Auvinen Group: Epidemiology
Bova Group: PELICAN-Personalized Cancer Medicine
Rautajoki Group: Cancer Regulation and Immunology
Murtola Group: Pharmacoepidemiology and Chemoprevention
Nykter Group: Computational Biology
Ruusuvuori Group: Bioimage Informatics
Schleutker Group: Genetic Predisposition to Prostate Cancer
Urbanucci Group: Genomic Regulation for Precision Cancer Medicine
Visakorpi Group: Molecular Biology of Prostate Cancer
Tolonen Group: Histopathology
Anssi Auvinen | Epidemiology
Auvinen A, Tammela T, Mirtti T, Lilja H, Tolonen T, Kenttämies A, Rinta-Kiikka I, Lehtimäki T, Natunen K, Nevalainen J, Raitanen J, Ronkainen J, van der Kwast T, Riikonen J, Pétas A, Matikainen M, Taari K, Kilpeläinen T, Rannikko AS. Prostate cancer screening with PSA, kallikrein panel and MRI: The ProScreen randomized trial. JAMA 2024;331:1452-59
Rannikko A, Leht M, Mirtti T, Kenttämies A, Tolonen T, Rinta-Kiikka I, Kilpeläinen TP, Natunen K, Lilja H, Lehtimäki T, Raitanen J, Kujala P, Ronkainen J, Matikainen M, Petas A, Taari K, Tammela T, Auvinen A. Population-based randomized trial of screening for clinically significant prostate cancer: A pilot study. BJU Int 2022;130:193-199
Vaccarella S, Li M, Bray F, Kvale R, Serraino D, Lorenzoni V, Auvinen A, dal Maso L. Prostate cancer incidence and mortality in Europe. BMJ 2024;386:e077738
Talala K, Walter SD, Taari K, Tammela TL, Kujala P, Auvinen A. Screening history and risk of death from prostate cancer: a nested case-control study. Cancer Causes Control 2024;35:695-703
Nevalainen J, Raitanen J, Natunen K, Rannikko A, Kilpeläinen T, Tammela TL, Auvinen A. Early detection of clinically significant prostate cancer: Protocol summary and statistical analysis plan for the ProScreen trial. BMJopen 2024;14:e075595
Pylväläinen J, Hofström J, Kenttämies A, Auvinen A, Mirtti T, Rannikko A. Risk of clinically significant prostate cancer after a non-suspicious prostate MRI. Cancer Epidemiol Biomarkers Prev 2024;33:749-756
Hietikko R, Mirtti T, Kilpeläinen TP, Tolonen T, Räisänen-Sokolowski A, Nordling S, Hannus J, Laurila M, Taari K, Tammela TLJ, Autio R, Natunen K, Auvinen A, Rannikko A. Expected
impact of MRI-targeted biopsy inter-reader variability among uropathologist on ProScreen prostate cancer screening trial World J Urol 2024;42:217
Pasanen N, Talala K, Remmers S, Tammela T, Hugosson J, Roobol M, Taari K, Godtman RA, Bangma C, Auvinen A. Which men benefit most from prostate cancer screening? BJU Int 2024;134:291-299
Ola I, Tammela T, Taari K, Murtola T, Talala K, Raitanen J, Auvinen A. Prostate cancer incidence in men with PSA below 3 ng/ml. Int J Cancer 2023;152:672-678
Siltari A, Lönnerbro R, Pang K, Shiranov K, Asiimwe A, Evans-Axelson S, Franks B, Kiran A, Murtola TJ, Schalken J, Steinbeisser C, Bjartell A, Auvinen A. How well do polygenic risk scores identify men at high risk of prostate cancer? Systematic review and meta-analysis. Clin Genitourin Cancer 2023;21:316.e1-316.e11
Remmers S, Bangma CH, Godtman RA, Carlsson SV, Auvinen A, Tammela TLJ, Denis LJ, Nelen V, Villers A, Rebillard X, Kwiatkowski M, Recker F, Wyler S, Zappa M, Puliti D, Gorini G, Paez A, Lujan M, Nieboer D, Schröder FH, Roobol MJ. Relationship between baseline prostate-specific antigen on cancer detection and prostate cancer death. Eur Urol2023;84:503-309
Bratt O, Auvinen A, Arnsrud Godtman R, Hellström M, Hugosson J, Lilja H, Wallström J, Roobol MJ. Screening for prostate cancer. BMJ Oncol 2023;2:e000039
Steven Bova | PELICAN-Personalized Cancer Medicine
Woodcock DJ, Sahli A, Teslo R, Bhandari V, Gruber AJ, Ziubroniewicz A, Gundem G, Xu Y, Butler A, Anokian E, Pope BJ, Jung CH, Tarabichi M, Dentro SC, Farmery JHR; CRUK ICGC Prostate Group; Van Loo P, Warren AY, Gnanapragasam V, Hamdy FC, Bova GS, Foster CS, Neal DE, Lu YJ, Kote-Jarai Z, Fraser M, Bristow RG, Boutros PC, Costello AJ, Corcoran NM, Hovens CM, Massie CE, Lynch AG, Brewer DS, Eeles RA, Cooper CS, Wedge DC. Genomic evolution shapes prostate cancer disease type. Cell Genom. 2024 Mar 13;4(3):100511. doi: 10.1016/j.xgen.2024.100511. Epub 2024 Feb 29. PMID: 38428419
Kaljunen H, Taavitsainen S, Kaarijärvi R, Takala E, Paakinaho V, Nykter M, Bova GS, Ketola K. Fanconi anemia pathway regulation by FANCI in prostate cancer. Front Oncol. 2023 Oct 30;13:1260826. doi: 10.3389/fonc.2023.1260826. eCollection 2023. PMID: 38023254
Nurminen A, Jaatinen S, Taavitsainen S, Högnäs G, Lesluyes T, Ansari-Pour N, Tolonen T, Haase K, Koskenalho A, Kankainen M, Jasu J, Rauhala H, Kesäniemi J, Nikupaavola T, Kujala P, Rinta-Kiikka I, Riikonen J, Kaipia A, Murtola T, Tammela TL, Visakorpi T, Nykter M, Wedge DC, Van Loo P, Bova GS. Cancer origin tracing and timing in two high-risk prostate cancers using multisample whole genome analysis: prospects for personalized medicine. Genome Med. 2023 Oct 12;15(1):82. doi: 10.1186/s13073-023-01242-y. PMID: 37828555
Jasu J, Tolonen T, Antonarakis ES, Beltran H, Halabi S, Eisenberger MA, Carducci MA, Loriot Y, Van der Eecken K, Lolkema M, Ryan CJ, Taavitsainen S, Gillessen S, Högnäs G, Talvitie T, Taylor RJ, Koskenalho A, Ost P, Murtola TJ, Rinta-Kiikka I, Tammela T, Auvinen A, Kujala P, Smith TJ, Kellokumpu-Lehtinen PL, Isaacs WB, Nykter M, Kesseli J, Bova GS. Combined Longitudinal Clinical and Autopsy Phenomic Assessment in Lethal Metastatic Prostate Cancer: Recommendations for Advancing Precision Medicine. Eur Urol Open Sci. 2021 Jul 2;30:47-62. doi: 10.1016/j.euros.2021.05.011. PMID: 34337548; PMCID: PMC8317817.
Woodcock DJ, Riabchenko E, Taavitsainen S, Kankainen M, Gundem G, Brewer DS, Ellonen P, Lepistö M, Golubeva YG, Warner AC, Tolonen TT, Jasu J, Isaacs WB, Emmert-Buck MR, Nykter M, Visakorpi T, Bova GS, Wedge DC. Prostate cancer evolution from multilineage primary to single lineage metastasis in ten men with implications for liquid biopsy. Nat Commun. 2020 Oct 8;11(1):5070. PMID: 33033260.
ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. Pan-cancer analysis of whole genomes. Nature. 2020 Feb;578(7793):82-93.
Bova GS, Cancer Genomics: Human metastases under scrutiny. Nature, 2017 548(7667):287-288.
Behjati S, Gundem G, Wedge DC, Roberts ND, Tarpey PS, Cooke SL, Van Loo P, Alexandrov LB, Ramakrishna M, Davies H, Nik-Zainal S, Hardy C, Latimer C, Raine KM, Stebbings L, Menzies A, Jones D, Shepherd R, Butler AP, Teague JW, Jorgensen M, Khatri B, Pillay N, Shlien A, Futreal PA, Badie C; ICGC Prostate Group, McDermott U, Bova GS, Richardson AL, Flanagan AM, Stratton MR, Campbell PJ. Mutational signatures of ionizing radiation in second malignancies. Nat Commun. 2016 Sep 12;7:12605.
Gundem G, Van Loo P, Kremeyer B, Alexandrov LB, Tubio JMC, Papaemmanuil E, Brewer DS, Kallio HML, Högnäs G, Annala M, Kivinummi K, Goody V, Latimer C, O’Meara S, Dawson KJ, Isaacs W, Emmert-Buck MR, Nykter M, Foster C, Kote-Jarai Z, Easton D, Whitaker HC, Neal DE, Cooper CS,Eeles RA, Visakorpi T, Campbell PJ, McDermott U, Wedge DC, and Bova GS. The Evolutionary History of Lethal Metastatic Prostate Cancer. Nature, 520, 353-7, 2015.
Tubio JM, Li Y, Ju YS, Martincorena I, Cooke SL, Tojo M, Gundem G, Pipinikas CP, Zamora J, Raine K, Menzies A, Roman-Garcia P, Fullam A, Gerstung M, Shlien A, Tarpey PS, Papaemmanuil E, Knappskog S, Van Loo P, Ramakrishna M, Davies HR, Marshall J, Wedge DC, Teague JW, Butler AP, Nik-Zainal S, Alexandrov L, Behjati S, Yates LR, Bolli N, Mudie L, Hardy C, Martin S, McLaren S, O’Meara S, Anderson E, Maddison M, Gamble S; ICGC Breast Cancer Group; ICGC Bone Cancer Group; ICGC Prostate Cancer Group, Foster C, Warren AY, Whitaker H, Brewer D, Eeles R, Cooper C, Neal D, Lynch AG, Visakorpi T, Isaacs WB, van’t Veer L, Caldas C, Desmedt C, Sotiriou C, Aparicio S, Foekens JA, Eyfjörd JE, Lakhani SR, Thomas G, Myklebost O, Span PN, Børresen-Dale AL, Richardson AL, Van de Vijver M, Vincent-Salomon A, Van den Eynden GG, Flanagan AM, Futreal PA, Janes SM, Bova GS, Stratton MR, McDermott U, Campbell PJ. Mobile DNA in cancer. Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes. Science. 2014 Aug 1;345(6196):1251343.
Liu W, Laitinen S, Khan S, Vihinen M, Kowalski J, Yu G, Chen L, Ewing CM, Eisenberger MA, Carducci MA, Nelson WG, Yegnasubramanian S, Luo J, Wang Y, Xu J, Isaacs WB, Visakorpi T, Bova GS. Copy Number Analysis Indicates Monoclonal Origin of Lethal Metastatic Prostate Cancer. Nature Medicine 2009; 15: 560-565.
Kirsi Rautajoki (nee Granberg) | Cancer Regulation and Immunology
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. Nat.Commun. 12:5307.
Kukkonen, K., Taavitsainen, S., Huhtala, L., Uusi-Makelä, J., Granberg, K.J., Nykter, M., Urbanucci, A. (2021) Chromatin and Epigenetic Dysregulation of Prostate Cancer Development, Progression, and Therapeutic Response. Cancers. 13:3325.
Rajamäki, K., Taira, A., Katainen, R., Välimäki, N., Kuosmanen, A., Plaketti, R-M., Seppälä, T.T., Ahtiainen, M., Wirta, E-V., Vartiainen, E., Sulo, P., Ravantti, J., Lehtipuro, S., Granberg, K.J., Nykter, M., Tanskanen, T., Ristimäki, A., Koskensalo, S., Renkonen-Sinisalo, L., Lepistö, A., Böhm, J., Taipale, J., Mecklin, J-P., Aavikko, M., Palin, K., Aaltonen, L.A. (2021) Genetic and Epigenetic Characteristics of Inflammatory Bowel Disease-Associated Colorectal Cancer. Gastroenterology 161:592-607.
Filppu, P., Ramanathan, J.T., Granberg, K.J., Gucciardo, E., Haapasalo, H., Lehti, K., Nykter, M., Le Joncour, V., Laakkonen, P. (2021) CD109 – GP130 interaction drives glioblastoma stem cell plasticity and chemoresistance through STAT3 activity. JCI Insight 6:e141486.
Dufva, O., Pölönen, P., Brück, O., Keränen, M., Klievink, J., Mehtonen, J., Huuhtanen, J., Kumar, A., Malani, D., Siitonen, S., Kankainen, M., Ghimire, B., Lahtela, J., Mattila, P., Vähä-Koskela, M., Wennerberg, K., Granberg, K., Leivonen, S-K., Meriranta, L., Heckman, C., Leppä, S., Nykter, M., Lohi, O., Heinäniemi, M.*, Mustjoki, S.* (2020) Immunogenomic landscape of hematological malignancies. Cancer Cell. 38: 424-428.
Mehtonen, J., Pölönen, P., Häyrynen, S., Dufva, O., Lin, J., Liuksiala, T., Granberg, K., Lohi, O., Hautamäki, V., Nykter, M.*, Heinäniemi, M.* (2019) Data-driven characterization of molecular phenotypes across heterogeneous sample collections. Nucleic Acids Research 47:e76.
Pölönen, P., Mehtonen, J., Lin, J., Liuksiala, T., Häyrynen, S., Teppo. S., Mäkinen, A., Kumar, A., Malani, D., Pohjolainen, V., Porkka, K., Heckman, C.A., May, P., Hautamäki, V., Granberg, K., Lohi, O., Nykter, M.*, Heinäniemi, M.* (2019) Hemap: An interactive online resource for characterizing molecular phenotypes across hematologic malignancies. Cancer res. 79:2466-2479.
Luoto, S., Hermelo, I., Vuorinen, E., Hannus, P., Kesseli, J., Nykter, M.*, Granberg, K.J.* (2018) Computational characterization of suppressive immune microenvironments in glioblastoma. Cancer Res. 78:5574-5585.
Nordfors, K., Haapasalo, J., Afyounian, E., Tuominen, J., Annala, M., Häyrynen, S., Karhu, R., Helén, P., Lohi, O., Nykter, M., Haapasalo, H., Granberg, K.J. (2018) Whole-exome sequencing identifies germline mutation in TP53 and ATRX in a child with genomically aberrant AT/RT and her mother with anaplastic astrocytoma. Cold Spring Harb. Mol. Case Stud. 4:a002246.
Granberg, K.J., Annala, M., Lehtinen, B., Kesseli, J., Haapasalo, J., Yli-Harja, O., Visakorpi, T., Haapasalo, H., Nykter, M., Zhang, W. (2017) Strong FGFR3 staining is a marker for FGFR3 fusions in diffuse gliomas. Neuro-Oncol. 19:1206-1216.
Teemu Murtola | Pharmacoepidemiology and Chemoprevention
Raittinen P, Niemistö K, Pennanen E, Syvälä H, Auriola S, Riikonen J, Lehtimäki T, Ilmonen P, Murtola T. Circulatory and prostatic tissue lipidomic profiles shifts after high-dose atorvastatin use in men with prostate cancer. Sci Rep. 2020 Jul 21;10(1):12016.
Siltari A, Murtola TJ, Talala K, Taari K, Tammela TLJ, Auvinen A. Antihypertensive drug use and prostate cancer-specific mortality in Finnish men. PLoS One. 2020 Jun 29;15(6):e0234269.
Riikonen J, Pakarainen T, Siltari A, Pienimäki JP, Koskimäki J, Murtola TJ. Urine colour as an indicator for anastomotic leakage after robot-assisted radical prostatectomy. Scand J Urol. 2020
Siltari A, Riikonen J, Fode M, Murtola TJ. Effects of Preoperative Atorvastatin Treatment On Erectile Function After Radical Prostatectomy: Results From a Subgroup of ESTO1, a Randomized, Double-Blind, Placebo-Controlled Study. J Sex Med. 2019 Oct;16(10):1597-1605.
Joentausta RM, Murtola TJ. Prostate cancer survival among statin users after prostatectomy in a Finnish nationwide cohort. Prostate. 2019;79:583-591.
Knuuttila E, Riikonen J, Syvälä H, Auriola S, Murtola TJ. Access and concentrations of atorvastatin in the prostate in men with prostate cancer. Prostate. 2019 Sep;79(12):1412-1419.
Murtola TJ, Veitonmäki T. Aspirin and Prostate Cancer Mortality: The Role of Tumor Grading Misclassification? Ann Intern Med. 2019 Apr 2;170(7):499-500.
Murtola TJ, Sälli SM, Talala K, Taari K, Tammela TLJ, Auvinen A. Blood glucose, glucose balance, and disease-specific survival after prostate cancer diagnosis in the Finnish Randomized Study of Screening for Prostate Cancer. Prostate Cancer Prostatic Dis. 2019 Sep;22(3):453-460.
Santala EE, Rannikko A, Murtola TJ Antihypertensive drugs and prostate cancer survival after radical prostatectomy in Finland-A nationwide cohort study. Int J Cancer. 2019 Feb 1;144(3):440-447.
Murtola TJ, Syvälä H, Tolonen T, Helminen M, Riikonen J, Koskimäki J, Pakarainen T, Kaipia A, Isotalo T, Kujala P, Tammela TL. Atorvastatin Versus Placebo for Prostate Cancer Before Radical Prostatectomy-A Randomized, Double-blind, Placebo-controlled Clinical Trial. J.Eur Urol. 2018 Dec;74(6):697-701.
Matti Nykter | Computational Biology
Kohvakka A, Sattari M, Shcherban A, Annala M, Urbanucci A, Kesseli J, Tammela TLJ, Kivinummi K, Latonen L, Nykter M, Visakorpi T. AR and ERG drive the expression of prostate cancer specific long noncoding RNAs. Oncogene. 2020 Jul;39(30):5241-5251. doi: 10.1038/s41388-020-1365-6. Epub 2020 Jun 17. PMID: 32555329.
Dufva O, Pölönen P, Brück O, Keränen MAI, Klievink J, Mehtonen J, Huuhtanen J, Kumar A, Malani D, Siitonen S, Kankainen M, Ghimire B, Lahtela J, Mattila P, Vähä-Koskela M, Wennerberg K, Granberg K, Leivonen SK, Meriranta L, Heckman C, Leppä S, Nykter M, Lohi O, Heinäniemi M, Mustjoki S. Immunogenomic Landscape of Hematological Malignancies. Cancer Cell. 2020 Sep 14;38(3):380-399.e13. doi: 10.1016/j.ccell.2020.06.002. Epub 2020 Jul 9. Erratum in: Cancer Cell. 2020 Sep 14;38(3):424-428. PMID: 32649887.
Vandekerkhove G, Struss WJ, Annala M, Kallio HML, Khalaf D, Warner EW, Herberts C, Ritch E, Beja K, Loktionova Y, Hurtado-Coll A, Fazli L, So A, Black PC, Nykter M, Tammela T, Chi KN, Gleave ME, Wyatt AW. Circulating Tumor DNA Abundance and Potential Utility in De Novo Metastatic Prostate Cancer. Eur Urol. 2019 Apr;75(4):667-675. doi: 10.1016/j.eururo.2018.12.042. Epub 2019 Jan 10. PMID: 30638634.
Taavitsainen S, Annala M, Ledet E, Beja K, Miller PJ, Moses M, Nykter M, Chi KN, Sartor O, Wyatt AW. Evaluation of Commercial Circulating Tumor DNA Test in Metastatic Prostate Cancer. JCO Precis Oncol. 2019 Jun 12;3:PO.19.00014. doi: 10.1200/PO.19.00014. PMID: 32914020; PMCID: PMC7446428.
Pölönen P, Mehtonen J, Lin J, Liuksiala T, Häyrynen S, Teppo S, Mäkinen A, Kumar A, Malani D, Pohjolainen V, Porkka K, Heckman CA, May P, Hautamäki V, Granberg KJ, Lohi O, Nykter M, Heinäniemi M. Hemap: An Interactive Online Resource for Characterizing Molecular Phenotypes across Hematologic Malignancies. Cancer Res. 2019 May 15;79(10):2466-2479. doi: 10.1158/0008-5472.CAN-18-2970. Epub 2019 Apr 2. PMID: 30940663.
Mehtonen J, Pölönen P, Häyrynen S, Dufva O, Lin J, Liuksiala T, Granberg K, Lohi O, Hautamäki V, Nykter M, Heinäniemi M. Data-driven characterization of molecular phenotypes across heterogeneous sample collections. Nucleic Acids Res. 2019 Jul 26;47(13):e76. doi: 10.1093/nar/gkz281. PMID: 31329928; PMCID: PMC6648337.
Latonen L, Afyounian E, Jylhä A, Nättinen J, Aapola U, Annala M, Kivinummi KK, Tammela TTL, Beuerman RW, Uusitalo H, Nykter M, Visakorpi T. Integrative proteomics in prostate cancer uncovers robustness against genomic and transcriptomic aberrations during disease progression. Nat Commun. 2018 Mar 21;9(1):1176. doi: 10.1038/s41467-018-03573-6. PMID: 29563510; PMCID: PMC5862881.
Annala M, Vandekerkhove G, Khalaf D, Taavitsainen S, Beja K, Warner EW, Sunderland K, Kollmannsberger C, Eigl BJ, Finch D, Oja CD, Vergidis J, Zulfiqar M, Azad AA, Nykter M, Gleave ME, Wyatt AW, Chi KN. Circulating Tumor DNA Genomics Correlate with Resistance to Abiraterone and Enzalutamide in Prostate Cancer. Cancer Discov. 2018 Apr;8(4):444-457. doi: 10.1158/2159-8290.CD-17-0937. Epub 2018 Jan 24. PMID: 29367197.
Annala M, Taavitsainen S, Vandekerkhove G, Bacon JVW, Beja K, Chi KN, Nykter M, Wyatt AW. Frequent mutation of the FOXA1 untranslated region in prostate cancer. Commun Biol. 2018 Aug 24;1:122. doi: 10.1038/s42003-018-0128-1. PMID: 30272002; PMCID: PMC6123809.
Gao Q, Liang WW, Foltz SM, Mutharasu G, Jayasinghe RG, Cao S, Liao WW, Reynolds SM, Wyczalkowski MA, Yao L, Yu L, Sun SQ; Fusion Analysis Working Group; Cancer Genome Atlas Research Network, Chen K, Lazar AJ, Fields RC, Wendl MC, Van Tine BA, Vij R, Chen F, Nykter M, Shmulevich I, Ding L. Driver Fusions and Their Implications in the Development and Treatment of Human Cancers. Cell Rep. 2018 Apr 3;23(1):227-238.e3. doi: 10.1016/j.celrep.2018.03.050. PMID: 29617662; PMCID: PMC5916809.
Pekka Ruusuvuori | Bioimage Informatics
Valkonen, M., Högnäs, G., Bova, G.S., Ruusuvuori, P. Generalized fixation invariant nuclei detection through domain adaptation based deep learning, IEEE Journal of Biomedical and Health Informatics, 12 pages, in press, 2020
Ström, P., Kartasalo, K., Olsson, H., Solorzano, L., Delahunt, B., Berney, D. M., …Ruusuvuori, P. … & Eklund, M. (2020). Artificial intelligence for diagnosis and grading of prostate cancer in biopsies: a population-based, diagnostic study. The Lancet Oncology, 21(2), 222-232.
Valkonen, J. Isola, O. Ylinen, V. Muhonen, A. Saxlin, T. Tolonen, M. Nykter, P. Ruusuvuori. (2020). Cytokeratin-supervised deep learning for automatic recognition of epithelial cells in breast cancers stained for ER, PR, and Ki-67. IEEE Transactions on Medical Imaging, 39(2), 534-542.
Liimatainen, L. Kananen, L. Latonen, P. Ruusuvuori. Iterative unsupervised domain adaptation for generalized cell detection from brightfield z-stacks. BMC Bioinformatics, 20 (1), 80, 2019. 10.1186/s12859-019-2605-z
Kartasalo, L. Latonen.M. Vihinen, T. Visakorpi, M. Nykter, P. Ruusuvuori. Comparative analysis of tissue reconstruction algorithms for 3D histology. Bioinformatics, bty210, 2018
Ehteshami Bejnordi, M. Veta, PJ van Diest, B. van Ginneken, N. Karssemeijer, G. Litjens, JAWM van der Laak, The CAMELYON16 Consortium. Diagnostic assessment of deep learning algorithms for detection of lymph node metastases in women with breast cancer. JAMA 318 (22), 2199-2210
Valkonen, K. Kartasalo, K. Liimatainen, M. Nykter, L. Latonen, P. Ruusuvuori, Metastasis detection from whole slide images using local features and random forests. Cytometry A, 2017. doi:10.1002/cyto.a.23089
Valkonen, P. Ruusuvuori, K. Kartasalo, M. Nykter, T. Visakorpi, L. Latonen, Analysis of spatial heterogeneity in normal epithelium and preneoplastic alterations in mouse prostate tumor models. Scientific Reports, 2017. dx.doi.org/10.1038/srep44831
Ruusuvuori, L. Paavolainen, K. Rutanen, A. Mäki, H. Huttunen, V. Marjomäki. (2014) Quantitative Analysis of Dynamic Association in Live Biological Fluorescent Samples. PLoS ONE 9(4): e94245. doi:10.1371/journal.pone.0094245
Ruusuvuori, J. Lin, AC. Scott, Z. Tan, S. Sorsa, A. Kallio, M. Nykter, O. Yli-Harja, I. Shmulevich, AM. Dudley, Quantitative analysis of colony morphology in yeast, BioTechniques, Vol. 56, No. 1, Jan 2014, pp. 18–27.
Johanna Schleutker | Genetic Predisposition to Prostate Cancer
Rantapero T, Wahlfors T, Kähler A, Hultman C, Lindberg J, Tammela TL, Nykter M, Schleutker J, Wiklund F. Inherited DNA Repair Gene Mutations in Men with Lethal Prostate Cancer. Genes (Basel), 2020,11(3):E314.
Chen SL, Fann JC, Sipeky C, Yang TK, Chiu SY, Yen AM, Laitinen V, Tammela TL, Stenman UH, Auvinen A, Schleutker J, Chen HH. Risk Prediction of Prostate Cancer with Single Nucleotide Polymorphisms (SNPs) and Prostate-Specific Antigen (PSA). J Urol, 2019; 201(3):486-495.
Kaikkonen E, Rantapero T, Zhang Q, Taimen P, Laitinen V, Kallajoki M, Jambulingam D, Ettala O, Knaapila J, Boström PJ, Wahlström G, Sipeky C, Pursiheimo J-P, Tammela T, Kellokumpu-Lehtinen P-L, PRACTICAL Consortium, Fey V, Maehle L, Wiklund F, Wei G-H, Schleutker J. ANO7 is associated with aggressive prostate cancer. Int J Cancer, 2018;143(10):2479-2487.
Sipeky C, Gao P, Zhang Q, Wang L, Ettala O, Talala KM, Tammela TLJ, Auvinen A, PRACTICAL Consortium, Wiklund F, Wei G-H, Schleutker J. Synergistic interaction of HOXB13 and CIP2A predispose to aggressive prostate cancer. Clin Cancer Res, 2018;24(24):6265-6276.
Chen Y, Zhang Q, Wang Q, Li J, Sipeky C, Xia J, Gao P, Hu Y, Zhang H, Yang X, Chen H, Jiang Y, Yang Y, Yao Z, Chen Y, Gao Y, Tan A, Liao M, Schleutker J, Xu J, Sun Y, Wei GH, Mo Z. Genetic association analysis of the RTK/ERK pathway with aggressive prostate cancer highlights the potential role of CCND2 in disease progression. Sci Rep, 2017; 7(1):4538.
Laitinen V, Rantapero T, Fischer D, Vuorinen EM, Tammela TLJ, PRACTICAL consortium, Wahlfors T, Schleutker J. Fine-mapping the 2q37 and 17q11.2-q22 loci for novel genes and sequence variants associated with a genetic predisposition to prostate cancer. Int J Cancer, 2015; 5;136(10):2316-2327..
Breyer JP, Bradley KM, Dorset DC, Clark TA, McReynolds K, Hock RL, Pereira JK, Maynard WH, Chang SS, Cookson MS, Smith JA, Schleutker J, Dupont WD, Smith JR. An expressed retrogene of master embryonic stem cell factor OCT4 alters prostate cancer susceptibility. Am J Hum Genet,2014; 6;94(3):395-404.
Chen LS, Fann JC, Chiu SY, Yen AM, Wahlfors T, Tammela TL, Chen HH, Auvinen A, Schleutker J. Assessing interactions of two loci (rs4242382 and rs10486567) in Familial Prostate Cancer: Statistical Evaluation of Epistasis. PLoS ONE, 2014; 9(2):e89508.
Cropp CD, Simpson CL, Wahlfors T, Ha N, George A, Jones MS, Harper U, Ponciano-Jackson D, Green TA, Tammela TL, Bailey-Wilson J, Schleutker J. Genome-wide linkage scan for prostate cancer susceptibility in Finland: Evidence for a novel locus on 2q37.2 and confirmation of signal on 17q21-q22. Int J Cancer, 2011; 129(10):2400-2407.
Nurminen R, Wahlfors T, Fischer D, Tammela TLJ, Schleutker J. Identification of an aggressive prostate cancer predisposing variant at 11q13. Int J Cancer, 2011;129(3):599-606.
Alfonso Urbanucci | Genomic Regulation for Precision Cancer Medicine
- Bischof, K, Cremaschi, A, Eroukhmanoff, L, Landskron, J, Flage-Larsen, LL, Gade, A et al.. Patient-derived acellular ascites fluid affects drug responses in ovarian cancer cell lines through the activation of key signalling pathways. Mol Oncol. 2024; :. doi: 10.1002/1878-0261.13726. PubMed PMID:39245677 .
- Cavanaugh, D, Urbanucci, A, Mohamed, NE, Tewari, AK, Figueiro, M, Kyprianou, N et al.. Link between circadian rhythm and benign prostatic hyperplasia (BPH)/lower urinary tract symptoms (LUTS). Prostate. 2024;84 (5):417-425. doi: 10.1002/pros.24656. PubMed PMID:38193363 PubMed Central PMC10922447.
- Severson, TM, Zhu, Y, Prekovic, S, Schuurman, K, Nguyen, HM, Brown, LG et al.. Enhancer profiling identifies epigenetic markers of endocrine resistance and reveals therapeutic options for metastatic castration-resistant prostate cancer patients. medRxiv. 2023; :. doi: 10.1101/2023.02.24.23286403. PubMed PMID:36865297 PubMed Central PMC9980263.
- Parry, MA, Grist, E, Mendes, L, Dutey-Magni, P, Sachdeva, A, Brawley, C et al.. Clinical testing of transcriptome-wide expression profiles in high-risk localized and metastatic prostate cancer starting androgen deprivation therapy: an ancillary study of the STAMPEDE abiraterone Phase 3 trial. Res Sq. 2023; :. doi: 10.21203/rs.3.rs-2488586/v1. PubMed PMID:36798177 PubMed Central PMC9934744.
Tapio Visakorpi | Molecular Biology of Prostate Cancer
- Lawlor, A, Beyer, K, Russell, B, Steinbeisser, C, Bjartell, A, De Meulder, B et al.. PIONEER big data platform for prostate cancer: lessons for advancing future real-world evidence research. Nat Rev Urol. 2024; :. doi: 10.1038/s41585-024-00925-4. PubMed PMID:39251785 .
- Kohvakka, A, Sattari, M, Nättinen, J, Aapola, U, Gregorová, P, Tammela, TLJ et al.. Long noncoding RNA EPCART regulates translation through PI3K/AKT/mTOR pathway and PDCD4 in prostate cancer. Cancer Gene Ther. 2024;31 (10):1536-1546. doi: 10.1038/s41417-024-00822-3. PubMed PMID:39147845 PubMed Central PMC11489079.
- Olotu, O, Koskenniemi, AR, Ma, L, Paramonov, V, Laasanen, S, Louramo, E et al.. Germline-specific RNA helicase DDX4 forms cytoplasmic granules in cancer cells and promotes tumor growth. Cell Rep. 2024;43 (7):114430. doi: 10.1016/j.celrep.2024.114430. PubMed PMID:38963760 .
- Russell, B, Beyer, K, Lawlor, A, Roobol, MJ, Venderbos, LDF, Remmers, S et al.. Survivorship Data in Prostate Cancer: Where Are We and Where Do We Need To Be?. Eur Urol Open Sci. 2024;59 :27-29. doi: 10.1016/j.euros.2023.11.004. PubMed PMID:38298764 PubMed Central PMC10829596.
Fizazi K, Shore N, Tammela TL, Ulys A, Vjaters E, Polyakov S, Jievaltas M, Luz M, Alekseev B, Kuss I, Le Berre MA, Petrenciuc O, Snapir A, Sarapohja T, Smith MR; ARAMIS Investigators. Nonmetastatic, Castration-Resistant Prostate Cancer and Survival with Darolutamide. N Engl J Med. 2020 Sep 10;383(11):1040-1049.
Talala K, Heinävaara S, Taari K, Tammela TLJ, Kujala P, Stenman UH, Malila N, Auvinen A. Long-term health-related quality of life among men with prostate cancer in the Finnish randomized study of screening for prostate cancer. Cancer Med. 2020 Aug;9(15):5643-5654. doi: 10.1002/cam4.3181. Epub 2020 Jun 4.
Kohvakka A, Sattari M, Shcherban A, Annala M, Urbanucci A, Kesseli J, Tammela TLJ, Kivinummi K, Latonen L, Nykter M, Visakorpi T. AR and ERG drive the expression of prostate cancer specific long noncoding RNAs. Oncogene. 2020 Jul;39(30):5241-5251.
Booth N, Rissanen P, Tammela TLJ, Kujala P, Stenman UH, Taari K, Talala K, Auvinen A. Cost-effectiveness analysis of PSA-based mass screening: Evidence from a randomised controlled trial combined with register data. PLoS One. 2019 Nov 5;14(11):e0224479.
Assel M, Sjöblom L, Murtola TJ, Talala K, Kujala P, Stenman UH, Taari K, Auvinen A, Vickers A, Visakorpi T, Tammela TL, Lilja H. A Four-kallikrein Panel and β-Microseminoprotein in Predicting High-grade Prostate Cancer on Biopsy: An Independent Replication from the Finnish Section of the European Randomized Study of Screening for Prostate Cancer. Eur Urol Focus. 2019 Jul;5(4):561-567.
Na R, Helfand BT, Chen H, Conran CA, Crawford SE, Hayward SW, Tammela TLJ, Hoffman-Bolton J, Zheng SL, Walsh PC, Schleutker J, Platz EA, Isaacs WB, Xu J. A genetic variant near GATA3 implicated in inherited susceptibility and etiology of benign prostatic hyperplasia (BPH) and lower urinary tract symptoms (LUTS). Prostate. 2017 Aug;77(11):1213-1220.
Assel M, Sjöblom L, Murtola TJ, Talala K, Kujala P, Stenman UH, Taari K, Auvinen A, Vickers A, Visakorpi T, Tammela TL, Lilja H. A Four-kallikrein Panel and β-Microseminoprotein in Predicting High-grade Prostate Cancer on Biopsy: An Independent Replication from the Finnish Section of the European Randomized Study of Screening for Prostate Cancer. Eur Urol Focus. 2019 Jul;5(4):561-567.
Gusev A, Shi H, Kichaev G, Pomerantz M, Li F, Long HW, Ingles SA, Kittles RA, Strom SS, Rybicki BA, Nemesure B, Isaacs WB, Zheng W, Pettaway CA, Yeboah ED, Tettey Y, Biritwum RB, Adjei AA, Tay E, Truelove A, Niwa S, Chokkalingam AP, John EM, Murphy AB, Signorello LB, Carpten J, Leske MC, Wu SY, Hennis AJ, Neslund-Dudas C, Hsing AW, Chu L, Goodman PJ, Klein EA, Witte JS, Casey G, Kaggwa S, Cook MB, Stram DO, Blot WJ, Eeles RA, Easton D, Kote-Jarai Z, Al Olama AA, Benlloch S, Muir K, Giles GG, Southey MC, Fitzgerald LM, Latonen L, Afyounian E, Jylhä A, Nättinen J, Aapola U, Annala M, Kivinummi KK, Tammela TTL, Beuerman RW, Uusitalo H, Nykter M, Visakorpi T. Integrative proteomics in prostate cancer uncovers robustness against genomic and transcriptomic aberrations during disease progression. Nat Commun. 2018 Mar 21;9(1):1176.
Gronberg H, Wiklund F, Aly M, Henderson BE, Schleutker J, Wahlfors T, Tammela TL, Nordestgaard BG, Key TJ, Travis RC, Neal DE, Donovan JL, Hamdy FC, Pharoah P, Pashayan N, Khaw KT, Stanford JL, Thibodeau SN, McDonnell SK, Schaid DJ, Maier C, Vogel W, Luedeke M, Herkommer K, Kibel AS, Cybulski C, Wokolorczyk D, Kluzniak W, Cannon-Albright L, Teerlink C, Brenner H, Dieffenbach AK, Arndt V, Park JY, Sellers TA, Lin HY, Slavov C, Kaneva R, Mitev V, Batra J, Spurdle A, Clements JA, Teixeira MR, Pandha H, Michael A, Paulo P, Maia S, Kierzek A; PRACTICAL consortium, Conti DV, Albanes D, Berg C, Berndt SI, Campa D, Crawford ED, Diver WR, Gapstur SM, Gaziano JM, Giovannucci E, Hoover R, Hunter DJ, Johansson M, Kraft P, Le Marchand L, Lindström S, Navarro C, Overvad K, Riboli E, Siddiq A, Stevens VL, Trichopoulos D, Vineis P, Yeager M, Trynka G, Raychaudhuri S, Schumacher FR, Price AL, Freedman ML, Haiman CA, Pasaniuc B. Atlas of prostate cancer heritability in European and African-American men pinpoints tissue-specific regulation. Nat Commun. 2016 Apr 7;7:10979.
Ylipää A, Kivinummi K, Kohvakka A, Annala M, Latonen L, Scaravilli M, Kartasalo K, Leppänen SP, Karakurt S, Seppälä J, Yli-Harja O, Tammela TL, Zhang W, Visakorpi T, Nykter M. Transcriptome Sequencing Reveals PCAT5 as a Novel ERG-Regulated Long Noncoding RNA in Prostate Cancer. Cancer Res. 2015 Oct 1;75(19):4026-31.
Teemu Tolonen | Histopathology
Woodcock DJ, Riabchenko E, Taavitsainen S, Kankainen M, Gundem G, Brewer DS, Ellonen P, Lepistö M, Golubeva YG, Warner AC, Tolonen TT, Jasu J, Isaacs WB, Emmert-Buck MR, Nykter M, Visakorpi T, Bova GS, Wedge DC. Prostate cancer evolution from multilineage primary to single lineage metastasis in ten men with implications for liquid biopsy. Nat Commun. 2020 Oct 8;11(1):5070.
Sainio M, Visakorpi T, Tolonen T, Ilvesaro J, Bova GS. Expression of neuroendocrine differentiation markers in lethal metastatic castration-resistant prostate cancer. Pathol Res Pract. 2018 Apr 26. pii: 0344-0338(18)30003-7.
Högnäs G, Kivinummi K, Kallio HML, Hieta R, Ruusuvuori P, Koskenalho A, Kesseli J, Tammela TLJ, Riikonen J, Ilvesaro J, Kares S, Hirvikoski PP, Laurila M, Mirtti T, Nykter M, Kujala PM, Visakorpi T, Tolonen T, Bova GS. Feasibility of Prostate PAXgene Fixation for Molecular Research and Diagnostic Surgical Pathology: Comparison of Matched Fresh Frozen, FFPE, and PFPE Tissues. Am J Surg Pathol. 2018 Jan;42(1):103-115.
Tolonen TT, Tammela TL, Kujala PM, Tuominen VJ, Isola JJ, Visakorpi T. Histopathological variables and biomarkers enhancer of zeste homologue 2, Ki-67 and minichromosome maintenance protein 7 as prognosticators in primarily endocrine-treated prostate cancer. BJU Int. 2011;108:1430-1438.
Tolonen TT, Kujala PM, Laurila M, Tirkkonen M, Ilvesaro J, Tuominen VJ, Tammela TL, Isola J. Routine dual-color immunostaining with a 3-antibody cocktail improves the detection of small cancers in prostate needle biopsies. Hum Pathol. 2011;42:1635-1642.
Koivusalo L, Kaipia A, Kujala P, Isola J, Tolonen TT. Digital image analysis of the tissue surface areas of site-designated and bilaterally pooled prostate biopsies. Histol Histopathol 2018;33:399-405.
Tolonen T, Riikonen J, Tammela TLJ, Koivusalo L, Haapasalo H, Kujala P, Kaipia A. Extraprostatic extension in prostate biopsies is an under-recognized feature indicating high risk disease. Ann Diag Pathol 2018. doi: 10.1016/j.anndiagpath.2018.06.001
Tolonen TT, Kujala PM, Tammela TL, Tuominen VJ, Isola JJ, Visakorpi T. Overall and worst gleason scores are equally good predictors of prostate cancer progression. BMC Urol. 2011;11:21.
Näpänkangas, J., & Tolonen, T. Adoption of diagnostic digital pathology in Finland. Finnish Journal of EHealth and EWelfare. 2019:11;320–325.