Article

Human Plasma Metabolomics for Biomarker Discovery:

Targeting the Molecular Subtypes in Breast Cancer
Leticia Díaz-Beltrán 1,† , Carmen González-Olmedo 1,† , Natalia Luque-Caro 1, Caridad Díaz 2,* ,
Ariadna Martín-Blázquez 2, Mónica Fernández-Navarro 1, Ana Laura Ortega-Granados 1,
Fernando Gálvez-Montosa 1, Francisca Vicente 2 , José Pérez del Palacio 2 and Pedro Sánchez-Rovira 1,*
[email protected] (N.L.-C.); [email protected] (M.F.-N.);
[email protected] (A.L.O.-G.); [email protected] (F.G.-
M.)
2
Citation: Díaz-Beltrán, L.; Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía,
González-Olmedo, C.; Luque-Caro, 18016 Granada, Andalucía, Spain; [email protected] (A.M.-B.);
[email protected] (F.V.); [email protected] (J.P.d.P.)
N.; Díaz, C.; Martín-Blázquez, A.;
* Correspondence: [email protected] (C.D.); pedro.sanchez.rovira.sspa@juntadeandalucía.es
Fernández-Navarro, M.;
or [email protected] (P.S.-R.); Tel.: +34-958-993-965 (C.D.); +34-953-220-306 (P.S.-R.) † These
Ortega-Granados, A.L.;
authors contributed equally to this work.
Gálvez-Montosa, F.; Vicente, F.;
Pérez del Palacio, J.; et al. Human
Plasma Metabolomics for Biomarker Simple Summary: Breast cancer is the leading cause of female cancer-related deaths worldwide.
Discovery: Targeting the Molecular New technologies with enhanced sensitivity and specificity for early diagnosis and tailored
Subtypes in Breast Cancer. Cancers monitoring are in critical demand. Thus, metabolomics appears to be a growing tool in order to
2021, 13, 147. https://doi.org/
detect molecular differences between distinct groups. In this case, an untargeted analytical
10.3390/cancers13010147
approach was used to identify metabolomics differences between molecular subtypes of breast
cancer in comparison with healthy matched controls. Footprints for each breast cancer subtype
Received: 7 December 2020
provided diagnostic capacities with an area under the receiver-operating characteristic curve
Accepted: 31 December 2020
above 0.85, which suggests that our results may represent a major advance towards the
Published: 5 January 2021
improvement of personalized medicine and precise targeted therapies for the various breast
cancer phenotypes. To validate these molecular profiling as potential therapeutic strategies for the
different breast cancer subtypes, further analysis and larger cohorts would be necessary in the
Publisher’s Note: MDPI stays neutral
near future.
with regard to jurisdictional claims
in published maps and institutional
affiliations. Abstract: Purpose: The aim of this study is to identify differential metabolomic signatures in
plasma samples of distinct subtypes of breast cancer patients that could be used in clinical practice
as diagnostic biomarkers for these molecular phenotypes and to provide a more individualized and
accurate therapeutic procedure. Methods: Untargeted LC-HRMS metabolomics approach in
Copyright: © 2021 by the authors.
positive and negative electrospray ionization mode was used to analyze plasma samples from LA,
Licensee MDPI, Basel, Switzerland.
LB, HER2+ and TN breast cancer patients and healthy controls in order to determine specific
This article is an open access article
metabolomic profiles through univariate and multivariate statistical data analysis. Results: We
distributed under the terms and
tentatively identified altered metabolites displaying concentration variations among the four
conditions of the Creative Commons breast cancer molecular subtypes. We found a biomarker panel of 5 candidates in LA, 7 in LB, 5 in
Attribution (CC BY) license (https:// HER2 and 3 in TN that were able to discriminate each breast cancer subtype with a false discovery
creativecommons.org/licenses/by/ range corrected p-value < 0.05 and a fold-change cutoff value > 1.3. The model clinical value was
4.0/). evaluated with the AUROC, providing diagnostic capacities above 0.85. Conclusion: Our study
1
Medical Oncology Unit, identifies metabolic profiling differences in molecular phenotypes of breast cancer. This may
University Hospital of Jaén, represent a key step towards therapy improvement in personalized medicine and prioritization of
23007 Jaén, Andalucía,
tailored therapeutic intervention strategies.
Spain;
leticia.diaz@juntadeandalu
cia.es (L.D.-B.); Keywords: human plasma metabolomics; breast cancer; molecular subtypes; metabolic profiling;
[email protected] personalized medicine
(C.G.-O.);

Cancers 2021, 13, 147. https://doi.org/10.3390/cancers13010147 https://www.mdpi.com/journal/cancers

1. Introduction
Breast cancer (BC) is currently the most common malignancy in women, both in
developed and less developed countries, and the leading cause of cancer-related
deaths among women worldwide, with a high incidence rate [1,2]. Every breast cancer
Cancers 2021, 13, 147 2 of 19
subtype is characterized by intrinsic molecular features and metastatic lesions, and

their natural heterogeneity leads to a high diversity in prognosis and clinical responses
to available medical treatments, even for patients with similar diagnosis, histology and
stage of disease [3–9].
Therefore, determining the molecular subtypes of breast cancer becomes crucial
for personalized treatment. In fact, there is evidence reporting that patients receiving
molecular-matched therapy have an increased overall response rate, longer period of
time to treatment failure and a longer survival rate in comparison to patients with
non-matched therapy [3,9]. Successive biopsy procedures and subsequent
histopathological analysis are normally used to study molecular and genetic
information from tumor cells in order to diagnose and classify BC into a subtype. This
analytical technique is invasive and time consuming [3]. Thus, non-invasive, fast,
sensible and precise analytical methods for distinction of different BC subtypes are in
critical demand [10,11].
In this sense, metabolomics has quickly arisen as a novel approach in the cancer
biomarker field to overcome the current limitations of standard diagnostic techniques
[12]. This expanding research area provides a dynamic portrait of an individual overall
metabolic status, assessing the final products of the myriad of intrinsic molecular
processes and intercellular pathways that may be altered in response to genetic,
pathological and/or environmental factors [3,13]. Hence, the end products of the
diverse biological processes known as metabolites can be analyzed from high-
throughput screening technologies such as nuclear magnetic resonance (NMR) and
mass spectrometry (MS) enabling the discovery of altered pathways that may give us
new insights into dysregulated metabolism in tumor development and progression.
Therefore, the altered metabolites reflecting these pathophysiological changes might
be considered as potential new therapeutic targets for breast cancer diagnosis,
prognosis, early recurrence and drug efficacy [14–16].
Several studies have already been conducted to explore the possibility of using
metabolite panels as biomarkers for early diagnosis, tumor characterization and
clinical outcome prediction [3,14–20]. Human body fluids such as saliva, urine, serum
and plasma have been re-discovered as a great source of potential biological markers,
and hence analyzed in the search of a metabolic profile that may be representative of
systemic metabolic dysregulation in breast cancer patients [19–23]. However, up to
today, efforts on proving highly accurate markers or proven targets for tailored
therapeutic treatments have not yet delivered the expected results [24–28] due to the
high heterogeneity displayed by breast cancer, from histology to prognosis, early
recurrence, risk of metastatic progression or response to treatment and survival rates
[29].
With this aim in view, we explore whether metabolomics is able to provide an
accurate pathological diagnosis, phenotypic classification and a tailored follow-up of
individuals with this malignancy. A high-throughput untargeted metabolic approach
was used to identify the capacity of different metabolic profiles to predict various BC
subtypes. Based on a liquid chromatography-mass spectrometry (HPLC/Q-TOF 5600)
platform-based metabolomics study, we propose and test the notion that a
differential metabolic signature representative of the distinct breast cancer subtypes
exists, and it can be ultimately detected in plasma of individuals with this disease.

2. Results
2.1. Patients’ Characteristics
To avoid the effect of potential confounding variables like age and Body Mass
Index (BMI), the homogeneity of BC group and its corresponding HC subjects was
evaluated. Normality’s distribution was checked with a Shapiro-Wilk normality test
and the equality of variances of both study groups was studied with the Levene´s test
when corresponded.
Finally, the appropriated t test was applied without significant differences observed in
any case.

2.2. LC-HRMS Analysis

Cancers 2021, 13, 147 3 of 19
Four different liquid chromatography-high resolution mass spectrometry (LC-

HRMS) analyses were carried out for each ionization mode, in order to determine the
molecular differences between the major subtypes of breast cancer (luminal A (LA),
luminal B (LB), triple negative (TN) and human growth factor receptor 2 positive
(HER2) and the healthy control (HC) groups. The reverse phase (RP) column is
recommended for the separation of medium-polar metabolites (such as
phospholipids, lysophospholipids or steroids) and non-polar metabolites. Total ion
chromatograms (TICs) in positive electrospray ionization mode (ESI+) are shown in
Figure 1, where clear differences are observed between BC subtypes and HC groups
corresponding to the most significant discriminatory features detected: very polar
metabolites eluted in the first 3 min (Figure 1a,c); medium-polar metabolites were
found to elute from 8.5 to 12.5 min (Figure 1a,b,d); non-polar metabolites were not
found in our work to be discriminatory after all the statistical analysis.

Figure 1. Representative RPLC-ESI+-HRMS TICs of a LA_BC (light blue) (a), HER2_BC (orange) (b), TN_BC (yellow) (c) and
LB_BC (pink) (d) sample compared to a HC sample (green). Remarkable differences were observed between BC and HC
samples.

2.3. Chemometric Analysis

Different data matrices were obtained depending on the ionization mode and
the set of BC molecular subtype analyzed. Retention time (RT) windows and mass
tolerances were determined for each analyzed set based on the data of selected
chromatographic peaks. After monoisotopic selection, contaminants were removed
based on the organic solvent (OS) filtration and several features presented in the
quality control (QC) samples were excluded for unacceptable variability (relative
standard deviation > 30%). Remaining variables were evaluated by multivariate
statistical analysis (Table S1). The close clustering of the QC samples in Figure 2
indicates that the separation observed between the corresponding study groups was
mainly due to biological reasons in ESI −. The authors found that PC1 and PC2
explained 54.6%, 47.9%, 40.5% and 39% of the total of variance in LA, HER2, TN,
LB in the ESI− mode analysis, respectively. The variance obtained with PC1 and PC2
was 42.5%, 40.5%, 44.8% and 43% in LA, HER2, TN, LB in the ESI+ mode analysis,
respectively. Unsupervised principal component analysis (PCA) score plots obtained by
ESI+ are shown in Figure S1. Score plots of the partial least squares-discriminant
analysis (PLS-DA) models illustrated a marked separation between the HC group and
Cancers 2021, 13, 147 4 of 19
BC molecular subtypes by both ESI modes (Figure 3 and Figure S2); the “goodness” of

the PLS-DA model, measured by R 2 and Q2, showed that no over-fitting was observed
and, consequently, these models are acknowledged for successful discernment
between HC patients and the LA, LB, TN and HER2 BC molecular subtypes [30] (Table
S1). Signals with false discovery range (FDR) corrected p-values < 0.05 were selected
as altered metabolites; those with a fold-change (FC) value of at least 1.3 between the
study groups were selected as potential biomarkers (BM) to identify.

Figure 2. 2D score plots of the unsupervised PCA of HC group (green) and LA_BC (light blue) (a), HER2_BC (orange) (b),
TN_BC (yellow) (c) and LB_BC (pink) (d) patients by ESI− showed that the separation observed between the groups was due
to biological reasons according to the close clustering of the QC samples (dark blue).
Cancers 2021, 13, 147 5 of 19

Figure 3. 2D score plots of the supervised PLS-DA of HC group (green) and LA_BC (light blue) (a), HER2_BC (orange) (b),
TN_BC (yellow) (c) and LB_BC (pink) (d) patients by ESI−determined a notably separation between BC molecular subtypes
and matched controls.

2.4. Differential Metabolomic Profiling

A tentative identification of the final candidates was achieved as it was
previously reported by the Schymansky classification. All identified metabolites were
classified at level 1 and 2, therefore, their identities or probable structures are
confirmed [31,32]. Hence, 5 metabolites were defined for the LA phenotype, 7 for LB,
5 for HER2 and 3 for TN (Table 1). The rest of metabolites (Table S2) met the criteria
established for potential biomarkers of BC, although they could not be identified due
to their MS/MS pattern, which did not match any of the queries of the compound
databases searched (Metlin, Human Metabolome Database, Lipid Maps, PubChem,
MassBank and NIST) or commercial standards used. This is likely to happen since the
major part of the identity queries belonged to a similar molecular family whose virtual
MS/MS spectra differences needed to be clarified, or because some of the signals
have not been discovered yet.
Cancers 2021, 13, 147

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Table 1. Differential identified metabolites of molecular subtypes in BC.

BC Tentative ID m/z RT Mass Error (ppm) p (FDR) FC * (BC/HC) Adduct Molecular
Molecular Formula
Subtype
ESI+
LysoPE(18:2) 478.291 11.34 −2.5 1.670 × 0.6008 [M+ C23H44NO
LysoPE(18:1(11Z/9Z)) 6 12.15 4.8 10−8 0.6303 H] 7P
LysoPE(18:1(11Z/9Z)) 480.310 12.47 −2.5 5.365 × 0.4713 [M+ C23H46NO
8 10−3 H] 7P
480.307 9.058 × [M+H] C23H46NO
3 7P
LB 10−10
LysoPC(20:3) 546.353 12.16 −2.7 2.214 × 0.7303 [M+H] C28H52NO
9 10−2 7P
Biliverdin 583.256 8.95 2.6 7.390 × 1.5681 [M+H] C33H34N4
6 10−9 O6
1 188.070 3.73 0.5 2.503 × 0.6362 [M+H-NH3] C11H12N2
7 10−2 O2
LysoPC(14:0) 468.308 9.66 −0.2 3.745 × 0.5849 [M+H] C22H46NO
4 10−2 7P
LysoPE(18:1(11Z)/9Z) 480.310 12.31 6.192 × 0.6407 [M+H] C23H46NO
9 10−3 7P

LysoPC(0:0/16:0) 496.341 11.71 2.6 6.396 × 0.6701 [M+H] C24H50NO

1 10−6 7P
Biliverdin 583.252 8.65 −4.5 2.0621 1.6265579 [M+H] C33H34N4
5 × 10−6 O6
L-Tryptophan 1 188.070 3.4 2.1 4.153 × 0.625911 [M+H-NH3] C11H12N2
TN
LysoPC(16:0/0:0) 2 10.07 1.3 10−2 0.5289669 [M+Na] O2
518.322 0.03043 C24H50NO
4 7P
452.279 ESI− C21H44NO
LB LysoPE(16:0) 6 5.71 2.9 0.5342 [M-H-H2O] 7P
Cancers 2021, 13, 147

5.427 ×
10−14
LysoPE(18:2) 476.280 5.59 4.4 1.304 × 0.5498 [M-H] C23H44NO
4 10−8 7P
L-Tryptophan 2 203.082 1.27 −1 1.637 × 0.6543 [M-H] C11H12N2
Glycoursodeoxych 4
3.24 −0.4 10−2 0.5646 [M-H]
O2
olic acid 3 448.306 C18H34O
2.861 ×
6 4
LA 10−2
LysoPE(18:2) 476.276 5 −3.6 3.489 × 0.6711 [M-H] C23H44NO
6 10−2 7P
L-Tryptophan 2 203.083 1 4.9 7.536 × 0.67 [M-H] C11H12N2
HE LysoPE(18:2) 6 5. 7.8 10−5 44 [M+K-2H] O2
R2 514.238 5 3.403 × 0.64 C23H44NO
1 10−4 08 7P
TN LysoPE(18:1(11Z)/9Z) 957.597 5.86 2.6 0.02790 0.4407772 [2M-H] C23H46NO
6 8 7P
Features statistically significant (FDR < 0.05 and FC > 1.3) with a tentative identification based on their accurate mass (m/z), MS/MS pattern or comparison with commercial standards 1,2,3, were selected to create the proposed
multivariate model. * Fold change (FC) expressed as the ratio of two averages (BC/HC); BC varies depending on the molecular subtype. BC: breast cancer; HC: healthy control; LA: luminal A; LB: luminal B; HER2: overexpressing
human epidermal growth factor 2; TN: triple negative.
Cancers 2021, 13, 147 8 of 19

Thus, RT and MS/MS spectra of L-Tryptophan and Glycoursodeoxycholic acid

(GUDCA) could be compared with their commercial standards under the same analytical
conditions (Figure 4a,b and Figure S3). The experimental pattern of these metabolites matched
with their standards so that the tentative identity could be confirmed.

Figure 4. Characteristic MS/MS spectra of m/z 188.0707 in a biological sample (green) (a.1) and the L-Tryptophan standard at 3.73
min in ESI + (blue) (a.2) and m/z 203.0824 at 1.27 min in a biological sample (green) (b.1) and the L-Tryptophan standard in ESI −
(blue) (b.2). MS/MS spectra revealed the characteristic fragmentation pattern of L-Tryptophan both in ESI+ and ESI −.
Cancers 2021, 13, 147 9 of 19

2.5. Biomarker Evaluation and Model Creation

The diagnostic ability of the final tentatively identified candidates was evaluated with a
multivariate receiver-operating characteristic (ROC) analysis. In this regard, we applied a PLS-DA
model to combine our set of biomarkers to obtain the area under curve (AUC), which is a
measure of how well a parameter can distinguish between two diagnostic groups. The AUC
values obtained for each set of metabolites (Table 1) to discriminate between healthy patients
and subtypes of breast cancer were 0.870, 0.919, 0.961 and 0.954 in LA, HER2+, TN and LB
respectively. The performance of this biomarker model was evaluated using a balanced Monte
Carlo cross-validation procedure. Although the model might improve when adding more of the
potential biomarkers proposed in our work (Table S2), these features did not have a reliable
structure ID since they could be only identified by their m/z and RT. Therefore, we preferred to
use those metabolites based on the FDR corrected p value < 0.05, FC value > 1.3 and a tentative
identification with a level classification of 1 or 2 by Schymansky (Table 1). The outcomes
obtained for diagnostic potential of the selected biomarkers are summarized in Figure 5 and
Table 2.

Figure 5. ROC curves for combined biomarkers model in LA_BC (a), HER2_BC (b), TN_BC (c) and LB_BC (d) by ESI+ and ESI−; 100 cross-
validations were performed, and the results were averaged to generate the plot.

MetaboAnalyst 4.0 Web Server software (Wishart Research Group at the University of
Alberta, Alberta, Canada) provided an average of predicted class probabilities of each sample in
the 100 cross-validations. Confusion matrix in LA_BC revealed 14 BC and 16 HC samples correctly
classified. Concurrently, 26 HER2_BC samples were correctly classified, whereas 28 samples
were correctly distributed in the HC group. In TN_BC samples 13 BC and 11 HC samples were
Cancers 2021, 13, 147 10 of 19

correctly classified; while 50 BC and 54 HC samples were properly assigned in LB_BC molecular
subtype.

Table 2. AUC scores of selected biomarkers (BM) for the proposed models and confusion matrices of the BC
subtypes.
BC Molecular Subtype BM AUC 95% CI Confusion Matrix
BC HC
LA 5 0.87 0.651–0.992 14/20 16/21
HER2 5 0.919 0.819–0.985 26/31 28/34
TN 3 0.961 0.8–1 13/15 14/15
LB 7 0.954 0.886–0.995 50/56 54/62
2.6. Pathway Analysis
We have found a set of biomarkers, which were able to discriminate each breast cancer
subtype significantly. These first funding to distinguish at molecular level using untargeted
metabolomics may improve the treatment of breast cancer and move towards to the priority of
personalized medicine and customized therapeutic intervention strategies.
According to the deregulated metabolites tentatively identified in each BC molecular
subtype by ESI+ and ESI−, we determined the major altered pathways implicated in the four
different subtypes. The outcomes were obtained by analyzing results in ESI+ and ESI −,
differentiating by phenotypes. Thus, pathway analysis revealed that porphyrin and chlorophyll
metabolism, glycerophospholipid metabolism, tryptophan metabolism and aminoacyl-tRNA
biosynthesis appeared to be altered (Table S3). Statistically significant pathways (p < 0.05) are
shown in Table 3.

Table 3. Altered pathways associated with BC molecular subtypes by ESI+ and ESI −.
Altered Pathways BC Molecular Subtype p-Value
Porphyrin and chlorophyll metabolism LB and HER2 0.038347
Glycerophospholipid metabolism LA, LB, TN and HER2 0.045927
Pathway Analysis using MetaboAnalyst 4.0 Web Server software revealed two statistically
significant dysregulated pathways (p value < 0.05) in breast cancer molecular subtypes.

3. Discussion
The advent of the –omics techniques is substantially accelerating predictive, preventing
and personalized medicine. Next-generation sequencing (NGS), genomics and transcriptomics
provide a better understanding of the genomic architecture of cancer and allow the discovery of
differentially expressed genes that drive and maintain tumorigenesis. Genomic profiling has
yielded potential biomarkers clinically relevant for early diagnosis of breast cancer, but these
analytical platforms have some disadvantages, like shorter read lengths that challenges genome
alignment and assemble, how to navigate through mega-datasets and, additionally, their cost is
still high in comparison with other techniques. In contrast with the gene panels discovered by
other techniques, metabolites are closer to the phenotype of the organism than genes and
proteins, so the metabolome can be a point of convergence for genetic variation influencing
complex traits, and can efficiently elucidate the mechanisms underlying phenotypic variation.
Thus, metabolomics profiling is considered as a relatively more rapid, accurate and non-invasive
method to discover diagnostic and prognostic biomarkers. In this work, we applied an
untargeted high-throughput metabolomics approach to compare the plasma metabolic profiling
changes associated with the distinct BC molecular subtypes (LA, LB, TN and HER2) versus healthy
controls. By using RPLC-HRMS in ESI+ and ESI − modes, we were able to detect statistically
significant differences in certain metabolites with high diagnostic capacity in the four different
BC phenotypes, which are involved in relevant biological cancer-related pathways such as:
Cancers 2021, 13, 147 11 of 19

glycerophospholipid metabolism, porphyrin and chlorophyll metabolism, tryptophan

metabolism and aminoacyl-tRNA biosynthesis.
Otto Warbug described in great detail how cancer cells increase their glucose consumption
as a fuel source to support the anabolic processes that promote their uncontrolled proliferation.
Not only have Warburg’s findings been confirmed, but other catabolic pathways have
demonstrated their fundamental role in cancer progression [33,34]. Our findings go in
accordance with the essential necessity of upregulating the energy supply in breast cancer cell
growth and proliferation. Interestingly, a significant decreased concentration of L-Tryptophan
(Trp) was observed in plasma of LA, TN and HER2 molecular subtypes of BC in comparison with
healthy controls (FDR corrected p value < 0.05, FC < 0.6). Decreased tryptophan in plasma and
serum of BC patients has also been reported in several studies [35–38]. Although the role of Trp
catabolism in tumor proliferation is still unclear, it has been discovered to indirectly promote the
degradation of the extracellular matrix and invasion on cancer cells [39]. Two main enzymes
catalyze tryptophan into metabolites of the kynurenine (Kyn) pathway: tryptophan-degrading
dioxygenases indoleamine-2,3dioxygenase (IDO1) and tryptophan-2,3-dioxygenase (TDO2)
[40,41]. Kyn activates the aryl hydrocarbon receptor (AhR) which contributes to cancer immune
escape since it promotes an immunosuppressive tumor microenvironment by an increase of IL-
10, Treg cells and suppressing immune activation cells [42]. Therefore, in cancer with an
overexpression of IDO1/TDO2, increased Trp catabolism could lead to the depletion of its serum
concentration and the accumulation of Kyn metabolites, which enhanced cancer scenario [43–
46]. Nevertheless, up to date there are no IDO1/TDO2 inhibitors currently approved by the US
Food and Drug Administration. The most recent clinical trial publishing the effect of an
IDO1/TDO2 inhibitor, Indoximod (D-1MT/NLG-8189), did not show a clinical benefit in metastatic
BC patients when combined with taxane chemotherapy [47]. In fact, a lot more research is
needed in order to warrant the efficacy of these inhibitors in clinical practice [48].
The reprogramming of lipid metabolism is a hallmark of many cancers, including breast
cancer. Several lipoids were identified to be differentially altered in LA, LB, TN and HER2
molecular subtypes when comparing with healthy controls, which emphasize the importance of
investigating the lipid metabolism differences in breast cancer. Phospholipids are a main
component of cell membranes, they play a major role in cell signaling and cycle regulation and
are a source of fatty acids (FA) which oxidative metabolism and ATP production is critical, not
only in normal cells but also in cancer function [49]. In particular, a decreased plasma
concentration of phosphoethanolamines (LysoPE (16:0), (18:1), (18:2) FDR < 0.05 and fold
change < 0.6) and phosphocholines (LysoPC (14:0), (16:0), (20:3) FDR < 0.05 and fold change <
0.7) was observed. Our findings are in line with the already suggested distinction in membrane
dynamics across molecular subtypes of breast cancer, where the acyl-chain constituents of PC
and PE is remodeled by the action of phospholipases and lysohpospholipid acyltransferases with
the delivery of fatty acid molecules for structural, signaling, and energy-producing purposes of
breast cancer cells [50]. However, in accordance with other studies, breast cancer cells adapt to
metabolic stress under given experimental conditions (glutamine deprivation or serum
deficiency), by changing PE and DAG homeostasis. In both cases, an accumulation of
phosphoethanolamine (PEtn) was observed in breast cancer cells with reduced expression of
PCYT2, suggesting tumor progression in response to glutamine deprivation [51,52]. Moreover, in
conformity with a recent prospective study where 1624 first primary incident invasive breast
cancer cases were compared by their molecular phenotypes with 1624 matched controls, a
phosphatidylcholine (LysoPC (20:3)) was found to have a negative association with risk of breast
cancer as we found in our analysis [53]. These biomarkers might open the possibility of
identifying an early poor prognosis as well as detecting residual disease after neoadjuvant
treatment (NAT).
Furthermore, only two non-related metabolites were found to be differently expressed
under our experimental conditions in luminal A, luminal B and HER2 molecular subtypes:
biliverdin and glycoursodeoxycholic acid. High levels of biliverdin (FDR < 0.05 and FC > 1.5) were
Cancers 2021, 13, 147 12 of 19

detected in plasma of luminal B and HER2 cancer patients. Although both biliverdin (BV) and its
catabolite bilirubin (BR) are non-toxic molecules that, under most conditions, act as anti-oxidants
by scavenging or neutralizing reactive oxygen species (ROS) [54], they are also endogenous
activators of aromatic hydrocarbon receptors [aryl hydrocarbon receptor (AhR)] [55]. So, the
increment of BV in plasma of LB and HER2 cancer patients would suggest its implication in
signaling and gene expression related to cell growth and cancer progression either by its
increased plasma concentration, an up-regulation of the heme oxygenase-1 (HO-1) or a
dysregulation of its catabolic enzyme biliverdin reductase (BLVR-A or BLVR-B) [56–58].
Moreover, not many studies have had an impact on our understanding on how the bile acid
pattern differs in BC subtypes until now. Although an influence of bile acids on the development
of breast cancer cells and the estrogen receptor function had been suggested [59], both pro and
anti-proliferative effects of bile acids in different breast cancer cell models have been
determined. Plasma deoxycholic acid (DA) concentrations were found to be higher in breast
cancer patients than in controls without considering the BC molecular differences [60], while
deoxycholate (DC) inhibited human luminal A breast cancer cell lines proliferation and
glycochenodeoxycholate (GCDC) enhanced patient survival in another study [61]. In this aspect,
our results show low levels of GUDCA in plasma of 21 luminal A cancer patients when compared
with 21 healthy controls (FDR < 0.05 and FC < 0.06), which makes it interesting for further study
in order to clarify its function in breast cancer development.
Finally, this study demonstrated that the four major BC subtypes could be discriminated
using an untargeted metabolomics approach. Precise classification of these phenotypes has
important implications in breast cancer personalized treatment, tailored follow up and detection
of early recurrence.

4. Materials and Methods

4.1. Participants and Ethics
A total of 131 breast cancer patients and 134 healthy control subjects were recruited over
12 months at the Medical Oncology Unit of the University Hospital of Jaén (Spain). The study
was approved by the Institutional Review Board of the Clinical Research Ethics Committee of
Jaén and all clinical investigations were conducted under the Helsinki Declaration guidelines and
the International Conference on Harmonization-Good Clinical
Practices (ICH-GCP) guidelines. Every patient provided written informed consent for
participation prior to blood sample extraction. The patient selection protocol was set as follows:
female subjects being at least 18 years old with histological confirmation of BC, no detectable
macro metastases and no previous anticancer treatment. Demographic details and clinical
diagnosis of studied subjects are summarized in Table 4. The cancer stage was classified
according to the 2002 Tumor Nodes Metastasis (TNM) system. Particularly, those BC patients
diagnosed with HER2- and ER+ with Ki67 > 20% were defined as luminal B group and patients
diagnosed with HER2- and ER+ with Ki67 < 20% were categorized as luminal A. As for non-
luminal subtypes, all BC patients who neither expressed hormone receptors (PR-, ER-) nor
overexpressed human epidermal growth factor 2 (HER2-) were considered as triple negative
breast cancer patients; and finally, patients overexpressing human epidermal growth factor 2
were diagnosed as HER2+ breast cancer patients.

4.2. Plasma Sample Preparation

Samples were collected in EDTA tubes after at least 8 h fasting using standard venipuncture
procedures. Blood was then centrifuged at 1400 × g for 10 min at 4 ◦C and the supernatant was
carefully aspirated and transferred into new vials, and immediately stored at −80 ◦C until the
analysis.
Cancers 2021, 13, 147

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Table 4. Demographic and clinical characteristics of breast cancer patients and healthy control subjects.
Characteristics LB HC LA HC TN HC HER2 HC
Subjects 61 64 21 21 15 15 34 34
Age (Range) 49 (27–75) 50 (42–56) 50 (32–81) 49 (34–60) 49 (29–71) 51 (26–63) 51 (33–70) 49 (28–62)
− 25.63 (16.9–40.5) 25.35 (19.8–30.0) 24.90 (20.0–37.2) 25.00 (18.0–28.3) 27.60 (21.60–41.23) 26.5 (21.3–30.0) 26.10 (21.0–33.3) 25.30 (20.80–29.80)
BMI (Kg·m 2)
HER2 Negative - Negative - Negative - Positive -
PR Neg/Pos - Neg/Pos - Negative - Neg/Pos -
ER Positive - Positive - Negative - Neg/Pos -
Ki67 >20% - <20% - - - - -
TNM-stage IA 0 - 1 - 0 - 1 -
TNM-stage IIA 26 - 10 - 9 - 9 -
TNM-stage IIIA 12 - 0 - 0 - 3 -
TNM-stage IIB 19 - 9 - 3 - 19 -
TNM-stage IIIB 2 - 1 - 2 - 1 -
TNM-stage IC 2 - 0 - 1 - 1 -
HC and BC patients were matched in terms of age and BMI. BC: breast cancer; LB: luminal B; HC: healthy control; LA: luminal A; TN: triple negative; HER2: human epidermal growth factor receptor 2 positive; BMI: body mass index;
PR: progesterone receptor; ER: estrogen receptor; TNM: tumor nodes metastasis.
Cancers 2021, 13, 147 14 of 19

4.3. Metabolite Extraction

An aliquot of 600 µL of acetonitrile (AcN) was added to 75 µL of plasma and the mixture
was shaken for 2 min. Then, samples were centrifuged at 15,200 × g for 10 min at 4 ◦C. The
supernatant was collected in HPLC analytical vials. After that, it was evaporated in a GeneVac
HT-8 evaporator (Savant, Holbrook, NY, USA) and kept frozen at −80 ◦C till the analysis. Finally,
dry residues were reconstituted in 210 µL of water:AcN (50:50) with 0.1% formic acid and 250
ppb of L-leucine (1–13C, 99%), Roxithromycin, Caffeine-d3, Creatine (methyl-d3) monohydrate,
L-abrine (methyl-d3) monohydrate and Bisphenol A-d16 as internal standards.

4.4. LC-HRMS Analysis

Samples were analyzed using an Agilent 1290 LC system (Agilent Technologies, Santa Clara,
CA, USA) coupled to a quadrupole-time-of-flight 5600 mass spectrometer (AB SCIEX
Q-TOF 5600, Concord, ON, Canada) in positive and negative electrospray ionization modes
(ESI+, ESI−). A high performance liquid chromatography (HPLC) mode separation in
ESI+ was carried out using an Atlantis T3 HPLC C18 column (2.1 mm × 150 mm, 3 µm; Waters
Corporation, Milford, MA, USA) kept at 25 ◦C. Organic Solvent (OS) consisted of water:AcN
(90:10) with 0.1% formic acid (eluent A) and AcN:water (90:10) with 0.1% formic acid (eluent B).
The column was eluted with the following gradient: 0–0.5 min 1% eluent B; 0.5–11 min 99%
eluent B; 11–15.50 min 99% eluent B; 15.50–15.60 min 1% eluent B and 15.60–20 min 1% eluent
B. The elution flow rate was set at 300 µL/min [62]. Then, chromatographic separation was
performed using a Gemini HPLC C18 column (100 mm × 2 mm, 3 µm; Phenomenex, CA, USA)
kept at 25 ◦C in ESI− mode. The flow rate was 300 µL/min with mobile phases A (90% water: 10%
AcN) and B (10% water: 90% AcN), both containing 0.1% ammonia at 20%. The gradient
consisted of 0–0.3 min 1% eluent B; 0.3–7.3 min 99% eluent B, 7.3–10.3 min 99% eluent B and
10.3–13.3 min 1% eluent B. The TOF method operated with the Q-TOF 5600 allowed mass
selection (80–1600 Da) with high resolution, in combination with an information dependent
acquisition (IDA) method, which enabled the fragmentation of the eight most intense ions, to
collect full-scan HRMS and MS/MS information simultaneously.
The exact mass calibration was automatically performed for every 10 injections of 5 µL of
randomly injected plasma samples. Organic solvent samples were analyzed along the sequence
for every 30 injections; quality control samples were analyzed for every 10 injections. The
analysis of OS samples provided high impurity identification on either organic solvents or
extraction procedure, and allowed discarding of carryover contamination. System stability and
performance are evaluated by QC samples—a pool of equal volume of all plasma samples used
in the study.

4.5. Data Processing

MarkerView software (version 1.2.1, AB SCIEX, Concord, ON, Canada) was used for LC-
HRMS raw data processing. This tool performs peak detection, alignment and data filtering,
providing a data matrix where the measured mass-to-charge ratio (m/z), retention time (RT) and
intensities are defined for each sample. Afterwards, to minimize mass redundancy and enhance
the true molecular feature selection, only monoisotopic peaks were considered. Background and
contaminants were removed from the OS by applying an additional filtering procedure with fold
change (<1.5) and a t test (p > 0.05) between OS samples and study samples. Finally, according
to FDA criteria for untargeted metabolomics, features with relative standard deviation higher
than 30% were discarded because of their unacceptable variability in the QC samples [63]. The
next steps were carried out using MetaboAnalyst 4.0 Web Server software (Wishart Research
Group at the University of Alberta, Alberta, Canada) [64].
4.6. Normalization and Analytical Validation
Prior to the statistical analysis, normalization by a QC reference sample (probabilistic
quotient normalization), transformation and scaling were applied to convert data set into a more
Cancers 2021, 13, 147 15 of 19

Gaussian-type distribution [65,66]. Then, the PCA was used to assess the quality of the analytical
system performance [67]. Analytical system stability was validated by QC samples presentation
on a PCA plot. In parallel, the PLS-DA score plot showed possible outliers. Parameters R 2 and Q2,
which estimate goodness of fit and goodness of prediction respectively, were calculated to
evaluate the statistical quality model description.

4.7. Statistical Analysis

Univariate analysis (UVA) was carried out using the non-parametric Wilcoxon ranksum test
to evaluate differences between BC patients and HC subjects. Benjamini-Hochberg false
discovery rate (FDR) correction was performed afterwards to minimize the expected proportion
of false positives (Type I errors) [68]. In this regard, a p value of 0.05 (corrected by FDR) for the t
test is generally used in metabolomics as a cutoff threshold. Signals selected as potential
candidates for a final discriminatory model were selected also based on their fold change (FC >
1.3). Eventually, a multivariate analysis was applied to identify features responsible for
discriminating both study groups [30,69].

4.8. Metabolite Identification

PeakView software (version 1.0 with Formula Finder plug-in version 1.0, AB SCIEX, Concord,
ON, Canada) was used to predict the elemental formula of selected candidates from accurate
mass, isotopic clustering and fragmentation patterns. The assignment of a tentative
identification for each selected metabolite was possible by searching different compound
databases (Metlin, Human Metabolome Database, Lipid Maps, PubChem [70–73]) for accurate
mass values. Structural identification of the molecular formula was achieved comparing the
experimental fragmentation spectra against spectral databases (MassBank [74], NIST2014:
version 2.2, Scientific Instrument Services, Inc, Ringoes, NJ, USA).

4.9. Biomarker Evaluation

Clinical relevance of the candidate metabolites was evaluated with the area under the
receiver-operating characteristic curves (AUROC). In order to check the classifier performance of
the biomarkers proposed for the diagnostic model, a multivariate ROC analysis was performed.

4.10. Pathway Analysis

MetaboAnalyst 4.0 Web Server software was used for the identification of altered
metabolic pathways [64]. The metabolite ID matching was performed with Human Metabolome
Database and KEGG database [71,75]. The analysis was adjusted by a hypergeometric test and
the impact on pathway topology was based on relative-betweenness centrality.

5. Conclusions
Here we present an untargeted LC-HRMS metabolomics approach as a non-invasive
technique to identify differential metabolomics signatures for BC subgroups. We found distinct
molecular profiles representative for LA, LB, HER2 and TN BC phenotypes, which may act as
crucial biomarkers for accurate diagnosis, phenotypic discrimination and personalized
therapeutic intervention. It is worth highlighting the importance of a deep understanding of the
molecular differences among BC subtypes within the realm of personalized medicine to avoid
unnecessary side effects or inadequate target engagement. The metabolomics profiles
discovered could be used as a powerful tool in clinical practice, not only to determine the
existence of residual disease after neoadjuvant therapy and, thereby, contribute to the
identification of patients who will absolutely benefit from additional treatment, but also to
enlighten the development of new therapeutic strategies for each BC molecular subtype and
tailored follow up. Finally, our findings reinforce a foundation to identify new biological targets
in key metabolic pathways that may help to identify early subsequent relapses in the different
BC phenotypes. Further analyses in larger prospective cohort of patients would be necessary to
Cancers 2021, 13, 147 16 of 19

validate the prognostic/diagnostic capability of the different metabolomics profiles found among
the four major BC subtypes.

Supplementary Materials: The following are available online at https://www.mdpi.com/2072-6

694/13/1/147/s1. Figure S1: 2D score plots of the unsupervised PCA of HC group (green) and LA_BC (light
blue) (a), HER2_BC (orange) (b), TN_BC (yellow) (c) and LB_BC (pink) (d) patients by ESI+ showed that the
separation observed between the groups was due to biological reasons according to the close clustering of
the QC samples (dark blue). Figure S2: 2D score plots of the supervised PLS-DA of HC group (green) and
LA_BC (light blue) (a), HER2_BC (orange) (b), TN_BC (yellow) (c) and LB_BC (pink) (d) patients by ESI−
determined a notably separation between BC molecular subtypes and matched controls. Figure S3:
Characteristic MS/MS spectra of m/z 448.3066 in a biological sample (green) (a) and the
glycoursodeoxycholic acid (GUDCA) standard (blue) (b) at 3.24 min. MS/MS spectra revealed the
characteristic fragmentation pattern of GUDCA in ESI −. Table S1: Extracted peaks from RPLC ESI+ and ESI −
HRMS, significant altered metabolites and quality model description. Table S2: Features identified by
accurate mass (m/z) and retention time (RT). Table S3: Altered non-significant pathways associated with BC
molecular subtypes by ESI+ and ESI−.

Author Contributions: Conceptualization, J.P.d.P. and P.S.-R.; methodology, A.M.-B. and C.G.-O.; formal
analysis, J.P.d.P., C.G.-O., C.D. and L.D.-B.; investigation, M.F.-N. and L.D.B.; resources, M.F.-N., N.L.-C.,
A.L.O.-G., F.G.-M., L.D.-B., C.D. and C.G.-O.; data curation, A.M.-B. and L.D.-B; writing—original draft
preparation, L.D.-B. and C.G.-O.; writing—review and editing, C.D., P.S.-R. and L.D.-B.; visualization, L.D.-B.
and C.G.-O.; supervision, P.S.-R. and F.V.; project administration, P.S.-R.; funding acquisition, P.S.-R. All
authors have read and agreed to the published version of the manuscript.

Funding: This research was funded by the Consejería de Salud of the Junta de Andalucía, grant number PI-
0455-2016 and the APC was funded by Fundación Pública Andaluza para la Investigación Biosanitaria de
Andalucía Oriental Alejandro Otero (FIBAO).
Institutional Review Board Statement: The study was conducted according to the guidelines of the
Declaration of Helsinki and the International Conference on Harmonization-Good Clinical Practices (ICH-
GCP), and approved by the Institutional Review Board of the Clinical Research Ethics Committee of Jaén
(protocol code: PI-0455-2016 and date of approval: 27 October 2016).
Informed Consent Statement: Informed consent was obtained from all subjects involved in the study.
Data Availability Statement: All data generated or analyzed during this study are included in this published
article and its supplementary materials. Raw data are not publicly available due to ethical restrictions, since
they contain information that could compromise the privacy of research participants, but are available
from the corresponding author on reasonable request.

Acknowledgments: We are especially grateful to all the patients and their families who contributed the
data that made this study possible. In addition, we thank the staff of the Clinical Research Unit of the
Medical Oncology Service of the University Hospital of Jaén for their time, and assistance; as well as the
technical support from Fundación MEDINA. We would also like to thank Shivan Barungi, whose valuable
assistance substantially improved the quality of the manuscript. We thank the reviewers and the editor for
their constructive contributions and comments. We finally thank the Junta de Andalucía and Fundación
Pública Andaluza para la Investigación Biosanitaria de Andalucía Oriental Alejandro Otero (FIBAO) for their
financial support.

Conflicts of Interest: The authors declare no conflict of interest.

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