Progress and challenges of sequencing and analyzing circulating tumor cells

Abstract

Circulating tumor cells (CTCs) slough off primary tumor tissues and are swept away by the circulatory system. These CTCs can remain in circulation or colonize new sites, forming metastatic clones in distant organs. Recently, CTC analyses have been successfully used as effective clinical tools to monitor tumor progression and prognosis. With advances in next-generation sequencing (NGS) and single-cell sequencing (SCS) technologies, scientists can obtain the complete genome of a CTC and compare it with corresponding primary and metastatic tumors. CTC sequencing has been successfully applied to monitor genomic variations in metastatic and recurrent tumors, infer tumor evolution during treatment, and examine gene expression as well as the mechanism of the epithelial-mesenchymal transition. However, compared with cancer biopsy sequencing and circulating tumor DNA sequencing, the sequencing of CTC genomes and transcriptomes is more complex and technically difficult. Challenges include enriching pure tumor cells from a background of white blood cells, isolating and collecting cells without damaging or losing DNA and RNA, obtaining unbiased and even whole-genome and transcriptome amplification material, and accurately analyzing CTC sequencing data. Here, we review and summarize recent studies using NGS on CTCs. We mainly focus on CTC genome and transcriptome sequencing and the biological and potential clinical applications of these methodologies. Finally, we discuss challenges and future perspectives of CTC sequencing.

Profiling of circulating tumor DNA in plasma of non‐small cell lung cancer patients, monitoring of epidermal growth factor receptor p.T790M mutated allelic fraction using beads, emulsion, amplification, and magnetics companion assay and evaluation in future application in mimicking circulating tumor cells

“…A CTC population is representative of the heterogeneity and the plasticity of tumoral cells of all tumoral sites into the body. These cells may undergo an epithelial to mesenchymal transition (EMT) or acquire stem cell features to sequester themselves from their initial site of origin or to migrate into secondary metastatic sites through lymph and/or whole blood systems. Currently, CTC analyses are mainly performed to gain insights of tumor progression by transcrptional and/or epigenetic mechanisms.…”

Live single cell mass spectrometry reveals cancer‐specific metabolic profiles of circulating tumor cells

“…Previous studies in genomics, transcriptomics, and proteomics succeeded in depicting the effective role of CTC analyses in monitoring tumor progression and prognosis as well as its clinical impact. As metabolomics is the final frontier of omics, it is essential to study the metabolic phenotypes of CTCs to gain a comprehensive understanding on the primary and metastatic tumor biology.…”

“…Despite the prognostic value of CTC enumeration, it is still not enough to gain a comprehensive understanding of the tumor nature and its characteristics. Recent studies have reported genome and transcriptome analyses of single CTCs using a next generation sequencer . Circulating tumor cell sequencing proved to be an efficient liquid biopsy tool that can monitor the variation in gene expression among different cancer stages, which could be used to investigate tumor origin, evolution, and tumor progression during treatment.…”

“…Recent studies have reported genome and transcriptome analyses of single CTCs using a next generation sequencer. 12 Circulating tumor cell sequencing proved to be an efficient liquid biopsy tool that can monitor the variation in gene expression among different cancer stages, which could be used to investigate tumor origin, evolution, and tumor progression during treatment. However, there is an untapped potential that lies in CTC metabolomic profiling that can shed light on the heterogeneity of cancer cells as well as the possible role played by CTCs in cancer progression and metastasis.…”

The future is now: cutting edge science and understanding toxicology

“…This has provided insights into the metastatic progression of breast cancer (McGranahan and Swanton 2017), leukemia , and kidney cancer ). Zhu et al also described the application of CTCs single cell sequencing to delineate signaling pathway alterations during tumor evolution, which led to the discovery of the extracellular matrix protein SPARC as a key mediator of dysregulated signaling in pancreatic cancer progression (Ting et al 2014) and drug metabolism pathway enrichment in refractory colorectal cancer (Grillet et al 2017;Zhu et al 2017). We believe that this paper is highly suitable for CBT, because cancer research-related toxicology is a major topic of the journal.…”