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Ferrata Storti Foundation
Haematologica 2019 Volume 104(8):1572-1579
Myeloproliferative Neoplasms
Epigenomic profiling of myelofibrosis reveals widespread DNA methylation changes in enhancer elements and ZFP36L1 as
a potential tumor suppressor gene
that is epigenetically regulated
Nicolás Martínez-Calle,1,2# Marien Pascual,1,2# Raquel Ordoñez,1,2# Edurne San
José Enériz,1,2 Marta Kulis,3 Estíbaliz Miranda,1,2 Elisabeth Guruceaga,4 Víctor
Segura,4 María José Larráyoz,5 Beatriz Bellosillo,6 María José Calasanz,2,5
and
1Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Pamplona; 2Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid; 3Fundació Clínic per a la Recerca Biomèdica, Barcelona; 4Unidad de Bioinformática, Centro de Investigación Médica Aplicada, Universidad de Navarra, Pamplona; 5CIMA Laboratory of Diagnostics, Universidad de Navarra, Pamplona; 6Departmento de Patología, Hospital del Mar, Barcelona; 7Departmento de Hematología, Hospital del Mar, Barcelona; 8Departamento de Hematología, Clínica Universidad de Navarra, Universidad de Navarra, Pamplona; 9Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona and 10Departament de Fonaments Clinics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain.
ABSTRACT
In this study we interrogated the DNA methylome of myelofibrosis patients using high-density DNA methylation arrays. We detected 35,215 differentially methylated CpG, corresponding to 10,253 genes, between myelofibrosis patients and healthy controls. These changes were present both in primary and secondary myelofibrosis, which showed no differences between them. Remarkably, most differentially methylated CpG were located outside gene promoter regions and showed significant association with enhancer regions. This aberrant enhancer hypermethyla- tion was negatively correlated with the expression of 27 genes in the myelofibrosis cohort. Of these, we focused on the ZFP36L1 gene and vali- dated its decreased expression and enhancer DNA hypermethylation in an independent cohort of patients and myeloid cell-lines. In vitro reporter assay and 5’-azacitidine treatment confirmed the functional relevance of hyper- methylation of ZFP36L1 enhancer. Furthermore, in vitro rescue of ZFP36L1 expression had an impact on cell proliferation and induced apoptosis in SET-2 cell line indicating a possible role of ZFP36L1 as a tumor suppressor gene in myelofibrosis. Collectively, we describe the DNA methylation pro- file of myelofibrosis, identifying extensive changes in enhancer elements and revealing ZFP36L1 as a novel candidate tumor suppressor gene.
Introduction
Philadelphia chromosome-negative myeloproliferative neoplasms, namely poly- cythemia vera (PV), essential thrombocythemia (ET) and primary myelofibrosis (MF), are characterized by a clonal transformation of hematopoietic progenitors leading to expansion of fully differentiated myeloid cells.1 Primary MF carries the worst prognosis of all Philadelphia chromosome-negative myeloproliferative neo- plasms, with progressive marrow fibrosis, extramedullary hematopoiesis, mild to severe splenomegaly and an increased risk of transformation into leukemia.2 Secondary MF can also arise from PV and ET (hereafter referred to as post-PV and
7 2,8 2,9,10 1,2* Carles Besses, José Rifón, José I. Martín-Subero, Xabier Agirre
Felipe Prosper1,2,8*
#These authors share first authorship *These authors share senior authorship
Correspondence:
XABIER AGIRRE
xaguirre@unav.es
FELIPE PROSPER
fprosper@unav.es
Received: August 23, 2018.
Accepted: January 15, 2019. Pre-published: January 17, 2019. doi:10.3324/haematol.2018.204917
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