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Next-Generation Technologies for Next-Generation Cancer Models

, by Cindy Kyi, Ph.D. and Eva Tonsing-Carter, Ph.D

NCI's Next generation technology for next generation cancer models program

NCI's Next-Generation Technology for Next-Generation Cancer Models Program

The Next-Generation Technologies for Next-generation Cancer Models program (NGT; RFA-CA-19-055) supports the development of technologies and tools that will facilitate, accelerate, and enhance research using advanced, human-derived, next-generation cancer models (NGCMs) such as organoids, conditionally reprogrammed cells, and others. The tools developed under this program will focus on utilizing NGCMs generated under the auspices of Human Cancer Models Initiative (HCMI). Both the HCMI and NGT programs are associated with the Beau Biden Cancer MoonshotSM Initiative to accelerate cancer research.

Patient-derived HCMI NGCMs are improved upon traditional cell lines. The models encapsulate the cellular architecture of original tumors, are associated with genomic and clinical data from the originating tumors, and represent broad cancer types such as rare cancers, pediatric cancers and cancers from racial and ethnic minorities. Currently, there are 148 HCMI models from 18 different primary anatomic sites; the available models can be browsed on HCMI Searchable Catalog. 

The primary goal of the NGT program is to facilitate broad application of HCMI’s NGCMs by providing researchers robust and reproducible genome editing/manipulating protocols and reagents and to enable advanced data interpretation. The new tools and broader use of HCMI NGCMs will contribute to progress in understanding the important pathways in cancer initiation, progression and metastasis, identifying mechanisms of resistance, discovering novel therapeutic targets, developing diagnostic and/or predictive biomarkers, and other aspects relevant to precision oncology. Protocols, knowledge, and materials developed by this program will be shared broadly with the research community.

There are three Centers working towards developing next-generation technologies and tools under this program: Broad Institute, Dana Farber Cancer Institute, and Massachusetts Institute of Technology.

The Broad Institute Center, co-led by Todd R. Golub, M.D., and John G. Doench, Ph.D., plans to develop genome editing vector systems and high-throughput screening methods suitable for slowly proliferating HCMI NGCMs as well as characterization methods to predict their metastatic potential in vivo.

Slow-proliferating cells present challenges to standard genome editing approaches due to the experimental need for large quantities of starting cell material. Therefore, instead of creating NGCMs that stably express Cas9 and then introducing guide RNAs, Broad will develop all-in-one genome editing vector systems. Additionally, alternative readouts will be required for efficient screening of the HCMI NGCMs, and the Center will be using short-term single cell RNA sequencing (scRNA-seq) methods that will serve as surrogate readouts for long-term cell viability. The group will also utilize multiplexed Cas 12/gRNA gene editing system for genetic perturbation studies and develop methods to determine organ-specific in vivo metastatic potential for NGCMs. The Broad Institute plans to create a public resource of the metastasis potential map (MetMap) for at least 50 HCMI NGCMs.

The Dana Farber Cancer Institute (DFCI) Center, led by William C. Hahn, M.D., Ph.D., will develop genome scale informatics methods as well as high-throughput approaches to profile genetic characteristics of HCMI NGCMs and study their responses to small molecule or genetic perturbations and sensitivity to drugs. Using innovative MIX-Seq (Multiplexed Interrogation of gene eXpression through single-cell RNA Sequencing) and computational methods, the team will explore cell state plasticity and heterogeneity in these models. These studies will allow the cancer research community to perform both high- and low-throughput analyses in HCMI NGCMs and provide a deeper insight into the stability and phenotypes represented by these models.

The team will build on the preliminary studies that indicated that pancreatic NGCMs exhibit heterogeneity and cell state plasticity when compared to the originating tumor. Using newly developed sequencing technology, the DFCI Center will interrogate the dynamics of these state changes and assess the degree of heterogeneity in the NGCMs. Additionally, the group will build on Project Achilles and the DepMap to create and implement an optimized genome scale CRISPR-Cas9 library that permits the systematic genetic interrogation of genetic dependencies in NGCMs.

The Massachusetts Institute of Technology (MIT) Center, led by Timothy K. Lu, M.D., Ph.D., Ömer H. Yilmaz, M.D., Ph.D., and Bonnie Berger, Ph.D., plans to develop innovative experimental and computational tools combining synthetic biology, cancer organoid technology, and bioinformatics. The Synthetic Tools to Annotate Reporter Organoids for Cancer Heterogeneity and Recurrence Development (StarOrchard) toolbox will include Synthetic Promoter Activated Recombination of Kaleidoscopic Organoids (SPARKO), Combinatorial Genetics EMasse (CombiGEM), and single-cell RNA sequencing panorama (Scanorama).

The SPARKO tool allows annotation of heterogeneous cancer populations within living cells via fluorescent protein expression libraries to make multi-colored tumor organoids. CombiGEM can rapidly identify potential therapeutic targets via large-scale, massively parallel, and unbiased combinatorial genetic screens. CombiGEM will be used to assemble a library of barcoded genetic libraries of perturbations created using a pair-wise guide RNA-mediated CRISPR system to investigate novel synthetic lethality and identify therapeutic targets. Scanorama is an efficient tool that integrates large single-cell transcriptomics (scRNA-seq) datasets from diverse cell types and tumor types via sophisticated bioinformatics algorithms. Scanorama can, then, find nearest neighbors among other datasets and group similar cell types together in a panoramic fashion. The Center reports that the StarOrchard tools focus on barcoding strategies to enable accurate longitudinal tracking and analysis of individual tumor cells that harbor distinct genetic aberrations and substantially expand the utility of NGCMs.

All data and resources such as protocols and reagents from the NGT program will be made publicly available to maximize the translational impact of these findings. These studies will generate protocols that will enable systematic functional investigations using NGCMs and facilitate the discovery of novel biomarkers and therapeutic targets. These tools and technologies can be used by the research community to ask specific questions using HCMI NGCMs in the efforts toward precision oncology. Visit the NGT program page for more information and future updates on the program.

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