. B) Mutant protein with truncated N-termini predicted from the mutant transcript.
13 Supplementary Figure 9. An example of inter-chromosomal re-arrangement resulting in fusion of the 5 UTR of ST6GAL1 with exon 1 of NSD2 Junction reads in RNA-seq that span 5 UTR of ST6GAL1 (left box, in blue) and the first coding exon of NSD2 (right box, in black) resulting from inter-chromosomal translocation in sample LGG039. The junction reads mapped to ST6GAL1 were marked as the soft-clipped reads by bwa (shown in light blue color in Bambino viewer at the left).
14 Supplementary Table 1. Cell lines screened by global histone profiling Cell Line Name Cluster Tissue of Origin Haematological Subtype t(4;14) translocation NSD2 variants EZH2 variants KARPAS422 A Heme/Lymph BCL Y641N Pfeiffer A Heme/Lymph BCL A677G SUDHL6 A Heme/Lymph BCL Y641N SUDHL4 A Heme/Lymph BCL Y641S RL A Heme/Lymph BCL Y641N WSUDLCL2 A Heme/Lymph BCL Y641F DB A Heme/Lymph BCL Y641N SUDHL10 A Heme/Lymph BCL Y641F 253JBV B Urinary A956P 5637 B Urinary SW1710 B Urinary KMBC2 B Urinary HEC108 B Endometrium K361Q RT4 B Urinary MOLM16 B Heme/Lymph AML L1236 B Heme/Lymph HL SCaBER B Urinary HT1376 B Urinary KHM1B B Heme/Lymph MM J82 B Urinary NCIH650 B Lung CAL29 B Urinary DEL B Heme/Lymph NS KMS20 B Heme/Lymph MM EB2 B Heme/Lymph BL KMS27 B Heme/Lymph MM UMUC3 B Urinary NCIH3255 B Lung BV173 B Heme/Lymph CML NB4 B Heme/Lymph AML T236A UBLC1 B Urinary QGP1 B Pancreas CMK115 B Heme/Lymph AML G945fs OCILY19 B Heme/Lymph BCL CMK B Heme/Lymph AML KMS12BM B Heme/Lymph MM MOLM6 B Heme/Lymph CML K361Q
15 MUTZ5 B Heme/Lymph ALL ML1 B Thyroid HDLM2 B Heme/Lymph HL SUPT11 B Heme/Lymph TCL PC3 B Prostate MonoMac1 B Heme/Lymph AML MonoMac6 B Heme/Lymph AML Nomo1 B Heme/Lymph AML Toledo B Heme/Lymph BCL GA10 B Breast KOPN8 B Heme/Lymph ALL KP4 B Pancreas Y696C TF1 B Heme/Lymph AML MDAMB157 B Breast OCIAML2 B Heme/Lymph AML NCIH1568 B Lung U937 B Heme/Lymph BCL UMUC1 C Urinary MOLM13 C Heme/Lymph AML JHUEM7 C Endometrium D672Y EJM C Heme/Lymph MM SUDHL5 C Heme/Lymph BCL KLE C Endometrium OCILY3 C Heme/Lymph BCL 647V C Urinary 639V C Urinary L428 C Heme/Lymph HL Y641S KMS26 D Heme/Lymph MM yes MM1S D Heme/Lymph MM E1099K KMS28BM D Heme/Lymph MM yes KMS34 D Heme/Lymph MM yes LP1 D Heme/Lymph MM yes OPM2 D Heme/Lymph MM yes KMS11 D Heme/Lymph MM yes RPMI8402 D Heme/Lymph ALL E1099K RS411 D Heme/Lymph ALL E1099K SEM D Heme/Lymph ALL E1099K MOLT13 D Heme/Lymph ALL E1099K RCHACV D Heme/Lymph ALL E1099K HPBALL D Heme/Lymph ALL E1099K
16 KMRC3 E Kidney G945fs IGR1 E Skin Y641N OVISE E Ovarian Set2 E Heme/Lymph ET MDAMB361 E Breast ZR7530 E Breast S619C LNCAP E Prostate THP1 E Heme/Lymph AML VMCUB1 E Urinary S804L TOV21G E Ovarian NAMALWA E Heme/Lymph BL KU1919 E Urinary HEL9217 E Heme/Lymph AML SKMEL30 E skin W624* BFTC905 E Urinary RT112 E Urinary L363 E Heme/Lymph MM T24 E Urinary NCIH1930 E Lung NCIH209 E Lung IGROV1 E Ovarian L33 E Pancreas MV411 E Heme/Lymph AML JJN3 E Heme/Lymph MM N268D SUIT2 E Pancreas SW780 E Urinary RERFLCAd2 E Lung TT E Oesophagus K361Q PL21 E Heme/Lymph AML ESS1 E Endometrium R685C JHOM1 E Ovarian KO52 E Heme/Lymph AML TALL1 F Heme/Lymph ALL I708M SW579 F Thyroid E1099K JMSU1 F Urinary G623D SKM1 F Heme/Lymph AML Y641C KE37 F Heme/Lymph ALL H279Y OCIAML5 F Heme/Lymph AML R685H Note: cell lines appear in the same order (left to right) as in Fig. 1 and Supplementary Fig. 1.
17 Supplementary Table 2. Summary of EZH2 status of 5 cell lines in cluster F by RNA-seq. Cell Line cdna_change Protein_Change t_alt_count t_ref_count JMSU1 c.1868g>a p.g623d KE37 c.835c>t p.h279y OCIAML5 c.2054g>a p.r685h SKM1 c.1922a>g p.y641c TALL1 c.1665c>a p.n555k TALL1 c.2124a>g p.i708m Set domain sequence alignment of five human methyltransferases performed by CLUSTALW. (*. : indicated identical residues, and residues showing different degrees of homology). Highlighted in yellow (G623), grey (Y641), green (R685) and red (I708) in the SET domain of EZH2. NSD2_ SETD2_ EZH2_ SUV39H1_ SETD7_ NSD2_ SETD2_ EZH2_ SUV39H1_ SETD7_ NSD2_ SETD2_ EZH2_ SUV39H1_ SETD7_ PETKIIKTD-GKGWGLVAKRDIRKGEFVNEYVGELIDEEECMARIKHAHE ADVEVILTE-KKGWGLRAAKDLPSNTFVLEYCGEVLDHKEFKARVKEYAR KHLLLAPSD-VAGWGIFIKDPVQKNEFISEYCGEIISQDEADRRGKVYD- YDLCIFRTDDGRGWGVRTLEKIRKNSFVMEYVGEIITSEEAERRGQIYDR GEGLFSKVAVGPNTVMSFYNGVRITHQEVDSRDWALNG * *: :..: * * :.* * NDITHFYMLTIDKDR-IIDAGPKGN-YSRFMNHSCQPNCETLKWTVN--- NKNIHYYFMALKNDE-IIDATQKGN-CSRFMNHSCEPNCETQKWTVN--- -KYMCSFLFNLNNDF-VVDATRKGN-KIRFANHSVNPNCYAKVMMVN--- QGATYLFDLDYVEDVYTVDAAYYGN-ISHFVNHSCDPNLQVYNVFIDNLD NTLSLDEETVIDVPEPYNHVSKYCASLGHKANHSFTPNCIYDMFVHPR--.. : *** ** -GDTRVGLFAVCDIPAGTELTFNYNLDCLGN -GQLRVGFFTTKLVPSGSELTFDYQFQRYGK -GDHRIGIFAKRAIQTGEELFFDYRYSQADA ERLPRIAFFATRTIRAGEELTFDYN FGPIKCIRTLRAVEADEELTVAYG : : : :. **. *
18 Supplementary Table 3. Summary of CCLE cell lines with NSD2 E1099K mutation. Cell lines HIST_SUBTYPE NSD2 protein change GENDER AGE_YRS sem acute_lymphoblastic_b_cell_leukaemia p.e1099k female 5 rs411 acute_lymphoblastic_b_cell_leukaemia p.e1099k female 32 rchacv acute_lymphoblastic_leukaemia p.e1099k female 8 hpball acute_lymphoblastic_t_cell_leukaemia p.e1099k male 14 rpmi8402 acute_lymphoblastic_t_cell_leukaemia p.e1099k female 16 molt13 acute_lymphoblastic_t_cell_leukaemia p.e1099k female 2 sw579 anaplastic_carcinoma p.e1099k male 59 mm1s plasma_cell_myeloma p.e1099k
19 Supplementary Table 4. Summary of colony growth in soft agar of 24 ALL cell lines.
20 Supplementary Table 5. Mutant Allele Fraction (MAF) of NSD2 somatic mutations in DNA and mrna samples of PCGP analyzed by WGS, custom capture and RNA-seq. MAF 0.1 was highlighted. The exon number of the four deletions were based on isoform 1 of NSD2 (accession NM_133330). * NGS read count in DNA combines data from WGS and custom capture when available ^MAF stands for mutant allele fraction, i.e. number of NGS reads with the mutant allele/number of all NGS at the site. Mutations with MAF <0.1 are matching normal sample of this tumor has approximately 20% contaminating tumor material.
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22 Supplementary Table 6. Examples of synthetic peptides for many possible peptide/modification combinations on histone H3. Mass [m/z] Start time [min] End time [min] Normalized HCD Collision Energy (%) Charge State [z] Targeted Species* H3K4me2-L H3K4me2-H H3K27me2K36me2-L H3K4ac1-L H3K4me3-L H3K27me2K36me2-H H3K27me3K36me2-L+H3K27me2K36me3-L H3K4ac1-H H3K4me3-H H3K27me3K36me2-H+H3K27me2K36me3-H H3K27me3K36me3-L H3K4me0-L H3K27me3K36me3-H H3K4me0-H H3K4me1-L H3K4me1-H H3K9me2K14ac1-L H3K9me2K14ac1-H H3K9ac1K14ac1-L H3K9me3K14ac1-L H3K9me2K14ac0-L H3K9ac1K14ac1-H H3K9me3K14ac1-H H3K9me2K14ac0-H H3K9ac1K14ac0-L+H3K9me0K14ac1-L H3K9me3K14ac0-L H3K9ac1K14ac0-H+H3K9me0K14ac1-H H3K9me3K14ac0-H H3K9me0K14ac0-L H3K9me1K14ac1-L H3K27ac1K36me2-L H3K9me0K14ac0-H H3K9me1K14ac1-H
23 H3K9me1K14ac0-L H3K27ac1K36me2-H H3K27ac1K36me3-L H3K27me2K36me0-L H3K27me0K36me2-L H3(41-49)-L H3K9me1K14ac0-H H3K27me2K36me0-H H3K27me0K36me2-H H3K27ac1K36me3-H H3K27ac1K36me0-L H3K27me1K36me2-L H3K27me0K36me3-L H3K27me2K36me1-L H3K27me3K36me0-L H3K27ac1K36me0-H H3K27me1K36me2-H H3K27me3K36me0-H H3K27me2K36me1-H H3K27me0K36me3-H H3K27me0K36me0-L+H3K27ac1K36me1-L H3K27me1K36me3-L H3K27me3K36me1-L H3K9me2S10ph1K14ac1-L H3(41-49)-H H3K27ac1K36me1-H+H3K27me0K36me0-H H3K27me1K36me3-H H3K27me3K36me1-H H3K27me1K36me0-L H3K27me0K36me1-L H3.3K27me0K36me0-L H3K9me2S10ph1K14ac1-H H3K9ac1S10ph1K14ac1-L H3K9me3S10ph1K14ac1-L H3K9me2S10ph1K14ac0-L H3K27me1K36me0-H H3K27me0K36me1-H H3.3K27me0K36me0-H H3K27me1K36me1-L H3K18ac1K23ac1-L
24 H3K27me1K36me1-H H3K9ac1S10ph1K14ac1-H H3K9me3S10ph1K14ac1-H H3K9me2S10ph1K14ac0-H H3K9ac1S10ph1K14ac0-L+H3K9me0S10ph1K14ac1- L H3K9me3S10ph1K14ac0-L H3K18ac1K23ac1-H H3K18ac1K23ac0-L+H3K18ac0K23ac1-L H3K9ac1S10ph1K14ac0-H+H3K9me0S10ph1K14ac1- H H3K9me3S10ph1K14ac0-H H3K9me0S10ph1K14ac0-L H3K9me1S10ph1K14ac1-L H3K18ac1K23ac0-H+H3K18ac0K23ac1-H H3K18ac0K23ac0-L H3K9me1S10ph1K14ac1-H H3K9me0S10ph1K14ac0-H H3K9me1S10ph1K14ac0-L H3K18ac0K23ac0-H H3K9me1S10ph1K14ac0-H H3K18ub1K23ac0-L+H3K18ac0K23ub1-L H3K18ub1K23ac0-H+H3K18ac0K23ub1-H H3K56me2-L H3K56me2-H H3K56me0-L H3K56me0-H H3K56me1-L H3K56me1-H H3K79me2-L H3K79me2-H H3K79me0-L H3K79me0-H H3K79me1-L H3K79me1-H *The label of the species targeted refers to the resultant derivatized peptide containing the stated modification after preparation as described in the Methods section. In some cases one set of (m/z, time window) coordinates may cover multiple species. -L denotes light peptides derived from the CCLE cell line while -H denotes heavy peptides derived from the R 10 standard mix cell lines.
25 Supplementary Table 7. Peptides monitored by Global Chromatin Profiling with histone nomenclature and biochemical abbreviations Nomenclature Base Sequence Modified Sequence H3K4me0 TKQTAR (pr)-t(kpr)qtar H3K4me1 TKQTAR (pr)-t(kme1pr)qtar H3K4me2 TKQTAR (pr)-t(kme2)qtar H3K4ac1 TKQTAR (pr)-t(kac)qtar H3K9me0K14ac0 KSTGGKAPR (pr)-(kpr)stgg(kpr)apr H3K9me0K14ac1 KSTGGKAPR (pr)-(kpr)stgg(kac)apr H3K9me1K14ac0 KSTGGKAPR (pr)-(kme1pr)stgg(kpr)apr H3K9me1K14ac1 KSTGGKAPR (pr)-(kme1pr)stgg(kac)apr H3K9me2K14ac0 KSTGGKAPR (pr)-(kme2)stgg(kpr)apr H3K9me2K14ac1 KSTGGKAPR (pr)-(kme2)stgg(kac)apr H3K9me3K14ac0 KSTGGKAPR (pr)-(kme3)stgg(kpr)apr H3K9me3K14ac1 KSTGGKAPR (pr)-(kme3)stgg(kac)apr H3K9ac1K14ac0 KSTGGKAPR (pr)-(kac)stgg(kpr)apr H3K9ac1K14ac1 KSTGGKAPR (pr)-(kac)stgg(kac)apr H3K18ac0K23ac0 KQLATKAAR (pr)-(kpr)qlat(kpr)aar H3K18ac1K23ac0 KQLATKAAR (pr)-(kac)qlat(kpr)aar H3K18ac0K23ac1 KQLATKAAR (pr)-(kpr)qlat(kac)aar H3K18ac1K23ac1 KQLATKAAR (pr)-(kac)qlat(kac)aar H3K18ac0K23ubq1 KQLATKAAR (pr)-(kpr)qlat(kggpr)aar H3K27me0K36me0 KSAPATGGVKKPHR (pr)-(kpr)sapatggv(kpr)(kpr)phr H3K27me0K36me1 KSAPATGGVKKPHR (pr)-(kpr)sapatggv(kme1pr)(kpr)phr H3K27me0K36me2 KSAPATGGVKKPHR (pr)-(kpr)sapatggv(kme2)(kpr)phr H3K27me0K36me3 KSAPATGGVKKPHR (pr)-(kpr)sapatggv(kme3)(kpr)phr H3K27me1K36me0 KSAPATGGVKKPHR (pr)-(kme1pr)sapatggv(kpr)(kpr)phr H3K27me1K36me1 KSAPATGGVKKPHR (pr)- (Kme1pr)SAPATGGV(Kme1pr)(Kpr)PHR H3K27me1K36me2 KSAPATGGVKKPHR (pr)-(kme1pr)sapatggv(kme2)(kpr)phr H3K27me1K36me3 KSAPATGGVKKPHR (pr)-(kme1pr)sapatggv(kme3)(kpr)phr H3K27me2K36me0 KSAPATGGVKKPHR (pr)-(kme2)sapatggv(kpr)(kpr)phr H3K27me2K36me1 KSAPATGGVKKPHR (pr)-(kme2)sapatggv(kme1pr)(kpr)phr H3K27me2K36me2 KSAPATGGVKKPHR (pr)-(kme2)sapatggv(kme2)(kpr)phr H3K27me3K36me0 KSAPATGGVKKPHR (pr)-(kme3)sapatggv(kpr)(kpr)phr H3K27me3K36me1 KSAPATGGVKKPHR (pr)-(kme3)sapatggv(kme1pr)(kpr)phr H3K27ac1K36me0 KSAPATGGVKKPHR (pr)-(kac)sapatggv(kpr)(kpr)phr H3K27ac1K36me1 KSAPATGGVKKPHR (pr)-(kac)sapatggv(kme1pr)(kpr)phr H3K27ac1K36me2 KSAPATGGVKKPHR (pr)-(kac)sapatggv(kme2)(kpr)phr H3K27ac1K36me3 KSAPATGGVKKPHR (pr)-(kac)sapatggv(kme3)(kpr)phr H3.3K27me0K36me0 KSAPSTGGVKKPHR (pr)-(kpr)sapstggv(kpr)(kpr)phr H3Y41ph0 YRPGTVALR (pr)-yrpgtvalr
26 H3K56me0 YQKSTELLIR (pr)-yq(kpr)stellir H3K56me1 YQKSTELLIR (pr)-yq(kme1pr)stellir H3K79me0 EIAQDFKTDLR (pr)-eiaqdf(kpr)tdlr H3K79me1 EIAQDFKTDLR (pr)-eiaqdf(kme1pr)tdlr H3K79me2 EIAQDFKTDLR (pr)-eiaqdf(kme2)tdlr Abbreviations: Chemical derivatives: Pr Ac me1 me2 me3 proprionyl acetyl monomethyl dimethyl trimethyl Nomenclature not defined above: Ubq me0 = ac0 ubiquityl stub (GG) unmodified
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p.r623c p.p976l p.d2847fs p.t2671 p.d2847fs p.r2922w p.r2370h p.c1201y p.a868v p.s952* RING_C BP PHD Cbp HAT_KAT11
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a Control shrna#9 shrna#12 c Control shrna#9 shrna#12 e Control shrna#9 shrna#12 h 14 12 CFU-E BFU-E GEMM GM b Colony number 7 6 5 4 3 2 1 6 pm A pa pc CFU-E BFU-E GEMM GM pu pgm A p pg B d f CD11b-APC
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IP: Flag a Mascot PTM Modified Mass Error Position Gene Names Score Score Sequence m/z [ppm] 81 MAT2A;AMS2;MATA2 35.6 137.28 _AAVDYQK(ac)VVR_ 595.83-2.28 b Pre-immu After-immu Flag- WT K81R WT K81R / Flag
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Supplementary Figure 1 a γ-h2ax MDC1 RNF8 FK2 BRCA1 U2OS Cells sgrna-1 ** 60 sgrna 40 20 0 % positive Cells (>5 foci per cell) b ** 80 sgrna sgrna γ-h2ax MDC1 γ-h2ax RNF8 FK2 MDC1 BRCA1 RNF8 FK2 BRCA1
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