1.-Identification of predictive epigenetic biomarkers in the appearance of resistance to treatment in solid tumors. Within the oncological markers, those for predictive use are the most necessary to help direct therapies since the vast majority of patients are diagnosed when the tumor needs to be treated. Platinum-derived compounds are the standard treatment for high-incidence tumors such as those of the lung, ovary, and rectum, so the fact of finding markers of response to their use would allow the selection of patients, optimizing treatment and associated healthcare costs.

  1.1- Lung cancer: In this line we have identified the methylation of the IGFBP3 gene promoter, whose epigenetic silencing is related to platinum resistance, extending its validation to cohorts of lung cancer patients likely to benefit from its use. In addition, the effectiveness of this biomarker is being tested in liquid biopsy as a non-invasive test. This line of research has given rise to three concatenated publications (Oncogene 2010 PMID: 20023704, Oncogene 2013 PMID: 22543588, Epigenetics 2014 PMID: 25482372) and a patent in the joint exploitation phase with a Spanish biotechnology company that has licensed said patent. This patent has passed a Pre-commercial Public Purchase in SERGAS and its validation in national phases has had the support of two concatenated RETOS projects.
 1.2. Brain Tumors: Regarding our line with brain tumors, we assess the methylation status of the MGMT gene in glioblastomas, as a care and research task since 2014 in our laboratory, developing advanced high-sensitivity technology for its detection in liquid biopsy. The data obtained to date in more than 200 patients in a prospective trial has given rise to a recent publication (Clinical epigenetics 2021 PMID: 33750464) and a second article in process, in addition to a European patent that has just passed PCT extension, and the award of two competitive public projects, one of them a DTS20 technological project for diagnosis and blood monitoring of patients with glioblastomas, and a PLEC project (RETOS) in collaboration with Val`deHebron for fine-tuning diagnostic technologies and monitoring with tracers PET. In addition, these results have allowed the defense in 2021 of the doctoral thesis of Rocío Rosas, a member of our team, who has just started her independent line in January 2022 as a "Juan Rodés" researcher.
 1.3. Ovarian Cancer: We also have an open line in ovarian cancer, in which we have published a recent article (Clinial Epigenetics 2021 PMID: 34454589) and has allowed us to participate as work package leaders in a Transcan European project led by Italy, which has just successfully passed the first round of evaluation.
 1.4 Melanoma. In this emerging line, we are focusing on the characterization of the oncogenic role of MAFG in the response to immunotherapy in melanoma. Dr. Olga Vera, recently has incorporated to the group as a Sara Borrell postdoctoral researcher to lead this line. Previous studies of Olga have identified MAFG as a potential oncogene in melanoma and with potential therapeutic applications. The successful completion of our study will significantly advance our understanding of the role of MAFG in melanoma, determine new therapeutic targets and open new lines of research focused on dissecting the oncogenic role of MAFG.  
 

2.-Study of the molecular mechanisms underlying simultaneous resistance to platinum in cancer, through the epigenetic regulation of regulatory non-coding RNAs. In this line, changes in the expression of microRNAs and lncRNAs in platinum-sensitive and -resistant human NSCLC and ovarian cancer cell lines established in our research group are studied. We have identified 7 microRNAs whose expression appears to be under epigenetic regulation. One of them under the epigenetic regulation of its regulatory region (miRNA-7) as a potential predictive biomarker of response to platinum in ovarian cancer in terms of overall survival and time to progression. Product of the development of this line has been the publication of an article in the journal (Theranostics 2017 PMID: 29158814), as well as a patent that is in the PCT phase. Based on these findings, in 2016 we began a collaboration with the MOFFITT cancer center in Tampa (USA) to study Long Non-Coding RNAs (lnc-RNAs) and their possible regulation through DNA methylation in these cell lines. With this project we assess the changes in the expression of lncRNAs and their epigenetic regulation at the level of DNA methylation, characterizing two groups of lncRNAs differentially regulated in the development of resistance to cisplatin, and thus opening the way for the identification of new ones. As a result of the activity of this collaboration, highly innovative results were obtained in this field (Epigenetics PMID: 29436261 and Translational Research 2018, PMID: 30053382), and the research activity focused on the characterization of these novel biomarkers is maintained thanks to the funding supported for the PI21/00145 and Caixa Impulse projects.
 

3. Identification of new therapeutic targets. In recent years we have also identified the direct regulation of the MAFG gene through miR-7 in our experimental models. The function of MAFG is associated with detoxification in a situation of oxidative stress and our in vitro studies have shown its involvement in the appearance of cisplatin-resistant phenotypes. Our translational approach indicates that MAFG could be a diagnostic marker in patients with lung and ovarian cancer treated with platinum-based chemotherapy. To date, this line has provided four articles (Translational Research 2018, PMID: 30053382; Cell Biosci. 2019 PMID: 31406565; Arch Bronconeumol (Engl Ed). 2020.PMID: 31780284; Antioxidants (Basel).PMID: 32492865) and one European patent that has just been extended to national phases in the USA and Europe, which describes the clinical use of MAFG in patients with lung and ovarian cancer. We have currently addressed the study and use of MAFG as a therapeutic target through in vitro and in vivo assays after editing the MAFG gene using CRISPR/Cas9 technology, a project funded by the ISCIII (PI18/00050, P21/000145 ) in addition to extending and validating its use with the potential development of a kit for clinical use thanks to obtaining a RETOS project (RTC2019-007229-1) from the 2019 call and which is ongoing with the collaboration of H. Ramón y Cajal and the companies Aptus and Atrys.
 

4. Identification of biomarkers in exosomes such as liquid biopsy in patients with lung and ovarian cancer. With this line we intend, through a first basic approach, to characterize and compare the protein and microRNA content of exosomes from the secretome of paired sensitive and resistant lung cancer cell lines. In the translational study of the project, the candidates identified in the cell lines in circulating exosomes from samples of lung and ovarian cancer patients are being validated, which have given rise to different results. On the one hand, two candidate miRNAs with prognostic significance in this pathology, and on the other hand, a miRNA with possible universal value has been identified as endogenous capable of normalizing the value of the content of the exosomal miRNoma, both in healthy individuals and in individuals with different tumor types. These results have given rise to a European patent that is in national phases and the obtaining of a Caixa Impulse Validate project for the constitution of a Spin-off, in our institution focused on the development of a first RUO product for the normalization of exosomal content. in human blood samples, in addition to two manuscripts in preparation, as well as the defense of Julia Jiménez's thesis in July 2019.
 

5. Identification of pharmacogenetic biomarkers associated with efficacy and toxicity of cancer treatments. Led by Dr R Rosas. Pharmacogenetics is the field of knowledge that seeks to identify genetic variants to provide information that will allow a better understanding of drug response in terms of efficacy and toxicity, thus contributing to personalised precision medicine. Despite progress in the research and development of new cancer treatments, the efficacy and safety of these drugs vary widely between patients. In this context, this line of research aims to understand how genetic variations in individuals may influence the efficacy and toxicity of cancer treatments. The use of pharmacogenetic biomarkers is a reality in routine clinical practice and has been shown to improve the efficacy and reduce the side effects of treatments, resulting in a better quality of life for patients and reduced costs for the national healthcare system. Our ultimate goal is to identify new pharmacogenetic biomarkers that will allow better selection of cancer treatments for each patient, thus promoting the medicine of the future with a personalised and individualised approach. This line currently has two projects awarded in public (PI22/00128) and private (Jose Luis Castaño-SEQC Foundation) competitive calls, led by Dr Rocío Rosas.
 

6.  Identification of microRNA hypermethylation patterns associated with an increased risk of developing non-small cell lung cancer in patients with mild COPD and moderate to high tobacco consumption. In recent years, the potential role of epigenetic alterations in the development of lung cancer in COPD patients, mediated by changes in the activity of various microRNAs, small non-coding RNA molecules (19-25 nucleotides) with a regulatory function of gene expression, which induce the degradation of messenger RNA or inhibit its translation, has gained particular importance. It is therefore interesting to consider whether there may be hypermethylation profiles of different microRNAs that are associated with an increased risk of lung cancer in COPD patients, which would facilitate appropriate risk selection for screening programmes.This line currently has one project, which was awarded in a competitive public call (PI22/001764), under the co-direction of Olga Pernía Arias.
 

7. Fine-tuning of high performance techniques available to the National Health System (NHS). (NGS and Characterization of DNA methylation status). Implicit in the group's cross-cutting lines and in our commitment to support the implementation in the NHS of the technological advances derived from our research activity, we have fine-tuned the characterization of the methylation status at the PAZ genetics facilities of DNA through the use of these new aspects of NGS applied to the field of epigenetics, both from a global approach and limited to certain regions, to implement its possible care applicability in cancer patients through personalized panels in solid tumors including glioblastomas, through the use of Methylseq technology and the 850K EPIC-arrays. Likewise, in these years we have fine-tuned the use of commercial NGS panels in strict compliance with quality regulations to address the characterization of the genetic profile of tumors in patients with lung cancer. Thanks to the addition to our team such as Dra Rocío Rosas, Juan Rodés from 2022, we are starting the hospital implementation phase, in which we have already tested careers with various platforms from different commercial houses. Its fine-tuning would allow its use both for research activities and its future healthcare applicability, especially in the classification of brain tumors. This activity is financed by the Spanish Group of Transversal Oncology and Rare Orphan Tumors (Getthi), which has just financed the group with a competitive project for this purpose. Given the experience acquired by the group in the use of massive data, we have been able to participate in the EU ISIDORE project and have begun the study of predictive bioinformatic matrices of response to platinum treatment. We intend to combine the information available in public domain databases with relevant clinical information associated with our own experimental results (methylation and gene expression microarrays and microRNAs, bisulfite sequencing, RNAseq and miRNAseq) to generate a predictive matrix of response to treatment. With these analytical models, we intend to identify "global markers" that define a predictive profile for treatment with platinum in lung and ovarian cancer based on the transcriptome, microRNome, and/or methylome.

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