Biology subjects

Smith, L. A.

Publications and source records attributed to Smith, L. A..

9 recordsLinked to original sources

bioRxiv2026

Neuroinflammation and metabolic dysfunction in POLG-related mitochondrial epilepsy

Super-refractory status epilepticus is a common neurological manifestation of mitochondrial disease caused by bi-allelic pathogenic variants in POLG. Epilepsy in POLG-related disease typically presents with an explosive onset of status epilepticus, often from an occipital focus, and is associated with extensive neurodegeneration. The neuropathological mechanisms underlying POLG-related mitochondrial epilepsy remain poorly understood, however, neuroinflammation and glial dysfunction are hypothesised to play a significant role. In this study, we performed a neuropathological and proteomic investigation of post-mortem brain tissues from 12 patients with POLG-related mitochondrial epilepsy (age range: 3 - 28 years) and matched control cases. Given that the primary visual cortex is prominently involved in this epileptic disorder, occipital cortical tissues (Brodmann area 17) were compared to frontal cortical tissues (Brodmann area 9). Liquid chromatography-mass spectrometry (LC-MS/MS) analysis identified a distinct immunometabolic signature in the occipital cortex, and to a lesser extent in the frontal cortex, in POLG-related epilepsy. This was characterised by decreased abundance of mitochondrial proteins coupled to an increased expression of innate immune and inflammatory proteins, consistent with neuroinflammation. To validate these observations, we confirmed an increased density of cells immunoreactive for acute phase proteins (C-reactive protein, osteopontin and serpin A3), immune co-receptors (CD14 and HLA-DR), the inflammatory glycoprotein YKL40, the cytokine TNF-alpha, and mitochondrial translocator protein (TSPO). We also demonstrate a decreased expression of mitochondrial oxidative phosphorylation (OXPHOS) subunits within POLG patient microglia, indicative of mitochondrial dysfunction. Finally, we show enrichment of mitochondrial OXPHOS and interneuron proteins in the control primary visual cortex compared with the frontal cortex, which may underlie the selective regional vulnerability observed in POLG-related mitochondrial disease. Overall, these findings provide strong neuropathological evidence implicating neuroinflammation and glial dysfunction in POLG-related epilepsy.

neuroscience↗

bioRxiv2026

The Paipu framework enables creation of a large-scale mammalian cancer transcriptomics atlas

A plethora of studies have identified shared molecular mechanisms involved in tumor development across humans and other mammalian species. While these two-species analyses advance understanding of human disease, extending them across many species would provide evolutionary insight into molecular mechanisms driving human cancers. However, this expansion requires knowledge transfer and harmonization across species. Genomic differences between species, including variation in genome annotation quality, have historically hindered multi-species large-scale atlas creation. To overcome these challenges, we present Paipu, a comprehensive pipeline designed to streamline querying, preprocessing, harmonization, and retrieval of large-scale RNA-seq data and associated metadata from the NCBI Sequence Read Archive (SRA). Paipu facilitates multi-species analysis by creating a harmonized atlas from user-defined search terms and species. It consists of three components: reference genome preparation, SRA metadata retrieval, and RNA-seq data processing. We apply Paipu to 188 cancer-related terms in 239 non-human mammalian species, creating a harmonized atlas of 3,484 RNA-seq samples spanning 17 species and 35 cancers. This pan-mammalian pan-cancer atlas enables myriad comparative genomics analyses that leverage genetic variation to better understand rare human cancers. As such, Paipu serves as a resource for cross-species cancer genomics and supports atlas creation for any set of species and search terms. Graphical Abstract

bioinformatics↗

bioRxiv2026

Deciphering sepsis molecular subtypes using large-scale data to identify subtype-specific drug repurposing

Sepsis is a life-threatening dysregulated response to infection, the heterogeneity of which precludes effective targeted therapies. To address this, we created a transcriptomic atlas of publicly available adult sepsis data, on which we performed molecular subtyping and identified potential subtype-specific drug repurposing opportunities. In total, we harmonized data from 3,713 samples across 28 datasets, of which 2,251 were from sepsis patients. Using this data, we identified four molecular subtypes of sepsis (C1 - C4) by clustering the sepsis samples based on expression differences in immune-and lipid-related genes. We next identified gene signatures unique to each molecular subtype. Pathway analysis of these signatures revealed patterns of immune exhaustion and metabolic dysregulation in C1, suggesting potential benefit from corticosteroid treatment. C2 had the youngest patient population and the lowest mortality, and C2 expression patterns were often anti-correlated with those of C1. C3 was enriched for inflammatory and cellular stress pathways, while the highest mortality subtype, C4, showed evidence of immunosuppression and metabolic reprogramming. Gene and pathway-level analysis of our molecular subtypes statistically correlated with results from analysis of 28-day mortality, with the best (C2) and worst subtypes (C4) exhibiting similar molecular dysregulation as survivors and non-survivors, respectively. For each subtype, we then evaluated potential targeted therapies. Using a large-scale pharmacogenomics database, we identified drugs targeting the subtype gene signatures and assessed the potential clinical impacts of these drugs. We identified several potential candidate therapies for each molecular subtype, including possible responsiveness to Methylene Blue therapy for patients from our highest mortality subtype, C4. Notably, our drug repurposing analysis revealed a significant representation of anti-inflammatory monoclonal antibody therapies across molecular subtypes. The anti-correlated signatures in C1 and C2 suggest that monoclonal antibody therapies may not be effective for patients in both subtypes, which may explain why prior clinical trials have been unsuccessful. Altogether, our detailed molecular subtyping and analysis identify potential drug targets within each molecular subtype, with implications for future precision medicine for sepsis.

bioinformatics↗

bioRxiv2023

Regulation of inositol 5-phosphatase activity by the C2 domain of SHIP1 and SHIP2

SHIP1, an inositol 5-phosphatase, plays a central role in cellular signalling. As such, it has been implicated in many conditions. Exploiting SHIP1 as a drug target will require structural knowledge and the design of selective small molecules. We have determined apo, and magnesium and phosphate-bound structures of the phosphatase and C2 domains of SHIP1. The C2 domains of SHIP1 and the related SHIP2 modulate the activity of the phosphatase domain. To understand the mechanism, we performed activity assays, hydrogen-deuterium-exchange mass spectrometry and molecular dynamics on SHIP1 and SHIP2. Our findings demonstrate that the influence of the C2 domain is more pronounced for SHIP2 than SHIP1. We determined 91 structures of SHIP1 with fragments bound, with some near the interface between the two domains. We performed a mass spectrometry screen and determined four structures with covalent fragments. These structures could act as starting points for the development of potent, selective probes.

biochemistry↗

bioRxiv2023

Calorie Restriction Outperforms Bariatric Surgery in a Murine Model of Obesity and Triple-Negative Breast Cancer

Obesity promotes triple-negative breast cancer (TNBC), and effective interventions are urgently needed to break the obesity-TNBC link. Epidemiologic studies indicate that bariatric surgery reduces TNBC risk, while evidence is limited or conflicted for weight loss via low-fat diet (LFD) or calorie restriction (CR). Using a murine model of obesity- driven TNBC, we compared the antitumor effects of vertical sleeve gastrectomy (VSG) with LFD, chronic CR, and intermittent CR. Each intervention generated weight and fat loss and suppressed tumor growth relative to obese mice (greatest suppression with CR). VSG and CR regimens exerted both similar and unique effects, as assessed using multi-omic approaches, in reversing obesity-associated transcriptional, epigenetic, secretome, and microbiota changes and restoring antitumor immunity. Thus, in a murine model of TNBC, bariatric surgery and CR each reverse obesity-driven tumor growth via shared and distinct antitumor mechanisms, and CR is superior to VSG in reversing obesitys procancer effects.

cancer biology↗

bioRxiv2021

Differential chemoarchitecture of Purkinje neurons contributes to intrinsic firing properties

Purkinje cells (PCs) are central to cerebellar information coding and appreciation for the diversity of their firing patterns and molecular profiles is growing. Heterogeneous subpopulations of PCs have been identified that display differences in intrinsic firing properties without clear mechanistic insight into what underlies the divergence in firing parameters. Although long used as a general PC marker, we report that the calcium binding protein parvalbumin labels a subpopulation of PCs with a conserved distribution pattern across the animals examined. We trained a convolutional neural network to recognize the parvalbumin-positive subtype and create maps of whole cerebellar distribution and find that PCs within these areas have differences in spontaneous firing that can be modified by altering calcium buffer content. These subtypes also show differential responses to potassium and calcium channel blockade, suggesting a mechanistic role for variability in PC intrinsic firing through differences in ion channel composition. It is proposed that ion channels drive the diversity in PC intrinsic firing phenotype and parvalbumin calcium buffering provides capacity for the highest firing rates observed. These findings open new avenues for detailed classification of PC subtypes.

neuroscience↗

bioRxiv2019

Conditional, inducible gene silencing in dopamine neurons reveals a sex-specific role for Rit2 GTPase in acute cocaine response and striatal function

Dopamine (DA) signaling is critical for movement, motivation, and addictive behavior. The neuronal GTPase, Rit2, is enriched in DA neurons (DANs), binds directly to the DA transporter (DAT), and is implicated in several DA-related neuropsychiatric disorders. However, it remains unknown whether Rit2 plays a role in either DAergic signaling and/or DA-dependent behaviors. Here, we leveraged the TET-OFF system to conditionally silence Rit2 in Pitx3IRES2-tTA mouse DANs. Following DAergic Rit2 knockdown (Rit2-KD), mice displayed an anxiolytic phenotype, with no change in baseline locomotion. Further, males exhibited increased acute cocaine sensitivity, whereas DAergic Rit2-KD suppressed acute cocaine sensitivity in females. DAergic Rit2-KD did not affect presynaptic TH and DAT protein levels in females, nor was TH was affected in males; however, DAT was significantly diminished in males. Paradoxically, despite decreased DAT levels in males, striatal DA uptake was enhanced, but was not due to enhanced DAT surface expression in either dorsal or ventral striatum. Finally, patch recordings in nucleus accumbens (NAcc) medium spiny neurons (MSNs) revealed reciprocal changes in spontaneous EPSP (sEPSP) frequency in male and female D1+ and D2+ MSNs following DAergic Rit2-KD. In males, sEPSP frequency was decreased in D1+, but not D2+, MSNs, whereas in females sEPSP frequency decreased in D2+, but not D1+, MSNs. Moreover, DAergic Rit2-KD abolished the ability of cocaine to reduce sEPSP frequency in D1+, but not D2+, male MSNs. Taken together, our studies are among the first to acheive AAV-mediated, conditional and inducible DAergic knockdown in vivo. Importantly, our results provide the first evidence that DAergic Rit2 expression differentially impacts striatal function and DA-dependent behaviors in males and females.

neuroscience↗

bioRxiv2019

Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types

Identification of the cis-regulatory elements (CREs) that regulate gene expression in specific cell types is critical for defining the gene regulatory networks (GRNs) that control normal physiology and disease states. We previously utilized non-coding RNA (ncRNA) profiling to define CREs that comprise a GRN in the adult mouse heart1. Here, we applied ncRNA profiling to the mouse retina in the presence and absence of Nrl, a rod photoreceptor-specific transcription factor required for rod versus cone photoreceptor cell fate. Differential expression of Nrl-dependent ncRNAs positively correlated with differential expression of Nrl-dependent local genes. Two distinct Nrl-dependent regulatory networks were discerned in parallel: Nrl-activated ncRNAs were enriched for accessible chromatin in rods but not cones whereas Nrl-repressed ncRNAs were enriched for accessible chromatin in cones but not rods. Furthermore, differential Nrl-dependent ncRNA expression levels quantitatively correlated with photoreceptor cell type-specific ATAC-seq read density. Direct assessment of Nrl-dependent ncRNA-defined loci identified functional cone photoreceptor CREs. This work supports differential ncRNA profiling as a platform for identifying context-specific regulatory elements and provides insight into the networks that define photoreceptor cell types.

molecular biology↗

bioRxiv2018

Movement imitation depends on an abstract trajectory representation in dorsal premotor cortex

Humans are particularly good at copying novel and meaningless gestures. The mechanistic and anatomical basis for this specialized imitation ability remains largely unknown. One idea is that imitation occurs by matching body configurations. Here we propose an alternative route to imitation that depends on a body-independent representation of the trajectory path of the end-effector. We studied a group of patients with strokes in the left frontoparietal cortices. We found that they were equally impaired at imitating movement trajectories using the ipsilesional limb (i.e., the non-paretic side) that were cued either by an actor using their whole arm or just by a cursor, suggesting that body configuration is not always critical for imitation and that a representation of abstract trajectory shape may suffice. In addition, imitation ability was uncorrelated to the ability to identify the trajectory shape, suggesting a dissociation between producing trajectory shapes and perceiving their paths. Finally, a lesion-symptom mapping analysis found that imitation deficits were associated with lesions in left dorsal premotor but not parietal cortex. Together, these findings suggest a novel body-independent route to imitation that relies on the ability to plan abstract movement trajectories within dorsal premotor cortex.\n\nSignificance StatementThe ability to imitate is critical for rapidly learning to produce new gestures and actions, but how the brain translates observed movements into motor commands is poorly understood. Examining the ability of patients with strokes affecting the left hemisphere revealed that meaningless gestures can be imitated by succinctly representing only the motion of the hand in space, rather than the posture of the entire arm. Moreover, performance deficits correlated with lesions in dorsal premotor cortex, an area not previously associated with impaired imitation of arm postures. These findings thus describe a novel route to imitation that may also be impaired in some patients with apraxia.

neuroscience↗