DLEC1 methylation is associated with a better clinical outcome in patients with intrahepatic cholangiocarcinoma of the small duct subtype

  • Younghoon Kim
  • Kyoungbun Lee
  • Seorin Jeong
  • Xianyu Wen
  • Nam-Yun Cho
  • Gyeong Hoon KangEmail author
Original Article


Intrahepatic cholangiocarcinoma is a complex disease with three different histologic subtypes, the large duct, small duct, and bile ductular types. In the present study, we elucidated whether the three histological subtypes have differences in their methylation profiles and developed a DNA methylation marker that might help identify a subset of ICC with a different prognosis. We screened 113 promoter CpG island loci against 10 cases of intrahepatic cholangiocarcinoma and normal cystic ducts using the MethyLight assay and selected 30 CpG island loci with cancer-associated hypermethylation. Then, we analyzed 172 intrahepatic cholangiocarcinomas for the methylation state at these 30 loci. Six loci, including DLEC1, were more frequently methylated in the bile ductular type and small duct type, whereas six loci were more frequently methylated in the large duct type. Of these 30 loci, DLEC1 methylation was found mainly in the bile ductular type and small duct type but rarely in the large duct type. DLEC1 methylation was significantly associated with a better clinical outcome in intrahepatic cholangiocarcinomas of the small duct type but not of the bile ductular type. DLEC1 methylation was an independent prognostic variable in both cancer-specific survival and recurrence-free survival. For patients with intrahepatic cholangiocarcinoma of the small duct type (n = 68), DLEC1 methylation was found in 26 (38.2%) and was associated with a better clinical outcome for both cancer-specific survival and recurrence-free survival. Our findings suggest that DLEC1 methylation can be utilized to identify a subset with a better prognosis in intrahepatic cholangiocarcinomas of the small duct type.


Biomarker CpG island DLEC1 Histologic type Intrahepatic cholangiocarcinoma Methylation Prognosis 



YK performed the analysis, collected part of the data, and wrote part of the paper; KL collected the data, contributed data, conceived the work, and performed the analysis; SJ, NYC and XW performed the analysis, collected the data, contributed to the interpretation of data; GHK conceived the work, wrote the draft, and interpreted the data. All the authors (YK, KL, SJ, XW, NYC, GHK) will participate in the final approval of the version to be published and express agreement to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.

Funding sources

This work was financially supported by grants from the National Research Foundation (NRF) funded by the Korean Ministry of Science, ICT and Future Planning (2016M3A9B6026921), a grant from the Korea Health Technology R&D Project through the Korea Health Industry Development Institute funded by the Korean Ministry of Health and Welfare (HI14C1277), and a grant from SNUH Research Fund (0320170070 (2017-1176)).

Compliance with ethical standards

This study was approved by the institutional review board of Seoul National University Hospital (IRB No. 1804-168-942). Under the condition of retrospective archival tissue collection and patient data anonymization, our study was exempted from the acquisition of informed consent from patients.

Conflicts of interest

The authors declare that they have no conflict of interest.

Supplementary material

428_2018_2511_MOESM1_ESM.jpg (1.5 mb)
Supplementary Figure 1 Representative photomicrographs of three histological subtypes; bile ductular subtype (A, original magnification (X200)), small duct subtype (B, original magnification (X200)), and large duct subtype (C, original magnification (X100)). (JPG 1541 kb)
428_2018_2511_MOESM2_ESM.jpg (125 kb)
Supplementary Figure 2 Ten cases of intrahepatic cholangiocarcinomas and ten cases of normal cystic ducts were analyzed to determine their methylation states at 113 CpG island loci using MethyLight assay. The methylation level is represented with different colors. Dark brown, percentage of methylated reference (PMR) ≥50%; brown, 50% > PMR ≥ 20%; light brown, 20% > PMR ≥ 4%; white, PMR < 4%. (JPG 125 kb)
428_2018_2511_Fig3_ESM.png (196 kb)
Supplementary Figure 3

DNA methylation heat map of 30 CpG island loci in 172 intrahepatic cholangiocarcinomas. The methylation level is represented with different colors. Dark brown, percentage of methylated reference (PMR) ≥50%; brown, 50% > PMR ≥ 20%; light brown, 20% > PMR ≥ 4%; white, PMR < 4%. Gross type: mass-forming type, green; periductal infiltrative type, red; intraductal growing type, purple; mixed type, white. Histological subtype: bile ductular type, light blue; small duct type, blue; large duct type, deep blue. (PNG 195 kb)

428_2018_2511_MOESM3_ESM.tif (518 kb)
High resolution image (TIF 517 kb)
428_2018_2511_Fig4_ESM.png (131 kb)
Supplementary Figure 4

Fifty-four cases of hepatocellular carcinomas and 57 cases of extrahepatic cholangiocarcinomas were analyzed using the MethyLight assay to determine their methylation states at 12 CpG island loci, which were significantly different in regard to the methylation frequencies between intrahepatic cholangiocarcinomas of the large duct type and small duct or bile ductular type. The methylation level is represented with different colors. Dark brown, percentage of methylated reference (PMR) ≥50%; brown, 50% > PMR ≥ 20%; light brown, 20% > PMR ≥ 4%; white, PMR < 4%. (PNG 131 kb)

428_2018_2511_MOESM4_ESM.tif (266 kb)
High resolution image (TIF 265 kb)
428_2018_2511_MOESM5_ESM.docx (16 kb)
Supplementary Table 1 (DOCX 15 kb)
428_2018_2511_MOESM6_ESM.docx (18 kb)
Supplementary Table 2 (DOCX 18 kb)
428_2018_2511_MOESM7_ESM.docx (18 kb)
Supplementary Table 3 (DOCX 17 kb)
428_2018_2511_MOESM8_ESM.docx (15 kb)
Supplementary Table 4 (DOCX 14 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Laboratory of Epigenetics, Cancer Research InstituteSeoul National University College of MedicineSeoulSouth Korea
  2. 2.Department of PathologySeoul National University College of MedicineSeoulSouth Korea

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