Epigenetic regulation of lysine acetylation: targeting writers, readers and erasers in cancer

Abstract

Cancer is considered nowadays a genetic and epigenetic disease. Aberrancies in epigenetic marks in DNA and histone tails together with alterations in epigenetic regulators responsible of catalyzing these marks have been shown to be crucial in tumorigenesis. These epigenetic regulators are commonly known as writers, readers and erasers. The plasticity of the epigenetic landscape compared to the unchangeable nature of genetic alterations has led to an increasing interest in the last years in finding specific drugs able to modulate and correct the epigenetic aberrancies present in tumors. At present, there are six epigenetic drugs already used in the clinics for the treatment of hematological cancers, two DNA methyltransferase inhibitors and four Histone deacetylases (HDACs) inhibitors. There is also a vast number of clinical trials ongoing with several drugs targeting the epigenetic modulators of the epigenome. The fact that some HDAC inhibitors are already in clinics makes particularly interesting the study of histone acetylation and its enzymatic regulators. Thus, lysine acetylation is regulated by: 1) Histone acetyltransferases (HATs) responsible of adding the acetylation mark in histone tails, being the ‘writers’; 2) Histone Deacetylases (HDACs) that remove the acetyl group acting as ‘erasers’ and 3) the bromodomains are the ‘readers’, that bind to acetyl groups and doing so recruit to specific sites in chromatin other molecular machinery involved in DNA-related processes. Moreover, it has also been described that HDACs and HATs also regulate acetylation in proteins different from histones but also very important in cancer such as the well-known p53 or Myc. The present Doctoral Thesis has been devoted to study epigenetic regulators involved in acetylation of histones and non-histones substrates, as also its targeting with small-inhibitors in cancer. The project was divided in three lines of study. Study I: We investigated the role of the HAT KAT6B in Small Cell Lung Cancer (SCLC). We reported that KAT6B undergoes homozygous deletion in SCLC and that it has tumor suppressor-like properties in vitro and in vivo in this type of cancer. KAT6B catalyzes the acetylation of lysine 23 of histone H3, being the first acetylation site described for this protein. Moreover, KAT6B impairment predicts an increased sensitivity to Irinotecan in SCLC models. Study II: Our objective was to unveil the molecular implications of bromodomain inhibitor JQ1 treatment in breast cancer. We found that JQ1 decreases cell viability in human

luminal breast cancer cell lines and downregulates PDZK1 and BCAS1, two important genes in breast cancer tumorigenesis. In addition, JQ1 used as curative treatment in a luminal breast cancer mice model leads to the appearance of smaller tumors. As a preventive treatment in the same mice model JQ1 treatment increases overall survival and delays the offset of the tumors. Study III: We studied a new HDAC6 inhibitor (QTX125) in cancer. We found that this new drug is highly specific for HDAC6 over the other HDACs and increases acetylation levels of α-tubulin, a well-known target of HDAC6, in a dose-dependent manner. It has antitumoral effect in 48 human cancer cell lines and Mantle Cell Lymphoma (MCL) cell lines are highly sensitive to QTX125. This drug induces apoptosis by cleavage of Caspase 3, 8 and 9 and PARP in vitro in MCL and it also exerts antitumoral effect by decreasing tumor growth in MCL xenografts. Interestingly, we observed that MCL primary cells from patients are more sensitive to QTX125 than PBMCs, CD3+ and CD19+ cell from healthy donors

El cáncer se define actualmente como una enfermedad genética y epigenética. En los tumores son frecuentes las alteraciones en marcas epigenéticas en el ADN y en colas de histonas, así como en las enzimas reguladoras de estas marcas, denominadas escritoras, lectoras o borradoras. Concretamente, la marca de acetilación está regulada por: 1) Histonas acetiltransferasas (HATs); 2) Histonas deacetilasas (HDACs) y 3) bromodominios. Además, estas enzimas también pueden regular la acetilación de otras proteínas importantes en cáncer diferentes a las histonas. Una de las ventajas de la epigenética frente a la genética es la naturaleza reversible de las marcas epigenéticas. Por ello, es interesante el estudio de fármacos que permitan modular y corregir las aberraciones epigenéticas presentes en los tumores. Esta tesis doctoral tiene como objetivo el estudio de los reguladores epigenéticos de la acetilación de histonas y otras proteínas en cáncer, así como su tratamiento con inhibidores específicos. El proyecto fue dividido en tres líneas de estudio. Estudio I: Estudiamos el papel de la HAT KAT6B en cáncer de pulmón de células pequeñas (SCLC). Describimos la deleción homocigota de KAT6B y su papel como supresor tumoral en SCLC y encontramos que KAT6B acetila la lisina 23 de la histona H3. Además, esta deleción predice una elevada sensibilidad al fármaco irinotecán en SCLC. Estudio II: Centrado en estudiar las implicaciones moleculares del fármaco inhibidor de bromodominios JQ1 en cáncer de mama de tipo luminal. JQ1 reduce el crecimiento tumoral in vitro disminuyendo la expresión de PDZK1 y BCAS1, dos genes importantes en cáncer de mama. JQ1 también disminuye el desarrollo tumoral, aumenta la supervivencia y retrasa la aparición de tumores en un modelo murino de cáncer de mama luminal. Estudio III: Consiste en el estudio de un nuevo fármaco (QTX125) inhibidor de HDAC6 en cáncer. Reportamos su efecto antitumoral en cáncer, y una elevada sensibilidad en linfoma de células del manto (MCL). QTX125 es altamente específico para HDAC6 e inhibe el crecimiento tumoral in vitro e in vivo en este tipo de linfoma. Además, células primarias de pacientes de MCL son más sensibles a QTX125 que PBMCs procedentes de donantes sanos.