PUBLICATIONS



Recent publications from the group


Cancer research

Mäkelä R, Arjonen A, Härmä V, Rintanen N, Paasonen L, Paprotka T, Rönsch K, Kuopio T, Kononen J, Rantala JK. Ex vivo modelling of drug efficacy in a rare metastatic urachal carcinoma. BMC Cancer. 20:590, 2020.

Arjonen A, Mäkelä R, Härmä V, Rintanen N, Kuopio T, Kononen J, Rantala JK. Image-based ex vivo drug screen to assess targeted therapies in recurrent thymoma. Lung Cancer. 145:27-32, 2020.

Lehtomaki KI, Lahtinen LI, Rintanen N, Kuopio T, Kholova I, Mäkelä R, Rantala JK, Kellokumpu-Lehtinen PL, Kononen J. Clonal Evolution of MEK/MAPK Pathway Activating Mutations in a Metastatic Colorectal Cancer Case. Anticancer Res. 39(11):5867-5877, 2019.

Kettunen K, Boström PJ, Lamminen T, Heinosalo T, West G, Saarinen I, Kaipio K, Rantala J, Albanese C, Poutanen M, Taimen P. Personalized Drug Sensitivity Screening for Bladder Cancer Using Conditionally Reprogrammed Patient-derived Cells. Eur. J. Urol. 76(4):430-434, 2019.

Ahtiainen M, Wirta EV, Kuopio T, Seppälä T, Rantala JK, Mecklin JP, Böhm J. Combined prognostic value of CD274 (PD-L1)/PDCDI (PD-1) expression and immune cell infiltration in colorectal cancer as per mismatch repair status. Modern Pathology. 6:866-883. 2019.

Risom T, Langer EM, Chapman MP, Rantala J, Fields AJ, Boniface C, Alvarez MJ, Kendsersky ND, Pelz CR, Johnson-Camacho K, Dobrolecki LE, Chin K, Aswani AJ, Wang NJ, Califano A, Lewis MT, Tomlin CJ, Spellman PT, Adey A, Gray JW, Sears RC. Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer. Nat Commun. 9(1):3815, 2018.

He T, Surdez D, Rantala JK, Haapa-Paananen S, Ban J, Kauer M, Tomazou E, Fey V, Alonso J, Kovar H, Delattre O, Iljin K. High-throughput RNAi screen in Ewing sarcoma cells identifies leucine rich repeats and WD repeat domain containing 1 (LRWD1) as a regulator of EWS-FLI1 driven cell viability. Gene. S0378-1119(16)30827-7, 2016.

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. 136(11):2535-2545, 2015.

Rantala JK. Converting imaging-based cell biology to high-throughput biology. Eur. Phar. Rev. 19(1): 62-66, 2014.


Toxicology research

Oki NO, Farcal L, Abdelaziz A, Florean O, Doktorova TY, Exner T, Kohonen P, Grafström R, Hardy B. Integrated analysis of in vitro data and the adverse outcome pathway framework for prioritization and regulatory applications: An exploratory case study using publicly available data on piperonyl butoxide and liver models. Toxicol In Vitro. 2019. 54:23-32. doi: 10.1016/j.tiv.2018.09.002.

Nymark P, Kohonen P, Hongisto V, Grafström RC. Toxic and Genomic Influences of Inhaled Nanomaterials as a Basis for Predicting Adverse Outcome. Ann Am Thorac Soc. 2018. 15(Suppl 2):S91-S97.

Nymark P, Rieswijk L, Ehrhart F, Jeliazkova N, Tsiliki G, Sarimveis H, Evelo CT, Hongisto V, Kohonen P, Willighagen E, Grafström RC. A Data Fusion Pipeline for Generating and Enriching Adverse Outcome Pathway Descriptions. Toxicol Sci. 2018. 162(1):264-275. doi: 10.1093/toxsci/kfx252.

Kohonen P, Parkkinen JA, Willighagen EL, Ceder R, Wennerberg K, Kaski S, Grafström RC. A transcriptomics data-driven gene space accurately predicts liver cytopathology and drug-induced liver injury. Nat Commun. 2017. 8:15932. doi: 10.1038/ncomms15932.

Montalvão S, Demirel Z, Devi P, Lombardi V, Hongisto V, Perälä M, Hattara J, Imamoglu E, Tilvi SS, Turan G, Dalay MC, Tammela P. Large-scale bioprospecting of cyanobacteria, micro- and macroalgae from the Aegean Sea. N Biotechnol. 2016.

Grafström RC, Nymark P, Hongisto V, Spjuth O, Ceder R, Willighagen E, Hardy B, Kaski S, Kohonen P. Toward the Replacement of Animal Experiments through the Bioinformatics-driven Analysis of ‘Omics’ Data from Human Cell Cultures. Altern Lab Anim. 2015.

Jeliazkova N, Chomenidis C, Doganis P, Fadeel B, Grafström R, Hardy B, Hastings J, Hegi M, Jeliazkov V, Kochev N, Kohonen P, Munteanu CR, Sarimveis H, Smeets B, Sopasakis P, Tsiliki G, Vorgrimmler D, Willighagen E. The eNanoMapper database for nanomaterial safety information. Beilstein J Nanotechnol. 2015

Kohonen P, Ceder R, Smit I, Hongisto V, Myatt G, Hardy B, Spjuth O, Grafström R. Cancer Biology, Toxicology and Alternative Methods Development Go Hand-in-Hand. Basic & Clinical Pharmacology & Toxicology 2014.

Nymark P, Wijshoff P, Cavill R, van Herwijnen M, Coonen ML, Claessen S, Catalán J, Norppa H, Kleinjans JC, Briedé JJ. Extensive temporal transcriptome and microRNA analyses identify molecular mechanisms underlying mitochondrial dysfunction induced by multi-walled carbon nanotubes in human lung cells. Nanotoxicology. 2015.

Kohonen P, Benfenati E, Bower D, Ceder R, Crump M, Cross K, Grafström RC, Healy L, Helma C, Jeliazkova N, Jeliazkov V, Maggioni S, Miller S, Myatt G, Rautenberg M, Stacey G, Willighagen E, Wiseman J, Hardy B. The ToxBank Data Warehouse: Supporting the Replacement of In Vivo Repeated Dose Systemic Toxicity Testing. Mol Inform. 2013.

Nymark P, Catalán J, Suhonen S, Järventaus H, Birkedal R, Clausen PA, Jensen KA, Vippola M, Savolainen K, Norppa H. Genotoxicity of polyvinylpyrrolidone-coated silver nanoparticles in BEAS 2B cells. Toxicology. 2013.