Abstract

Background: Breast cancer is biologically heterogeneous, and gene-expression studies have demonstrated clinically relevant intrinsic subtypes with differing patterns of prognosis and treatment response. Contemporary management, however, does not rely on intrinsic subtype alone; clinicopathological factors, immunohistochemistry (IHC), in situ hybridization, validated genomic assays, germline alterations, and treatment-specific biomarkers are integrated to guide therapy. Objective: This paper aims to review the evolution of molecular classification of breast cancer and critically summarize how molecular and biomarker information informs contemporary diagnosis, prognostication, systemic treatment, and precision-oncology strategies. Methods: A PRISMA-guided narrative review was conducted using PubMed/MEDLINE, Scopus, Web of Science, Cochrane Library, and Google Scholar, with reference-list screening of landmark molecular studies, clinical trials, and major guidelines. Searches covered database inception through June 2025. Titles and abstracts were screened, followed by full-text assessment; two reviewers independently screened and extracted data, with disagreements resolved by discussion and, when necessary, a third reviewer. Evidence was synthesized narratively, with explicit separation of intrinsic molecular subtypes, prognostic assays, predictive biomarkers, and treatment-eligibility biomarkers. Results: The reviewed evidence supports a layered model of classification. Intrinsic subtypes are transcriptomic constructs and are not interchangeable with routine IHC-defined clinical categories; in particular, HER2-enriched is not defined by ERBB2 amplification. Validated genomic assays have assay- and population-specific roles in HR-positive/HER2-negative early breast cancer, ranging from recurrence-risk estimation to chemotherapy-benefit assessment in defined populations. In TNBC, treatment selection is driven primarily by disease setting and validated biomarkers such as germline BRCA1/2 and PD-L1 in specific metastatic contexts, whereas proposed transcriptomic subclasses remain investigational. HER2-low is a treatment-relevant IHC expression category rather than an intrinsic molecular subtype. Overall, molecular information is most useful when integrated with stage, pathology, receptor status, and patient factors. Conclusion: Molecular classification has moved breast oncology from morphology-based categorization toward biologically informed treatment selection. Its greatest clinical value arises when molecular information is interpreted in context rather than used as a substitute for stage, histological features, receptor status, patient factors, and validated treatment-specific biomarkers.

Keywords

Breast Cancer, Molecular Classification, Intrinsic Subtypes, HER2-Enriched, Triple-Negative Breast Cancer, HER2-Low, Genomic Assays, Precision Oncology

Share and Cite:

1. Introduction

Breast cancer is the most frequently diagnosed cancer among women worldwide and remains a major cause of cancer mortality. Its biological heterogeneity is reflected in substantial differences in natural history, endocrine sensitivity, response to chemotherapy, sensitivity to targeted therapies, and patterns of recurrence. Conventional histopathology, tumour grade, stage, and receptor assessment remain essential, but they do not capture the full biological diversity of breast cancer.

Gene-expression profiling provided the foundation for intrinsic molecular classification. Perou and colleagues identified reproducible gene-expression patterns that included luminal, HER2-related, basal-like, and normal-breast-like groups; subsequent work refined these categories and demonstrated associations with clinical outcome [1] [2]. Importantly, intrinsic molecular subtypes and routine clinical biomarkers overlap but are not synonymous. A tumour classified as HER2-enriched by a transcriptomic assay may be HER2-negative by conventional IHC/ISH, while many clinically HER2-positive tumours do not necessarily belong to the HER2-enriched intrinsic subtype.

The therapeutic relevance of molecular information has expanded substantially. Endocrine therapy remains central to hormone-receptor-positive disease, HER2-directed treatment is determined by validated clinical HER2 testing, and genomic assays can refine recurrence-risk estimation and, in selected populations, inform chemotherapy decisions [3]-[8].

This review therefore focuses on the clinically meaningful relationship between molecular classification and treatment while avoiding conflation of prognostic classification, predictive biomarkers, and treatment eligibility.

2. Methods

2.1. Review Design

This systematic narrative review was reported using the PRISMA 2020 framework for transparent identification, screening, eligibility assessment, and reporting of the literature. The review was designed to synthesize landmark molecular studies, contemporary clinical trials, validated genomic assays, and major clinical-practice guidelines rather than to perform a quantitative meta-analysis [9]. Searches were conducted through June 2025 (final search month: June 2025).

2.2. Information Sources and Search Strategy

The information sources were PubMed/MEDLINE, Scopus, Web of Science, Cochrane Library, and Google Scholar. Reference lists of key molecular studies, clinical trials, and guideline documents were also screened. The search covered database inception through June 2025. The core concept combined breast cancer with molecular classification/intrinsic subtypes and clinically relevant treatment, biomarker, prognosis, or genomic-assay terms. Database-specific syntax was adapted to each platform; the reproducible search strings used for this revision are provided in Supplementary Table S1.

2.3. Eligibility Criteria

Eligible literature comprised peer-reviewed human studies addressing breast-cancer molecular classification, intrinsic subtypes, clinically validated biomarkers, genomic assays, targeted treatment, immunotherapy, antibody-drug conjugates, or precision-oncology approaches. Landmark molecular studies, randomized clinical trials, prospective validation studies, systematic reviews, and major international guidelines were prioritized. Non-human studies, duplicate publications, conference abstracts without adequate full text, and publications without direct relevance to the review question were excluded.

2.4. Screening, Data Extraction, and Reviewer Roles

Titles and abstracts were screened against the predefined eligibility criteria, followed by full-text assessment of potentially relevant reports. Two reviewers independently screened records and extracted data. Disagreements were resolved by discussion and, when required, by a third reviewer. The extraction fields included study design, population, molecular classification or biomarker, clinical setting, treatment decision addressed, principal outcomes, and whether the evidence was prognostic, predictive, or treatment-eligibility defining.

2.5. Full-Text Exclusion

At full-text review, reports were excluded when they did not address the review question or eligible population, used a non-clinical/research-only classification without a relevant management implication, represented a duplicate or overlapping cohort, lacked sufficient clinical information, or did not provide usable full text. The documented aggregate flow was 176 full-text reports assessed and 82 studies retained; therefore, 94 reports were excluded at full-text stage. The exclusion categories are listed in Supplementary Table S2.

2.6. Synthesis

Evidence was synthesized narratively. Particular attention was given to distinguishing intrinsic molecular subtype from IHC-defined clinical subtype, prognostic risk estimation from prediction of treatment benefit, and exploratory molecular associations from validated treatment-selection biomarkers. No quantitative meta-analysis was performed.

3. Results

The evidence synthesis was organized into intrinsic molecular classification, luminal disease, HER2-related disease, TNBC, HER2-low expression, genomic assays, and emerging precision-oncology strategies. The principal finding was that molecular information is most clinically useful when integrated with conventional pathology, anatomical stage, receptor testing, patient characteristics, and the treatment context. The study-selection process is summarized in Figure 1.

Figure 1. PRISMA 2020 study-selection flow diagram.

3.1. Evolution and Interpretation of Molecular Classification

The original intrinsic taxonomy included Luminal A, Luminal B, HER2-enriched, basal-like, and normal-like patterns. Gene-expression profiling demonstrated reproducible biological patterns, while subsequent work established the clinical relevance and limitations of these intrinsic categories [1] [2]. Importantly, intrinsic subtypes are transcriptomic constructs and are not interchangeable with routine IHC-defined clinical categories. The relationship between intrinsic molecular patterns and routine clinical testing is summarized in Table 1 and Figure 2. Intrinsic subtypes should not be reconstructed solely from ER, PR, HER2, and Ki-67 values; IHC and ISH remain the standard methods for defining clinical receptor status.

Table 1. Intrinsic molecular patterns and their relationship to routine clinical testing.

Figure 2. Relationship between intrinsic molecular classification, routine biomarkers, and treatment-specific biomarkers.

3.2. Luminal A and Luminal B Disease

Hormone-receptor-positive, HER2-negative breast cancer constitutes the largest clinical group. Endocrine therapy is the foundation of treatment, but recurrence risk varies widely. The labels Luminal A and Luminal B are useful biological concepts rather than stand-alone treatment algorithms. Tumour size, nodal status, histological grade, receptor expression, proliferation, patient age/menopausal status, and genomic assay results may all contribute to adjuvant decisions. Table 1 summarizes the relationship between intrinsic molecular patterns and routine clinical testing.

CDK4/6 inhibitors have expanded adjuvant treatment options for selected higher-risk HR-positive/HER2-negative early breast cancer. In monarchE, abemaciclib plus endocrine therapy improved invasive disease-free survival in a high-risk, node-positive population, with sustained benefit at longer follow-up [10] [11]. NATALEE subsequently demonstrated improved invasive disease-free survival with ribociclib plus a nonsteroidal aromatase inhibitor in a broader stage II/III HR-positive/HER2-negative population [12]. These results should be interpreted within their trial-defined populations rather than assigned generically to all Luminal B tumours.

3.3. HER2-Enriched versus Clinically HER2-Positive Breast Cancer

HER2-enriched is a gene-expression subtype and is not defined by ERBB2 amplification. HER2-enriched tumours may show high expression of HER2-related genes and pathway activation, but transcriptomic HER2-enriched status is not equivalent to HER2 amplification or IHC 3+ status [13]. Therefore, HER2-enriched should not be used as a synonym for clinically HER2-positive disease. For treatment purposes, clinical HER2 status remains based on validated IHC and ISH testing.

For treatment purposes, clinical HER2 status remains based on validated IHC and ISH testing. HER2-positive early breast cancer may receive neoadjuvant and/or adjuvant HER2-directed therapy according to stage and risk, while advanced disease can be treated with HER2-directed agents according to treatment line and clinical context [14] [15].

3.4. Triple-Negative Breast Cancer

TNBC is defined clinically by the absence of ER and PR expression and lack of HER2 overexpression/amplification according to accepted testing criteria. It is biologically heterogeneous, with basal-like, mesenchymal, luminal-androgen-receptor, immune-related, and other proposed transcriptomic groups. These research classifications have not been established as routine treatment-selection biomarkers [16].

In early TNBC, pembrolizumab combined with neoadjuvant chemotherapy and continued after surgery improved event-free outcomes in the KEYNOTE-522 population [17] [18]. PD-L1 expression did not define eligibility for the early-stage KEYNOTE-522 regimen. In metastatic TNBC, however, PD-L1 testing can guide pembrolizumab-containing therapy in appropriate patients, including the KEYNOTE-355 population with PD-L1 combined positive score thresholds specified by the trial and applicable guidance [19]. Thus, PD-L1 is a treatment-specific biomarker in defined metastatic settings and is not a universal molecular definition of TNBC or a requirement for early-disease pembrolizumab.

Germline BRCA1/2 status is another clinically validated biomarker. In OlympiA, adjuvant olaparib improved invasive and distant disease-free outcomes in patients with high-risk, HER2-negative early breast cancer carrying germline pathogenic or likely pathogenic BRCA1/2 variants after local treatment and chemotherapy [20]. This illustrates the distinction between a molecular alteration that identifies a treatment opportunity and an intrinsic subtype that describes tumour biology.

Sacituzumab govitecan has demonstrated activity in previously treated metastatic TNBC, including in the phase 3 ASCENT trial [21]. Its use should be described according to the disease setting and prior-treatment context rather than as therapy selected solely by an intrinsic TNBC molecular subclass.

3.5. HER2-Low Expression

HER2-low is not an intrinsic molecular subtype. It is a treatment-relevant IHC expression category generally referring to HER2 IHC 1+ or IHC 2+ with negative ISH in the context of clinical-trial eligibility. The ASCO/CAP guideline update retained the established HER2 testing framework while acknowledging the therapeutic relevance of trastuzumab deruxtecan in tumours with IHC 1+ or 2+ without amplification [14] [22]. The biological heterogeneity of HER2-low tumours means that HER2-low should not be presented as a discrete intrinsic molecular class.

DESTINY-Breast04 demonstrated improved progression-free and overall survival with trastuzumab deruxtecan compared with physician’s-choice chemotherapy in previously treated HER2-low advanced breast cancer [22]. The clinical implication is treatment-specific: low HER2 expression can provide a target for an antibody-drug conjugate even when the tumour is not HER2-positive by conventional amplification/overexpression criteria.

Emerging evidence has also examined very low HER2 expression, including HER2-ultralow categories. These categories are treatment- and jurisdiction-specific and should not be interpreted as new intrinsic molecular subtypes. Their clinical use should follow the applicable regulatory indication, assay, and guideline.

3.6. Genomic Assays: Prognostic versus Predictive Utility

Multigene assays have an important but specific role in selected HR-positive/HER2-negative early breast cancers. Their clinical roles differ by assay and population. Some assays are primarily prognostic, whereas prospective evidence supports chemotherapy-benefit assessment for specific assays in defined populations [4]-[8]. Table 2 summarizes the validated clinical context and the distinction between prognostic and predictive utility.

Table 2. Genomic assays: validated populations and prognostic versus predictive roles.

TAILORx showed that many women with HR-positive/HER2-negative, node-negative disease and intermediate 21-gene recurrence scores can avoid adjuvant chemotherapy without compromising invasive disease-free outcomes, although age and recurrence-score range modify the magnitude of chemotherapy benefit [4] [5]. RxPONDER further demonstrated that menopausal status matters in node-positive disease: postmenopausal women with one to three positive nodes and recurrence scores of 25 or lower did not derive a clinically meaningful chemotherapy benefit, whereas premenopausal women did derive benefit [6]. These findings illustrate why genomic scores should not be interpreted independently of clinical and patient characteristics.

MINDACT provided prospective evidence for use of a 70-gene signature in selected patients with discordant clinical and genomic risk, particularly those with high clinical risk and low genomic risk [7]. Its principal contribution is risk stratification and chemotherapy decision support in its validated population, not a universal prediction of chemotherapy sensitivity.

3.7. Precision Oncology and Actionable Genomic Alterations

Next-generation sequencing can identify alterations with therapeutic implications, particularly in advanced disease. Examples include PIK3CA alterations in HR-positive/HER2-negative breast cancer, ESR1 alterations associated with endocrine resistance, and AKT-pathway alterations. Germline BRCA1/2 status can identify candidates for PARP inhibition in appropriate settings. Molecular testing should therefore be linked to a specific therapeutic decision; broad genomic profiling does not automatically imply that every detected alteration is clinically actionable.

Precision oncology also increasingly includes circulating tumour DNA, minimal residual disease approaches, transcriptomic signatures, digital pathology, artificial intelligence, and multi-omics integration. These technologies are promising but vary substantially in analytical and clinical validation. Research findings should therefore be distinguished from biomarkers already incorporated into treatment guidance. The clinical questions and corresponding validated uses are summarized in Table 3.

3.8. Clinical Integration of Molecular Information

Table 3. Clinical integration of molecular information in contemporary breast-cancer management.

4. Discussion

The principal clinical contribution of molecular classification is not the replacement of conventional pathology but its integration with it. Intrinsic subtypes provide a framework for understanding tumour biology, whereas treatment decisions usually depend on receptor status, anatomical stage, histological features, validated biomarkers, patient characteristics, and evidence supporting a particular therapy. The evidence summarized in this review therefore supports a layered rather than a subtype-only model of decision-making.

The distinction between HER2-enriched and clinically HER2-positive disease is important because a transcriptomic label does not establish eligibility for conventional anti-HER2 treatment. Conversely, clinically HER2-positive tumours are defined by validated pathology testing regardless of whether their transcriptomic profile is labelled HER2-enriched [13]-[15].

The role of genomic assays is assay- and population-specific. The 21-gene assay has prospective evidence informing chemotherapy decisions in defined HR-positive/HER2-negative populations, while other assays have predominantly prognostic roles or different validated indications [4]-[8]. The review therefore avoids the unsupported generalization that all multigene assays predict chemotherapy benefit.

TNBC demonstrates a similar principle. Proposed molecular subtypes have biological and research value, but treatment selection currently relies more heavily on clinical stage, receptor testing, germline BRCA status, PD-L1 in specific metastatic settings, and evidence for particular systemic therapies [16]-[21]. The distinction between early and metastatic disease is particularly important for PD-L1 because the biomarker does not define eligibility for the KEYNOTE-522 early-TNBC regimen [17] [18].

HER2-low further illustrates the difference between taxonomy and therapeutics. HER2-low is best viewed as a treatment-relevant IHC expression category rather than a stable intrinsic molecular subtype [14] [22]. The emergence of antibody-drug conjugates demonstrates that therapeutic classification can evolve faster than biological taxonomy.

Several limitations should be acknowledged. Molecular classifications are influenced by assay platform, tumour heterogeneity, sampling, and temporal evolution. Intrinsic subtype assignment can vary between platforms and may not fully capture changes between primary and metastatic disease or after treatment. Selection of literature in a narrative review can also introduce interpretive bias, and the evidence base for emerging biomarkers evolves rapidly. Access to molecular testing and targeted therapies varies across healthcare systems.

Future research will likely integrate transcriptomic, genomic, epigenomic, proteomic, spatial, radiomic, digital-pathology, and circulating-tumour-DNA data. However, increasingly complex molecular classification will only improve patient care if biomarkers demonstrate analytical validity, clinical validity, clinical utility, and reproducible effects on meaningful patient outcomes.

5. Conclusion

Molecular classification has transformed the understanding and management of breast cancer, but its clinical value lies in integration rather than replacement of clinicopathological assessment. Intrinsic subtypes provide a biologically informative framework; validated receptor testing defines major therapeutic categories; genomic assays refine risk and, in selected populations, chemotherapy decisions; and treatment-specific biomarkers such as germline BRCA1/2 and PD-L1 identify particular therapeutic opportunities. HER2-enriched should be understood as a gene-expression subtype rather than a synonym for ERBB2 amplification, while HER2-low should be regarded as a clinically relevant IHC expression category rather than an intrinsic molecular subtype. Contemporary precision oncology therefore depends on matching each molecular measurement to the specific clinical decision it has been validated to inform.

Declaration of AI Use

The authors declare that AI tools were used to assist with data analysis and figure preparation.

Author Contributions

‌Both authors contributed equally to the preparation of this manuscript.

Supplementary Tables

Table S1. Database-specific search strategies used for the literature search (searches through June 2025).

Table S2. Primary categories used to document reasons for full-text exclusion. The archived draft supplied aggregate counts but not reason-specific frequencies.

Conflicts of Interest

The authors declare no conflicts of interest regarding the publication of this paper.

References