Advances in Liquid Biopsy Technology and Implications for Pancreatic Cancer
Abstract
:1. Introduction
2. ctDNA
2.1. Methods for Detecting and Analyzing ctDNA
2.2. ctDNA as a Screening Tool
2.3. cctDNA to Guide Treatment and Monitor for Recurrence
3. Exosomes
3.1. Methods for Capturing Exosomes
3.2. Exosomes as a Screening Tool
3.3. Exosomes to Guide Treatment and Monitor for Recurrence
4. Circulating Tumor Cells
4.1. Methods for Capturing CTCs
4.2. CTCs as a Screening Tool
4.3. CTCs to Guide Treatment and Monitor for Recurrence
5. microRNAs
Potential Use of microRNAs in Pancreatic Cancer
6. Challenges and Limitations of Liquid Biopsy in PDAC
7. Conclusions
Author Contributions
Funding
Conflicts of Interest
References
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---|---|---|---|---|---|
Sorenson et al., 1994 [48] | 3 | Stage IV PDAC | PCR and allele specific amplification | KRAS | KRAS mutation detected in 3/3 PDAC pts and 0/5 pts without PDAC. |
Maire et al., 2002 [49] | 47 | PDAC, all stages | qPCR and allele specific amplification | KRAS | KRAS mutation detected in 47% of 47 PDAC pts and 13% of 31 controls with chronic pancreatitis (p < 0.002). The combination of KRAS and CA19-9 gave a sensitivity and specificity of 98% and 77%, respectively for identifying PDAC pts. |
Zill et al., 2015 [26] | 18 | Advanced pancreato-biliary cancers | NGS | KRAS, TP53, APC, SMAD4, and FBXW7 | Mutations detected in 90.3% of pts. |
Sausen et al., 2015 [50] | 77 | Stage II PDAC | NGS and ddPCR | KRAS | KRAS mutation detected in 43% of pts. Detection of ctDNA after resection predicted clinical relapse and poor prognosis. ctDNA could detect recurrence 6.5 months earlier than CT. |
Kinugasa et al., 2015 [51] | 75 | PDAC, all stages | ddPCR | KRAS | KRAS mutation rate 74.7% in tissue and 62.6% in ctDNA from 75 pts with PDAC. OS significantly longer in pts without detectable KRAS mutations in ctDNA. |
Berger et al., 2016 [52] | 24 | Metastatic PDAC | ddPCR | KRAS | KRAS mutation detected in 41.7% of 24 PDAC pts and 0/101 pts with IPMN, borderline IPMN, resected SCAs or no pathology. |
Henriksen et al., 2016 [53] | 95 | PDAC, all stages | Methylation-specific PCR | BMP3, RASSF1A, BNC1, MESTv2, TFPI2, APC, SFRP1 and SFRP2 | Mean methylated genes detected in 95 PDAC pts was 8.41 compared with 4.74 in control group of 97 pts with chronic pancreatitis, 59 with acute pancreatitis and 27 without evidence of PDAC (p < 0.001). A diagnostic prediction model using age and methylation pattern had 76% sensitivity 76% and 83% specificity for detecting PDAC. |
Tjensvoll et al., 2016 [54] | 14 | PDAC, all stages | PNA-clamp PCR | KRAS | KRAS mutation detected in 71% of pts with PDAC. Pre-therapy ctDNA predicted decreased DFS and OS. Changes in ctDNA levels correlated with radiological findings and CA19-9 levels. |
Cheng et al., 2017 [55] | 188 | Metastatic PDAC | NGS and ddPCR | KRAS, BRCA2, EGFR and KDR | KRAS mutation detected in 72% of pts. |
Pietrasz et al., 2017 [56] | 135 | PDAC, all stages | NGS | KRAS | ctDNA was detected in 48% of pts with advanced PDAC, and was an independent prognostic marker in advanced PDAC. ctDNA was associated with shorter DFS and OS when detected after resection of localized PDAC. |
Cohen et al., 2017 [57] | 221 | Resectable PDAC | ddPCR | KRAS | KRAS mutation detected in 30% of 221 pts with resectable PDAC and 1/182 control pts. All KRAS mutations in ctDNA concordant with those detected in tissue. Screening for PDAC using ctDNA positivity or elevation of any of 4 protein biomarkers cutoffs produced a sensitivity of 64% and specificity of 99.5%. |
Sugimori et al., 2019 [58] | 45 | Metastatic PDAC | dPCR | KRAS | In the 6 locally advanced cases, KRAS mutation appeared concurrently with liver metastasis. Among the 6 cases with liver metastasis, KRAS mutation disappeared during the duration of stable disease or a partial response, and reappeared at the time of progressive disease. |
Patel et al., 2019 [59] | 112 | Metastatic PDAC | NGS | KRAS, TP53 | Concordance for KRAS alterations between ctDNA and tissue DNA from metastatic sites was significantly higher than between ctDNA and primary tumor DNA (72% vs. 39%, p = 0.01). Higher VAF was an independent prognostic factor for worse OS (HR, 4.35; 95% confidence interval: 1.85–10.24). |
Lee et al., 2019 [60] | 112 | Resectable PDAC | ddPCR | KRAS | Patients with ctDNA-positive status postoperatively had reduced DFS and (HR 5.4; p < 0.0001) and OS (HR 4.0; p = 0.003). |
Guler et al., 2020 [36] | 64 | PDAC, all stages | Methylation-specific NGS | Many | Differential hydroxymethylation of genes related to pancreas development or function and cancer pathogenesis were identified in a discovery cohort and used to differentiate PDAC-associated from normal plasma samples in a validation cohort. |
Jiang et al., 2020 [61] | 27 | Resectable PDAC | NGS | KRAS, TP53 | Patients with ctDNA-positive status postoperatively had reduced DFS compared to those with ctDNA-negative status (HR, 5.20; p = 0.019). |
Toledano-Fonseca et al., 2020 [62] | 61 | Metastatic PDAC | dPCR | KRAS | Higher RAS VAF and higher cfDNA levels correlated with worse DFS and OS. The combination of CA19-9 with VAF, cfDNA levels improved prognostic stratification. |
Uesato et al., 2020 [63] | 104 | Metastatic PDAC | NGS | Many | Detectable ctDNA correlated with worse PFS and OS. ctDNA correlated with number of liver metastases and with the presence of metastases at other sites. |
Wei et al., 2020 [64] | 70 | Metastatic PDAC | NGS | Many | Higher VAF was associated with increased CA19-9, metastasis, and worse prognosis. CNAs were concordant over time even in patients with progressive disease. Patients with more abundant baseline CNAs exhibited a better response to chemotherapy. |
Nakamura et al., 2020 [65] | 363 | Metastatic PDAC | NGS | TP53, KRAS and GNAS | PDAC patients had lower MSI prevalence and TMB score, but higher rates of germline BRCA mutations than patients with gastroesophageal and colon cancer. |
Bachet et al., 2020 [66] | 113 | Metastatic PDAC | NGS | TP53, KRAS and others | ctDNA was positive at baseline in 68% of patients. Detectable ctDNA was an independent negative prognostic factor for OS and PFS. Early change in ctDNA levels correlated with ORR. |
Hussung et al., 2021 [67] | 25 | Resectable PDAC | ddPCR | KRAS | Integration of cell free mutant KRAS cfDNA levels and CA19–9 levels outperformed either individual marker when predicting PFS and OS. |
Pietrasz et al., 2022 [68] | 255 | Metastatic PDAC | ddPCR | HOXD8 and POU4F1 methylated markers | 56.8% of patients were ctDNA positive. Median PFS and OS were 5.3 and 8.2 months in ctDNA-positive and 6.2 and 12.6 months in ctDNA-negative patients, respectively. ctDNA positivity was associated with young age and high CA19-9 level and was an independent prognostic marker for PFS and OS. |
Renouf et al., 2022 [69] | 174 | Metastatic PDAC | NGS | KRAS and others | KRAS wild type metastatic PDAC may derive benefit from immunotherapy. |
Huang et al., 2022 [18] | 74 | Stage III-IV PDAC | NGS | KRAS | cfDNA concentration of >9.71 ng/mL before and after first two courses of chemotherapy was strongly predictive of the development of new distant metastasis (NDM) on CT scans 3 months later (accuracy 94.4%, AUC 0.971, p < 0.0001). |
Study | No. of pts | Type of pts | Isolated Component | Platform | Markers | Findings |
---|---|---|---|---|---|---|
Allenson et al., 2017 [77] | 68 | PDAC, all stages | ctDNA and exomes | ddPCR | KRAS | KRAS mutation in exoDNA, identified in 7.4%, 66.7%, 80%, and 85% of age-matched controls (54), localized, locally advanced, and metastatic PDAC pts, respectively. KRAS mutation in cfDNA was detected in 14.8%, 45.5%, 30.8%, and 57.9% of these individuals. Higher exoKRAS VAFs associated with decreased DFS in pts with localized disease. |
Yang et al., 2017 [78] | 48 | Resectable PDAC | Exomes | dPCR | KRAS, TP53 | KRAS and TP53 mutations identified in exosomal DNA of 39.6% and 4.2% of PDAC cases, respectively. In 114 healthy controls 2.6% and 0% had KRAS and TP53 mutations in exosomal DNA, respectively. |
Bernard et al., 2019 [17] | 194 | PDAC, all stages | ctDNA and exomes | ddPCR and NGS | KRAS | In 34 pts with potentially resectable PDAC, increase in exoDNA level after neoadjuvant therapy was significantly associated with disease progression (p = 0.003). Concordance rate of KRAS mutation between liquid biopsy and surgical resection >95%. In stage IV PDAC, detectable ctDNA correlated with decreased DFS and OS. |
Castillo et al., 2018 [79] | 103 | PDAC, all stages | Exomes | ddPCR | KRAS, exosome surface proteins | KRAS mutation in exoDNA of 73% of PDAC pts following exosome capture using selected biomarkers. |
Study | No. of pts | Type of pts | Platform | Markers | Findings |
---|---|---|---|---|---|
Allard et al., 2004 [100] | 16 | Stage IV PDAC (within study of multiple cancer types) | Antibody detection | CellSearch system | 19% of 21 samples from 19 pts with stage IV PDAC had ≥2 CTCs per 7.5 mL blood. In the larger cohort of patients with metastatic carcinoma from various sites, 36% (781/2183) pts had had ≥2 CTCs per 7.5 mL blood |
Nagrath et al., 2007 [101] | 15 | Stage IV PDAC (within study of multiple cancer types) | Antibody detection | CTC-chip system using EpCAM-coated microposts | CTCs identified in 115/116 pts with metastatic carcinoma (15/15 PDAC pts). Temporal changes in CTC numbers correlated with radiologic response/progression. |
Kulemann et al., 2017 [116] | 58 | PDAC, all stages | CTC detection based on size and genomic analysis | Size-based CTC isolation | CTCs identified in 53/58 pts with PDAC and 0/10 healthy controls. Pts with >3 CTCs/mL had non-significantly reduced OS. KRAS mutations in CTCs were discordant with those in primary tumor in 11/26 pts and concordant in 15/26 pts with KRAS mutated CTCs. Pts with KRAS mutations in CTCs had longer OS than other pts. |
Effenberger et al., 2018 [117] | 69 | PDAC, all stages | Antibody detection | Anti-cyto-keratin/anti-EpCAM staining | CTCs identified in 23/69 pts with PDAC, ranging from 1–19 cells. Detectable CTCs correlated with decreased DFS and OS. |
Arnoletti et al., 2018 [118] | 11 | Resectable PDAC | Antibody detection | FACS-isolation system | CTC proliferation and resistance to T cell cytotoxicity were decreased among patients who received neoadjuvant chemotherapy. |
Gemene-tzis et al., 2018 [119] | 200 | PDAC, all stages | Size followed by antibody detection | ISET assay | Neoadjuvant chemotherapy and surgery both significantly lowered total CTCs. |
Liu et al., 2018 [120] | 29 | Advanced PDAC | Antibody detection | EasySep Human CD45 Depletion Kit | Absolute number of CTCs in portal vein was significantly higher than that in peripheral circulation and was associated with intrahepatic metastases and poor prognosis. |
Wei et al., 2019 [121] | 76 | PDAC, all stages | Density followed by antibody detection | CytoQuest CR system | Combined vimentin+ CTCs and CA19-9 identified PDAC cases with an area under the curve of 0.968. |
Chen et al., 2022 [115] | 80 | PDAC and IPMNs | Antibody detection | NE-imFISH | CTCs isolated from 80 patients with increased specificity/sensitivity in detecting PDAC compared to CA19-9 alone. |
Dopico et al., 2022 [114] | 8 | Resectable PDAC | ctDNA by ddPCR, CTCs by antibody detection | Microfluidic droplet digital PCR (DDPRC) | Both cfDNA and CTCs (81% and 91%, respectively) can be isolated in patients after starting neoadjuvant therapy and before surgical resection. |
Date Initiated | Analyte | No. of pts | Disease Setting | Trial Number |
---|---|---|---|---|
12 June 2019 | CTCs | 50 | Resectable PDAC | NCT04289961 |
7 November 2017 | ctDNA, Exosomes, CTCs | 700 | Screening/and response to treatment | NCT03334708 |
15 August 2017 | ctDNA, Exosomes | 100 | PDAC screening | NCT0325½8 |
2 January 2019 | Exosomes | 200 | PDAC screening | NCT03791073 |
15 March2015 | Exosomes | 111 | PDAC (any stage) | NCT02393703 |
3 November 2022 | ctDNA | 150 | PDAC (any stage) | NCT05604573 |
18 February 2019 | ctDNA | 40 | Resectable PDAC | NCT03435536 |
29 January 2020 | ctDNA | 200 | Resectable PDAC | NCT04246203 |
1 June 2022 | ctDNA | 200 | Resectable PDAC | NCT05400681 |
21 September 2021 | ctDNA | 15 | PDAC (any stage) | NCT05497531 |
29 July 2022 | ctDNA | 150 | Resectable PDAC | NCT05479708 |
15 June 2022 | ctDNA | 50 | Resectable PDAC | NCT05052671 |
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Raufi, A.G.; May, M.S.; Hadfield, M.J.; Seyhan, A.A.; El-Deiry, W.S. Advances in Liquid Biopsy Technology and Implications for Pancreatic Cancer. Int. J. Mol. Sci. 2023, 24, 4238. https://doi.org/10.3390/ijms24044238
Raufi AG, May MS, Hadfield MJ, Seyhan AA, El-Deiry WS. Advances in Liquid Biopsy Technology and Implications for Pancreatic Cancer. International Journal of Molecular Sciences. 2023; 24(4):4238. https://doi.org/10.3390/ijms24044238
Chicago/Turabian StyleRaufi, Alexander G., Michael S. May, Matthew J. Hadfield, Attila A. Seyhan, and Wafik S. El-Deiry. 2023. "Advances in Liquid Biopsy Technology and Implications for Pancreatic Cancer" International Journal of Molecular Sciences 24, no. 4: 4238. https://doi.org/10.3390/ijms24044238
APA StyleRaufi, A. G., May, M. S., Hadfield, M. J., Seyhan, A. A., & El-Deiry, W. S. (2023). Advances in Liquid Biopsy Technology and Implications for Pancreatic Cancer. International Journal of Molecular Sciences, 24(4), 4238. https://doi.org/10.3390/ijms24044238