Our Research

Our projects span the translational spectrum: from patient care to molecular discovery and computational innovation, all centered around improving outcomes for individuals with breast cancer. By combining clinical insights with data-driven methodologies, we explore how tumors evolve, resist treatment, and respond to new therapeutic strategies.

Each project is shaped by collaboration across disciplines within the lab and with external partners in academia, healthcare, and industry. Together, we aim to translate biological understanding into real-world clinical benefit. To learn more about our ongoing projects or to explore collaborative opportunities, please get in touch with us. We welcome new ideas, partnerships, and perspectives that can drive innovation in breast cancer research.

Research themes

Clinical Trials

Clinical studies are essential for improving breast cancer care by translating discoveries into evidence-based treatments. In this section, we present our portfolio of investigator-led and collaborative studies that evaluate new therapies, optimize existing regimens, and refine treatment intensity to maximize benefit while minimizing toxicity. Across these trials, we integrate robust clinical endpoints with translational analyses, linking patient outcomes to tumor biology, biomarkers, and treatment response to accelerate precision medicine for people with breast cancer.

Contact person: Alexios Matikas (alexios.matikas@ki.se)

Epidemiology

Clinical trials show how breast cancer treatments work in controlled settings. They usually include younger, healthier individuals and do not capture the diversity of patients seeking care in breast cancer clinics. Our research looks at how breast cancer develops and how treatments perform in everyday situations. Through epidemiological studies we can study a broader and more representative population than clinical trials - better reflecting the diverseness of breast cancer patients, including older patients and those with other health conditions. Using nationwide registers that link information on patients, tumors characteristics, treatments, and long-term follow-up events, we can investigate biomarker dynamics during treatments, treatment adherence and usage, and identify factors that impact on or lead to better outcomes in a variety of scenarios. Real-world data (RWD) and evidence (RWE) support improvements in clinical care, guide future research, and help in the design of new clinical trials.

Contact person: Louise Eriksson (louise.eriksson@ki.se)

Associated members: Louise Eriksson, Xingrong Liu, Andri Papankonstantinou, Alexios Matikas

  1. Prevalence and prognosis of patients with breast cancer eligible for adjuvant abemaciclib or ribociclib: a nationwide population-based study.
    X. Liu, B. Binicy, B. Acs, L. Eriksson Bergman, S. Loibl, M. Gnant, M. Untch, A. Valachis, J. Bergh, J. Hartman, T. Foukakis, and A. Matikas.
    Lancet Regional Health Europe, vol. 59, Dec. 2025

  2. Prognostic significance of tumour Ki-67 dynamics during neoadjuvant treatment in patients with breast cancer: a population-based cohort study.
    M. A. Toli, X. Liu, D. Massa, S. Lando, C. Boman, N. Tsiknakis, C. Tranchell, A. Papakonstantinou, G. Fotia, C. Vernieri, V. Guarneri, J. Bergh, M. V. Dieci, L. E. Bergman, A. Matikas, and T. Foukakis.
    Lancet Regional Health Europe, vol. 58, Nov. 2025

  3. Adherence to adjuvant endocrine therapy including GnRH-analogues and survival: a population-based cohort study.
    L. Eriksson Bergman, A. Matikas, X. Liu, and T. Foukakis.
    EClinicalMedicine, vol. 88, Oct. 2025

  4. Prognosis After Pathologic Complete Response to Neoadjuvant Therapy in Early-Stage Breast Cancer: A Population-Based Study.
    C. Boman, C. Tranchell, X. Liu, L. Eriksson Bergman, M. A. Toli, J. Bergh, T. Foukakis, and A. Matikas.
    J Natl Compr Canc Netw, vol. 23, no. 4, Mar. 2025

  5. Long-term outcome for neoadjuvant versus adjuvant chemotherapy in early breast cancer and the prognostic impact of nodal therapy response: A population-based study.
    X. Liu, L. Eriksson Bergman, C. Boman, T. Foukakis, and A. Matikas.
    Eur J Surg Oncol, vol. 51, no. 3, Mar. 2025

  6. A population-based study on trajectories of HER2 status during neoadjuvant chemotherapy for early breast cancer and metastatic progression.
    C. Boman, X. Liu, L. Eriksson Bergman, W. Sun, C. Tranchell, M. A. Toli, B. Acs, J. Bergh, T. Foukakis, and A. Matikas.
    Br J Cancer, vol. 131, no. 4, Sep. 2024

Cancer Immunology & Immunotherapy

Breast cancer is an immunologically heterogeneous disease, where the composition and function of the tumor immune microenvironment critically influence treatment response and clinical outcomes. Although immunotherapy has transformed the management of breast cancer patients, there is still an unmet need for biomarker development and a deeper understanding of treatment resistance. Our research aims to identify biomarkers of immunotherapy response and long-term prognosis, unravel mechanisms of primary and acquired resistance, and define the immunomodulatory effects of chemotherapy and targeted therapies. By integrating multi-omics methodology, with data from national and international clinical trials and population-based cohorts, we seek to uncover clinically relevant biomarkers and novel therapeutic targets that will advance precision immuno-oncology and improve outcomes for patients with breast cancer.

Contact person: Ioannis Zerdes (ioannis.zerdes@ki.se)

Associated members: Ioannis Zerdes, Andri Papakonstantinou, Xingrong Liu, Kang Wang, Nikolaos Tsiknakis, Emilia Morales

  1. The interplay between the immune response and neoadjuvant therapy in breast cancer.
    N. Thomas, T. Foukakis, and K. Willard-Gallo.
    Front Oncol, vol. 15, May 2025

  2. Machine learning-based spatial characterization of tumor-immune microenvironment in the EORTC 10994/BIG 1-00 early breast cancer trial.
    I. Zerdes, A. Matikas, A. Mezheyeuski, G. Manikis, B. Acs, H. Johansson, C. Boyaci, C. Boman, C. Poncet, M. Ignatiadis, Y. Bai, D. L. Rimm, D. Cameron, H. Bonnefoi, J. Bergh, G. MacGrogan, and T. Foukakis.
    NPJ Breast Cancer, vol. 11, no. 1, Mar. 2025

  3. Longitudinal molecular profiling elucidates immunometabolism dynamics in breast cancer.
    K. Wang, I. Zerdes, H. J. Johansson, D. Sarhan, Y. Sun, D. C. Kanellis, E. G. Sifakis, A. Mezheyeuski, X. Liu, N. Loman, I. Hedenfalk, J. Bergh, J. Bartek, T. Hatschek, J. Lehtio, A. Matikas, and T. Foukakis.
    Nature Communications, vol. 15, no. 1, May 2024

  4. PD-1 protein and gene expression as prognostic factors in early breast cancer.
    A. Matikas, I. Zerdes, J. Lovrot, E. Sifakis, F. Richard, C. Sotiriou, G. Rassidakis, J. Bergh, A. Valachis, and T. Foukakis.
    ESMO Open, vol. 5, no. 6, Nov. 2020

  5. Prognostic Implications of PD-L1 Expression in Breast Cancer: Systematic Review and Meta-analysis of Immunohistochemistry and Pooled Analysis of Transcriptomic Data.
    A. Matikas, I. Zerdes, J. Lovrot, F. Richard, C. Sotiriou, J. Bergh, A. Valachis, and T. Foukakis.
    Clin Cancer Res, vol. 25, no. 18, Sep. 2019

Translational Biomarker Research

Breast cancer is a biologically and clinically heterogeneous disease, and patients with similar clinicopathological characteristics may experience markedly different responses to therapy and clinical outcomes. Our translational biomarker research aims to identify prognostic and predictive biomarkers that improve patient stratification and guide treatment selection across breast cancer subtypes and treatment settings. We combine comprehensive molecular profiling of tumour tissue and blood samples with detailed clinical data from prospective clinical trials and well-annotated patient cohorts. We use multi-omics approaches – including RNA sequencing, DNA sequencing, proteomics, single-cell and single-nucleus RNA sequencing, spatial transcriptomics, and digital pathology – to investigate tumour-intrinsic biology as well as the tumour microenvironment to better understand mechanisms of treatment response, resistance, and disease progression. A central component of our work is the integration of translational molecular analyses within prospective neoadjuvant clinical trials, enabling direct links between tumour biology, treatment exposure, and clinical outcomes. By integrating multi-omics data with detailed clinical annotation and applying advanced computational and statistical approaches for biomarker development and validation, we aim to identify biologically meaningful tumour subgroups and develop biomarkers that inform treatment escalation, de-escalation, and patient selection for specific therapies. Ultimately, our goal is to advance precision medicine in breast cancer by improving patient selection for therapy and enabling more individualized treatment strategies that maximize benefit while minimizing unnecessary toxicity.

Contact person: Emmanouil Sifakis (emmanouil.sifakis@ki.se)

Associated members: Emmanouil Sifakis, Kang Wang, Michail Sarafidis, Sen Li, Emilia Morales

  1. Prognostic and predictive implications of sterile alpha motif and HD domain-containing protein 1 (SAMHD1) expression in breast cancer.
    M. Kouvaraki, I. Zerdes, E. G. Sifakis, M. Sarafidis, A. Matikas, E. Tzoras, U. Kjallquist, K. Stathopoulou, J. Lovrot, A. Alkodsi, J. Hartman, C. Sotiriou, F. Richard, T. Hatschek, N. Herold, J. Bergh, G. Z. Rassidakis, and T. Foukakis.
    Int J Cancer, vol. 156, no. 8, Apr. 2025

  2. Prognostic role of serum thymidine kinase 1 kinetics during neoadjuvant chemotherapy for early breast cancer.
    A. Matikas, K. Wang, E. Lagoudaki, B. Acs, I. Zerdes, J. Hartman, E. Azavedo, J. Bjohle, L. Carlsson, Z. Einbeigi, I. Hedenfalk, M. Hellstrom, T. Lekberg, N. Loman, A. Saracco, A. von Wachenfeldt, S. Rotstein, M. Bergqvist, J. Bergh, T. Hatschek, and T. Foukakis.
    ESMO Open, vol. 6, no. 2, Apr. 2021

  3. Programmed death-ligand 1 gene expression is a prognostic marker in early breast cancer and provides additional prognostic value to 21-gene and 70-gene signatures in estrogen receptor-positive disease.
    I. Zerdes, E. G. Sifakis, A. Matikas, S. Chretien, N. P. Tobin, J. Hartman, G. Z. Rassidakis, J. Bergh, and T. Foukakis.
    Mol Oncol, vol. 14, no. 5, May 2020

  4. STAT3 Activity Promotes Programmed-Death Ligand 1 Expression and Suppresses Immune Responses in Breast Cancer.
    I. Zerdes, M. Wallerius, E. G. Sifakis, T. Wallmann, S. Betts, M. Bartish, N. Tsesmetzis, N. P. Tobin, C. Coucoravas, J. Bergh, G. Z. Rassidakis, C. Rolny, and T. Foukakis.
    Cancers (Basel), vol. 11, no. 10, Oct. 2019

Artificial Intelligence & Digital Pathology

One of our research themes centers on advancing data-driven and AI-based analyses in breast cancer, spanning biomarker discovery and validation, methodological development, and critical evaluation of artificial intelligence approaches. Within this theme, we develop and benchmark new computational methods, validate emerging biomarkers for patient prognostication and therapy response, and systematically compare AI models to understand their strengths, limitations, and clinical relevance. Our work integrates handcrafted pathomics with machine learning, deep learning, foundation models, and multimodal analyses of histopathology, spatial and molecular data, and clinical information, contributing to state-of-the-art digital pathology and supporting more precise and personalized breast cancer care.

Contact person: Nikos Tsiknakis (nikolaos.tsiknakis@ki.se)

Associated members: Georgios Manikis, Evangelos Tzoras, Kang Wang, Maria Angeliki Toli

  1. Optimization of guidelines for Risk Of Recurrence/Prosigna testing using a machine learning model: a Swedish multicenter study.
    U. Kjallquist, N. Tsiknakis, B. Acs, S. Margolin, L. E. Kessler, S. Levy, M. Ekholm, C. Lundgren, E. Olsson, H. Lindman, A. Valachis, J. Hartman, T. Foukakis, and A. Matikas.
    Breast, vol. 82, Aug. 2025

  2. Pathologist-Read vs AI-Driven Assessment of Tumor-Infiltrating Lymphocytes in Melanoma.
    T. N. Aung, M. Liu, D. Su, S. Shafi, C. Boyaci, S. Steen, N. Tsiknakis, J. M. Vidal, N. Maher, G. Micevic, S. X. Tan, M. D. Vesely, S. Nourmohammadi, Y. Bai, D. Djureinovic, P. F. Wong, K. Bates, N. N. N. Chan, N. Gavirelatou, M. He, S. Burela, R. Barna, M. Bosic, K. Brautigam, I. Illabochaca, Z. Chenhao, J. Gama, B. Kreis, R. Mohacsi, N. Pillar, J. Pinto, C. Poulios, M. A. Toli, E. Tzoras, Y. Bracero, F. Bosisio, G. Cserni, A. Dema, F. Fortarezza, M. S. Gonzalez, I. Gullo, F. J. Queipo Gutierrez, E. Hacihasanoglu, V. Jovic, B. Lazar, M. Olinca, C. Neppl, R. C. Oliveira, F. Pezzuto, D. Gomes Pinto, V. Plotar, O. Pop, T. Rau, K. Skok, W. Sun, E. D. Serbes, W. Solass, O. Stanowska, M. Szasz, K. Szymonski, F. Thimm, D. Vignati, A. Vigdorovits, V. Prieto, T. Sinnberg, J. Wilmott, S. Cowper, J. Warrell, Y. Saenger, J. Hartman, J. Plummer, I. Osman, D. L. Rimm, and B. Acs.
    JAMA Network Open, vol. 8, no. 7, Jul. 2025

  3. The analytical and clinical validity of AI algorithms to score TILs in TNBC: can we use different machine learning models interchangeably?
    J. M. Vidal, N. Tsiknakis, J. Staaf, A. Bosch, A. Ehinger, E. Nimeus, R. Salgado, Y. Bai, D. L. Rimm, J. Hartman, and B. Acs.
    EClinicalMedicine, vol. 78, Dec. 2024

  4. Unveiling the Power of Model-Agnostic Multiscale Analysis for Enhancing Artificial Intelligence Models in Breast Cancer Histopathology Images.
    N. Tsiknakis, G. Manikis, E. Tzoras, D. Salgkamis, J. M. Vidal, K. Wang, D. Zaridis, E. Sifakis, I. Zerdes, J. Bergh, J. Hartman, B. Acs, K. Marias, and T. Foukakis.
    IEEE J Biomed Health Inform, vol. 28, no. 9, Sep. 2024