Methodological Advancements for Investigating Intra-tumoral Heterogeneity in Breast Cancer at the Bench and Bedside

Mokryun Baek,Gloria V Echeverria,Jeffrey T Chang

doi:10.1007/s10911-020-09470-3

Abstract

There is a major need to overcome therapeutic resistance and metastasis that eventually arises in many breast cancer patients. Therapy resistant and metastatic tumors are increasingly recognized to possess intra-tumoral heterogeneity (ITH), a diversity of cells within an individual tumor. First hypothesized in the 1970s, the possibility that this complex ITH may endow tumors with adaptability and evolvability to metastasize and evade therapies is now supported by multiple lines of evidence. Our understanding of ITH has been driven by recent methodological advances including next-generation sequencing, computational modeling, lineage tracing, single-cell technologies, and multiplexed in situ approaches. These have been applied across a range of specimens, including patient tumor biopsies, liquid biopsies, cultured cell lines, and mouse models. In this review, we discuss these approaches and how they have deepened our understanding of the mechanistic origins of ITH amongst tumor cells, including stem cell-like differentiation hierarchies and Darwinian evolution, and the functional role for ITH in breast cancer progression. While ITH presents a challenge for combating tumor evolution, in-depth analyses of ITH in clinical biopsies and laboratory models hold promise to elucidate therapeutic strategies that should ultimately improve outcomes for breast cancer patients.

Highlights

Breast cancer is the most frequently diagnosed cancer and the leading cause of cancer deaths in women worldwide [1]
While barcodes enable highthroughput analysis of hundreds to thousands of unique clones simultaneously, they are not directly linked to molecular events within the cells they mark, necessitating further downstream investigations to identify drivers of the observed patterns of intratumor heterogeneity (ITH). This technology has been used in cell line and patient-derived xenograft (PDX) in vivo models of breast cancer to track patterns of ITH during xenograft passaging and primary tumor growth, revealing substantial ITH and diversity of clonal growth patterns between samples derived from distinct models [82]
One of the most critical remaining questions is the correlation of ITH with therapeutic response and metastasis

Summary

Introduction

Breast cancer is the most frequently diagnosed cancer and the leading cause of cancer deaths in women worldwide [1]. In addition to the inter-patient heterogeneity, across patients, of protein levels of established prognostic and predictive biomarkers (estrogen receptor, ER, progesterone receptor, PR, and human epidermal growth factor receptor 2, HER2) [2], the cells within each tumor are diverse with respect to their somatic mutations, gene expression and epigenetic profiles, and proteomic and metabolic programming. Numerous methods have been used to identify ITH in breast cancer specimens, including bulk and single-cell genomic and transcriptomic sequencing, lineage tracing, analysis of circulating tumor cells and DNA, and in situ analyses on tissues These methods have been implemented in patient tumor biopsies and laboratory models including cell lines, genetically engineered mouse models (GEMMs), and patient-derived xenograft (PDX) mouse models. This diversity of approaches and models is painting an ever-clearer picture of the heterogeneous composition of tumors, which is providing a deeper understanding of breast cancer biology

Bulk Methods to Assess ITH

Method type ITH analyzed Pros

Findings

Concluding Remarks