Programs & Groups

Biomedical Research Division Clinical Research Division Core Transversal Groups and Units Transversal Services

Cancer Genomics Group

Molecular Oncology Group

Proteomics Group

Molecular Prescreening Program

VHIOTECA

Group Leader Ana Vivancos Laboratory Manager Agatha Martín Project Manager Ester Castillo Postdoctoral Fellows Eva Rodríguez, Antonis Klonizakis Specialized Technicians Vanessa Bach, Giuseppe Buono, Berta Mas, Ana Onieva, Montserrat Ricart Predoctoral Fellows Francheska Cadacio, Diego Gómez, Alberto Hernando, Paula Romero Bioinformaticians Elena Campoy, Nuria García, Marina Gómez, Maria Vila Research Support Technicians Ana Isabel Corao, Touria Laajaj

Core Transversal Groups and Units

Cancer Genomics Group

Summary

VHIO’s Cancer Genomics Group serves as a Core Facility. Our laboratory provides access to a range of cutting-edge applications and technologies in cancer genomics including three NextGen Sequencers, MiSeq, NextSeq, and NovaSeq6000 from Illumina, and a ddPCR from BIORAD.

We also pioneer the development of new, fully validated genomic tests that are currently used in the clinical research setting.

We have developed and routinely implemented several NGS-based tests: VHIO300, a 435-gene capture panel (Illumina); VHIO Epsilon Panel, an RNA- based enrichment panel for the detection of gene fusions and expression patterns in tumors, and VHIO360, a cutting-edge test for liquid biopsy, technology transfer of the Guardant 360® DX test (Guardant Health). Notably, VHIO was the first cancer research center in Europe to incorporate this avant-garde platform. Aimed at overcoming the limitations associated with traditional tissue biopsy, this technology provides complete genomic results in all solid tumors from a simple blood draw in seven days.

Molecular Prescreening at VHIO is co-led by Ana Vivancos, Head of our group, alongside Paolo Nuciforo, Elena Garralda, and Rodrigo Dienstmann, who lead our Molecular Oncology, Early Clinical Drug Development, and Oncology Data Science – OdysSey Groups, respectively. Through our institutional Advanced Molecular Diagnostics Program – DIAMAV, supported by the FERO Foundation, we perform molecular profiling in patients as potential candidates for enrolment in our phase I clinical trials led by VHIO’s Research Unit for Molecular Therapy of Cancer (UITM) – CaixaResearch, directed by Elena Garralda.

In 2025, we performed tumor molecular profiling of more than 2,300 patients’ tumors. Over 50% of these tests were performed using liquid biopsy.

Reflective of our dedication to excellence and quality in the services that we provide, all of our panels have received ISO 15189 flexible accreditation (VHIO300, VHIO Epsilon and VHIO360), and we operate as a fully IVDR-compliant laboratory for all available tests in tumor tissue and liquid biopsy.

Our research activities focus on the development of novel multiplexed tests that are optimized to FFPE-derived nucleic acids and liquid biopsy. Once developed, these assays are validated and used in both clinical and translational research. We are also involved in several translational research projects. These include the identification of mechanisms of resistance to targeted therapies as well as predictive biomarkers of response to immunotherapy. Based on genome-wide RNA seq and array-based Nanostring technologies, we have developed the VIGex predictive pan cancer platform to help guide patient selection for personalized immune-based therapies (see Figure).

Figure: VIGex tool: a pan-cancer immune gene expression signature encompassing 12 immune-related genes that predicts immunotherapy benefit and prioritizes immunotherapy combinations in early phase clinical trials.
  • Develop and implement large-scale pan-cancer panels to optimize strategies for routine patient prescreening.
  • Pioneer the development of cutting-edge tests for comprehensive liquid biopsy analysis.
  • Provide cutting-edge applications in cancer genomics by implementing novel technologies and developing new protocols.
  • Prioritize translational research projects and promote team science to further strengthen VHIO's renowned excellence in oncology.
  • VHIO is a founding partner of the Cancer Core Europe (CCE), along with the Gustave Roussy Cancer Campus Grand Paris (Villejuif, France), Cambridge Cancer Centre (Cambridge, UK), Karolinska Institute (Stockholm, Sweden), Netherlands Cancer Institute – NKI (Amsterdam, The Netherlands), National Center for Tumor Diseases–DKFZ- NCT (Heidelberg, Germany), and the National Cancer Institute of Milan (INT). Our group serves as co-leader of CCE’s Genomics Task Force and is responsible for aligning genomic testing across all member institutions.
  • Thanks to our institutional Advanced Molecular Diagnostics Program - DIAMAV (supported by the FERO Foundation), VHIO has become a reference center in Europe in molecular prescreening. In 2025, we performed molecular profiling of 2,300 patients, representing a significant increase compared to the last 10 years, when the number of patients profiled per year averaged 1,100. These patients are candidates for enrolment in early phase clinical trials conducted at our Research Unit for Molecular Therapy of Cancer (UITM) – CaixaResearch. Based on the molecular characteristics and therapeutic vulnerabilities of each person’s tumor, this program enables us to match an increasing number of patients to a particular clinical study.
  • Implement improved strategies for routine patient prescreening with a large pan-cancer panel.
  • Continue to provide cutting-edge applications in cancer genomics using novel technologies and protocol development.
  • Prioritize translational projects and partnerships that reinforce VHIO's renowned excellence in oncology.
  • Nozawa K, Sawaki M, Uemura Y, Tsuneizumi M, Takano T, Gondo N, Hara F, Harao M, Toyama T, Taira N, Vivancos A, Perou CM, Sanfeliu E, Brasó-Maristany F, Parker JS, Buckingham W, Paré L, Villacampa G, Marín-Aguilera M, Villagrasa P, Prat A, Iwata H. HER2DX in older patients with HER2-positive early breast cancer: extended follow-up from the RESPECT trial of trastuzumab ± chemotherapy. Nat Commun. 2025 Nov 4;16(1):9585.
  • Perachino M, Ortiz C, Carmona J, Saura C, Vivancos A. Expanding screening through the use of liquid biopsy for early cancer detection. Commun Med (Lond). 2025 May 10;5(1):167.
  • Martín M, Stecklein SR, Gluz O, Villacampa G, Monte-Millán M, Nitz U, Cobo S, Christgen M, Brasó-Maristany F, Álvarez EL, Echavarría I, Conte B, Kuemmel S, Bueno-Muiño C, Jerez Y, Kates R, Cebollero M, Kolberg-Liedtke C, Bueno O, García-Saenz JÁ, Moreno F, Grischke EM, Forstbauer H, Braun M, Warm M, Hackmann J, Uleer C, Aktas B, Schumacher C, Wuerstleins R, Graeser M, Zu Eulenburg C, Kreipe HH, Gómez H, Massarrah T, Herrero B, Paré L, Bohn U, López-Tarruella S, Vivancos A, Sanfeliu E, Parker JS, Perou CM, Villagrasa P, Prat A, Sharma P, Harbeck N. TNBC-DX genomic test in early-stage triple-negative breast cancer treated with neoadjuvant taxane-based therapy. Ann Oncol. 2025 Feb;36(2):158-171.
  • Villacampa G, Pascual T, Tarantino P, Cortés J, Perez-García J, Llombart-Cussac A, Conte P, Mancino M, Guarneri V, Dieci MV, Waks AG, Schettini F, Brasó-Maristany F, Griguolo G, de Castro BA, Reboredo C, Antolín S, Bueno-Muiño C, Echavarría I, López-Tarruella S, Massarrah T, Del Monte-Millán M, Martín M, Buckingham W, Parker JS, Vivancos A, Polyak K, Filho OM, Wolff AC, DeMichele A, Tung NM, Perou CM, Paré L, Villagrasa P, Prat A, Tolaney SM. HER2DX and survival outcomes in early-stage HER2-positive breast cancer: an individual patient-level meta-analysis. Lancet Oncol. 2025 Aug;26(8):1100-1112.
  1. Project title: CGI-Clinics. Data-Driven Cancer Genome Interpretation for Personalized Cancer Treatment.
    Funding: HORIZON-HLTH-2021-CARE-05-02. HORIZON-RIA 101057509.
    Award period: 01/11/2022 – 31/10/2027.
    Principal Investigator: Ana Vivancos.
  2. Project title: Factores de liberación y eliminación de ADN circulante libre en sangre.
    Funding: Instituto de Salud Carlos III (ISCIII). Reference: PI24/00177.
    Award period: 01/01/2025 – 31/12/2028.
    Principal Investigator: Ana Vivancos.
  3. RETOS – Proyectos de Colaboración Público – Privado: Developing a new diagnostic test for personalized treatment of triple negative breast cancer
    Funding: Agencia Estatal de Investigación. Reference: CPP2024-011794
    Award period: 01/01/2024 – 31/12/2027.
    Principal Investigator: Ana Vivancos.
  1. Villacampa G, Pascual T, Tarantino P, Cortés J, Perez-García J, Llombart-Cussac A, Conte P, Mancino M, Guarneri V, Dieci MV, Waks AG, Schettini F, Brasó-Maristany F, Griguolo G, de Castro BA, Reboredo C, Antolín S, Bueno-Muiño C, Echavarría I, López-Tarruella S, Massarrah T, Del Monte-Millán M, Martín M Buckingham W, Parker JS, Vivancos A, Polyak K, Filho OM, Wolff AC, DeMichele A, Tung NM, Perou CM, Paré L, Villagrasa P, Prat A, Tolaney SM. HER2DX and survival outcomes in early-stage HER2-positive breast cancer: an individual patient-level meta-analysis. Lancet Oncol. 2025 Aug;26(8):1100-1112. doi: 10.1016/S1470-2045(25)00276-1. Epub 2025 Jul 14. PMID: 40675165.
  2. Martín M, Stecklein SR, Gluz O, Villacampa G, Monte-Millán M, Nitz U, Cobo S, Christgen M, Brasó-Maristany F, Álvarez EL, Echavarría I, Conte B, Kuemmel S, Bueno-Muiño C, Jerez Y, Kates R, Cebollero M, Kolberg-Liedtke C, Bueno O, García-Saenz JÁ, Moreno F, Grischke EM, Forstbauer H, Braun M, Warm M, Hackmann J, Uleer C, Aktas B, Schumacher C, Wuerstleins R, Graeser M, Zu Eulenburg C, Kreipe HH, Gómez H, Massarrah T, Herrero B, Paré L, Bohn U, López-Tarruella S, Vivancos A, Sanfeliu E, Parker JS, Perou CM, Villagrasa P, Prat A, Sharma P, Harbeck N. TNBC-DX genomic test in early-stage triple-negative breast cancer treated with neoadjuvant taxane-based therapy. Ann Oncol. 2025 Feb;36(2):158-171. doi: 10.1016/j.annonc.2024.10.012. Epub 2024 Oct 16. PMID: 39419289.
  3. Alsina M, Villacampa G, de Andrea C, Vivancos A, Ponz-Sarvise M, Arrazubi V, Jimenez-Fonseca P, Diez M, Sanz-Garcia E, Martínez E, Guardeño R, Calvo M, Bugés C, Longo F, Navarro V, García-Galea E, Gros A, Ochoa MC, Lopez-Janeiro A, Sanchez-Gregorio S, Herrero C, Labiano I, Vila-Casadesús M, López D, Alexandru R, Muñoz S, Tabernero J, Melero I. A Phase II Study of Perioperative Avelumab plus Chemotherapy for Patients with Resectable Gastric Cancer or Gastroesophageal Junction Cancer - The MONEO Study. Clin Cancer Res. 2025 Jul 15;31(14):2890-2898. doi: 10.1158/1078-0432.CCR-25-0369. PMID: 40388549; PMCID: PMC12260514.
  4. Castet F, Salcedo MT, Nuciforo P, Aguilar S, Vivancos A. Best practices in sample management and molecular profiling of cholangiocarcinoma: a practical guide. Expert Rev Mol Diagn. 2025 Aug;25(8):479-494. doi: 10.1080/14737159.2025.2518145. Epub 2025 Jun 12. PMID: 40497693.
  5. Arce-Gallego S, Cresta Morgado P, Delgado-Serrano L, Simonetti S, Gonzalez M, Romero-Lozano P, Marmolejo D, Morales-Barrera R, Arnau GM, Semidey ME, Aguilar D, Cordoba-Terreros S, Mast R, de Albert M, Planas J, Cuadras M, Maldonado X, Suarez C, Casanova-Salas I, Figols M, Cros S, Mas A, Nonell L, Dienstmann R, Nuciforo P, Vivancos A, Llop-Guevara A, Carles J, Serra V, Mateo J. Homologous recombination repair status in metastatic prostate cancer by next-generation sequencing and functional immunofluorescence. Cell Rep Med. 2025 Feb 18;6(2):101937. doi: 10.1016/j.xcrm.2025.101937. Epub 2025 Feb 5. PMID: 39914385; PMCID: PMC11866514.
  6. Angelats L, Paré L, Rubio-Perez C, Sanfeliu E, González A, Seguí E, Villacampa G, Marín-Aguilera M, Pernas S, Conte B, Albarrán-Fernández V, Martínez-Sáez O, Aguirre Á, Galván P, Fernandez-Martinez A, Cobo S, Rey M, Martínez-Romero A, Walbaum B, Schettini F, Vidal M, Buckingham W, Muñoz M, Adamo B, Agrawal Y, Guedan S, Pascual T, Agudo J, Grzelak M, Borcherding N, Heyn H, Vivancos A, Parker JS, Villagrasa P, Perou CM, Prat A, Brasó-Maristany F. Linking tumor immune infiltration to enhanced longevity in recurrence-free breast cancer. ESMO Open. 2025 Jan;10(1):104109. doi: 10.1016/j.esmoop.2024.104109. Epub 2025 Jan 6. PMID: 39765189; PMCID: PMC11758579.
  7. Dienstmann R, Ruiz-García E, Alsina M, Ruiz-Pace F, Groen-van Schooten TS, Martínez-Ciarpaglini C, Fernández-Figueroa EA, Herrera-Goepfert R, Díaz-Romero C, Lino-Silva L, Hernandez-Guerrero AI, Valdez-Reyes NM, León-Takahashi A, Falcón-Martínez JC, Pouw RE, Romero S, Villagrasa R, Cabeza-Segura M, Alarcón- Molero L, Jimenez-Martí E, Miralles A, Boggino H, Gauna C, Pereira R, Lezcano H, Cantero D, Vivancos A, Matito J, Martin A, Gómez M, Castillo E, Vila M, Ferreira RM, Barros R, Santos-Antunes J, Mendes-Rocha M, Costa A, Riquelme E, Roa JC, Latorre G, Freile B, Caro L, Esteso F, O'Connor J, Riquelme A, Owen G, Garrido M, Diez-García M, Figueiredo C, Caballero C, Lordick F, Farrés J, Derks S, Carneiro F, Cervantes A, Fleitas T. Integrated clinico-molecular analysis of gastric cancer in European and Latin American populations: LEGACY project. ESMO Open. 2025 Mar;10(3):104482. doi: 10.1016/j.esmoop.2025.104482. Epub 2025 Mar 3. PMID: 40036904; PMCID: PMC11926697.
  8. Perachino M, Ortiz C, Carmona J, Saura C, Vivancos A. Expanding screening through the use of liquid biopsy for early cancer detection. Commun Med (Lond). 2025 May 10;5(1):167. doi: 10.1038/s43856-025-00885-9. PMID: 40348826; PMCID: PMC12065791.
  9. Cruellas M, Papakonstantinou A, López-Fernández A, Castillo E, Matito J, Gómez M, Rezqallah A, Vega S, Navarro V, Torres M, Moles-Fernández A, Saura C, Vivancos A, Balmaña J, Oliveira M. Identifying germline pathogenic variants in breast cancer using tumor sequencing. Breast. 2025 Jun;81:104439. doi: 10.1016/j.breast.2025.104439. Epub 2025 Mar 12. PMID: 40090122; PMCID: PMC11952849.
  10. Catani G, Morchón-Araujo D, Mirallas O, Sánchez-Pérez V, Nuciforo P, Villacampa G, Dienstmann R, Vivancos A, Garralda E, Hernando-Calvo A. Optimizing early-phase immunotherapy trials: the role of biomarker enrichment strategies. Front Immunol. 2025 Oct 22;16:1664443. doi: 10.3389/fimmu.2025.1664443. PMID: 41200168; PMCID: PMC12586187.
  11. Martínez-Ciarpaglini C, Barros R, Caballero C, Boggino H, Alarcón-Molero L, Peleteiro B, Ruiz-García E, Fernandez-Figueroa E, Herrera-Goepfert R, Díaz- Romero C, Ferreira R, Groen-van Schooten TS, Gauna C, Pereira R, Cantero D, Lezcano H, Esteso F, O Connor J, Riquelme A, Owen GI, Garrido M, Roa JC, Ruiz- Pace F, Vivancos A, Diez-García M, Alsina M, Matito J, Martin A, Gómez M, Castillo E, Vila M, Santos-Antunes J, Costa A, Lordick F, Farrés J, Palomar-De Lucas B, Cabeza-Segura M, Villagrasa R, Jimenez-Martí E, Miralles-Marco A, Dienstmann R, Derks S, Figueiredo C, Cervantes A, Carneiro F, Fleitas- Kanonnikoff T. Comprehensive histopathological analysis of gastric cancer in European and Latin America populations reveals differences in PDL1, HER2, p53 and MUC6 expression. Gastric Cancer. 2025 Mar;28(2):160-173. doi: 10.1007/s10120-024-01578-3. Epub 2025 Jan 5. PMID: 39755998; PMCID: PMC11842524.
  12. Nozawa K, Sawaki M, Uemura Y, Tsuneizumi M, Takano T, Gondo N, Hara F, Harao M, Toyama T, Taira N, Vivancos A, Perou CM, Sanfeliu E, Brasó-Maristany F, Parker JS, Buckingham W, Paré L, Villacampa G, Marín-Aguilera M, Villagrasa P, Prat A, Iwata H. HER2DX in older patients with HER2-positive early breast cancer: extended follow-up from the RESPECT trial of trastuzumab ± chemotherapy. Nat Commun. 2025 Nov 4;16(1):9585. doi: 10.1038/s41467-025-65599-x. PMID: 41188218; PMCID: PMC12586486.
  13. Lynce F, Martínez-Sáez O, Walbaum B, Brasó-Maristany F, Waks AG, Villagrasa P, Villacampa Javierre G, Sanfeliu E, Galván P, Paré L, Anderson LM, Perou CM, Parker JS, Vivancos A, DiLullo MK, Pernas S, Winer EP, Overmoyer B, Mittendorf EA, Bueno-Muiño C, Martín M, Prat A, Tolaney SM. HER2DX in HER2-positive inflammatory breast cancer: correlative insights and comparative analysis with noninflammatory breast cancers. ESMO Open. 2025 Feb;10(2):104100. doi: 10.1016/j.esmoop.2024.104100. Epub 2025 Jan 17. PMID: 39826476; PMCID: PMC11786065.
  14. Cicala CM, Matito J, Quindos M, Gómez-Peregrina D, Romero-Lozano P, Fernández-Suárez P, Valverde C, González M, Landolfi S, Pérez-Albert P, Gros L, Vivancos A, Serrano C. Targeted Next-Generation Sequencing in Succinate Dehydrogenase-Deficient GI Stromal Tumor Identifies Actionable Alterations in the PI3K/mTOR Pathway. JCO Precis Oncol. 2025 Jan;9:e2400497. doi: 10.1200/PO-24-00497. Epub 2025 Jan 9. PMID: 39787462.
  15. Biagioni C, Fimereli D, Irrthum A, Guerrero-Zotano A, Piccart M, Cameron D, Caballero C, Raimbault A, Martins-Branco D, Romagnoli D, Agostinetto E, Venet D, Llinas-Bertran A, Seoane JA, Zoppoli G, Vivancos A, Vingiani A, Oliveira M, Curigliano G, Crestani T, Sotiriou C, Nili Gal-Yam E, Hilbers FS, Aftimos P, Benelli M. Molecular and clinical analyses of gene fusions identify therapeutic targets in paired primary and metastatic breast cancer from the AURORA program (BIG 14-01). Clin Cancer Res. 2025 Dec 22. doi: 10.1158/1078-0432.CCR-25-2707. Epub ahead of print. PMID: 41427961.
  16. Seguí E, Brasó-Maristany F, Pascual T, Sanfeliu E, Victoria I, Saura C, Hierro C, López-González A, Izarzugaza Y, Ciruelos E, Gavilá J, Racca F, Cejalvo JM, Amillano K, Paz-Ares L, Juan M, Felip E, Garralda E, González B, Arance A, Martín-Liberal J, Conte B, Walbaum B, Indacochea A, Castillo O, Blasco P, Pardo F, Aguirre Á, Sirenko V, González X, Galván P, Vivancos A, Ferrero-Cafiero JM, Mulero-Sánchez A, Salvador F, Villacampa G, Mesía R, Cervantes A, Prat A, Tabernero J. Efficacy of anti-PD1 therapy in PD1-high mRNA tumors across multiple cancer types: results from cohort 1 and cohort 2 of the phase II SOLTI-1904 ACROPOLI trial. ESMO Open. 2025 Oct;10(10):105838. doi: 10.1016/j.esmoop.2025.105838. Epub 2025 Sep 30. PMID: 41033278; PMCID: PMC12514499.
  17. Dienstmann R, Vivancos A, Nuciforo P, Aguilar S, Ruiz-Pace F, Viaplana C, Gonzalez J, Fite B, Pedrola A, Elez E, Saura C, Felip E, Macarulla T, Capdevila J, Fariñas-Madrid L, Carles J, Mateo J, Muñoz-Cosuelo E, Balmaña J, Braña I, Garralda E, Tabernero J. Genomic actionability and matched targeted therapy in a decade-long institutional precision medicine program for solid tumors. ESMO Open. 2025 Nov;10(11):105888. doi: 10.1016/j.esmoop.2025.105888. Epub 2025 Nov PMID: 41202500; PMCID: PMC12639418.

Group Leader Paolo Nuciforo Attending Physicians Roberta Fasani, Siarhei Mauchanski, Artur Mezheyeuski, Sara Simonetti Laboratory Supervisor Jose Antonio Jiménez Research Support Technicians Laura Boleda, Mª Ángeles Diaz, Joel Luque Postdoctoral Fellows Mònica Aguilera, Francisca Gallego, Stefania Napoli, Alba Santiago, Garazi Serna PhD Student Diego Alfonso Arregui Technicians Lidia Alonso, Nuria Aybar, Luis Garcia, Margarita Gonzalez, Xavier Guàrdia, Paula León, Anaïs Mallén, Paola Martinez, Júlia Reig, Gertrudis Sánchez, César Javier Sevillano

Core Transversal Groups and Units

Molecular Oncology Group

Summary

The Molecular Oncology Group at VHIO applies state-of-the-art tissue-based technologies in basic, translational, and clinical research to develop and validate novel tumor biomarkers for precision oncology.

In collaboration with VHIO’s Cancer Genomics Group led by Ana Vivancos, Oncology Data Science - ODysSey Group headed by Rodrigo Dienstmann, and the Research Unit for Molecular Therapy of Cancer (UITM) – CaixaResearch, directed by Elena Garralda, we co-lead VHIO's Molecular Prescreening Program, supported by the FERO Foundation. Each year, we perform molecular profiling for over 1,100 patients eligible for enrolment in early phase clinical trials at UITM-CaixaResearch.

Our group also serves as one of VHIO’s core technology platforms, and our laboratory contributes to VHIO’s research lines and programs. Our work includes biomarker analyses for patient stratification, digital pathology, tissue banking, and the development of primary patient-derived xenograft (PDX) models. In 2024, our contributions were reflected in multiple co-authored publications in high-impact journals.

As an independent group, we investigate the link between the gut microbiome and cancer. These investigations have led to important contributions in this field, such as the demonstration of Fusobacterium nucleatum and its associated microbiota in colorectal cancer (CRC) liver metastasis (Bullman et al, Science 2017) and the prognostic role of Fusobacterium persistence after neoadjuvant chemoradiotherapy (nCRT) in locally advanced rectal cancers (Serna et al, Ann Oncol 2020). Building on these findings, we co-lead WP3 of the OPTIMISTICC Cancer Grand Challenge project funded by Cancer Research UK (CRUK). Supported by the Mutua Madrileña Foundation and Instituto de Salud Carlos III (ISCIII), we also lead the FUSOMAP project to develop microbiota-based diagnostic and prognostic models for early-stage CRC.

As a core facility, we have supported over 400 clinical studies conducted at Vall d’Hebron Hospital, contributing to 70% of all ongoing trials at our Institute. Our involvement includes the coordination of sample collection, storage and shipment, developing and conducting 'real-time' assays to guide patient inclusion in these studies, and performing pharmacodynamic monitoring and dose-finding studies.

In 2024, we performed more than 3,500 molecular assays on samples for trial enrolment and over 20,000 tests to support basic and translation research. We also served as the central laboratory of choice for several international studies and successfully maintained our ISO15189 accreditation, ensuring continued excellence in quality and competence.

Figure: Workflow for the automated generation of tumor and immune segmentation masks from Pan-keratin (PanCK) and CD3 performed on the same slide using NGI (Next-Generation Immunohistochemistry), a sequential IHC technique. After alignment with the H&E obtained from the same slide, the resulting segmentations are used to train an AI model capable of directly predicting segmentation on H&E. Serna G, et al, European Congress on Digital Pathology (ECDP), P15, 2025.

As a core facility:

  • Apply molecular pathology strategies to support early clinical drug development.
  • Define target epidemiology to help develop personalized treatment strategies in oncology.
  • Serve as a central and local academic laboratory in clinical trials and a core technology platform for clinical and experimental pathology at VHIO.

As an independent group:

  • Advance insights into the cancer microbiome by interrogating cancer-associated microbiota to identify diagnostic, prognostic and/or predictive biomarkers in colorectal cancer and other tumor types.
  • Develop novel methodologies to enhance biomarker quantification and reproducibility in cancer, with a focus on breast and colorectal cancers.
  • Investigate the value of immune contexture analysis of the tumor microenvironment as a biomarker of response to immunotherapy in different cancer types.
  • Explore the utility of artificial intelligence (AI) in pathology and precision oncology by developing multimodal approaches using H&E and IHC stained slides for reproducible and weekly supervised biomarker quantification and clinically relevant image patterns recognition.
  • We co-lead VHIO's Molecular Prescreening Program (supported by the FERO Foundation). In 2025, we performed more than 3,500 molecular assays in over 2000 patients who are candidates for enrolment in early phase clinical trials conducted at our Research Unit for Molecular Therapy of Cancer (UITM) - CaixaResearch.
  • We supported over 400 clinical studies conducted at Vall d’Hebron Hospital, contributing to more than 70% of all ongoing trials at our Institute.
  • We performed around 10,000 tests to support basic and translation research programs.
  • We collected and analysed more than 1000 samples from over 500 patients for translational microbiome research projects.
  • We developed and implemented computational pathology approaches on routine H&E and IHC whole-slide images to support quantitative analysis of tumor composition, immune contexture, and host–microbiome interactions.
  • Advance research on cancer microbiome by investigating its potential role as diagnostic, prognostic and/or predictive indicators in colorectal cancer and other tumor types.
  • Apply spatial analyses to precision medicine in oncology.
  • Explore the utility of artificial intelligence (AI) in digital pathology.
  • Garralda E, Abbott C, Calahorro A, Mirallas O, Pugh J, Moreno-Cárdenas AB, Keough K, Galvao V, Alonso G, Olano AM, Vieito Villar M, Oberoi A, Lostes Bardaji J, Hernando-Calvo A, Braña I, Pretelli G, Ortega B, Arenillas C, Czerniak N, Navarro FCP, Li B, Pyke RM, Ravi N, Zatse C, Grussu F, Sanz M, Viaplana C, Raskina K, Jimenez J, Fasani R, Casbas-Hernandez P, Oflazoglu E, Hodgson D, Reis-Filho J, Felip E, Élez E, Muñoz E, Dienstmann R, Tabernero J, Lopez-Perez R, Nuciforo P, Chen RO, Boyle SM, Toledo RA. Broad Utility of Ultrasensitive Analysis of ctDNA Dynamics across Solid Tumors Treated with Immunotherapy. Clin Cancer Res. 2025. doi: 10.1158/1078-0432.CCR-25-2312.
  • Dienstmann R, Vivancos A, Nuciforo P, Aguilar S, Ruiz-Pace F, Viaplana C, Gonzalez J, Fite B, Pedrola A, Elez E, Saura C, Felip E, Macarulla T, Capdevila J, Fariñas-Madrid L, Carles J, Mateo J, Muñoz-Cosuelo E, Balmaña J, Braña I, Garralda E, Tabernero J. Genomic actionability and matched targeted therapy in a decade-long institutional precision medicine program for solid tumors. ESMO Open. 2025 Nov;10(11):105888.
  • Karta J, Meyers M, Rodriguez F, Koncina E, Gilson C, Klein E, Gabola M, Benzarti M, Pérez Escriva P, Molina Tijeras JA, Correia Tavares Bernardino C, Ponath F, Carpentier A, Pujabet MA, Schmoetten M, Tsenkova M, Saoud P, Gaigneaux A, Ternes D, Alonso L, Zügel N, Willemssen E, Koppes P, Léonard D, Casanova LP, Haan S, Mittelbronn M, Meiser J, Pozdeev VI, Vogel J, Nuciforo PG, Wilmes P, Letellier E. Fusobacterium nucleatum interacts with cancer-associated fibroblasts to promote colorectal cancer. EMBO J. 2025 Oct;44(19):5375-5393.
  • Moreno-Cárdenas AB, Ros J, Gil-Vila A, Datta D, Fasani R, Serna G, Jimenez J, Trallero-Araguás E, Viaplana C, Lostes J, Milisenda JC, Grau-Junyent JM, Lopez-Perez R, Pinal-Fernández I, Nuciforo P, Toledo RA, Selva-O'Callaghan A. Frequent genetic alterations in myositis autoantigen genes in cancer-associated dermatomyositis. Ann Rheum Dis. 2025 Nov 24:S0003-4967(25)04457-7.
  • Siarhei Mauchanski was awarded for the best mini-oral communication titled: Concordance analysis of HER2-low status in breast cancer and correlation with protein levels by mass spectrometry, at the 32nd National Congress of the Spanish Society of Pathological Anatomy – International Academy of Pathology (SEAP – IAP), 21-23 May, San Sebastián, Basque Country.
  1. Opportunity: To Investigate the Microbiome’s Impact on Science and Treatment In Colorectal Cancer - OPTIMISTICC, Grand Challenge, Cancer Research UK. 2018-2025.
  2. Development and validation of Fusobacterium and its associated microbiota as risk stratification biomarker for predicting outcome after standard of care treatment in locally advanced rectal cancer. Agència de Gestió d’Ajuts Universitaris i de Recerca (AGAUR). 2024 – 2025.
  3. A Multimodal Approach to study locally ColoRectal Cancer host-ONcomIcrobiome interactions and their prognostic and therapeutic implications (MARCONI PROJECT). FIS - Instituto de Salud Carlos III (ISCIII). 2024-2027.
  4. Microbiota-based relapse risk prediction in locally advanced rectal cancer. Agència de Gestió d’Ajuts Universitaris i de Recerca (AGAUR). 2025 – 2027.
  1. Garralda E, Abbott C, Calahorro A, Mirallas O, Pugh J, Moreno-Cárdenas AB, Keough K, Galvao V, Alonso G, Olano AM, Vieito Villar M, Oberoi A, Lostes Bardaji J, Hernando-Calvo A, Braña I, Pretelli G, Ortega B, Arenillas C, Czerniak N, Navarro FCP, Li B, Pyke RM, Ravi N, Zatse C, Grussu F, Sanz M, Viaplana C, Raskina K, Jimenez J, Fasani R, Casbas-Hernandez P, Oflazoglu E, Hodgson D, Reis-Filho J, Felip E, Élez E, Muñoz E, Dienstmann R, Tabernero J, Lopez-Perez R, Nuciforo P, Chen RO, Boyle SM, Toledo RA. Broad Utility of Ultrasensitive Analysis of ctDNA Dynamics across Solid Tumors Treated with Immunotherapy. Clin Cancer Res. 2026 Jan 16;32(2):333-349. doi: 10.1158/1078-0432.CCR-25-2312. PubMed PMID: 41400436; PubMed Central PMCID: PMC12809116.
  2. Navarro-Garcia D, Grussu F, Zatse C, Klümper N, Macarro C, Hernando-Calvo A, Sanz M, Vieito M, Braña I, Mirallas O, Alonso G, Galvao V, Pretelli G, Lostes J, Oberoi A, Toledo R, Nuciforo P, Garralda E, Perez-Lopez R. Integrating C-reactive protein flare and early MRI dynamics for enhanced prediction of immunotherapy response. J Immunother Cancer. 2025 Dec 21;13(12). doi: 10.1136/jitc-2025-012143. PubMed PMID: 41423273; PubMed Central PMCID: PMC12718596.
  3. Grigoriou A, Macarro C, Palombo M, Navarro-Garcia D, Voronova AK, Bernatowicz K, Barba I, Escriche A, Greco E, Abad M, Simonetti S, Serna G, Mast R, Merino X, Roson N, Escobar M, Vieito M, Nuciforo P, Toledo R, Garralda E, Sala-Llonch R, Fieremans E, Novikov DS, Perez-Lopez R, Grussu F. Histology-informed microstructural diffusion simulations for MRI cancer characterisation-the Histo-μSim framework. Commun Biol. 2025 Nov 26;8(1):1695. doi: 10.1038/s42003-025-09096-3. PubMed PMID: 41298809; PubMed Central PMCID: PMC12657972.
  4. Moreno-Cárdenas AB, Ros J, Gil-Vila A, Datta D, Fasani R, Serna G, Jimenez J, Trallero-Araguás E, Viaplana C, Lostes J, Milisenda JC, Grau-Junyent JM, Lopez-Perez R, Pinal-Fernández I, Nuciforo P, Toledo RA, Selva-O'Callaghan A. Frequent genetic alterations in myositis autoantigen genes in cancer-associated dermatomyositis. Ann Rheum Dis. 2025 Nov 24;. doi: 10.1016/j.ard.2025.10.018. [Epub ahead of print] PubMed PMID: 41290487.
  5. Grussu F, Grigoriou A, Bernatowicz K, Palombo M, Casanova-Salas I, Navarro-Garcia D, Barba I, Simonetti S, Serna G, Macarro C, Voronova AK, Garay V, Corral JF, Vidorreta M, García-Polo García P, Merino X, Mast R, Rosón N, Escobar M, Vieito M, Toledo R, Nuciforo P, Mateo J, Garralda E, Perez-Lopez R. Clinically feasible liver tumour cell size measurement through histology-informed in vivo diffusion MRI. Commun Med (Lond). 2025 Nov 20;5(1):535. doi: 10.1038/s43856-025-01246-2. PubMed PMID: 41266804; PubMed Central PMCID: PMC12749696.
  6. Rondon-Lorefice I, Lopez JI, Ugalde-Olano A, Zufiaurre M, Astobiza I, Martin-Martin N, Bozal-Basterra L, Garcia-Longarte S, Zabala-Letona A, Rey S, Santos-Martin A, Unda M, Loizaga-Iriarte A, Graupera M, Nuciforo P, Carracedo A, Mendizabal I. Transcriptional network analysis of PTEN-protein-deficient prostate tumors reveals robust stromal reprogramming and signs of senescent paracrine communication. Mol Oncol. 2025 Nov 17;. doi: 10.1002/1878-0261.70164. [Epub ahead of print] PubMed PMID: 41247227.
  7. Dienstmann R, Vivancos A, Nuciforo P, Aguilar S, Ruiz-Pace F, Viaplana C, Gonzalez J, Fite B, Pedrola A, Elez E, Saura C, Felip E, Macarulla T, Capdevila J, Fariñas-Madrid L, Carles J, Mateo J, Muñoz-Cosuelo E, Balmaña J, Braña I, Garralda E, Tabernero J. Genomic actionability and matched targeted therapy in a decade-long institutional precision medicine program for solid tumors. ESMO Open. 2025 Nov;10(11):105888. doi: 10.1016/j.esmoop.2025.105888. Epub 2025 Nov 6. PubMed PMID: 41202500; PubMed Central PMCID: PMC12639418.
  8. Catani G, Morchón-Araujo D, Mirallas O, Sánchez-Pérez V, Nuciforo P, Villacampa G, Dienstmann R, Vivancos A, Garralda E, Hernando-Calvo A. Optimizing early-phase immunotherapy trials: the role of biomarker enrichment strategies. Front Immunol. 2025;16:1664443. doi: 10.3389/fimmu.2025.1664443. eCollection 2025. Review. PubMed PMID: 41200168; PubMed Central PMCID: PMC12586187.
  9. Pascual T, Villacampa G, Oliveira M, Escrivá-de-Romaní S, Pernas S, Paré L, Adamo B, Martínez E, Cortés J, Perelló A, Galan M, Melé M, Villanueva L, Gonzalez-Rodriguez M, Tolosa P, González-Farré B, Galván P, Canes J, Nuciforo P, Ferrero-Cafiero JM, González-Farré X, Villagrasa P, Prat A, Ciruelos E. Palbociclib and trastuzumab for HER2-positive metastatic breast cancer: final overall survival results of cohort A and B of SOLTI-1303-PATRICIA trial. ESMO Open. 2025 Sep;10(9):105572. doi: 10.1016/j.esmoop.2025.105572. Epub 2025 Sep 1. PubMed PMID: 40896880; PubMed Central PMCID: PMC12424417.
  10. Karta J, Meyers M, Rodriguez F, Koncina E, Gilson C, Klein E, Gabola M, Benzarti M, Pérez Escriva P, Molina Tijeras JA, Correia Tavares Bernardino C, Ponath F, Carpentier A, Pujabet MA, Schmoetten M, Tsenkova M, Saoud P, Gaigneaux A, Ternes D, Alonso L, Zügel N, Willemssen E, Koppes P, Léonard D, Casanova LP, Haan S, Mittelbronn M, Meiser J, Pozdeev VI, Vogel J, Nuciforo PG, Wilmes P, Letellier E. Fusobacterium nucleatum interacts with cancer-associated fibroblasts to promote colorectal cancer. EMBO J. 2025 Oct;44(19):5375-5393. doi: 10.1038/s44318-025-00542-w. Epub 2025 Aug 22. PubMed PMID: 40846900; PubMed Central PMCID: PMC12488894.
  11. Castet F, Salcedo MT, Nuciforo P, Aguilar S, Vivancos A. Best practices in sample management and molecular profiling of cholangiocarcinoma: a practical guide. Expert Rev Mol Diagn. 2025 Aug;25(8):479-494. doi: 10.1080/14737159.2025.2518145. Epub 2025 Jun 12. Review. PubMed PMID: 40497693.
  12. Pedretti F, Abdalfttah M, Pellegrino B, Mateo F, Martínez-Sanz P, Herencia-Ropero A, Òdena A, Clavell-Revelles P, Casali G, Domènech H, Monserrat L, Papić D, Mas Malavila A, Pascual-Reguant A, Eixarch H, Guzmán M, Rodríguez O, Grueso J, Simonetti S, Fasani R, Nuciforo P, Espejo C, Florian S, Pujana MÁ, Nonell L, Seoane J, Valge-Archer V, O'Connor MJ, Nieto JC, Heyn H, Balmaña J, Llop-Guevara A, Serra V. Harnessing STING Signaling and Natural Killer Cells Overcomes PARP Inhibitor Resistance in Homologous Recombination-Deficient Breast Cancer. Cancer Res. 2025 May 15;85(10):1888-1908. doi: 10.1158/0008-5472.CAN-24-2531. PubMed PMID: 40067927.
  13. Arenillas C, Celada L, Ruiz-Cantador J, Calsina B, Datta D, García-Galea E, Fasani R, Moreno-Cárdenas AB, Alba-Linares JJ, Miranda-Barrio B, Martínez-Montes ÁM, Alvarez-Escola C, Lecumberri B, González García A, K Flores S, Esquivel E, Ding Y, Peitzsch M, Robles-Guirado JÁ, Regojo Zapata RM, Pozo-Kreilinger JJ, Iglesias C, Dwight T, Muir CA, Oleaga A, Garrido-Lestache Rodríguez-Monte ME, Del Cerro MJ, Martínez-Bendayán I, Álvarez-González E, Cubiella T, Lourenço DM Jr, A Pereira MA, Burnichon N, Buffet A, Broberg C, Dickson PV, Fraga MF, Llorente Pendás JL, Rueda Soriano J, Buendía Fuentes F, Toledo SPA, Clifton-Bligh R, Dienstmann R, Villanueva J, Capdevila J, Gimenez-Roqueplo AP, Favier J, Nuciforo P, Young WF Jr, Bechmann N, Opotowsky AR, Vaidya A, Bancos I, Weghorn D, Robledo M, Casteràs A, Dos-Subirà L, Adameyko I, Chiara MD, Dahia PLM, Toledo RA. Convergent Genetic Adaptation in Human Tumors Developed Under Systemic Hypoxia and in Populations Living at High Altitudes. Cancer Discov. 2025 May 2;15(5):1037-1062. doi: 10.1158/2159-8290.CD-24-0943. PubMed PMID: 40199338; PubMed Central PMCID: PMC12046333.
  14. El-Khoueiry A, Saavedra O, Thomas J, Livings C, Garralda E, Hintzen G, Kohlhas L, Vanosmael D, Koch J, Rajkovic E, Ravenstijn P, Nuciforo P, Fehniger TA, Foster M, Berrien-Elliott MM, Wingert S, Stäble S, Morales-Espinosa D, Rivas D, Emig M, Lopez J. First-in-Human Phase I Study of a CD16A Bispecific Innate Cell Engager, AFM24, Targeting EGFR-Expressing Solid Tumors. Clin Cancer Res. 2025 Apr 1;31(7):1257-1267. doi: 10.1158/1078-0432.CCR-24-1991. PubMed PMID: 39846810; PubMed Central PMCID: PMC11964176.
  15. Voronova AK, Grigoriou A, Bernatowicz K, Simonetti S, Serna G, Roson N, Escobar M, Vieito M, Nuciforo P, Toledo R, Garralda E, Fieremans E, Novikov DS, Palombo M, Perez-Lopez R, Grussu F. SpinFlowSim: A blood flow simulation framework for histology-informed diffusion MRI microvasculature mapping in cancer. Med Image Anal. 2025 May;102:103531. doi: 10.1016/j.media.2025.103531. Epub 2025 Mar 7. PubMed PMID: 40073583; PubMed Central PMCID: PMC12034030.
  16. Arce-Gallego S, Cresta Morgado P, Delgado-Serrano L, Simonetti S, Gonzalez M, Romero-Lozano P, Marmolejo D, Morales-Barrera R, Arnau GM, Semidey ME, Aguilar D, Cordoba-Terreros S, Mast R, de Albert M, Planas J, Cuadras M, Maldonado X, Suarez C, Casanova-Salas I, Figols M, Cros S, Mas A, Nonell L, Dienstmann R, Nuciforo P, Vivancos A, Llop-Guevara A, Carles J, Serra V, Mateo J. Homologous recombination repair status in metastatic prostate cancer by next-generation sequencing and functional immunofluorescence. Cell Rep Med. 2025 Feb 18;6(2):101937. doi: 10.1016/j.xcrm.2025.101937. Epub 2025 Feb 5. PubMed PMID: 39914385; PubMed Central PMCID: PMC11866514.
  17. Bernatowicz K, Amat R, Prior O, Frigola J, Ligero M, Grussu F, Zatse C, Serna G, Nuciforo P, Toledo R, Escobar M, Garralda E, Felip E, Perez-Lopez R. Radiomics signature for dynamic monitoring of tumor inflamed microenvironment and immunotherapy response prediction. J Immunother Cancer. 2025 Jan 11;13(1). doi: 10.1136/jitc-2024-009140. PubMed PMID: 39800381; PubMed Central PMCID: PMC11749429.
In 2025, we were active as a central laboratory in the following clinical studies:
  1. A Phase 1b Study to Evaluate the Safety, Pharmacokinetics, and Anti-Tumour Activity of the Myc Inhibitor OMO-103 Administered Intravenously in Patients with Advanced Solid Tumors (OMO-103-02). ClinicalTrials.gov Identifier: NCT06059001.
  2. Predicting olaparib sensitivity in patients with unresectable locally advanced/metastatic HER2-negative breast cancer with BRCA1, BRCA2, PALB2, RAD51C or RAD51D mutations or RAD51-foci low test: RADIOLA TRIAL. ClinicalTrials.gov Identifier: NCT05340413.
  3. Pembrolizumab and Olaparib in Homologous-recombination Deficient (HRD) Advanced Colorectal Cancer (CRC). (PEMBROLA). ClinicalTrials.gov Identifier: NCT05201612
  4. Real World Clinical Practice Study to Assess the Feasibility and Impact of Liquid Biopsy-based Genomic Profiling on Treatment Decision Making for Patients with Metastatic Prostate Cancer in Spain (SOLTI-2102) (HOPE-PROSTATE). ClinicalTrials.gov Identifier: NCT05885009.
  5. Olaparib and durvalumab (MEDI4736) in patients with metastatic pancreatic cancer and DNA Damage Repair genes alterations (TTD-20-04). ClinicalTrials.gov Identifier: NCT05659914.
  6. Spanish Registry of Digestive Tumours RETUD (RETUD) A Descriptive, Multicentre, Observational Epidemiological Study on Digestive Tumours (TTD-20-01). ClinicalTrials.gov Identifier: NCT06711211.
  7. Analyzing and Solving Exceptional Long-term Survivors in Solid Tumors with Poor Prognosis: A 3 Cohorts Case Control Matched Study (ROSALIND). ClinicalTrials.gov Identifier: NCT06160596.
  8. The Basket of Baskets: A Modular, Open-label, Phase II, Multicentre Study To Evaluate Targeted Agents in Molecularly Selected Populations With Advanced Solid Tumours (BOB). ClinicalTrials.gov Identifier: NCT03767075.
  9. Non-Randomized, Open-Label, Prospective Phase II Trial to Better Characterize the Status of HRD Leading to a Benefit From Olaparib in Combination With Bevacizumab in Patients With Advanced FIGO Stage III-IV High Grade Serous or Endometrioid Ovarian, Fallopian Tube, or Peritoneal Cancer After Standard First-Line Treatment (STROBE) ClinicalTrials.gov Identifier: NCT06377267.
  10. Bevacizumab plus encoRAfenib-cetuximab in BRAF-V600E mutated metastatic colorectal cancer, a phase II study with a safety lead-in cohort, the BRAVE trial. ClinicalTrials.gov Identifier: NCT06411600.
  11. Real-world patient-centric study to assess the feasibility of a molecular diagnosis on treatment decision making for patients with metastatic breast cancer in Spain (SOLTI 2401 HOPE-Focus). NCT06991946.
  12. Sotorasib combined with first-line chemotherapy for advanced pancreatic adenocarcinoma with KRAS p.G12C mutation. (PANSOTO) EuCT number: 2024-516233-12-00.
  13. Phase I, first-in human, open-label, dose escalation and cohort expansion study for the evaluation of safety, pharmacokinetics, pharmacodynamics, and antitumour activity of LB-208 (HTR1B antagonist) in adult patients with relapsed or refractory solid tumours and lymphoma. (SERONCO-1) (LB-208-001).
  14. Adjuvant pembrolizumab or surveillance in Early Triple Negative breAst cancer with high stromal tumor-infiltrating lymphocytes (TILs) score (ETNA). EuCT number: 2023-504620-26-00.

Unit Head Francesc Canals Senior Researcher Josep Villanueva Post-Doctoral Fellow Joan Navarro Graduate Students Paula Carrillo, Carla Mayans, José Ángel Robles Technicians Paula Lorda, Luna Martín, Daniela Ruiz

Core Transversal Groups and Units

Proteomics Group

Summary

Our group serves as a Core Technology Platform, providing VHIO investigators with state-of-the-art proteomic methodologies. We also incorporate the latest technological advances to provide the very latest approaches and technologies.

We apply proteomic and phosphoproteomic analyses to characterize patient-derived xenograft (PDX) models of colorectal cancer (CRC), complementing genomic classifications , and exploring proteome-based tumor subtyping strategies. We have also established mass spectometry-based approaches for drug monitoring in biological samples to assess pharmacokinetics and bioavailability in preclinical models, as well as to interrogate protein-protein and protein-drug interactions.

A central research focus is the quantitative proteomic profiling of sub-proteomes linked to cellular communication, including the secretome, exosomes, and cell surface proteome. Our work has evolved from large-scale data generation toward hypothesis-driven studies of tumor cell protein communication. Notably, we demonstrated that an alternative extracellular function of the nuclear protein HMGA1 exerts an extracellular function that promotes invasion and metastasis in triple-negative breast cancer through interaction with RAGE.

In parallel, we contribute to clinical studies by identifying predictive biomarkers of treatment response and resistance mechanisms, particularly in triple-negative breast cancer.

Figure: Schematic overview of the pipeline for extracellular vesicle proteomic analysis. The workflow starts from preclinical models (e.g., mouse xenografts and PDX-derived organoids) and cancer patient samples (plasma) for the isolation of extracellular vesicles (EVs). EVs are enriched using size exclusion chromatography (SEC) and ultracentrifugation (UC), and their cargo is analyzed by mass spec proteomic platforms. The resulting molecular profiles are integrated using computational and network-based approaches to identify EV-associated biomarker candidates. These candidates are then assessed for their ability to stratify patients and predict clinical outcome, supporting personalized treatment decisions.
  • Conduct proteomic screenings aimed at identifying biomarkers for drug discovery and development.
  • Development of mass spectrometry-based assays for the analysis of biomarkers in clinical samples.
  • Identification and characterization of protein factors associated with drug resistance in breast cancer.
  • Development and implementation of proteomic methodologies aimed at advancing insights into cellular communication in cancer biology.
  • We applied proteomic and phosphoproteomic screenings to characterize patient-derived xenograft (PDX) models of colorectal cancer (CRC).
  • Setting up of mass spectrometry-based analytical methods for monitoring specific drugs in plasma and tumor tissue to assess preliminary pharmacokinetics in preclinical mouse models.
  • Characterization of specific protein interactomes.
  • Developed immunoprecipitation-mass spectrometry approaches for proteomic analysis of chromatin-associated protein complexes.
  • Advance proteomic discovery pipelines to identify and functionally validate novel therapeutic targets and secreted biomarkers, with particular focus on metalloprotease-derived proteins in breast cancer and phosphoproteomic vulnerabilities in CRC PDX models.
  • Translate MS-based assays into clinically applicable platforms for monitoring cancer biomarkers in patient samples.
  • Expand next-generation cell surface and extracellular vesicle proteomics to support translational oncology and precision medicine initiatives.
  • Further dissect RAGE-driven signaling in triple-negative breast cancer and advance the preclinical development of novel RAGE antagonists.
  • Continue strengthening the platform’s technological capabilities to support VHIO programs with cutting-edge, quantitative proteomic solutions.
  • Pujols J, Fornt-Suñé M, Gil-García M, Bartolomé-Nafría A, Canals F, Cerofolini L, Teilum K, Banci L, Esperante SA, Ventura S. MIA40 circumvents the folding constraints imposed by TRIAP1 function. J Biol Chem. 2025 Mar;301(3):108268.
  • Area-Navarro M, Pastor-Moreno A, Scholz E, Cerqueira A, Tirado-Herranz A, Marcilla M, Canals F, Juan M, Palacio JR, Alvarez I. Specific Instability of HLA-A*03:01 Expression in HEK-293 Cells. Int J Mol Sci. 2025 Nov 24;26(23):11357.
  • Arenillas C, Celada L, Ruiz-Cantador J, Calsina B, Datta D, García-Galea E, Fasani R, Moreno-Cárdenas AB, Alba-Linares JJ, Miranda-Barrio B, Martínez-Montes ÁM, Alvarez-Escola C, Lecumberri B, González García A, K Flores S, Esquivel E, Ding Y, Peitzsch M, Robles-Guirado JÁ, Regojo Zapata RM, Pozo-Kreilinger JJ, Iglesias C, Dwight T, Muir CA, Oleaga A, Garrido-Lestache Rodríguez-Monte ME, Del Cerro MJ, Martínez-Bendayán I, Álvarez-González E, Cubiella T, Lourenço DM Jr, A Pereira MA, Burnichon N, Buffet A, Broberg C, Dickson PV, Fraga MF, Llorente Pendás JL, Rueda Soriano J, Buendía Fuentes F, Toledo SPA, Clifton-Bligh R, Dienstmann R, Villanueva J, Capdevila J, Gimenez-Roqueplo AP, Favier J, Nuciforo P, Young WF Jr, Bechmann N, Opotowsky AR, Vaidya A, Bancos I, Weghorn D, Robledo M, Casteràs A, Dos-Subirà L, Adameyko I, Chiara MD, Dahia PLM, Toledo RA. Convergent Genetic Adaptation in Human Tumors Developed Under Systemic Hypoxia and in Populations Living at High Altitudes. Cancer Discov. 2025 May 2;15(5):1037-1062.
  • De Bolòs A, Carreras-Caballé M, Sureda-Gómez M, Rodríguez ML, Charalampopoulou S, Albero R, Maiques-Diaz A, Playa-Albinyana H, Clot G, López C, Colomer D, Martin-Subero JI, Campo E, Reverter D, Villanueva J, Amador V. The SOX11:SMARCA4 complex is a driver of oncogenic transcriptional programs in mantle cell lymphoma. Blood Cancer J. 2025 Jul 30;15(1):127.
  1. We are a member of CIBERONC’s Programa de Tumores del Tracto Digestivo, as part of the group (Program ID: CB16/12/00259) led by VHIO’s Director Josep Tabernero (PI: Teresa Macarulla).
  2. Project title: Nuevos conjugados anticuerpo-fármaco biespecíficos basados en her3 para el tratamiento de tumores sólidos agresivos. Funding Agency: RETOS-MINECO. Award period: 2023-2025. PI: Josep Villanueva.
  3. Project title: Targeting and Monitoring Non-genetic Cancer cell Plasticity in Triple-Negative Breast Cancer. Funding Agency: MINECO. Award period: 2024-2026. PI: Josep Villanueva.
  4. Project title: Overcoming resistant tumors using CCR9-focused ADCs. Funding Agency: RETOS-MINECO. Award period: 2024-2026. PI: Josep Villanueva.
  5. Project title: Descubriendo nuevas combinaciones de fármacos para evitar la persistencia del cáncer colorrectal. Funding Agency: Instituto de Salud Carlos III. Award period: 2025-2027. PI: Isabel Puig. Participation as a collaborator.

Co-leadership Ana Vivancos, Head of Cancer Genomics, Elena Garralda, Director of the Research Unit for Molecular Therapy of Cancer (UITM) – CaixaResearch and Head of Early Clinical Drug Development, Paolo Nuciforo, Director of Core Transversal Groups and Units and Head of Molecular Oncology, Rodrigo Dienstmann, Head of Oncology Data Science (ODysSey) Program Coordination Susana Aguilar, Head of the VHIOTECA Unit Research Support Technicians Jenifer González, Laura González

Core Transversal Groups and Units

Molecular Prescreening Program

Summary

VHIO's Molecular Prescreening Program, supported by FERO’s Institutional Advanced Diagnostics Program – DIAMAV, was established in 2010 as a strategic program for the detection of validated and emerging cancer biomarkers to help guide clinicians in selecting both standard-of-care and investigational anti-cancer treatments, and spur clinical-molecular correlative research at VHIO.

This program is co-led by VHIO’s Ana Vivancos, Paolo Nuciforo, Elena Garralda, and Rodrigo Dienstmann, Heads of our Cancer Genomics, Molecular Oncology, Early Clinical Drug Development, and Oncology Data Science – OdysSey Groups, respectively. Activities are coordinated by Susana Aguilar, Head of the VHIOTECA Unit, in collaboration with Research Support Technicians, Jenifer González and Laura González.

The main objective of molecular prescreening at VHIO is to facilitate the clinical implementation of emerging cancer biomarkers that help to optimize the selection of therapies for patients being considered for enrolment in clinical trials. Diagnostic tests are developed and validated in-house for the cost-effective and streamlined identification of tumor molecular alterations of major interest in drug development.

Tumor profiling includes a variety of genomic techniques such as next-generation sequencing panels (NGS) in tissue or liquid biopsy samples for the detection of mutations, copy number variations, gene fusions, and RNA expression signatures, as well as histopathological techniques such as immunohistochemistry (IHC) and in situ hybridization (ISH) for protein and gene expression profiling.

In 2025, we performed molecular profiling of 2,529 patients (Figure 1A), a volume similar to that of the previous two years and more than double the annual numbers recorded between 2014 and 2022. Since 2022, the VHIO360 liquid biopsy test has been implemented, which was initially used for the detection of genomic alterations in small subsets of patients. Over the past three years, this test has been applied to an increasing number of patients who may have acquired resistance to targeted therapies or patients lacking metastatic tissue biopsies for testing, opening opportunities for expanding personalized treatments and clinical trials. In 2025, we have been able to offer this test to 1,512 patients on a routine basis, representing 55% of all samples profiled (Figure 1A).

VHIO’s Cancer Genomics Group has also implemented a more precise technique to detect gene fusions, replacing the small Nanostring panel with an RNA-based enrichment panel for the detection of gene fusions and expression patterns in tumors (Epsilon Panel). This test was introduced at the end of 2023 and has since become the reference test based on RNA sequencing. Importantly, in 2025, an ENAC ISO1589 accreditation was granted for this test.

In 2025, we implemented a new data management and notification model for Prescreening test results. To integrate test orders from the pathology and genomics laboratories with result reporting and clinician alerts, we leverage multiple data capture and query platforms (VHIOPAT, COGNOS, and REDCap) that feed into a unified SQL database (Figure 1B). This integration and automation of processes was possible thanks to the work of the VHIO’s Data Science (ODysSey) Group and the Data Engineering for Research Unit, led by Anna Pedrola.

We also prioritize educating clinicians on the interpretation of next-generation sequencing tests and emerging biomarkers. During Molecular Tumor Board and Genetic Tumor Board meetings, we facilitate data exchange among a broad range of experts. To help guide treatment decision-making and prevention strategies, we collectively review patients’ medical histories and tumor molecular profiles.

Figure: Molecular Prescreening Program at VHIO. A) Distribution of patients and tissue profiled in 2025. B) Interrelationship between Genomic and Molecular Pathology laboratories with clinical oncologists, and the functionality of the Prescreening Program.
  • Clinical implementation of advanced molecular diagnostics to optimize the selection of therapies for patients being considered for enrolment in clinical trials.
  • Continued medical education with standardized reports of genomic alterations and weekly Molecular Tumor Boards.
  • Continued revision and update of molecular diagnostic tests to cover emerging cancer biomarkers for precision oncology.
  • VHIO is an active member of the American Association for Cancer Research’s (AACR) Genomics Evidence Neoplasia Information Exchange (GENIE) project. This multi-phase, multi-year, international study catalyzes precision oncology through the development of a regulatory-grade registry, which aggregates and links clinical-grade cancer genomic data with clinical outcomes from tens of thousands of cancer patients treated at the participating institutions.
  • We have sustained the molecular profiling by liquid biopsy to help patients who may have acquired resistance to targeted therapies, or patients without metastatic tumor tissue biopsies for testing.
  • We have consolidated a monthly Molecular Tumor Board. We discuss the results of somatic next-generation sequencing (NGS) panels and other biomarkers within the clinicopathological context of patients and provide updates on the latest results reported in the literature on the interpretation of alterations and their actionability for targeted therapies.
  • Continued implementation and utilization of novel biomarkers based on gene expression panels and digital pathology, among others.
  • Delivery of new integrative, enhanced molecular prescreening reports to help guide treatment decision-making and optimize the selection of therapies for patients being considered for enrolment in clinical trials.
  • Closely monitor the impact of the recent implementation of the liquid biopsy and the ongoing development of genomic and transcriptomic signatures.
  • Dienstmann R, Vivancos A, Nuciforo P, Aguilar S, Ruiz-Pace F, Viaplana C, Gonzalez J, Fite B, Pedrola A, Elez E, Saura C, Felip E, Macarulla T, Capdevila J, Fariñas-Madrid L, Carles J, Mateo J, Muñoz-Cosuelo E, Balmaña J, Braña I, Garralda E, Tabernero J. Genomic actionability and matched targeted therapy in a decade-long institutional precision medicine program for solid tumors. ESMO Open. 2025 Nov;10(11):105888.
  • Arce-Gallego S, Cresta Morgado P, Delgado-Serrano L, Simonetti S, Gonzalez M, Romero-Lozano P, Marmolejo D, Morales-Barrera R, Arnau GM, Semidey ME, Aguilar D, Cordoba-Terreros S, Mast R, de Albert M, Planas J, Cuadras M, Maldonado X, Suarez C, Casanova-Salas I, Figols M, Cros S, Mas A, Nonell L, Dienstmann R, Nuciforo P, Vivancos A, Llop-Guevara A, Carles J, Serra V, Mateo J. Homologous recombination repair status in metastatic prostate cancer by next-generation sequencing and functional immunofluorescence. Cell Rep Med. 2025 Feb 18;6(2):101937.
  • Catani G, Morchón-Araujo D, Mirallas O, Sánchez-Pérez V, Nuciforo P, Villacampa G, Dienstmann R, Vivancos A, Garralda E, Hernando-Calvo A. Optimizing early-phase immunotherapy trials: the role of biomarker enrichment strategies. Front Immunol. 2025 Oct 22;16:1664443.

Unit Head Susana Aguilar Clinical Research Oncology Nurses Ana Baizan, Ana Maria Castiñeira, Ariadna García, Anna Martínez, Helena Palma, Marta Sanz, Alex Sierra, Mireia Soleda, Anna Suñol, Sandra Vidal Research Support Technicians Marta Jiménez, Claudia Martínez, Inés Suárez

Core Transversal Groups and Units

VHIOTECA

Summary

The VHIOTECA Unit supports the collection, registration, and preservation of non-tumoral biological samples, such as plasma, feces, and saliva, etc. from cancer patients , enabling their use in translational and clinical research projects.

The use of liquid biopsy testing in cancer patients for the identification of new biomarkers of response and resistance to therapy, coupled with its incorporation in clinical research projects requiring plasma, has led to a significant increase in the extraction of blood samples from cancer patients.

The growing integration of liquid biopsy into oncology research, particularly for identifying biomarkers of response and resistance, has significantly increased the demand for high-quality blood sample collection. To meet this need, the Unit has strengthened operational circuits, optimized logistics, and standardized processes to ensure reliability, traceability, and optimal sample handling conditions (Figure: A). We also actively support investigators in designing and implementing projects that require coordinated sample acquisition, working closely with clinical teams to obtain blood samples at the time of surgical procedures and other clinical procedures.

In 2025 alone, we have collected, registered, and preserved over 7,500 blood samples from 3,000 patients across multiple cancer types, including upper gastrointestinal, genitourinary, colorectal, breast, and lung cancers. Since its creation, VHIOTECA has markedly expanded its activity, reflecting the increasing centrality of liquid biopsy and translational biospecimen research at VHIO (Figure: B).

Figure: VHIOTECA circuit and activity for blood samples. (A) VHIOTECA workflow: The workflow model for blood collection, storage, distribution and quality control evaluation. (B) Blood samples collected since VHIOTECA was established in 2021.
  • Beyond supporting established research circuits, the Unit also develops tailored collection pathways for tumor types with fewer patients or more limited resources, ensuring equitable access to high-quality biospecimens across VHIO programs, including coordinated blood and tumor sampling.
  • An expanding area of activity is microbiome research in oncology. Studies in colorectal cancer and other tumor types increasingly require standardized stool collection, molecular profiling, and associated epidemiological data. The clinical research nurses from VHIOTECA oversee patient education, sample collection logistics, and coordination with laboratory teams to ensure adherence, quality control, and proper storage.
  • Our team comprises clinical and translational oncology research nurses and dedicated technical staff responsible for sample processing, traceability, distribution management, and database maintenance, providing an integrated operational backbone for biospecimen-based research at VHIO.
  • Further expansion of standardized blood collection across clinical programs, adapting procedures to the specific needs of each team while maintaining quality and traceability.
  • Consolidation of secure, end-to-end sample registration and tracking using NorayBanks software ensuring robust data integrity and regulatory compliance.Successful implementation of biospecimen collection workflows within additional clinical teams, broadening institutional research capacity.
  • Continue expanding structured biospecimen collection pathways to support emerging clinical and preclinical research programs.
  • Develop and implement a dedicated digital platform to enhance database management, real-time tracking, and advanced data extraction capabilities.
  • Broaden support to additional clinical teams and tumor programs, reinforcing VHIOTECA as a central infrastructure for translational oncology at VHIO.
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