High HER2 Intratumoral Heterogeneity Is Resistant to Anti-HER2 Neoadjuvant Chemotherapy in Early Stage and Locally Advanced HER2-Positive Breast Cancer

<b>Background/Objectives</b>: Breast cancer tumors possess intratumoral heterogeneity (ITH), which is associated with therapeutic resistance. Tumors with high ITH exhibit human epidermal growth factor receptor 2 (HER2) heterogeneity, affecting the effectiveness of HER2-targeted therapies. Our recent study identified HER2 ITH as an independent prognostic factor for poor outcomes in HER2-positive breast cancer. We here investigated the association between HER2 ITH and anti-HER2 neoadjuvant chemotherapy (NAC) resistance. <b>Methods</b>: This study included 97 patients with primary HER2-positive breast cancer treated with anti-HER2 NAC. Breast tumor samples were obtained from vacuum-assisted breast biopsy before NAC. HER2 gene amplification was assessed using fluorescence in situ hybridization (FISH), and HER2 gene copy number histograms were generated. Using the Gaussian mixture model, histogram data were analyzed and categorized into the high (HH) and low HER2 heterogeneity (LH) groups. The association between HER2 ITH and treatment response was evaluated using the pathological complete response (pCR) rate. <b>Results</b>: Of the 97 patients, 18 (18.6%) and 79 (81.4%) were classified into the HH and LH groups, respectively. The pCR rate in the HH group was significantly lower at 28% (5/18) than that in the LH group at 65% (51/79) (<i>p</i> < 0.01). Multivariate analysis of pathological parameters revealed that the most significant predictor of pCR rate was HER2 ITH (<i>p</i> = 0.02). <b>Conclusions</b>: HER2 ITH assessment may be valuable in predicting therapeutic outcomes in HER2-positive breast cancer. Our novel approach of the HER2 ITH method using FISH histograms could serve as a useful tool for predicting anti-HER2 NAC resistance.