Publications

Supplementary Tables from A Mouse Skin Multistage Carcinogenesis Model Reflects the Aberrant DNA Methylation Patterns of Human Tumors

Supplementary Tables from A Mouse Skin Multistage Carcinogenesis Model Reflects the Aberrant DNA Methylation Patterns of Human Tumors

A DNA methylation database of human and mouse hematological malignancy cell lines

Abstract PL01-03: Epigenetics, aging, and cancer: From DNA methylation to microRNAs

Abstract An altered pattern of epigenetic modifications is central to many common human diseases, including cancer. Many studies have explored the mosaic patterns of DNA methylation and histone modifications in cancer cells on a gene-by-gene basis, among them the seminal finding of transcriptional silencing of tumor suppressor genes by CpG island promoter hypermethylation. Epigenetic gene inactivation in transformed cells involves many “belts of silencing”. We are in the process of completing the molecular dissection of the entire epigenetic machinery involved in methylation-associated silencing, such as DNA methyltransferases, methyl-CpG binding domain proteins, histone deacetylases, histone methyltransferases, histone demethylases and Polycomb proteins. The first indications are also starting to emerge about how the combination of cellular selection and targeted pathways leads to abnormal DNA methylation. In addition to classical tumorsuppressor and DNA repair genes, epigenetic gene silencing includes genes involved in premature aging and microRNAs with growth inhibitory functions. Recent technological advances are now enabling cancer epigenetics to be studied genome-wide. It is time to “upgrade” cancer epigenetics research and put together an ambitious plan to tackle the many unanswered questions in this field using genomics approaches to unravel the epigenome. Citation Information: Cancer Prev Res 2010;3(1 Suppl):PL01-03.

Aberrant promoter methylation of the transcription factor genes PAX5 alpha and beta in human cancers.

Aberrant methylation of 5'CpG islands is a key epigenetic event in many human cancers. A PCR-based technique of methylated CpG island amplification followed by representational difference analysis was used to identify genes methylated in cancer. Two of the CpG islands identified mapped to the 5' untranslated region of the PAX5 alpha and beta genes. These genes, located on chromosome 9p13, are transcribed from two distinct promoters and form two alternative first exons that are subsequently spliced to the common exons 2-10. The resulting splice variants encode two distinct transcription factors important in cell differentiation and embryonic development. Examination of the methylation status of each gene using methylation-specific PCR revealed that both genes are methylated in approximately 65% of breast and lung tumors. Bisulfite sequencing revealed dense methylation patterns within each 5'CpG island, strongly correlating with transcriptional silencing. Expression in cell lines with dense methylation of either the PAX5 alpha or beta promoter region was restored after treatment with the demethylating agent 5-Aza-2'-deoxycytidine. The PAX5 beta gene encodes for the transcription factor B cell-specific activating protein that, in turn, directly regulates CD19, a gene shown to negatively control cell growth. A strong association was observed between PAX5 beta methylation and loss of expression of the CD19 gene demonstrating that inactivation of the PAX5 beta gene likely contributes to neoplastic development by inhibiting growth regulation through effects on CD19 gene expression. Recent studies have demonstrated the importance of PAX5 gene alterations in human cancer. Our results are the first to identify aberrant promoter methylation as a common mechanism for dysregulation of these genes in solid tumors.

A two‐phase epigenome‐wide four‐way gene–smoking interaction study of overall survival for early‐stage non‐small cell lung cancer

The Human Epigenome: Implications for the Understanding of Human Disease

Epigenetic processes, defined as the heritable patterns of gene expression that do not involve changes in the sequence of the genome, and their effects on gene repression are increasingly understood to be such a way of modulating phenotype transmission and development. The patterns of DNA methylation, histone modifications, microRNAs, and several chromatin-related proteins of sick cells usually differ from those of healthy cells, highlighting the importance of epigenetic regulation in most human pathologies. This chapter provides an overview of how epigenetic factors contribute to the development of human diseases, such as abnormal imprinting-causative pathologies, cancer malignancies, as well as autoimmune, cardiovascular, and neurological disorders. These studies have provided extensive information about the mechanisms that contribute to the phenotype of human diseases, but also provided opportunities for therapy.

Figure S10 from Single-cell Multiomics Analysis of Myelodysplastic Syndromes and Clinical Response to Hypomethylating Therapy

<p>Effect of AZA treatment on wild-type cell populations in responder patients</p>

Alterations of the p16INK4a/Rb/cyclin-D1 pathway in vulvar carcinoma, vulvar intraepithelial neoplasia, and lichen sclerosus

Abstract 6160: Design and preclinical evaluation of a first-in-class covalent reversible inhibitor of IRAK4 with immunomodulatory properties and selective anti-lymphoma effect

Abstract Oncogenic activating mutations in the myeloid differentiation primary response gene 88 (MyD88) and the consequent activation of the Toll-like receptor pathway are hallmarks of the activated B-cell-like (ABC) subtype of diffuse large B-cell lymphoma (DLBCL). This cascade includes phosphorylation of interleukin-1 receptor-associated kinase 4 (IRAK4), triggering downstream NF-κB activation and driving tumor survival, proliferation, and chemotherapeutic resistance. Although several IRAK4 small-molecule inhibitors (IRAK4-i) are undergoing clinical evaluation for various cancers, most are non-covalent inhibitors with limited activity and specificity.To address this, we employed computer-aided drug design to create a library of reversible covalent IRAK4-i based on a pyrido[2, 3-d]pyrimidine scaffold with lysine-targeting warheads. From this library, the ten most promising candidates were synthesized using organometallic reactions and microwave-assisted techniques. Subsequent multikinase screening identified four potential IRAK4-specific inhibitors, with GGP314 emerging as the most potent. GGP314 exhibited IC50 values of 6.6-7.3 μM at 24 hours and 1.8-2.8 μM at 72 hours in MyD88mut ABC-DLBCL cell lines, while showing minimal activity against non-ABC-DLBCL cells and normal peripheral blood mononuclear cells (PBMCs). Mechanistically, GGP314 reduced IRAK4 phosphorylation and impaired NF-κB signaling, as evidenced by the downregulation of several target genes. The compound demonstrated antitumor activity in 3D spheroid cultures of ABC-DLBCL cells, achieving a 50-60% reduction in Ki67 levels. However, the cytostatic effect was partially attenuated in the presence of follicular dendritic or mesenchymal stromal cells, though not with M2-polarized macrophages. Single-cell RNA sequencing (scRNA-seq) analysis of 3D spheroids revealed that GGP314 preferentially targets tumor-associated macrophages, shifting the tumor microenvironment towards a pro-inflammatory state via upregulation of interferon-gamma response pathways. Finally, GGP314 efficacy was validated in vivo in an immunocompetent chicken embryo chorioallantoic membrane (CAM) model of MYD88-mutant ABC-DLBCL. Twice-weekly dosing resulted in up to 55% tumor growth inhibition in a dose-dependent manner without systemic toxicity. In conclusion, we report here the development and preclinical validation of GGP314, a first-in-class reversible covalent IRAK4 inhibitor. GGP314 exhibits significant antitumor activity, high specificity, and the ability to modulate both tumor-intrinsic and microenvironment-dependent signals, supporting its potential as a therapeutic candidate for ABC-DLBCL. Citation Format: Gema Gorjon de Pablo, Nuria Profitos-Peleja, Miek Jacobs, Aitor Gonzalez-Herrero, Jeronimo Parra, Elisabetta Mereu, Paula Cifuentes, Melissa Orphali, Jordi Teixido, Manel Esteller, Jose I. Borrell, Roger Estrada-Tejedor, Gael Roue. Design and preclinical evaluation of a first-in-class covalent reversible inhibitor of IRAK4 with immunomodulatory properties and selective anti-lymphoma effect [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 6160.

A Synthetic mRNA Cell Reprogramming Method Using <i>CYCLIN D1</i> Promotes DNA rEpair, Generating Improved Genetically Stable Human Induced Pluripotent Stem Cells

A key challenge for clinical application of induced pluripotent stem cells (iPSC) to accurately model and treat human pathologies depends on developing a method to generate genetically stable cells to reduce long-term risks of cell transplant therapy. Here, we hypothesized that CYCLIN D1 repairs DNA by highly efficient homologous recombination (HR) during reprogramming to iPSC that reduces genetic instability and threat of neoplastic growth. We adopted a synthetic mRNA transfection method using clinically compatible conditions with CYCLIN D1 plus base factors (OCT3/4, SOX2, KLF4, LIN28) and compared with methods that use C-MYC. We demonstrate that CYCLIN D1 made iPSC have (a) lower multitelomeric signal, (b) reduced double-strand DNA breaks, (c) correct nuclear localization of RAD51 protein expression, and (d) reduced single-nucleotide polymorphism (SNP) changes per chromosome, compared with the classical reprogramming method using C-MYC. CYCLIN D1 iPSC have reduced teratoma Ki67 cell growth kinetics and derived neural stem cells successfully engraft in a hostile spinal cord injury (SCI) microenvironment with efficient survival, differentiation. We demonstrate that CYCLIN D1 promotes double-stranded DNA damage repair predominantly through HR during cell reprogramming to efficiently produce iPSC. CYCLIN D1 reduces general cell stress associated with significantly lower SIRT1 gene expression and can rescue Sirt1 null mouse cell reprogramming. In conclusion, we show synthetic mRNA transfection of CYCLIN D1 repairs DNA during reprogramming resulting in significantly improved genetically stable footprint in human iPSC, enabling a new cell reprogramming method for more accurate and reliable generation of human iPSC for disease modeling and future clinical applications.

Faculty Opinions recommendation of Mutations in DNMT1 cause autosomal dominant cerebellar ataxia, deafness and narcolepsy.

The transcribed pseudogene RPSAP52 enhances the oncofetal HMGA2-IGF2BP2-RAS axis through LIN28B-dependent and independent let-7 inhibition

One largely unknown question in cell biology is the discrimination between inconsequential and functional transcriptional events with relevant regulatory functions. Here, we find that the oncofetal HMGA2 gene is aberrantly reexpressed in many tumor types together with its antisense transcribed pseudogene RPSAP52. RPSAP52 is abundantly present in the cytoplasm, where it interacts with the RNA binding protein IGF2BP2/IMP2, facilitating its binding to mRNA targets, promoting their translation by mediating their recruitment on polysomes and enhancing proliferative and self-renewal pathways. Notably, downregulation of RPSAP52 impairs the balance between the oncogene LIN28B and the tumor suppressor let-7 family of miRNAs, inhibits cellular proliferation and migration in vitro and slows down tumor growth in vivo. In addition, high levels of RPSAP52 in patient samples associate with a worse prognosis in sarcomas. Overall, we reveal the roles of a transcribed pseudogene that may display properties of an oncofetal master regulator in human cancers.

Figure S13 from ERBB4-Mediated Signaling Is a Mediator of Resistance to PI3K and BTK Inhibitors in B-cell Lymphoid Neoplasms

&lt;p&gt;Immunoblotting for total and p-ERBB4, p-AKT and p-ERK in parental (left) and resistant (right) Karpas1718 cells (A-B), and TMD8 cells (C). All blots are representative of two independent experiments. Karpas1718 or TMD8 cells were stimulated with PBS or HBEGF (30ng/mL) for 4 hours, washed-up and treated with DMSO (0.1%), idelalisib (1µM), lapatinib (1µM) or the combination. Levels of phospho proteins were normalized to vinculin and total protein. Data on the barplots represent the mean of two experiments, errors bars represent standard deviation of the mean. * for p&lt;0.05, ** for p&lt;0.01 and ns for not significant from a t-test.&lt;/p&gt;

Genome-wide study of chromatin remodeling factor CHD8 role in transcription

Poster presentado al 22nd IUBMB & 37th FEBS Congress: From Single Molecules to Systems Biology, celebrado en Sevilla (Espana) del 4 al 9 de septiembre de 2012

Clonal evolution of a lethal prostate cancer: Integrated whole genome analysis case study

Supplementary Tables from NID2 and HOXA9 Promoter Hypermethylation as Biomarkers for Prevention and Early Detection in Oral Cavity Squamous Cell Carcinoma Tissues and Saliva

Supplementary Tables from NID2 and HOXA9 Promoter Hypermethylation as Biomarkers for Prevention and Early Detection in Oral Cavity Squamous Cell Carcinoma Tissues and Saliva

Polychlorinated Biphenyls Affect Histone Modification Pattern in Early Development of Rats: A Role for Androgen Receptor-Dependent Modulation?

Background: The epigenome represents an important target of environmental pollution. Early-life exposure to polychlorinated biphenyls (PCBs) modifies sex steroid enzymes and receptor transcription patterns. Steroid receptors, such as androgen receptor (AR), function as coregulators of histone modification enzymes. Aim: To clarify if a PCB early-life exposure might affect the epigenome in rat liver, we analyzed some histone post-translational modifications (H3K4me3 and H4K16Ac) and the corresponding histone remodeling enzymes, and the AR as a histone enzyme coregulator. Results: We observed a decrease of H4K16Ac and H3K4me3 levels, possibly linked to the induction of chromatin-modifying enzymes SirtT1 and Jarid1b, and a decrease of AR. PCBs also seem to induce AR transcriptional activity. Some of the observed effects are sex dimorphic. Conclusion: Our data suggest that an early-life exposure to PCB sometimes modifies the epigenome in the offspring liver in a dimorphic way. AR might be involved in modulating PCB effects on the epigenome.

Genetic predisposition to clinical AD and AD pathology is differentially associated with baseline and 3‐year period change for specific AD‐related markers

Abstract Background Alzheimer’s disease (AD) is a complex neurodegenerative disorder characterized by early changes in brain structure and cognitive function before the age of onset. This study investigated whether the genetic load for clinical AD and AD pathology predicts AD‐related brain and cognitive changes over a 3‐year period, targeting the preclinical phase in cognitively unimpaired (CU) middle‐aged individuals. Method The sample of the study was defined by 429 CU middle‐aged participants at risk of AD from the ALFA+ nested cohort with available information on genetics, brain imaging markers and cognitive data [Table 1]. A subset of them had information at two‐time points (N = 367) [Figure 1]. Genetic predisposition for clinical AD (PRSAD and PRSADnoAPOE) and AD pathology (PRSAβ42‐CSF and PRSpTau‐CSF) were calculated. We used linear regression models to assess the association between each PRS and global amyloid PET deposition expressed in Centiloids, AD Dickerson MRI‐signature, hippocampal volume and cognitive outcomes, at baseline and rate of change over visits after controlling for confounders. PET and MRI outcomes were defined as the annual rate of change. Cognitive outcomes were z‐scores of the two‐time points difference. Models were adjusted for time between visits. Result At baseline, higher genetic predisposition to clinical AD was associated with increased amyloid‐PET levels and higher average thickness of AD‐affected regions. Additionally, higher PRSAD was associated with reduced AD‐related cognitive performance and worse language [Figure 2]. Over the three‐year period, AD‐genetic load predicted higher annual amyloid accumulation in the brain, independently of APOE. Conversely, genetic predisposition to higher CSF Aβ42 levels predicted lower annual rate of change for Centiloids. PRSAD was also associated with annual reduction of hippocampal volume. Finally, genetic predisposition to AD beyond the APOE region was associated with executive functioning rate of change[Figure 2]. Conclusion The results of this study showed the role of genetic predisposition to AD, affecting amyloid PET deposition, brain structure changes, and cognitive decline. These findings emphasized the importance of considering a comprehensive range of genetic markers in risk assessments for AD, particularly in its early stages, and highlight the potential of personalized genetic approaches to enhance predictions and interventions in the management of AD.

Supplementary Table 3 from Discovery of Epigenetically Silenced Genes by Methylated DNA Immunoprecipitation in Colon Cancer Cells

Supplementary Table 3 from Discovery of Epigenetically Silenced Genes by Methylated DNA Immunoprecipitation in Colon Cancer Cells