|
1
|
Bonin S and Stanta G: Pre-analytics and
tumor heterogeneity. N Biotechnol. 55:30–35. 2020. View Article : Google Scholar
|
|
2
|
Dagogo-Jack I and Shaw AT: Tumour
heterogeneity and resistance to cancer therapies. Nat Rev Clin
Oncol. 15:81–94. 2018. View Article : Google Scholar
|
|
3
|
Falzone L, Bordonaro R and Libra M:
SnapShot: Cancer chemotherapy. Cell. 186:1816–1816.e1. 2023.
View Article : Google Scholar
|
|
4
|
Baylin SB and Jones PA: Epigenetic
determinants of cancer. Cold Spring Harb Perspect Biol.
8:a0195052016. View Article : Google Scholar : PubMed/NCBI
|
|
5
|
Ilango S, Paital B, Jayachandran P, Padma
PR and Nirmaladevi R: Epigenetic alterations in cancer. Front
Biosci (Landmark Ed). 25:1058–1109. 2020. View Article : Google Scholar : PubMed/NCBI
|
|
6
|
Klutstein M, Nejman D, Greenfield R and
Cedar H: DNA methylation in cancer and aging. Cancer Res.
76:3446–3450. 2016. View Article : Google Scholar : PubMed/NCBI
|
|
7
|
Moore LD, Le T and Fan G: DNA methylation
and its basic function. Neuropsychopharmacology. 38:23–38. 2013.
View Article : Google Scholar
|
|
8
|
Dhar GA, Saha S, Mitra P and Nag Chaudhuri
R: DNA methylation and regulation of gene expression: Guardian of
our health. Nucleus (Calcutta). 64:259–270. 2021. View Article : Google Scholar : PubMed/NCBI
|
|
9
|
Hao X, Luo H, Krawczyk M, Wei W, Wang W,
Wang J, Flagg K, Hou J, Zhang H, Yi S, et al: DNA methylation
markers for diagnosis and prognosis of common cancers. Proc Natl
Acad Sci USA. 114:7414–7419. 2017. View Article : Google Scholar : PubMed/NCBI
|
|
10
|
Pettini F, Visibelli A, Cicaloni V,
Iovinelli D and Spiga O: Multi-omics model applied to cancer
genetics. Int J Mol Sci. 22:57512021. View Article : Google Scholar : PubMed/NCBI
|
|
11
|
Papanicolau-Sengos A and Aldape K: DNA
methylation profiling: An emerging paradigm for cancer diagnosis.
Annu Rev Pathol. 17:295–321. 2022. View Article : Google Scholar
|
|
12
|
Grunau C, Clark SJ and Rosenthal A:
Bisulfite genomic sequencing: SYstematic investigation of critical
experimental parameters. Nucleic Acids Res. 29:E652001. View Article : Google Scholar : PubMed/NCBI
|
|
13
|
Tanaka K and Okamoto A: Degradation of DNA
by bisulfite treatment. Bioorg Med Chem Lett. 17:1912–1915. 2007.
View Article : Google Scholar : PubMed/NCBI
|
|
14
|
Li Q, Hermanson PJ and Springer NM:
Detection of DNA methylation by whole-genome bisulfite sequencing.
Methods Mol Biol. 1676:185–196. 2018. View Article : Google Scholar
|
|
15
|
Mehrmohamadi M, Sepehri MH, Nazer N and
Norouzi MR: A comparative overview of epigenomic profiling methods.
Front Cell Dev Biol. 9:7146872021. View Article : Google Scholar : PubMed/NCBI
|
|
16
|
Kurdyukov S and Bullock M: DNA methylation
analysis: Choosing the right method. Biology (Basel).
5:32016.PubMed/NCBI
|
|
17
|
Šestáková Š, Šálek C and Remešová H: DNA
methylation validation methods: A coherent review with practical
comparison. Biol Proced Online. 21:192019. View Article : Google Scholar : PubMed/NCBI
|
|
18
|
Beikircher G, Pulverer W, Hofner M,
Noehammer C and Weinhaeusel A: Multiplexed and sensitive DNA
methylation testing using methylation-sensitive restriction enzymes
'MSRE-qPCR'. Methods Mol Biol. 1708:407–424. 2018. View Article : Google Scholar
|
|
19
|
Melnikov AA, Gartenhaus RB, Levenson AS,
Motchoulskaia NA and Levenson Chernokhvostov VV: MSRE-PCR for
analysis of gene-specific DNA methylation. Nucleic Acids Res.
33:e932005. View Article : Google Scholar : PubMed/NCBI
|
|
20
|
Chapman KB and Higgs BW: Selective
amplification of hypermethylated DNA from diverse tumor types via
MSRE-PCR. Oncotarget. 11:4387–4400. 2020. View Article : Google Scholar : PubMed/NCBI
|
|
21
|
Nell RJ, van Steenderen D, Menger NV,
Weitering TJ, Versluis M and van der Velden PA: Quantification of
DNA methylation independent of sodium bisulfite conversion using
methylation-sensitive restriction enzymes and digital PCR. Hum
Mutat. 41:2205–2216. 2020. View Article : Google Scholar : PubMed/NCBI
|
|
22
|
Wang D, O'Rourke D, Sanchez-Garcia JF, Cai
T, Scheuenpflug J and Feng Z: Development of a liquid biopsy based
purely quantitative digital droplet PCR assay for detection of MLH1
promoter methylation in colorectal cancer patients. BMC Cancer.
21:7972021. View Article : Google Scholar : PubMed/NCBI
|
|
23
|
van Zogchel LMJ, Lak NSM, Verhagen OJHM,
Tissoudali A, Gussmalla Nuru M, Gelineau NU, Zappeij-Kannengieter
L, Javadi A, Zijtregtop EAM, Merks JHM, et al: Novel circulating
hypermethylated RASSF1A ddPCR for liquid biopsies in patients with
pediatric solid tumors. JCO Precis Oncol.
5:PO.21.001302021.PubMed/NCBI
|
|
24
|
Metzenmacher M, Hegedüs B, Forster J,
Schramm A, Horn PA, Klein CA, Bielefeld N, Ploenes T, Aigner C,
Theegarten D, et al: Combined multimodal ctDNA analysis and
radiological imaging for tumor surveillance in Non-small cell lung
cancer. Transl Oncol. 15:1012792022. View Article : Google Scholar
|
|
25
|
Olmedillas-López S, Olivera-Salazar R,
García-Arranz M and García-Olmo D: Current and emerging
applications of droplet digital PCR in oncology: An updated review.
Mol Diagn Ther. 26:61–87. 2022. View Article : Google Scholar
|
|
26
|
Gattuso G, Falzone L, Costa C, Giambò F,
Teodoro M, Vivarelli S, Libra M and Fenga C: Chronic pesticide
exposure in farm workers is associated with the epigenetic
modulation of hsa-miR-199a-5p. Int J Environ Res Public Health.
19:70182022. View Article : Google Scholar : PubMed/NCBI
|
|
27
|
Crimi S, Falzone L, Gattuso G, Grillo CM,
Candido S, Bianchi A and Libra M: Droplet digital PCR analysis of
liquid biopsy samples unveils the diagnostic Role of
hsa-miR-133a-3p and hsa-miR-375-3p in oral cancer. Biology (Basel).
9:3792020.PubMed/NCBI
|
|
28
|
Pharo HD, Andresen K, Berg KCG, Lothe RA,
Jeanmougin M and Lind GE: A robust internal control for
high-precision DNA methylation analyses by droplet digital PCR.
Clin Epigenetics. 10:242018. View Article : Google Scholar : PubMed/NCBI
|
|
29
|
Lin WH, Xiao J, Ye ZY, Wei DL, Zhai XH, Xu
RH, Zeng ZL and Luo HY: Circulating tumor DNA methylation marker
MYO1-G for diagnosis and monitoring of colorectal cancer. Clin
Epigenetics. 13:2322021. View Article : Google Scholar : PubMed/NCBI
|
|
30
|
Salemi R, Falzone L, Madonna G, Polesel J,
Cinà D, Mallardo D, Ascierto PA, Libra M and Candido S: MMP-9 as a
candidate marker of response to BRAF inhibitors in melanoma
patients with BRAFV600E mutation detected in
circulating-free DNA. Front Pharmacol. 9:8562018. View Article : Google Scholar
|
|
31
|
Barros-Silva D, Marques CJ, Henrique R and
Jerónimo C: Profiling DNA methylation based on next-generation
sequencing approaches: New insights and clinical applications.
Genes (Basel). 9:4292018. View Article : Google Scholar : PubMed/NCBI
|
|
32
|
Nikolouzakis TK, Falzone L, Lasithiotakis
K, Krüger-Krasagakis S, Kalogeraki A, Sifaki M, Spandidos DA,
Chrysos E, Tsatsakis A and Tsiaoussis J: Current and future trends
in molecular biomarkers for diagnostic, prognostic, and predictive
purposes in non-melanoma skin cancer. J Clin Med. 9:28682020.
View Article : Google Scholar : PubMed/NCBI
|
|
33
|
Merkel A and Esteller M: Experimental and
bioinformatic approaches to studying DNA methylation in cancer.
Cancers (Basel). 14:3492022. View Article : Google Scholar : PubMed/NCBI
|
|
34
|
Gai W and Sun K: Epigenetic biomarkers in
cell-free DNA and applications in liquid biopsy. Genes (Basel).
10:322019. View Article : Google Scholar : PubMed/NCBI
|
|
35
|
Smith J, Day RC and Weeks RJ:
Next-generation bisulfite sequencing for targeted DNA methylation
analysis. Methods Mol Biol. 2458:47–62. 2022. View Article : Google Scholar : PubMed/NCBI
|
|
36
|
Leti F, Llaci L, Malenica I and Di Stefano
JK: Methods for CpG methylation array profiling via bisulfite
conversion. Methods Mol Biol. 1706:233–254. 2018. View Article : Google Scholar : PubMed/NCBI
|
|
37
|
Kint S, De Spiegelaere W, De Kesel J,
Vandekerckhove L and Van Criekinge W: Evaluation of bisulfite kits
for DNA methylation profiling in terms of DNA fragmentation and DNA
recovery using digital PCR. PLoS One. 13:e01990912018. View Article : Google Scholar : PubMed/NCBI
|
|
38
|
Hong SR and Shin KJ: Bisulfite-converted
DNA quantity evaluation: A multiplex quantitative real-time PCR
system for evaluation of bisulfite conversion. Front Genet.
12:6189552021. View Article : Google Scholar : PubMed/NCBI
|
|
39
|
Lavoro A, Scalisi A, Candido S, Zanghì GN,
Rizzo R, Gattuso G, Caruso G, Libra M and Falzone L: Identification
of the most common BRCA alterations through analysis of germline
mutation databases: Is droplet digital PCR an additional strategy
for the assessment of such alterations in breast and ovarian cancer
families? Int J Oncol. 60:582022. View Article : Google Scholar : PubMed/NCBI
|
|
40
|
Van Wesenbeeck L, Janssens L, Meeuws H,
Lagatie O and Stuyver L: Droplet digital PCR is an accurate method
to assess methylation status on FFPE samples. Epigenetics.
13:207–213. 2018. View Article : Google Scholar : PubMed/NCBI
|
|
41
|
Candido S, Tomasello B, Lavoro A, Falzone
L, Gattuso G, Russo A, Paratore S, McCubrey JA and Libra M:
Bioinformatic analysis of the LCN2-SLC22A17-MMP9 network in cancer:
The role of DNA methylation in the modulation of tumor
microenvironment. Front Cell Dev Biol. 10:9455862022. View Article : Google Scholar : PubMed/NCBI
|
|
42
|
Chi Y, Remsik J, Kiseliovas V, Derderian
C, Sener U, Alghader M, Saadeh F, Nikishina K, Bale T,
Iacobuzio-Donahue C, et al: Cancer cells deploy lipocalin-2 to
collect limiting iron in leptomeningeal metastasis. Science.
369:276–282. 2020. View Article : Google Scholar : PubMed/NCBI
|
|
43
|
Liu F, Li N, Yang W, Wang R, Yu J and Wang
X: The expression analysis of NGAL and NGALR in clear cell renal
cell carcinoma. Gene. 676:269–278. 2018. View Article : Google Scholar : PubMed/NCBI
|
|
44
|
Gomez-Chou SB, Swidnicka-Siergiejko AK,
Badi N, Chavez-Tomar M, Lesinski GB, Bekaii-Saab T, Farren MR, Mace
TA, Schmidt C, Liu Y, et al: Lipocalin-2 promotes pancreatic ductal
adenocarcinoma by regulating inflammation in the tumor
microenvironment. Cancer Res. 77:2647–2660. 2017. View Article : Google Scholar : PubMed/NCBI
|
|
45
|
Miyamoto T, Kashima H, Yamada Y, Kobara H,
Asaka R, Ando H, Higuchi S, Ida K, Mvunta DH and Shiozawa T:
Lipocalin 2 enhances migration and resistance against cisplatin in
endometrial carcinoma cells. PLoS One. 11:e01552202016. View Article : Google Scholar : PubMed/NCBI
|
|
46
|
Wei J, Gao X, Qin Y, Liu T and Kang Y: An
iron metabolism-related SLC22A17 for the prognostic value of
gastric cancer. Onco Targets Ther. 13:12763–12775. 2020. View Article : Google Scholar : PubMed/NCBI
|
|
47
|
Frouin E, Maudelonde T, Senal R, Larrieux
M, Costes V, Godreuil S, Vendrell JA and Solassol J: Comparative
methods to improve the detection of BRAF V600 mutations in highly
pigmented melanoma specimens. PLoS One. 11:e01586982016. View Article : Google Scholar : PubMed/NCBI
|
|
48
|
Vicente ALSA, Bianchini RA, Laus AC,
Macedo G, Reis RM and Vazquez VL: Comparison of protocols for
removal of melanin from genomic DNA to optimize PCR amplification
of DNA purified from highly pigmented lesions. Histol Histopathol.
34:1089–1096. 2019.PubMed/NCBI
|
