Headed by José A. Seoane, VHIO’s Cancer Computational Biology Group leverages epi(genetic) cancer datasets to identify the molecular mechanisms implicated in cancer initiation, progression, drug resistance and metastasis toward improving outcomes for patients.
We aim to advance insights into the role of chromatin regulatory elements in treatment response and metastasis, develop novel epigenetic synthetic lethality-based therapeutic options, improve patient stratification guided by multi-omics analysis, and discover novel epigenetic biomarkers of treatment response.
We have previously shown how the genetic modifiers of chromatin structure are associated with chemotherapy resistance in breast cancer (Seoane et al. 2019). Our group focuses on how these epigenetic alterations affect drug resistance and how epigenetic therapies can be used to target tumor suppressor genes.
We are also exploring how the machine learning-based horizontal and vertical integration of multi-omics datasets can facilitate the discovery of new cancer subgroups and biomarkers, as well as help to better predict treatment outcomes and drug response.
Our group has participated/participates in multiple international consortia including The Cancer Genome Atlas, the Human Tumor Atlas Network, Cancer Target Discovery and Development (CTD 2) Network, and, most recently, AURORA (metastatic breast cancer multi-omics cohort).
- Understand the role of chromatin regulatory elements in treatment response and metastasis.
- Discover new epigenetic biomarkers of drug response.
- Potentiate therapeutic options by combining epigenetic therapies with other agents.
- Discover potential environmental causes of early onset cancer.
- Develop clinically actionable machine learning algorithms for prediction and patient stratification.
Group Leader
José Antonio Seoane
Post-Doctoral Fellow
Silvana Maas
Lea Lemler
hubert Bretonniere
Graduate students
M José Fariña
María Butjosa
Enric Álvarez,
Juan Rafael Valera
Arnau Llinàs
Laia Ollé
More relevant publications 2024
- Llinas-Bertran A, Bellet-Ezquerra M, Seoane JA. Epigenetic Control of Cancer Cell Dormancy and Awakening in Endocrine Therapy Resistance. Cancer Discov. 2024 May 1;14(5):704-706.
- Miera-Maluenda M, Pérez-Torres M, Mañas A, Rubio-San-Simón A, Butjosa-Espín M, Ruiz-Duran P, Seoane JA, Moreno L, Segura MF. Advances in the approaches used to repurpose drugs for neuroblastoma. Expert Opin Drug Discov. 2024 Nov;19(11):1309-1319.
All publications
- Salahudeen AA, Seoane JA, Yuki K, Mah AT, Smith AR, Kolahi K, De la O SM, Hart DJ, Ding J, Ma Z, Barkal SA, Shukla ND, Zhang CH, Cantrell MA, Batish A, Usui T, Root DE, Hahn WC, Curtis C, Kuo CJ. Functional screening of amplification outlier oncogenes in organoid models of early tumorigenesis. Cell Rep. 2023 Nov 28;42(11):113355.
- Kaiser AM, Gatto A, Hanson KJ, Zhao RL, Raj N, Ozawa MG, Seoane JA, Bieging-Rolett KT, Wang M, Li I, Trope WL, Liou DZ, Shrager JB, Plevritis SK, Newman AM, Van Rechem C, Attardi LD. p53 governs an AT1 differentiation programme in lung cancer suppression. Nature. 2023 Jul;619(7971):851-859.
- Strand SH, Rivero-Gutiérrez B, Houlahan KE, Seoane JA, King LM, Risom T, Simpson LA, Vennam S, Khan A, Cisneros L, Hardman T, Harmon B, Couch F, Gallagher K, Kilgore M, Wei S, DeMichele A, King T, McAuliffe PF, Nangia J, Lee J, Tseng J, Storniolo AM, Thompson AM, Gupta GP, Burns R, Veis DJ, DeSchryver K, Zhu C, Matusiak M, Wang J, Zhu SX, Tappenden J, Ding DY, Zhang D, Luo J, Jiang S, Varma S, Anderson L, Straub C, Srivastava S, Curtis C, Tibshirani R, Angelo RM, Hall A, Owzar K, Polyak K, Maley C, Marks JR, Colditz GA, Hwang ES, West RB. Molecular classification and biomarkers of clinical outcome in breast ductal carcinoma in situ: Analysis of TBCRC 038 and RAHBT cohorts. Cancer Cell . 2022 Dec 12;40(12):1521-1536.e7.
- Nobre AR, Dalla E, Yang J, Huang X, Wullkopf L, Risson E, Razghandi P, Anton ML, Zheng W, Seoane JA, Curtis C, Kenigsberg E, Wang J, Aguirre-Ghiso JA. ZFP281 drives a mesenchymal-like dormancy program in early disseminated breast cancer cells that prevents metastatic outgrowth in the lung. Nat Cancer . 2022 Oct;3(10):1165-1180.
- Raj N, Wang M, Seoane JA, Zhao RL, Kaiser AM, Moonie NA, Demeter J, Boutelle AM, Kerr CH, Mulligan AS, Moffatt C, Zeng SX, Lu H, Barna M, Curtis C, Chang HY, Jackson PK, Attardi LD. The Mettl3 epitranscriptomic writer amplifies p53 stress responses. Mol Cell . 2022 Jul 7;82(13):2370-2384.e10.
- Liñares-Blanco J, Fernandez-Lozano C, Seoane JA, López-Campos G. Machine Learning Based Microbiome Signature to Predict Inflammatory Bowel Disease Subtypes. Front Microbiol . 2022 May 17;13:872671..
- DCIS genomic signatures define biology and correlate with clinical outcome: a Human Tumor Atlas Network (HTAN) analysis of TBCRC 038 and RAHBT cohorts
Siri H Strand, Belén Rivero-Gutiérrez, Kathleen E Houlahan, Jose A Seoane, Lorraine King, …,Christina Curtis, Rob Tibshirani, Robert Michael Angelo, Allison Hall, Kouros Owzar, Kornelia Polyak, Carlo Maley, Jeffrey R Marks, Graham A Colditz, E Shelley Hwang, Robert B West
bioRxiv, Jun 2021
10.1101/2021.06.16.448585 - CRISPR screens in cancer spheroids identify 3D growth-specific vulnerabilities
Kyuho Han, Sarah E Pierce, Amy Li, Kaitlyn Spees, Grace R Anderson, Jose A Seoane, Yuan-Hung Lo, Michael Dubreuil, Micah Olivas, Roarke A Kamber, Michael Wainberg, Kaja Kostyrko, Marcus R Kelly, Maryam Yousefi, Scott W Simpkins, David Yao, Keonil Lee, Calvin J Kuo, Peter K Jackson, Alejandro Sweet-Cordero, Anshul Kundaje, Andrew J Gentles, Christina Curtis, Monte M Winslow, Michael C Bassik
Nature, 580(7801):136-141, April. 2020 - Convergent mutations in tissue-specific regulatory regions reveal novel cancer drivers
Nasa Sinnott-Armstrong, Jose A Seoane, Jonathan K Pritchard, Christina Curtis, Michael P Snyder
BioRxiv, Nov. 2020 - Chromatin regulators mediate anthracycline sensitivity in breast cancer
Jose A Seoane, Jacob G Kirkland, Jennifer L Caswell-Jin, Gerald R Crabtree, Christina Curtis
Nature medicine, 25(11):1721-1727, Nov. 2019 - Dynamics of breast-cancer relapse reveal late-recurring ER-positive genomic subgroups
Oscar M Rueda, Stephen-John Sammut, Jose A Seoane, Suet-Feung Chin, Jennifer L Caswell-Jin, Maurizio Callari, Rajbir Batra, Bernard Pereira, Alejandra Bruna, H Raza Ali, Elena Provenzano, Bin Liu, Michelle Parisien, Cheryl Gillett, Steven McKinney, Andrew R Green, Leigh Murphy, Arnie Purushotham, Ian O Ellis, Paul D Pharoah, Cristina Rueda, Samuel Aparicio, Carlos Caldas, Christina Curtis
Nature, 567(7748):399-404, Mar. 2019 - Assessment of ERBB2/HER2 status in HER2-equivocal breast cancers by FISH and 2013/2014 ASCO-CAP guidelines
Michael F Press, Jose A Seoane, Christina Curtis, Emmanuel Quinaux, Roberta Guzman, Guido Sauter, Wolfgang Eiermann, John R Mackey, Nicholas Robert, Tadeusz Pienkowski, John Crown, Miguel Martin, Vicente Valero, Valerie Bee, Yanling Ma, Ivonne Villalobos, Dennis J Slamon
JAMA oncology, 5(3):366-375, Mar. 2019 - The chromatin accessibility landscape of primary human cancers
M Ryan Corces, Jeffrey M Granja, Shadi Shams, Bryan H Louie, Jose A Seoane, Wanding Zhou, Tiago C Silva, Clarice Groeneveld, Christopher K Wong, Seung Woo Cho, Ansuman T Satpathy, Maxwell R Mumbach, Katherine A Hoadley, A Gordon Robertson, Nathan C Sheffield, Ina Felau, Mauro AA Castro, Benjamin P Berman, Louis M Staudt, Jean C Zenklusen, Peter W Laird, Christina Curtis, William J Greenleaf, Howard Y Chang
Science, 362(6413), Oct. 2018 - Canonical correlation analysis for gene-based pleiotropy discovery
Jose A Seoane, Colin Campbell, Ian NM Day, Juan P Casas, Tom R Gaunt
PLoS Computational Biology, 10(10), Oct. 2014 - A pathway-based data integration framework for prediction of disease progression
Jose A Seoane, Ian NM Day, Tom R Gaunt, Colin Campbell
Bioinformatics, 30(6):838-845, Mar. 2014
- Characterizing Heterogeneous Regulatory prOgraMs in ER+ breast cancer (CHROME). Funded by: Agencia Estatal de Investigación – Ministerio de Ciencia e Innovación. Reference: PID2024-162678OB-I00. Execution period: 01/09/2025 – 31/08/2028. PI: José Antonio Seoane
- Targeting synthetic lethality in Chromatin Regulatory Genes for gastrointestinal cancer treatment. Ref PID2020-115097RA-I00.
Agencia Estatal de Investigación. 9/2021-8/2025. PI: Jose A. Seoane
- Ramon y Cajal Grant.
Agencia Estatal de Investigación. 2021-2025 - Epigenetic differences associated with hormone treatment resistant breast cancer heterogeneity Fundación FERO. 2022-2024
- Identificación in Silico de Respuesta a fármacos especifica de metastasis
Entidad Financiadora: MCIN/AEI/10.13039/501100011033Ref: CNS2022-135424Periodo de Ejecución: 01/09/2023 – 31/12/2026. PI: Jose Antonio Seoane
Grant funded by the European Union NextGenerationEU/Plan de Recuperación, Transformación y Resilencia (PRTR) - TACTIC: Explorando soluciones a los retos de salud mediante ciencia disruptiva, terapias avanzadas y medicina de sistemas. Programa FORTALECE ISCIII REF: FORT23/00034. 2024-2027
- José A. Seoane was awarded with a Consolidación Investigadora grant from the State Investigation Agency (Agencia Estatal de Investigación – AEI).
- Our group is a member of the Vall d’Hebron TACTICS project. This project was awarded with a FORTALECE grant from the Carlos III Health Institute (ISCIII). In total, 2.4 million euros will be allocated over four years.
- José Liñares read his PhD dissertation and graduated with distinction. He is currently a postdoc in Julio Saez-Rodriguez’s lab at the Institute for Computational Biomedicine in Heidelberg, Germany.
- In collaboration with Laura Attardi’s group at the Stanford University School of Medicine, USA, we identified that p53 is a key regulator in AT1 differentiator in lung adenocarcinoma.
This group is supported by CaixaResearch
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