Selected publications

Qiao X, Routila J, Tienhaara M, Irjala H, Santhi PP, Huusko T, Nissi L, Paatero I, Lehtinen N, Rantala J, Viljanen T, Leivo I, Koivunen P, Jouppila-Mättö A, Taulu R, Bäck L, Wilkman T, Haapio E, Kinnunen I, Kurppa K, Westermarck J, Ventelä S. LIMA1-alpha staining predicts curative intent surgery response in HPV negative head and neck cancer. EMBO Mol Med. 2025;(8):2095-2114. doi: 10.1038/s44321-025-00266-8.

Rahman MM, Wells G, Rantala JK, Helleday T, Muthana M, Danson SJ. In-vitro assays for immuno-oncology drug efficacy assessment and screening for personalized cancer therapy: scopes and challenges. Expert Rev Clin Immunol. 2024;(8):821-838. doi: 10.1080/1744666X.2024.2336583.

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. Ex-vivo drug screening of surgically resected glioma stem cells to replace murine avatars and provide personalise cancer therapy for glioblastoma patients. F1000Res. 2024;12:954. doi: 10.12688/f1000research.

Lehtinen N, Suhonen J, Rice K, Välimäki E, Toriseva M, Routila J, Halme P, Rahi M, Irjala H, Leivo I, Kallajoki M, Nees M, Kuopio T, Ventelä S, Rantala JK. Assessment of targeted therapy opportunities in sinonasal cancers using patient-derived functional tumor models. Transl Oncol. 2024;44:101935.

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

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. FBXL12 degrades FANCD2 to regulate replication recovery and promote cancer cell survival under conditions of replication stress. Mol Cell. 2023 Oct 19;83(20):3720-3739.e8.

Williams ST, Wells G, Conroy S, Gagg H, Allen R, Rominiyi O, Helleday T, Hullock K, Pennington CEW, Rantala J, Collis SJ, Danson SJ. Precision oncology using ex vivo technology: a step towards individualised cancer care? Expert Rev Mol Med. 2022;3:1-48.

Routila J, Qiao X, Weltner J, Rantala JK, Carpén T, Hagström J, Mäkitie A, Leivo I, Ruuskanen M, Söderlund J, Rintala M, Hietanen S, Irjala H, Minn H, Westermarck J, Ventelä S. Cisplatin overcomes radiotherapy resistance in OCT4-expressing head and neck squamous cell carcinoma. Oral Oncol. 2022;127:105772.

Shen JZ, Qiu Z, Wu Q, Zhang G, Harris R, Sun D, Rantala J, Barshop WD, Zhao L, Lv D, Won KA, Wohlschlegel J, Sangfelt O, Laman H, Rich JN, Spruck C. A FBXO7/EYA2-SCFFBXW7 axis promotes AXL-mediated maintenance of mesenchymal and immune evasion phenotypes of cancer cells. Mol Cell. 2022;82(6):1123-1139.e8.

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

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

Mäkelä R, Härmä V, Badra Fajardo N, Wells G, Lygerou Z, Sangfelt O, Kononen J, Rantala JK. Ex vivo analysis of DNA repair targeting in extreme rare cutaneous apocrine sweat gland carcinoma. Oncotarget. 2021;12(11):1100-1109.

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

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

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. PTEN and DNA-PK determine sensitivity and recovery in response to WEE1 inhibition in human breast cancer. Elife. 2020;9:e57894.

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

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. 2020;20(1):590.

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. 2020;145:27-32.

Pellinen T, Tuomi S, Arjonen A, Wolf M, Edgren H, Meyer H, Grosse R, Kitzing T, Rantala JK, Kallioniemi O, Fässler R, Kallio M, Ivaska J. Integrin trafficking regulated by Rab21 is necessary for cytokinesis. Dev Cell. 15(3): 371-385, 2008.

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 JK, 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. Mod Pathol. 32(6):866-883. 2019.

Rantala JK. Diagnostic therapy efficacy assessment in genomic medicine and rare cancer care. Sci. Tech. 3(28). 2018.

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.

Rozanov DV, Rozanov ND, Chiotti KE, Reddy A, Wilmarth PA, David LL, Cha SW, Woo S, Pevzner P, Bafna V, Burrows GG, Rantala JK, Levin T, Anur P, Johnson-Camacho K, Tabatabaei S, Munson DJ, Bruno TC, Slansky JE, Kappler JW, Hirano N, Boegel S, Fox BA, Egelston C, Simons DL, Jimenez G, Lee PP, Gray JW, Spellman PT. MHC class I loaded ligands from breast cancer cell lines: A potential HLA-I-typed antigen collection. J Proteomics. 176. 2018.

Lue HW, Podolak J, Kolahi K, Cheng L, Rao S, Garg D, Xue CH, Rantala JK, Tyner JW, Thornburg KL, Martinez-Acevedo A, Liu JJ, Amling CL, Truillet C, Louie SM, Anderson KE, Evans MJ, O’Donnell VB, Nomura DK, Drake JM, Ritz A, Thomas GV. Metabolic reprogramming ensures cancer cell survival despite oncogenic signaling blockade. Genes Dev. 31(20):2067-2084. 2017.

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. 596:137-146, 2017.

Balistreri G, Viiliäinen J, Turunen M, Diaz R, Lyly L, Pekkonen P, Rantala J, Ojala K, Sarek G, Teesalu M, Denisova O, Peltonen K, Julkunen I, Varjosalo M, Kainov D, Kallioniemi O, Laiho M, Taipale J, Hautaniemi S, Ojala PM. Oncogenic Herpesvirus Utilizes Stress- Induced Cell Cycle Checkpoints for Efficient Lytic Replication. PLoS Pathog. 12(2):e1005424, 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.

Christensen LL, Holm A, Rantala J, Kallioniemi O, Rasmussen MH, Ostenfeld MS, Dagnaes- Hansen F, Øster B, Schepeler T, Tobiasen H, Thorsen K, Sieber OM, Gibbs P, Lamy P, Hansen TF, Jakobsen A, Riising EM, Helin K, Lubinski J, Hagemann-Madsen R, Laurberg S, Ørntoft TF, Andersen CL. Functional screening identifies miRNAs influencing apoptosis and proliferation in colorectal cancer. PLoS One.9(6): e96767, 2014.

Mai A, Muharram G, Barrow R, Baghirov H, Rantala J, Kermorgant S, Ivaska J. Distinct c- Met Activation Mechanisms Induce Cell Rounding or Invasion Through Pathways Involving Integrins, RhoA, and Hip1. J Cell Sci. 127(Pt 9): 1938-1952, 2014.

Costantino L*, Sotiriou SK*, Rantala JK*, Magin S, Mladenov E, Helleday T, Haber JE, Iliakis G, Kallioniemi OP, Halazonetis TD. Break-induced replication repair of damaged forks induces genomic duplications in human cells. Science. 343(6166): 88-91, 2014.

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

Cepeda D, Ng HF, Sharifi HR, Mahmoudi S, Cerrato VS, Fredlund E, Magnusson K, Nilsson H, Malyukova A, Rantala J, Klevebring D, Viñals F, Bhaskaran N, Zakaria SM, Rahmanto AS, Grotegut S, Nielsen ML, Szigyarto CA, Sun D, Lerner M, Navani S, Widschwendter M, Uhlén M, Jirström K, Pontén F, Wohlschlegel J, Grandér D, Spruck C, Larsson LG, Sangfelt O. CDK- mediated activation of the SCF(FBXO) (28) ubiquitin ligase promotes MYC-driven transcription and tumorigenesis and predicts poor survival in breast cancer. EMBO Mol Med. 5(7): 999-1018, 2013.

Dao KH, Rotelli MD, Brown BR, Yates JE, Rantala J, Tognon C, Tyner JW, Druker BJ, Bagby GC. The PI3K/Akt1 pathway enhances steady-state levels of FANCL. Mol Biol Cell. 24(16): 2582-2592, 2013

Rantala JK, Kwon S, Korkola J, Gray JW. Expanding the diversity of imaging-based RNAi screen applications using cell spot microarrays. Microarrays. 2: 97-114, 2013.

Cekaite L*, Rantala JK*, Bruun J, Guriby M, Ågesen TH, Danielsen SA, Lind GE, Nesbakken A, Kallioniemi O, Lothe RA, Skotheim RI. MiR-9, -31 and -182 deregulation promote proliferation and tumor cell survival in colon cancer. Neoplasia. 14(9): 868-81, 2012.

Fredlund E, Staaf J, Rantala JK, Kallioniemi O, Borg A, Ringnér M. The gene expression landscape of breast cancer is shaped by tumor protein p53 status and epithelial-mesenchymal transition. Breast Cancer Res. 14(4): R113, 2012.

Virtakoivu R, Pellinen T, Rantala JK, Perälä M, Ivaska J. Distinct roles of AKT isoforms in regulating β1-integrin activity, migration and invasion in prostate cancer. Mol Biol Cell. 23(17): 3357–3369, 2012

Pellinen T*, Rantala JK*, Arjonen A, Mpindi JP, Kallioniemi O, Ivaska J. A functional genomic analysis of β1-integrin activity regulators. J Cell Sci. 125(3): 649-61, 2012.

Björkman M, Ostling 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. 31: 3444-3456, 2012.

Rantala JK*, Pouwels J*, Pellinen T, Laasola P, Potter C, Sundberg JP, Kallioniemi O, Parsons M, Salmi M, Ivaska J. Sharpin is an endogenous inhibitor of b1 integrin activation. Nat. Cell Biol. 13(11): 1315-1324, 2011.

Rantala JK, Mäkelä R, Aaltola AR, Laasola P, Mpindi JP, Nees M, Saviranta P, Kallioniemi O. A cell spot microarray method for production of high density siRNA transfection microarrays. BMC Genomics. 28(12): 162, 2011.

Björkman M, Rantala J, Nees M, Kallioniemi O. Epigenetics of prostate cancer and the prospect of identification of novel drug targets by RNAi screening of epigenetic enzymes. Epigenomics. 2(5): 683–689, 2010.

Gupta S, Iljin K, Sara H, Mpindi JP, Mirtti T, Vainio P, Rantala J, Alanen K, Nees M, Kallioniemi O. FZD4 as a mediator of ERG oncogene-induced WNT signaling and epithelial-to- mesenchymal transition in human prostate cancer cells. Cancer Res. 70(17): 6735- 6745, 2010.

Rantala JK, Edgren H, Lehtinen L, Wolf M, Kleivi K, Vollan HK, Aaltola AR, Laasola P, Kilpinen S, Saviranta P, Iljin K, Kallioniemi O. Integrative functional genomics analysis of sustained polyploidy phenotypes in breast cancer cells identifies an oncogenic profile for GINS2. Neoplasia.12(11): 877-888, 2010