Biology subjects

Pathak, H.

Publications and source records attributed to Pathak, H..

10 recordsLinked to original sources

bioRxiv2026

Accelerated amyloid neurodegeneration in HIV-1-infected APP-KI Alzheimer's disease mice

STRUCTURED ABSTRACTO_ST_ABSINTRODUCTIONC_ST_ABSA higher incidence of dementia, including Alzheimer s-like pathology, is observed in aged people living with HIV-1. However, mechanisms linking HIV-1 to Alzheimers disease (AD) pathology remain unclear, due to the lack of animal models that allow for concurrent study. METHODSWe created a novel APP knock-in (KI) AD mouse, NOG/APPKM670,671NL/IL-34 (hNAIL) that permits study of progressive brain HIV-1 replication. The mice harbor human microglia-like cells. Four-month-old CD34+ human cell reconstituted mice infected with the HIV-1ADA strain facilitated studies of HIV-1 replication on AD pathologies. RESULTSHIV-1 replication increased A{beta} levels and reduced synaptic and neuronal integrity. Spatial transcriptomics demonstrated distinct A{beta} and HIV-1 transcriptional patterns, whereas dual diseased combinations amplified AD pathology. Neurons showed highest transcriptional change, with genes linked to neuroinflammation, protein trafficking, and synaptic dysfunction. DISCUSSIONThe hNAIL mice enable interrogation of HIV-AD comorbidities, with a future potential for the development of novel therapeutic interventions.

neuroscience↗

bioRxiv2026

CRISP enables comparisons of image-based spatial transcriptomicsegmentation quality across ten organs

Image-based spatial transcriptomics depends on cell segmentation to assign transcripts to individual cells, but how segmentation algorithms perform across tissues with distinct cellular architectures is poorly understood. This study presents the broadest independent benchmark to date of cell segmentation algorithms for spatial transcriptomics, comparing five approaches across ten mouse tissues using a 5,006-gene Xenium panel. To quantify segmentation errors, Co-expression Rejection in Segmentation Purity (CRISP) was developed, an open-source tool available in R and Python that measures cell purity through tissue-specific mutually exclusive marker co-expression without requiring ground truth annotations. This benchmark revealed that segmentation algorithms face a fundamental tradeoff between maximizing transcript capture and maintaining cell purity, and that the severity of this tradeoff is tissue-dependent. Proseg achieved the highest average performance across tissues, though the magnitude of its advantage varies with tissue architecture. Overall, CRISP provides per-tissue performance profiles as a practical resource for algorithm selection.

bioinformatics↗

bioRxiv2025

Macrophage-derived WNT regulates tumor immune microenvironment to reduce colitis-associated colon cancer

Prolonged colonic inflammation and ulcerative colitis lead to colon cancer. The rapid growth and treatment-resistant nature of these tumors are primarily influenced by an immunosuppressive tumor microenvironment, which is led by tumor-associated macrophages (TAMs). However, factors influencing or regulating the immunosuppressive nature of TAMs have not been sufficiently studied. In this manuscript, we use a mouse model of colitis-associated colorectal cancer (CRC) to demonstrate that WNT expression in TAMs regulates their immunosuppressive function by inhibiting Glycogen synthase kinase-3 beta (GSK-3{beta}) within the macrophages, possibly through an autofeedback loop. GSK3{beta} is a positive regulator of PD-1 and PDL1 expression in macrophages and promotes an immunosuppressive microenvironment. Therefore, GSK-3{beta} inhibition alters the immunosuppressive nature of the immune microenvironment and effectively controls tumor growth. In Csf1r-iCre; Porcnfl/fl mice, the absence of macrophage-derived WNT promotes tumor growth in the model of colitis-associated colon cancer. Absence of macrophage-derived WNT stabilizes GSK-3{beta} in macrophages and promotes an immunosuppressive tumor microenvironment. We also show that pharmacological inhibition of GSK-3{beta} in a macrophage-specific manner, achieved by systemic delivery of a lipo-GSK3{beta} inhibitor, effectively inhibits tumor growth. Therefore, this manuscript demonstrates for the first time that the macrophage-specific modulation of GSK3{beta} can be a potential target to treat colitis-associated colon cancer.

cancer biology↗

bioRxiv2024

Niche-Based Priority Effects Predict Microbe Resistance to Erwinia amylovora in Pear Nectar

Fire blight is a devastating disease affecting pome fruit trees that is caused by Erwinia amylovora and leads to substantial annual losses worldwide. While antibiotic-based management approaches like streptomycin can be effective, there are concerns over evolved resistance of the pathogen and non-target effects on beneficial microbes and insects. Using microbial biological control agents (mBCAs) to combat fire blight has promise, but variable performance necessitates the discovery of more effective solutions. Here we used a niche-based predictive framework to assess the strength of priority effects exerted by prospective mBCAs, and the mechanisms behind growth suppression in floral nectar. Through in vitro and in vivo assays, we show that antagonist impacts on nectar pH and sucrose concentration were the primary predictors of priority effects. Surprisingly, overlap in amino acid use, and the degree of phylogenetic relatedness between mBCA and Erwinia did not significantly predict pathogen suppression in vitro, suggesting that competition for limited shared resources played a lesser role than alterations in the chemical environment created by the initial colonizing species. We also failed to detect an association between our measures of in vitro and in vivo Erwinia suppression, suggesting other mechanisms may dictate mBCA establishment and efficacy in flowers, including priming of host defenses.

plant biology↗

bioRxiv2022

Differential pathogenesis of SARS-CoV-2 variants of concern in human ACE2-expressing mice

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a pandemic resulting in millions of deaths worldwide. Increasingly contagious variants of concern (VoC) have fueled recurring global infection waves. A major question is the relative severity of disease caused by the previous and currently circulating variants of SARS-CoV-2. In this study, we evaluated the pathogenesis of SARS-CoV-2 variants in human ACE-2-expressing (K18-hACE2) mice. Eight-week-old K18-hACE2 mice were inoculated intranasally with a representative virus from the original B.1 lineage, or the emerging B.1.1.7 (alpha), B.1.351 (beta), B.1.617.2 (delta) or B.1.1.529 (omicron) lineages. We also infected a group of mice with the mouse-adapted SARS-CoV-2 (MA10). Our results demonstrate that B.1.1.7, B.1.351 and B.1.617.2 viruses are significantly more lethal than B.1 strain in K18-hACE2 mice. Infection with B.1.1.7, B.1.351 and B.1.617.2 variants resulted in significantly higher virus titers in the lungs and brain of mice compared to the B.1 virus. Interestingly, mice infected with the B.1.1.529 variant exhibited less severe clinical signs and high survival rate. We found that B.1.1.529 replication was significantly lower in the lungs and brain of infected mice in comparison to other VoC. Transcription levels of cytokines and chemokines in the lungs of the B.1.1.529-infected mice were significantly less when compared to those challenged with the B.1.1.7 virus. Together, our data provide insights into the pathogenesis of the previous and circulating SARS-CoV-2 VoC in mice.

microbiology↗

bioRxiv2021

SARS-CoV-2 variants of concern infect the respiratory tract and induce inflammatory response in wild-type laboratory mice

The emergence of new severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants of concern poses a major threat to the public health due to possible enhanced virulence, transmissibility and immune escape. These variants may also adapt to new hosts in part through mutations in the spike protein. In this study, we evaluated the infectivity and pathogenicity of SARS-CoV-2 variants of concern in wild-type C57BL/6 mice. Six-week-old mice were inoculated intranasally with a representative virus from the original B.1 lineage or emerging B.1.1.7 and B.1.351 lineages. We also infected a group of mice with a mouse-adapted SARS-CoV-2 (MA10). Viral load and mRNA levels of multiple cytokines and chemokines were analyzed in the lung tissues on day 3 after infection. Our data show that unlike the B.1 virus, the B.1.1.7 and B.1.351 viruses are capable of infecting C57BL/6 mice and replicating at high concentrations in the lungs. The B.1.351 virus replicated to higher titers in the lungs compared to the B.1.1.7 and MA10 viruses. The levels of cytokines (IL-6, TNF-, IL-1{beta}) and chemokine (CCL2) were upregulated in response to the B.1.1.7 and B.1.351 infection in the lungs. Overall, these data indicate a greater potential for infectivity and adaptation to new hosts by emerging SARS-CoV-2 variants.

microbiology↗

bioRxiv2021

MinION nanopore sequencing provides similar methylation estimates to Sanger bisulfite sequencing in the TRPA1 promoter region

Bisulfite sequencing has long been considered the gold standard for measurement of DNA methylation at single CpG resolution. In the meantime, several new approaches have been developed, which are regarded as less error-prone. Since these errors were shown to be sequence-specific, we aimed to verify the methylation data of a particular region of the TRPA1 promoter obtained from our previous studies. For this purpose, we compared methylation rates obtained via direct bisulfite sequencing and nanopore sequencing. Thus, we were able to confirm our previous findings to a large extent.

molecular biology↗

bioRxiv2020

Neuroinvasion and encephalitis following intranasal inoculation of SARS-CoV-2 in K18-hACE2 mice

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection can cause neurological disease in humans, but little is known about the pathogenesis of SARS-CoV-2 infection in the central nervous system. Herein, using K18-hACE2 mice, we demonstrate that SARS-CoV-2 neuroinvasion and encephalitis is associated with mortality in these mice. Intranasal infection of K18-hACE2 mice with 105 plaque-forming units of SARS-CoV-2 resulted in 100% mortality by day 6 after infection. The highest virus titers in the lungs were observed at day 3 and declined at days 5 and 6 after infection. In contrast, very high levels of infectious virus were uniformly detected in the brains of all the animals at days 5 and 6. Onset of severe disease in infected mice correlated with peak viral levels in the brain. SARS-CoV-2-infected mice exhibited encephalitis hallmarks characterized by production of cytokines and chemokines, leukocyte infiltration, hemorrhage and neuronal cell death. SARS-CoV-2 was also found to productively infect cells within the nasal turbinate, eye and olfactory bulb, suggesting SARS-CoV-2 entry into the brain by this route after intranasal infection. Our data indicate that direct infection of CNS cells together with the induced inflammatory response in the brain resulted in the severe disease observed in SARS-CoV-2-infected K18-hACE2 mice.

microbiology↗

bioRxiv2019

Regulation of starvation-mediated hyperactivity and triglyceride metabolism by Short neuropeptide F and Insulin Like Peptide in Drosophila

The circadian clock regulates various behavioral, metabolic and physiological processes to occur at the most suitable time of the day. Internal energy stores and nutrient availability modulates the most apparent circadian clock mediated locmotor activity rhythm in Drosophila. Although previous studies unraveled the role of circadian clock in metabolism and activity rest rhythm, the precise pathway through which the circadian neuropeptidergic signaling regulates internal energy storage and the starvation-mediated increase in activity resembling foraging remains largely unclear. This study was aimed to elucidate the role of circadian neuropeptide, short neuropeptide F (sNPF) in triglyceride metabolism, starvation resistance and starvation-mediated increased locomotor activity in Drosophila. The results showed that snpf transcripts exhibits significant rhythmicity in wild type flies under 12:12 hour light-dark cycles (LD) and constant darkness (DD) whereas snpf transcript level in period null flies did not exhibit any significant rhythmicity under LD. Knockdown of sNPF in circadian clock neurons reduced the triglyceride level, starvation resistance and increased the starvation-mediated hyperactivity response after 24 hour of starvation. Further studies showed that knock down of sNPF receptors (sNPFR) expressed in insulin producing cells (IPC) increased the starvation resistance and reduced starvation-induced hyperactivity response after 24 hour of starvation. Collectively, our results suggest that transcriptional oscillation of snpf mRNA is endogenously controlled by the circadian clock and elucidate the role of sNPF in modulating locomotor activity in accordance with the nutrient availability in Drosophila.

animal behavior and cognition↗

bioRxiv2019

Edem1 activity in the fat body regulates insulin signalling and metabolic homeostasis in Drosophila

In Drosophila, nutrient status is sensed by the fat body, a functional homolog of mammalian liver and white adipocytes. The fat body conveys nutrient information to insulin-producing cells (IPCs) through humoral factors which regulate Drosophila insulin-like peptide (DILP) levels and insulin signalling. Insulin signalling has pleiotropic functions, which include the management of growth and metabolic pathways. Here, we report that Edem1 (endoplasmic reticulum degradation-enhancing -mannosidase-like protein 1), an endoplasmic reticulum-resident protein involved in protein quality control, acts in the fat body to regulate insulin signalling and thereby the metabolic status in Drosophila. Edem1 limits the fat body derived Drosophila TNF Eiger activity on IPCs and maintains systemic insulin signalling in fed conditions. During food deprivation, edem1 gene expression levels drop, which aids in the reduction of systemic insulin signalling crucial for survival. Overall we demonstrate that Edem1 plays a vital role in helping the organism to endure a fluctuating nutrient environment by managing insulin signalling and metabolic homeostasis.

developmental biology↗