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Researchers at MD Anderson Cancer Center recently used a Cellecta CloneTracker Barcode Library to label patient-derived xenograft (PDX) cells and establish a stable population of aggressive tumorigenic cells with a specific set of barcodes. With this population of barcoded tumorigenic clones, the investigators analyzed tumor development and investigated how sub-populations of these tumor-initiating cells responded differently to several therapeutic treatments.

A tumor evolves from different founder clones whose progeny rapidly grow and diverge into more diverse sub-types. Lentiviral vector-based libraries with large numbers of uniquely identifiable sequences (i.e., “barcodes”) combined with high throughput DNA sequencing provide a powerful tracking tool to investigate clonal dynamics and tumor-initiating cell (TIC) heterogeneity in these models.

In this tumorigenic cell tracking study, the researchers used one of Cellecta’s CloneTracker pooled libraries of barcodes in lentiviral constructs to label patient-derived pancreatic cancer and then analyze the heterogeneity of this population over serial passages in culture and in recipient mice. The researchers found that after several passages, the resulting tumor cells in the various in vivo and in vitro cultures shared similar lineages. The “same set of common barcodes, although just a fraction of detected barcodes, represented almost the entire mass of tumors formed under both conditions (96% of in vitro-stabilized tumor mass versus 68% of in vivo-passaged tumor mass).” Thus, a core population of long-term tumorigenic cells present in the original barcoded population was responsible for initiating and maintaining tumor growth in different environments.

Given the stable population dynamics of the long-term tumorigenic cells, the investigators were able to produce cohorts of tumors and cultured cells harboring similar overlapping profiles of barcodes which they dubbed “clonal replicate tumors.” These clonal replicates with largely overlapping barcode profiles were then employed by the researchers to evaluate how sub-populations and tumor diversity changed in response to different therapeutic approaches. Although treatment with various targeted therapeutics (e.g., MEK1 inhibitor, PI3K/mTOR inhibitors, etc.) significantly reduced the heterogeneity of the cultures, a treatment-specific sub-population of the common tumor-initiating clones was resistant to each type of treatment and enabled the rapid regrowth of the tumors.

The ability to track the same barcoded population across cultures and in different animals enabled the researchers to demonstrate “the existence of genomically and transcriptomically heterogeneous pools of tumorigenic cells that sustain tumor evolution and exhibit differential responses to external perturbations.” The data suggest that “tumors are likely sustained by a small pool of tumorigenic cells that maintained this capacity even in the different microenvironmental contexts of in vitro versus in vivo growth.”

You can read more details about the study in the article


Clonal replicate tumors generated with CloneTracker barcodes

After multiple passages of barcoded PDX cells, the researchers were able to establish tumors with largely overlapping barcode profiles. These “clonal replicate tumors” with the same barcoded cells in different animals enabled the researchers to evaluate and compare the effects of different treatments on the clonal sub-populations that formed the tumors.