Cancer Genomics, Biomedicine, Data Visualization
"Data really powers everything that we do”
“Anyone who has never made a mistake has never tried anything new.” Albert Einstein
Biomedical researcher with ten years of experience in the genomics field. I have participated in various projects across a broad range of areas including oncology, computational genomics and clinical data.
I developed this project at the Institute of Biomedicine-Gothenburg University, Sweden. The projects consisted on the identifcation of mutation present in cancer tumor samples and analyzed their impact on RNA binding proteins (RBPs). In addition these data was integrated with eCLIP and shRNAs experiments to unveil RBPs-RNA interactions which could be disregulated in cancer.'
In collaboration with my colleague Emre Guney, we did some data visualization of IMI projects
The results from my PhD project led to the following patent application, in which I am co-inventor: Title: Compounds targeting lncRNA for the treatment of cancer. Patent application: US2020/0087666 A1
In this work we analyzed >7000 tumor samples, we found amplified lncRNA associated with lung cancer-1 (ALAL-1) as frequently amplified in lung adenocarcinomas. ALAL-1 is also overexpressed in additional tumor types, such as lung squamous carcinoma. The RNA product of ALAL-1 is able to promote the proliferation and tumorigenicity of lung cancer cells. ALAL-1 is a TNFα− and NF-κB–induced cytoplasmic lncRNA that specifically interacts with SART3, regulating the subcellular localization of the protein deubiquitinase USP4 and, in turn, its function in the cell. Interestingly, ALAL-1 expression inversely correlates with the immune infiltration of lung squamous tumors, while tumors with ALAL-1 amplification show lower infiltration of several types of immune cells. We have thus unveiled a pro-oncogenic lncRNA that mediates cancer immune evasion, pointing to a new target for immune potentiation
In this book chapter, we summarize current knowledge about the prevalence of different DNA repair gene alterations across different stages of prostate cancer and review the clinical relevance of such events in terms of prognosis and treatment stratification.
In collaboration with Joaquin Mateo and Sara Arce, I wrote this review about DNA damage repair in prostate cancer and the current use of precision medicine.
In collaboration with Maite Huarte PhD, I wrote this preview report in Cancer Cell. We described the findings of Hu and colleagues where they discover the oncogenic lncRNA FAL1.
In this work we described the transcriptional landscape regulated by the tumor suppressor p53 in colon cancer cell lines. I performed the ChIP-seq analysis and integrate these results with RNA-seq data, resulting in the identification of a set of DNA damage induced lncRNAs which are p53 direct targets.
This work is the follow up of our previous publication of Pint lincRNA, this time we decided to focus on the human version: lncRNA LINC-PINT which is downregulated in various cancer types. Interestingly, we discovered a conserved sequence element which mediates this lncRNA's function.
In this work we report the discovery of the p53 regulated lncRNA named Pint. In particular I analyzed gene expression data (microarrays) from a colon cancer tumor cohort where we found that PINT expression is downregulated in colon primary tumors. In addition experimental evidences suggest its role as a tumor suppressor.
In this work we discovered the transmembrane protein CUP-1 that is involved in dietary cholesterol uptake in C. elegans. For this project I peformed a wide range of molecular biology experiments. In addition I carried out evolutionary conservation analysis which led to the identification of CRAC motifs in CUP-1 mammalian homologous.
For this publication I performed a computational analysis using the miRanda algorithm to predict a set of mRNAs targets for those microRNAs localized in synaptoneurosomes (SN). Gene Ontology (GO) enrichment analysis showed that the most predicted targets belong to genes associated with learning and memory.
2018-current
Prostate Cancer Research: I am currently working in a project to identify copy number profiles signatures in Whole Genomes associated with alterations in DNA Damage Response (DDR) genes. In addition I am analyzing genomics and transcriptomic data from liquid biopsy samples.
2012-2017
Integrative Genomic Analysis: Analyzed the genome of 7,448 tumors from cancer patients to identify copy number altered regions harboring a class of genes called: lncRNAs. Integrated these data with RNA-seq to identify novel cancer genes. In addition, experimentally validated the function of a discovered lncRNA and confirmed its roles in lung cancer.
Analysis of Cancer Mutations: Identified the mutations present in cancer tumors samples and analyzed their impact in RNA binding proteins (RBPs). In addition these data was integrated with eCLIP and shRNAs experiments to unveil RBPs-RNA interactions involved in the disease.
2010-2011
Breast Cancer Research: Experimentally explored the regulation of the tumor suppressor PTEN performing molecular biology techniques.
Emerging Roles of the Sirtuin Family: I wrote the academic review where I described the key aspects of sirtuin's biology, presents the current situation of sirtuins in the biotechnology industry, an its function in cell metabolism, chromatin regulation and cancer. This review is available at Columbia University Academic Commons: https://doi.org/10.7916/D8X354FT.
2006-2010
Influenza Virus Detection: Conducted sequence comparison analysis for the design of molecular beacon probes to differentially detect Influenza virus subtypes during the global flu outbreak in 2009.