Genomic and transcriptomic landscapes of acute promyelocy3c leukemia Kankan Wang

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1 Genomic and transcriptomic landscapes of acute promyelocy3c leukemia Kankan Wang State Key Laboratory of Medical Genomics Rui-Jin Hospital Shanghai Jiaotong University School of Medicine

2 Understanding the pathogenesis and treatment of APL using high-throughput technologies RNA polymerase CH 3 ChIP-seq RNA-seq? PML/RARα APL Effects of ATRA and ATO (co-regulators)?

3 Hallmarks of acute promyelocy3c leukemia How does PML/RARα drive the development of APL?

4 Genome-wide PML/RARα binding sites PML/RARα retains the DNA binding domain of wild-type RARα. PML/RARα acts as a strong transcriptional repressor. Myeloid commitment is hardly affected in various RAR-deficient mice. ChIP-chip/ChIP-seq

5 Genome-wide binding pictures of PML/RARα ATRA ATRA! PU.1-mediated transactivation was restored! Genes repressed by PML/RARα were reactivated! Increased in H3K9K14 acetylation! Induced transcriptional changes correlate with H3K9K14 acetylation Wang et al. Cancer Cell 2010 Martens et al. Cancer Cell 2010

6 PU.1 and RARE half sites are the most significant mo3fs in the PML/RARα ChIP regions Wang et al. Cancer Cell 2010

7 PML/RARα predominantly represses PU.1-regulated genes Recruitment of PML/RARα to chromaen pre-bound by PU.1 Repression of PU.1-dependent transacevaeon through both PU.1 and RARE half sites Wang et al. Cancer Cell 2010

8 PML/RARα tends to colocalize with RXR preferen3ally on promoter regions Martens et al. Cancer Cell 2010

9 ATRA treatment increases the level of H3K9K14ac but not H3K9me3 and H3K27me3 Martens et al. Cancer Cell 2010

10 Regulatory features and func3ons of PML/RARα key targets in APL Genome-wide PML/RARα binding Detailed analysis of key targets PML/ RARα POL II PML/ PU.1 PU.1 RARα PU.1 PU.1 PML/ RARα PMSB8 PMSB9 ER8 CDKN2D Tissue factor HCK Indirect binding Binding to multiple PU.1 Coordinated regulation Binding to ER8 PU.1 PMSB10 PML/ RARα Hemorrhage Tumor suppression Antigen presentation Differentiation & Cell cycle Yan JS, et al, PNAS Zou DD, et al, Leukemia Res Yang XW, et al, Oncogene Wang YW, et al, Cell Death Dis. 2014

11 PML/RARα transac3vates the 3ssue factor promoter through an indirect interac3on Yan et al. PNAS 2010

12 PML/RARα exerted both repressive and ac3va3ng func3ons Unpublished data

13 Func3onally importance of both PML/RARα-repressed and -ac3vated targets Unpublished data

14 Repression was associated with RARα, whereas ac3va3on was independent of RARα Unpublished data

15 Dis3nct ATRA effects on PML/RARα-ac3vated and -repressed genes Unpublished data

16 PML/RARα preferen3ally existed within super-enhancer regions Unpublished data

17 Transcriptome analysis of the mechanism of ATRA action RNA-seq/microarray Ribo-minus RNA-seq

18 ATRA regulates gene expression at the transcriptomic level, whereas ATO func3ons at the proteomic level Transcriptome Proteome 12 h RA 0.1 µm 48 h h ATO 0.5 µm h RA 0.1 µm ATO 0.5 µm h 48 h Zheng et al. PNAS 2005

19 Molecular networks underlying the combina3on of ATRA and ATO in NB4 cells camp-pka Pathway Calcium Pathway AC G protein Receptor ATP AKAP9 camp AKAP1 AKAP13 PKA PDE4DIP RA Pathway RA TFs/CoFs CGREF1 S100A8 S100A9 PLSCR1 IRF1 Ca2+ CALM CBP ID1 CEBPE HHEX NCOA3 P/CAF ID2 CEBPG CEBPZ PML-RARα TIF EP300 BHLHB2 CEBPD CEBPB PLCB G protein Receptor PIP2 DG2 IP3 PKC PKA AKAP9 ITPR ER Ca2+ NUCB2 ANK3 RYR3 PSME2 PML SP110 SP140 SP100 others Restoration of NB IFN Pathway IFNAR2 G-CSF-R IFNGR JAK1 TYK2 JAK1 JAK2 STAT1 STAT2 ISGF3G STAT1 ISGF3 IRF7 STAT1 Nucleus MAPK-JNK-p38 Pathway Receptor Daxx TRAF2 ASK1 G-CSF-R SHP2 Rac MEKK1 MKK3 PTPN9 MKK4/7 P38 JNK2 TFs/CoFs Receptor GRB2 SOS2 Ras Raf MEK1 MAPK6 SELPLG SELL CD44 ICAM1 CD11b CD18 Surface Molecules Plasma Membrane SENP5 EIF4B UBE1L UBE4B EIF4A1 EIF4G1 80S DNAJB1 EEF1B2 AHSA1 HSPCA HSPA8 EEF1A1 EEF1D EEF1G AUG DNAJA1 Proteins UBE2L6 UBE3C 40S 60S SUMO1 PML-RARα PSMC3 PSMB8 PSMD13 PSMB10 PSMC2 PSMB9 Ubiquitiated PML-RARα Sumoylated PML-RARα proteasome MAP2 MYOM1 Degradation of MYH3 PML-RARα FBN2 Stress Protein Synthesis PML-RARα Degradation Cytoskeleton Cytoplasm CDKN1A CDKN1B CDKN2D CDK4 CCND2 G1 CDK2 CCNE1 IFI16b ARHI GAS7 CDK2 CCNA2 S BCL2 PDCD6IP GADD45B BCL2A1 Mitochondria Apoptosis CHEK1 CASP9 STK24 PCNA cytc APAF1 BAK1 CDC25A CDC25B CDK7 CDK1 CCNH CCNA2 Cell Cycle Arrest Cell Cycle G2 CDK1 CCNB1 PEG10 M CASP3 CASP1 CASP7 CASP10 CASP8 IRF1 FADD FADD TRADD PIBF1 CCNG2 TRAIL-R Apoptosis TNF-R Zheng et al. PNAS 2005

20 Circular RNA genera3ng from the fusion site of PML/RARα is oncogenic and contributes to cellular transforma3on Zepp et al. Cell 2017

21 Dynamic regulated cicrrna profiling upon ATRA treatment of APL cells Unpublished data

22 cicrrna regula3on independent of their host linear mrna Unpublished data

23 Requirement of circ-rell1 in ATRA-induced differen3a3on of APL cells Unpublished data

24 Summary " Genome-wide binding pictures of PML/RARα - PML/RARα selectively targets PU.1-regulated genes. - PML/RARα is colocalized with RXR on chromatin. - PML/RARα exerts both activation and repression roles of in driving APL. " Regulatory features and functions of key targets of PML/ RARα. " Transcriptomic view of the mechanism of ATRA action - ATRA induces transcriptional remodeling and a series of signaling pathways in APL cells. - ATRA dynamically regulates a number of cicrrnas upon ATRA treatment.

25 Acknowledgements Omics platforms Yun Tan Ping Wang Yizhen Li Xuehua Zhu Functional studies Wen Jin Xianwen Yang Xuefei Ma Yewei Wang Bioinformatics analysis Hai Fang Ming Zhao Jiantao Shi Huanwei Wang