Molecular characterization of circulating colorectal tumor cells defines genetic signatures for individualized cancer care

Abstract

Studies on circulating tumor cells (CTCs) have largely focused on platform development and CTC enumeration rather than on the genomic characterization of CTCs. To address this, we performed targeted sequencing of CTCs of colorectal cancer patients and compared the mutations with the matched primary tumors. We collected preoperative blood and matched primary tumor samples from 48 colorectal cancer patients. CTCs were isolated using a label-free microfiltration device on a silicon microsieve. Upon whole genome amplification, we performed amplicon-based targeted sequencing on a panel of 39 druggable and frequently mutated genes on both CTCs and fresh-frozen tumor samples. We developed an analysis pipeline to minimize false-positive detection of somatic mutations in amplified DNA. In 60% of the CTC-enriched blood samples, we detected primary tumor matching mutations. We found a significant positive correlation between the allele frequencies of somatic mutations detected in CTCs and abnormal CEA serum level. Strikingly, we found driver mutations and amplifications in cancer and druggable genes such as APC, KRAS, TP53, ERBB3, FBXW7 and ERBB2. In addition, we found that CTCs carried mutation signatures that resembled the signatures of their primary tumors. Cumulatively, our study defined genetic signatures and somatic mutation frequency of colorectal CTCs. The identification of druggable mutations in CTCs of preoperative colorectal cancer patients could lead to more timely and focused therapeutic interventions.

Fast and efficient microfluidic cell filter for isolation of circulating tumor cells from unprocessed whole blood of colorectal cancer patients

“…Nevertheless, false-negative results cannot be ruled out due to the low amount of starting DNA. A recent work confirmed that in all CRC patients analyzed, the mutational status of APC in both CTCs and the primary tumor matched, with 60% concordance 85 . However, to the best of our knowledge this is the first study reporting the analysis of APC alterations by ddPCR in CTCs isolated from CRC patients.…”

Tracking cancer progression: from circulating tumor cells to metastasis

“…Single-cell analyses have revealed that CTCs often comprise a heterogeneous population of cells. Logically, this heterogeneity may reflect the extent of intratumor heterogeneity (ITH) [65][66][67][68][69][70] and may have important implications for prognosis and resistance to therapy. Indeed, a recent study of archived samples from patients with metastatic breast cancer found 85% concordance between CTCs and metastatic sites in terms of mutations and copy-number profile [71].…”

Liquid biopsy - emergence of a new era in personalized cancer care

“…And, due to apoptosis of CTCs, which begins soon after separation from the tumor of origin, they are extremely fragile [21]. Next generation sequencing (NGS) has revealed CTCs carry mutation signatures that resemble the signatures of their primary tumors including driver and druggable mutations like APC, KRAS, TP53, ERBB3, FBXW7 and ERBB2 [22].…”