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

Project Information

HERCULES

Grant agreement ID: 667403

DOI 10.3030/667403

Project closed

EC signature date 2 December 2015

Start date 1 January 2016

End date 30 June 2021

Funded under

• SOCIETAL CHALLENGES - Health, demographic change and well-being

Total cost € 5 994 868,75

EU contribution € 5 994 868,75

Coordinated by

HELSINGIN YLIOPISTO
Finland

Deliverables

Other (3)

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

Websites, patent fillings, videos etc. (2)

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

Documents, reports (3)

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

Demonstrators, pilots, prototypes (1)

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

Open Research Data Pilot (1)

Data Management Plan

Publications

Thesis and dissertations (5)

Clinical Application of Novel Circulatory Biomarkers in Epithelial Ovarian Cancer

Author(s): Salminen, Liina
Published in: 2020
Publisher: University of Turku

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

Author(s): Facciotto, Chiara
Published in: 2021, ISBN 978-951-51-7427-7
Publisher: University of Helsinki

Transcriptomics analysis and its applications in cancer

Author(s): Cervera, Alejandra
Published in: 2020, ISBN 978-951-51-6866-5
Publisher: University of Helsinki

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

Author(s): Azzalini, Eros.
Published in: 2020
Publisher: Università degli Studi di Trieste

Proteogenomics methods for translational cancer research

Author(s): Casado, Julia
Published in: 2021, ISBN 978-951-51-7220-4
Publisher: University of Helsinki

Peer reviewed articles (27)

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

Author(s): 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
Published in: Briefings in Bioinformatics, 2021, ISSN 1467-5463
Publisher: Oxford University Press
DOI: 10.1093/bib/bbab272

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

Author(s): Eros Azzalini, Nodira Abdurakhmanova, Pietro Parisse, Michele Bartoletti, Vincenzo Canzonieri, Giorgio Stanta, Loredana Casalis, Serena Bonin
Published in: Nanomedicine: Nanotechnology, Biology and Medicine, Issue 37, 2021, Page(s) 102452, ISSN 1549-9634
Publisher: Elsevier BV
DOI: 10.1016/j.nano.2021.102452

Agile workflow for interactive analysis of mass cytometry data

Author(s): 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
Published in: Bioinformatics, 2020, Page(s) 1-6, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btaa946

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

Author(s): 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
Published in: Scientific Reports, Issue 11/1, 2021, Page(s) 1-12, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-021-88382-6

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

Author(s): 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
Published in: Nature Communications, Issue 12/1, 2021, ISSN 2041-1723
Publisher: 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

Author(s): 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
Published in: Cancers, Issue 12/5, 2020, Page(s) 1175, ISSN 2072-6694
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers12051175

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

Author(s): 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
Published in: Bioinformatics, 2021, Page(s) 1-7, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btab178

Human cell transformation by combined lineage conversion and oncogene expression

Author(s): Biswajyoti Sahu, Päivi Pihlajamaa, Kaiyang Zhang, Kimmo Palin, Saija Ahonen, Alejandra Cervera, Ari Ristimäki, Lauri A. Aaltonen, Sampsa Hautaniemi, Jussi Taipale
Published in: Oncogene, 2021, ISSN 0950-9232
Publisher: Nature Publishing Group
DOI: 10.1038/s41388-021-01940-0

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

Author(s): Emilia Kozłowska, Anniina Färkkilä, Tuulia Vallius, Olli Carpén, Jukka Kemppainen, Seija Grénman, Rainer Lehtonen, Johanna Hynninen, Sakari Hietanen, Sampsa Hautaniemi
Published in: Cancer Research, Issue 78/14, 2018, Page(s) 4036-4044, ISSN 0008-5472
Publisher: 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

Author(s): J. Hynninen, M. Laasik, T. Vallius, J. Kemppainen, S. Grönroos, J. Virtanen, J. Casado, S. Hautaniemi, S. Grenman, M. Seppänen, A. Auranen
Published in: Clinical Oncology, Issue 30/8, 2018, Page(s) 507-514, ISSN 0936-6555
Publisher: W. B. Saunders Co., Ltd.
DOI: 10.1016/j.clon.2018.04.007

Identifying differentially methylated sites in samples with varying tumor purity

Author(s): Antti Häkkinen, Amjad Alkodsi, Chiara Facciotto, Kaiyang Zhang, Katja Kaipio, Sirpa Leppä, Olli Carpén, Seija Grénman, Johanna Hynninen, Sakari Hietanen, Rainer Lehtonen, Sampsa Hautaniemi
Published in: Bioinformatics, Issue 34/18, 2018, Page(s) 3078-3085, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/bty310

Network module identification—A widespread theoretical bias and best practices

Author(s): Iryna Nikolayeva, Oriol Guitart Pla, Benno Schwikowski
Published in: Methods, Issue 132, 2018, Page(s) 19-25, ISSN 1046-2023
Publisher: 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

Author(s): Maren Laasik, Jukka Kemppainen, Annika Auranen, Sakari Hietanen, Seija Grénman, Marko Seppänen, Johanna Hynninen
Published in: Cancer Imaging, Issue 19/1, 2019, ISSN 1470-7330
Publisher: Springer Nature
DOI: 10.1186/s40644-019-0215-7

Anduril 2: upgraded large-scale data integration framework

Author(s): 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
Published in: Bioinformatics, Issue 35/19, 2019, Page(s) 3815-3817, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btz133

Prospective Longitudinal ctDNA Workflow Reveals Clinically Actionable Alterations in Ovarian Cancer

Author(s): 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
Published in: JCO Precision Oncology, Issue 3, 2019, Page(s) 1-12, ISSN 2473-4284
Publisher: American Society of Clinical Oncology
DOI: 10.1200/po.18.00343

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

Author(s): Veli-Matti Isoviita, Liina Salminen, Jimmy Azar, Rainer Lehtonen, Pia Roering, Olli Carpén, Sakari Hietanen, Seija Grénman, Johanna Hynninen, Anniina Färkkilä, Sampsa Hautaniemi
Published in: JCO Clinical Cancer Informatics, Issue 3, 2019, Page(s) 1-16, ISSN 2473-4276
Publisher: American Society of Clinical Oncology
DOI: 10.1200/cci.18.00132

Virtual clinical trials identify effective combination therapies in ovarian cancer

Author(s): Emilia Kozłowska, Tuulia Vallius, Johanna Hynninen, Sakari Hietanen, Anniina Färkkilä, Sampsa Hautaniemi
Published in: Scientific Reports, Issue 9/1, 2019, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-019-55068-z

ALDH1A1‐related stemness in high‐grade serous ovarian cancer is a negative prognostic indicator but potentially targetable by EGFR/mTOR‐PI3K/aurora kinase inhibitors

Author(s): 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
Published in: The Journal of Pathology, Issue 250/2, 2019, Page(s) 159-169, ISSN 0022-3417
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/path.5356

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

Author(s): Yevhen Akimov, Daria Bulanova, Sanna Timonen, Krister Wennerberg, Tero Aittokallio
Published in: Molecular Systems Biology, Issue 16/3, 2020, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.20199195

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

Author(s): 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
Published in: Bioinformatics, 2020, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btaa637

Reliability of miRNA Analysis from Fixed and Paraffin-Embedded Tissues

Author(s): Eros Azzalini, Eleonora De Martino, Paolo Fattorini, Vincenzo Canzonieri, Giorgio Stanta, Serena Bonin
Published in: International Journal of Molecular Sciences, Issue 20/19, 2019, Page(s) 4819, ISSN 1422-0067
Publisher: 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

Author(s): 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
Published in: Clinical Cancer Research, 2018, ISSN 1078-0432
Publisher: 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

Author(s): Liina Salminen, Nimrah Nadeem, Shruti Jain, Seija Grènman, Olli Carpén, Sakari Hietanen, Sinikka Oksa, Urpo Lamminmäki, Kim Pettersson, Kamlesh Gidwani, Kaisa Huhtinen, Johanna Hynninen
Published in: Gynecologic Oncology, Issue 156/3, 2020, Page(s) 689-694, ISSN 0090-8258
Publisher: Academic Press
DOI: 10.1016/j.ygyno.2019.12.025

FUNGI: FUsioN Gene Integration toolset

Author(s): 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
Published in: Bioinformatics, 2021, Page(s) 1-3, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btab206

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

Author(s): Liina Salminen, Kamlesh Gidwani, Seija Grènman, Olli Carpén, Sakari Hietanen, Kim Pettersson, Kaisa Huhtinen, Johanna Hynninen
Published in: Acta Oncologica, Issue 59/12, 2020, Page(s) 1461-1468, ISSN 0284-186X
Publisher: Taylor & Francis
DOI: 10.1080/0284186x.2020.1827157

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

Author(s): 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
Published in: Cancer Discovery, Issue 11/2, 2021, Page(s) 384-407, ISSN 2159-8274
Publisher: 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

Author(s): Hippen AA, Falco MM, Weber LM, Erkan EP, Zhang K, Doherty JA. Vähärautio A,Greene CS, Hicks SC.
Published in: PLOS Computational Biology, 2021, ISSN 1553-734X
Publisher: Public Library of Science
DOI: 10.1371/journal.pcbi.1009290

Other (2)

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

Author(s): Ozisik, Ozan; Facciotto, Chiara; Häkkinen, Antti; Zhang, Kaiyang; Tumiati, Manuela; Hautaniemi, Sampsa; Schwikowski, Benno
Published in: https://hal.archives-ouvertes.fr/hal-02276581, Issue 1, 2019
Publisher: CCSD
DOI: 10.13140/rg.2.2.18954.82883

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

Author(s): Ozisik, Ozan; Facciotto, Chiara; Häkkinen, Antti; Zhang, Kaiyang; Tumiati, Manuela; Hautaniemi, Sampsa; Schwikowski, Benno
Published in: Advances and Future of High-Grade Serous Ovarian Cancer Research Symposium, Issue 1, 2019
Publisher: CCSD
DOI: 10.13140/rg.2.2.13921.66404

Non-peer reviewed articles (1)

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

Author(s): Maren Laasik, Johanna Hynninen, Sarita Forsback, Tommi Noponen, Marko Seppänen, Sakari Hietanen
Published in: EJNMMI Research, Issue 10/1, 2020, ISSN 2191-219X
Publisher: Springer Berlin
DOI: 10.1186/s13550-020-00689-z