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

Informacje na temat projektu

HYPER-INSIGHT

Identyfikator umowy o grant: 757700

DOI 10.3030/757700

Projekt został zamknięty

Data podpisania przez KE 19 Września 2017

Data rozpoczęcia 1 Lutego 2018

Data zakończenia 31 Stycznia 2024

Finansowanie w ramach

• EXCELLENT SCIENCE - European Research Council (ERC)

Koszt całkowity € 1 499 812,50

Wkład UE € 1 499 812,50

Koordynowany przez

FUNDACIO INSTITUT DE RECERCA BIOMEDICA (IRB BARCELONA)
Spain

Publikacje

Peer reviewed articles (23)

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

Autorzy: Marina Salvadores, Francisco Fuster-Tormo, Fran Supek
Opublikowane w: Science Advances, Numer 6/27, 2020, Strona(/y) eaba1862, ISSN 2375-2548
Wydawca: 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

Autorzy: Josep Biayna; Isabel Garcia-Cao; Miguel M. Álvarez; Marina Salvadores; Jose Espinosa-Carrasco; Marcel McCullough; Fran Supek; Travis H. Stracker
Opublikowane w: PLoS Biology, Numer 15449173, 2022, Strona(/y) e3001176, ISSN 1544-9173
Wydawca: Public Library of Science
DOI: 10.1371/journal.pbio.3001176

The evolutionary signal in metagenome phyletic profiles predicts many gene functions

Autorzy: Vedrana Vidulin, Tomislav Šmuc, Sašo Džeroski, Fran Supek
Opublikowane w: Microbiome, Numer 6/1, 2018, ISSN 2049-2618
Wydawca: 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

Autorzy: 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
Opublikowane w: Genome Biology, Numer 20/1, 2019, ISSN 1474-760X
Wydawca: BioMed Central
DOI: 10.1186/s13059-019-1892-z

The impact of rare germline variants on human somatic mutation processes

Autorzy: Mischan Vali-Pour, Ben Lehner, Fran Supek
Opublikowane w: Nature Communications, Numer 20411723, 2022, Strona(/y) 3724, ISSN 2041-1723
Wydawca: 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

Autorzy: Marina Salvadores, Fran Supek
Opublikowane w: Nature Cancer, Numer 5, 2024, Strona(/y) 330-346, ISSN 2662-1347
Wydawca: Springer Nature
DOI: 10.1038/s43018-023-00707-8

Proton and alpha radiation-induced mutational profiles in human cells

Autorzy: Tiffany Delhomme, Maia Munteanu, Manuela Buonanno, Veljko Grilj, Josep Biayna, Fran Supek
Opublikowane w: Scientific Reports, Numer 13, 2023, Strona(/y) 9791, ISSN 2045-2322
Wydawca: Nature Publishing Group
DOI: 10.1038/s41598-023-36845-3

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

Autorzy: David Mas-Ponte, Fran Supek
Opublikowane w: Nature Genetics, Numer 52/9, 2020, Strona(/y) 958-968, ISSN 1061-4036
Wydawca: Nature Publishing Group
DOI: 10.1038/s41588-020-0674-6

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

Autorzy: Bruno Fito-Lopez, Marina Salvadores, Miguel-Martin Alvarez, Fran Supek
Opublikowane w: BMC Biology, Numer 21, 2023, Strona(/y) 92, ISSN 1741-7007
Wydawca: BioMed Central
DOI: 10.1186/s12915-023-01595-1

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

Autorzy: David Mas-Ponte, Fran Supek
Opublikowane w: Nucleic Acids Research, 2024, Strona(/y) gkae252, ISSN 0305-1048
Wydawca: 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

Autorzy: David Mas-Ponte, Marcel McCullough, Fran Supek
Opublikowane w: Clinical Science, Numer 01435221, 2022, Strona(/y) 383–404, ISSN 0143-5221
Wydawca: Portland Press, Ltd.
DOI: 10.1042/cs20210682

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

Autorzy: 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.
Opublikowane w: Nature Genetics, Numer 52/3, 2020, Strona(/y) 306-319, ISSN 1061-4036
Wydawca: 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.

Autorzy: Fran Supek; Ben Lehner; Ben Lehner; Rik G.H. Lindeboom
Opublikowane w: Trends in Genetics, Numer 01689525, 2022, Strona(/y) 657-668, ISSN 0168-9525
Wydawca: 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

Autorzy: 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
Opublikowane w: Nature Cell Biology, Numer 20/12, 2018, Strona(/y) 1400-1409, ISSN 1465-7392
Wydawca: Nature Publishing Group
DOI: 10.1038/s41556-018-0233-x

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

Autorzy: Matej Mihelčić, Tomislav Šmuc, Fran Supek
Opublikowane w: Scientific Reports, Numer 9/1, 2019, ISSN 2045-2322
Wydawca: Nature Publishing Group
DOI: 10.1038/s41598-019-55984-0

Passenger mutations accurately classify human tumors

Autorzy: Marina Salvadores, David Mas-Ponte, Fran Supek
Opublikowane w: PLOS Computational Biology, Numer 15/4, 2019, Strona(/y) e1006953, ISSN 1553-7358
Wydawca: Public Library of Science
DOI: 10.1371/journal.pcbi.1006953

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

Autorzy: Fran Supek, Ben Lehner
Opublikowane w: DNA Repair, Numer 81, 2019, Strona(/y) 102647, ISSN 1568-7864
Wydawca: Elsevier BV
DOI: 10.1016/j.dnarep.2019.102647

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

Autorzy: Rik Lindeboom, Michiel Vermeulen, Ben Lehner, Fran Supek
Opublikowane w: Nature Genetics, Numer in press, 2019, ISSN 1061-4036
Wydawca: 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

Autorzy: 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
Opublikowane w: Genome Biology, Numer 20/1, 2019, ISSN 1474-760X
Wydawca: BioMed Central
DOI: 10.1186/s13059-019-1835-8

A framework for mutational signature analysis based on DNA shape parameters

Autorzy: Aleksandra Karolak; Jurica Levatić; Fran Supek
Opublikowane w: PLoS ONE, Numer 19326203, 2022, Strona(/y) e0262495, ISSN 1932-6203
Wydawca: Public Library of Science
DOI: 10.1371/journal.pone.0262495

Mutational signatures are markers of drug sensitivity of cancer cells

Autorzy: Jurica Levatic, Marina Salvadores, Francisco Fuster-Tormo, Fran Supek
Opublikowane w: Nature Communications, Numer 20411723, 2022, Strona(/y) 2926, ISSN 2041-1723
Wydawca: 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

Autorzy: Miguel Alvarez, Josep Biayna, Fran Supek
Opublikowane w: Nature Communications, Numer 20411723, 2022, Strona(/y) 4520, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-022-32285-1

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

Autorzy: Park, Solip; Supek, Fran; Lehner, Ben; park
Opublikowane w: Nature Communications, Numer 20411723, 2021, Strona(/y) 7051, ISSN 2041-1723
Wydawca: 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

Autorzy: Guillermo Palou-Marquez, Fran Supek
Opublikowane w: bioRxiv, Numer 2024.02.29.582778, 2024, ISSN 2692-8205
Wydawca: 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

Autorzy: Elizaveta Besedina, Fran Supek
Opublikowane w: bioRxiv, Numer 2023.08.05.552104, 2023, ISSN 2692-8205
Wydawca: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.08.05.552104

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

Autorzy: Ignasi Toledano, Fran Supek, Ben Lehner
Opublikowane w: bioRxiv, Numer 2023.08.07.552350, 2023, ISSN 2692-8205
Wydawca: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.08.07.552350