Longitudinal Copy-Number Alteration Analysis in Plasma Cell-Free DNA of Neuroendocrine Neoplasms is a Novel Specific Biomarker for Diagnosis, Prognosis, and Follow-up

Abstract

Purpose: As noninvasive biomarkers are an important unmet need for neuroendocrine neoplasms (NEN), biomarker potential of genome-wide molecular profiling of plasma cell-free DNA (cfDNA) was prospectively studied in patients with NEN. Experimental Design: Longitudinal plasma samples were collected from patients with well-differentiated, metastatic gastroenteropancreatic and lung NEN. cfDNA was subjected to shallow whole-genome sequencing to detect genome-wide copy-number alterations (CNA) and estimate circulating tumor DNA (ctDNA) fraction, and correlated to clinicopathologic and survival data. To differentiate pancreatic NENs (PNEN) from pancreatic adenocarcinomas (PAAD) using liquid biopsies, a classification model was trained using tissue-based CNAs and validated in cfDNA. Results: One hundred and ninety-five cfDNA samples from 43 patients with NEN were compared with healthy control cfDNA (N = 100). Plasma samples from patients with PNEN (N = 21) were used for comparison with publicly available PNEN tissue (N = 98), PAAD tissue (N = 109), and PAAD cfDNA (N = 96). Thirty percent of the NEN cfDNA samples contained ctDNA and 44% of the patients had at least one ctDNA-positive (ctDNA+) sample. CNAs detected in cfDNA were highly specific for NENs and the classification model could distinguish PAAD and PNEN cfDNA samples with a sensitivity, specificity, and AUC of 62%, 86%, and 79%, respectively. ctDNA-positivity was associated with higher World Health Organization (WHO) grade, primary tumor location, and higher chromogranin A and neuron-specific enolase values. Overall survival was significantly worse for ctDNA+ patients and increased ctDNA fractions were associated with poorer progression-free survival. Conclusions: Sequential genome-wide profiling of plasma cfDNA is a novel, noninvasive biomarker with high specificity for diagnosis, prognosis, and follow-up in metastatic NENs.

Circulating Neuroendocrine Tumor Biomarkers: Past, Present and Future

“…It has been reported that the presence of ctDNA in body fluids is linked to the localization of the primary tumor and metastatic lesions [ 129 , 130 , 131 , 132 ]. Oversoe et al described elevated levels of cfDNA in panNET and siNET patients compared to healthy controls [ 133 ].…”

“…Boons et al, described a correlation between the presence of ctDNA and a higher grading [ 132 ]. On the contrary to NECs, NETs (which are generally slow growing tumors) have a lower cell loss index and ctDNA release and can often be ctDNA negative [ 130 ]. Quantitative analysis of ctDNA may also be useful to assess tumor volume and in an early diagnosis of relapse after surgery and as a predictive factor of response to treatment [ 134 , 135 , 136 , 137 ].…”

Predictive Factors for Resistant Disease with Medical/Radiologic/Liver-Directed Anti-Tumor Treatments in Patients with Advanced Pancreatic Neuroendocrine Neoplasms: Recent Advances and Controversies

“…In the last decade there has been a steadily increasing need for the identification of predictive/prognostic factors in all stages of the management of panNEN/NEN patients with advanced disease [ 7 , 383 , 384 , 385 ]. This has occurred for a number of reasons, but is largely related to the increasing complexity of treating these patients.…”

Neuroendocrine Tumors and Peptide Receptor Radionuclide Therapy: When Is the Right Time?

“…Although not evaluated in the setting of PRRT to date, the presence and increased fractions of circulating tumor DNA were associated with poorer PFS. 48 Further work using circulating tumor cells and DNA may add additional value in understanding who will benefit the most from PRRT.…”