RESISTANCE UNDER COMBINATORIAL TREATMENT IN ER+ AND ER- BREAST CANCER.

Risultati finali

MTD Assessment protocol.

For standardized MTD assessments in drug combination studies

Performance of the segmentation and IG approach on images.

Trained network and report on performance of the segmentation and IG approach on images.

Quality plan & risk registry

Quality plan & risk registry, used to monitor risks and assess quality/timing of results.

Data Integration Report

Data integration report Describing the data integration process from existing datasets from CTs

Dissemination Plan

Dissemination Plan, describing the actions foreseen for dissemination and reporting on the dissemination framework established for the project.

Data management database

Data management database with front end ready.

Bayesian modelling framework for predicting drug synergies

An open-source software implementation of the developed Bayesian modelling framework for predicting drug synergistic effects in drug combination experiments

Data management plan

The DMP needs to be updated over the course of the project whenever significant changes arise, such as (but not limited to): - new data - changes in consortium policies (e.g. new innovation potential, decision to file for a patent) - changes in consortium composition and external factors (e.g. new consortium members joining or old members leaving).

Pubblicazioni

Correlative Biomarker Analysis of Intrinsic Subtypes and Efficacy Across the MONALEESA Phase III Studies

Autori: Aleix Prat; Anwesha Chaudhury; Nadia Solovieff; Laia Paré; D. Martinez; Nuria Chic; Olga Martínez-Sáez; Fara Brasó-Maristany; Agnes Lteif; Tetiana Taran; Naveen Babbar; Fei Su
Pubblicato in: J Clin Oncol., Numero 1, 2021, ISSN 1527-7755
Editore: American Society of Clinical Oncology
DOI: 10.1200/jco.20.02977

A scalable solver for a stochastic, hybrid cellular automaton model of personalized breast cancer therapy.

Autori: Xiaoran Lai; Håkon A. Taskén; Torgeir Mo; Simon W. Funke; Arnoldo Frigessi; Arnoldo Frigessi; Marie E. Rognes; Alvaro Köhn-Luque
Pubblicato in: International Journal for Numerical Methods in Biomedical Engineering, Numero 16, 2021, Pagina/e e3542, ISSN 2040-7939
Editore: John Wiley & Sons Ltd.
DOI: 10.48550/arxiv.2105.00448

bayesynergy: flexible Bayesian modelling of synergistic interaction effects in in vitro drug combination experiments

Autori: Leiv Rønneberg, Andrea Cremaschi, Robert Hanes, Jorrit M Enserink, Manuela Zucknick
Pubblicato in: Briefings in Bioinformatics, 2021, ISSN 1467-5463
Editore: Oxford University Press
DOI: 10.1093/bib/bbab251

A Prognostic Model Based on PAM50 and Clinical Variables (PAM50MET) for Metastatic Hormone Receptor–positive HER2-negative Breast Cancer

Autori: Aleix Prat, Yi-Hsuan Tsai, Tomás Pascual, Laia Paré, Barbara Adamo, Maria Vidal, Fara Brasó-Maristany, Patricia Galván, Jan Christoph Brase, Vanessa Rodrik-Outmezguine, Stephen Johnston, Eva Ciruelos, Joel S. Parker
Pubblicato in: Clinical Cancer Research, Numero 26/23, 2020, Pagina/e 6141-6148, ISSN 1078-0432
Editore: American Association for Cancer Research
DOI: 10.1158/1078-0432.ccr-20-2793

FGFR4 regulates tumor subtype differentiation in luminal breast cancer and metastatic disease

Autori: Susana García-Recio; Aatish Thennavan; Michael P. East; Joel S. Parker; Juan Miguel Cejalvo; Joseph P. Garay; Daniel P. Hollern; Xiaping He; Kevin R. Mott; Patricia Galván; Cheng Fan; Sara R. Selitsky; Alisha R. Coffey; David Marron; Fara Brasó-Maristany; Octavio Burgues; Joan Albanell; Federico Rojo; Ana Lluch; Eduardo Martínez de Dueñas; Jeffery M. Rosen; Gary L. Johnson; Lisa A. Carey; Ale
Pubblicato in: instname:, Numero 12, 2020, ISSN 0021-9738
Editore: American Society for Clinical Investigation
DOI: 10.1172/jci130323

Intrinsic subtypes and therapeutic decision-making in hormone receptor-positive/HER2-negative metastatic breast cancer with visceral crisis: A case report

Autori: Francesco Schettini, Elia Seguí, Benedetta Conte, Esther Sanfeliu, Blanca Gonzalez-Farre , Pedro Jares , Sergi Vidal-Sicart , Sergi Ganau , Isaac Cebrecos, Fara Brasó-Maristany , Montserrat Muñoz, Aleix Prat, Maria Vidal
Pubblicato in: Frontiers Oncol., Numero 12, 2022, ISSN 2234-943X
Editore: Frontiers Media S. A.
DOI: 10.3389/fonc.2022.1009352

Quantification of Tumor Hypoxia through Unsupervised Modelling of Consumption and Supply Hypoxia MR Imaging in Breast Cancer

Autori: Torgeir Mo; Siri Helene Bertelsen Brandal; Alvaro Köhn-Luque; Olav Engebraaten; Vessela N. Kristensen; Thomas Fleischer; Tord Hompland; Therese Seierstad
Pubblicato in: Cancers; Volume 14; Numero 5; Pages: 1326, Numero 3, 2022, ISSN 2072-6694
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers14051326

Efficient gene expression signature for a breast cancer immuno-subtype

Autori: Ben Galili, Xavier Tekpli, Vessela N. Kristensen, Zohar Yakhini
Pubblicato in: PLOS ONE, Numero 16/1, 2021, Pagina/e e0245215, ISSN 1932-6203
Editore: Public Library of Science
DOI: 10.1371/journal.pone.0245215

EnrichIntersect: an R package for custom set enrichment analysis and interactive visualization of intersecting sets

Autori: Zhi Zhao, Manuela Zucknick, Tero Aittokallio
Pubblicato in: Bioinformatics Advances, Numero 2(1), 2022, Pagina/e vbac073, ISSN 2635-0041
Editore: Oxford Academic
DOI: 10.1093/bioadv/vbac073

Compressive stress-mediated p38 activation required for ERα + phenotype in breast cancer

Autori: Pauliina M, Munne; Lahja, Martikainen; Iiris, Räty; Kia, Bertula; , Nonappa; Janika, Ruuska; Hanna, Ala-Hongisto; Aino, Peura; Babette, Hollmann; Lilya, Euro; Kerim, Yavuz; Linda, Patrikainen; Maria, Salmela; Juho, Pokki; Mikko, Kivento; Juho, Väänänen; Tomi, Suomi; Liina, Nevalaita; Minna, Mutka; Panu, Kovanen; Marjut, Leidenius; Tuomo, Meretoja; Katja, Hukkinen; Outi, Monni; Jeroen, Pouwels;
Pubblicato in: Nature Communications, Numero 14, 2022, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-021-27220-9

Multiple kernel learning for integrative consensus clustering of omic datasets

Autori: Alessandra Cabassi, Paul D W Kirk
Pubblicato in: Bioinformatics, Numero 36/18, 2020, Pagina/e 4789-4796, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btaa593

Tissue-specific identification of multi-omics features for pan-cancer drug response prediction

Autori: Zhi Zhao, Shixiong Wang, Manuela Zucknick, Tero Aittokallio
Pubblicato in: iScience, Numero 25(8), 2022, Pagina/e 104767, ISSN 2589-0042
Editore: Cell Press
DOI: 10.1016/j.isci.2022.104767

POIBM: batch correction of heterogeneous RNA-seq datasets through latent sample matching.

Autori: Susanna Holmström, Sampsa Hautaniemi, Antti Häkkinen
Pubblicato in: Bioinformatics, 2022, ISSN 1460-2059
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btac124

screenwerk: a modular tool for the design and analysis of drug combination screens

Autori: Robert Hanes, Pilar Ayuda-Durán, Leiv Rønneberg, Sigve Nakken, Eivind Hovig, Manuela Zucknick, Jorrit M Enserink
Pubblicato in: Bioinformatics, Numero btac840, 2022, Pagina/e 1-3, ISSN 1477-4054
Editore: Oxford Academic
DOI: 10.1093/bioinformatics/btac840

Spatial transcriptomics inferred from pathology whole-slide images links tumor heterogeneity to survival in breast and lung cancer

Autori: Alona Levy-Jurgenson, Xavier Tekpli, Vessela N. Kristensen, Zohar Yakhini
Pubblicato in: Scientific Reports, Numero 10/1, 2020, ISSN 2045-2322
Editore: Nature Publishing Group
DOI: 10.1038/s41598-020-75708-z

Decitabine potentiates efficacy of doxorubicin in a preclinical trastuzumab-resistant HER2-positive breast cancer models

Autori: Verona Buocikova, Eleonora Marta Longhin, Eleftherios Pilalis, Chara Mastrokalou, Svetlana Miklikova, Marina Cihova, et al.
Pubblicato in: Biomedicine & Pharmacotherapy, Numero Volume 147, March 2022, 112662, 2022, ISSN 1950-6007
Editore: Elsevier
DOI: 10.1016/j.biopha.2022.112662

Assessment of the WAP-Myc mouse mammary tumor model for spontaneous metastasis

Autori: Begüm Utz, Rita Turpin, Johanna Lampe, Jeroen Pouwels, Juha Klefström
Pubblicato in: Scientific Reports, Numero 10/1, 2020, ISSN 2045-2322
Editore: Nature Publishing Group
DOI: 10.1038/s41598-020-75411-z

BayesSUR: An R Package for High-Dimensional Multivariate Bayesian Variable and Covariance Selection in Linear Regression

Autori: Zhi Zhao; Marco Banterle; Leonardo Bottolo; Sylvia Richardson; Alex Lewin; Manuela Zucknick
Pubblicato in: Journal of Statistical Software; Vol. 100 (2021); 1 - 32, Numero 4, 2021, ISSN 1548-7660
Editore: University of California at Los Angeles
DOI: 10.48550/arxiv.2104.14008

Topological approximate Bayesian computation for parameter inference of an angiogenesis model

Autori: Thomas Thorne, Paul D W Kirk, Heather A Harrington
Pubblicato in: Bioinformatics, Numero btac118, 2020, Pagina/e 2529–2535, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btac118

12P Gene expression profiling in early breast cancer treated with neoadjuvant ribociclib plus letrozole (R+L) versus chemotherapy (CT): A correlative analysis of the SOLTI-1402/CORALLEEN phase II trial

Autori: Nuria Chic; Blanca Gonzalez-Farre; Laia Paré; T. Pascual; Cristina Saura; C. Hernando Melia; Montse Muñoz; Pascual Fernández; Dianny Martínez; Esther Sanfeliu; Fara Brasó-Maristany; X. González-Farré; Mafalda Oliveira; Miguel Gil-Gil; Pamela Céliz; E.M. Ciruelos; Patricia Villagrasa; J. Gavila Gregori; Andreu Prat
Pubblicato in: Annals of Oncology, Numero 13, 2020, ISSN 0923-7534
Editore: Oxford University Press
DOI: 10.1016/j.annonc.2020.03.148

Clinical implications of the intrinsic molecular subtypes in hormone receptor-positive and HER2-negative metastatic breast cancer

Autori: Claudette Falato; Francesco Schettini; Tomás Pascual; Fara Brasó-Maristany; Aleix Prat
Pubblicato in: cancer treatment reviews, Numero 9, 2022, ISSN 0305-7372
Editore: W. B. Saunders Co., Ltd.
DOI: 10.1016/j.ctrv.2022.102496

ERBB2 mRNA Expression and Response to Ado-Trastuzumab Emtansine (T-DM1) in HER2-Positive Breast Cancer.

Autori: Gaia Griguolo; Fara Brasó-Maristany; Blanca Gonzalez-Farre; Tomás Pascual; Nuria Chic; Tamara Saurí; Ronald E. Kates; Oleg Gluz; D. Martinez; Laia Paré; Vassilena Tsvetkova; David Pesantez; Maria Vidal; Barbara Adamo; Montserrat Muñoz; Patricia Galván; Laura Barberá; Miriam Cuatrecasas; Mathias Christgen; Hans Kreipe; Inés Monge-Escartín; Patricia Villagrasa; Dolors Soy; Tommaso Giarratan
Pubblicato in: Cancers (Basel), Numero 11, 2020, ISSN 2072-6694
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers12071902

A single-cell map of intratumoral changes during anti-PD1 treatment of patients with breast cancer

Autori: Ayse Bassez, Hanne Vos, Laurien Van Dyck, Giuseppe Floris, Ingrid Arijs, Christine Desmedt, Bram Boeckx, Marlies Vanden Bempt, Ines Nevelsteen, Kathleen Lambein, Kevin Punie, Patrick Neven, Abhishek D. Garg, Hans Wildiers, Junbin Qian, Ann Smeets, Diether Lambrechts
Pubblicato in: Nature Medicine, Numero 27/5, 2021, Pagina/e 820-832, ISSN 1078-8956
Editore: Nature Publishing Group
DOI: 10.1038/s41591-021-01323-8

A perspective on the development and lack of interchangeability of the breast cancer intrinsic subtypes

Autori: Francesco Schettini, Fara Brasó-Maristany, Nicole M. Kuderer & Aleix Prat
Pubblicato in: npj breast cancer, Numero 8:85, 2022, ISSN 2374-4677
Editore: Springer Nature
DOI: 10.1038/s41523-022-00451-9

Tailored Bayes: a risk modeling framework under unequal misclassification costs

Autori: Solon Karapanagiotis, Umberto Benedetto, Sach Mukherjee, Paul D W Kirk, Paul J Newcombe
Pubblicato in: Biostatistics, 2021, ISSN 1465-4644
Editore: Oxford University Press
DOI: 10.1093/biostatistics/kxab023

ABC of the future

Autori: Henri Pesonen, Umberto Simola, Alvaro Köhn-Luque, Henri Vuollekoski, Xiaoran Lai, Arnoldo Frigessi, Samuel Kaski, David T. Frazier, Worapree Maneesoonthorn, Gael M. Martin, Jukka Corander
Pubblicato in: International Statistical Review, Numero n/a, 2022, Pagina/e n/a, ISSN 1751-5823
Editore: Wiley
DOI: 10.1111/insr.12522

Gene expression profiles of breast cancer metastasis according to organ site

Autori: Fara Brasó-Maristany; Laia Paré; Nuria Chic; Olga Martínez-Sáez; Tomás Pascual; Meritxell Mallafre-Larrosa; Francesco Schettini; Blanca Gonzalez-Farre; Esther Sanfeliu; D. Martinez; Patricia Galván; Esther Barnadas; Belinda Salinas; P. Tolosa; Eva Ciruelos; Esther Carcelero; Cecilia Guillen; Barbara Adamo; Reinaldo Moreno; Maria Vidal; Montserrat Muñoz; Aleix Prat
Pubblicato in: Molecular Oncology, Numero 8, 2021, ISSN 1574-7891
Editore: Elsevier BV
DOI: 10.1002/1878-0261.13021

Dose-response prediction for in-vitro drug combination datasets: a probabilistic approach

Autori: Leiv Rønneberg, Paul D.W. Kirk, Manuela Zucknick
Pubblicato in: ResearchSquare, Numero rs-1465185, 2022, Pagina/e 2529–2535, ISSN 2693-5015
Editore: Research Square Platform LLC
DOI: 10.21203/rs.3.rs-1465185/v2

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