Biology subjects

Rahman, I.

Publications and source records attributed to Rahman, I..

17 recordsLinked to original sources

bioRxiv2025

Deposition of microplastics associated with bioaccumulation of heavy metals in human lungs of smokers: Implications of adsorption and mobilization of metals via microplastics

BackgroundAirborne micro- and nano plastics (MNPs), generated from synthetic textiles, vehicle tires and plastic wastes, are omnipresent in the environment and known to deposit in human lungs. Bioaccumulation of MNPs in lung tissues has been studied, but effect of tobacco smoking on deposition is not well understood. Tobacco smoke is known to contain heavy metals which can get adsorbed to the MNP surface, leading to increased environmental bioavailability. We hypothesized that smoking leads to enhanced chelation of heavy metals with airborne MNPs leading to accentuated lung bioaccumulation, thereby leading to lung pathologies. MethodsAge (20-75 years) and sex-matched archival lung tissue samples from smokers (n = 9) and non-smokers (n = 10) were procured and quantified to assess: (a) the levels of MNPs by pyro-GC/MS and (b) heavy metals by ICP-MS. Furthermore, to establish if there exists a correlation between MNP deposition and disease occurrence in current smokers, tissue samples from age-matched patients with COPD (n = 4) and IPF (n = 4) underwent pyro-GC/MS analyses. ResultsA relatively higher level of MNPs were found in the lungs of smokers (43.67 mcg/gm) as compared to non-smoker (34.53 mcg/gm) upon pyro-GC/MS analyses. We observed a marked increase in the levels of polyethylene (PE; p< 0.0076), polycarbonate (PC; p< 0.0947) and nylon6 (N6; p < 0.0653) polymers in the lungs of smokers as compared to non-smokers. Metal analyses showed a significant (p <0.0001) increase in the levels of cadmium (Cd) in the lungs of smokers with the levels of deposited Cd being more pronounced for female smokers. Importantly, we observed a strong correlation (p < 0.05) between the amounts of accumulated PE and levels of Cd in the lungs. Pyro-GC/MS analyses did not reveal any relation between MNP deposition and disease occurrence in our study. Furthermore, little to no change in the level of deposited MNPs was observed in the lungs of current versus ex-smokers in disease cohorts. ConclusionsOverall, our results show that smoking promotes bioaccumulation of certain MNPs (PE) with heavy metals (Cd) which may lead to adverse lung effects in smokers.

pharmacology and toxicology↗

bioRxiv2025

An Intrinsic-hoc Framework for Heterogeneous Cellular Senescence Elucidation Using Deep Graph Representation Learning and Experimental Validation

Cellular senescence is a primordial driver of tissue and organ aging, and the accumulation of senescent cells (SnCs) has been implicated in numerous age-related diseases. A major barrier to studying senescence is the rarity and heterogeneity of SnCs, which are not a uniform population but instead comprise diverse senotypes shaped by cell-of-origin and microenvironmental context. Such heterogeneity exceeds what classical senescence hallmarks can resolve at single-cell resolution, motivating the need for computational frameworks that can capture senotype-level diversity intrinsically. Here, we introduce DeepSAS, a deep graph representation learning framework that robustly identifies cell-type-specific SnCs and their senescence-associated genes (SnGs). DeepSAS incorporates a heterogeneous graph that integrates intracellular transcriptional states with intercellular communication cues, enabling the joint inference of senescent cells and senescence-linked genes through attention-based contrastive learning. Applied to public healthy eye and lung atlases, DeepSAS identified SnCs whose proportions positively correlate with aging. From in-house idiopathic pulmonary fibrosis (IPF) patient scRNA-seq data, DeepSAS detected 1,678 SnCs (out of 24,125 cells) and 263 SnGs across 26 cell types, including 43 SnGs that are uniquely associated with a single cell type. We generated high-resolution Xenium spatial transcriptomics data to further validate SnGs in IPF, revealing NFE2L2 as a SnG specifically enriched in CTHRC1+ fibroblasts. Notably, the ex vivo bleomycin-induced senescence in human precision-cut lung slice (hPCLS) samples similarly identified NFE2L2 as an SnG in CTHRC1+ fibroblasts, albeit with stronger transcriptional signals, suggesting mechanistic differences in senescence cells associated with chronic and acute injury. Overall, DeepSAS uncovers distinct senescence programs and infers cell-type-specific SnGs that are difficult to resolve using existing marker-based approaches. We believe it offers a generalizable and translationally relevant strategy for advancing senescence biology and therapeutic development.

bioinformatics↗

bioRxiv2025

Single-cell transcriptomics identifies a dampened neutrophil function and accentuated T-cell cytotoxicity in tobacco flavored e-cigarette exposed mouse lungs

E-cigarettes (e-cigs) are a public health concern for young adults due to their rising popularity despite evidence of harmful effects. Yet an extensive study defining the cell-specific immune changes upon exposure to flavored e-cigs remains elusive. To determine the immunological lung landscape upon acute nose-only exposure of C57BL/6J to flavored e-cig aerosols, we performed single-cell RNA sequencing (scRNA seq). Analyses of the levels of metals in the e-cig aerosol generated daily during exposure revealed a flavor-dependent variation in the day-to-day leaching of the levels of metals like Ni, Cu, K and Zn, among others. scRNA profiles of 71,725 cells generated from control and treatment groups (n=2/sex/group) found maximum dysregulation of (a) myeloid cell function in menthol (324 differentially enriched genes (DEG)) and tobacco (553 DEGs) -flavor exposed and (b) lymphoid cell function in fruit (112 DEGs)-flavored e-cig aerosol exposed mouse lungs as compared to air. Flow cytometry analyses identified marked increase in the neutrophil percentage and a decrease in the eosinophil count in menthol and tobacco-flavored e-cig aerosol exposed mouse lungs which corroborated with our scRNA seq data. We further found an: (a) increase in CD8+ T cell percentages, (b) upregulation of inflammatory genes like Stat4, Il1bos, Il1b, Il1ra and Cxcl3 and (c) enrichment of terms like T-helper cell 1cytokine function and NK cell degranulation in the lungs of e-cig aerosol exposed mouse when compared to control. Interestingly, the increase in the level of immature neutrophils characterized by Ly6G deficiency and reduction in the S100A8 (marker for neutrophil activation) using immunofluorescence in tobacco-flavored e-cig aerosol exposed mouse lung sections point towards a possible shift in the neutrophil dynamics upon exposure to e-cigs. Overall, this study identifies flavor dependent changes in myeloid and lymphoid-cell mediated responses in the mouse lungs exposed to acute nose-only e-cig aerosols and provides a resource to influence future research in select /specific cell types to understand the immunological implications of long-term use of e-cigs.

pharmacology and toxicology↗

bioRxiv2024

SenSet, a novel human lung senescence cell gene signature, identifies cell-specific senescence mechanisms

Cellular senescence is a major hallmark of aging. Senescence is defined as an irreversible growth arrest observed when cells are exposed to a variety of stressors including DNA damage, oxidative stress, or nutrient deprivation. While senescence is a well-established driver of aging and age-related diseases, it is a highly heterogeneous process with significant variations across organisms, tissues, and cell types. The relatively low abundance of senescence in healthy aged tissues represents a major challenge to studying senescence in a given organ, including the human lung. To overcome this limitation, we developed a Positive-Unlabeled (PU) learning framework to generate a comprehensive senescence marker gene list in human lungs (termed SenSet) using the largest publicly available single-cell lung dataset, the Human Lung Cell Atlas (HLCA). We validated SenSet in a highly complex ex vivo human 3D lung tissue culture model subjected to the senescence inducers bleomycin, doxorubicin, or irradiation, and established its sensitivity and accuracy in characterizing senescence. Using SenSet, we identified and validated cell-type specific senescence signatures in distinct lung cell populations upon aging and environmental exposures. Our study presents the first comprehensive analysis of senescent cells in the healthy aging lung and uncovers cell-specific gene signatures of senescence, presenting fundamental implications for our understanding of major lung diseases, including cancer, fibrosis, chronic obstructive pulmonary disease, or asthma.

genomics↗

bioRxiv2024

Seabird and sea duck mortalities were lower during the second breeding season in eastern Canada following the introduction of Highly Pathogenic Avian Influenza A H5Nx viruses

H5N1 clade 2.3.4.4b viruses have caused significant mortality events in various wild bird species across Europe, North America, South America, and Africa. In North America, the largest impacts on wild birds have been in eastern Canada, where over 40,391 wild birds were reported to have died from highly pathogenic avian influenza (HPAI) between April and September 2022. In the year following, we applied previously established methods to quantify total reported mortality in eastern Canada for a full year October 2022, to September 2023. In this study, we (i) document the spatial, temporal and taxonomic patterns of wild bird mortality in the 12 months that followed the mass mortality event in the summer of 2022 and (ii) quantify the observed differences in mortality across the breeding season (April to September) of 2022 and 2023. In eastern Canada, there was high uncertainty about whether 2023 would bring another year of devastating HPAI-linked mortalities. Mortalities in the breeding season were 93% lower in 2023 compared to 2022 but encompassed a more taxonomically diverse array of species. We found that mortalities in the fall and winter (non-breeding season) were dominated by waterfowl, while mortalities during the spring and summer (breeding season) were dominated by seabirds. Due to a low prevalence of HPAI among the subset of tested birds, we refrained from broadly attributing reported mortalities in 2023 to HPAI. However, our analysis did identify three notable mortality events linked to HPAI, involving at least 1,646 Greater Snow Geese, 232 Canada Geese, and 212 Northern Gannets. This study emphasizes the ongoing need for H5NX surveillance and mortality assessments as the patterns of mortality in wild populations continue to change.

ecology↗

bioRxiv2024

Avian influenza virus circulation and immunity in a wild urban duck population prior to and during a highly pathogenic H5N1 outbreak

Highly pathogenic avian influenza (HPAI) H5N1 clade 2.3.4.4b viruses were first detected in St. Johns, Newfoundland, Canada in late 2021, with the virus rapidly spreading across the western hemisphere over the next year. To investigate the patterns of avian influenza virus (AIV) infection and immune responses subsequent to the arrival of H5N1, we sampled the wild urban duck population in St. Johns for a period of 16 months after the start of the outbreak and compared these findings to archived samples. Antibody seroprevalence was relatively stable before the outbreak (2011-2014) at 27.6% and 3.9% for anti-AIV (i.e., NP) and H5-specific antibodies, respectively. During the winter of 2022, AIV-NP and H5-specific antibody seroprevalence both reached 100%, signifying a population-wide infection event. As expected, population-level immunity waned over time, and we found that ducks were seropositive for anti- AIV-NP antibodies for around twice as long as for H5-specific antibodies. The population was H5 seronegative to the latter approximately six months after the initial H5N1 incursion. In late February 2023, H5N1 clade 2.3.4.4b viruses were again detected in the duck population as a result of a second incursion into Newfoundland from Eurasia, which resulted in a second population-wide infection event. We observed a clear relationship of increasing antibody levels with decreasing viral RNA loads that allowed for interpretation of the course of infection and immune response in infected individuals and applied these findings to two cases of resampled ducks to infer infection history. Our study highlights the significance of applying both AIV surveillance and seroprevalence monitoring to provide a better understanding of AIV dynamics in wild populations, which may be crucial following the arrival of 2.3.4.4b H5Nx subtypes to assess the threats they pose to both wild and domestic animals, and to humans.

microbiology↗

bioRxiv2024

Geographic, ecological, and temporal patterns of seabird mortality during the 2022 HPAI H5N1 outbreak on the island of Newfoundland

Highly pathogenic avian influenza (HPAI) H5N1 caused mass seabird mortality across the North Atlantic in 2022. Following outbreaks in Europe, the first case in North America was detected on the island of Newfoundland (NFLD), Canada in November 2021, before spreading through all North American flyways. During the following breeding season, NFLD experienced the second-highest number of seabird mortalities in Canadian provinces. Surveys and citizen reports identified 13543 seabird mortalities from April to September 2022. Many carcasses occurred on the west coast of NFLD in May and June 2022. Reported mortalities peaked in July along the southeastern coast. In August and September, mortalities were concentrated along the northeastern coast. With the exception of two colony surveys, reported mortalities decreased in September. Most mortality was found among Northern Gannet (6622), Common Murre (5992), Atlantic Puffin (282), and Black-legged Kittiwake (217). Using comprehensive knowledge of seabird ecology, we formulated exploratory hypotheses regarding traits that could contribute to mortality. Species differences in mortality were most strongly associated with nesting density, timing of breeding, and at-sea overlap with allospecifics from other colonies. Unprecedented seabird mortality and ongoing transmission within the circulating avian influenza viruses highlight the need for continued monitoring and development of conservation strategies.

zoology↗

bioRxiv2024

Wild bird mass mortalities in eastern Canada associated with the Highly Pathogenic Avian Influenza A(H5N1) virus, 2022

In 2022, a severe outbreak of clade 2.3.4.4b Highly Pathogenic Avian Influenza (HPAI) H5N1 virus resulted in unprecedented mortality among wild birds in eastern Canada. Tens of thousands of birds were reported sick or dead, prompting a comprehensive assessment of mortality spanning the breeding season between April 1 and September 30, 2022. Mortality reports were collated from federal, Indigenous, provincial, and municipal agencies, the Canadian Wildlife Health Cooperative, non-governmental organizations, universities, and citizen science platforms. A scenario analysis was conducted to refine mortality estimates, accounting for potential double counts from multiple sources under a range of spatial and temporal overlap. Correcting for double counting, an estimated 40,966 wild birds were reported sick or dead in eastern Canada during the spring and summer of 2022. Seabirds and sea ducks, long-lived species that are slow to recover from perturbations, accounted for 98.7% of reported mortalities. Mortalities were greatest among Northern Gannets (Morus bassanus; 26,193), Common Murres (Uria aalge; 8,133), and American Common Eiders (Somateria mollissima dresseri; 1,945), however, these figures underestimate total mortality as they exclude unreported deaths on land and at sea. In addition to presenting mortality estimates, we compare mortalities with known population sizes and trends and make an initial assessment of whether population-level impacts are possible for the Northern Gannet, a species that has suffered significant global mortality, and two harvested species, Common Murre and American Common Eider, to support management decisions. We hypothesize that population-level impacts in eastern Canada are possible for Northern Gannets and American Common Eiders but are unlikely for Common Murres. This study underscores the urgent need for further research to understand the broader ecological ramifications of the HPAI outbreak on wild bird populations.

zoology↗

bioRxiv2023

Avian influenza viruses in wild birds in Canada following incursion of the highly pathogenic H5N1 virus from Eurasia in 2021/2022

Following detection of novel highly pathogenic avian influenza virus (HPAIV) H5N1 clade 2.3.4.4b in Newfoundland, Canada in late 2021, avian influenza surveillance in wild birds was scaled-up across Canada. Herein, we present results of Canadas Interagency Surveillance Program for Avian Influenza in wild birds during the first year (November 2021 - November 2022) following the incursions of HPAIV from Eurasia. Key objectives of the surveillance program were to (i) detect the presence, distribution and spread of HPAIV and other avian influenza viruses (AIVs), (ii) detect wild bird morbidity and mortality associated with HPAIV, (iii) identify the range of wild bird species infected by HPAIV, and (iv) characterize detected AIV. A total of 6,246 sick and dead wild birds were tested, of which 27.4% were HPAIV positive across 12 taxonomic orders and 80 species. Geographically, HPAIV detections occurred in all Canadian provinces and territories, with the highest numbers in the Atlantic and Central flyways. Temporally, peak detections differed across flyways, though the national peak occurred in April 2022. In an additional 11,295 asymptomatic harvested or live captured wild birds, 5.2% were HPAIV positive across 3 taxonomic orders and 19 species. Whole genome sequencing identified HPAIV of Eurasian origin as most prevalent in the Atlantic flyway, along with multiple reassortants of mixed Eurasian and North American origins distributed across Canada, with moderate structuring at the flyway scale. Wild birds were victims and reservoirs of HPAIV H5N1 2.3.4.4b, underscoring the importance of surveillance encompassing samples from sick and dead, as well as live and harvested birds to provide insights into the dynamics and potential impacts of the HPAIV H5N1 outbreak. This dramatic shift in presence and distribution of HPAIV in wild birds in Canada highlights a need for sustained investment in wild bird surveillance and collaboration across One Health partners.

zoology↗

bioRxiv2022

Flavor Classification/Categorization and Differential Toxicity of Oral Nicotine Pouches (ONPs) in Lung Epithelial Cells

The prevalence of flavored tobacco product usage amongst youth in the United States is partly due to the emergence of non-combustible nicotine-containing products (NCNPs), including oral nicotine pouches (ONPs) and smokeless tobacco products. ONPs are available in various different flavors (mint, fruity, tobacco, dessert, citrus, coffee, wintergreen, and berry) and may use either Tobacco-Derived Nicotine (TDN) or Tobacco-Free Nicotine (TFN). Currently, several brands of ONPs are sold in the U.S and comprise a significant portion of NCNP sales in the U.S. There is a growing concern that flavored ONPs may not only induce oral health effects, but may also induce systemic toxic effects due to nicotine and other ONP byproducts being absorbed into systemic circulation through the oral mucosa. These byproducts can act locally on other tissues and may potentially cause redox dysregulation and heightened inflammatory responses systemically in the respiratory, cardiovascular, and/or renal systems. Hence, we determined the effects of flavored ONPs from four of the most widely sold brands in the U.S in inducing toxicological effects on the respiratory epithelium. Prior to analyzing the effects ONPs, we first classified ONPs sold in the US based on their flavor and the flavor category to which they belong to using a wheel diagram. Subsequently, using human bronchial epithelial cells (16-HBE and BEAS-2B) exposed to extracts of flavored ONPs, we assessed the levels of ONP-induced inflammatory cytokine release (IL-6 and IL-8), cellular Reactive Oxygen Species (ROS) production, and cytotoxicity in the airway epithelium. Our data showed that cells exposed to the lowest concentration treatments showed increased cytotoxicity, differential cellular ROS production, and proinflammatory cytokine release. The most striking response was observed among cells treated with the spearmint ONP, whereas ONPs containing original tobacco and fruity flavors showed varied levels of ROS release in 16-HBE cells. Our data suggest that flavored ONPs are unsafe and likely to cause systemic and local toxicological responses during chronic usage. Our study is a part of ongoing efforts to use in vitro, ex-vivo, and in vivo systems to understand how the usage of various flavored ONPs may cause both oral and pulmonary toxicity, and impact human periodontal health.

pharmacology and toxicology↗

bioRxiv2022

Nose-only Exposure to Cherry and Tobacco Flavored E-cigarettes Induced Lung Inflammation in Mice in a Sex-dependent Manner

Flavoring chemicals utilized in electronic nicotine delivery systems (ENDS) have been shown to result in an increase in cellular inflammation, meanwhile, the effects of fruit and tobacco flavors on lung inflammation by nose-only exposures to mice are relatively unknown. We hypothesized that C57BL/6J mice exposed to flavored e-cigarettes would result in an increase in lung inflammation. C57BL/6J mice were exposed to air, propylene glycol/vegetable glycerin (PG/VG), and e-liquids "Apple", "Cherry", "Strawberry", "Wintergreen", and "Smooth & Mild Tobacco", for one hour per day for a three day exposure. Quantification of flavoring chemicals was measured by proton nuclear magnetic resonance spectroscopy (1H NMR), differential cell counts by flow cytometry, pro-inflammatory cytokines/chemokines by ELISA, and matrix metalloproteinase levels by western blot. Exposure to PG/VG, Apple, and Smooth & Mild Tobacco resulted in an increase in neutrophil cell count in lung bronchoalveolar lavage fluid (BALF). Strawberry exposure increased KC levels in BALF while in lung homogenate KC levels were increased in PG/VG, Cherry, and Smooth & Mild Tobacco exposure. Exposure to PG/VG and Cherry increased IL-6 levels and in all exposed mice there was a male-specific decrease in MCP-1 levels in lung homogenate. Mice exposed to PG/VG, Apple, Cherry, and Wintergreen resulted in an increase in MMP2 levels. Our results indicate that female mice exposed to cherry flavored e-liquids and male mice exposed to tobacco flavored e-liquids resulted in an increase in inflammation, while exposure to mint flavored e-liquids resulted in a decrease in inflammatory cytokine and an increase in tissue repair proteins. This study revealed that flavored-based e-cigarette exposure elicited sex-specific alterations in lung inflammation, with cherry flavors/benzaldehyde eliciting female-specific increases in inflammation. This highlights the toxicity of flavored chemicals and the further need for regulation of flavoring chemicals.

pharmacology and toxicology↗

bioRxiv2022

Synthetic Coolant WS-23 increases E-Cigarette Generated Aerosolized Acellular Reactive Oxygen Species (ROS) Levels

There has been a substantial rise in e-cigarette (e-cig) use or vaping in the past decade, prompting growing concerns about their adverse health effects. Recently, e-cig manufacturers have been using synthetic cooling agents, like WS-23 and WS-3, to provide a cooling sensation without the "menthol taste". Studies have shown that aerosols/vapes generated by e-cigs can contain significant levels of reactive oxygen species (ROS). However, studies investigating the role of synthetic coolants in modulating ROS levels generated by e-cigs are lacking. This study seeks to understand the potential of synthetic coolants, e-cigarette additives that have become increasingly prevalent in e-liquids sold in the United States (US), on acellular ROS production. Aerosols were generated from e-liquids with and without synthetic coolants through a single-puff aerosol generator; subsequently, acellular ROS was semi-quantified in H2O2 equivalents via fluorescence spectroscopy. Our data suggest that adding WS-3 to e-liquid base (PG:VG), regardless of nicotine content, has a minimal impact on modifying e-cigarette-generated acellular ROS levels. Additionally, our data also suggest that the addition of WS-23 to nicotine-containing e-liquid base significantly modifies e-cigarette-generated acellular ROS levels. Together, our data provide insight into whether adding synthetic coolants to e-liquids significantly impacts vaping-induced oxidative stress in the lungs.

pharmacology and toxicology↗

bioRxiv2022

E-Cigarette Synthetic Cooling Agent WS-23 and Nicotine Aerosols Differentially Modulate Airway Epithelial Cell Responses

Electronic cigarette (e-cig) aerosol/vape exposures are strongly associated with pulmonary dysfunctions, and the airway epithelial cells (AECs) of respiratory passages play a pivotal role in understanding this association. However, not much is known about the effect of synthetic cooling agents such as WS-23 on AECs. WS-23 is a synthetic menthol-like cooling agent widely used to enhance the appeal of e-cigs and to suppress the harshness and bitterness of other e-cig constituents. Using primary human AECs, we compared the effects of aerosolized WS-23 with propylene glycol/vegetable glycerin (PG/VG) vehicle control and nicotine aerosol exposures. AECs treated with 3% WS-23 aerosols showed a significant increase in viable cell numbers compared to PG/VG-vehicle aerosol exposed cells and cell growth was comparable following 2.5% nicotine aerosol exposure. AEC inflammatory factors, IL-6 and ICAM-1 levels were significantly suppressed by WS-23 aerosols compared to PG/VG-controls. When differentiated AECs were challenged with WS-23 aerosols, there was a significant increase in MUC5AC+ goblet cells with no discernible change in SCGB1A1+ secretory cells. Compared to PG/VG-controls, WS-23 or nicotine aerosols presented with increased goblet cell numbers, but there was no synergistic effect of WS-23+nicotine combination exposure. Thus, WS-23 and nicotine aerosols modulate the AEC responses and induce goblet cell hyperplasia, which could impact the airway physiology and susceptibility to respiratory diseases.

pharmacology and toxicology↗

bioRxiv2022

An evaluation of RNA-seq differential analysis methods

RNA-seq is a high-throughput sequencing technology widely used for gene transcript discovery and quantification under different biological or biomedical conditions. A fundamental research question in most RNA-seq experiments is the identification of differentially expressed genes among experimental conditions or sample groups. Numerous statistical methods for RNA-seq differential analysis have been proposed since the emergence of the RNA-seq assay. To evaluate popular differential analysis methods used in the open source R and Bioconductor packages, we conducted multiple simulation studies to compare the performance of eight RNA-seq differential analysis methods used in RNA-seq data analysis (edgeR, DESeq, DESeq2, baySeq, EBSeq, NOISeq, SAMSeq, Voom). The comparisons were across different scenarios with either equal or unequal library sizes, different distribution assumptions and sample sizes. We measured performance using false discovery rate (FDR) control, power, and stability. No significant differences were observed for FDR control, power, or stability across methods, whether with equal or unequal library sizes. For RNA-seq count data with negative binomial distribution, when sample size is 3 in each group, EBSeq performed better than the other methods as indicated by FDR control, power, and stability. When sample sizes increase to 6 or 12 in each group, DESeq2 performed slightly better than other methods. All methods have improved performance when sample size increases to 12 in each group except DESeq. For RNA-seq count data with log-normal distribution, both DESeq and DESeq2 methods performed better than other methods in terms of FDR control, power, and stability across all sample sizes. Real RNA-seq experimental data were also used to compare the total number of discoveries and stability of discoveries for each method. For RNA-seq data analysis, the EBSeq method is recommended for studies with sample size as small as 3 in each group, and the DESeq2 method is recommended for sample size of 6 or higher in each group when the data follow the negative binomial distribution. Both DESeq and DESeq2 methods are recommended when the data follow the log-normal distribution.

bioinformatics↗

bioRxiv2021

p16-3MR: a novel model to study cellular senescence in cigarette smoke-induced lung injuries during aging

Cellular senescence and lung aging are associated with the pathogenesis of Chronic Obstructive Pulmonary Disease (COPD). COPD progresses with aging, and chronic smoking is the key susceptibility factor in lung pathological changes concurrent with biological aging. However, these processes involving cigarette smoke (CS)-mediated lung cellular senescence are difficult to distinguish. One of the impediments to study cellular senescence in relation to age-related lung pathologies is the lack of a suitable in vivo model. In view of this, we provide evidence that supports the suitability of p16-3MR mice to study cellular senescence in CS-mediated and age-related lung pathologies. p16-3MR mice has a trimodal reporter fused to the promoter of p16INK4a gene that enables detection, isolation and selective elimination of senescent cells, thus making it a suitable model to study cellular senescence. To determine its suitability in CS-mediated lung pathologies, we exposed young (12-14 months) and old (17-20 months) p16-3MR mice to 30-day CS exposure and studied the expression of senescent genes (p16, p21 and p53) and SASP-associated markers (MMP9, MMP12, PAI-1, and FN-1) in air- and CS-exposed mouse lungs. Our results showed that this model could detect cellular senescence using luminescence and isolate cells undergoing senescence with the help of tissue fluorescence in CS-challenged young and old mice. Our results from the expression of senescence markers and SASP-associated genes in CS-challenged young and old p16-3MR mice were comparable with increased lung cellular senescence and SASP in COPD. We further showed age-dependent alteration in the (i) tissue luminescence and fluorescence, (ii) mRNA and protein expressions of senescent markers and SASP genes, and (iii) SA-{beta}-gal activity in CS-challenged young and old p16-3MR mice as compared to their air controls. Overall, we showed that p16-3MR is a competent model to study cellular senescence in age-related pathologies and could help understand the pathobiology of cellular senescence in lung conditions like COPD and fibrosis.

pharmacology and toxicology↗

bioRxiv2020

Pulmonary toxicity and inflammatory response of e-cigarettes containing medium-chain triglyceride oil and vitamin E acetate: Implications in the pathogenesis of EVALI but independent of SARS-COV-2 COVID-19 related proteins

Recently, there has been an outbreak associated with the use of e-cigarette or vaping products, associated lung injury (EVALI). The primary components of vaping products, vitamin E acetate (VEA) and medium-chain triglycerides (MCT) may be responsible for acute lung toxicity. Currently, little information is available on the physiological and biological effects of exposure to these products. We hypothesized that these e-cig cartridges and their constituents (VEA and MCT) induce pulmonary toxicity, mediated by oxidative damage and inflammatory responses, leading to acute lung injury. We studied the potential mechanisms of cartridge aerosol induced inflammatory response by evaluating the generation of reactive oxygen species by MCT, VEA, and cartridges, and their effects on the inflammatory state of pulmonary epithelium and immune cells both in vitro and in vivo. Cells exposed to these aerosols generated reactive oxygen species, caused cytotoxicity, induced epithelial barrier dysfunction, and elicited an inflammatory response. Using a murine model, the parameters of acute toxicity to aerosol inhalation were assessed. Infiltration of neutrophils and lymphocytes was accompanied by significant increases in IL-6, eotaxin, and G-CSF in the bronchoalveolar lavage fluid (BALF). In mouse plasma, eicosanoid inflammatory mediators, leukotrienes, were significantly increased. Plasma from e-cig users also showed increased levels of hydroxyeicosatetraenoic acid (HETEs) and various eicosanoids. Exposure to e-cig cartridge aerosols showed the most significant effects and toxicity compared to MCT and VEA. In addition, we determined at SARS-COV-2 related proteins and found no impact associated with aerosol exposures from these tested cartridges. Overall, this study demonstrates acute exposure to specific e-cig cartridges induces in vitro cytotoxicity, barrier dysfunction, and inflammation and in vivo mouse exposure induces acute inflammation with elevated pro-inflammatory markers in the pathogenesis of EVALI.Competing Interest StatementThe authors have declared no competing interest.View Full Text

pharmacology and toxicology↗

bioRxiv2020

Chemical constituents involved in e-cigarette, or vaping product use-associated lung injury (EVALI)

BackgroundThe Centers for Disease Control (CDC) declared e-cigarette (e-cig), or vaping product use-associated lung injury (EVALI) a national outbreak due to the high incidence of emergency department admissions and deaths. Investigators have identified vitamin E acetate (VEA) as the plausible cause for EVALI, based on compounds found in bronchoalveolar lavage fluid. ObjectivesWe defined the chemical constituents present in e-cig cartridges associated with EVALI and compared constituents to medical-grade and cannabidiol (CBD) containing cartridges. MethodsWe measured chemicals and elemental metals in e-liquid and vapor phases of e-cig counterfeit cartridges by Gas Chromatography (GC) and Mass Spectrometry (MS), EPA method TO-15 by GCMS, and ICP-MS analysis. ResultsWe have identified chemical constituents in e-cig vaping tetrahydrocannabinol (THC)-containing counterfeit cartridges compared to medical-grade and cannabidiol (CBD) containing cartridges. Apart from VEA and THC, other potential toxicants correlated with EVALI included solvent-derived hydrocarbons, silicon conjugated compounds, various terpenes, pesticides/plasticizers/polycaprolactones, and metals. These chemicals are known to cause symptoms, such as cough, shortness of breath or chest pain, nausea, vomiting or diarrhea, fatigue, fever, or weight loss, all symptoms presenting in patients with EVALI. ConclusionThis study provides insights into understanding the chemical-induced disease mechanism of acute lung injury.

pharmacology and toxicology↗