Biology subjects

Adamson, S. I.

Publications and source records attributed to Adamson, S. I..

6 recordsLinked to original sources

bioRxiv2026

LRP2: A proteogenomics pipeline for long-read informed protein isoform analysis and discovery

Most human genes produce multiple RNA isoforms, yet it remains unclear which isoforms are translated into stable, functional proteins. Long-read RNA sequencing resolves full-length transcript structures and, when paired with mass spectrometry, can provide empirical evidence of isoform translation. Despite this opportunity, comprehensive workflows integrating isoform discovery, open reading frame prediction, peptide identification, and protein inference remain limited, leaving users to handle these steps piecemeal. Here, we present LRP2, a modular, end-to-end long-read proteogenomics pipeline built in Nextflow. LRP2 scales transcript discovery to hundreds of samples via PacBio's latest Isocall tool, removes technical artifacts with SQANTI QC, generates and classifies predicted proteomes via CPAT and SQANTI Protein, performs multi-group differential expression and usage analysis via edgeR, DRIMSeq, and a long-read adaptation of LeafCutter, and integrates protein-level evidence from DDA and DIA MS data through FragPipe. For cross-dataset comparison of novel isoforms, LRP2 employs deterministic splice-junction, coordinate-based isoform identifiers. Used as an integrated pipeline, LRP2 enables the detection of novel peptides and improves the protein isoform inference to confirm protein isoform translation.

bioinformatics↗

bioRxiv2024

Alternating hemiplegia of childhood associated mutations in Atp1a3 reveal diverse neurological alterations in mice.

Pathogenic variants in the neuronal Na+/K+ ATPase transmembrane ion transporter (ATP1A3) cause a spectrum of neurological disorders including alternating hemiplegia of childhood (AHC). The most common de novo pathogenic variants in AHC are p.D801N ([~]40% of patients) and p.E815K ([~]25% of patients), which lead to early mortality by spontaneous death in mice. Nevertheless, knowledge of the development of clinically relevant neurological phenotypes without the obstacle of premature death, is critical for the identification of pathophysiological mechanisms and ultimately, for the testing of therapeutic strategies in disease models. Here, we used hybrid vigor attempting to mitigate the fragility of AHC mice and then, performed behavioral, electrophysiological, biochemical, and molecular testing to comparatively analyze mice that carry either of two most common AHC patient observed variants in the Atp1a3 gene. Collectively, our data reveal the presence but also the differential impact of the p.D801N and p.E815K variants on disease relevant alterations such as spontaneous and stress-induced paroxysmal episodes, motor function, behavioral and neurophysiological activity, and neuroinflammation. Our alternate AHC mouse models with their phenotypic deficits open novel avenues for the investigation of disease biology and therapeutic testing for ATP1A3 research.

neuroscience↗

bioRxiv2021

Functional characterization of splicing regulatory elements

BackgroundRNA binding protein-RNA interactions mediate a variety of processes including pre-mRNA splicing, translation, decay, polyadenylation and many others. Previous high-throughput studies have characterized general sequence features associated with increased and decreased splicing of certain exons, but these studies are limited by not knowing the mechanisms, and in particular, the mediating RNA binding proteins, underlying these associations. ResultsHere we utilize ENCODE data from diverse data modalities to identify functional splicing regulatory elements and their associated RNA binding proteins. We identify features which make splicing events more sensitive to depletion of RNA binding proteins, as well as which RNA binding proteins act as splicing regulators sensitive to depletion. To analyze the sequence determinants underlying RBP-RNA interactions impacting splicing, we assay tens of thousands of sequence variants in a high-throughput splicing reporter called Vex-seq and confirm a small subset in their endogenous loci using CRISPR base editors. Finally, we leverage other large transcriptomic datasets to confirm the importance of RNA binding proteins which we designed experiments around and identify additional RBPs which may act as additional splicing regulators of the exons studied. ConclusionsThis study identifies sequence and other features underlying splicing regulation mediated specific RNA binding proteins, as well as validates and identifies other potentially important regulators of splicing in other large transcriptomic datasets.

genomics↗

bioRxiv2021

Defects in translation-dependent quality control pathways lead to convergent molecular and neurodevelopmental pathology

Translation-dependent quality control pathways such as no-go decay (NGD), non-stop decay (NSD) and nonsense-mediated decay (NMD) govern protein synthesis and proteostasis by resolving non-translating ribosomes and preventing the production of potentially toxic peptides derived from faulty and aberrant mRNAs. However, how translation is altered and the in vivo defects that arise in the absence of these pathways are poorly understood. Here, we show that the NGD/NSD factors Pelo and Hbs1l are critical for cerebellar neurogenesis but expendable for survival of these neurons after development. Analysis of mutant embryonic fibroblasts revealed translational pauses, alteration of signaling pathways, and translational reprogramming. Similar effects on signaling pathways, the translatome and cerebellar development were observed upon deletion of the NMD factor Upf2. These data reveal that these quality control pathways that function to mitigate errors at distinct steps in translation can evoke similar cellular responses.

cell biology↗

bioRxiv2020

GTPBP1 resolves paused ribosomes to maintain neuronal homeostasis

Ribosome-associated quality control pathways respond to defects in translational elongation to recycle arrested ribosomes and degrade aberrant polypeptides and mRNAs. Loss of an individual tRNA gene leads to ribosomal pausing that is resolved by the translational GTPase GTPBP2, and in its absence causes neuron death. Here we show that loss of the homologous protein GTPBP1 during tRNA deficiency in the mouse brain also leads to codon-specific ribosome pausing and neurodegeneration, suggesting that these non-redundant translational GTPases function in the same pathway to mitigate ribosome pausing. Ribosome stalling in the mutant brain led to activation of the integrated stress response (ISR) mediated by GCN2 and decreased mTORC1 signaling. However, in contrast to the ISR, which enhanced neuron survival, reduced mTORC1 signaling increased neuronal death. Our data demonstrate that GTPBP1 functions as an important quality control mechanism during translation elongation and suggest that translational signaling pathways intricately interact to regulate neuronal homeostasis during defective translation elongation.

neuroscience↗

bioRxiv2017

High-Throughput Identification of Genetic Variation Impact on pre-mRNA Splicing Efficiency

AbstractUnderstanding the functional impact of genomic variants is a major goal of modern genetics and personalized medicine. Although many synonymous and non-coding variants act through altering the efficiency of pre-mRNA splicing, it is difficult to predict how these variants impact pre-mRNA splicing. Here, we describe a massively parallel approach we used to test the impact of 2,059 human genetic variants spanning 110 alternative exons on pre-mRNA splicing. This method yields data that reinforces known mechanisms of pre-mRNA splicing, can rapidly identify genomic variants that impact pre-mRNA splicing, and will be useful for increasing our understanding of genome function.

genomics↗