Biology subjects

Leonard, C.

Publications and source records attributed to Leonard, C..

8 recordsLinked to original sources

bioRxiv2025

Proteomic profiling of Elp1-deficient trigeminal ganglia reveals disruption of neurotrophic and metabolic pathways in a familial dysautonomia mouse model

BackgroundElp1, a subunit of the Elongator complex, is essential for tRNA modification and neuronal development. Mutations in ELP1 underlie familial dysautonomia (FD), a disorder marked by sensory and autonomic neuropathy. While loss of Elp1 disrupts trigeminal ganglion formation and survival, the downstream molecular consequences remain poorly defined. ResultsWe performed quantitative proteomic profiling of trigeminal ganglia from Elp1 conditional knockout (CKO) and control embryos at E13.5. Across 5,650 detected proteins, 25 were significantly upregulated and 26 downregulated in Elp1 CKO embryos. EnrichR analysis revealed enrichment of upregulated proteins in amino acid transport and tRNA aminoacylation pathways, with links to neuromuscular and neuropathic diseases. Downregulated proteins were associated with RNA modification, cholesterol biosynthesis, and synaptic organization. Validation by immunohistochemistry confirmed decreased expression of the neurotrophic receptor Gfra3 and the neuropeptide Galanin, and increased levels of the chromatin regulator Chd1, in Elp1 CKO embryos relative to controls. ConclusionsThese findings demonstrate that Elp1 loss disrupts metabolic, RNA modification, and neurotrophic signaling pathways in the developing trigeminal ganglion. Proteomic analysis thus provides new insight into the molecular consequences of Elp1 deficiency and highlights candidate mechanisms contributing to sensory neuron vulnerability in FD.

developmental biology↗

bioRxiv2025

Explainable machine learning identifies features and thresholds predictive of immunotherapy response

BackgroundImmunotherapy has improved patient survival for multiple cancer types, including melanoma. While a variety of molecular features have been linked to response to immune checkpoint inhibitors (ICI) treatment, clinically established biomarkers, such as tumour mutation burden (TMB) and PD-L1 expression, have shown limitations in accurately categorising responders versus non-responders. Due to the complex nature of ICI response, which includes cancer intrinsic and extrinsic features within the tumour microenvironment (TME), using a single biomarker to predict response is insufficient, necessitating the need to identify accurate clinical and multi-omic molecular predictors. MethodsWe integrate clinical, DNA and RNA sequencing data from four datasets, comprising 138 melanoma patients treated with ICI, to develop machine learning models for predicting ICI response. The performance of each model was evaluated using an independent dataset of patients with cutaneous melanoma (n=53). Interactions between trained models and features were rationalised using the explainability method SHAP. ResultsThe most optimal model was the multi-omic random forest model, with AUC-ROC of 0.78 when predicting response in the independent test dataset. Using SHAP, we predicted thresholds for mutational signatures, neoantigen load, immune cell-type abundance and immune receptor LAG3 expression. The relationship between these influential features and their SHAP scores revealed numerical thresholds constituting good and poor patient response. ConclusionsThis approach highlights patient response to ICI is influenced by both cancer intrinsic and extrinsic features, as well as identifies candidate biomarkers that could inform the use of ICI and potentially assist in the selection of combination therapy in melanoma treatment.

bioinformatics↗

bioRxiv2024

Identification of a sub-population of synovial mesenchymal stem cells with enhanced treatment efficacy in a rat model of Osteoarthritis

Osteoarthritis (OA) is a painful and debilitating disease which has no cure and there are no treatments which can predictably stop/reverse its progression. Treating this disease is particularly difficult since the articular cartilage lacks intrinsic repair capacity even though mesenchymal stem cells (MSCs) are present in the joint environment and have robust chondrogenic potential. We have previously shown that there is heterogeneity of MSC sub-types within the human synovium, yet it remains unclear if any of these MSC types can regenerate cartilage and/or impact OA disease progression. Therefore, we have undertaken this study focusing on clonally derived MSC populations derived from the synovium of normal and OA patients to characterize if any MSC populations can positively impact OA disease trajectory in a rat model of OA. MSCs were clonally isolated by indexed flow cytometry, expanded in culture and then characterized for differentiation capacity and by quantitative proteomics. MSC clones were then transplanted into a xenograft rat OA model and treatment effect was determined by histology and immunofluorescence outcomes. We identified heterogeneity in putative MSCs derived from within and between patient groups (normal vs. OA) and the ability of these cells to effect repair in a rat OA model. However, these different sub-types of MSCs could not be distinguished by traditional cell surface markers showing the need for a better understanding of these populations at the single cell level. Using an unbiased proteomics approach, CD47 was identified a novel marker of human MSCs. Using the same rat model of OA, CD47Hi expressing cells were found to have robust treatment efficacy and directly contributed to the formation of new articular cartilage tissue. Characterizing MSCs is essential to understand which sub-types are appropriate for further clinical investigation. If OA patients still have functional MSCs in their synovium, then it is possible these cells can be exploited for cartilage regeneration / OA treatment strategies.

cell biology↗

bioRxiv2021

DJ-1 depletion slows down immunoaging in T-cell compartments

Decline in immune function during aging increases susceptibility to different aging related diseases. However, the underlying molecular mechanisms, especially the genetic factors contributing to imbalance of naive/memory T-cell subpopulations, still remain largely elusive. Here we show that loss of DJ-1 encoded by PARK7/DJ-1, causing early-onset familial Parkinsons disease (PD), unexpectedly delayed immunoaging in both human and mice. Compared with two gender-matched unaffected sibling carriers of similar ages, the index PD patient with DJ-1 deficiency showed a decline in many critical immunoaging features, including almost doubled frequencies of non-senescent T cells. The observation of a younger immune system in the index patient was further consolidated by the results in aged DJ-1 knockout mice. Our data from bone marrow chimera models and adoptive transfer experiments demonstrated that DJ-1 regulates several immunoaging features via hematopoietic-intrinsic and naive-CD8-intrinsic mechanisms. Our finding suggests an unrecognized critical role of DJ-1 in regulating immunoaging, discovering a potent target to interfere with immunoaging- and aging-associated diseases.

immunology↗

bioRxiv2020

FAM13A regulates maturation and effector functions of natural killer cells

The polymorphism of the gene FAM13A (family with sequence similarity 13, member A) is strongly linked to the risk of lung cancer and chronic obstructive pulmonary disease, which are among the leading causes of mortality and morbidity in lung-related diseases worldwide. However, the underlying molecular and cellular mechanisms through which FAM13A contributes to the pathogenesis of these diseases largely remain unclear. Here, using a Fam13a knock out (KO) mouse model, we showed that Fam13a depletion upregulated the expression of the terminal differentiation and inhibitory marker, KLRG1 (killer cell lectin-like receptor G1) in natural killer (NK) cells. NK cells from Fam13a-deficient mice showed impaired IFN-{gamma} production either against target tumor cells or following various cytokine cocktail stimulations. Furthermore, the number of lung metastases induced by B16F10 melanoma cells was increased in Fam13a-KO mice. Collectively, our data suggest a key role of FAM13A in regulating NK cell functions, indicating that the key lung-disease risk gene FAM13A might contribute to the pathogenesis of several lung diseases via regulating NK cells.

immunology↗

bioRxiv2019

PARK7/DJ-1 promotes pyruvate dehydrogenase activity and maintains Treg homeostasis

Pyruvate dehydrogenase (PDH) is the gatekeeper enzyme into the tricarboxylic acid (TCA) cycle. Here we show that PARK7/DJ-1, a key familial Parkinsons disease (PD) gene, is a pacemaker controlling PDH activity in CD4 regulatory T cells (Tregs). DJ-1 bound to PDH-E1 beta (PDHB), inhibiting the phosphorylation of PDH-E1 alpha (PDHA), thus promoting PDH activity and oxidative phosphorylation (OXPHOS). Dj-1 depletion impaired Treg proliferation and cellularity maintenance in older mice, increasing the severity during the remission phase of experimental autoimmune encephalomyelitis (EAE). The compromised proliferation and differentiation of Tregs in Dj-1 knockout mice were caused via regulating PDH activity. These findings provide novel insight into the already complicated regulatory machinery of the PDH complex and demonstrate that the DJ-1-PDHB axis represents a potent target to maintain Treg homeostasis, which is dysregulated in many complex diseases.

biochemistry↗

bioRxiv2018

Rampant cryptic sex chromosome drive in Drosophila

Theory predicts that selfish genetic elements that increase their transmission are prone to originate on sex chromosomes but create strong selective pressure to evolve suppressors due to reduced fertility and distorted population sex ratios. Here we show that recurrent genetic conflict over sex chromosome transmission appears to be an important evolutionary force that has shaped gene content evolution of sex chromosomes in Drosophila. We demonstrate that convergent acquisition and amplification of spermatid expressed gene families are common on Drosophila sex chromosomes, and especially on recently formed ones, and harbor characteristics typical of meiotic drivers. We carefully characterize one putative novel cryptic sex chromosome distortion system that arose independently several times in members of the Drosophila obscura group. Co-amplification of the S-Lap1/GAPsec gene pair on both the X and the Y chromosome occurred independently several times in members of the D. obscura group, where this normally autosomal gene pair is sex-linked due to a sex chromosome - autosome fusion. Investigation of gene expression and short RNA profiles at the S-Lap1/GAPsec system suggest that meiotic drive and suppression likely involves RNAi mechanisms. Our finding suggests that recurrent conflict over sex chromosome transmission has shaped widespread genomic and evolutionary patterns, including the epigenetic regulation of sex chromosomes, the distribution of sex-biased genes, and the evolution of hybrid sterility.

genomics↗

bioRxiv2017

The role of chromosomal inversions in speciation

The chromosomal inversions of D. persimilis and D. pseudoobscura have deeply influenced our understanding of the evolutionary forces that shape natural variation, speciation, and selfish chromosome dynamics. Here, we perform a comprehensive reconstruction of the evolutionary histories of the chromosomal inversions in these species. We provide a solution to the puzzling origins of the selfish Sex-Ratio chromosome in D. persimilis and show that this Sex-Ratio chromosome directly descends from an ancestrally-arranged chromosome. Our results further show that all fixed inversions between D. persimilis and D. pseudoobscura were segregating in the ancestral population long before speciation, and that the genes contributing to reproductive barriers between these species must have evolved within them afterwards. We propose a new model for the role of chromosomal inversions in speciation and suggest that higher levels of divergence and an association with hybrid incompatibilities are emergent properties of ancestrally segregating inversions. These findings force a reconsideration of the role of chromosomal inversions in speciation, not as protectors of existing hybrid incompatibility alleles, but as fertile grounds for their formation.

evolutionary biology↗