Research

JAMA Oncology | Original Investigation

Targeting the PI3K/AKT/mTOR Pathway for the Treatment

of Mesenchymal Triple-Negative Breast Cancer
Evidence From a Phase 1 Trial of mTOR Inhibition in
Combination With Liposomal Doxorubicin and Bevacizumab
Reva K. Basho, MD; Michael Gilcrease, MD, PhD; Rashmi K. Murthy, MD; Thorunn Helgason; Daniel D. Karp, MD;
Funda Meric-Bernstam, MD; Kenneth R. Hess, PhD; Shelley M. Herbrich; Vicente Valero, MD;
Constance Albarracin, MD, PhD; Jennifer K. Litton, MD; Mariana Chavez-MacGregor, MD, MS;
Nuhad K. Ibrahim, MD; James L. Murray III, MD, MPH; Kimberly B. Koenig, MD; David Hong, MD;
Vivek Subbiah, MD; Razelle Kurzrock, MD; Filip Janku, MD, PhD; Stacy L. Moulder, MD, MS

Supplemental content
IMPORTANCE Triple-negative breast cancer (TNBC) classified by transcriptional profiling as
the mesenchymal subtype frequently harbors aberrations in the phosphoinositide 3-kinase
(PI3K) pathway, raising the possibility of targeting this pathway to enhance chemotherapy
response. Up to 30% of mesenchymal TNBC can be classified histologically as metaplastic
breast cancer, a chemorefractory group of tumors with a mixture of epithelial and
mesenchymal components identifiable by light microscopy. While assays to identify
mesenchymal TNBC are under development, metaplastic breast cancer serves as a clinically
identifiable surrogate to evaluate potential regimens for mesenchymal TNBC.

OBJECTIVE To assess safety and efficacy of mammalian target of rapamycin (mTOR)

inhibition in combination with liposomal doxorubicin and bevacizumab in patients with
advanced metaplastic TNBC.

DESIGN, SETTING, AND PARTICIPANTS Phase 1 study with dose escalation and dose expansion
at the University of Texas MD Anderson Cancer Center of patients with advanced metaplastic
TNBC. Patients were enrolled from April 16, 2009, to November 4, 2014, and followed for
outcomes with a cutoff date of November 1, 2015, for data analysis.

INTERVENTIONS Liposomal doxorubicin, bevacizumab, and the mTOR inhibitors temsirolimus

or everolimus using 21-day cycles.

MAIN OUTCOMES AND MEASURES Safety and response. When available, archived tissue was
evaluated for aberrations in the PI3K pathway.

RESULTS Fifty-two women with metaplastic TNBC (median age, 58 years; range, 37-79 years)
were treated with liposomal doxorubicin, bevacizumab, and temsirolimus (DAT) (N = 39) or
liposomal doxorubicin, bevacizumab, and everolimus (DAE) (N = 13). The objective response
rate was 21% (complete response = 4 [8%]; partial response = 7 [13%]) and 10 (19%) patients
had stable disease for at least 6 months, for a clinical benefit rate of 40%. Tissue was
available for testing in 43 patients, and 32 (74%) had a PI3K pathway aberration. Presence of
PI3K pathway aberration was associated with a significant improvement in objective
response rate (31% vs 0%; P = .04) but not clinical benefit rate (44% vs 45%; P > .99).

CONCLUSIONS AND RELEVANCE Using metaplastic TNBC as a surrogate for mesenchymal

Author Affiliations: Author
TNBC, DAT and DAE had notable activity in mesenchymal TNBC. Objective response was affiliations are listed at the end of this
limited to patients with PI3K pathway aberration. A randomized trial should be performed to article.
test DAT and DAE for metaplastic TNBC, as well as nonmetaplastic, mesenchymal TNBC, Corresponding Author: Stacy L.
especially when PI3K pathway aberrations are identified. Moulder, MD, MS, The University of
Texas MD Anderson Cancer Center,
Dan L. Duncan Bldg (CPB5.3542),
1515 Holcombe Blvd, Unit 1354,
JAMA Oncol. doi:10.1001/jamaoncol.2016.5281 Houston, TX 77030 (smoulder
Published online November 23, 2016. @mdanderson.org).

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 Research Original Investigation
T
riple-negative breast cancer (TNBC) is defined as inva-
sive breast carcinoma that lacks estrogen receptor ex-
pression, progesterone receptor expression, and hu-
man epidermal growth factor receptor 2 overexpression. It is
a heterogeneous group of tumors with varying prognoses.1 Be-
cause of the lack of well-defined molecular targets, cytotoxic
chemotherapy remains the mainstay of treatment, and prog-
nosis is poor in patients whose disease is resistant to stan-
dard chemotherapy.2-4 Recently, gene expression profiling has
identified subgroups of TNBC with unique molecular aberra-
tions that may be actionable.1,5 Mesenchymal TNBC is one such
group that comprises approximately 30% of TNBCs.1,5 This sub-
group has been labeled by various investigators as claudin-
low, mesenchymal, or mesenchymal stemlike and has
been associated with a worse prognosis.1,5-9 Mesenchymal
TNBCs are enriched in epithelial-to-mesenchymal transition
(EMT) and cancer stem cell (CSC) features and contain
frequent aberrations in the phosphoinositide 3-kinase
(PI3K)/AKT/mammalian target of rapamycin (mTOR) path-
way, raising the possibility of targeting this axis for
treatment.1,5,7,8 Mesenchymal stemlike tumors are also en-
riched in genes involved in angiogenesis including VEGFR2,
EPAS1, TEK, and TIE1.5
Although Clinical Laboratory Improvement Amendment
certified diagnostic assays are under development, at this time,
the clinical identification of mesenchymal TNBC remains a
challenge, making patient selection for therapeutic trials of tar-
geted therapy difficult. Metaplastic breast cancer is a rare sub-
type of TNBC composed of a diverse group of histologic sub-
types in which epithelial and mesenchymal components are
admixed.10-16 Approximately 10% to 30% of tumors profiled
as mesenchymal TNBCs are metaplastic on the basis of mor-
phologic features identified by light microscopy.7,17 Similar to
mesenchymal TNBCs, metaplastic TNBCs are enriched in CSC
and EMT features, are chemorefractory, and carry a poor
prognosis.8,18-21 Furthermore, metaplastic TNBCs also have fre-
quent aberrations in the PI3K/AKT/mTOR pathway and promi-
nent expression of vascular endothelial growth factor (VEGF).8
As a result, metaplastic TNBC is a subset of mesenchymal TNBC
that can be recognized by light microscopy and used as a clini-
cally identifiable population to validate targeted regimens for
mesenchymal TNBC.
On the basis of these data, patients with metastatic
metaplastic breast cancer were enrolled in a phase 1 trial of
doxorubicin, bevacizumab, and temsirolimus (DAT) or lipo-
somal doxorubicin, bevacizumab, and everolimus (DAE) at
MD Anderson. Toxicity and maximum tolerated dose have
been previously reported for DAT; so herein, we report the
efficacy results for patients with metaplastic TNBC treated
with DAT or DAE.22
Methods
Patient Selection and Data Collection
A phase 1 trial with dose escalation of DAT conducted in pa-
tients with advanced solid malignant tumors at MD Anderson
has been previously reported (NCT00761644).22 Expansion
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PI3K/AKT/mTOR Pathway for Mesenchymal Triple-Negative Breast Cancer
Key Points
Question Using metaplastic breast cancer as a surrogate, is
phosphoinositide 3-kinase (PI3K) pathwaydirected therapy
effective in the treatment of mesenchymal triple-negative breast
cancer (TNBC)?
Findings In this cohort of patients with metaplastic TNBC, the
combination of liposomal doxorubicin, bevacizumab, and the
mammalian target of rapamycin inhibitors temsirolimus or
everolimus had a higher objective response rate than has
historically been seen in this chemorefractory subset of tumors.
There was a high incidence of PI3K pathway aberrations, and
patients whose tumors had pathway aberrations had a
significantly higher objective response rate compared with
patients with tumors lacking pathway aberrations.
Meaning Further investigation of PI3K pathwaydirected therapy
is warranted in the treatment of metaplastic TNBC, as well as
mesenchymal TNBC as a whole, once diagnostic assays are
available.
cohorts were undertaken in specific tumor types including
metaplastic TNBC due to an observed response signal during
dose escalation. The MD Anderson institutional review board
approved the study, and written informed consent was
obtained from all patients. Treatment was conducted at MD
Anderson. Later in the trial, the protocol was amended to allow
treatment with DAE because oral administration of everolimus
was less cumbersome compared with weekly intravenous
temsirolimus. Additional patients with metaplastic TNBC were
also treated with these regimens off study but per protocol
guidelines using a second institutional review boardapproved
protocol to observe patients for documentation of toxic effects
and response. Patients were enrolled from April 16, 2009, to
November 4, 2014, and followed for outcomes with a cutoff
date of November 1, 2015, for data analysis. Treatment was
administered on an outpatient basis with intravenous
liposomal doxorubicin and bevacizumab on the first day of
every cycle with weekly intravenous temsirolimus (DAT) or
daily oral everolimus (DAE). Each cycle was 21 days.
Herein, we report the results for 52 patients with meta-
plastic TNBC treated with DAT or DAE. The diagnosis of meta-
plastic TNBC was confirmed by pathology review at MD
Anderson. Of note, 2 patients were found to have invasive duc-
tal carcinoma on biopsy of localized disease and squamous
metaplasia on pathology review of subsequent metastatic le-
sions. These patients were considered to have metaplastic
TNBC and were included in the study. All patients who re-
ceived 1 dose of any of the study agents were considered evalu-
able for safety and efficacy. The severity of adverse events was
graded according to the Common Terminology Criteria for Ad-
verse Events, version 3.0.23 Patients with prior cumulative
doxorubicin dose more than 300 mg/m2 were excluded, and
all patients underwent close cardiac monitoring as defined in
the phase 1 study.22 Radiographic imaging studies were re-
peated after every 2 cycles (6 weeks) of therapy to assess re-
sponse using Response Evaluation Criteria in Solid Tumors.24
jamaoncology.com
 PI3K/AKT/mTOR Pathway for Mesenchymal Triple-Negative Breast Cancer
Table. Number of Patients With Metaplastic Triple-Negative
Breast Cancer Undergoing Each Type of Molecular Study
Study Patients, No.
Hot spot mutation testing 32
PTEN loss by immunohistochemistry 9
Sequencing by Foundation Medicine 23
Molecular Correlative Studies
When archived tissue was available, DNA was analyzed by a
polymerase chain reactionbased DNA sequencing method for
hot spot mutations in select genes of interest.25,26 After 2011,
mass spectrometric detection (Sequenom MassARRAY) was
used, and after 2012, a 46- or 50-gene Ampliseq Ion Torrent
Assay was used.27,28 When possible, loss of PTEN was as-
sessed using immunohistochemical analysis (Dako). Loss of
PTEN was defined as the complete absence of PTEN staining
in tumor cells. All of this molecular testing was conducted in
a Clinical Laboratory Improvement Amendmentcertified mo-
lecular diagnostic laboratory at MD Anderson. Additionally, tu-
mors from some patients underwent next-generation sequenc-
ing through Foundation Medicine (182- and 236-gene panel).
The numbers of patients who underwent various types of mo-
lecular testing are presented in the Table. Only patients who
had some form of testing for mutations in PIK3CA were in-
cluded in analyses based on mutation status.
Statistical Analysis
Descriptive summary statistics were used to assess demograph-
ic characteristics, safety, and antitumor activity. Categorical data
were summarized using frequencies and relative frequencies (ie,
proportions). Confidence intervals for proportions were com-
puted using the exact binomial method. Continuous data were
summarized by median and range. Differences in categorical vari-
ables were assessed using Fisher exact tests. Progression-free sur-
vival was estimated using the Kaplan-Meier method and com-
pared between groups using Cox proportional hazards regression
analysis. Statistical inferences were based on 2-sided tests at a
significance level of P < .05.
Results
Patient Characteristics
A total of 52 female patients with metaplastic TNBC (median
age, 58 years; range, 37-79 years) were treated with DAT (N = 39;
2 dose levels) or DAE (N = 13; 3 dose levels). Bevacizumab was
omitted in 1 patient treated with DAT due to a history of gas-
trointestinal bleeding. Baseline patient characteristics are pre-
sented in eTable 1 in the Supplement. The median number of
prior regimens for metastatic disease was 1 (range, 0-5). Most
patients had received prior anthracycline-based (39 [75%])
and/or taxane-based (42 [81%]) therapy, either in the local-
ized or metastatic setting.
Safety
Overall, therapy was well tolerated in all patients enrolled in
the phase 1 trial that established the maximum tolerated dose
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Original Investigation Research
of DAT, and toxicity was similar for DAE.22 The incidence of
grade 3 to 4 toxic effects in patients with metaplastic TNBC
treated with DAT or DAE is presented in eTable 2 in the Supple-
ment. Generally, grade 3 to 4 toxic effects were managed by
dose reductions and/or delays in treatment. One patient dis-
continued treatment with DAT due to adverse events includ-
ing grade 3 mucositis and grade 3 pancreatitis. One patient died
with pneumonia after 1 cycle of DAT, but this was not be-
lieved to be treatment related because the patient had a his-
tory of postobstructive pneumonia due to pulmonary metas-
tases. The sole patient treated with everolimus, 10 mg, had
grade 3 mucositis. Furthermore, at 1 dose level below, with
everolimus dosed at 7.5 mg daily, 1 of 9 patients experienced
grade 4 mucositis with bleeding gastric ulcers requiring hos-
pitalization and urgent transfusion of blood. No other grade 3
to 4 mucositis events were observed at this dose level. Grade
3 heart failure was seen in 1 patient treated with DAT; this pa-
tient had prior exposure to anthracyclines in both the adju-
vant and metastatic setting. Additionally, 1 patient treated with
DAE had grade 2 pulmonary toxic effects; this patient had a
history of everolimus-associated pulmonary toxic effects.
Antitumor Activity
Patients who were removed from the study before the first
scheduled restaging workup because of discontinuation of
treatment were excluded from waterfall plots of best re-
sponse. Patients who were removed from the study because
of progression in nonmeasurable or new lesions were arbi-
trarily designated as having 20% increase in tumor size on wa-
terfall plots showing best tumor response and were counted
as progression events. All responses were confirmed on at least
1 subsequent staging evaluation. The objective response rate
(ORR) was 21% (complete response [CR] = 4 [8%]; partial re-
sponse [PR] = 7 [13%]; 95% CI, 11%-35%), and 10 (19%) pa-
tients had stable disease (SD) for at least 6 months, for a clini-
cal benefit rate (CBR) of 40% (95% CI, 27%-55%). Figure 1A
displays the waterfall plot of best response for all patients with
metaplastic TNBC.
Tissue was available for testing in 43 patients and 32 (74%)
of them had PI3K pathway aberrations that were considered
to be pathway activating (Figure 2). In patients with PI3K path-
way activation, the ORR was 31% (CR = 4 [13%]; PR = 6 [19%];
95% CI, 16%-50%), and 4 patients had SD for at least 6 months,
for a CBR of 44% (95% CI, 26%-62%). One patient has had a
durable CR for more than 5 years, and this patient was found
to have a mutation in NF2. No response was seen in the 11 pa-
tients lacking PI3K pathway aberrations (ORR, 0%; 95% CI, 0%-
28%), but 5 patients had SD for at least 6 months, for a CBR of
45% (95% CI, 17%-77%). As a result, PI3K pathway activation
was associated with a significant improvement in ORR (P = .04)
but not CBR (P > .99). Figure 1B and 1C display the waterfall
plots of best response for patients with and without PI3K path-
way activation. The improvement in ORR seen in patients with
PI3K pathway activation was also associated with longer pro-
gression-free survival, but this was not significant (median, 5.1
vs 2.9 months; P = .35; hazard ratio, 0.69; 95% CI, 0.33-1.46)
(eFigure in the Supplement). Because mutation in PIK3CA was
the most common aberration seen in the PI3K pathway,
(Reprinted) JAMA Oncology Published online November 23, 2016 E3
 Research Original Investigation
Figure 1. Waterfall Plots of Best Response in Patients With Metaplastic Triple-Negative Breast Cancer (TNBC)
A Metaplastic TNBC B Metaplastic TNBC with P13K Pathway Aberration
150 150
100 100
Change in Tumor Size, %
Change in Tumor Size, %
50 50
0 0
50 + 50
100 100
52 Patients
PI3K indicates phosphoinositide 3-kinase. Dotted line indicates 30% decrease
in size of target lesions, consistent with partial response according to Response
Evaluation Criteria in Solid Tumors (RECIST), version 1.1. Asterisks indicate
patients with progression in nontarget or new lesions designated as having
responses were further assessed by their location in the heli-
cal or kinase domain of PIK3CA. Outcomes were similar if mu-
tations in PIK3CA were located in the helical or kinase do-
main (ORR, 22% vs 23%; P > .99; and CBR, 33% vs 46%; P = .67,
respectively).
Discussion
Metaplastic breast cancer is an aggressive subtype of TNBC that
has historically been refractory to standard chemotherapeu-
tic treatments.21 Although rare, metaplastic TNBCs account for
several hundred new breast cancer cases in the United States
annually, representing a therapeutic dilemma. To our knowl-
edge, we report the largest series to date of prospectively
treated patients with metastatic metaplastic TNBC. Response
rates with the DAT or DAE regimens, which target the PI3K
pathway through mTOR inhibition, were much higher than has
historically been reported with chemotherapy in metaplastic
TNBC.21 The use of anthracycline-based chemotherapy likely
enhanced the response of these regimens due to the shared
features between metaplastic TNBCs and sarcomas. In addi-
tion to DAT or DAE, various combinations of temsirolimus, be-
vacizumab, and taxane-, platinum-, or anthracycline-based
chemotherapy have been tested in patients with metaplastic
TNBC at MD Anderson.29 Six of a total of 24 patients treated
achieved response, and all of these patients were treated with
liposomal doxorubicin-containing regimens. Patients treated
with paclitaxel- and carboplatin-containing regimens did not
achieve response. Similarly, in an analysis of 100 breast can-
cer patients with biphasic metaplastic sarcomatoid carci-
noma treated at MD Anderson, patients treated with anthra-
cycline-containing regimens had a higher likelihood of being
alive and recurrence-free at 5 years compared with patients
treated with nonanthracycline-containing regimens, al-
though this difference was not significant.18 Limited statisti-
cal power precludes definitive interpretation of these data, but
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PI3K/AKT/mTOR Pathway for Mesenchymal Triple-Negative Breast Cancer
C Metaplastic TNBC without P13K Pathway Aberration
150
100
Change in Tumor Size, %
50
0
+ 50
100
32 Patients 11 Patients
20% progression. Plus sign indicates patient with a subcentimeter lesion that
was evaluable but not measurable by RECIST. This lesion decreased by a
maximum dimension of 40% with therapy and was counted as a partial
response.
they raise the hypothesis that anthracyclines are the pre-
ferred chemotherapy backbone of choice for the treatment of
metaplastic TNBC.
The DAT or DAE regimens were generally well tolerated,
with expected adverse events including mucositis, myelosup-
pression, and hand-foot syndrome. Only 1 patient discontin-
ued treatment as a result of adverse events, and most adverse
events were otherwise managed with dose reductions and/or
delays. A high incidence of grade 3 to 4 mucositis was seen with
higher doses of everolimus, suggesting that 10 mg of everoli-
mus in combination with liposomal doxorubicin and bevaci-
zumab is unlikely to be tolerated. Although 1 patient death was
observed with DAT therapy, this was not believed to be treat-
ment related. Despite prior anthracycline exposure in the ma-
jority of patients, only 1 patient treated with DAT had grade 3
congestive heart failure. Similarly, grade 2 pulmonary toxic ef-
fects with DAE therapy was only seen in 1 patient, and this
patient had a history of everolimus-associated lung toxic
effects.
In this cohort, PI3K pathway aberrations were present in
the majority of patients, suggesting an important role of this
pathway in metaplastic TNBC. More importantly, tumor re-
sponses in patients with metaplastic TNBC were limited to pa-
tients with PI3K pathway aberrations, suggesting that path-
way aberrations render metaplastic tumors susceptible to
pathway-directed therapy. Interestingly, a subset of patients
lacking PI3K pathway aberrations achieved stable disease last-
ing longer than 6 months, suggesting that even patients with
metaplastic TNBC who lack a detectable aberration may ben-
efit from PI3K pathwaydirected therapy. The possible ben-
efits of these regimens in this subgroup, however, might be ex-
plained by the fact that molecular testing for PI3K pathway
aberrations was frequently limited to hot spot testing in se-
lect genes of interest, permitting some pathway aberrations to
remain undetected. The significantly higher response rate seen
in patients with PI3K pathway aberration was associated with
longer progression-free survival. However, this was not
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 PI3K/AKT/mTOR Pathway for Mesenchymal Triple-Negative Breast Cancer Original Investigation Research

Figure 2. Spectrum of Mutations in Patients With Metaplastic Breast Cancer

A PI3K pathway aberrations

Any activating aberration

PIK3CA mutation
p.H1047R
p.E545K
p.G1007R
p.E545A
p.H1047Y
p.K111E
p.E542K
PTEN mutation
PTEN loss
AKT1 p.E17K mutation
PIK3R1 mutation
PIK3CA amplification
AKT2 amplification
NF2 p.K159fs*16 mutation

0 10 20 30 40 50 60 70 80 90 100
Percent

B Spectrum of aberrations

TP53
PIK3CA
PTEN loss (immunohistochemistry)
PTEN
HRAS
RB1
PTEN loss (Foundation Medicine)
KIT
PIK3R1 A, Incidence of phosphoinositide
MLL2 3-kinase (PI3K) pathway aberrations
MET
KDM6A
in patients with metaplastic breast
ATM cancer. Only mutations predicted to
ARID1A be pathway activating are depicted.
AKT Some tumors had more than
SMAD4 1 aberration detected. B, Spectrum of
PTPN11
PIK3CA amplification
aberrations seen in patients with
NF2 metaplastic breast cancer, detected
NF1 by means of polymerase chain
JAK2 reactionbased DNA sequencing of
FANCA hot spots in select genes of interest,
EPHB1
EGFR
next-generation sequencing through
CDH1 Foundation Medicine, and
BRCA2 immunohistochemical analysis for
BRAF PTEN loss. Mutations predicted to be
APC germline variants are excluded.
AKT2 amplification
Response for each patient is also
Complete Partial Stable Disease Stable Disease Progressive Disease depicted except one; this patient
Response Response 6 mo <6 mo died due to pneumonia after 2 cycles
Patients (n = 43) of DAT and was not evaluated for
response.

statistically significant, and larger numbers of patients are
needed to confirm this observation.
Increased signaling through the PI3K pathway has been as-
sociated with primary and secondary resistance to standard
therapy in breast cancer.31-36 However, pathway aberrations
have not consistently been associated with improved re-
sponse to pathway-directed therapy.37,38 It is interesting to note,
however, that despite the association of pathway aberrations
and response in this cohort of patients with metaplastic TNBC,
patients with mutations in PTEN did not respond to DAT or DAE
(Figure 2). In contrast, 1 patient achieved a CR that has been
durable for longer than 5 years, and this patient had a muta-
tion in NF2, which encodes a tumor suppressor that inhibits
the PI3K pathway.30 Before treatment, this patient had sev-
eral perihepatic abdominal tumor implants, with the largest
measuring 3.8 cm in longest dimension, as well as nodular pleu-
ral changes measuring 4.1 cm and subcarinal adenopathy mea-
suring 3.4 cm in longest dimension. Thus, the implication of
specific pathway aberrations in patients with metaplastic TNBC
is a subject that requires ongoing investigation.
The use of bevacizumab for the treatment of breast can-
cer is controversial as a result of the US Food and Drug Admin-
istrations ruling to withdraw the breast cancer indication in
2011; however, the drug does remain available for the treat-
ment of breast cancer in other countries. Given the design of
this phase 1 study, it is impossible to determine whether the

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 Research Original Investigation PI3K/AKT/mTOR Pathway for Mesenchymal Triple-Negative Breast Cancer

use of bevacizumab added any additional benefit to mTOR
inhibition in combination with chemotherapy. In preclinical
models, treatment with bevacizumab and subsequent intra-
tumoral hypoxia results in increased production of hypoxia-
induced factor 1. Hypoxia-induced factor 1 has been shown
to mediate enrichment of the CSC population, which is accom-
panied by increased levels of phosphorylated AKT, priming tu-
mors for treatment with PI3K pathwaydirected therapy.39-41
As such, bevacizumab may hypothetically enhance the ef-
fects of mTOR inhibition and should be further studied in ran-
domized clinical trials to determine drug benefit in appropri-
ately selected patients.
The results from this study may have further implica-
tions in the treatment of mesenchymal TNBC, a subset that ac-
counts for up to 30% of TNBCs characterized by microarray pro-
filing. Approximately 10% to 30% of tumors identified as
claudin-low or mesenchymal TNBCs by gene signature are
identified as metaplastic breast cancers using light micros-
copy. Not surprisingly, metaplastic breast cancers share mo-
lecular features with tumors characterized as claudin-low and
mesenchymal TNBCs, including EMT features, enrichment of
angiogenesis, and frequent PI3K/AKT/mTOR pathway
aberrations.5-8 Like metaplastic TNBCs, mesenchymal TNBCs
have been associated with poor response to chemotherapy and
worse outcomes compared with other subtypes, including
lower rates of pathologic complete response with standard an-
thracycline- or taxane-based chemotherapy and decreased sur-
vival, making it crucial to find novel therapeutic strategies.9
Thus, the use of metaplastic TNBC as a clinically recogniz-
able subgroup of mesenchymal TNBC to assess response to po-
tential therapies can provide insight into the treatment of mes-
enchymal TNBC, which remains identifiable only by gene
expression profiling at this time.
Limitations
This study has limitations due in most part to the rarity of meta-
plastic breast cancer. First, patients were accrued over a pro-
longed periodduring which substantial changes developed in
the technology of molecular characterization. Thus, tumors
analyzed earlier in accrual were not as extensively profiled as
those analyzed later. Second, this was not a randomized trial
and historical data regarding outcomes of standard chemo-
therapy in metastatic, metaplastic breast cancer are limited to
retrospective reviews of medical records, so it is difficult to
gauge the magnitude of impact for the targeted therapy regi-
men. As such, these limitations emphasize the need for pro-
spective randomized studies.
Conclusions
In this cohort of patients with metaplastic TNBC, the DAT or DAE
regimens were well tolerated and led to better outcomes than has
historically been seen in this chemorefractory subset of tumors.
There was a high incidence of PI3K pathway aberrations, and pa-
tients with aberrations were responsive to pathway-directed
therapy with the DAT or DAE regimens, with a subset of patients
achieving CR. These promising data warrant further investiga-
tion of PI3K pathwaydirected therapy in the treatment of meta-
plastic TNBC, as well as mesenchymal TNBC as a whole.

ARTICLE INFORMATION
Accepted for Publication: September 2, 2016.
Published Online: November 23, 2016.
doi:10.1001/jamaoncol.2016.5281
Author Affiliations: Division of Cancer Medicine,
The University of Texas MD Anderson Cancer
Center, Houston (Basho); Department of Pathology,
The University of Texas MD Anderson Cancer
Center, Houston (Gilcrease, Albarracin); Breast
Medical Oncology, The University of Texas MD
Anderson Cancer Center, Houston (Murthy, Valero,
Litton, Chavez-MacGregor, Ibrahim, Murray, Koenig,
Moulder); Investigational Cancer Therapeutics
(Phase I Trials Program), The University of Texas MD
Anderson Cancer Center, Houston (Helgason, Karp,
Meric-Bernstam, Hong, Subbiah, Kurzrock, Janku,
Moulder); Sheikh Khalifa Bin Zayed Al Nahyan
Institute for Personalized Cancer Therapy, The
University of Texas MD Anderson Cancer Center,
Houston (Meric-Bernstam); Breast Surgical
Oncology, The University of Texas MD Anderson
Cancer Center, Houston (Meric-Bernstam);
Biostatistics, The University of Texas MD Anderson
Cancer Center, Houston (Hess); Pediatrics, The
University of Texas MD Anderson Cancer Center,
Houston (Herbrich); Health Services Research, The
University of Texas MD Anderson Cancer Center,
Houston (Chavez-MacGregor); Division of
Hematology and Oncology, University of California
San Diego Moores Cancer Center, La Jolla
(Kurzrock).
Author Contributions: Drs Basho and Moulder had
full access to all the data in the study and take
responsibility for the integrity of the data and the
accuracy of the data analysis. Drs Janku and
Moulder contributed equally to this work.
Study concept and design: Kurzrock, Janku,
Moulder.
Acquisition, analysis, or interpretation of data: All
authors.
Drafting of the manuscript: Basho, Valero, Chavez-
MacGregor, Janku, Moulder.
Critical revision of the manuscript for important
intellectual content: All authors.
Statistical analysis: Helgason, Hess, Herbrich,
Chavez-MacGregor, Janku, Moulder.
Obtained funding: Janku.
Administrative, technical, or material support:
Helgason, Karp, Meric-Bernstam, Valero, Subbiah,
Kurzrock, Janku, Moulder.
Conflict of Interest Disclosures: Dr Moulder has
received consulting fees from Novartis. No other
disclosures are reported.
Previous Presentations: This work was presented
at the European Cancer Congress; Vienna, Austria;
September 25, 2015; the San Antonio Breast Cancer
Symposium; December 10, 2015; San Antonio,
Texas; and the American Association for Cancer
Research Annual Meeting; April 18, 2016;
New Orleans, Louisiana.
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