Abascal, Federico

Martincorena Group

Federico’s current research interest is in the study of somatic mutation to better understand cancer evolution and organism development.

The characterisation of somatic mutations allows the possibility of answering a range of questions. I am particularly interested in understanding how different genomic contexts influence mutation and evolution, and how these effects compare at the somatic (either normal or cancer cells) and germline levels. Also of interest is how mutation signatures can help understand cellular processes like DNA repair and how they relate to environmental exposure. The interplay between genomic context and mutational processes is key to unraveling adaptive evolution (causality) during cancer progression. Somatic mutation is also very promising to help understand embryonic development and the organisation of cells within tissues and organs. This is not only important to understanding cancer progression, but also to query the developmental plan for evolutionary adaptive strategies.

Publications

Alternative Splicing May Not Be the Key to Proteome Complexity.

Tress ML, Abascal F and Valencia A

Trends in biochemical sciences 2017;42;2;98-110

PUBMED: 27712956; PMC: 6526280; DOI: 10.1016/j.tibs.2016.08.008
Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx.

Abascal F, Corvelo A, Cruz F, Villanueva-Cañas JL, Vlasova A et al.

Genome biology 2016;17;1;251

PUBMED: 27964752; PMC: 5155386; DOI: 10.1186/s13059-016-1090-1
Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level.

Abascal F, Ezkurdia I, Rodriguez-Rivas J, Rodriguez JM, del Pozo A et al.

PLoS computational biology 2015;11;6;e1004325

PUBMED: 26061177; PMC: 4465641; DOI: 10.1371/journal.pcbi.1004325
The evolutionary fate of alternatively spliced homologous exons after gene duplication.

Abascal F, Tress ML and Valencia A

Genome biology and evolution 2015;7;6;1392-403

PUBMED: 25931610; PMC: 4494069; DOI: 10.1093/gbe/evv076
Alternative splicing and co-option of transposable elements: the case of TMPO/LAP2α and ZNF451 in mammals.

Abascal F, Tress ML and Valencia A

Bioinformatics (Oxford, England) 2015;31;14;2257-61

PUBMED: 25735770; PMC: 4495291; DOI: 10.1093/bioinformatics/btv132
Subfunctionalization via adaptive evolution influenced by genomic context: the case of histone chaperones ASF1a and ASF1b.

Abascal F, Corpet A, Gurard-Levin ZA, Juan D, Ochsenbein F et al.

Molecular biology and evolution 2013;30;8;1853-66

PUBMED: 23645555; DOI: 10.1093/molbev/mst086
LRRC8 proteins share a common ancestor with pannexins, and may form hexameric channels involved in cell-cell communication.

Abascal F and Zardoya R

BioEssays : news and reviews in molecular, cellular and developmental biology 2012;34;7;551-60

PUBMED: 22532330; DOI: 10.1002/bies.201100173
Evolutionary analyses of gap junction protein families.

Abascal F and Zardoya R

Biochimica et biophysica acta 2013;1828;1;4-14

PUBMED: 22366062; DOI: 10.1016/j.bbamem.2012.02.007
TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations.

Abascal F, Zardoya R and Telford MJ

Nucleic acids research 2010;38;Web Server issue;W7-13

PUBMED: 20435676; PMC: 2896173; DOI: 10.1093/nar/gkq291
Parallel evolution of the genetic code in arthropod mitochondrial genomes.

Abascal F, Posada D, Knight RD and Zardoya R

PLoS biology 2006;4;5;e127

PUBMED: 16620150; PMC: 1440934; DOI: 10.1371/journal.pbio.0040127
Automatic annotation of protein function based on family identification.

Abascal F and Valencia A

Proteins 2003;53;3;683-92

PUBMED: 14579359; DOI: 10.1002/prot.10449
Reductive genome evolution in Buchnera aphidicola.

van Ham RC, Kamerbeek J, Palacios C, Rausell C, Abascal F et al.

Proceedings of the National Academy of Sciences of the United States of America 2003;100;2;581-6

PUBMED: 12522265; PMC: 141039; DOI: 10.1073/pnas.0235981100

Few SINEs of life: Alu elements have little evidence for biological relevance despite elevated translation.

Martinez-Gomez L, Abascal F, Jungreis I, Pozo F, Kellis M et al.

NAR genomics and bioinformatics 2020;2;1;lqz023

PUBMED: 31886458; PMC: 6924539; DOI: 10.1093/nargab/lqz023
Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis.

Carlevaro-Fita J, Lanzós A, Feuerbach L, Hong C, Mas-Ponte D et al.

Communications biology 2020;3;1;56

PUBMED: 32024996; DOI: 10.1038/s42003-019-0741-7
Combined burden and functional impact tests for cancer driver discovery using DriverPower.

Shuai S, PCAWG Drivers and Functional Interpretation Working Group, Gallinger S, Stein L and PCAWG Consortium

Nature communications 2020;11;1;734

PUBMED: 32024818; DOI: 10.1038/s41467-019-13929-1
Integrative pathway enrichment analysis of multivariate omics data.

Paczkowska M, Barenboim J, Sintupisut N, Fox NS, Zhu H et al.

Nature communications 2020;11;1;735

PUBMED: 32024846; DOI: 10.1038/s41467-019-13983-9
Pathway and network analysis of more than 2500 whole cancer genomes.

Reyna MA, Haan D, Paczkowska M, Verbeke LPC, Vazquez M et al.

Nature communications 2020;11;1;729

PUBMED: 32024854; DOI: 10.1038/s41467-020-14367-0
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.

Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O et al.

Nature 2020;578;7793;102-111

PUBMED: 32025015; DOI: 10.1038/s41586-020-1965-x
Pan-cancer analysis of whole genomes.

ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium

Nature 2020;578;7793;82-93

PUBMED: 32025007; DOI: 10.1038/s41586-020-1969-6

Genomic landscape and chronological reconstruction of driver events in multiple myeloma.

Maura F, Bolli N, Angelopoulos N, Dawson KJ, Leongamornlert D et al.

Nature communications 2019;10;1;3835

PUBMED: 31444325; PMC: 6707220; DOI: 10.1038/s41467-019-11680-1

De novo assembly of English yew (Taxus baccata) transcriptome and its applications for intra- and inter-specific analyses.

Olsson S, Pinosio S, González-Martínez SC, Abascal F, Mayol M et al.

Plant molecular biology 2018;97;4-5;337-345

PUBMED: 29850988; DOI: 10.1007/s11103-018-0742-9

Alternative Splicing May Not Be the Key to Proteome Complexity.

Tress ML, Abascal F and Valencia A

Trends in biochemical sciences 2017;42;2;98-110

PUBMED: 27712956; PMC: 6526280; DOI: 10.1016/j.tibs.2016.08.008

Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx.

Abascal F, Corvelo A, Cruz F, Villanueva-Cañas JL, Vlasova A et al.

Genome biology 2016;17;1;251

PUBMED: 27964752; PMC: 5155386; DOI: 10.1186/s13059-016-1090-1

Alternative splicing and co-option of transposable elements: the case of TMPO/LAP2α and ZNF451 in mammals.

Abascal F, Tress ML and Valencia A

Bioinformatics (Oxford, England) 2015;31;14;2257-61

PUBMED: 25735770; PMC: 4495291; DOI: 10.1093/bioinformatics/btv132
Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level.

Abascal F, Ezkurdia I, Rodriguez-Rivas J, Rodriguez JM, del Pozo A et al.

PLoS computational biology 2015;11;6;e1004325

PUBMED: 26061177; PMC: 4465641; DOI: 10.1371/journal.pcbi.1004325
The evolutionary fate of alternatively spliced homologous exons after gene duplication.

Abascal F, Tress ML and Valencia A

Genome biology and evolution 2015;7;6;1392-403

PUBMED: 25931610; PMC: 4494069; DOI: 10.1093/gbe/evv076

Subfunctionalization via adaptive evolution influenced by genomic context: the case of histone chaperones ASF1a and ASF1b.

Abascal F, Corpet A, Gurard-Levin ZA, Juan D, Ochsenbein F et al.

Molecular biology and evolution 2013;30;8;1853-66

PUBMED: 23645555; DOI: 10.1093/molbev/mst086
Evolutionary analyses of gap junction protein families.

Abascal F and Zardoya R

Biochimica et biophysica acta 2013;1828;1;4-14

PUBMED: 22366062; DOI: 10.1016/j.bbamem.2012.02.007

LRRC8 proteins share a common ancestor with pannexins, and may form hexameric channels involved in cell-cell communication.

Abascal F and Zardoya R

BioEssays : news and reviews in molecular, cellular and developmental biology 2012;34;7;551-60

PUBMED: 22532330; DOI: 10.1002/bies.201100173

TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations.

Abascal F, Zardoya R and Telford MJ

Nucleic acids research 2010;38;Web Server issue;W7-13

PUBMED: 20435676; PMC: 2896173; DOI: 10.1093/nar/gkq291

Parallel evolution of the genetic code in arthropod mitochondrial genomes.

Abascal F, Posada D, Knight RD and Zardoya R

PLoS biology 2006;4;5;e127

PUBMED: 16620150; PMC: 1440934; DOI: 10.1371/journal.pbio.0040127

Automatic annotation of protein function based on family identification.

Abascal F and Valencia A

Proteins 2003;53;3;683-92

PUBMED: 14579359; DOI: 10.1002/prot.10449
Reductive genome evolution in Buchnera aphidicola.

van Ham RC, Kamerbeek J, Palacios C, Rausell C, Abascal F et al.

Proceedings of the National Academy of Sciences of the United States of America 2003;100;2;581-6

PUBMED: 12522265; PMC: 141039; DOI: 10.1073/pnas.0235981100

Career/Research Highlights

A DIRS1-like retrotransposon inserted within two genes (TMPO/LAP2alpha and ZNF451) in the ancestor of mammals and was co-opted for important new cellular functions. Interestingly, the alternative splicing of the retrotransposed sequence allowed the production of both the new and the untouched original isoforms in the two genes, which may have contributed to the success of this double colonization process.
Proteomics evidence, evolutionary conservation, protein structure and population genetics data strongly suggest that most of the annotated alternative transcripts do not code for functionally relevant proteins
Genes within genes... The subfunctionalization experienced by histone chaperones ASF1a and ASF1b in vertebrates has been influenced by genomic context and has been driven by adaptive evolution. Interestingly, ASF1a relocated into another gene (MCM9) in the ancestor of tetrapods. This relocation possibly had an additional adaptive value as both genes show opposite cell-cycle regulation programs, matching the subfunctionalization of ASF1a.
We proposed that LRRC8 proteins share a common ancestor with pannexins and may form hexameric channels involved in cell-cell communication. Recent studies have confirmed the proposed membrane topology and channel activity, revealing that LRRC8 are essential components of volume-regulated anion channels.
We found that the mitochondrial genome of some arthropods is translated according to an alternative genetic code in which the AGG codon is translated as Lys. Interestingly, this new genetic code evolved in parallel in different arthropod lineages, in a complex interplay between GC content, number of AGG codon instances and specific mutations at tRNA anticodons.

Federico Abascal | Postdoctoral Fellow