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Genomic Regulation for Precision Cancer Medicine Lab

Publications

2024

  1. Kiviaho, A, Eerola, SK, Kallio, HML, Andersen, MK, Hoikka, M, Tiihonen, AM et al.. Single cell and spatial transcriptomics highlight the interaction of club-like cells with immunosuppressive myeloid cells in prostate cancer. Nat Commun. 2024;15 (1):9949. doi: 10.1038/s41467-024-54364-1. PubMed PMID:39550375 PubMed Central PMC11569175.
  2. 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 .
  3. 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.

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2023

  1. Bhasin, N, Dabral, P, Senavirathna, L, Pan, S, Chen, R. Inhibition of TRAP1 Accelerates the DNA Damage Response, Activation of the Heat Shock Response and Metabolic Reprogramming in Colon Cancer Cells. Front Biosci (Landmark Ed). 2023;28 (9):227. doi: 10.31083/j.fbl2809227. PubMed PMID:37796715 PubMed Central PMC10727129.
  2. 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.
  3. 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.

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2022

  1. 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.
  2. Engedal, N, Sønstevold, T, Beese, CJ, Selladurai, S, Melcher, T, Simensen, JE et al.. Measuring Autophagic Cargo Flux with Keima-Based Probes. Methods Mol Biol. 2022;2445 :99-115. doi: 10.1007/978-1-0716-2071-7_7. PubMed PMID:34972988 .

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2021

  1. 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.
  2. 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.
  3. Eerola, SK, Kohvakka, A, Tammela, TLJ, Koskinen, PJ, Latonen, L, Visakorpi, T et al.. Expression and ERG regulation of PIM kinases in prostate cancer. Cancer Med. 2021;10 (10):3427-3436. doi: 10.1002/cam4.3893. PubMed PMID:33932111 PubMed Central PMC8124112.
  4. 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.
  5. Nakken, S, Lilleby, W, Switlyk, MD, Knudsen, KE, Lilleby, O, Zhao, S et al.. The Quandary of DNA-Based Treatment Assessment in De Novo Metastatic Prostate Cancer in the Era of Precision Oncology. J Pers Med. 2021;11 (5):. doi: 10.3390/jpm11050330. PubMed PMID:33922147 PubMed Central PMC8143497.

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2020

  1. Itkonen, HM, Poulose, N, Steele, RE, Martin, SES, Levine, ZG, Duveau, DY et al.. Inhibition of O-GlcNAc Transferase Renders Prostate Cancer Cells Dependent on CDK9. Mol Cancer Res. 2020;18 (10):1512-1521. doi: 10.1158/1541-7786.MCR-20-0339. PubMed PMID:32611550 PubMed Central PMC7541471.
  2. Lavelle, TJ, Alver, TN, Heintz, KM, Wernhoff, P, Nygaard, V, Nakken, S et al.. Dysregulation of MITF Leads to Transformation in MC1R-Defective Melanocytes. Cancers (Basel). 2020;12 (7):. doi: 10.3390/cancers12071719. PubMed PMID:32605315 PubMed Central PMC7408466.
  3. 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 .
  4. Pace, M, Falappa, M, Freschi, A, Balzani, E, Berteotti, C, Lo Martire, V et al.. Loss of Snord116 impacts lateral hypothalamus, sleep, and food-related behaviors. JCI Insight. 2020;5 (12):. doi: 10.1172/jci.insight.137495. PubMed PMID:32365348 PubMed Central PMC7406246.

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2019

  1. Eerola, SK, Santio, NM, Rinne, S, Kouvonen, P, Corthals, GL, Scaravilli, M et al.. Phosphorylation of NFATC1 at PIM1 target sites is essential for its ability to promote prostate cancer cell migration and invasion. Cell Commun Signal. 2019;17 (1):148. doi: 10.1186/s12964-019-0463-y. PubMed PMID:31730483 PubMed Central PMC6858710.
  2. Handle, F, Prekovic, S, Helsen, C, Van den Broeck, T, Smeets, E, Moris, L et al.. Drivers of AR indifferent anti-androgen resistance in prostate cancer cells. Sci Rep. 2019;9 (1):13786. doi: 10.1038/s41598-019-50220-1. PubMed PMID:31551480 PubMed Central PMC6760229.
  3. Braadland, PR, Ramberg, H, Grytli, HH, Urbanucci, A, Nielsen, HK, Guldvik, IJ et al.. The β-Adrenergic Receptor Is a Molecular Switch for Neuroendocrine Transdifferentiation of Prostate Cancer Cells. Mol Cancer Res. 2019;17 (11):2154-2168. doi: 10.1158/1541-7786.MCR-18-0605. PubMed PMID:31395667 .
  4. Itkonen, HM, Urbanucci, A, Martin, SE, Khan, A, Mathelier, A, Thiede, B et al.. High OGT activity is essential for MYC-driven proliferation of prostate cancer cells. Theranostics. 2019;9 (8):2183-2197. doi: 10.7150/thno.30834. PubMed PMID:31149037 PubMed Central PMC6531294.
  5. Braadland, PR, Urbanucci, A. Chromatin reprogramming as an adaptation mechanism in advanced prostate cancer. Endocr Relat Cancer. 2019;26 (4):R211-R235. doi: 10.1530/ERC-18-0579. PubMed PMID:30844748 .

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2018

  1. Gerhauser, C, Favero, F, Risch, T, Simon, R, Feuerbach, L, Assenov, Y et al.. Molecular Evolution of Early-Onset Prostate Cancer Identifies Molecular Risk Markers and Clinical Trajectories. Cancer Cell. 2018;34 (6):996-1011.e8. doi: 10.1016/j.ccell.2018.10.016. PubMed PMID:30537516 PubMed Central PMC7444093.
  2. Perera, AP, Sajnani, K, Dickinson, J, Eri, R, Körner, H. NLRP3 inflammasome in colitis and colitis-associated colorectal cancer. Mamm Genome. 2018;29 (11-12):817-830. doi: 10.1007/s00335-018-9783-2. PubMed PMID:30206651 .
  3. Urbanucci, A, Mills, IG. Bromodomain-containing proteins in prostate cancer. Mol Cell Endocrinol. 2018;462 (Pt A):31-40. doi: 10.1016/j.mce.2017.06.007. PubMed PMID:28624514 .

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2017

  1. Kivinummi, K, Urbanucci, A, Leinonen, K, Tammela, TLJ, Annala, M, Isaacs, WB et al.. The expression of AURKA is androgen regulated in castration-resistant prostate cancer. Sci Rep. 2017;7 (1):17978. doi: 10.1038/s41598-017-18210-3. PubMed PMID:29269934 PubMed Central PMC5740165.
  2. Urbanucci, A, Mills, IG. Bromodomain-containing proteins in prostate cancer. Mol Cell Endocrinol. 2018;462 (Pt A):31-40. doi: 10.1016/j.mce.2017.06.007. PubMed PMID:28624514 .
  3. Urbanucci, A, Barfeld, SJ, Kytölä, V, Itkonen, HM, Coleman, IM, Vodák, D et al.. Androgen Receptor Deregulation Drives Bromodomain-Mediated Chromatin Alterations in Prostate Cancer. Cell Rep. 2017;19 (10):2045-2059. doi: 10.1016/j.celrep.2017.05.049. PubMed PMID:28591577 PubMed Central PMC5675034.
  4. Itkonen, HM, Brown, M, Urbanucci, A, Tredwell, G, Ho Lau, C, Barfeld, S et al.. Lipid degradation promotes prostate cancer cell survival. Oncotarget. 2017;8 (24):38264-38275. doi: 10.18632/oncotarget.16123. PubMed PMID:28415728 PubMed Central PMC5503531.
  5. Barfeld, SJ, Urbanucci, A, Itkonen, HM, Fazli, L, Hicks, JL, Thiede, B et al.. c-Myc Antagonises the Transcriptional Activity of the Androgen Receptor in Prostate Cancer Affecting Key Gene Networks. EBioMedicine. 2017;18 :83-93. doi: 10.1016/j.ebiom.2017.04.006. PubMed PMID:28412251 PubMed Central PMC5405195.
  6. Zuber, V, Bettella, F, Witoelar, A, PRACTICAL Consortium, CRUK GWAS, BCAC Consortium et al.. Bromodomain protein 4 discriminates tissue-specific super-enhancers containing disease-specific susceptibility loci in prostate and breast cancer. BMC Genomics. 2017;18 (1):270. doi: 10.1186/s12864-017-3620-y. PubMed PMID:28359301 PubMed Central PMC5374680.
  7. Sajnani, K, Islam, F, Smith, RA, Gopalan, V, Lam, AK. Genetic alterations in Krebs cycle and its impact on cancer pathogenesis. Biochimie. 2017;135 :164-172. doi: 10.1016/j.biochi.2017.02.008. PubMed PMID:28219702 .
  8. McNair, C, Urbanucci, A, Comstock, CE, Augello, MA, Goodwin, JF, Launchbury, R et al.. Cell cycle-coupled expansion of AR activity promotes cancer progression. Oncogene. 2017;36 (12):1655-1668. doi: 10.1038/onc.2016.334. PubMed PMID:27669432 PubMed Central PMC5364060.

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