Global hypomethylation and promoter methylation in small intestinal neuroendocrine tumors: an in vivo and in vitro study.
Aberrant DNA methylation is a feature of human cancer affecting gene expression and tumor phenotype. Here, we quantified promoter methylation of candidate genes and global methylation in 44 small intestinal-neuroendocrine tumors (SI-NETs) from 33 patients by pyrosequencing. Findings were compared with gene expression, patient outcome and known tumor copy number alterations. Promoter methylation was observed for WIF1, RASSF1A, CTNNB1, CXCL14, NKX2-3, P16, LAMA1, and CDH1. By contrast APC, CDH3, HIC1, P14, SMAD2, and SMAD4 only had low levels of methylation. WIF1 methylation was significantly increased (P = 0.001) and WIF1 expression was reduced in SI-NETs vs. normal references (P = 0.003). WIF1, NKX2-3, and CXCL14 expression was reduced in metastases vs. primary tumors (P<0.02). Low expression of RASSF1A and P16 were associated with poor overall survival (P = 0.045 and P = 0.011, respectively). Global methylation determined by pyrosequencing of LINE1 repeats was reduced in tumors vs. normal references, and was associated with loss in chromosome 18. The tumors fell into three clusters with enrichment of WIF1 methylation and LINE1 hypomethylation in Cluster I and RASSF1A and CTNNB1 methylation and loss in 16q in Cluster II. In Cluster III, these alterations were low-abundant and NKX2-3 methylation was low. Similar analyses in the SI-NET cell lines HC45 and CNDT2 showed methylation for CDH1 and WIF1 and/or P16, CXCL14, NKX2-3, LAMA1, and CTNNB1. Treatment with the demethylating agent 5-azacytidine reduced DNA methylation and increased expression of these genes in vitro. In conclusion, promoter methylation of tumor suppressor genes is associated with suppressed gene expression and DNA copy number alterations in SI-NETs, and may be restored in vitro.
Department of Oncology-Pathology; Karolinska Institutet; Karolinska University Hospital; Stockholm, Sweden.
Omid
O
Fotouhi
Unit of Epidemiology; Institute of Environmental Medicine; Karolinska Institutet; Stockholm, Sweden.
Maral
M
Adel Fahmideh
Department of Molecular Medicine and Surgery; Endocrine and Sarcoma Surgery Unit; Karolinska Institutet; Karolinska University Hospital; Stockholm, Sweden.
Magnus
M
Kjellman
Department of Oncology-Pathology; Karolinska Institutet; Karolinska University Hospital; Stockholm, Sweden.
Luqman
L
Sulaiman
Department of Oncology-Pathology; Karolinska Institutet; Karolinska University Hospital; Stockholm, Sweden.
Anders
A
Höög
Department of Molecular Medicine and Surgery; Endocrine and Sarcoma Surgery Unit; Karolinska Institutet; Karolinska University Hospital; Stockholm, Sweden.
Jan
J
Zedenius
Department of Oncology-Pathology; Karolinska Institutet; Karolinska University Hospital; Stockholm, Sweden.
Jamileh
J
Hashemi
Department of Oncology-Pathology; Karolinska Institutet; Karolinska University Hospital; Stockholm, Sweden.
Catharina
C
Larsson
D000964:Antimetabolites, Antineoplastic / Q000494:pharmacology; D001374:Azacitidine / Q000494:pharmacology; D045744:Cell Line, Tumor; D002887:Chromosomes, Human, Pair 18; D016000:Cluster Analysis; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000378:metabolism; D056915:DNA Copy Number Variations; D019175:DNA Methylation; D005260:Female; D015894:Genome, Human; D006801:Humans; D007414:Intestinal Neoplasms / Q000378:metabolism* / Q000401:mortality / Q000473:pathology; D007421:Intestine, Small / Q000187:drug effects / Q000378:metabolism*; D020084:Long Interspersed Nucleotide Elements; D008297:Male; D009362:Neoplasm Metastasis; D018358:Neuroendocrine Tumors / Q000378:metabolism* / Q000401:mortality / Q000473:pathology; D011401:Promoter Regions, Genetic; D012333:RNA, Messenger / Q000378:metabolism; D015996:Survival Rate; D025521:Tumor Suppressor Proteins / Q000235:genetics / Q000378:metabolism
D000964:Antimetabolites, Antineoplastic; D012333:RNA, Messenger; D025521:Tumor Suppressor Proteins; D004248:DNA (Cytosine-5-)-Methyltransferases; D001374:Azacitidine
DNA methylation; SI-NET; carcinoid; neuroendocrine; pyrosequencing