Biology subjects

Sharma, A.

Publications and source records attributed to Sharma, A..

At least 379 records · Page 21Linked to original sources

bioRxiv2020

IL-27 enhances the lymphocyte mediated innate resistance to primary hookworm infection in the lungs

Interleukin-27 (IL-27) is a heterodimeric cytokine of the IL-12 family, formed by non-covalent association of the promiscuous EBI3 subunit and selective p28 subunit. IL-27 is produced by mononuclear phagocytes and unfolds pleiotropic immune-modulatory functions through high affinity ligation to IL-27 receptor alpha (IL-27RA). While IL-27 is known to contribute to immunity and to end inflammation following numerous types of infections, its relevance for host defense against multicellular parasites is still poorly defined. Here, we investigated the role of IL-27 during infection with the soil-transmitted hookworm, Nippostrongylus brasiliensis, in its early intrapulmonary life cycle. IL-27(p28) was detectable in broncho-alveolar lavage fluids of C57BL/6J wild type mice on day 1 after subcutaneous N. brasiliensis inoculation. The expression of IL-27RA was most abundant on lung invading {gamma}{delta} T cells followed by CD8+ T cells, CD4+ T cells and NK cells. IL-27RA was weakly present on CD19+ B cells and absent on neutrophils, alveolar macrophages and eosinophils. Il27ra-/- mice showed increased parasite burden together with aggravated pulmonary hemorrhage and higher alveolar albumin leakage as a surrogate for disruption of the epithelial/vascular barrier. Conversely, recombinant mouse IL-27 injections of wild type mice reduced parasite burdens and lung injury. In multiplex screens, we identified higher airway accumulations of IL-6, TNF and MCP-3 (CCL7) in Il27ra-/- mice, while rmIL-27 treatment showed a reciprocal effect. Finally, {gamma}{delta} T cell infiltration of the airways required endogenous IL-27 expression. In summary, this report demonstrates protective functions of IL-27 to control the early larval stage of hookworm infection in the lungs.

immunology↗

bioRxiv2020

E-cigarettes compromise the gut barrier and trigger gut inflammation

E-cigarette and vaping device use continue to rise, particularly in adolescents and young adults, but the safety of inhaling the multitude of chemicals within e-cigarette aerosols has been questioned. While several studies have evaluated vaping effects on the lungs and heart; effects on the gastrointestinal tract remain unknown. Using established murine models of acute (1 week) and chronic (3 month) daily e-cigarette aerosol inhalation, both with nicotine-containing and vehicle control e-liquids, murine colon transcriptomics and organoid co-culture models, we assessed the effects of e-cigarette use on the gut barrier and mucosal health. Histologic analyses revealed that chronic exposure to nicotine-free e-cigarette aerosols induced mucosal inflammation. Transcriptome analyses revealed that chronic, but not acute, nicotine-free e-cigarette use significantly reduced expression of tight junction markers, including occluding, and drove expression of pro-inflammatory cytokines. Exposure of murine and human enteroid-derived monolayers (EDMs) to nicotine-free e-cigarette aerosols alone, or in co-culture with invasive E. coli, confirmed that repetitive exposure was sufficient to recapitulate the key findings observed in vivo, i.e., barrier-disruption, downregulation of occludin, inflammation, and an accentuated risk of and response to bacterial infection. These data highlight an unexpected harmful effect of e-cigarette use on the gut barrier and pinpoint non-nicotine chemical components common across >90% of e-cigarette e-liquids as the source of harm. Given the ever-expanding importance of the integrity of the gut barrier for host fitness, and impact of gut mucosal inflammation on a multitude of chronic diseases, these findings are broadly relevant to medicine and public health. SIGNIFICANCEThe safety of electronic cigarettes has been questioned amidst emerging evidence that they may derail our immune system and increase our susceptibility to infections. Despite these insights, their impact on the most critical entity that separates trillions of microbes from the largest immune system in our body, i.e., the gut barrier, remains unexplored. Using a combination of mouse models, gut transcriptomics, and murine and human gut-derived organoids, here we show that chronic exposure to aerosols of electronic-cigarette disrupts the gut barrier, increases its susceptibility to bacterial infections and triggers inflammation. Given the importance of the gut barrier in the maintenance of immune homeostasis, these findings provide valuable insights into the potential long-term harmful effects of electronic cigarettes on health.

immunology↗

bioRxiv2020

FEATS: Feature selection based clustering of single-cell RNA-seq data

Advances in next-generation sequencing (NGS) have made it possible to carry out transcriptomic studies at single-cell resolution and generate vast amounts of single-cell RNA-seq data rapidly. Thus, tools to analyze this data need to evolve as well to improve accuracy and efficiency. We present FEATS, a python software package that performs clustering on single-cell RNA-seq data. FEATS is capable of performing multiple tasks such as estimating the number of clusters, conducting outlier detection, and integrating data from various experiments. We develop a univariate feature selection based approach for clustering, which involves the selection of top informative features to improve clustering performance. This is motivated by the fact that cell types are often manually determined using the expression of only a few known marker genes. On a variety of single-cell RNA-seq datasets, FEATS gives superior performance compared to the current tools, in terms of adjusted rand index (ARI) and estimating the number of clusters. In addition to cluster estimation, FEATS also performs outlier detection and data integration while giving an excellent computational performance. Thus, FEATS is a comprehensive clustering tool capable of addressing the challenges during the clustering of single-cell RNA-seq data. The installation instructions and documentation of FEATS is available at https://edwinv87.github.io/feats/.

bioinformatics↗

bioRxiv2020

AE-LGBM: Sequence-Based Novel Approach To Detect Interacting Protein Pairs via Ensemble of Autoencoder and LightGBM.

Protein-protein interactions (PPIs) are a vital phenomenon for every biological process. Prediction of PPI can be very helpful in the probing of protein functions which can further help in the development of new and powerful therapy designs for disease prevention. A lot of experimental studies have been done previously to study PPIs. However, lab-based experimental studies of PPI prediction are resource-extensive and time-consuming. In recent years, several high throughput, computational approaches to predict PPI have been developed but they could be fallible in terms of accuracy and false-positive rate. To overcome these shortcomings, we propose a novel approach AE-LGBM to predict the PPI more accurately. This method is based on the LightGBM classifier and utilizes the Autoencoder, which is an artificial neural network, to efficiently produce lower-dimensional, discriminative, and noise-free features. We incorporate conjoint triad (CT) features along with Composition-Transition-Distribution (CTD) features into the model and obtained promising results. The ten-fold cross-validation results indicate that the prediction accuracies obtained for Human and Yeast datasets are 98.7% and 95.4% respectively. This method was further evaluated on other datasets and has achieved excellent accuracies of 100%, 100%, 99.9%, 99.2% on E.coli, M.musculus, C.elegans, and H.sapiens respectively. We also executed AE-LGBM over three important PPI networks namely, single-core network (CD9), the multiple-core network (The Ras/Raf/MEK/ERK pathway), and the cross-connection network (Wnt Network). The method was successful in predicting the pathway with an impressive accuracy of 100%, 100%, and 98.9% respectively. These figures are significantly higher than previous methods that are based on state-of-the-art models and models including LightGBM or Autoencoder, proving AE-LGBM to be highly versatile, efficient, and robust.Competing Interest StatementThe authors have declared no competing interest.View Full Text

bioinformatics↗

bioRxiv2020

SARS-CoV-2 Infection of Pluripotent Stem Cell-derived Human Lung Alveolar Type 2 Cells Elicits a Rapid Epithelial-Intrinsic Inflammatory Response

The most severe and fatal infections with SARS-CoV-2 result in the acute respiratory distress syndrome, a clinical phenotype of coronavirus disease 2019 (COVID-19) that is associated with virions targeting the epithelium of the distal lung, particularly the facultative progenitors of this tissue, alveolar epithelial type 2 cells (AT2s). Little is known about the initial responses of human lung alveoli to SARS-CoV-2 infection due in part to inability to access these cells from patients, particularly at early stages of disease. Here we present an in vitro human model that simulates the initial apical infection of the distal lung epithelium with SARS-CoV-2, using AT2s that have been adapted to air-liquid interface culture after their derivation from induced pluripotent stem cells (iAT2s). We find that SARS-CoV-2 induces a rapid global transcriptomic change in infected iAT2s characterized by a shift to an inflammatory phenotype predominated by the secretion of cytokines encoded by NF-kB target genes, delayed epithelial interferon responses, and rapid loss of the mature lung alveolar epithelial program. Over time, infected iAT2s exhibit cellular toxicity that can result in the death of these key alveolar facultative progenitors, as is observed in vivo in COVID-19 lung autopsies. Importantly, drug testing using iAT2s confirmed an antiviral dose-response to remdesivir and demonstrated the efficacy of TMPRSS2 protease inhibition, validating a putative mechanism used for viral entry in human alveolar cells. Our model system reveals the cell-intrinsic responses of a key lung target cell to infection, providing a physiologically relevant platform for further drug development and facilitating a deeper understanding of COVID-19 pathogenesis.

molecular biology↗

bioRxiv2020

Harvest and Culture of Porcine Adipose-Derived Mesenchymal Stem Cells for Autologous Transplantation

ImportanceTransplantation of adipose-derived (mesenchymal) stem cells (ADSCs) are currently under investigation for numerous novel regenerative cell therapies of the head, neck and periphery. Critical to the development of these techniques is the availability of large-animal models that can be used to test the safety and efficacy of these approaches in a manner that provides source material (in this case MSC) analogous to those developed in humans. ObjectiveTo describe the surgical technique and laboratory procedures for harvesting and isolating porcine ADSCs that are functionally equivalent to human ADSCs without sacrificing the donor animal. MethodsThe reagents and methods used in the porcine model described were purposefully focused to be able to be sufficiently analogous to those used in humans such that data developed using these techniques should support the use of porcine models for regulatory submissions. ResultsWe describe a method and confirm the activity of functionally analogous adipose derived porcine MSC. Two conditions were critical to move gain analogous performance: the cells needed to be incubated at porcine body temperature (39{degrees}C) and the cells were more sensitive to initial plating densities with plating densities of 20,000 cells/cm2 being optimal. DiscussionThis approach will allow reproducible and predictable use of an autologous large-animal model for testing AMDSC therapies.

cell biology↗

bioRxiv2020

Antiviral Drug Screen of Kinase inhibitors Identifies Cellular Signaling Pathways Critical for SARS-CoV-2 Replication

Emergence of a highly contagious novel coronavirus, SARS-CoV-2 that causes COVID-19, has precipitated the current global health crisis with over 479,000 deaths and more than 9.3 million confirmed cases. Currently, our knowledge of the mechanisms of COVID-19 disease pathogenesis is very limited which has hampered attempts to develop targeted antiviral strategies. Therefore, we urgently need an effective therapy for this unmet medical need. Viruses hijack and dysregulate cellular machineries in order for them to replicate and infect more cells. Thus, identifying and targeting dysregulated signaling pathways that have been taken over by viruses is one strategy for developing an effective antiviral therapy. We have developed a high-throughput drug screening system to identify potential antiviral drugs targeting SARS-CoV-2. We utilized a small molecule library of 430 protein kinase inhibitors, which are in various stages of clinical trials. Most of the tested kinase antagonists are ATP competitive inhibitors, a class of nucleoside analogs, which have been shown to have potent antiviral activity. From the primary screen, we have identified 34 compounds capable of inhibiting viral cytopathic effect in epithelial cells. Network of drug and protein relations showed that these compounds specifically targeted a limited number of cellular kinases. More importantly, we have identified mTOR-PI3K-AKT, ABL-BCR/MAPK, and DNA-Damage Response (DDR) pathways as key cellular signaling pathways critical for SARS-CoV-2 infection. Subsequently, a secondary screen confirmed compounds such as Berzosertib (VE-822), Vistusertib (AZD2014), and Nilotinib with anti SARS-CoV-2 activity. Finally, we found that Berzosertib, an ATR kinase inhibitor in the DDR pathway, demonstrated potent antiviral activity in a human epithelial cell line and human induced pluripotent stem cell (hIPSC)-derived cardiomyocytes. These inhibitors are already in clinical trials of phase 2 or 3 for cancer treatment, and can be repurposed as promising drug candidates for a host-directed therapy of SARS-CoV-2 infection. In conclusion, we have identified small molecule inhibitors exhibiting anti SARS-CoV-2 activity by blocking key cellular kinases, which gives insight on important mechanism of host-pathogen interaction. These compounds can be further evaluated for the treatment of COVID-19 patients following additional in vivo safety and efficacy studies. DisclosuresNone declared.

microbiology↗

bioRxiv2020

CYCLODEXTRIN DERIVATIVE ENHANCES THE OPHTHALMIC DELIVERY OF POORLY SOLUBLE AZITHROMYCIN.

Azithromycin (AZM), a macrolide antibiotic used for the treatment of Chlamydial conjunctivitis, is less effective for the treatment of this disease due to its poor bioavailability (38%). Various alternatives have been developed for improving the physico-chemical properties (i.e., solubility) of the AZM without much success. To overcome the problems associated with AZM, an inclusion complex employing a modified cyclodextrin i.e., sulfobutylether-{beta}-cyclodextrin (SBE-{beta}-CD) was prepared and characterized by phase solubility studies, pXRD and FTIR techniques. The results portrayed the formation of the inclusion complex of AZM with sulfobutylether {beta}-cyclodextrin (SBE-{beta}-CD) in 1:2 molar stoichiometric ratios. This inclusion complex was later incorporated into a polymer matrix to prepare an in situ gel. Various combinations of carbopol 934P and hydroxypropyl methylcellulose (HPMC K4M) polymers were used and evaluated by rheological and in vitro drug release studies. The optimized formulation (F4), containing carbopol 934P 0.2% (w/v) and HPMC K4M 0.2% (w/v), was evaluated for clarity, pH, gelling capacity, drug content, rheological properties, in vitro drug release pattern, ocular irritation test and antimicrobial efficacy. Finally, owing to the improved antimicrobial efficacy and increased residence time, AZM:SBE-{beta}-CD in situ gel was found to be a promising formulation for the efficient treatment of bacterial ocular disease.

microbiology↗

bioRxiv2020

In silico multi-epitope vaccine against covid19 showing effective interaction with HLA-B*15:03

The recent outbreak of severe acute respiratory syndrome (SARS) coronavirus (CoV)-2 (SARS-CoV-2) causing coronavirus disease (covid19) has posed a great threat to human health. Previous outbreaks of SARS-CoV and Middle East respiratory Syndrome CoV (MERS-CoV) from the same CoV family had posed similar threat to human health and economic growth. To date, not even a single drug specific to any of these CoVs has been developed nor any anti-viral vaccine is available for the treatment of diseases caused by CoVs. Subunits present in spike glycoproteins of SARS-CoV and SARS-CoV-2 are involved in binding to human ACE2 Receptor which is the primary method of viral invasion. As it has been observed in the previous studies that there are very minor differences in the spike glycoproteins of SARS-CoV and SARS-CoV-2. SARS-CoV-2 has an additional furin cleavage site that makes it different from SARS-CoV (Walls et al., 2020). In this study, we have analyzed spike glycoproteins of SARS-CoV-2 and SARS-CoV phylogenetically and subjected them to selection pressure analysis. Selection pressure analysis has revealed some important sites in SARS-CoV-2 and SARS-CoV spike glycoproteins that might be involved in their pathogenicity. Further, we have developed a potential multi-epitope vaccine candidate against SARS-CoV-2 by analyzing its interactions with HLA-B*15:03 subtype. This vaccine consists of multiple T-helper (TH) cells, B-cells, and Cytotoxic T-cells (CTL) epitopes joined by linkers and an adjuvant to increase its immunogenicity. Conservation of selected epitopes in SARS, MERS, and human hosts, suggests that the designed vaccine could provide cross-protection. The vaccine is designed in silico by following a reverse vaccinology method acknowledging its antigenicity, immunogenicity, toxicity, and allergenicity. The vaccine candidate that we have designed as a result of this work shows promising result indicating its potential capability of simulating an immune response.

bioinformatics↗

bioRxiv2020

DNA glycosylase NEIL2 prevents Fusobacterium-mediated inflammation and DNA damage in colonic epithelial cells

Colorectal cancer (CRC) is the third most prevalent and deadly cancer. Approximately, 15-20 % of CRCs display microsatellite instability (MSI); however, the majority (80-85%) of cases are sporadic and known as microsatellite stable (MSS). Several recent studies indicated that infection and uncontrolled inflammation initiate DNA damage and lead to cancer progression. One of the major microbes, Fusobacterium nucleatum (Fn) is highly associated with CRC, but the role of DNA repair in microbe-associated CRC has been largely unknown. Here we show that NEIL2, an oxidized base-specific DNA glycosylase, is significantly downregulated among all the key DNA repair proteins involved in various DNA repair pathways, after infection of Fn with stem-cell-based enteroid-derived monolayers (EDMs) of murine and human healthy subjects. Furthermore, following Fn infection, NEIL2-null mouse-derived EDMs showed significantly higher level of DNA damage, including double strand breaks, and inflammatory cytokines.. Murine CRC model also showed downregulation of the NEIL2 transcript and accumulation of DNA damage. Importantly, analysis of publicly available transcriptomic data showed that the downregulation of NEIL2 is specific for MSS compared to MSI CRCs. We thus conclude that the pathogenic bacterial infection-induced downregulation of NEIL2, and consequent accumulation of DNA damage, play critical roles in the progression of CRC.

immunology↗

bioRxiv2020

Minimal system for assembly of SARS-CoV-2 virus like particles

SARS-CoV-2 virus is the causative agent of COVID-19. Here we demonstrate that non-infectious SARS-CoV-2 virus like particles (VLPs) can be assembled by co-expressing the viral proteins S, M and E in mammalian cells. The assembled SARS-CoV-2 VLPs possess S protein spikes on particle exterior, making them ideal for vaccine development. The particles range in shape from spherical to elongated with a characteristic size of 129 {+/-} 32 nm. We further show that SARS-CoV-2 VLPs dried in ambient conditions can retain their structural integrity upon repeated scans with Atomic Force Microscopy up to a peak force of 1 nN.

biophysics↗

bioRxiv2020

Condensed chromatin behaves like a solid on the mesoscale in vitro and in living cells

The association of nuclear DNA with histones to form chromatin is essential to the temporal and spatial control of eukaryotic genomes. In this study, we examined the physical state of chromatin in vitro and in vivo. Our in vitro studies demonstrate that MgCl2-dependent self-association of native chromatin fragments or reconstituted nucleosomal arrays produced supramolecular condensates whose constituents are physically constrained and solid-like. Liquid chromatin condensates could be generated in vitro, but only using non-physiological conditions. By measuring DNA mobility within heterochromatin and euchromatin in living cells, we show that chromatin also exhibits solid-like behavior in vivo. Representative heterochromatin proteins, however, displayed liquid-like behavior and coalesced around a solid chromatin scaffold. Remarkably, both euchromatin and heterochromatin showed solid-like behavior even when transmission electron microscopy revealed limited interactions between chromatin fibers. Our results therefore argue that chromatin is not liquid but exists in a solid-like material state whose properties are tuned by fiber-fiber interactions.

biochemistry↗

bioRxiv2020

PCNA has specific functions in regulation of metabolism in haematological cells

PCNAs essential roles in DNA replication and repair are well established, while its recently discovered cytosolic roles are less explored. Here we show that impairing PCNAs cytosolic scaffold functions led to massive changes in cellular signaling, and most strikingly, a strong reduction in glycolytic metabolite and nucleoside phosphate pools in haematological cancer cells. This was not detected in cells from solid tissues nor in primary monocytes from healthy donors. However, lipopolysaccharide stimulated monocytes responded to targeting PCNAs scaffold function similarly to haematological cancer cells, suggesting that cellular stress is an important factor for the observed response. Integrated transcriptome, proteome and metabolome analysis revealed that pathways involved in protein stability/folding and immune responses were affected in haematopoietic cancer cells. Altogether, our data suggests that PCNA has an important role in regulation of cytoplasmic stress via regulation of central carbon metabolism in haematological cells, which potentially can be targeted in cancer treatment. HighlightA strong reduction in glycolytic metabolites and the nucleoside phosphate pools was detected in haematological cancer cells upon inhibiting PCNA scaffold functions. These metabolic changes were not found in cancer cells from other tissues, indicating a special role of PCNA in regulation of metabolism in cells of haematological origin.

cell biology↗

bioRxiv2020

Microglia-targeted dendrimer-2PMPA therapy robustly inhibits GCPII and improves cognition in a mouse model of multiple sclerosis

Roughly half of all individuals with multiple sclerosis (MS) experience cognitive impairment, but there are no approved treatments that target this aspect of the disease. Recent studies link reduced brain N-acetylaspartylglutamate (NAAG) levels to impaired cognition in various neurological diseases, including MS. NAAG levels are regulated by glutamate carboxypeptidase II (GCPII), which hydrolyzes the neuropeptide to N-acetyl-aspartate (NAA) and glutamate. Although several GCPII inhibitors, such as 2-(phosphonomethyl)-pentanedioic acid (2-PMPA), elevate brain NAAG levels and restore cognitive function in preclinical studies when given at high systemic doses or via direct brain injection, no GCPII inhibitors are clinically available due to poor bioavailability and limited brain penetration. Systemic hydroxyl dendrimers (~4 nm) have been successfully used to enhance brain delivery of drugs selectively to activated glia. We recently discovered that GCPII is highly upregulated in activated microglia after brain injury. To determine if dendrimer conjugation could enhance the brain delivery of GCPII inhibitors, specifically in the context of MS, we attached 2-PMPA to hydroxyl polyamidoamicne (PAMAM) dendrimers (D-2PMPA) using a highly efficient click chemistry approach. Targeted uptake of D-2PMPA into activated glia was subsequently confirmed in glial cultures where it showed robust anti-inflammatory activity, including an elevation in TGF{beta} and a reduction in TNF. Given these positive effects, D-2PMPA (20mg/kg) or vehicle dendrimer were dosed twice weekly to experimental autoimmune encephalomyelitis (EAE)-immunized mice starting at disease onset (therapeutic paradigm). D-2PMPA significantly improved cognition in EAE as assessed by Barnes maze performance, even though physical severity was not impacted. Glial target engagement was confirmed, as CD11b+ enriched cells isolated from hippocampi in D-2PMPA-treated mice exhibited almost complete loss of GCPII activity. These data demonstrate the utility of hydroxyl dendrimers to enhance brain penetration and support the development of D-2PMPA to treat cognitive impairment in MS. FundingThis work was funded by the National Multiple Sclerosis Society (RG-1507-05403 to BSS), the National Institute of Health NINDS (R01NS093416 to SK, RM and BSS), and Ashvattha Therapeutics. We would also like to acknowledge support for the statistical analysis from the National Center for Research Resources and NIH NCATS (1UL1TR001079). HighlightsO_LIThe GCPII inhibitor 2-PMPA was conjugated to hydroxyl PAMAM dendrimers (D-2PMPA) C_LIO_LID-2PMPA targeted activated glia in culture and displayed anti-inflammatory activity C_LIO_LIWhen dosed systemically to EAE mice, D-2PMPA inhibited CD11b+ cell GCPII activity C_LIO_LIWhen dosed systemically to EAE mice, D-2PMPA improved cognitive function C_LI

neuroscience↗

bioRxiv2020

Human iPSC-Derived Cardiomyocytes are Susceptible to SARS-CoV-2 Infection

Coronavirus disease 2019 (COVID-19) is a viral pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 is predominantly defined by respiratory symptoms, but cardiac complications including arrhythmias, heart failure, and viral myocarditis are also prevalent. Although the systemic ischemic and inflammatory responses caused by COVID-19 can detrimentally affect cardiac function, the direct impact of SARS-CoV-2 infection on human cardiomyocytes is not well-understood. We used human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) as a model system to examine the mechanisms of cardiomyocyte-specific infection by SARS-CoV-2. Microscopy and immunofluorescence demonstrated that SARS-CoV-2 can enter and replicate within hiPSC-CMs, localizing at perinuclear locations within the cytoplasm. Viral cytopathic effect induced hiPSC-CM apoptosis and cessation of beating after 72 hours of infection. These studies show that SARS-CoV-2 can infect hiPSC-CMs in vitro, establishing a model for elucidating the mechanisms of infection and potentially a cardiac-specific antiviral drug screening platform.

cell biology↗

bioRxiv2020

A Novel Model of Pancreatic Cancer Dormancy Reveals Mechanistic Insights and a Dormancy Gene Signature with Human Relevance

Latent recurrences following curative-intent pancreatic cancer surgery is a major clinical problem thought to be due to the reactivation of dormant tumor cells that disseminate before the primary tumor has been removed. How dormancy is established and ultimately reversed to drive recurrence is poorly understood. Here we introduce a novel model of pancreatic cancer dormancy that mimics early and latent survival outcomes of resected patients. Using single-cell transcriptomics we compared primary, dormant, and reactivated tumor cells and found the primary and reactivated tumor cell transcriptomes clustered together with and away from the dormant tumor cells. Using a chromatin accessibility assay we found dormancy exhibits large scale changes in chromatin remodeling. Dormant tumor cells express cancer stem cell markers that are lost upon reactivation and are chemotherapy resistant. We identified a dormancy gene signature and investigated this in patients undergoing surgery for localized PC by isolating cells from the primary tumor and liver disseminated tumor cells (DTCs) for single-cell transcriptomics. We found the signature correlated with DTCs indicating that these cells are dormant at the time of surgery. The signature also identified CCL5 as a novel dormancy marker in PC. Mechanisms of PC dormancy include upregulation of the transcriptional repressor Dec2 which drives quiescence, monoallelic suppression of the mutant KRAS allele by DNA methylation, and immunoregulation. We conclude that PC dormancy is a highly plastic and heterogeneous cellular state governed by tumor cell autonomous and non-autonomous mechanisms. One Sentence SummaryA novel model of resectable pancreatic cancer reveals pancreatic cancer dormancy is characterized by significant cellular plasticity, heterogeneity and chromatin remodeling

cancer biology↗

bioRxiv2020

scRNA-seq reveals ACE2 and TMPRSS2 expression in TROP2+ Liver Progenitor Cells: Implications in COVID-19 associated Liver Dysfunction

The recent pandemic of coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 was first reported in China (December 2019) and now prevalent in [~]170 countries across the globe. Entry of SARS-CoV-2 into mammalian cells require the binding of viral Spike (S) proteins to the ACE2 (angiotensin converting enzyme 2) receptor. Once entered the S protein is primed by a specialised serine protease, TMPRSS2 (Transmembrane Serine Protease 2) in the host cell. Importantly, beside respiratory symptoms, consistent with other common respiratory virus infection when patients become viraemic, a significant number of COVID-19 patients also develop liver comorbidities. We explored if specific target cell-type in the mammalian liver, could be implicated in disease pathophysiology other than the general deleterious response to cytokine storms. Here we employed single-cell RNA-seq (scRNA-seq) to survey the human liver and identified potentially implicated liver cell-type for viral ingress. We report the co-expression of ACE2 and TMPRSS2 in a TROP2+ liver progenitor population. Importantly, we fail to detect the expression of ACE2 in hepatocyte or any other liver (immune and stromal) cell types. These results indicated that in COVID-19 associated liver dysfunction and cell death, viral infection of TROP2+ progenitors in liver may significantly impaired liver regeneration and could lead to pathology. Highlights- EPCAM+ Liver progenitors co-express ACE2 and TMPRSS2 - ACE2 and TMPRSS2 expression is highest in TROP2high progenitors - ACE2 and TMPRSS2 cells express cholangiocyte biased fate markers - ACE2 and TMPRSS2 positive cells are absent in human fetal liver

genomics↗

bioRxiv2020

Cholinergic basal forebrain degeneration due to obstructive sleep apnoeaincreases Alzheimer's pathology in mice

Epidemiological studies indicate that obstructive sleep apnoea is a strong risk factor for the development of Alzheimers disease but the mechanisms of the risk remain unclear. We developed a method of modelling obstructive sleep apnoea in mice that replicates key features of human obstructive sleep apnoea: altered breathing during sleep, sleep disruption, moderate intermittent hypoxemia and cognitive impairment. When we induced obstructive sleep apnoea in a familial Alzheimers disease model, the mice displayed exacerbation of cognitive impairment and pathological features of Alzheimers disease, including increased levels of amyloid-beta and inflammatory markers, as well as selective degeneration of cholinergic basal forebrain neurons. These pathological features were not induced by chronic hypoxia or sleep disruption alone. Our results also revealed that the neurodegeneration was mediated by the oxygen-sensitive p75 neurotrophin receptor and hypoxia inducible factor 1 alpha activity. Furthermore, restoring blood oxygen levels during sleep to prevent intermittent hypoxia prevented the pathological changes induced by the OSA. These findings provide a signalling mechanism by which obstructive sleep apnoea induces cholinergic basal forebrain degeneration and could thereby increase the risk of developing Alzheimers disease, as well as providing a rationale for testing a range of possible prophylactic treatment options for people with obstructive sleep apnoea and hypoxia including increased compliance of continuous positive airway pressure therapy.

neuroscience↗