This document discusses molecular profiling of breast cancer. It begins by introducing breast cancer as the most common cancer in women. It then discusses traditional classifications based on histological and clinical features. However, up to half of hormone receptor positive cancers do not respond to treatment, showing clinical classifications are insufficient. Molecular profiling uses high-throughput techniques to better understand breast cancer biology and refine classifications. Gene expression profiling has identified major molecular subtypes, like luminal A/B, HER2-positive, and basal-like. Multigene assays provide prognostic and predictive information beyond traditional clinics-pathological factors. Several common assays are discussed, including Oncotype DX, Mammaprint, and PAM50. Next generation sequencing is also discussed for

1. MOLECULAR PROFILING OF BREAST CANCER
Dr Hriman Sharma Sarkar

2. INTRODUCTION
 Worldwide Breast cancer is the most common
cancer that women may face in their lifetime
(except for skin cancer). It can occur at any age,
but the risk goes up as you get older.
 They are traditionally classified on the basis of
 morphological feature,
 histological features,
 tumor grade, and stage
 proliferation status,
 Lymphovascular invasion.

5. Two key determinations to make in the
morphologic study of breast carcinoma are: (1)
whether the tumor is confined to the epithelial
component of the organ (in situ carcinoma) or
has invaded the stroma (invasive carcinoma); and
(2) whether it is of ductal or lobular type.

6. Figure 23-23 Grading of invasive carcinoma. A, A well-differentiated carcinoma of
no special type consists of tubules or a cribriform pattern of cells with small
monomorphic nuclei. B, A moderately differentiated carcinoma of no special type
shows less tubule formation and more solid nests of cells and pleomorphic
nuclei. C, A poorly differentiated carcinoma of no special type infiltrates as ragged
sheets of pleomorphic cells and contains numerous mitotic figures and central
areas of tumor necrosis.

7. Figure 23-24 Special histologic types of invasive carcinoma. A, Lobular
carcinoma. B, Mucinous carcinoma. C, Tubular carcinoma. D, Papillary
carcinoma. E, Apocrine carcinoma. F, Micropapillary carcinoma. G,
Medullary carcinoma. H, Secretory carcinoma.
A B C
HG

8. The clinical-pathological paradigm estimates the probability
of breast cancer recurrence using
•Physical characteristics such as tumor size, histological grade,
and number of metastatic axillary lymph nodes.
• Estrogen and progesterone receptor (ER/PR) expression levels
are determined by IHC .
•Human epidermal growth factor receptor 2 (HER2) is
determined by IHC or in situ hybridization (ISH).
•The levels of each are used as predictive markers to identify
subgroups of patients who are likely to benefit from anti–
estrogen or anti–HER2-directed therapies.

10. However..
…Up to half of all hormone receptor positive breast
cancers do not respond to endocrine treatment at initial
presentation (intrinsic resistance) or there is inevitable
development of resistance over time (acquired resistance)
Osborne CK. Tamoxifen in the treatment of breast cancer.
N Engl J Med 1998; 339: 1609e18.

11. Thus, the clinicopathologic classification and staging of Tumor
based on histology, tumor grade, nodal spread,
Lymphovascular invasion, proliferation status and
hormone sensitivity is important but not sufficient.
We also now know that Breast cancer is caused by heterogeneous
group of tumor cells whose behavior and response to therapy
depends on biological features.

12.  Tumors of similar clinicopathologic features exhibit
dissimilar behavior and response to specific therapy.
 Advances in high output molecular techniques and
bioinformatics have improved our understanding of
cancer biology, refined molecular taxonomies and led to
development of novel prognosis and predictive
molecular arrays.
 Molecular testing is becoming relevant to diagnosis and
treatment of breast cancer.

13. We have thus arrived at an important
juncture in the treatment of breast cancer.
We stand between the clinical-pathological
paradigm, which has been dominant for
several decades, and the emerging genomic
paradigm.

14. A ‘gene expression signature’ can be defined as a single or a
combined gene expression alteration with validated
specificity in terms of diagnosis, prognosis or prediction of
therapeutic response.
Molecular profiling is a method of testing, that looks at each
person's cancer tumor and studies the genetic
characteristics as well as any unique biomarkers. The
information gathered is used to identify and create targeted
therapies that are designed to work better for a specific
cancer tumor profile.

15. Purpose of Molecular testing in breast cancer is therefore to:
Classify tumor types,
Recognize hereditary implications (e.g. BRCA1 mutations)
Identify appropriate therapeutic agents (e.g. HER2+ disease
or ER/PR + disease),
Determine the prognosis of the disease by giving the risk
score,
Identify biomarkers that can predict or monitor the
response to treatment
To avoid unnecessary treatment to all cancer patients

16. Sections taken from the primary tumour displayed distinct well-segregated
spatial morphological heterogeneity with H&E . IHC heterogeneity largely
conforming to these same areas was observed

17. GENE EXPRESSION PROFILING(GEP)
Although GEP based molecular subtyping is promising but
cost, access to the technology and need for fresh tumor
material pose problem.
More recently, molecular intrinsic subtyping that uses
formalin fixed paraffin embedded material has become
available.
Gene expression profiling is the measurement of the
activity (the expression) of thousands of genes at the level of
transcription, at once, to create a global picture of cellular
function. It measures relative levels of mRNA expression.

19. •The first use of GEP to stratify breast cancer into molecularly
distinct classes was introduced by Perou and colleagues in 2000.
•They demonstrated that breast cancer at transcriptone level is not
a single disease. Individual tumor possesses a unique genetic
profile.
•However, tumors clustered together to produce distinct
reproducible classes based on transcriptome profiles.
•The classification of breast cancer was based on the expression
of a subset of differentially expressed genes termed the
“intrinsic” gene set.

20. •In Perou’s study two main tumor clusters were identified.
a)ER- positive cluster and was termed luminal in reference to its
molecular similarity to luminal mammary epithelial cells
b)ER- negative cluster which exhibited three sub classes termed
HER 2 positive, basal like and normal breast type.
Subsequent GEP studies indicated that luminal class which
comprise the majority of breast cancer is heterogenous with respect
of expression of other gene and outcome and was devided into
subclasses luminal A and Luminal B.
Despite the different microarray platforms and different intrinsic
gene lists most studies have consistently reported at least four
classes luminal A and B, HER 2-positive and basal like.
Other novel molecular classes claudin-low and apocrine subtypes
have triple negative phenotypes.

21. Major Molecular Subtypes of breast cancer determined by GEP

22. ESMO CLINICAL PRACTICE GUIDELINE
Luminal A Luminal B Basal Like Her2 positive
ER&PR-Positve
Her2-Negative
Ki67 low,<10%
Her2 positive or
negative, High
Ki67>30%
Defined as triple
negative
Her2
overexpression/
gene
amplification
Low risk
molecular
signature(if
available)
PR low or
showing poor
prognostic gene
expression
signature(if
available)
Absence of ER
or PR.

23. SUMMARY OF MOLECULAR TESTS MOST
COMMONLY USED FOR BREAST CANCER IN
CURRENT CLINICAL PRACTICE

24. MULTIGENE PROGNOSTIC AND PREDICTIVE
SIGNATURE
 Under the current clinical-pathologic paradigm, the typical
approach is to use clinical features that are surrogates for
metastatic potential such as tumor size, tumor grade, lymph node
involvement, and hormone receptor status to determine the
average 10-year risk of recurrence.
 One of the most important uses of these Multigene Assay is
prognosis, that is, to more accurately estimate the risk of breast
cancer recurrence in women with early stage breast cancer and to
select patients who would benefit most from cytotoxic
chemotherapy, at the same time sparing those who would derive
little or no benefit from treatment.

25.  The first generation gene signature mainly associated with
proliferation associated genes and showed highest
discriminatory power in ER positive disease.
 Subsequent studies have strived to generate multigene
predictors based on genes characteristic of a biological
process, e.g. genes associated with host immune response,
wound healing, and other stromal gene signatures that carry
prognostic value independent of ER status and
proliferation.

26. MULTIGENE ASSAY
•Oncotype DX
•Mammaprint
•PAM50
•Breast cancer index
•Endopredict index
•IHC4 Score
•Next generation sequencing

27. ONCOTYPE DX
 Based on RT-PCR
 Biological material is FFPE.
 Measures the expression of 21 genes (16 cancer-related genes and 5 reference
genes that serve as internal controls).
 The cancer-related genes include
 Estrogen group gene
 Her2 group gene
 Proliferation gene
 invasion groups genes.
 A Recurrence Score scale range from 0 to 100
 Kaplan-Meier estimates of the rates of distant recurrence at 10 years in patients
with score
 < 18 (low risk)
 >31 (high risk)
 18 to 30 (intermediate risk)

28.  Scoring is done by measuring the different gene expression and multiplying
by sets of multiplication factors and adding the total value
 And uses that information to predict the
1. Risk of recurrence (the risk of the cancer coming back after
treatment),
2. How likely a patient is to benefit from chemotherapy treatment after
surgery in early stage cancer,
3. The benefit from receiving radiation therapy after DCIS surgery.
 This test may be used for DCIS (ductal carcinoma in situ), stage I or II
breast cancers that are ER+ (estrogen receptor positive) and have no
cancer in the lymph nodes.
 Oncotype DX has demonstrated benefit from adjuvant chemotherapy
primarily in patients with high recurrence score.

31. MAMMAPRINT
 Microarray based
 Fresh tissue or FFPE.
 Uses 70 gene expression to asses the prognosis of breast
tumor
 The biological functions of the 70 genes are
 regulating cell cycle,
 invasion, metastasis,
 proliferation,
 survival in circulation,
 extravasasion,
 adaptation to the micro-environment as well as
angiogenesis

32.  It is approved by US(FDA) for breast cancer patients >61 years
of age with stage I/II, lymph node-negative or 1-3 node-positive
disease.
 It stratifies patients into low-risk or high-risk prognostic groups.
 Though it is applicable to tumors regardless of ER expression,
the prognostic risk discrimination is mainly for ER positive
tumor while ER negative tumor are almost classified high risk.
 Mammaprint test has been validated in retrospective studies but
its clinical utility is under evaluation in a large prospective phase
III trail:MINDACT (microarray in node-negative and 1-3 node
positive disease may avoid chemotherapy)

34. PAM50
 Commercially it is called as Prosigna kit
 FFPE
 Based on RT-PCR
 50 gene expression is assessed
 cell cycle regulating genes
 gene for proliferation
 Developed to provide
 breast cancer classification into the intrinsic subtypes
 to give risk of recurrence score

35. Prosigna can be used to estimate short and long term recurrence-
free survival for stage I/II (including 1-3 positive nodes)
ER-positive breast cancer in postmenopausal women
treated with adjuvant hormone therapy.
Prosigna assay results are reported as a risk of recurrence (ROR)
score from 0 to 100 in two ways:
 Node-negative cancers classified as, Low (0-40) risk,
Intermediate (41-60) risk,
High (61-100) risk.
 Node-positive cancers classified as, Low (0-40) risk,
High (41-100) risk

36.  Knowing if a woman has a high or low risk of distant
recurrence more than 5 years after diagnosis, may be
able to help doctors figure out, whether 5 years or 10
years of hormonal therapy is better for her situation.
Research has shown that taking tamoxifen for 10 years
instead of 5 years can better lower the risk of recurrence
and improve overall survival for many women.
But if doctors knew that a woman had a low risk of distant
recurrence, they might be able spare her the extra 5 years
of hormonal therapy treatment.

37.  It has been approved for OPTIMA (Optimal personalised
treatment of early breast cancer using Multi-parameter Analysis)
main trail.
 This clinical trail aims to reduce the use of chemotherapy in
hormone response HER2-negative breast cancer patients with
lymph node-positive status(pN1-2 or pN0 andpT>30mm) who
are currently offered chemotherapy as standard treatment.

38. THEROS BREAST CANCER INDEX
 It is based on RT-PCR
 FFPE
This assay includes combination of two independently developed
gene signature :
 The two gene ratio (HOXB13:IL17BR) signature, a homeo
domain–containing protein and interleukin 17 receptor B .
 Molecular grade index (MGI) which analyze the expression
of 5 gene which involves in proliferation and cell cycle.
 Compared to Oncotype DX and IHC4, BCI is a predictor of
early distant recurrence and is the only significant prognostic
for risk of late recurrence.

39. ENDOPREDICT TEST
 Based on RT PCR,
 FFPE tissue.
 Assay measures the expression of eight cancer
genes and three housekeeping control genes
 Risk score is been combined with clinical variables
like
 LN status
 Tumor size
 It stratifies ER-positive breast cancer patients
treated with adjuvant therapy into low and high risk
of recurrence.

40. IHC4 ASSAY
 Uses IHC technique
 FFPE tissues
 Based on the assessment of ER, PR, HER2, Ki67
 It uses semiquantitative expression values of these four
markers and produces a ROR score.
 IHC is inexpensive and can be performed in local
laboratories but standardization and quality assurance
required.

41. NEXT GENERATION SEQUENCING
 NGS-based assays that can detect gene mutations from small
amounts of DNA are also in development;
 DNA from fine needle aspirates or
 circulating tumor DNA (ctDNA) from blood samples
 Several studies have shown a high degree of concordance between
mutations in ctDNA (detected using NGS techniques) and mutations
from the primary tumors
 NGS has been used to characterize genomic alterations such as copy
number changes, insertions/deletions and mutations; to facilitate
sequencing at a greater depth(at base pair level) to enable
identification of subclonal mutation, also differentiate driver from
passenger mutation.

42.  NGS revealed the Spatial and Temporal intratumor heterogeneity.
 NGS showed that the constellation of somatic mutation between
primary tumor and its metastasis (temporal h)and between distinct
areas within the primary tumor (spatial heterogeneity) are not
identical indicating that breast cancer evolve over the course of the
disease.
 This clonal heterogenety may explain resistance of some breast
cancer to therapy.

43. CONCLUSION
 Breast cancer is a diverse spectrum of diseases featuring distinct
histological biological, molecular and clinical phenotypes.
 Studies indicate that traditional classification systems are
insufficient to reflect the biological and clinical heterogenity of
breast cancer.
 Advances in high-throughput molecular techniques and
bioinformatics have improved our understanding and refined
molecular taxonomies.
 Molecular testing is evolving and is increasingly becoming
relevant to the prevention, dignosis and treatment of breast
cancer.

44. SO THE FUTURE….
July1,2034
Ultimogenetics has determined patient’s
T2N1 primary breast cancer, as having following molecular profile
, and interventions recommended are as follows ;
Recommendation
Tumor: Pi3k-activating mutation -Pipatah
Her2 amplification -T-parth
Telomerase activation -Deka-tip
Myc overexpression -Myindra
Stroma: VEGR pathway activation -Utss200
Bone tropism -Krish1
This will reduce your patiets estimated 10-year risk of recurrence from
72% to 3.7%