Aging-like Spontaneous Epigenetic Silencing Facilitates Wnt Activation, Stemness, and BrafV600E-Induced Tumorigenesis

Tao Y, Kang B, Petkovich DA, Bhandari YR, In J, Stein-O’Brien G, Kong X, Xie W, Zachos N, Maegawa S, Vaidya H, Brown S, Chiu Yen RW, Shao X, Thakor J, Lu Z, Cai Y, Zhang Y, Mallona I, Peinado MA, Zahnow CA, Ahuja N, Fertig E, Issa JP, Baylin SB, Easwaran H.

Cancer Cell. 2019 Feb 11;35(2):315-328.e6. doi: 10.1016/j.ccell.2019.01.005.

Interplay between post-translational cyclooxygenase-2 modifications and the metabolic and proteomic profile in a colorectal cancer cohort.

Prieto P, Jaén RI, Calle D, Gómez-Serrano M, Núñez E, Fernández-Velasco M, Martín-Sanz P, Alonso S, Vázquez J, Cerdán S, Peinado MÁ, Boscá L.

World J Gastroenterol. 2019 Jan 28;25(4):433-446. doi: 10.3748/wjg.v25.i4.433.

Modular dynamics of DNA co-methylation networks exposes the functional organization of colon cancer cells’ genome

Izaskun Mallona, Susanna Ausso, Anna Diez-Villanueva, Victor Moreno, Miguel A. Peinado

bioRxiv doi: https://doi.org/10.1101/428730

Adipose tissue mitochondrial dysfunction in human obesity is linked to a specific DNA methylation signature in adipose-derived stem cells

Ejarque M, Ceperuelo-Mallafré V, Serena C, Maymo-Masip E, Duran X, Díaz-Ramos A, Millan-Scheiding M, Núñez-Álvarez Y, Núñez-Roa C, Gama P, Garcia-Roves PM, Peinado MA, Gimble JM, Zorzano A, Vendrell J, Fernández-Veledo S.

Int J Obes (Lond). 2019 Jun;43(6):1256-1268. doi: 10.1038/s41366-018-0219-6. Epub 2018 Sep 27.

Kallikreins Stepwise Scoring Reveals Three Subtypes of Papillary Thyroid Cancer with Prognostic Implications

Buj R, Mallona I, Díez-Villanueva A, Zafon C, Mate JL, Roca M, Puig-Domingo M, Reverter JL, Mauricio D, Peinado MA, Jordà M

Thyroid. 2018 May;28(5):601-612. doi: 10.1089/thy.2017.0501.

The Pancancer DNA Methylation Trackhub: A Window to The Cancer Genome Atlas Epigenomics Data.

Mallona I, Sierco A, Peinado MA. The Pancancer DNA Methylation Trackhub: A Window to The Cancer Genome Atlas Epigenomics Data. Methods Mol Biol. 2018;1766:123-135. doi: 10.1007/978-1-4939-7768-0_7.

CpG Islands. Methods and Protocols

CpG islands constitute key genomic elements playing a fundamental role in essential biological processes such as development and cell differentiation. CpG islands are short stretches of DNA enriched in CpG dinucleotides, firstly identified by Adrian Bird in the 80’s. The human genome contains about 28,000 of these elements that are tightly associated to the regulation of 40% of the genes. Epigenetic alterations of specific CpG islands constitute molecular landmarks of multiple diseases including cancer, cardiovascular and neurological diseases, becoming principal targets as biomarkers and advanced therapeutic strategies.

The authoritative series Methods in Molecular Biology published by Springer Nature has released a new volume devoted to cover different aspects related with the study of these genomic elements. The book covers bioinformatic and molecular biology methods useful to identify and to explore the functions of CpG islands, as well as reviews on key applications of its study. Tanya Vavouri and Miguel A. Peinado, from the IJC and the IGTP, are the editors and have counted with the contribution of internationally renowned scientists in the fields of genomics and epigenomics.

The book contents and the online version may be found at: https://link.springer.com/book/10.1007/978-1-4939-7768-0.

Reference: Vavouri T, Peinado MA (ed.) CpG Islands: Methods and Protocols. Methods Mol Biol. 2018;1766. https://doi.org/10.1007/978-1-4939-7768-0

Increased global DNA hypomethylation in distant metastatic and dedifferentiated thyroid cancer.

Klein Hesselink EN, Zafon C, Villalmanzo N, Iglesias C, van Hemel BM, Klein Hesselink MS, Montero-Conde C, Buj R, Mauricio D, Peinado MA, Puig-Domingo M, Riesco-Eizaguirre G, Reverter JL, Robledo M, Links TP, Jordà M. Increased global DNA hypomethylation in distant metastatic and dedifferentiated thyroid cancer. J Clin Endocrinol Metab. 2018 Feb 1;103(2):397-406. doi: 10.1210/jc.2017-01613.

Survivin, a key player in cancer progression, increases in obesity and protects adipose tissue stem cells from apoptosis.

Ejarque M, Ceperuelo-Mallafré V, Serena C, Pachón G, Núñez-Álvarez Y, Terrón-Puig M, Calvo E, Núñez-Roa C, Oliva-Olivera W, Tinahones FJ, Peinado MA, Vendrell J, Fernández-Veledo S. Survivin, a key player in cancer progression, increases in obesity and protects adipose tissue stem cells from apoptosis. Cell Death Dis. 2017 May 18;8(5):e2802. doi: 10.1038/cddis.2017.209.

Truke, a web tool to check for and handle excel misidentified gene symbols

Izaskun Mallona and Miguel A. Peinado. Truke, a web tool to check for and handle excel misidentified gene symbols. BMC Genomics (2017) 18:242