36P Multiplexed RNA-FISH-guided laser capture microdissection RNA sequencing improves breast cancer molecular subtyping and prognostic classification

• DOI: 10.1016/j.esmoop.2024.103044
• Publication Date: 2024-05-17T11:08:45Z
• Authors: E.D. Paul; B. Huraiová; N. Valková; N. Matyašovská; D. Gábrišová; S. Gubová; H. Ignačáková; T. Ondris; S. Bendíková; D. Lovíšek; M. Gala; M. Ristová; I. Comino-Méndez; P. Morozov; F. Pareja; J.N. Kather; P. Cekan
• Keywords: Subtyping; Laser capture microdissection; Microdissection

Multigene tests provide information that may guide the optimal treatment regimen for breast cancer (BCa) patients. However, assignment of an individual tumor to any subtype/prognostic risk group shows only moderate reproducibility depending on assay, composition, gene list and expression thresholds. This single-sample discordance impedes clinical use raises important questions about which is right test whether multiple are better than one. We used multiplexed RNA fluorescent in situ hybridization four BCa biomarkers, estrogen/progesterone/Her2/Ki67, laser capture microdissection followed by RNAseq. technique, called mFISHseq, ensures purity, facilitates interrogation heterogeneity, permitting unbiased whole transcriptome analysis. To ascertain multigene discordance, we applied mFISHseq a cohort 1,082 FFPE tumors with detailed clinicopathological data derived molecular subtypes using research based PAM50, AIMS, our own 293-gene subtyping classifier. also assigned patients prognostic groups OncotypeDX, GENE70, recurrence subtype, GGI. observed considerable 24% 61% having at least one disagreement assignment, respectively. improve single sample concordance, implemented simple voting scheme classifiers assign consensus subtype/risk group. Consensus reclassified 30% into fit their transcriptomic outcome, further identified 60% these received suboptimal treatment. Likewise, approach mitigated provided insights high, low, ultra-low risk. By leveraging spatially resolved, enriched profiling, alleviated sample-level individuals subtypes/prognostic matched thus resolving limitations adoption.