navigating the ovarian cancer (epi) genome - brian gloss
TRANSCRIPT
![Page 1: Navigating the Ovarian Cancer (Epi) Genome - Brian Gloss](https://reader034.vdocuments.net/reader034/viewer/2022052619/556e2cf7d8b42a6a698b4d4d/html5/thumbnails/1.jpg)
Navigating the Ovarian Cancer (Epi)Genome
Dr Brian Gloss –Kinghorn Cancer Centre, Garvan Institute, Sydney
AMATA 2013
CANCER RESEARCH
![Page 2: Navigating the Ovarian Cancer (Epi) Genome - Brian Gloss](https://reader034.vdocuments.net/reader034/viewer/2022052619/556e2cf7d8b42a6a698b4d4d/html5/thumbnails/2.jpg)
• 5th most
common cause
of cancer death
in women
• Mostly presents
at advanced
stage
• Poor outcome
• Complex
biology
Ovarian cancer
CANCER RESEARCH Siegel CA Cancer J Clin 2011
Naora H. Expert Rev Mol Med 2007
Estimated deaths Estimated new cases
![Page 3: Navigating the Ovarian Cancer (Epi) Genome - Brian Gloss](https://reader034.vdocuments.net/reader034/viewer/2022052619/556e2cf7d8b42a6a698b4d4d/html5/thumbnails/3.jpg)
Aims
• Ovarian cancer presents at advanced
stage
– Identify and develop epigenetic
biomarkers of ovarian cancer for clinical
application
• Ovarian cancer is complicated
– Evaluate the role of novel genes identified
above in the development of ovarian
cancer
CANCER RESEARCH
![Page 4: Navigating the Ovarian Cancer (Epi) Genome - Brian Gloss](https://reader034.vdocuments.net/reader034/viewer/2022052619/556e2cf7d8b42a6a698b4d4d/html5/thumbnails/4.jpg)
Epigenetic Biomarker Discovery
• Screening
– Indirect (expression)
– Direct (methylation profiling)
• Target validation
(Sequenom)
– Cell lines
– Tumours
• Clinical application
(headloop PCR)
– Archival tumour samples
– Plasma
• Novel ovarian cancer
genes
CANCER RESEARCH
Num
ber
of re
gio
ns e
valu
ate
d
Num
ber o
f sam
ple
s te
ste
d
![Page 5: Navigating the Ovarian Cancer (Epi) Genome - Brian Gloss](https://reader034.vdocuments.net/reader034/viewer/2022052619/556e2cf7d8b42a6a698b4d4d/html5/thumbnails/5.jpg)
Epigenetic Biomarker Screening
• Screening
– Indirect (expression)
– Direct (methylation profiling)
• Target validation
(Sequenom)
– Cell lines
– Tumours
• Clinical application
(headloop PCR)
– Archival tumour samples
– Plasma
• Novel ovarian cancer
genes
CANCER RESEARCH Gloss et Al. Cancer Letters 2012
Num
be
r o
f re
gio
ns e
valu
ate
d
Num
ber o
f sam
ple
s te
ste
d
![Page 6: Navigating the Ovarian Cancer (Epi) Genome - Brian Gloss](https://reader034.vdocuments.net/reader034/viewer/2022052619/556e2cf7d8b42a6a698b4d4d/html5/thumbnails/6.jpg)
Epigenetic Biomarker Validation
• Screening
– Indirect (expression)
– Direct (methylation profiling)
• Target validation
(Sequenom)
– Cell lines
– Tumours
• Clinical application
(headloop PCR)
– Archival tumour samples
– Plasma
• Novel ovarian cancer
genes
CANCER RESEARCH Gloss et Al. Cancer Letters 2012
Normal Im-
mortal Cancer
Num
be
r o
f re
gio
ns e
valu
ate
d
Num
ber o
f sam
ple
s te
ste
d
Methylation Level
![Page 7: Navigating the Ovarian Cancer (Epi) Genome - Brian Gloss](https://reader034.vdocuments.net/reader034/viewer/2022052619/556e2cf7d8b42a6a698b4d4d/html5/thumbnails/7.jpg)
Epigenetic Biomarker Application
• Screening
– Indirect (expression)
– Direct (methylation profiling)
• Target validation
(Sequenom)
– Cell lines
– Tumours
• Clinical application
(headloop PCR)
– Archival tumour samples
– Plasma
• Novel ovarian cancer
genes
CANCER RESEARCH Gloss et Al. Cancer Letters 2012
Num
be
r o
f re
gio
ns e
valu
ate
d
Num
ber o
f sam
ple
s te
ste
d
Cancer Samples Methylated
Normal Samples Methylated
![Page 8: Navigating the Ovarian Cancer (Epi) Genome - Brian Gloss](https://reader034.vdocuments.net/reader034/viewer/2022052619/556e2cf7d8b42a6a698b4d4d/html5/thumbnails/8.jpg)
Epigenetic Biomarker: ZNF300P1
• Screening
– Indirect (expression)
– Direct (methylation profiling)
• Target validation
(Sequenom)
– Cell lines
– Tumours
• Clinical application
(headloop PCR)
– Archival tumour samples
– Plasma
• Novel ovarian cancer
genes: ZNF300P1
CANCER RESEARCH Gloss et Al. Cancer Letters 2012
Num
be
r o
f re
gio
ns e
valu
ate
d
Num
ber o
f sam
ple
s te
ste
d
Cancer Normal
![Page 9: Navigating the Ovarian Cancer (Epi) Genome - Brian Gloss](https://reader034.vdocuments.net/reader034/viewer/2022052619/556e2cf7d8b42a6a698b4d4d/html5/thumbnails/9.jpg)
A novel noncoding gene
CANCER RESEARCH Gloss, O’Brien & Clark WO Patent 2,012,142,656, 2012
• ZNF300P1
– Unprocessed
Pseudogene of
ZNF300 (84%)
• 2.4kb transcript
• Chr 5q33.1
Scalechr5:
100 kb hg18150,150,000 150,200,000 150,250,000 150,300,000 150,350,000 150,400,000
RefSeq Genes
CpG Islands (Islands < 300 Bases are Light Green)
DCTN4DCTN4DCTN4
SMIM3 IRGM ZNF300ZNF300ZNF300
ZNF300P1 GPX3TNIP1TNIP1TNIP1TNIP1TNIP1TNIP1TNIP1TNIP1TNIP1TNIP1
CpG: 36 CpG: 36 CpG: 23 CpG: 25 CpG: 43
chr5 (q33.1) 5p15.2 14.3 14.1 p13.3 13.2 p12 5q11.2 13.2 14.1 5q14.3 5q15 q21.1 q21.3 5q23.1 q23.2 31.1 5q32 33.1 33.3 5q34 35.1 35.2 35.3
![Page 10: Navigating the Ovarian Cancer (Epi) Genome - Brian Gloss](https://reader034.vdocuments.net/reader034/viewer/2022052619/556e2cf7d8b42a6a698b4d4d/html5/thumbnails/10.jpg)
A novel noncoding gene
CANCER RESEARCH Gloss, O’Brien & Clark WO Patent 2,012,142,656, 2012
• Targeted for silencing in
cancer?
Scalechr5:
100 kb hg18150,150,000 150,200,000 150,250,000 150,300,000 150,350,000 150,400,000
RefSeq Genes
CpG Islands (Islands < 300 Bases are Light Green)
DCTN4DCTN4DCTN4
SMIM3 IRGM ZNF300ZNF300ZNF300
ZNF300P1 GPX3TNIP1TNIP1TNIP1TNIP1TNIP1TNIP1TNIP1TNIP1TNIP1TNIP1
CpG: 36 CpG: 36 CpG: 23 CpG: 25 CpG: 43
Methylation Level
TN
IP1
GP
X3
ZN
F300P
1
ZN
F300
MS
T150
DC
N4
Ovaria
n C
ancer C
ell L
ines
![Page 11: Navigating the Ovarian Cancer (Epi) Genome - Brian Gloss](https://reader034.vdocuments.net/reader034/viewer/2022052619/556e2cf7d8b42a6a698b4d4d/html5/thumbnails/11.jpg)
A Major Player in Cancer?
• Accumulating
methylation in
multiple cancer
types
• Candidate
lncRNA
Khalil et Al. PNAS 2009
Gloss, O’Brien & Clark WO Patent 2,012,142,656, 2012 CANCER RESEARCH
Vita Lin
Wenjia Qu
Nicola Currey
![Page 12: Navigating the Ovarian Cancer (Epi) Genome - Brian Gloss](https://reader034.vdocuments.net/reader034/viewer/2022052619/556e2cf7d8b42a6a698b4d4d/html5/thumbnails/12.jpg)
siRNA expression profiling
CANCER RESEARCH Gloss et al under review 2013
GO terms
KEGG pathways
Networks (IPA)
GSEA
Affy Gene ST v1
Arrays
-Single specific siRNA
(not affecting ZNF300)
-Biological triplicate knockdown
(immortalised normal epithelium)
Cancer/TSG/Cell Death terms
Cell Cycle DOWN
Cell/Cell interaction and motility apparatus UP
![Page 13: Navigating the Ovarian Cancer (Epi) Genome - Brian Gloss](https://reader034.vdocuments.net/reader034/viewer/2022052619/556e2cf7d8b42a6a698b4d4d/html5/thumbnails/13.jpg)
Cell Motility: Scratch/Wound Assay
Immortal
Ovarian
Epithelium
siRNA
Knockdown
CANCER RESEARCH Dr Kim Moran Jones
Gloss et al under review 2013
![Page 14: Navigating the Ovarian Cancer (Epi) Genome - Brian Gloss](https://reader034.vdocuments.net/reader034/viewer/2022052619/556e2cf7d8b42a6a698b4d4d/html5/thumbnails/14.jpg)
Control Knockdown
Cell Polarity Front
Back
Middle
CANCER RESEARCH Dr Kim Moran Jones
Gloss et al under review 2013
Golgi
Dire
ction
of (n
orm
al) m
ove
me
nt
Scratch
Ovarian cancers spread by direct means
An initiating molecular event?
![Page 15: Navigating the Ovarian Cancer (Epi) Genome - Brian Gloss](https://reader034.vdocuments.net/reader034/viewer/2022052619/556e2cf7d8b42a6a698b4d4d/html5/thumbnails/15.jpg)
Conclusions • Insights into epigenetics
of ovarian cancer using many whole-genome and targeted tools
• Novel noncoding gene that is silenced in multiple cancer types
• Expression profiling highlights loss of cell polarity as the likely culprit
Hanahan & Weinberg 2000 & 2011, Cell CANCER RESEARCH
![Page 16: Navigating the Ovarian Cancer (Epi) Genome - Brian Gloss](https://reader034.vdocuments.net/reader034/viewer/2022052619/556e2cf7d8b42a6a698b4d4d/html5/thumbnails/16.jpg)
Acknowledgments • Dr Goli Samimi & Prof. Sue Clark
• Ovarian and Epigenetic Cancer groups
• Cancer department
• Tissue culture
• ACRF
• Peter Wills Bioinformatics
• Support
• Marcel Dinger: Genome Informatics Research team – At AMATA: Mark Cowley, Mark
McCabe, Jesper Maag
CANCER RESEARCH
![Page 17: Navigating the Ovarian Cancer (Epi) Genome - Brian Gloss](https://reader034.vdocuments.net/reader034/viewer/2022052619/556e2cf7d8b42a6a698b4d4d/html5/thumbnails/17.jpg)
Questions
xkcd.com Thanks!
![Page 18: Navigating the Ovarian Cancer (Epi) Genome - Brian Gloss](https://reader034.vdocuments.net/reader034/viewer/2022052619/556e2cf7d8b42a6a698b4d4d/html5/thumbnails/18.jpg)
Relationship with ZNF300
CANCER RESEARCH