Liquid Biopsy from Bile-Circulating Tumor DNA in Patients with Biliary Tract Cancer
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Patients
2.2. Bile Collection
2.3. Chemicals and Reagents
2.4. Preparation of Blood Collection
2.5. DNA Extraction from Bile, Plasma, and FFPE Samples
2.6. Droplet Digital PCR
2.7. Direct Extraction of Single-Stranded RNA
2.8. SMARTer smRNA Library
2.9. mRNA-Seq Data Analysis
2.10. Statistical Analysis
3. Results
3.1. Patient Characteristics
3.2. DNA Fragment Size Distributions and Histograms of KRAS Mutations in Bile ctDNA, FFPE, and Plasma Samples
3.3. Concordance of KRAS Mutations among ctDNA in Bile, Plasma, and FFPE DNA Samples from BTC Patients
3.4. Transcriptomic Sequencing in Bile, and Paired Plasma and Tissue
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Bile (N = 42) | FFPE (N = 20) | Plasma (N = 16) | |||||||
---|---|---|---|---|---|---|---|---|---|
Wild Type (N = 22) | KRAS Mutant (N = 20) | p | Wild Type (N = 10) | KRAS Mutant (N = 10) | p | Wild Type (N = 13) | KRAS Mutant (N = 3) | p | |
Age (Mean, SD) | 74.4 ± 9.6 | 71.9 ± 9.5 | 0.408 | 75.3 ± 8.3 | 65.7 ± 8.8 | 0.022 | 73.1 ± 8.3 | 74.3 ± 1.5 | 0.802 |
Sex (Male, %) | 10 (45.5) | 13 (65.0) | 0.337 | 6 (60.0) | 7 (70.0) | 0.774 | 7 (53.8) | 2 (66.7) | 1.000 |
AJCC stage (I, II/III, IV) | 5 (22.7)/ 17 (77.3) | 3 (15.0)/ 17 (85.0) | 0.808 | 3 (30.0)/ 7 (70.0) | 5 (50.0)/ 5 (50.0) | 0.478 | 7 (53.8)/ 6 (46.2) | 0 (0.0)/ 3 (100.0) | 0.238 |
Type of cancer | 0.544 | 0.589 | 0.809 | ||||||
eCCA | 19 (86.4) | 17 (85.0) | 9 (90.0)) | 8 (80.0) | 12 (92.3) | 3 (100.0) | |||
GBC | 3 (13.6) | 2 (10.0) | 1 (10.0) | 1(10.0) | 0 (0.0) | 0 (0.0) | |||
AC | 0 (0.0) | 1 (5.0) | 0 (0.0) | 1 (10.0) | 1 (7.7) | 0 (0.0) | |||
Treatment | 0.476 | 1.000 | 0.809 | ||||||
Surgery | 10 (45.5) | 6 (30.0) | 7 (70.0) | 8 (80.0) | 12 (92.3) | 2 (66.7) | |||
Palliative care | 12 (54.5) | 14 (70.0) | 3 (30.0) | 2 (20.0) | 1 (7.7) | 1 (33.3) |
Bile (N = 42) | FFPE (N = 20) | Plasma (N = 16) | ||||
---|---|---|---|---|---|---|
N (%) | Concentration of DNA (Copies/mL) | N (%) | Concentration of DNA (Copies/mL) | N (%) | Concentration of DNA(Copies/mL) | |
KRAS multiplex mutation | 20 (47.6) | 14,995.0 ± 17,602.6 | 10 (50.0) | 24,515.0 ± 17,128.9 | 3 (18.7) | 12.5 ± 26.9 |
KRASpoint mutation | ||||||
p. G12D | 20 (100.0) | 7917 ± 15,436.7 | 9 (90.0) | 6982.0 ± 14,951.6 | 1 (33.3) | 4.3 ± 17.5 |
p. G12V | 9 (45.0) | 1775.5 ± 3782.3 | 10 (100.0) | 5647.0 ± 8185.9 | 3 (100.0) | 11.8 ± 25.6 |
p. G12D + p. G12V | 20 (100.0) | 9692.5 ± 15,287.9 | 10 (100.0) | 12,632.0 ± 15,207.5 | 3 (100.0) | 16.2 ± 37.5 |
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Han, J.-Y.; Ahn, K.S.; Kim, T.-S.; Kim, Y.H.; Cho, K.B.; Shin, D.W.; Baek, W.-K.; Suh, S.-I.; Jang, B.-C.; Kang, K.J. Liquid Biopsy from Bile-Circulating Tumor DNA in Patients with Biliary Tract Cancer. Cancers 2021, 13, 4581. https://doi.org/10.3390/cancers13184581
Han J-Y, Ahn KS, Kim T-S, Kim YH, Cho KB, Shin DW, Baek W-K, Suh S-I, Jang B-C, Kang KJ. Liquid Biopsy from Bile-Circulating Tumor DNA in Patients with Biliary Tract Cancer. Cancers. 2021; 13(18):4581. https://doi.org/10.3390/cancers13184581
Chicago/Turabian StyleHan, Jin-Yi, Keun Soo Ahn, Tae-Seok Kim, Yong Hoon Kim, Kwang Bum Cho, Dong Woo Shin, Won-Ki Baek, Seong-Il Suh, Byeong-Churl Jang, and Koo Jeong Kang. 2021. "Liquid Biopsy from Bile-Circulating Tumor DNA in Patients with Biliary Tract Cancer" Cancers 13, no. 18: 4581. https://doi.org/10.3390/cancers13184581