Biology subjects

McConnell, M.

Publications and source records attributed to McConnell, M..

9 recordsLinked to original sources

bioRxiv2026

The structure of the Salmonella phage epsilon15 tailspike reveals multiple O-antigen binding sites and a protruding esterase domain

Many bacteriophages use tailspikes to degrade host bacterial polysaccharides, facilitating access to the outer membrane. The homotrimeric tailspikes of the Salmonella phage epsilon15 feature a slender phage-binding domain, a kink, and a barrel-shaped section with three petal-like protrusions. Here, we present the crystal structures of the monomeric protruding petal domain alone and of the trimeric barrel-shaped section with three petal domains. The barrel-shaped section includes a trimeric beta-helix, typical of phage tailspikes, alongside a trimeric beta-sandwich domain. The petal domain exhibits a fold characteristic of the serine-glycine-asparagine-histidine (SGNH) esterase family. Co-crystallisation with O-antigen fragments identified four binding sites on the tailspike: two adjacent sites on the surface of the triple beta-helix, one in the beta-sandwich domain and a fourth near the petal esterase site. These binding sites align with the expected orientation of the phage just before DNA transfer. Nuclear magnetic resonance spectroscopy and site-directed mutagenesis revealed an endorhamnosidase activity, showed that the reaction mechanism proceeds by inversion of the configuration and revealed that the active site is located at the junction of the two beta-helix binding sites. Analogous experiments also revealed an esterase site in the petal domain. Together, the structural and functional insights suggest a dual role for the phage epsilon15 tailspike: de-acetylation of the O-antigen, potentially affecting the local structure and lipopolysaccharide flexibility, plus cleavage of the O-antigen, enabling the phage to approach the bacterial membrane.

biochemistry↗

bioRxiv2026

Dismantling Chromosomal Stasis Across the Eukaryotic Tree of Life

Chromosome number shapes genome organization, recombination, and speciation, yet how fast it evolves across the tree of life has never been measured. We analyzed 63,682 karyotypes across 55 eukaryotic clades and found that dysploidy rates vary by 844-fold, from approximately 0.0008 to 0.7 events per million years. This variation does not follow kingdom boundaries or deep phylogeny; intraclade variance exceeds interclade differences by more than an order of magnitude. Even birds, the textbook example of chromosomal stasis, exceed the global median rate once microchromosome dynamics are resolved. Contrasting the stasis of Odonata with the volatility of Orchidaceae reveals that life history and population structure, rather than deep phylogenetic constraints, govern the tempo of karyotypic change.

evolutionary biology↗

bioRxiv2024

Cortical inhibitory parvalbumin interneurons exhibit metabolic specializations coordinated by PGC-1α that are lost in rodents and humans after traumatic brain injury

Parvalbumin-positive interneurons (PV-INs) regulate neuronal and circuit activity, and their dysfunction is observed across neurological conditions, including traumatic brain injury (TBI), epilepsy, Alzheimers disease, and schizophrenia. PV-INs are particularly vulnerable to cell loss, potentially due to their increased metabolic demands arising from their uniquely high level of electrical activity, which render them susceptible to metabolic pressure. Here, we use single-nucleus RNA-sequencing (snRNAseq) data from a rodent model of TBI, as well as human TBI data, and demonstrate PV-INs have unique metabolic specializations that are lost after injury and can be rescued by in vivo treatment with the glycolytic inhibitor, 2-deoxyglucose. We generated a novel PV-IN transcriptional identity module comprised primarily of genes encoding specialized ion channels, metabolic enzymes, and synaptic machinery, that identifies heterogenous subsets of injury-associated PV-INs with loss of PV-IN transcriptional identity. We show that changes in metabolic specialization are coupled to changes in transcriptional identity in PV-INs and implicate the PV-IN-enriched transcriptional co-activator, Ppargc1a, as a key driver of PV-IN transcriptional metabolic dysfunction. We also identify a family of long non-coding RNAs enriched in this subset of transcriptionally dysfunctional PV-INs that negatively correlates with PV-IN metabolic specialization. Lastly, we utilize these tools to interrogate a published human TBI snRNAseq data set and find nearly identical changes, underscoring the importance of PV-IN metabolic dysfunction in the pathology of TBI.

neuroscience↗

bioRxiv2024

Cbfβ regulates Wnt/β-catenin, Hippo/Yap, and TGFβ signaling pathways in articular cartilage homeostasis and protects from ACLT surgery-induced osteoarthritis

As the most common degenerative joint disease, osteoarthritis (OA) contributes significantly to pain and disability during aging. Several genes of interest involved in articular cartilage damage in OA have been identified. However, the direct causes of OA are poorly understood. Evaluating the public human RNA-seq dataset showed that Cbf{beta}, (subunit of a heterodimeric Cbf{beta}/Runx1,Runx2, or Runx3 complex) expression is decreased in the cartilage of patients with OA. Here, we found that the chondrocyte-specific deletion of Cbf{beta} in tamoxifen-induced Cbf{beta}f/fCol21-CreERT mice caused a spontaneous OA phenotype, worn articular cartilage, increased inflammation, and osteophytes. RNA-sequencing analysis showed that Cbf{beta} deficiency in articular cartilage resulted in reduced cartilage regeneration, increased canonical Wnt signaling and inflammatory response, and decreased Hippo/YAP signaling and TGF-{beta} signaling. Immunostaining and western blot validated these RNA-seq analysis results. ACLT surgery-induced OA decreased Cbf{beta} and Yap expression and increased active {beta}-catenin expression in articular cartilage, while local AAV-mediated Cbf{beta} overexpression promoted Yap expression and diminished active {beta}-catenin expression in OA lesions. Remarkably, AAV-mediated Cbf{beta} overexpression in knee joints of mice with OA showed the significant protective effect of Cbf{beta} on articular cartilage in the ACLT OA mouse model. Overall, this study, using loss-of-function and gain-of-function approaches, uncovered that low expression of Cbf{beta} may be the cause of OA. Moreover, Local admission of Cbf{beta} may rescue and protect OA through decreasing Wnt/{beta}-catenin signaling, and increasing Hippo/Yap signaling and TGF{beta}/Smad2/3 signaling in OA articular cartilage, indicating that local Cbf{beta} overexpression could be an effective strategy for treatment of OA.

pathology↗

bioRxiv2021

Quantitative systems pharmacology modeling of avadomide-induced neutropenia enables virtual clinical dose and schedule finding studies

Avadomide is a cereblon E3 ligase modulator and a potent antitumor and immunomodulatory agent. Avadomide trials are challenged by neutropenia as a major adverse event and a dose-limiting toxicity. Intermittent dosing schedules supported by preclinical data provide a strategy to reduce frequency and severity of neutropenia, however the identification of optimal dosing schedules remains a clinical challenge. Quantitative Systems Pharmacology (QSP) modeling offers opportunities for virtual screening of efficacy and toxicity levels produced by alternative dose and schedule regimens, thereby supporting decision-making in translational drug development. We formulated a QSP model to capture the mechanism of avadomide-induced neutropenia, which involves cereblon-mediated degradation of transcription factor Ikaros, resulting in a maturation block of the neutrophil lineage. The neutropenia model was integrated with avadomide-specific pharmacokinetic and pharmacodynamic models to capture dose-dependent effects. Additionally, we generated a disease-specific virtual patient population to represent the variability in patient characteristics and response to treatment observed for a diffuse large B-cell lymphoma trial cohort. Model utility was demonstrated by simulating avadomide effect in the virtual population for various dosing schedules and determining the incidence of high-grade neutropenia, its duration, and the probability of recovery to low grade-neutropenia.

pharmacology and toxicology↗

bioRxiv2020

Alcohol-induced Hsp90 acetylation is a novel driver of liver sinusoidal endothelial dysfunction and alcoholic liver disease

BackgroundIt is unknown whether liver sinusoidal endothelial cells (LSECs) metabolize alcohol. Chronic alcohol consumption decreases endothelial nitric oxide synthase (eNOS)-derived NO production typical of LSEC dysfunction. Heat shock protein 90 (Hsp90) interacts with eNOS to increase its activity. Cytochrome P450 2E1 (CYP2E1) is a key enzyme in alcohol metabolism and facilitates protein acetylation via acetyl-CoA, but its expression in LSECs is unknown. This study investigates alcohol metabolism by LSECs, the mechanism of alcohol-induced LSEC dysfunction and a potential therapeutic approach for alcohol-induced liver injury. MethodsPrimary human, rat and mouse LSECs were used. Histone deacetylase 6 (HDAC6) was overexpressed specifically in liver ECs using an adeno-associated virus (AAV)-mediated gene delivery system to decrease Hsp90 acetylation in ethanol fed mice. ResultsLSECs expressed CYP2E1 and alcohol dehydrogenase 1 (ADH1) and metabolized alcohol. Ethanol induced CYP2E1 in LSECs, but not ADH1. Alcohol metabolism by CYP2E1 increased Hsp90 acetylation and decreased its interaction with eNOS along with a decrease in NO production. A non-acetylation mutant of Hsp90 increased its interaction with eNOS and NO production, whereas a hyper-acetylation mutant decreased NO production, compared with wildtype Hsp90. These results indicate that Hsp90 acetylation is responsible for decreases in its interaction with eNOS and eNOS-derived NO production. Adeno-associated virus 8 (AAV8)-driven HDAC6 overexpression specifically in liver ECs deacetylated Hsp90, restored Hsp90s interaction with eNOS and ameliorated alcohol-induced liver injury in mice. ConclusionRestoring LSEC function is important for ameliorating alcohol-induced liver injury. To this end, blocking acetylation of Hsp90 specifically in LSECs via AAV-mediated gene delivery has the potential to be a new therapeutic strategy.

molecular biology↗

bioRxiv2020

Enhanced meningeal lymphatic drainage ameliorates neuroinflammation and hepatic encephalopathy in cirrhotic rats

Background and aimsHepatic encephalopathy (HE) is a serious neurological complication in patients with liver cirrhosis. Nothing is known about the role of the meningeal lymphatic system in HE. We tested our hypothesis that enhancement of meningeal lymphatic drainage could decrease neuroinflammation and ameliorate HE. MethodsA 4-week bile duct ligation (BDL) model was used to develop cirrhosis with HE in rats. Brain inflammation in patients with HE was evaluated using archived GSE41919. Motor function of rats was assessed by the rotarod test. AAV8-VEGF-C was injected into the cisterna magna of BDL rats one day after surgery to induce meningeal lymphangiogenesis. ResultsCirrhotic rats with HE showed significantly increased microglia activation in the middle region of the cortex (p<0.001) as well as increased neuroinflammation as indicated by significant increases in IL-1{beta}, INF{gamma}, TNF and Iba1 expression in at least one of the three regions of the cortex. Motor function was also impaired in rats with HE (p<0.05). Human brains of cirrhotic patients with HE also exhibited upregulation of pro-inflammatory genes (NF-{kappa}{beta}, Iba1, TNF and IL-1{beta}) (n=6). AAV8-VEGF-C injection significantly increased meningeal lymphangiogenesis (p=0.035) and tracer dye uptake in the anterior and middle regions of the cortex (p=0.006 & 0.003, respectively), their corresponding meninges (p=0.086 & 0.006, respectively) and the draining lymph nodes (p=0.02). Further, AAV8-VEGF-C decreased microglia activation (p<0.001) and neuroinflammation, and ameliorated motor dysfunction (p=0.024). ConclusionPromoting meningeal lymphatic drainage and enhancing waste clearance improves HE. Manipulation of meningeal lymphangiogenesis could be a new therapeutic strategy for the treatment of HE.

neuroscience↗

bioRxiv2020

Single-cell transcriptomics reveals zone-specific alterations of liver sinusoidal endothelial cells in cirrhosis

Dysfunction of liver endothelial cells (ECs), particularly sinusoidal endothelial cells (LSECs), is permissive for the progression of liver fibrosis/cirrhosis and responsible for its clinical complications. Here, we have mapped the spatial distribution of heterogeneous liver ECs in normal versus cirrhotic mouse livers and identified zone-specific transcriptomic changes of LSECs associated with liver cirrhosis using single-cell RNA sequencing technology. We identified 6 clusters of liver EC populations including 3 clusters of LSECs, 2 clusters of vascular ECs and 1 cluster of lymphatic ECs. To add finer detail, we mapped the 3 clusters of LSECs to Zones 1 to 3. We found that heterogeneous liver EC identities are conserved even in liver cirrhosis and that Zone 3 LSECs are most susceptible to damage associated with liver cirrhosis, demonstrating increased capillarization and decreased ability to regulate endocytosis. Altogether, this study deepens our knowledge of the pathogenesis of liver cirrhosis at a spatial, cell-specific level, which is indispensable for the development of novel therapeutic strategies to target the most highly dysfunctional liver ECs.

cell biology↗

bioRxiv2019

ADAPTS: Automated Deconvolution Augmentation of Profiles for Tissue Specific cells

Immune cell infiltration of tumors can be an important component for determining patient outcomes, e.g. by inferring immune cell presence by deconvolving gene expression data drawn from a heterogenous mix of cell types. One particularly powerful family of deconvolution techniques uses signature matrices of genes that uniquely identify each cell type as determined from cell type purified gene expression data. Many methods of this type have been recently published, often including new signature matrices appropriate for a single purpose, such as investigating a specific type of tumor. The package ADAPTS helps users make the most of this expanding knowledge base by introducing a framework for cell type deconvolution. ADAPTS implements modular tools for customizing signature matrices for new tissue types by adding custom cell types or building new matrices de novo, including from single cell RNAseq data. It includes a common interface to several popular deconvolution algorithms that use a signature matrix to estimate the proportion of cell types present in heterogenous samples. ADAPTS also implements a novel method for clustering cell types into groups that are hard to distinguish by deconvolution and then re-splitting those clusters using hierarchical deconvolution. We demonstrate that the techniques implemented in ADAPTS improve the ability to reconstruct the cell types present in a single cell RNAseq data set in a blind predictive analysis. ADAPTS is currently available for use in R on CRAN and GitHub.

biophysics↗