Impact Of Cell-Free Plasma DNA In Metastatic And Non-Metastatic Prostate Cancer

2021 ◽  
Vol 21 ◽  
Author(s):  
Abdelraouf A. Abonar ◽  
Shymaa E. Ayoub ◽  
Ibrahim A. Tagreda ◽  
Marwa N. Abdelhafez ◽  
Mohammed M Khamiss ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Cancer Patients ◽  
Metastatic Prostate Cancer ◽  
Plasma Dna ◽  
Cell Free Dna ◽  
Group Iii ◽  
Free Dna ◽  
Group I ◽  
Total Psa ◽  
Free Plasma

: Increased cell-free DNA (cfDNA) is observed in many diseases such as cancer, myocardial infarction, and autoimmune diseases. It has the ability to alter the receptor cell phenotype, triggering events related to malignant transformation. Our study aims at assessing the use of Cell-free plasma DNA in the diagnosis of metastatic and non-metastatic prostate cancer. The study included 180 subjects who were classified into four groups: Group I (GI) included 50 in perfect health subjects as the control group, Group II (GII) included 40 patients with prostatitis, group III (GIII) included 40 patients with benign prostatic hyperplasia (BPH) and Group IV (GIV) included 50 patients with pre-operative prostate cancer (PC). Evaluation of the plasma level of circulating cell-free DNA by real-time PCR and measurement of total PSA (tPSA) and free to total PSA percent (f/tPSA%) were done for all groups. Our study revealed that the level of tPSA was significantly higher in prostate cancer patients while levels of f/t PSA were found to be significantly lower. The level of cfDNA was significantly higher in prostate cancer patients (399.9±88.6ng/ul) when compared to that of the group I (12.1±1.5ng/ul) (p<0.01), group II (14.7±2.4 ng/ul) (p<0.01), and group III (26.6±45.6 ng/ul) (p<0.01) respectively. There was a statistically significant difference in yields of cfDNA between metastatic and non- metastatic groups (P=0.03) with a higher level in the metastatic group.

scholarly journals Cell-Free DNA Alterations in the AR Enhancer and Locus Predict Resistance to AR-Directed Therapy in Patients With Metastatic Prostate Cancer

2020 ◽  
pp. 680-713 ◽  
Author(s):  
Ha X. Dang ◽  
Pradeep S. Chauhan ◽  
Haley Ellis ◽  
Wenjia Feng ◽  
Peter K. Harris ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Androgen Receptor ◽  
Metastatic Prostate Cancer ◽  
Progression Free Survival ◽  
Therapy Resistance ◽  
Cancer Resistance ◽  
Liquid Biopsies ◽  
Genomic Alterations ◽  
Cell Free Dna ◽  
Free Dna

PURPOSE Cell-free DNA (cfDNA) and circulating tumor cell (CTC)–based liquid biopsies have emerged as potential tools to predict responses to androgen receptor (AR)–directed therapy in metastatic prostate cancer. However, because of complex mechanisms and incomplete understanding of genomic events involved in metastatic prostate cancer resistance, current assays (eg, CTC AR-V7) demonstrate low sensitivity and remain underutilized. The recent discovery of AR enhancer amplification in > 80% of patients with metastatic disease and its association with disease resistance presents an opportunity to improve on current assays. We hypothesized that tracking AR/enhancer genomic alterations in plasma cfDNA would detect resistance with high sensitivity and specificity. PATIENTS AND METHODS We developed a targeted sequencing and analysis method as part of a new assay called Enhancer and Neighboring Loci of Androgen Receptor Sequencing (EnhanceAR-Seq). We applied EnhanceAR-Seq to plasma collected from 40 patients with metastatic prostate cancer treated with AR-directed therapy to monitor AR/enhancer genomic alterations and correlated these events with therapy resistance, progression-free survival (PFS), and overall survival (OS). RESULTS EnhanceAR-Seq identified genomic alterations in the AR/enhancer locus in 45% of cases, including a 40% rate of AR enhancer amplification. Patients with AR/enhancer alterations had significantly worse PFS and OS than those without (6-month PFS, 30% v 71%; P = .0002; 6-month OS, 59% v 100%; P = .0015). AR/enhancer alterations in plasma cfDNA detected 18 of 23 resistant cases (78%) and outperformed the CTC AR-V7 assay, which was also run on a subset of patients. CONCLUSION cfDNA-based AR locus alterations, including of the enhancer, are strongly associated with resistance to AR-directed therapy and significantly worse survival. cfDNA analysis using EnhanceAR-Seq may enable more precise risk stratification and personalized therapeutic approaches for metastatic prostate cancer.

Determining Tumor Load and Biallelic Mutation in Patients with CALR Mutation Using Peripheral Blood Plasma

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 1818-1818
Author(s):  
Kevin Diep ◽  
Wanlong Ma ◽  
Ferras Albitar ◽  
Ivan De Dios ◽  
Sally Agersborg ◽  
...  
Keyword(s):  
Sanger Sequencing ◽  
Plasma Dna ◽  
Biallelic Mutation ◽  
Cell Free Dna ◽  
Free Dna ◽  
Tumor Load ◽  
Peripheral Blood Plasma ◽  
Cellular Dna ◽  
Free Plasma ◽  
Calr Mutation

Abstract Background: CALR gene is frequently mutated in patients with myeloproliferative neoplasmas (MPN). Almost all mutations are indel - some with large (>50 bp) deletion. Detecting this type of mutations with acceptable sensitivity is difficult by sequencing. Fragment length analysis (FLA) is a reliable technique in detecting this type of mutations. Furthermore, FLA allows quantifying the mutant DNA and better evaluation of tumor load. Determining tumor load can be confusing and difficult when the mutation is biallelic. Distinguishing between patients with single allele mutation from those with biallelic mutations might add another dimension in predicting clinical behavior and determining the tumor load. We explored using cell free DNA in peripheral blood plasma to test for CALR mutations and determining tumor load. Methods: Using Direct bidirectional sequencing and FLA, we detected CALR indel mutations in 71 of 522 (14%) patients suspected of having MPN and referred for testing for CALR mutation. No sample showed point mutation. DNA from cells and cell free DNA in plasma was available from 31 of the 71 cases. The mutant DNA peak was quantified and the relative percentage of mutant DNA was calculated in both cellular DNA and cell free plasma DNA. FLA and Sanger sequencing data were compared between cellular DNA and cell free plasma DNA. Any ratio >55% was considered as evidence of biallelic mutation. Results: As expected all positive samples by cellular DNA testing also showed the indel mutation in cell free plasma by FLA. However, four of the 31 (13%) positive samples by FLA failed to show the mutation on Sanger sequencing. The most likely cause for failing to detect the mutation by Sanger is low level mutation load and the lower sensitivity of Sanger sequencing. When we compared ratios of mutant peak (tumor load) between cellular DNA and cell free DNA in plasma, mutant CALR DNA was significantly higher (P=0.0002, Wilcoxon matched pairs test) in cell free DNA in plasma than in cellular DNA. More importantly, we were able to determine the presence of homozygous mutation (>55% mutant DNA) in 5 of 31 (16%) patients when cell free DNA in plasma is used. In contrast, only 1 of 31 (3%) patients showed evidence of biallelic mutation when cellular DNA is used. Most of the mutations (25 of 31, 81%) were deletions. As deletions results in smaller size amplicon on the FLA and better amplification efficiency, we set 55% as a cut-off for biallelic mutation to account for the more efficient amplification of the deleted peak. Conclusion: Cell free DNA in plasma is more reliable than cellular DNA for the detection of CALR mutations and for determining tumor load. Testing for CALR must include fragment length analysis. More importantly, biallelic CALR mutation is frequent and the clinical relevance of biallelic CALR mutation needs to be investigated. Disclosures No relevant conflicts of interest to declare.

Cell-free plasma DNA as biochemical biomarker for the diagnosis and follow-up of prostate cancer patients

Tumor Biology ◽  
2013 ◽  
Vol 34 (5) ◽  
pp. 2921-2927 ◽  
Author(s):  
Marcelo L. Wroclawski ◽  
Ary Serpa-Neto ◽  
Fernando L. A. Fonseca ◽  
Oseas Castro-Neves-Neto ◽  
Alexandre S. F. L. Pompeo ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Cancer Patients ◽  
Plasma Dna ◽  
Free Plasma

AR enhancer and locus genomic alterations as cell-free DNA biomarkers of primary resistance to AR-directed treatment of metastatic prostate cancer.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. 5529-5529
Author(s):  
Chris Maher ◽  
Ha X. Dang ◽  
Pradeep S. Chauhan ◽  
Haley Ellis ◽  
Wenjia Feng ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Metastatic Prostate Cancer ◽  
Dna Analysis ◽  
Clinical Decision Making ◽  
Cancer Center ◽  
Genomic Alterations ◽  
Primary Resistance ◽  
Cell Free Dna ◽  
Free Dna

5529 Background: Predicting primary resistance to androgen receptor (AR)-directed therapies is critical for personalizing treatment of metastatic prostate cancer (mPCa). Analyses of liquid biopsies are potential tools but remained underutilized due to limited sensitivity. We developed a cell-free DNA (cfDNA) assay (EnhanceAR-Seq) to monitor genomic alterations in mPCa including AR enhancer duplication, a resistance marker recently discovered in ~81% of mPCa patients. Here we show that applying EnhanceAR-Seq to plasma cfDNA to monitor alterations of AR gene and enhancer ( AR/enhancer) predicted primary resistance with high sensitivity and outperformed the clinically validated CTC AR-V7 assay. Methods: Forty mPCa patients were prospectively enrolled at the Washington University School of Medicine Siteman Cancer Center with plasma cfDNA analyzed by EnhanceAR-Seq. Twenty-five of them also had the Oncotype DX AR-V7 Nucleus Detect CTC assay performed at a similar timepoint at the discretion of the treating oncologist. All patients received AR-directed therapy (eg. abiraterone, enzalutamide) and underwent standard-of-care clinical and laboratory follow-up. Primary resistance was defined as PSA progression, change of treatment or death within 4 months of treatment initiation, or radiographic progression within 6 months. Results: Median clinical follow up after diagnosis was 50 months. EnhanceAR-Seq detected alterations targeting AR/enhancer in 18 patients (45%), TP53 in 8 patients (20%), and PTEN in 6 patients (15%). We found that AR/enhancer alterations (copy gain, tandem duplication, and point mutation) in cfDNA were strongly predictive of primary resistance to AR-directed therapy (PPV = 100%, Sens. = 89%). Our assay outperformed the CTC AR-V7 assay, which was positive in only two patients (PPV = 50%, Sens. = 6%). Furthermore, patients with AR/enhancer alterations had significantly worse progression-free survival (P = 0.0015; HR = 11.5) and overall survival (P = 0.0002; HR = 6.8). Finally, serial cell-free DNA analysis of 10 patients showed that AR/enhancer copy number gain was maintained or acquired in 5 of 6 AR-resistant cases, and neutrality maintained in 4 of 4 AR-sensitive cases. Conclusions: cfDNA-based AR/enhancer locus genomic alterations could potentially be used to predict primary resistance to AR-directed therapy with higher sensitivity than the clinically validated CTC AR-V7 assay, be used for serial timepoint monitoring and guiding personalized clinical decision-making.

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