Identification of DNA Methylation Prognostic Signature of Acute Myelocytic Leukemia

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2018 Jun 23

PMID 29933410

Citations 7

Authors

Haiguo Zhang

Guanli Song

Guanbo Song

Ruolei Li

Min Gao

Ling Ye

Chengfang Zhang

Affiliations

Soon will be listed here.

Abstract

Background: The aim of this study is to find the potential survival related DNA methylation signature capable of predicting survival time for acute myelocytic leukemia (AML) patients.

Methods: DNA methylation data were downloaded. DNA methylation signature was identified in the training group, and subsequently validated in an independent validation group. The overall survival of DNA methylation signature was performed. Functional analysis was used to explore the function of corresponding genes of DNA methylation signature. Differentially methylated sites and CpG islands were also identified in poor-risk group.

Results: A DNA methylation signature involving 8 DNA methylation sites and 6 genes were identified. Functional analysis showed that protein binding and cytoplasm were the only two enriched Gene Ontology terms. A total of 70 differentially methylated sites and 6 differentially methylated CpG islands were identified in poor-risk group.

Conclusions: The identified survival related DNA methylation signature adds to the prognostic value of AML.

Citing Articles

Assessing the Differential Methylation Analysis Quality for Microarray and NGS Platforms.

Budkina A, Medvedeva Y, Stupnikov A Int J Mol Sci. 2023; 24(10).

PMID: 37239934 PMC: 10218268. DOI: 10.3390/ijms24108591.

A DNA methylation signature for the prediction of tumour recurrence in stage II colorectal cancer.

Li M, Zhu C, Xue Y, Miao C, He R, Li W Br J Cancer. 2023; 128(9):1681-1689.

PMID: 36828869 PMC: 10133253. DOI: 10.1038/s41416-023-02155-8.

Systematic review of epigenetic targets in acute myeloid leukemia.

Verma S, Dhanda H, Singh A, Rishi B, Tanwar P, Chaudhry S Am J Blood Res. 2021; 11(5):458-471.

PMID: 34824880 PMC: 8610793.

DNA Methylation Signatures Predict Cytogenetic Subtype and Outcome in Pediatric Acute Myeloid Leukemia (AML).

Krali O, Palle J, Backlin C, Abrahamsson J, Noren-Nystrom U, Hasle H Genes (Basel). 2021; 12(6).

PMID: 34200630 PMC: 8229099. DOI: 10.3390/genes12060895.

Meta-analysis of gene signatures and key pathways indicates suppression of JNK pathway as a regulator of chemo-resistance in AML.

Modarres P, Mohamadi Farsani F, Nekouie A, Vallian S Sci Rep. 2021; 11(1):12485.

PMID: 34127725 PMC: 8203646. DOI: 10.1038/s41598-021-91864-2.

References

Deneberg S, Grovdal M, Karimi M, Jansson M, Nahi H, Corbacioglu A . Gene-specific and global methylation patterns predict outcome in patients with acute myeloid leukemia. Leukemia. 2010; 24(5):932-41. DOI: 10.1038/leu.2010.41. View

Tse K, Su W, Chang K, Tsang N, Yu C, Tang P . Genome-wide association study reveals multiple nasopharyngeal carcinoma-associated loci within the HLA region at chromosome 6p21.3. Am J Hum Genet. 2009; 85(2):194-203. PMC: 2725267. DOI: 10.1016/j.ajhg.2009.07.007. View

Dohner H, Weisdorf D, Bloomfield C . Acute Myeloid Leukemia. N Engl J Med. 2015; 373(12):1136-52. DOI: 10.1056/NEJMra1406184. View

Yoshinaga S, Mabuchi K, Sigurdson A, Doody M, Ron E . Cancer risks among radiologists and radiologic technologists: review of epidemiologic studies. Radiology. 2004; 233(2):313-21. DOI: 10.1148/radiol.2332031119. View

Wolters J, van Breda S, Claessen S, de Kok T, Kleinjans J . Data on novel DNA methylation changes induced by valproic acid in human hepatocytes. Data Brief. 2017; 16:161-171. PMC: 5702865. DOI: 10.1016/j.dib.2017.11.031. View

Braun T, Bober E, Winter B, Rosenthal N, Arnold H . Myf-6, a new member of the human gene family of myogenic determination factors: evidence for a gene cluster on chromosome 12. EMBO J. 1990; 9(3):821-31. PMC: 551742. DOI: 10.1002/j.1460-2075.1990.tb08179.x. View

Miyawaki S . [Guideline for AML]. Rinsho Ketsueki. 2013; 54(10):1633-42. View

Hay N, Sonenberg N . Upstream and downstream of mTOR. Genes Dev. 2004; 18(16):1926-45. DOI: 10.1101/gad.1212704. View

Ting W, Chen L, Pao J, Yang Y, You B, Chang T . Genetic polymorphisms of matrix metalloproteinases and clinical outcomes in colorectal cancer patients. Int J Med Sci. 2013; 10(8):1022-7. PMC: 3691801. DOI: 10.7150/ijms.6686. View

10.

Larkin K, Blum W . Novel therapies in AML: reason for hope or just hype?. Am Soc Clin Oncol Educ Book. 2014; :e341-51. DOI: 10.14694/EdBook_AM.2014.34.e341. View

11.

Masaki T, Matsuoka H, Sugiyama M, Abe N, Goto A, Sakamoto A . Matrilysin (MMP-7) as a significant determinant of malignant potential of early invasive colorectal carcinomas. Br J Cancer. 2001; 84(10):1317-21. PMC: 2363635. DOI: 10.1054/bjoc.2001.1790. View

12.

Plass C, Oakes C, Blum W, Marcucci G . Epigenetics in acute myeloid leukemia. Semin Oncol. 2008; 35(4):378-87. PMC: 3463865. DOI: 10.1053/j.seminoncol.2008.04.008. View

13.

Tang M, Lautenberger J, Gao X, Sezgin E, Hendrickson S, Troyer J . The principal genetic determinants for nasopharyngeal carcinoma in China involve the HLA class I antigen recognition groove. PLoS Genet. 2012; 8(11):e1003103. PMC: 3510037. DOI: 10.1371/journal.pgen.1003103. View

14.

Kushwaha G, Dozmorov M, Wren J, Qiu J, Shi H, Xu D . Hypomethylation coordinates antagonistically with hypermethylation in cancer development: a case study of leukemia. Hum Genomics. 2016; 10 Suppl 2:18. PMC: 4965721. DOI: 10.1186/s40246-016-0071-5. View

15.

Hanspal M, Smockova Y, Uong Q . Molecular identification and functional characterization of a novel protein that mediates the attachment of erythroblasts to macrophages. Blood. 1998; 92(8):2940-50. View

16.

Benton M, Johnstone A, Eccles D, Harmon B, Hayes M, Lea R . An analysis of DNA methylation in human adipose tissue reveals differential modification of obesity genes before and after gastric bypass and weight loss. Genome Biol. 2015; 16:8. PMC: 4301800. DOI: 10.1186/s13059-014-0569-x. View

17.

Ishikawa F, Yoshida S, Saito Y, Hijikata A, Kitamura H, Tanaka S . Chemotherapy-resistant human AML stem cells home to and engraft within the bone-marrow endosteal region. Nat Biotechnol. 2007; 25(11):1315-21. DOI: 10.1038/nbt1350. View

18.

Rao A, Valk P, Metzeler K, Acharya C, Tuchman S, Stevenson M . Age-specific differences in oncogenic pathway dysregulation and anthracycline sensitivity in patients with acute myeloid leukemia. J Clin Oncol. 2009; 27(33):5580-6. DOI: 10.1200/JCO.2009.22.2547. View

19.

Horwitz M, Goode E, Jarvik G . Anticipation in familial leukemia. Am J Hum Genet. 1996; 59(5):990-8. PMC: 1914843. View

20.

Levine R . Molecular pathogenesis of AML: translating insights to the clinic. Best Pract Res Clin Haematol. 2013; 26(3):245-8. PMC: 3869618. DOI: 10.1016/j.beha.2013.10.003. View