Biology subjects

Atkinson, C.

Publications and source records attributed to Atkinson, C..

11 recordsLinked to original sources

bioRxiv2026

Vitamin D3 Deficiency Exacerbates Abdominal Aortic Aneurysm Progression Via Complement C3a Activation

Abdominal aortic aneurysm (AAA) is a chronic inflammatory vascular disease characterized by progressive extracellular matrix degradation, vascular smooth muscle cell (VSMC) loss, and immune cell infiltration, ultimately leading to aortic dilation and rupture. Although vitamin 25(OH)D3 deficiency has been associated with cardiovascular inflammation, its mechanistic role in AAA pathogenesis remains poorly defined. Here, we investigated the role of vitamin D{square} mediated signaling to regulate complement pathway activation, particularly the C3a axis, to modulate aneurysm development. Single cell-RNA sequencing analysis of human tissue demonstrated significant differences in Vitamin D and complement pathway-related genes in VSMCs in AAAs compared to control aortic tissue. Using a murine elastase-induced AAA model, we observed that vitamin D3-deficient diet significantly enhances aortic dilation, leukocyte infiltration, proinflammatory cytokine expression and elastin fragmentation, as well as decreases SMC -actin expression compared with vitamin D3-sufficient conditions. Furthermore, vitamin D3 deficiency was accompanied by increased aortic expression of complement component C3a that correlated with vascular inflammation and remodeling during AAA progression. Pharmacological blockade with a C3a receptor antagonist (C3aRA) markedly attenuated AAA formation in two established murine AAA models with concomitant reductions in proinflammatory cytokines and preservation of aortic wall structure. In vitro studies demonstrated that stimulation of VSMCs significantly increased C3a production, which was suppressed by calcitriol (active form of Vitamin D) treatment. These studies suggest that the vitamin D-C3a axis is a critical regulator of vascular inflammation and AAA progression, and postulate that restoring vitamin D{square} sufficiency or targeting C3a signaling may represent a novel therapeutic strategy to limit AAA growth and rupture. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=162 SRC="FIGDIR/small/730431v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@1e6a56dorg.highwire.dtl.DTLVardef@176b1b9org.highwire.dtl.DTLVardef@18e1fcdorg.highwire.dtl.DTLVardef@1c9eb4d_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2026

Neural mechanisms underlying leg muscle responses during cervical transcutaneous spinal cord stimulation

Transcutaneous spinal cord stimulation (tSCS) of the cervical spinal cord has been thought to modulate lumbar networks, leading to the hypothesis that leg muscle recruitment may occur via recruitment of long-range spinal connections between cervical and lumbar circuits. To directly test this hypothesis, we compared arm and leg muscle responses elicited in unimpaired participants (N = 12) by cervical tSCS with the anodes placed over the iliac crests, with the anodes placed over the clavicles, and with lumbar tSCS as a control for leg muscle recruitment via the posterior root-muscle reflex. The idea of tSCS targeting cervico-lumbar connectivity would suggest that cervical stimulation could evoke responses in leg muscles. However, in our experiments, leg responses via cervical tSCS were only observed when the anodes were placed over the iliac crests, but not over the clavicles. These leg muscle responses had shorter latencies than those with lumbar tSCS and showed minimal post-activation depression, indicating efferent rather than afferent recruitment. Therefore, changes in leg muscle excitability by cervical-iliac tSCS previously attributed to descending cervical circuits could instead be explained by direct recruitment of efferent fibers near the iliac anodes. These findings suggest that cervical tSCS alone does not engage leg muscle motoneurons via long-range spinal or bidirectional pathways. Therefore, our study highlights the need to carefully consider electrode configuration when interpreting cervical tSCS mechanisms and additional or unexpected rehabilitative effects that extend caudally from the cervical spinal cord.

neuroscience↗

bioRxiv2025

Exogenous BMP9 therapy ameliorates primary graft dysfunction post lung transplantation

Primary graft dysfunction (PGD) is a leading cause of early mortality after lung transplantation and is driven by ischemia-reperfusion injury (IRI), which destabilizes the pulmonary endothelium. Bone morphogenetic protein 9 (BMP9), a vascular quiescence factor of the TGF superfamily, maintains endothelial homeostasis through ALK-1/BMPR2-mediated signaling. Herein, this work identified a previously unrecognized suppression of BMP9 signaling during early reperfusion in a murine orthotopic lung transplant model. Allograft transcriptomic profiling revealed rapid downregulation of BMP9 pathway components, including Bmpr2, Acvrl1, Smad5, and Eng. Recombinant BMP9 administered at reperfusion enhanced Id1 expression in pulmonary endothelium, reduced neutrophil infiltration, preserved vascular barrier function, and improved oxygenation. In vitro, BMP9 attenuated proinflammatory cytokine release following simulated cold ischemia-reperfusion injury in human lung endothelial cells. Plasma from lung transplant recipients, regardless of PGD status, had impaired BMP9-induced ID1 expression in endothelial cells, with the most profound suppression observed in patients with interstitial lung disease. These findings implicate transient loss of BMP9 signaling as a key feature of transplant-induced vascular injury and support the therapeutic potential of BMP9 supplementation to restore endothelial homeostasis and improve early graft outcomes.

immunology↗

bioRxiv2025

Evaluation of Ventilation at 10C as the Optimal Storage Condition for Donor Lungs in a Murine Model

RationaleCold static preservation at 4{degrees}C is the clinical standard for donor lung storage but is limited to 6-8 hours of cold ischemia. Static storage at 10{degrees}C has been shown to extend ischemia times and improve lung health. Given that lungs can maintain aerobic metabolism ex vivo, we hypothesized that adding ventilation at 10{degrees}C would further prolong preservation by stimulating aerobic metabolism. MethodsLungs were procured from C57Bl/6 mice and then stored for 24h with ventilation at 10{degrees}C (n=4), statically at 10{degrees}C (n=4), or statically at 4{degrees}C (n=4). Respiratory mechanics were evaluated using a FlexiVent system. Cellular viability was assessed via flow cytometry. Complement shedding was evaluated by enzyme-linked immunosorbent assay. Histologic evidence of lung injury was assessed by H&E staining. ResultsDonor lungs stored with ventilation at 10{degrees}C exhibited significantly reduced histologic injury scores compared to static storage at 4{degrees}C (p = 0.0062). Ventilation also decreased complement C3 shedding (p < 0.01), apoptosis (p < 0.05), cytochrome c release (p = 0.0014), and ROS production (p = 0.0008) compared to statically stored lungs at 4{degrees}C and 10{degrees}C. Functionally, ventilated lungs demonstrated improved respiratory mechanics with lower airway resistance (p = 0.021) and increased compliance (p = 0.023) compared to static storage at 10{degrees}C. ConclusionsVentilating lungs at 10{degrees}C compared to static cold storage appears to result in healthier and more functional lung tissue and may extend the preservation times of donor organs for lung transplantation.

physiology↗

bioRxiv2025

Transient effects in corticospinal and reticulospinal tract excitability induced by motor skill and isometric resistance training

Motor skill and resistance training are commonly used in rehabilitation to enhance neural plasticity. Nonetheless, how each modality impacts the excitability of corticospinal and reticulospinal pathways controlling the lower limb remains poorly understood. Here, we tested how single 30-minute sessions of cue-paced motor skill and isometric resistance training modulate corticospinal, reticulospinal, and spinal excitability in unimpaired adults (N = 23). Using motor-evoked potentials via transcranial magnetic stimulation, we found that both training types increased corticospinal excitability, with more substantial effects following motor skill training. In contrast, reticulospinal tract excitability--assessed by StartReact responses--and spinal excitability--assessed by H/M ratios, F-wave response amplitude, and persistence--remained largely unchanged. These results suggest that short-term training selectively enhances corticospinal tract excitability without a measurable impact on spinal or reticulospinal circuits. This pathway-specific response may inform strategies for targeting neural plasticity in rehabilitation.

neuroscience↗

bioRxiv2024

Predicting Primary Graft Dysfunction in Lung Transplantation: Machine Learning-Guided Biomarker Discovery

BACKGROUNDThere is an urgent need to better understand the pathophysiology of primary graft dysfunction (PGD) so that point-of-care methods can be developed to predict those at risk. Here we utilize a multiplex multivariable approach to define cytokine, chemokines, and growth factors in patient-matched biospecimens from multiple biological sites to identify factors predictive of PGD. METHODSBiospecimens were collected from patients undergoing bilateral LTx from three distinct sites: donor lung perfusate, post-transplant bronchoalveolar lavage (BAL) fluid (2h), and plasma (2h and 24h). A 71-multiplex panel was performed on each biospecimen. Cross-validated logistic regression (LR) and random forest (RF) machine learning models were used to determine whether analytes in each site or from combination of sites, with or without clinical data, could discriminate between PGD grade 0 (n = 9) and 3 (n = 8). RESULTSUsing optimal AUROC, BAL fluid at 2h was the most predictive of PGD (LR, 0.825; RF, 0.919), followed by multi-timepoint plasma (LR, 0.841; RF, 0.653), then perfusate (LR, 0.565; RF, 0.448). Combined clinical, BAL, and plasma data yielded strongest performance (LR, 1.000; RF, 1.000). Using a LASSO of the predictors obtained using LR, we selected IL-1RA, BCA-1, and Fractalkine, as most predictive of severe PGD. CONCLUSIONSBAL samples collected 2h post-transplant were the strongest predictors of severe PGD. Our machine learning approach not only identified novel cytokines not previously associated with PGD, but identified analytes that could be used as a point-of-care cytokine panel aimed at identifying those at risk for developing severe PGD.

immunology↗

bioRxiv2024

Lipoxin A4/FPR2 signaling mitigates ferroptosis of alveolar epithelial cells via NRF2-dependent pathway during lung ischemia-reperfusion injury

BACKGROUNDPost-lung transplantation (LTx) injury can involve sterile inflammation due to ischemia-reperfusion injury (IRI). We investigated the cell-specific role of ferroptosis (excessive iron-mediated cell death) in mediating lung IRI and determined if specialized pro-resolving mediators such as Lipoxin A4 (LxA4) can protect against ferroptosis in lung IRI. METHODSSingle-cell RNA sequencing of lung tissue from post-LTx patients was analyzed. Lung IRI was evaluated in C57BL/6 (WT), formyl peptide receptor 2 knockout (Fpr2-/-) and nuclear factor erythroid 2-related factor 2 knockout (Nrf2-/-) mice using a hilar-ligation model with or without LxA4 administration. Furthermore, the protective efficacy of LxA4 was evaluated employing a murine orthotopic LTx model and in vitro studies using alveolar type II epithelial (ATII) cells. RESULTSDifferential expression of ferroptosis-related genes was observed in post-LTx patient samples compared to healthy controls. A significant increase in the levels of oxidized lipids and reduction in the levels of intact lipids were observed in mice subjected to IRI compared to shams. Furthermore, pharmacological inhibition of ferroptosis with liproxstatin-1 mitigated lung IRI and lung dysfunction. Importantly, LxA4 treatment attenuated pulmonary dysfunction, ferroptosis and inflammation in WT mice subjected to lung IRI, but not in Fpr2-/- or Nrf2-/-mice, after IRI. In the murine LTx model, LxA4 treatment increased PaO2 levels and attenuated lung IRI. Mechanistically, LxA4-mediated protection involves increase in NRF2 activation and glutathione concentration as well as decrease in MDA levels in ATII cells. CONCLUSIONSLxA4/FPR2 signaling on ATII cells mitigates ferroptosis via NRF2 activation and protects against lung IRI.

immunology↗

bioRxiv2024

MerTK-dependent efferocytosis by monocytic-MDSCs mediates resolution of post-lung transplant injury

ABSTRACTO_ST_ABSRationaleC_ST_ABSPatients with end stage lung diseases require lung transplantation (LTx) that can be impeded by ischemia-reperfusion injury (IRI) leading to subsequent chronic lung allograft dysfunction (CLAD) and inadequate outcomes. ObjectivesWe examined the undefined role of MerTK (receptor Mer tyrosine kinase) on monocytic myeloid-derived suppressor cells (M-MDSCs) in efferocytosis (phagocytosis of apoptotic cells) to facilitate resolution of lung IRI. MethodsSingle-cell RNA sequencing of lung tissue and BAL from post-LTx patients was analyzed. Murine lung hilar ligation and allogeneic orthotopic LTx models of IRI were used with Balb/c (WT), cebpb-/- (MDSC-deficient), Mertk-/- or MerTK-CR (cleavage resistant) mice. Lung function, IRI (inflammatory cytokine and myeloperoxidase expression, immunohistology for neutrophil infiltration), and flow cytometry of lung tissue for efferocytosis of apoptotic neutrophils were assessed in mice. Measurements and Main ResultsA significant downregulation in MerTK-related efferocytosis genes in M-MDSC populations of CLAD patients compared to healthy subjects was observed. In the murine IRI model, significant increase in M-MDSCs, MerTK expression and efferocytosis was observed in WT mice during resolution phase that was absent in cebpb-/- Land Mertk-/- mice. Adoptive transfer of M-MDSCs in cebpb-/- mice significantly attenuated lung dysfunction, and inflammation leading to resolution of IRI. Additionally, in a preclinical murine orthotopic LTx model, increases in M-MDSCs were associated with resolution of lung IRI in the transplant recipients. In vitro studies demonstrated the ability of M-MDSCs to efferocytose apoptotic neutrophils in a MerTK-dependent manner. ConclusionsOur results suggest that MerTK-dependent efferocytosis by M-MDSCs can significantly contribute to the resolution of post-LTx IRI.

immunology↗

bioRxiv2022

Kidney tubular epithelial cell ferroptosis links glomerular injury to tubulointerstitial pathology in lupus nephritis

ObjectiveAn appreciation of factors that lead to tubular injury in lupus nephritis is lacking. Iron accumulates in the kidney tubules of nephritic patients and lupus-prone nephritic mice. Ferroptosis is a druggable, iron-dependent form of cell death that has received little attention in lupus nephritis. This study investigated whether intra-renal ferroptosis is a target for intervention in lupus nephritis. MethodsKidneys of lupus nephritis patients and two spontaneous murine models of lupus nephritis were characterized for ferroptosis using protein, RNA, and lipidomics-based approaches. Susceptibility of heavy chain ferritin (FtH1; an essential iron sequestration protein) deficient proximal tubular epithelial cells (PTECs) was studied using nephrotoxic serum nephritis and FtH1 knockdown human PTECs. The benefit of Liproxstatin-2, a novel second-generation ferroptosis, was evaluated using human PTECs exposed to lupus nephritis patients serum. ResultsHuman and murine nephritic kidneys have the characteristic markers of ferroptosis, such as 4-hydroxynonenal and acyl-CoA synthetase long-chain family member 4, mainly in the tubular segments. Murine kidneys showed impairment in the glutathione synthesis pathway, decreased expression of glutathione peroxidase 4, a glutathione-dependent ferroptosis inhibitor, and characteristic ferroptotic lipid signature. Loss of FtH1 increased PTEC pathology independent of glomerular injury. These findings were recapitulated in human PTECs. Of translational relevance, Liproxstatin-2 demonstrated a prophylactic and therapeutic benefit in mitigating lupus nephritis patient serum-induced PTEC ferroptosis. ConclusionOur findings highlight tubular cell ferroptosis as a pathological feature in human and murine lupus nephritis and identify ferroptosis inhibitors as potential novel adjunct therapeutics to treat lupus nephritis.

immunology↗

bioRxiv2022

Computational modeling of macrophage iron sequestration during host defense against Aspergillus

Iron is essential to the virulence of Aspergillus species, and restricting iron availability is a critical mechanism of antimicrobial host defense. Macrophages recruited to the site of infection are at the crux of this process, employing multiple intersecting mechanisms to orchestrate iron sequestration from pathogens. To gain an integrated understanding of how this is achieved in invasive aspergillosis, we generated a transcriptomic time-series of the response of human monocyte-derived macrophages to Aspergillus and used this and the available literature to construct a mechanistic computational model of iron handling of macrophages during this infection. We found an overwhelming macrophage response beginning 2-4 hours after exposure to the fungus, which included upregulated transcription of iron import proteins transferrin receptor-1, divalent metal transporter-1, and ZIP family transporters, and downregulated transcription of the iron exporter ferroportin. The computational model, based on a discrete dynamical systems framework, consisted of 21 3-state nodes, and was validated with additional experimental data that were not used in model generation. The model accurately captures the steady state and the trajectories of most of the quantitatively measured nodes. In the experimental data, we surprisingly found that transferrin receptor-1 upregulation preceded the induction of inflammatory cytokines, a feature that deviated from model predictions. Model simulations suggested that direct induction of TfR1 after fungal recognition, independent of the Iron Regulatory Protein - Labile Iron Pool system, explains this finding. We anticipate that this model will contribute to a quantitative understanding of iron regulation as a fundamental host defense mechanism during aspergillosis. ImportanceInvasive pulmonary aspergillosis is a major cause of death among immunosuppressed individuals despite the best available therapy. Depriving the pathogen of iron is an essential component of host defense in this infection, but the mechanisms by which the host achieves this are complex. To understand how recruited macrophages mediate iron deprivation during the infection, we developed and validated a mechanistic computational model that integrates the available information in the field. The insights provided by this approach can help in designing iron modulation therapies as anti-fungal treatments.

immunology↗

bioRxiv2021

Phenogenomic characterization of a newly domesticated and novel species from the genus Verrucosispora

The concept of bacterial dark matter stems from our inability to culture most microbes and represents a fundamental hole in our knowledge of microbial diversity. Herein we present the domestication of such an organism: a previously uncultured, novel species from the rare-Actinomycetes genus Verrucosispora. Although initial recovery took >4 months, isolation of phenotypically distinct, domesticated generations occurred within weeks. Two isolates were subjected to phenogenomic analyses, revealing domestication correlated with enhanced growth rates in nutrient-rich media, but diminished capacity to metabolize diverse amino acids. This is seemingly mediated by genomic decay through the pseudogenization of amino acids metabolism genes. Conversely, later generational strains had enhanced spore germination rates, potentially through the reversion of a sporulation-associated kinase from pseudogene to true gene status. We observed that our most wild-type isolate had the greatest potential for antibacterial activity, which correlated with extensive mutational attrition of biosynthetic gene clusters in domesticated strains. Comparative analyses revealed wholesale genomic reordering in strains, with widespread SNP, indel and pseudogene mutations observed. We hypothesize that domestication of this previously unculturable organism resulted from the shedding of genomic flexibility required for life in a dynamic marine environment, parsing out genetic redundancy to allow for a newfound cultivable amenability.

microbiology↗