Biology subjects

Malik, A. B.

Publications and source records attributed to Malik, A. B..

11 recordsLinked to original sources

bioRxiv2026

E3 ubiquitin ligase SYVN1 mediates K63-linked ubiquitination of DDX3X to activate Macrophage NLRP3 Inflammasome

DDX3X (DEAD box helicase 3, X linked) is a common and essential component for both stress granules and NLRP3 inflammasome assembly and their activation; however, the upstream cellular stress signals driving DDX3X to activate the contrasting cellular pathway remain unclear. We identified the pivotal role of the E3 ubiquitin ligase SYVN1(Synoviolin) as the upstream regulator of DDX3X and thereby controlling NLRP3 activation and stress granule assembly. We observed SYVN1 silencing in macrophages prevented both NLRP3 driven inflammation and stress granule formation. SYVN1 deficiency prevented LPS induced inflammatory lung injury and increased the survival rate of the mice. SYVN1 sustains DDX3X gene expression and promotes stimulus-dependent ubiquitination of DDX3X. Under inflammatory conditions, SYVN1 mediated 63 linked ubiquitination of DDX3X, a requirement for NLRP3 inflammasome activation. Conversely, stress conditions reduced K63 linked DDX3X ubiquitination in coordination with activity of the deubiquitinase OTUB1 (OTU domain-containing ubiquitin aldehyde-binding protein 1). Thus, the balance between SYVN1 and OTUB1 functioned to optimize DDX3X activity and activation of NLRP3 or stress granule. These findings show the upstream role of SYVN1 OTUB1 axis in integrating cellular stress signals to decide the cell fate and suggest that ubiquitination of DDX3X is a potential target for inflammasome driven inflammation.

immunology↗

bioRxiv2026

Innate Immune Function of Neutrophil Cytoplasts Generated Post-Vital NETosis

The migration of polymorphonuclear neutrophils (PMN) into the site of infection such as lungs during pneumonia is a canonical feature of innate immunity. Formation of neutrophil-derived extracellular traps (NETs), web-like strands of varying lengths comprising DNA, histones, elastase, and myeloperoxidase, is an important determinant of PMN-mediated innate immunity. NETs form in microvessels, entrap bacteria and effete matter, and dampen PMN-mediated inflammatory injury at specific sites. However, studies have largely focused on NET release secondary to lytic NETosis and lysis of PMN. Far less is known about vital NETosis occurring in the absence of PMN rupture. As vital NETosis is characterized by generation of anuclear PMN termed cytoplasts (PMNcyto), we addressed the function of PMNcyto as a critical determinant of PMN-mediated innate immunity. Studies were made in mice challenged with live Pseudomonas aeruginosa (PA) i.t. to induce fulminant pneumonia characterized by tissue injury in which we determined the role of generated PMNcyto population. Using Tomato Red (tDTomato) transgenic mice to mark PMN, we observed PA pneumonia induced PMN transmigration leading to PMNcyto generation in the airspace. In contrast, PMNcyto transmigration, was minimal. PMNcyto accumulating in lung tissue actively phagocytosed and killed PA. Instillation of ex vivo generated PMNcyto also prevented PA-induced inflammatory lung injury and reduced mortality as compared to control mice. We demonstrated that the salutary effects of PMNcyto required functional microchondria. Proteomic analysis revealed that PMNcyto retained bactericidal and ROS generating pathways, consistent with an intact plasma membrane. Genetic deletion of peptidyl arginine deaminase 4 (PAD4), which mediates histone citrullination and promotes NETosis, facilitates PMNcyto generation and thereby abrogated pneumonia-induced mortality. Thus, we have identified the crucial host defense function of PMNcyto generated post-vital NETosis, suggesting that PMNcyto hold promise as cell based anti-bacterial therapy in pneumonia.

immunology↗

bioRxiv2025

CaMKKβ regulates transcription factor Elf2 gene methylation to maintain endothelial junctional barrier integrity

The expression of endothelial-enriched receptor tyrosine kinase Tie2 and vascular endothelial cadherin VE-cadherin in endothelial cells (EC) is essential for maintaining endothelial barrier integrity and vascular homeostasis. The Ets family of transcription factors plays a critical role in regulating the expression of Tie2 and VE-cadherin in EC. However, the transcriptional regulation of these factors remains poorly understood. In this study, we performed whole genome methylation analysis and found that the gene encoding the Ets family transcription factor Elf2/Nerf2 was hypermethylated in Camkk{beta}-deficient (Camkk{beta}-/-) mice. Notably, these mice exhibited significantly reduced mRNA and protein levels of Elf2, Tie2, and VE-cadherin, along with uncontrolled lung vascular injury following LPS challenge. Additionally, either depletion of CaMKK{beta} in human lung microvascular endothelial cells or EC-specific deletion of Camkk{beta} in mice led to a decrease in the expression of Elf2, Tie2, and VE-cadherin. Furthermore, administration of the DNA methyltransferase inhibitor 5-azacytidine (5-AZA) or EC-specific expression of wild-type CaMKK{beta} but not the kinase-defective mutant restored the expression of Elf2, Tie2, and VE-cadherin in Camkk{beta}-/-mice. We find that under baseline conditions, methyl CpG binding protein MeCP2 repressed Elf2 expression in EC. Importantly, in EC-restricted Elf2 knockout mice (Elf21EC), lung endothelial barrier integrity was compromised due to dramatically reduced levels of Tie2 and VE-cadherin. Together, these findings underscore the crucial role of CaMKK{beta} in regulating endothelial junctional barrier integrity by controlling Elf2 expression.

cell biology↗

bioRxiv2024

Tissue Regeneration Requires Edema Fluid Clearance by Compensatory Lymphangiogenesis in Zebrafish

Lymphangiogenesis is essential for tissue regeneration and edema clearance, and delayed or failed lymphangiogenesis is a critical cause of impaired healing. However, elucidating the dynamic changes in lymphangiogenesis during tissue regeneration in animal models in real-time has been challenging; thus, the mechanisms of compensatory lymphatic activation for edema clearance remain unclear. To address this, zebrafish were subjected to osmotic stress using a hypertonic solution (375 mOsm/L) and hypotonic solution (37.5 mOsm/L) to induce tissue damage followed by edema formation. Intravital imaging of Tg(mrc1a:egfp; kdrl:mcherry) larvae unveiled substantial lymphatic vessel remodeling during tissue regeneration. The increase of lymphatic endothelial progenitor cells accompanied by sustained expansion and remodeling of primary lymphatics during recovery suggested active lymphangiogenesis during tissue repair. We developed a novel method using translating ribosome affinity purification to scrutinize the translatome of lymphatic endothelial cells in vivo. This analysis revealed the upregulation of key pro-lymphangiogenic genes, notably vegfr2 and vegfr3, during tissue regeneration. Pharmacological inhibition of these Vegfr2/Vegfr3 prevented compensatory lymphangiogenesis and impaired healing. Our findings provide a new model of in vivo live imaging of regenerative lymphangiogenesis, presenting a novel approach to investigating lymphatic activation during tissue regeneration.

developmental biology↗

bioRxiv2022

Endosomal Trafficking of Two Pore K+ Efflux Channel TWIK2 to Plasmalemma Mediates NLRP3 Inflammasome Activation and Inflammatory Injury

Potassium efflux via the two pore K+ channel TWIK2 is a requisite step for the activation of the NLRP3 inflammasome, however it is unclear how the efflux is activated in response to cues. Here we report that during homeostasis, TWIK2 resides in endosomal compartments. TWIK2 is transported by endosomal fusion to the plasmalemma in response to increased extracellular ATP resulting in extrusion of K+ ATP-induced endosomal TWIK2 plasmalemma translocation is regulated by Rab11a. Deleting Rab11a or ATP ligated purinergic receptor P2X7 prevented endosomal fusion with the plasmalemma and K+ efflux and NLRP3 inflammasome activation in macrophages. Adoptive transfer of Rab11a-deleted macrophages into mouse lungs prevented NLRP3 inflammasome activation and inflammatory lung injury. Rab11a-mediated endosomal trafficking in macrophages thus regulates TWIK2 abundance and activity on the cell surface and downstream activation of the NLRP3 inflammasome. Endosomal trafficking of TWIK2 to the plasmalemma is therefore a potential therapy target in acute or chronic inflammatory states.

cell biology↗

bioRxiv2022

An engineered ACE2 decoy receptor can be administered by inhalation and potently targets the BA.1 and BA.2 omicron variants of SARS-CoV-2

Monoclonal antibodies targeting the SARS-CoV-2 spike (S) glycoprotein neutralize infection and are efficacious for the treatment of mild-to-moderate COVID-19. However, SARS-CoV-2 variants have emerged that partially or fully escape monoclonal antibodies in clinical use. Notably, the BA.2 sublineage of B.1.1.529/omicron escapes nearly all monoclonal antibodies currently authorized for therapeutic treatment of COVID-19. Decoy receptors, which are based on soluble forms of the host entry receptor ACE2, are an alternative strategy that broadly bind and block S from SARS-CoV-2 variants and related betacoronaviruses. The high-affinity and catalytically active decoy sACE22.v2.4-IgG1 was previously shown to be effective in vivo against SARS-CoV-2 variants when administered intravenously. Here, the inhalation of sACE22.v2.4-IgG1 is found to increase survival and ameliorate lung injury in K18-hACE2 transgenic mice inoculated with a lethal dose of the virulent P.1/gamma virus. Loss of catalytic activity reduced the decoys therapeutic efficacy supporting dual mechanisms of action: direct blocking of viral S and turnover of ACE2 substrates associated with lung injury and inflammation. Binding of sACE22.v2.4-IgG1 remained tight to S of BA.1 omicron, despite BA.1 omicron having extensive mutations, and binding exceeded that of four monoclonal antibodies approved for clinical use. BA.1 pseudovirus and authentic virus were neutralized at picomolar concentrations. Finally, tight binding was maintained against S from the BA.2 omicron sublineage, which differs from S of BA.1 by 26 mutations. Overall, the therapeutic potential of sACE22.v2.4-IgG1 is further confirmed by inhalation route and broad neutralization potency persists against increasingly divergent SARS-CoV-2 variants.

microbiology↗

bioRxiv2021

Engineered High-Affinity ACE2 Peptide Mitigates ARDS and Death Induced by Multiple SARS-CoV-2 Variants

Vaccine hesitancy and continuing emergence of SARS-CoV-2 variants of concern that may escape vaccine-induced immune responses highlight the urgent need for effective COVID-19 therapeutics. Monoclonal antibodies used in the clinic have varying efficacies against distinct SARS-CoV-2 variants; thus, there is considerable interest in engineered ACE2 peptides with augmented binding affinities for SARS-CoV-2 Spike protein. These could have therapeutic benefit against multiple viral variants. Using molecular dynamics simulations, we show how three amino acid substitutions in an engineered soluble ACE2 peptide (sACE22.v2.4-IgG1) markedly increase affinity for the SARS-CoV-2 Spike (S) protein. We demonstrate high binding affinity to S protein of the early SARS-CoV-2 WA-1/2020 isolate and also to multiple variants of concern: B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), and B.1.617.2 (Delta) SARS-CoV-2 variants. In humanized K18-hACE2 mice, prophylactic and therapeutic administration of sACE22.v2.4-IgG1 peptide prevented acute lung vascular endothelial injury and lung edema (essential features of ARDS) and significantly improved survival after infection by SARS-CoV-2 WA-1/2020 as well as P.1 variant of concern. These studies demonstrate for the first time broad efficacy in vivo of an ACE2 decoy peptide against multiple SARS-CoV-2 variants and point to its therapeutic potential.

pharmacology and toxicology↗

bioRxiv2021

Computer-Vision Stabilized Intravital Imaging Reveals Lung Capillary Neutrophil Dynamics Crucial for Lung Host-Defense Function

Polymorphonuclear neutrophils (PMN) are highly dynamic innate immune cells which are essential for lung host defense. However, in vivo intravital imaging in moving organs such as the lung remains challenging due to motion artifacts. Here we describe a novel intravital imaging method with high-throughput analytical capability based on a computer vision stabilization algorithm, Computer-vision-Assisted STabilized intravital imaging (CASTii). The sub-micron precision of this approach enables analysis of compartmentalized intravital PMN dynamics. We quantified in real-time a novel patrolling function of lung intracapillary circulating PMN. We also describe the dynamics of intracapillary PMN pooling (marginated PMN pool) using direct imaging of PMNs. The pool was formed by repeated catch-and-release kinetics involving PMN deformation inside microvessels during the passage of PMNs in vessels. We observed rapid PMN recruitment into the lung tissue compartments from pooled PMNs in response to alveolar chemoattract exposure. In contrast, endotoxemia-induced intracapillary sequestration of PMN impaired PMN transmigration into the alveolar space and defective phagocytosis of live bacteria. Intravital imaging of PMN dynamics with CASTii provides fundamental insights into host-defense functions of lung capillary PMN.

microbiology↗

bioRxiv2020

Selective Nanotherapeutic Targeting of the Neutrophil Subset Mediating Inflammatory Injury

Inflammatory tissue injury such as acute lung injury (ALI) is a disorder that leads to respiratory failure, a major cause of morbidity and mortality worldwide. Excessive neutrophil influx is a critical pathogenic factor in the development of ALI. Here, we identify the subset of neutrophils that is responsible for ALI and lethality in polymicrobial sepsis. The pro-inflammatory neutrophil subpopulation was characterized by its unique ability to endocytose albumin nanoparticles (ANP), upregulation of pro-inflammatory cytokines and chemokines as well as the excessive production of reactive oxygen species (ROS) in models of endotoxemia and septicemia. ANP delivery of the drug piceatannol, a spleen tyrosine kinase (Syk) inhibitor, to the susceptible subset of neutrophils, prevented ALI and mortality in mice subjected to polymicrobial infection. Targeted inhibition of Syk in ANP-susceptible neutrophils had no detrimental effect on neutrophil-dependent host defense because the subset of ANPlow neutrophils effectively controlled polymicrobial infection. The results show that neutrophil heterogeneity can be leveraged therapeutically to prevent ALI without compromising host defense.Competing Interest StatementABM, AS, KB have interests in the biotechnology company Nano Biotherapeutics Inc.View Full Text

immunology↗

bioRxiv2019

TAK1 Regulates Endothelial Integrity Through Stabilization of Junctions via GSK3β and FoxO1

TLR4 signaling in endothelial cells (ECs) induces vascular injury by disrupting the endothelial junctional barrier. However, it is not known whether TLR4 signaling can also promote endothelial barrier repair after vascular injury. Here we addressed the role of TAK1 activation downstream of TLR4 in the mechanism of vascular integrity. In inducible EC-restricted TAK1 knockout (TAK1i{Delta}EC) mice, the endothelial barrier was compromised. Blocking TAK1 activity caused spontaneous loss of the endothelial barrier. Importantly, TAK1 inactivated GSK3{beta} via AKT to prevent {beta}-catenin downregulation. We observed in ECs of GSK3{beta}i{Delta}EC mice an increase in {beta}-catenin transfer to the nucleus to form a complex with transcription factor FoxO1, thus repressing the expression of the tight junction protein claudin-5 and causing vascular leak. Strikingly, in TAK1i{Delta}EC mice, FoxO1 expression was dramatically increased while expression of AKT was suppressed, and in vivo inhibition of FoxO1 prevented sepsis-induced lung vascular leak in GSK3{beta}i{Delta}EC and TAK1i{Delta}EC mice. Further, EC-restricted deletion of FoxO1 in mice suppressed sepsis-induced lung vascular leak and mortality. Our findings point to the potential of targeting the TAK1-AKT-GSK3{beta}-FoxO1 axis as a therapeutic approach to treat uncontrolled lung vascular leak in sepsis.

cell biology↗

bioRxiv2019

EphB1 in Endothelial Cells Regulates Caveolae Formation and Endocytosis

Caveolae, the cave-like structures abundant in endothelial cells (ECs), are important in regulating key functions such as caveolae-mediated endocytosis and generation of nitric oxide. Here we show that deletion of the receptor tyrosine kinase EphB1 (EphB1-/-) in mice markedly reduced the caveolae number in ECs of heart and lung vessels and prevented caveolae-mediated endocytosis. EphB1 expressed in adult ECs was shown to bind the caveolin-1 (Cav-1) scaffold domain (CSD) via the CSD binding motif (CSDBM) on EphB1. We demonstrated that activation of EphB1 by the native ligand Ephrin B1 uncoupled EphB1 from Cav-1, and licensed Src-dependent Y-14 Cav-1 phosphorylation. Deletion of CSDBM on EphB1 prevented EphB1/Cav-1 interaction and the activation of Src and Src mediated Y-14 Cav-1 phosphorylation. These studies identify the central role of endothelium expressed EphB1 in regulating caveolae biogenesis and caveolae-mediated endocytosis.

cell biology↗