Biology subjects

Fenton, R. A.

Publications and source records attributed to Fenton, R. A..

8 recordsLinked to original sources

bioRxiv2026

Deep visual proteomics reveals distinct proximal tubular and glomerular injury programs in experimental diabetic kidney disease

Background: Diabetic kidney disease (DKD) is the leading cause of chronic kidney disease (CKD). However, most proteomic studies of DKD rely on bulk kidney tissue, which cannot distinguish the contribution or response of individual nephron compartments to injury. Methods: Diabetes was induced in male mice by streptozotocin (STZ) injections. After 16-weeks, the mice and vehicle-treated controls were characterized physiologically, biochemically, and histologically. A deep learning-powered Deep Visual Proteomics (DVP) pipeline, validated against manual annotation, was adapted to isolate proximal tubule (PT) and glomeruli from Megalin stained kidney sections by automated laser microdissection. Bulk kidney, PT, and glomerular proteomes were generated by data independent acquisition mass spectrometry. PT-enriched candidates were prioritized using a composite scoring approach and compared with human tubulointerstitial proteomic data from the Kidney Precision Medicine Project. Results: STZ mice developed sustained hyperglycaemia and albuminuria, alongside elevated markers of tubular injury and interstitial fibrosis. Segmentation models isolated PT and glomeruli with high fidelity (Dice coefficients 0.878 and 0.914; area correlations r=0.993 and r=0.996). Compartment-resolved proteomics determined that PT and glomeruli underwent largely distinct, non-overlapping remodelling: PT exhibited loss of proteostatic, cell cycle, and structural programs with compensatory mitochondrial and lipid metabolic upregulation, whereas glomeruli showed broad loss of oxidative metabolic capacity without any compensatory metabolic program. Fourteen of the top twenty prioritized PT candidates, including LARS2 and ANXA2, changed in the same direction in human CKD tubulointerstitial proteomic data. The STZ PT proteome correlated significantly with this human dataset, while the glomerular comparison did not. Conclusions: Compartment-resolved and deep learning-guided visual proteomics can uncover divergent, biologically coherent PT and glomerular injury programs in DKD that are masked in bulk tissue analysis. A PT injury signature was uncovered that is partially conserved in human CKD, identifying novel candidate mechanisms and biomarkers for future exploration.

pathology↗

bioRxiv2026

Interstitial macrophages drive chronic lung allograft dysfunction

Despite immunosuppressive regimens targeting adaptive immunity, chronic lung allograft dysfunction (CLAD) remains the major obstacle to durable lung allograft survival. Here, we identify colony-stimulating factor 1 receptor (CSF1R)-expressing interstitial macrophages as critical orchestrators of CLAD. Using lung tissue from patients with CLAD and a mouse model of mismatched lung transplantation, we show that both donor-derived tissue-resident and recipient- monocyte-derived interstitial macrophages spatially co-localize within peribronchial immune aggregates in patients with CLAD. These interstitial macrophages express distinct cytokine programs that include those implicated in the recruitment of T and B cells. Pharmacological inhibition of CSF1R after lung transplantation in mice reduced interstitial macrophage abundance and attenuated CLAD pathology. Our findings identify donor- and recipient-derived interstitial macrophages as upstream regulators of CLAD and suggest CSF1R as a therapeutic target for its prevention and treatment.

immunology↗

bioRxiv2026

Regulation of the Na-K-2Cl cotransporter NKCC2 by ubiquitylation

NKCC2, localized to the apical membrane of thick ascending limb epithelial cells, is essential for renal salt handling and systemic electrolyte homeostasis. NKCC2 undergoes extensive ubiquitylation, with the E3 protein ligase Nedd4-2 implicated as a key regulator. However, progress has been limited by challenges expressing NKCC2 in mammalian cell lines, hindering mechanistic studies of NKCC2 ubiquitylation. Therefore, the aims of this study were to develop a mammalian cell model enabling mechanistic investigations of NKCC2 ubiquitylation, including the role of Nedd4-2 and the functional consequences of site-specific modification. A tetracycline-inducible MDCKI cell line was generated expressing human NKCC2 and used to assess Nedd4-2-dependent and site-specific ubiquitylation of NKCC2 using biochemical, imaging, and functional assays. The MDCKI cell line demonstrated stable, inducible expression of full-length human NKCC2. In this cell line, mutating the ubiquitylation site at K871 increased membrane abundance and uptake activity, without altering internalization rates. Nedd4-2 co-immunoprecipitated with NKCC2, and Nedd4-2 deletion increased total, but not membrane NKCC2 abundance. In summary, ubiquitylation on NKCC2 at K871 plays a key role in controlling NKCC2 membrane localization and thus function. Although Nedd4-2 can modulate NKCC2 abundance, it is not involved in NKCC2 trafficking. We conclude that the generated cell line provides a robust model for mechanistic studies of NKCC2 and will aid studies examining posttranslational regulation of NKCC2.

molecular biology↗

bioRxiv2026

Glutamate transporter xCT is important for cGAS-dependent interferon responses to DNA and to HSV-1

Metabolic reprogramming is a key component of antiviral immunity, yet how metabolite transport regulates innate immune signaling remains incompletely understood. Here, we show that infection with herpes simplex virus 1 (HSV-1) and stimulation with cytosolic DNA induce the cellular export of glutamate via the xCT (SLC7A11) transporter and that inhibition of xCT reduces cellular resistance to viral replication. Mechanistically, xCT inhibition impaired cGAS-STING signaling by reducing DNA-induced cGAMP production, thereby diminishing type I interferon (IFN/{beta}) responses and downstream induction of interferon-stimulated genes. Interestingly, modulating intracellular glutamate levels through inhibition of other glutamate pathways, e.g., glutaminolysis or glutamate import, also affected cellular IFN responses, suggesting that glutamate is a central control knob for DNA sensing. Finally, we demonstrate that HSV-1 suppresses xCT expression via a mechanism dependent on the immediate early viral protein ICP27, thereby promoting viral replication by limiting cGAS-dependent IFN induction. Together, these findings identify xCT-dependent glutamate transport as a critical metabolic regulator of cGAS-STING-mediated antiviral immunity.

immunology↗

bioRxiv2026

Sex-specific remodeling of the human adipose tissue vascular niche in obesity

AO_SCPLOWBSTRACTC_SCPLOWObesity remodels the subcutaneous adipose tissue (SAT) vasculature and contributes to cardiometabolic risk, yet potential sex differences in this process remain poorly defined. Here, we integrated single-nucleus transcriptomics and histological analyses of human SAT to reveal pronounced sexual dimorphism within the vascular niche. Obese males exhibit mural cell loss, increased collagen deposition, and inflammatory endothelial activation, including enhanced antigen presentation programs. In contrast, females display preserved mural coverage and increased lipid-handling and redox-adaptive pathways. These coordinated structural and transcriptional differences position the adipose endothelium as a sex-divergent regulator of obesity-associated cardiometabolic vulnerability.

cell biology↗

bioRxiv2025

Single-cell proteomics: a powerful new tool to study kidney cell heterogeneity

BackgroundTechnological advancements in protein mass spectrometry have significantly enhanced analytical sensitivity and throughput, enabling single-cell proteomics by mass spectrometry (SCP-MS) to become reality. SCP-MS allows high-resolution analysis of cellular heterogeneity and function, bypassing bulk analysis limitations. Here, we used SCP-MS to document at the protein level the cellular diversity of mouse kidney cells. We further focused SCP-MS on low abundance distal convoluted tubule (DCT) cells that are essential for body electrolyte homeostasis and blood pressure control. MethodsMouse kidney cells were isolated via enzymic digestion and single-cells isolated using fluorescence- activated cell sorting (FACS). DCT cells were isolated from mice with GFP expression specifically in the DCT (parvalbumin-GFP) using a similar workflow. SCP-MS analyses was performed using an Orbitrap Ascend Mass Spectrometer with a FAIMS Pro Duo interface coupled with Wide ISolation window High-resolution MS1 Data Independent Acquisition (WISH-DIA). Spectronaut was used for protein identification and quantification, and cell-type annotation and clustering were performed in Python by scanpy implementation. ResultsWorkflow benchmarking using Hela cells confirmed a successful SCP-MS setup. From 768 single mouse kidney cells, SCP-MS identified 2626 unique proteins. Computational approaches resolved various nephron segments, including distinct DCT populations. From enriched DCT cells, 1912 proteins were identified, enabling classification of three populations - DCT1, DCT2, and a proliferative subset (ProLIF) that represented a transient state between DCT1 and DCT2. ProLIF cells had elevated abundance of the sodium-chloride cotransporter NCC and represented approximately 33% of DCT cells, substantially exceeding previous transcriptomic estimates of ProLIF cell frequency (~0.1%). High proliferation (~39%) of DCT cells was confirmed using immunohistochemistry. ConclusionsThis SCP-MS analysis of mouse kidney uncovered significant cellular heterogeneity not captured effectively using transcriptomics. Despite imitations in proteome depth and throughput, SCP-MS provides a powerful approach for investigating kidney cellular dynamics at the protein level. Key pointsO_LIWe developed a single-cell proteomics by mass spectrometry (SCP-MS) workflow identifying up to ~2,000 proteins in a single mouse kidney cell C_LIO_LISCP-MS identified a substantial proliferative subset of cells in the DCT underestimated by transcriptomics C_LIO_LISCP-MS could inform on clinical strategies for kidney disease monitoring, offering robust indicators of tubular injury or regeneration. C_LI

biochemistry↗

bioRxiv2021

Potassium effects on NCC are attenuated during inhibition of Cullin E3-ubiquitin ligases

The thiazide sensitive sodium-chloride co-transporter (NCC) plays a vital role in maintaining sodium (Na+) and potassium (K+) homeostasis. NCC activity is modulated by the with-no-lysine kinases 1 and 4 (WNK1 and WNK4), the abundance of which are controlled by the RING-type E3 ligase Cullin 3 (Cul3) and its substrate adapter Kelch-like protein 3. Dietary K+ intake has an inverse correlation with NCC activity, but the mechanism underlying this phenomenon remains to be fully elucidated. Here, we investigated the involvement of other members of the Cullin family in mediating K+ effects on NCC phosphorylation (active form) and abundance. In kidneys from mice fed diets varying in K+ content, there were negative correlations between NCC (phosphorylated and total) and active (neddylated) forms of Cullins (Cul1, 3, 4 and 5). High dietary K+ effects on phosphorylated NCC were attenuated in Cul3 mutant mice (CUL3-Het/{Delta}9). Short-term (30 min) and long-term (24 h) alterations in the extracellular K+ concentration did not affect Cullin neddylation levels in ex vivo renal tubules. Short-term, the ability of high extracellular K+ to decrease NCC phosphorylation was preserved in the presence of MLN4924 (pan Cullin inhibitor), but the response to low extracellular K+ was absent. Long-term, MLN4924 attenuated the effects of high extracellular K+ on NCC phosphorylation and responses to low extracellular K+ were absent. Our data suggest that in addition to Cul3, other Cullins are involved in mediating the effects of K+ on NCC phosphorylation and abundance.

physiology↗

bioRxiv2021

Cryo-EM structure of the human NKCC1 transporter reveals mechanisms of ion coupling and specificity

The sodium-potassium-chloride transporter NKCC1 (SLC12A2) performs Na+-dependent Cl- and K+ ion uptake across plasma membranes. NKCC1 is important for regulating e.g. cell volume, hearing, blood pressure, and chloride gradients defining GABAergic and glycinergic signaling in brain. Here, we present a 2.6 [A] resolution cryo-electron microscopy (cryo-EM) structure of human NKCC1 in the substrate-loaded (Na+, K+, 2 Cl-) and inward-facing conformation adopting an occluded state that has also been observed for the SLC6 type transporters MhsT and LeuT. Cl- binding at the Cl1 site together with the nearby K+ ion provide a crucial bridge between the LeuT-fold scaffold and bundle domains. Cl- ion binding at the Cl2 site seems to undertake a structural role similar to a conserved glutamate of SLC6 transporters and may allow for chloride-sensitive regulation of transport. Supported by functional studies in mammalian cells and computational simulations we describe the Na+ binding site and a putative Na+ release pathway along transmembrane helix 5. The results provide insight into the structure-function relationship of NKCC1 with broader implications for other SLC12 family members.

biochemistry↗