Breast Cancer Under the Microscope: How Pathologists Diagnose and Classify the Disease

From specimen to diagnosis

A breast cancer diagnosis begins with tissue. Whether the sample arrives as a core needle biopsy (a thin cylinder of tissue sampled under imaging guidance) or as a larger surgical excision, the pathologist's first job is the same: to determine whether a malignancy is present, and if so, what kind. The tissue is fixed in formalin, embedded in paraffin, sliced into micron-thin sections, and stained with hematoxylin and eosin (H&E) — a stain that colors nuclei blue-purple and cytoplasm and stroma pink. This humble stain remains the backbone of diagnosis: architecture, cell shape, and the relationship of tumor cells to surrounding tissue are all read first on H&E.

The single most important question on H&E is whether the lesion is in situ (confined within the duct-lobular system) or invasive (breaching the basement membrane into stroma). This distinction hinges on the myoepithelial layer — the outer cell coat of normal ducts and lobules. When that layer is intact, the proliferation is in situ; when it is absent and tumor cells infiltrate stroma freely, the lesion is invasive. Where H&E is ambiguous, immunohistochemistry (IHC) for myoepithelial markers such as p63, calponin, and smooth-muscle myosin heavy chain (SMMHC) settles the question [1, 2].

Every invasive carcinoma is then characterized by a standard biomarker panel — estrogen receptor (ER), progesterone receptor (PR), and HER2 — assessed on essentially every case, because these markers define eligibility for endocrine and HER2-directed drug classes and shape prognosis [1, 2].

The H&E picture

Across the catalogue of breast carcinomas, recurring morphologic themes organize the diagnosis. Pathologists read architecture (do cells form tubules, sheets, single files, sieve-like cribriform islands, or papillary fronds?), cytology (nuclear size, uniformity, nucleoli, cytoplasm), mitotic activity, and stromal response (desmoplasia, mucin, necrosis). A few patterns are nearly diagnostic at a glance: single-file infiltration with loss of cohesion suggests lobular carcinoma; well-formed angulated tubules with low-grade nuclei suggest tubular carcinoma; tumor clusters floating in mucin lakes signal mucinous carcinoma; and morule-like clusters sitting in empty lacunar spaces with reversed "inside-out" polarity define invasive micropapillary carcinoma [1].

When morphology alone cannot resolve a case, ancillary tests refine it. E-cadherin loss with cytoplasmic relocalization of p120 catenin supports lobular differentiation [1]. Certain rare subtypes carry defining molecular lesions that double as diagnostic tools: MYB::NFIB fusion in adenoid cystic carcinoma, ETV6::NTRK3 fusion in secretory carcinoma, and the IDH2 R172 hotspot mutation in tall cell carcinoma with reversed polarity [1].

The major categories

In situ lesions. Ductal carcinoma in situ (DCIS) is a neoplastic epithelial proliferation confined by an intact myoepithelial layer, displaying comedo, cribriform, micropapillary, papillary, or solid patterns, and graded low/intermediate/high by nuclear grade and necrosis [1, 2]. Lobular carcinoma in situ (LCIS) is a dyscohesive proliferation expanding acini with E-cadherin loss; classic LCIS is a risk indicator and non-obligate precursor and is not staged as pTis, whereas pleomorphic and florid variants behave more aggressively [1, 3, 2].

The common invasive carcinomas. Invasive breast carcinoma of no special type (IBC-NST) — formerly "invasive ductal carcinoma, NOS" — is the most common invasive cancer and a diagnosis of exclusion for tumors lacking sufficient special-type features [1]. Invasive lobular carcinoma (ILC) shows single-file, discohesive, targetoid growth, usually ER-positive/HER2-negative, with characteristic (though not obligatory) E-cadherin loss and a distinctive metastatic pattern [1].

Favorable-prognosis special types. Tubular and cribriform carcinomas are low-grade, strongly ER/PR-positive tumors with excellent outcomes [1]. Mucinous carcinoma (types A and B) is favorable when pure [1]. Invasive papillary carcinoma belongs to the papillary-lesion family, classified by the presence of myoepithelium and true invasion [1].

Salivary-gland-analogue and fusion-driven tumors. Adenoid cystic carcinoma is typically triple-negative yet indolent in classic form, driven by MYB rearrangement [1]. Secretory carcinoma carries the ETV6::NTRK3 fusion, making it a candidate for the TRK-inhibitor drug class in advanced disease [1]. Also in this family: acinic cell carcinoma, mucoepidermoid carcinoma, and the very rare polymorphous adenocarcinoma [1].

Aggressive and distinctive types. Invasive micropapillary carcinoma is prognostically adverse with high lymphovascular invasion even as a minor component [1]. Metaplastic carcinoma shows squamous and/or mesenchymal differentiation, is usually triple-negative, and is relatively chemoresistant [1]. Carcinoma with apocrine differentiation often occupies the triple-negative, androgen-receptor-positive space [1]. Neuroendocrine tumor (NET) and neuroendocrine carcinoma (NEC) are grouped under neuroendocrine neoplasms in the current classification [1, 4].

Newly recognized and biphasic entities. WHO5 introduced mucinous cystadenocarcinoma and tall cell carcinoma with reversed polarity as new entities [1, 5]. Malignant adenomyoepithelioma and phyllodes tumor (benign/borderline/malignant) round out the biphasic and fibroepithelial categories [1].

How grading and staging work

For most invasive carcinomas, grade is assigned by the Nottingham combined histologic grade, which sums three scored components — tubule formation, nuclear pleomorphism, and mitotic count — to yield grade 1, 2, or 3 [1, 2]. Some special types are low-grade by definition (tubular, cribriform). DCIS uses its own nuclear-grade-plus-necrosis scheme, and phyllodes tumors use a three-tier system based on stromal cellularity, atypia, mitoses, overgrowth, and margins [1].

Staging is separate from grading and follows the AJCC system, integrating tumor size, nodal status, and distant spread, with prognostic stage groups now incorporating biomarker status [3]. Notably, classic LCIS was removed from the pTis category in AJCC 8th edition, reflecting its status as a risk marker rather than a true in situ carcinoma [3].

Why classification matters

Classification is not academic labeling. Subtype, grade, and biomarker profile together determine prognosis and eligibility for entire therapeutic drug classes — endocrine therapy for ER-positive disease, HER2-directed agents for HER2-positive disease, and, for fusion-positive secretory carcinoma, TRK inhibitors in the advanced setting [1, 2]. The evidence suggests that accurate subtyping also explains otherwise puzzling behavior: a triple-negative immunophenotype is ominous in metaplastic carcinoma but compatible with excellent outcomes in classic adenoid cystic carcinoma [1].

What's current

The 5th-edition WHO classification reshaped breast pathology, and these changes are worth flagging explicitly because older reports may use superseded names. Several formerly "special" patterns — oncocytic, lipid-rich, glycogen-rich (clear cell), sebaceous, choriocarcinomatous, melanocytic, pleomorphic, and osteoclast-like-giant-cell carcinomas — were folded into IBC-NST rather than retained as standalone entities [1, 5]. The medullary carcinoma group was removed as a distinct entity owing to poor interobserver reproducibility and is now described as IBC-NST with a basal-like/medullary pattern and prominent tumor-infiltrating lymphocytes [5]. Conversely, new entities were added, including mucinous cystadenocarcinoma and tall cell carcinoma with reversed polarity [1, 5]. These reclassifications are a fast-moving area; pathologists verify each diagnosis against the current WHO blue book and the current CAP protocol before reporting [1, 2].

References

1. WHO Classification of Tumours Editorial Board. Breast Tumours. WHO Classification of Tumours, 5th ed., vol. 2. IARC, Lyon; 2019. ISBN 978-92-832-4500-1.
2. College of American Pathologists. Protocol for the Examination of Specimens From Patients With Invasive Carcinoma of the Breast. CAP Cancer Protocols (current version).
3. Amin MB, Edge S, Greene F, et al. (eds). AJCC Cancer Staging Manual, 8th ed. Springer, New York; 2017. ISBN 978-3-319-40617-6.
4. Neuroendocrine Neoplasms of the Breast: WHO Classification and Review. Review literature; 2022. PMC8750232.
5. What's new in breast pathology: WHO 5th edition and biomarker updates. Journal of Pathology and Translational Medicine (and equivalent review literature); 2022.