Genomic Regulation for Precision Cancer Medicine Lab Publications

Publications 2024

Bischof K, Cremaschi A, Eroukhmanoff L, Landskron J, Flage-Larsen LL, Gade A, Bjørge L, Urbanucci A, Taskén K (2024)
Patient-derived acellular ascites fluid affects drug responses in ovarian cancer cell lines through the activation of key signalling pathways
Mol Oncol (in press)
DOI 10.1002/1878-0261.13726, PubMed 39245677

Cavanaugh D, Urbanucci A, Mohamed NE, Tewari AK, Figueiro M, Kyprianou N (2024)
Link between circadian rhythm and benign prostatic hyperplasia (BPH)/lower urinary tract symptoms (LUTS)
Prostate, 84 (5), 417-425
DOI 10.1002/pros.24656, PubMed 38193363

Kiviaho A, Eerola SK, Kallio HML, Andersen MK, Hoikka M, Tiihonen AM, Salonen I, Spotbeen X, Giesen A, Parker CTA, Taavitsainen S, Hantula O, Marttinen M, Hermelo I, Ismail M, Midtbust E, Wess M, Devlies W, Sharma A, Krossa S, Häkkinen T, Afyounian E, Vandereyken K, Kint S, Kesseli J et al. (2024)
Single cell and spatial transcriptomics highlight the interaction of club-like cells with immunosuppressive myeloid cells in prostate cancer
Nat Commun, 15 (1), 9949
DOI 10.1038/s41467-024-54364-1, PubMed 39550375

Publications 2023

Parry MA, Grist E, Mendes L, Dutey-Magni P, Sachdeva A, Brawley C, Murphy L, Proudfoot J, Lall S, Liu Y, Friedrich S, Ismail M, Hoyle A, Ali A, Haran A, Wingate A, Zakka L, Wetterskog D, Amos CL, Atako NB, Wang V, Rush HL, Jones RJ, Leung H, Cross WR et al. (2023)
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
DOI 10.21203/rs.3.rs-2488586/v1, PubMed 36798177

Severson TM, Zhu Y, Prekovic S, Schuurman K, Nguyen HM, Brown LG, Hakkola S, Kim Y, Kneppers J, Linder S, Stelloo S, Lieftink C, van der Heijden M, Nykter M, van der Noort V, Sanders J, Morris B, Jenster G, van Leenders GJ, Pomerantz M, Freedman ML, Beijersbergen RL, Urbanucci A, Wessels L, Corey E et al. (2023)
Enhancer profiling identifies epigenetic markers of endocrine resistance and reveals therapeutic options for metastatic castration-resistant prostate cancer patients
medRxiv
DOI 10.1101/2023.02.24.23286403, PubMed 36865297

Publications 2022

Cao S, Wang JR, Ji S, Yang P, Dai Y, Guo S, Montierth MD, Shen JP, Zhao X, Chen J, Lee JJ, Guerrero PA, Spetsieris N, Engedal N, Taavitsainen S, Yu K, Livingstone J, Bhandari V, Hubert SM, Daw NC, Futreal PA, Efstathiou E, Lim B, Viale A, Zhang J et al. (2022)
Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression
Nat Biotechnol, 40 (11), 1624-1633
DOI 10.1038/s41587-022-01342-x, PubMed 35697807

Engedal N, Sønstevold T, Beese CJ, Selladurai S, Melcher T, Simensen JE, Frankel LB, Urbanucci A, Torgersen ML (2022)
Measuring Autophagic Cargo Flux with Keima-Based Probes
Methods Mol Biol, 2445, 99-115
DOI 10.1007/978-1-0716-2071-7_7, PubMed 34972988

Publications 2021

Cangiano M, Grudniewska M, Salji MJ, Nykter M, Jenster G, Urbanucci A, Granchi Z, Janssen B, Hamilton G, Leung HY, Beumer IJ (2021)
Gene Regulation Network Analysis on Human Prostate Orthografts Highlights a Potential Role for the JMJD6 Regulon in Clinical Prostate Cancer
Cancers (Basel), 13 (9)
DOI 10.3390/cancers13092094, PubMed 33925994

Kukkonen K, Taavitsainen S, Huhtala L, Uusi-Makela J, Granberg KJ, Nykter M, Urbanucci A (2021)
Chromatin and Epigenetic Dysregulation of Prostate Cancer Development, Progression, and Therapeutic Response
Cancers (Basel), 13 (13)
DOI 10.3390/cancers13133325, PubMed 34283056

Nakken S, Lilleby W, Switlyk MD, Knudsen KE, Lilleby O, Zhao S, Kaveh F, Ekstrøm PO, Urbanucci A, Hovig E (2021)
The Quandary of DNA-Based Treatment Assessment in De Novo Metastatic Prostate Cancer in the Era of Precision Oncology
J Pers Med, 11 (5)
DOI 10.3390/jpm11050330, PubMed 33922147

Pällmann N, Deng K, Livgård M, Tesikova M, Jin Y, Frengen NS, Kahraman N, Mokhlis HM, Ozpolat B, Kildal W, Danielsen HE, Fazli L, Rennie PS, Banerjee PP, Üren A, Jin Y, Kuzu OF, Saatcioglu F (2021)
Stress-Mediated Reprogramming of Prostate Cancer One-Carbon Cycle Drives Disease Progression
Cancer Res, 81 (15), 4066-4078
DOI 10.1158/0008-5472.CAN-20-3956, PubMed 34183356

Taavitsainen S, Engedal N, Cao S, Handle F, Erickson A, Prekovic S, Wetterskog D, Tolonen T, Vuorinen EM, 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 TLJ, Murtola T et al. (2021)
Single-cell ATAC and RNA sequencing reveal pre-existing and persistent cells associated with prostate cancer relapse
Nat Commun, 12 (1), 5307
DOI 10.1038/s41467-021-25624-1, PubMed 34489465

Publications 2020

Itkonen HM, Poulose N, Steele RE, Martin SES, Levine ZG, Duveau DY, Carelli R, Singh R, Urbanucci A, Loda M, Thomas CJ, Mills IG, Walker S (2020)
Inhibition of O-GlcNAc Transferase Renders Prostate Cancer Cells Dependent on CDK9
Mol Cancer Res, 18 (10), 1512-1521
DOI 10.1158/1541-7786.MCR-20-0339, PubMed 32611550

Kohvakka A, Sattari M, Shcherban A, Annala M, Urbanucci A, Kesseli J, Tammela TLJ, Kivinummi K, Latonen L, Nykter M, Visakorpi T (2020)
AR and ERG drive the expression of prostate cancer specific long noncoding RNAs
Oncogene, 39 (30), 5241-5251
DOI 10.1038/s41388-020-1365-6, PubMed 32555329

Lavelle TJ, Alver TN, Heintz KM, Wernhoff P, Nygaard V, Nakken S, Øy GF, Bøe SL, Urbanucci A, Hovig E (2020)
Dysregulation of MITF Leads to Transformation in MC1R-Defective Melanocytes
Cancers (Basel), 12 (7)
DOI 10.3390/cancers12071719, PubMed 32605315

Pace M, Falappa M, Freschi A, Balzani E, Berteotti C, Lo Martire V, Kaveh F, Hovig E, Zoccoli G, Amici R, Cerri M, Urbanucci A, Tucci V (2020)
Loss of Snord116 impacts lateral hypothalamus, sleep, and food-related behaviors
JCI Insight, 5 (12)
DOI 10.1172/jci.insight.137495, PubMed 32365348

Yin YP, Shi WH, Deng K, Liu XL, Li H, Lv XT, Lui VWY, Ding C, Hong B, Lin WC (2020)
Combinations of proteasome inhibitors with obatoclax are effective for small cell lung cancer
Acta Pharmacol Sin, 42 (8), 1298-1310
DOI 10.1038/s41401-020-00544-w, PubMed 33139838

Publications 2019

Braadland PR, Ramberg H, Grytli HH, Urbanucci A, Nielsen HK, Guldvik IJ, Engedal A, Ketola K, Wang W, Svindland A, Mills IG, Bjartell A, Taskén KA (2019)
The β₂-Adrenergic Receptor Is a Molecular Switch for Neuroendocrine Transdifferentiation of Prostate Cancer Cells
Mol Cancer Res, 17 (11), 2154-2168
DOI 10.1158/1541-7786.MCR-18-0605, PubMed 31395667

Braadland PR, Urbanucci A (2019)
Chromatin reprogramming as an adaptation mechanism in advanced prostate cancer
Endocr Relat Cancer, 26 (4), R211-R235
DOI 10.1530/ERC-18-0579, PubMed 30844748

Handle F, Prekovic S, Helsen C, Van den Broeck T, Smeets E, Moris L, Eerlings R, Kharraz SE, Urbanucci A, Mills IG, Joniau S, Attard G, Claessens F (2019)
Drivers of AR indifferent anti-androgen resistance in prostate cancer cells
Sci Rep, 9 (1), 13786
DOI 10.1038/s41598-019-50220-1, PubMed 31551480

Itkonen HM, Urbanucci A, Martin SE, Khan A, Mathelier A, Thiede B, Walker S, Mills IG (2019)
High OGT activity is essential for MYC-driven proliferation of prostate cancer cells
Theranostics, 9 (8), 2183-2197
DOI 10.7150/thno.30834, PubMed 31149037

Li H, Wang H, Deng K, Han W, Hong B, Lin W (2019)
The ratio of Bcl-2/Bim as a predictor of cisplatin response provides a rational combination of ABT-263 with cisplatin or radiation in small cell lung cancer
Cancer Biomark, 24 (1), 51-59
DOI 10.3233/CBM-181692, PubMed 30614795

Publications 2018

Deng K, Shen J, Wang W, Li M, Li H, Chen C, Zhao H, Zhang M, Xue T, Liu Q, Lui VWY, Hong B, Lin W (2018)
Sodium chloride (NaCl) potentiates digoxin-induced anti-tumor activity in small cell lung cancer
Cancer Biol Ther, 20 (1), 52-64
DOI 10.1080/15384047.2018.1504723, PubMed 30183476

Gerhauser C, Favero F, Risch T, Simon R, Feuerbach L, Assenov Y, Heckmann D, Sidiropoulos N, Waszak SM, Hübschmann D, Urbanucci A, Girma EG, Kuryshev V, Klimczak LJ, Saini N, Stütz AM, Weichenhan D, Böttcher LM, Toth R, Hendriksen JD, Koop C, Lutsik P, Matzk S, Warnatz HJ, Amstislavskiy V et al. (2018)
Molecular Evolution of Early-Onset Prostate Cancer Identifies Molecular Risk Markers and Clinical Trajectories
Cancer Cell, 34 (6), 996-1011.e8
DOI 10.1016/j.ccell.2018.10.016, PubMed 30537516

Publications 2017

Barfeld SJ, Urbanucci A, Itkonen HM, Fazli L, Hicks JL, Thiede B, Rennie PS, Yegnasubramanian S, DeMarzo AM, Mills IG (2017)
c-Myc Antagonises the Transcriptional Activity of the Androgen Receptor in Prostate Cancer Affecting Key Gene Networks
EBioMedicine, 18, 83-93
DOI 10.1016/j.ebiom.2017.04.006, PubMed 28412251

Hong B, Wang H, Deng K, Wang W, Dai H, Yan Lui VW, Lin W (2017)
Combination treatment of RAD001 and BEZ235 exhibits synergistic antitumor activity via down-regulation of p-4E-BP1/Mcl-1 in small cell lung cancer
Oncotarget, 8 (63), 106486-106498
DOI 10.18632/oncotarget.18984, PubMed 29290965

Itkonen HM, Brown M, Urbanucci A, Tredwell G, Ho Lau C, Barfeld S, Hart C, Guldvik IJ, Takhar M, Heemers HV, Erho N, Bloch K, Davicioni E, Derua R, Waelkens E, Mohler JL, Clarke N, Swinnen JV, Keun HC, Rekvig OP, Mills IG (2017)
Lipid degradation promotes prostate cancer cell survival
Oncotarget, 8 (24), 38264-38275
DOI 10.18632/oncotarget.16123, PubMed 28415728

Kivinummi K, Urbanucci A, Leinonen K, Tammela TLJ, Annala M, Isaacs WB, Bova GS, Nykter M, Visakorpi T (2017)
The expression of AURKA is androgen regulated in castration-resistant prostate cancer
Sci Rep, 7 (1), 17978
DOI 10.1038/s41598-017-18210-3, PubMed 29269934

Urbanucci A, Barfeld SJ, Kytölä V, Itkonen HM, Coleman IM, Vodák D, Sjöblom L, Sheng X, Tolonen T, Minner S, Burdelski C, Kivinummi KK, Kohvakka A, Kregel S, Takhar M, Alshalalfa M, Davicioni E, Erho N, Lloyd P, Karnes RJ, Ross AE, Schaeffer EM, Vander Griend DJ, Knapp S, Corey E et al. (2017)
Androgen Receptor Deregulation Drives Bromodomain-Mediated Chromatin Alterations in Prostate Cancer
Cell Rep, 19 (10), 2045-2059
DOI 10.1016/j.celrep.2017.05.049, PubMed 28591577

Urbanucci A, Mills IG (2017)
Bromodomain-containing proteins in prostate cancer
Mol Cell Endocrinol, 462 (Pt A), 31-40
DOI 10.1016/j.mce.2017.06.007, PubMed 28624514

Wang H, Hong B, Li X, Deng K, Li H, Yan Lui VW, Lin W (2017)
JQ1 synergizes with the Bcl-2 inhibitor ABT-263 against MYCN-amplified small cell lung cancer
Oncotarget, 8 (49), 86312-86324
DOI 10.18632/oncotarget.21146, PubMed 29156797

Zuber V, Bettella F, Witoelar A, PRACTICAL Consortium, CRUK GWAS, BCAC Consortium, TRICL Consortium, Andreassen OA, Mills IG, Urbanucci A (2017)
Bromodomain protein 4 discriminates tissue-specific super-enhancers containing disease-specific susceptibility loci in prostate and breast cancer
BMC Genomics, 18 (1), 270
DOI 10.1186/s12864-017-3620-y, PubMed 28359301

Publications 2016

Fiorito E, Sharma Y, Gilfillan S, Wang S, Singh SK, Satheesh SV, Katika MR, Urbanucci A, Thiede B, Mills IG, Hurtado A (2016)
CTCF modulates Estrogen Receptor function through specific chromatin and nuclear matrix interactions
Nucleic Acids Res, 44 (22), 10588-10602
DOI 10.1093/nar/gkw785, PubMed 27638884

McNair C, Urbanucci A, Comstock CE, Augello MA, Goodwin JF, Launchbury R, Zhao SG, Schiewer MJ, Ertel A, Karnes J, Davicioni E, Wang L, Wang Q, Mills IG, Feng FY, Li W, Carroll JS, Knudsen KE (2016)
Cell cycle-coupled expansion of AR activity promotes cancer progression
Oncogene, 36 (12), 1655-1668
DOI 10.1038/onc.2016.334, PubMed 27669432

Tekpli X, Urbanucci A, Hashim A, Vågbø CB, Lyle R, Kringen MK, Staff AC, Dybedal I, Mills IG, Klungland A, Staerk J (2016)
Changes of 5-hydroxymethylcytosine distribution during myeloid and lymphoid differentiation of CD34+ cells
Epigenetics Chromatin, 9, 21
DOI 10.1186/s13072-016-0070-8, PubMed 27252783

Publications 2015

Barfeld SJ, Fazli L, Persson M, Marjavaara L, Urbanucci A, Kaukoniemi KM, Rennie PS, Ceder Y, Chabes A, Visakorpi T, Mills IG (2015)
Myc-dependent purine biosynthesis affects nucleolar stress and therapy response in prostate cancer
Oncotarget, 6 (14), 12587-602
DOI 10.18632/oncotarget.3494, PubMed 25869206

Khanna A, Rane JK, Kivinummi KK, Urbanucci A, Helenius MA, Tolonen TT, Saramäki OR, Latonen L, Manni V, Pimanda JE, Maitland NJ, Westermarck J, Visakorpi T (2015)
CIP2A is a candidate therapeutic target in clinically challenging prostate cancer cell populations
Oncotarget, 6 (23), 19661-70
DOI 10.18632/oncotarget.3875, PubMed 25965834

Lund K, Dembinski JL, Solberg N, Urbanucci A, Mills IG, Krauss S (2015)
Slug-dependent upregulation of L1CAM is responsible for the increased invasion potential of pancreatic cancer cells following long-term 5-FU treatment
PLoS One, 10 (4), e0123684
DOI 10.1371/journal.pone.0123684, PubMed 25860483

Publications 2014

Barfeld SJ, Itkonen HM, Urbanucci A, Mills IG (2014)
Androgen-regulated metabolism and biosynthesis in prostate cancer
Endocr Relat Cancer, 21 (4), T57-66
DOI 10.1530/ERC-13-0515, PubMed 24497572

Publications 2012

Jalava SE, Urbanucci A, Latonen L, Waltering KK, Sahu B, Jänne OA, Seppälä J, Lähdesmäki H, Tammela TL, Visakorpi T (2012)
Androgen-regulated miR-32 targets BTG2 and is overexpressed in castration-resistant prostate cancer
Oncogene, 31 (41), 4460-71
DOI 10.1038/onc.2011.624, PubMed 22266859

Lehmusvaara S, Erkkilä T, Urbanucci A, Jalava S, Seppälä J, Kaipia A, Kujala P, Lähdesmäki H, Tammela TL, Visakorpi T (2012)
Goserelin and bicalutamide treatments alter the expression of microRNAs in the prostate
Prostate, 73 (1), 101-12
DOI 10.1002/pros.22545, PubMed 22674191

Lehmusvaara S, Erkkilä T, Urbanucci A, Waltering K, Seppälä J, Larjo A, Tuominen VJ, Isola J, Kujala P, Lähdesmäki H, Kaipia A, Tammela TLj, Visakorpi T (2012)
Chemical castration and anti-androgens induce differential gene expression in prostate cancer
J Pathol, 227 (3), 336-45
DOI 10.1002/path.4027, PubMed 22431170

Waltering KK, Urbanucci A, Visakorpi T (2012)
Androgen receptor (AR) aberrations in castration-resistant prostate cancer
Mol Cell Endocrinol, 360 (1-2), 38-43
DOI 10.1016/j.mce.2011.12.019, PubMed 22245783

Publications 2011

Urbanucci A, Marttila S, Jänne OA, Visakorpi T (2011)
Androgen receptor overexpression alters binding dynamics of the receptor to chromatin and chromatin structure
Prostate, 72 (11), 1223-32
DOI 10.1002/pros.22473, PubMed 22212979

Urbanucci A, Sahu B, Seppälä J, Larjo A, Latonen LM, Waltering KK, Tammela TL, Vessella RL, Lähdesmäki H, Jänne OA, Visakorpi T (2011)
Overexpression of androgen receptor enhances the binding of the receptor to the chromatin in prostate cancer
Oncogene, 31 (17), 2153-63
DOI 10.1038/onc.2011.401, PubMed 21909140

Publications 2010

Waltering KK, Porkka KP, Jalava SE, Urbanucci A, Kohonen PJ, Latonen LM, Kallioniemi OP, Jenster G, Visakorpi T (2010)
Androgen regulation of micro-RNAs in prostate cancer
Prostate, 71 (6), 604-14
DOI 10.1002/pros.21276, PubMed 20945501

Publications 2009

Urbanucci A, Myrmel M, Berg I, von Bonsdorff CH, Maunula L (2009)
Potential internalisation of caliciviruses in lettuce
Int J Food Microbiol, 135 (2), 175-8
DOI 10.1016/j.ijfoodmicro.2009.07.036, PubMed 19720414

Publications 2008

Urbanucci A, Waltering KK, Suikki HE, Helenius MA, Visakorpi T (2008)
Androgen regulation of the androgen receptor coregulators
BMC Cancer, 8, 219
DOI 10.1186/1471-2407-8-219, PubMed 18673534