Hypermutated tumors: insight into genome maintenance and cancer vulnerabilities provided by an extreme burden of somatic mutations

Informazioni relative al progetto

HYPER-INSIGHT

ID dell’accordo di sovvenzione: 757700

DOI 10.3030/757700

Progetto chiuso

Data della firma CE 19 Settembre 2017

Data di avvio 1 Febbraio 2018

Data di completamento 31 Gennaio 2024

Finanziato da

• EXCELLENT SCIENCE - European Research Council (ERC)

Costo totale € 1 499 812,50

Contributo UE € 1 499 812,50

Coordinato da

FUNDACIO INSTITUT DE RECERCA BIOMEDICA (IRB BARCELONA)
Spain

Pubblicazioni

Peer reviewed articles (23)

Matching cell lines with cancer type and subtype of origin via mutational, epigenomic, and transcriptomic patterns

Autori: Marina Salvadores, Francisco Fuster-Tormo, Fran Supek
Pubblicato in: Science Advances, Numero 6/27, 2020, Pagina/e eaba1862, ISSN 2375-2548
Editore: American Association for the Advancement of Science
DOI: 10.1126/sciadv.aba1862

Loss of the abasic site sensor HMCES is synthetic lethal with the activity of the APOBEC3A cytosine deaminase in cancer cells

Autori: Josep Biayna; Isabel Garcia-Cao; Miguel M. Álvarez; Marina Salvadores; Jose Espinosa-Carrasco; Marcel McCullough; Fran Supek; Travis H. Stracker
Pubblicato in: PLoS Biology, Numero 15449173, 2022, Pagina/e e3001176, ISSN 1544-9173
Editore: Public Library of Science
DOI: 10.1371/journal.pbio.3001176

The evolutionary signal in metagenome phyletic profiles predicts many gene functions

Autori: Vedrana Vidulin, Tomislav Šmuc, Sašo Džeroski, Fran Supek
Pubblicato in: Microbiome, Numero 6/1, 2018, ISSN 2049-2618
Editore: BioMed Central
DOI: 10.1186/s40168-018-0506-4

Whole genome DNA sequencing provides an atlas of somatic mutagenesis in healthy human cells and identifies a tumor-prone cell type

Autori: Irene Franco, Hafdis T. Helgadottir, Aldo Moggio, Malin Larsson, Peter Vrtačnik, Anna Johansson, Nina Norgren, Pär Lundin, David Mas-Ponte, Johan Nordström, Torbjörn Lundgren, Peter Stenvinkel, Lars Wennberg, Fran Supek, Maria Eriksson
Pubblicato in: Genome Biology, Numero 20/1, 2019, ISSN 1474-760X
Editore: BioMed Central
DOI: 10.1186/s13059-019-1892-z

The impact of rare germline variants on human somatic mutation processes

Autori: Mischan Vali-Pour, Ben Lehner, Fran Supek
Pubblicato in: Nature Communications, Numero 20411723, 2022, Pagina/e 3724, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-022-31483-1

Cell cycle gene alterations associate with a redistribution of mutation risk across chromosomal domains in human cancers

Autori: Marina Salvadores, Fran Supek
Pubblicato in: Nature Cancer, Numero 5, 2024, Pagina/e 330-346, ISSN 2662-1347
Editore: Springer Nature
DOI: 10.1038/s43018-023-00707-8

Proton and alpha radiation-induced mutational profiles in human cells

Autori: Tiffany Delhomme, Maia Munteanu, Manuela Buonanno, Veljko Grilj, Josep Biayna, Fran Supek
Pubblicato in: Scientific Reports, Numero 13, 2023, Pagina/e 9791, ISSN 2045-2322
Editore: Nature Publishing Group
DOI: 10.1038/s41598-023-36845-3

DNA mismatch repair promotes APOBEC3-mediated diffuse hypermutation in human cancers

Autori: David Mas-Ponte, Fran Supek
Pubblicato in: Nature Genetics, Numero 52/9, 2020, Pagina/e 958-968, ISSN 1061-4036
Editore: Nature Publishing Group
DOI: 10.1038/s41588-020-0674-6

Prevalence, causes and impact of TP53-loss phenocopying events in human tumors

Autori: Bruno Fito-Lopez, Marina Salvadores, Miguel-Martin Alvarez, Fran Supek
Pubblicato in: BMC Biology, Numero 21, 2023, Pagina/e 92, ISSN 1741-7007
Editore: BioMed Central
DOI: 10.1186/s12915-023-01595-1

Mutation rate heterogeneity at the sub-gene scale due to local DNA hypomethylation

Autori: David Mas-Ponte, Fran Supek
Pubblicato in: Nucleic Acids Research, 2024, Pagina/e gkae252, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkae252

Spectrum of DNA mismatch repair failures viewed through the lens of cancer genomics and implications for therapy

Autori: David Mas-Ponte, Marcel McCullough, Fran Supek
Pubblicato in: Clinical Science, Numero 01435221, 2022, Pagina/e 383–404, ISSN 0143-5221
Editore: Portland Press, Ltd.
DOI: 10.1042/cs20210682

Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

Autori: Bernardo Rodriguez-Martin, Eva G. Alvarez, Adrian Baez-Ortega, Jorge Zamora, Fran Supek, Jonas Demeulemeester, Martin Santamarina, Young Seok Ju, Javier Temes, Daniel Garcia-Souto, Harald Detering, Yilong Li, Jorge Rodriguez-Castro, Ana Dueso-Barroso, Alicia L. Bruzos, Stefan C. Dentro, Miguel G. Blanco, Gianmarco Contino, Daniel Ardeljan, Marta Tojo, Nicola D. Roberts, Sonia Zumalave, Paul A. W.
Pubblicato in: Nature Genetics, Numero 52/3, 2020, Pagina/e 306-319, ISSN 1061-4036
Editore: Nature Publishing Group
DOI: 10.1038/s41588-019-0562-0

To NMD or Not To NMD: Nonsense-Mediated mRNA Decay in Cancer and Other Genetic Diseases.

Autori: Fran Supek; Ben Lehner; Ben Lehner; Rik G.H. Lindeboom
Pubblicato in: Trends in Genetics, Numero 01689525, 2022, Pagina/e 657-668, ISSN 0168-9525
Editore: Elsevier BV
DOI: 10.1016/j.tig.2020.11.002

Loss of G9a preserves mutation patterns but increases chromatin accessibility, genomic instability and aggressiveness in skin tumours

Autori: Alexandra Avgustinova, Aikaterini Symeonidi, Andrés Castellanos, Uxue Urdiroz-Urricelqui, Llorenç Solé-Boldo, Mercè Martín, Ivan Pérez-Rodríguez, Neus Prats, Ben Lehner, Fran Supek, Salvador Aznar Benitah
Pubblicato in: Nature Cell Biology, Numero 20/12, 2018, Pagina/e 1400-1409, ISSN 1465-7392
Editore: Nature Publishing Group
DOI: 10.1038/s41556-018-0233-x

Patterns of diverse gene functions in genomic neighborhoods predict gene function and phenotype

Autori: Matej Mihelčić, Tomislav Šmuc, Fran Supek
Pubblicato in: Scientific Reports, Numero 9/1, 2019, ISSN 2045-2322
Editore: Nature Publishing Group
DOI: 10.1038/s41598-019-55984-0

Passenger mutations accurately classify human tumors

Autori: Marina Salvadores, David Mas-Ponte, Fran Supek
Pubblicato in: PLOS Computational Biology, Numero 15/4, 2019, Pagina/e e1006953, ISSN 1553-7358
Editore: Public Library of Science
DOI: 10.1371/journal.pcbi.1006953

Scales and mechanisms of somatic mutation rate variation across the human genome

Autori: Fran Supek, Ben Lehner
Pubblicato in: DNA Repair, Numero 81, 2019, Pagina/e 102647, ISSN 1568-7864
Editore: Elsevier BV
DOI: 10.1016/j.dnarep.2019.102647

The impact of nonsense-mediated mRNA decay on genetic disease, gene editing and cancer immunotherapy

Autori: Rik Lindeboom, Michiel Vermeulen, Ben Lehner, Fran Supek
Pubblicato in: Nature Genetics, Numero in press, 2019, ISSN 1061-4036
Editore: Nature Publishing Group
DOI: 10.1038/s41588-019-0517-5

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Autori: Naihui Zhou, Yuxiang Jiang, Timothy R. Bergquist, Alexandra J. Lee, Balint Z. Kacsoh, Alex W. Crocker, Kimberley A. Lewis, George Georghiou, Huy N. Nguyen, Md Nafiz Hamid, Larry Davis, Tunca Dogan, Volkan Atalay, Ahmet S. Rifaioglu, Alperen Dalkıran, Rengul Cetin Atalay, Chengxin Zhang, Rebecca L. Hurto, Peter L. Freddolino, Yang Zhang, Prajwal Bhat, Fran Supek, José M. Fernández, Branislava Ge
Pubblicato in: Genome Biology, Numero 20/1, 2019, ISSN 1474-760X
Editore: BioMed Central
DOI: 10.1186/s13059-019-1835-8

A framework for mutational signature analysis based on DNA shape parameters

Autori: Aleksandra Karolak; Jurica Levatić; Fran Supek
Pubblicato in: PLoS ONE, Numero 19326203, 2022, Pagina/e e0262495, ISSN 1932-6203
Editore: Public Library of Science
DOI: 10.1371/journal.pone.0262495

Mutational signatures are markers of drug sensitivity of cancer cells

Autori: Jurica Levatic, Marina Salvadores, Francisco Fuster-Tormo, Fran Supek
Pubblicato in: Nature Communications, Numero 20411723, 2022, Pagina/e 2926, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-022-30582-3

TP53-dependent toxicity of CRISPR/Cas9 cuts is differential across genomic loci and can confound genetic screening

Autori: Miguel Alvarez, Josep Biayna, Fran Supek
Pubblicato in: Nature Communications, Numero 20411723, 2022, Pagina/e 4520, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-022-32285-1

Higher order genetic interactions switch cancer genes from two-hit to one-hit drivers.

Autori: Park, Solip; Supek, Fran; Lehner, Ben; park
Pubblicato in: Nature Communications, Numero 20411723, 2021, Pagina/e 7051, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-021-27242-3

Other (3)

Variable efficiency of nonsense-mediated mRNA decay across human tissues, tumors and individuals

Autori: Guillermo Palou-Marquez, Fran Supek
Pubblicato in: bioRxiv, Numero 2024.02.29.582778, 2024, ISSN 2692-8205
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.02.29.582778

Copy number losses of oncogenes and gains of tumor suppressor genes generate common driver events of human cancer

Autori: Elizaveta Besedina, Fran Supek
Pubblicato in: bioRxiv, Numero 2023.08.05.552104, 2023, ISSN 2692-8205
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.08.05.552104

Genome-scale quantification and prediction of pathogenic stop codon readthrough by small molecules

Autori: Ignasi Toledano, Fran Supek, Ben Lehner
Pubblicato in: bioRxiv, Numero 2023.08.07.552350, 2023, ISSN 2692-8205
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.08.07.552350