Transcript-based circulating tumor and cancer stem cell detection in inflammatory breast cancer: a six-year prospective evaluation of assay yield and prognostic performance

Inflammatory breast cancer (IBC) is a rare and aggressive presentation for which no validated blood-based monitoring tool exists, and the tumor emboli that define its biology have motivated interest in circulating tumor cell (CTC) assays. We prospectively evaluated a transcript-based platform combining epithelial CTC markers (MUC1, HER2, GA733-2) and cancer stem cell (CSC)-associated markers (TWIST, AKT, PI3K, ALDH1) in patients with stage III breast cancer enrolled from 2013 to 2020, comparing 54 patients with IBC against 23 with non-IBC disease across 222 quality-controlled serial samples. Using the manufacturer-defined positivity thresholds, 14% of samples were CTC-positive and 29% CSC-positive. No marker distinguished IBC from non-IBC at baseline: GA733-2 was positive in 7 of 54 IBC versus 1 of 23 non-IBC patients (p = 0.42), and the composite positive categories did not differ (p = 0.71 for CTC, p = 0.11 for CSC). HER2 and TWIST transcripts were undetectable at threshold in all 77 patients. Among 44 IBC patients evaluable for event-free survival over a median 65 months of follow-up, neither baseline CTC positivity (log-rank p = 0.10) nor CSC positivity (p = 0.55) stratified outcome. Threshold sensitivity analysis showed that detectable signal clustered an order of magnitude below the positivity cutoffs, so that no threshold produced both an adequate positivity rate and outcome discrimination. Positivity at any draw during follow-up, and an additive classification combining both marker classes, likewise showed no association with outcome. Benchmarked against a tumor-informed ctDNA assay evaluated by our group in the same disease setting, the two platforms showed near-identical sample-level positivity (29% versus 27%) and technical QC performance, yet only ctDNA positivity tracked disease trajectory and preceded radiographic relapse. These findings indicate that transcript-based CTC and CSC detection, as implemented here, does not provide clinically actionable risk stratification in IBC, and they support prioritizing sequencing-based circulating tumor DNA and next-generation CTC platforms for minimal residual disease monitoring in this population.