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

Informazioni relative al progetto

HERCULES

ID dell’accordo di sovvenzione: 667403

DOI 10.3030/667403

Progetto chiuso

Data della firma CE 2 Dicembre 2015

Data di avvio 1 Gennaio 2016

Data di completamento 30 Giugno 2021

Finanziato da

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

Costo totale € 5 994 868,75

Contributo UE € 5 994 868,75

Coordinato da

HELSINGIN YLIOPISTO
Finland

Risultati finali

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

Pubblicazioni

Thesis and dissertations (5)

Clinical Application of Novel Circulatory Biomarkers in Epithelial Ovarian Cancer

Autori: Salminen, Liina
Pubblicato in: 2020
Editore: University of Turku

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

Autori: Facciotto, Chiara
Pubblicato in: 2021, ISBN 978-951-51-7427-7
Editore: University of Helsinki

Transcriptomics analysis and its applications in cancer

Autori: Cervera, Alejandra
Pubblicato in: 2020, ISBN 978-951-51-6866-5
Editore: University of Helsinki

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

Autori: Azzalini, Eros.
Pubblicato in: 2020
Editore: Università degli Studi di Trieste

Proteogenomics methods for translational cancer research

Autori: Casado, Julia
Pubblicato in: 2021, ISBN 978-951-51-7220-4
Editore: University of Helsinki

Peer reviewed articles (27)

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

Autori: 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
Pubblicato in: Briefings in Bioinformatics, 2021, ISSN 1467-5463
Editore: Oxford University Press
DOI: 10.1093/bib/bbab272

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

Autori: Eros Azzalini, Nodira Abdurakhmanova, Pietro Parisse, Michele Bartoletti, Vincenzo Canzonieri, Giorgio Stanta, Loredana Casalis, Serena Bonin
Pubblicato in: Nanomedicine: Nanotechnology, Biology and Medicine, Numero 37, 2021, Pagina/e 102452, ISSN 1549-9634
Editore: Elsevier BV
DOI: 10.1016/j.nano.2021.102452

Agile workflow for interactive analysis of mass cytometry data

Autori: 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
Pubblicato in: Bioinformatics, 2020, Pagina/e 1-6, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btaa946

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

Autori: 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
Pubblicato in: Scientific Reports, Numero 11/1, 2021, Pagina/e 1-12, ISSN 2045-2322
Editore: Nature Publishing Group
DOI: 10.1038/s41598-021-88382-6

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

Autori: 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
Pubblicato in: Nature Communications, Numero 12/1, 2021, ISSN 2041-1723
Editore: 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

Autori: 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
Pubblicato in: Cancers, Numero 12/5, 2020, Pagina/e 1175, ISSN 2072-6694
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers12051175

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

Autori: 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
Pubblicato in: Bioinformatics, 2021, Pagina/e 1-7, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btab178

Human cell transformation by combined lineage conversion and oncogene expression

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

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

Autori: Emilia Kozłowska, Anniina Färkkilä, Tuulia Vallius, Olli Carpén, Jukka Kemppainen, Seija Grénman, Rainer Lehtonen, Johanna Hynninen, Sakari Hietanen, Sampsa Hautaniemi
Pubblicato in: Cancer Research, Numero 78/14, 2018, Pagina/e 4036-4044, ISSN 0008-5472
Editore: 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

Autori: J. Hynninen, M. Laasik, T. Vallius, J. Kemppainen, S. Grönroos, J. Virtanen, J. Casado, S. Hautaniemi, S. Grenman, M. Seppänen, A. Auranen
Pubblicato in: Clinical Oncology, Numero 30/8, 2018, Pagina/e 507-514, ISSN 0936-6555
Editore: W. B. Saunders Co., Ltd.
DOI: 10.1016/j.clon.2018.04.007

Identifying differentially methylated sites in samples with varying tumor purity

Autori: Antti Häkkinen, Amjad Alkodsi, Chiara Facciotto, Kaiyang Zhang, Katja Kaipio, Sirpa Leppä, Olli Carpén, Seija Grénman, Johanna Hynninen, Sakari Hietanen, Rainer Lehtonen, Sampsa Hautaniemi
Pubblicato in: Bioinformatics, Numero 34/18, 2018, Pagina/e 3078-3085, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/bty310

Network module identification—A widespread theoretical bias and best practices

Autori: Iryna Nikolayeva, Oriol Guitart Pla, Benno Schwikowski
Pubblicato in: Methods, Numero 132, 2018, Pagina/e 19-25, ISSN 1046-2023
Editore: 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

Autori: Maren Laasik, Jukka Kemppainen, Annika Auranen, Sakari Hietanen, Seija Grénman, Marko Seppänen, Johanna Hynninen
Pubblicato in: Cancer Imaging, Numero 19/1, 2019, ISSN 1470-7330
Editore: Springer Nature
DOI: 10.1186/s40644-019-0215-7

Anduril 2: upgraded large-scale data integration framework

Autori: 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
Pubblicato in: Bioinformatics, Numero 35/19, 2019, Pagina/e 3815-3817, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btz133

Prospective Longitudinal ctDNA Workflow Reveals Clinically Actionable Alterations in Ovarian Cancer

Autori: 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
Pubblicato in: JCO Precision Oncology, Numero 3, 2019, Pagina/e 1-12, ISSN 2473-4284
Editore: American Society of Clinical Oncology
DOI: 10.1200/po.18.00343

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

Autori: Veli-Matti Isoviita, Liina Salminen, Jimmy Azar, Rainer Lehtonen, Pia Roering, Olli Carpén, Sakari Hietanen, Seija Grénman, Johanna Hynninen, Anniina Färkkilä, Sampsa Hautaniemi
Pubblicato in: JCO Clinical Cancer Informatics, Numero 3, 2019, Pagina/e 1-16, ISSN 2473-4276
Editore: American Society of Clinical Oncology
DOI: 10.1200/cci.18.00132

Virtual clinical trials identify effective combination therapies in ovarian cancer

Autori: Emilia Kozłowska, Tuulia Vallius, Johanna Hynninen, Sakari Hietanen, Anniina Färkkilä, Sampsa Hautaniemi
Pubblicato in: Scientific Reports, Numero 9/1, 2019, ISSN 2045-2322
Editore: 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

Autori: 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
Pubblicato in: The Journal of Pathology, Numero 250/2, 2019, Pagina/e 159-169, ISSN 0022-3417
Editore: John Wiley & Sons Inc.
DOI: 10.1002/path.5356

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

Autori: Yevhen Akimov, Daria Bulanova, Sanna Timonen, Krister Wennerberg, Tero Aittokallio
Pubblicato in: Molecular Systems Biology, Numero 16/3, 2020, ISSN 1744-4292
Editore: Nature Publishing Group
DOI: 10.15252/msb.20199195

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

Autori: 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
Pubblicato in: Bioinformatics, 2020, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btaa637

Reliability of miRNA Analysis from Fixed and Paraffin-Embedded Tissues

Autori: Eros Azzalini, Eleonora De Martino, Paolo Fattorini, Vincenzo Canzonieri, Giorgio Stanta, Serena Bonin
Pubblicato in: International Journal of Molecular Sciences, Numero 20/19, 2019, Pagina/e 4819, ISSN 1422-0067
Editore: 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

Autori: 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
Pubblicato in: Clinical Cancer Research, 2018, ISSN 1078-0432
Editore: 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

Autori: Liina Salminen, Nimrah Nadeem, Shruti Jain, Seija Grènman, Olli Carpén, Sakari Hietanen, Sinikka Oksa, Urpo Lamminmäki, Kim Pettersson, Kamlesh Gidwani, Kaisa Huhtinen, Johanna Hynninen
Pubblicato in: Gynecologic Oncology, Numero 156/3, 2020, Pagina/e 689-694, ISSN 0090-8258
Editore: Academic Press
DOI: 10.1016/j.ygyno.2019.12.025

FUNGI: FUsioN Gene Integration toolset

Autori: 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
Pubblicato in: Bioinformatics, 2021, Pagina/e 1-3, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btab206

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

Autori: Liina Salminen, Kamlesh Gidwani, Seija Grènman, Olli Carpén, Sakari Hietanen, Kim Pettersson, Kaisa Huhtinen, Johanna Hynninen
Pubblicato in: Acta Oncologica, Numero 59/12, 2020, Pagina/e 1461-1468, ISSN 0284-186X
Editore: Taylor & Francis
DOI: 10.1080/0284186x.2020.1827157

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

Autori: 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
Pubblicato in: Cancer Discovery, Numero 11/2, 2021, Pagina/e 384-407, ISSN 2159-8274
Editore: 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

Autori: Hippen AA, Falco MM, Weber LM, Erkan EP, Zhang K, Doherty JA. Vähärautio A,Greene CS, Hicks SC.
Pubblicato in: PLOS Computational Biology, 2021, ISSN 1553-734X
Editore: 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

Autori: Ozisik, Ozan; Facciotto, Chiara; Häkkinen, Antti; Zhang, Kaiyang; Tumiati, Manuela; Hautaniemi, Sampsa; Schwikowski, Benno
Pubblicato in: https://hal.archives-ouvertes.fr/hal-02276581, Numero 1, 2019
Editore: CCSD
DOI: 10.13140/rg.2.2.18954.82883

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

Autori: Ozisik, Ozan; Facciotto, Chiara; Häkkinen, Antti; Zhang, Kaiyang; Tumiati, Manuela; Hautaniemi, Sampsa; Schwikowski, Benno
Pubblicato in: Advances and Future of High-Grade Serous Ovarian Cancer Research Symposium, Numero 1, 2019
Editore: 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

Autori: Maren Laasik, Johanna Hynninen, Sarita Forsback, Tommi Noponen, Marko Seppänen, Sakari Hietanen
Pubblicato in: EJNMMI Research, Numero 10/1, 2020, ISSN 2191-219X
Editore: Springer Berlin
DOI: 10.1186/s13550-020-00689-z