Epigenetic targets in breast cancer

Epigenetic targets
in breast cancer
Kornelia Polyak, MD, PhD
Dana-Farber Cancer Institute
Harvard Medical School
Boston, MA
KDM5B/JARID1B/PLU-1, histone H3 K4 demethylase
Highly expressed in Her2+ breast cancer (Plu-1)
histone H3 K4 demethylase (tri, di, and mono)
Required for embryonic survival and ESC differentiation
Role in melanoma maintenance and treatment resistance
H3K4 histone methyl transferases and demethylases in cancer
MLL : frequent mutations and rearrangements in diverse cancer types
KDM5A/JARID1A: fusion protein, overexpression in multiple cancer types
KDM5B/JARID1B: gain in breast, prostate cancer, somatic mutations
KDM5C/JARID1C: mutated in RCC
LSD1: overexpression in multiple cancer types
Intertumor heterogeneity in breast cancer
Major subtypes:
Luminal A
Luminal B
HER2+
Basal-like
Normal breast-like
Relevance:
Different risk factors
Different response to treatment
Different risk of progression
Different site of metastasis
Perou et al, Nature, 2000
JARID1B in breast cancer:
common copy number gain and overexpression
Most significant in luminal A and HER2+ tumors,
but seen across all tumor subtypes
Yamamoto et al. unpublished data
JARID1B in breast cancer:
common copy number gain and overexpression
Most significant in luminal A and HER2+ tumors,
but seen across all tumor subtypes
Loss of JARID1B decreases breast cancer cell growth
shRNA screen results
Most significant in luminal A breast cancer cells but also seen in some basal cells
siRNAs
Changes in histone H3K4me3/2 levels after siJARID1B
Slight increase in H3K4me3 in luminal A breast cancer cell lines
Changes in gene expression patterns after siJARID1B
Up genes
Down genes
Increased expression of basal/stem cell genes in luminal A cells
Upregulation of TGFb signaling after siJARID1B in MCF7 cells
Downregulation of TGFb signaling after siJARID1B in SUM159PT cells
Role TGFb in JARID1B-loss-induced growth arrest
Inhibition of TGFb signaling rescues Jarid1b-loss-induced growth arrest
in MCF7 luminal but not in SUM159PT basal cells
Breast tumor subtype-specific Jarid1b ChIP-seq patterns
More promoter binding in luminal than in basal breast cancer cells
Breast tumor subtype-specific Jarid1b ChIP-seq patterns
Non-promoter signal is more subtype-specific than promoter signal
Changes in global H3K4me3/me2 ratios after siJARID1B in MCF7 cells
Increase in H3K4m3/m2 ratio after siJARID1B
Jarid1b and H4K4me3/me2 signal overlaps
Jarid1b is enriched in H3K4me3/me2 bounds regions in all cell types
Jarid1b binding to H4K4me3/me2-enriched expressed genes
Jarid1b is enriched in H3K4me3/me2 bound expressed genes in all cell types
Jarid1b binding is enriched in luminal-high genes
Overlap with ER targets
Overlap of peaks
Overlap of target genes
(ChIP-seq data)
(expression and ChIP-seq data)
ER
Jarid1b
14,490
1,129
17,011
Genes with Jarid1b promoter binding
2,194 1,263
8,548
p value: 1.34087e-96
High luminal Jarid1b activity score is prognostic in ER+ tumors
Jarid1b chromatin binding overlaps with CTCF
Jarid1b is associated with CTCF in most breast cancer cells
CTCF may modulate Jarid1b’s binding and H3K4 HDM activity
Decreased H3K4me3 signal at Jarid1b-CTCF overlapping peaks
More pronounced in promoters and luminal cells
CTCF may modulate Jarid1b chromatin binding
MCF7
siCTCF -
+
-
SUM185PE
+
-
+
-
+
CTCF
Jarid1b
H3K4me3
Histone H3
Decreased Jarid1b binding after siCTCF
In MCF7 cells
b-actin
Increased H3K4me3 after siCTCF
In MCF7 cells
Somatic mutations in JARID1B in breast tumors
K1435R mutant in HCC2157 basal breast cancer cells
may lead to expression of luminal genes
K1435R mutant Jarid1b has a unique binding pattern
MCF7
Pa
4,000,8000
Exogenous transfection of myc-tagged wt or mutant JARID1B in SUM159PT cells
D
Pa
10 15 20 25 30 35
5
0
0
5
Pr
*
*
*
*
*
r
**
1,000
0
500
1,000
0
F
ChIP-qPCR
0
500
1,000
0
500
1,000
0
5
**
500
5
**
**
0
10 15 20 25 30 35
er
**
10 15 20 25 30 35
*
*
10 15 20 25 30 35
er
V
V
qRT-PCR
MCF7
ESRP1 is a mutant Jarid1b target and
it changes splicing patterns in basal-like breast cancer cells
Endogenous splice variants
Changes in splice variants after exogenous transfection
K1435R JARID1B mutation may influence interaction with CTCF
HCC2157-unique Jarid1b peaks do not overlap with CTCF
Mutant Jarid1b has decreased
Binding to CTCF
5
10 15 20 25 30 35
10 15 20 25 30 35
1,000
0
500
1,000
0
500
1,000
0
500
1,000
5
10 15 20 25 30 35
500
10 15 20 25 30 35
0
0
0
5
r
er
0
0
5
Pr
er
Functional differences between wt and K1435R mutant Jarid1b
HCC2157-unique Jarid1b peaks in promoters have lower H3K4me3/me2 signal
SUMMARY
JARID1B amplified and overexpressed in breast cancer (luminal A and HER2+)
Its downregulation inhibits breast cancer cell growth (mostly luminal A ER+)
Its downregulation in luminal cells leads to activation of TGFb signaling
and expression of basal-specific genes
Inhibition of TGFb signaling rescues growth arrest in siJARID1B-transfected cells
Jarid1b chromatin-binding is breast tumor subtype-specific
Jarid1b is enriched in H3K4me3/me2 bound expressed genes in all cell types
Jarid1b associates with CTCF and this may modulate its KDM activity
JARID1B mutation in basal breast cancer cells may lead to gain of luminal features
High luminal Jarid1b activity is associated with worse outcome in ER+ tumors
Shoji Yamamoto
Reo Maruyama
Hege Russnes
http://polyaklab.dfci.harvard.edu/
Zhenhua Wu
Guillermo Peluffo
Muhammad Ekram
Kristopher Carver
Taku Yoshida
Mattia Zucca
Vanessa Almendro
Jun Yao
Jee Hyung Kim
Laura Mulvey
Shinji Takagi
Dana-Farber Cancer Institute
Shirley X. Liu
Hanfei Su
Five3 Genomics LLC
Charles Vaske
Thompson-Reuters
Yuri Nikolsky
Marina Bessarabova
Oslo University Hospital
Hege G Russnes
Hans Kristina Moen Vollan
Xi Zhao
University of Cambridge
Oscar Rueda
Carlos Caldas