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Zhong H, Sian V, Johari M, Katayama S, Oghabian A, Jonson PH, Hackman P, Savarese M, Udd B. Revealing myopathy spectrum: integrating transcriptional and clinical features of human skeletal muscles with varying health conditions. Commun Biol 2024; 7:438. [PMID: 38600180 PMCID: PMC11006663 DOI: 10.1038/s42003-024-06143-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 04/03/2024] [Indexed: 04/12/2024] Open
Abstract
Myopathy refers to a large group of heterogeneous, rare muscle diseases. Bulk RNA-sequencing has been utilized for the diagnosis and research of these diseases for many years. However, the existing valuable sequencing data often lack integration and clinical interpretation. In this study, we integrated bulk RNA-sequencing data from 1221 human skeletal muscles (292 with myopathies, 929 controls) from both databases and our local samples. By applying a method similar to single-cell analysis, we revealed a general spectrum of muscle diseases, ranging from healthy to mild disease, moderate muscle wasting, and severe muscle disease. This spectrum was further partly validated in three specific myopathies (97 muscles) through clinical features including trinucleotide repeat expansion, magnetic resonance imaging fat fraction, pathology, and clinical severity scores. This spectrum helped us identify 234 genuinely healthy muscles as unprecedented controls, providing a new perspective for deciphering the hallmark genes and pathways among different myopathies. The newly identified featured genes of general myopathy, inclusion body myositis, and titinopathy were highly expressed in our local muscles, as validated by quantitative polymerase chain reaction.
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Affiliation(s)
- Huahua Zhong
- Department of Neurology, Huashan Rare Disease Center, Huashan Hospital, Fudan University, Shanghai, China.
| | - Veronica Sian
- Department of Precision Medicine, "Luigi Vanvitelli" University of Campania, Via L. De Crecchio 7, Naples, Italy
| | - Mridul Johari
- Department of Medical and Clinical Genetics, Folkhälsan Research Center, Medicum, University of Helsinki, Helsinki, Finland
- Harry Perkins Institute of Medical Research, Centre for Medical Research, University of Western Australia, Nedlands, WA, Australia
| | - Shintaro Katayama
- Department of Medical and Clinical Genetics, Folkhälsan Research Center, Medicum, University of Helsinki, Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Ali Oghabian
- Department of Medical and Clinical Genetics, Folkhälsan Research Center, Medicum, University of Helsinki, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Per Harald Jonson
- Department of Medical and Clinical Genetics, Folkhälsan Research Center, Medicum, University of Helsinki, Helsinki, Finland
| | - Peter Hackman
- Department of Medical and Clinical Genetics, Folkhälsan Research Center, Medicum, University of Helsinki, Helsinki, Finland
| | - Marco Savarese
- Department of Medical and Clinical Genetics, Folkhälsan Research Center, Medicum, University of Helsinki, Helsinki, Finland
| | - Bjarne Udd
- Department of Medical and Clinical Genetics, Folkhälsan Research Center, Medicum, University of Helsinki, Helsinki, Finland
- Tampere Neuromuscular Center, University Hospital, Tampere, Finland
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Tamlander M, Jermy B, Seppälä TT, Färkkilä M, Widén E, Ripatti S, Mars N. Genome-wide polygenic risk scores for colorectal cancer have implications for risk-based screening. Br J Cancer 2024; 130:651-659. [PMID: 38172535 PMCID: PMC10876651 DOI: 10.1038/s41416-023-02536-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Hereditary factors, including single genetic variants and family history, can be used for targeting colorectal cancer (CRC) screening, but limited data exist on the impact of polygenic risk scores (PRS) on risk-based CRC screening. METHODS Using longitudinal health and genomics data on 453,733 Finnish individuals including 8801 CRC cases, we estimated the impact of a genome-wide CRC PRS on CRC screening initiation age through population-calibrated incidence estimation over the life course in men and women. RESULTS Compared to the cumulative incidence of CRC at age 60 in Finland (the current age for starting screening in Finland), a comparable cumulative incidence was reached 5 and 11 years earlier in persons with high PRS (80-99% and >99%, respectively), while those with a low PRS (< 20%) reached comparable incidence 7 years later. The PRS was associated with increased risk of post-colonoscopy CRC after negative colonoscopy (hazard ratio 1.76 per PRS SD, 95% CI 1.54-2.01). Moreover, the PRS predicted colorectal adenoma incidence and improved incident CRC risk prediction over non-genetic risk factors. CONCLUSIONS Our findings demonstrate that a CRC PRS can be used for risk stratification of CRC, with further research needed to optimally integrate the PRS into risk-based screening.
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Affiliation(s)
- Max Tamlander
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Bradley Jermy
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Toni T Seppälä
- Faculty of Medicine and Health Technology, University of Tampere and TAYS Cancer Centre, Tampere, Finland
- Department of Gastroenterology and Alimentary Tract Surgery, Tampere University Hospital, Tampere, Finland
- Applied Tumor Genomics Research Program, University of Helsinki, Helsinki, Finland
- Abdominal Center, Helsinki University Hospital, Helsinki University, Helsinki, Finland
| | - Martti Färkkilä
- Abdominal Center, Helsinki University Hospital, Helsinki University, Helsinki, Finland
| | - Elisabeth Widén
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
- Clinicum, Department of Public Health, University of Helsinki, Helsinki, Finland
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nina Mars
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Mirzaie M, Gholizadeh E, Miettinen JJ, Ianevski F, Ruokoranta T, Saarela J, Manninen M, Miettinen S, Heckman CA, Jafari M. Designing patient-oriented combination therapies for acute myeloid leukemia based on efficacy/toxicity integration and bipartite network modeling. Oncogenesis 2024; 13:11. [PMID: 38429288 PMCID: PMC10907624 DOI: 10.1038/s41389-024-00510-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 03/03/2024] Open
Abstract
Acute myeloid leukemia (AML), a heterogeneous and aggressive blood cancer, does not respond well to single-drug therapy. A combination of drugs is required to effectively treat this disease. Computational models are critical for combination therapy discovery due to the tens of thousands of two-drug combinations, even with approved drugs. While predicting synergistic drugs is the focus of current methods, few consider drug efficacy and potential toxicity, which are crucial for treatment success. To find effective new drug candidates, we constructed a bipartite network using patient-derived tumor samples and drugs. The network is based on drug-response screening and summarizes all treatment response heterogeneity as drug response weights. This bipartite network is then projected onto the drug part, resulting in the drug similarity network. Distinct drug clusters were identified using community detection methods, each targeting different biological processes and pathways as revealed by enrichment and pathway analysis of the drugs' protein targets. Four drugs with the highest efficacy and lowest toxicity from each cluster were selected and tested for drug sensitivity using cell viability assays on various samples. Results show that ruxolitinib-ulixertinib and sapanisertib-LY3009120 are the most effective combinations with the least toxicity and the best synergistic effect on blast cells. These findings lay the foundation for personalized and successful AML therapies, ultimately leading to the development of drug combinations that can be used alongside standard first-line AML treatment.
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Affiliation(s)
- Mehdi Mirzaie
- Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki, Finland
| | - Elham Gholizadeh
- Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki, Finland
| | - Juho J Miettinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Filipp Ianevski
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Tanja Ruokoranta
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Jani Saarela
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | | | - Susanna Miettinen
- Adult Stem Cell Group, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Tays Research Services, Wellbeing Services County of Pirkanmaa, Tampere University Hospital, Tampere, Finland
| | - Caroline A Heckman
- Institute for Molecular Medicine Finland - FIMM, HiLIFE - Helsinki Institute of Life Science, iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland.
| | - Mohieddin Jafari
- Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki, Finland.
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Reinholm A, Maljanen S, Jalkanen P, Altan E, Tauriainen S, Belik M, Skön M, Haveri A, Österlund P, Iakubovskaia A, Pasternack A, Naves RA, Ritvos O, Miettinen S, K Häkkinen H, Ivaska L, Tähtinen PA, Lempainen J, Kantele A, Kakkola L, Julkunen I, Kolehmainen P. Neutralizing antibodies after the third COVID-19 vaccination in healthcare workers with or without breakthrough infection. Commun Med (Lond) 2024; 4:28. [PMID: 38396065 PMCID: PMC10891120 DOI: 10.1038/s43856-024-00457-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND Vaccinations against the SARS-CoV-2 are still crucial in combating the ongoing pandemic that has caused more than 700 million infections and claimed almost 7 million lives in the past four years. Omicron (B.1.1.529) variants have incurred mutations that challenge the protection against infection and severe disease by the current vaccines, potentially compromising vaccination efforts. METHODS We analyzed serum samples taken up to 9 months post third dose from 432 healthcare workers. Enzyme-linked immunosorbent assays (ELISA) and microneutralization tests (MNT) were used to assess the prevalence of vaccine-induced neutralizing antibodies against various SARS-CoV-2 Omicron variants. RESULTS In this serological analysis we show that SARS-CoV-2 vaccine combinations of BNT162b2, mRNA-1273, and ChAdOx1 mount SARS-CoV-2 binding and neutralizing antibodies with similar kinetics, but with differing neutralization capabilities. The most recent Omicron variants, BQ.1.1 and XBB.1.5, show a significant increase in the ability to escape vaccine and infection-induced antibody responses. Breakthrough infections in thrice vaccinated adults were seen in over 50% of the vaccinees, resulting in a stronger antibody response than without infection. CONCLUSIONS Different three-dose vaccine combinations seem to induce considerable levels of neutralizing antibodies against most SARS-CoV-2 variants. However, the ability of the newer variants BQ1.1 and XBB 1.5 to escape vaccine-induced neutralizing antibody responses underlines the importance of updating vaccines as new variants emerge.
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Affiliation(s)
- Arttu Reinholm
- Institute of Biomedicine, University of Turku, Turku, Finland.
| | - Sari Maljanen
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Pinja Jalkanen
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Eda Altan
- Institute of Biomedicine, University of Turku, Turku, Finland
| | | | - Milja Belik
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Marika Skön
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Anu Haveri
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | | | - Alina Iakubovskaia
- Department of Physiology, Medicum, University of Helsinki, Helsinki, Finland
| | - Arja Pasternack
- Department of Physiology, Medicum, University of Helsinki, Helsinki, Finland
| | - Rauno A Naves
- Department of Physiology, Medicum, University of Helsinki, Helsinki, Finland
| | - Olli Ritvos
- Department of Physiology, Medicum, University of Helsinki, Helsinki, Finland
| | - Simo Miettinen
- Department of Infectious Diseases, Meilahti Vaccination Research Center, MeVac, Helsinki, University Hospital and University of Helsinki, Helsinki, Finland
| | - Hanni K Häkkinen
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - Lauri Ivaska
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland
- InFlames Research Flagship Center, University of Turku, Turku, Finland
| | - Paula A Tähtinen
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland
| | - Johanna Lempainen
- Institute of Biomedicine, University of Turku, Turku, Finland
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland
- Clinical Microbiology, Turku University Hospital, Turku, Finland
| | - Anu Kantele
- Department of Infectious Diseases, Meilahti Vaccination Research Center, MeVac, Helsinki, University Hospital and University of Helsinki, Helsinki, Finland
| | - Laura Kakkola
- Institute of Biomedicine, University of Turku, Turku, Finland
- InFlames Research Flagship Center, University of Turku, Turku, Finland
- Clinical Microbiology, Turku University Hospital, Turku, Finland
| | - Ilkka Julkunen
- Institute of Biomedicine, University of Turku, Turku, Finland
- InFlames Research Flagship Center, University of Turku, Turku, Finland
- Clinical Microbiology, Turku University Hospital, Turku, Finland
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5
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Fan X, Sun AR, Young RSE, Afara IO, Hamilton BR, Ong LJY, Crawford R, Prasadam I. Spatial analysis of the osteoarthritis microenvironment: techniques, insights, and applications. Bone Res 2024; 12:7. [PMID: 38311627 PMCID: PMC10838951 DOI: 10.1038/s41413-023-00304-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/21/2023] [Accepted: 11/27/2023] [Indexed: 02/06/2024] Open
Abstract
Osteoarthritis (OA) is a debilitating degenerative disease affecting multiple joint tissues, including cartilage, bone, synovium, and adipose tissues. OA presents diverse clinical phenotypes and distinct molecular endotypes, including inflammatory, metabolic, mechanical, genetic, and synovial variants. Consequently, innovative technologies are needed to support the development of effective diagnostic and precision therapeutic approaches. Traditional analysis of bulk OA tissue extracts has limitations due to technical constraints, causing challenges in the differentiation between various physiological and pathological phenotypes in joint tissues. This issue has led to standardization difficulties and hindered the success of clinical trials. Gaining insights into the spatial variations of the cellular and molecular structures in OA tissues, encompassing DNA, RNA, metabolites, and proteins, as well as their chemical properties, elemental composition, and mechanical attributes, can contribute to a more comprehensive understanding of the disease subtypes. Spatially resolved biology enables biologists to investigate cells within the context of their tissue microenvironment, providing a more holistic view of cellular function. Recent advances in innovative spatial biology techniques now allow intact tissue sections to be examined using various -omics lenses, such as genomics, transcriptomics, proteomics, and metabolomics, with spatial data. This fusion of approaches provides researchers with critical insights into the molecular composition and functions of the cells and tissues at precise spatial coordinates. Furthermore, advanced imaging techniques, including high-resolution microscopy, hyperspectral imaging, and mass spectrometry imaging, enable the visualization and analysis of the spatial distribution of biomolecules, cells, and tissues. Linking these molecular imaging outputs to conventional tissue histology can facilitate a more comprehensive characterization of disease phenotypes. This review summarizes the recent advancements in the molecular imaging modalities and methodologies for in-depth spatial analysis. It explores their applications, challenges, and potential opportunities in the field of OA. Additionally, this review provides a perspective on the potential research directions for these contemporary approaches that can meet the requirements of clinical diagnoses and the establishment of therapeutic targets for OA.
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Affiliation(s)
- Xiwei Fan
- Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, QLD, Australia
- School of Mechanical, Medical & Process Engineering, Queensland University of Technology, Brisbane, QLD, Australia
| | - Antonia Rujia Sun
- Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, QLD, Australia
- School of Mechanical, Medical & Process Engineering, Queensland University of Technology, Brisbane, QLD, Australia
| | - Reuben S E Young
- Central Analytical Research Facility, Queensland University of Technology, Brisbane, QLD, Australia
- Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia
| | - Isaac O Afara
- Department of Technical Physics, University of Eastern Finland, Kuopio, Finland
- School of Electrical Engineering and Computer Science, Faculty of Engineering, Architecture and Information Technology, University of Queensland, Brisbane, QLD, Australia
| | - Brett R Hamilton
- Centre for Microscopy and Microanalysis, University of Queensland, Brisbane, QLD, Australia
| | - Louis Jun Ye Ong
- Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, QLD, Australia
- School of Mechanical, Medical & Process Engineering, Queensland University of Technology, Brisbane, QLD, Australia
| | - Ross Crawford
- Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, QLD, Australia
- The Prince Charles Hospital, Brisbane, QLD, Australia
| | - Indira Prasadam
- Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, QLD, Australia.
- School of Mechanical, Medical & Process Engineering, Queensland University of Technology, Brisbane, QLD, Australia.
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6
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Koistinen VM, Haldar S, Tuomainen M, Lehtonen M, Klåvus A, Draper J, Lloyd A, Beckmann M, Bal W, Ross AB, Brandt K, Fawcett L, Seal C, Hanhineva K. Metabolic changes in response to varying whole-grain wheat and rye intake. NPJ Sci Food 2024; 8:8. [PMID: 38291073 PMCID: PMC10828387 DOI: 10.1038/s41538-024-00247-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 01/08/2024] [Indexed: 02/01/2024] Open
Abstract
Epidemiological studies have shown associations between whole-grain intake and lowered disease risk. A sufficient level of whole-grain intake to reach the health benefits has not been established, and there is limited knowledge about the impact of whole-grain intake on metabolite levels. In this clinical intervention study, we aimed to identify plasma and urine metabolites associated with two different intake levels of whole-grain wheat and rye and to correlate them with clinical plasma biomarkers. Healthy volunteers (N = 68) were divided into two groups receiving either whole-grain wheat or whole-grain rye in two four-week interventions with 48 and 96 g/d of whole grains consumed. The metabolomics of the plasma samples was performed with UPLC-QTOF-MS. Plasma alkylresorcinols were quantified with GC-MS and plasma and urinary mammalian lignans with HPLC-ECD. The high-dose intervention impacted the metabolite profile, including microbial metabolites, more in the rye-enriched diet compared with wheat. Among the increased metabolites were alkylresorcinol glucuronides, sinapyl alcohol, and pipecolic acid betaine, while the decreased metabolites included acylcarnitines and ether lipids. Plasma alkylresorcinols, urinary enterolactone, and total mammalian lignans reflected the study diets in a dose-dependent manner. Several key metabolites linked with whole-grain consumption and gut microbial metabolism increased in a linear manner between the two interventions. The results reveal that an increase in whole-grain intake, particularly rye, is strongly reflected in the metabolite profile, is correlated with clinical variables, and suggests that a diet rich in whole grains promotes the growth and/or metabolism of microbes producing potentially beneficial microbial metabolites.
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Affiliation(s)
- Ville M Koistinen
- Food Sciences Unit, Department of Life Technologies, University of Turku, Turku, Finland.
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland.
| | - Sumanto Haldar
- Clinical Nutrition Research Centre, Singapore Institute of Food and Biotechnology Innovations (SIFBI), Yong Loo Lin School of Medicine, Singapore, 117599, Singapore
| | - Marjo Tuomainen
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Marko Lehtonen
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Anton Klåvus
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - John Draper
- Department of Biological, Environmental and Rural Sciences, Aberystwyth University, Wales, UK
| | - Amanda Lloyd
- Department of Biological, Environmental and Rural Sciences, Aberystwyth University, Wales, UK
| | - Manfred Beckmann
- Department of Biological, Environmental and Rural Sciences, Aberystwyth University, Wales, UK
| | - Wendy Bal
- Human Nutrition and Exercise Research Centre, Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | - Kirsten Brandt
- Human Nutrition and Exercise Research Centre, Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Lee Fawcett
- School of Mathematics, Statistics and Physics, Newcastle University, Newcastle upon Tyne, UK
| | - Chris Seal
- Human Nutrition and Exercise Research Centre, Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Kati Hanhineva
- Food Sciences Unit, Department of Life Technologies, University of Turku, Turku, Finland
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
- Food and Nutrition Science Division, Chalmers University of Technology, Gothenburg, Sweden
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Vasilescu C, Colpan M, Ojala TH, Manninen T, Mutka A, Ylänen K, Rahkonen O, Poutanen T, Martelius L, Kumari R, Hinterding H, Brilhante V, Ojanen S, Lappalainen P, Koskenvuo J, Carroll CJ, Fowler VM, Gregorio CC, Suomalainen A. Recessive TMOD1 mutation causes childhood cardiomyopathy. Commun Biol 2024; 7:7. [PMID: 38168645 PMCID: PMC10761686 DOI: 10.1038/s42003-023-05670-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024] Open
Abstract
Familial cardiomyopathy in pediatric stages is a poorly understood presentation of heart disease in children that is attributed to pathogenic mutations. Through exome sequencing, we report a homozygous variant in tropomodulin 1 (TMOD1; c.565C>T, p.R189W) in three individuals from two unrelated families with childhood-onset dilated and restrictive cardiomyopathy. To decipher the mechanism of pathogenicity of the R189W mutation in TMOD1, we utilized a wide array of methods, including protein analyses, biochemistry and cultured cardiomyocytes. Structural modeling revealed potential defects in the local folding of TMOD1R189W and its affinity for actin. Cardiomyocytes expressing GFP-TMOD1R189W demonstrated longer thin filaments than GFP-TMOD1wt-expressing cells, resulting in compromised filament length regulation. Furthermore, TMOD1R189W showed weakened activity in capping actin filament pointed ends, providing direct evidence for the variant's effect on actin filament length regulation. Our data indicate that the p.R189W variant in TMOD1 has altered biochemical properties and reveals a unique mechanism for childhood-onset cardiomyopathy.
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Affiliation(s)
- Catalina Vasilescu
- Research Programs Unit, Stem Cells and Metabolism, Biomedicum-Helsinki, University of Helsinki, 00290, Helsinki, Finland
| | - Mert Colpan
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program, The University of Arizona, Tucson, AZ, 85724, USA
| | - Tiina H Ojala
- Department of Pediatric Cardiology, Helsinki University Hospital and University of Helsinki, 00290, Helsinki, Finland
| | - Tuula Manninen
- Research Programs Unit, Stem Cells and Metabolism, Biomedicum-Helsinki, University of Helsinki, 00290, Helsinki, Finland
| | - Aino Mutka
- Department of Pathology, Helsinki University Hospital and University of Helsinki, 00290, Helsinki, Finland
| | - Kaisa Ylänen
- Tampere Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University and University Hospital, 33521, Tampere, Finland
| | - Otto Rahkonen
- Department of Pediatric Cardiology, Helsinki University Hospital and University of Helsinki, 00290, Helsinki, Finland
| | - Tuija Poutanen
- Tampere Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University and University Hospital, 33521, Tampere, Finland
| | - Laura Martelius
- Department of Pediatric Radiology, Helsinki University Hospital and University of Helsinki, 00290, Helsinki, Finland
| | - Reena Kumari
- HiLIFE Institute of Biotechnology, University of Helsinki, 00014, Helsinki, Finland
| | - Helena Hinterding
- Research Programs Unit, Stem Cells and Metabolism, Biomedicum-Helsinki, University of Helsinki, 00290, Helsinki, Finland
| | - Virginia Brilhante
- Research Programs Unit, Stem Cells and Metabolism, Biomedicum-Helsinki, University of Helsinki, 00290, Helsinki, Finland
| | - Simo Ojanen
- Research Programs Unit, Stem Cells and Metabolism, Biomedicum-Helsinki, University of Helsinki, 00290, Helsinki, Finland
| | - Pekka Lappalainen
- HiLIFE Institute of Biotechnology, University of Helsinki, 00014, Helsinki, Finland
| | | | - Christopher J Carroll
- Research Programs Unit, Stem Cells and Metabolism, Biomedicum-Helsinki, University of Helsinki, 00290, Helsinki, Finland
- Molecular and Clinical Sciences, St. George's, University of London, London, United Kingdom
| | - Velia M Fowler
- Department of Biological Sciences, University of Delaware, Newark, DE, 19711, USA
| | - Carol C Gregorio
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program, The University of Arizona, Tucson, AZ, 85724, USA.
- Cardiovascular Research Institute, Department of Medicine, Icahn School of Medicine, New York, NY, 10029, USA.
| | - Anu Suomalainen
- Research Programs Unit, Stem Cells and Metabolism, Biomedicum-Helsinki, University of Helsinki, 00290, Helsinki, Finland.
- HUSlab, Helsinki University Hospital, University of Helsinki, 00290, Helsinki, Finland.
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8
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Quixabeira DCA, Pakola S, Jirovec E, Havunen R, Basnet S, Santos JM, Kudling TV, Clubb JHA, Haybout L, Arias V, Grönberg-Vähä-Koskela S, Cervera-Carrascon V, Kerkelä E, Pasanen A, Anttila M, Tapper J, Kanerva A, Hemminki A. Boosting cytotoxicity of adoptive allogeneic NK cell therapy with an oncolytic adenovirus encoding a human vIL-2 cytokine for the treatment of human ovarian cancer. Cancer Gene Ther 2023; 30:1679-1690. [PMID: 37949944 PMCID: PMC10721546 DOI: 10.1038/s41417-023-00674-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/31/2023] [Accepted: 09/29/2023] [Indexed: 11/12/2023]
Abstract
Despite good results in the treatment of hematological malignancies, Natural killer (NK) cells have shown limited effectiveness in solid tumors, such as ovarian cancer (OvCa). Here, we assessed the potential of an oncolytic adenovirus expressing a variant interleukin-2 (vIL-2) cytokine, Ad5/3-E2F-d24-vIL2 (vIL-2 virus), also known as TILT-452, to enhance NK cell therapy efficacy in human OvCa ex vivo. Human OvCa surgical specimens were processed into single-cell suspensions and NK cells were expanded from healthy blood donors. OvCa sample digests were co-cultured ex vivo with NK cells and vIL-2 virus and cancer cell killing potential assessed in real time through cell impedance measurement. Proposed therapeutic combination was evaluated in vivo with an OvCa patient-derived xenograft (PDX) in mice. Addition of vIL-2 virus significantly enhanced NK cell therapy killing potential in treated OvCa co-cultures. Similarly, vIL-2 virus in combination with NK cell therapy promoted the best in vivo OvCa tumor control. Mechanistically, vIL-2 virus induced higher percentages of granzyme B in NK cells, and CD8+ T cells, while T regulatory cell proportions remained comparable to NK cell monotherapy in vivo. Ad5/3-E2F-d24-vIL2 virus treatment represents a promising strategy to boost adoptive NK cell therapeutic effect in human OvCa.
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Affiliation(s)
- D C A Quixabeira
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- TILT Biotherapeutics Ltd, Helsinki, Finland
| | - S Pakola
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - E Jirovec
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - R Havunen
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- TILT Biotherapeutics Ltd, Helsinki, Finland
| | - S Basnet
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - J M Santos
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- TILT Biotherapeutics Ltd, Helsinki, Finland
| | - T V Kudling
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - J H A Clubb
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- TILT Biotherapeutics Ltd, Helsinki, Finland
| | - L Haybout
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - V Arias
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - S Grönberg-Vähä-Koskela
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - V Cervera-Carrascon
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- TILT Biotherapeutics Ltd, Helsinki, Finland
| | - E Kerkelä
- Finnish Red Cross Blood Service, Helsinki, Finland
| | - A Pasanen
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - M Anttila
- Pathology, Finnish Food Authority, Helsinki, Finland
| | - J Tapper
- Department of Obstetrics and Gynecology, Helsinki University Central Hospital, Helsinki, Finland
| | - A Kanerva
- Department of Obstetrics and Gynecology, Helsinki University Central Hospital, Helsinki, Finland
| | - A Hemminki
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- TILT Biotherapeutics Ltd, Helsinki, Finland.
- Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.
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9
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Siljamäki E, Riihilä P, Suwal U, Nissinen L, Rappu P, Kallajoki M, Kähäri VM, Heino J. Inhibition of TGF-β signaling, invasion, and growth of cutaneous squamous cell carcinoma by PLX8394. Oncogene 2023; 42:3633-3647. [PMID: 37864034 PMCID: PMC10691969 DOI: 10.1038/s41388-023-02863-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/28/2023] [Accepted: 10/04/2023] [Indexed: 10/22/2023]
Abstract
Cutaneous squamous cell carcinoma (cSCC) is the most common metastatic skin cancer. The prognosis of patients with metastatic cSCC is poor emphasizing the need for new therapies. We have previously reported that the activation of Ras/MEK/ERK1/2 and transforming growth factor β (TGF-β)/Smad2 signaling in transformed keratinocytes and cSCC cells leads to increased accumulation of laminin-332 and accelerated invasion. Here, we show that the next-generation B-Raf inhibitor PLX8394 blocks TGF-β signaling in ras-transformed metastatic epidermal keratinocytes (RT3 cells) harboring wild-type B-Raf and hyperactive Ras. PLX8394 decreased phosphorylation of TGF-β receptor II and Smad2, as well as p38 activity, MMP-1 and MMP-13 synthesis, and laminin-332 accumulation. PLX8394 significantly inhibited the growth of human cSCC tumors and in vivo collagen degradation in xenograft model. In conclusion, our data indicate that PLX8394 inhibits several serine-threonine kinases in malignantly transformed human keratinocytes and cSCC cells and inhibits cSCC invasion and tumor growth in vitro and in vivo. We identify PLX8394 as a potential therapeutic compound for advanced human cSCC.
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Affiliation(s)
- Elina Siljamäki
- MediCity Research Laboratory, University of Turku, Tykistökatu 6A, FI-20520, Turku, Finland
- Department of Life Technologies and InFLAMES Research Flagship, University of Turku, FI-20014, Turku, Finland
| | - Pilvi Riihilä
- Department of Dermatology, University of Turku and Turku University Hospital, Hämeentie 11 TE6, FI-20520, Turku, Finland
- FICAN West Cancer Research Laboratory, University of Turku and Turku University Hospital, Kiinamyllynkatu 10, FI-20520, Turku, Finland
| | - Ujjwal Suwal
- MediCity Research Laboratory, University of Turku, Tykistökatu 6A, FI-20520, Turku, Finland
- Department of Life Technologies and InFLAMES Research Flagship, University of Turku, FI-20014, Turku, Finland
| | - Liisa Nissinen
- Department of Dermatology, University of Turku and Turku University Hospital, Hämeentie 11 TE6, FI-20520, Turku, Finland
- FICAN West Cancer Research Laboratory, University of Turku and Turku University Hospital, Kiinamyllynkatu 10, FI-20520, Turku, Finland
| | - Pekka Rappu
- MediCity Research Laboratory, University of Turku, Tykistökatu 6A, FI-20520, Turku, Finland
- Department of Life Technologies and InFLAMES Research Flagship, University of Turku, FI-20014, Turku, Finland
| | - Markku Kallajoki
- Department of Pathology, University of Turku and Turku University Hospital, Kiinamyllynkatu 10, FI-20520, Turku, Finland
| | - Veli-Matti Kähäri
- Department of Dermatology, University of Turku and Turku University Hospital, Hämeentie 11 TE6, FI-20520, Turku, Finland.
- FICAN West Cancer Research Laboratory, University of Turku and Turku University Hospital, Kiinamyllynkatu 10, FI-20520, Turku, Finland.
| | - Jyrki Heino
- MediCity Research Laboratory, University of Turku, Tykistökatu 6A, FI-20520, Turku, Finland.
- Department of Life Technologies and InFLAMES Research Flagship, University of Turku, FI-20014, Turku, Finland.
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10
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Chiaro J, Antignani G, Feola S, Feodoroff M, Martins B, Cojoc H, Russo S, Fusciello M, Hamdan F, Ferrari V, Ciampi D, Ilonen I, Räsänen J, Mäyränpää M, Partanen J, Koskela S, Honkanen J, Halonen J, Kuryk L, Rescigno M, Grönholm M, Branca RM, Lehtiö J, Cerullo V. Development of mesothelioma-specific oncolytic immunotherapy enabled by immunopeptidomics of murine and human mesothelioma tumors. Nat Commun 2023; 14:7056. [PMID: 37923723 PMCID: PMC10624665 DOI: 10.1038/s41467-023-42668-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 10/18/2023] [Indexed: 11/06/2023] Open
Abstract
Malignant pleural mesothelioma (MPM) is an aggressive tumor with a poor prognosis. As the available therapeutic options show a lack of efficacy, novel therapeutic strategies are urgently needed. Given its T-cell infiltration, we hypothesized that MPM is a suitable target for therapeutic cancer vaccination. To date, research on mesothelioma has focused on the identification of molecular signatures to better classify and characterize the disease, and little is known about therapeutic targets that engage cytotoxic (CD8+) T cells. In this study we investigate the immunopeptidomic antigen-presented landscape of MPM in both murine (AB12 cell line) and human cell lines (H28, MSTO-211H, H2452, and JL1), as well as in patients' primary tumors. Applying state-of-the-art immuno-affinity purification methodologies, we identify MHC I-restricted peptides presented on the surface of malignant cells. We characterize in vitro the immunogenicity profile of the eluted peptides using T cells from human healthy donors and cancer patients. Furthermore, we use the most promising peptides to formulate an oncolytic virus-based precision immunotherapy (PeptiCRAd) and test its efficacy in a mouse model of mesothelioma in female mice. Overall, we demonstrate that the use of immunopeptidomic analysis in combination with oncolytic immunotherapy represents a feasible and effective strategy to tackle untreatable tumors.
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Affiliation(s)
- Jacopo Chiaro
- Drug Research Program (DRP), ImmunoViroTherapy Lab (IVT), Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5E, 00790, Helsinki, Finland
- Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Fabianinkatu 33, 00710, Helsinki, Finland
- Translational Immunology Program (TRIMM), Faculty of Medicine Helsinki University, University of Helsinki, Haartmaninkatu 8, 00290, Helsinki, Finland
- Digital Precision Cancer Medicine Flagship (iCAN), University of Helsinki, 00014, Helsinki, Finland
| | - Gabriella Antignani
- Drug Research Program (DRP), ImmunoViroTherapy Lab (IVT), Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5E, 00790, Helsinki, Finland
- Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Fabianinkatu 33, 00710, Helsinki, Finland
- Translational Immunology Program (TRIMM), Faculty of Medicine Helsinki University, University of Helsinki, Haartmaninkatu 8, 00290, Helsinki, Finland
- Digital Precision Cancer Medicine Flagship (iCAN), University of Helsinki, 00014, Helsinki, Finland
| | - Sara Feola
- Drug Research Program (DRP), ImmunoViroTherapy Lab (IVT), Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5E, 00790, Helsinki, Finland
- Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Fabianinkatu 33, 00710, Helsinki, Finland
- Translational Immunology Program (TRIMM), Faculty of Medicine Helsinki University, University of Helsinki, Haartmaninkatu 8, 00290, Helsinki, Finland
- Digital Precision Cancer Medicine Flagship (iCAN), University of Helsinki, 00014, Helsinki, Finland
| | - Michaela Feodoroff
- Drug Research Program (DRP), ImmunoViroTherapy Lab (IVT), Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5E, 00790, Helsinki, Finland
- Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Fabianinkatu 33, 00710, Helsinki, Finland
- Translational Immunology Program (TRIMM), Faculty of Medicine Helsinki University, University of Helsinki, Haartmaninkatu 8, 00290, Helsinki, Finland
- Digital Precision Cancer Medicine Flagship (iCAN), University of Helsinki, 00014, Helsinki, Finland
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Beatriz Martins
- Drug Research Program (DRP), ImmunoViroTherapy Lab (IVT), Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5E, 00790, Helsinki, Finland
- Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Fabianinkatu 33, 00710, Helsinki, Finland
- Translational Immunology Program (TRIMM), Faculty of Medicine Helsinki University, University of Helsinki, Haartmaninkatu 8, 00290, Helsinki, Finland
- Digital Precision Cancer Medicine Flagship (iCAN), University of Helsinki, 00014, Helsinki, Finland
| | - Hanne Cojoc
- Valo Therapeutics Oy, Viikinkaari 6, Helsinki, Finland, 00790, Helsinki, Finland
| | - Salvatore Russo
- Drug Research Program (DRP), ImmunoViroTherapy Lab (IVT), Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5E, 00790, Helsinki, Finland
- Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Fabianinkatu 33, 00710, Helsinki, Finland
- Translational Immunology Program (TRIMM), Faculty of Medicine Helsinki University, University of Helsinki, Haartmaninkatu 8, 00290, Helsinki, Finland
- Digital Precision Cancer Medicine Flagship (iCAN), University of Helsinki, 00014, Helsinki, Finland
| | - Manlio Fusciello
- Drug Research Program (DRP), ImmunoViroTherapy Lab (IVT), Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5E, 00790, Helsinki, Finland
- Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Fabianinkatu 33, 00710, Helsinki, Finland
- Translational Immunology Program (TRIMM), Faculty of Medicine Helsinki University, University of Helsinki, Haartmaninkatu 8, 00290, Helsinki, Finland
- Digital Precision Cancer Medicine Flagship (iCAN), University of Helsinki, 00014, Helsinki, Finland
| | - Firas Hamdan
- Drug Research Program (DRP), ImmunoViroTherapy Lab (IVT), Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5E, 00790, Helsinki, Finland
- Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Fabianinkatu 33, 00710, Helsinki, Finland
- Translational Immunology Program (TRIMM), Faculty of Medicine Helsinki University, University of Helsinki, Haartmaninkatu 8, 00290, Helsinki, Finland
- Digital Precision Cancer Medicine Flagship (iCAN), University of Helsinki, 00014, Helsinki, Finland
| | - Valentina Ferrari
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20090, Pieve Emanuele, MI, Italy
| | - Daniele Ciampi
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20090, Pieve Emanuele, MI, Italy
| | - Ilkka Ilonen
- Department of General Thoracic and Esophageal Surgery, Heart and Lung Center, Helsinki University Hospital, 00029, Helsinki, Finland
- Department of Surgery, Clinicum, University of Helsinki, 00029, Helsinki, Finland
| | - Jari Räsänen
- Department of General Thoracic and Esophageal Surgery, Heart and Lung Center, Helsinki University Hospital, 00029, Helsinki, Finland
- Department of Surgery, Clinicum, University of Helsinki, 00029, Helsinki, Finland
| | - Mikko Mäyränpää
- Department of Pathology, Helsinki University Hospital, Helsinki, Finland
| | - Jukka Partanen
- Research & Development Finnish Red Cross Blood Service Helsinki, Kivihaantie 7, 00310, Helsinki, Finland
| | - Satu Koskela
- Finnish Red Cross Blood Service Biobank, Härkälenkki 13, 01730, Vantaa, Finland
| | - Jarno Honkanen
- Finnish Red Cross Blood Service Biobank, Härkälenkki 13, 01730, Vantaa, Finland
| | - Jussi Halonen
- Finnish Red Cross Blood Service Biobank, Härkälenkki 13, 01730, Vantaa, Finland
| | - Lukasz Kuryk
- Valo Therapeutics Oy, Viikinkaari 6, Helsinki, Finland, 00790, Helsinki, Finland
- Department of Virology, National Institute of Public Health NIH-National Research Institute, 24 Chocimska Str., 00-791, Warsaw, Poland
| | - Maria Rescigno
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20090, Pieve Emanuele, MI, Italy
- IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089, Rozzano, MI, Italy
| | - Mikaela Grönholm
- Drug Research Program (DRP), ImmunoViroTherapy Lab (IVT), Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5E, 00790, Helsinki, Finland
- Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Fabianinkatu 33, 00710, Helsinki, Finland
- Translational Immunology Program (TRIMM), Faculty of Medicine Helsinki University, University of Helsinki, Haartmaninkatu 8, 00290, Helsinki, Finland
- Digital Precision Cancer Medicine Flagship (iCAN), University of Helsinki, 00014, Helsinki, Finland
| | - Rui M Branca
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Janne Lehtiö
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Vincenzo Cerullo
- Drug Research Program (DRP), ImmunoViroTherapy Lab (IVT), Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5E, 00790, Helsinki, Finland.
- Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Fabianinkatu 33, 00710, Helsinki, Finland.
- Translational Immunology Program (TRIMM), Faculty of Medicine Helsinki University, University of Helsinki, Haartmaninkatu 8, 00290, Helsinki, Finland.
- Digital Precision Cancer Medicine Flagship (iCAN), University of Helsinki, 00014, Helsinki, Finland.
- Department of Molecular Medicine and Medical Biotechnology and CEINGE, Naples University Federico II, 80131, Naples, Italy.
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11
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Quixabeira DCA, Jirovec E, Pakola S, Havunen R, Basnet S, Santos JM, Kudling TV, Clubb JHA, Haybout L, Arias V, Grönberg-Vähä-Koskela S, Cervera-Carrascon V, Pasanen A, Anttila M, Tapper J, Kanerva A, Hemminki A. Improving the cytotoxic response of tumor-infiltrating lymphocytes towards advanced stage ovarian cancer with an oncolytic adenovirus expressing a human vIL-2 cytokine. Cancer Gene Ther 2023; 30:1543-1553. [PMID: 37666898 PMCID: PMC10645590 DOI: 10.1038/s41417-023-00658-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 07/19/2023] [Accepted: 08/02/2023] [Indexed: 09/06/2023]
Abstract
While the presence of tumor-infiltrating lymphocytes (TILs) associates with improved survival prognosis in ovarian cancer (OvCa) patients, TIL therapy benefit is limited. Here, we evaluated an oncolytic adenovirus coding for a human variant IL-2 (vIL-2) cytokine, Ad5/3-E2F-d24-vIL2 (vIL-2 virus), also known as TILT-452, as an immunotherapeutic strategy to enhance TIL responsiveness towards advanced stage OvCa tumors. Fragments of resected human OvCa tumors were processed into single-cell suspensions, and autologous TILs were expanded from said samples. OvCa tumor specimens were co-cultured with TILs plus vIL-2 virus, and cell killing was assessed in real time through cell impedance measurement. Combination therapy was further evaluated in vivo through a patient-derived xenograft (PDX) ovarian cancer murine model. The combination of vIL-2 virus plus TILs had best cancer cell killing ex vivo compared to TILs monotherapy. These results were supported by an in vivo experiment, where the best OvCa tumor control was obtained when vIL-2 virus was added to TIL therapy. Furthermore, the proposed therapy induced a highly cytotoxic phenotype demonstrated by increased granzyme B intensity in NK cells, CD4+ T, and CD8+ T cells in treated tumors. Our results demonstrate that Ad5/3-E2F-d24-vIL2 therapy consistently improved TILs therapy cytotoxicity in treated human OvCa tumors.
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Affiliation(s)
- D C A Quixabeira
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- TILT Biotherapeutics Ltd, Helsinki, Finland
| | - E Jirovec
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - S Pakola
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - R Havunen
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- TILT Biotherapeutics Ltd, Helsinki, Finland
| | - S Basnet
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - J M Santos
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- TILT Biotherapeutics Ltd, Helsinki, Finland
| | - T V Kudling
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - J H A Clubb
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- TILT Biotherapeutics Ltd, Helsinki, Finland
| | - L Haybout
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - V Arias
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - S Grönberg-Vähä-Koskela
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - V Cervera-Carrascon
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- TILT Biotherapeutics Ltd, Helsinki, Finland
| | - A Pasanen
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - M Anttila
- Pathology, Finnish Food Authority, Helsinki, Finland
| | - J Tapper
- Department of Obstetrics and Gynecology, Helsinki University Central Hospital, Helsinki, Finland
| | - A Kanerva
- Department of Obstetrics and Gynecology, Helsinki University Central Hospital, Helsinki, Finland
| | - A Hemminki
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- TILT Biotherapeutics Ltd, Helsinki, Finland.
- Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.
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12
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Santangeli A, Weigel B, Antão LH, Kaarlejärvi E, Hällfors M, Lehikoinen A, Lindén A, Salemaa M, Tonteri T, Merilä P, Vuorio K, Ovaskainen O, Vanhatalo J, Roslin T, Saastamoinen M. Mixed effects of a national protected area network on terrestrial and freshwater biodiversity. Nat Commun 2023; 14:5426. [PMID: 37704608 PMCID: PMC10499833 DOI: 10.1038/s41467-023-41073-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 08/22/2023] [Indexed: 09/15/2023] Open
Abstract
Protected areas are considered fundamental to counter biodiversity loss. However, evidence for their effectiveness in averting local extinctions remains scarce and taxonomically biased. We employ a robust counterfactual multi-taxon approach to compare occupancy patterns of 638 species, including birds (150), mammals (23), plants (39) and phytoplankton (426) between protected and unprotected sites across four decades in Finland. We find mixed impacts of protected areas, with only a small proportion of species explicitly benefiting from protection-mainly through slower rates of decline inside protected areas. The benefits of protection are enhanced for larger protected areas and are traceable to when the sites were protected, but are mostly unrelated to species conservation status or traits (size, climatic niche and threat status). Our results suggest that the current protected area network can partly contribute to slow down declines in occupancy rates, but alone will not suffice to halt the biodiversity crisis. Efforts aimed at improving coverage, connectivity and management will be key to enhance the effectiveness of protected areas towards bending the curve of biodiversity loss.
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Affiliation(s)
- Andrea Santangeli
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
- Animal Demography and Ecology Unit, Institute for Mediterranean Studies (IMEDEA), CSIC-UIB, 07190, Esporles, Spain.
| | - Benjamin Weigel
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- INRAE, EABX, Cestas, France
| | - Laura H Antão
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Elina Kaarlejärvi
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Maria Hällfors
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Nature Solutions Unit, Finnish Environment Institute (SYKE), Helsinki, Finland
| | - Aleksi Lehikoinen
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | | | - Maija Salemaa
- Natural Resources Institute (LUKE), Helsinki, Finland
| | - Tiina Tonteri
- Natural Resources Institute (LUKE), Helsinki, Finland
| | - Päivi Merilä
- Natural Resources Institute (LUKE), Helsinki, Finland
| | - Kristiina Vuorio
- Nature Solutions Unit, Finnish Environment Institute (SYKE), Helsinki, Finland
| | - Otso Ovaskainen
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35 (Survontie 9C), FI-40014, Jyväskylä, Finland
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jarno Vanhatalo
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, Faculty of Science, University of Helsinki, Helsinki, Finland
| | - Tomas Roslin
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Spatial Foodweb Ecology Group, Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
- Spatial Foodweb Ecology Group, Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Marjo Saastamoinen
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
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13
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Karttunen K, Patel D, Xia J, Fei L, Palin K, Aaltonen L, Sahu B. Transposable elements as tissue-specific enhancers in cancers of endodermal lineage. Nat Commun 2023; 14:5313. [PMID: 37658059 PMCID: PMC10474299 DOI: 10.1038/s41467-023-41081-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 08/23/2023] [Indexed: 09/03/2023] Open
Abstract
Transposable elements (TE) are repetitive genomic elements that harbor binding sites for human transcription factors (TF). A regulatory role for TEs has been suggested in embryonal development and diseases such as cancer but systematic investigation of their functions has been limited by their widespread silencing in the genome. Here, we utilize unbiased massively parallel reporter assay data using a whole human genome library to identify TEs with functional enhancer activity in two human cancer types of endodermal lineage, colorectal and liver cancers. We show that the identified TE enhancers are characterized by genomic features associated with active enhancers, such as epigenetic marks and TF binding. Importantly, we identify distinct TE subfamilies that function as tissue-specific enhancers, namely MER11- and LTR12-elements in colon and liver cancers, respectively. These elements are bound by distinct TFs in each cell type, and they have predicted associations to differentially expressed genes. In conclusion, these data demonstrate how different cancer types can utilize distinct TEs as tissue-specific enhancers, paving the way for comprehensive understanding of the role of TEs as bona fide enhancers in the cancer genomes.
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Affiliation(s)
- Konsta Karttunen
- Applied Tumor Genomics Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Divyesh Patel
- Applied Tumor Genomics Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Jihan Xia
- Applied Tumor Genomics Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Liangru Fei
- Applied Tumor Genomics Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kimmo Palin
- Applied Tumor Genomics Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Lauri Aaltonen
- Applied Tumor Genomics Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Biswajyoti Sahu
- Applied Tumor Genomics Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland.
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway.
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14
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Rehan S, Tranter D, Sharp PP, Craven GB, Lowe E, Anderl JL, Muchamuel T, Abrishami V, Kuivanen S, Wenzell NA, Jennings A, Kalyanaraman C, Strandin T, Javanainen M, Vapalahti O, Jacobson MP, McMinn D, Kirk CJ, Huiskonen JT, Taunton J, Paavilainen VO. Signal peptide mimicry primes Sec61 for client-selective inhibition. Nat Chem Biol 2023; 19:1054-1062. [PMID: 37169961 PMCID: PMC10449633 DOI: 10.1038/s41589-023-01326-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 04/06/2023] [Indexed: 05/13/2023]
Abstract
Preventing the biogenesis of disease-relevant proteins is an attractive therapeutic strategy, but attempts to target essential protein biogenesis factors have been hampered by excessive toxicity. Here we describe KZR-8445, a cyclic depsipeptide that targets the Sec61 translocon and selectively disrupts secretory and membrane protein biogenesis in a signal peptide-dependent manner. KZR-8445 potently inhibits the secretion of pro-inflammatory cytokines in primary immune cells and is highly efficacious in a mouse model of rheumatoid arthritis. A cryogenic electron microscopy structure reveals that KZR-8445 occupies the fully opened Se61 lateral gate and blocks access to the lumenal plug domain. KZR-8445 binding stabilizes the lateral gate helices in a manner that traps select signal peptides in the Sec61 channel and prevents their movement into the lipid bilayer. Our results establish a framework for the structure-guided discovery of novel therapeutics that selectively modulate Sec61-mediated protein biogenesis.
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Affiliation(s)
- Shahid Rehan
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Dale Tranter
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Phillip P Sharp
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Gregory B Craven
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Eric Lowe
- Kezar Life Sciences, South San Francisco, CA, USA
| | | | | | - Vahid Abrishami
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Suvi Kuivanen
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nicole A Wenzell
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | | | - Chakrapani Kalyanaraman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of California, San Francisco, CA, USA
| | - Tomas Strandin
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Matti Javanainen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Olli Vapalahti
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of California, San Francisco, CA, USA
| | | | | | - Juha T Huiskonen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.
| | - Ville O Paavilainen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland.
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15
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Pavic K, Gupta N, Omella JD, Derua R, Aakula A, Huhtaniemi R, Määttä JA, Höfflin N, Okkeri J, Wang Z, Kauko O, Varjus R, Honkanen H, Abankwa D, Köhn M, Hytönen VP, Xu W, Nilsson J, Page R, Janssens V, Leitner A, Westermarck J. Structural mechanism for inhibition of PP2A-B56α and oncogenicity by CIP2A. Nat Commun 2023; 14:1143. [PMID: 36854761 PMCID: PMC9974998 DOI: 10.1038/s41467-023-36693-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 02/09/2023] [Indexed: 03/02/2023] Open
Abstract
The protein phosphatase 2A (PP2A) heterotrimer PP2A-B56α is a human tumour suppressor. However, the molecular mechanisms inhibiting PP2A-B56α in cancer are poorly understood. Here, we report molecular level details and structural mechanisms of PP2A-B56α inhibition by an oncoprotein CIP2A. Upon direct binding to PP2A-B56α trimer, CIP2A displaces the PP2A-A subunit and thereby hijacks both the B56α, and the catalytic PP2Ac subunit to form a CIP2A-B56α-PP2Ac pseudotrimer. Further, CIP2A competes with B56α substrate binding by blocking the LxxIxE-motif substrate binding pocket on B56α. Relevant to oncogenic activity of CIP2A across human cancers, the N-terminal head domain-mediated interaction with B56α stabilizes CIP2A protein. Functionally, CRISPR/Cas9-mediated single amino acid mutagenesis of the head domain blunted MYC expression and MEK phosphorylation, and abrogated triple-negative breast cancer in vivo tumour growth. Collectively, we discover a unique multi-step hijack and mute protein complex regulation mechanism resulting in tumour suppressor PP2A-B56α inhibition. Further, the results unfold a structural determinant for the oncogenic activity of CIP2A, potentially facilitating therapeutic modulation of CIP2A in cancer and other diseases.
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Affiliation(s)
- Karolina Pavic
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Nikhil Gupta
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Judit Domènech Omella
- Laboratory of Protein Phosphorylation & Proteomics, Department of Cellular & Molecular Medicine, University of Leuven (KU Leuven), B-3000, Leuven, Belgium
| | - Rita Derua
- Laboratory of Protein Phosphorylation & Proteomics, Department of Cellular & Molecular Medicine, University of Leuven (KU Leuven), B-3000, Leuven, Belgium
- SyBioMa, University of Leuven (KU Leuven), B-3000, Leuven, Belgium
| | - Anna Aakula
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Riikka Huhtaniemi
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Juha A Määttä
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland and Fimlab Laboratories, 33520, Tampere, Finland
| | - Nico Höfflin
- Faculty of Biology, Institute of Biology III, University of Freiburg, 79104, Freiburg, Germany
| | - Juha Okkeri
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Zhizhi Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Otto Kauko
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Roosa Varjus
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Henrik Honkanen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Daniel Abankwa
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Maja Köhn
- Faculty of Biology, Institute of Biology III, University of Freiburg, 79104, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Vesa P Hytönen
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland and Fimlab Laboratories, 33520, Tampere, Finland
| | - Wenqing Xu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jakob Nilsson
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Rebecca Page
- Department of Chemistry and Biochemistry University of Arizona, Tucson, AZ, USA
| | - Veerle Janssens
- Laboratory of Protein Phosphorylation & Proteomics, Department of Cellular & Molecular Medicine, University of Leuven (KU Leuven), B-3000, Leuven, Belgium
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093, Zurich, Switzerland
| | - Jukka Westermarck
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland.
- Institute of Biomedicine, University of Turku, 20520, Turku, Finland.
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16
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Pihlajamaa P, Kauko O, Sahu B, Kivioja T, Taipale J. A competitive precision CRISPR method to identify the fitness effects of transcription factor binding sites. Nat Biotechnol 2023; 41:197-203. [PMID: 36163549 PMCID: PMC9931575 DOI: 10.1038/s41587-022-01444-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 07/20/2022] [Indexed: 12/26/2022]
Abstract
Here we describe a competitive genome editing method that measures the effect of mutations on molecular functions, based on precision CRISPR editing using template libraries with either the original or altered sequence, and a sequence tag, enabling direct comparison between original and mutated cells. Using the example of the MYC oncogene, we identify important transcriptional targets and show that E-box mutations at MYC target gene promoters reduce cellular fitness.
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Affiliation(s)
- Päivi Pihlajamaa
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Otto Kauko
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Biswajyoti Sahu
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Teemu Kivioja
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Jussi Taipale
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden.
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17
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Belik M, Jalkanen P, Lundberg R, Reinholm A, Laine L, Väisänen E, Skön M, Tähtinen PA, Ivaska L, Pakkanen SH, Häkkinen HK, Ortamo E, Pasternack A, Ritvos MA, Naves RA, Miettinen S, Sironen T, Vapalahti O, Ritvos O, Österlund P, Kantele A, Lempainen J, Kakkola L, Kolehmainen P, Julkunen I. Comparative analysis of COVID-19 vaccine responses and third booster dose-induced neutralizing antibodies against Delta and Omicron variants. Nat Commun 2022; 13:2476. [PMID: 35513437 PMCID: PMC9072399 DOI: 10.1038/s41467-022-30162-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/19/2022] [Indexed: 11/08/2022] Open
Abstract
Two COVID-19 mRNA (of BNT162b2, mRNA-1273) and two adenovirus vector vaccines (ChAdOx1 and Janssen) are licensed in Europe, but optimization of regime and dosing is still ongoing. Here we show in health care workers (n = 328) that two doses of BNT162b2, mRNA-1273, or a combination of ChAdOx1 adenovirus vector and mRNA vaccines administrated with a long 12-week dose interval induce equally high levels of anti-SARS-CoV-2 spike antibodies and neutralizing antibodies against D614 and Delta variant. By contrast, two doses of BNT162b2 with a short 3-week interval induce 2-3-fold lower titers of neutralizing antibodies than those from the 12-week interval, yet a third BNT162b2 or mRNA-1273 booster dose increases the antibody levels 4-fold compared to the levels after the second dose, as well as induces neutralizing antibody against Omicron BA.1 variant. Our data thus indicates that a third COVID-19 mRNA vaccine may induce cross-protective neutralizing antibodies against multiple variants.
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Affiliation(s)
- Milja Belik
- Institute of Biomedicine, University of Turku, Turku, Finland.
| | - Pinja Jalkanen
- Institute of Biomedicine, University of Turku, Turku, Finland
| | | | - Arttu Reinholm
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Larissa Laine
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Elina Väisänen
- Institute of Biomedicine, University of Turku, Turku, Finland
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Marika Skön
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Paula A Tähtinen
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland
| | - Lauri Ivaska
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland
| | - Sari H Pakkanen
- Department of Infectious Diseases, Meilahti Vaccination Research Center, MeVac, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Hanni K Häkkinen
- Department of Infectious Diseases, Meilahti Vaccination Research Center, MeVac, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Eeva Ortamo
- Department of Infectious Diseases, Meilahti Vaccination Research Center, MeVac, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Arja Pasternack
- Department of Physiology, University of Helsinki, Helsinki, Finland
| | - Mikael A Ritvos
- Department of Physiology, University of Helsinki, Helsinki, Finland
| | - Rauno A Naves
- Department of Physiology, University of Helsinki, Helsinki, Finland
| | - Simo Miettinen
- Department of Virology, University of Helsinki and HUSLAB, Helsinki, Finland
| | - Tarja Sironen
- Department of Virology, University of Helsinki and HUSLAB, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Olli Vapalahti
- Department of Virology, University of Helsinki and HUSLAB, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Olli Ritvos
- Department of Physiology, University of Helsinki, Helsinki, Finland
| | | | - Anu Kantele
- Department of Infectious Diseases, Meilahti Vaccination Research Center, MeVac, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Johanna Lempainen
- Institute of Biomedicine, University of Turku, Turku, Finland
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland
- Clinical Microbiology, Turku University Hospital, Turku, Finland
| | - Laura Kakkola
- Institute of Biomedicine, University of Turku, Turku, Finland
| | | | - Ilkka Julkunen
- Institute of Biomedicine, University of Turku, Turku, Finland.
- Clinical Microbiology, Turku University Hospital, Turku, Finland.
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18
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Sahu B, Pihlajamaa P, Zhang K, Palin K, Ahonen S, Cervera A, Ristimäki A, Aaltonen LA, Hautaniemi S, Taipale J. Human cell transformation by combined lineage conversion and oncogene expression. Oncogene 2021; 40:5533-5547. [PMID: 34302118 PMCID: PMC8429043 DOI: 10.1038/s41388-021-01940-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 06/17/2021] [Accepted: 07/01/2021] [Indexed: 02/07/2023]
Abstract
Cancer is the most complex genetic disease known, with mutations implicated in more than 250 genes. However, it is still elusive which specific mutations found in human patients lead to tumorigenesis. Here we show that a combination of oncogenes that is characteristic of liver cancer (CTNNB1, TERT, MYC) induces senescence in human fibroblasts and primary hepatocytes. However, reprogramming fibroblasts to a liver progenitor fate, induced hepatocytes (iHeps), makes them sensitive to transformation by the same oncogenes. The transformed iHeps are highly proliferative, tumorigenic in nude mice, and bear gene expression signatures of liver cancer. These results show that tumorigenesis is triggered by a combination of three elements: the set of driver mutations, the cellular lineage, and the state of differentiation of the cells along the lineage. Our results provide direct support for the role of cell identity as a key determinant in transformation and establish a paradigm for studying the dynamic role of oncogenic drivers in human tumorigenesis.
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Affiliation(s)
- Biswajyoti Sahu
- Applied Tumor Genomics Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Päivi Pihlajamaa
- Applied Tumor Genomics Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Kaiyang Zhang
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kimmo Palin
- Applied Tumor Genomics Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Saija Ahonen
- Applied Tumor Genomics Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Alejandra Cervera
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico, Finland
| | - Ari Ristimäki
- Applied Tumor Genomics Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Pathology, HUSLAB and HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Lauri A Aaltonen
- Applied Tumor Genomics Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Sampsa Hautaniemi
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jussi Taipale
- Applied Tumor Genomics Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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19
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Koskela O, Montonen T, Belay B, Figueiras E, Pursiainen S, Hyttinen J. Gaussian Light Model in Brightfield Optical Projection Tomography. Sci Rep 2019; 9:13934. [PMID: 31558755 PMCID: PMC6763473 DOI: 10.1038/s41598-019-50469-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 09/12/2019] [Indexed: 01/27/2023] Open
Abstract
This study focuses on improving the reconstruction process of the brightfield optical projection tomography (OPT). OPT is often described as the optical equivalent of X-ray computed tomography, but based on visible light. The detection optics used to collect light in OPT focus on a certain distance and induce blurring in those features out of focus. However, the conventionally used inverse Radon transform assumes an absolute focus throughout the propagation axis. In this study, we model the focusing properties of the detection by coupling Gaussian beam model (GBM) with the Radon transform. The GBM enables the construction of a projection operator that includes modeling of the blurring caused by the light beam. We also introduce the concept of a stretched GBM (SGBM) in which the Gaussian beam is scaled in order to avoid the modeling errors related to the determination of the focal plane. Furthermore, a thresholding approach is used to compress memory usage. We tested the GBM and SGBM approaches using simulated and experimental data in mono- and multifocal modes. When compared with the traditionally used filtered backprojection algorithm, the iteratively computed reconstructions, including the Gaussian models GBM and SGBM, provided smoother images with higher contrast.
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Affiliation(s)
- Olli Koskela
- Faculty of Medicine and Health Technology and BioMediTech Institute, Tampere University, Tampere, 33014, Finland.
- HAMK Smart Research Unit, Häme University of Applied Sciences, Hämeenlinna, 13100, Finland.
| | - Toni Montonen
- Faculty of Medicine and Health Technology and BioMediTech Institute, Tampere University, Tampere, 33014, Finland
| | - Birhanu Belay
- Faculty of Medicine and Health Technology and BioMediTech Institute, Tampere University, Tampere, 33014, Finland
| | - Edite Figueiras
- Champalimaud Research, Champalimaud Foundation, Lisbon, 1400-038, Portugal
| | - Sampsa Pursiainen
- Faculty of Information Technology and Communication Sciences, Tampere University, Tampere, 33014, Finland
| | - Jari Hyttinen
- Faculty of Medicine and Health Technology and BioMediTech Institute, Tampere University, Tampere, 33014, Finland
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