Fragment size and level of cell-free DNA provide prognostic information in patients with advanced pancreatic cancer

Abstract

BackgroundIt was recently demonstrated that the size of cell-free DNA (cfDNA) fragments that originates from tumor cells are shorter than cfDNA fragments that originates from non-malignant cells. We investigated whether cfDNA fragment size and cfDNA levels might have prognostic value in patients with advanced pancreatic cancer.MethodsBlood samples were obtained from patients with advanced pancreatic cancer, before (n = 61) initiation of chemotherapy and after the first cycle of chemotherapy (n = 39). Samples were separated with density centrifugation and plasma DNA was isolated. Mode cfDNA fragment size and cfDNA levels were then determined using a 2100 Bioanalyzer. A cohort of partially age-matched healthy volunteers (n = 28) constituted the control group.ResultsBoth a pre-treatment cfDNA fragment size of ≤ 167 bp (mode) and high pre-treatment cfDNA levels were associated with shorter progression-free survival (PFS) (p = 0.002 and p < 0.001, respectively) and overall survival (OS) (p = 0.001 and p = 0.001, respectively). Furthermore, multivariable Cox regression analyses demonstrated that pre-treatment cfDNA levels could independently predict prognosis for both PFS (HR = 3.049, p = 0.005) and OS (HR = 2.236, p = 0.028).ConclusionThis study demonstrates that cfDNA fragment size and cfDNA levels can be used to predict disease outcome in patients with advanced pancreatic cancer. The described approach, using a rapid, economic and simple test to reveal prognostic information, has potential for future treatment stratification and monitoring.Electronic supplementary materialThe online version of this article (10.1186/s12967-018-1677-2) contains supplementary material, which is available to authorized users.

Cell-free DNA as a biomarker for prostate cancer: elevated concentration and decreased fragment size

“…While the biological mechanisms underlying decreased fragment size in cancer patients are not well-understood, differences in nucleosome positioning and DNA methylation may result in varied DNA degradation. Our finding that the overall average fragment size in localized patients was shorter and more fragmented than in healthy individuals is consistent with the findings of studies assessing fragment size in patients with hepatocellular carcinoma and advanced pancreatic cancer 18,25 . The proportion of cfDNA fragments shorter than 150bp is also increased for multiple cancer types when compared to healthy fragment sizes with shallow genome-wide sequencing 17 We processed samples in a manner that maximized the quality and quantity of extracted cfDNA [27][28][29][30] .…”

“…However, the slightly increased cfDNA concentrations observed in controls may be due to cell lysis during transit, since whole blood was collected from individuals at a donor center in Kent, Washington and shipped overnight to San Francisco, California, whereas the patient samples were collected and processed onsite. Additionally, the lower overall cfDNA concentrations found in the localized cohort may be due to the subduing effect of anesthetic agents on cell death, which were administered prior to blood sample collection before surgery 31 A previous study demonstrated that in pre-treatment speciments, shorter cfDNA fragment size and elevated cfDNA concentrations were associated with shorter progression-free survival and overall survival in patients with advanced pancreatic cancer 25 . Due to the relatively short follow-up time in this study, future longitudinal studies evaluating disease progression from localized to metastatic disease are necessary to elucidate the value of analyzing cfDNA concentration and fragment size in the context of prostate cancer.…”

“…DNA integrity, which measures the ratio of all cfDNA fragments (ALU 247bp) to shorter fragments (ALU 115bp) has distinguished prostate cancer from benign prostatic hyperplasia (BPH) 15 . Pre-treatment cfDNA concentration and fragment size were predictive of advanced pancreatic cancer progression-free survival and overall survival 16 . Furthermore, tumor fragments in cfDNA appeared shorter in size than fragments that originated from non-malignant cells [17][18][19] .…”

Comparison of Somatic Mutation Profiles Between Formalin-Fixed Paraffin Embedded Tissues and Plasma Cell-Free DNA from Ovarian Cancer Patients Before and After Surgery

“…[9][10][11][12][13][14] Circulating tumor DNA (ctDNA) originate from apoptotic or necrotic cancer cells, perhaps even from active cellular secretion, and its fragment size is most commonly less than 180 bp. [15][16][17][18][19][20] Moreover, ctDNA usually constitutes a small fraction (<20%) of total cfDNA concentration that is generally low. While its levels correlate with disease grading, staging, and metastasis, this can vary among patients.…”

Quick assessment of cell-free DNA in seminal fluid and fragment size for early non-invasive prostate cancer diagnosis

“…Each above mentioned compartment releases different forms of cfDNA into the bloodstream or other biological fluids [6,7]. Previous studies associated high cfDNA concentrations with specific size-distribution patterns to cancer diagnosis [8,9]. However, levels of cfDNA/ctDNA in blood samples vary depending on cancer type.…”