Next-Generation Sequencing Applications for Preclinical Oncology Research

Advances in preclinical oncology research are dependent on gaining insights into tumor biology and applying these insights to the development of novel diagnostics or therapeutics. Next-generation sequencing (NGS) technology has been instrumental in bridging basic immuno-oncology findings and preclinical applications. Here we provide an overview of NGS applications that are transforming preclinical oncology research.

Teasing Apart the Tumor Microenvironment

Solid tumors are now understood to have dynamic and unique tumor microenvironments (TMEs) that influence the immune response as well as tumor progression. Combined with flow cytometry and immunohistochemistry, single-cell NGS methods such as scRNA sequencing (scRNA-seq) and Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-Seq) allow scientists to measure and understand which cells are present in the TME. These findings may characterize how different stromal cells are present and contributing to tumorigenesis[1] and how the TME can create an immunosuppressive environment[2].

Elevating Liquid Biopsies

Liquid biopsies have gained popularity as a method to measure circulating tumor cells (CTCs) related to either solid tumor metastasis or hematological malignancies. NGS methods have greatly improved insights gained from this sampling method[3]. Previous bulk sampling methods for quantifying CTCs were hampered by sample contamination with leukocytes and the extremely low frequency of CTCs. Single-cell NGS methods, including methods to measure single nucleotide variations as well as large-scale mutations such as copy number variations or chromosomal rearrangements, have provided unprecedented information about CTC specimens in different anatomical locations or over time. These methods have also driven the development of liquid biopsy methods that can be used to track treatment efficacy and the emergence of resistance.

Better Biomarkers

Tumor mutation burden (TMB) is a measurement of mutations within a tumor’s genomic sequence and has emerged as a potential biomarker associated with immune checkpoint inhibitor (ICI) efficacy. Numerous studies have now applied NGS methods to measure TMB in relation to ICI efficacy[4], and robust methods are now being validated for use clinically[5]. These findings have consistently found that high TMB correlates with ICI efficacy, and other NGS-based studies have been used to compare TMB with other genomic aberrations like microsatellite instability[6].

NGS data will continue to provide critical insights into preclinical oncology research and is certain to drive the development of better diagnostics and therapeutics.

[1] Lambrechts D, Wauters E, Boeckx B, et al. (2018). Phenotype molding of stromal cells in the lung tumor microenvironment. Nature Medicine, 24(8), 1277-1289.

[2] Devalaraja S, To TK, Folkert IW, et al. (2020). Tumor-derived retinoic acid regulates intratumoral monocyte differentiation to promote immune suppression. Cell.180(6):1098-114.

[3] Lim SB, Di Lee W, Vasudevan J, et al. (2019). Liquid biopsy: one cell at a time. NPJ Precision Oncology. 3(1):1-9.

[4] Goodman AM, Kato S, Bazhenova L, et al. (2017). Tumor Mutational Burden as an Independent Predictor of Response to Immunotherapy in Diverse Cancers. Mol Cancer Ther. 16(11):2598-2608.

[5] Fenizia F, Alborelli I, Costa JL, et al. (2021). Validation of a Targeted Next-Generation Sequencing Panel for Tumor Mutation Burden Analysis: Results from the Onconetwork Immuno-Oncology Consortium. J. Mol. Diagn. S1525-1578(21)00117-3.

[6] Goodman AM, Sokol ES, Frampton GM, et al. Microsatellite-Stable Tumors with High Mutational Burden Benefit from Immunotherapy. (2019). Cancer Immunol. Res. 10:1570-1573.