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1.
PLoS Biol ; 22(3): e3002240, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38547242

ABSTRACT

MYCN activates canonical MYC targets involved in ribosome biogenesis, protein synthesis, and represses neuronal differentiation genes to drive oncogenesis in neuroblastoma (NB). How MYCN orchestrates global gene expression remains incompletely understood. Our study finds that MYCN binds promoters to up-regulate canonical MYC targets but binds to both enhancers and promoters to repress differentiation genes. MYCN binding also increases H3K4me3 and H3K27ac on canonical MYC target promoters and decreases H3K27ac on neuronal differentiation gene enhancers and promoters. WDR5 facilitates MYCN promoter binding to activate canonical MYC target genes, whereas MYCN recruits G9a to enhancers to repress neuronal differentiation genes. Targeting both MYCN's active and repressive transcriptional activities using both WDR5 and G9a inhibitors synergistically suppresses NB growth. We demonstrate that MYCN cooperates with WDR5 and G9a to orchestrate global gene transcription. The targeting of both these cofactors is a novel therapeutic strategy to indirectly target the oncogenic activity of MYCN.


Subject(s)
Cell Transformation, Neoplastic , Nuclear Proteins , Humans , Nuclear Proteins/metabolism , N-Myc Proto-Oncogene Protein/genetics , N-Myc Proto-Oncogene Protein/metabolism , Histone Methyltransferases/genetics , Cell Line, Tumor , Cell Transformation, Neoplastic/genetics , Carcinogenesis/genetics , Gene Expression Regulation, Neoplastic , Transcription, Genetic , Intracellular Signaling Peptides and Proteins/genetics , Intracellular Signaling Peptides and Proteins/metabolism
2.
Cell ; 142(3): 456-67, 2010 Aug 06.
Article in English | MEDLINE | ID: mdl-20691904

ABSTRACT

RNA import into mammalian mitochondria is considered essential for replication, transcription, and translation of the mitochondrial genome but the pathway(s) and factors that control this import are poorly understood. Previously, we localized polynucleotide phosphorylase (PNPASE), a 3' --> 5' exoribonuclease and poly-A polymerase, in the mitochondrial intermembrane space, a location lacking resident RNAs. Here, we show a new role for PNPASE in regulating the import of nuclear-encoded RNAs into the mitochondrial matrix. PNPASE reduction impaired mitochondrial RNA processing and polycistronic transcripts accumulated. Augmented import of RNase P, 5S rRNA, and MRP RNAs depended on PNPASE expression and PNPASE-imported RNA interactions were identified. PNPASE RNA processing and import activities were separable and a mitochondrial RNA targeting signal was isolated that enabled RNA import in a PNPASE-dependent manner. Combined, these data strongly support an unanticipated role for PNPASE in mediating the translocation of RNAs into mitochondria.


Subject(s)
Mitochondria/metabolism , Polyribonucleotide Nucleotidyltransferase/metabolism , RNA/metabolism , Animals , Cell Line , Gene Knockout Techniques , Humans , Mice , Mice, Inbred C57BL , Polyribonucleotide Nucleotidyltransferase/genetics , RNA Processing, Post-Transcriptional , Ribonuclease P/metabolism , Saccharomyces cerevisiae/metabolism
3.
Article in English | MEDLINE | ID: mdl-38568479

ABSTRACT

RATIONALE: Idiopathic Pulmonary Arterial Hypertension (IPAH) is characterized by extensive pulmonary vascular remodeling due to plexiform and obliterative lesions, media hypertrophy, inflammatory cell infiltration, and alterations of the adventitia. OBJECTIVE: Test the hypothesis that microscopic IPAH vascular lesions express unique molecular profiles, which collectively are different from control pulmonary arteries. METHODS: We used digital spatial transcriptomics to profile the genome-wide differential transcriptomic signature of key pathological lesions (plexiform, obliterative, intima+media hypertrophy, and adventitia) in IPAH lungs (n= 11) and compared these data to the intima+media and adventitia of control pulmonary artery (n=5). RESULTS: We detected 8273 transcripts in the IPAH lesions and control lung pulmonary arteries. Plexiform lesions and IPAH adventitia exhibited the greatest number of differentially expressed genes when compared with intima-media hypertrophy and obliterative lesions. Plexiform lesions in IPAH showed enrichment for (i) genes associated with TGFß-signaling and (ii) mutated genes affecting the extracellular matrix and endothelial-mesenchymal transformation. Plexiform lesions and IPAH adventitia showed upregulation of genes involved in immune and interferon signaling, coagulation, and complement pathways. Cellular deconvolution indicated variability in the number of vascular and inflammatory cells between IPAH lesions, which underlies the differential transcript profiling. CONCLUSIONS: IPAH lesions express unique molecular transcript profiles enriched for pathways involving pathogenetic pathways, including genetic disease drivers, innate and acquired immunity, hypoxia sensing, and angiogenesis signaling. These data provide a rich molecular-structural framework in IPAH vascular lesions that inform novel biomarkers and therapeutic targets in this highly morbid disease.

4.
Plant Biotechnol J ; 2024 Jun 03.
Article in English | MEDLINE | ID: mdl-38831638

ABSTRACT

The foundation of most food production systems underpinning global food security is the careful management of soil resources. Embedded in the concept of soil health is the impact of diverse soil-borne pests and pathogens, and phytoparasitic nematodes represent a particular challenge. Root-knot nematodes and cyst nematodes are severe threats to agriculture, accounting for annual yield losses of US$157 billion. The control of soil-borne phytoparasitic nematodes conventionally relies on the use of chemical nematicides, which can have adverse effects on the environment and human health due to their persistence in soil, plants, and water. Nematode-resistant plants offer a promising alternative, but genetic resistance is species-dependent, limited to a few crops, and breeding and deploying resistant cultivars often takes years. Novel approaches for the control of phytoparasitic nematodes are therefore required, those that specifically target these parasites in the ground whilst minimizing the impact on the environment, agricultural ecosystems, and human health. In addition to the development of next-generation, environmentally safer nematicides, promising biochemical strategies include the combination of RNA interference (RNAi) with nanomaterials that ensure the targeted delivery and controlled release of double-stranded RNA. Genome sequencing has identified more than 75 genes in root knot and cyst nematodes that have been targeted with RNAi so far. But despite encouraging results, the delivery of dsRNA to nematodes in the soil remains inefficient. In this review article, we describe the state-of-the-art RNAi approaches targeting phytoparasitic nematodes and consider the potential benefits of nanotechnology to improve dsRNA delivery.

5.
Respir Res ; 25(1): 192, 2024 May 03.
Article in English | MEDLINE | ID: mdl-38702687

ABSTRACT

This review examines how single-cell omics technologies, particularly single-cell RNA sequencing (scRNAseq), enhance our understanding of pulmonary arterial hypertension (PAH). PAH is a multifaceted disorder marked by pulmonary vascular remodeling, leading to high morbidity and mortality. The cellular pathobiology of this heterogeneous disease, involving various vascular and non-vascular cell types, is not fully understood. Traditional PAH studies have struggled to resolve the complexity of pathogenic cell populations. scRNAseq offers a refined perspective by detailing cellular diversity within PAH, identifying unique cell subsets, gene networks, and molecular pathways that drive the disease. We discuss significant findings from recent literature, summarizing how scRNAseq has shifted our understanding of PAH in human, rat, and mouse models. This review highlights the insights gained into cellular phenotypes, gene expression patterns, and novel molecular targets, and contemplates the challenges and prospective paths for research. We propose ways in which single-cell omics could inform future research and translational efforts to combat PAH.


Subject(s)
Single-Cell Analysis , Humans , Animals , Single-Cell Analysis/methods , Pulmonary Arterial Hypertension/genetics , Pulmonary Arterial Hypertension/metabolism , Pulmonary Arterial Hypertension/physiopathology , Pulmonary Arterial Hypertension/pathology , Sequence Analysis, RNA/methods , Hypertension, Pulmonary/genetics , Hypertension, Pulmonary/metabolism , Hypertension, Pulmonary/pathology
6.
Phytopathology ; 114(6): 1161-1175, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38427594

ABSTRACT

The loss of the soil fumigant methyl bromide (MeBr) and adoption of soil fumigant alternatives has been challenging for farmers, particularly for those crops in which pathogens previously controlled by MeBr have emerged as significant problems, but it has resulted in some unanticipated benefits for the scientific community and the environment. Applauded as one of the most effective environmental agreements to date, the universally accepted Montreal Protocol on Ozone Depleting Substances has had a significant impact on the environment, reducing the release of halogenated compounds from anthropogenic sources enough to mitigate global warming by an estimated 1.1°C by 2021. The funding associated with various MeBr transition programs has increased collaboration across scientific disciplines, commodity groups, industry, and regulatory agencies. Chemical alternatives and improved application strategies, including the development of gas-retentive agricultural films, coupled with sound efficacy data and grower ingenuity have resulted in the sustained production of many of the impacted crops; although there has been some loss of acreage and value, particularly for Florida fumigated crops, for some, value has continued to increase, allowing production to continue. The loss of a single, broad-spectrum tool for pest control has led to a deeper understanding of the specific pest complexes impacting these at-risk crops, as well as the development of new, biologically based management tools for their control while increasing our understanding of the role of the soil microbiome in pest control and crop production.


Subject(s)
Fumigation , Hydrocarbons, Brominated , Soil , Soil/chemistry , Crops, Agricultural/microbiology , Agriculture , Plant Diseases/prevention & control , Plant Diseases/microbiology
7.
Am J Respir Cell Mol Biol ; 68(4): 381-394, 2023 04.
Article in English | MEDLINE | ID: mdl-36252184

ABSTRACT

The identification and role of endothelial progenitor cells in pulmonary arterial hypertension (PAH) remain controversial. Single-cell omics analysis can shed light on endothelial progenitor cells and their potential contribution to PAH pathobiology. We aim to identify endothelial cells that may have stem/progenitor potential in rat lungs and assess their relevance to PAH. Differential expression, gene set enrichment, cell-cell communication, and trajectory reconstruction analyses were performed on lung endothelial cells from single-cell RNA sequencing of Sugen-hypoxia, monocrotaline, and control rats. Relevance to human PAH was assessed in multiple independent blood and lung transcriptomic data sets. Rat lung endothelial cells were visualized by immunofluorescence in situ, analyzed by flow cytometry, and assessed for tubulogenesis in vitro. A subpopulation of endothelial cells (endothelial arterial type 2 [EA2]) marked by Tm4sf1 (transmembrane 4 L six family member 1), a gene strongly implicated in cancer, harbored a distinct transcriptomic signature enriched for angiogenesis and CXCL12 signaling. Trajectory analysis predicted that EA2 has a less differentiated state compared with other endothelial subpopulations. Analysis of independent data sets revealed that TM4SF1 is downregulated in lungs and endothelial cells from patients and PAH models, is a marker for hematopoietic stem cells, and is upregulated in PAH circulation. TM4SF1+CD31+ rat lung endothelial cells were visualized in distal pulmonary arteries, expressed hematopoietic marker CD45, and formed tubules in coculture with lung fibroblasts. Our study uncovered a novel Tm4sf1-marked subpopulation of rat lung endothelial cells that may have stem/progenitor potential and demonstrated its relevance to PAH. Future studies are warranted to further elucidate the role of EA2 and Tm4sf1 in PAH.


Subject(s)
Endothelial Progenitor Cells , Pulmonary Arterial Hypertension , Animals , Humans , Rats , Antigens, Surface/metabolism , Disease Models, Animal , Endothelium , Familial Primary Pulmonary Hypertension/metabolism , Monocrotaline , Neoplasm Proteins/metabolism , Pulmonary Arterial Hypertension/metabolism , Pulmonary Artery/metabolism
8.
Am J Respir Crit Care Med ; 206(2): 186-196, 2022 07 15.
Article in English | MEDLINE | ID: mdl-35504005

ABSTRACT

Rationale: Idiopathic pulmonary arterial hypertension (PAH) is a terminal pulmonary vascular disease characterized by increased pressure, right ventricular failure, and death. PAH exhibits a striking sex bias and is up to four times more prevalent in females. Understanding the molecular basis behind sex differences could help uncover novel therapies. Objectives: We previously discovered that the Y chromosome is protective against hypoxia-induced experimental pulmonary hypertension (PH), which may contribute to sex differences in PAH. Here, we identify the gene responsible for Y-chromosome protection, investigate key downstream autosomal genes, and demonstrate a novel preclinical therapy. Methods: To test the effect of Y-chromosome genes on PH development, we knocked down each Y-chromosome gene expressed in the lung by means of intratracheal instillation of siRNA in gonadectomized male mice exposed to hypoxia and monitored changes in right ventricular and pulmonary artery hemodynamics. We compared the lung transcriptome of Uty knockdown mouse lungs to those of male and female PAH patient lungs to identify common downstream pathogenic chemokines and tested the effects of these chemokines on human pulmonary artery endothelial cells. We further inhibited the activity of these chemokines in two preclinical pulmonary hypertension models to test the therapeutic efficacy. Measurements and Main Results: Knockdown of the Y-chromosome gene Uty resulted in more severe PH measured by increased right ventricular pressure and decreased pulmonary artery acceleration time. RNA sequencing revealed an increase in proinflammatory chemokines Cxcl9 and Cxcl10 as a result of Uty knockdown. We found CXCL9 and CXCL10 significantly upregulated in human PAH lungs, with more robust upregulation in females with PAH. Treatment of human pulmonary artery endothelial cells with CXCL9 and CXCL10 triggered apoptosis. Inhibition of Cxcl9 and Cxcl10 expression in male Uty knockout mice and CXCL9 and CXCL10 activity in female rats significantly reduced PH severity. Conclusions:Uty is protective against PH. Reduction of Uty expression results in increased expression of proinflammatory chemokines Cxcl9 and Cxcl10, which trigger endothelial cell death and PH. Inhibition of CLXC9 and CXLC10 rescues PH development in multiple experimental models.


Subject(s)
Chemokines , Hypertension, Pulmonary , Minor Histocompatibility Antigens , Nuclear Proteins , Animals , Chemokines/metabolism , Disease Models, Animal , Endothelial Cells/metabolism , Familial Primary Pulmonary Hypertension/genetics , Female , Genes, Y-Linked , Humans , Hypertension, Pulmonary/genetics , Hypoxia , Male , Mice , Minor Histocompatibility Antigens/genetics , Nuclear Proteins/genetics , Pulmonary Artery , Rats
9.
J Soc Pers Relat ; 40(5): 1579-1600, 2023 May.
Article in English | MEDLINE | ID: mdl-38603400

ABSTRACT

Main effect models contend that perceived social support benefits mental health in the presence and the absence of stressful events, whereas stress-buffering models contend that perceived social support benefits mental health especially when individuals are facing stressful events. We tested these models of how perceived social support impacts mental health during the COVID-19 pandemic and evaluated whether characteristics of everyday social interactions statistically mediated this association - namely, (a) received support, the visible and deliberate assistance provided by others, and (b) pleasantness, the extent to which an interaction is positive, flows easily, and leads individuals to feel understood and validated. 591 United States adults completed a 3-week ecological momentary assessment protocol sampling characteristics of their everyday social interactions that was used to evaluate between-person average values and within-person daily fluctuations in everyday social interaction characteristics. Global measures of perceived social support and pandemic-related stressors were assessed at baseline. Psychiatric symptoms of depression and anxiety were assessed at baseline, at the end of each day of ecological momentary assessment, and at 3-week follow-up. Consistent with a main effect model, higher baseline perceived social support predicted decreases in psychiatric symptoms at 3-week follow-up (ß = -.09, p = .001). Contrary to a stress-buffering model, we did not find an interaction of pandemic-stressors × perceived social support. The main effect of perceived social support on mental health was mediated by the pleasantness of everyday social interactions, but not by received support in everyday social interactions. We found evidence for both main effects and stress-buffering effects of within-person fluctuations in interaction pleasantness on daily changes in mental health. Results suggest the importance of everyday social interaction characteristics, especially their pleasantness, in linking perceived social support and mental health.

10.
Am J Respir Crit Care Med ; 203(8): 1006-1022, 2021 04 15.
Article in English | MEDLINE | ID: mdl-33021809

ABSTRACT

Rationale: The cellular and molecular landscape and translational value of commonly used models of pulmonary arterial hypertension (PAH) are poorly understood. Single-cell transcriptomics can enhance molecular understanding of preclinical models and facilitate their rational use and interpretation.Objectives: To determine and prioritize dysregulated genes, pathways, and cell types in lungs of PAH rat models to assess relevance to human PAH and identify drug repositioning candidates.Methods: Single-cell RNA sequencing was performed on the lungs of monocrotaline (MCT), Sugen-hypoxia (SuHx), and control rats to identify altered genes and cell types, followed by validation using flow-sorted cells, RNA in situ hybridization, and immunofluorescence. Relevance to human PAH was assessed by histology of lungs from patients and via integration with human PAH genetic loci and known disease genes. Candidate drugs were predicted using Connectivity Map.Measurements and Main Results: Distinct changes in genes and pathways in numerous cell types were identified in SuHx and MCT lungs. Widespread upregulation of NF-κB signaling and downregulation of IFN signaling was observed across cell types. SuHx nonclassical monocytes and MCT conventional dendritic cells showed particularly strong NF-κB pathway activation. Genes altered in SuHx nonclassical monocytes were significantly enriched for PAH-associated genes and genetic variants, and candidate drugs predicted to reverse the changes were identified. An open-access online platform was developed to share single-cell data and drug candidates (http://mergeomics.research.idre.ucla.edu/PVDSingleCell/).Conclusions: Our study revealed the distinct and shared dysregulation of genes and pathways in two commonly used PAH models for the first time at single-cell resolution and demonstrated their relevance to human PAH and utility for drug repositioning.


Subject(s)
Antihypertensive Agents/therapeutic use , Cells, Cultured/drug effects , Drug Repositioning , Gene Expression Regulation/drug effects , Pulmonary Arterial Hypertension/drug therapy , Pulmonary Arterial Hypertension/genetics , Pulmonary Arterial Hypertension/physiopathology , Animals , Disease Models, Animal , Humans , Male , Rats , Rats, Sprague-Dawley
11.
Pervasive Mob Comput ; 75: 101439, 2021 Aug.
Article in English | MEDLINE | ID: mdl-36569467

ABSTRACT

Smartphone-based contact-tracing apps are a promising solution to help scale up the conventional contact-tracing process. However, low adoption rates have become a major issue that prevents these apps from achieving their full potential. In this paper, we present a national-scale survey experiment ( N = 1963 ) in the U.S. to investigate the effects of app design choices and individual differences on COVID-19 contact-tracing app adoption intentions. We found that individual differences such as prosocialness, COVID-19 risk perceptions, general privacy concerns, technology readiness, and demographic factors played a more important role than app design choices such as decentralized design vs. centralized design, location use, app providers, and the presentation of security risks. Certain app designs could exacerbate the different preferences in different sub-populations which may lead to an inequality of acceptance to certain app design choices (e.g., developed by state health authorities vs. a large tech company) among different groups of people (e.g., people living in rural areas vs. people living in urban areas). Our mediation analysis showed that one's perception of the public health benefits offered by the app and the adoption willingness of other people had a larger effect in explaining the observed effects of app design choices and individual differences than one's perception of the app's security and privacy risks. With these findings, we discuss practical implications on the design, marketing, and deployment of COVID-19 contact-tracing apps in the U.S.

12.
J Mol Cell Cardiol ; 148: 25-33, 2020 11.
Article in English | MEDLINE | ID: mdl-32835666

ABSTRACT

The novel 2019 coronavirus disease (COVID-19), resulting from severe acute respiratory syndrome coronarvirus-2 (SARS-CoV-2) infection, typically leads to respiratory failure in severe cases; however, cardiovascular injury is reported to contribute to a substantial proportion of COVID-19 deaths. Preexisting cardiovascular disease (CVD) is among the most common risk factors for hospitalization and death in COVID-19 patients, and the pathogenic mechanisms of COVID-19 disease progression itself may promote the development of cardiovascular injury, increasing risk of in-hospital death. Sex differences in COVID-19 are becoming more apparent as mounting data indicate that males seem to be disproportionately at risk of severe COVID-19 outcome due to preexisting CVD and COVID-19-related cardiovascular injury. In this review, we will provide a basic science perspective on current clinical observations in this rapidly evolving field and discuss the interplay sex differences, preexisting CVD and COVID-19-related cardiac injury.


Subject(s)
COVID-19/epidemiology , Cardiovascular Diseases/epidemiology , Sex Factors , Angiotensin-Converting Enzyme 2/genetics , Arrhythmias, Cardiac/complications , Arrhythmias, Cardiac/epidemiology , COVID-19/complications , COVID-19/genetics , Cardiovascular Diseases/complications , Disease Progression , Disease Susceptibility , Endothelium, Vascular/pathology , Female , Humans , Inflammation , Male , Microcirculation , Obesity/complications , Risk Factors , Smoking , Thrombosis/complications , Thrombosis/epidemiology
13.
J Biol Chem ; 294(50): 18952-18966, 2019 12 13.
Article in English | MEDLINE | ID: mdl-31578281

ABSTRACT

Intercellular propagation of protein aggregation is emerging as a key mechanism in the progression of several neurodegenerative diseases, including Alzheimer's disease and frontotemporal dementia (FTD). However, we lack a systematic understanding of the cellular pathways controlling prion-like propagation of aggregation. To uncover such pathways, here we performed CRISPR interference (CRISPRi) screens in a human cell-based model of propagation of tau aggregation monitored by FRET. Our screens uncovered that knockdown of several components of the endosomal sorting complexes required for transport (ESCRT) machinery, including charged multivesicular body protein 6 (CHMP6), or CHMP2A in combination with CHMP2B (whose gene is linked to familial FTD), promote propagation of tau aggregation. We found that knocking down the genes encoding these proteins also causes damage to endolysosomal membranes, consistent with a role for the ESCRT pathway in endolysosomal membrane repair. Leakiness of the endolysosomal compartment significantly enhanced prion-like propagation of tau aggregation, likely by making tau seeds more available to pools of cytoplasmic tau. Together, these findings suggest that endolysosomal escape is a critical step in tau propagation in neurodegenerative diseases.


Subject(s)
Endosomal Sorting Complexes Required for Transport/metabolism , Lysosomes/metabolism , tau Proteins/metabolism , Cells, Cultured , HEK293 Cells , Humans , Protein Aggregates
14.
Neurobiol Dis ; 141: 104877, 2020 07.
Article in English | MEDLINE | ID: mdl-32360664

ABSTRACT

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease in which motor neurons throughout the brain and spinal cord progressively degenerate resulting in muscle atrophy, paralysis and death. Recent studies using animal models of ALS implicate multiple cell-types (e.g., astrocytes and microglia) in ALS pathogenesis in the spinal motor systems. To ascertain cellular vulnerability and cell-type specific mechanisms of ALS in the brainstem that orchestrates oral-motor functions, we conducted parallel single cell RNA sequencing (scRNA-seq) analysis using the high-throughput Drop-seq method. We isolated 1894 and 3199 cells from the brainstem of wildtype and mutant SOD1 symptomatic mice respectively, at postnatal day 100. We recovered major known cell types and neuronal subpopulations, such as interneurons and motor neurons, and trigeminal ganglion (TG) peripheral sensory neurons, as well as, previously uncharacterized interneuron subtypes. We found that the majority of the cell types displayed transcriptomic alterations in ALS mice. Differentially expressed genes (DEGs) of individual cell populations revealed cell-type specific alterations in numerous pathways, including previously known ALS pathways such as inflammation (in microglia), stress response (ependymal and an uncharacterized cell population), neurogenesis (astrocytes, oligodendrocytes, neurons), synapse organization and transmission (microglia, oligodendrocyte precursor cells, and neuronal subtypes), and mitochondrial function (uncharacterized cell populations). Other cell-type specific processes altered in SOD1 mutant brainstem include those from motor neurons (axon regeneration, voltage-gated sodium and potassium channels underlying excitability, potassium ion transport), trigeminal sensory neurons (detection of temperature stimulus involved in sensory perception), and cellular response to toxic substances (uncharacterized cell populations). DEGs consistently altered across cell types (e.g., Malat1), as well as cell-type specific DEGs, were identified. Importantly, DEGs from various cell types overlapped with known ALS genes from the literature and with top hits from an existing human ALS genome-wide association study (GWAS), implicating the potential cell types in which the ALS genes function with ALS pathogenesis. Our molecular investigation at single cell resolution provides comprehensive insights into the cell types, genes and pathways altered in the brainstem in a widely used ALS mouse model.


Subject(s)
Amyotrophic Lateral Sclerosis/metabolism , Amyotrophic Lateral Sclerosis/pathology , Brain Stem/metabolism , Brain Stem/pathology , Superoxide Dismutase-1/metabolism , Amyotrophic Lateral Sclerosis/genetics , Animals , Female , Mice, Transgenic , Mutation , Neurons/metabolism , Neurons/pathology , Sequence Analysis, RNA , Signal Transduction , Single-Cell Analysis , Superoxide Dismutase-1/genetics , Transcriptome
15.
Respir Res ; 21(1): 303, 2020 Nov 18.
Article in English | MEDLINE | ID: mdl-33208169

ABSTRACT

Pulmonary hypertension (PH) developing secondarily in pulmonary fibrosis (PF) patients (PF-PH) is a frequent co-morbidity. The high prevalence of PH in PF patients is very concerning since the presence of PH is a strong predictor of mortality in PF patients. Until recently, PH was thought to arise solely from fibrotic destruction of the lung parenchyma, leading to hypoxic vasoconstriction and loss of vascular bed density. Thus, potential cellular and molecular dysregulation of vascular remodeling as a driver of PF-PH has been under-investigated. The recent demonstrations that there is no correlation between the severity of the fibrosis and development of PH, along with the finding that significant vascular histological and molecular differences exist between patients with and without PH have shifted the etiological paradigm of PF-PH. This review aims to provide a comprehensive translational overview of PH in PF patients from clinical diagnosis and outcome to the latest understanding of the histology and molecular pathophysiology of PF-PH.


Subject(s)
Hypertension, Pulmonary/etiology , Hypertension, Pulmonary/pathology , Lung/pathology , Pulmonary Fibrosis/complications , Pulmonary Fibrosis/pathology , Vascular Remodeling/physiology , Animals , Echocardiography/methods , Humans , Hypertension, Pulmonary/metabolism , Inflammation Mediators/metabolism , Lung/metabolism , Pulmonary Fibrosis/metabolism , Respiratory Function Tests/methods
16.
Arch Biochem Biophys ; 678: 108116, 2019 12 15.
Article in English | MEDLINE | ID: mdl-31568751

ABSTRACT

Exposure to ambient particulate matter has been shown to promote a variety of disorders, including cardiovascular diseases predominantly of ischemic etiology. However, the mechanisms linking inhaled particulates with systemic vascular effects, resulting in worsened atherosclerosis, are not well defined. We assessed the potential role of macrophages in translating these effects by analyzing gene expression patterns in response to diesel exhaust particles (DEP) at the average cell level, using Affymetrix microarrays in peritoneal macrophages in culture (in vitro), and at the individual cell level, using single-cell RNA sequencing (scRNA-seq) in alveolar macrophages collected from exposed mice (in vivo). Peritoneal macrophages were harvested from C57BL/6J mice and treated with 25 µg/mL of a DEP methanol extract (DEPe). These cells exhibited significant (FDR < 0.05) differential expression of a large number of genes and enrichment in pathways, especially engaged in immune responses and antioxidant defense. DEPe led to marked upregulation of heme oxygenase 1 (Hmox1), the most significantly upregulated gene (FDR = 1.75E-06), and several other antioxidant genes. For the in vivo work, C57BL/6J mice were subjected to oropharyngeal aspiration of 200 µg of whole DEP. The gene expression profiles of the alveolar macrophages harvested from these mice were analyzed at the single-cell level using scRNA-seq, which showed significant dysregulation of a broad number of genes enriched in immune system pathways as well, but with a large heterogeneity in how individual alveolar macrophages responded to DEP exposures. Altogether, DEP pollutants dysregulated immunological pathways in macrophages that may mediate the development of pulmonary and systemic vascular effects.


Subject(s)
Air Pollutants/toxicity , Macrophages/drug effects , Macrophages/immunology , Oligonucleotide Array Sequence Analysis , RNA, Small Cytoplasmic/genetics , RNA-Seq , Vehicle Emissions/toxicity , Animals , Antioxidants/metabolism , Immunity, Innate/drug effects , Immunity, Innate/genetics , Macrophages/metabolism , Macrophages, Alveolar/drug effects , Macrophages, Alveolar/immunology , Macrophages, Alveolar/metabolism , Macrophages, Peritoneal/drug effects , Macrophages, Peritoneal/immunology , Macrophages, Peritoneal/metabolism , Male , Mice , Mice, Inbred C57BL
17.
Mol Cell ; 39(6): 873-85, 2010 Sep 24.
Article in English | MEDLINE | ID: mdl-20864035

ABSTRACT

During an immune response, B cells undergo rapid proliferation and activation-induced cytidine deaminase (AID)-dependent remodeling of immunoglobulin (IG) genes within germinal centers (GCs) to generate memory B and plasma cells. Unfortunately, the genotoxic stress associated with the GC reaction also promotes most B cell malignancies. Here, we report that exogenous and intrinsic AID-induced DNA strand breaks activate ATM, which signals through an LKB1 intermediate to inactivate CRTC2, a transcriptional coactivator of CREB. Using genome-wide location analysis, we determined that CRTC2 inactivation unexpectedly represses a genetic program that controls GC B cell proliferation, self-renewal, and differentiation while opposing lymphomagenesis. Inhibition of this pathway results in increased GC B cell proliferation, reduced antibody secretion, and impaired terminal differentiation. Multiple distinct pathway disruptions were also identified in human GC B cell lymphoma patient samples. Combined, our data show that CRTC2 inactivation, via physiologic DNA damage response signaling, promotes B cell differentiation in response to genotoxic stress.


Subject(s)
B-Lymphocytes/cytology , Cell Cycle Proteins/metabolism , Cell Differentiation/immunology , Cytidine Deaminase/genetics , DNA Damage/immunology , DNA-Binding Proteins/metabolism , Protein Serine-Threonine Kinases/metabolism , Tumor Suppressor Proteins/metabolism , AMP-Activated Protein Kinase Kinases , Active Transport, Cell Nucleus/drug effects , Active Transport, Cell Nucleus/radiation effects , Animals , Ataxia Telangiectasia Mutated Proteins , B-Lymphocytes/drug effects , B-Lymphocytes/immunology , B-Lymphocytes/metabolism , B-Lymphocytes/radiation effects , Cell Cycle Proteins/antagonists & inhibitors , Cell Cycle Proteins/genetics , Cell Differentiation/drug effects , Cell Differentiation/radiation effects , Cell Line, Tumor , DNA Breaks, Double-Stranded/drug effects , DNA Breaks, Double-Stranded/radiation effects , DNA Damage/drug effects , DNA Damage/radiation effects , DNA-Binding Proteins/antagonists & inhibitors , DNA-Binding Proteins/genetics , Gene Expression/drug effects , Gene Expression/immunology , Gene Expression/radiation effects , Gene Expression Regulation/immunology , Germinal Center/cytology , Humans , Immunoglobulin Class Switching/physiology , Lymphoma, B-Cell/genetics , Lymphoma, B-Cell/metabolism , Metformin/pharmacology , Mice , Mice, Knockout , Phosphorylation/drug effects , Phosphorylation/radiation effects , Plasma Cells/cytology , Plasma Cells/immunology , Protein Serine-Threonine Kinases/antagonists & inhibitors , Protein Serine-Threonine Kinases/genetics , Proto-Oncogene Proteins/genetics , Signal Transduction/drug effects , Signal Transduction/genetics , Signal Transduction/immunology , Signal Transduction/radiation effects , Transcription Factors/genetics , Transcription Factors/metabolism , Tumor Suppressor Proteins/antagonists & inhibitors , Tumor Suppressor Proteins/genetics
18.
Clin Med Res ; 15(1-2): 41-44, 2017 Jun.
Article in English | MEDLINE | ID: mdl-28751467

ABSTRACT

We present the case of a patient with primary APS who had a recurrence of thrombotic event while on treatment with rivaroxaban and had to be restarted on warfarin. The current literature on recurrence of thrombotic events in patients with antiphospholipid syndrome (APS) treated with newer oral anticoagulants (NOAC) is also reviewed. Relevant case reports and case series were identified by searching the Medline database using the key words antiphospholipid syndrome, anticoagulants and names of the NOACs, and data on individual patients was abstracted. We identified several reports on the failure of newer anticoagulants in APS, as well as cases and clinical trial results reporting efficacy. We conclude that treatment strategies for APS should be tailored cautiously when using NOACs.


Subject(s)
Anticoagulants , Antiphospholipid Syndrome/drug therapy , Rivaroxaban , Thrombosis , Warfarin , Administration, Oral , Anticoagulants/administration & dosage , Anticoagulants/adverse effects , Antiphospholipid Syndrome/diagnosis , Female , Humans , Middle Aged , Rivaroxaban/administration & dosage , Rivaroxaban/adverse effects , Thrombosis/chemically induced , Thrombosis/diagnosis , Thrombosis/drug therapy , Warfarin/administration & dosage , Warfarin/adverse effects
19.
J Nematol ; 48(4): 231-240, 2016 Dec.
Article in English | MEDLINE | ID: mdl-28154429

ABSTRACT

Two years of field trials conducted in a Meloidogyne incognita-infested field evaluated grafting and Paladin Pic-21 (dimethyl disulfide:chloropicrin [DMDS:Pic] 79:21) for root-knot nematode and weed control in tomato and melon. Tomato rootstocks evaluated were; 'TX301', 'Multifort', and 'Aloha'. 'Florida 47' was the scion and the nongrafted control. A double crop of melon was planted into existing beds following tomato harvest. Melon rootstocks, C. metulifer and 'Tetsukabuto', were evaluated with nongrafted 'Athena' in year 1. In year 2, watermelon followed tomato with scion variety 'Tri-X Palomar' as the control and also grafted onto 'Emphasis' and 'Strongtosa' rootstocks. Four soil treatments were applied in fall both years under Canslit metalized film; Paladin Pic-21, methyl bromide:chloropicrin (MeBr:C33, 67:33), Midas (iodomethane:chloropicrin 50:50), and a herbicide-treated control. M. incognita J2 in soil were highest in herbicide control plots and nongrafted tomato. All soil treatments produced similar tomato growth, which was greater than the herbicide control. All treatments reduced M. incognita J2 in roots compared to the herbicide control. 'Multifort' rootstock produced the largest and healthiest roots; however, the number of M. incognita isolated from roots did not differ among the tomato rootstocks tested. Galling on tomato was highest in herbicide control plots and nongrafted plants. In melon, M. incognita J2 in soil did not differ among melon rootstocks, but numbers isolated from melon rootstocks increased in 'Tetsukabuto' compared with C. metuliferus. 'Tetsukabuto' were larger root systems than nongrafted 'Athena'. All fumigants provided protection for all melon rootstocks against galling by M. incognita compared to the herbicide control. Galling on C. metuliferus rootstock was less in all fumigant treatments compared with nongrafted 'Athena' and 'Tetsukabuto'. In watermelon, M. incognita in soil and roots did not differ among soil treatments or watermelon rootstocks, and yield was lower in both grafted rootstocks compared with the nongrafted control. All soil treatments increased average fruit weight of watermelon compared with the herbicide control, and provided effective weed control, keeping the most predominant weed, purple nutsedge (Cyperus rotundus L.), density at or below 1/m row. Grafting commercial scions onto M. incognita-resistant rootstocks has potential for nematode management combined with soil treatments or as a stand-alone component in crop production systems.

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