Spatial Transcriptomics and Bulk RNA-Seq Analysis Revealed Molecular Classification of Invasive Lobular Carcinoma

Invasive lobular carcinoma (ILC) is a special type of breast cancer. The histological subtypes of ILC exhibit diverse morphological features, and the prognosis differs accordingly. Compared with patients with classic-ILC (C-ILC), patients with pleomorphic-ILC (P-ILC) have a worse prognosis, owing to high-grade nuclear atypia and mitotic cells. However, the molecular differences between C-ILC and P-ILC remain unclear. To address this gap, we performed spatial transcriptomic profiling on four fresh-frozen C-ILC samples and four fresh-frozen P-ILC samples, followed by confirmation of reproducibility in bulk RNA-seq datasets. We identified significant enrichment of cellular response to heat stress in P-ILC. Furthermore, molecular clustering analysis using genes differentially expressed across ILC samples in spatial transcriptome revealed that ILC has three molecular subtypes: proliferative (PR), immunoreactive (IM), and stroma-rich (ST), associated with distinct prognostic outcomes. Although these molecular subtypes did not completely correspond to C-ILC or P-ILC, PR tended to include P-ILC, and ST tended to include C-ILC. These molecular clusters exhibited features comparable to previously reported subtypes. Despite these phenotypic features, ILC is generally treated similarly to invasive ductal carcinoma (IDC), with limited consideration of molecular subtype classification. Our findings suggest that molecular profiling may more accurately reflect prognosis than conventional histological classification and may provide potential diagnostic markers and therapeutic targets.