Publications

  1. Bulanova D, Akimov Y, Senkowski W, Oikkonen J, Gall-Mas L, Timonen S, Elmadani M, Hynninen J, Hautaniemi S, Aittokallio T, Wennerberg K. A synthetic lethal dependency on casein kinase 2 in response to replication-perturbing therapeutics in RB1-deficient cancer cells. Science Advances 2024. 10.1126/sciadv.adj1564
  2. Rausio H, Cervera A, Heuser V, West G, Oikkonen J, Pianfetti E, Lovino M, Ficarra E, Taimen P, Hynninen J, Lehtonen R, Hautaniemi S, Carpén S, Huhtinen K. PIK3R1 fusion drives chemoresistance in ovarian cancer by activating ERK1/2 and inducing rod and ring-like structures. ScienceDirect 2024. https://doi.org/10.1016/j.neo.2024.100987
  3. Perkiö A, Pradhan B, Genc F, Pirttikoski A, Pikkusaari S, Erkan E, Falco M, Huhtinen K, Narva S, Hynninen J, Kauppi L, Vähärautio A. Locus-specific LINE-1 expression in clinical ovarian cancer specimens at the single-cell level. Scientific Reports 2024. https://doi.org/10.1038/s41598-024-54113-w
  4. Jamalzadeh S, Dai J, Lavikka K, Li Y, Jiang J, Huhtinen K, Virtanen A, Oikkonen J, Hietanen S, Hynninen J, Vähärautio A, Häkkinen A, Hautaniemi S. Genome-wide quantification of copy-number aberration impact on gene expression in ovarian high-grade serous carcinoma. BMC Cancer 2024. https://doi.org/10.1186/s12885-024-11895-6
  5. Koskela H*, Li Y*, Joutsiniemi T, Muranen T, Isoviita V-M, Huhtinen K, Micoli G, Lavikka K, Marchi G, Hietanen S, Virtanen A, Hautaniemi S, Oikkonen J*, Hynninen J*. HRD related signature 3 predicts clinical outcome in advanced tubo-ovarian high-grade serous carcinoma. Gynecologic Oncology 2023. https://doi.org/10.1016/j.ygyno.2023.11.027
  6. Skorda A, Lauridsen AR, Huhtinen K, Lahtinen A, Senkowski W, Oikkonen J, Hynninen J, Hautaniemi S, Kallunki T. Quantification of cell death and proliferation of patient-derived ovarian cancer organoids through 3D imaging and image analysis. Cell Press 2023. https://doi.org/10.1016/j.xpro.2023.102683
  7. Marchi G*, Rajavuori A*, Nguyen M, Huhtinen K, Oksa S, Hietanen S, Hautaniemi S, Hynninen J*, Oikkonen J*. Extensive mutational ctDNA profiles reflect High-grade serous cancer tumors and reveal emerging mutations at recurrence. Translational Oncology (39) 2023. https://doi.org/10.1016/j.tranon.2023.101814
  8. Rannikko JH, Bono P, Hynninen J, Hollmén M. Bexmarilimab activates human tumor-associated macrophages to support adaptive immune responses in interferon-poor immune microenvironments. Cancer Immunology Research 2023. https://doi.org/10.1158/2326-6066.CIR-23-0350
  9. Ariotta V, Lehtonen O, Salloum S, Micoli G, Lavikka K, Rantanen V, Hynninen J, Virtanen A, Hautaniemi S. H&E image analysis pipeline for quantifying morphological features. Journal of Pathology Informatics 2023. https://doi.org/10.1016/j.jpi.2023.100339
  10. Nguyen M, Rajavuori A, Huhtinen K, Hietanen S, Hynninen J, Oikkonen J, Hautaniemi S. Circulating tumor DNA-based copy-number profiles enable monitoring treatment effects during therapy in high-grade serous carcinoma. Biomedicine & Pharmacotherapy (168) 2023. https://doi.org/10.1016/j.biopha.2023.115630
  11. Lahtinen A, Lavikka K, Virtanen A, Li Y, Jamalzadeh S, Skorda A, Lauridsen AR, Zhang K, Marchi G, Isoviita VM, Ariotta V, Lehtonen O, Muranen TA, Huhtinen K, Carpén O, Hietanen S, Senkowski W, Kallunki T, Häkkinen A, Hynninen J, Oikkonen J, Hautaniemi S. Evolutionary states and trajectories characterized by distinct pathways stratify patients with ovarian high grade serous carcinoma. Cancer Cell 2023. 10.1016/j.ccell.2023.04.017
  12. Senkowski W, Gall-Mas L, Falco MM, Li Y, Lavikka K, Kriegbaum MC, Oikkonen J, Bulanova D, Pietras EJ, Voßgröne K, Chen YJ, Erkan EP, Dai J, Lundgren A, Grønning Høg MK, Larsen IM, Lamminen T, Kaipio K, Huvila J, Virtanen A, Engelholm L, Christiansen P, Santoni-Rugiu E, Huhtinen K, Carpén O, Hynninen J, Hautaniemi S, Vähärautio A, Wennerberg K. A platform for efficient establishment and drug-response profiling of high-grade serous ovarian cancer organoids. Dev Cell 2023. 10.1016/j.devcel.2023.04.012 
  13. Deng F, Laasik M, Salminen L, Lapatto L, Huhtinen K, Li Y, Hautaniemi S, Hynninen J, Niemi M, Lehtonen R. Toxicity and therapy outcome associations in LIG3, SLCO1B3, ABCB1, OPRM1 and GSTP1 in high-grade serous ovarian cancer. BCPT 2023. https://doi.org/10.1111/bcpt.13866
  14. Pikkusaari S,  Tumiati M, Virtanen A, Oikkonen J, Li Y, Perez-Villatoro F, Muranen T, Salko M, Huhtinen K, Kanerva A, Koskela H, Tapper J, Koivisto-Korander R, Joutsiniemi T, Haltia U-M, Lassus H, Hautaniemi S, Färkkilä A, Hynninen J, Hietanen S, Carpén O, Kauppi L. Functional Homologous Recombination Assay on FFPE Specimens of Advanced High-Grade Serous Ovarian Cancer Predicts Clinical Outcomes. Clinical Cancer Research OF1–OF14, 2023. https://doi.org/10.1158/1078-0432.CCR-22-3156.
  15. Perez-Villatoro F, Oikkonen J, Casado J, Chernenko A, Gulhan DC,  Tumiati M, Li Y, Lavikka K, Hietanen S, Hynninen J, Haltia U-M, Tyrmi JS, Laivuori H, Konstantinopoulos PA, Hautaniemi S, Kauppi L & Färkkilä A. Optimized detection of homologous recombination deficiency improves the prediction of clinical outcomes in cancer. npj Precision Oncology volume 6, Article number: 96 (2022).
  16. 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. eCollection 2022.
  17. Carroll MJ, Kaipio K, Hynninen J, Carpen O, Hautaniemi S, Page D, Kreeger PK. A Subset of Secreted Proteins in Ascites Can Predict Platinum-Free Interval in Ovarian Cancer. Cancers (Basel). 2022 Sep 1;14(17):4291. doi: 10.3390/cancers14174291.
  18. Zhang K, Erkan EP, Jamalzadeh S, Dai J, Andersson N, Kaipio K, Lamminen T, Mansuri N, Huhtinen K, Carpén O, Hietanen S, Oikkonen J, Hynninen J, Virtanen A, Häkkinen A, Hautaniemi S, Vähärautio A. Longitudinal single-cell RNA-seq analysis reveals stress-promoted chemoresistance in metastatic ovarian cancer. Sci Adv. 2022 Feb 25;8(8):eabm1831. doi: 10.1126/sciadv.abm1831. Epub 2022 Feb 23.
  19. Jamalzadeh S, Häkkinen A, Andersson N, Huhtinen K, Laury A, Hietanen S, Hynninen J, Oikkonen J, Carpén O, Virtanen A, Hautaniemi S. QuantISH: RNA in situ hybridization image analysis framework for quantifying cell type-specific target RNA expression and variability. Lab Invest. 2022 Jul;102(7):753-761. doi: 10.1038/s41374-022-00743-5. Epub 2022 Feb 15.
  20. Narva SI, Seppänen MP, Raiko JRH, Forsback SJ, Orte KJ, Virtanen JM, Hynninen J, Hietanen S. Imaging of Tumor Hypoxia With 18F-EF5 PET/MRI in Cervical Cancer. Clin Nucl Med. 2021 Dec 1;46(12):952-957. doi: 10.1097/RLU.0000000000003914.
  21. Hautaniemi S, Hynninen J. Syöpäsolujen lääkeresistenssi ja miten se voitetaan – valokeilassa munasarjasyöpä. Duodecim 2021;137(18):1871-7
  22. He L, Bulanova D, Oikkonen J, Häkkinen A, Zhang K, Zheng S, Wang W, Erkan EP, Carpén O, Joutsiniemi T, Hietanen S, Hynninen J, Huhtinen K, Hautaniemi S,Vähärautio A, Tang J, Wennerberg K, Aittokallio T. Network-guided identificationof cancer-selective combinatorial therapies in ovarian cancer. Brief Bioinform. 2021
  23. Pietilä EA, Gonzalez-Molina J, Moyano-Galceran L, Jamalzadeh S, Zhang K, Lehtinen L, Turunen SP, Martins TA, Gultekin O, Lamminen T, Kaipio K, Joneborg U, Hynninen J, Hietanen S, Grénman S, Lehtonen R, Hautaniemi S, Carpén O, Carlson JW, Lehti K. Co-evolution of matrisome and adaptive adhesion dynamics drives ovarian cancer chemoresistance. Nat Commun. 2021
  24. Casado J, Lehtonen O, Rantanen V, Kaipio K, Pasquini L, Häkkinen A, Petrucci E, Hynninen J, Hietanen S, Carpén O, Biffoni M, Färkkilä A, Hautaniemi S. Agile workflow for interactive analysis of mass cytometry data. Bioinformatics. 2021
  25. Cervera A*, Rausio H*, Kähkönen T, Andersson N, Partel G, Rantanen V, Paciello G, Ficarra E, Hynninen J, Hietanen S, Carpén O, Lehtonen R, Hautaniemi S, Huhtinen K. FUNGI Fusion gene integration toolset. Bioinformatics. 2021 Mar 27;37(19):3353-5
  26. Salminen L, Braicu E, Lääperi M, Jylhä A, Oksa S, Hietanen S, Sehouli J, Kulbe H, DuBois A, Mahner S, Harter P, Carpen O, Huhtinen K, Hynninen J, Hilvo M. A novel two-lipid signature is a strong and independent prognostic factor in ovarian cancer. Cancers (Basel). 2021 Apr 7;13(8):1764. doi: 10.3390/cancers13081764.
  27. Jukonen J, Moyano-Galceran L, Höpfner K, Pietilä EA, Lehtinen L, Huhtinen K, Gucciardo E, Hynninen J, Hietanen S, Grénman S, Ojala PM, Carpén O, Lehti K. Aggressive and recurrent ovarian cancers upregulate ephrinA5, a non-canonical effector of EphA2 signaling duality. Sci Rep. 2021
  28. Häkkinen A, Zhang K, Alkodsi A, Andersson N, Erkan EP, Dai J, Kaipio K, Lamminen T, Mansuri N, Huhtinen K, Vähärautio A, Carpén O, Hynninen J, Hietanen S, Lehtonen R, Hautaniemi S. PRISM: Recovering cell type specific expression profiles from composite RNA-seq data. Bioinformatics. 2021 Mar 15. doi: 10.1093/bioinformatics/btab178
  29. Iyer S, Zhang S, Yucel S, Horn H, Smith S, Reinhardt F, Hoefsmit E, Assatova B, Casado J, Meinsohn M, Barrasa M, Bell G, Perez-Villatoro F, Huhtinen K, Hynninen J, Oikkonen J, Galhenage P, Pathania S, Hammond P, Neel B, Färkkilä A, Pépin D, Weinberg R. Genetically defined syngeneic mouse models of ovarian cancer as tools for the discovery of combination immunotherapy. Cancer Discov. 2020 Nov 6:CD-20-0818. doi: 10.1158/2159-8290.CD-20-0818.
  30. Salminen L, Gidwani K, Grènman S, Carpén O, Hietanen S, Pettersson K, Huhtinen K, Hynninen J. HE4 in the evaluation of tumor load and prognostic stratification of high grade serous ovarian carcinoma. Acta Oncol. 2020 Dec;59(12):1461-1468. doi: 10.1080/0284186X.2020.1827157.</li
  31. Häkkinen A, Koiranen J, Casado J, Kaipio K, Lehtonen O, Petrucci E, Hynninen J, Hietanen S, Carpén O, Pasquini L, Biffoni M, Lehtonen R, Hautaniemi S. qSNE: quadratic rate t-SNE optimizer with automatic parameter tuning for large datasets, Bioinformatics, Volume 36, Issue 20, 15 October 2020, Pages 5086–5092
  32. Laasik M, Hynninen J, Forsback S, Noponen T, Seppänen M, Hietanen S. The feasibility of [18F]EF5-PET/CT to image hypoxia in ovarian tumors: a clinical study.  EJNMMI Res. 2020 Sep 10;10(1):103. doi:10.1186/s13550-020-00689-z.
  33. Bayoumy S, Hyytiä H, Leivo J, Talha SM, Huhtinen K, Poutanen M, Hynninen J, Perheentupa A, Lamminmäki U, Gidwani K, Pettersson K. Glycovariant-based lateral flow immunoassay to detect ovarian cancer-associated serum CA125. Commun Biol. 2020 Aug 21;3(1):460. doi: 10.1038/s42003-020-01191-x.
  34. Salminen L, Nadeem N, Jain S, Grènman S, Carpén O, Hietanen S, Oksa S, Lamminmäki U, Pettersson K, Gidwani K, Huhtinen K, Hynninen J. A longitudinal analysis of CA125 glycoforms in the monitoring and follow up of high grade serous ovarian cancer. Gynecol Oncol. 2020 Mar;156(3):689-694. doi: 10.1016/j.ygyno.2019.12.025.
  35. Salminen L, Nadeem N, Rolfsen A, Dørum A, Grénman S, Hietanen S, Heinosalo T, Perheentupa A, Poutanen M, Bolstad N, Carpén O, Lamminmäki U, Pettersson K, Gidwani K, Hynninen J, and Huhtinen K. Exploratory analysis of CA125-MGL and -STn glycoforms in the differential diagnostics of pelvic masses.J Appl Lab Med. 2020 Mar 1;5(2):263-272. doi: 10.1093/jalm/jfz012.
  36. Kaipio K, Chen P, Roering P, Huhtinen K, Mikkonen P, Östling P, Lehtinen L, Korpela T, Potdar S, Hynninen J, Auranen A, Grénman S, Wennerberg K, Hautaniemi S and 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. 2019 Oct 9. doi: 10.1002/path.5356.
  37. Isoviita VM, Salminen L, Azar J, Lehtonen R, Roering P, Carpén O, Hietanen S, Grénman S, Hynninen J, Färkkilä A, Hautaniemi S. Open Source Infrastructure for Health Care Data Integration and Machine Learning Analyses. JCO Clin Cancer Inform. 2019 Aug;3:1-16. doi: 10.1200/CCI.18.00132. PMID: 31454273.
  38. Gidwani K, Nadeem N, Huhtinen K, Kekki H, Heinosalo T, Hynninen J, Perheentupa A, Poutanen M, Carpen O, Pettersson K, and Lamminmäki U. Europium Nanoparticle-Based Sialyl-Tn monoclonal antibody discriminates Epithelial Ovarian Cancer -associated CA125 from benign sources. J Appl Lab Med. 2019; 4(3):299-310.
  39. Oikkonen J, Zhang K, Salminen L, Schulman I, Lavikka K, Andersson N, Ojanperä E, Hietanen S, Grénman S, Lehtonen R, Huhtinen K, Carpén O, Hynninen J, Färkkilä A and Hautaniemi A. Prospective longitudinal ctDNA workflow reveals clinically actionable alterations in ovarian cancer. JCO Precision Oncology. DOI:10.1200/PO.18.00343. Published May 3, 2019
  40. Kozłowska E, Vallius T, Hynninen J, Hietanen S, Färkkilä A, Hautaniemi S. Virtual clinical trials identify effective combination therapies in ovarian cancer. Sci Rep. 2019 Dec 10;9(1):18678. doi: 10.1038/s41598-019-55068-z
  41. Tumiati M, Hietanen S, Hynninen J, Pietilä E, Färkkilä A, Kaipio K, Roering P, Huhtinen K, Alkodsi A, Li Y, Lehtonen R, Erkan EP, Tuominen M, Lehti K, Hautaniemi S, Vähärautio A, Grénman S, Carpén O, and Kauppi L. A functional homologous recombination assay predicts primary chemotherapy response and long-term survival in ovarian cancer patients. Clin Cancer Res. 2018 Jun 1. doi: 10.1158/1078-0432.CCR-17-3770
  42. Häkkinen A, Alkodsi A, Facciotto C, Zhang K, Kaipio K, Leppä S, Carpén O, Grénman S, Hynninen J, Hietanen S, Lehtonen R, Hautaniemi S. Identifying differentially methylated sites in samples with varying tumor purity. Bioinformatics, 34:3078-85, 2018
  43. Kozlowska E, Färkkilä A, Vallius T, Carpén O, Kemppainen J, Grénman S, Lehtonen R, Hynninen J, Hietanen S, Hautaniemi S. Mathematical model predicts response to chemotherapy and drug combinations in ovarian cancer. Cancer Res. 78:4036-44, 2018
  44. Kemiläinen H, Huhtinen K, Auranen A, Carpén O, Strauss L, Poutanen M. The expression of HSD17B12 is associated with COX2, and is increased in high-grade epithelial ovarian cancer. Oncology. 2018, 94: 233-242.
  45. Vallius T, Hynninen J, Kemppainen J, Alves V, Auranen K, Matomäki J, Oksa S, Virtanen J, Grénman S, Auranen A, Seppänen M.18F-FDG-PET/CT based total metabolic tumor volume change during neoadjuvant chemotherapy predicts outcome in advanced epithelial ovarian cancer. Eur J Nucl Med Mol Imaging. 2018 Jul;45(7):1224-1232. doi: 10.1007/s00259-018-3961-z. Epub 2018 Feb 23
  46. Nguyen EV*, Huhtinen K*, Goo YA, Kaipio K, Andersson N, Rantanen V, Hynninen J, Lahesmaa R, Carpen O, Goodlett DR. Proteomic and phosphoproteomic analysis of cisplatin resistance in patient derived serous ovarian cancer cells. Mol Cell Proteomics. 2017, 16: 1377-1392. *equal contribution
  47. Lund RJ*, Huhtinen K*, Salmi J, Nguyen EV, Moulder R, Goodlett DR, Lahesmaa R, Carpén O. DNA methylation and Transcriptome Changes Associated with Cisplatin Resistance in Ovarian Cancer. Sci Rep. 2017, 7: 1469. *equal contribution
  48. Vallius T, Hynninen J, Auranen A, Matomäki J, Oksa S, Roering P, Grènman S.Postoperative human epididymis protein 4 predicts primary therapy outcome in advanced epithelial ovarian cancer. Tumour Biol. 2017 Feb;39(2):1010428317691189. doi: 10.1177/1010428317691189.
  49. Gidwani K*, Huhtinen K*, Kekki H, van Vliet S, Koivuviita N, Perheentupa A, Poutanen M, Hynninen J, Auranen A, Grenman S, Lamminmäki U, Carpen O, van Kooyk Y, Pettersson K. A nanoparticle-lectin-immunoassay improves discrimination of serum CA125 from malignant 1 and benign sources. Clinical Chemistry. 2016, 62:1390-400. *equal contribution
  50. Tambe M, Pruikkonen S, Mäki-Jouppila J, Chen P, Elgaaen BV, Birkeland EE, Huhtinen K, Cárpen O, Lønning PE, Davidson B, Hautaniemi S, and Kallio MJ. Mad2 targeting miR-493-3p perturbs spindle assembly checkpoint signalling and confers resistance to paclitaxel. Oncotarget. 2016, 7: 12267-85
  51. Chen P*, Huhtinen K*, Kaipio K, Mikkonen P, Aittomäki V, Lindell R, Hynninen J, Auranen A, Grenman S, Lehtonen R, Carpen O, Hautaniemi S. Identification of Prognostic Groups in High-Grade Serous Ovarian Cancer Treated with Platinum-Taxane Chemotherapy. Cancer Res. 2015, 75: 2987-2998. *equal contribution
  52. Vallius T, Hynninen J, Auranen A, Carpén O, Matomäki J, Oksa S, Virtanen J, Grénman S: Serum HE4 and CA125 as predictors of response and outcome during neoadjuvant chemotherapy of advanced high grade serous ovarian cancer. Tumor Biology 2014 Dec;35(12):12389-95
  53. Vallius T, Peter A, Auranen A, Carpén O, Kemppainen J, Matomäki J, Oksa S, Roering P, Seppänen M, Grénman S, Hynninen J: 118F-FDG-PET/CT can identify histopathological non-responders to platinum-based neoadjuvant chemotherapy in advanced epithelial ovarian cancer. Gynecol Oncol 2016 Jan; 140(1):29-35.
  54. Hynninen J, Auranen A, Carpén O, Dean K, Seppänen M, Kemppainen J, Lavonius M, Lisinen I, Virtanen J, Grénman S: FDG PET/CT in staging of advanced epithelial ovarian cancer: frequency of supradiaphragmatic lymph node metastasis challenges the traditional pattern of disease spread. Gynecol Oncol. 2012 Jul; 126(1): 64-8.
  55. Hynninen J, Lavonius M, Oksa S, Grénman S, Carpén Olli, Auranen Annika: Is perioperative visual estimation of intra-abdominal tumor spread reliable in ovarian cancer surgery after neoadjuvant chemotherapy? Gynecol Oncol 2013 Feb; 128(2): 229-232.
  56. Hynninen J, Kemppainen J, Lavonius M, Virtanen J, Matomäki J, Oksa S, Carpén O, Grénman S, Seppänen M, Auranen A: A prospective comparison of integrated FDG-PET/contrast-enhanced CT and contrast-enhanced CT for pretreatment imaging of advanced epithelial ovarian cancer. Gynecol Oncol 2013 Nov; 131(2): 389-394
  57. Hynninen J, Auranen A, Dean K, Lavonius M, Carpen O, Perheentupa A, Seppänen M, Grénman S. Serum HE4 Profile During Primary Chemotherapy of Epithelial Ovarian Cancer.
     Int J Gynecol Cancer. 2011 Dec;21(9):1573-8. doi: 10.1097/IGC.0b013e3182225509.