Page 36 - GTM-3-3

Global Translational Medicine Computational advances in cancer liquid biopsy

sequencing of single-cell genomes and transcriptomes. Nat 70. Ponomaryova AA, Rykova EY, Gervas PA, Cherdyntseva NV,
Methods. 2015;12(6):519-522. Mamedov IZ, Azhikina TL. Aberrant methylation of LINE-1
transposable elements: A search for cancer biomarkers.
doi: 10.1038/nmeth.3370
Cells. 2020;9(9):2017.
60. Cheng YH, Chen YC, Lin E, et al. Hydro-Seq enables
contamination-free high-throughput single-cell RNA- doi: 10.3390/cells9092017
sequencing for circulating tumor cells. Nat Commun. 71. Su SF, De Castro Abreu AL, Chihara Y, et al. A panel of three
2019;10(1):2163. markers hyper- and hypomethylated in urine sediments
accurately predicts bladder cancer recurrence. Clin Cancer
doi: 10.1038/s41467-019-10122-2
Res. 2014;20(7):1978-1989.
61. Pixberg C, Schulz W, Stoecklein N, Neves R. Characterization doi: 10.1158/1078-0432.CCR-13-2637
of DNA methylation in circulating tumor cells. Genes.
2015;6(4):1053-1075. 72. Ross JP, Rand KN, Molloy PL. Hypomethylation of repeated
DNA sequences in cancer. Epigenomics. 2010;2(2):245-269.
doi: 10.3390/genes6041053
doi: 10.2217/epi.10.2
62. Gkountela S, Castro-Giner F, Szczerba BM, et al. Circulating
tumor cell clustering shapes DNA methylation to enable 73. Burns KH. Transposable elements in cancer. Nat Rev Cancer.
metastasis seeding. Cell. 2019;176(1-2):98-112.e14. 2017;17(7):415-424.
doi: 10.1016/j.cell.2018.11.046 doi: 10.1038/nrc.2017.35
63. Chimonidou M, Strati A, Tzitzira A, et al. DNA methylation 74. Annapragada AV, Niknafs N, White JR, et al. Genome-wide
of tumor suppressor and metastasis suppressor genes in repeat landscapes in cancer and cell-free DNA. Sci Transl
circulating tumor cells. Clin Chem. 2011;57(8):1169-1177. Med. 2024;16(738):eadj9283.
doi: 10.1373/clinchem.2011.165902 doi: 10.1126/scitranslmed.adj9283
64. Peneder P, Stütz AM, Surdez D, et al. Multimodal analysis 75. Park MK, Lee JC, Lee JW, Hwang SJ. Alu cell-free DNA
of cell-free DNA whole-genome sequencing for pediatric concentration, Alu index, and LINE-1 hypomethylation as
cancers with low mutational burden. Nat Commun. a cancer predictor. Clin Biochem. 2021;94:67-73.
2021;12(1):3230. doi: 10.1016/j.clinbiochem.2021.04.021
doi: 10.1038/s41467-021-23445-w 76. Douville C, Lahouel K, Kuo A, et al. Machine learning to detect
65. Cristiano S, Leal A, Phallen J, et al. Genome-wide cell- the SINEs of cancer. Sci Transl Med. 2024;16(731):eadi3883.
free DNA fragmentation in patients with cancer. Nature. doi: 10.1126/scitranslmed.adi3883
2019;570(7761):385-389.
77. Reggiardo RE, Maroli SV, Peddu V, et al. Profiling of
doi: 10.1038/s41586-019-1272-6 repetitive RNA sequences in the blood plasma of patients
66. Ulz P, Perakis S, Zhou Q, et al. Inference of transcription with cancer. Nat Biomed Eng. 2023;7(12):1627-1635.
factor binding from cell-free DNA enables tumor doi: 10.1038/s41551-023-01081-7
subtype prediction and early detection. Nat Commun.
2019;10(1):4666. 78. Aceto N, Bardia A, Wittner BS, et al. AR expression in breast
cancer CTCs associates with bone metastases. Mol Cancer
doi: 10.1038/s41467-019-12714-4 Res. 2018;16(4):720-727.
67. Wong D, Luo P, Oldfield LE, et al. Early cancer detection in doi: 10.1158/1541-7786.MCR-17-0480
Li-Fraumeni syndrome with cell-free DNA. Cancer Discov.
2024;14(1):104-119. 79. Chen C, Mahalingam D, Osmulski P, et al. Single‐cell analysis
of circulating tumor cells identifies cumulative expression
doi: 10.1158/2159-8290.CD-23-0456 patterns of EMT‐related genes in metastatic prostate cancer.
68. Grabuschnig S, Soh J, Heidinger P, et al. Circulating cell- Prostate. 2013;73(8):813-826.
free DNA is predominantly composed of retrotransposable doi: 10.1002/pros.22625
elements and non-telomeric satellite DNA. J Biotechnol. 80. D’Avola D, Villacorta-Martin C, Martins-Filho SN, et al.
2020;313:48-56.
High-density single cell mRNA sequencing to characterize
doi: 10.1016/j.jbiotec.2020.03.002 circulating tumor cells in hepatocellular carcinoma. Sci
Rep. 2018;8(1):11570.
69. Papasotiriou I, Pantopikou K, Apostolou P. L1
retrotransposon expression in circulating tumor cells. PLoS doi: 10.1038/s41598-018-30047-y
One. 2017;12(2):e0171466.
81. Papadaki MA, Stoupis G, Theodoropoulos PA, Mavroudis D,
doi: 10.1371/journal.pone.0171466 Georgoulias V, Agelaki S. Circulating tumor cells with

Volume 3 Issue 3 (2024) 13 doi: 10.36922/gtm.3063