Molecular Classification of BC
Molecular Classification of BC
Molecular Classification of BC
B re a s t Ca n c e r
Elena Provenzano, MBBS, PhD, FRCPatha,b, Gary A. Ulaner, MD, PhDc,d,
Suet-Feung Chin, BSc, PhDe,*
KEYWORDS
Breast cancer Molecular classification Genes Mutations Copy number alterations
KEY POINTS
Breast cancer is a heterogeneous disease.
It can be classified based on its molecular profiles.
These molecular subtypes have different prognostic indices and may require different clinical
management.
a
Cambridge Experimental Cancer Medicine Centre (ECMR), NIHR Cambridge Biomedical Research Centre,
Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; b Department of Histopathol-
ogy, Addenbrookes Hospital, Box 235, Hills Road, Cambridge CB2 0QQ, UK; c Department of Radiology, Me-
morial Sloan Kettering Cancer Center, 1275 York Avenue, Box 77, New York, NY 10065, USA; d Department
pet.theclinics.com
of Radiology, Weill Cornell Medical School, New York, NY 10065, USA; e Cancer Research UK Cambridge Insti-
tute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
* Corresponding author.
E-mail address: [email protected]
harmful drugs in patients with a good prognosis, been dropped, as it is thought to represent
and more aggressive intervention with first-line contamination by normal glands. Classification of
chemotherapy in patients with a poor prog- cohorts of breast cancers into the intrinsic sub-
nosis.16–18 However, use of algorithms based on types seems robust across studies; however,
these histologic variables result in a significant assignment of individual tumors to a subgroup
number of patients being overtreated, with as shows only moderate reproducibility depending
many as 85% of patients deriving no benefit from on the array platform used, composition of the
chemotherapy. At the other extreme, 20% of pa- entire tumor population, and setting of gene
tients still die despite receiving maximum expression thresholds.24–26 Identification of the
therapy.19 basal-like group is most reproducible, with the
The ultimate goal of modern oncological man- luminal B and HER2 groups the most poorly repro-
agement is personalized medicine, with a more ducible.26,27 The commercially available Predic-
precise determination of patient prognosis based tion Analysis of Microarray 50(PAM50) classifier
on tumor biology and the opportunity for targeted (Prosigna),28,29 based on expression of 50 genes
treatment directed at the underlying molecular that can separate tumors into the intrinsic sub-
aberrations driving individual tumor growth. HT types, has been shown to be an independent
molecular techniques offer the potential to revolu- marker of prognosis.30–33 Attempts to replicate
tionize patient management in this way. But these these groups using IHC-based panels, including
techniques are currently expensive compared with ER, PR, HER2, Ki67, and basal cytokeratins,
standard methods, such as immunohistochem- have produced modest concordance between
istry (IHC); the vast amounts of data generated gene expression and IHC-defined intrinsic sub-
require complex bioinformatic analyses limiting types at best.22,34
their clinical use currently.20
Luminal Breast Cancer
Intrinsic Subtypes
Luminal breast cancers are enriched for ER-
The mainstays of breast cancer characterization positive tumors and include special type cancers,
are still histologic subtype, tumor grade, and such as tubular, cribriform, lobular, and mucinous
stage, which provide a basic reflection of the de- carcinomas. Luminal cancers form a continuous
gree of tumor differentiation (tubule formation) spectrum that can be arbitrarily divided into 2
and growth rate (size and mitotic count). The sem- subgroups based on the expression of
inal article that led to the identification of 5 intrinsic proliferation-related genes. Luminal A tumors are
subtypes was published by Perou and colleagues5 typically low grade with an excellent prognosis,
in 2000. The investigators took a series of 38 inva- ER/PR positive and HER2 negative, with high
sive breast cancers (36 ductal and 2 lobular), 1 expression of ER-related genes and low expres-
case of ductal carcinoma in situ (DCIS), and 4 sion of proliferation-related genes.23,35 In contrast,
benign samples and undertook complementary luminal B tumors are higher grade with worse
DNA microarray gene expression analysis fol- prognosis and may be PR negative and/or HER2
lowed by hierarchical clustering of differentially positive with high expression of proliferation-
expressed genes and identified 5 subtypes pri- related genes.36,37 Clinically, the luminal A group
marily separated by estrogen receptor (ER) is likely to benefit from hormonal therapy alone,
expression; 2 ER-positive luminal subtypes, and whereas luminal B tumors with their increased pro-
3 ER-negative subtypes (HER2 enriched, basal liferation may be candidates for chemotherapy.
and normal-like). A follow-up study showed that Molecular signatures that separate ER-positive
these subtypes were associated with differences tumors into good and poor prognosis subgroups
in survival.21 form the basis for many of the multi-gene assays
These 5 intrinsic subtypes have been validated that are currently available for clinical use,
in other series and have changed how we think such as Oncotype Dx, Mammaprint, and
about the taxonomy of breast cancer.22,23 The EndoPredict.38–40 Although there is little overlap
separation into good and poor prognosis in the specific genes that make up these signa-
ER-positive, HER2-positive, and triple-negative tures, they all include genes involved in prolifera-
(ER, progesterone receptor [PR], and HER2 nega- tion and ER signaling.27,41 In studies whereby
tive: triple-negative breast cancer [TNBC]) groups multiple signatures are applied to the same patient
is highly clinically relevant, given that current ther- cohort, they all identify low- and high-risk groups
apeutic regimens are centered on antiestrogen with a significantly different prognosis; however,
therapy, chemotherapy, and HER2-targeted there is disagreement at the individual patient level
agents. The normal-like subtype has subsequently in many cases.42–46
Molecular Classification of Breast Cancer 327
Because of the present high cost of these com- 7% basal-like, and 18% normal-like. Of note, the
mercial multi-gene assays, attempts have been HER2-enriched tumors had a significantly higher
made to recapitulate the luminal A and B subtypes pathologic complete response (pCR) rate versus
using IHC markers of proliferation, such as Ki67. HER2-luminal tumors (53% vs 29% respectively)
Cheang and colleagues37 looked at a series of 357 and had a larger improvement in event-free sur-
cancers with known gene expression profiling and vival with the addition of trastuzumab.50
identified an optimum Ki67 cut point of 13.25% for
distinguishing luminal A from B tumors, with a sensi-
Basal-Like/Triple-Negative Breast Cancers
tivity of 72% and a specificity of 77%. This cut point
was rounded to 14% for clinical use. Hence, the sur- The basal-like breast cancers are typically high-
rogate IHC definition of luminal A tumors was ER grade TNBC that are characterized by upregula-
positive and HER2 negative with a Ki67 index less tion of genes expressed by basal/myoepithelial
than 14% and of luminal B tumors was ER positive cells, including high-molecular-weight cytokera-
and HER2 negative with a Ki67 index of greater tins (CK5 and 14), P-cadherin, and epidermal
than 14% or HER2 positive. In 2 large clinical trial us- growth factor receptor.23 The basal-like group
ing this IHC surrogate definition, 81% to 85% of includes diverse histologic types of breast cancer;
luminal A tumors were correctly classified, whereas although most are high-grade IDC, they also
35% to 52% of luminal B tumors were misclassified include medullarylike cancers with a prominent
as IHC luminal A.35 The IHC definition of luminal A lymphocytic infiltrate; metaplastic cancers, which
tumors was subsequently modified to include PR may show squamous or spindle cell differentiation;
expression of greater than 20% to better identify a and rare special type cancers like adenoid
good prognosis subgroup akin to the luminal A tu- cystic carcinoma (AdCC), which carry a good
mors defined by gene expression profiling. Despite prognosis.51–55
the initial enthusiasm, Ki67 is not currently accepted Breast cancers arising in BRCA1 mutation car-
as a routine prognostic marker in breast cancer by riers are typically basal-like; BRCA1 dysfunction
the American Society of Clinical Oncology because mediated by alternative mechanisms, such as
of disagreement as to the best scoring method and methylation, has been identified in non-BRCA1
suboptimal reproducibility in scoring.47 mutated basal-like tumors.51,56,57 The terms
basal-like and TNBC have been used interchange-
ably; however, not all TNBC are of the basal type.
Human Epidermal Growth Factor Receptor
On gene expression profiling, TNBCs have been
2–Positive Breast Cancer
subdivided into 6 subgroups with different molec-
ER-negative cancers comprise biologically distinct ular drivers and variable clinical outcomes and
entities with different drivers that can be divided response to neoadjuvant chemotherapy, although
into 2 main groups: HER2 enriched and basal- this has subsequently been revised to 4
like/TNBC. The HER2-enriched group is driven groups.58–60
by overexpression of HER2 and genes associated An important subgroup is the luminal androgen
with related pathways or with the HER2 amplicon receptor (LAR) group, characterized by high
on chromosome 17q12. Before the introduction expression of androgen receptor and hormonally
of HER2-targeted therapies, they had the worst regulated pathways with similarities to the molec-
prognosis of all breast cancer subtypes. Although ular apocrine group of breast cancers.61 They have
most tumors within this subgroup (>80%) show a relatively good prognosis and show a lower pCR
HER2 gene amplification or HER2 protein over- rate following neoadjuvant chemotherapy (10%)
expression on IHC, not all clinically defined more akin to ER-positive tumors.60 As well as
HER2-positive tumors fall into this subgroup; expressing androgen receptor, LAR tumors
many ER-positive/HER2-positive tumors fall into frequently have PIK3CA mutations and may be
the luminal B group mentioned earlier.23,48 In one candidates for antiandrogenic agents and/or
series looking at clinically HER2-positive breast phosphatidylinositide 3-kinase (P13K) pathway
cancers, 47% were of the HER2-enriched sub- inhibitors.62
type, whereas conversely only 65% of HER2- There are 2 basal-like subgroups, BL1 and BL2,
enriched subtype cancers were clinically HER2 enriched for genes involved in proliferation, DNA
positive.49 In a retrospective analysis of the damage response (BL1), and growth factor recep-
NeoAdjuvant Herceptin (NOAH) clinical trial look- tor signaling pathways (BL2). The BL1 group
ing at neoadjuvant therapy with or without trastu- shows high pCR rates following neoadjuvant
zumab for clinically HER2-positive breast cancer, chemotherapy (52%), whereas the BL2 group
on PAM50 testing only 55% of the cancers were shows poor response.60 The immune modulatory
classed as HER2 enriched; 21% were luminal, group is enriched for genes involved in immune
328 Provenzano et al
cell processes, such as B- and T-cell receptor these special-type cancers are described in
signaling, cytokine signaling, and antigen presen- more detail later.
tation, and is now thought to reflect infiltration by
immune cells rather than represent a true TNBC
Invasive Lobular Carcinoma
subtype.59 The mesenchymal (M) group shows
enrichment for genes involved in cell motility, dif- The most common special-type cancer is invasive
ferentiation, growth signaling pathways, and lobular carcinoma (ILC), accounting for 5% to 15%
extracellular matrix interactions, with low expres- of breast cancers (Fig. 1).2 ILC is composed of
sion of proliferation-related genes and high small, monotonous cells with round nuclei that
expression of genes associated with stem cells. lack cohesion, infiltrating as cords and single files
The last group was associated with worse 5-year around existing normal breast structures. There is
distant recurrence-free survival consistent with often minimal stromal reaction; this absence of
upregulation of pathways involved in motility and disruption to background breast architecture is
metastasis; the M group also showed the poorest what results in the difficulties in radiological detec-
disease-free survival and overall survival following tion of these tumors, with up to 43% being occult
neoadjuvant chemotherapy.60 on standard mammography.69 ILCs are typically
TNBCs demonstrate particularly elevated up- ER positive (95%–99%) and HER2 negative
take of fluorodeoxyglucose (FDG) on PET.63,64 (>95%), and most fall into luminal subtypes with
They are also known to result in early metastatic 30% to 85% being luminal A and 20% to 64%
disease and have a propensity for extraskeletal luminal B.70 A small subset show more aggressive
metastases,65 increasing the importance of imag- histologic features, such as a solid growth pattern
ing for systemic staging. and/or severe nuclear pleomorphism. The latter
group are referred to as pleomorphic ILC and
Integrative Clusters can have a more aggressive biological phenotype
with ER negativity in up to 25% and HER2 gene
Breast cancer is a copy number disease.66
amplification in 15% to 35%.71,72
Recently, a classifier based on integrated analysis
The characteristic molecular feature of ILC is
of both genomic and transcriptomic data from
downregulation of the CDH1 gene on 16q that en-
2000 primary breast tumors MolEcular TAxonomy
codes the E-cadherin protein. E-cadherin is a cell
of BReast cancer International Consortium
adhesion molecule that forms part of the
(METABRIC) was produced, which revealed 10
cadherin-catenin complex and is responsible for
groups termed integrative clusters (IntClusts) with
the glandular architecture of the breast.73 How-
a distinct clinical outcome67 further refining the
ever, 12% to 16% of classic ILC retain expression
existing expression-based subgroups (Table 1).
of the E-cadherin protein on IHC and 25% to 50%
IntClust 5 is composed of HER2-positive tumors;
of IDCs may show reduced or absent E-cadherin
TNBCs predominantly fall in IntClust 10 with
expression, so ILC is defined by morphology and
some in IntClust 4, which is characterized by im-
not by absent E-cadherin staining alone.74–76
mune infiltration. The remaining 7 IntClusts are
Clinically, ILC have a similar prognosis to stage-
predominantly composed of ER-positive/HER2-
matched IDC in most series, although long-term
negative cancers highlighting the heterogeneity
prognosis may be poorer with higher rates of late
present within this subtype includes an ER-
relapse after 10 years.77 Grade is a significant
positive group (IntClust2) with a prognosis worse
prognostic factor, with grade 3 tumors showing a
than ER-negative disease characterized by
worse outcome. ILC show a poor response to neo-
CCND1 amplification.
adjuvant chemotherapy, with low pCR rates and a
lower rate of tumor downsizing and conversion to
Special Histologic Subtypes
breast-conservation therapy.78,79 On Oncotype
There are more than 20 special histologic sub- Dx testing, most fall into the low- (32%–77%)
types of breast cancer, each associated with a and intermediate-risk (23%–57%) groups, with
distinct histologic appearance and clinical only 1% to 10% having a high-risk recurrence
behavior.2 New genomic techniques have led to score, consistent with the limited benefit of
considerable interest in interrogating the molecu- chemotherapy in these patients.80
lar profiles of these special-type tumors to help un- Historically, ILC and IDC were thought to
derstand them.68 Although some special-type develop via separate pathways, with ILC origi-
tumors have been associated with characteristic nating in the lobules and IDC originating from
genetic changes, there is also considerable ge- ducts; it is now known that most breast cancers
netic heterogeneity within many special-type can- arise in the terminal duct lobular units, which is
cers despite their distinct morphology. Some of also the location of the stem cell niche.81 ILC and
Molecular Classification of Breast Cancer 329
Table 1
Description of the 10 integrative cluster subtypes
low-grade ER-positive IDC share many genetic Gene expression profiling of ILC has identified 2
similarities, including gain on chromosome 1q subtypes: one is hormone related with upregula-
and 16p and loss of 16q, and are now thought to tion of ESR1 and cell cycle and ER target genes
share common precursor lesions, such as atypical and the other is immune related with activation of
lobular hyperplasia, atypical ductal hyperplasia, immune signaling and cytokine pathways and
LCIS, and low-grade DCIS, that together form associated with an increased lymphocytic infiltrate
the low-grade ER-positive breast neoplasia on histology.84 In the METABRIC study, ILC fell
pathway.82 In a comparison with grade-matched across several intrinsic clusters, with approxi-
ER-positive IDC, ILC showed differential ex- mately one-third in IntClust 3 associated with
pression of CDH1 and other genes involved in CDH1 and PIK3CA mutations85,86; in fact, it was
cell assembly and cell-cell interactions as well as the increased number of ILC in IntClust 3 that
reduced expression of cell cycle genes.83 largely accounted for the CDH1 mutations87. The
Other genes commonly mutated in ILC include second largest group fell in IntClust 4, with low
PIK3CA (35%–48%), PTEN (14%), and ERBB2 genome instability and increased expression of
(4%–18%).70 immune signatures. Given the generally poor
330 Provenzano et al
Fig. 1. Invasive lobular carcinoma (ILC). (A) Screening mammogram from a 69-year-old woman showing a 20-mm
area of architectural distortion in the upper outer quadrant. (B) On MR imaging, the tumor was much larger than
apparent on the mammogram. (C) Core biopsy revealed ILC, with the characteristic single-file growth pattern and
minimal stromal reaction (H&E, original magnification x 10). (D) Higher power showing cells with regular round
nuclei and occasional mucin vacuoles, which demonstrates the potential limitations, including undermeasure-
ment of the malignancy, when imaging ILC by mammography (H&E, original magnification x 20).
response to traditional chemotherapy, these ge- The lobular subtype has important implications
netic profiles may offer new treatment opportu- for imaging studies (Fig. 1). Primary ILC lesions
nities, such as PI3K pathway and immune of the breast are more difficult to detect than
checkpoint inhibitors. ductal/IDC on all current imaging modalities,
Molecular Classification of Breast Cancer 331
Fig. 2. (A) FDG PET maximum-intensity-projection image of a patient with newly diagnosed lobular breast cancer
demonstrates physiologic FDG avidity, without abnormal foci. (B) Sagittal computed tomography (CT) on bone
window demonstrates widespread sclerotic osseous metastases (arrows). Biopsy-confirmed osseous metastases.
(C) Fused FDG PET/CT demonstrates the widespread osseous metastases are not appreciably FDG avid. This finding
demonstrates the potential for substantial ILC malignancy with little or no FDG avidity on PET.
332 Provenzano et al
Fig. 3. (A) FDG PET maximum-intensity-projection image of a patient with newly diagnosed lobular breast cancer
demonstrates physiologic FDG avidity, without abnormal foci. (B) Axial PET. (C) Axial CT. (D) Axial fused FDG
PET/CT demonstrates gastric wall thickening (arrow), peritoneal free fluid (arrowhead), and hydronephrosis
(curved arrow), better appreciated on CT than FDG PET. Endoscopy and biopsy confirmed ILC metastases to
the stomach. Hydronephrosis is probably from ILC metastases to the retroperitoneum obstructing the ureters.
This image is an example of widespread, multi-organ system ILC metastases with little or no FDG avidity.
Within the METABRIC cohort, mucinous carci- grade variants of spindle cell metaplastic carci-
nomas fell within the ER-positive IntClusts but noma (fibromatosislike metaplastic carcinoma),
were relatively evenly distributed across clusters low-grade adenosquamous carcinoma, and rare
and did not associate with any one cluster; hence, salivary glandlike tumors that occur in the breast,
despite their unique morphology, as a group including AdCC and secretory carcinoma, both
mucinous carcinomas show considerable hetero- characterized by the presence of specific fusion
geneity in terms of underlying genetic drivers.87 genes.53,55,108,109
Basal-like breast cancers are typically associ-
ated with aggressive clinical behavior and a poor
Adenoid Cystic Carcinoma
outcome, but there is a subset of special-type can-
cers that fall within the basal group but has an AdCCs are composed of a dual population of
excellent prognosis. This subset includes low- luminal and basaloid cells that form islands with
Fig. 4. A 49-year-old woman presented with a breast mass. (A) Mammogram showed dense breast tissue with no
apparent focal lesions. (B) Ultrasound showed a circumscribed lobulated lesion with heterogeneous echogenicity.
(C) MR imaging showed a 15-mm ring-enhancing lesion that did not reach threshold, with increased signal on T2
and low signal on T1. (D) Core biopsy showed an invasive mucinous carcinoma, with islands of tumor cells floating
in background mucin. (E) The tumor cells stained strongly positive for estrogen receptor but were negative for
HER2 (F). This finding demonstrates the potential limitations, including nonvisualization of the malignancy,
when imaging mucinous tumors by mammography.
Molecular Classification of Breast Cancer 333
a cribriform or sievelike architecture with spaces appear deceptively innocuous on imaging, partic-
filled with bluish mucin and pink basement mem- ularly in young women.53,104
branelike material, although solid and tubular Classic medullary carcinoma is defined by strict
patterns can also be seen.53,110 They were origi- histologic criteria that are poorly reproducible, and
nally described in the salivary gland but can it is now thought that the relatively favorable prog-
occur in the breast or lung. In the breast, AdCCs nosis compared with other grade-3 TNBCs is due
usually occur in older women and are low-grade to the associated immune response, so medullary,
with an excellent prognosis with adequate local atypical medullary, and medullarylike IDC are
therapy; lymph node and distant metastases grouped together in the most recent World Health
are rare.2 Regardless of site, AdCCs harbor a Organization classification as carcinoma with
chromosomal rearrangement involving the MYB medullary features.2 These tumors show high
gene, typically resulting in a t(6;9)(q22–23;p23– levels of genomic instability with complex copy
24) translocation with the formation of a MYB- number aberrations and structural gene rear-
NFIB fusion gene. This translocation has been rangements. Structural gene rearrangements
detected in 23% to 100% of breast AdCCs.53 resulting in the creation of neo-antigens, which
Apart from this translocation, the genome is sta- then activate the host immune response.114,115
ble and they lack copy number changes, such as The cancers that arise in BRCA1 mutation carriers
8q gain and 5q loss or mutations in TP53 and often have medullary features with a very high
PIK3CA that are commonly seen in other mitotic rate, although conversely only 13% of
TNBCs.111 Rare cases with progression to poorly women diagnosed with medullarylike cancers
differentiated basaloid carcinoma accompanied have BRCA1 mutations.116,117 Alternative mecha-
by accumulation of additional genetic alterations nisms, such as promoter hypermethylation, may
have been described.112 be responsible for BRCA1 downregulation in
cases lacking a germline mutation.118 Medullary-
like carcinomas also frequently contain TP53
Secretory Carcinoma
mutations; this was the only high-frequency muta-
Secretory carcinoma is a very rare tumor that was tion seen in medullary carcinomas within the
originally described in children and adolescents METABRIC cohort, present in more than 80% of
but can occur in patients of all ages and in cases.86
men.2,113 It is composed of cells with abundant In conclusion, new HT genetic technologies have
granular eosinophilic to foamy cytoplasm forming enhanced our understanding of breast cancer
microcystic, tubular and solid patterns, with peri- biology and changed the way we conceptualize
odic acid–Schiff–positive intracellular and extra- breast cancer classification. However, the tradi-
cellular secretory material that gives it its name. tional histologic subtypes of breast cancer retain
Despite being triple negative, they are low grade their value because of their clinical and radiological
and have an excellent prognosis. Secretory carci- correlations and provide some clues as to the un-
noma has a characteristic t(12;15) translocation derlying molecular biology. Hence, the two are
that produces a ETV6-NTRK3 fusion gene; this complementary; both play an important role at pre-
translocation is unique to secretory carcinoma in sent in determining patient management. The his-
the breast but has been described in other tumors, tologic and molecular subtypes of breast cancer
such as infantile fibrosarcoma and congenital have important implications for how tumors are
mesoblastic nephroma.53,109 Similar to AdCC, visualized on imaging studies. Several subtypes
the genome is otherwise stable with few copy of breast cancer are more difficult to image on
number alterations. Interestingly, a salivary gland mammography. Basal-like/TNBCs tend to be high-
counterpart to secretory carcinoma has now ly FDG avid on PET, whereas the lobular histologic
been recognized, in part because it harbors the subtype may be less avid and less perceptible on
same t(12;15) translocation. FDG PET imaging.
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