Single cell and spatial transcriptomics highlight the interaction of club-like cells with immunosuppressive myeloid cells in prostate cancer.

Autor: Kiviaho A; Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.; Prostate Cancer Research Center, Tampere University and TAYS Cancer Center, Tampere, Finland., Eerola SK; Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.; Prostate Cancer Research Center, Tampere University and TAYS Cancer Center, Tampere, Finland., Kallio HML; Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.; Prostate Cancer Research Center, Tampere University and TAYS Cancer Center, Tampere, Finland., Andersen MK; Department of Circulation and Medical Imaging, Norwegian University of Science and Technology, Trondheim, Norway.; Clinic of Surgery, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway., Hoikka M; Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.; Prostate Cancer Research Center, Tampere University and TAYS Cancer Center, Tampere, Finland., Tiihonen AM; Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.; Prostate Cancer Research Center, Tampere University and TAYS Cancer Center, Tampere, Finland., Salonen I; Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.; Prostate Cancer Research Center, Tampere University and TAYS Cancer Center, Tampere, Finland., Spotbeen X; Laboratory of Lipid Metabolism and Cancer, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium.; KU Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Belgium., Giesen A; Department of Urology, University Hospitals Leuven, Leuven, Belgium.; Department of Development and Regeneration, KU Leuven, Leuven, Belgium., Parker CTA; University College London Cancer Institute, London, UK., Taavitsainen S; Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.; Prostate Cancer Research Center, Tampere University and TAYS Cancer Center, Tampere, Finland., Hantula O; Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.; Prostate Cancer Research Center, Tampere University and TAYS Cancer Center, Tampere, Finland., Marttinen M; Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.; Prostate Cancer Research Center, Tampere University and TAYS Cancer Center, Tampere, Finland.; European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.; European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany., Hermelo I; Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.; Prostate Cancer Research Center, Tampere University and TAYS Cancer Center, Tampere, Finland., Ismail M; University College London Cancer Institute, London, UK., Midtbust E; Department of Circulation and Medical Imaging, Norwegian University of Science and Technology, Trondheim, Norway.; Clinic of Surgery, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway., Wess M; Department of Circulation and Medical Imaging, Norwegian University of Science and Technology, Trondheim, Norway.; Clinic of Surgery, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway., Devlies W; Department of Urology, University Hospitals Leuven, Leuven, Belgium.; Molecular Endocrinology Laboratory, Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium., Sharma A; Department of Public Health and Nursing, Norwegian University of Science and Technology (NTNU), Trondheim, Norway., Krossa S; Department of Circulation and Medical Imaging, Norwegian University of Science and Technology, Trondheim, Norway.; Central staff, St. Olavs Hospital HF, 7006, Trondheim, Norway., Häkkinen T; Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.; Prostate Cancer Research Center, Tampere University and TAYS Cancer Center, Tampere, Finland., Afyounian E; Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.; Prostate Cancer Research Center, Tampere University and TAYS Cancer Center, Tampere, Finland., Vandereyken K; KU Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Belgium.; Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, Belgium., Kint S; KU Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Belgium.; Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, Belgium., Kesseli J; Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.; Prostate Cancer Research Center, Tampere University and TAYS Cancer Center, Tampere, Finland., Tolonen T; Prostate Cancer Research Center, Tampere University and TAYS Cancer Center, Tampere, Finland.; Department of Pathology, Fimlab Laboratories, Ltd, Tampere University Hospital, Tampere, Finland., Tammela TLJ; Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.; Department of Urology, Tampere University Hospital, Tampere, Finland., Viset T; Department of Pathology, St. Olav's Hospital, Trondheim University Hospital, Trondheim, Norway., Størkersen Ø; Department of Pathology, St. Olav's Hospital, Trondheim University Hospital, Trondheim, Norway., Giskeødegård GF; Clinic of Surgery, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway.; Department of Public Health and Nursing, Norwegian University of Science and Technology (NTNU), Trondheim, Norway., Rye MB; Clinic of Surgery, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway.; Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway., Murtola T; Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.; Prostate Cancer Research Center, Tampere University and TAYS Cancer Center, Tampere, Finland., Erickson A; Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.; ICAN-Digital Precision Cancer Medicine Flagship, Helsinki, Finland.; Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK., Latonen L; Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland., Bova GS; Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.; Prostate Cancer Research Center, Tampere University and TAYS Cancer Center, Tampere, Finland., Mills IG; Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK.; Patrick G Johnston Centre for Cancer Research, Queen's University of Belfast, Belfast, UK., Joniau S; Department of Urology, University Hospitals Leuven, Leuven, Belgium.; Department of Development and Regeneration, KU Leuven, Leuven, Belgium., Swinnen JV; Laboratory of Lipid Metabolism and Cancer, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium.; KU Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Belgium., Voet T; KU Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Belgium.; Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, Belgium., Mirtti T; Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.; ICAN-Digital Precision Cancer Medicine Flagship, Helsinki, Finland.; Department of Pathology, University of Helsinki & Helsinki University Hospital, Helsinki, Finland., Attard G; University College London Cancer Institute, London, UK.; University College London Hospitals, London, UK., Claessens F; Molecular Endocrinology Laboratory, Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium., Visakorpi T; Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.; Prostate Cancer Research Center, Tampere University and TAYS Cancer Center, Tampere, Finland.; Fimlab Laboratories, Ltd, Tampere University Hospital, Tampere, Finland., Rautajoki KJ; Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.; Prostate Cancer Research Center, Tampere University and TAYS Cancer Center, Tampere, Finland., Tessem MB; Department of Circulation and Medical Imaging, Norwegian University of Science and Technology, Trondheim, Norway.; Clinic of Surgery, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway., Urbanucci A; Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland. alfonso.urbanucci@tuni.fi.; Prostate Cancer Research Center, Tampere University and TAYS Cancer Center, Tampere, Finland. alfonso.urbanucci@tuni.fi.; Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway. alfonso.urbanucci@tuni.fi., Nykter M; Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland. matti.nykter@tuni.fi.; Prostate Cancer Research Center, Tampere University and TAYS Cancer Center, Tampere, Finland. matti.nykter@tuni.fi.

Publikováno v: Nature communications [Nat Commun] 2024 Nov 16; Vol. 15 (1), pp. 9949. Date of Electronic Publication: 2024 Nov 16.

Cancer origin tracing and timing in two high-risk prostate cancers using multisample whole genome analysis: prospects for personalized medicine.

Autor: Nurminen A; Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland., Jaatinen S; Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland., Taavitsainen S; Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland., Högnäs G; Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland., Lesluyes T; The Francis Crick Institute, London, NW1 1AT, UK., Ansari-Pour N; MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK., Tolonen T; Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere, Finland., Haase K; The Francis Crick Institute, London, NW1 1AT, UK.; Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität Zu Berlin, ECRC Experimental and Clinical Research Center, Berlin, Germany., Koskenalho A; Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland., Kankainen M; Institute for Molecular Medicine Finland, University of Helsinki, Tukholmankatu 8, Helsinki, 00290, Finland., Jasu J; Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland., Rauhala H; Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland., Kesäniemi J; Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland., Nikupaavola T; Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland., Kujala P; Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere, Finland., Rinta-Kiikka I; Imaging Centre, Department of Radiology, Tampere University Hospital, Tampere, Finland., Riikonen J; Department of Urology, TAYS Cancer Center, Tampere University Hospital, Tampere, Finland., Kaipia A; Department of Urology, TAYS Cancer Center, Tampere University Hospital, Tampere, Finland., Murtola T; Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland.; Department of Urology, TAYS Cancer Center, Tampere University Hospital, Tampere, Finland., Tammela TL; Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland.; Department of Urology, TAYS Cancer Center, Tampere University Hospital, Tampere, Finland., Visakorpi T; Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland.; Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere, Finland., Nykter M; Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland., Wedge DC; Manchester Cancer Research Centre, Division of Cancer Sciences, University of Manchester, Manchester, M20 4GJ, UK., Van Loo P; The Francis Crick Institute, London, NW1 1AT, UK.; Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA., Bova GS; Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland. steve.bova@tuni.fi.

Publikováno v: Genome medicine [Genome Med] 2023 Oct 12; Vol. 15 (1), pp. 82. Date of Electronic Publication: 2023 Oct 12.

Single-cell ATAC and RNA sequencing reveal pre-existing and persistent cells associated with prostate cancer relapse

Autor: Taavitsainen, S., Engedal, N., Cao, S., Handle, F., Erickson, A., Prekovic, S., Wetterskog, D., Tolonen, T., Vuorinen, E. M., Kiviaho, A., Nätkin, R., Häkkinen, T., Devlies, W., Henttinen, S., Kaarijärvi, R., Lahnalampi, M., Kaljunen, H., Nowakowska, K., Syvälä, H., Bläuer, M., Cremaschi, P., Claessens, F., Visakorpi, T., Tammela, T. L. J., Murtola, T., Granberg, K. J., Lamb, A. D., Ketola, K., Mills, I. G., Attard, G., Wang, W., Nykter, M., Urbanucci, A.

Publikováno v: Taavitsainen, S, Engedal, N, Cao, S, Handle, F, Erickson, A, Prekovic, S, Wetterskog, D, Tolonen, T, Vuorinen, E M, Kiviaho, A, Nätkin, R, Häkkinen, T, Devlies, W, Henttinen, S, Kaarijärvi, R, Lahnalampi, M, Kaljunen, H, Nowakowska, K, Syvälä, H, Bläuer, M, Cremaschi, P, Claessens, F, Visakorpi, T, Tammela, T L J, Murtola, T, Granberg, K J, Lamb, A D, Ketola, K, Mills, I G, Attard, G, Wang, W, Nykter, M & Urbanucci, A 2021, ' Single-cell ATAC and RNA sequencing reveal pre-existing and persistent cells associated with prostate cancer relapse ', Nature Communications, vol. 12, no. 1 . https://doi.org/10.1038/s41467-021-25624-1
Nature Communications, Vol 12, Iss 1, Pp 1-16 (2021)
Nature Communications

Prostate cancer is heterogeneous and patients would benefit from methods that stratify those who are likely to respond to systemic therapy. Here, we employ single-cell assays for transposase-accessible chromatin (ATAC) and RNA sequencing in models of

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid_dedup__::66dd98a7ed2dc0560613c76ad1776551
https://lirias.kuleuven.be/handle/123456789/682242

Subclone eradication analysis identifies targets for enhanced cancer therapy and reveals L1 retrotransposition as a dynamic source of cancer heterogeneity

Autor: Ketola, K., Kaljunen, H., Taavitsainen, S., Kaarijärvi, R., Järvelä, E., Rodriguez Martin, B., Haase, K., Woodcock, D.J., Tubio, J., Wedge, D.C., Nykter, M., Bova, G.S.

Publikováno v: Ketola, K, Kaljunen, H, Taavitsainen, S, Kaarijärvi, R, Järvelä, E, Rodriguez Martin, B, Haase, K, Woodcock, D J, Tubio, J, Wedge, D C, Nykter, M & Bova, G S 2021, ' Subclone eradication analysis identifies targets for enhanced cancer therapy and reveals L1 retrotransposition as a dynamic source of cancer heterogeneity ', Cancer Research . https://doi.org/10.1158/0008-5472.CAN-21-0371

Treatment-eradicated cancer subclones have been reported in leukemia and have recently been detected in solid tumors. Here we introduce Differential Subclone Eradication and Resistance (DSER) analysis, a method developed to identify molecular targets

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid_dedup__::484db0fbb8cc03e2fc901dec4cda4810
https://trepo.tuni.fi/handle/10024/135173

Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression.

Autor: Cao S; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA., Wang JR; Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA., Ji S; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA., Yang P; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.; Department of Statistics, Rice University, Houston, TX, USA., Dai Y; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.; Baylor College of Medicine, Houston, TX, USA., Guo S; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA., Montierth MD; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.; Baylor College of Medicine, Houston, TX, USA., Shen JP; Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA., Zhao X; Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA., Chen J; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA., Lee JJ; Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.; Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.; Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA., Guerrero PA; Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.; Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA., Spetsieris N; Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA., Engedal N; Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway., Taavitsainen S; Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland., Yu K; Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA., Livingstone J; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA.; Department of Urology, University of California, Los Angeles, Los Angeles, CA, USA.; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA.; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA., Bhandari V; Department of Medical Biophysics, University of Toronto, Toronto ON, Canada., Hubert SM; Department of Thoracic Head Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA., Daw NC; Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA., Futreal PA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA., Efstathiou E; Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA., Lim B; Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA., Viale A; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA., Zhang J; Department of Thoracic Head Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA., Nykter M; Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland., Czerniak BA; Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA., Brown PH; Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA., Swanton C; The Francis Crick Institute, London, UK., Msaouel P; Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.; Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA., Maitra A; Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.; Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.; Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA., Kopetz S; Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA., Campbell P; Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK., Speed TP; Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VC, Australia.; School of Mathematics and Statistics, The University of Melbourne, Melbourne, VC, Australia., Boutros PC; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA.; Department of Urology, University of California, Los Angeles, Los Angeles, CA, USA.; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA.; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.; Department of Medical Biophysics, University of Toronto, Toronto ON, Canada., Zhu H; Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA., Urbanucci A; Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway., Demeulemeester J; Cancer Genomics Laboratory, The Francis Crick Institute, London, UK.; Department of Human Genetics, KU Leuven, Leuven, Belgium., Van Loo P; Cancer Genomics Laboratory, The Francis Crick Institute, London, UK.; Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA., Wang W; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. wwang7@mdanderson.org.; Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. wwang7@mdanderson.org.

Publikováno v: Nature biotechnology [Nat Biotechnol] 2022 Nov; Vol. 40 (11), pp. 1624-1633. Date of Electronic Publication: 2022 Jun 13.