genomic and transcriptomic landscapes of acute ... · -2 2 1 0-1-2 2 1 0-1-2 2 1 0-1-2 2 1 0-1-2 2...
TRANSCRIPT
Genomicandtranscriptomiclandscapesofacutepromyelocy3cleukemia
KankanWang
StateKeyLaboratoryofMedicalGenomics
Rui-JinHospitalShanghaiJiaotongUniversitySchoolofMedicine
UnderstandingthepathogenesisandtreatmentofAPLusinghigh-throughputtechnologies
CH3
RNA polymerase
ChIP-seq RNA-seq
PML/RARαAPLEffectsofATRAandATO(co-regulators)
? ?
Hallmarksofacutepromyelocy3cleukemia
HowdoesPML/RARαdrivethedevelopmentofAPL?
• 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.
Genome-widePML/RARαbindingsites
ChIP-chip/ChIP-seq
Wang et al. Cancer Cell 2010 Martens et al. Cancer Cell 2010
Genome-widebindingpicturesofPML/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
PU.1andRAREhalfsitesarethemostsignificantmo3fsinthePML/RARαChIPregions
Wang et al. Cancer Cell 2010
Wang et al. Cancer Cell 2010
RecruitmentofPML/RARαtochromaEnpre-boundbyPU.1
PML/RARαpredominantlyrepressesPU.1-regulatedgenes
RepressionofPU.1-dependenttransacEvaEonthroughbothPU.1andRAREhalfsites
PML/RARαtendstocolocalizewithRXRpreferen3allyonpromoterregions
Martens et al. Cancer Cell 2010
ATRAtreatmentincreasesthelevelofH3K9K14acbutnotH3K9me3andH3K27me3
Martens et al. Cancer Cell 2010
PML/RARα
PML/RARα
HCK PMSB8
Tissue factor
PU.1
PU.1
PMSB9
PMSB10 PML/RARα PU.1
PU.1 PU.1
POL II
Detailed analysis of key targets
Genome-wide PML/RARα binding
PML/RARα
CDKN2D
Indirect binding Binding to multiple PU.1 Coordinated regulation Binding to ER8
Hemorrhage
Yan JS, et al, PNAS. 2010
Antigen presentation
Yang XW, et al, Oncogene. 2014
Differentiation & Cell cycle
Wang YW, et al, Cell Death Dis. 2014
Tumor suppression
Zou DD, et al, Leukemia Res. 2010
Regulatoryfeaturesandfunc3onsofPML/RARαkeytargetsinAPL
ER8
PML/RARαtransac3vatesthe3ssuefactorpromoterthroughanindirectinterac3on
Yan et al. PNAS 2010
PML/RARαexertedbothrepressiveandac3va3ngfunc3ons
Unpublished data
Func3onallyimportanceofbothPML/RARα-repressedand-ac3vatedtargets
Unpublished data
RepressionwasassociatedwithRARα,whereasac3va3onwasindependentofRARα
Unpublished data
Dis3nctATRAeffectsonPML/RARα-ac3vatedand-repressedgenes
Unpublished data
PML/RARαpreferen3allyexistedwithinsuper-enhancerregions
Unpublished data
Transcriptome analysis of the mechanism of ATRA action
• RNA-seq/microarray
• Ribo-minusRNA-seq
RA 0.1 µM
ATO 0.5 µM
12 h 48 h
12 h 48 h
12 h 48 h
2
1
0
-1
-2
2
1
0
-1
-2
2
1
0
-1
-2
2
1
0
-1
-2
2
1
0
-1
-2
2
1
0
-1
-2
ATO 0.5 µM
RA 0.1 µM
RA 0.1 µM
ATO 0.5 µM
12 h 48 h
12 h 48 h
12 h 48 h
2
1
0
-1
-2
2
1
0
-1
-2
2
1
0
-1
-2
2
1
0
-1
-2
2
1
0
-1
-2
2
1
0
-1
-2
ATO 0.5 µM
RA 0.1 µM
ATRAregulatesgeneexpressionatthetranscriptomiclevel,whereasATOfunc3onsattheproteomiclevel
Transcriptome Proteome
Zheng et al. PNAS 2005
Molecularnetworksunderlyingthecombina3onofATRAandATOinNB4cells
CD
44
SE
LL
CD
11b
CD
18
ICA
M1
Surf
ace
Mole
cule
s
Restoration of NB
Plasma Membrane
Cytoplasm
IFNAR2
JAK1 TYK2
ISGF3GSTAT1 STAT2
IFNGR
JAK1 JAK2
STAT1IRF7ISGF3
STAT1
IFN PathwayG-CSF-R Receptor
GRB2
SOS2
Ras
Raf
MAPK6
Receptor
TRAF2Daxx
ASK1
MKK3
Rac
P38
MKK4/7
JNK2
PTPN9 MEK1
MAPK-JNK-p38 PathwayG-CSF-R
SHP2
TFs/CoFs
MEKK1
Protein Synthesis PML-RARα Degradation Cell Cycle
Nucleus
TRADDFADD
CASP10 CASP8
CASP3CASP7
cytcAPAF1
CASP9
BCL2
Mitochondria Apoptosis
Apoptosis
IRF1
CASP1
TRAIL-R
FADD
PDCD6IPBCL2A1
TNF-R
STK24
BAK1
M
CDK4CCND2
CDK2CCNE1
CDK2CCNA2
CDK7CCNH
CDK1CCNA2
CDK1CCNB1
CDKN2DCDKN1A
CDC25B
CHEK1
PCNA
GADD45B
CDC25A
G1 G2S
CDKN1B
Stress Cytoskeleton
AHSA1
HSPCA
DNAJA1
HSPA8
DNAJB1
ReceptorG proteinAC
ATP cAMP
PKA
cAMP-PKA Pathway
AKAP13
AKAP1
PDE4DIP
AKAP9
ReceptorG proteinPLCB
PIP2
IP3
DG2
ITPR
RYR3Ca2+
CALM
Ca2+
PKC
Calcium Pathway
PKA
ANK3
ERNUCB2
AKAP9
S100A8
S100A9PLSCR1
CGREF1
SP100
SP110 SP140
PSME2 PMLothers
PML-RARαP/CAFNCOA3
TIF
CBPRARA Pathway
EP300
ID1
BHLHB2ID2 CEBPZ
CEBPBCEBPGCEBPD
CEBPE HHEXTFs/CoFs
40S
AUG
Proteins
EIF4A1
EEF1B2
EEF1A1EEF1D
EEF1G
60S
EIF4B
EIF4G1
80S PML-RARα
SUMO1UBE2L6UBE1L UBE4B
UBE3C
PSMB9
PSMB8
PSMB10
PSMC3
PSMD13
PSMC2
SumoylatedPML-RARα
SENP5
MAP2
MYH3MYOM1
FBN2
UbiquitiatedPML-RARα
Degradation of PML-RARα
proteasome
Cell Cycle ArrestIFI16b
GAS7ARHI
PEG10
CCNG2
PIBF1
SE
LP
LG
CD
44
SE
LL
CD
11b
CD
18
ICA
M1
Surf
ace
Mole
cule
s
Restoration of NB
Plasma Membrane
Cytoplasm
IFNAR2
JAK1 TYK2
ISGF3GSTAT1 STAT2
IFNGR
JAK1 JAK2
STAT1IRF7ISGF3
STAT1
IFN PathwayG-CSF-R Receptor
GRB2
SOS2
Ras
Raf
MAPK6
Receptor
TRAF2Daxx
ASK1
MKK3
Rac
P38
MKK4/7
JNK2
PTPN9 MEK1
MAPK-JNK-p38 PathwayG-CSF-R
SHP2
TFs/CoFs
MEKK1
Protein Synthesis PML-RARα Degradation Cell Cycle
Nucleus
TRADDFADD
CASP10 CASP8
CASP3CASP7
cytcAPAF1
CASP9
BCL2
Mitochondria Apoptosis
Apoptosis
IRF1
CASP1
TRAIL-R
FADD
PDCD6IPBCL2A1
TNF-R
STK24
BAK1
M
CDK4CCND2
CDK2CCNE1
CDK2CCNA2
CDK7CCNH
CDK1CCNA2
CDK1CCNB1
CDKN2DCDKN1A
CDC25B
CHEK1
PCNA
GADD45B
CDC25A
G1 G2S
CDKN1B
Stress Cytoskeleton
AHSA1
HSPCA
DNAJA1
HSPA8
DNAJB1
AHSA1
HSPCA
DNAJA1
HSPA8
DNAJB1
ReceptorG proteinAC
ATP cAMP
PKA
cAMP-PKA Pathway
AKAP13
AKAP1
PDE4DIP
AKAP9
ReceptorG proteinPLCB
PIP2
IP3
DG2
ITPR
RYR3Ca2+
CALM
Ca2+
PKC
Calcium Pathway
PKA
ANK3
ERNUCB2
AKAP9
S100A8
S100A9PLSCR1
CGREF1S100A8
S100A9PLSCR1
CGREF1
SP100
SP110 SP140
PSME2 PMLothers
SP100
SP110 SP140
PSME2 PMLothers
PML-RARαP/CAFNCOA3
TIF
CBPRARA Pathway
EP300
ID1
BHLHB2ID2 CEBPZ
CEBPBCEBPGCEBPD
CEBPE HHEXTFs/CoFs
40S
AUGAUG
Proteins
EIF4A1
EEF1B2
EEF1A1EEF1D
EEF1G
60S60S
EIF4B
EIF4G1
80S PML-RARα
SUMO1UBE2L6UBE1L UBE4B
UBE3CUBE2L6UBE1L UBE4B
UBE3C
PSMB9
PSMB8
PSMB10
PSMC3
PSMD13
PSMC2 PSMB9
PSMB8
PSMB10
PSMC3
PSMD13
PSMC2
SumoylatedPML-RARα
SENP5
MAP2
MYH3MYOM1
FBN2
MAP2
MYH3MYOM1
FBN2
UbiquitiatedPML-RARα
Degradation of PML-RARα
proteasome
Cell Cycle ArrestIFI16b
GAS7ARHI
PEG10
CCNG2
PIBF1
SE
LP
LG
IRF1
Zheng et al. PNAS 2005
CircularRNAgenera3ngfromthefusionsiteofPML/RARαisoncogenicandcontributestocellulartransforma3on
Zepp et al. Cell 2017
DynamicregulatedcicrRNAprofilinguponATRAtreatmentofAPLcells
Unpublished data
cicrRNAregula3onindependentoftheirhostlinearmRNA
Unpublished data
Unpublished data
Requirementofcirc-RELL1inATRA-induceddifferen3a3onofAPLcells
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.
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