DNA Fragmentation

BackgroundCirculating DNA (ctDNA) is acknowledged as a potential diagnostic tool for various cancers including colorectal cancer, especially when considering the detection of mutations. Certainly due to lack of normalization of the experimental conditions, previous reports present many discrepancies and contradictory data on the analysis of the concentration of total ctDNA and on the proportion of tumour-derived ctDNA fragments.MethodologyIn order to rigorously analyse ctDNA, we thoroughly investigated ctDNA size distribution. We used a highly specific Q-PCR assay and athymic nude mice xenografted with SW620 or HT29 human colon cancer cells, and we correlated our results by examining plasma from metastatic CRC patients.Conclusion/significanceFragmentation and concentration of tumour-derived ctDNA is positively correlated with tumour weight. CtDNA quantification by Q-PCR depends on the amplified target length and is optimal for 60-100 bp fragments. Q-PCR analysis of plasma samples from xenografted mice and cancer patients showed that tumour-derived ctDNA exhibits a specific amount profile based on ctDNA size and significant higher ctDNA fragmentation. Metastatic colorectal patients (n = 12) showed nearly 5-fold higher mean ctDNA fragmentation than healthy individuals (n = 16).

Non-invasive approaches for cell-free DNA (cfDNA) assessment provide an opportunity for cancer detection and intervention. Here, we use a machine learning model for detecting tumor-derived cfDNA through genome-wide analyses of cfDNA fragmentation in a prospective study of 365 individuals at risk for lung cancer. We validate the cancer detection model using an independent cohort of 385 non-cancer individuals and 46 lung cancer patients. Combining fragmentation features, clinical risk factors, and CEA levels, followed by CT imaging, detected 94% of patients with cancer across stages and subtypes, including 91% of stage I/II and 96% of stage III/IV, at 80% specificity. Genome-wide fragmentation profiles across ~13,000 ASCL1 transcription factor binding sites distinguished individuals with small cell lung cancer from those with non-small cell lung cancer with high accuracy (AUC = 0.98). A higher fragmentation score represented an independent prognostic indicator of survival. This approach provides a facile avenue for non-invasive detection of lung cancer.

DNA that survives in museum specimens, bones and other tissues recovered by archaeologists is invariably fragmented and chemically modified. The extent to which such modifications accumulate over time is largely unknown but could potentially be used to differentiate between endogenous old DNA and present-day DNA contaminating specimens and experiments. Here we examine mitochondrial DNA sequences from tissue remains that vary in age between 18 and 60,000 years with respect to three molecular features: fragment length, base composition at strand breaks, and apparent C to T substitutions. We find that fragment length does not decrease consistently over time and that strand breaks occur preferentially before purine residues by what may be at least two different molecular mechanisms that are not yet understood. In contrast, the frequency of apparent C to T substitutions towards the 5'-ends of molecules tends to increase over time. These nucleotide misincorporations are thus a useful tool to distinguish recent from ancient DNA sources in specimens that have not been subjected to unusual or harsh treatments.

BackgroundCirculating tumor DNA (ctDNA) has emerged as a clinically valuable biomarker for cancer detection, treatment monitoring, and minimal residual disease assessment. Despite its growing clinical utility, the biological mechanisms governing ctDNA release remain incompletely understood. The objective of this study was to investigate how chemotherapy-induced cytotoxicity and chemoresistance influence the kinetics and fragmentation patterns of cfDNA released by cancer cells in vitro.MethodsHuman lung adenocarcinoma (A549) and esophageal adenocarcinoma (FLO-1, OE19) cell lines were used to investigate cell-free DNA (cfDNA) release and fragmentation in vitro. Cancer cells were treated with chemotherapy (cisplatin and 5-fluorouracil), and cfDNA released into the culture medium was quantified as total cfDNA by Qubit fluorometry and mutation-specific cfDNA by droplet digital PCR (ddPCR). A cisplatin-resistant OE19 model was generated to directly compare cfDNA release kinetics between chemosensitive and chemoresistant cells. Fragment size distributions were determined and evaluated alongside cell death mechanisms assessed by flow cytometry.ResultscfDNA release correlated positively with viable tumor cell number across all cell lines. Chemotherapy increased per-cell cfDNA release in all cell lines. Chemosensitive OE19 cells exhibited significantly higher cfDNA release compared to chemoresistant OE19 cells following cisplatin exposure, with distinct temporal release kinetics. Additionally, chemotherapy treatment induced a shift toward the release of larger DNA fragments in both chemosensitive and resistant cells. This was accompanied by changes in PI-positive and Annexin V/PI double-positive cell populations, suggesting altered cell death processes following cisplatin treatment.ConclusionsChemotherapy-induced cytotoxicity significantly influences cfDNA release kinetics and fragmentation patterns, with distinct effects in chemosensitive and chemoresistant cancer cells. These findings provide mechanistic insight into tumor-derived DNA release biology and may have important implications for the interpretation, timing, and standardization of liquid biopsy testing during treatment. Furthermore, they establish in vitro cancer models as a valuable platform for studying cfDNA dynamics and informing preclinical therapeutic development.