Genome-wide study of hypomethylated and induced genes in patients with liver cancer unravels novel anticancer targets.
OBJECTIVE
We utilized whole-genome mapping of promoters that are activated by DNA hypomethylation in hepatocellular carcinoma (HCC) clinical samples to shortlist novel targets for anticancer therapeutics. We provide a proof of principle of this approach by testing six genes short-listed in our screen for their essential role in cancer growth and invasiveness.


METHODS
We used siRNA- or shRNA-mediated depletion to determine whether inhibition of these genes would reduce human tumor xenograft growth in mice as well as cell viability, anchorage-independent growth, invasive capacities, and state of activity of nodal signaling pathways in liver, breast, and bladder cancer cell lines.


RESULTS
Depletion of EXOSC4, RNMT, SENP6, WBSCR22, RASAL2, and NENF effectively and specifically inhibits cancer cell growth and cell invasive capacities in different types of cancer, but, remarkably, there is no effect on normal cell growth, suggesting a ubiquitous causal role for these genes in driving cancer growth and metastasis. Depletion of RASAL2 and NENF in vitro reduces their growth as explants in vivo in mice. RASAL2 and NENF depletion interferes with AKT, WNT, and MAPK signaling pathways as well as regulation of epigenetic proteins that were previously demonstrated to drive cancer growth and metastasis.


CONCLUSIONS
Our results prove that genes that are hypomethylated and induced in tumors are candidate targets for anticancer therapeutics in multiple cancer cell types. Because these genes are particularly activated in cancer, they constitute a group of targets for specific pharmacologic inhibitors of cancer and cancer metastasis. Clin Cancer Res; 20(12); 3118-32. ©2014 AACR.
Authors' Affiliations: Departments of Pharmacology and Therapeutics and Medicine, McGill University Health Centre, Montreal; McGill Centre for Bioinformatics; and Sackler program for Psychobiology and Epigenetics at McGill University, Montreal, Quebec, Canada; Department of Nutrition Science, Purdue University, West Lafayette, Indiana; Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China; Department of Hepatology, Bangabandhu Sheikh Mujib Medical University; International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka, Dhaka District, Bangladesh; Department of Medical Sciences, Toshiba General Hospital, Tokyo, Kanto, Japan; and Department of Pathology, Fatima Memorial Hospital College of Medicine and Dentistry Lahore, PakistanAuthors' Affiliations: Departments of Pharmacology and Therapeutics and Medicine, McGill University Health Centre, Montreal; McGill Centre for Bioinformatics; and Sackler program for Psychobiology and Epigenetics at McGill University, Montreal, Quebec, Canada; Department of Nutrition Science, Purdue University, West Lafayette, Indiana; Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China; Department of Hepatology, Bangabandhu Sheikh Mujib Medical University; International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka, Dhaka District, Bangladesh; Department of Medical Sciences, Toshiba General Hospital, Tokyo, Kanto, Japan; and Department of Pathology, Fatima Memorial Hospital College of Medicine and Dentistry Lahore, Pakistan.
Barbara
B
Stefanska
Authors' Affiliations: Departments of Pharmacology and Therapeutics and Medicine, McGill University Health Centre, Montreal; McGill Centre for Bioinformatics; and Sackler program for Psychobiology and Epigenetics at McGill University, Montreal, Quebec, Canada; Department of Nutrition Science, Purdue University, West Lafayette, Indiana; Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China; Department of Hepatology, Bangabandhu Sheikh Mujib Medical University; International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka, Dhaka District, Bangladesh; Department of Medical Sciences, Toshiba General Hospital, Tokyo, Kanto, Japan; and Department of Pathology, Fatima Memorial Hospital College of Medicine and Dentistry Lahore, Pakistan.
David
D
Cheishvili
Authors' Affiliations: Departments of Pharmacology and Therapeutics and Medicine, McGill University Health Centre, Montreal; McGill Centre for Bioinformatics; and Sackler program for Psychobiology and Epigenetics at McGill University, Montreal, Quebec, Canada; Department of Nutrition Science, Purdue University, West Lafayette, Indiana; Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China; Department of Hepatology, Bangabandhu Sheikh Mujib Medical University; International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka, Dhaka District, Bangladesh; Department of Medical Sciences, Toshiba General Hospital, Tokyo, Kanto, Japan; and Department of Pathology, Fatima Memorial Hospital College of Medicine and Dentistry Lahore, Pakistan.
Matthew
M
Suderman
Authors' Affiliations: Departments of Pharmacology and Therapeutics and Medicine, McGill University Health Centre, Montreal; McGill Centre for Bioinformatics; and Sackler program for Psychobiology and Epigenetics at McGill University, Montreal, Quebec, Canada; Department of Nutrition Science, Purdue University, West Lafayette, Indiana; Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China; Department of Hepatology, Bangabandhu Sheikh Mujib Medical University; International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka, Dhaka District, Bangladesh; Department of Medical Sciences, Toshiba General Hospital, Tokyo, Kanto, Japan; and Department of Pathology, Fatima Memorial Hospital College of Medicine and Dentistry Lahore, Pakistan.
Ani
A
Arakelian
Authors' Affiliations: Departments of Pharmacology and Therapeutics and Medicine, McGill University Health Centre, Montreal; McGill Centre for Bioinformatics; and Sackler program for Psychobiology and Epigenetics at McGill University, Montreal, Quebec, Canada; Department of Nutrition Science, Purdue University, West Lafayette, Indiana; Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China; Department of Hepatology, Bangabandhu Sheikh Mujib Medical University; International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka, Dhaka District, Bangladesh; Department of Medical Sciences, Toshiba General Hospital, Tokyo, Kanto, Japan; and Department of Pathology, Fatima Memorial Hospital College of Medicine and Dentistry Lahore, Pakistan.
Jian
J
Huang
Authors' Affiliations: Departments of Pharmacology and Therapeutics and Medicine, McGill University Health Centre, Montreal; McGill Centre for Bioinformatics; and Sackler program for Psychobiology and Epigenetics at McGill University, Montreal, Quebec, Canada; Department of Nutrition Science, Purdue University, West Lafayette, Indiana; Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China; Department of Hepatology, Bangabandhu Sheikh Mujib Medical University; International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka, Dhaka District, Bangladesh; Department of Medical Sciences, Toshiba General Hospital, Tokyo, Kanto, Japan; and Department of Pathology, Fatima Memorial Hospital College of Medicine and Dentistry Lahore, Pakistan.
Michael
M
Hallett
Authors' Affiliations: Departments of Pharmacology and Therapeutics and Medicine, McGill University Health Centre, Montreal; McGill Centre for Bioinformatics; and Sackler program for Psychobiology and Epigenetics at McGill University, Montreal, Quebec, Canada; Department of Nutrition Science, Purdue University, West Lafayette, Indiana; Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China; Department of Hepatology, Bangabandhu Sheikh Mujib Medical University; International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka, Dhaka District, Bangladesh; Department of Medical Sciences, Toshiba General Hospital, Tokyo, Kanto, Japan; and Department of Pathology, Fatima Memorial Hospital College of Medicine and Dentistry Lahore, Pakistan.
Ze-Guang
ZG
Han
Authors' Affiliations: Departments of Pharmacology and Therapeutics and Medicine, McGill University Health Centre, Montreal; McGill Centre for Bioinformatics; and Sackler program for Psychobiology and Epigenetics at McGill University, Montreal, Quebec, Canada; Department of Nutrition Science, Purdue University, West Lafayette, Indiana; Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China; Department of Hepatology, Bangabandhu Sheikh Mujib Medical University; International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka, Dhaka District, Bangladesh; Department of Medical Sciences, Toshiba General Hospital, Tokyo, Kanto, Japan; and Department of Pathology, Fatima Memorial Hospital College of Medicine and Dentistry Lahore, Pakistan.
Mamun
M
Al-Mahtab
Authors' Affiliations: Departments of Pharmacology and Therapeutics and Medicine, McGill University Health Centre, Montreal; McGill Centre for Bioinformatics; and Sackler program for Psychobiology and Epigenetics at McGill University, Montreal, Quebec, Canada; Department of Nutrition Science, Purdue University, West Lafayette, Indiana; Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China; Department of Hepatology, Bangabandhu Sheikh Mujib Medical University; International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka, Dhaka District, Bangladesh; Department of Medical Sciences, Toshiba General Hospital, Tokyo, Kanto, Japan; and Department of Pathology, Fatima Memorial Hospital College of Medicine and Dentistry Lahore, Pakistan.
Sheikh Mohammad Fazle
SM
Akbar
Authors' Affiliations: Departments of Pharmacology and Therapeutics and Medicine, McGill University Health Centre, Montreal; McGill Centre for Bioinformatics; and Sackler program for Psychobiology and Epigenetics at McGill University, Montreal, Quebec, Canada; Department of Nutrition Science, Purdue University, West Lafayette, Indiana; Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China; Department of Hepatology, Bangabandhu Sheikh Mujib Medical University; International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka, Dhaka District, Bangladesh; Department of Medical Sciences, Toshiba General Hospital, Tokyo, Kanto, Japan; and Department of Pathology, Fatima Memorial Hospital College of Medicine and Dentistry Lahore, Pakistan.
Wasif Ali
WA
Khan
Authors' Affiliations: Departments of Pharmacology and Therapeutics and Medicine, McGill University Health Centre, Montreal; McGill Centre for Bioinformatics; and Sackler program for Psychobiology and Epigenetics at McGill University, Montreal, Quebec, Canada; Department of Nutrition Science, Purdue University, West Lafayette, Indiana; Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China; Department of Hepatology, Bangabandhu Sheikh Mujib Medical University; International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka, Dhaka District, Bangladesh; Department of Medical Sciences, Toshiba General Hospital, Tokyo, Kanto, Japan; and Department of Pathology, Fatima Memorial Hospital College of Medicine and Dentistry Lahore, Pakistan.
Rubhana
R
Raqib
Authors' Affiliations: Departments of Pharmacology and Therapeutics and Medicine, McGill University Health Centre, Montreal; McGill Centre for Bioinformatics; and Sackler program for Psychobiology and Epigenetics at McGill University, Montreal, Quebec, Canada; Department of Nutrition Science, Purdue University, West Lafayette, Indiana; Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China; Department of Hepatology, Bangabandhu Sheikh Mujib Medical University; International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka, Dhaka District, Bangladesh; Department of Medical Sciences, Toshiba General Hospital, Tokyo, Kanto, Japan; and Department of Pathology, Fatima Memorial Hospital College of Medicine and Dentistry Lahore, Pakistan.
Imrana
I
Tanvir
Authors' Affiliations: Departments of Pharmacology and Therapeutics and Medicine, McGill University Health Centre, Montreal; McGill Centre for Bioinformatics; and Sackler program for Psychobiology and Epigenetics at McGill University, Montreal, Quebec, Canada; Department of Nutrition Science, Purdue University, West Lafayette, Indiana; Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China; Department of Hepatology, Bangabandhu Sheikh Mujib Medical University; International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka, Dhaka District, Bangladesh; Department of Medical Sciences, Toshiba General Hospital, Tokyo, Kanto, Japan; and Department of Pathology, Fatima Memorial Hospital College of Medicine and Dentistry Lahore, Pakistan.
Haseeb Ahmed
HA
Khan
Authors' Affiliations: Departments of Pharmacology and Therapeutics and Medicine, McGill University Health Centre, Montreal; McGill Centre for Bioinformatics; and Sackler program for Psychobiology and Epigenetics at McGill University, Montreal, Quebec, Canada; Department of Nutrition Science, Purdue University, West Lafayette, Indiana; Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China; Department of Hepatology, Bangabandhu Sheikh Mujib Medical University; International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka, Dhaka District, Bangladesh; Department of Medical Sciences, Toshiba General Hospital, Tokyo, Kanto, Japan; and Department of Pathology, Fatima Memorial Hospital College of Medicine and Dentistry Lahore, Pakistan.
Shafaat A
SA
Rabbani
Authors' Affiliations: Departments of Pharmacology and Therapeutics and Medicine, McGill University Health Centre, Montreal; McGill Centre for Bioinformatics; and Sackler program for Psychobiology and Epigenetics at McGill University, Montreal, Quebec, Canada; Department of Nutrition Science, Purdue University, West Lafayette, Indiana; Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China; Department of Hepatology, Bangabandhu Sheikh Mujib Medical University; International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka, Dhaka District, Bangladesh; Department of Medical Sciences, Toshiba General Hospital, Tokyo, Kanto, Japan; and Department of Pathology, Fatima Memorial Hospital College of Medicine and Dentistry Lahore, PakistanAuthors' Affiliations: Departments of Pharmacology and Therapeutics and Medicine, McGill University Health Centre, Montreal; McGill Centre for Bioinformatics; and Sackler program for Psychobiology and Epigenetics at McGill University, Montreal, Quebec, Canada; Department of Nutrition Science, Purdue University, West Lafayette, Indiana; Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China; Department of Hepatology, Bangabandhu Sheikh Mujib Medical University; International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka, Dhaka District, Bangladesh; Department of Medical Sciences, Toshiba General Hospital, Tokyo, Kanto, Japan; and Department of Pathology, Fatima Memorial Hospital College of Medicine and Dentistry Lahore, Pakistan moshe.szyf@mcgill.ca.
Moshe
M
Szyf
D000818:Animals; D014408:Biomarkers, Tumor / Q000235:genetics*; D006528:Carcinoma, Hepatocellular / Q000235:genetics*; D002352:Carrier Proteins / Q000037:antagonists & inhibitors / Q000235:genetics; D002465:Cell Movement; D049109:Cell Proliferation; D003546:Cysteine Endopeptidases / Q000737:chemistry / Q000235:genetics; D019175:DNA Methylation; D063326:Exosome Multienzyme Ribonuclease Complex / Q000037:antagonists & inhibitors / Q000235:genetics; D020690:GTPase-Activating Proteins; D015972:Gene Expression Regulation, Neoplastic; D055106:Genome-Wide Association Study; D006801:Humans; D036341:Intercellular Signaling Peptides and Proteins / Q000235:genetics; D008113:Liver Neoplasms / Q000235:genetics*; D008297:Male; D008780:Methyltransferases / Q000037:antagonists & inhibitors / Q000235:genetics; D051379:Mice; D016688:Mice, Inbred NOD; D016513:Mice, SCID; D009419:Nerve Tissue Proteins / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics; D034741:RNA, Small Interfering / Q000235:genetics; D016601:RNA-Binding Proteins / Q000037:antagonists & inhibitors / Q000235:genetics; D015398:Signal Transduction
D014408:Biomarkers, Tumor; D002352:Carrier Proteins; D020690:GTPase-Activating Proteins; D036341:Intercellular Signaling Peptides and Proteins; C500818:NENF protein, human; D009419:Nerve Tissue Proteins; C576391:RASAL2 protein, human; D034741:RNA, Small Interfering; D016601:RNA-Binding Proteins; C455827:BUD23 protein, human; D008780:Methyltransferases; C055097:mRNA (guanine(N7))-methyltransferase; C415835:EXOSC4 protein, human; D063326:Exosome Multienzyme Ribonuclease Complex; D003546:Cysteine Endopeptidases; C408873:SENP6 protein, human