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Articles by Federico Abascal
Extensive and differential platinum chemotherapy mutagenesis in livers of children
Editor’s summary Structured Abstract Abstract Supplementary Materials References and Notes Information & Authors Metrics & Citations Check Access References Figures Tables Media Share This article has 0 eLetter . Editor’s summary Pediatric cancers are now more treatable than they have ever been before, but the treatments come with their own risks. Survivors of pediatric cancer can experience multiple long-term health consequences, some of which are not fully understood.
“¿No habréis montado un Watergate?”. Así se logró la gran exclusiva de la Transición
¿Por qué un texto que afecta a todos se mantiene oculto? Es la pregunta que se hizo la redacción de ‘Cuadernos para el diálogo’ en 1977, ante el secretismo que rodeaba el proyecto de la Constitución. Tres periodistas lograron hacerse con el borrador de la ley fundamental. Entre ellos, Soledad Gallego-Díaz, fallecida en Madrid el pasado martes. Fue su primera gran exclusiva.
Polyclonal selection of immune checkpoint mutations in thyroid autoimmunity
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Abstract Our immune system contains multiple checkpoints to prevent the activation of self-reactive lymphocytes. How some lymphocytes escape these constraints to cause autoimmune disease remains poorly understood. A long-standing hypothesis posits that somatic mutations in immune-regulatory genes may enable self-reactive lymphocytes to bypass tolerance checkpoints1–3, but testing this has been challenging due to technical limitations.
By Pantelis Nicola, Andrew Lawson, Yoshihiro Ishida, Luke Wylie, Paul Scott, Kenny Roberts, Luke Harvey, Stefanie V. Lensing, Wei Cheng, Federico Abascal, Daniel Leongamornlert, Yvette Hooks, Matthew Mayho, Nicole Müller-Sienerth, Laura Mincarelli, Flavia Peci, Bee Ling Ng, Georgeina L Jarman, Andrew Russell, Kourosh Saeb-Parsy, Anna L Paterson, Krishna Chatterjee, Raheleh Rahbari, Omer Ali Bayraktar, Michael Stratton, Peter Campbell, John Tadross, Iñigo Martincorena, Alexandra Tidd, Juliette Imbert, Sara Widaa, James Illing, Krishnaa T. A. Mahbubani, Nadia Schoenmakers
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Nature
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Sperm sequencing reveals extensive positive selection in the male germline - Nature
Abstract Mutations that occur in the cell lineages of sperm or eggs can be transmitted to offspring. In humans, positive selection of driver mutations during spermatogenesis can increase the birth prevalence of certain developmental disorders1,2,3. Until recently, characterizing the extent of this selection in sperm has been limited by the error rates of sequencing technologies. Here we used the duplex sequencing method NanoSeq4 to sequence 81 bulk sperm samples from individuals aged 24–75 years.
Somatic mutation and selection at population scale - Nature
Abstract As we age, many tissues become colonized by microscopic clones carrying somatic driver mutations1,2,3,4,5,6,7. Some of these clones represent a first step towards cancer whereas others may contribute to ageing and other diseases. However, our understanding of this phenomenon remains limited due to the challenge of detecting mutations in small clones.
Sperm sequencing reveals extensive positive selection in the male germline
I.M., M.R.S., and P.J.C. are co-founders, shareholders, and consultants for Quotient Therapeutics Ltd. R.E.A. is an employee of Quotient Therapeutics Ltd. M.E.H. is a co-founder of, consultant to and holds shares in Congenica, a genetics diagnostic company. This research is supported by core funding from Wellcome Trust. R.R. is funded by Cancer Research UK (C66259/A27114) and Medical Research Council (MR/W025353/1).
Saturation genome editing of DDX3X clarifies pathogenicity of germline and somatic variation - Nature Communications
Abstract Loss-of-function of DDX3X is a leading cause of neurodevelopmental disorders (NDD) in females. DDX3X is also a somatically mutated cancer driver gene proposed to have tumour promoting and suppressing effects. We perform saturation genome editing of DDX3X, testing in vitro the functional impact of 12,776 nucleotide variants. We identify 3432 functionally abnormal variants, in three distinct classes.
Effects of psoriasis and psoralen exposure on the somatic mutation landscape of the skin - Nature Genetics
Abstract Somatic mutations are hypothesized to play a role in many non-neoplastic diseases. We performed whole-exome sequencing of 1,182 microbiopsies dissected from lesional and nonlesional epidermis from 111 patients with psoriasis to search for evidence that somatic mutations in keratinocytes may influence the disease process. Lesional skin remained highly polyclonal, showing no evidence of large-scale spread of clones carrying potentially pathogenic mutations.
Effects of psoriasis and psoralen exposure on the somatic mutation landscape of the skin
Abstract Somatic mutations are hypothesised to play a role in many non-neoplastic diseases. These diseases may also shape the somatic mutation landscape of affected tissues after onset.
The longitudinal dynamics and natural history of clonal haematopoiesis - Nature
Abstract Clonal expansions driven by somatic mutations become pervasive across human tissues with age, including in the haematopoietic system, where the phenomenon is termed clonal haematopoiesis1,2,3,4. The understanding of how and when clonal haematopoiesis develops, the factors that govern its behaviour, how it interacts with ageing and how these variables relate to malignant progression remains limited5,6.
Clonal dynamics of haematopoiesis across the human lifespan - Nature
Abstract Age-related change in human haematopoiesis causes reduced regenerative capacity1, cytopenias2, immune dysfunction3 and increased risk of blood cancer4,5,6, but the reason for such abrupt functional decline after 70 years of age remains unclear. Here we sequenced 3,579 genomes from single cell-derived colonies of haematopoietic cells across 10 human subjects from 0 to 81 years of age.
Somatic mutation rates scale with lifespan across mammals - Nature
Abstract The rates and patterns of somatic mutation in normal tissues are largely unknown outside of humans1,2,3,4,5,6,7. Comparative analyses can shed light on the diversity of mutagenesis across species, and on long-standing hypotheses about the evolution of somatic mutation rates and their role in cancer and ageing. Here we performed whole-genome sequencing of 208 intestinal crypts from 56 individuals to study the landscape of somatic mutation across 16 mammalian species.
Inherited MUTYH mutations cause elevated somatic mutation rates and distinctive mutational signatures in normal human cells
Inherited MUTYH mutations cause elevated somatic mutation rates and distinctive mutational signatures in normal human cells Philip S Robinson, Laura E. Thomas, Federico Abascal, Hyunchul Jung, Luke Harvey, Hannah D. West, Sigurgeir Olafsson, Bernard C.H. Lee, Tim Coorens, Henry Lee-Six, Laura Butlin, Nicola Lander, Mathijs A. Sanders, Stefanie Lensing, Simon J.A. Buczacki, Rogier ten Hoppen, Nicholas Coleman, Roxanne Brunton-Sim, Simon Rushbrook, Kourosh Saeb-Parsy, Fiona Lalloo, Peter J.
Convergent somatic mutations in metabolism genes in chronic liver disease - Nature
Abstract The progression of chronic liver disease to hepatocellular carcinoma is caused by the acquisition of somatic mutations that affect 20–30 cancer genes1,2,3,4,5,6,7,8. Burdens of somatic mutations are higher and clonal expansions larger in chronic liver disease9,10,11,12,13 than in normal liver13,14,15,16, which enables positive selection to shape the genomic landscape9,10,11,12,13.
Somatic mutation rates scale with lifespan across mammals
New Results Alex Cagan, View ORCID ProfileAdrian Baez-Ortega, Natalia Brzozowska, Federico Abascal, Tim H. H. Coorens, Mathijs A. Sanders, Andrew R. J. Lawson, Luke M. R. Harvey, Shriram G. Bhosle, David Jones, Raul E. Alcantara, Timothy M. Butler, Yvette Hooks, Kirsty Roberts, Elizabeth Anderson, Edmund Flach, Simon Spiro, Inez Januszczak, Ethan Wrigglesworth, Matthew W. Perkins, Robert Deaville, Megan Druce, Ruzhica Bogeska, Michael D.
Somatic mutation landscapes at single-molecule resolution
Abstract Somatic mutations drive the development of cancer and may contribute to ageing and other diseases1,2. Despite their importance, the difficulty of detecting mutations that are only present in single cells or small clones has limited our knowledge of somatic mutagenesis to a minority of tissues.
Extensive heterogeneity in somatic mutation and selection in the human bladder
Genetic profiles of the bladder Depending on the environment of the individual, the human bladder can be exposed to carcinogens as they are flushed through the body. Lawson et al. and Li et al. examined the genetic composition of laser-dissected microbiopsies from normal and cancer cells collected from the urothelium, a specialized epithelium lining the lower urinary tract (see the Perspective by Rozen).
ENCODE 3
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Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
Abstract The discovery of drivers of cancer has traditionally focused on protein-coding genes1,2,3,4. Here we present analyses of driver point mutations and structural variants in non-coding regions across 2,658 genomes from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium5 of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA).
Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis
Abstract Long non-coding RNAs (lncRNAs) are a growing focus of cancer genomics studies, creating the need for a resource of lncRNAs with validated cancer roles. Furthermore, it remains debated whether mutated lncRNAs can drive tumorigenesis, and whether such functions could be conserved during evolution.
Somatic mutant clones colonize the human esophagus with age
As people age, they accumulate somatic mutations in healthy cells. About 25% of cells in normal, sun-exposed skin harbor cancer driver mutations. What about tissues not exposed to powerful mutagens like ultraviolet light? Martincorena et al. performed targeted gene sequencing of normal esophageal epithelium from nine human donors of varying age (see the Perspective by Chanock).
Somatic mutant clones colonize the human esophagus with age
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Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx
Eleven Iberian and one Eurasian lynx were sequenced in this project (Additional file 1: Table S1). A moderately inbred male born in Andújar in 2006 and kept as a founder of the captive population since then (Candiles) was selected to provide the reference genome for the species. Ten additional Iberian and one Eurasian male were sampled for whole-genome resequencing, four of them from the population in Doñana and six from Andújar.
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