Triple-negative breast cancer (TNBC) is a molecularly-defined subtype of breast cancer characterized by the absence of estrogen receptor (ER), progesterone receptor (PR), and HER2 expression. TNBC represents approximately 10-15% of breast cancers and is clinically aggressive with higher rates of recurrence and visceral/brain metastases. TNBC is molecularly heterogeneous, encompassing several intrinsic subtypes including basal-like, mesenchymal, and immunomodulatory. Treatment relies on chemotherapy and increasingly immunotherapy, as hormonal and HER2-targeted therapies are ineffective by definition.
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name: Triple-Negative Breast Cancer
creation_date: '2026-01-26T02:55:13Z'
description: >-
Triple-negative breast cancer (TNBC) is a molecularly-defined subtype of breast
cancer characterized by the absence of estrogen receptor (ER), progesterone
receptor (PR), and HER2 expression. TNBC represents approximately 10-15% of
breast cancers and is clinically aggressive with higher rates of recurrence
and visceral/brain metastases. TNBC is molecularly heterogeneous, encompassing
several intrinsic subtypes including basal-like, mesenchymal, and
immunomodulatory. Treatment relies on chemotherapy and increasingly immunotherapy,
as hormonal and HER2-targeted therapies are ineffective by definition.
categories:
- Molecularly-Defined Cancer
- Breast Cancer Subtype
- Solid Tumor
parents:
- breast carcinoma
has_subtypes:
- name: Basal-like TNBC
description: >-
The most common TNBC subtype (50-75%), characterized by expression of basal
cytokeratins (CK5/6, CK14, CK17), EGFR expression, high proliferation, and
frequent TP53 and BRCA1 mutations. Overlaps significantly with BRCA1-associated
breast cancer.
evidence:
- reference: PMID:21633166
reference_title: "Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies."
supports: SUPPORT
snippet: >-
BL1 and BL2 subtypes had higher expression of cell cycle and DNA damage
response genes, and representative cell lines preferentially responded to
cisplatin.
explanation: >-
The Lehmann et al. study identified basal-like subtypes (BL1 and BL2) with
high cell cycle and DNA damage response gene expression, consistent with
high proliferation and BRCA1 mutations.
- name: Mesenchymal TNBC
description: >-
Characterized by epithelial-mesenchymal transition features, enrichment in
cell motility and differentiation pathways. May respond to PI3K/mTOR inhibition.
evidence:
- reference: PMID:21633166
reference_title: "Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies."
supports: SUPPORT
snippet: >-
M and MSL subtypes were enriched in GE for epithelial-mesenchymal transition,
and growth factor pathways and cell models responded to NVP-BEZ235 (a PI3K/mTOR
inhibitor) and dasatinib (an abl/src inhibitor).
explanation: >-
The Lehmann et al. study confirmed mesenchymal subtypes are enriched for EMT
and growth factor pathways, responding to PI3K/mTOR inhibition.
- name: Luminal Androgen Receptor (LAR) TNBC
description: >-
Despite being ER/PR-negative, LAR tumors express androgen receptor and have
luminal gene expression patterns. May benefit from androgen receptor-targeted
therapy. Often have PIK3CA mutations.
evidence:
- reference: PMID:21633166
reference_title: "Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies."
supports: SUPPORT
snippet: >-
The LAR subtype includes patients with decreased relapse-free survival and
was characterized by androgen receptor (AR) signaling. LAR cell lines were
uniquely sensitive to bicalutamide (an AR antagonist).
explanation: >-
The Lehmann et al. study identified the LAR subtype characterized by AR
signaling and sensitivity to AR antagonists.
- name: Immunomodulatory TNBC
description: >-
Characterized by immune cell infiltration and immune checkpoint expression.
Best responders to immune checkpoint inhibitor therapy.
evidence:
- reference: PMID:21633166
reference_title: "Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies."
supports: SUPPORT
snippet: >-
Cluster analysis identified 6 TNBC subtypes displaying unique GE and
ontologies, including 2 basal-like (BL1 and BL2), an immunomodulatory (IM),
a mesenchymal (M), a mesenchymal stem-like (MSL), and a luminal androgen
receptor (LAR) subtype.
explanation: >-
The Lehmann et al. study identified the immunomodulatory (IM) subtype as
one of the six TNBC subtypes with unique gene expression profiles.
pathophysiology:
- name: Loss of Hormone Receptor Signaling
description: >-
TNBC lacks expression of estrogen receptor alpha (ESR1) and progesterone
receptor (PGR), eliminating the growth-promoting effects of estrogen signaling
that drive most breast cancers. This absence removes a key therapeutic target
but also indicates fundamentally different tumor biology.
evidence:
- reference: PMID:35987766
reference_title: "Triple negative breast cancer: Pitfalls and progress."
supports: SUPPORT
evidence_source: OTHER
snippet: >-
Triple negative breast cancer (TNBC) is characterized by the lack of
estrogen and progesterone receptor expression and lacks HER2 overexpression
or gene amplification.
explanation: >-
This review abstract defines TNBC by absent ER and PR expression with
absent HER2 overexpression, directly supporting loss of hormone receptor
signaling as a defining mechanistic feature.
biological_processes:
- preferred_term: estrogen receptor signaling pathway
modifier: ABSENT
term:
id: GO:0030520
label: estrogen receptor signaling pathway
downstream:
- target: Alternative Oncogenic Pathways
description: Other signaling pathways drive proliferation in absence of ER
- name: Alternative Oncogenic Pathways
description: >-
In the absence of hormone receptor signaling, TNBC is driven by alternative
oncogenic pathways including EGFR signaling, PI3K-AKT-mTOR activation, and
Wnt/beta-catenin signaling. Many TNBCs have TP53 mutations eliminating this
tumor suppressor checkpoint.
biological_processes:
- preferred_term: epidermal growth factor receptor signaling pathway
modifier: INCREASED
term:
id: GO:0007173
label: epidermal growth factor receptor signaling pathway
- preferred_term: phosphatidylinositol 3-kinase signaling
modifier: INCREASED
term:
id: GO:0043491
label: phosphatidylinositol 3-kinase/protein kinase B signal transduction
downstream:
- target: Aggressive Tumor Behavior
description: Multiple activated pathways drive aggressive phenotype
- name: DNA Repair Deficiency
description: >-
A significant subset of TNBC (~20%) harbors germline or somatic BRCA1/2
mutations resulting in homologous recombination deficiency. This creates
sensitivity to platinum chemotherapy and PARP inhibitors through synthetic
lethality.
biological_processes:
- preferred_term: homologous recombination
modifier: DECREASED
term:
id: GO:0035825
label: homologous recombination
evidence:
- reference: PMID:33475295
reference_title: "PARP Inhibitors in Triple-Negative Breast Cancer Including Those With BRCA Mutations."
supports: SUPPORT
evidence_source: OTHER
snippet: >-
PARP inhibition causes synthetic lethality in breast cancers associated
with germline BRCA1 and BRCA2 mutations and is routinely used in clinical
practice for metastatic breast cancer.
explanation: >-
Supports the therapeutic consequence of homologous-recombination deficiency
in BRCA-mutated breast cancer. It does not support the "~20% of TNBC"
prevalence figure in the node description, which remains uncited.
downstream:
- target: Genomic Instability
description: DNA repair defects lead to mutation accumulation
- name: Genomic Instability
conforms_to: "genome_instability_mutation#Mutator Phenotype and Chromosomal Instability"
description: >-
Loss of high-fidelity double-strand-break repair, compounded by near-universal
TP53 inactivation, produces a mutator phenotype and pervasive chromosomal
instability. This is the enabling characteristic that supplies the driver
lesions feeding the alternative oncogenic pathways and aggressive behavior of
TNBC.
biological_processes:
- preferred_term: DNA damage response
modifier: ABNORMAL
term:
id: GO:0006974
label: DNA damage response
- preferred_term: chromosome segregation
modifier: ABNORMAL
term:
id: GO:0007059
label: chromosome segregation
evidence:
- reference: PMID:31045815
reference_title: "Association of p53 expression with poor prognosis in patients with triple-negative breast invasive ductal carcinoma."
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: "TP53 gene is mutated in approximately 80% of triple-negative breast cancer (TNBC)."
explanation: >-
Supports near-universal loss of the TP53 checkpoint in TNBC, the principal
permissive lesion for the mutator/chromosomal-instability phenotype. Direct
TNBC genomic-scarring evidence is still needed.
downstream:
- target: Aggressive Tumor Behavior
description: >-
Accumulated driver lesions and chromosomal instability fuel clonal evolution
and the aggressive clinical course.
- name: Aggressive Tumor Behavior
description: >-
TNBC is characterized by high proliferation rates, early metastasis (especially
to viscera and brain), and shorter time to recurrence compared to other breast
cancer subtypes. The aggressive biology reflects activation of multiple
oncogenic pathways and loss of tumor suppressors.
evidence:
- reference: PMID:35987766
reference_title: "Triple negative breast cancer: Pitfalls and progress."
supports: SUPPORT
snippet: "It accounts for 10-15% of incident breast cancers and carries the worst prognosis."
explanation: "Abstract states TNBC carries the worst prognosis, supporting aggressive behavior."
biological_processes:
- preferred_term: cell population proliferation
modifier: INCREASED
term:
id: GO:0008283
label: cell population proliferation
histopathology:
- name: Invasive Ductal Carcinoma
finding_term:
preferred_term: Invasive Breast Carcinoma of No Special Type
term:
id: NCIT:C4194
label: Invasive Breast Carcinoma of No Special Type
frequency: VERY_FREQUENT
description: Invasive ductal carcinoma is the most common type of breast cancer.
evidence:
- reference: PMID:39806949
reference_title: "An Overview of Invasive Ductal Carcinoma (IDC) in Women's Breast Cancer."
supports: SUPPORT
snippet: "Invasive ductal carcinoma (IDC) is the most common type of breast cancer,"
explanation: Abstract states that invasive ductal carcinoma is the most common breast cancer type.
phenotypes:
- category: Neoplastic
name: Breast Carcinoma
frequency: OBLIGATE
diagnostic: true
description: >-
Triple-negative breast cancers are typically high-grade invasive ductal
carcinomas with high mitotic rates. Medullary and metaplastic histologies
are enriched in the TNBC population.
phenotype_term:
preferred_term: Breast carcinoma
term:
id: HP:0003002
label: Breast carcinoma
- category: Clinical
name: Early Visceral Metastases
frequency: FREQUENT
description: >-
TNBC has a predilection for visceral metastases (lung, liver) and brain
metastases, occurring earlier and more frequently than in ER+ breast cancer.
notes: >-
HPO has no generic metastasis term, so this is bound to the coarse parent
HP:0002664 Neoplasm. The binding does not convey the metastatic or visceral
specificity described here.
phenotype_term:
preferred_term: Neoplasm
term:
id: HP:0002664
label: Neoplasm
- category: Molecular
name: Triple-Negative Phenotype
frequency: OBLIGATE
diagnostic: true
description: >-
Defining feature is absence of ER (<1%), PR (<1%), and HER2 (IHC 0-1+ or
FISH non-amplified). This is a diagnosis of exclusion from other breast
cancer subtypes. Note: this is a receptor-status molecular classification,
not an HPO-modelled clinical abnormality; the HP:0002664 Neoplasm binding
below is a placeholder and does not represent the triple-negative state.
evidence:
- reference: PMID:35987766
reference_title: "Triple negative breast cancer: Pitfalls and progress."
supports: SUPPORT
evidence_source: OTHER
snippet: "Triple negative breast cancer (TNBC) is characterized by the lack of estrogen and progesterone receptor expression and lacks HER2 overexpression or gene amplification."
explanation: "Abstract defines TNBC by lack of ER/PR and HER2, matching the diagnostic phenotype."
phenotype_term:
preferred_term: Neoplasm
term:
id: HP:0002664
label: Neoplasm
biochemical:
- name: Hormone Receptor and HER2 Testing
notes: >-
Diagnosis requires testing for ER, PR (by IHC), and HER2 (by IHC and/or FISH).
Triple-negative is defined as ER <1%, PR <1%, and HER2 0-1+ or non-amplified.
PD-L1 testing (CPS or SP142) is recommended for treatment selection.
- name: BRCA1/2 Testing
notes: >-
Germline BRCA1/2 testing is recommended for all TNBC patients given high
prevalence of mutations (~15-20%) and therapeutic implications (PARP inhibitors).
Somatic testing may identify additional HRD-positive tumors.
genetic:
- name: TP53
gene_term:
preferred_term: TP53
term:
id: hgnc:11998
label: TP53
association: Somatic Mutations
relationship_type: SOMATIC_DRIVER
variant_origin: SOMATIC
notes: >-
TP53 mutations occur in approximately 80% of TNBC, the highest rate among
breast cancer subtypes. Mutations are typically missense in the DNA-binding
domain or truncating mutations.
evidence:
- reference: PMID:31045815
reference_title: "Association of p53 expression with poor prognosis in patients with triple-negative breast invasive ductal carcinoma."
supports: SUPPORT
snippet: "TP53 gene is mutated in approximately 80% of triple-negative breast cancer (TNBC)."
explanation: "Abstract reports TP53 mutation frequency in TNBC, supporting this genetic association."
- name: BRCA1
gene_term:
preferred_term: BRCA1
term:
id: hgnc:1100
label: BRCA1
association: Germline and Somatic Mutations
relationship_type: RISK_FACTOR
variant_origin: GERMLINE_AND_SOMATIC
notes: >-
BRCA1 germline mutations are enriched in TNBC, occurring in 10-15% of cases.
BRCA1-associated breast cancers are predominantly triple-negative and basal-like.
Somatic BRCA1 mutations and promoter methylation also occur.
- name: PIK3CA
gene_term:
preferred_term: PIK3CA
term:
id: hgnc:8975
label: PIK3CA
association: Somatic Mutations
relationship_type: SOMATIC_DRIVER
variant_origin: SOMATIC
notes: >-
PIK3CA mutations occur in approximately 10-20% of TNBC, particularly in the
LAR subtype. May identify patients who benefit from PI3K inhibitors.
treatments:
- name: Neoadjuvant Chemotherapy
description: >-
Standard treatment includes anthracycline and taxane-based regimens given
before surgery. Pathologic complete response (pCR) rates are higher in TNBC
than other subtypes and strongly predict long-term outcomes.
treatment_term:
preferred_term: Neoadjuvant Chemotherapy
term:
id: NCIT:C213450
label: Neoadjuvant Chemotherapy
evidence:
- reference: PMID:32046998
reference_title: "Pathologic Complete Response after Neoadjuvant Chemotherapy and Impact on Breast Cancer Recurrence and Survival: A Comprehensive Meta-analysis."
supports: SUPPORT
snippet: >-
Patients with a pCR after NAT had significantly better EFS (HR = 0.31; 95%
PI, 0.24-0.39), particularly for triple-negative (HR = 0.18; 95% PI,
0.10-0.31) and HER2+ (HR = 0.32; 95% PI, 0.21-0.47) disease.
explanation: >-
Meta-analysis confirms that achieving pCR after neoadjuvant therapy is
strongly associated with improved event-free survival, particularly for TNBC.
- name: Pembrolizumab Plus Chemotherapy
description: >-
PD-1 inhibitor pembrolizumab combined with chemotherapy improves outcomes
in early-stage and metastatic TNBC. KEYNOTE-522 established pembrolizumab
in the neoadjuvant/adjuvant setting regardless of PD-L1 status.
treatment_term:
preferred_term: immunotherapy
term:
id: NCIT:C15262
label: Immunotherapy
therapeutic_agent:
- preferred_term: pembrolizumab
term:
id: NCIT:C106432
label: Pembrolizumab
evidence:
- reference: PMID:32101663
reference_title: "Pembrolizumab for Early Triple-Negative Breast Cancer."
supports: SUPPORT
snippet: >-
Among patients with early triple-negative breast cancer, the percentage
with a pathological complete response was significantly higher among those
who received pembrolizumab plus neoadjuvant chemotherapy than among those
who received placebo plus neoadjuvant chemotherapy.
explanation: >-
KEYNOTE-522 demonstrated significantly higher pCR rates with pembrolizumab
plus chemotherapy versus chemotherapy alone in early TNBC.
- name: PARP Inhibitors
description: >-
Olaparib and talazoparib are approved for germline BRCA-mutated metastatic
TNBC. They exploit synthetic lethality in HRD-positive tumors unable to
repair DNA double-strand breaks.
treatment_term:
preferred_term: targeted therapy
term:
id: NCIT:C93352
label: Targeted Therapy
evidence:
- reference: PMID:33475295
reference_title: "PARP Inhibitors in Triple-Negative Breast Cancer Including Those With BRCA Mutations."
supports: SUPPORT
snippet: >-
PARP inhibition causes synthetic lethality in breast cancers associated
with germline BRCA1 and BRCA2 mutations and is routinely used in clinical
practice for metastatic breast cancer.
explanation: >-
Review confirms PARP inhibitors cause synthetic lethality in BRCA-mutated
breast cancers and are standard of care for metastatic disease.
- name: Sacituzumab Govitecan
description: >-
Antibody-drug conjugate targeting Trop-2 with an SN-38 payload. Approved
for previously treated metastatic TNBC with significant survival benefit
demonstrated in ASCENT trial.
treatment_term:
preferred_term: Pharmacotherapy
term:
id: NCIT:C15986
label: Pharmacotherapy
therapeutic_agent:
- preferred_term: sacituzumab govitecan
term:
id: NCIT:C102783
label: Sacituzumab Govitecan
evidence:
- reference: PMID:33882206
reference_title: "Sacituzumab Govitecan in Metastatic Triple-Negative Breast Cancer."
supports: SUPPORT
snippet: >-
Progression-free and overall survival were significantly longer with
sacituzumab govitecan than with single-agent chemotherapy among patients
with metastatic triple-negative breast cancer.
explanation: >-
ASCENT trial demonstrated significant PFS and OS benefit with sacituzumab
govitecan versus chemotherapy in metastatic TNBC.
- name: Platinum Chemotherapy
description: >-
Carboplatin improves pCR rates in neoadjuvant therapy, particularly in
BRCA-mutated or HRD-positive TNBC. Used in combination with taxanes.
treatment_term:
preferred_term: chemotherapy
term:
id: NCIT:C15632
label: Chemotherapy
evidence:
- reference: PMID:21633166
reference_title: "Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies."
supports: SUPPORT
snippet: >-
BL1 and BL2 subtypes had higher expression of cell cycle and DNA damage
response genes, and representative cell lines preferentially responded to
cisplatin.
explanation: >-
Basal-like TNBC subtypes with DNA damage response gene expression
preferentially respond to platinum chemotherapy.
disease_term:
preferred_term: triple-negative breast carcinoma
term:
id: MONDO:0005494
label: triple-negative breast carcinoma
mappings:
mondo_mappings:
- term:
id: MONDO:0005494
label: triple-negative breast carcinoma
mapping_predicate: skos:exactMatch
mapping_source: MONDO
mapping_justification: MONDO provides an exact disease term for triple-negative breast carcinoma.
classifications:
icdo_morphology:
classification_value: Adenocarcinoma
harrisons_chapter:
- classification_value: ONCOLOGY_HEMATOLOGY
references:
- reference: DOI:10.2147/bctt.s516542
title: 'Diagnosis, Prognosis, and Treatment of Triple-Negative Breast Cancer: A Review'
found_in:
- Triple_Negative_Breast_Cancer-deep-research-falcon.md
findings:
- statement: TNBC is defined by absence of ER, PR, and HER2 and remains clinically aggressive despite growing therapeutic options.
supporting_text: 'Diagnosis, Prognosis, and Treatment of Triple-Negative Breast Cancer: A Review'
- reference: DOI:10.3389/fonc.2024.1405491
title: 'Advancements and challenges in triple-negative breast cancer: a comprehensive review of therapeutic and diagnostic strategies'
found_in:
- Triple_Negative_Breast_Cancer-deep-research-falcon.md
findings:
- statement: Contemporary TNBC management is increasingly shaped by immunotherapy, antibody-drug conjugates, and molecular stratification, but heterogeneity remains a central obstacle.
supporting_text: 'Advancements and challenges in triple-negative breast cancer: a comprehensive review of therapeutic and diagnostic strategies'
- reference: DOI:10.3390/cancers17020228
title: Triple-Negative Breast Cancer Progression and Drug Resistance in the Context of Epithelial–Mesenchymal Transition
found_in:
- Triple_Negative_Breast_Cancer-deep-research-falcon.md
findings:
- statement: EMT-associated plasticity is a major contributor to TNBC progression, metastatic behavior, and therapy resistance.
supporting_text: 'Triple-Negative Breast Cancer Progression and Drug Resistance in the Context of Epithelial–Mesenchymal Transition'
- reference: DOI:10.53022/oarjbp.2024.10.2.0013
title: 'Triple Negative Breast Cancer (TNBC): Signalling pathways-Role of plant-based inhibitors'
found_in:
- Triple_Negative_Breast_Cancer-deep-research-falcon.md
findings:
- statement: Multiple signaling pathways remain mechanistically relevant in TNBC and motivate continued pathway-directed therapeutic exploration.
supporting_text: 'Triple Negative Breast Cancer (TNBC): Signalling pathways-Role of plant-based inhibitors'
datasets:
- accession: ega:EGAS00001003196
title: Exome-sequencing of paired docetaxel sensitive and resistant triple-negative breast cancer
description: Taxane-based regimens constitute the most common therapeutic option in patients with triple-negative breast cancer (TNBC). Resistance to treatment often arises although the molecular mechanisms responsible for this process are unknown. To unravel chemoresistance mechanisms, exome sequencing was performed on matched docetaxel sensitive and resistant TNBC patient-derived xenografts (PDX).
organism:
preferred_term: human
term:
id: NCBITaxon:9606
label: Homo sapiens
data_type: WES
notes: 'European Genome-phenome Archive study, matched because the disease is named in the study''s own title ("Triple-Negative Breast Cancer"); description-level mentions were not accepted. EGA study_type: Exome Sequencing. Controlled access -- data require a Data Access Agreement. EGA metadata retrieved 2026-08-01.'
- accession: ega:EGAS00001005892
title: Functional Mapping of AKT Signaling and Biomarkers of Response From the FAIRLANE Trial of Neoadjuvant Ipatasertib Plus Paclitaxel for Triple-Negative Breast Cancer
description: 'Purpose: Despite extensive genomic and transcriptomic profiling, it remains unknown how signaling pathways are differentially activated and how tumors are differentially sensitized to certain perturbations. Here, we aim to characterize AKT signaling activity and its association with other genomic or immunohistochemistry-based PI3K/AKT pathway biomarkers as well as the clinical activity of ipatasertib (AKT inhibitor) in the FAIRLANE trial. Experimental Design: In FAIRLANE, 151 patients with early triple-negative breast cancer were randomized 1:1 to receive paclitaxel with ipatasertib or placebo for 12 weeks prior to surgery.'
organism:
preferred_term: human
term:
id: NCBITaxon:9606
label: Homo sapiens
notes: 'European Genome-phenome Archive study, matched because the disease is named in the study''s own title ("Triple-Negative Breast Cancer"); description-level mentions were not accepted. EGA study_type: Other. Controlled access -- data require a Data Access Agreement. EGA metadata retrieved 2026-08-01.'
- accession: ega:EGAS00001006079
title: Comprehensive Molecular Profiling Identifies Features of Disease Resistance to Neoadjuvant Chemotherapy in Triple-Negative Breast Cancer
organism:
preferred_term: human
term:
id: NCBITaxon:9606
label: Homo sapiens
notes: 'European Genome-phenome Archive study, matched because the disease is named in the study''s own title ("Triple-Negative Breast Cancer"); description-level mentions were not accepted. EGA study_type: Cancer Genomics. Controlled access -- data require a Data Access Agreement. EGA metadata retrieved 2026-08-01.'
- accession: metabolomics_workbench:ST002408
title: Multi-omic Analysis of ClpP Activation in Triple-Negative Breast Cancer Cells
notes: Located via OmicsDI, which aggregates across omics repositories; this record comes from metabolomics_workbench. Only repositories with no other discovery route in this project and with a working accession resolver are curated from OmicsDI -- GEO, ArrayExpress, PRIDE, MetaboLights and EGA hits are excluded as duplicates of dedicated passes. Matched because the disease is named in the dataset's own title ("Triple-Negative Breast Cancer"). Retrieved 2026-08-02.
- accession: metabolomics_workbench:ST002235
title: Application of Artificial Intelligence to Plasma Metabolomics Profiles to Predict Response to Neoadjuvant Chemotherapy in Triple-Negative Breast Cancer
notes: Located via OmicsDI, which aggregates across omics repositories; this record comes from metabolomics_workbench. Only repositories with no other discovery route in this project and with a working accession resolver are curated from OmicsDI -- GEO, ArrayExpress, PRIDE, MetaboLights and EGA hits are excluded as duplicates of dedicated passes. Matched because the disease is named in the dataset's own title ("Triple-Negative Breast Cancer"). Retrieved 2026-08-02.
- accession: metabolomics_workbench:ST002290
title: Metabolic impact of anticancer drugs Pd2Spermine and Cisplatin on the polar metabolome of brain from cell-derived xenograft mouse model of Triple-Negative Breast Cancer (part 1)
organism:
preferred_term: mouse
term:
id: NCBITaxon:10090
label: Mus musculus
data_type: METABOLOMICS
notes: Located via OmicsDI, which aggregates across omics repositories; this record comes from metabolomics_workbench. Only repositories with no other discovery route in this project and with a working accession resolver are curated from OmicsDI -- GEO, ArrayExpress, PRIDE, MetaboLights and EGA hits are excluded as duplicates of dedicated passes. Matched because the disease is named in the dataset's own title ("Triple-Negative Breast Cancer"). Retrieved 2026-08-02.
Pathophysiology description (narrative) Triple-negative breast cancer is defined by the absence of ER, PR, and HER2 expression and accounts for about 15–20% of breast cancers. It is enriched in younger patients and in germline BRCA1 carriers, shows rapid early recurrence, and tends to metastasize viscerally. As a recent review summarized: “TNBC is characterized by its aggressive nature, limited treatment options, and poorer prognosis compared to other breast cancer subtypes,” with targeted strategies focusing on PARP inhibitors and immune checkpoint blockade but with persistent biomarker challenges (Frontiers in Oncology, 28 May 2024, https://doi.org/10.3389/fonc.2024.1405491). Mechanistically, TNBC exhibits profound genomic instability (frequent TP53 mutation; HRD in BRCA1/2 or broader HRR genes), PI3K/AKT/mTOR and EGFR pathway activation in subsets (including the luminal androgen receptor [LAR] subtype), epithelial–mesenchymal transition (EMT) and cancer stemness driving invasion and therapeutic resistance, and an often immunologically active yet variably suppressive tumor microenvironment (TME). Clinically, neoadjuvant chemotherapy remains foundational; however, residual disease after chemotherapy is common and portends high recurrence risk, underscoring the need to address EMT/stemness, DNA-repair defects, and immune evasion in combination regimens (Frontiers in Oncology, 2024; Breast Cancer: Targets and Therapy, 13 Mar 2025, https://doi.org/10.2147/bctt.s516542) (xiong2024advancementsandchallenges pages 1-2, jie2025diagnosisprognosisand pages 7-9).
Core Pathophysiology - Primary mechanisms - Homologous recombination deficiency (HRD) due to BRCA1/2 or broader HRR gene disruption creates genomic scarring, high mutation burden, and sensitivity to DNA-damaging agents (carboplatin) and PARP inhibition; HRD/TIL enrichment may also interface with ICI responsiveness (Breast Cancer: Targets and Therapy, 2025, https://doi.org/10.2147/bctt.s516542) (jie2025diagnosisprognosisand pages 7-9). - EMT and stemness: EMT programs downregulate E-cadherin and upregulate vimentin/N-cadherin, enabling motility, invasion, and resistance; EMT fosters cancer stem cell traits and post-chemotherapy minimal residual disease (Cancers, 12 Jan 2025, https://doi.org/10.3390/cancers17020228) (błaszczak2025triplenegativebreastcancer pages 2-4, błaszczak2025triplenegativebreastcancer pages 1-2). - PI3K/AKT/mTOR and EGFR signaling: frequently activated in TNBC and particularly in LAR or EGFR-high tumors, promoting proliferation, survival, and metabolic reprogramming (Breast Cancer: Targets and Therapy, 2025; review of EGFR ~70% positivity in TNBC and PI3K/AKT/mTOR involvement) (jie2025diagnosisprognosisand pages 7-9). - Tumor immune microenvironment: TNBCs often show higher TILs and PD-L1 expression, supporting chemo-ICI combinations; yet ICI monotherapy responses are modest, highlighting immune evasion and need for better biomarkers (Frontiers in Oncology, 2024) (xiong2024advancementsandchallenges pages 1-2). - Dysregulated molecular pathways - DNA repair: BRCA1/2-HRD axis (jie2025diagnosisprognosisand pages 7-9). - Growth/survival: EGFR→PI3K/AKT/mTOR; FGFR4 signaling altering lipid metabolism (jie2025diagnosisprognosisand pages 7-9). - EMT networks: canonical EMT TFs/signals (e.g., TGF-β, WNT/NOTCH/Hedgehog cross-talk) highlighted in EMT-focused reviews (błaszczak2025triplenegativebreastcancer pages 2-4, błaszczak2025triplenegativebreastcancer pages 1-2). - Cellular processes affected - Invasion/metastasis via EMT; therapy resistance linked to EMT/stemness; metabolic rewiring to support proliferation; context-dependent immune activation/suppression influencing NAC/ICI outcomes (błaszczak2025triplenegativebreastcancer pages 2-4, błaszczak2025triplenegativebreastcancer pages 1-2, xiong2024advancementsandchallenges pages 1-2, jie2025diagnosisprognosisand pages 7-9).
Key Molecular Players - Genes/Proteins (HGNC) - BRCA1 (HGNC:1100), BRCA2 (HGNC:1101): HRR; loss/HRD sensitizes to platinum/PARPi (jie2025diagnosisprognosisand pages 7-9). - TP53 (HGNC:11998): frequently mutated in TNBC; contributes to genomic instability (xiong2024advancementsandchallenges pages 1-2). - EGFR (HGNC:3236): overexpressed in ~70% of TNBC; activates PI3K/AKT/mTOR (jie2025diagnosisprognosisand pages 7-9). - FGFR4 (HGNC:3689): upregulated in TNBC; promotes proliferation/invasion and lipid metabolic changes (jie2025diagnosisprognosisand pages 7-9). - AR (HGNC:644): defines LAR subtype; therapeutic target under investigation (xiong2024advancementsandchallenges pages 1-2, yan2024understandingmechanismsof pages 30-35). - EMT markers/regulators: CDH1/E-cadherin (HGNC:1748) down; VIM (HGNC:12692) and CDH2/N-cadherin (HGNC:1749) up (błaszczak2025triplenegativebreastcancer pages 2-4, błaszczak2025triplenegativebreastcancer pages 1-2). - Chemical Entities (ChEBI) - Carboplatin (CHEBI:31355): platinum agent; higher pCR in HRD-positive TNBC (jie2025diagnosisprognosisand pages 7-9). - PARP inhibitors (class; e.g., olaparib, CHEBI:89745): effective in gBRCA-mutant TNBC (xiong2024advancementsandchallenges pages 1-2, jie2025diagnosisprognosisand pages 7-9). - Immune checkpoint inhibitors (e.g., pembrolizumab): benefit in PD-L1–positive TNBC with chemotherapy (xiong2024advancementsandchallenges pages 1-2). - Cell Types (CL) - Malignant basal-like epithelial cells (CL:0000066 derivative) exhibiting EMT/stemness (błaszczak2025triplenegativebreastcancer pages 2-4, błaszczak2025triplenegativebreastcancer pages 1-2). - Tumor-infiltrating lymphocytes (T cells; CL:0000084) variably abundant (xiong2024advancementsandchallenges pages 1-2). - Myeloid cells/macrophages (CL:0000235) and CAFs (CL:0000635) implicated in TME remodeling (overview) (xiong2024advancementsandchallenges pages 1-2). - Anatomical Locations (UBERON) - Mammary gland (UBERON:0001911); propensity for visceral metastases (lung UBERON:0002048; liver UBERON:0002107; brain UBERON:0000955) (xiong2024advancementsandchallenges pages 1-2).
Biological Processes (GO) disrupted - DNA repair via homologous recombination (GO:0000724) (jie2025diagnosisprognosisand pages 7-9). - Signal transduction via EGFR/PI3K/AKT (GO:0007173; GO:0043491; GO:0038083) (jie2025diagnosisprognosisand pages 7-9). - Epithelial to mesenchymal transition (GO:0001837) and regulation of cell migration (GO:0030334) (błaszczak2025triplenegativebreastcancer pages 2-4, błaszczak2025triplenegativebreastcancer pages 1-2). - Regulation of apoptotic process (GO:0042981) and cell cycle (GO:0051726) downstream of PI3K/AKT/EGFR (jie2025diagnosisprognosisand pages 7-9). - Immune response (GO:0006955), T cell activation (GO:0042110), and negative regulation within TME (overview) (xiong2024advancementsandchallenges pages 1-2).
Cellular Components (GO) implicated - Nucleus (GO:0005634) and DNA repair foci (GO:0035861) for HRR (jie2025diagnosisprognosisand pages 7-9). - Plasma membrane (GO:0005886) for EGFR/FGFR and AR (jie2025diagnosisprognosisand pages 7-9, xiong2024advancementsandchallenges pages 1-2). - Adherens junction (GO:0005912)/cell-cell junctions affected in EMT (błaszczak2025triplenegativebreastcancer pages 2-4, błaszczak2025triplenegativebreastcancer pages 1-2). - Extracellular space (GO:0005615)/ECM (GO:0031012) in invasion and CAF remodeling (overview) (xiong2024advancementsandchallenges pages 1-2).
Disease Progression (sequence) 1) Initiation: HRD/TP53 mutation and basal-like lineage programs drive genomic instability and rapid proliferation (xiong2024advancementsandchallenges pages 1-2, jie2025diagnosisprognosisand pages 7-9). 2) Local invasion: EMT program reduces E-cadherin and increases mesenchymal proteins, enabling dissemination; EGFR/PI3K signaling supports motility and survival (błaszczak2025triplenegativebreastcancer pages 2-4, błaszczak2025triplenegativebreastcancer pages 1-2, jie2025diagnosisprognosisand pages 7-9). 3) Systemic metastasis: preferential early visceral spread; immune contexture variably hot/cold; subsets exhibit LAR signaling (xiong2024advancementsandchallenges pages 1-2). 4) Treatment response/resistance: NAC induces pCR in a subset; residual disease (RCB-II/III) common and at high recurrence risk; EMT/stemness and HRD status influence sensitivity to platinum/PARPi and to chemo-ICI combinations (błaszczak2025triplenegativebreastcancer pages 1-2, jie2025diagnosisprognosisand pages 7-9, xiong2024advancementsandchallenges pages 1-2).
Phenotypic Manifestations (HP terms) - High histologic grade and high proliferative index (Ki-67) (HP:0030079; HP:0030064) (błaszczak2025triplenegativebreastcancer pages 1-2). - Early visceral metastasis (HP:0002725 for abnormal immune response context; clinical pattern: lung/liver/brain spread) (xiong2024advancementsandchallenges pages 1-2). - Poor response durability to monotherapy ICI; improved with chemo-ICI in PD-L1+ disease (clinical phenotype) (xiong2024advancementsandchallenges pages 1-2).
Subtype and biomarker context - Transcriptomic TNBC subtypes include basal-like, immunomodulatory (IM), mesenchymal (M), and LAR; LAR tumors show AR signaling and often PI3K pathway dependence (Frontiers in Oncology, 2024; review of LAR subgroup) (xiong2024advancementsandchallenges pages 1-2, yan2024understandingmechanismsof pages 30-35). - PD-L1 and TILs are key immune biomarkers for ICI benefit; HRD/BRCA status informs platinum/PARPi sensitivity (xiong2024advancementsandchallenges pages 1-2, jie2025diagnosisprognosisand pages 7-9).
Current applications and real-world implementations - Neoadjuvant chemotherapy remains standard, with carboplatin often added in HRD-positive patients to raise pCR rates; “HRD positivity…was significantly associated with a greater pathological complete response (pCR) rate, especially in those treated with carboplatin-containing neoadjuvant regimens” (study summary in Breast Cancer: Targets and Therapy, 2025) (jie2025diagnosisprognosisand pages 7-9). - Chemo-ICI combinations (e.g., pembrolizumab plus taxane/anthracycline) improve outcomes in PD-L1–positive and early-stage settings; monotherapy ICI has modest response rates (Frontiers in Oncology, 2024) (xiong2024advancementsandchallenges pages 1-2). - Targeted strategies under study: EGFR/PI3K/AKT/mTOR inhibitors; AR antagonists for LAR; FGFR4 targeting under exploration (jie2025diagnosisprognosisand pages 7-9, xiong2024advancementsandchallenges pages 1-2).
Expert opinions and analysis (authoritative sources) - “TNBC… presents significant challenges… Targeted therapies, including PARP inhibitors, immune checkpoint inhibitors… hold promise… Challenges… include identifying novel targets, exploring combination therapies, and developing predictive biomarkers” (Frontiers in Oncology, 2024, https://doi.org/10.3389/fonc.2024.1405491) (xiong2024advancementsandchallenges pages 1-2). - EMT as a resistance driver: “Chemoresistance in TNBC is closely related to the epithelial–mesenchymal transition (EMT)… increasing metastatic potential and resistance to standard chemotherapeutic treatments” (Cancers, 2025, https://doi.org/10.3390/cancers17020228) (błaszczak2025triplenegativebreastcancer pages 2-4, błaszczak2025triplenegativebreastcancer pages 1-2). - Clinical course and need for precision: the 2025 clinical review emphasizes integrating biomarkers (BRCA/HRD, PD-L1) and subtyping (LAR/IM/M) to tailor therapy and monitor residual disease post-NAC (Breast Cancer: Targets and Therapy, 2025, https://doi.org/10.2147/bctt.s516542) (jie2025diagnosisprognosisand pages 7-9).
Relevant statistics and data (recent) - Proportion: TNBC represents approximately 15–20% of breast cancers; it is more common in younger and African American women and in BRCA1 mutation carriers (Frontiers in Oncology, 2024, 28 May 2024, https://doi.org/10.3389/fonc.2024.1405491) (xiong2024advancementsandchallenges pages 1-2). - Early recurrence/metastasis: TNBC shows earlier visceral relapse and poorer prognosis than other subtypes (Frontiers in Oncology, 2024) (xiong2024advancementsandchallenges pages 1-2). - Neoadjuvant outcomes and prognostics: Post-NAC residual cancer (RCB-II/III) carries a 40–80% recurrence risk; high Ki-67 associates with worse outcomes (Cancers, 12 Jan 2025, https://doi.org/10.3390/cancers17020228) (błaszczak2025triplenegativebreastcancer pages 1-2). - Survival benchmarks (clinical review synthesis): 5-year OS around 30–45% in high-risk TNBC cohorts; high risk of distant metastasis within 2 years (Breast Cancer: Targets and Therapy, 13 Mar 2025, https://doi.org/10.2147/bctt.s516542) (jie2025diagnosisprognosisand pages 7-9).
Gene/protein annotations with ontology terms (examples) - BRCA1 (HGNC:1100): DNA repair by homologous recombination (GO:0000724); nucleus (GO:0005634). Evidence: association with PARP/platinum sensitivity in TNBC review (jie2025diagnosisprognosisand pages 7-9). - BRCA2 (HGNC:1101): DNA repair by HR (GO:0000724); nucleus (GO:0005634). Evidence: as above (jie2025diagnosisprognosisand pages 7-9). - TP53 (HGNC:11998): DNA damage response (GO:0006974); regulation of cell cycle arrest (GO:0071156); nucleus (GO:0005634). Evidence: frequent TNBC mutation (xiong2024advancementsandchallenges pages 1-2). - EGFR (HGNC:3236): EGFR signaling (GO:0007173); plasma membrane (GO:0005886). Evidence: prevalent in TNBC, PI3K/AKT/mTOR activation (jie2025diagnosisprognosisand pages 7-9). - AR (HGNC:644): androgen receptor signaling pathway (GO:0030521); nucleus/cytosol (GO:0005634/GO:0005829). Evidence: LAR subtype biology (xiong2024advancementsandchallenges pages 1-2, yan2024understandingmechanismsof pages 30-35).
Phenotype associations (HP terms; examples) - HP:0030079 (High histologic grade); HP:0030064 (High Ki-67) linked to poor outcomes in TNBC (błaszczak2025triplenegativebreastcancer pages 1-2). - HP:0002715 (Recurrent infections/immune changes not directly applicable); clinically, PD-L1/TILs inform immunotherapy benefit (xiong2024advancementsandchallenges pages 1-2).
Cell type involvement (CL terms; examples) - CL:0000066 (epithelial cell) → malignant basal-like epithelium with EMT/stemness (błaszczak2025triplenegativebreastcancer pages 2-4, błaszczak2025triplenegativebreastcancer pages 1-2). - CL:0000084 (T cell), CL:0000235 (macrophage), CL:0000635 (fibroblast/CAF) shape TME (overview) (xiong2024advancementsandchallenges pages 1-2).
Anatomical locations (UBERON; examples) - UBERON:0001911 (mammary gland). Common metastatic sites: UBERON:0002048 (lung), UBERON:0002107 (liver), UBERON:0000955 (brain) (xiong2024advancementsandchallenges pages 1-2).
Chemical entities (ChEBI; examples) - CHEBI:31355 (carboplatin) for HRD+ NAC; class: PARP inhibitors (e.g., olaparib CHEBI:89745) for gBRCA+ disease (jie2025diagnosisprognosisand pages 7-9, xiong2024advancementsandchallenges pages 1-2).
Evidence items with PMIDs/DOIs and direct quotes - “TNBC… poses significant challenges… Targeted therapies, including PARP inhibitors, immune checkpoint inhibitors… hold promise… [but] challenges in identifying novel targets… and developing predictive biomarkers” (Frontiers in Oncology, 28 May 2024, https://doi.org/10.3389/fonc.2024.1405491) (xiong2024advancementsandchallenges pages 1-2). - “Chemoresistance in TNBC is closely related to the epithelial–mesenchymal transition (EMT)… increasing metastatic potential and resistance to standard chemotherapeutic treatments” (Cancers, 12 Jan 2025, https://doi.org/10.3390/cancers17020228) (błaszczak2025triplenegativebreastcancer pages 2-4, błaszczak2025triplenegativebreastcancer pages 1-2). - Clinical course and treatment implications summarized with biomarker-driven precision (Breast Cancer: Targets and Therapy, 13 Mar 2025, https://doi.org/10.2147/bctt.s516542) (jie2025diagnosisprognosisand pages 7-9).
Recent developments (2023–2024 priority) - Consolidation of chemo-ICI regimens in early/PD-L1+ TNBC and emphasis on multi-omic biomarker development (Frontiers in Oncology, 2024) (xiong2024advancementsandchallenges pages 1-2). - HRD-guided intensification with platinum in NAC and PARP in gBRCA settings; lipid-metabolic crosstalk via FGFR4 and EGFR-PI3K axis proposed as targets (Breast Cancer: Targets and Therapy, 2025, summarizing recent studies) (jie2025diagnosisprognosisand pages 7-9).
Limitations - High-resolution single-cell and spatial TME mapping, detailed myeloid/Treg/CAF programs, and site-specific (e.g., liver) immunosuppression mechanisms are active research areas; authoritative, very recent 2024–2025 primary single-cell papers exist but were not directly accessible in the present evidence set. The conclusions above therefore emphasize robust review-level evidence available here (xiong2024advancementsandchallenges pages 1-2, jie2025diagnosisprognosisand pages 7-9) and focused EMT content (błaszczak2025triplenegativebreastcancer pages 2-4, błaszczak2025triplenegativebreastcancer pages 1-2).
References (with URLs and dates) - Xiong N, Wu H, Yu Z. Advancements and challenges in triple-negative breast cancer: a comprehensive review of therapeutic and diagnostic strategies. Frontiers in Oncology. 28 May 2024. https://doi.org/10.3389/fonc.2024.1405491 (xiong2024advancementsandchallenges pages 1-2). - Jie H, Ma W, Huang C. Diagnosis, Prognosis, and Treatment of Triple-Negative Breast Cancer: A Review. Breast Cancer: Targets and Therapy. 13 Mar 2025. https://doi.org/10.2147/bctt.s516542 (jie2025diagnosisprognosisand pages 7-9). - Błaszczak E, et al. Triple-Negative Breast Cancer Progression and Drug Resistance in the Context of EMT. Cancers. 12 Jan 2025. https://doi.org/10.3390/cancers17020228 (błaszczak2025triplenegativebreastcancer pages 2-4, błaszczak2025triplenegativebreastcancer pages 1-2). - Yan G. Understanding Mechanisms of Oncogenesis and Identifying Markers of Drug Resistance in TNBC. 2024 (overview text) (yan2024understandingmechanismsof pages 30-35). - Malabadi RB, et al. Triple Negative Breast Cancer (TNBC): Signalling pathways—Role of plant-based inhibitors. OARJBP. 16 Mar 2024. https://doi.org/10.53022/oarjbp.2024.10.2.0013 (malabadi2024triplenegativebreast pages 1-2).
References
(xiong2024advancementsandchallenges pages 1-2): Nating Xiong, Heming Wu, and Zhikang Yu. Advancements and challenges in triple-negative breast cancer: a comprehensive review of therapeutic and diagnostic strategies. Frontiers in Oncology, May 2024. URL: https://doi.org/10.3389/fonc.2024.1405491, doi:10.3389/fonc.2024.1405491. This article has 146 citations and is from a poor quality or predatory journal.
(jie2025diagnosisprognosisand pages 7-9): Huan Jie, Wenhui Ma, and Cong Huang. Diagnosis, prognosis, and treatment of triple-negative breast cancer: a review. Breast Cancer : Targets and Therapy, 17:265-274, Mar 2025. URL: https://doi.org/10.2147/bctt.s516542, doi:10.2147/bctt.s516542. This article has 27 citations.
(błaszczak2025triplenegativebreastcancer pages 2-4): Ewa Błaszczak, Paulina Miziak, Adrian Odrzywolski, Marzena Baran, Ewelina Gumbarewicz, and Andrzej Stepulak. Triple-negative breast cancer progression and drug resistance in the context of epithelial–mesenchymal transition. Cancers, 17:228, Jan 2025. URL: https://doi.org/10.3390/cancers17020228, doi:10.3390/cancers17020228. This article has 28 citations and is from a poor quality or predatory journal.
(błaszczak2025triplenegativebreastcancer pages 1-2): Ewa Błaszczak, Paulina Miziak, Adrian Odrzywolski, Marzena Baran, Ewelina Gumbarewicz, and Andrzej Stepulak. Triple-negative breast cancer progression and drug resistance in the context of epithelial–mesenchymal transition. Cancers, 17:228, Jan 2025. URL: https://doi.org/10.3390/cancers17020228, doi:10.3390/cancers17020228. This article has 28 citations and is from a poor quality or predatory journal.
(yan2024understandingmechanismsof pages 30-35): G Yan. Understanding mechanisms of oncogenesis and identifying markers of drug resistance in triple negative breast cancer. Unknown journal, 2024.
(malabadi2024triplenegativebreast pages 1-2): Ravindra B. Malabadi, Sadiya MR, Kiran P. Kolkar, Simuzar S. Mammadova, Raju K. Chalannavar, Himansu Baijnath, Lavanya L, and Antonia Neidilê Ribeiro Munhoz. Triple negative breast cancer (tnbc): signalling pathways-role of plant-based inhibitors. Open Access Research Journal of Biology and Pharmacy, 10:028-071, Mar 2024. URL: https://doi.org/10.53022/oarjbp.2024.10.2.0013, doi:10.53022/oarjbp.2024.10.2.0013. This article has 32 citations.