Chromosomal Instability and Clonal Heterogeneity in Breast Cancer: From Mechanisms to Clinical Applications

Abstract

Background: Chromosomal instability (CIN) and clonal heterogeneity (CH) are fundamental hallmarks of breast cancer that drive tumor evolution, disease progression, and therapeutic resistance. Understanding the mechanisms underlying these phenomena is essential for improving cancer diagnosis, prognosis, and treatment strategies.

Methods: In this review, we provide a comprehensive overview of the biological processes contributing to CIN and CH, highlighting their molecular determinants and clinical relevance.

Results: We discuss the latest advances in detection methods, including single-cell sequencing and other high-resolution techniques, which have enhanced our ability to characterize intratumoral heterogeneity. Additionally, we explore how CIN and CH influence treatment responses, their potential as therapeutic targets, and their role in shaping the tumor immune microenvironment, which has implications for immunotherapy effectiveness.

Conclusions: By integrating recent findings, this review underscores the impact of CIN and CH on breast cancer progression and their translational implications for precision medicine.

Keywords: aneuploidy; breast cancer; chromosomal instability; clonal heterogeneity; gene expression; single-cell sequencing.

Figure 1

Cellular mechanisms leading to numerical chromosomal instability (CIN) in cancer. Numerical CIN arises from errors in chromosome segregation during mitosis (mitotic nondisjunction), leading to daughter cells with aneuploid or polyploid karyotypes. Key mechanisms involved include (A) cohesion defects, where a loss of cohesin (blue) prevents proper chromatid alignment in metaphase, causing segregation errors in anaphase; (B) kinetochore–microtubule attachment errors, where incorrect spindle attachment results in sister chromatids migrating to the same pole, leading to missegregation; (C) centrosome amplification, where extra centrosomes increase erroneous kinetochore attachments and chromosome lagging; (D) cell cycle regulation defects, where checkpoint failures allow cells with missegregated chromosomes to continue division; and (E) spindle assembly checkpoint (SAC) errors, where improperly attached chromosomes should activate SAC to delay anaphase, but undetected errors lead to missegregation.

Figure 2

Cellular mechanisms leading to structural chromosomal instability (CIN) in cancer. Structural CIN results from deficiencies in genome integrity maintenance, primarily affecting (A) double-strand break (DSB) repair. (B) Homologous recombination (HR) ensures accurate DSB repair by using an undamaged homologous sequence as a template. HR defects lead to increased reliance on error-prone pathways. (C) Non-homologous end joining (NHEJ) leads to an increased reliance on error-prone pathways, as it joins DNA ends without the guidance of a homologous sequence. (D) When either of these mechanisms fails to function properly, the affected DNA strand ends remain exposed, potentially leading to structural chromosomal alterations such as deletions, translocations, inversions, derivatives chromosomes, amplifications, dicentric chromosomes, ring chromosomes, and chromothripsis. Several processes contribute to the formation of these chromosomal alterations, including splicing, resection, alignment, strand invasion, and/or replication, all of which promote the induction of CIN.

Figure 3

The role of the CIN phenotype in breast cancer progression, therapy resistance, and patient outcomes. CIN plays a crucial role in tumor evolution and progression, contributing to both (A) intertumoral and intratumoral heterogeneity. The administration of chemotherapy or radiotherapy to tumor cells (B) can increase CIN (C) and alter gene expression (D), both of which are associated with a rise in tumor heterogeneity (E). This increased heterogeneity can lead to the induction of apoptosis (F), resulting in tumor regression, or the clonal expansion of new oncogenic alterations, further enhancing heterogeneity (G) and CIN (H) and driving resistance to therapy (I). Given the strong association between CIN and variations in gene expression (J), signatures such as CIN25 and CIN70 have been investigated as potential biomarkers to evaluate CIN (K) and stratify BC patients based on their risk (L). These signatures hold the potential to improve the accuracy of diagnostic predictions and patient outcome assessments (M).

Figure 4

Application of scRNA-seq in tumor biology. scRNA-seq enables the identification of CIN expression signatures at the single-cell level, uncovering tumor heterogeneity and key molecular mechanisms. It facilitates differential expression analysis, cell–cell interaction characterization, and transcriptomic dynamics tracking, providing a high-resolution view of CIN in cancer development.