Publications

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HTB services have been used in the following publications:

2020

Hansson K, Radke K, Aaltonen K, Saarela J, Mañas A, Sjölund J, Smith E, Wennerberg K, Gisselsson D, Bexell D. Therapeutic targeting of KSP in preclinical models of high-risk neuroblastoma. Science Translational Medicine. Accepted for publication.

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. Moderate inter-metastatic heterogeneity of drug sensitivities in organoids from patients with multiple colorectal cancer liver metastases. Clinical Cancer Research. Accepted for publication.

 

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, Feb 18. pii: jbc.RA119.011265. doi: 10.1074/jbc.RA119.011265. [Epub ahead of print]

 

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, accepted for publication. *equal contribution. doi: 10.1093/bioinformatics/btaa138

 

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, https://doi.org/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). pii: E92. 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.org/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.org/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). pii: e00440-18. 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. Sci Transl Med. 2018, 10(450). pii: eaaq1093. 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.

Pietiainen 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.

 

Acknowledgements:

Adnan Awad S, Kankainen M, Ojala T, Koskenvesa P, Eldfors S, Ghimire B, Kumar A, Kytölä S, Kamel MM, Heckman CA, Porkka K, Mustjoki S. Mutation accumulation in cancer genes relates to nonoptimal outcome in chronic myeloid leukemia. Blood Adv. 2020, 4(3):546-559. doi: 10.1182/bloodadvances.2019000943.

 

Dufva O, Koski J, Maliniemi P, Ianevski A, Klievink J, Leitner J, Pölönen P, Hohtari H, Saeed K, Hannunen T, Ellonen P, Steinberger P, Kankainen M, Aittokallio T, Keränen MAI, Korhonen M, Mustjoki S. Integrated drug profiling and CRISPR screening identify essential pathways for CAR T cell cytotoxicity. Blood. 2019, pii: blood.2019002121. doi: 10.1182/blood.2019002121. [Epub ahead of print]

 

Kuusanmäki H, Leppä AM, Pölönen P, Kontro M, Dufva O, Deb D, Yadav B, Brück O, Kumar A, Everaus H, Gjertsen BT, Heinäniemi M, Porkka K, Mustjoki S, Heckman CA. Phenotype-based drug screening reveals association between venetoclax response and differentiation stage in acute myeloid leukemia. Haematologica. 2019, pii: haematol.2018.214882. doi: 10.3324/haematol.2018.214882. [Epub ahead of print]

 

Majumder MM, Leppä AM, Hellesøy M, Dowling P, Malyutina A, Kopperud R, Bazou D, Andersson E, Parsons A, Tang J, Kallioniemi O, Mustjoki S, O'Gorman P, Wennerberg K, Porkka K, Gjertsen BT, Heckman CA. Multi-parametric single cell evaluation defines distinct drug responses in healthy hematological cells that are retained in corresponding malignant cell types. Haematologica. 2019, pii: haematol.2019.217414. doi: 10.3324/haematol.2019.217414. [Epub ahead of print]

 

Kivioja JL, Thanasopoulou A, Kumar A, Kontro M, Yadav B, Majumder MM, Javarappa KK, Eldfors S, Schwaller J, Porkka K, Heckman CA. Dasatinib and navitoclax act synergistically to target NUP98-NSD1+/FLT3-ITD+ acute myeloid leukemia. Leukemia. 2019, 33(6):1360-1372. doi: 10.1038/s41375-018-0327-2.

 

Karjalainen R, Liu M, Kumar A, He L, Malani D, Parsons A, Kontro M, Kallioniemi O, Porkka K, Heckman CA. Elevated expression of S100A8 and S100A9 correlates with resistance to the BCL-2 inhibitor venetoclax in AML. Leukemia. 2019, 33(10):2548-2553. doi: 10.1038/s41375-019-0504-y.

 

Javarappa KK, Tsallos D, Heckman CA. A Multiplexed Screening Assay to Evaluate Chemotherapy-Induced Myelosuppression Using Healthy Peripheral Blood and Bone Marrow. SLAS Discov. 2018, 23(7):687-696. doi: 10.1177/2472555218777968. 

 

Medarametla P, Gatta V, Kajander T, Laitinen T, Tammela P, Poso A. Structure‐Based Virtual Screening of LsrK Kinase Inhibitors to Target Quorum Sensing. ChemMedChem. 2018, 13(22):2400-2407. doi: 10.1002/cmdc.201800548.

 

Dufva O, Kankainen M, Kelkka T, Sekiguchi N, Awad SA, Eldfors S, Yadav B, Kuusanmäki H, Malani D, Andersson EI, Pietarinen P, Saikko L, Kovanen PE, Ojala T, Lee DA, Loughran TP Jr, Nakazawa H, Suzumiya J, Suzuki R, Ko YH, Kim WS, Chuang SS, Aittokallio T, Chan WC, Ohshima K, Ishida F, Mustjoki S. Aggressive natural killer-cell leukemia mutational landscape and drug profiling highlight JAK-STAT signaling as therapeutic target. Nat Commun. 2018, 9(1):1567. doi: 10.1038/s41467-018-03987-2.

 

Alzrigat M, Párraga AA, Majumder MM, Ma A, Jin J, Österborg A, Nahi H, Nilsson K, Heckman CA, Öberg F, Kalushkova A, Jernberg-Wiklund H. The polycomb group protein BMI-1 inhibitor PTC-209 is a potent anti-myeloma agent alone or in combination with epigenetic inhibitors targeting EZH2 and the BET bromodomains. Oncotarget. 2017, 8(61):103731-103743. doi: 10.18632/oncotarget.21909. 

Majumder MM, Silvennoinen R, Anttila P, Tamborero D, Eldfors S, Yadav B, Karjalainen R, Kuusanmäki H, Lievonen J, Parsons A, Suvela M, Jantunen E, Porkka K, Heckman CA. Identification of precision treatment strategies for relapsed/refractory multiple myeloma by functional drug sensitivity testing. Oncotarget. 2017, 8(34):56338-56350. doi: 10.18632/oncotarget.17630. 

Paasonen L, Sharma S, Braun GB, Kotamraju VR, Chung TD, She ZG, Sugahara KN, Yliperttula M, Wu B, Pellecchia M, Ruoslahti E, Teesalu T. New p32/gC1qR Ligands for Targeted Tumor Drug Delivery. Chembiochem. 2016, 1;17(7):570-5. doi: 10.1002/cbic.201500564.

Kontro M, Kuusanmäki H, Eldfors S, Burmeister T, Andersson EI, Bruserud Ø, Brümmendorf TH, Edgren H, Gjertsen BT, Itälä-Remes M, Lagström S, Lohi O, Lundán T, Martı´ JML, Majumder MM, Parsons A, Pemovska T, Rajala H, Vettenranta K, Kallioniemi O, Mustjoki S, Porkka K and Heckman CA. 2014 Novel activating STAT5B mutations as putative drivers of T-cell acute lymphoblastic leukemia. Leukemia. 2014, 28, 1738–1742. doi: 10.1038/leu.2014.89.

Andersson EI, Rajala HL, Eldfors S, Ellonen P, Olson T, Jerez A, Clemente MJ, Kallioniemi O, Porkka K, Heckman C, Loughran TP Jr, Maciejewski JP, Mustjoki S. Novel somatic mutations in large granular lymphocytic leukemia affecting the STAT-pathway and T-cell activation. Blood Cancer J. 2013, 3:e168. doi: 10.1038/bcj.2013.65.

Nybond S, Karp M, Tammela P. Antimicrobial assay optimization and validation for HTS in 384-well format using a bioluminescent E. coli K-12 strain. European Journal of Pharmaceutical Sciences. 2013, 49, 782–789. doi: 10.1016/j.ejps.2013.05.024.

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