Our strength relies in our multidisciplinary approach and in the combination of state-of-the-art technologies, including single-cell sequencing, high-throughput profiling, and powerful bioinformatic analysis, which have led to ground-breaking discoveries in the medical field. We primarily use patients’ immune and cancer cells in dynamic co-culture models, hoping that the results will be more readily incorporated into clinical patient care.
Moreover, we have several academic and company-sponsored clinical trials ongoing (both phase I and phase II) studying the effects of tyrosine kinase inhibitors (imatinib, dasatinib, nilotinib, bosutinib) in combination with other drugs.
Engaging our own immune system to fight against the cancer has become an increasingly important and promising therapy in many solid tumors, such as melanoma. Disappointingly, the responses to these novel immune activating therapies have been very modest in many blood cancers and limited to only some of the patients. It is not known in detail how blood cancer cells escape the immune cell attack, and which individual mechanisms may account for a patient’s resistance to treatment. We aim to discover more effective immunotherapies, as well as individual resistance and sensitivity mechanisms of cancer cells to the immune system and be able to develop more personalized treatment options (personalized medicine).
Immunogenomic landscape and resistance and sensitivity mechanisms in blood cancers. Together with our collaborators, we analyze gene expression patterns in large-scale genomic data sets and characterize the immune environment in the bone marrow and blood samples with multicolor flow cytometry and multiplexed immunohistochemistry to understand the immune checkpoint molecule expression. The ultimate goal is to identify the patient subsets which may benefit from immune-based therapies. To better understand the immunological landscape of hematologic cancers, we have performed extensive immunogenomic analyses and discovered immunological features that are related to different blood cancer subtypes and the survival of patients and described novel cancer-type specific immune checkpoint, epigenetic and genetic alterations (Dufva&Polonen Cancer Cell 2020).
In addition to immunogenomic analysis, our group has also recently aimed to understand mechanisms that allow blood cancer cells to avoid chimeric antigen receptor (CAR) T cell or natural killer (NK) cells killing (Dufva, Blood 2020, Dufva&Gandolfi, Immunity 2023).
We studied different blood cancer types (leukemia, lymphoma, myeloma) in the interaction with NK cells and found that NK cells do not react similarly to all cancer cells: some cancers cause the NK cells to activate and destroy the cancer cells, while others do not induce any response. To identify cancer cell–intrinsic factors conferring resistance or sensitivity to CART and NK cell cytotoxicity, we used genome-wide CRISPR screens in a range of hematologic malignancies and uncovered several genes involved in the sensitivity and resistance mechanisms to NK cells including already known mechanisms (such as antigen presentation) and new, previously unappreciated culprits (for example adhesion-related glycoproteins, protein fucosylation genes, and transcriptional regulators). The proteins produced by these genes could be targeted by different types of treatments, such as antibodies, which could lead to improved cancer immunotherapies in the future (Dufva&Gandolfi, Immunity 2023).
In CART cell cytotoxicity, we revealed the essentiality of death receptor signaling. Further, with the high-throughput profiling of over 500 drugs, we discovered drug classes which either inhibit or potentiate CART cytotoxicity (Dufva, Blood 2020).
Thanks to the availability of samples from the iCAN cohort, we are currently studying the sensitivity mechanisms of acute myloid leukimia (AML) primary cells to NK cells at the single-cell resolution. With over 100 samples analysed, we discovered the presence of both sensitive and resistant AML subgroups (Duán, ASH abstract 2024).
Chronic myeloid leukemia (CML). During our early years, we studied the anti-leukemia immune effects in CML widely. We discovered that especially the 2nd generation tyrosine kinase inhibitor (TKI) dasatinib has immunomodulatory properties (Kreutzman, Blood 2010; Kreutzman, Leukemia 2011; Mustjoki, Leukemia 2013; Kreutzman, Oncoimmunology 2014). Interestingly, the immune-related adverse events of dasatinib have been associated with better treatment responses in advanced CML. Despite the success of TKIs, it is believed that these drugs do not eradicate CML stem cells, and relapses occur often after treatment discontinuation. However, our studies suggest that a proportion of CML patients can discontinue the treatment and that NK cells are important in this successful treatment cessation (Ilander, Leukemia 2017). Recently, we also studied how BCR::ABL1-independent pathways can contribute to primary resistance to TKI and hilighted potential mechanisms for primary TKI resistance and non-BCR::ABL1-targeting drugs, offering insights for optimizing CML treatment (Adnan-Awad, Cell rep med 2024)
Accumulation of acquired genetic alterations (somatic mutations) has been considered as a hallmark of cancer progression. Mutations occur more frequently during DNA replication, and thus cancers originate more commonly from rapidly proliferating cell types. Recently, we discovered novel somatic mutations in CML and showed how they impact disease prognosis and response both to targeted and immunotherapies (Adnan-Awad Leukemia 2020, Blood Adv 2021, Leukemia 2021, Blood Cancer J 2022). We also studied the immune response at the single-cell level after TKI discontinuation and highlighted the role of NK cells and anti-PR1 T cells in anti-leukemic immune responses in CML (Huuhtanen, Leukemia 2024).
Finally, our recent work showed that IFN-α broadens the immune repertoire and restores immunological function, supporting the combination of IFN-α with TKI therapy in CML (Huuhtanen, J Clin Invest 2022).
Improving immunotherapies with oncology drugs. In another line of work, we have aimed to improve the cytotoxicity of NK cells against leukemic cells, thus leveraging the full potential of cellular immunotherapies against hematological cancers. To this end, we have conducted an extensive analysis of over 500 approved or investigational oncology drug compounds to explore synergistic approaches with NK cells against different blood cell lines, using a high-throughput drug sensitivity and resistance testing (DSRT) platform. These results will be soon published (Nygren et al., manuscript submitted, Bouhlal et al, manuscript in preparation),
Solid tumors. In addition to hematological malignancies, our group is also investigating the immune system in solid tumors (Hekim&Ilander et al, Cancer Immunol Res 2017). We analyzed over 10 million T cell receptors (TCRs) from 515 patients with primary or metastatic melanoma and compared it to 783 healthy controls and built an artificial intelligence model for predicting anti-melanoma T cells (Huuhtanen Nat Commun 2022).
We are also interested in renal cell carcinoma (RCC): we are studying how somatic mutations in tumor infiltrating T cells affect tumor immune responses and tumor microenvironment.
Somatic mutations not only occur in cancer patients, but also in hematopoietic stem cells of healthy individuals, and their frequency increases with age. We hypothesize that during normal immune responses when T cells undergo rapid clonal expansion, they may also acquire genetic changes, which may alter their behaviour. In our model disease, large granular lymphocyte (LGL) leukaemia, chronic antigen stimulation is appreciated as a potential initiator for the disease. Interestingly, in LGL leukaemia, somatic mutations in STAT3 gene predispose the patients to autoimmune co-manifestations, such as rheumatoid arthritis (RA) and immune-mediated cytopenias (Koskela HLM&Eldfors S NEJM 2012; Rajala Hematologica 2014). Therefore, LGL leukemia may be considered as an extreme example of autoimmune response. Recently, we studied the TCR repertoire in T-LGLL patients and showed that T-LGLL clonotypes are restricted to individual patients, suggesting that there is not one shared target antigen in T-LGLL (Huuhtanen Nat comm, 2022). However, we also discovered that the majority of leukemic T-LGLL clonotypes share TCR similarities with their non-leukemic repertoire. Thus, an aberrant oligoclonal immune response against a specific antigen can be a disease-inducing and evolution-driving trigger in T-LGLL. The antigen can be both autoantigen or alloantigen, as T-LGLL patients have autoimmune-like symptoms and LGL proliferations have also been observed after viral infections.
Chronic inflammation has been accepted as a potential risk factor for cancer. Our hypothesis is that the pathogenesis of some autoimmune diseases may share similar mechanisms with LGL leukemia. We showed that patients with untreated RA harbour somatic mutations in their clonally expanded cytotoxic lymphocytes (Savola P&Kelkka T et al, Nat Commun 2017). Thus, by using state-or-art technologies, we identified a novel connection between autoimmune inflammation and cancer.
Recently, we showed how somatic mutations influence T cell function and phenotype not only in RA, but also in other auto- and alloimmune diseases including immune mediated bone marrow failure and graft versus host disease (Mustjoki NEJM 2021; Kim Haematologica 2022, Kim Leukemia 2021, Lundgren Leukemia 2021; Savola Haematologica 2020; Kim Nat Comm 2020). In our last study, we also examined somatic mutations in CD4+ and CD8+ T cells from 90 patients with hematological and immunological disorders and discovered that somatic mutations contribute to CD8+ T cell expansions without malignant transformation (Lundgren Sci Adv 2024).
In collaboration with Pentti Tienari’s lab, we studied somatic mutations in multiple sclerosis. We demonstrated that STAT3 is an outstanding mutational hotspot in CD8+ cells, but the overall mutation prevalence was not increased in CD8+ cells derived from MS patients (Valori PLoS One 2022).
In close collaboration with the Institute for Molecular Medicine Finland (FIMM), we apply the cancer cell Drug Sensitivity and Resistance Testing (DSRT) platform to functionally characterize the ex vivo sensitivity to hundreds of compounds in different leukemias both using fresh patient-derived samples as well as using established and experimental cell lines. Our discoveries in T-cell prolymphocytic leukemia (Andersson et al., Leukemia 2017), chronic myeloid leukemia (CML) (Pietarinen et al., Blood Cancer J 2015; Pietarinen et al., Oncotarget 2017) and STAT3-driven lymphocytic malignancies (Kuusanmäki et al., Oncotarget 2017) highlight the importance of the method in disease characterization as well as in the discovery of novel therapy options for different leukemias. We therefore applied high-throughput flow cytometry-based drug profiling to understand the single-cell heterogeneity of drug responses in myeloid leukemias and to develop novel assays to discover immunomodulatory effects of oncology drugs that could synergize with cancer immunotherapies.
We discovered erythroid/megakaryocytic AML to be highly sensitive for BCL-XL inhibition which provides a novel treatment possibility for patients with currently have extremely poor prognosis (Kuusanmäki&Dufva et al., Blood 2023). We also discovered novel pathogenetic mechanisms and targeted therapies for rare aggressive T and NK cell malignancies (Dufva et al., Nat Comm 2018; Huuhtanen et al., Nat Comm 2022; Bhattacharya et al., Blood Cancer J 2022) and some of these discoveries are already now applied in diagnostics.
We have set up a biomarker discovery program, which is performed concurrent to the clinical drug studies, both academic and company sponsored. In the frame of Nordic CML study group we analysed the leukemic stem cell burden at the diagnosis and during TKI therapy and its importance for the therapy response. These analyses have been performed during NordCML006 study, NordCML007 study Enest1st study. In addition to stem cell analysis, we are performing various immunological measurements aiming to understand immunological determinants of successful treatment response. We also headed an immunology biomarker substudy in European wide Euro-Ski study, which evaluated the probability of successful treatment discontinuation in CML.
Moreover, we established significant research collaborations with pharmaceutical companies in which our unit serves as the central immunological biomarker discovery laboratory in international Phase I/II clinical studies.
Recently, we carried out immunological analyses and identified novel biomarkers that correlate to the response to immunotherapies (Huuhtanen J Clin Invest 2022; Hakanen, Cancer Immunol Immunother 2020).