José Fernández Navarro obtained a Bachelor’s degree in Computer Science in Spain and Ireland in 2010, followed by a Master’s degree in Computational Biology at the prestigious Royal Institute of Technology (KTH) in Stockholm, Sweden.
From 2011-2020 he worked at the internationally acclaimed Karolinska Institute in Stockholm where he also obtained his PhD in Computational Biology. During this time; he, together with others, developed a technology for the spatially resolved analysis and visualization of the transcriptome (Spatial Transcriptomics). This technology was acquired by 10x Genomics in 2018 and was named method of the year 2020 by Nature. During his time at the Karolinska Institute he collaborated in multiple projects. As an example, he applied Spatial Transcriptomics in combination with other omics to molecularly characterize the mouse brain and study neurogenerative diseases in mouse models.
In 2020, he returned to Spain to join the Vall d’Hebron Institute of Oncology (VHIO) as PI of the newly created Bioinformatics Unit.
VHIO’s Bioinformatics Support Unit, led by José Fernández Navarro, promotes digital transformation and sets optimal standards and best-practices for the processing, analysis and visualization of omics datasets.
We provide support and expertise across multiple projects in collaboration with other investigators at VHIO including Joaquín Arribas, Héctor G. Palmer, Alena Gros, Joaquin Mateo, Ana Vivancos, Raquel Pérez-López, Rodrigo Toledo, and Sara Rodriguez, to name but a few. Projects range from mentorship, the development of pipelines and tools for the processing of multi-omics datasets, to the analysis, integration and visualization of omics datasets by applying machine learning and statistics.
We have also started to represent our Institute as a member of various consortia and taskforces, and have also developed state-of-the-art pipelines and tools for the processing of different omics using modern standards. In collaboration with other VHIO groups, we aim to establish our own research lines.
Ana Vivancos obtained her PhD in 2006 in Biochemistry and Molecular Biology from the Universitat Pompeu Fabra, Barcelona, supervised by E. Hidalgo. During this period, she worked on the response of fission yeast to oxidative stress and characterized the redox switch Tpx1-Pap1 that acts as the H2O2-sensor in this organism.
In 2007 she joined the Colorectal Cancer Lab at the Institut de Recerca de Barcelona (IRB), where she worked on WNT signaling in colorectal cancer. She then moved to the Centre for Genomic Regulation (CRG, Barcelona), where she set up the Ultrasequencing Core Facility that incorporated the very first 2nd generation instrument in Spain (Genome Analyzer, Illumina). During this time, she specialized in protocol design and improvement of NextGen sequencing applications.
In early 2010 Ana moved to the Vall d’Hebron Institute of Oncology (VHIO) to assume the position as Principal Investigator of the Cancer Genomics Group. The Lab is focused on performing molecular prescreening of Phase I trial patients as well as in developing genomic tests to be used with FFPE-derived nucleic acids, liquid biopsy. As a reflection of our dedication to excellence and quality in the services we provide, we have attained ISO 15189 flexible accreditation for our Amplicon-seq testing method as well as for our large 450-gene capture panel.
Our research activities focus on developing novel multiplexed tests that are optimized to FFPE-derived nucleic acids. Once developed, they are validated and used in both clinical and translational research.
We are also involved in a number of translational research projects including the identification of mechanisms of resistance to targeted therapies, as well as predictive biomarkers for immunotherapeutics. Presently, our group is particularly interested in liquid biopsy and on RNA-based profiling of tumors for microenvironment profiling.
VHIO’s Cancer Genomics Group serves as a Core Technology laboratory. We are also dedicated to translational research as well as the development of novel genomic tests.
Our group provides cutting-edge applications in cancer genomics through state-of-the-art technologies and the development of novel, fully validated tests that are used in the clinical research setting. Our lab is equipped with an n-Counter (Nanostring) platform, two digital PCR platforms (BEAMing Sysmex and ddPCR, BIO-RAD) and three NextGen Sequencers; MiSeq, NextSeq and HiSeq2500, Illumina. We are also starting to work with Minion Oxford Nanopore technology.
Our Molecular Prescreening Program, is headed by Rodrigo Dienstmann, PI of VHIO’s Oncology Data Science – ODysSey – Group, and co-led by our PI, Ana Vivancos, Paolo Nuciforo, PI of VHIO's Molecular Oncology Group, and Elena Garralda, who leads VHIO’s Early Clinical Drug Development Group.
Our Advanced Molecular Diagnostics Program – DIAMAV, is supported by the FERO Foundation. We perform molecular profiling in over 1100 patients each year as potential candidates for enrollment in our Phase I clinical trials led by VHIO’s Research Unit for Molecular Therapy of Cancer (UITM) – CaixaResearch, directed by Elena Garralda.
Patients’ suitability for inclusion in any given clinical trial is assessed based on their respective genomic or pathologic profile. We have developed and routinely implemented several tests for our Molecular Prescreening Program.
Two are based on NGS: an Amplicon-seq approach to sequence 67 genes as well as a 450-gene capture panel (Illumina). We use nCounter (Nanostring) for our RNA- based gene fusion panel, with the capacity of detecting over 100 recurrent gene fusions (also enabling us to assess gene expression patterns in tumors), and our Copy Number Alterations panel, evaluating a 59 gene panel for genes with frequent gains or losses in cancer.
As a reflection of our dedication to excellence and quality in the services we provide, we have attained ISO 15189 flexible accreditation for our Amplicon-seq testing as well as for our large 450-gene capture panel. Research activities focus on developing novel multiplexed tests that are optimized to FFPE-derived nucleic acids. Once developed, they are validated and used in both clinical and translational research.
We are also involved in a number of translational research projects including the identification of mechanisms of resistance to targeted therapies, as well as predictive biomarkers for immunotherapeutics. Based on nanostring and RNA-seq technologies for the detection of an immune signature, we use the VIGex tool (see figure). Our group is particularly interested in liquid biopsy and RNA-based analysis of tumors for microenvironment profiling.
Paolo obtained his medical degree in Catania and received board certification in Pathology from the University of Milan (Italy).
As cancer treatment is evolving towards a more personalized approach, skills and competencies of professionals in oncology are also changing. Pathologists are at the front-line in combating cancer, and knowledge concerning translational research and novel genetic and genomic technologies is consequently imperative. To respond to this rapidly emerging landscape, Paolo moved to the IFOM, the FIRC Institute of Molecular Oncology, Milan (Italy) in 2003. Devoted to basic and translational cancer research, IFOM enabled him to expand his clinical and surgical pathology background and skill set with molecular biology and experience in novel post-genomic technologies. During this period, he initially worked as Research Fellow and was later appointed to lead the Molecular Pathology Unit that now serves IFOM´s research groups. At FIRC he co-authored numerous publications in translational research.
In 2007 Paolo moved to Novartis, a leading and international pharmaceutical company, where he joined the Oncology Biomarkers Group which comprised a multicultural team focused on implementing and supporting innovative biomarker strategies in early and late drug development programs to better enable decision-making, proof of mechanism, and patient selection.
During his time at Novartis he created a new group from scratch, set up his laboratory, recruited and led a small team of talented scientists to deliver on the company’s strategic goals. He also provided support for preclinical research activities as well as several clinical oncology biomarker programs.
Paolo joined VHIO in 2012 as Principal Investigator of the Molecular Pathology Group to significantly contribute to the development of new biomarkers and diagnostic tests for precision oncology, leveraging over 10 years’ experience in clinical and translational oncology.
In 2016, he obtained his PhD in Morphology, Structural and Molecular Pathology (now Surgery and Morphological Sciences), at the Universitat Autònoma de Barcelona, Spain.
Paolo has co-authored over 100 publications in peer-reviewed journals, mainly focused on the discovery and validation of novel biomarkers using tissue-based technologies. Most recently, his Molecular Oncology Group at VHIO has been studying the link between the gut microbiome and cancer, leading to important contributions to the field (Science2017, Annals of Oncology2020).
VHIO’s Molecular Oncology Group applies state-of-the-art tissue-based technologies to basic, translational, and clinical research with a clear focus on developing and validating novel tumor biomarkers for precision medicine in oncology.
Together with VHIO’s Cancer Genomics Group (PI Ana Vivancos), and Oncology Data Science - ODysSey Group (PI Rodrigo Dienstmann, we participate in our in-house Molecular Prescreening Program. We molecularly profile over 1500 patients per year as candidates for enrolment in early phase clinical trials at our Research Unit for Molecular Therapy of Cancer (UITM) – CaixaResearch, directed by Elena Garralda.
Our group also serves as one of VHIO’s Core Technology Platforms and our laboratory is therefore key to VHIO’s translational research lines and programs. We actively participate in all projects involving the use of human tissue collected from patients, including biomarker analyses for patient stratification and inclusion in clinical trials, digital pathology, tissue banking and the development of primary patient-derived xenograft (PDX) models. Our contribution is reflected by several high-impact factor collaborative papers published throughout 2020.
Our team also continues to work both independently as well as in partnership to establish the impact of microbiome in colorectal cancer development and progression. In particular, we developed a Fusobacterium nucleatum diagnostic assay that permits the simultaneous visualization and quantification of bacteria within tumors. Using this assay we identified, for the very first time, Fusobacterium nucleatum as a biomarker of relapse in rectal cancer (Annals of Oncology 2020). We are also leading the FUSOMAP, a 3-year project funded by the Mutua Madrileña Foundation and Instituto de Salud Carlos III - ISCIII (Institute of Health Carlos III), to develop microbiota-based diagnostic and prognostic models by mapping intratumoral Fusobacterium and associated gut microbiota in early-stage colorectal cancer.
As a Core Facility we have provided support for approximately 340 clinical studies conducted at Vall d’Hebron, representing 72% of all currently open trials at our institution. Our involvement in clinical trials ranges from the coordination of sample collection, storage and shipment, developing and running multiple assays for real-time patient inclusion, as well as pharmacodynamic monitoring and dose finding.
In 2020, we performed more than 3000 molecular determinations on samples for patient inclusion in clinical trials, and over 19,000 tests to support basic and translation research. We have also served as the central laboratory of choice for 10 international studies, and successfully maintained the prestigious ISO15189 accreditation that endorses quality and competence.
Francesc Canals graduated in Organic Chemistry from the Institut Químic de Sarrià (Barcelona, Spain), in 1982 from where he also obtained his PhD in 1989 under the supervision of J -J. Bonet working on organic photochemistry. Part of his PhD work was carried out during a one year stay in M. Demuth´s laboratory at the Max-Plank-Institut für Strahlenchemie, Mülheim a.d. Ruhr (Germany). He also obtained a degree in Biochemistry from the Universitat Autònoma de Barcelona in 1987.
From 1989 to 1991 he worked as a postdoctoral fellow in the laboratory of J. Kyte, at the University of California San Diego (USA). He performed protein chemistry studies on the signaling mechanism of the epidermal growth factor receptor, demonstrating that the tyrosine kinase of the receptor is activated after its dimerization. In 1991 he moved to the laboratory of F. X. Avilés, at the Institut de Biotecnologia i Biomedicina (Universitat Autònoma de Barcelona), where he worked as a postdoc until 1995. During this time his research focused on protein chemistry and protein engineering studies on metallocarboxypeptidase inhibitors, aimed at characterizing structure-activity relationships and disulfide folding mechanisms.
From 1995 - 2003 he was in charge of the Proteomics Facility at the Universitat Autònoma de Barcelona. In addition to providing proteomic services to other research groups, he also contributed to several studies on the biological applications of mass spectrometry.
He joined the Medical Oncology Research program at VHIO in 2003, and is currently Principal Investigator of VHIO´s Proteomics Group. Since then, Francesc has set up the different separation and mass spectrometry-based proteomic technologies offered by the facility. His research centers on the development and application of proteomic strategies for the screening and validation of biomarkers for cancer diagnostics, personalized therapies and the tracking of disease.
Our group serves as a Core Technology Platform. We provide state-of-the-art proteomic methodologies to investigators at VHIO, and incorporate new developments within the field to offer the very latest strategies and technologies in the field.
We employ mass spectrometry-based proteomic strategies for the screening and validation of biomarkers for cancer diagnostics, precision therapy and the closer monitoring of disease.
One of our research lines focuses on the development of mass spectrometry-based assays for the analysis of biomarkers in clinical samples. We have developed immune-MS based assays with improved selectivity and accuracy in the analysis of low abundance biomarker proteins in plasma or CSF samples.
Our group also develops MS based assays for marker proteins in FFPE tissue samples in order to provide accurate quantitative measurements that can translate in superior stratification compared with routine IHC scoring methods.
We have set up workflows for the proteomic and phosphoproteomic characterization of patient- derived xenograft (PDX) models of colorectal cancer. PDX constitute an ideal platform for the molecular characterization at the proteomic level of this tumor type.
Complementing genomic classification, we are exploring the suitability of this characterization as a tool for tumor subtype classification.