A Case Series Exploration of Multi-Regional Expression Heterogeneity in Triple-Negative Breast Cancer Patients

Abstract

Extensive intratumoral heterogeneity (ITH) is believed to contribute to therapeutic failure and tumor recurrence, as treatment-resistant cell clones can survive and expand. However, little is known about ITH in triple-negative breast cancer (TNBC) because of the limited number of single-cell sequencing studies on TNBC. In this study, we explored ITH in TNBC by evaluating gene expression-derived and imaging-derived multi-region differences within the same tumor. We obtained tissue specimens from 10 TNBC patients and conducted RNA sequencing analysis of 2–4 regions per tumor. We developed a novel analysis framework to dissect and characterize different types of variability: between-patients (inter-tumoral heterogeneity), between-patients across regions (inter-tumoral and region heterogeneity), and within-patient, between-regions (regional intratumoral heterogeneity). We performed a Bayesian changepoint analysis to assess and classify regional variability as low (convergent) versus high (divergent) within each patient feature (TNBC and PAM50 subtypes, immune, stroma, tumor counts and tumor infiltrating lymphocytes). Gene expression signatures were categorized into three types of variability: between-patients (108 genes), between-patients across regions (183 genes), and within-patients, between-regions (778 genes). Based on the between-patient gene signature, we identified two distinct patient clusters that differed in menopausal status. Significant intratumoral divergence was observed for PAM50 classification, tumor cell counts, and tumor-infiltrating T cell abundance. Other features examined showed a representation of both divergent and convergent results. Lymph node stage was significantly associated with divergent tumors. Our results show extensive intertumoral heterogeneity and regional ITH in gene expression and image-derived features in TNBC. Our findings also raise concerns regarding gene expression based TNBC subtyping. Future studies are warranted to elucidate the role of regional heterogeneity in TNBC as a driver of treatment resistance.

Phenotypic heterogeneity drives differential disease outcome in a mouse model of triple negative breast cancer

“…Two tumor epithelial cell populations that showed distinct GFP expression levels were obtained from the GFP+ fraction -a GFP High (High GFP expression) and a GFP Low (Low GFP expression) cell population. Interestingly, these cell populations also displayed different morphological appearance when cultured in vitro which was similar to observations made by Xiang and colleagues (Figure 1B) (14). The GFP High cells showed a round and loosely adherent morphology whereas GFP Low cell population exhibited adherent, 4T1 like morphology.…”

“…Unfortunately, only 20% of TNBC cases respond to conventional chemotherapy (13) and is characterized by aggressive clinical course with cerebral and visceral metastasis. Compared to other subtypes, TNBC patients show significantly poor prognosis and lower overall survival (14,15) making it imperative to devise new therapeutic strategies for targeting the disease.…”

Recent Advances in Breast Cancer Research

“…These factors are promising biomarkers for optimizing the clinical management of metastatic BC [7]. Another study investigated tumor specimens from 10 triple-negative breast cancer (TNBC) patients [8]. This BC type exhibited profound intratumoral heterogeneity.…”

“…This BC type exhibited profound intratumoral heterogeneity. Therefore, single biopsy specimens may show only a portion of genetic aberrations of the entire tumor [8]. Genetic aberrations are involved in various cancer-specific biological processes, like tumorigenicity, induction of cell signaling, senescence, angiogenesis, migration, and response to treatment [8].…”

“…Therefore, single biopsy specimens may show only a portion of genetic aberrations of the entire tumor [8]. Genetic aberrations are involved in various cancer-specific biological processes, like tumorigenicity, induction of cell signaling, senescence, angiogenesis, migration, and response to treatment [8]. The authors concluded that medications used on the basis of the molecular profile of diagnostic biopsies may fail to remove the tumor, thus resulting in tumor recurrence.…”