Quantitative analysis of plasma cell-free DNA and its DNA integrity in patients with metastatic prostate cancer using ALU sequence

Abstract

Highly significant levels of cf-DNA and its integrity in PC patients compared to BPH. Twenty-eight (56%) patients with prostate cancer had bone metastasis. ALU115 qpcr is superior to the other markers in discriminating metastatic patients with a sensitivity of 96.4% and a specificity of 86.4% and (AUC=0.981) CONCLUSION: ALU115 qpcr could be used as a valuable biomarker helping in identifying high risk patients, indicating early spread of tumor cells as a potential seed for future metastases.

Circulating Cell-Free DNA in Dogs with Mammary Tumors: Short and Long Fragments and Integrity Index

“…In agreement with previously published data mainly in humans, in our work, the neoplastic subjects showed a higher amount of both short and long cfDNA fragments than the non-neoplastic diseased and healthy controls [11–15, 23, 43–47]. Only one study [16] compared circulating DNA in non-neoplastic with neoplastic dogs (lymphoma and other cancers) and found similar results.…”

“…In a more simplistic vision, it seems that the rate of evasion of apoptosis taking place in the studied tumors was not sufficient to determine an increased ratio, since both short and long fragments were augmented. In our samples, instead, the presence of necrosis was able to significantly increase the integrity index causing more long fragments to circulate within the plasma, in accordance with other works [20,21,23,30,43–47] and further supporting the necrotic origin of the fragments amplified by the LINE-218 primer pairs.…”

“…They show that cfDNA fragments (short and long) and integrity index allow identification of malignant and necrotic CMTs and might therefore be further studied as potential diagnostic and prognostic tests also in veterinary medicine. In addition, it seems that both apoptosis and necrosis cause an increase of circulating DNA with necrosis as major source of long fragments and related increase of integrity index as already demonstrated in humans [23,43–47]. This is the first study of cfDNA quantification and cfDNA integrity index evaluation in dogs carrying CMTs, and its results suggest that further studies should be designed to strengthen the diagnostic/prognostic role of cfDNA levels and integrity index, including the establishment of verified cut-off values associated with different diagnoses and prognoses.…”

“…The use of repetitive DNA elements with a high copy number distributed throughout the genomic DNA can ensure a good sensitivity and accurate data also for those samples with very low quantity and degraded cfDNA [10]. Particularly, amplification of ALU repeats (ALU-qPCR 247/115) to detect long (247bp) and short (115bp) DNA fragments and cfDNA integrity index is now used in human cancer diagnostic and prognostic studies [23, 43–47]. …”

“…Therefore, there has been an explosion of technologies for the quantification and analysis of both these markers from the non-invasive and highly accessible “liquid biopsies”, however there is still a lack of standardization [55,56,59]. Quantification and integrity index of cfDNA are still proved to be valid diagnostic and prognostic markers in human cancer [23,43–47,60]. However, enormous improvement in sensitivity and specificity of downstream analysis has been achieved for example by next generation sequencing (NGS), digital droplet PCR (ddPCR), and beads, emulsion, amplification, magnetics (BEAMing) PCR for tumor association, mutational analysis, and patient monitoring [55,61].…”