Abstract Introduction and rationale: There is a wide-spread urgent need for an objective reproducible diagnostic tool capable of precisely classifying atypical mammary lesions into cancer vs. benign. Current diagnostic methods in pathology rely on routine and highly subjective histomorphologic and immunophenotypic features. Some authors report a 35% error rate in pathologic interpretation of atypical lesions of the breast (Elmore, 2015). Diagnostic variability can drop to the flip-of-the-coin 50%, even amongst expert breast pathologists (Tozbekian, 2017; Samples, 2017) and is largely attributed to the lack of innovative tools to adequately distinguish biologic differences (Allison, 2016), resulting in diagnoses that are described as “murky” and “arbitrary” (Khoury, 2022). Genomic imprinting, a vital epigenetic regulatory mechanism, is critical in mammalian development and tumorigenesis (Barlow, 2014, Murrell, 2006). Typically, imprinted genes exhibit parent-specific allele silencing through differential methylation. However, in cancer, this regulation often breaks down, resulting in the aberrant activation of the typically silenced allele—a phenomenon known as loss of imprinting (LOI) (Jelinic, 2016). LOI is considered one of the earliest molecular changes in cancer development, occurs early in tumorigenesis, making it ideal for identifying precursor lesions. Objectives: We hypothesize loss of imprinting (LOI) can be developed as a diagnostic, predictive and prognostic novel epigenetic marker (Quantitative Chromogenic Imprinted Gene In-Situ Hybridization, QCIGISH) for breast precancerous lesions and cancer detection. Our objective is to initiate a proof of concept for atypical breast lesions with QCIGISH and develop a diagnostic model. Methods: We retrospectively identified benign, atypical, and carcinoma core needle specimens from year 2023 in the Department of Pathology at Mayo Clinic Florida. Inclusion criteria included female patients, ages 18-99, with archived breast material obtained through standard of care (n=20). All diagnoses were ascertained by a breast pathologist (MKK). Following a thorough literature review, we processed the material for in situ hybridization, and pretreated with RNA scope preparation procedure using probes targeting noncoding intronic regions of nascent RNAs (QCIGISH). Based on high Area Under the Receiver Operating Characteristics Curve (AUROC), 2 genes - HM13 and GRB10 were identified as the most promising candidates for classification with QCIGISH. Upon test completion, the detected gene-expression site appeared as a distinct red dot on the slide under the common bright-field microscope. Next, the gene expression signals were counted and further classified as bi-allelic (BAE), multi-allelic (MAE) and total expression (TE). Results: A decision tree model based on BAE, MAE, and TE metrics showed differential signal expression. High MAE was a strong predictor for malignancy. We achieved 100% sensitivity and specificity with the ground truth, thereby initiating proof of concept. Furthermore, one histomorphologically challenging atypical lesion, for which the positive LOI finding accurately classified as ductal carcinoma in situ (DCIS), was confirmed indeed DCIS by ground truth validation on the excision specimen. Conclusion: We have demonstrated a breakthrough molecular biomarker that is fully objective, reproducible, and practical. First of its kind, the innovative QCIGISH has superior performance than the current standard of care in breast cancer diagnostics allowing for single-cell resolution of epigenetic changes. Next, we seek to undergo full model validation. Citation Format: M. Abdollahi Neisani, R. Guo, T. Cheng, M. K. Komforti. Epigenetic Imprinting as a Novel Precision Biomarker for Early Breast Cancer and Precancer Diagnosis and Detection abstract. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(4 Suppl):Abstract nr PS2-07-09.
Neisani et al. (Tue,) studied this question.