Biology subjects

Gallagher, D.

Publications and source records attributed to Gallagher, D..

7 recordsLinked to original sources

bioRxiv2026

Predicting cellular functions of human phosphosites

Protein phosphorylation is a regulatory switch that controls essentially all cellular processes, including metabolism, cell cycle progression, and DNA repair. Furthermore, by modulating specific regions and activities of a protein, phosphorylation sites can independently coordinate the proteins involvement in distinct cellular processes. Despite the importance of this regulatory mechanism, the majority of human phosphosites have not been functionally characterized. Here we have developed biologically informed predictors of phosphosite cellular function by integrating protein functional annotation, recognition by upstream kinases, and regulation across phosphoproteomics perturbations. To enable this we harmonized public phosphoproteomics data into an atlas of nearly 2,000 perturbations and more than 16 million quantifications, providing a powerful resource for studying phosphosite regulation. We applied our predictors to functionally characterise thousands of understudied phosphosites, revealing many phosphosite functions that could not be inferred from protein functional annotation, and functionally divergent phosphosites within the same protein. Using cancer multi-omics data we characterized connections between these phosphosites and other molecular layers. Finally, we illuminated novel signaling axes within the DNA repair pathway, and demonstrated that phosphosites on PPM1G and KHSRP modulate cell survival under DNA damage. Our work represents a powerful resource for dissecting the cellular consequences of protein phosphorylation.

genomics↗

bioRxiv2026

Non-Canonical ERP Patterns in Second-language Sentence Processing: Evidence from Syntactic, Semantic, and Phonological Violations in Japanese Learners of English

Background/ObjectivesDespite notable advances in the neural mechanisms of second-language (L2) processing, few studies have systematically compared syntactic, semantic, and phonological processing of L2 within a single experimental design. We investigate the neurocognitive mechanisms underlying L2 sentence processing in native Japanese speakers with intermediate English proficiency. By integrating behavioral measures and event-related potentials (ERPs), we examined how syntactic, semantic, and phonological information influenced sentence comprehension. MethodsTwenty-seven participants completed an auditory sentence judgment task involving English sentences with a syntactic, semantic, or phonological error. ResultsBehavioral results revealed the highest accuracy in the control and semantic conditions, while syntactic and phonological violations led to significantly lower performance, indicating greater processing difficulty in these domains. Among the three linguistic violation types, phonological violations elicited the robust ERP negativities across both time 300-500 ms and 500-800 ms time windows, while syntactic and semantic violations evoked less consistent neural responses in this L2 auditory sentence judgment task. These results suggest that mismatches in expected phonological forms hinder lexical activation, triggering a negativity that resembles an N400 but reflects different underlying processes. ConclusionWe found non-canonical neural response patterns in L2 learners, characterized by sensitivity to phonological anomalies but minimal neural disruption for semantic or syntactic anomalies. The current study contributes to our understanding of L2 sentence processing in native Japanese speakers, particularly by aligning real-time neural responses with behavioral performance. This work offers implications for pedagogical practices and assessment strategies tailored to neurodiverse bilingual populations.

neuroscience↗

bioRxiv2025

Two Sites, Two Languages: Dual-site tDCS and EEG Evidence for L1 Feature Transfer in L2

The neural bases of syntactic and semantic processing remain unclear. While prior transcranial direct current stimulation (tDCS) studies have targeted either the inferior frontal gyrus (LIFG) or left superior temporal gyrus (LSTG), we test whether dual stimulation of both alters second language (L2) anomaly based on native language (L1). Chinese and Korean participants evaluated Japanese sentence correctness; Japanese shares morpho-syntax with Korean and semantic radicals with Chinese. For the N400, dual anodal tDCS elicited a significant interaction stimulation and L1 (F (1,960.7) = 5.48, p = 0.0194), stimulation and sentence type (F (5,960.7) = 2.28, p = .0448), and L1 and sentence type (F (5, 960) = 2.28, p = 0.045). For the P600, a significant effect of stimulation and L1 interaction (F (1,1303.1) = 9.86, p = 0.0017), and stimulation x sentence type (F (5,1303.1) = 2.35, p = 0.039), suggesting L1 typology affected semantic integration during dual-stimulation tDCS.

neuroscience↗

bioRxiv2025

Modeling Dyslexia in Neurotypical Adults by Combining Neuroimaging and Neuromodulation Techniques: A Hypothesis Paper

Dyslexia is a prevalent developmental disorder marked by deficits in literacy skills. Given that the core deficits of dyslexia are uniquely human, animal models have not been as useful in dyslexia research as they have been in other areas of research. While significant progress has been made through behavioral and neuroimaging studies, a viable model could facilitate controlled investigations into the neural mechanisms underlying dyslexia and accelerate the development of targeted interventions. In this hypothesis article, we propose a two-pronged approach to model dyslexia in neurotypical adults using neuroimaging and neuromodulation techniques. First, we propose using functional and structural MRI data to cluster individuals into neuropathologically derived subgroups in order to facilitate the classification of dyslexia subtypes based on neuropathological characteristics. Second, we propose employing transcranial temporal interference stimulation (tTIS) to temporarily downregulate activity in brain regions specified in the clustering analysis, inducing subtype-specific dyslexic symptoms in neurotypical individuals. This approach enables the establishment of causal or probabilistic relationships between neuropathologies and dyslexia subtypes, while at the same time creating dyslexia models to facilitate investigation into subtype-specific interventions. By integrating neuroimaging and neuromodulation, we hope to offer a viable substitute for animal models in dyslexia and accelerate the development of personalized therapeutic strategies for dyslexia.

neuroscience↗

bioRxiv2023

Accelerated physiology and increased energy expenditure in animals and humans with mitochondrial defects: A meta-analysis

Mitochondria are key energy transforming organelles in mammalian cells. However, how defects in oxidative phosphorylation (OxPhos) and other mitochondrial functions influence whole-body energy expenditure (EE) has not been rigorously studied. Cellular and organismal responses to OxPhos defects likely involve a combination of functional downregulation to conserve energy and compensatory upregulation of stress responses. If the energy cost of compensatory responses exceeds the potential energy savings of functional downregulation, as recent work suggests, the result would be an increase in total EE. To address the hypothesis that OxPhos defects increase the energetic cost of living, we performed a meta-analysis of available studies reporting EE in animal models with mitochondrial gene defects. Of all reported experimental conditions (n = 91, from 29 studies), 51% reported a >10% elevation in EE relative to control animals, compared to 11% reporting <10% reduction in EE (p<0.0001, Chi-square). Of the experimental conditions where locomotor activity was also quantified, 39% showed that OxPhos-deficient animals had elevated EE despite reduced locomotor activity, which would be expected to decrease EE. To extend this finding in humans, we re-analyzed a high-quality clinical and multi-omics dataset (Sharma et al. 2021) of mitochondrial disease patients with the m.3243A>G mutation. This analysis similarly indicates an upregulation of energetically costly physiological, immune, and metabolic parameters in people with OxPhos deficiency. These results suggest that animals and humans with mitochondrial defects must expend more energy to sustain life, a state clinically called hypermetabolism. High-quality human energetics studies are needed to understand the magnitude, mechanisms, and modifiability of hypermetabolism in mitochondrial disorders.

cell biology↗

bioRxiv2023

Epitope Engineered Human Haematopoietic Stem Cells are Shielded from CD123-targeted Immunotherapy

Targeted eradication of transformed or otherwise dysregulated cells using monoclonal antibodies (mAb), antibody-drug conjugates (ADC), T cell engagers (TCE) or chimeric antigen receptor (CAR) cells is very effective for haematologic diseases. Unlike the breakthrough progress achieved for B cell malignancies, there is a pressing need to find suitable antigens for immunotherapy of myeloid malignancies. CD123, the interleukin-3 (IL-3) receptor alpha-chain, is highly expressed in various haematological malignancies, including acute myeloid leukaemia (AML) and blastic plasmacytoid dendritic cell neoplasm (BPDCN). However, shared expression of CD123 on healthy haematopoietic stem and progenitor cells (HSPCs) bears the risk for extensive myelotoxicity upon targeted depletion. Here, we demonstrate that rationally designed, epitope-engineered HSPCs were completely shielded from CD123-targeted immunotherapy but remained fully functional while CD123-deficient HSPCs displayed a competitive disadvantage. Thus, molecularly shielded HSPCs could allow tumor-selective targeted immunotherapy and in parallel enable rebuilding a fully functional haematopoietic system. We envision that this approach is broadly applicable to many targets and cells, could render hitherto undruggable targets accessible to immunotherapy and will allow continued posttransplant immunotherapy, for instance to treat minimal residual disease (MRD) or be used as a salvage therapy. Since the function of the engineered targets is preserved, multiplexed molecular shielding could also enable targeted combination immunotherapies to address tumor heterogeneity. More generally, epitope shielding will be applicable for replacement of other cell types including the many immune cells which are currently being considered for engineered cellular therapies.

bioengineering↗

bioRxiv2020

A Rad51-Independent P{-}ath{-}way Promotes Single-Strand Template Repair in Gene Editing

The Rad51/RecA family of recombinases perform a critical function in typical repair of double-strand breaks (DSBs): strand invasion of a resected DSB end into a homologous double-stranded DNA (dsDNA) template sequence to facilitate repair. However, repair of a DSB using single stranded DNA (ssDNA) as a template, a common method of CRISPR/Cas9-mediated gene editing, is Rad51-independent. We have analyzed the genetic requirements for these Rad51-independent events in Saccharomyces cerevisiae in two different assays. Gene editing events were carried out either by creating a DSB with the site-specific HO endonuclease and repairing the DSB with 80-nt single-stranded oligonucleotides (ssODNs) or by using a bacterial retron system that produces ssDNA templates in vivo in combination with DSBs created by Cas9. We show that single strand template repair (SSTR), is dependent on Rad52, Rad59, Srs2 and the Mre11-Rad50-Xrs2 (MRX) complex, but not Rad51, Rad54 or Rad55. Srs2 acts to prevent overloading of Rad51 on the ssDNA filament, whereas Rad59 appears to alleviate the inhibition of Rad51 on Rad52s strand annealing activity; thus, deletion of RAD51 suppresses both the srs2{Delta} and rad59{Delta} phenotypes. This same suppression by rad51{Delta} of rad59{Delta} is found in another DSB repair pathway, single strand annealing (SSA). In contrast, gene targeting using an 80-bp dsDNA template of the same sequence is Rad51-dependent. We also examined SSTR events in which the ssODN carried several mismatches. In the absence of the mismatch repair protein, Msh2, we found that the fate of mismatches carried on the ssDNA template are very different at the 3 end, which can anneal directly to the resected DSB end, compared to the 5 end. We also find that DNA polymerase Pol{delta}s 3 to 5 proofreading activity frequently excises a mismatch close to the 3 end of the template, similar to its removal of heterologies close to the 3 invading end of the DSB. We further report that SSTR is accompanied by a 600-fold increase in mutations in a region adjacent to the sequences directly undergoing repair. These DNA polymerase {zeta}-dependent mutations may compromise the accuracy of gene editing.

genetics↗