Clonal Lineage Tracing with Recordable Barcodes Reveals Migration Histories of Metastatic Prostate Cancer

Geriatrics Urology Medicine Oncology
clonal lineage tracing metastatic prostate cancer barcodes tumor evolution mouse model tumor heterogeneity

title: “Utilizing Clonal Lineage Tracing with Recordable Barcodes Unveils the Migration History of Prostate Cancer Metastasis” author: Ryan N. Serio, Armin Scheben, *Billy Lu, *Domenic V. Gargiulo, Lucrezia Patruno, Caroline L. Buckholtz, Ryan J. Chaffee, Megan C. Jibilian, Steven G. Persaud, Stephen J. Staklinski, Rebecca Hassett, Lise M. Brault, Daniele Ramazzotti, Christopher E. Barbieri, Adam C. Siepel, #, Dawid G. Nowak journal: Cancer Discovery

date: July 16, 2024

Introduction

The development of early diagnostic and therapeutic strategies for Prostate Cancer (PCA) depends on a profound understanding of the tumor metastasis process. Yet, the patterns of tumor spread from the primary prostate cancer foci to metastatic sites remain unclear. Thus, the research team used PCR/Cas9 barcode technology to design and validate a chimeric cell lineage tracing technique to reveal the dynamic migratory history of metastatic prostate cancer and provide a new perspective to understand the evolution and migratory pathways of tumor clones.

Background and Source of the Paper

The authors of this academic paper hail from renowned research institutions such as Weill Cornell Medicine, Cold Spring Harbor Laboratory, and University of Milano-Bicocca, and it was published in the prestigious journal Cancer Discovery. Major authors include Ryan N. Serio, Armin Scheben, Billy Lu, Domenic V. Gargiulo, Lucrezia Patruno, Caroline L. Buckholtz, and others. The article discusses the mechanisms of prostate cancer metastasis and explains how the patterns of prostate cancer metastasis influence disease progression and the development of therapeutic strategies.

Research Process

Experimental Models and Methods

The paper employed a novel intravenous mouse model called EvoCaP (Evolutionary Prostate Cancer) with highly invasive metastatic characteristics to bone, liver, lung, and lymph nodes. To track the migratory history between primary tumors and metastatic sites, the research team used the EvoTracer pipeline to track different tumor clones containing recordable barcodes.

  1. Modeling Process:

    • In the EvoCaP mouse model, genes were modified via a lentiviral injection in the prostate to induce prostate cancer. The process included:
      • Deletion of Pten and Trp53 genes, a common genomic combination in patients with metastatic disease.
      • Tracking cancer evolution through accumulated heritable barcodes (BC10).

  2. Data Collection and Analysis:

    • Quantitative analysis was conducted using synthetic barcode BC10 that contained multiple gene-editing primers, via the EvoTracer software package.
    • The analysis revealed a high degree of clonal heterogeneity and defined founder clone populations (CPs) between the prostate and metastatic sites.
    • The migratory history was inferred using population smoothing techniques and the Cassiopeia algorithm, combined with Machina software.

  3. Experimental Results:

    • Tracking cancer clones through injection of barcoded viruses into mice subjected to genetic modification revealed a wide range of highly heterogeneous clone populations.
    • Many shared Cas9 editing events (landmark mutations) were detected, defining the founder CPs between the prostate and metastatic sites.
    • A small number of highly invasive clones played a major role in the migration process, while a large number of tumor cells remained stationary within the metastatic sites.

Experimental Details and Innovation of Methods

The EvoCaP model is a newly designed mutant mouse model by the research team, characterized by mimicking the evolution and metastasis of human prostate cancer through in vivo genetic processing (e.g., using lentiviral injections). The barcode recording system BC10 used by the researchers also added significant innovation to the experiment, enabling precise tracking of the evolution and migratory history of cancer clones over a long period.

  1. Construction of the EvoCaP Model:

    • Cre recombinase and firefly luciferase (Fluc) expression were introduced into the mouse prostate through lentiviral injection, leading to focal loss of Pten and Trp53 genes.
    • This induction mechanism effectively mimicked human prostate cancer from an initial focus to metastases in bone, lung, liver, and even lymph nodes.

  2. Barcode (BC10) System:

    • BC10 barcode consists of 10 Cas9 target sites of 20 nucleotides each and is designed using a machine learning (cutting frequency determination, CFD) scoring algorithm to ensure its efficient editing function.
    • The integrated BC10 barcode records accumulated genetic markers, allowing for observation of complex evolutionary relationships among clone populations over time.

  3. Data Collection and Analysis:

    • High-sensitivity quantitative analysis was achieved using the EvoTracer software package, employing advanced bioinformatic analysis tools including Cassiopeia and Machina, to reconstruct the clonal tree and infer potential migration trajectories.
    • The dose of virus injected and the capacity to silence foreign genes ensured the stability of the animal model and the consistency of the data.

Main Results

The experimental results show that in this study: - The multiclonal nature of the initial tumor is marked, with highly invasive clones playing a major role in expanding their ecological niches. - Clonal heterogeneity reflects fundamental migration patterns from the prostate to distant metastatic sites. The migration process is primarily linear propagation, with few metastasis-to-metastasis transmission events. - Specific metastatic patterns, such as direct (primary-to-metastatic) transmission from prostate sites to bone, liver, lung, etc., were discovered.

These data indicate that a few dominant clones expand their distribution through migration, overcoming constraints that keep them in place, thus exhibiting high invasiveness and monopolization.

Conclusion

Significance of the Research

The importance of this study lies in: - Providing a detailed understanding of prostate cancer metastasis, revealing how tumor clones evolve and migrate within different body sites. - The EvoCaP model and barcode tracking technology used in this study demonstrate their potential to identify tumor clone populations and infer their migration paths. - These findings have profound implications for developing novel treatment approaches for prostate cancer.

Key Findings

The study highlighted the systemic characteristics of prostate cancer, driven by some highly invasive clones, exhibiting complex migration and expansion patterns. These highly invasive clones are able to overcome physiological barriers and extend to more distant metastatic sites, providing a new perspective on systemic diseases.

Novelty of the Methods and Process

The EvoCaP model employed in the study is a novel approach to genetic processing, allowing accurate simulation of human prostate cancer evolution within mice. The Barcode (BC10) system further enhances the efficiency and accuracy of tracking the evolution of tumor clones, highlighting great potential in cancer research.

The EvoCaP model and barcode tracking platform confirm their effectiveness and innovation in studying prostate cancer migration and expansion. These technologies and methods can be applied not only to prostate cancer but also extended to other types of cancer and disease research, providing valuable tools and perspectives for academia and clinical practice.