Genomic and transcriptomic landscapes of acute promyelocy3c leukemia - PowerPoint PPT Presentation

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

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)

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

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

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

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

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

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

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

Regulatory features and func3ons of PML/RARα key targets in APL Genome-wide PML/RAR α binding Detailed analysis of key targets PMSB10 PU.1 PML/ PML/ PML/ PML/ RAR α PU.1 RAR α PU.1 RAR α PU.1 RAR α PU.1 POL II PMSB8 PMSB9 ER8 CDKN2D Tissue factor HCK Indirect binding Binding to multiple PU.1 Coordinated regulation Binding to ER8 Hemorrhage Tumor suppression Antigen presentation Differentiation & Cell cycle Yan JS, et al , Zou DD, et al , Yang XW, et al , Wang YW , et al , PNAS. 2010 Leukemia Res. 2010 Oncogene. 2014 Cell Death Dis. 2014

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

PML/RARα exerted both repressive and ac3va3ng func3ons Unpublished data

Func3onally importance of both PML/RARα-repressed and -ac3vated targets Unpublished data

Repression was associated with RARα, whereas ac3va3on was independent of RARα Unpublished data

Dis3nct ATRA effects on PML/RARα-ac3vated and -repressed genes Unpublished data

PML/RARα preferen3ally existed within super-enhancer regions Unpublished data

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

ATRA regulates gene expression at the transcriptomic level, whereas ATO func3ons at the proteomic level Transcriptome Proteome 12 h 48 h 12 h 48 h 2 2 2 2 1 1 1 1 M M 0 0 0 0 -1 -1 -1 -1 -2 -2 -2 -2 12 h 48 h 12 h 48 h 2 2 2 2 1 1 1 1 M M 0 0 0 0 -1 -1 -1 -1 -2 -2 -2 -2 12 h 48 h 12 h 48 h 2 2 2 2 1 1 1 1 M M 0 0 0 0 M M -1 -1 -1 -1 -2 -2 -2 -2 Zheng et al. PNAS 2005

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

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

Dynamic regulated cicrRNA profiling upon ATRA treatment of APL cells Unpublished data

cicrRNA regula3on independent of their host linear mRNA Unpublished data

Requirement of circ-RELL1 in ATRA-induced differen3a3on of APL cells Unpublished data

Summary � Genome-wide binding pictures of PML/RAR α PML/RAR α selectively targets PU.1-regulated genes. - PML/RAR α is colocalized with RXR on chromatin. - PML/RAR α exerts both activation and repression roles of in - driving APL. � Regulatory features and functions of key targets of PML/ RAR α . � 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.

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