Barcelona conference on epigenetics and cancer: 50 years of histone acetylation

The Barcelona Conference on Epigenetics and Cancer (BCEC) was held in Barcelona, Spain, on October 1 and 2 , 2014. The meeting was co-organized by the Cancer Epigenetics and Biology Program (PEBC-IDIBELL) and B·Debate, an initiative of Biocat, with the support of 'la Caixa' Foundation. The scientific committee was comprised of leading scientists in the field of epigenetics: Dr. Manel Esteller, director of PEBC-IDIBELL, Dr. Alejandro Vaquero and Dr. Esteban Ballestar, from PEBC-IDIBELL, Juan Ausió from the University of Victoria (Canada), and Marcus Buschbeck, from the Institute of Predictive and Personalized Medicine of Cancer (IMPPC), as BCEC series coordinator. This meeting was the second edition of the BCEC series, which was launched by 5 leading Barcelonan institutes to bring together leading investigators in the fields of epigenetics and chromatin research. The topics discussed during the meeting included the current challenges, opportunities, and perspectives surrounding the study of histone modifications (focusing in acetylation), chromatin structure and gene expression, and the involvement of histone acetylation in physiology and diseases, such as cancer or neurological diseases

Circular RNA CpG island hypermethylation-associated silencing in human cancer

Noncoding RNAs (ncRNAs), such as microRNAs and long noncoding RNAs (lncRNAs), participate in cellular transformation. Work done in the last decade has also demonstrated that ncRNAs with growth-inhibitory functions can undergo promoter CpG island hypermethylation-associated silencing in tumorigenesis. Herein, we wondered whether circular RNAs (circRNAs), a type of RNA transcripts lacking 5′-3′ ends and forming closed loops that are gaining relevance in cancer biology, are also a target of epigenetic inactivation in tumors. To tackle this issue, we have used cancer cells genetically deficient for the DNA methyltransferase enzymes in conjuction with circRNA expression microarrays. We have found that the loss of DNA methylation provokes a release of circRNA silencing. In particular, we have identified that promoter CpG island hypermethylation of the genes TUSC3 (tumor suppressor candidate 3), POMT1 (protein O-mannosyltransferase 1), ATRNL1 (attractin-like 1) and SAMD4A (sterile alpha motif domain containing 4A) is linked to the transcriptional downregulation of both linear mRNA and the hosted circRNA. Although some circRNAs regulate the linear transcript, we did not observe changes in TUSC3 mRNA levels upon TUSC3 circ104557 overexpression. Interestingly, we found circRNA-mediated regulation of target miRNAs and an in vivo growth inhibitory effect upon TUSC3 circ104557 transduction. Data mining for 5′-end CpG island methylation of TUSC3, ATRNL1, POMT1 and SAMD4A in cancer cell lines and primary tumors showed that the epigenetic defect was commonly observed among different tumor types in association with the diminished expression of the corresponding transcript. Our findings support a role for circRNA DNA methylation-associated loss in human cancer

Germline variation in O6-methylguanine-DNA methyltransferase (MGMT) as cause of hereditary colorectal cancer

Somatic epigenetic inactivation of the DNA repair protein O6-methylguanine DNA methyltransferase (MGMT) is frequent in colorectal cancer (CRC); however, its involvement in CRC predisposition remains unexplored. We assessed the role and relevance of MGMT germline mutations and epimutations in familial and early-onset CRC. Mutation and promoter methylation screenings were performed in 473 familial and/or early-onset mismatch repair-proficient nonpolyposis CRC cases. No constitutional MGMT inactivation by promoter methylation was observed. Of six rare heterozygous germline variants identified, c.346C > T (p.H116Y) and c.476G > A (p.R159Q), detected in three and one families respectively, affected highly conserved residues and showed segregation with cancer in available family members. In vitro, neither p.H116Y nor p.R159Q caused statistically significant reduction of MGMT repair activity. No evidence of somatic second hits was found in the studied tumors. Case-control data showed over-representation of c.346C > T (p.H116Y) in familial CRC compared to controls, but no overall association of MGMT mutations with CRC predisposition. In conclusion, germline mutations and constitutional epimutations in MGMT are not major players in hereditary CRC. Nevertheless, the over-representation of c.346C > T (p.H116Y) in our familial CRC cohort warrants further research

Bromodomain inhibition shows antitumoral activity in mice and human luminal breast cancer

BET bromodomain inhibitors, which have an antitumoral effect against various solid cancer tumor types, have not been studied in detail in luminal breast cancer, despite the prevalence of this subtype of mammary malignancy. Here we demonstrate that the BET bromodomain inhibitor JQ1 exerts growth-inhibitory activity in human luminal breast cancer cell lines associated with a depletion of the C-MYC oncogene, but does not alter the expression levels of the BRD4 bromodomain protein. Interestingly, expression microarray analyses indicate that, upon JQ1 administration, the antitumoral phenotype also involves downregulation of relevant breast cancer oncogenes such as the Breast Carcinoma-Amplified Sequence 1 (BCAS1) and the PDZ Domain-Containing 1 (PDZK1). We have also applied these in vitro findings in an in vivo model by studying a transgenic mouse model representing the luminal B subtype of breast cancer, the MMTV-PyMT, in which the mouse mammary tumor virus promoter is used to drive the expression of the polyoma virus middle T-antigen to the mammary gland. We have observed that the use of the BET bromodomain inhibitor for the treatment of established breast neoplasms developed in the MMTV-PyMT model shows antitumor potential. Most importantly, if JQ1 is given before the expected time of tumor detection in the MMTV-PyMT mice, it retards the onset of the disease and increases the survival of these animals. Thus, our findings indicate that the use of bromodomain inhibitors is of great potential in the treatment of luminal breast cancer and merits further investigation

In vitro and in vivo activity of a new small-molecule inhibitor of HDAC6 in mantle cell lymphoma

Cancer origin and development is associated not only with genetic alterations, but also with the disturbance of epigenetic profiles.1 In this regard, the tumoral epigenome is characterized by both specific and general shifts in the DNA methylation and histone-modification landscapes.1 However, in contrast to genetic disruption, the effect of epigenetic modifications or marks may potentially be reversed by the use of drugs that target enzymes involved in adding, removing or signaling DNA methylation and histone modifications.1 This basic knowledge has been adopted into clinical practice, and inhibitors of histone deacetylases and DNA demethylating agents have been approved for use in the therapy of hematologic malignancies, such as cutaneous T-cell lymphoma and myelodysplastic syndrome, respectively.2 Other promising epigenetic drugs include inhibitors of histone methyltransferases,2 histone demethylases,2 histone kinases,3 and bromodomain proteins that interfere with the 'reading' of acetylated histone residues

Epigenetic loss of RNA‑methyltransferase NSUN5 in glioma targets ribosomes to drive stress adaptive translational program

Tumors have aberrant proteomes that often do not match their corresponding transcriptome profiles. One possible cause of this discrepancy is the existence of aberrant RNA modification landscapes in the so-called epitranscriptome. Here, we report that human glioma cells undergo DNA methylation-associated epigenetic silencing of NSUN5, a candidate RNA methyltransferase for 5-methylcytosine. In this setting, NSUN5 exhibits tumor-suppressor characteristics in vivo glioma models. We also found that NSUN5 loss generates an unmethylated status at the C3782 position of 28S rRNA that drives an overall depletion of protein synthesis, and leads to the emergence of an adaptive translational program for survival under conditions of cellular stress. Interestingly, NSUN5 epigenetic inactivation also renders these gliomas sensitive to bioactivatable substrates of the stress-related enzyme NQO1. Most importantly, NSUN5 epigenetic inactivation is a hallmark of glioma patients with long-term survival for this otherwise devastating disease

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

[eng] 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[spa] 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

Bromodomain inhibitors and cancer therapy: From structures to applications

Aberrations in the epigenetic landscape are a hallmark of cancer. Alterations in enzymes that are “writers,” “erasers,” or “readers” of histone modification marks are common. Bromodomains are “readers” that bind acetylated lysines in histone tails. Their most important function is the regulation of gene transcription by the recruitment of different molecular partners. Moreover, proteins containing bromodomains are also epigenetic regulators, although little is known about the specific function of these domains. In recent years, there has been increasing interest in developing small molecules that can target specific bromodomains. First, this has helped clarify biological functions of bromodomain-containing proteins. Secondly, it opens a new front for combatting cancer. In this review we will describe the structures and mechanisms associated with Bromodomain and Extra-Terminal motif (BET) inhibitors and non-BET inhibitors, their current status of development, and their promising role as anti-cancer agents

Barcelona conference on epigenetics and cancer: 50 years of histone acetylation

The Barcelona Conference on Epigenetics and Cancer (BCEC) was held in Barcelona, Spain, on October 1 and 2 , 2014. The meeting was co-organized by the Cancer Epigenetics and Biology Program (PEBC-IDIBELL) and B·Debate, an initiative of Biocat, with the support of 'la Caixa' Foundation. The scientific committee was comprised of leading scientists in the field of epigenetics: Dr. Manel Esteller, director of PEBC-IDIBELL, Dr. Alejandro Vaquero and Dr. Esteban Ballestar, from PEBC-IDIBELL, Juan Ausió from the University of Victoria (Canada), and Marcus Buschbeck, from the Institute of Predictive and Personalized Medicine of Cancer (IMPPC), as BCEC series coordinator. This meeting was the second edition of the BCEC series, which was launched by 5 leading Barcelonan institutes to bring together leading investigators in the fields of epigenetics and chromatin research. The topics discussed during the meeting included the current challenges, opportunities, and perspectives surrounding the study of histone modifications (focusing in acetylation), chromatin structure and gene expression, and the involvement of histone acetylation in physiology and diseases, such as cancer or neurological diseases