RESEARCH AREAS
A central goal of somatic cell division is the accurate partitioning of the duplicated genome between two daughter cells. Mitotic errors can alter chromosome number and structure, generating genetically distinct cells upon which selection can act. Whereas some genomic alterations accumulate gradually, others arise simultaneously during a single catastrophic event and trigger punctuated bursts of genome evolution. Understanding how transient mitotic errors impart heritable genomic changes and how these changes influence subsequent evolutionary trajectories is therefore fundamental to our understanding of cancer development.
The Ly Laboratory investigates this process at three interconnected scales – within individual cells, between neighboring cells, and during cancer development. We have established experimental systems that enable defined genomic events to be induced and tracked in human cells. By combining genome engineering, high-resolution fixed- and live-cell microscopy, molecular cytogenetics, and genomics, we seek to establish how altered genomes arise within individual cells, propagate between neighboring cells, and shape cancer evolution.
Cell-intrinsic mechanisms of genomic instability
Sequencing of cancer genomes has revealed complex structural alterations that previously escaped detection by classical cytogenetic approaches. This is epitomized by chromothripsis – a catastrophic event in which a chromosome is shattered into tens to hundreds of fragments that are subsequently reassembled in the incorrect order. Chromothripsis can be initiated by mitotic errors that isolate mis-segregated chromosomes within abnormal compartments called micronuclei. Defective compartmentalization disrupts normal nuclear processes within micronuclei – including DNA replication and repair – rendering the entrapped chromosome vulnerable to extensive DNA damage and fragmentation. We have developed chromosome-specific experimental systems that allow us to follow individual chromosomes from the initiating mitotic error through the formation of stable, rearranged chromosomes. Using these approaches, we are interested in defining how chromosomes are damaged within micronuclei, how their fragments are inherited and repaired, and how this process generates diverse genomic outcomes – including DNA copy-number alterations, complex rearrangements, and oncogene-containing extrachromosomal DNA.
Propagation of genome instability across neighboring cells
Most models of cancer evolution assume that genomic alterations arise within individual cells and are transmitted vertically to their descendants during cell division. We discovered that genomic DNA can also move horizontally between neighboring human cells through a process we termed intercellular DNA transfer. These findings challenge the strictly cell-autonomous view of somatic evolution. Genomic DNA entrapped in micronuclei can transfer between adjacent cells through cytoskeleton-based nanotube connections. The transferred DNA can persist as stable, functional genetic material within recipient cells and confer new phenotypic traits, thus providing an unexpected route through which genomic alterations generated in one cell may influence the genomes and behavior of surrounding cells. We are working to define the principles that govern how the genome is mobilized, which types of genetic material can be transferred, and what happens to this DNA within recipient cells. Our long-term goal is to determine whether and how intercellular DNA transfer contributes to genetic heterogeneity, tumor evolution, and therapeutic resistance by propagating cancer-associated genomic alterations across cell populations.
Genomic instability as a driver of tumorigenesis
Numerical and structural chromosome aberrations are pervasive in cancer, yet how they shape tumor evolution remains challenging to model. Some alterations – including whole-chromosome and arm-level aneuploidy – initially reduce cellular fitness, creating evolutionary bottlenecks in which rare cells acquire the adaptations needed to survive and expand. We have engineered human cell-based models harboring specific chromosomal alterations, enabling us to mechanistically interrogate how they impact cellular fitness and influence subsequent genome evolution. We currently use clear cell renal cell carcinoma as an experimental platform because it is initiated by loss of chromosome 3p and proceeds through a defined sequence of genetic alterations. By reconstructing this trajectory in non-transformed human renal epithelial cells, we can determine how an initiating chromosome alteration reshapes the fitness landscape during malignant transformation. We seek to uncover how tissue context and natural selection govern the consequences of mitotic errors and to identify therapeutic vulnerabilities that emerge as cancer genomes evolve.
