Genome-Wide DNA Methylation Analysis Reveals Epigenetic Dysregulation of MicroRNA-34A in TP53-Associated Cancer Susceptibility.

PURPOSE Although the link between mutant TP53 and human cancer is unequivocal, a significant knowledge gap exists in clinically actionable molecular targets in Li-Fraumeni syndrome (LFS), a highly penetrant cancer predisposition syndrome associated with germline mutations in TP53. This study surveyed the epigenome to identify functionally and clinically relevant novel genes implicated in LFS. PATIENTS AND METHODS We performed genome-wide methylation analyses of peripheral blood leukocyte DNA in germline TP53 mutation carriers (n = 72) and individuals with TP53 wild type in whom histologically comparable malignancies developed (n = 111). Targeted bisulfite pyrosequencing was performed on a validation cohort of 30 TP53 mutation carriers and 46 patients with TP53 wild type, and candidate sites were evaluated in primary tumors from patients with LFS across multiple histologic tumor types. RESULTS In 183 patients, distinct DNA methylation signatures were associated with deleterious TP53 mutations in peripheral blood leukocytes. TP53-associated DNA methylation marks occurred in genomic regions that harbored p53 binding sites and in genes encoding p53 pathway proteins. Moreover, loss-of-function TP53 mutations were significantly associated with differential methylation at the locus encoding microRNA miR-34A, a key component of the p53 regulatory network (adjusted P < .001), and validated in an independent patient cohort (n = 76, P < .001). Targeted bisulfite pyrosequencing demonstrated that miR-34A was inactivated by hypermethylation across many histologic types of primary tumors from patients with LFS. Moreover, miR-34A tumor hypermethylation was associated with decreased overall survival in a cohort of 29 patients with choroid plexus carcinomas, a characteristic LFS tumor (P < .05). CONCLUSION Epigenetic dysregulation of miR-34A may comprise an important path in TP53-associated cancer predisposition and represents a therapeutically actionable target with potential clinical relevance.

[1]  Mathieu Lemire,et al.  Long-range epigenetic regulation is conferred by genetic variation located at thousands of independent loci , 2015, Nature Communications.

[2]  Nada Jabado,et al.  Molecular Characterization of Choroid Plexus Tumors Reveals Novel Clinically Relevant Subgroups , 2014, Clinical Cancer Research.

[3]  F. Bunz,et al.  A PTCH1 Homolog Transcriptionally Activated by p53 Suppresses Hedgehog Signaling* , 2014, The Journal of Biological Chemistry.

[4]  Rocky Cipriano,et al.  Conserved Oncogenic Behavior of the FAM83 Family Regulates MAPK Signaling in Human Cancer , 2014, Molecular Cancer Research.

[5]  R. Weksberg,et al.  Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray , 2013, Epigenetics.

[6]  M. Negrini,et al.  Synthetic miR-34a Mimics as a Novel Therapeutic Agent for Multiple Myeloma: In Vitro and In Vivo Evidence , 2012, Clinical Cancer Research.

[7]  M. Bissell,et al.  FAM83A confers EGFR-TKI resistance in breast cancer cells and in mice. , 2012, The Journal of clinical investigation.

[8]  H. Hermeking,et al.  MicroRNAs in the p53 network: micromanagement of tumour suppression , 2012, Nature Reviews Cancer.

[9]  A. Bader.  miR-34 – a microRNA replacement therapy is headed to the clinic , 2012, Front. Gene..

[10]  John J Dunn,et al.  Distinct p53 genomic binding patterns in normal and cancer-derived human cells , 2011, Cell cycle.

[11]  F. Slack,et al.  Systemic delivery of tumor suppressor microRNA mimics using a neutral lipid emulsion inhibits lung tumors in mice. , 2011, Molecular therapy : the journal of the American Society of Gene Therapy.

[12]  S. Sommer,et al.  Beyond Li Fraumeni Syndrome: clinical characteristics of families with p53 germline mutations. , 2009, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[13]  Carola Berking,et al.  Inactivation of miR-34a by aberrant CpG methylation in multiple types of cancer , 2008, Cell cycle.

[14]  Ivo G Gut,et al.  DNA methylation analysis by pyrosequencing , 2007, Nature Protocols.

[15]  L. Lim,et al.  A microRNA component of the p53 tumour suppressor network , 2007, Nature.

[16]  Michael A. Beer,et al.  Transactivation of miR-34a by p53 broadly influences gene expression and promotes apoptosis. , 2007, Molecular cell.

[17]  Moshe Oren,et al.  Transcriptional activation of miR-34a contributes to p53-mediated apoptosis. , 2007, Molecular cell.

[18]  M. Olivier,et al.  The TP53 mutation, R337H, is associated with Li-Fraumeni and Li-Fraumeni-like syndromes in Brazilian families. , 2007, Cancer letters.

[19]  Z. Weng,et al.  A Global Map of p53 Transcription-Factor Binding Sites in the Human Genome , 2006, Cell.

[20]  A. Levine,et al.  Surfing the p53 network , 2000, Nature.