Metformin pharmacogenomics: a genome-wide association study to identify genetic and epigenetic biomarkers involved in metformin anticancer response using human lymphoblastoid cell lines.
Metformin is currently considered as a promising anticancer agent in addition to its anti-diabetic effect. To better individualize metformin therapy and explore novel molecular mechanisms in cancer treatment, we conducted a pharmacogenomic study using 266 lymphoblastoid cell lines (LCLs). Metformin cytotoxicity assay was performed using the MTS assay. Genome-wide association (GWA) analyses were performed in LCLs using 1.3 million SNPs, 485k DNA methylation probes, 54k mRNA expression probe sets, and metformin cytotoxicity (IC50s). Top candidate genes were functionally validated using siRNA screening, followed by MTS assay in breast cancer cell lines. Further study of one top candidate, STUB1, was performed to elucidate the mechanisms by which STUB1 might contribute to metformin action. GWA analyses in LCLs identified 198 mRNA expression probe sets, 12 SNP loci, and 5 DNA methylation loci associated with metformin IC50 with P-values <10−4 or <10−5. Integrated SNP/methylation loci-expression-IC50 analyses found 3 SNP loci or 5 DNA methylation loci associated with metformin IC50 through trans-regulation of expression of 11 or 26 genes with P-value <10−4. Functional validation of top 61 candidate genes in 4 IPA networks indicated down regulation of 14 genes significantly altered metformin sensitivity in two breast cancer cell lines. Mechanistic studies revealed that the E3 ubiquitin ligase, STUB1, could influence metformin response by facilitating proteasome-mediated degradation of cyclin A. GWAS using a genomic data-enriched LCL model system, together with functional and mechanistic studies using cancer cell lines, help us to identify novel genetic and epigenetic biomarkers involved in metformin anticancer response.
Division of Clinical Pharmacology, Mayo Clinic College of Medicine, Rochester, MN, USA.
Nifang
N
Niu
Division of Oncology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, MN, USA.
Tongzheng
T
Liu
Division of Clinical Pharmacology, Mayo Clinic College of Medicine, Rochester, MN, USA.
Junmei
J
Cairns
Division of Clinical Pharmacology, Mayo Clinic College of Medicine, Rochester, MN, USA.
Reynold C
RC
Ly
UMDNJ/The Cancer Institute of New Jersey, New Brunswick, NJ, USA.
Xianglin
X
Tan
Division of Oncology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, MN, USA.
Min
M
Deng
University of Kansas Medical Center, Kansas City, Kansas City, KS, USA.
Brooke L
BL
Fridley
Division of Biostatistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN, USA.
Krishna R
KR
Kalari
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
Ryan P
RP
Abo
Division of Biostatistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN, USA.
Gregory
G
Jenkins
Division of Biostatistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN, USA.
Anthony
A
Batzler
Division of Biostatistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN, USA.
Erin E
EE
Carlson
Division of Biostatistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN, USA.
Poulami
P
Barman
Bellvitge Biomedical Research Institute (IDIBELL), L Hospitalet de Llobregat, Barcelona, Spain.
Sebastian
S
Moran
Bellvitge Biomedical Research Institute (IDIBELL), L Hospitalet de Llobregat, Barcelona, Spain.
Holger
H
Heyn
Bellvitge Biomedical Research Institute (IDIBELL), L Hospitalet de Llobregat, Barcelona, Spain.|Institucio Catalana de Recerca i Estudis Avançats, Barcelona, Catalonia, Spain|Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain
Manel
M
Esteller
Division of Clinical Pharmacology, Mayo Clinic College of Medicine, Rochester, MN, USA.
Liewei
L
Wang
D000970:Antineoplastic Agents / Q000378:metabolism; D054316:Biomarkers, Pharmacological / Q000378:metabolism; D045744:Cell Line, Tumor / Q000187:drug effects; D019175:DNA Methylation; D044127:Epigenesis, Genetic / Q000235:genetics; D057890:Epigenomics; D055106:Genome-Wide Association Study; D005838:Genotype; D006801:Humans; D008687:Metformin / Q000378:metabolism* / Q000494:pharmacology*; D010597:Pharmacogenetics / Q000379:methods; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D034741:RNA, Small Interfering / Q000378:metabolism; D059467:Transcriptome / Q000235:genetics; D044767:Ubiquitin-Protein Ligases / Q000187:drug effects / Q000235:genetics
D000970:Antineoplastic Agents; D054316:Biomarkers, Pharmacological; D034741:RNA, Small Interfering; D008687:Metformin; C467728:STUB1 protein, human; D044767:Ubiquitin-Protein Ligases