Exploring the spatiotemporal genetic heterogeneity in metastatic lung adenocarcinoma using a nuclei flow‐sorting approach

Abstract

Variable tumor cellularity can limit sensitivity and precision in comparative genomics because differences in tumor content can result in misclassifying truncal mutations as region‐specific private mutations in stroma‐rich regions, especially when studying tissue specimens of mediocre tumor cellularity such as lung adenocarcinomas (LUADs). To address this issue, we refined a nuclei flow‐sorting approach by sorting nuclei based on ploidy and the LUAD lineage marker thyroid transcription factor 1 and applied this method to investigate genome‐wide somatic copy number aberrations (SCNAs) and mutations of 409 cancer genes in 39 tumor populations obtained from 16 primary tumors and 21 matched metastases. This approach increased the mean tumor purity from 54% (range 7–89%) of unsorted material to 92% (range 79–99%) after sorting. Despite this rise in tumor purity, we detected limited genetic heterogeneity between primary tumors and their metastases. In fact, 88% of SCNAs and 80% of mutations were propagated from primary tumors to metastases and low allele frequency mutations accounted for much of the mutational heterogeneity. Even though the presence of SCNAs indicated a history of chromosomal instability (CIN) in all tumors, metastases did not have more SCNAs than primary tumors. Moreover, tumors with biallelic TP53 or ATM mutations had high numbers of SCNAs, yet they were associated with a low interlesional genetic heterogeneity. The results of our study thus provide evidence that most macroevolutionary events occur in primary tumors before metastatic dissemination and advocate for a limited degree of CIN over time and space in this cohort of LUADs. Sampling of primary tumors thus may suffice to detect most mutations and SCNAs. In addition, metastases but not primary tumors had seeded additional metastases in three of four patients; this provides a genomic rational for surgical treatment of such oligometastatic LUADs. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Deciphering the clonal relationship between glandular and squamous components in adenosquamous carcinoma of the lung using whole exome sequencing

“…Our gene copy number data suggest persistent genomic instability as chromosomal aberrations are detected even after branching of the two components. The high overall concordance between the chromosomal copy number aberrations profiles of the components support our previous data from metastatic LUAD showing that most aberrant genomic events are truncal with only limited heterogeneity between primary tumors and matched metastases [34]. Nevertheless, the two ASC components had private CNVs, which were similar to the CNVs known to be typical for their pure morphological counterparts, i.e.…”

ctDNA as a Cancer Biomarker: A Broad Overview

“…The total ctDNA represented in the body fluid is a sum of the tumor localization, phenotype and differentiation grade. Tumor samples with less than 10% neoplastic cell content may lose the low rate of genetic aberration sensitivity (Lorber et al, 2019;Méhes, 2019;Schwarzenbach et al, 2011). Therefore, the ctDNA concentration is not controllable, as tumor composition and localization are major preanalytical variables.…”

Genomic evolutionary trajectory of metastatic squamous cell carcinoma of the lung

“…Nuclei isolation from FF and FFPE samples was conducted as described previously (9)(10)(11)(12). All nuclei were DAPI stained for sorting, DNA quantification and ploidy analysis.…”

“…Molecular profiling of LUSC is further challenged by the often low tumor cell content of LUSC tissue (8). To overcome this hurdle, we previously showed that the tumor purity of LUAD can be greatly enhanced by an advanced nuclei flow-sorting technique (9). Briefly, cells were stained with 4',6-Diamin-2-phenylindol (DAPI) and an antibody for TTF-1 to isolate LUAD specific cells.…”

“…Briefly, cells were stained with 4',6-Diamin-2-phenylindol (DAPI) and an antibody for TTF-1 to isolate LUAD specific cells. This flow-sorting approach allowed us to distinguish and isolate aneuploid and diploid populations enabling highly informative genomic profiling (9).…”