Comprehensive characterization and effective combinatorial targeting of high-grade serous ovarian cancer via single-cell analysis

Rezultaty

Novel drug response scoring model based on flow cytometry / imaging-based
Network-based algorithm that predicts drug combinations for identified subpopulations
One or more software components that automate import and integration of modelling data into Cytoscape

Knowledge Management System up and running
Project Office with Operational Project Manager in place and Project Management Committee

Report on raising public participation and awareness
Project presentation produced
A workflow for obtaining consents from advanced HGS-OvCa patients, and for collecting samples from the patients

Evaluation of flow cytometry and imaging-based clonal drug response assays

Data Management Plan

Publikacje

Clinical Application of Novel Circulatory Biomarkers in Epithelial Ovarian Cancer

Autorzy: Salminen, Liina
Opublikowane w: 2020
Wydawca: University of Turku

In vitro and in silico methods to investigate and overcome drug resistance in cancer

Autorzy: Facciotto, Chiara
Opublikowane w: 2021, ISBN 978-951-51-7427-7
Wydawca: University of Helsinki

Transcriptomics analysis and its applications in cancer

Autorzy: Cervera, Alejandra
Opublikowane w: 2020, ISBN 978-951-51-6866-5
Wydawca: University of Helsinki

Comprehensive characterization and effective combinatorial targeting of high-grade serous ovarian cancer via single-cell analysis.

Autorzy: Azzalini, Eros.
Opublikowane w: 2020
Wydawca: Università degli Studi di Trieste

Proteogenomics methods for translational cancer research

Autorzy: Casado, Julia
Opublikowane w: 2021, ISBN 978-951-51-7220-4
Wydawca: University of Helsinki

Network-guided identification of cancer-selective combinatorial therapies in ovarian cancer

Autorzy: Liye He, Daria Bulanova, Jaana Oikkonen, Antti Häkkinen, Kaiyang Zhang, Shuyu Zheng, Wenyu Wang, Erdogan Pekcan Erkan, Olli Carpén, Titta Joutsiniemi, Sakari Hietanen, Johanna Hynninen, Kaisa Huhtinen, Sampsa Hautaniemi, Anna Vähärautio, Jing Tang, Krister Wennerberg, Tero Aittokallio
Opublikowane w: Briefings in Bioinformatics, 2021, ISSN 1467-5463
Wydawca: Oxford University Press
DOI: 10.1093/bib/bbab272

Cell-stiffness and morphological architectural patterns in clinical samples of high grade serous ovarian cancers

Autorzy: Eros Azzalini, Nodira Abdurakhmanova, Pietro Parisse, Michele Bartoletti, Vincenzo Canzonieri, Giorgio Stanta, Loredana Casalis, Serena Bonin
Opublikowane w: Nanomedicine: Nanotechnology, Biology and Medicine, Numer 37, 2021, Strona(/y) 102452, ISSN 1549-9634
Wydawca: Elsevier BV
DOI: 10.1016/j.nano.2021.102452

Agile workflow for interactive analysis of mass cytometry data

Autorzy: Julia Casado, Oskari Lehtonen, Ville Rantanen, Katja Kaipio, Luca Pasquini, Antti Häkkinen, Elenora Petrucci, Johanna Hynninen, Sakari Hietanen, Olli Carpén, Mauro Biffoni, Anniina Färkkilä, Sampsa Hautaniemi
Opublikowane w: Bioinformatics, 2020, Strona(/y) 1-6, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/btaa946

Aggressive and recurrent ovarian cancers upregulate ephrinA5, a non-canonical effector of EphA2 signaling duality

Autorzy: Joonas Jukonen, Lidia Moyano-Galceran, Katrin Höpfner, Elina A. Pietilä, Laura Lehtinen, Kaisa Huhtinen, Erika Gucciardo, Johanna Hynninen, Sakari Hietanen, Seija Grénman, Päivi M. Ojala, Olli Carpén, Kaisa Lehti
Opublikowane w: Scientific Reports, Numer 11/1, 2021, Strona(/y) 1-12, ISSN 2045-2322
Wydawca: Nature Publishing Group
DOI: 10.1038/s41598-021-88382-6

Co-evolution of matrisome and adaptive adhesion dynamics drives ovarian cancer chemoresistance

Autorzy: Elina A. Pietilä, Jordi Gonzalez-Molina, Lidia Moyano-Galceran, Sanaz Jamalzadeh, Kaiyang Zhang, Laura Lehtinen, S. Pauliina Turunen, Tomás A. Martins, Okan Gultekin, Tarja Lamminen, Katja Kaipio, Ulrika Joneborg, Johanna Hynninen, Sakari Hietanen, Seija Grénman, Rainer Lehtonen, Sampsa Hautaniemi, Olli Carpén, Joseph W. Carlson, Kaisa Lehti
Opublikowane w: Nature Communications, Numer 12/1, 2021, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-021-24009-8

The Extracellular Matrix Influences Ovarian Carcinoma Cells’ Sensitivity to Cisplatinum: A First Step towards Personalized Medicine

Autorzy: Andrea Balduit, Chiara Agostinis, Alessandro Mangogna, Veronica Maggi, Gabriella Zito, Federico Romano, Andrea Romano, Rita Ceccherini, Gabriele Grassi, Serena Bonin, Deborah Bonazza, Fabrizio Zanconati, Giuseppe Ricci, Roberta Bulla
Opublikowane w: Cancers, Numer 12/5, 2020, Strona(/y) 1175, ISSN 2072-6694
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers12051175

PRISM: recovering cell-type-specific expression profiles from individual composite RNA-seq samples

Autorzy: Antti Häkkinen, Kaiyang Zhang, Amjad Alkodsi, Noora Andersson, Erdogan Pekcan Erkan, Jun Dai, Katja Kaipio, Tarja Lamminen, Naziha Mansuri, Kaisa Huhtinen, Anna Vähärautio, Olli Carpén, Johanna Hynninen, Sakari Hietanen, Rainer Lehtonen, Sampsa Hautaniemi
Opublikowane w: Bioinformatics, 2021, Strona(/y) 1-7, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/btab178

Human cell transformation by combined lineage conversion and oncogene expression

Autorzy: Biswajyoti Sahu, Päivi Pihlajamaa, Kaiyang Zhang, Kimmo Palin, Saija Ahonen, Alejandra Cervera, Ari Ristimäki, Lauri A. Aaltonen, Sampsa Hautaniemi, Jussi Taipale
Opublikowane w: Oncogene, 2021, ISSN 0950-9232
Wydawca: Nature Publishing Group
DOI: 10.1038/s41388-021-01940-0

Mathematical Modeling Predicts Response to Chemotherapy and Drug Combinations in Ovarian Cancer

Autorzy: Emilia Kozłowska, Anniina Färkkilä, Tuulia Vallius, Olli Carpén, Jukka Kemppainen, Seija Grénman, Rainer Lehtonen, Johanna Hynninen, Sakari Hietanen, Sampsa Hautaniemi
Opublikowane w: Cancer Research, Numer 78/14, 2018, Strona(/y) 4036-4044, ISSN 0008-5472
Wydawca: American Association for Cancer Research
DOI: 10.1158/0008-5472.can-17-3746

Clinical Value of 18 F-fluorodeoxyglucose Positron Emission Tomography/Computed Tomography in Response Evaluation after Primary Treatment of Advanced Epithelial Ovarian Cancer

Autorzy: J. Hynninen, M. Laasik, T. Vallius, J. Kemppainen, S. Grönroos, J. Virtanen, J. Casado, S. Hautaniemi, S. Grenman, M. Seppänen, A. Auranen
Opublikowane w: Clinical Oncology, Numer 30/8, 2018, Strona(/y) 507-514, ISSN 0936-6555
Wydawca: W. B. Saunders Co., Ltd.
DOI: 10.1016/j.clon.2018.04.007

Identifying differentially methylated sites in samples with varying tumor purity

Autorzy: Antti Häkkinen, Amjad Alkodsi, Chiara Facciotto, Kaiyang Zhang, Katja Kaipio, Sirpa Leppä, Olli Carpén, Seija Grénman, Johanna Hynninen, Sakari Hietanen, Rainer Lehtonen, Sampsa Hautaniemi
Opublikowane w: Bioinformatics, Numer 34/18, 2018, Strona(/y) 3078-3085, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/bty310

Network module identification—A widespread theoretical bias and best practices

Autorzy: Iryna Nikolayeva, Oriol Guitart Pla, Benno Schwikowski
Opublikowane w: Methods, Numer 132, 2018, Strona(/y) 19-25, ISSN 1046-2023
Wydawca: Academic Press
DOI: 10.1016/j.ymeth.2017.08.008

Behavior of FDG-avid supradiaphragmatic lymph nodes in PET/CT throughout primary therapy in advanced serous epithelial ovarian cancer: a prospective study

Autorzy: Maren Laasik, Jukka Kemppainen, Annika Auranen, Sakari Hietanen, Seija Grénman, Marko Seppänen, Johanna Hynninen
Opublikowane w: Cancer Imaging, Numer 19/1, 2019, ISSN 1470-7330
Wydawca: Springer Nature
DOI: 10.1186/s40644-019-0215-7

Anduril 2: upgraded large-scale data integration framework

Autorzy: Alejandra Cervera, Ville Rantanen, Kristian Ovaska, Marko Laakso, Javier Nuñez-Fontarnau, Amjad Alkodsi, Julia Casado, Chiara Facciotto, Antti Häkkinen, Riku Louhimo, Sirkku Karinen, Kaiyang Zhang, Kari Lavikka, Lauri Lyly, Maninder Pal Singh, Sampsa Hautaniemi
Opublikowane w: Bioinformatics, Numer 35/19, 2019, Strona(/y) 3815-3817, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/btz133

Prospective Longitudinal ctDNA Workflow Reveals Clinically Actionable Alterations in Ovarian Cancer

Autorzy: Jaana Oikkonen, Kaiyang Zhang, Liina Salminen, Ingrid Schulman, Kari Lavikka, Noora Andersson, Erika Ojanperä, Sakari Hietanen, Seija Grénman, Rainer Lehtonen, Kaisa Huhtinen, Olli Carpén, Johanna Hynninen, Anniina Färkkilä, Sampsa Hautaniemi
Opublikowane w: JCO Precision Oncology, Numer 3, 2019, Strona(/y) 1-12, ISSN 2473-4284
Wydawca: American Society of Clinical Oncology
DOI: 10.1200/po.18.00343

Open Source Infrastructure for Health Care Data Integration and Machine Learning Analyses

Autorzy: Veli-Matti Isoviita, Liina Salminen, Jimmy Azar, Rainer Lehtonen, Pia Roering, Olli Carpén, Sakari Hietanen, Seija Grénman, Johanna Hynninen, Anniina Färkkilä, Sampsa Hautaniemi
Opublikowane w: JCO Clinical Cancer Informatics, Numer 3, 2019, Strona(/y) 1-16, ISSN 2473-4276
Wydawca: American Society of Clinical Oncology
DOI: 10.1200/cci.18.00132

Virtual clinical trials identify effective combination therapies in ovarian cancer

Autorzy: Emilia Kozłowska, Tuulia Vallius, Johanna Hynninen, Sakari Hietanen, Anniina Färkkilä, Sampsa Hautaniemi
Opublikowane w: Scientific Reports, Numer 9/1, 2019, ISSN 2045-2322
Wydawca: Nature Publishing Group
DOI: 10.1038/s41598-019-55068-z

Autorzy: Katja Kaipio, Ping Chen, Pia Roering, Kaisa Huhtinen, Piia Mikkonen, Päivi Östling, Laura Lehtinen, Naziha Mansuri, Taina Korpela, Swapnil Potdar, Johanna Hynninen, Annika Auranen, Seija Grénman, Krister Wennerberg, Sampsa Hautaniemi, Olli Carpén
Opublikowane w: The Journal of Pathology, Numer 250/2, 2019, Strona(/y) 159-169, ISSN 0022-3417
Wydawca: John Wiley & Sons Inc.
DOI: 10.1002/path.5356

Improved detection of differentially represented DNA barcodes for high‐throughput clonal phenomics

Autorzy: Yevhen Akimov, Daria Bulanova, Sanna Timonen, Krister Wennerberg, Tero Aittokallio
Opublikowane w: Molecular Systems Biology, Numer 16/3, 2020, ISSN 1744-4292
Wydawca: Nature Publishing Group
DOI: 10.15252/msb.20199195

qSNE: Quadratic rate t-SNE optimizer with automatic parameter tuning for large data sets

Autorzy: Antti Häkkinen, Juha Koiranen, Julia Casado, Katja Kaipio, Oskari Lehtonen, Eleonora Petrucci, Johanna Hynninen, Sakari Hietanen, Olli Carpén, Luca Pasquini, Mauro Biffoni, Rainer Lehtonen, Sampsa Hautaniemi
Opublikowane w: Bioinformatics, 2020, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/btaa637

Reliability of miRNA Analysis from Fixed and Paraffin-Embedded Tissues

Autorzy: Eros Azzalini, Eleonora De Martino, Paolo Fattorini, Vincenzo Canzonieri, Giorgio Stanta, Serena Bonin
Opublikowane w: International Journal of Molecular Sciences, Numer 20/19, 2019, Strona(/y) 4819, ISSN 1422-0067
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms20194819

A Functional Homologous Recombination Assay Predicts Primary Chemotherapy Response and Long-Term Survival in Ovarian Cancer Patients

Autorzy: Manuela Tumiati, Sakari Hietanen, Johanna Hynninen, Elina Pietilä, Anniina Färkkilä, Katja Kaipio, Pia Roering, Kaisa Huhtinen, Amjad Alkodsi, Yilin Li, Rainer Lehtonen, Erdogan Pekcan Erkan, Minna M. Tuominen, Kaisa Lehti, Sampsa K. Hautaniemi, Anna Vähärautio, Seija Grénman, Olli Carpén, Liisa Kauppi
Opublikowane w: Clinical Cancer Research, 2018, ISSN 1078-0432
Wydawca: American Association for Cancer Research
DOI: 10.1158/1078-0432.ccr-17-3770

A longitudinal analysis of CA125 glycoforms in the monitoring and follow up of high grade serous ovarian cancer

Autorzy: Liina Salminen, Nimrah Nadeem, Shruti Jain, Seija Grènman, Olli Carpén, Sakari Hietanen, Sinikka Oksa, Urpo Lamminmäki, Kim Pettersson, Kamlesh Gidwani, Kaisa Huhtinen, Johanna Hynninen
Opublikowane w: Gynecologic Oncology, Numer 156/3, 2020, Strona(/y) 689-694, ISSN 0090-8258
Wydawca: Academic Press
DOI: 10.1016/j.ygyno.2019.12.025

FUNGI: FUsioN Gene Integration toolset

Autorzy: Alejandra Cervera, Heidi Rausio, Tiia Kähkönen, Noora Andersson, Gabriele Partel, Ville Rantanen, Giulia Paciello, Elisa Ficarra, Johanna Hynninen, Sakari Hietanen, Olli Carpén, Rainer Lehtonen, Sampsa Hautaniemi, Kaisa Huhtinen
Opublikowane w: Bioinformatics, 2021, Strona(/y) 1-3, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/btab206

HE4 in the evaluation of tumor load and prognostic stratification of high grade serous ovarian carcinoma

Autorzy: Liina Salminen, Kamlesh Gidwani, Seija Grènman, Olli Carpén, Sakari Hietanen, Kim Pettersson, Kaisa Huhtinen, Johanna Hynninen
Opublikowane w: Acta Oncologica, Numer 59/12, 2020, Strona(/y) 1461-1468, ISSN 0284-186X
Wydawca: Taylor & Francis
DOI: 10.1080/0284186x.2020.1827157

Genetically Defined Syngeneic Mouse Models of Ovarian Cancer as Tools for the Discovery of Combination Immunotherapy

Autorzy: Sonia Iyer, Shuang Zhang, Simge Yucel, Heiko Horn, Sean G. Smith, Ferenc Reinhardt, Esmee Hoefsmit, Bimarzhan Assatova, Julia Casado, Marie-Charlotte Meinsohn, M. Inmaculada Barrasa, George W. Bell, Fernando Pérez-Villatoro, Kaisa Huhtinen, Johanna Hynninen, Jaana Oikkonen, Pamoda M. Galhenage, Shailja Pathania, Paula T. Hammond, Benjamin G. Neel, Anniina Farkkila, David Pépin, Robert A. Weinber
Opublikowane w: Cancer Discovery, Numer 11/2, 2021, Strona(/y) 384-407, ISSN 2159-8274
Wydawca: American Association for Cancer Research Inc.
DOI: 10.1158/2159-8290.cd-20-0818

miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data

Autorzy: Hippen AA, Falco MM, Weber LM, Erkan EP, Zhang K, Doherty JA. Vähärautio A,Greene CS, Hicks SC.
Opublikowane w: PLOS Computational Biology, 2021, ISSN 1553-734X
Wydawca: Public Library of Science
DOI: 10.1371/journal.pcbi.1009290

Technical Report: Towards Prediction of Platinum Resistance from Expression Levels of Genes Related to Homologous Recombination

Autorzy: Ozisik, Ozan; Facciotto, Chiara; Häkkinen, Antti; Zhang, Kaiyang; Tumiati, Manuela; Hautaniemi, Sampsa; Schwikowski, Benno
Opublikowane w: https://hal.archives-ouvertes.fr/hal-02276581, Numer 1, 2019
Wydawca: CCSD
DOI: 10.13140/rg.2.2.18954.82883

Prediction of Platinum Resistance from Expression Levels of Genes Related to Homologous Recombination

Autorzy: Ozisik, Ozan; Facciotto, Chiara; Häkkinen, Antti; Zhang, Kaiyang; Tumiati, Manuela; Hautaniemi, Sampsa; Schwikowski, Benno
Opublikowane w: Advances and Future of High-Grade Serous Ovarian Cancer Research Symposium, Numer 1, 2019
Wydawca: CCSD
DOI: 10.13140/rg.2.2.13921.66404

The feasibility of [18F]EF5-PET/CT to image hypoxia in ovarian tumors: a clinical study

Autorzy: Maren Laasik, Johanna Hynninen, Sarita Forsback, Tommi Noponen, Marko Seppänen, Sakari Hietanen
Opublikowane w: EJNMMI Research, Numer 10/1, 2020, ISSN 2191-219X
Wydawca: Springer Berlin
DOI: 10.1186/s13550-020-00689-z

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