Biology subjects

Singh, A.

Publications and source records attributed to Singh, A..

At least 235 records · Page 13Linked to original sources

bioRxiv2025

Acquisition of discrete immune suppressive barriers contributes to the initiation and progression of preinvasive to invasive human lung cancer.

Computerized chest tomography (CT)-guided screening in populations at risk for lung cancer has increased the detection of preinvasive subsolid nodules, which progress to solid invasive adenocarcinoma. Despite the clinical significance, there is a lack of effective therapies for intercepting the progression of preinvasive to invasive adenocarcinoma. To uncover determinants of early disease emergence and progression, we used integrated single-cell approaches, including scRNA-seq, multiplexed imaging mass cytometry and spatial transcriptomics, to construct the first high-resolution map of the composition, lineage/functional states, developmental trajectories and multicellular crosstalk networks from microdissected non-solid (preinvasive) and solid compartments (invasive) of individual part-solid nodules. We found that early disease initiation and subsequent progression are associated with the evolution of immune-suppressive cellular phenotypes characterized by decreased cytotoxic CD8 T and NK cells, increased T cell exhaustion and accumulation of immunosuppressive regulatory T cells (Tregs) and M2-like macrophages expressing TREM2. Within Tregs, we identified a unique population of 4-1BB+ Treg subset enriched for the IL2-STAT5 suppressive pathway with transcription profiles supporting discrete metabolic alterations. Spatial analysis showed increased density of suppressive immune cells around tumor cells, increased exhaustion phenotype of both CD4 and CD8 T cells expressing chemokine CXCL13, and spatial micro-complex of endothelial and lymphocyte interactions within tertiary lymphoid structures. The single-cell architecture identifies determinants of early disease emergence and progression, which may be developed not only as diagnostic/prognostic biomarkers but also as targets for disease interception. Additionally, our dataset constitutes a valuable resource for the preinvasive lung cancer research community.

cancer biology↗

bioRxiv2024

Transient glycan-shield reduction induces CD4-binding site broadly neutralizing antibodies in SHIV-infected macaques

Broadly neutralizing antibodies (bNAbs) targeting the HIV-1 CD4-binding site (CD4bs) occur infrequently in macaques and humans and have not been reproducibly elicited in any outbred animal model. To address this challenge, we first isolated RHA10, an infection-induced rhesus bNAb with 51% breadth. The cryo-EM structure of RHA10 with HIV-1 envelope (Env) resembled prototypic human CD4bs bNAbs with CDR-H3-dominated binding. Env-antibody co-evolution revealed transient elimination of two Env CD4bs-proximal glycans near the time of RHA10-lineage initiation, and these glycan-deficient Envs bound preferentially to early RHA10 intermediates, suggesting glycan deletions in infecting SHIVs could consistently induce CD4bs bNAbs. To test this, we constructed SHIV.CH505.D3 with CD4bs-proximal glycan deletions. Infection of 10 macaques resulted in accelerated CD4bs bNAb responses in 8, compared with 1 of 115 control macaques. Glycan hole-based immunofocusing coupled to Env-Ab co-evolution can consistently induce broad CD4bs responses in macaques and thus serve as a model for HIV vaccine design. HighlightsO_LIOut of 115 wildtype HIV-1 Env bearing SHIV infected macaques, only one macaque (T681) developed CD4bs bNAbs C_LIO_LICD4bs bNAbs in macaque T681 recognized Env similarly to previously described CDR-H3 dominated human CD4bs bNAbs and exhibited comparable breadth and potency C_LIO_LITransient CD4bs-proximal glycan deletions in macaque T681 preceded bNAb induction C_LIO_LIA novel SHIV with CD4bs-proximal glycan holes and enhanced CD4bs antigenicity immunofocused B cell responses to the CD4bs and elicited cross-clade neutralizing responses in 80% of macaques C_LI

microbiology↗

bioRxiv2024

Hydrogen sulfide (H2S) coordinates redox balance, carbon metabolism, and mitochondrial bioenergetics to suppress SARS-CoV-2 infection.

Viruses exploit host metabolism for replication and immune-regulation. Understanding how SARS-CoV-2 alters the host metabolism may lead to treatments for COVID-19. We report that a ubiquitous gaseous molecule, hydrogen sulfide (H2S), regulates redox, metabolism, and mitochondrial bioenergetics to control SARS-CoV-2. Virus replication is associated with down-regulation of the H2S-producing enzymes cystathionine-{beta}-synthase (CBS), cystathionine-{gamma}-lyase (CTH), and 3-mercaptopyruvate sulfurtransferase (3-MST), resulting in diminished endogenous H2S levels. Inhibition of CTH resulted in SARS-CoV-2 proliferation. A slow-releasing H2S donor, GYY4137, diminished virus replication by inducing Nrf2/Keap1 pathway, restoring redox balance and mitochondrial bioenergetics. Treatment of SARS-CoV-2-infected animals with GYY4137 suppressed viral replication, ameliorated respiratory pathology, and restored antioxidant gene expression. Notably, whole-body plethysmography showed improved pulmonary function variables, including pulmonary obstruction and end-expiratory pause upon GYY4137 treatment in vivo. Data extend our understanding of H2S-mediated regulation of viral-infections, and open new avenues for investigating the pathogenic mechanisms and therapeutic opportunities for coronavirus-associated disorders.

microbiology↗

bioRxiv2024

Sporophyte Directed Gametogenesis via the Ubiquitin Proteasome System

Plants alternate between diploid sporophyte and haploid gametophyte generations. In mosses which retain features of ancestral land plants, the gametophyte is dominant and has an independent existence. However, in flowering plants the gametophyte has undergone evolutionary reduction to just a few cells enclosed within the sporophyte. The gametophyte is thought to retain genetic control of its development even after reduction. Here we demonstrate that male gametophyte development in Arabidopsis, long considered to be autonomous, is also under genetic control of the sporophyte via a repressive mechanism involving large-scale regulation of protein turnover. We identify an Arabidopsis gene SHUKR as an inhibitor of male gametogenesis. SHUKR is unrelated to proteins of known function and acts sporophytically in meiosis to control gametophyte development by negatively regulating expression of a large set of ubiquitination genes specific to post-meiotic gametogenesis. This control is late-emerging as SHUKR homologs are found only in eudicots. We show that SHUKR is rapidly evolving under positive selection suggesting that variation in control of protein turnover during male gametogenesis has played an important role in evolution within eudicots.

plant biology↗

bioRxiv2024

Using deep generative models for simultaneous representational and predictive modeling of brain and behavior: A graded supervised-to-unsupervised modeling framework.

This paper uses a generative neural network architecture combining unsupervised (generative) and supervised (discriminative) models with a model comparison strategy to evaluate assumptions about the mappings between brain states and behavior. Most modeling in cognitive neuroscience publications assume a one-to-one brain-behavior relationship that is linear, but never test these assumptions or the consequences of violating them. We systematically varied these assumptions using simulations of four ground-truth brain-behavior mappings that involve progressively more complex relationships, ranging from one-to-one linear mappings to many-to-one nonlinear mappings. We then applied our Variational AutoEncoder-Classifier framework to the simulations to show how it accurately captured diverse brain-behavior mappings,provided evidence regarding which assumptions are supported by the data, and illustrated the problems that arise when assumptions are violated. This integrated approach offers a reliable foundation for cognitive neuroscience to effectively model complex neural and behavioral processes, allowing more justified conclusions about the nature of brain-behavior mappings.

neuroscience↗

bioRxiv2024

An in-cell approach to evaluate E3 ligases for use in targeted protein degradation.

One of the major challenges in evaluating the suitability of potential [~]700 E3 ligases for target protein degradation (TPD) is the lack of binders specific to each E3 ligase. Here we apply genetic code expansion (GCE) to encode a tetrazine-containing non-canonical amino acid (Tet-ncAA) site-specifically into the E3 ligase, which can be conjugated with strained trans-cyclooctene (sTCO) tethered to a neo-substrate protein binder by click chemistry within living cells. The resulting E3 ligase minimally modified and functionalized in an E3-ligand free (ELF) manner, can be evaluated for TPD of the neo-substrate. We demonstrate that CRBN encoded with clickable Tet-ncAA, either in the known immunomodulatory drug (IMiD)-binding pocket or across surface, can be covalently tethered to sTCO-linker-JQ1 and recruit BRD2/4 for CRBN mediated degradation, indicating the high plasticity of CRBN for TPD. The degradation efficiency is dependent on location of the Tet-ncAA encoding on CRBN as well as the length of the linker, showing the capability of this approach to map the surface of E3 ligase for identifying optimal TPD pockets. This ELF-degrader approach has the advantages of not only maintaining the native state of E3 ligase, but also allowing the interrogation of E3 ligases and target protein partners under intracellular conditions and can be applied to any known E3 ligase.

cell biology↗

bioRxiv2024

IVISc-L: A quick and simple in vivo assay to study the regulation of gene expression

Several methods are available to study the regulation of gene expression at cellular and molecular levels. Adaptation of these methods in vivo is cumbersome and often requires animal sacrifice. Here, we report an assay (IVISc-L, In Vivo Imaging of Subcutaneous Luminescence) to study gene regulation in vivo. This assay involves subcutaneous injection of a plasmid DNA encoding firefly luciferase, whose expression is under the regulatory mechanism to be investigated. We could infer its regulated expression by detecting the subcutaneous luminescence using an in vivo imaging system. Using this assay, we have demonstrated the regulation of gene expression mediated by a promoter, micro-RNAs, stop codon readthrough, and rare codons. This minimally invasive assay does not require animal sacrifice or any tissue extraction. The entire assay can be completed within 24 hours. Therefore, this assay will be useful in investigating the mechanisms of gene expression regulation, and screening molecules that can alter gene expression in vivo.

molecular biology↗

bioRxiv2024

The PRMT5-splicing axis is a critical oncogenic vulnerability that regulates detained intron splicing

Protein arginine methyltransferase 5 (PRMT5) is a promising cancer target, yet its unclear which PRMT5 roles underlie this vulnerability. Here, we establish that PRMT5 inhibition induces a special class of unspliced introns, called detained introns (DIs). To interrogate the impact of DIs, we depleted CLNS1A, a PRMT5 cofactor that specifically enables Sm protein methylation. We found that many, but not all, cell lines are CLNS1A-dependent and established that loss of viability is linked to loss of Sm protein methylation and DI upregulation. Finally, we discovered that PRMT5-regulated DIs, and the impacted genes, are highly conserved across human, and also mouse, cell lines but display little interspecies conservation. Despite this, human and mouse DIs have convergent impacts on proliferation by affecting essential components of proliferation-regulating complexes. Together, these data argue that the PRMT5-splicing axis, including appropriate DI splicing, underlies cancers vulnerability to PRMT5 inhibitors.

cancer biology↗

bioRxiv2024

Reduced enteric BDNF-TrkB signaling drives glucocorticoid-mediated GI dysmotility

Stress is a key contributor to gastrointestinal (GI) dysmotility, particularly in patients with disorders of gut-brain interactions (DGBI). Since GI motility is governed by the enteric nervous system (ENS), stress may act by altering ENS function. While stress activates glucocorticoid signaling via the hypothalamic-pituitary-adrenal axis, the impact of stress-mediated glucocorticoid signaling on ENS biology remains poorly understood. In the central nervous system, glucocorticoids reduce specific isoforms of brain-derived neurotrophic factor (BDNF), impairing signaling through its receptor, TrkB, and contributing to behavioral dysfunction. However, the identity of ENS-specific Bdnf isoforms, their glucocorticoid sensitivity, and the effect of enhanced TrkB signaling on GI motility in stressed animals has not been characterized. Here, using male and female mice, we show that >85% of post-natal ENS Bdnf transcripts are glucocorticoid-responsive isoforms. We also demonstrate that both BDNF and its receptor TrkB (Ntrk2) are expressed by enteric neurons. In male mice, stress and administration of dexamethasone--a synthetic glucocorticoid receptor (GR) agonist--cause GI dysmotility, which we demonstrate is associated with significantly reduced Bdnf transcripts in the longitudinal muscle - myenteric plexus (LM-MP) tissue in vivo. Dexamethasone exposure also represses Bdnf transcript and mature protein levels in LM-MP tissue in vitro. Notably, treatment with HIOC, a selective TrkB agonist, rescues GI transit defects in dexamethasone-treated animals. These findings identify BDNF-TrkB signaling as a key modulator of stress-induced ENS dysfunction and highlight TrkB as a promising therapeutic target for GI dysmotility in DGBI. Significance statementHow stress causes gastrointestinal (GI) dysmotility is not well understood. GI motility is regulated by the enteric nervous system (ENS), which is responsive to brain-derived neurotrophic factor (BDNF), which signals through its receptor tropomyosin related kinase B (TrkB). By altering glucocorticoid signaling, stress modulates brains BDNF levels to cause behavioral changes. However, if this pathway is similarly responsible for stresss effects on GI dysmotility is not well understood. Here, by identifying the nature of ENS-specific Bdnf isoforms, studying their response to stress and glucocorticoid signaling, and testing the effect of a TrkB agonist to improve gut motility in a model of glucocorticoid-driven dysmotility, we implicate altered BDNF-TrkB signaling as an important mechanism driving stress-associated dysmotility.

neuroscience↗

bioRxiv2024

Implications of diabetes mellitus on pathophysiology of Tuberculosis: Role of AGE-RAGE Axis and Glycated Proteins

Chronic hyperglycemia in diabetes mellitus promotes the formation of advanced glycation end products (AGEs) via non-enzymatic glycation of plasma proteins. AGEs and their receptor RAGE are central to diabetic complications, as they activate inflammatory pathways and oxidative stress. We studied the AGE-RAGE axis in uncontrolled diabetic individuals having pulmonary TB (PTB+DM), uncontrolled diabetic individuals with no infection (DM), and pulmonary TB patients (PTB). Levels of AGEs and RAGE were measured across these groups and compared to controls. The results showed significantly higher AGEs and RAGE levels in the diabetic milieu, reflecting chronic hyperglycemia. These AGEs were shown to be associated with impaired macrophage function, evidenced by reduced phagocytic capacity. Increased AGEs correlated with disease severity in tuberculosis patients co-affected by diabetes, indicating compromised immune responses. RAGE expression also showed a higher trend in TB patients, although not statistically significant, potentially influencing infection outcomes. Glycated calmodulin was also elevated in diabetic and TB-diabetes comorbid patients and negatively correlated with nitric oxide (NO) levels, suggesting that calmodulin glycation hinders NO production in diabetic conditions. Molecular dynamic studies revealed that glycosylation disrupts calmodulins interaction with inducible nitric oxide synthase (iNOS), potentially explaining the decreased NO levels in TB-diabetes comorbid patients. These findings underscore the detrimental impact of AGEs and RAGE in diabetic immune dysregulation, highlighting the need for therapeutic strategies to mitigate their effects on macrophage function and restore immune responses. HighlightsO_LIWe conducted this study to examine how hyperglycemia-driven AGEs and RAGE contribute to immune dysfunction and disease severity in diabetic and TB-diabetes patients. C_LIO_LIHigh AGEs and RAGE impairs macrophage function, decreasing phagocytic capacity and worsening disease severity in TB-diabetes comorbidity. C_LIO_LIGlycosylation disrupts calmodulins interaction with iNOS, contributing to lower NO levels and weakened immune responses in TB-diabetes comorbidity. C_LIO_LIThe AGE-RAGE axis should be studied further for these comorbid conditions to assess and improve macrophage function and restore immune responses. C_LI

immunology↗

bioRxiv2024

Salmonella Typhimurium Manipulates Syntaxin 7 to Navigate Endo-Lysosomal Trafficking in Host Cells

Intracellular pathogens rely on manipulating host endocytic pathways to ensure survival. Legionella and Chlamydia exploit host SNARE proteins, with Legionella cleaving syntaxin 17 (STX17) and Chlamydia interacting with VAMP8 and VAMP7. Similarly, Salmonella targets the hosts endosomal fusion machinery, using SPI effectors like SipC and SipA to interact with syntaxin 6 (STX6) and syntaxin 8 (STX8), respectively, maintaining its vacuolar niche. Recent evidence highlights syntaxin 7 (STX7), a Qa-SNARE involved in endo-lysosomal fusion, as a potential Salmonella target. BioID screening revealed STX7 interactions with SPI-2 effectors SifA and SopD2, suggesting a critical role in Salmonella pathogenesis. We investigated the role of STX7 in Salmonella-containing vacuole (SCV) biogenesis and pathogenesis in macrophages and epithelial cells. Our findings indicate that STX7 levels and localization differ between these cell types during infection, reflecting the distinct survival strategies of Salmonella. Live cell imaging showed that STX7 is recruited to SCVs at different infection stages, with significantly altered distribution in HeLa cells at the late stage of infection. STX7 knockdown resulted in reduced bacterial survival, which was rescued upon overexpression of STX7 in both HeLa and RAW264.7 cells, suggesting Salmonella hijacks STX7 to evade lysosomal fusion and secure nutrients for intracellular replication. These results underscore the essential role of STX7 in maintaining SCVs and facilitating Salmonella survival. Further, the temporal expression of STX7 adaptor/binding partners in macrophages showed dynamic interactions with STX7 facilitating Salmonella infection and survival in host cells. Together, our study highlights STX7 as a critical host factor exploited by Salmonella, providing insights into the molecular mechanisms underlying its pathogenesis in macrophages and epithelial cells. These findings may in form strategies for targeting host-pathogen interactions to combat Salmonella infections.

microbiology↗

bioRxiv2024

Designing a multi-serotype Dengue virus vaccine: an in silico approach to broad-spectrum immunity

Dengue virus infection represents a major global health issue, with four distinct serotypes complicating the challenge of developing a vaccine due to the need for balanced, long-lasting immunity against all serotypes. Current vaccines have limitations, including an increased risk of severe dengue in seronegative individuals and moderate efficacy, highlighting the need for more effective solutions. Our study aimed to design a multi-serotype Dengue virus vaccine using a computational approach to achieve broad-spectrum immunity. We employed advanced computational tools and algorithms to predict B-cell and T-cell epitopes, ensuring the selection of antigenic targets that provide comprehensive protection against all four serotypes. The methodology included tools for B-cell epitope prediction, tools for MHC class II and I peptide predictions, and tools for toxicity and allergenicity screening to ensure the safety of the vaccine candidates. Our results identified 21 B-cell epitopes, 15 CTL peptides, and 12 HTL peptides, validated for safety regarding toxicity and allergenic potential. The vaccine construct incorporated the adjuvant {beta}-defensin-3 and specific linkers to enhance immunogenicity and stability. Tertiary structure prediction, Ramachandran plot analysis, and stereochemical examination confirmed the stability and quality of the vaccine model. These findings demonstrate the potential of computational methods in addressing the complex challenges of Dengue virus vaccine development. Our computational approach offers a novel pathway for vaccine design, potentially accelerating the development of effective multi-serotype vaccines. This study provides a promising foundation for future research and clinical validation, marking a significant step forward in dengue vaccine development.

immunology↗

bioRxiv2024

Design and synthesis of triazine-based hydrogel for combined targeted doxorubicin delivery and PI3Kinhibition

Melanoma, an aggressive skin cancer originating from melanocytes, presents substantial challenges due to its high metastatic potential and resistance to conventional therapies. Hydrogels, three-dimensional networks of hydrophilic polymers with high water-retention capacities, offer significant promise for controlled drug delivery applications. In this study, we report the synthesis and characterization of hydrogelators based on the triazine molecular scaffold, which self-assemble into fibrous networks conducive to hydrogel formation. Rheological analysis confirmed their hydrogelation properties, while microscopic techniques including FE-SEM and FEG-TEM provided insights into their morphological networks. The drug delivery capability of these hydrogelators was evaluated using doxorubicin, a widely employed anticancer agent, demonstrating enhanced biocompatibility and reduced side effects compared to free doxorubicin. Additionally, the hydrogelators exhibited inhibitory activity against phosphoinositide 3-kinase (PI3K), a key enzyme frequently mutated in cancer, and also involved in melanoma progression. The dual functionality of this delivery system - controlled drug release and PI3K inhibition - highlights the potential of triazine-based hydrogelators as innovative therapeutic platforms for melanoma treatment.

cancer biology↗

bioRxiv2024

TRPV4 overactivation enhances cellular contractility and drives ocular hypertension in TGFβ2 overexpressing eyes

The risk for developing primary open-angle glaucoma (POAG) correlates with the magnitude of ocular hypertension (OHT) and the concentration of transforming growth factor-{beta}2 (TGF{beta}2) in the aqueous humor. Effective treatment of POAG requires detailed understanding of interaction between pressure sensing mechanisms in the trabecular meshwork (TM) and biochemical risk factors. Here, we employed molecular, optical, electrophysiological and tonometric strategies to establish the role of TGF{beta}2 in transcription and functional expression of mechanosensitive channel isoforms alongside studies of TM contractility in biomimetic hydrogels, and intraocular pressure (IOP) regulation in a mouse model of TGF{beta}2 -induced OHT. TGF{beta}2 upregulated expression of TRPV4 and PIEZO1 transcripts and time-dependently augmented functional TRPV4 activation. TRPV4 agonists induced contractility of TM-seeded hydrogels whereas pharmacological inhibition suppressed TGF{beta}2-induced hypercontractility and abrogated OHT in eyes overexpressing TGF{beta}2. Trpv4-deficient mice resisted TGF{beta}2-driven increases in IOP, but nocturnal OHT was not additive to TGF{beta}-evoked OHT. Our study establishes the fundamental role of TGF{beta} as a modulator of mechanosensing in nonexcitable cells, identifies the TRPV4 channel as the final common mechanism for TM contractility and circadian and pathological OHT, and offers insights for future treatments that can lower IOP in the sizeable cohort of hypertensive glaucoma patients that resist current treatments.

physiology↗

bioRxiv2024

Potassium ferric oxalate nanoparticles prevent human blood clotting and thrombosis in a mouse model

Blood clot creates occlusion in the veins and arteries, which leads to pernicious effects. Here, the anticoagulation properties of potassium ferric oxalate nanoparticles (KFeOx-NPs) in human blood were demonstrated for blood clot management. The mechanism involves the chelation of calcium ions from the blood by the oxalate present in the KFeOx-NPs. Various commercial assays were used to determine the clotting time for the KFeOx-NPs and identified the hindrance in activating factor XII in the intrinsic pathway. We used animal models to show toxicity and biodistribution profiles and determined the safety and efficacy. Intravenously injected KFeOx-NPs increased clotting time and thrombosis prevention in a mouse model confirmed by ultrasound and the power Doppler images. Coating catheters with KFeOx-NPs prevents clot formation with reduced protein attachment when incubated with blood, enhancing blood flow properties. In biological applications, KFeOx-NPs may improve the long-term prevention of blood clot formation and enhance the efficiency of medical devices. TOC O_FIG O_LINKSMALLFIG WIDTH=188 HEIGHT=200 SRC="FIGDIR/small/621820v1_ufig1.gif" ALT="Figure 1"> View larger version (68K): org.highwire.dtl.DTLVardef@1292afeorg.highwire.dtl.DTLVardef@1c5ba81org.highwire.dtl.DTLVardef@576f23org.highwire.dtl.DTLVardef@4186e9_HPS_FORMAT_FIGEXP M_FIG C_FIG PVP-stabilized novel potassium ferric oxalate nanoparticles were synthesized for the application of blood clot management and thrombosis prevention.

pathology↗

bioRxiv2024

Identifying Prognostic Cell State Interactions in the TumorMicroenvironment of IDH-Mutant Gliomas Using CSI-TME

Intercellular communication between distinct transcriptional states of various cell types in the tumor microenvironment (TME) influence the progression and clinical outcome of the tumors. Details of such clinically relevant cellular state interactions (CSIs) in IDH-mutant gliomas remain obscure. Here we developed CSI-TME, a computational pipeline that deconvolves cell type-specific gene expression from bulk transcriptomic data, identifies distinct cell states, and uncovers prognostic cell state interactions by modelling the clinical data based on the joint activity of cell state pairs. We found a significantly reproducible cell state interaction network (CSIN) that is (i) predominantly pro-tumor, (ii) likely mediated through the interaction between cell surface molecules, (iii) differentially activated in IDH-mut astrocytoma and oligodendroglioma, and (iv) significantly associated with response to immune checkpoint blockade therapy. The distinct malignant cell states involved in CSIs resembled neuronal lineages such as astrocyte-like and oligodendrocyte progenitor cells-like states and captured key interactions between glioma stem cells and immune cells. Integration of CSIN with somatic mutation data suggests the anti-tumor role of CSIs in the early stages that transitions towards pro-tumor role as glioma progresses. In summary, CSI-TME provides valuable insights into the physiology of the TME in IDH-mutant glioma and provides a framework to prioritize ligand-receptor interactions or patients stratification for therapeutic interventions.

cancer biology↗

bioRxiv2024

Pathophysiological Implications of Nucleotide Self-Assembly: Adenine-Derived Nucleotides Aggregation in Disease Mechanisms

Adenine nucleotides, including adenosine monophosphate, adenosine diphosphate, and adenosine triphosphate, play pivotal roles in cellular bioenergetics, nucleic acid metabolism, and signal transduction. However, their propensity to undergo self-assembly and form supramolecular aggregates under certain conditions is not well-characterized. In this study, we examined the self-assembly, aggregation, and cytotoxicity of AMP, ADP, and ATP in both fresh and aged conditions. Utilizing advanced microscopy techniques, Thioflavin T (ThT) fluorescence assays, and cross-seeding experiments, we identified oligomer formation in freshly prepared nucleotide solutions, which progressed to larger, more stable aggregates over time. The cytotoxic potential of these nucleotide aggregates was assessed using in vitro models, including human retinal pigment epithelial (RPE-1) and colorectal carcinoma (HCT-116) cell lines. Our findings demonstrate that nucleotide aggregation induces significant cytotoxic effects, particularly in aged conditions. Further investigations into bacterial toxicity models revealed similar deleterious impacts, indicating a broad-spectrum biological stress response to nucleotide aggregates. These results suggest that nucleotide self-assembly and aggregation may contribute to cellular dysfunction, offering new insights into their non-canonical roles in disease pathophysiology, potentially analogous to protein misfolding disorders.

bioengineering↗

bioRxiv2024

Disruption of molecular interactions between G3BP1 stress granule host protein and nucleocapsid (NTD-N) protein impedes SARS-CoV-2 virus replication

The Ras GTPase-activating protein SH3-domain-binding protein 1 (G3BP1) serves as a formidable barrier to viral replication by generating stress granules (SGs) in response to viral infections. Interestingly, viruses, including SARS-CoV-2, have evolved defensive mechanisms to hijack SG proteins like G3BP1 for the dissipation of SGs that lead to the evasion of hosts immune responses. Previous research has demonstrated that the interaction between the NTF2-like domain of G3BP1 (G3BP1NTF-2) and the intrinsically disordered N-terminal domain (NTD-N1-25) of the N protein plays a crucial role in regulating viral replication and pathogenicity. Interestingly, the current study identified an additional upstream stretch of residues (128KDGIIWVATEG138) (N128-138) within the N-terminal domain of the N protein (NTD-N41-174) that also forms molecular contacts with the G3BP1 protein, as revealed through in silico analysis, site-directed mutagenesis and biochemical analysis. Remarkably, WIN-62577, and fluspirilene, the small molecules targeting the conserved peptide binding pocket in G3BP1NTF-2, not only disrupted the protein-protein interactions (PPIs) between the NTD-N41-174 and G3BP1NTF-2 but also exhibited significant antiviral efficacy against SARS-CoV-2 replication with EC50 values of [~]1.8 {micro}M and [~]1.3 {micro}M, respectively. The findings of this study, validated by biophysical thermodynamics and biochemical investigations, advance the potential of developing therapeutics targeting the SG host protein against SARS-CoV-2, which may also serve as a broad-spectrum antiviral target.

biochemistry↗