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Xing L, Gkini V, Nieminen AI, Zhou HC, Aquilino M, Naumann R, Reppe K, Tanaka K, Carmeliet P, Heikinheimo O, Pääbo S, Huttner WB, Namba T. Functional synergy of a human-specific and an ape-specific metabolic regulator in human neocortex development. Nat Commun 2024; 15:3468. [PMID: 38658571 PMCID: PMC11043075 DOI: 10.1038/s41467-024-47437-8] [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: 11/03/2023] [Accepted: 04/02/2024] [Indexed: 04/26/2024] Open
Abstract
Metabolism has recently emerged as a major target of genes implicated in the evolutionary expansion of human neocortex. One such gene is the human-specific gene ARHGAP11B. During human neocortex development, ARHGAP11B increases the abundance of basal radial glia, key progenitors for neocortex expansion, by stimulating glutaminolysis (glutamine-to-glutamate-to-alpha-ketoglutarate) in mitochondria. Here we show that the ape-specific protein GLUD2 (glutamate dehydrogenase 2), which also operates in mitochondria and converts glutamate-to-αKG, enhances ARHGAP11B's ability to increase basal radial glia abundance. ARHGAP11B + GLUD2 double-transgenic bRG show increased production of aspartate, a metabolite essential for cell proliferation, from glutamate via alpha-ketoglutarate and the TCA cycle. Hence, during human evolution, a human-specific gene exploited the existence of another gene that emerged during ape evolution, to increase, via concerted changes in metabolism, progenitor abundance and neocortex size.
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Affiliation(s)
- Lei Xing
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada.
| | - Vasiliki Gkini
- Neuroscience Center, HiLIFE - Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Anni I Nieminen
- FIMM Metabolomics Unit, Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Hui-Chao Zhou
- Center for Cancer Biology (CCB), VIB-KU Leuven, B-3000, Leuven, Belgium
| | - Matilde Aquilino
- Neuroscience Center, HiLIFE - Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Ronald Naumann
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Katrin Reppe
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Kohichi Tanaka
- Laboratory of Molecular Neuroscience, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Peter Carmeliet
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, B-3000, Leuven, Belgium
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, B-3000, Leuven, Belgium
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Oskari Heikinheimo
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Human Evolutionary Genomics Unit, Okinawa Institute of Science and Technology, Okinawa, Onna-son, Japan
| | - Wieland B Huttner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
| | - Takashi Namba
- Neuroscience Center, HiLIFE - Helsinki Institute of Life Science, University of Helsinki, Helsinki, 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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3
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Kallionpää RA, Johansson E, Böckerman P, Peltonen J, Peltonen S. The contribution of morbidity and unemployment for the reduced labor market participation of individuals with neurofibromatosis 1 in Finland. Eur J Hum Genet 2024; 32:83-90. [PMID: 37460655 PMCID: PMC10772102 DOI: 10.1038/s41431-023-01426-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 12/13/2022] [Revised: 05/24/2023] [Accepted: 06/29/2023] [Indexed: 01/09/2024] Open
Abstract
Neurofibromatosis 1 (NF1) is a multisystem disorder associated with, for example, a high risk for cancer, a variety of behavioral and cognitive deficits, low educational attainment and decreased income. We now examined the labor market participation of individuals with NF1. We analyzed the numbers of days of work, unemployment, and sickness allowance among 742 Finnish individuals with NF1 aged 20-59 years using nationwide register data from Statistics Finland and the Social Insurance Institution of Finland. The individuals with NF1 were compared with a control cohort of 8716 individuals matched with age, sex, and the area of residence. Individuals with NF1 had a significantly lower number of working days per year than the controls (rate ratio [RR] 0.93, 95% CI 0.91-0.95). Unemployment (RR 1.79, 95% CI 1.58-2.02), and sickness absence (RR 1.44, 95% CI 1.25-1.67) were more frequent in the NF1 than in the control group. The causes of sickness allowances were highly concordant with the previously reported morbidity profile of NF1 including neoplasms, cardiovascular disease, mental and behavioral diseases, and neurological diseases. In conclusion, NF1 significantly interferes with labor market participation via both unemployment and morbidity. Unemployment seems to cause more days of not working than sickness absence.
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Affiliation(s)
- Roope A Kallionpää
- Cancer Research Unit and FICAN West Cancer Centre, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Edvard Johansson
- Faculty of Social Sciences, Business, and Economics, Åbo Akademi University, Turku, Finland
| | - Petri Böckerman
- Jyväskylä University School of Business and Economics, Jyväskylä, Finland
- Labour Institute for Economic Research LABORE, Helsinki, Finland
- IZA Institute of Labor Economics, Bonn, Germany
| | - Juha Peltonen
- Cancer Research Unit and FICAN West Cancer Centre, Institute of Biomedicine, University of Turku, Turku, Finland.
| | - Sirkku Peltonen
- Department of Dermatology and Venereology, University of Turku, Turku, Finland
- Department of Dermatology, Turku University Hospital, Turku, Finland
- Department of Dermatology and Venereology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Dermatology and Venereology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Dermatology and Allergology, University of Helsinki, Helsinki, Finland
- Skin and Allergy Hospital, Helsinki University Hospital, Helsinki, Finland
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4
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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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5
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Olkinuora A, Nieminen TT, Douglas S, Kauppinen A, Kontro M, Väänänen J, Kankainen M, Ristimäki A, Mäkinen M, Lahermo P, Heckman C, Saarela J, Salonen M, Lepistö A, Järvinen H, Mecklin JP, Kilpivaara O, Wartiovaara-Kautto U, Porkka K, Peltomäki P. Identification of DHX40 as a candidate susceptibility gene for colorectal and hematological neoplasia. Leukemia 2023; 37:2301-2305. [PMID: 37696923 PMCID: PMC10624609 DOI: 10.1038/s41375-023-02021-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/15/2023] [Accepted: 09/01/2023] [Indexed: 09/13/2023]
Affiliation(s)
- Alisa Olkinuora
- Department of Medical and Clinical Genetics, University of Helsinki, 00014, Helsinki, Finland.
| | - Taina T Nieminen
- Department of Medical and Clinical Genetics, University of Helsinki, 00014, Helsinki, Finland.
| | - Suvi Douglas
- Department of Medical and Clinical Genetics, University of Helsinki, 00014, Helsinki, Finland
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
| | - Anni Kauppinen
- Department of Medical and Clinical Genetics, University of Helsinki, 00014, Helsinki, Finland
| | - Mika Kontro
- Department of Hematology, Helsinki University Hospital, Comprehensive Cancer Center and University of Helsinki, 00014, Helsinki, Finland
- HiLIFE Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00014, Helsinki, Finland
- Foundation for the Finnish Cancer Institute, 00014, Helsinki, Finland
| | - Juho Väänänen
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
| | - Matti Kankainen
- HUSLAB Laboratory of Genetics, HUS Diagnostic Center, HUS, Helsinki University Hospital, 00029, Helsinki, Finland
- Hematology Research Unit Helsinki, University of Helsinki, 00014, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014, Helsinki, Finland
| | - Ari Ristimäki
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
- Department of Pathology, HUSLAB, HUS Diagnostic Center, Helsinki University Hospital and University of Helsinki, 00014, Helsinki, Finland
| | - Markus Mäkinen
- Research Unit of Cancer and Translational Medicine, Department of Pathology, 90014, University of Oulu, and Department of Pathology, Oulu University Hospital, OYS, 90029, Oulu, Finland
| | - Päivi Lahermo
- HiLIFE Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00014, Helsinki, Finland
| | - Caroline Heckman
- HiLIFE Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00014, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Janna Saarela
- HiLIFE Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00014, Helsinki, Finland
- Centre for Molecular Medicine Norway, NCMM, University of Oslo, 0318, Oslo, Norway
| | - Milla Salonen
- Department of Medical and Clinical Genetics, University of Helsinki, 00014, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, 00014, Helsinki, Finland
- Folkhälsan Research Center, 00290, Helsinki, Finland
| | - Anna Lepistö
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
- Department of Abdominal Surgery, Helsinki University Hospital and University of Helsinki, 00014, Helsinki, Finland
| | - Heikki Järvinen
- Department of Abdominal Surgery, Helsinki University Hospital and University of Helsinki, 00014, Helsinki, Finland
| | - Jukka-Pekka Mecklin
- Department of Education & Research and Surgery, Jyväskylä Central Hospital, 40620, Jyväskylä, Finland
- Department of Sports & Health Sciences, Jyväskylä University, 40014, Jyväskylä, Finland
| | - Outi Kilpivaara
- Department of Medical and Clinical Genetics, University of Helsinki, 00014, Helsinki, Finland
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
- HUSLAB Laboratory of Genetics, HUS Diagnostic Center, HUS, Helsinki University Hospital, 00029, Helsinki, Finland
| | - Ulla Wartiovaara-Kautto
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
- Department of Hematology, Helsinki University Hospital, Comprehensive Cancer Center and University of Helsinki, 00014, Helsinki, Finland
| | - Kimmo Porkka
- Department of Hematology, Helsinki University Hospital, Comprehensive Cancer Center and University of Helsinki, 00014, Helsinki, Finland.
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland.
| | - Päivi Peltomäki
- Department of Medical and Clinical Genetics, University of Helsinki, 00014, Helsinki, Finland.
- HUSLAB Laboratory of Genetics, HUS Diagnostic Center, HUS, Helsinki University Hospital, 00029, Helsinki, Finland.
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6
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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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7
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Virtanen V, Paunu K, Kukkula A, Niva S, Junila Y, Toriseva M, Jokilehto T, Mäkelä S, Huhtaniemi R, Poutanen M, Paatero I, Sundvall M. Glucocorticoid receptor-induced non-muscle caldesmon regulates metastasis in castration-resistant prostate cancer. Oncogenesis 2023; 12:42. [PMID: 37573448 PMCID: PMC10423232 DOI: 10.1038/s41389-023-00485-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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 07/18/2023] [Accepted: 07/25/2023] [Indexed: 08/14/2023] Open
Abstract
Lethal prostate cancer (PCa) is characterized by the presence of metastases and development of resistance to therapies. Metastases form in a multi-step process enabled by dynamic cytoskeleton remodeling. An actin cytoskeleton regulating gene, CALD1, encodes a protein caldesmon (CaD). Its isoform, low-molecular-weight CaD (l-CaD), operates in non-muscle cells, supporting the function of filaments involved in force production and mechanosensing. Several factors, including glucocorticoid receptor (GR), have been identified as regulators of l-CaD in different cell types, but the regulation of l-CaD in PCa has not been defined. PCa develops resistance in response to therapeutic inhibition of androgen signaling by multiple strategies. Known strategies include androgen receptor (AR) alterations, modified steroid synthesis, and bypassing AR signaling, for example, by GR upregulation. Here, we report that in vitro downregulation of l-CaD promotes epithelial phenotype and reduces spheroid growth in 3D, which is reflected in vivo in reduced formation of metastases in zebrafish PCa xenografts. In accordance, CALD1 mRNA expression correlates with epithelial-to-mesenchymal transition (EMT) transcripts in PCa patients. We also show that CALD1 is highly co-expressed with GR in multiple PCa data sets, and GR activation upregulates l-CaD in vitro. Moreover, GR upregulation associates with increased l-CaD expression after the development of resistance to antiandrogen therapy in PCa xenograft mouse models. In summary, GR-regulated l-CaD plays a role in forming PCa metastases, being clinically relevant when antiandrogen resistance is attained by the means of bypassing AR signaling by GR upregulation.
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Affiliation(s)
- Verneri Virtanen
- Cancer Research Unit, Institute of Biomedicine, and FICAN West Cancer Center Laboratory, University of Turku, and Turku University Hospital, Kiinamyllynkatu 10, 20520, Turku, Finland
| | - Kreetta Paunu
- Cancer Research Unit, Institute of Biomedicine, and FICAN West Cancer Center Laboratory, University of Turku, and Turku University Hospital, Kiinamyllynkatu 10, 20520, Turku, Finland
| | - Antti Kukkula
- Cancer Research Unit, Institute of Biomedicine, and FICAN West Cancer Center Laboratory, University of Turku, and Turku University Hospital, Kiinamyllynkatu 10, 20520, Turku, Finland
| | - Saana Niva
- Cancer Research Unit, Institute of Biomedicine, and FICAN West Cancer Center Laboratory, University of Turku, and Turku University Hospital, Kiinamyllynkatu 10, 20520, Turku, Finland
| | - Ylva Junila
- Cancer Research Unit, Institute of Biomedicine, and FICAN West Cancer Center Laboratory, University of Turku, and Turku University Hospital, Kiinamyllynkatu 10, 20520, Turku, Finland
| | - Mervi Toriseva
- Cancer Research Unit, Institute of Biomedicine, and FICAN West Cancer Center Laboratory, University of Turku, and Turku University Hospital, Kiinamyllynkatu 10, 20520, Turku, Finland
| | - Terhi Jokilehto
- Cancer Research Unit, Institute of Biomedicine, and FICAN West Cancer Center Laboratory, University of Turku, and Turku University Hospital, Kiinamyllynkatu 10, 20520, Turku, Finland
| | - Sari Mäkelä
- Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, and FICAN West Cancer Center, University of Turku, Kiinamyllynkatu 10, 20520, Turku, Finland
| | - Riikka Huhtaniemi
- Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, and FICAN West Cancer Center, University of Turku, Kiinamyllynkatu 10, 20520, Turku, Finland
| | - Matti Poutanen
- Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, and FICAN West Cancer Center, University of Turku, Kiinamyllynkatu 10, 20520, Turku, Finland
| | - Ilkka Paatero
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520, Turku, Finland
| | - Maria Sundvall
- Cancer Research Unit, Institute of Biomedicine, and FICAN West Cancer Center Laboratory, University of Turku, and Turku University Hospital, Kiinamyllynkatu 10, 20520, Turku, Finland.
- Department of Oncology, Turku University Hospital, PL52, 20521, Turku, Finland.
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8
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Kastinen M, Sirniö P, Elomaa H, Ahtiainen M, Väyrynen SA, Herzig KH, Meriläinen S, Aro R, Häivälä R, Rautio T, Saarnio J, Wirta EV, Helminen O, Seppälä TT, Kuopio T, Böhm J, Tuomisto A, Mecklin JP, Mäkinen MJ, Väyrynen JP. Immunological and prognostic significance of tumour necrosis in colorectal cancer. Br J Cancer 2023; 128:2218-2226. [PMID: 37031328 PMCID: PMC10241859 DOI: 10.1038/s41416-023-02258-2] [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: 11/03/2022] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 04/10/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) causes the second most cancer deaths worldwide, but the disease course varies according to tumour characteristics and immunological factors. Our objective was to examine the associations of tumour necrosis with tumour characteristics, immune cell infiltrates, serum cytokine concentrations, as well as prognosis in CRC. METHODS Three independent CRC cohorts, including 1413 patients, were analysed. Associations of the areal percentage of tumour necrosis with clinicopathologic parameters, tumour infiltrating immune cells, cytokine concentrations in systemic and mesenteric vein blood, and survival were examined. RESULTS Higher tumour necrosis percentage associated with shorter colorectal cancer-specific survival independent of tumour grade, T, N or M-class, mismatch repair status, BRAF status, and other possible confounding factors. In the largest cohort (N = 1100), the HR for high tumour necrosis percentage (≥40% vs. <3%) was 3.22 (95% CI 1.68-6.17, Ptrend < 0.0001). Tumour necrosis percentage positively correlated with peripheral serum levels of CXCL8, a proinflammatory chemokine, and negatively correlated with mesenteric serum levels of CXCL10 and mast cell densities in the invasive margin of the tumour. CONCLUSIONS Our results support the value of tumour necrosis as a prognostic factor in colorectal cancer. CXCL8 may have a role in the systemic effects of tumour necrosis.
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Affiliation(s)
- Meeri Kastinen
- Translational Medicine Research Unit, Medical Research Center Oulu, Oulu University Hospital, and University of Oulu, Oulu, Finland
| | - Päivi Sirniö
- Translational Medicine Research Unit, Medical Research Center Oulu, Oulu University Hospital, and University of Oulu, Oulu, Finland
| | - Hanna Elomaa
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
- Department of Education and Research, Wellbeing services county of Central Finland, Jyväskylä, Finland
| | - Maarit Ahtiainen
- Department of Pathology, Wellbeing services county of Central Finland, Jyväskylä, Finland
| | - Sara A Väyrynen
- Department of Internal Medicine, Oulu University Hospital, Oulu, Finland
| | - Karl-Heinz Herzig
- Research Unit of Biomedicine, Medical Research Center Oulu, University of Oulu, Oulu University Hospital, Oulu, Finland
- Department of Pediatric Gastroenterology and Metabolism, Poznan University of Medical Sciences, Poznan, Poland
| | - Sanna Meriläinen
- Translational Medicine Research Unit, Medical Research Center Oulu, Oulu University Hospital, and University of Oulu, Oulu, Finland
| | - Raila Aro
- Translational Medicine Research Unit, Medical Research Center Oulu, Oulu University Hospital, and University of Oulu, Oulu, Finland
| | - Reetta Häivälä
- Translational Medicine Research Unit, Medical Research Center Oulu, Oulu University Hospital, and University of Oulu, Oulu, Finland
| | - Tero Rautio
- Translational Medicine Research Unit, Medical Research Center Oulu, Oulu University Hospital, and University of Oulu, Oulu, Finland
| | - Juha Saarnio
- Translational Medicine Research Unit, Medical Research Center Oulu, Oulu University Hospital, and University of Oulu, Oulu, Finland
| | - Erkki-Ville Wirta
- Department of Gastroenterology and Alimentary Tract Surgery, Tampere University Hospital, Tampere, Finland
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Olli Helminen
- Translational Medicine Research Unit, Medical Research Center Oulu, Oulu University Hospital, and University of Oulu, Oulu, Finland
| | - Toni T Seppälä
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
- Department of Gastrointestinal Surgery, Helsinki University Central Hospital, University of Helsinki, Helsinki, Finland
- Applied Tumor Genomics, Research Program Unit, University of Helsinki, Helsinki, Finland
| | - Teijo Kuopio
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
- Department of Pathology, Wellbeing services county of Central Finland, Jyväskylä, Finland
| | - Jan Böhm
- Department of Pathology, Wellbeing services county of Central Finland, Jyväskylä, Finland
| | - Anne Tuomisto
- Translational Medicine Research Unit, Medical Research Center Oulu, Oulu University Hospital, and University of Oulu, Oulu, Finland
| | - Jukka-Pekka Mecklin
- Department of Education and Research, Wellbeing services county of Central Finland, Jyväskylä, Finland
- Faculty of Sport and Health Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Markus J Mäkinen
- Translational Medicine Research Unit, Medical Research Center Oulu, Oulu University Hospital, and University of Oulu, Oulu, Finland
| | - Juha P Väyrynen
- Translational Medicine Research Unit, Medical Research Center Oulu, Oulu University Hospital, and University of Oulu, Oulu, Finland.
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9
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Murumägi A, Ungureanu D, Khan S, Arjama M, Välimäki K, Ianevski A, Ianevski P, Bergström R, Dini A, Kanerva A, Koivisto-Korander R, Tapper J, Lassus H, Loukovaara M, Mägi A, Hirasawa A, Aoki D, Pietiäinen V, Pellinen T, Bützow R, Aittokallio T, Kallioniemi O. Drug response profiles in patient-derived cancer cells across histological subtypes of ovarian cancer: real-time therapy tailoring for a patient with low-grade serous carcinoma. Br J Cancer 2023; 128:678-690. [PMID: 36476658 PMCID: PMC9938120 DOI: 10.1038/s41416-022-02067-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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 12/12/2022] Open
Abstract
Many efforts are underway to develop novel therapies against the aggressive high-grade serous ovarian cancers (HGSOCs), while our understanding of treatment options for low-grade (LGSOC) or mucinous (MUCOC) of ovarian malignancies is not developing as well. We describe here a functional precision oncology (fPO) strategy in epithelial ovarian cancers (EOC), which involves high-throughput drug testing of patient-derived ovarian cancer cells (PDCs) with a library of 526 oncology drugs, combined with genomic and transcriptomic profiling. HGSOC, LGSOC and MUCOC PDCs had statistically different overall drug response profiles, with LGSOCs responding better to targeted inhibitors than HGSOCs. We identified several subtype-specific drug responses, such as LGSOC PDCs showing high sensitivity to MDM2, ERBB2/EGFR inhibitors, MUCOC PDCs to MEK inhibitors, whereas HGSOCs showed strongest effects with CHK1 inhibitors and SMAC mimetics. We also explored several drug combinations and found that the dual inhibition of MEK and SHP2 was synergistic in MAPK-driven EOCs. We describe a clinical case study, where real-time fPO analysis of samples from a patient with metastatic, chemorefractory LGSOC with a CLU-NRG1 fusion guided clinical therapy selection. fPO-tailored therapy with afatinib, followed by trastuzumab and pertuzumab, successfully reduced tumour burden and blocked disease progression over a five-year period. In summary, fPO is a powerful approach for the identification of systematic drug response differences across EOC subtypes, as well as to highlight patient-specific drug regimens that could help to optimise therapies to individual patients in the future.
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Affiliation(s)
- Astrid Murumägi
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.
| | - Daniela Ungureanu
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Suleiman Khan
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Helsinki Institute for Information Technology (HIIT), Department of Computer Science, Aalto University, Espoo, Finland
| | - Mariliina Arjama
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Katja Välimäki
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Aleksandr Ianevski
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Helsinki Institute for Information Technology (HIIT), Department of Computer Science, Aalto University, Espoo, Finland
| | - Philipp Ianevski
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Rebecka Bergström
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Solna, Sweden
| | - Alice Dini
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Anna Kanerva
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Riitta Koivisto-Korander
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Johanna Tapper
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Heini Lassus
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Mikko Loukovaara
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | | | - Akira Hirasawa
- Department of Clinical Genomic Medicine, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Daisuke Aoki
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
| | - Vilja Pietiäinen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Teijo Pellinen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Ralf Bützow
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Helsinki Institute for Information Technology (HIIT), Department of Computer Science, Aalto University, Espoo, Finland
- Institute for Cancer Research, Department of Cancer Genetics, Oslo University Hospital, Oslo, Norway
- Centre for Biostatistics and Epidemiology (OCBE), Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Olli Kallioniemi
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland.
- Science for Life Laboratory (SciLifeLab), Department of Oncology and Pathology, Karolinska Institutet, Solna, Sweden.
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10
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Bulten W, Kartasalo K, Chen PHC, Ström P, Pinckaers H, Nagpal K, Cai Y, Steiner DF, van Boven H, Vink R, Hulsbergen-van de Kaa C, van der Laak J, Amin MB, Evans AJ, van der Kwast T, Allan R, Humphrey PA, Grönberg H, Samaratunga H, Delahunt B, Tsuzuki T, Häkkinen T, Egevad L, Demkin M, Dane S, Tan F, Valkonen M, Corrado GS, Peng L, Mermel CH, Ruusuvuori P, Litjens G, Eklund M. Artificial intelligence for diagnosis and Gleason grading of prostate cancer: the PANDA challenge. Nat Med 2022; 28:154-163. [PMID: 35027755 PMCID: PMC8799467 DOI: 10.1038/s41591-021-01620-2] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [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: 03/05/2021] [Accepted: 11/08/2021] [Indexed: 12/12/2022]
Abstract
Artificial intelligence (AI) has shown promise for diagnosing prostate cancer in biopsies. However, results have been limited to individual studies, lacking validation in multinational settings. Competitions have been shown to be accelerators for medical imaging innovations, but their impact is hindered by lack of reproducibility and independent validation. With this in mind, we organized the PANDA challenge-the largest histopathology competition to date, joined by 1,290 developers-to catalyze development of reproducible AI algorithms for Gleason grading using 10,616 digitized prostate biopsies. We validated that a diverse set of submitted algorithms reached pathologist-level performance on independent cross-continental cohorts, fully blinded to the algorithm developers. On United States and European external validation sets, the algorithms achieved agreements of 0.862 (quadratically weighted κ, 95% confidence interval (CI), 0.840-0.884) and 0.868 (95% CI, 0.835-0.900) with expert uropathologists. Successful generalization across different patient populations, laboratories and reference standards, achieved by a variety of algorithmic approaches, warrants evaluating AI-based Gleason grading in prospective clinical trials.
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Affiliation(s)
- Wouter Bulten
- Department of Pathology, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Kimmo Kartasalo
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
| | | | - Peter Ström
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Hans Pinckaers
- Department of Pathology, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | | | | | - Hester van Boven
- Department of Pathology, Antoni van Leeuwenhoek Hospital, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Robert Vink
- Laboratory of Pathology East Netherlands, Hengelo, The Netherlands
| | | | - Jeroen van der Laak
- Department of Pathology, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Center for Medical Image Science and Visualization, Linköping University, Linköping, Sweden
| | - Mahul B Amin
- Department of Pathology and Laboratory Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Andrew J Evans
- Laboratory Medicine, Mackenzie Health, Toronto, Ontario, Canada
| | - Theodorus van der Kwast
- Department of Pathology, Laboratory Medicine and Pathology, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Robert Allan
- Pathology and Laboratory Medicine Service, North Florida/South Georgia Veterans Health System, Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Peter A Humphrey
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Henrik Grönberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Surgery, Capio St. Göran's Hospital, Stockholm, Sweden
| | | | - Brett Delahunt
- Department of Pathology and Molecular Medicine, Wellington School of Medicine and Health Sciences, University of Otago, Wellington, New Zealand
| | - Toyonori Tsuzuki
- Department of Surgical Pathology, School of Medicine, Aichi Medical University, Nagakute, Japan
| | - Tomi Häkkinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Lars Egevad
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | | | | | | | - Masi Valkonen
- Institute of Biomedicine, Cancer Research Unit and FICAN West Cancer Centre, University of Turku and Turku University Hospital, Turku, Finland
| | | | | | | | - Pekka Ruusuvuori
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Institute of Biomedicine, Cancer Research Unit and FICAN West Cancer Centre, University of Turku and Turku University Hospital, Turku, Finland
| | - Geert Litjens
- Department of Pathology, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Martin Eklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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11
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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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