Johan Staaf

Senior Lecturer, Associate Professor, Associate Professor, PhD, MSc, MSc

Research areas and keywords

UKÄ subject classification

  • Cancer and Oncology
  • Bioinformatics (Computational Biology)

Keywords

  • Lung cancer, biomarkers, genomic characterization, NGS, Bioinformatics, prognostic factors, predictive factors

Research

Lung cancer, the leading cause of cancer death, is divided into several histological subtypes with large differences in molecular alterations, clinical presentation, and patient outcome. By a combined clinical and molecular approach the current project focuses on improving the molecular understanding of lung cancer and translate research findings into a clinical diagnostic setting.

By characterization of the genomic, transcriptional, and DNA methylation landscape in lung cancer subgroups defined by histology and other clinicopathological factors in both own and public cohorts we search for new molecular subgroups of potential clinical relevance, additional targets for synergistic treatment, and a deepened understanding of the molecular pathogenesis.

To identify operable lung cancer patients with risk for metastatic relapse we search for new prognostic biomarkers based on analysis of genome-wide gene expression data and conventional protein marker validation based on analysis of primary tumor tissue. By analysis of patient specific alterations in circulating tumor DNA in blood samples we aim to establish blood-based assays for early detection of lung cancer, treatment monitoring, and early detection of relapse in the primary and advanced setting.

Research

Breast cancer is the most common malignancy in women and a heterogeneous disease at the molecular level. This heterogeneity translates into differences in clinical manifestation, patient therapies, and ultimately patient outcome. TNBC is a subgroup of breast cancer, representing ~10% of all cases (9% in Sweden 2015). To date, this patient subgroup has often had a poorer clinical outcome, early relapses, and without obvious available targeted therapies compared to other breast subgroups. Consequently, in TNBC there is a clear need of identifying new targets for selective inhibition to improve patient outcome.

The main aims of this project is to:

1) Characterize the molecular landscape in TNBC on the DNA, RNA, epigenetic and protein level, through broad high-dimensional analysis techniques and advanced bioinformatics.

2) Identify novel markers of DNA repair deficiency and neoantigens peptides in triple negative breast cancer  that may be relevant for future diagnostics and interpretation of response to current systemic therapies and emerging immune therapies.

3) Characterize the immunogenic landscape of TNBC through molecular data and in situ analyses.

4) Redefine the molecular taxonomy of TNBC through data integration of multiple -omics layers using advanced bioinformatics and machine-learning.

 

Based  on experiences and knowledge gained in TNBC we  are now expanding analyses of DNA repair deficiency to ER-positive and HER2-neegative disease,  representing   the largest subgroup of breast cancer. Here,  we  will use similar  techniques and multi-omics approaches.

Highlighted research outputs

Johan Staaf, Dominik Glodzik, Ana Bosch, Johan Vallon-Christersson, Christel Reuterswärd, Jari Häkkinen, Andrea Degasperi, Tauanne Dias Amarante, Lao H Saal, Cecilia Hegardt, Hilary Stobart, Anna Ehinger, Christer Larsson, Lisa Rydén, Niklas Loman, Martin Malmberg, Anders Kvist, Hans Ehrencrona, Helen R Davies, Åke Borg & 1 others, Serena Nik-Zainal, 2019, In: Nature Medicine. 25, p. 1526–1533

Research output: Contribution to journalArticle

Serena Nik-Zainal, Helen Davies, Johan Staaf, Manasa Ramakrishna, Dominik Glodzik, Xueqing Zou, Inigo Martincorena, Ludmil B Alexandrov, Sancha Martin, David C Wedge, Peter Van Loo, Young Seok Ju, Marcel Smid, Arie B Brinkman, Sandro Morganella, Miriam R Aure, Ole Christian Lingjærde, Anita Langerød, Markus Ringnér, Sung-Min Ahn & 68 others, Sandrine Boyault, Jane E Brock, Annegien Broeks, Adam Butler, Christine Desmedt, Luc Dirix, Serge Dronov, Aquila Fatima, John A Foekens, Moritz Gerstung, Gerrit K J Hooijer, Se Jin Jang, David R Jones, Hyung-Yong Kim, Tari A King, Savitri Krishnamurthy, Hee Jin Lee, Jeong-Yeon Lee, Yilong Li, Stuart McLaren, Andrew Menzies, Ville Mustonen, Sarah O'Meara, Iris Pauporté, Xavier Pivot, Colin A Purdie, Keiran Raine, Kamna Ramakrishnan, F Germán Rodríguez-González, Gilles Romieu, Anieta M Sieuwerts, Peter T Simpson, Rebecca Shepherd, Lucy Stebbings, Olafur A Stefansson, Jon Teague, Stefania Tommasi, Isabelle Treilleux, Gert G Van den Eynden, Peter Vermeulen, Anne Vincent-Salomon, Lucy Yates, Carlos Caldas, Laura van't Veer, Andrew Tutt, Stian Knappskog, Benita Kiat Tee Tan, Jos Jonkers, Åke Borg, Naoto T Ueno, Christos Sotiriou, Alain Viari, P Andrew Futreal, Peter J Campbell, Paul N Span, Steven Van Laere, Sunil R Lakhani, Jorunn E Eyfjord, Alastair M Thompson, Ewan Birney, Hendrik G Stunnenberg, Marc J van de Vijver, John W M Martens, Anne-Lise Børresen-Dale, Andrea L Richardson, Gu Kong, Gilles Thomas & Michael R Stratton, 2016 Jun 2, In: Nature. 534, 7605, p. 47-54 8 p.

Research output: Contribution to journalArticle

Anna Karlsson, Hans Brunnström, Patrick Micke, Srinivas Veerla, Johanna M Mattsson, Linnea La Fleur, Johan Botling, Mats Jönsson, Christel Reuterswärd, Maria Planck & Johan Staaf, 2017, In: Journal of Thoracic Oncology. 12, 8, p. 1257-1267

Research output: Contribution to journalArticle

Anna Karlsson, Helena Cirenajwis, Kajsa Ericson-Lindquist, Hans Brunnström, Christel Reuterswärd, Mats Jönsson, Cristian Ortiz-Villalón, Aziz Hussein, Bengt Bergman, Anders Vikström, Nastaran Monsef, Eva Branden, Hirsh Koyi, Luigi de Petris, Patrick Micke, Annika Patthey, Annelie F. Behndig, Mikael Johansson, Maria Planck & Johan Staaf, 2019 Mar 26, In: Scientific Reports. 9, 1, 5207.

Research output: Contribution to journalArticle

Arie B. Brinkman, Serena Nik-Zainal, Femke Simmer, F. Germán Rodríguez-González, Marcel Smid, Ludmil B. Alexandrov, Adam Butler, Sancha Martin, Helen Davies, Dominik Glodzik, Xueqing Zou, Manasa Ramakrishna, Johan Staaf, Markus Ringnér, Anieta Sieuwerts, Anthony Ferrari, Sandro Morganella, Thomas Fleischer, Vessela Kristensen, Marta Gut & 9 others, Marc J. van de Vijver, Anne Lise Børresen-Dale, Andrea L. Richardson, Gilles Thomas, Ivo G. Gut, John W.M. Martens, John A. Foekens, Michael R. Stratton & Hendrik G. Stunnenberg, 2019 Apr 15, In: Nature Communications. 10, 1, 1749.

Research output: Contribution to journalArticle

Anna K Karlsson, Markus Ringnér, Martin Lauss, Johan Botling, Patrick Micke, Maria Planck & Johan Staaf, 2014, In: Clinical Cancer Research. 20, 18, p. 4912-4924

Research output: Contribution to journalArticle

Helen R. Davies, Dominik Glodzik, Sandro Morganella, Lucy R. Yates, Johan Staaf, Xueqing Zou, Manasa Ramakrishna, Sancha Martin, Sandrine Boyault, Anieta M. Sieuwerts, Peter T Simpson, Tari A King, Keiran Raine, Jorunn E. Eyfjord, Gu Kong, Åke Borg, Ewan Birney, Hendrik G. Stunnenberg, Marc J van de Vijver, Anne-Lise Børresen-Dale & 13 others, John W. M. Martens, Paul N. Span, Sunil R. Lakhani, Anne Vincent-Salomon, Christos Sotiriou, Andrew Tutt, Alastair M Thompson, Steven Van Laere, Andrea L. Richardson, Alain Viari, Peter J. Campbell, Michael R. Stratton & Serena Nik-Zainal, 2017 Apr, In: Nature Medicine. 23, 4, p. 517-525 9 p.

Research output: Contribution to journalArticle

Dominik Glodzik, Sandro Morganella, Helen R. Davies, Peter T Simpson, Yilong Li, Xueqing Zou, Javier Diez-Perez, Johan Staaf, Ludmil B. Alexandrov, Marcel Smid, Arie B Brinkman, Inga Hansine Rye, Hege Russnes, Keiran Raine, Colin A Purdie, Sunil R. Lakhani, Alastair M Thompson, Ewan Birney, Hendrik G. Stunnenberg, Marc J van de Vijver & 10 others, John W M Martens, Anne-Lise Børresen-Dale, Andrea L. Richardson, Gu Kong, Alain Viari, Douglas Easton, Gerard Evan, Peter J. Campbell, Michael R. Stratton & Serena Nik-Zainal, 2017 Mar 1, In: Nature Genetics. 49, 3, p. 341-348 8 p.

Research output: Contribution to journalArticle

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