Supplemental Information Jmjd1c is Required for MLL-AF9 and HOXA9 Mediated AML Stem Cell Self- Renewal Nan Zhu, Mo Chen, Rowena Eng, Joshua DeJong, Amit U. Sinha, Noushin F. Rahnamay, Richard Koche, Fatima Al-Shahrour, Janna C. Minehart, Chun-Wei Chen, Aniruddha J. Deshpande, Haiming Xu, S. Haihua Chu, Benjamin L. Ebert, Robert G. Roeder, Scott A. Armstrong Inventory of Supplemental Information Supplemental Figure Legends Supplemental Figures Figure S1. Related to Figure 1. Figure S. Related to Figure &4. Figure S. Related to Figure &5. Figure S4. Related to Figure 6. Figure S5. Related to Figure 7. Figure S6. Related to Figure 7. Supplemental Tables Table S1. Related to Figure 1. Table S. Related to Figure 1. Table S. Related to Figure S Table S4. Related to Figure. Table S5. Related to Figure 5. Table S6. Related to Figure 7.
Figure S1 A B Number of Illumina reads C Log (Median Fold Change Bone Marrow vs. T0) R =0.89 Log (Median Fold Change Spleen vs. T0) Row min Relative Row max D MLL t (8;1) t (15;17) Adult Inv 16 M7 other T_MLL Hoxa9 probe 1 Hoxa9 probe -.5 + Row relative HOXA9 HOXA10 JMJD1C MEIS1 SENP6 TSCD HIPK HOXA7 CDK6 RDX WNK1 PHIP CHD PDEB RUNX
Figure S1. In vivo shrna screen of MLL-AF9 targets. Related to Figure 1. (A) Number of reads obtained from Illumina sequencing of eight experimental replicates. (B) Unsupervised hierarchical clustering of normalized reads of all hairpins in eight replicates. Hairpins are ranked by their depletion level in the bone marrow using log median foldchange. (C) Scatter plot showing correlation of Log Fold Change in the BM vs. SPL. (D) Heatmap of MLL-AF9 target genes (14) (upper panel) and scatter plot of Hoxa9 and Jmjd1c expression level (bottom panel) in human leukemias (9).
Figure S A B C Jmjd1c f/f MIT CRE D Jmjd1c f/f :CRE M NTC f/f Jmjd1c f/f :MIT E F G Jmjd1c f/f Jmjd1c -/- H I Cleaved caspase Total H
Figure S continued J K L M Cell line HOXA9 expression THP1 + Molm1 + Nomo1 + MonoMac6 + Oci-AML + Kasumi - HL60 - N O
Figure S. Effect of loss of Jmjd1c in MLL-AF9 leukemia. Related to Figure &. (A) Colony counts of MLL-AF9 transformed pre-leukemic cells derived from Jmjd1c f/f and wt background 7 days after transduction of CRE or MIT control viruses in methylcellulose. Results from two to three independent experiments. (B) Morphology 9 days after CRE transduction: colony image (top [x40 original magnification]) and Wright- Giemsa staining (bottom [x400 original magnification]). (C) Proliferation assay of sorted GFP+/Tomato+ MLL- AF9 leukemia cells from Jmjd1c f/f (triplicate samples from three leukemias) and wt (triplicate samples) background after transduction with MIT control or CRE virus. (D) Limiting dilution transplantation of cells in (C) see also Table S1. Right panel: Genotyping PCR of BM cells. (E)-(H) Analysis of BM cells from secondary recipient mice. (E) Flow cytometry analysis of c- Kit expression, n=4&7 for Jmjd1c MIT & CRE in BM cells from secondary recipients as in (D). (F) Wright-Giemsa staining of sorted GFP+/Tomato+ (Jmjd1c -/- ) or GFP+ (Jmjd1c f/f ) MLL-AF9 leukemia cells from secondary recipients (x400 original magnification), Colony counts of sorted leukemic cells as in (F) in methylcellulose after 7 days. Duplicate samples from two leukemias are shown. (H) Western blot of cleaved caspase in BM cells as in (F). (I) Colony counts of sorted peripheral blood GFP+ cells in methylcellulose after 7 days from mice transplanted in Figure B 9 days after pipc administration. Duplicate samples from three pipc treated Jmjd1c f/f : Mx1Cre leukemias and a non-treated leukemia are shown. (J) Colony counts of MLL-AF9 transformed pre-leukemic cells derived from Jmjd1c f/f :Vav1Cre and controls. Shown are duplicate samples. (K) Survival curve of primary recipient mice that received,000 MLL-AF9 transformed LSKs from Jmjd1c f/f : Vav1Cre and controls. (L) Proliferation of human leukemia cells transduced with shrna (two independent shrnas were used) against Jmjd1c compared to shluc control, as measured by live cell counts. Results from four independent experiments. (M) RT-QPCR performed using cells from (L). Results from three independent experiments. (N) Apoptosis assay of transduced cells as in (L). Shown are duplicate samples. Color key same as in (L) and different shades of the same color represents different time point: lighter day4 and darker day7. NA: no day7 data available because of insufficient number of cells. (O) Colony counts of Hoxa9/Meis1 transformed pre-leukemic cells derived from Jmjd1c f/f :Vav1Cre and controls. Results from two independent experiments in duplicates. Data are represented as mean+ SEM in (A), (E), (G), (I), (J) & (L)-(O). *p<0.05; **p<0.01 student s t-test.
Figure S A f/f NES=1.44 -/- p=0.08 q=0.05 f/f NES=1.7 -/- p=0.06 q=0.08 f/f NES=1. -/- p=0.5 q=0.5 B α-jmjd1c Streptavidin pull down - + 5% Input - + Bio-Jmjd1c Jmjd1c HA-IP flag-jmjd1c + + HA-Hoxa9 - + flag-jmjd1c C Jmjd1c f/f M Jmjd1c -/- HK9me H K9me1 α- Hoxa10 Hoxa10 HA-Hoxa9 Total H 1 4 D Genes negatively regulated by Jmjd1c Genes bound and negatively regulated by Hoxa9 Log Fold change CRE/MIT Genes positively regulated by Jmjd1c Log Fold change CRE/MIT Genes bound and positively regulated by Hoxa9 HK9me CRE/MIT HK9me CRE/MIT E f/f NES=-1.44 -/- p=0.0 q=0.09 f/f NES=-1.41 -/- f/f NES=1.5 -/- p=0.0 q=0.15 p=0.09 q=0.
Figure S. Loss of Jmjd1c on gene expression and histone methylation. Related to Figure 4. (A) GSEA analysis result showing enrichment of differentiation and apoptosis pathway in MLL-AF9 leukemia cells 6 days after loss of Jmjd1c. (B) Left panel : Coimmunoprecipitation of HOXA10 and JMJD1C in 9T cells transfected with indicated plasmids. Right panel: In vitro protein-protein interaction assay between purified HA-Hoxa9 from 9T cells and baculovirus system expressed and purified flag-jmjd1c. (C) Western on HK9me/me1 in BM cells from secondary MLL-AF9 recipient mice. (D) Scatter plots of Log gene expression changes (CRE/MIT Y axis) vs. HK9me level. Highlighted in red populations: upper left: genes that are up-regulated upon loss of Jmjd1c; lower left: genes that are down-regulated upon loss of Jmjd1c; upper right: genes that are bound and repressed by Hoxa9; lower right: genes that are bound and activated by Hoxa9 (44). (E) GSEA analysis result showing enrichment of differentiation and negative regulation of cell cycle signatures in Hoxa9/Meis1 leukemia cells 6 days after loss of Jmjd1c.
Figure S4 A C B LK LSK GMP CMP MEP c-kit CD48 FcγR II/III Vav1Cre Sca-1 CD150 CD4 Lin- Lin- CLP Flt C-Kit Vav1Cre IL-7Rα Sca-1
Figure S4. Effect of loss of Jmjd1c in normal hematopoiesis. Related to Figure 6. (A) RT-QPCR analysis of Jmjd1c level in hematopoietic compartments (n= biological replicates). LT-HSC [LSK Flt - CD4 - ], ST-HSC [LSK Flt - CD4 + ], LMPP [LSK Flt + CD4 + ], CMP [LK CD4 + FcγR II/III lo ], GMP [LK CD4 + FcγR II/III hi ], MEP [LK CD4 - FcγR II/III lo ]. (B) Colony formation of normal hematopoietic progenitors using whole bone marrow from Jmjd1c f/f :Vav1Cre mice. Summary of three independent experiments. (C) Representative stem progenitors flow cytometry plots from (top panel) and Vav1Cre (bottom) mice (LK [Lin - c-kit + ], CLP [Lin - IL7R + Flt + Sca-1 lo c-kit +lo ], HSC [LSK CD150+ CD48-]). Data are represented as mean+ SEM in (A)&(C).
Figure S5 A B C Vav1Cre Vav1Cre Vav1Cre 1 Non-competitive transplant D E F Vav1Cre Vav1Cre Vav1Cre Non-competitive transplant G Mac1Gr1 B0 CD Vav1Cre H Vav1Cre I Vav1Cre 1 Competitive transplant J K L Vav1Cre Vav1Cre Vav1Cre M 1 Competitive transplant N Vav1Cre
Figure S5 continued O P Jmjd1c f/f Figure S5. Effect of loss of Jmjd1c in regenerative hematopoiesis. Related to Figure 7. (A) -(L) Flow cytometry analysis results of chimerism of recipient mice from transplantation experiments. (A)-(C) Two million BM cells from Vav1Cre or Jmjd1c f/f : Vav1Cre were transplanted into lethally irradiated CD45.1 recipients. (n=10) (D)-(F) Two million BM cells from primary non-competitive transplantation were serially transplanted into secondary CD45.1 recipients (n=10). (G)-(I) Chimerism of PB Mac-1 Gr-1(G), B0 (H) and CD (I) in primary competitive transplant as in Figure 7(A)-(C). (J)-(K) Two hundred HSC (CD150 + CD48 - Lin - Sca-1 + c-kit + ) cells from Vav1Cre or Jmjd1c f/f : Vav1Cre were mixed 1:1 with 00 CD45.1 HSC cells plus 0. million CD45.1 helper cells and transplanted into lethally irradiated CD45.1 recipients. (n=15). Chimerism in peripheral blood (A),(D),(G)- (I)&(J); bone marrow and spleen (B),(E)&(K); stem and progenitor populations in BM (C),(F)&(L). (M) Homing of whole bone marrow from Jmjd1c f/f :Vav1Cre mice analyzed 18 hours after transplantation (n=8). Two donor mice and eight recipients were used. (N) Cell cycle analysis by BrdU and Sytox blue (n= per genotype). (O) HSPC frequency two weeks after 5-Fu treatment (n=-4 per genotype). (P) Survival curve of Jmjd1c f/f : Vav1Cre mice after weekly 5-Fu treatment (indicated by arrows) (n=5 per genotype). Data are represented as mean+ SEM. *p<0.05 student s t-test.
Figure S6 A Mx1Cre Jmjd1c f/f Mx1Cre B Mx1Cre Jmjd1c f/f Mx1Cre C Mx1Cre Jmjd1c f/f Mx1Cre 1 Non-competitive transplant D Mx1Cre Jmjd1c f/f Mx1Cre E Mx1Cre Jmjd1c f/f Mx1Cre F Mx1Cre Jmjd1c f/f Mx1Cre 1 Competitive transplant Figure S6 Characterization of loss of Jmjd1c in regenerative hematopoiesis using Mx1Cre system. Related to Figure 7. (A)-(C) Two million BM cells from Mx1Cre or Jmjd1c f/f : Mx1Cre were transplanted into lethally irradiated CD45.1 recipients (n=5). (D)-(F) One million BM cells from Mx1Cre or Jmjd1c f/f : Mx1Cre were mixed 1:1 with CD45.1 BM and transplanted into lethally irradiated CD45.1 recipients (n=5). Chimerism in peripheral blood (A)&(D) ; bone marrow and spleen (B)&(E); stem and progenitor populations in BM (C)& (F). Data are represented as mean+ SEM. *p<0.05 student s t-test.
Supplemental Tables Table S1. Related to Figure 1. Genes Targeted in the shrna Screen. 111000E01Rik 111004A4Rik 1110059E4Rik 41000ORik 810407C0Rik 491408C0Rik Aff1 AI14180 Ankib1 Ano6 Arhgap19 Arid1b Arid Arih Atp11b Bgnt B4galt6 Baz1a Bazb Bcor Bfsp1 Cacnb Cbx Cd47 Cdk17 Cdk6 Cdkn1b Cenpv Chd Chd7 Chd9 Copb1 Crlf Ctnnb1 D90015E06Rik Dach1 Dcun1d1 Dirc Dock8 Dsp Eifa Eif5b Elf1 Emb Erbbip Etv6 F6004A04Rik Fam108b Fam6a Fcho Fhdc1 Frat Fut8 Gda Gfi1 GFP Gm710 Gxylt1 Hectd1 Hhex Hjurp Hnrpll Hoxa10 Hoxa11 Hoxa Hoxa7 Hoxa9 Hpgd Hsd17b11 Ift80 Ikzf1 Il1a Jmjd1c Kctd1 Kif11 Klhdc Krit1 lacz Lass Lass6 Lmo Lnpep Lrrc Lta4h LUCIFERASE March7 Mbnl1 Meis1 Mgat Mgat5 Mppe1 Mrp6 Mtus1 Myb N4bp Naa16 Ncor1 Nipbl Npr1 Nrg Parp8 Pdeb Pds5a Pex1 Pgd Phtf1 Pigl Pitpnc1 Poli Prkarb Psma1 Pus10 Rap1gds1 Rdx Reep Rev1 RFP Rhob Rnf1 Rnf0 Rod1 Rpl6al Rreb1 Rsbn1l Runx Satb Serp1 Sfi1 Sgk Siah Six1 Six4 Slc8a1 Sltm Smc4 Snx1 Snx9 Sos Stxbp5 Supth Susd1 Tmem181a Tnpo1 Trim Trim59 Trip4 Trpm8 Tscd Ubek Ugt1a1 Vcpip1 Vps54 Wbp4 Zcchc
Table S. Related to Figure 1. Positive hits in the shrna screen Gene Symbol March7 111000E01Rik 111004A4Rik 810407C0Rik Ano6 Arid1b Arid Atp11b B4galt6 Bcor Cbx Cdk17 Cenpv Chd Chd7 Copb1 D90015E06Rik Dcun1d1 Dirc Eifa Eif5b Erbbip Etv6 Fam6a Fhdc1 Gda Gfi1 Gm710 Gxylt1 Hectd1 Hhex Hnrpll #shrnas Depleted >10-fold in BM 4 4 4 4 4 5 5 4 Gene Symbol Hoxa10 Hoxa11 Hoxa9 Hsd17b11 Ift80 Il1a Jmjd1c Kif11 Klhdc Lass Lmo Lrrc Meis1 Mgat Mppe1 Mrp6 Mtus1 Ncor1 Nipbl Npr1 Nrg Parp8 Pds5a Pex1 Phtf1 Pitpnc1 Poli Prkarb Psma1 Pus10 Rap1gds1 Rdx #shrnas Depleted >10-fold in BM 4 4 4 4 4 4
Gene Symbol Reep Rev1 Rnf1 Rod1 Rreb1 Rsbn1l Satb Serp1 Sfi1 Siah Six1 Six4 #shrnas Depleted >10-fold in BM 5 Gene Symbol Smc4 Sos Supth Tnpo1 Trim59 Tscd Ubek Ugt1a1 Vcpip1 Vps54 Wbp4 Zcchc #shrnas Depleted >10-fold in BM
Table S. Limiting dilution assay result of MLL-AF9 leukemia Dose Response/Tested P value MIT CRE MIT vs Cre 00,000 6/6 4/5 0.0476 100,000 6/6 6/7 0.0007 0,000 7/8 6/8 0.66 5,000 5/8 /8 0.044 LIC frequency 1 in 7,000 1 in 5,000
Table S4. Related to Figure. Differentially regulated genes (fold> 1.5, p<0.05), between Jmjd1c f/f and Jmjd1c -/- Mll-AF9 leukemic cells Log fold Adjusted Jmjd1c -1.04466 1.11E-15 Slc8a -0.7889 1.7E-06 Cbx6-0.8166.76E-06 Celsr1-1.0689 4.78E-06 Pak1-0.8197 6.94E-06 Gm14085-0.7965 1.98E-05 Ascl -1.11069.9E-05 Cbs -1.1648 5.5E-05 Ogdhl -0.9876 0.00007 Fam1a -0.9908 0.0004 Snhg4-0.66807 0.00085 Ms4a -0.81898 0.00094 Wdr4-0.8871 0.00096 Adrbk -1.06 0.00119 B4galnt4-0.969 0.00194 Megf8-0.697 0.0015 Sarm1-1.0575 0.00165 Dancr -0.614 0.00165 Docg -0.6747 0.001681 Rab4-0.98188 0.00411 Tbc1d16-0.70577 0.00458 Smpd -0.89456 0.00555 Nefh -0.8901 0.006075 Spag4-0.8846 0.00658 Fam69b -0.67687 0.006584 Bcl7a -0.7799 0.008908 Gga -0.611 0.01084 Lmo1-0.979 0.011071 Elfn -1.01907 0.01178 Shd5-0.6810 0.014798 Lzts -0.6416 0.01656 Gtdc -0.8075 0.01841 Log fold Adjusted Arhgef10-0.9 0.0177 Slc9a -0.6404 0.0054 Arhgef5-0.856 0.04187 Samd4-1.04005 0.0619 Snord47-0.78796 0.0619 Gspt -1.0604 0.0718 Prickle1-0.7159 0.08597 Art5-0.7898 0.09591 50406O09Rik -0.59476 0.01161 Cdh17-0.9765 0.051 Acer -0.775 0.0876 Arxes -1.0474 0.04475 Pcdhgb4-0.61768 0.0677 Pcdhga1-0.6440 0.0710 Cftr -1.0409 0.0876 Ltbp4-0.88001 0.04665 Bhlhb9-0.7916 0.04665 Rtn4r -0.7461 0.04718 Pcdhgb5-0.6041 0.04865 Unc79-0.857 0.04415 Pcdhgb6-0.5951 0.04469 Alms1-ps -0.7059 0.047744 Cabp1-0.97949 0.04891 Pcdhga -0.61616 0.04891 Gria -0.66066 0.049001 Itgb.1955 9.85E-7 Abca1.99841 7.E-5 Rcbtb 0.911.1E- Ablim1 1.9867 8.E-0 Gas7 1.6059.56E-18 Abcg1 1.919096 1.8E-16 Thbd 1.46946 6.94E-1
Log fold Adjusted Ptplad 1.67055 5.91E-1 Galnt9 1.88804 5.07E-11 Clec4a.1555 5.07E-11 Chn 1.686 1.14E-10 Tgfbr 1.005 1.59E-09 Emb 0.754.0E-09 Hpse 1.41579.17E-08 Eps8 1.657.E-08 Bank1 1.7469.48E-08 Gapt 0.68589.8E-08 Arhgap4 1.988 5.54E-08 Dab 1.40641 1.01E-07 Sema4d 1.096698 1.06E-07 Milr1 1.05148 1.8E-07 Rab 0.755518 1.8E-07 Tuba8 0.67794.51E-07 Tmcc 1.67484.65E-07 Ptgs1 0.86461 6.66E-07 910019P16Rik 1.11841.1E-06 Tpm4 0.94081 5.58E-06 Pikcg 1.714589 6.61E-06 Cd180 1.4666 7.E-06 Dse 1.6947 7.41E-06 Irf8 1.1485 9.95E-06 Rgl1 1.65077 1.E-05 Dpep 1.45881 1.67E-05 Cd8 1.55147 1.88E-05 Psap 0.904.74E-05 Siglec1 1.6177.09E-05 Ahr 1.566.1E-05 Trps1 1.09951 4.E-05 Cytip 0.7874 7.57E-05 Log fold Adjusted Prx7 1.40745 8.14E-05 Clec4a1 1.4085 0.000106 Pry6 1.6547 0.000106 Rassf4 0.885495 0.000115 Gm6116 1.59708 0.000141 Itgb7 0.99194 0.00017 Casp6 0.64108 0.00018 Il15 1.05 0.000191 Stgal1 0.764674 0.000 Tlr9 1.46061 0.000 Gm6904 1.55104 0.00067 Cdkn1a 0.8178 0.00001 Csfrb 0.71174 0.00007 Cd9 0.876 0.00007 Cd74 1.0847 0.00007 Mgst1 0.7944 0.0008 Rapb 0.59855 0.000 1810011H11Rik 0.697994 0.0004 Gpr5 1.4969 0.00045 Ninj1 0.8657 0.00049 Tlr7 1.68991 0.00049 Tlr 1.117165 0.000469 Myo1e 0.7151 0.00054 Tpd5 0.795116 0.000658 Neurl 0.797467 0.000751 Mafb 1.9057 0.00076 Vwa5a 0.869746 0.0008 Ssxb9 1.96 0.0008 Gngt 1.07444 0.00084 Cd164 0.676565 0.00096 Csfrb 0.77507 0.0010 Hmox1 0.855608 0.0010
Log fold Adjusted Ston 0.8564 0.00107 54045GRik 1.06810 0.001097 Plk 1.08151 0.00119 Tnfsf9 1.94997 0.00198 900617O0Rik 0.71004 0.00148 Rgs 0.7198 0.001446 Lrp1 1.1411 0.0015 Pde7b 1.54865 0.0015 Abcc 0.941484 0.001666 580416P10Rik 0.7018 0.001811 Trp5inp1 0.7678 0.00049 Camkk1 0.8848 0.00049 Nov 1.08977 0.00049 Prr5l 1.14504 0.00049 Htra 1.0479 0.00049 Sc5d 0.614511 0.00089 Mndal 1.017784 0.00089 Lair1 0.888594 0.004 Slc9a9 0.87959 0.0091 Cpeb 0.80695 0.0095 Kcnn4 0.90791 0.0095 Haao 0.7405 0.00468 Gm19689 1.056 0.00559 Bmf 0.74496 0.00654 Ms4a7 1.05401 0.0081 Slc5a15 0.7499 0.008 Tle 0.7088 0.0059 Zfp608 0.848658 0.0046 Mr1 1.11045 0.0046 Ptafr 1.08505 0.00461 Cxcl1 1.9795 0.00794 Rara 0.914714 0.0080 Log fold Adjusted Fblim1 1.117164 0.004057 Cd97 0.8456 0.004077 Smim 0.665106 0.00411 Nos 1.8475 0.004119 Hlx 0.87996 0.0046 Pde8b 0.871051 0.00449 Vwf 1.1079 0.0045 F1a1 1.14199 0.00458 Trem 1.66 0.004605 Ugt1a7c 0.67866 0.004815 A600H0Rik 1.16418 0.004815 Gfra1 1.951 0.004815 Gm51 1.56649 0.004815 Tscd1 1.00116 0.004977 Angptl 1.6805 0.00504 Gfi1b 1.95 0.00508 Zmat 0.70585 0.00508 Filip1l 0.65971 0.00514 Cd00lb 0.90606 0.0056 Sirpa 0.668059 0.0054 Mgam 0.8686 0.00556 Arhgef 0.65161 0.006051 Gal 0.75496 0.006051 Mx 1.19047 0.006051 Parp1 0.665018 0.006148 Ugt1a10 0.644697 0.006548 Ugt1a5 0.644595 0.00655 Ugt1a1 0.644979 0.00655 Ugt1a9 0.6488 0.006584 Ugt1a 0.64657 0.006584 Fbp1 1.114 0.006584 Ppt1 0.619918 0.0066
Log fold Adjusted Ugt1a6b 0.64107 0.006657 Ugt1a6a 0.641147 0.007059 Clvs1 0.8698 0.008001 Ndst1 0.6460 0.0090 Ptkb 0.5904 0.009555 Nxpe5 1.04981 0.009685 Arhgap1 0.6877 0.010654 AU079 1.07586 0.010654 Il1rb 0.6057 0.01155 A1cf 1.1558 0.011689 Trim9 0.60506 0.01186 Lct 0.75159 0.01186 Cgn 0.9784 0.01186 Emp1 1.151407 0.01186 Abhd5 0.585817 0.019 Serpinaf 1.1944 0.01101 Smad 0.6081 0.014868 Ubel6 1.011999 0.016879 0610040F04Rik 0.96445 0.017685 C1qc 1.066999 0.018461 Krt80 0.880684 0.018551 Klk1b9 1.18404 0.018566 Adamts 0.99114 0.005 Irs 0.59489 0.0754 A7000M07Rik 1.00985 0.04187 Rhov 0.878516 0.044 Mefv 0.771 0.05414 Oas 0.899 0.05414 Socs1 0.64574 0.0544 Igf1 1.0781 0.0619 Gm14005 0.848907 0.06588 Gbp7 0.667154 0.0716 Log fold Adjusted Lrp1 0.7454 0.0716 Tcf7l 0.915086 0.0718 AF51705 0.58914 0.074 S100a4 1.04084 0.08074 Stat4 0.6980 0.0846 Gdpd5 0.69614 0.08699 BC01767 1.0456 0.08987 Ndrg1 0.655756 0.015 Tubb1 1.04801 0.015 Zch1d 1.07701 0.015 Slc5a 0.761571 0.01959 Lpar6 0.58515 0.005 Asb 1.06198 0.05 Ap5s1 0.8547 0.006 Siglec5 0.84061 0.0565 Rasgrp 1.056 0.0565 Klk1b4 1.06615 0.0565 Lif 0.978898 0.0876 Denndc 0.69089 0.099 Krt86 0.8894 0.099 Gng 0.6017 0.0406 Ptpro 1.061994 0.0406 Klk1b16 1.0566 0.064 Klk1b4 1.05474 0.06449 Tspan18 0.95784 0.0889 Cd00e 1.056 0.0889 Fgf1 1.007764 0.09701 Maf 0.96674 0.040167 Fcrls 0.96404 0.04046 Plcb1 0.77484 0.040519 Nlrp1b 0.967911 0.040654 Ceacam18 0.86994 0.04151
Log fold Adjusted Klk1b7 0.99791 0.04151 Hbegf 0.874976 0.0415 Sulf 0.914505 0.0415 Il18 1.008716 0.044145 Iqgap 0.6417 0.04541 Trim7 1.0456 0.045766 Ssxb1 1.000 0.047744 Gm16897 0.797845 0.04797 Trim0d 0.81498 0.0487 Nlrp1a 0.8454 0.049001 Insl6 0.91467 0.049001 Ccrl 0.91196 0.049497
Table S5. Related to Figure 5. Differentially regulated genes (fold> 1.5, p<0.05), between Jmjd1c f/f and Jmjd1c -/- Hoxa9/Meis1 leukemic cells Log fold Adjusted Pcdh7-0.6696.1E-11 Plekhh -0.7997 1.6E-09 Eltd1-1.0949 5.80E-08 Armcx4-0.86084.45E-06 Cth -1.04 5.1E-06 Zcchc14-1.0095 7.8E-06 Fam174b -0.781 7.E-05 Aldh1l -0.86677 0.000155 Gm1709-0.685 0.00097 Pcdhgc -0.59696 0.0005 Glyat -0.7095 0.000444 Rgs8-0.80111 0.000461 Mir17hg -0.5987 0.00115 Sgip1-0.5858 0.0067 Kdelc -0.59198 0.00579 Prrg4-0.61959 0.00646 Ggact -0.69016 0.0054 Slc6a9-0.7075 0.004488 Sacs -0.65441 0.00565 Ccdc40-0.61917 0.00651 Hid1-0.69969 0.006586 Pitpnm -0.6597 0.00764 Cdrl -0.6909 0.007799 Ctnna -0.6 0.007861 Col5a -0.601 0.00867 Nr0b -0.59415 0.010108 Six4-0.66491 0.010717 Hmgn -0.6107 0.011606 Cpeb1-0.609 0.011814 Extl1-0.64644 0.015151 Aldh1a -0.691 0.019066 B1004C11Rik -0.6497 0.0194 Log fold Adjusted 490565N06Rik -0.58678 0.0445 Tacc -0.61591 0.0467 Tfr -0.61115 0.08009 Pcsk9-0.5944 0.005 Msantd -0.59049 0.0051 Spry4-0.5969 0.0571 Dab 1.5776.88E-5 Wfdc17 1.769478 5.E-4 Cd74.1111 1.15E- Rgl1 1.60868 1.74E-1 Tlr7 1.511707 7.86E-1 Itgb 1.14444.75E-19 Tscd1 1.11069 4.09E-19 Ndrg1 0.785 1.54E-18 C1qb 1.8999 1.74E-18 Msr1 1.850818.8E-18 Fyb 1.519498.4E-18 Gpnmb 1.49614 5.1E-18 Sdc 1.18179.5E-17 Pira1 1.54865.0E-16 Gm14548 1.5901 9.56E-16 Hmox1 1.15987 9.94E-16 Pira11 1.51776 1.87E-15 Pira6 1.51911 1.89E-15 Bank1 1.5865.40E-15 Abca1 1.75816 5.E-15 Car1 1.68516 8.8E-4 Ctss 1.5444 4.70E-40 Pira4 1.45476 9.88E-1 Pira7 1.45457 5.7E-7 Fos 1.405475 1.77E-6 AI60787 1.681568 4.49E-6
Log fold Adjusted Rara 0.91405 5.51E-15 Tgfbi 1.55144 1.01E-14 Stk17b 1.01944.57E-14 Ahnak 1.454799 5.89E-14 Rap1gap 1.141 8.44E-14 Gas7 1.16808.66E-1 Hlx 0.75554.70E-1 C1qc 1.5869.86E-1 Sema4d 0.6161.86E-1 Plek 1.11969.99E-1 Arl4c 1.1081 4.6E-1 Abcg1 0.897 4.4E-1 Ifi04 1.5788 4.48E-1 C1qa 1.570706 9.7E-1 Ptpro 1.5149 9.91E-1 Ccl 0.966588 9.9E-1 Ifi7la 0.906601 1.E-1 Lgmn 1.4507 1.E-1 Chn 0.768674 1.7E-1 Slfn5 1.06769.66E-1 Fosl 0.91659.94E-1 Id 1.110961 5.77E-1 Zfp6 0.99184 6.1E-1 Mir5107 1.51075 6.49E-1 Lpl 1.7098 6.49E-1 Marcks 1.48658 1.0E-11 Trem 1.45766 1.51E-11 Gapt 0.917488 1.55E-11 Fcgr1 1.475111.1E-11 Mpeg1 1.044586.56E-11 Mapk8 1.00465.74E-11 Spint1 1.47058 7.8E-11 Log fold Adjusted Itgb5 0.74976 1.60E-10 Abi 1.0017 1.66E-10 Maf 1.795.00E-10 Pira 1.746.60E-10 Olfm1 1.808.6E-10 Oas 0.6487 6.84E-10 Ifit1 1.1581 9.E-10 Tpd5 0.595469 1.09E-09 Ms4a4c 1.61147 1.19E-09 Lrrc 0.9151 1.45E-09 Nlrp 0.849 1.5E-09 Cd80 1.68676.9E-09 Adorab 0.769775.9E-09 Asph 0.7481.4E-09 Il10ra 0.7841 4.14E-09 Shdc 0.9651 5.87E-09 Slc15a 1.8687 7.76E-09 Cd00r4 0.8977 9.81E-09 Lgals 0.884147 9.81E-09 Ier5 0.910574 1.0E-08 Abcg 1.15904 1.1E-08 Clec4a 1.9151 1.0E-08 Jun 0.91595 1.E-08 Htra 1.78086 1.E-08 Psap 0.8986 1.40E-08 Pry1 1.86848 1.40E-08 Ptgs 1.0081 1.5E-08 Rcbtb 0.7599 1.60E-08 Xdh 1.0567 1.67E-08 Ptafr 1.14194.08E-08 Mmp1 1.07811.7E-08 Mtss1 0.61567.45E-08
Log fold Adjusted Ddx60 0.8754 1.10E-06 Atp7a 0.89088 1.5E-06 Hpse 0.6104 1.45E-06 AF51705 0.9469 1.5E-06 Dusp5 0.61887 1.5E-06 Krt80 1.046971 1.6E-06 Egr 1.117191 1.67E-06 Egr1 0.96867 1.7E-06 Tnfaip 0.798601 1.85E-06 Plxdc 1.10674.00E-06 Stk10 0.648879.1E-06 Ccr5 1.0591.6E-06 Galnt6 0.66651.6E-06 Gm541 1.095884.67E-06 Nrp1 0.87058.8E-06 Zbp1 0.650097.08E-06 Btg1 0.6787.14E-06 Csf1 0.85166.69E-06 Il6ra 0.9695.87E-06 Rasgrp4 0.707174 4.00E-06 Neurl 0.7757 4.1E-06 Ndst1 0.66589 4.60E-06 Klf 0.64919 5.04E-06 Myof 1.065667 5.E-06 Trim0d 0.69185 5.7E-06 Slca 0.8588 5.70E-06 Mapk5 0.684 6.57E-06 Phospho1 0.955146 7.89E-06 Rbms1 0.888 7.89E-06 B4006N0Rik 0.878714 7.99E-06 Stx 1.0081 9.04E-06 Lyn 0.61806 1.0E-05 Log fold Adjusted Serpinb 1.0189 1.11E-05 Slfn 0.78181 1.16E-05 Nt5e 0.99 1.6E-05 Klf6 0.76579 1.45E-05 Mitf 0.68657 1.48E-05 Cd6 1.00595 1.54E-05 Sfxn5 0.940947 1.54E-05 Tnfrsf9 0.9118 1.58E-05 Zch1d 0.98046 1.81E-05 Dse 0.74895 1.90E-05 Ifit 0.98564.95E-05 Vcan 0.874651.0E-05 Cd9 0.8615.1E-05 H-DMb 0.87087.7E-05 Emp1 0.991584.54E-05 Oit 0.96087.54E-05 Lilra6 0.9894.66E-05 Nos 0.959185.84E-05 910019P16Rik 0.67481 4.41E-05 Evia 0.61416 4.67E-05 Wipi1 0.61696 4.74E-05 Sgms1 0.8598 5.1E-05 AA467197 0.9196 5.14E-05 Ahr 0.95196 5.E-05 Gbp9 0.77578 5.41E-05 Plaur 0.79759 5.5E-05 Pydc4 0.95491 5.57E-05 Siglec1 0.9648 6.56E-05 Ankrdb 0.95066 7.71E-05 Lif 0.8016 8.01E-05 Clvs1 0.641664 8.17E-05 Tlr5 0.9178 8.89E-05
Log fold Adjusted Bcll11 0.599555 8.99E-05 Zfhx 0.799855 9.6E-05 Ifnlr1 0.97 0.000107 Osgin1 0.7556 0.000108 Gcnt 0.907464 0.000115 Hgf 0.717698 0.000116 Gsn 0.91154 0.00016 Cox4i 0.8601 0.00014 Trim0b 0.914968 0.00014 Pikr6 0.60479 0.00016 Dusp1 0.79161 0.000174 Ms4a6c 0.7604 0.000181 Gm10684 0.8097 0.000186 Tnip 0.90984 0.000189 Cd5 0.61994 0.00019 Pry6 0.84541 0.00018 4648N05Rik 0.70070 0.000 Adora 0.89515 0.0008 Upp1 0.900904 0.0004 Mylk 0.641149 0.00045 Ly6g5b 0.81850 0.00055 Samhd1 0.674 0.00055 Pry14 0.846147 0.00058 Cd00ld 0.74418 0.0001 Fam19a 0.815761 0.000 Arhgef 0.6591 0.0004 Grina 0.608174 0.0004 Csf1r 0.879604 0.000 Pirb 0.87761 0.00041 Zcwpw1 0.77607 0.00075 Fam49a 0.7089 0.00075 Pikr5 0.695478 0.00079 Log fold Adjusted Klk1b9 0.8055 0.0008 Tlr8 0.8616 0.00089 Card6 0.85549 0.00099 Cd8 0.8655 0.00040 Tgm 0.84185 0.000405 Hbegf 0.68647 0.000409 Arg 0.86907 0.00041 Prx7 0.879 0.000417 Susd 0.6848 0.0004 Tagap 0.7946 0.0004 Ccl 0.864609 0.000445 Tgfbr 0.6078 0.000468 Havcr 0.860498 0.000511 Serpinb10 0.841698 0.0005 Anxa1 0.8448 0.000556 LOC10008947 0.797 0.00060 Anxa11 0.666 0.00061 Mnda 0.790576 0.00067 Adam8 0.8166 0.00066 Card10 0.809776 0.00069 Lsp1 0.85 0.000766 Cdc4ep 0.89408 0.000794 Nfkbiz 0.67691 0.00088 Mir147 0.806 0.000886 Tesc 0.698141 0.000899 Cnr 0.6809 0.000904 Spatc1 0.8865 0.00091 0610040F04Rik 0.679999 0.000945 Dfna5 0.64989 0.000965 Pag1 0.60187 0.000995 Pgf 0.805878 0.001054 Smpd5 0.64101 0.00109
Log fold Adjusted Rassf4 0.5887 0.001095 Zmat 0.608775 0.00118 Rab7 0.74788 0.001194 AI89979 0.7069 0.00107 Ublcp1 0.769 0.00108 Gpr55 0.775807 0.00149 Serpinaf 0.64789 0.0015 Clec7a 0.71878 0.00154 Gm17455 0.705 0.00154 Epb4.1l1 0.74961 0.001597 Mertk 0.756 0.001597 Slc7a 0.706546 0.001687 Klra 0.785 0.00170 Usp18 0.6514 0.00170 Gbp4 0.61075 0.00170 Tulp4 0.7561 0.00170 Tnfrsf 0.77744 0.00175 Lyz 0.790456 0.00177 Bcla1b 0.769015 0.001795 Gp49a 0.78854 0.00181 Prr 0.78844 0.001848 Scel 0.771557 0.001848 Tnfsf1 0.601574 0.001949 Rnase6 0.7989 0.00005 Bmf 0.65051 0.0001 Itpr 0.70875 0.00047 Il1r 0.767484 0.00049 Saa 0.77761 0.0011 Il1b 0.77959 0.00147 Galnt9 0.67996 0.00147 Nov 0.75157 0.0019 Cpeb 0.60167 0.0019 Log fold Adjusted Cd101 0.767077 0.00195 Pf4 0.7700 0.0006 Sulf 0.74517 0.0067 Nedd9 0.644775 0.0071 Ptms 0.74615 0.005 Myo1e 0.61911 0.00595 Mctp1 0.64768 0.00597 501414D18Rik 0.6198 0.00617 Aif1 0.7089 0.0077 Atf 0.608 0.00009 Dpep 0.7577 0.00019 Sirpb1b 0.66065 0.0018 Kcne 0.6974 0.00 Zfp6l1 0.750779 0.0061 Wfdc18 0.67018 0.00945 Rnf150 0.74099 0.00456 Arg1 0.75609 0.00451 Nos1ap 0.6848 0.004561 Tmcc 0.6655 0.004647 Ly6a 0.655151 0.00469 Nrg1 0.60681 0.00516 Adoraa 0.69058 0.00516 Irgc1 0.64986 0.005186 Scn1b 0.7599 0.00507 Ceacam1 0.601987 0.0055 Antxr 0.67479 0.00589 Gpr5 0.69155 0.005498 Ccdc80 0.699847 0.005505 Clec4n 0.64169 0.005754 1-Mar 0.6175 0.005754 Bcla1d 0.661164 0.005794 Cd00lf 0.6987 0.005859
Log fold Adjusted Slc7a8 0.61 0.006001 Lifr 0.710515 0.0065 Cd00c 0.71449 0.006 01000M1Rik 0.701788 0.00608 Abtb 0.705477 0.006548 Grk5 0.700011 0.006598 Ppp1rd 0.67786 0.00669 Rhov 0.70794 0.006786 Axl 0.676 0.00686 Il1rb 0.64475 0.0071 Plk 0.7069 0.007514 Gm97 0.67400 0.00759 Klk1b11 0.595797 0.00764 H-Eb1 0.6981 0.00789 Slc44a1 0.64507 0.0086 Dhrs9 0.640046 0.0086 Epma 0.684668 0.008805 Fas 0.664474 0.009115 Phlda1 0.68851 0.009176 Scrg1 0.58701 0.010496 H-Aa 0.656786 0.01055 Ctse 0.664618 0.010608 Hck 0.650795 0.010901 Sycp 0.6486 0.01097 Mir667 0.6609 0.01097 Reps 0.6704 0.011046 Fcnb 0.61709 0.01187 Tlr1 0.6169 0.01151 Bcla1a 0.665986 0.01156 Gm677 0.6149 0.011594 Klk1b1 0.586761 0.01199 Cyp4f18 0.66987 0.01466 Gas6 0.6440 0.015064 Log fold Adjusted Camk1d 0.649447 0.015106 Tnfsf8 0.61679 0.015415 Il18r1 0.65057 0.0154 Ipcef1 0.6871 0.0168 840408GRik 0.58719 0.017749 Creb5 0.64759 0.01865 C0046G1Rik 0.608 0.018616 Rragd 0.598578 0.01869 60409D0Rik 0.6405 0.01866 Col1a1 0.65884 0.0191 Il7 0.687 0.01905 C1006I1Rik 0.609898 0.019409 Plxna1 0.598917 0.0018 49159L05Rik 0.6969 0.0196 Clec4b 0.59947 0.0196 Kcnk1 0.6159 0.0167 Inhba 0.614645 0.050 Rasgrp1 0.65614 0.047 Arl5c 0.6164 0.0418 Car 0.58885 0.0569 Ltb 0.59616 0.06545 A600H0Rik 0.587179 0.07667 Pilrb1 0.60611 0.07711 Trp5inp1 0.6094 0.0774 Ppp1r16b 0.609004 0.0886 Lpcat 0.589851 0.0881 Mir190 0.60676 0.095 Grap 0.604711 0.09955 Pikcb 0.597985 0.07 Tg 0.5955 0.04157 Mapk9 0.59181 0.0566 Mxd1 0.590848 0.05767 Gm167 0.59011 0.0607 Jmjd1c ranks #14 in all down-regulated genes with Log fold change of -0.50105 and adjusted p value of.86e-05.
Table S6. Related to Figure 7. Differentially regulated genes (fold> 1.5, p<0.05) in LSK cells between Vav1Cre and Jmjd1c f/f :Vav1Cre mice Log fold Adjusted Wdfy1-1.07858 1.0E-1 Ly6c -0.7907 1.9E-11 Jmjd1c -0.8878.E-09 Gm15446-1.751 4.00E-06 Fn1-1.10458 0.0007 Fcnb -0.61544 0.00096 Ighgc -5.17506 0.009648 Clec1a -0.75467 0.01114 Gimap4-1.0787 0.01656 Rnase4-1.0881 0.016917 Il7r -0.9576 0.0007 Ccl -1.1 0.00804 Hepacam -1.5491 0.00904 Ighv1-6 -.79986 0.0657 F1a1-0.688 0.047106 Chtf8 0.9176.76E-06 Prep 0.798554 1.65E-05 Ints1 0.9448 1.9E-05 Ppif 0.608105 6.4E-05 Ncdn 0.84471 0.0007 Igfbp4 0.675156 0.000715 Sfb4 0.68951 0.0007 Clnk 0.86648 0.0007 Cad 0.67985 0.000801 Cd76 1.501615 0.00199 Atf6b 0.7481 0.00 Ppa 0.819458 0.006 Mri1 1.4676 0.00544 Srrt 0.659789 0.004194 Nop9 0.78961 0.004417 Med16 0.667674 0.009648 Gtdc -0.8075 0.01841 Log fold Adjusted Ptk7 1.051968 0.010065 Tcof1 0.58574 0.01197 Rae1 0.596786 0.0159 Lmnb 0.709808 0.0115 Tcf 0.8558 0.01656 BC00867 0.615055 0.01787 Runx 0.670999 0.01787 Igkv4-91.898587 0.01787 Sumf1 1.1148 0.01888 Eifb 0.665685 0.000 Zfp55 0.701895 0.000 Cdc0 0.65764 0.00804 Ubap 0.66551 0.00804 Prpsap1 1.0591 0.00804 Pkmyt1 0.95077 0.084 Emid1 1.5481 0.0606 Arhgef1 0.6975 0.0476 Il1rb1 0.9980 0.0476 Vars 0.7797 0.0515 Sf1 0.6418 0.05498 Eifb5 1.166 0.05498 Padi4 0.96041 0.00017 Znhit 1.68875 0.00017 Tbc1d9b 0.70911 0.00904 Ttyh 0.74959 0.00904 Impdh1 0.84509 0.01644 Vps7b 0.650417 0.061 Cdk9 0.8550 0.0466 Uaf 0.6 0.0657 Phrf1 0.668619 0.0657 Cpne 0.78869 0.0417 Polra 0.65485 0.0454
Log fold Adjusted Mybl 0.80781 0.0478 Itgab 0.6088 0.047106 Med0 1.856448 0.04755 Mgat 0.69051 0.04848 Pola 0.6978 0.049