Biology subjects

Baeza-Centurion, P.

Publications and source records attributed to Baeza-Centurion, P..

5 recordsLinked to original sources

bioRxiv2024

Deep indel mutagenesis reveals the regulatory and modulatory architecture of alternative exon splicing

Altered splicing is a frequent mechanism by which genetic variants cause disease and antisense oligonucleotides (AONs) that target pre-mRNA splicing have been approved as therapeutics for multiple pathologies including patient-customized treatments for rare diseases. However, the regulatory architecture of human exons remains poorly understood and AON discovery is currently slow and expensive, limiting the wider adoption of the approach. Here we show that that systematic deletion scans -which can be made experimentally at very low cost - provide an efficient strategy to chart the regulatory landscape of human exons and to rapidly identify effective splicing-modulating oligonucleotides in a fully quantitative manner. Our results suggest a mechanism for the evolutionary origins of unusually short microexons and the repression of transmembrane domain-encoding exons, and reveal a checkerboard architecture of sequential enhancers and silencers in a model alternative exon. Accurate prediction of the effects of deletions using deep learning provides a resource, DANGO, that maps the splicing regulatory landscape of all human exons and predicts effective splicing-altering antisense oligonucleotides genome-wide.

genetics↗

bioRxiv2023

An interactive cellular ecosystem blocks epithelial transformation in naked mole-rat

Long-lived species suppress cancer despite accumulating somatic mutations throughout life, but how this is achieved in renewing tissues remains unclear. Here, we show that naked mole-rat skin uncouples high cellular turnover from cancer risk through coordinated epithelial and stromal mechanisms that constrain clonal outgrowth and suppress tumor-promoting inflammation. Despite elevated epidermal proliferation and mutational burden, naked mole-rat skin maintains tissue integrity through an expanded pool of early committed progenitor (hybrid) cells and replication-coupled genome maintenance pathways. Under chronic carcinogenic stress, undifferentiated basal cells replenish the hybrid progenitor pool. This dilutes initiated clones and permits only limited selective expansion of rare cancer gene-mutant clones. Depletion of the hybrid compartment shifts this protective state toward clonal expansion and inflammatory activation. These expanding clones are further constrained by a highly tumor-suppressive stromal microenvironment, driven by fibroblasts that adopt a metabolically restricted, non-inflammatory program. Together, our data uncover a multi-layered tumor-suppressive strategy that couples turnover-driven regeneration with an anti-permissive stromal niche to prevent malignant progression under mutagenic stress.

cancer biology↗

bioRxiv2020

Mutations primarily alter the inclusion of alternatively spliced exons

Genetic analyses and systematic mutagenesis have revealed that synonymous, non-synonymous and intronic mutations frequently alter the inclusion levels of alternatively spliced exons, consistent with the concept that altered splicing might be a common mechanism by which mutations cause disease. However, most exons expressed in any cell are highly-included in mature mRNAs. Here, by performing deep mutagenesis of highly-included exons and by analysing the association between genome sequence variation and exon inclusion across the transcriptome, we report that mutations only very rarely alter the inclusion of highly-included exons. This is true for both exonic and intronic mutations as well as for perturbations in trans. Therefore, mutations that affect splicing are not evenly distributed across primary transcripts but are focussed in and around alternatively spliced exons with intermediate inclusion levels. These results provide a resource for prioritising synonymous and other variants as disease-causing mutations.

genomics↗

bioRxiv2020

DiMSum: an error model and pipeline for analyzing deep mutational scanning data and diagnosing common experimental pathologies

Deep mutational scanning (DMS) enables multiplexed measurement of the effects of thousands of variants of proteins, RNAs and regulatory elements. Here, we present a customizable pipeline - DiMSum - that represents an end-to-end solution for obtaining variant fitness and error estimates from raw sequencing data. A key innovation of DiMSum is the use of an interpretable error model that captures the main sources of variability arising in DMS workflows, outperforming previous methods. DiMSum is available as an R/Bioconda package and provides summary reports to help researchers diagnose common DMS pathologies and take remedial steps in their analyses.

bioinformatics↗

bioRxiv2019

Changes in gene expression shift and switch genetic interactions

An important goal in disease genetics and evolutionary biology is to understand how mutations combine to alter phenotypes and fitness. Non-additive interactions between mutations occur extensively and change across conditions, cell types, and species, making genetic prediction a difficult challenge. To understand the reasons for this, we reduced the problem to a minimal system where we combined mutations in a single protein performing a single function (a transcriptional repressor inhibiting a target gene). Even in this minimal system, a change in gene expression altered both the strength and type of genetic interactions. These seemingly complicated changes could, however, be predicted by a mathematical model that propagates the effects of mutations on protein folding to the cellular phenotype. We show that similar changes will be observed for many genes. These results provide fundamental insights into genotype-phenotype maps and illustrate how changes in genetic interactions can be predicted using hierarchical mechanistic models.\n\nOne sentence SummaryDeep mutagenesis of the lambda repressor reveals that changes in gene expression will alter the strength and direction of genetic interactions between mutations in many genes.\n\nHighlightsO_LIDeep mutagenesis of the lambda repressor at two expression levels reveals extensive changes in mutational effects and genetic interactions\nC_LIO_LIGenetic interactions can switch from positive (suppressive) to negative (enhancing) as the expression of a gene changes\nC_LIO_LIA mathematical model that propagates the effects of mutations on protein folding to the cellular phenotype accurately predicts changes in mutational effects and interactions\nC_LIO_LIChanges in expression will alter mutational effects and interactions for many genes\nC_LIO_LIFor some genes, perfect mechanistic models will never be able to predict how mutations of known effect combine without measurements of intermediate phenotypes\nC_LI

genetics↗