2024
Ianevski A, Nader K, Driva K, Senkowski W, Bulanova D, Moyano-Galceran L, Ruokoranta T, Kuusanmäki H, Ikonen N, Sergeev P, Vähä-Koskela M, Giri AK, Vähärautio A, Kontro M, Porkka K, Pitkänen E, Heckman CA, Wennerberg K, Aittokallio T. Single-cell transcriptomes identify patient-tailored therapies for selective co-inhibition of cancer clones. Nat Commun. 2024 Oct 3;15(1):8579. doi: 10.1038/s41467-024-52980-5. PMID: 39362905
Kytölä S, Vänttinen IM, Ruokoranta T, Partanen A, Holopainen A, Saad J, Kuusisto MEL, Koskela S, Räty RK, Itälä-Remes M, Västrik I, Suvela M, Parsons AO, Porkka K, Wennerberg K, Heckman CA, Jalkanen T, Huttunen T, Ettala P MD, Rimpiläinen J, Siitonen T, Pyörälä M, Kuusanmäki H, Kontro M. Ex Vivo Venetoclax Sensitivity Predicts Clinical Response in Acute Myeloid Leukemia in the Prospective VenEx Trial. Blood. 2024 Oct 2:blood.2024024968. doi: 10.1182/blood.2024024968. Epub ahead of print. PMID: 39357056.
Korelin K, Oostveen M, Wahbi W, Ianevski F, Cavalcante B, Turunen L, Belevich I, Al-Samadi A, Salo T. Evaluation of BH3 mimetics as a combination therapy with irradiation in head and neck squamous cell carcinoma. Biomed Pharmacother. 2024 Jun;175:116719. doi: 10.1016/j.biopha.2024.116719. Epub 2024 May 15.
Adnan Awad S, Dufva O, Klievink J, Karjalainen E, Ianevski A, Pietarinen P, Kim D, Potdar S, Wolf M, Lotfi K, Aittokallio T, Wennerberg K, Porkka K, Mustjoki S. Integrated drug profiling and CRISPR screening identify BCR::ABL1-independent vulnerabilities in chronic myeloid leukemia. Cell Rep Med. 2024 Apr 10:101521. doi: 10.1016/j.xcrm.2024.101521. Online ahead of print.
Mendiola M, Saarela J, Escudero FJ, Heredia-Soto V, Potdar S, Rodriguez-Marrero S, Miguel M, Pozo-Kreilinger JJ, Berjon A, Ortiz-Cruz E, Feliu J, Redondo A. Characterisation of new in vitro models and identification of potentially active drugs in angiosarcoma. Biomedicine & Pharmacotherapy. 2024 Apr:173:116397. doi: 10.1016/j.biopha.2024.116397.
Mirzaie M, Gholizadeh E, Miettinen JJ, Ianevski F, Ruokoranta T, Saarela J, Manninen M, Miettinen S, Heckman CA, Jafari M. Designing patient-oriented combination therapies for acute myeloid leukemia based on efficacy/toxicity integration and bipartite network modeling. Oncogenesis. 2024 13:11. doi: 10.1038/s41389-024-00510-9.
Pehkonen H, Filippou A, Väänänen J, Lindfors I, Vänttinen M, Ianevski P, Mäkelä A, Munne P, Klefström J, Toppila-Salmi S, Grénman R, Hagström J, Mäkitie AA, Karhemo PR, Monni O. Liprin-α1 contributes to oncogenic MAPK signaling by counteracting ERK activity. Mol Oncol. 2024 Mar;18(3):662-676. doi: 10.1002/1878-0261.13593.
Bogacheva MS, Kuivanen S, Potdar S, Hassinen A, Huuskonen S, Pöhner I, Luck TJ, Turunen L, Feodoroff M, Szirovicza L, Savijoki K, Saarela J, Tammela P, Paavolainen L, Poso A, Varjosalo M, Kallioniemi O, Pietiäinen V, Vapalahti O. Drug repurposing platform for deciphering the druggable SARS-CoV-2 interactome. Antiviral Research. 2024 Mar:223:105813. doi: 10.1016/j.antiviral.2024.105813.
Chen Y, He L, Ianevski A, Ayuda-Durán P, Potdar S, Saarela J, Miettinen JJ, Kytölä S, Miettinen S, Manninen M, Heckman CA, Enserink JM, Wennerberg K, Tero Aittokallio T. Robust scoring of selective drug responses for patient-tailored therapy selection. Nature Protocols. 2024 Jan;19(1):60-82. doi: 10.1038/s41596-023-00903-x.
2023
Rizzo A, Maresca C, D’Angelo C, Porru M, Di Vito S, Salvati E, Sacconi A, Berardinelli F, Sgura A, Kuznetsov S, Potdar S, Hassinen A, Stoppacciaro A, Zizza P, Biroccio A. Drug repositioning strategy for the identification of novel telomere-targeting agents: a role for NAMPT inhibitors. Aging Cell. 2023 Nov;22(11):e13944. doi: 10.1111/acel.13944.
Pietiäinen V, Polso M, Migh E, Guckelsberger C, Harmati M, Diosdi A, Turunen L, Hassinen A, Potdar S, Koponen A, Sebestyen EG, Kovacs F, Kriston A, Hollandi R, Burian K, Terhes G, Visnyovszki A, Fodor E, Lacza Z, Kantele A, Kolehmainen P, Kakkola L, Strandin T, Levanov L, Kallioniemi O, Kemeny L, Julkunen I, Vapalahti O, Buzas K, Paavolainen L, Horvath P, Hepojoki J. Image-based and machine learning-guided multiplexed serology test for SARS-CoV-2. Cell Rep Methods. 2023 Aug 22;3(8):100565. doi: 10.1016/j.crmeth.2023.100565.
Kuusanmäki H, Kytölä S, Vänttinen I, Ruokoranta T, Ranta A, Huuhtanen J, Suvela M, Parsons A, Holopainen A, Partanen A, Kuusisto MEL, Koskela S, Räty R, Itälä-Remes M, Västrik I, Dufva O, Siitonen S, Porkka K, Wennerberg K, Heckman CA, Ettala P, Pyörälä M, Rimpiläinen J, Siitonen T, Kontro M. Ex vivo venetoclax sensitivity testing predicts treatment response in acute myeloid leukemia. Haematologica. 2023 Jul 1;108(7):1768-1781. doi: 10.3324/haematol.2022.281692.
Potdar S, Ianevski F, Ianevski A, Tanoli Z, Wennerberg K, Seashore-Ludlow B, Kallioniemi O, Östling P, Aittokallio T, Saarela J. Breeze 2.0: an interactive web-tool for visual analysis and comparison of drug response data. Nucleic Acids Research. 2023. Jul 5;51(W1):W57-W61. doi: 10.1093/nar/gkad390.
Angori S, Banaei-Esfahani A, Mühlbauer K, Bolck HA, Kahraman A, Karakulak T, Poyet C, Feodoroff M, Potdar S, Kallioniemi O, Pietiäinen V, Schraml P, Moch H. Ex Vivo Drug Testing in Patient-derived Papillary Renal Cancer Cells Reveals EGFR and the BCL2 Family as Therapeutic Targets. Eur Urol Focus. 2023 Sep;9(5):751-759. doi: 10.1016/j.euf.2023.03.005.
Feodoroff M, Mikkonen P, Turunen L, Hassinen A, Paasonen L, Paavolainen L, Potdar S, Murumägi A, Kallioniemi O, Pietiäinen V. Comparison of two supporting matrices for patient-derived cancer cells in 3D drug sensitivity and resistance testing assay (3D-DSRT). SLAS Discovery. 2023 Jun;28(4):138-148. doi: 10.1016/j.slasd.2023.03.002.
Feodoroff M, Mikkonen P, Arjama M, Murumägi A, Kallioniemi O, Potdar S, Turunen L, Pietiäinen V. Protocol for 3D Drug Sensitivity and Resistance Testing of Patient-Derived Cancer Cells in 384-Well Plates. SLAS Discovery. 2023 28(2):36-41. doi: 10.1016/j.slasd.2022.11.003.
Kuusanmäki H, Dufva O, Vähä-Koskela M, Leppä AM, Huuhtanen J, Vänttinen IM, Nygren PJ, Klievink J, Bouhlal JOV, Pölönen P, Zhang Q, Adnan Awad S, Mancebo-Pérez C, Saad J, Miettinen JJ, Javarappa KK, Aakko S, Ruokoranta T, Eldfors S, Heinäniemi M, Theilgaard-Mönch K, Wartiovaara-Kautto U, Keränen MAI, Porkka K, Konopleva M, Wennerberg K, Kontro M, Heckman CA, Mustjoki S. Erythroid/megakaryocytic differentiation confers BCL-XL dependency and venetoclax resistance in acute myeloid leukemia. Blood. 2023 Mar 30;141(13):1610-1625. doi: 10.1182/blood.2021011094.
Wang Z, Mačáková M, Bugai A, Kuznetsov SG, Hassinen A, Lenasi T, Potdar S, Friedel CC, Barborič M. P-TEFb promotes cell survival upon p53 activation by suppressing intrinsic apoptosis pathway. Nucleic Acids Research. 2023 Feb 28;51(4):1687-1706. doi: 10.1093/nar/gkad001.
Murumägi A, Ungureanu D, Khan S, Arjama M, Välimäki K, Ianevski A, Ianevski P, Bergström R, Dini A, Kanerva A, Koivisto-Korander R, Tapper J, Lassus H, Loukovaara M, Mägi A, Hirasawa A, Aoki D, Pietiäinen V, Pellinen T, Bützow R, Aittokallio T, Kallioniemi O. Drug response profiles in patient-derived cancer cells across histological subtypes of ovarian cancer: real-time therapy tailoring for a patient with low-grade serous carcinoma. Br J Cancer. 2023 Feb;128(4):678-690. doi: 10.1038/s41416-022-02067-z.
2022
Peterziel H, Jamaladdin N, ElHarouni D, Gerloff XF, Herter S, Fiesel P, Berker Y, Blattner-Johnson M, Schramm K, Jones BC, Reuss D, Turunen L, Friedenauer A, Holland-Letz T, Sill M, Weiser L, Previti C, Balasubramanian G, Gerber NU, Gojo J, Hutter C, Øra I, Lohi O, Kattamis A, de Wilde B, Westermann F, Tippelt S, Graf N, Nathrath M, Sparber-Sauer M, Sehested A, Kramm CM, Dirksen U, Kallioniemi O, Pfister SM, van Tilburg CM, Jones DTW, Saarela J, Pietiäinen V, Jäger N, Schlesner M, Kopp-Schneider A, Oppermann S, Milde T, Witt O, Oehme I. Drug sensitivity profiling of 3D tumor tissue cultures in the pediatric precision oncology program INFORM. NPJ Precis Oncol. 2022 Dec 27;6(1):94. doi: 10.1038/s41698-022-00335-y.
Roering P, Siddiqui A, Heuser VD, Potdar S, Mikkonen P, Oikkonen J, Li Y, Pikkusaari S, Wennerberg K, Hynninen J, Grenman S, Huhtinen K, Auranen A, Carpén O, Kaipio K. Effects of Wee1 inhibitor adavosertib on patient-derived high-grade serous ovarian cancer cells are multiple and independent of homologous recombination status. Front Oncol. 2022 Aug 23;12:954430. doi: 10.3389/fonc.2022.954430.
Kainulainen V, von Schantz-Fant C, Kovanen RM, Potdar S, Laamanen K, Saarela J, Satokari R. Genome-wide siRNA screening reveals several host receptors for the binding of human gut commensal Bifidobacterium bifidum. Npj Biofilms and microbiomes. 2022 Jun 29;8(1):50. doi:10.1038/s41522-022-00312-0.
Skaga E, Kulesskiy E, Potdar S, Panagopoulos I, Micci F, Langmoen IA, Sandberg CJ, Vik-Mo EO. Functional temozolomide sensitivity testing of patient-specific glioblastoma stem cell cultures is predictive of clinical outcome. Transl Oncol. 2022 Dec:26:101535. doi: 10.1016/j.tranon.2022.101535.
Denisova OV, Merisaari J, Kaur A, Yetukuri L, Jumppanen M, von Schantz-Fant C, Ohlmeyer M, Wennerberg K, Aittokallio T, Taipale M, Westermarck J. Development of actionable targets of multi-kinase inhibitors (AToMI) screening platform to dissect kinase targets of staurosporines in glioblastoma cells. Scientific Reports. 2022 Aug 13;12(1):13796. doi: 10.1038/s41598-022-18118-7.
Laukkanen S, Bacquelaine Veloso A, Yan C, Oksa L, Alpert EJ, Do D, Hyvärinen N, McCarthy K, Adhikari A, Yang Q, Iyer S, Garcia SP, Pello A, Ruokoranta T, Moisio S, Adhikari S, Yoder JA, Gallagher KM, Whelton L, Allen JR, Jin AH, Loontiens S, Heinäniemi M, Kelliher MA, Heckman CA, Lohi O, Langenau DM. Combination therapies to inhibit LCK tyrosine kinase and mTOR signaling in T-cell Acute Lymphoblastic Leukemia. Blood. 2022 140 (17): 1891–1906. doi: 10.1182/blood.2021015106.
Hohtari H, Kankainen M, Adnan-Awad S, Yadav B, Potdar S, Ianevski A, Dufva O, Heckman C, Sexl V, Kytölä S, Mustjoki S, Porkka K. Targeting Apoptosis Pathways With BCL2 and MDM2 Inhibitors in Adult B-cell Acute Lymphoblastic Leukemia. Hemasphere. 2022 Feb 24;6(3):e701. doi: 10.1097/HS9.0000000000000701.
Kohtamäki L, Arjama M, Mäkelä S, Ianevski P, Välimäki K, Juteau S, Ilmonen S, Ungureanu D, Kallioniemi O, Murumägi A, Hernberg M. High-throughput ex vivo drug testing identifies potential drugs and drug combinations for NRAS-positive malignant melanoma. Transl Oncol. 2022 Jan;15(1):101290. doi: 10.1016/j.tranon.2021.101290.
ElHarouni D, Berker Y, Peterziel H, Gopisetty A, Turunen L, Kreth S, Stainczyk SA, Oehme I, Pietiäinen V, Jäger N, Witt O, Schlesner M, Oppermann S. iTReX: Interactive exploration of mono- and combination therapy dose response profiling data. Pharmacol Res. 2022 Jan;175:105996. doi: 10.1016/j.phrs.2021.105996.
Malani D, Kumar A, Bruck O, Kontro M, Yadav B, Hellesoy M, Kuusanmaki H, Dufva O, Kankainen M, Eldfors S, Potdar S, Saarela J, Turunen L, Parsons A, Vastrik I, Kivinen K, Saarela J, Raty R, Lehto M, Wolf M, Gjertsen BT, Mustjoki S, Aittokallio T, Wennerberg K, Heckman CA, Kallioniemi O, Porkka K. Implementing a functional precision medicine tumor board for acute myeloid leukemia. Cancer Discovery. 2022 12:1–14. doi: 10.1158/2159-8290.CD-21-0410.
Tanoli Z, Aldahdooh J, Alam F, Wang Y, Seemab U, Fratelli M, Pavlis P, Hajduch M, Bietrix F, Gribbon P, Zaliani A, Hall MD, Shen M, Brimacombe K, Kulesskiy E, Saarela J, Wennerberg K, Vähä-Koskela M, Tang J. Minimal information for chemosensitivity assays (MICHA): a next-generation pipeline to enable the FAIRification of drug screening experiments. Briefings in Bioinformatics. 2022 23(1), 1–7 doi: 10.1093/bib/bbab350.
2021
White BS, Khan SA, Mason MJ, Ammad-Ud-Din M, Potdar S, Malani D, Kuusanmäki H, Druker BJ, Heckman C, Kallioniemi O, Kurtz SE, Porkka K, Tognon CE, Tyner JW, Aittokallio T, Wennerberg K, Guinney J. Bayesian multi-source regression and monocyte-associated gene expression predict BCL-2 inhibitor resistance in acute myeloid leukemia. NPJ Precis Oncol. 2021 Jul 23;5(1):71. doi: 10.1038/s41698-021-00209-9.
Talwelkar SS, Mäyränpää MI, Søraas L, Potdar S, Bao J, Hemmes A, Linnavirta N, Lømo J, Räsänen J, Knuuttila A, Wennerberg K, Verschuren EW. Functional diagnostics using fresh uncultured lung tumor cells to guide personalized treatments. Cell Rep Med. 2021 Aug 17;2(8):100373. doi: 10.1016/j.xcrm.2021.100373
Tuomainen K, Hyytiäinen A, Al-Samadi A, Ianevski P, Ianevski A, Potdar S, Turunen L, Saarela J, Kuznetsov S, Wahbi W, Risteli M, Mäkitie A, Monni O, Salo T. High-throughput compound screening identifies navitoclax combined with irradiation as a candidate therapy for HPV-negative head and neck squamous cell carcinoma. Scientific Reports. 2021 Jul 20;11(1):14755. doi: 10.1038/s41598-021-94259-5.
Jamshidi M, Fagerholm R, Muranen TA, Kaur S, Potdar S, Khan S, Netti E, Mpindi J-P, Yadav B, Kiiski JI, Aittomäki K, Heikkilä P, Saarela J, Bützow R, Blomqvist C, Nevanlinna H. High miR-30 expression associates with improved breast cancer patient survival and treatment outcome. Cancers (Basel). 2021 Jun 10;13(12):2907. doi: 10.3390/cancers13122907.
Wang L, Poque S, Laamanen K, Saarela J, Poso A, Laitinen T, Valkonen J. In vitro identification and in vivo confirmation of inhibitors for SPCSV RNA silencing suppressor, a viral RNase III. Journal of Virology. 2021 May 24;95(12):e00107-21. doi: 10.1128/JVI.00107-21.
Ianevski A, Lahtela J, Javarappa KK, Sergeev P, Ghimire BR, Gautam P, Vähä-Koskela M, Turunen L, Linnavirta N, Kuusanmäki H, Kontro M, Porkka K, Heckman CA, Mattila P, Wennerberg K, Giri AK, Aittokallio T. Patient-tailored design for selective co-inhibition of leukemic cell subpopulations. Science Advances. 2021 Feb 19;7(8):eabe4038. doi: 10.1126/sciadv.abe4038.
Adnan-Awad S, Kim D, Hohtari H, Javarappa KK, Brandstoetter T, Mayer I, Potdar S, Heckman CA, Kytölä S, Porkka K, Doma E, Sexl V, Kankainen M, Mustjoki S. Characterization of p190-Bcr-Abl chronic myeloid leukemia reveals specific signaling pathways and therapeutic targets. Leukemia. 2021 Jul;35(7):1964-1975. doi: 10.1038/s41375-020-01082-4.
2020
Ianevski A, Yao R, Biza S, Zusinaite E, Mannik A, Kivi G, Planken A, Kurg K, Tombak EM, Ustav M Jr, Shtaida N, Kulesskiy E, Jo E, Yang J, Lysvand H, Løseth K, Oksenych V, Aas PA, Tenson T, Vitkauskienė A, Windisch MP, Fenstad MH, Nordbø SA, Ustav M, Bjørås M, Kainov DE. Identification and Tracking of Antiviral Drug Combinations. Viruses. 2020 12(10):1178. doi: 10.3390/v12101178.
Torrente L, Maan G, Rezig AO, Quinn J, Jackson A, Grilli A, Casares L, Zhang Y, Kulesskiy E, Saarela J, Bicciato S, Edwards J, Dinkova-Kostova A, de la Vega L. High NRF2 levels correlate with poor prognosis in colorectal cancer patients and with sensitivity to the kinase inhibitor AT9283 in vitro. Biomolecules. 2020 10(10):1365. doi: 10.3390/biom10101365.
Malani D, Yadav B, Kumar A, Potdar S, Kontro M, Kankainen M, Javarappa KK, Porkka K, Wolf M, Aittokallio T, Wennerberg K, Heckman CA, Murumägi A, Kallioniemi O. KIT pathway upregulation predicts dasatinib efficacy in acute myeloid leukemia. Leukemia. 2020 34(10):2780-2784. doi: 10.1038/s41375-020-0978-7.
Hansson K, Radke K, Aaltonen K, Saarela J, Mañas A, Sjölund J, Smith EM, Pietras K, Påhlman S, Wennerberg K, Gisselsson D, Bexell D. Therapeutic targeting of KSP in preclinical models of high-risk neuroblastoma. Science Translational Medicine. 2020 12, eaba4434. doi: 10.1126/scitranslmed.aba4434.
Bruun J, Kryeziu K, Eide PW, Hossein Moosavi S, Eilertsen I, Langerud J, Røsok B, Totland MZ, Brunsell T, Pellinen T, Saarela J, Bergsland CH, Brudvik K, Guren T, Dienstmann R, Guren MG, Nesbakken A, Atle Bjørnbeth B, Sveen A, Lothe RA. Patient-Derived Organoids from Multiple Colorectal Cancer Liver Metastases Reveal Moderate Intra-patient Pharmacotranscriptomic Heterogeneity. Clinical Cancer Research. 2020 26, 4107–19. doi:10.1158/1078-0432.CCR-19-3637.
Ianevski A, Kulesskiy E, Krpina K, Lou G, Aman Y, Bugai A, Aasumets K, Akimov Y, Bulanova D, Gildemann K, Arutyunyan AF, Susova OY, Zhuze AL, Ji P, Wang W, Holien T, Bugge M, Zusinaite E, Oksenych V, Lysvand H, Gerhold JM, Bjørås M, Johansen P, Waage A, Heckman CA, Fang EF, Kainov DE. Chemical, Physical and Biological Triggers of Evolutionary Conserved Bcl-xL-Mediated Apoptosis. Cancers (Basel). 2020 Jun 25;12(6):1694. doi: 10.3390/cancers12061694.
Wang L, Saarela J, Poque S, Valkonen JPT. Development of FRET-Based High-Throughput Screening for viral RNase III Inhibitors. Molecular Plant Pathology. 2020 21, 961–974. doi: 10.1111/mpp.12942.
Kauko O, Imanishi SY, Kulesskiy E, Yetukuri L, Laajala TD, Sharma M, Pavic K, Aakula A, Rupp C, Jumppanen M, Haapaniemi P, Ruan L, Yadav B, Suni V, Varila T, Corthals GL, Reimand J, Wennerberg K, Aittokallio T, Westermarck J. Phosphoproteome and drug response effects mediated by the three Protein Phosphatase 2A inhibitor proteins CIP2A, SET and PME-1. J Biol Chem. 2020 295(13):4194-4211. doi: 10.1074/jbc.RA119.011265.
Potdar S, Ianevski A, Mpindi JP, Bychkov D, Fiere C, Ianevski P, Yadav B, Wennerberg K, Aittokallio T, Kallioniemi O, Saarela J*, Östling P*. Breeze: an integrated quality control and data analysis application for high-throughput drug screening. Bioinformatics. 2020 36(11), 3602–3604. doi: 10.1093/bioinformatics/btaa138. *shared authorship.
Gupta A, Gautam P, Wennerberg K, Aittokallio T. A normalized drug response metric improves accuracy and consistency of anticancer drug sensitivity quantification in cell-based screening. Communications biology. 2020 3:42. doi: 10.1038/s42003-020-0765-z.
Kaipio K, Chen P, Roering P, Huhtinen K, Mikkonen P, Östling P, Lehtinen L, Mansuri N, Korpela T, Potdar S, Hynninen J, Auranen A, Grénman S, Wennerberg K, Hautaniemi S, Carpén O. ALDH1A1-related stemness in high-grade serous ovarian cancer is a negative prognostic indicator but potentially targetable by EGFR/mTOR-PI3K/aurora kinase inhibitors. J Pathol. 2020 250(2):159-169. doi: 10.1002/path.5356.
Tanoli Z, Alam Z, Ianevski A, Wennerberg K, Vähä-Koskela M, Aittokallio T. Interactive visual analysis of drug-target interaction networks using Drug Target Profiler, with applications to precision medicine and drug repurposing. Brief Bioinform. 2020 21 (1), 211–220, doi: 10.1093/bib/bby119.
2019
Tuomainen K, Al-Samadi A, Potdar S, Turunen L, Turunen M, Karhemo PR, Bergman P, Risteli M, Åström P, Tiikkaja R, Grenman R, Wennerberg K, Monni O, Salo T. Human Tumor-Derived Matrix Improves the Predictability of Head and Neck Cancer Drug Testing. Cancers (Basel). 2019 12(1). doi: 10.3390/cancers12010092.
Wang W, Malyutina A, Pessia A, Saarela J, Heckman C, Tang J. Combined gene essentiality scoring (CES) improves the prediction of cancer dependency map. EBioMedicine. 2019 67-80. doi: 10.1016/j.ebiom.2019.10.051.
Facciotto C, Casado J, Turunen L, Leivonen S-K, Tumiati M, Rantanen V, Kauppi L, Lehtonen R, Leppä S, Wennerberg K, Hautaniemi S. Drug screening approach combines epigenetic sensitization with immunochemotherapy in cancer. Clin Epigenet. 2019 11, 192. Doi: 10.1186/s13148-019-0781-3.
Ianevski A, Giri AK, Gautam P, Kononov A, Potdar S, Saarela J, Wennerberg K, Aittokallio T. Prediction of drug combination effects with a minimal set of experiments. Nat Mach Intell. 2019 1, 568–577. doi: 10.1038/s42256-019-0122-4.
Skaga E, Kulesskiy E, Brynjulvsen M, Sandberg CJ, Potdar S, Langmoen IA, Laakso A, Gaál-Paavola E, Perola M, Wennerberg K, Vik-Mo EO. Feasibility study of using high-throughput drug sensitivity testing to target recurrent glioblastoma stem cells for individualized treatment. Clin Transl Med. 2019 8(1):33. doi: 10.1186/s40169-019-0253-6.
Skaga E, Kulesskiy E, Fayzullin A, Sandberg CJ, Potdar S, Kyttälä A, Langmoen IA, Laakso A, Gaál-Paavola E, Perola M, Wennerberg K, Vik-Mo EO. Intertumoral heterogeneity in patient-specific drug sensitivities in treatment-naïve glioblastoma. BMC Cancer. 2019 19(1):628. doi: 10.1186/s12885-019-5861-4.
Talwelkar SS, Nagaraj AS, Devlin JR, Hemmes A, Potdar S, Kiss EA, Saharinen P, Salmenkivi K, Mäyränpää MI, Wennerberg K, Verschuren EW. Receptor Tyrosine Kinase Signaling Networks Define Sensitivity to ERBB Inhibition and Stratify Kras-Mutant Lung Cancers. Mol Cancer Ther. 2019 18(10):1863-1874. doi: 10.1158/1535-7163.MCT-18-0573.
Tang J, Gautam P, Gupta A, He L, Timonen S, Akimov Y, Wang W, Szwajda A, Jaiswal A, Turei D, Yadav B, Kankainen M, Saarela J, Saez-Rodriguez J, Wennerberg K, Aittokallio T. Network pharmacology modeling identifies synergistic Aurora B and ZAK interaction in triple-negative breast cancer. npj systems biology and applications. 2019 5:20. doi.org/10.1038/s41540-019-0098-z.
Ianevski A, Zusinaite E, Shtaida N, Kallio-Kokko H, Valkonen M, Kantele A, Telling K, Lutsar I, Letjuka P, Metelitsa N, Oksenych V, Dumpis U, Vitkauskiene A, Stašaitis K, Öhrmalm C, Bondeson K, Bergqvist A, Cox RJ, Tenson T, Merits A, Kainov DE. Low Temperature and Low UV Indexes Correlated with Peaks of Influenza Virus Activity in Northern Europe during 2010–2018. Viruses. 2019 11, 207. doi: 10.3390/v11030207.
Jaiswal A, Yadav B, Wennerberg K, Aittokallio T. Integrated Analysis of Drug Sensitivity and Selectivity to Predict Synergistic Drug Combinations and Target Coaddictions in Cancer. Methods Mol Biol. 2019 1888:205-217. doi: 10.1007/978-1-4939-8891-4_12.
Pulkka OP, Gebreyohannes YK, Wozniak A, Mpindi JP, Tynninen O, Icay K, Cervera A, Keskitalo S, Murumägi A, Kulesskiy E, Laaksonen M, Wennerberg K, Varjosalo M, Laakkonen P, Lehtonen R, Hautaniemi S, Kallioniemi O, Schöffski P, Sihto H, Joensuu H. Anagrelide for Gastrointestinal Stromal Tumor. Clin Cancer Res. 2019 25(5):1676-1687. doi: 10.1158/1078-0432.CCR-18-0815.
Buettner R, Nguyen LXT, Kumar B, Morales C, Liu C, Chen LS, Pemovska T, Synold TW, Palmer J, Thompson R, Li L, Hoang DH, Zhang B, Ghoda L, Kowolik C, Kontro M, Leitch C, Wennerberg K, Yu X, Chen CC, Horne D, Gandhi V, Pullarkat V, Marcucci G, Rosen ST. 8-chloro-adenosine activity in FLT3-ITD acute myeloid leukemia. J Cell Physiol. 2019 234:16295–16303. doi: 10.1002/jcp.28294.
Brodin BA, Wennerberg K, Lidbrink E, Brosjö O, Potdar S, Wilson JN, Ma L, Moens LN, Hesla A, Porovic E, Bernhardsson E, Papakonstantinou A, Bauer H, Tsagkozis P, von Sivers K, Wejde J, Östling P, Kallioniemi O, Stragliotto CL. Drug sensitivity testing on patient-derived sarcoma cells predicts patient response to treatment and identifies c-Sarc inhibitors as active drugs for translocation sarcomas. Br J Cancer. 2019 120 (4):435-443. doi: 10.1038/s41416-018-0359-4.
2018
Tanoli Z, Alam Z, Vähä-Koskela M, Ravikumar B, Malyutina A, Jaiswal A, Tang J, Wennerberg K, Aittokallio T. Drug Target Commons 2.0: a community platform for systematic analysis of drug-target interaction profiles. Database (Oxford). 2018 1-13. doi: 10.1093/database/bay083.
Vaseva AV, Blake DR, Gilbert TSK, Ng S, Hostetter G, Azam SH, Ozkan-Dagliyan I, Gautam P, Bryant KL, Pearce KH, Herring LE, Han H, Graves LM, Witkiewicz AK, Knudsen ES, Pecot CV, Rashid N, Houghton PJ, Wennerberg K, Cox AD, Der CJ. KRAS Suppression-Induced Degradation of MYC Is Antagonized by a MEK5-ERK5 Compensatory Mechanism. Cancer Cell. 2018 34(5):807-822.e7. doi: 10.1016/j.ccell.2018.10.001.
Zusinaite E, Ianevski A, Niukkanen D, Poranen MM, Bjørås M, Afset JE, Tenson T, Velagapudi V, Merits A, Kainov DE. A Systems Approach to Study Immuno- and Neuro-Modulatory Properties of Antiviral Agents. Viruses. 2018 10(8). doi: 10.3390/v10080423. Review.
Loevenich S, Ianevski A, Oitmaa E, Kainov DE, Anthonsen MW. Single Passage of Human Metapneumovirus in LLC-MK2 Cells Does Not Affect Viral Protein-Coding Capacity. Genome Announc. 2018 6(21). doi: 10.1128/genomeA.00440-18.
Ianevski A, Zusinaite E, Kuivanen S, Strand M, Lysvand H, Teppor M, Kakkola L, Paavilainen H, Laajala M, Kallio-Kokko H, Valkonen M, Kantele A, Telling K, Lutsar I, Letjuka P, Metelitsa N, Oksenych V, Bjørås M, Nordbø SA, Dumpis U, Vitkauskiene A, Öhrmalm C, Bondeson K, Bergqvist A, Aittokallio T, Cox RJ, Evander M, Hukkanen V, Marjomaki V, Julkunen I, Vapalahti O, Tenson T, Merits A, Kainov D. Novel activities of safe-in-human broad-spectrum antiviral agents. Antiviral Res. 2018 154:174-182. doi: 10.1016/j.antiviral.2018.04.016.
Kauko O, O’Connor CM, Kulesskiy E, Sangodkar J, Aakula A, Izadmehr S, Yetukuri L, Yadav B, Padzik A, Laajala TD, Haapaniemi P, Momeny M, Varila T, Ohlmeyer M, Aittokallio T, Wennerberg K, Narla G, Westermarck J. PP2A inhibition is a druggable MEK inhibitor resistance mechanism in KRAS mutant lung cancer cells. Science Translational Medicine. 2018 10(450). doi: 10.1126/scitranslmed.aaq1093.
Nepal C, O'Rourke CJ, Oliveira DV, Taranta A, Shema S, Gautam P, Calderaro J, Barbour A, Raggi C, Wennerberg K, Wang XW, Lautem A, Roberts LR, Andersen JB. Genomic Perturbations Reveal Distinct Regulatory Networks in Intrahepatic Cholangiocarcinoma. Hepatology. 2018 68(3):949-963. doi: 10.1002/hep.29764.
Lepikhova T, Karhemo PR, Louhimo R, Yadav B, Murumägi A, Kulesskiy E, Kivento M, Sihto H, Grénman R, Syrjänen SM, Kallioniemi O, Aittokallio T, Wennerberg K, Joensuu H, Monni O. Drug sensitivity screening and genomic characterization of 45 HPV-negative head and neck carcinoma cell lines for novel biomarkers of drug efficacy. Mol Cancer Ther. 2018 17(9):2060-2071. doi: 10.1158/1535-7163.MCT-17-0733.
Andersson EI, Pützer S, Yadav B, Dufva O, Khan S, He L, Sellner L, Schrader A, Crispatzu G, Oleś M, Zhang H, Adnan-Awad S, Lagström S, Bellanger D, Mpindi JP, Eldfors S, Pemovska T, Pietarinen P, Lauhio A, Tomska K, Cuesta-Mateos C, Faber E, Koschmieder S, Brümmendorf TH, Kytölä S, Savolainen ER, Siitonen T, Ellonen P, Kallioniemi O, Wennerberg K, Ding W, Stern MH, Huber W, Anders S, Tang J, Aittokallio T, Zenz T, Herling M, Mustjoki S. Discovery of novel drug sensitivities in T-PLL by high-throughput ex vivo drug testing and mutation profiling. Leukemia. 2018 32(3):774-787. doi: 10.1038/leu.2017.252.
Härmä H, Tong-Ochoa N, van Adrichem AJ, Jelesarov I, Wennerberg K, Kopra K. Toward universal protein post-translational modification detection in high throughput format. Chem Commun (Camb). 2018 54(23):2910-2913. doi: 10.1039/c7cc09575a.
He L, Tang J, Andersson EI, Timonen S, Koschmieder S, Wennerberg K, Mustjoki S, Aittokallio T. Patient-customized Drug Combination Prediction and Testing for T-cell Prolymphocytic Leukemia Patients. Cancer Res. 2018 78(9):2407-2418. doi: 10.1158/0008-5472.CAN-17-3644.
Tang J, Tanoli ZU, Ravikumar B, Alam Z, Rebane A, Vähä-Koskela M, Peddinti G, van Adrichem AJ, Wakkinen J, Jaiswal A, Karjalainen E, Gautam P, He L, Parri E, Khan S, Gupta A, Ali M, Yetukuri L, Gustavsson AL, Seashore-Ludlow B, Hersey A, Leach AR, Overington JP, Repasky G, Wennerberg K, Aittokallio T. Drug Target Commons: A Community Effort to Build a Consensus Knowledge Base for Drug-Target Interactions. Cell Chem Biol. 2018 25(2):224-229.e2. doi: 10.1016/j.chembiol.2017.11.009.
He L, Kulesskiy E, Saarela J, Turunen L, Wennerberg K, Aittokallio T, Tang J. Methods for High-throughput Drug Combination Screening and Synergy Scoring. Methods in molecular biology. 2018 1711, 351-398, ISSN: 1064-3745. doi: 10.1007/978-1-4939-7493-1_17.
Tang J, Tanoli ZU, Ravikumar B, Alam Z, Rebane A, Vähä-Koskela M, Peddinti G, van Adrichem AJ, Wakkinen J, Jaiswal A, Karjalainen E, Gautam P, He L, Parri E, Khan S, Gupta A, Ali M, Yetukuri L, Gustavsson AL, Seashore-Ludlow B, Hersey A, Leach AR, Overington JP, Repasky G, Wennerberg K, Aittokallio T. Drug Target Commons: A Community Effort to Build a Consensus Knowledge Base for Drug-Target Interactions. Cell Chem Biol. 2018 25(2):224-229.e2. doi: 10.1016/j.chembiol.2017.11.009.
Ali M, Khan SA, Wennerberg K, Aittokallio. Global proteomics profiling improves drug sensitivity prediction: results from a multi-omics, pan-cancer modeling approach. Bioinformatics. 2018 34(8):1353-1362. doi: 10.1093/bioinformatics/btx766.
2017
Bulanova D, Ianevski A, Bugai A, Akimov Y, Kuivanen S, Paavilainen H, Kakkola L, Nandinia J, Turunen L, Öhman T, Ala-Hongisto H, Pesonen H, Kuisma M, Honkimaa A, Walton E, Oksenych V, Lorey M, Guschin D, Shim JM, Kim J, Than T, Chang SY, Hukkanen V, Kulesskiy E, Marjomäki V, Julkunen I, Nyman T, Matikainen S, Saarela J, Sané F, Hober D, Gabriel G, De Brabander J, Martikainen M, Windich M, Min J-Y, Bruzzone R, Aittokallio T, Vähä-Koskela M, Vapalahti O, Pulk A, Velagapudi V, Kainov D. Antiviral properties of chemical inhibitors of cellular anti-apoptotic Bcl-2 proteins. Viruses. 2017 9, 271; doi: 10.3390/v9100271.
Kuusanmäki H, Dufva O, Parri E, van Adrichem AJ, Rajala H, Majumder MM, Yadav B, Parsons A, Chan WC, Wennerberg K, Mustjoki S, Heckman CA. Drug sensitivity profiling identifies potential therapies for lymphoproliferative disorders with overactive JAK/STAT3 signaling. Oncotarget. 2017 8, (57), 97516-97527. doi: 10.18632/oncotarget.22178.
Ianevski A, He L, Aittokallio T, Tang J. SynergyFinder: a web application for analyzing drug combination dose-response matrix data. Bioinformatics. 2017 33(15):2413-2415. doi: 10.1093/bioinformatics/btx162.
Kreutzman A, Colom-Fernández B, Jiménez AM, Ilander M, Cuesta-Mateos C, Pérez-García Y, Arévalo CD, Brück O, Hakanen H, Saarela J, Ortega-Carrión A, de Rosendo A, Juanes-García A, Steegmann JL, Mustjoki S, Vicente-Manzanares M, Muñoz-Calleja C. Dasatinib reversibly disrupts endothelial vascular integrity by increasing non-muscle myosin II contractility in a ROCK-dependent manner. Clin Cancer Res. 2017 23(21):6697-6707. doi: 10.1158/1078-0432.CCR-16-0667.
Ammad-Ud-Din M, Khan SA, Wennerberg K, Aittokallio T. Systematic identification of feature combinations for predicting drug response with Bayesian multi-view multi-task linear regression. Bioinformatics. 2017 33(14):i359-i368. doi: 10.1093/bioinformatics/btx266.
Cichonska A, Ravikumar B, Parri E, Timonen S, Pahikkala T, Airola A, Wennerberg K, Rousu J, Aittokallio T. Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors. PLOS Computational Biology. 2017 13(8): e1005678. doi: 10.1371/journal.pcbi.1005678.
Kohonen P, Parkkinen JA, Willighagen EL, Ceder R, Wennerberg K, Kaski S, Grafstrom RC. A transcriptomics data-driven gene space accurately predicts liver cytopathology and drug-induced liver injury. Nature Communications. 2017 8, 15932. doi: 10.1038/ncomms15932.
Jaiswal A, Peddinti G, Akimov Y, Wennerberg K, Kuznetsov S, Tang J, Aittokallio T. Seed-effect modeling improves the consistency of genome-wide loss-of-function screens and identifies synthetic lethal vulnerabilities in cancer cells. Genome medicine. 2017 9, 51. doi: 10.1186/s13073-017-0440-2.
Kopra K, van Adrichem AJ, Salo-Ahen OMH, Peltonen J, Wennerberg K, Harma H. High-Throughput Dual Screening Method for Ras Activities and Inhibitors. Analytical Chemistry. 2017 89, 8, 4508-4516. doi: 10.1021/acs.analchem.6b04904.
Karjalainen R, Pemovska T, Popa M, Liu M, Javarappa KK, Majumder MM, Yadav B, Tamborero D, Tang J, Bychkov D, Kontro M, Parsons A, Suvela M, Safont MM, Porkka K, Aittokallio T, Kallioniemi O, McCormack E, Gjertsen BT, Wennerberg K, Knowles J, Heckman CA. JAK1/2 and BCL2 inhibitors synergize to counteract bone marrow stromal cell-induced protection of AML. Blood. 2017 130(6):789-802. doi: https://doi.org/10.1182/blood-2016-02-699363.
Kuivanen S, Bespalov MM, Nandania J, Ianevski A, Velagapudi V, De Brabander JK, Kainov DE, Vapalahti O. Obatoclax, saliphenylhalamide and gemcitabine inhibit Zika virus infection in vitro and differentially affect cellular signaling, transcription and metabolism. Antiviral Research. 2017 139, 117-128. doi: 10.1016/j.antiviral.2016.12.022.
Uusi-Rauva K, Blom T, von Schantz-Fant C, Blom T, Jalanko A, Kyttälä A. Induced Pluripotent Stem Cells Derived from a CLN5 Patient Manifest Phenotypic Characteristics of Neuronal Ceroid Lipofuscinoses. Int. J. Mol. Sci. 2017 18, 955. doi: 10.3390/ijms18050955.
Pietarinen PO, Eide CA, Ayuda-Durán P, Potdar S, Kuusanmäki H, Andersson EI, Mpindi JP, Pemovska T, Kontro M, Heckman CA, Kallioniemi O, Wennerberg K, Hjorth-Hansen H, Druker BJ, Enserink JM, Tyner JW, Mustjoki S, Porkka K. Differentiation status of primary chronic myeloid leukemia cells affects sensitivity to BCR-ABL1 inhibitors. Oncotarget. 2017 8, 22606-22615. doi: 10.18632/oncotarget.15146.
Haltia U-M, Andersson N, Yadav B, Farkkila A, Kulesskiy E, Kankainen M, Tang J, Butzow R, Riska A, Leminen A, Heikinheimo M, Kallioniemi O, Unkila-Kallio L, Wennerberg K, Aittokallio T, Anttonen M. Systematic drug sensitivity testing reveals synergistic growth inhibition by dasatinib or mTOR inhibitors with paclitaxel in ovarian granulosa cell tumor cells. Gynecologic Oncology. 2017 144, 3, 621-630. doi: 10.1016/j.ygyno.2016.12.016.
Malani D, Murumägi A, Yadav B, Kontro M, Eldfors S, Kumar A, Karjalainen R, Majumder MM, Ojamies P, Pemovska T, Wennerberg K, Heckman C, Porkka K, Wolf M, Aittokallio T, Kallioniemi O. Enhanced sensitivity to glucocorticoids in cytarabine-resistant AML. Leukemia. 2017 31, 1187–1195. doi: 10.1038/leu.2016.314.
Ojamies PN, Kontro M, Edgren H, Ellonen P, Lagström S, Almusa H, Miettinen T, Eldfors S, Tamborero D, Wennerberg K, Heckman C, Porkka K, Wolf M, Kallioniemi O. Monitoring therapy responses at the leukemic subclone level by ultra-deep amplicon resequencing in acute myeloid leukemia. Leukemia. 2017 31, 1048–1058. doi:10.1038/leu.2016.286.
Fagerholm R, Khan S, Schmidt MK, García-Closas M, Heikkilä P, Saarela J, Beesley J, Jamshidi M, Aittomäki K, Liu J, Ali HR, Andrulis IL, Beckmann MW, Behrens S, Blows FM, Brenner H, Chang-Claude J, Couch FJ, Czene K, Fasching PA, Figueroa J, Floris G, Glendon G, Guo Q, Hall P, Hallberg E, Hamann U, Holleczek B, Hooning MJ, Hopper JL, Jager A, Kabisch M, kConFab/AOCS Investigators, Keeman R, Kosma VM, Lambrechts D, Lindblom A, Mannermaa A, Margolin S, Provenzano E, Shah M, Southey MC, Dennis J, Lush M, Michailidou K, Wang Q, Bolla MK, Dunning AM, Easton DF, Pharoah PD, Chenevix-Trench G, Blomqvist C, Nevanlinna H. TP53-based interaction analysis identifies cis-eQTL variants for TP53BP2, FBXO28, and FAM53A that associate with survival and treatment outcome in breast cancer. Oncotarget. 2017 8, 18381-18398. doi: 10.18632/oncotarget.15110.
Eldfors S, Kuusanmäki H, Kontro M, Majumder MM, Parsons A, Edgren H, Pemovska T, Kallioniemi O, Wennerberg K, Gökbuget N, Burmeister T, Porkka K, Heckman CA. Idelalisib sensitivity and mechanisms of disease progression in relapsed TCF3-PBX1 acute lymphoblastic leukemia. Leukemia. 2017 31, 51-57. doi: 10.1038/leu.2016.202.
Saeed K, Rahkama V, Eldfors S, Bychkov D, Mpindi JP, Yadav B, Paavolainen L, Aittokallio T, Heckman C, Wennerberg K, Peehl DM, Horvath P, Mirtti T, Rannikko A, Kallioniemi O, Östling P, af Hällström TM. Comprehensive Drug Testing of Patient-derived Conditionally Reprogrammed Cells from Castration-resistant Prostate Cancer. European Urology. 2017 71, 319-327.
Kontro M, Kumar A, Majumder MM, Eldfors S, Parsons A, Pemovska T, Saarela J, Yadav B, Malani D, Fløisand Y, Höglund M, Remes K, Gjertsen BT, Kallioniemi O, Wennerberg K, Heckman CA, Porkka K. HOX gene expression predicts response to BCL-2 inhibition in acute myeloid leukemia. Leukemia. 2017 31, 301–309; doi:10.1038/leu.2016.222.
2016
Mpindi JP, Yadav B, Östling P, Gautam P, Malani D, Murumägi A, Hirasawa A, Kangaspeska S, Wennerberg K, Kallioniemi O, Aittokallio T. Consistency in drug response profiling. Nature. 2016 540, 7631, E5-E6. doi: 10.1038/nature20171.
Söderholm S, Kainov DE, Öhman T, Denisova OV, Schepens B, Kulesskiy E, Imanishi SY, Corthals G, Hintsanen P, Aittokallio T, Saelens X, Matikainen S, Nyman TA. Phosphoproteomics to Characterize Host Response During Influenza A Virus Infection of Human Macrophages. Mol Cell Proteomics. 2016 15(10):3203-3219. doi:10.1074/mcp.M116.057984.
Wennerberg K. Cancer Cell Drug Response Transcriptomes in 3D. Cell chemical biology. 2016 23, 11, 1323-1324. doi: 10.1016/j.chembiol.2016.11.002.
Lindholm D, Pham DD, Cascone A, Eriksson O, Wennerberg K, Saarma M. c-Abl Inhibitors Enable Insights into the Pathophysiology and Neuroprotection in Parkinson's Disease. Frontiers in aging neuroscience. 2016 8, 254. doi:10.3389/fnagi.2016.00254.
Sieberts SK, Zhu F, Garcia-Garcia J, Stahl E, Pratap A, Pandey G, Pappas D, Aguilar D, Anton B, Bonet J, Eksi R, Fornes O, Guney E, Li H, Marin MA, Panwar B, Planas-Iglesias J, Poglayen D, Cui J, Falcao AO, Suver C, Hoff B, Balagurusamy VSK, Dillenberger D, Neto EC, Norman T, Aittokallio T, Ammad-ud-din M, Azencott C-A, Bellon V, Boeva V, Bunte K, Chheda H, Cheng L, Corander J, Dumontier M, Goldenberg A, Gopalacharyulu P, Hajiloo M, Hidru D, Jaiswal A, Kaski S, Khalfaoui B, Khan SA, Kramer ER, Marttinen P, Mezlini AM, Molparia B, Pirinen M, Saarela J, Samwald M, Stoven V, Tang H, Tang J, Torkamani A, Vert J-P, Wang B, Wang T, Wennerberg K, Wineinger NE, Xiao G, Xie Y, Yeung R, Zhan X, Zhao C, Greenberg J, Kremer J, Michaud K, Barton A, Coenen M, Mariette X, Miceli C, Shadick N, Weinblatt M, de Vries N, Tak PP, Gerlag D, Huizinga TWJ, Kurreeman F, Allaart C F, Bridges SL, Criswell L, Moreland L, Klareskog L, Saevarsdottir S, Padyukov L, Gregersen PK, Friend S, Plenge R, Stolovitzky G, Oliva B, Guan Y, Mangravite LM, Rheumatoid Arth Challenge. Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis. Nature Communications. 2016 7, 12460. doi: 10.1038/ncomms12460.
Hayes TK, Neel NF, Hu C, Gautam P, Chenard M, Long B, Aziz M, Kassner M, Bryant KL, Pierobon M, Marayati R, Kher S, George SD, Xu M, Wang-Gillam A, Samatar AA, Maitra A, Wennerberg K, Petricoin EF 3rd, Yin HH, Nelkin B, Cox AD, Yeh JJ, Der CJ. Long-Term ERK Inhibition in KRAS-Mutant Pancreatic Cancer Is Associated with MYC Degradation and Senescence-like Growth Suppression. Cancer Cell. 2016 29, 75-89. doi: 10.1016/j.ccell.2015.11.011.
von Schantz C, Saarela J. High Throughput siRNA Screening Using Reverse Transfection. Methods Molecular Biology. 2016 1470, p. 25-37, ISBN: 978-1-4939-6335-5. doi: 10.1007/978-1-4939-6337-9_3.
Gautam P, Karhinen L, Szwajda A, Jha SK, Yadav B, Aittokallio T, Wennerberg K. Identification of selective cytotoxic and synthetic lethal drug responses in triple negative breast cancer cells. Mol Cancer. 2016 15(1):34. doi: 10.1186/s12943-016-0517-3.
Varghese FS, Kaukinen P, Glasker S, Bespalov M, Hanski L, Wennerberg K, Kummerer BM, Ahola T. Discovery of berberine, abamectin and ivermectin as antivirals against chikungunya and other alphaviruses. Antiviral Research. 2016 126, 117-124. doi:10.1016/j.antiviral.2015.12.012.
Gu Y, Helenius M, Väänänen K, Bulanova D, Saarela J, Sokolenko A, Martens J, Imyanitov E, and Kuznetsov S. BRCA1-deficient breast cancer cell lines are resistant to MEK inhibitors and show distinct sensitivities to 6-thioguanine; Sci. Rep. 2016 6, 28217; doi: 10.1038/srep28217.
Kulesskiy E*, Saarela J*, Turunen L*, Wennerberg K. Precision Cancer Medicine in the Acoustic Dispensing Era: Ex Vivo Primary Cell Drug Sensitivity Testing. J. Lab. Autom. 2016 21, 27-36. doi: 10.1177/2211068215618869. *shared authorship.
Hayes TK, Neel NF, Hu C, Gautam P, Chenard M, Long B, Aziz M, Kassner M, Bryant KL, Pierobon M, Marayati R, Kher S, George SD, Xu M, Wang-Gillam A, Samatar AA, Maitra A, Wennerberg K, Petricoin EF, Yin HH, Nelkin B, Cox AD, Yeh JJ, Der CJ. Long-Term ERK Inhibition in KRAS-Mutant Pancreatic Cancer Is Associated with MYC Degradation and Senescence-like Growth Suppression. Cancer Cell. 2016 29, 1, 75-89. doi:10.1016/j.ccell.2015.11.011.
2015
Mpindi JP, Potdar S, Bychkov D, Saarela J, Saeed K, Wennerberg K, Aittokallio T, Östling P, Kallioniemi O. Impact of normalization methods on high-throughput screening data with high hit rates and drug testing with dose-response data. Bioinformatics. 2015 31(23), 3815-3821. doi:10.1093/bioinformatics/btv455.
van Adrichem AJ, Wennerberg K. MgcRacGAP inhibition stimulates JAK-dependent STAT3 activity. FEBS Letters. 2015 589, 24, 3859-3865. doi: 10.1016/j.febslet.2015.11.013.
Pokharel YR*, Saarela J*, Szwajda A*, Rupp C, Rokka A, Karna SKL, Teittinen K, Corthals G, Kallioniemi O, Wennerberg K, Aittokallio T, Westermarck J. Relevance Rank Platform (RRP) for functional filtering of high content protein-protein interaction data. Molecular and Cellular Proteomics. 2015 14, 3274-83. doi: 10.1074/mcp.M115.050773. *shared authorship.
Swajda A, Gautam P, Karhinen L, Kumar Jha S, Saarela J, Shakyawar S, Turunen L, Yadav B, Tang J, Wennerberg K, Aittokallio T. Systematic Mapping of Kinase Addiction Combinations in Breast Cancer Cells by Integrating Drug Sensitivity and Selectivity Profiles. Chemistry & Biology. 2015 22, 1–12. doi.org/10.1016/j.chembiol.2015.06.021.
Pietarinen PO, Pemovska T, Kontro M, Yadav B, Mpindi JP, Andersson EI, Majumder MM, Kuusanmäki H, Koskenvesa P, Kallioniemi O, Wennerberg K, Heckman CA, Mustjoki S, Porkka K. Novel drug candidates for blast phase chronic myeloid leukemia from high-throughput drug sensitivity and resistance testing. Blood Cancer Journal. 2015 5, e309; doi:10.1038/bcj.2015.30.
Yadav B, Gopalacharyulu P, Pemovska T, Khan, SA, Szwajda A, Tang J, Wennerberg K, Aittokallio T. From drug response profiling to target addiction scoring in cancer cell models. Disease Models & Mechanisms. 2015 8, 10, 1255-1264. doi: 10.1242/dmm.021105.
Aakula A, Leivonen S-K, Hintsanen P, Aittokallio T, Ceder Y, Børresen-Dale A-L, Perälä M, Östling P and Kallioniemi O. MicroRNA-135b regulates ERα, AR and HIF1AN and affects breast and prostate cancer cell growth. Mol Oncol. 2015 9(7):1287-300. doi: 10.1016/j.molonc.2015.03.001.
Pemovska T, Johnson E, Kontro M, Repasky GA, Chen J, Wells P, Cronin CN, McTigue M, Kallioniemi O, Porkka K, Murray BW, Wennerberg K. Axitinib effectively inhibits BCR-ABL1(T315I) with a distinct binding conformation. Nature. 2015 519(7541):102-5. doi: 10.1038/nature14119.
He L, Wennerberg K, Aittokallio T, Tang J. TIMMA-R: an R package for predicting synergistic multi-targeted drug combinations in cancer cell lines or patient-derived samples. Bioinformatics. 2015 31(11):1866-8. doi: 10.1093/bioinformatics/btv067.
Tang J, Wennerberg K, Aittokallio T. What is synergy? The Saariselka agreement revisited. Frontiers in Pharmacology. 2015 6:181. doi: 10.3389/fphar.2015.00181.
van Adrichem AJ, Fagerholm A, Turunen L, Lehto A, Saarela J, Koskinen A, Repasky GA, Wennerberg K. Discovery of MINC1, a GTPase-activating protein small molecule inhibitor, targeting MgcRacGAP. Comb Chem High Throughput Screen. 2015 18(1):3-17. doi:10.2174/1386207318666141205112730.
Li Y, Lu W, Chen D, Boohaker RJ, Zhai L, Padmalayam I, Wennerberg K, Xu B, Zhang W. KIFC1 is a novel potential therapeutic target for breast cancer. Cancer Biology & Therapy. 2015 16, 9, 1316-1322. doi: 10.1080/15384047.2015.1070980.
Yadav B, Wennerberg K, Aittokallio T, Tang J. Searching for Drug Synergy in Complex Dose–Response Landscapes Using an Interaction Potency Model. Computational and Structural Biotechnology Journal. 2015 13, 504 - 513. doi: 10.1016/j.csbj.2015.09.001.
Larne O, Östling P, Haflidadóttir BS, Hagman Z, Aakula A, Kohonen P, Kallioniemi O, Edsjö A, Bjartell A, Lilja H, Lundwall Å, Ceder Y. miR-183 in Prostate Cancer Cells Positively Regulates Synthesis and Serum Levels of Prostate-specific Antigen. Eur Urol. 2015 68, 581-8. doi: 10.1016/j.eururo.2014.12.025.
Saeed K, Östling P, Björkman M, Mirtti T, Alanen K, Vesterinen T, Sankila A, Lundin J, Lundin M, Rannikko A, Nordling S, Mpindi JP, Kohonen P, Iljin K, Kallioniemi O, Rantala JK. Androgen receptor interacting protein HSPBAP1 facilitates growth of prostate cancer cells in androgen-deficient conditions. Int. J. Cancer. 2015 136, 2535–2545. doi: 10.1002/ijc.29303.
2014
Gu Y, Bouwman P, Greco D, Saarela J, Yadav B, Jonkers J & Kuznetsov SG, Suppression of BRCA1 sensitizes cells to proteasome inhibitors. Cell Death and Disease. 2014 5, e1580. doi: 10.1038/cddis.2014.537.
Bansal M, Yang J, Karan C, Menden MP, Costello JC, Tang H, Xiao G, Li Y, Allen J, Zhong R, Chen B, Kim M, Wang T, Heiser LM, Realubit R, Mattioli M, Alvarez MJ, Shen Y; NCI-DREAM Community, Gallahan D, Singer D, Saez-Rodriguez J, Xie Y, Stolovitzky G, Califano A; NCI-DREAM Community. A community computational challenge to predict the activity of pairs of compounds. Nat. Biotechnol. 2014 32(12):1213-22. doi: 10.1038/nbt.3052.
Costello JC, Heiser LM, Georgii E, Gönen M, Menden MP, Wang NJ, Bansal M, Ammad-ud-din M, Hintsanen P, Khan SA, Mpindi JP, Kallioniemi O, Honkela A, Aittokallio T, Wennerberg K; NCI DREAM Community, Collins JJ, Gallahan D, Singer D, Saez-Rodriguez J, Kaski S, Gray JW, Stolovitzky G. A community effort to assess and improve drug sensitivity prediction algorithms. Nat. Biotechnol. 2014 32(12):1202-12. doi: 10.1038/nbt.2877.
Vidugiriene J, Leippe D, Sobol M, Vidugiris G, Zhou W, Meisenheimer P, Gautam P, Wennerberg K, Cali JJ. Bioluminescent cell-based NAD(P)/NAD(P)H assays for rapid dinucleotide measurement and inhibitor screening. Assay Drug Dev. Technol. 2014 12(9-10):514-26. doi: 10.1089/adt.2014.605.
Khan SA, Virtanen S, Kallioniemi OP, Wennerberg K, Poso A, Kaski S. Identification of structural features in chemicals associated with cancer drug response: a systematic data-driven analysis. Bioinformatics. 2014 30(17):i497-504. doi: 10.1093/bioinformatics/btu456.
Ammad-ud-din M, Georgii E, Gönen M, Laitinen T, Kallioniemi O, Wennerberg K, Poso A, Kaski S. Integrative and personalized QSAR analysis in cancer by kernelized Bayesian matrix factorization. J Chem Inf Model. 2014 54(8):2347-59. doi: 10.1021/ci500152b.
Denisova OV, Söderholm S, Virtanen S, von Schantz C, Bychkov D, Vashchinkina E, Desloovere J, Tynell J, Ikonen N, Theisen LL, Nyman TA, Matikainen S, Kallioniemi O, Julkunen I, Muller CP, Saelens X, Verkhusha VV, Kainov DE. Akt inhibitor MK2206 prevents influenza pH1N1 virus infection in vitro. Antimicrob Agents Chemother. 2014 58(7):3689-96. doi: 10.1128/AAC.02798-13.
Yadav B, Pemovska T, Szwajda A, Kulesskiy E, Kontro M, Karjalainen R, Majumder MM, Malani D, Murumägi A, Knowles J, Porkka K, Heckman C, Kallioniemi O, Wennerberg K, Aittokallio T. Quantitative scoring of differential drug sensitivity for individually optimized anticancer therapies. Sci Rep. 2014 4:5193. doi: 10.1038/srep05193.
Pietiäinen V, Saarela J, von Schantz C, Turunen L, Östling P, Wennerberg K. The high throughput biomedicine unit at the institute for molecular medicine Finland: high throughput screening meets precision medicine. Comb Chem High Throughput Screen. 2014 17(4):377-86. doi:10.2174/1386207317666140323195927.
Tang J, Szwajda A, Shakyawar S, Xu T, Hintsanen P, Wennerberg K, Aittokallio T. Making sense of large-scale kinase inhibitor bioactivity data sets: a comparative and integrative analysis. J Chem Inf Model. 2014 54(3):735-43. doi: 10.1021/ci400709d.
Antila H, Autio H, Turunen L, Harju K, Tammela P, Wennerberg K, Yli-Kauhaluoma J, Huttunen HJ, Castrén E, Rantamäki T. Utilization of in situ ELISA method for examining Trk receptor phosphorylation in cultured cells. J Neurosci Methods. 2014 222:142-6. doi: 10.1016/j.jneumeth.2013.11.001.
Atkins C, Evans CW, Nordin B, Patricelli MP, Reynolds R, Wennerberg K, Noah JW. Global Human-Kinase Screening Identifies Therapeutic Host Targets against Influenza. J Biomol Screen. 2014 19(6):936-946. doi: 10.1177/1087057113518068.
Stylianou M, Kulesskiy E, Lopes JP, Granlund M, Wennerberg K, Urban CF. Antifungal application of nonantifungal drugs. Antimicrob Agents Chemother. 2014 58(2):1055-62. doi: 10.1128/AAC.01087-13.
2013
Tang J, Karhinen L, Xu T, Szwajda A, Yadav B, Wennerberg K, Aittokallio T. Target inhibition networks: predicting selective combinations of druggable targets to block cancer survival pathways. PLoS Comput Biol. 2013 9(9):e1003226. doi: 10.1371/journal.pcbi.1003226.
Pemovska T, Kontro M, Yadav B, Edgren H, Eldfors S, Szwajda A, Almusa H, Bespalov MM, Ellonen P, Elonen E, Gjertsen BT, Karjalainen R, Kulesskiy E, Lagström S, Lehto A, Lepistö M, Lundán T, Majumder MM, Marti JM, Mattila P, Murumägi A, Mustjoki S, Palva A, Parsons A, Pirttinen T, Rämet ME, Suvela M, Turunen L, Västrik I, Wolf M, Knowles J, Aittokallio T, Heckman CA, Porkka K, Kallioniemi O, Wennerberg K. Individualized systems medicine strategy to tailor treatments for patients with chemorefractory acute myeloid leukemia. Cancer Discov. 2013 3(12):1416-29. doi: 10.1158/2159-8290.CD-13-0350.
Jin S, Mutvei AP, Chivukula IV, Andersson ER, Ramsköld D, Sandberg R, Lee KL, Kronqvist P, Mamaeva V, Östling P, Mpindi JP, Kallioniemi O, Screpanti I, Poellinger L, Sahlgren C, Lendahl U. Non-canonical Notch signaling activates IL-6/JAK/STAT signaling in breast tumor cells and is controlled by p53 and IKKα/IKKβ. Oncogene. 2013 32(41):4892-902. doi: 10.1038/onc.2012.517.
Wolfe LM, Veeraraghavan U, Idicula-Thomas S, Schürer S, Wennerberg K, Reynolds R, Besra GS, Dobos KM. A chemical proteomics approach to profiling the ATP-binding proteome of Mycobacterium tuberculosis. Mol Cell Proteomics. 2013 12(6):1644-60. doi: 10.1074/mcp.M112.025635.
Rajala HL, Eldfors S, Kuusanmäki H, van Adrichem AJ, Olson T, Lagström S, Andersson EI, Jerez A, Clemente MJ, Yan Y, Zhang D, Awwad A, Ellonen P, Kallioniemi O, Wennerberg K, Porkka K, Maciejewski JP, Loughran TP Jr, Heckman C, Mustjoki S. Discovery of somatic STAT5b mutations in large granular lymphocytic leukemia. Blood. 2013 121(22):4541-50. doi: 10.1182/blood-2012-12-474577.
Pietiäinen V., Vassilev B., Blom T., Wang W., Nelson J., Bittman R., Bäck N., Zelcer N., Ikonen E. NDRG1 functions in LDLR trafficking by regulating endosomal recycling and degradation. Journal of Cell Science. 2013 1;126(Pt 17):3961-71. doi: 10.1242/jcs.128132.
2012
Björkman M, Östling P, Härmä V, Virtanen J, Mpindi JP, Rantala J, Mirtti T, Vesterinen T, Lundin M, Sankila A, Rannikko A, Kaivanto E, Kohonen P, Kallioniemi O, Nees M. Systematic knockdown of epigenetic enzymes identifies a novel histone demethylase PHF8 overexpressed in prostate cancer with an impact on cell proliferation, migration and invasion. Oncogene. 2012 31(29):3444-56. doi: 10.1038/onc.2011.512.
Khan SA, Faisal A, Mpindi JP, Parkkinen JA, Kalliokoski T, Poso A, Kallioniemi OP, Wennerberg K, Kaski S. Comprehensive data-driven analysis of the impact of chemoinformatic structure on the genome-wide biological response profiles of cancer cells to 1159 drugs. BMC Bioinformatics. 2012 13:112. doi: 10.1186/1471-2105-13-112.
Koskela HL, Eldfors S, Ellonen P, van Adrichem AJ, Kuusanmäki H, Andersson EI, Lagström S, Clemente MJ, Olson T, Jalkanen SE, Majumder MM, Almusa H, Edgren H, Lepistö M, Mattila P, Guinta K, Koistinen P, Kuittinen T, Penttinen K, Parsons A, Knowles J, Saarela J, Wennerberg K, Kallioniemi O, Porkka K, Loughran TP Jr, Heckman CA, Maciejewski JP, Mustjoki S. Somatic STAT3 mutations in large granular lymphocytic leukemia. N Engl J Med. 2012 366(20):1905-13. doi: 10.1056/NEJMoa1114885.
Schmiedt ML, Blom T, Blom T, Kopra O, Wong A, von Schantz-Fant C, Ikonen E, Kuronen M, Jauhiainen M, Cooper JD, Jalanko A. Cln5-deficiency in mice leads to microglial activation, defective myelination and changes in lipid metabolism. Neurobiol Dis. 2012 46(1):19-29. doi: 10.1016/j.nbd.2011.12.009.
2011
Östling P, Leivonen SK, Aakula A, Kohonen P, Mäkelä R, Hagman Z, Edsjö A, Kangaspeska S, Edgren H, Nicorici D, Bjartell A, Ceder Y, Perälä M, Kallioniemi O. Systematic Analysis of MicroRNAs Targeting the Androgen Receptor in Prostate Cancer Cells. Cancer Research. 2011 71(5):1956-1967. doi: 10.1158/0008-5472.CAN-10-2421.
Leivonen SK, Rokka A, Östling P, Kohonen P, Corthals G, Perälä M, Kallioniemi O. Identification of miR-193b targets in breast cancer cells and systems biological analysis of their functional impact. Mol Cell Proteomics. 2011 10(7), M110.005322. doi: 10.1074/mcp.M110.005322.
Manuvakhova MS, Johnson GG, White MC, Ananthan S, Sosa M, Maddox C, McKellip S, Rasmussen L, Wennerberg K, Hobrath JV, White EL, Maddry JA, Grimaldi M. Identification of novel small molecule activators of nuclear factor-κB with neuroprotective action via high-throughput screening. J Neurosci Res. 2011 89(1):58-72. doi: 10.1002/jnr.22526.
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