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The Susan G. Komen for the Cure® Tissue
Bank at the IU Simon Cancer Center:
How normal breast tissue can facilitate
breast cancer research
Susan E. Clare, MD, PhD
Division of Breast Surgical Oncology
Department of Surgery
July 17, 2015
REPORT OF THE BREAST CANCER PROGRESS REVIEW GROUP
1.
Our limited understanding of the biology and
developmental genetics of the normal mammary gland is a
barrier to progress. Much of our biological research in breast
cancer has focused on understanding the initiation and
development of the disease. This research has been fruitful,
but it is now clear that a more complete understanding of the
normal mammary gland at each stage of development—from
infancy through adulthood—will be a critical underpinning of
continued advances in detecting, preventing, and treating
breast cancer. This focus represents a major shift in breast
biology research and requires increased support for these
studies and the materials needed to conduct them.
Charting the Course: Priorities for Breast Cancer Research
Report of the Breast Cancer Review Group
National Cancer Institute
1998
IMPEDIMENTS TO CONDUCTING
RESEARCH ON “PRE-CANCERS”
• insufficient understanding of normal and
“pre-cancer” biology
• limited access to appropriate specimens
• a highly subjective, histology-based
classification scheme
• the lack of strategic partnerships among
research communities
November 2004 NCI Workshop on Pre-Cancers
Cancer Detect Prev. 2006;30:387-94
TYPES OF SPECIMENS
A repository of richly annotated biologic specimens from
volunteers without evidence of breast cancer.
Whole Blood
Blood
DNA
Saliva
DNA
Breast tissue (10 GA core biopsy x 2-4)
Fresh-frozen
Formalin-fixed, paraffin-embedded
Epithelial and stromal cell lines derived from the cores
Serum
Plasma
Fat (10 GA core biopsy x 2-3)
SPECIMENS
4/7/2010
7000
6872
6000
5000
4000
3186
3000
2000
1749
893
503
1000
0
Tissue
DNA
Serum
Plasma
FFPE
Increased diversity of the Bank as a
result of targeted collections
14
12
10
prior to
2009
2009
8
%
6
4
2
0
Jewish Descent
African American
Hispanic
AGE DISTRIBUTION
ALL SPECIMENS
200
180
160
140
120
100
80
60
40
20
0
18 20 22 24 26 28 30 32 34 36 38 40 42 44 46 48 50 52 54 56 58 60 62 64 66 68 70 72 74 76 78 80 82 84 86 88
AGE DISTRIBUTION
TISSUE
50
45
40
35
30
25
20
15
10
5
0
18 20 22 24 26 28 30 32 34 36 38 40 42 44 46 48 50 52 54 56 58 60 62 64 66 68 70 72 74 76 78 80 82 84 86
AGE
GAIL RISK MODELING/TISSUE
90
80
70
60
50
# of donors
40
30
20
10
0
2
4
6
8
10
12
14
16
18
20
22
24
% lifetime risk
26
28
30
32
34
36
38
40
More
NEXT-GENERATION SEQUENCING
• A new method of sequencing in a massively
parallel fashion
No need for prior gene selection
Unlimited dynamic range
Digital quantification
TRANSCRIPTOME ANALYSIS
• Search space is limited to only actively
transcribed areas… compared to studying
whole genomes
• Expression of all coding and non-coding
RNAs
• Identification of alternative splicing events
• Expressed SNPs (single nucleotide
polymorphisms) or mutations
• Translocations and fusion transcripts
• Identify allele specific expression patterns
LASER CAPTURE
MICRODISSECTION
before
after
cap
Normals are quite different…
Phase of the menstrual cycle can explain
some of the difference
9
5
25
13
27
26
4
14
29
19
We identified 299 microRNAs* in breast tissues (first time such survey has been
completed!)
Most abundant microRNAs include:
25
20
Frequency
•
hsa-mir-1978,1975,
1826,1977,1974,1973,1979,12
48,1291,1244,1300,663,663b
(13 in total, RPKM >100)
15
10
5
0
microRNAs*: set filter
average RPKM ≥ 0.5
0.01
0.1
0
10
100
1000
Average RPKM numbers for miRs
WHAT ABOUT NOVEL GENES?
NORMAL BREAST TISSUE AS A CONTROL
FOR BREAST CANCER EXPERIMENTS
• Dr. Bryan Schneider, Hematology/Oncology and Milan
Radovich, Medical and Molecular Genetics
• Compare the transcriptomes of 10 triple-negative breast
tumors and 10 normal tissues from the Komen Tissue
Bank
Identify transcripts/targets that can be further
characterized for therapeutic development
• All samples are from pre-menopausal women.
• Normals were distributed among phases of the
menstrual cycle
• All normals were microdissected
• TNBC samples contained high tumor cell content
and were pathologically verified by Dr. Sunil Badve
TNBC vs. NORMAL
GENE EXPRESSION
281 Genes are significantly differentially expressed between tumor and normal!
TOP 10 DIFFERENTIALLY EXPRESSED
GENES
Gene Symbol
COBRA1
USP39
DBNL
C6orf150
CENPL
SLC25A44
RAD51
MARS
LRP8
DRAP1
P-value (ANOVA)
7.26E-10
1.28E-09
1.99E-09
2.36E-09
2.72E-09
2.76E-09
2.77E-09
2.82E-09
3.31E-09
4.59E-09
Fold Change
3.17
3.28
2.96
8.58
3.87
4.09
3.52
3.71
5.51
3.42
COMING ATTRACTIONS
HOW TO MAKE AN EXTREMELTY
LIMITED RESOURCE ALMOST
UNLILMITED
Oracle
Commitment Grant/Virtual Tissue Bank
 Cell lines
CELL LINES
• 26 primary epithelial cell lines from 36 cores
• 30 primary stromal cell lines from 36 cores
Brittney-Shea Herbert, Ph.D.
Department of Medical and Molecular Genetics
ACKNOWLEDGEMENTS
•
•
•
•
•
The Catherine Peachey Fund, Inc.
Susan G. Komen for the Cure®
Oracle Giving
The Breast Cancer Research
Foundation
Indiana University School of Medicine
Department of Surgery
Department of Medicine
IU Simon Cancer Center
THANK YOU
Donors!
VOLUNTEERS
co-PI
Anna Maria Storniolo
co-PI
Susan Clare
Consumer Representative
Connie Rufenbarger
COO
Jill Henry
Biospecimen Manager
Theresa Mathieson
Database Manager
Heng Zhang
Grants Coordinator
Elizabeth Parsons
Administrative Assistant
Patricia Mitchum