Publications


Recent publications from the group

Cancer research

Defined extracellular matrix compositions support stiffness-insensitive cell spreading and adhesion signaling. Conway JRW, Isomursu A, Follain G, Härmä V, Jou-Ollé E, Pasquier N, Välimäki EPO, Rantala JK, Ivaska J.  Proc Natl Acad Sci U S A. 2023 Oct 24;120(43):e2304288120. doi: 10.1073/pnas.2304288120

Ex-vivo drug screening of surgically resected glioma stem cells to replace murine avatars and provide personalise cancer therapy for glioblastoma patients. Gagg H, Williams ST, Conroy S, Myers KN, McGarrity-Cottrell C, Jones C, Helleday T, Rantala J, Rominiyi O, Danson SJ, Collis SJ, Wells G. F1000Res. 2023 Aug 8;12:954. doi: 10.12688/f1000research.135809.1

FBXL12 degrades FANCD2 to regulate replication recovery and promote cancer cell survival under conditions of replication stress. Brunner A, Li Q, Fisicaro S, Kourtesakis A, Viiliäinen J, Johansson HJ, Pandey V, Mayank AK, Lehtiö J, Wohlschlegel JA, Spruck C, Rantala JK, Orre LM, Sangfelt O. Mol Cell. 2023 Aug 9:S1097-2765(23)00599-3. doi: 10.1016/j.molcel.2023.07.026

High-throughput screen in vitro identifies dasatinib as a candidate for combinatorial treatment with HER2-targeting drugs in breast cancer. Normann LS, Haugen MH, Hongisto V, Aure MR, Leivonen SK, Kristensen VN, Tahiri A, Engebraaten O, Sahlberg KK, Mælandsmo GM. PLoS One. 2023 Jan 27;18(1):e0280507. doi: 10.1371/journal.pone.0280507.

Precision oncology using ex vivo technology: a step towards individualised cancer care? Williams ST, Wells G, Conroy S, Gagg H, Allen R, Rominiyi O, Helleday T, Hullock K, Pennington CEW, Rantala J, Collis SJ, Danson SJ.  Expert Rev Mol Med. 2022 Oct 3;24:e39.

Cisplatin overcomes radiotherapy resistance in OCT4-expressing head and neck squamous cell carcinoma.  Routila J, Qiao X, Weltner J, Rantala JK, et al. Oral Oncol. 2022 Apr;127:105772

A FBXO7/EYA2-SCFFBXW7 axis promotes AXL-mediated maintenance of mesenchymal and immune evasion phenotypes of cancer cells. Shen JZ, Qiu Z, Wu Q, Zhang G, Harris R, Sun D, Rantala J, et al. Mol Cell. 2022 Mar 17;82(6):1123-1139.e8. doi: 10.1016/j.molcel.2022.01.022. Epub 2022 Feb 18. PMID: 35182481

Ex Vivo Drug Screening Informed Targeted Therapy for Metastatic Parotid Squamous Cell Carcinoma. Nykänen N, Mäkelä R, Arjonen A, Härmä V, Lewandowski L, Snowden E, Blaesius R, Jantunen I, Kuopio T, Kononen J, Rantala JK. Front Oncol. 2021 Sep 16;11:735820. doi: 10.3389/fonc.2021.735820. PMID: 34604070

Substrate-biased activity-based probes identify proteases that cleave receptor CDCP1. Kryza T, Khan T, Lovell S, Harrington BS, Yin J, Porazinski S, Pajic M, Koistinen H, Rantala JK et al. Nat Chem Biol. 2021;Apr 15.

FBXO44 promotes DNA replication-coupled repetitive element silencing in cancer cells. Shen JZ, Qiu Z, Wu Q, Finlay D, Garcia G, Sun D, Rantala J et al. Cell. 2021;184(2):352-369.e23.

Ex vivo assessment of targeted therapies in a rare metastatic epithelial-myoepithelial carcinoma. Mäkelä R, Arjonen A, Suryo Rahmanto A, Härmä V, Lehtiö J, Kuopio T, Helleday T, Sangfelt O, Kononen J, Rantala JK. Neoplasia. 2020;22(9):390-398.

PTEN and DNA-PK determine sensitivity and recovery in response to WEE1 inhibition in human breast cancer. Brunner A, Suryo Rahmanto A, Johansson H, Franco M, Viiliäinen J, Gazi M, Frings O, Fredlund E, Spruck C, Lehtiö J, Rantala JK, Larsson LG, Sangfelt O. Elife. 2020;9:e57894.

Ex vivo modelling of therapy efficacy for rare Krugenberg tumors – a report of two cases. Arjonen A, Mäkelä R, Virtakoivu R, Härmä V, Kuopio T, Hakkarainen H, Hollmén M, Kononen J, Rantala JK. Clin. Onc. Res. 2020;3(7).

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

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

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

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

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

Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer. 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. Nat Commun. 9(1):3815, 2018.

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. 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. Gene. S0378-1119(16)30827-7, 2016.

Androgen receptor-interacting protein HSPBAP1 facilitates growth of prostate cancer cells in androgen-deficient conditions.  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. Int J Cancer. 136(11):2535-2545, 2015.

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

Toxicology research

Reply to: Prospects and challenges for FAIR toxicogenomics data. Grafström R, Haase A, Kohonen P, Jeliazkova N, Nymark P. Nat Nanotechnol. 2022 Jan;17(1):19-20.

Towards FAIR nanosafety data. Jeliazkova N, Apostolova MD, Andreoli C, Barone F, Barrick A, et al. Nat Nanotechnol. 2021 Jun;16(6):644-654.

Transcriptomics in Toxicogenomics, Part III: Data Modelling for Risk Assessment. Serra A, Fratello M, Cattelani L, Liampa I, Melagraki G, Kohonen P, et al. Nanomaterials (Basel). 2020 Apr 8;10(4):708.

NanoSolveIT Project: Driving nanoinformatics research to develop innovative and integrated tools for in silico nanosafety assessment. Afantitis A, Melagraki G, Isigonis P, Tsoumanis A, Varsou DD, et al. Comput Struct Biotechnol J. 2020 Mar 7;18:583-602. doi: 10.1016/j.csbj.2020.02.023.

Toward Rigorous Materials Production: New Approach Methodologies Have Extensive Potential to Improve Current Safety Assessment Practices. Nymark P, Bakker M, Dekkers S, Franken R, Fransman W, García-Bilbao A, Greco D, Gulumian M, Hadrup N, Halappanavar S, Hongisto V, Hougaard KS, Jensen KA, Kohonen P, Koivisto AJ, Dal Maso M, Oosterwijk T, Poikkimäki M, Rodriguez-Llopis I, Stierum R, Sørli JB, Grafström R.  Small. 2020 Feb;16(6):e1904749.

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. Oki NO, Farcal L, Abdelaziz A, Florean O, Doktorova TY, Exner T, Kohonen P, Grafström R, Hardy B.  Toxicol In Vitro. 2019. 54:23-32. doi: 10.1016/j.tiv.2018.09.002.

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

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

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

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

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

The eNanoMapper database for nanomaterial safety information. 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. Beilstein J Nanotechnol. 2015

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

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

The ToxBank Data Warehouse: Supporting the Replacement of In Vivo Repeated Dose Systemic Toxicity Testing. 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. Mol Inform. 2013.

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