Biology subjects

Pathak, V.

Publications and source records attributed to Pathak, V..

10 recordsLinked to original sources

bioRxiv2026

Oxidative Stress Susceptibility, Complement Dysregulation, and Metabolic Reprogramming in CFH Y402H Patient-Derived Choriocapillaris Endothelial Cells

Age-related macular degeneration (AMD) is a leading cause of central vision loss. Immunofluorescence and gene expression studies in human donor eyes have shown that choriocapillaris endothelial cells (CECs) are lost before retinal pigment epithelium (RPE) degeneration, leaving extracellular matrix-filled empty lumens known as "ghost vessels." To investigate disease mechanisms, we generated CECs from patient-specific induced pluripotent stem cells (iPSCs) carrying the high-risk CFH Y402H variant and CRISPR-Cas9-corrected isogenic controls. The iPSC-derived CECs expressed canonical endothelial markers, formed fenestrations, maintained barrier function, and assembled capillary-like structures. Although baseline metabolism was preserved, Y402H CECs showed heightened sensitivity to hydroquinone-induced oxidative stress, with increased cytotoxicity and deposition of the complement membrane attack complex (C5b-9). RNA sequencing revealed oxidative stress-driven upregulation of lipid biosynthesis, mTORC signalling, endothelial-to-mesenchymal transition, and angiogenic pathways, alongside an imbalance in the complement pathway. These findings demonstrate that the CFH Y402H polymorphism increases CEC vulnerability to environmental stress, linking complement dysregulation and metabolic reprogramming to choriocapillaris dysfunction in AMD and highlighting CECs as a potential therapeutic target.

Cell Biology↗

bioRxiv2026

Urine proteomic profiling at admission reveals complement biomarkers linked to alcohol-associated liver disease.

Background and aimsCirculating complement is associated with occurrence of alcohol-associated hepatitis (AH) and is a potential biomarker to distinguish AH from alcohol cirrhosis (AC). Complement contributes to kidney injury, a condition often occurring in patients with alcohol-associated liver disease (ALD). However, little is known regarding complement in cross talk between liver and kidney in ALD. Here we tested the hypothesis that urinary complement would provide potential biomarkers for ALD and insights into mechanisms of liver-kidney crosstalk in the pathogenesis of ALD. MethodsPlasma and urine were collected at admission from patients with sAH, healthy controls (HC), and heavy drinkers without liver disease (HD) (from the multicenter Alcohol Hepatitis Network) and with AC (from the Northern Ohio Alcohol Center). Urine was subjected to unbiased proteomics analysis and plasma complement assessed by multiplex/ELISA assays. 30- and 90-day mortality was tracked in patients with sAH. ResultsAll three complement activation pathways were perturbed in plasma and urine of patients with sAH and AC compared to HC and HD. Components of the lectin and classical pathways in urine were associated with 30- and 90-day mortality in patients with sAH. When 4 complement proteins were combined, they distinguished sAH from AC (AUC 0.78), equivalent to that of MELD (AUC 0.65). There was no correlation between complement in plasma and urine, suggesting an independent impact of sAH on complement in kidney and liver. ConclusionThe urinary proteome revealed complement protein signatures associated with sAH and AC, providing valuable insights into the potential for complement biomarkers and the mechanisms of liver-kidney crosstalk in ALD.

immunology↗

bioRxiv2025

Mitochondria-derived dsRNA-induced stress granules promote IRF3-mediated fibrotic responses

Nucleic acid-induced activation of the anti-viral transcription factor interferon regulatory factor 3 (IRF3) promotes transforming growth factor-beta (TGF{beta})-induced fibrotic responses of hepatic stellate cells in vitro. Herein, we identified molecular mechanisms underlying TGF{beta}-induced IRF3 activation. Gene silencing of IRF3 with short interfering RNA (siRNA) in LX2 human hepatic stellate cells decreased TGF{beta}-induced fibrotic responses. An unbiased proteomic analysis of homeostatic IRF3-interacting proteins revealed striking enrichment in cytoplasmic stress granule components, including G3BP stress granule assembly factor 1 (G3BP1), G3BP2, and cell cycle associated protein 1 (CAPRIN1). TGF{beta} induced cytoplasmic accumulation of mitochondria-derived double-stranded RNA (mt-dsRNA) and assembly of IRF3-containing stress granules. Finally, blockade of G3BP1 activity or depletion of mt-dsRNA decreased TGF{beta}-induced fibrotic responses. Collectively, these findings identify a novel TGF{beta}-mt-dsRNA-stress granule axis in hepatic stellate cells that promotes IRF3-mediated fibrotic responses and potentially implicate cytoplasmic stress granules as a global regulator of fibrosis.

cell biology↗

bioRxiv2024

Pan-cortical cellular imaging in freely behaving mice using a miniaturized micro-camera array microscope (mini-MCAM)

Understanding how circuits in the brain simultaneously coordinate their activity to mediate complex ethnologically relevant behaviors requires recording neural activities from distributed populations of neurons in freely behaving animals. Current miniaturized imaging microscopes are typically limited to imaging a relatively small field of view, precluding the measurement of neural activities across multiple brain regions. Here we present a miniaturized micro-camera array microscope (mini-MCAM) that consists of four fluorescence imaging micro-cameras, each capable of capturing neural activity across a 4.5 mm x 2.55 mm field of view (FOV). Cumulatively, the mini-MCAM images over 30 mm2 area of sparsely expressed GCaMP6s neurons distributed throughout the dorsal cortex, in regions including the primary and secondary motor, somatosensory, visual, retrosplenial, and association cortices across both hemispheres. We demonstrate cortex-wide cellular resolution in vivo Calcium (Ca2+) imaging using the mini-MCAM in both head-fixed and freely behaving mice.

neuroscience↗

bioRxiv2023

Membrane Bound O-Acyltransferase 7 (MBOAT7) Shapes Lysosomal Lipid Homeostasis and Function to Control Alcohol-Associated Liver Injury

Several recent genome-wide association studies (GWAS) have identified single nucleotide polymorphism (SNPs) near the gene encoding membrane-bound O-acyltransferase 7 (MBOAT7) that is associated with advanced liver diseases. In fact, a common MBOAT7 variant (rs641738), which is associated with reduced MBOAT7 expression, confers increased susceptibility to non-alcoholic fatty liver disease (NAFLD), alcohol-associated liver disease (ALD), and liver fibrosis in those chronically infected with hepatitis viruses B and C. The MBOAT7 gene encodes a lysophosphatidylinositol (LPI) acyltransferase enzyme that produces the most abundant form of phosphatidylinositol 38:4 (PI 18:0/20:4). Although these recent genetic studies clearly implicate MBOAT7 function in liver disease progression, the mechanism(s) by which MBOAT7-driven LPI acylation regulates liver disease is currently unknown. Previously we showed that antisense oligonucleotide (ASO)-mediated knockdown of Mboat7 promoted non-alcoholic fatty liver disease (NAFLD) in mice (Helsley et al., 2019). Here, we provide mechanistic insights into how MBOAT7 loss of function promotes alcohol-associated liver disease (ALD). In agreement with GWAS studies, we find that circulating levels of metabolic product of MBOAT7 (PI 38:4) are significantly reduced in heavy drinkers compared to age-matched healthy controls. Hepatocyte specific genetic deletion (Mboat7HSKO), but not myeloid-specific deletion (Mboat7MSKO), of Mboat7 in mice results in enhanced ethanol-induced hepatic steatosis and high concentrations of plasma alanine aminotransferase (ALT). Given MBOAT7 is a lipid metabolic enzyme, we performed comprehensive lipidomic profiling of the liver and identified a striking reorganization of the hepatic lipidome upon ethanol feeding in Mboat7HSKO mice. Specifically, we observed large increases in the levels of endosomal/lysosomal lipids including bis(monoacylglycero)phosphates (BMP) and phosphatidylglycerols (PGs) in ethanol-exposed Mboat7HSKO mice. In parallel, ethanol-fed Mboat7HSKO mice exhibited marked dysregulation of autophagic flux and lysosomal biogenesis when exposed to ethanol. This was associated with impaired transcription factor EB (TFEB)-mediated lysosomal biogenesis and accumulation of autophagosomes. Collectively, this works provides new molecular insights into how genetic variation in MBOAT7 impacts ALD progression in humans and mice. This work is the first to causally link MBOAT7 loss of function in hepatocytes, but not myeloid cells, to ethanol-induced liver injury via dysregulation of lysosomal biogenesis and autophagic flux.

cell biology↗

bioRxiv2022

Gut Microbial Trimethylamine is Elevated in Alcohol-Associated Hepatitis and Contributes to Ethanol-Induced Liver Injury in Mice

BACKGROUNDThere is mounting evidence that microbes resident in the human intestine contribute to diverse alcohol-associated liver diseases (ALD) including the most deadly form known as alcohol-associated hepatitis (AH). However, mechanisms by which gut microbes synergize with excessive alcohol intake to promote liver injury are poorly understood. Furthermore, whether drugs that selectively target gut microbial metabolism can improve ALD has never been tested. METHODSWe used liquid chromatography tandem mass spectrometry to quantify the levels of microbe and host choline co-metabolites in healthy controls and AH patients, finding elevated levels of the microbial metabolite trimethylamine (TMA) in AH. In subsequent studies, we treated mice with non-lethal bacterial choline TMA lyase (CutC/D) inhibitors to blunt gut microbe-dependent production of TMA in the context of chronic ethanol administration. Indices of liver injury were quantified by complementary RNA sequencing, biochemical, and histological approaches. In addition, we examined the impact of ethanol consumption and TMA lyase inhibition on gut microbiome structure via 16S rRNA sequencing. RESULTSWe show the gut microbial choline metabolite trimethylamine (TMA) is elevated in AH patients and correlates with reduced hepatic expression of the TMA oxygenase flavin-containing monooxygenase 3 (FMO3). Provocatively, we find that small molecule inhibition of gut microbial CutC/D activity protects mice from ethanol-induced liver injury. CutC/D inhibitor-driven improvement in ethanol-induced liver injury is associated with distinct reorganization of the gut microbiome and host liver transcriptome. CONCLUSIONSThe microbial metabolite TMA is elevated in patients with AH, and inhibition of TMA production from gut microbes can protect mice from ethanol-induced liver injury.

biochemistry↗

bioRxiv2021

The looping lullaby: closed-loop neurostimulation decreases sleepers' sensitivity to environmental noise

Study ObjectiveSleep is critical for physical and mental health. However, sleep disruption due to noise is a growing problem, causing long-lasting distress and fragilizing entire populations mentally and physically. Here for the first time, we tested an innovative and non-invasive potential countermeasure for sleep disruptions due to noise. MethodsWe developed a new, modeling-based, closed-loop acoustic neurostimulation procedure (CLNS) to precisely phase-lock stimuli to slow oscillations (SO). We used CLNS to align, soft sound pulses to the start of the SO positive deflection to boost SO and sleep spindles during non-rapid eye movement (NREM) sleep. Participants underwent three overnight EEG recordings. The first night served to determine each participants individual noise arousal threshold. The remaining two nights occurred in counterbalanced order: in the "Disturbing night", loud, real-life noises were repeatedly presented; in the "Intervention night", similar loud noises were played while using the CLNS to boost SO. All experimental manipulations were performed in the first three hours of sleep; participants slept undisturbed for the rest of the night. ResultsIn contrast to the Disturbing night, the probability of arousals caused by noise was significantly decreased in the Intervention night. Moreover, the CLNS intervention increased NREM duration and sleep spindle power across the night. ConclusionsThese results show that our CLNS procedure can effectively protect sleep from disruptions caused by noise. Remarkably, even in the presence of loud environmental noise, CLNS soft and precisely timed sound pulses played a beneficial role in protecting sleep continuity. This represents the first successful attempt at using CLNS in a noisy environment. Statement of SignificanceExposure to noise during sleep impairs sleep quality, leading to impaired biological functioning, decreased day-time performance and higher occurrence of accidents. Slow wave sleep is hallmarked by slow oscillations (SO) and sleep spindles, both of which are markers of sleep stability. In previous experiments, acoustic stimulation has shown potential in enhancing SO and sleep spindles. Whether these manipulations also work to stabilize sleep against the disrupting effects of environmental noise remains unclear. Here we use a new closed-loop approach to precisely align subtle acoustic stimuli with SO phase. We show that this method effectively stabilizes sleep in the presence of noise. Our results bear crucial relevance for improving sleep in the general public and in many high-risk professions.

neuroscience↗

bioRxiv2021

Surface expressed Plasmodium circumsporozoite protein (CSP) modulates cellular flexibility and motility

Plasmodium falciparum circumsporozoite protein (CSP) is a critically required abundant surface protein of sporozoites and a major vaccine candidate. However, neither the structure nor the role of CSP in sporozoite motility is well understood. Our recent in vitro data, from single-molecule pulling experiments suggested a mechanically pliable structure for P. falciparum CSP. By engineering vegetative cells of the cellular slime-mold Dictyostelium discoideum with regulatable CSP surface expression, we report evidence for direct involvement of CSP towards conferring elastic properties and motility of the cells. With an increase in the surface-CSP levels by 5-8-fold, the Youngs moduli of the cells, observed through atomic force microscopy, decreased around 2-fold, with a concomitant increase in motility by about 2-fold. Interestingly, only full length CSP expression conferred maximal flexibility and motility, as opposed to repeat region alone or the flanking domains of CSP. The enhanced motility of the CSP-expressing cells was abrogated with anti-CSP antibodies as well as phospholipase cleavage of CSP, indicating specific contribution of CSP towards motility. Measurements of the Youngs moduli of Plasmodium berghei midgut (MG) and salivary gland (SG) sporozoites revealed an inverse correlation with CSP levels with a decrease from 1.1 kPa to 0.3 kPa as the CSP concentration doubled from MG to SG sporozoites. We hypothesize that high CSP level lowers the stiffness of sporozoites possibly through its pliable surface-coat, leading to cellular flexibility. These findings may explain a sporozoites developmental ability to enhance its CSP levels during transition from midgut to salivary glands to suit a migratory mode in the host, needed for successful hepatocyte invasion.

cell biology↗

bioRxiv2020

Isoform-specific characterization implicates alternative splicing in APOBEC3B as a mechanism restricting APOBEC-mediated mutagenesis

APOBEC3A (A3A) and APOBEC3B (A3B) enzymes drive APOBEC-mediated mutagenesis, but the understanding of the regulation of their mutagenic activity remains limited. Here, we showed that mutagenic and non-mutagenic A3A and A3B enzymes are produced by canonical and alternatively spliced A3A and A3B isoforms, respectively. Notably, increased expression of the canonical A3B isoform, which encodes the mutagenic A3B enzyme, predicted shorter progression-free survival of bladder cancer patients. Expression of the mutagenic A3B isoform was reduced by exon 5 skipping, generating a non-mutagenic A3B isoform. The exon 5 skipping, which was dependent on the interaction between SF3B1 splicing factor and weak branch point sites in intron 4, could be enhanced by an SF3B1 inhibitor, decreasing the production of the mutagenic A3B enzyme. Thus, our results underscore the role of A3B, especially in bladder cancer, and implicate alternative splicing of A3B as a mechanism and therapeutic target to restrict APOBEC-mediated mutagenesis.

genomics↗

bioRxiv2020

Vascular dimorphism ensured by regulated proteoglycan dynamics favors rapid umbilical artery closure at birth

The umbilical artery lumen occludes rapidly at birth, preventing blood loss, whereas the umbilical vein remains patent, providing the newborn with a placental infusion. Here, we identify differential arterial-venous proteoglycan dynamics as a determinant of these contrasting vascular responses. We show that the umbilical artery, unlike the vein, has an inner layer enriched in the hydrated proteoglycan aggrecan, external to which lie contraction-primed smooth muscle cells (SMC). At birth, SMC contraction drives inner layer buckling and centripetal displacement to occlude the arterial lumen, a mechanism elicited by biomechanical and computational analysis. Vascular dimorphism arises from spatially regulated proteoglycan expression and breakdown in umbilical vessels. Mice lacking aggrecan or the metalloprotease ADAMTS1, which degrades proteoglycans, demonstrated their opposing roles in umbilical cord arterial-venous dimorphism and contrasting effects on SMC differentiation. Umbilical vessel dimorphism is conserved in mammals, suggesting that their differential proteoglycan dynamics were a positive selection step in mammalian evolution.Competing Interest StatementThe authors have declared no competing interest.View Full Text

developmental biology↗