Misaligned Chromosomes are a Major Source of Chromosomal Instability in Breast Cancer

Abstract

Chromosomal instability (CIN), the persistent reshuffling of chromosomes during mitosis, is a hallmark of human cancers that contributes to tumor heterogeneity and has been implicated in driving metastasis and altering responses to therapy. Though multiple mechanisms can produce CIN, lagging chromosomes generated from abnormal merotelic attachments are the major cause of CIN in a variety of cell lines, and are expected to predominate in cancer. Here, we quantify CIN in breast cancer using a tumor microarray, matched primary and metastatic samples, and patient-derived organoids from primary breast cancer. Surprisingly, misaligned chromosomes are more common than lagging chromosomes and represent a major source of CIN in primary and metastatic tumors. This feature of breast cancers is conserved in a majority of breast cancer cell lines. Importantly, though a portion of misaligned chromosomes align before anaphase onset, the fraction that remain represents the largest source of CIN in these cells. Metastatic breast cancers exhibit higher rates of CIN than matched primary cancers, primarily due to increases in misaligned chromosomes. Whether CIN causes immune activation or evasion is controversial. We find that misaligned chromosomes result in immune-activating micronuclei substantially less frequently than lagging and bridge chromosomes and that breast cancers with greater frequencies of lagging chromosomes and chromosome bridges recruit more stromal tumor-infiltrating lymphocytes (sTILs). These data indicate misaligned chromosomes represent a major mechanism of CIN in breast cancer and provide support for differential immunostimulatory effects of specific types of CIN.

CINner: modeling and simulation of chromosomal instability in cancer at single-cell resolution

“…We find that simultaneous parameter inference for both selection parameters and CNA probabilities in bulk DNA-sequencing data results in nonidentifiability issues. Previous works have observed around 1 – 9 × 10 −3 missegregations per division in cancer cell lines [28–30]. However, in CINner this figure can be explained by either (i) high CNA probabilities coupled with selection parameters close to 1, or (ii) low CNA probabilities and selection parameters farther from 1.…”

HPV16 E6 induces chromosomal instability due to polar chromosomes caused by E6AP-dependent degradation of the mitotic kinesin CENP-E

“…Lagging chromosomes and chromosome bridges often result in micronuclei which have been implicated in the formation of structural aneuploidy ( 70 , 71 ). In contrast, polar chromosomes are more likely to join with the main nucleus after chromosome segregation to spindle poles in early anaphase, leading to whole chromosome aneuploidy ( 72 ). Since HPV16 E6 specifically increases polar chromosomes, we wanted to determine whether HPV+ HNCs have higher levels of whole chromosome aneuploidy than HPV− HNCs.…”

Double-checking chromosome segregation

“…Recent evidence also indicated that many more merotelic kinetochore–microtubule attachments than previously thought result in anaphase lagging chromosomes that satisfy the SAC in human cultured cells ( Orr et al, 2021 ; Sen et al, 2021 ), but only rarely result in micronuclei, hinting at the existence of active surveillance and correction mechanisms during anaphase that we are just starting to understand. Interestingly, although most micronuclei in cancer cells derive from anaphase lagging chromosomes that rarely missegregate ( Thompson and Compton, 2011 ), a recent study has shown that misaligned chromosomes that satisfy the SAC often directly missegregate without lagging behind in anaphase and have the highest probability to form micronuclei ( Gomes et al, 2022 ), representing a major source of chromosomal instability in primary and metastatic breast tumors ( Tucker et al, 2023 ; Fig. 1 ).…”