Biology subjects

Ghosh, A.

Publications and source records attributed to Ghosh, A..

At least 109 records · Page 6Linked to original sources

bioRxiv2024

Peri-mitochondrial actin filaments inhibit Parkin assembly via disruption of ER-mitochondrial contact

Mitochondrial damage represents a dramatic change in cellular homeostasis, necessitating metabolic adaptation as well as clearance of the damaged organelle. One rapid response to mitochondrial damage is peri-mitochondrial actin polymerization within 2 mins, which we term ADA (Acute Damaged-induced Actin). ADA is vital for a metabolic shift from oxidative phosphorylation to glycolysis upon mitochondrial dysfunction. In the current study we investigated the effect of ADA on Pink1/Parkin mediated mitochondrial quality control. We show that inhibition of proteins involved in the ADA pathway significantly accelerates Parkin recruitment onto depolarized mitochondria. Addressing the mechanism by which ADA resists Parkin recruitment onto depolarized mitochondria, we found that ADA disrupts ER- mitochondrial contacts in an Arp2/3 complex-dependent manner. Interestingly, over-expression of ER-mitochondrial tethers overrides the effect of ADA, allowing rapid recruitment of not only Parkin but also LC3 after mitochondrial depolarization. During chronic mitochondrial dysfunction, Parkin and LC3 recruitment are completely blocked, which is reversed rapidly by inhibiting ADA. Taken together we show that ADA acts as a protective mechanism, delaying mitophagy following acute damage, and blocking mitophagy during chronic mitochondrial damage.

cell biology↗

bioRxiv2024

The timing of preceding tactile inputs modulates cortical processing

Sensory experiences in the real world cut across timescales from milliseconds to seconds. Emerging evidence suggests that somatosensory processing is sensitive to the temporal structure of the stimuli in the sub-second scale, yet only a few select ranges within this scale have been studied. To process real-world information, the integration of tactile inputs must occur over a much broader temporal range. To address temporal integration across timescales, we recorded scalp EEG signals from somatosensory cortex in response to a train of tactile pulses presented to the fingertips with varying inter-stimulus intervals (ISI) spanning 100 to 10,000 ms. To capture a rich variety of influences of the temporal structure on the cortical signals, we used a multi-dimensional event-related potential where the stimulations are separated according to the next interval structure. We tracked cortical tactile processing through its early (<75 ms), intermediate (75 to 150 ms) and late stages (150 to 300 ms). We find that the early and late stages of cortical activity were similarly dominated by the preceding ISI; EEG signals were suppressed with ISIs < 500 ms and enhanced with longer ISIs, with this effect persisting even when ISIs were approximately 8 seconds. The intermediate stage of cortical activity was sensitive to both the previous and the penultimate ISIs. Our findings suggest that the specific somatosensory cortical networks integrate temporal structure across timescales to enable complex sensory experiences.

neuroscience↗

bioRxiv2024

Neural microstates in real-world behaviour captured on the smartphone

Microstates are periods of quasi-stability in large-scale neural networks, and they are ubiquitous spanning sleep, rest and behaviour. One possibility is that the temporal and spatial features of these states vary from person to person contributing to inter-individual behavioural differences. Another possibility is that the microstates support momentary behavioural needs and as a result their properties may vary with behavioural fluctuations in the same person. Here, we leverage the history of smartphone touchscreen interaction dynamics and combined smartphone and EEG recordings (N = 61), to address if and how microstates contribute to real-world behaviour. We find that microstates measured when at rest correlated with the history ([~]30 days) of smartphone interaction dynamics captured in the real world, indicating their role in the behaviour. During smartphone behaviour, the configuration of microstates varied over time. However, this variance was largely unrelated to the rich behavioural dynamics, as in similar temporal and spatial features were observed during rapid and slow smartphone interactions. We show that in the real world microstates do not respond to the fluctuations of the ongoing behaviour. Still, as microstates measured at rest are correlated to the inter-individual behavioural differences captured on the smartphone, we propose that microstates exert a top-down influence to broadly orchestrate real-world behaviour.

neuroscience↗

bioRxiv2024

Control of cholesterol-induced adipocyte inflammation by the Nfe2l1-Atf3 pathway

While adipocytes are critical pillars of energy metabolism, their dysfunction is linked to adipose tissue (AT) inflammation, insulin resistance, and ectopic lipotoxicity in cardiometabolic diseases. However, the mechanisms causing adipocyte inflammation and insulin resistance remain unclear. Here, we show that excess cholesterol induces adipocyte dysfunction, which is suppressed by the transcription factor Nfe2l1 (nuclear factor erythroid derived-2, like-1). Nfe2l1 is required to sustain proteasome function in adipocytes and proteotoxic stress induces adipocyte inflammation via the activation of Atf3. In humans, the Nfe2l1-proteasome pathway is inversely correlated to body mass index (BMI) in an adipose-depot specific manner. In mice, loss of adipocyte Nfe2l1 caused AT inflammation with a pronounced infiltration of macrophages and T cells. Mice lacking adipocyte Nfe2l1 displayed severe adipocyte dysfunction during diet-induced obesity (DIO), characterized by lower adipokine levels, steatosis, glucose intolerance and insulin resistance. Nfe2l1{Delta}AT mice on an Apoe-deficient (Apoe-/-) background fed a cholesterol-rich Western Diet (WD), developed a lipoatrophy-like syndrome, dyslipidemia, and enhanced atherosclerosis. Our results reveal an important role for proteasome-mediated proteostasis in adipocytes and indicate that Nfe2l1 is linked to metabolic health in humans and preclinical mouse models. Promoting proteostasis in adipocytes may thus alleviate inflammation in obesity, potentially averting adverse cardiometabolic outcomes. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=191 SRC="FIGDIR/small/604614v1_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@145e32borg.highwire.dtl.DTLVardef@1454df1org.highwire.dtl.DTLVardef@1002383org.highwire.dtl.DTLVardef@1b7319_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2024

Meta-omics reveals role of photosynthesis in Microbially Induced Carbonate Precipitation at a CO2-rich Geyser

Microbially induced carbonate precipitation (MICP) is a natural process with potential biotechnological applications to address both carbon sequestration and sustainable construction needs. However, our understanding of the microbial processes involved in MICP is limited to a few well-researched pathways such as ureolytic hydrolysis. To expand our knowledge of MICP, we conducted an omics-based study on sedimentary communities from travertine around the CO2-driven Crystal Geyser near Green River, Utah. Using metagenomics and metaproteomics, we identified the community members and potential metabolic pathways involved in MICP. We found variations in microbial community composition between the two sites we sampled, but Rhodobacterales were consistently the most abundant order, including both chemoheterotrophs and anoxygenic phototrophs. We also identified several highly abundant genera of Cyanobacteriales. The dominance of these community members across both sites and the abundant presence of photosynthesis-related proteins suggest that photosynthesis could play a role in MICP at Crystal Geyser. We also found abundant bacterial proteins involved in phosphorous starvation response at both sites suggesting that P-limitation shapes both composition and function of the microbial community driving MICP. Our study emphasizes the possible involvement of photosynthesis in MICP processes at Crystal Geyser and suggests that P-limitation may either hinder or facilitate MICP within the community.

microbiology↗

bioRxiv2024

A Single Trophoblast Layer Acts as the Gatekeeper at the Endothelial-Hematopoietic Crossroad in the Placenta

During embryonic development the placental vasculature acts as a major hematopoietic niche, where endothelial to hematopoietic transition ensures emergence of hematopoietic stem cells (HSCs). However, the molecular mechanisms that regulate the placental hematoendothelial niche are poorly understood. Using a parietal trophoblast giant cell (TGC)-specific knockout mouse model and single-cell RNA-sequencing, we show that the paracrine factors secreted by the TGCs are critical in the development of this niche. Disruptions in the TGC-specific paracrine signaling leads to the loss of HSC population and the concomitant expansion of a KDR+/DLL4+/PROM1+ hematoendothelial cell-population in the placenta. Combining single- cell transcriptomics and receptor-ligand pair analyses, we also define the parietal TGC- dependent paracrine signaling network and identify Integrin signaling as a fundamental regulator of this process. Our study elucidates novel mechanisms by which non-autonomous signaling from the primary parietal TGCs maintain the delicate placental hematopoietic- angiogenic balance and ensures embryonic and extraembryonic development.

developmental biology↗

bioRxiv2024

METTL3 shapes m6A epitranscriptomic landscape for successful human placentation

Methyltransferase-like 3 (METTL3), the catalytic enzyme of methyltransferase complex for m6A methylation of RNA, is essential for mammalian development. However, the importance of METTL3 in human placentation remains largely unexplored. Here, we show that a fine balance of METTL3 function in trophoblast cells is essential for successful human placentation. Both loss-of and gain-in METTL3 functions are associated with adverse human pregnancies. A subset of recurrent pregnancy losses and preterm pregnancies are often associated with loss of METTL3 expression in trophoblast progenitors. In contrast, METTL3 is induced in pregnancies associated with fetal growth restriction (FGR). Our loss of function analyses showed that METTL3 is essential for the maintenance of human TSC self-renewal and their differentiation to extravillous trophoblast cells (EVTs). In contrast, loss of METTL3 in human TSCs promotes syncytiotrophoblast (STB) development. Global analyses of RNA m6A modification and METTL3-RNA interaction in human TSCs showed that METTL3 regulates m6A modifications on the mRNA molecules of critical trophoblast regulators, including GATA2, GATA3, TEAD1, TEAD4, WWTR1, YAP1, TFAP2C and ASCL2, and loss of METTL3 leads to depletion of mRNA molecules of these critical regulators. Importantly, conditional deletion of Mettl3 in trophoblast progenitors of an early post-implantation mouse embryo also leads to arrested self-renewal. Hence, our findings indicate that METLL3 is a conserved epitranscriptomic governor in trophoblast progenitors and ensures successful placentation by regulating their self-renewal and dictating their differentiation fate.

developmental biology↗

bioRxiv2024

TGFb-ANGPT2-Tie2 axis in cancer-associated fibroblasts reprograms oral cancer cells to embryonic-like cell state with predictive significance of poor prognosis

Myofibroblastic cancer-associated fibroblasts (CAFs) in tumor stroma is identified as poor-prognostic indicator in oral cancer; however, biological mechanisms are largely unexplored. Here, we discovered the role of autocrine or exogenous transforming growth factor beta (TGF{beta}) in inducing Tunica Interna Endothelial cell kinase 2 (Tie2) -signaling through histone deacetylase-mediated downregulation of Tie2-antagonist, Angiopoietin-2 in CAFs, responsible for induction and maintenance of myofibroblastic differentiation. To understand the influence of CAF-specific Tie2-signaling on cancer cell properties, we performed CAF-Cancer cell co-culture and its single-cell RNA sequencing (scRNA-Seq). Distinct clustering of CAFs suggested their transcriptional heterogeneity, driven by TGF{beta}-Tie2 activation. Interestingly, CAF-specific Tie2-signaling was responsible to reprogram cancer cells, producing embryonic-like cell state with increased stemness and EMT signatures. Importantly, both the Tie2-specific gene expression signature as well as reprogrammed cancer cell specific gene expression modules were validated respectively in fibroblasts clusters and malignant cell clusters in two independent earlier reported scRNAseq studies of HNSCC tumors. Highlighting the translatability of our study, the gene expression signature derived from reprogrammed cancer cells showed significant association with poor prognosis in HNSCC patient of TCGA cohort. Pharmacological inhibition of Tie2-signaling in CAFs, significantly abrogated the tumor initiating ability of co-cultured oral cancer cell lines. Overall, combining our molecular and computational analysis, we may propose Tie2 as a novel factor responsible for CAF mediated cancer cell plasticity, associated with aggressive nature of oral cancer. TeaserTie2-signaling is activated in myofibroblasts which impacts the behaviour of malignant cells by inducing cancer cell plasticity to acquire stemness.

cancer biology↗

bioRxiv2024

Role of VapBC4 toxin-antitoxin system of Sulfolobus acidocaldarius in heat stress adaptation

Toxin-antitoxin (TA) systems are important for stress adaptation in prokaryotes, including persistence, antibiotic resistance, pathogenicity, and biofilm formation. Toxins can cause cell death, reversible growth stasis, and direct inhibition of crucial cellular processes through various mechanisms, while antitoxins neutralize the effects of toxins. In bacteria, these systems have been studied in detail, whereas their function in archaea remains elusive. During heat stress, the thermoacidophilic archaeon Sulfolobus acidocaldarius exhibited an increase in the expression of several bicistronic type II vapBC TA systems, with the highest expression observed in the vapBC4 system. In the current study, we performed a comprehensive biochemical characterization of the VapBC4 TA system, establishing it as a bonafide type II toxin-antitoxin system. The VapC4 toxin is shown to have high-temperature catalyzed RNase activity specific for mRNA and rRNA, while the VapB4 antitoxin inhibits the toxic activity of VapC4 by interacting with it. VapC4 toxin expression led to heat-induced persister-like cell formation, allowing the cell to cope with the stress. Furthermore, this study explored the impact of vapBC4 deletion on biofilm formation, whereby deletion of vapC4 led to increased biofilm formation, suggesting its role in regulating biofilm formation. Thus, during heat stress, the liberated VapC4 toxin in cells could potentially signal a preference for persister cell formation over biofilm growth. Thus, our findings shed light on the diverse roles of the VapC4 toxin in inhibiting translation, inducing persister cell formation, and regulating biofilm formation in S. acidocaldarius, enhancing our understanding of TA systems in archaea. IMPORTANCEThis research enhances our knowledge of Toxin-antitoxin (TA) systems in archaea, specifically in the thermoacidophilic archaeon Sulfolobus acidocaldarius. TA systems are widespread in both bacterial and archaeal genomes, indicating their evolutionary importance. However, their exact functions in archaeal cellular physiology are still not well understood. This study sheds light on the complex roles of TA systems and their critical involvement in archaeal stress adaptation, including persistence and biofilm formation. By focusing on S. acidocaldarius, which lives in habitats with fluctuating temperatures that can reach up to 90, the study reveals the unique challenges and survival mechanisms of this organism. The detailed biochemical analysis of the VapBC4 TA system, and its crucial role during heat stress, provides insights into how extremophiles can survive in harsh conditions. The findings of this study show the various functions of the VapC4 toxin, including inhibiting translation, inducing persister-like cell formation, and regulating biofilm formation. This knowledge improves our understanding of TA systems in thermoacidophiles and has broader implications for understanding how microorganisms adapt to extreme environments.

microbiology↗

bioRxiv2024

A novel cholesterol dehydrogenase from Limosilactobacillus fermentum catalyzes the direct conversion of cholesterol to coprostanol

On the one hand, cholesterol is a foundational molecule for various structural and biochemical pathways, while elevated cholesterol levels are associated with cardiovascular diseases. Some selected strains of Lactobacilli are also known for modulating cholesterol levels. However, the molecular mechanism of cholesterol transformation by lactobacilli has remained challenging to reveal. This study reports the discovery and role of a microbial 3{beta}-OH-{Delta}5-6-cholesterol-5{beta}-reductase from Limosilactobacillus fermentum NKN51, which directly converts cholesterol to coprostanol, thereby resolving the enigma. Protein engineering of the reductase enzyme identified the cholesterol and NADP+ interacting amino acids, detailing the catalytic mechanism of 5{beta}ChR. Phylogenetic studies emphasize the abundance of 5{beta}ChRs in gut commensal lactobacilli, which shares a common ancestor with plant 5{beta} reductases. Meta-analysis results of healthy participant microbiomes underline the significance of 5{beta}ChR homologs, while a cohort study reveals an association between higher 5{beta}ChR abundance and diabetes. The discovery of the 5{beta}ChR enzyme and its molecular mechanism in cholesterol metabolism pave the way for a better understanding of the gut-associated microbiome and the design of practical applications to ameliorate dyslipidemia.

molecular biology↗

bioRxiv2024

Spatiotemporal dynamic models of Amblyomma americanum questing activity in the Central Great Plains

Ticks represent important vectors of a number of bacterial and viral disease agents, owing to their hematophagous nature and their questing behavior (the process in which they seek new hosts). Questing activity is notably seasonal with spatiotemporal dynamics that needs to be understood in detail as part of mediating and mitigating tick-borne disease risk. Models of the geography of tick questing activity developed to date, however, have ignored the temporal dimensions of that behavior; more fundamentally, they have often not considered the sampling underlying available occurrence data. Here, we have addressed these shortfalls for Amblyomma americanum, the most commonly encountered tick in the central Great Plains, via (1) detailed, longitudinal sampling to characterize the spatiotemporal dimensions of tick questing activity; (2) randomization tests to establish in which environmental dimensions a species is manifesting selective use; and (3) modeling methods that include both presence data and absence data, taking fullest advantage of the information available in the data resource. The outcome was a detailed picture of geographic and temporal variation in suitability for the species through the two-year course of this study. Such models that take full advantage of available information will be crucial in understanding the risk of tick-borne disease into the future.

ecology↗

bioRxiv2024

Design of High Affinity Binders to Convex Protein Target Sites

While there has been progress in the de novo design of small globular miniproteins (50-65 residues) to bind to primarily concave regions of a target protein surface, computational design of minibinders to convex binding sites remains an outstanding challenge due to low level of overall shape complementarity. Here, we describe a general approach to generate computationally designed proteins which bind to convex target sites that employ geometrically matching concave scaffolds. We used this approach to design proteins binding to TGF{beta}RII, CTLA-4 and PD-L1 which following experimental optimization have low nanomolar to picomolar affinities and potent biological activity. Co-crystal structures of the TGF{beta}RII and CTLA-4 binders in complex with the receptors are in close agreement with the design models. Our approach provides a general route to generating very high affinity binders to convex protein target sites.

biochemistry↗

bioRxiv2024

A novel micronemal protein, Scot1, is essential for apicoplast biogenesis and liver stage development in Plasmodium berghei

Plasmodium sporozoites invade hepatocytes, transform into liver stages, and replicate into thousands of merozoites that infect erythrocytes and cause malaria. Proteins secreted from micronemes play an essential role in hepatocyte invasion, and unneeded micronemes are subsequently discarded for replication. The liver-stage parasites are potent immunogens that prevent malarial infection. Late liver stage-arresting genetically attenuated parasites (GAPs) exhibit greater protective efficacy than early GAP. However, the number of late liver-stage GAPs for generating GAPs with multiple gene deletions is limited. Here, we identified Scot1 (Sporozoite Conserved Orthologous Transcript 1), which was previously shown to be upregulated in sporozoites, and by endogenous tagging with mCherry, we demonstrated that it is expressed in the sporozoite and liver stages in micronemes. Using targeted gene deletion in Plasmodium berghei, we showed that Scot1 is essential for late liver-stage development. Scot1 KO sporozoites grew normally into liver stages but failed to initiate blood-stage infection in mice due to impaired apicoplast biogenesis and merozoite formation. Bioinformatic studies suggested that Scot1 is a metal/small molecule carrier protein. Remarkably, supplementation with metals in the culture of infected Scot1 KO cells did not rescue their phenotype. Immunization with Scot1 KO sporozoites in C57BL/6 mice confers protection against a malaria challenge via infection. These proof-of-concept studies will enable the generation of P. falciparum Scot1 mutants that could be exploited to generate GAP malaria vaccines. ImportanceMalaria parasites experience significant bottlenecks as transmitted to the mammalian host during a mosquito bite. Sporozoites invade liver cells, reproducing into thousands of merozoites, which are released after liver cell ruptures. The specific arrest of sporozoites during liver stage development acts as a powerful immunogen and provides sterile protection against sporozoite infection. GAP leading to an arrest in late liver stage development offers superior protection. Here, we report that a micronemal protein, Scot1, is essential for parasite maturation in the liver. Deletion of Scot1 resulted in impaired apicoplast biogenesis and merozoite formation. Vaccination with Scot1 KO sporozoites protects against malaria challenge. We have identified a late arresting GAP that will aid in developing new as well as safeguarding existing whole parasite vaccines.

microbiology↗

bioRxiv2024

Paired transcriptomic analyses of atheromatous and control vessels reveal novel autophagy and immunoregulatory genes in peripheral artery disease

AbstractO_ST_ABSBackgroundC_ST_ABSPeripheral artery disease (PAD), a significant health burden worldwide, affects lower extremities due to atherosclerotic changes in the peripheral vessels. Although mechanisms of PAD have been studied, the molecular milieu of the plaques localized within peripheral arteries in patients are not well understood. Thus, to identify PAD lesion specific gene expression profiles precluding genetic, environmental and dietary biases, we studied the transcriptomic profile of plaque tissues normalized to non-plaque tissues from the same donors. MethodsTranscriptomic analysis of 9 paired samples of PAD patients from south Indian population was performed with institutional ethics approval and written consent. Plaque tissues were histologically confirmed. Expression of a select target gene set was done by qPCR from the same tissues. Bioinformatic and network analyses were performed using various statistical tools. ResultsA total of 296 upregulated, 274 downregulated genes and 186 non-coding RNAs were identified. STAG1, SPCC3, FOXQ1 and E2F3 were key downregulated genes and CD93 was top upregulated gene. Autophagosome assembly, cellular response to UV, cytoskeletal organization, TCR signaling and phosphatase activity were key dysregulated pathways identified in the study. Telomerase regulation and autophagy were identified as novel interacting pathways using network analysis. Plaque tissue was predominantly composed of immune cells and dedifferentiated cell populations indicated by cell specific marker imputed gene expression analysis. ConclusionThe current study identifies novel genes, non-coding RNAs, associated regulatory pathways and cell composition of the plaque tissue in PAD patients. The autophagy and immunoregulatory genes may drive novel mechanisms resulting in atheroma. These novel interacting networks and genes have the potential for PAD specific therapeutic applications.

molecular biology↗

bioRxiv2024

Heterotypic Seeding Generates Mixed Amyloid Polymorphs

Aggregation of the amyloid {beta} (A{beta}) peptide into fibrils represents one of the major biochemical pathways underlying the development of Alzheimers disease (AD). Extensive studies have been carried out to understand the role of fibrillar seeds on the overall kinetics of amyloid aggregation. However, the precise effect of seeds that are structurally or sequentially different from A{beta} on the structure of the resulting amyloid aggregates is yet to be fully understood. In this work, we use nanoscale infrared spectroscopy to probe the spectral facets of individual aggregates formed by aggregating A{beta}42 with antiparallel fibrillar seeds of A{beta} (16-22) and E22Q A{beta} (1-40) Dutch mutant and demonstrate that A{beta} can form heterotypic or mixed polymorphs that deviate significantly from its expected parallel cross {beta} structure. We further show that formation of heterotypic aggregates is not limited to coaggregation of A{beta} and its isomers, and that the former can form heterotypic fibrils with alpha synuclein and brain protein lysates. These findings highlight the complexity of A{beta} aggregation in AD and underscore the need to explore how A{beta} interacts with other brain components, which is crucial for developing better therapeutic strategies for AD.

biophysics↗

bioRxiv2024

Application of Quantum Tensor Networks for Protein Classification

Computational methods in drug discovery significantly reduce both time and experimental costs. Nonetheless, certain computational tasks in drug discovery can be daunting with classical computing techniques which can be potentially overcome using quantum computing. A crucial task within this domain involves the functional classification of proteins. However, a challenge lies in adequately representing lengthy protein sequences given the limited number of qubits available in existing noisy quantum computers. We show that protein sequences can be thought of as sentences in natural language processing and can be parsed using the existing Quantum Natural Language framework into parameterized quantum circuits of reasonable qubits, which can be trained to solve various proteinrelated machine-learning problems. We classify proteins based on their sub-cellular locations--a pivotal task in bioinformatics that is key to understanding biological processes and disease mechanisms. Leveraging the quantum-enhanced processing capabilities, we demonstrate that Quantum Tensor Networks (QTN) can effectively handle the complexity and diversity of protein sequences. We present a detailed methodology that adapts QTN architectures to the nuanced requirements of protein data, supported by comprehensive experimental results. We demonstrate two distinct QTNs, inspired by classical recurrent neural networks (RNN) and convolutional neural networks (CNN), to solve the binary classification task mentioned above. Our top-performing quantum model has achieved a 94% accuracy rate, which is comparable to the performance of a classical model that uses the ESM2 protein language model embeddings. Its noteworthy that the ESM2 model is extremely large, containing 8 million parameters in its smallest configuration, whereas our best quantum model requires only around 800 parameters. We demonstrate that these hybrid models exhibit promising performance, showcasing their potential to compete with classical models of similar complexity.

bioinformatics↗

bioRxiv2024

Identification of Key Regulators in Pancreatic Ductal Adenocarcinoma using Network theoretical Approach

Pancreatic Ductal Adenocarcinoma (PDAC) is a devastating disease with poor clinical outcomes, which is mainly because of delayed disease detection, resistance to chemotherapy, and lack of specific targeted therapies. The diseases development involves complex interactions among immunological, genetic, and environmental factors, yet its molecular mechanism remains elusive. A major challenge in understanding PDAC etiology lies in unraveling the genetic profiling that governs the PDAC network. To address this, we examined the gene expression profile of PDAC and compared it with that of healthy controls, identifying differentially expressed genes (DEGs). These DEGs formed the basis for constructing the PDAC protein interaction network, and their network topological properties were calculated. It was found that the PDAC network self-organizes into a scale-free fractal state with weakly hierarchical organization. Newman and Girvans algorithm (leading eigenvector (LEV) method) of community detection enumerated four communities leading to at least one motif defined by G (3,3). Our analysis revealed 33 key regulators were predominantly enriched in neuroactive ligand-receptor interaction, Cell adhesion molecules, Leukocyte transendothelial migration pathways; positive regulation of cell proliferation, positive regulation of protein kinase B signaling biological functions; G-protein beta-subunit binding, receptor binding molecular functions etc. Transcription Factor and mi-RNA of the key regulators were obtained. Recognizing the therapeutic potential and biomarker significance of PDAC Key regulators, we also identified approved drugs for specific genes. However, it is imperative to subject Key regulators to experimental validation to establish their efficacy in the context of PDAC.

systems biology↗

bioRxiv2024

Antigenic determinants of HAstV-VA1 neutralization and their relevance in the human immune response

Astroviruses are highly divergent and infect a wide variety of animal hosts. In 2009, a genetically divergent human astrovirus (HAstV) strain VA1 was first identified in an outbreak of acute gastroenteritis. This strain has also been associated with fatal central nervous system disease. In this work, we report the isolation of three high-affinity neutralizing monoclonal antibodies (Nt-MAbs) targeting the capsid spike domain of HAstV-VA1. These antibodies (7C8, 2A2, 3D8) were used to select individual HAstV-VA1 mutants resistant to their neutralizing activity and also select a HAstV-VA1 triple mutant that escapes neutralization from all three Nt-MAbs. Sequencing of the virus genome capsid region revealed escape mutations that map to the surface of the capsid spike domain, define three potentially independent neutralization epitopes, and help delineate four antigenic sites in rotaviruses. Notably, two of the escape mutations were found to be present in the spike sequence of the HAstV-VA1-PS strain isolated from an immunodeficient patient with encephalitis, suggesting that those mutations arose as a result of the immune pressure generated by the patients immunotherapy. In accordance with this observation, human serum samples exhibiting strong neutralization activity against wild-type HAstV-VA1 had a 2.6-fold reduction in neutralization titer when evaluated against the triple-escape HAstV-VA1 mutant, indicating shared neutralization epitopes between the mouse and human antibody response. The isolated Nt-MAbs reported in this work will help characterize the functional sites of the virus during cell entry and have the potential for developing a specific antibody therapy for the neurological disease associated with HAstV-VA1. ImportanceHuman astroviruses (HAstVs) have been historically associated with acute gastroenteritis. However, the genetically divergent HAstV-VA1 strain has been associated with central nervous system disease. This work isolated high-affinity neutralizing monoclonal antibodies directed to HAstV-VA1. The proposed binding sites for these antibodies, together with previously reported sites for neutralizing antibodies against classical HAstVs, suggest the existence of at least four neutralization sites on the capsid spike of astroviruses. Our data show that natural infection with human astrovirus VA1 elicits a robust humoral immune response that targets the same antigenic sites recognized by the mouse monoclonal antibodies and strongly suggests the emergence of a variant HAstV-VA1 virus in an immunodeficient patient with prolonged astrovirus infection. The isolated Nt-MAb reported in this work will be helpful in defining the functional sites of the virus involved in cell entry and hold promise for developing a specific antibody therapy for the neurological disease associated with HAstV-VA1.

microbiology↗