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Computational Biology

We are part of Academy of Finland Center of Excellence in Tumor Genetics

Publications 2020-2023

2023

  1. Kivioja, T, Posti, JP, Sipilä, J, Rauhala, M, Frantzén, J, Gardberg, M et al.. Motor dysfunction as a primary symptom predicts poor outcome: multicenter study of glioma symptoms. Front Oncol. 2023;13 :1305725. doi: 10.3389/fonc.2023.1305725. PubMed PMID:38239655 PubMed Central PMC10794640.
  2. Kaljunen, H, Taavitsainen, S, Kaarijärvi, R, Takala, E, Paakinaho, V, Nykter, M et al.. Fanconi anemia pathway regulation by FANCI in prostate cancer. Front Oncol. 2023;13 :1260826. doi: 10.3389/fonc.2023.1260826. PubMed PMID:38023254 PubMed Central PMC10643534.
  3. Lin, J, Moradi, E, Salenius, K, Lehtipuro, S, Häkkinen, T, Laiho, JE et al.. Distinct transcriptomic profiles in children prior to the appearance of type 1 diabetes-linked islet autoantibodies and following enterovirus infection. Nat Commun. 2023;14 (1):7630. doi: 10.1038/s41467-023-42763-9. PubMed PMID:37993433 PubMed Central PMC10665402.
  4. Rautajoki, KJ, Jaatinen, S, Hartewig, A, Tiihonen, AM, Annala, M, Salonen, I et al.. Genomic characterization of IDH-mutant astrocytoma progression to grade 4 in the treatment setting. Acta Neuropathol Commun. 2023;11 (1):176. doi: 10.1186/s40478-023-01669-9. PubMed PMID:37932833 PubMed Central PMC10629206.
  5. Nurminen, A, Jaatinen, S, Taavitsainen, S, Högnäs, G, Lesluyes, T, Ansari-Pour, N et al.. Cancer origin tracing and timing in two high-risk prostate cancers using multisample whole genome analysis: prospects for personalized medicine. Genome Med. 2023;15 (1):82. doi: 10.1186/s13073-023-01242-y. PubMed PMID:37828555 PubMed Central PMC10571458.
  6. Sattari, M, Kohvakka, A, Moradi, E, Rauhala, H, Urhonen, H, Isaacs, WB et al.. Identification of long noncoding RNAs with aberrant expression in prostate cancer metastases. Endocr Relat Cancer. 2023;30 (8):. doi: 10.1530/ERC-22-0247. PubMed PMID:37140987 PubMed Central PMC10326635.
  7. Hamis, S, Somervuo, P, Ågren, JA, Tadele, DS, Kesseli, J, Scott, JG et al.. Spatial cumulant models enable spatially informed treatment strategies and analysis of local interactions in cancer systems. J Math Biol. 2023;86 (5):68. doi: 10.1007/s00285-023-01903-x. PubMed PMID:37017776 PubMed Central PMC10076412.
  8. Ojanen, MJT, Caro, FM, Aittomäki, S, Ploquin, MJ, Ortutay, Z, Pekkarinen, M et al.. FURIN regulates cytotoxic T-lymphocyte effector function and memory cell transition in mice. Eur J Immunol. 2023;53 (6):e2250246. doi: 10.1002/eji.202250246. PubMed PMID:37015057 .
  9. Tolmeijer, SH, Boerrigter, E, Sumiyoshi, T, Kwan, EM, Ng, SWS, Annala, M et al.. Early On-treatment Changes in Circulating Tumor DNA Fraction and Response to Enzalutamide or Abiraterone in Metastatic Castration-Resistant Prostate Cancer. Clin Cancer Res. 2023;29 (15):2835-2844. doi: 10.1158/1078-0432.CCR-22-2998. PubMed PMID:36996325 .
  10. Alanen, E, Heikkinen, S, Nurminen, R, Nykter, M, Haapasalo, H, Hirvonen, E et al.. Early-onset grade 2-3 diffuse gliomas and schwannomas increase the risk of central nervous system tumors among the patients’ relatives. Neurooncol Adv. 2023;5 (1):vdad008. doi: 10.1093/noajnl/vdad008. PubMed PMID:36950216 PubMed Central PMC10025807.
  11. 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.
  12. Aakula, A, Sharma, M, Tabaro, F, Nätkin, R, Kamila, J, Honkanen, H et al.. RAS and PP2A activities converge on epigenetic gene regulation. Life Sci Alliance. 2023;6 (5):. doi: 10.26508/lsa.202301928. PubMed PMID:36858798 PubMed Central PMC9979842.
  13. Nätkin, R, Pennanen, P, Syvälä, H, Bläuer, M, Kesseli, J, Tammela, TLJ et al.. Adaptive and non-adaptive gene expression responses in prostate cancer during androgen deprivation. PLoS One. 2023;18 (2):e0281645. doi: 10.1371/journal.pone.0281645. PubMed PMID:36809527 PubMed Central PMC9942993.
  14. Saralahti, AK, Harjula, SE, Rantapero, T, Uusi-Mäkelä, MIE, Kaasinen, M, Junno, M et al.. Characterization of the innate immune response to Streptococcus pneumoniae infection in zebrafish. PLoS Genet. 2023;19 (1):e1010586. doi: 10.1371/journal.pgen.1010586. PubMed PMID:36622851 PubMed Central PMC9858863.

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2022

 

  1. Sjöström, M, Zhao, SG, Levy, S, Zhang, M, Ning, Y, Shrestha, R et al.. The 5-Hydroxymethylcytosine Landscape of Prostate Cancer. Cancer Res. 2022;82 (21):3888-3902. doi: 10.1158/0008-5472.CAN-22-1123. PubMed PMID:36251389 PubMed Central PMC9627125.
  2. Kukkonen, K, Autio-Kimura, B, Rauhala, H, Kesseli, J, Nykter, M, Latonen, L et al.. Nonmalignant AR-positive prostate epithelial cells and cancer cells respond differently to androgen. Endocr Relat Cancer. 2022;29 (12):717-733. doi: 10.1530/ERC-22-0108. PubMed PMID:36219867 PubMed Central PMC9644224.
  3. Buhigas, C, Warren, AY, Leung, WK, Whitaker, HC, Luxton, HJ, Hawkins, S et al.. The architecture of clonal expansions in morphologically normal tissue from cancerous and non-cancerous prostates. Mol Cancer. 2022;21 (1):183. doi: 10.1186/s12943-022-01644-3. PubMed PMID:36131292 PubMed Central PMC9494848.
  4. Rautajoki, KJ, Jaatinen, S, Tiihonen, AM, Annala, M, Vuorinen, EM, Kivinen, A et al.. PTPRD and CNTNAP2 as markers of tumor aggressiveness in oligodendrogliomas. Sci Rep. 2022;12 (1):14083. doi: 10.1038/s41598-022-14977-2. PubMed PMID:35982066 PubMed Central PMC9388569.
  5. Koivisto, M, Tolvanen, TA, Toimela, T, Miinalainen, I, Kiviaho, A, Kesseli, J et al.. Functional human cell-based vascularised cardiac tissue model for biomedical research and testing. Sci Rep. 2022;12 (1):13459. doi: 10.1038/s41598-022-17498-0. PubMed PMID:35931748 PubMed Central PMC9355975.
  6. Herberts, C, Annala, M, Sipola, J, Ng, SWS, Chen, XE, Nurminen, A et al.. Deep whole-genome ctDNA chronology of treatment-resistant prostate cancer. Nature. 2022;608 (7921):199-208. doi: 10.1038/s41586-022-04975-9. PubMed PMID:35859180 .
  7. L B Almeida, B, M Bahrudeen, MN, Chauhan, V, Dash, S, Kandavalli, V, Häkkinen, A et al.. The transcription factor network of E. coli steers global responses to shifts in RNAP concentration. Nucleic Acids Res. 2022;50 (12):6801-6819. doi: 10.1093/nar/gkac540. PubMed PMID:35748858 PubMed Central PMC9262627.
  8. Cao, S, Wang, JR, Ji, S, Yang, P, Dai, Y, Guo, S et al.. Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression. Nat Biotechnol. 2022;40 (11):1624-1633. doi: 10.1038/s41587-022-01342-x. PubMed PMID:35697807 PubMed Central PMC9646498.
  9. Fonseca, NM, Van der Eecken, K, Herberts, C, Verbeke, S, Ng, SWS, Lumen, N et al.. Genomic Features of Lung-Recurrent Hormone-Sensitive Prostate Cancer. JCO Precis Oncol. 2022;6 :e2100543. doi: 10.1200/PO.21.00543. PubMed PMID:35507889 .
  10. Rodriguez-Martinez, A, Vuorinen, EM, Shcherban, A, Uusi-Mäkelä, J, Rajala, NKM, Nykter, M et al.. Novel ZNF414 activity characterized by integrative analysis of ChIP-exo, ATAC-seq and RNA-seq data. Biochim Biophys Acta Gene Regul Mech. 2022;1865 (3):194811. doi: 10.1016/j.bbagrm.2022.194811. PubMed PMID:35318951 .
  11. Ruusuvuori, P, Valkonen, M, Kartasalo, K, Valkonen, M, Visakorpi, T, Nykter, M et al.. Spatial analysis of histology in 3D: quantification and visualization of organ and tumor level tissue environment. Heliyon. 2022;8 (1):e08762. doi: 10.1016/j.heliyon.2022.e08762. PubMed PMID:35128089 PubMed Central PMC8800033.
  12. Bacon, JVW, Müller, DC, Ritch, E, Annala, M, Dugas, SG, Herberts, C et al.. Somatic Features of Response and Relapse in Non-muscle-invasive Bladder Cancer Treated with Bacillus Calmette-Guérin Immunotherapy. Eur Urol Oncol. 2022;5 (6):677-686. doi: 10.1016/j.euo.2021.11.002. PubMed PMID:34895867 .

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2021

 

  1. Bacon, JVW, Müller, DC, Ritch, E, Annala, M, Dugas, SG, Herberts, C et al.. Somatic Features of Response and Relapse in Non-muscle-invasive Bladder Cancer Treated with Bacillus Calmette-Guérin Immunotherapy. Eur Urol Oncol. 2022;5 (6):677-686. doi: 10.1016/j.euo.2021.11.002. PubMed PMID:34895867 .
  2. Taavitsainen, S, Engedal, N, Cao, S, Handle, F, Erickson, A, Prekovic, S et al.. Single-cell ATAC and RNA sequencing reveal pre-existing and persistent cells associated with prostate cancer relapse. Nat Commun. 2021;12 (1):5307. doi: 10.1038/s41467-021-25624-1. PubMed PMID:34489465 PubMed Central PMC8421417.
  3. Ketola, K, Kaljunen, H, Taavitsainen, S, Kaarijärvi, R, Järvelä, E, Rodríguez-Martín, B et al.. Subclone Eradication Analysis Identifies Targets for Enhanced Cancer Therapy and Reveals L1 Retrotransposition as a Dynamic Source of Cancer Heterogeneity. Cancer Res. 2021;81 (19):4901-4909. doi: 10.1158/0008-5472.CAN-21-0371. PubMed PMID:34348967 PubMed Central PMC9397610.
  4. Jasu, J, Tolonen, T, Antonarakis, ES, Beltran, H, Halabi, S, Eisenberger, MA et al.. Combined Longitudinal Clinical and Autopsy Phenomic Assessment in Lethal Metastatic Prostate Cancer: Recommendations for Advancing Precision Medicine. Eur Urol Open Sci. 2021;30 :47-62. doi: 10.1016/j.euros.2021.05.011. PubMed PMID:34337548 PubMed Central PMC8317817.
  5. Kukkonen, K, Taavitsainen, S, Huhtala, L, Uusi-Makela, J, Granberg, KJ, Nykter, M et al.. Chromatin and Epigenetic Dysregulation of Prostate Cancer Development, Progression, and Therapeutic Response. Cancers (Basel). 2021;13 (13):. doi: 10.3390/cancers13133325. PubMed PMID:34283056 PubMed Central PMC8268970.
  6. Jacome Sanz, D, Saralahti, AK, Pekkarinen, M, Kesseli, J, Nykter, M, Rämet, M et al.. Proprotein convertase subtilisin/kexin type 9 regulates the production of acute-phase reactants from the liver. Liver Int. 2021;41 (10):2511-2522. doi: 10.1111/liv.14993. PubMed PMID:34174143 .
  7. Annala, M, Taavitsainen, S, Khalaf, DJ, Vandekerkhove, G, Beja, K, Sipola, J et al.. Evolution of Castration-Resistant Prostate Cancer in ctDNA during Sequential Androgen Receptor Pathway Inhibition. Clin Cancer Res. 2021;27 (16):4610-4623. doi: 10.1158/1078-0432.CCR-21-1625. PubMed PMID:34083234 .
  8. Filppu, P, Tanjore Ramanathan, J, Granberg, KJ, Gucciardo, E, Haapasalo, H, Lehti, K et al.. CD109-GP130 interaction drives glioblastoma stem cell plasticity and chemoresistance through STAT3 activity. JCI Insight. 2021;6 (9):. doi: 10.1172/jci.insight.141486. PubMed PMID:33986188 PubMed Central PMC8262342.
  9. Rajamäki, K, Taira, A, Katainen, R, Välimäki, N, Kuosmanen, A, Plaketti, RM et al.. Genetic and Epigenetic Characteristics of Inflammatory Bowel Disease-Associated Colorectal Cancer. Gastroenterology. 2021;161 (2):592-607. doi: 10.1053/j.gastro.2021.04.042. PubMed PMID:33930428 .
  10. Cangiano, M, Grudniewska, M, Salji, MJ, Nykter, M, Jenster, G, Urbanucci, A et al.. Gene Regulation Network Analysis on Human Prostate Orthografts Highlights a Potential Role for the Regulon in Clinical Prostate Cancer. Cancers (Basel). 2021;13 (9):. doi: 10.3390/cancers13092094. PubMed PMID:33925994 PubMed Central PMC8123677.
  11. Annala, M, Fu, S, Bacon, JVW, Sipola, J, Iqbal, N, Ferrario, C et al.. Cabazitaxel versus abiraterone or enzalutamide in poor prognosis metastatic castration-resistant prostate cancer: a multicentre, randomised, open-label, phase II trial. Ann Oncol. 2021;32 (7):896-905. doi: 10.1016/j.annonc.2021.03.205. PubMed PMID:33836265 .
  12. Cerqueira, JXM, Saavalainen, P, Kurppa, K, Laurikka, P, Huhtala, H, Nykter, M et al.. Independent and cumulative coeliac disease-susceptibility loci are associated with distinct disease phenotypes. J Hum Genet. 2021;66 (6):613-623. doi: 10.1038/s10038-020-00888-5. PubMed PMID:33446885 PubMed Central PMC8144013.
  13. Vandekerkhove, G, Lavoie, JM, Annala, M, Murtha, AJ, Sundahl, N, Walz, S et al.. Plasma ctDNA is a tumor tissue surrogate and enables clinical-genomic stratification of metastatic bladder cancer. Nat Commun. 2021;12 (1):184. doi: 10.1038/s41467-020-20493-6. PubMed PMID:33420073 PubMed Central PMC7794518.
  14. Warner, E, Herberts, C, Fu, S, Yip, S, Wong, A, Wang, G et al.. , , and Defects Differentially Shape Prostate Tumor Driver Genomics and Clinical Aggression. Clin Cancer Res. 2021;27 (6):1650-1662. doi: 10.1158/1078-0432.CCR-20-3708. PubMed PMID:33414135 .

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2020

 

  1. Woodcock, DJ, Riabchenko, E, Taavitsainen, S, Kankainen, M, Gundem, G, Brewer, DS et al.. Prostate cancer evolution from multilineage primary to single lineage metastases with implications for liquid biopsy. Nat Commun. 2020;11 (1):5070. doi: 10.1038/s41467-020-18843-5. PubMed PMID:33033260 PubMed Central PMC7545111.
  2. Dufva, O, Pölönen, P, Brück, O, Keränen, MAI, Klievink, J, Mehtonen, J et al.. Immunogenomic Landscape of Hematological Malignancies. Cancer Cell. 2020;38 (3):424-428. doi: 10.1016/j.ccell.2020.08.019. PubMed PMID:32931743 .
  3. Gundem, G, Van Loo, P, Kremeyer, B, Alexandrov, LB, Tubio, JMC, Papaemmanuil, E et al.. Author Correction: The evolutionary history of lethal metastatic prostate cancer. Nature. 2020;584 (7820):E18. doi: 10.1038/s41586-020-2581-5. PubMed PMID:32728210 .
  4. Yang, M, Petralia, F, Li, Z, Li, H, Ma, W, Song, X et al.. Community Assessment of the Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics. Cell Syst. 2020;11 (2):186-195.e9. doi: 10.1016/j.cels.2020.06.013. PubMed PMID:32710834 .
  5. Dufva, O, Pölönen, P, Brück, O, Keränen, MAI, Klievink, J, Mehtonen, J et al.. Immunogenomic Landscape of Hematological Malignancies. Cancer Cell. 2020;38 (3):380-399.e13. doi: 10.1016/j.ccell.2020.06.002. PubMed PMID:32649887 .
  6. Khalaf, DJ, Aragón, IM, Annala, M, Lozano, R, Taavitsainen, S, Lorente, D et al.. HSD3B1 (1245A>C) germline variant and clinical outcomes in metastatic castration-resistant prostate cancer patients treated with abiraterone and enzalutamide: results from two prospective studies. Ann Oncol. 2020;31 (9):1186-1197. doi: 10.1016/j.annonc.2020.06.006. PubMed PMID:32574722 .
  7. Kohvakka, A, Sattari, M, Shcherban, A, Annala, M, Urbanucci, A, Kesseli, J et al.. AR and ERG drive the expression of prostate cancer specific long noncoding RNAs. Oncogene. 2020;39 (30):5241-5251. doi: 10.1038/s41388-020-1365-6. PubMed PMID:32555329 .
  8. Herberts, C, Murtha, AJ, Fu, S, Wang, G, Schönlau, E, Xue, H et al.. Activating AKT1 and PIK3CA Mutations in Metastatic Castration-Resistant Prostate Cancer. Eur Urol. 2020;78 (6):834-844. doi: 10.1016/j.eururo.2020.04.058. PubMed PMID:32451180 .
  9. Tanjore Ramanathan, J, Lehtipuro, S, Sihto, H, Tóvári, J, Reiniger, L, Téglási, V et al.. Prostate-specific membrane antigen expression in the vasculature of primary lung carcinomas associates with faster metastatic dissemination to the brain. J Cell Mol Med. 2020;24 (12):6916-6927. doi: 10.1111/jcmm.15350. PubMed PMID:32390293 PubMed Central PMC7299712.
  10. Rantapero, T, Wahlfors, T, Kähler, A, Hultman, C, Lindberg, J, Tammela, TL et al.. Inherited DNA Repair Gene Mutations in Men with Lethal Prostate Cancer. Genes (Basel). 2020;11 (3):. doi: 10.3390/genes11030314. PubMed PMID:32183364 PubMed Central PMC7140841.
  11. Bacon, JVW, Annala, M, Soleimani, M, Lavoie, JM, So, A, Gleave, ME et al.. Plasma Circulating Tumor DNA and Clonal Hematopoiesis in Metastatic Renal Cell Carcinoma. Clin Genitourin Cancer. 2020;18 (4):322-331.e2. doi: 10.1016/j.clgc.2019.12.018. PubMed PMID:32046920 .
  12. Lindfors, K, Lin, J, Lee, HS, Hyöty, H, Nykter, M, Kurppa, K et al.. Metagenomics of the faecal virome indicate a cumulative effect of enterovirus and gluten amount on the risk of coeliac disease autoimmunity in genetically at risk children: the TEDDY study. Gut. 2020;69 (8):1416-1422. doi: 10.1136/gutjnl-2019-319809. PubMed PMID:31744911 PubMed Central PMC7234892.
  13. Ritch, E, Fu, SYF, Herberts, C, Wang, G, Warner, EW, Schönlau, E et al.. Identification of Hypermutation and Defective Mismatch Repair in ctDNA from Metastatic Prostate Cancer. Clin Cancer Res. 2020;26 (5):1114-1125. doi: 10.1158/1078-0432.CCR-19-1623. PubMed PMID:31744831 .
  14. Granberg, KJ, Raita, A, Lehtinen, B, Tiihonen, AM, Kesseli, J, Annala, M et al.. Moderate-to-strong expression of FGFR3 and TP53 alterations in a subpopulation of choroid plexus tumors. Histol Histopathol. 2020;35 (7):673-680. doi: 10.14670/HH-18-180. PubMed PMID:31660579 .
  15. Harjula, SE, Saralahti, AK, Ojanen, MJT, Rantapero, T, Uusi-Mäkelä, MIE, Nykter, M et al.. Characterization of immune response against Mycobacterium marinum infection in the main hematopoietic organ of adult zebrafish (Danio rerio). Dev Comp Immunol. 2020;103 :103523. doi: 10.1016/j.dci.2019.103523. PubMed PMID:31626817 .
  16. Valkonen, M, Isola, J, Ylinen, O, Muhonen, V, Saxlin, A, Tolonen, T et al.. Cytokeratin-Supervised Deep Learning for Automatic Recognition of Epithelial Cells in Breast Cancers Stained for ER, PR, and Ki-67. IEEE Trans Med Imaging. 2020;39 (2):534-542. doi: 10.1109/TMI.2019.2933656. PubMed PMID:31398111 .

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