Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 26
Filter
1.
Microbiol Spectr ; : e0351623, 2024 Apr 30.
Article in English | MEDLINE | ID: mdl-38687064

ABSTRACT

Recent case reports and epidemiological data suggest that fungal infections represent an underappreciated complication among people with severe COVID-19. However, the frequency of fungal colonization in patients with COVID-19 and associations with specific immune responses in the airways remain incompletely defined. We previously generated a single-cell RNA-sequencing data set characterizing the upper respiratory microenvironment during COVID-19 and mapped the relationship between disease severity and the local behavior of nasal epithelial cells and infiltrating immune cells. Our previous study, in agreement with findings from related human cohorts, demonstrated that a profound deficiency in host immunity, particularly in type I and type III interferon signaling in the upper respiratory tract, is associated with rapid progression to severe disease and worse clinical outcomes. We have now performed further analysis of this cohort and identified a subset of participants with severe COVID-19 and concurrent detection of Candida species-derived transcripts within samples collected from the nasopharynx and trachea. Here, we present the clinical characteristics of these individuals. Using matched single-cell transcriptomic profiles of these individuals' respiratory mucosa, we identify epithelial immune signatures suggestive of IL17 stimulation and anti-fungal immunity. Further, we observe a significant expression of anti-fungal inflammatory cascades in the nasal and tracheal epithelium of all participants who went on to develop severe COVID-19, even among participants without detectable genetic material from fungal pathogens. Together, our data suggest that IL17 stimulation-in part driven by Candida colonization-and blunted interferon signaling represent a common feature of severe COVID-19 infection. IMPORTANCE: In this paper, we present an analysis suggesting that symptomatic and asymptomatic fungal coinfections can impact patient disease progression during COVID-19 hospitalization. By looking into the presence of other pathogens and their effect on the host immune response during COVID-19 hospitalizations, we aim to offer insight into an underestimated scenario, furthering our current knowledge of determinants of severity that could be considered for future diagnostic and intervention strategies.

2.
medRxiv ; 2023 Sep 15.
Article in English | MEDLINE | ID: mdl-37745424

ABSTRACT

Background: Many questions remain unanswered regarding the implication of lipid metabolites in severe SARS-CoV-2 infections. By re-analyzed sequencing data from the nasopharynx of a previously published cohort, we found that alox genes, involved in eicosanoid synthesis, were up-regulated in high WHO score patients, especially in goblet cells. Herein, we aimed to further understand the roles played by eicosanoids during severe SARS-CoV-2 infection. Methods and findings: We performed a total fatty acid panel on plasma and bulk RNA-seq analysis on peripheral blood mononuclear cells (PBMCs) collected from 10 infected and 10 uninfected patients. Univariate comparison of lipid metabolites revealed that lipid metabolites were increased in SARS-CoV-2 patients including the lipid mediators Arachidonic Acid (AA) and Eicosapentaenoic Acid (EPA). AA, EPA and the fatty acids Docosahexaenoic acid (DHA) and Docosapentaenoic acid (DPA), were positively correlated to WHO disease severity score. Transcriptomic analysis demonstrated that COVID-19 patients can be segregated based on WHO scores. Ontology, KEGG and Reactome analysis identified pathways enriched for genes related to innate immunity, interactions between lymphoid and nonlymphoid cells, interleukin signaling and, cell cycling pathways. Conclusions: Our study offers an association between nasopharynx mucosa eicosanoid genes expression, specific serum inflammatory lipids and, subsequent DNA damage pathways activation in PBMCs to severity of COVID-19 infection.

3.
Am J Med Sci ; 365(6): 488-495, 2023 06.
Article in English | MEDLINE | ID: mdl-36842466

ABSTRACT

BACKGROUND: Most facets of Inflammatory Bowel Disease (IBD) have not been thoroughly compared among minority populations, including Black patients. Our study was designed to characterize the demographics, phenotypes, outcomes, healthcare utilization, and treatment of IBD in a large cohort with 38% Black patients. METHODS: Electronic health records of 3272 IBD patients seen in a tertiary academic medical network from 2012 to July 15th, 2019 were analyzed. RESULTS: Black patients with Crohn's disease were significantly more likely than White patients to suffer from perianal (p < 0.001), fistulizing (p < 0.001), and fibrostenotic phenotypes (p < 0.001). Black patients with IBD were significantly more likely to undergo IBD-related surgery (p = 0.042) and experience an IBD-related complication (p < 0.001). The proportion of patients with at least one colonoscopy, one visit to the gastroenterology clinic, one visit to the emergency department (ED), and one hospital admission were higher in Black patients (p < 0.001, p = 0.005, p < 0.001, and p < 0.001; respectively). CONCLUSIONS: Black IBD patients had more severe disease phenotypes and worse healthcare outcomes than White patients. Black patients also used healthcare facilities and IBD medications to an equal or greater extent, despite being of a lower average socioeconomic class than their White counterparts. Our study suggests that underlying factors that do not pertain to the utilization of healthcare resources may be responsible for these worse outcomes in Black patients.


Subject(s)
Colitis, Ulcerative , Crohn Disease , Inflammatory Bowel Diseases , Humans , Black People , Colitis, Ulcerative/complications , Crohn Disease/epidemiology , Inflammatory Bowel Diseases/epidemiology , Inflammatory Bowel Diseases/therapy , Retrospective Studies , White People
4.
Inflamm Bowel Dis ; 29(12): 1847-1853, 2023 Dec 05.
Article in English | MEDLINE | ID: mdl-36808256

ABSTRACT

BACKGROUND: Most studies on the safety and efficacy of antitumor necrosis factor alpha (anti-TNF) agents in the treatment of inflammatory bowel disease have included few Black patients. AIMS: We aimed to evaluate the therapeutic response rate in Black IBD patients compared with White patients. METHODS: We conducted a retrospective review of IBD patients who were treated with anti-TNF agents and assessed those with therapeutic drug levels for clinical, endoscopic, and radiologic response to anti-TNF treatment. RESULTS: We identified 118 patients who met the inclusion criteria. Black IBD patients had significantly higher prevalence of endoscopic and radiologic active disease compared with White patients (62% and 34%, respectively; P = .023), despite similar proportions reaching therapeutic titers (67% and 55%, respectively; P = .20). Moreover, Black patients had significantly higher rate of IBD-related hospitalizations than White patients (30% vs 13%, respectively; P = .025) while on anti-TNF agents. CONCLUSIONS: Black IBD patients on anti-TNF agents had a significantly higher prevalence of active disease and more IBD-related hospitalizations than White patients.


This study explores the question of how IBD therapeutic efficacy may vary among racial groups.


Subject(s)
Inflammatory Bowel Diseases , Tumor Necrosis Factor Inhibitors , Humans , Inflammatory Bowel Diseases/drug therapy , Inflammatory Bowel Diseases/epidemiology , Retrospective Studies , Tumor Necrosis Factor Inhibitors/therapeutic use , Black or African American , White
5.
Int J Mol Sci ; 24(2)2023 Jan 14.
Article in English | MEDLINE | ID: mdl-36675169

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus is the causative agent of the COVID-19 disease. COVID-19 viral infection can affect many cell types, including epithelial cells of the lungs and airways. Extracellular vesicles (EVs) are released by virtually all cell types, and their packaged cargo allows for intercellular communication, cell differentiation, and signal transduction. Cargo from virus-infected cells may include virally derived metabolites, miRNAs, nucleic acids, and proteins. We hypothesized that COVID-19 plasma EVs can induce the formation of signaling platforms known as lipid rafts after uptake by normal human small airway epithelial cells (SAECs). Circulating EVs from patients with or without COVID-19 were characterized by nanoparticle tracking analysis, Western blotting using specific antibodies, and transmission electron microscopy. Primary cultures of normal human small airway epithelial cells were challenged with EVs from the two patient groups, and lipid raft formation was measured by fluorescence microscopy and assessed by sucrose density gradient analysis. Collectively, our data suggest that circulating EVs from COVID-19-infected patients can induce the formation of lipid rafts in normal human small airway epithelial cells. These results suggest the need for future studies aimed at investigating whether the increased density of lipid rafts in these cells promotes viral entry and alteration of specific signaling pathways in the recipient cells.


Subject(s)
COVID-19 , Extracellular Vesicles , Humans , SARS-CoV-2 , Epithelial Cells , Extracellular Vesicles/metabolism , Membrane Microdomains/metabolism
6.
Br J Neurosurg ; : 1-6, 2022 Dec 21.
Article in English | MEDLINE | ID: mdl-36541810

ABSTRACT

OBJECTIVE: Case series presentation and literature review of patient group suffering from symptomatic tension subdural extra-arachnoid hygroma following decompressive surgery for degenerative lumbar stenosis or disc disease. The purpose was to better understand this rare post-operative complication with a pathognomic radiological sign to help recommend optimal strategies for clinical management. METHODS: Retrospective case series comprising seven cases from one tertiary Neurosurgical centre spanning a 10-year period from 2011 to 2021. Patients included were those known to have undergone a spinal procedure and subsequently to have developed a symptomatic spinal subdural extra-arachnoid hygroma (SSEH). A literature review was conducted using PubMed, MEDLINE and EMBASE (keywords 'subdural hygroma', 'lumbar CSF hygroma', 'extra arachnoid hygroma', 'extra-arachnoid CSF collection', 'CSF tension hygroma', 'lumbar extra arachnoid hygroma', 'lumbar spinal hygroma', 'post-operating spinal hygroma', 'post-operative spinal CSF collection') and through reading references cited in relevant articles. Articles involving post-operative SSEH following lumbar spinal surgery were included. RESULTS: Rare complication with only five other cases in the literature. Dural breach described intra-operatively in only 5 of 12 total cases from our series and the literature. 5 patients in our series were managed surgically with 2 being managed conservatively. All patients in our series improved symptomatically and radiologically following surgical or conservative management. CONCLUSIONS: This is a rare post-lumbar surgery complication that can cause rapidly deteriorating lower limb and sphincteric function. Surgical management with wide durotomy and arachnoid marsupialisation can lead to reversal of neurological deterioration and excellent clinical results. A delayed presentation with pseudomeningocele formation may be managed conservatively if neurology is stable or improving. It is a condition that it is important for the clinician to recognise in order to instigate appropriate management in a time-dependent fashion.

7.
medRxiv ; 2022 Oct 26.
Article in English | MEDLINE | ID: mdl-36324802

ABSTRACT

Recent case reports and epidemiological data suggest fungal infections represent an under-appreciated complication among people with severe COVID-19. However, the frequency of fungal colonization in patients with COVID-19 and associations with specific immune responses in the airways remain incompletely defined. We previously generated a single-cell RNA-sequencing (scRNA-seq) dataset characterizing the upper respiratory microenvironment during COVID-19, and mapped the relationship between disease severity and the local behavior of nasal epithelial cells and infiltrating immune cells. Our study, in agreement with findings from related human cohorts, demonstrated that a profound deficiency in host immunity, particularly in type I and type III interferon signaling in the upper respiratory tract, is associated with rapid progression to severe disease and worse clinical outcomes. We have now performed further analysis of this cohort and identified a subset of participants with severe COVID-19 and concurrent detection of Candida species-derived transcripts within samples collected from the nasopharynx and trachea. Here, we present the clinical characteristics of these individuals, including confirmatory diagnostic testing demonstrating elevated serum (1, 3)-ß-D-glucan and/or confirmed fungal culture of the predicted pathogen. Using matched single-cell transcriptomic profiles of these individuals' respiratory mucosa, we identify epithelial immune signatures suggestive of IL-17 stimulation and anti-fungal immunity. Further, we observe significant expression of anti-fungal inflammatory cascades in the nasal and tracheal epithelium of all participants who went on to develop severe COVID-19, even among participants without detectable genetic material from fungal pathogens. Together, our data suggests that IL-17 stimulation - in part driven by Candida colonization - and blunted type I/III interferon signaling represents a common feature of severe COVID-19 infection.

8.
J Ambul Care Manage ; 45(1): 55-62, 2022.
Article in English | MEDLINE | ID: mdl-34524176

ABSTRACT

Web-based health education provides access to information and better coordination of care. Demographic and geographical factors may impact use and effectiveness of these services. The purpose of this study was to identify factors associated with use of web-based health education programs among diabetic patients at ambulatory clinics of a safety-net hospital. This was a retrospective chart review. Total sample size was 300. Patients who completed a web-based video were younger, Caucasian, living outside inner city core, users of patient portal, and more likely to complete annual diabetic eye examination. Web-based education may empower patients to manage health conditions and improve health outcomes. Health care organizations must consider barriers to use of these tools.


Subject(s)
Ambulatory Care , Diabetes Mellitus , Diabetes Mellitus/therapy , Health Education , Humans , Internet , Retrospective Studies
9.
Am J Gastroenterol ; 116(12): 2474-2475, 2021 12 01.
Article in English | MEDLINE | ID: mdl-34515670
11.
J Clin Invest ; 131(19)2021 10 01.
Article in English | MEDLINE | ID: mdl-34375310

ABSTRACT

NKTR-255 is a PEG conjugate of recombinant human IL-15 (rhIL-15) being examined as a potential cancer immunotherapeutic. Since IL-15 responses can be mediated by trans or cis presentation via IL-15Rα or soluble IL-15/IL-15Rα complexes, we investigated the role of IL-15Rα in driving NKTR-255 responses using defined naive and memory OVA-specific CD8+ T cells (OT-I) and NK cells in mice. NKTR-255 induced a 2.5- and 2.0-fold expansion of CD8+ T and NK cells, respectively, in WT mice. In adoptive transfer studies, proliferation of naive and memory WT OT-I T cells in response to NKTR-255 was not impaired in IL-15Rα-/- mice, suggesting trans presentation was not utilized by NKTR-255. Interestingly, naive IL-15Rα-/- OT-I cells had deficient responses to NKTR-255, while memory IL-15Rα-/- OT-I cell responses were partially impaired, suggesting that naive CD8+ T cells are more dependent on cis presentation of NKTR-255 than memory CD8+ T cells. In bone marrow chimera studies, IL-15Rα-/- and WT NK cells present in WT recipients had similar responses to NKTR-255, suggesting that cis presentation is not utilized by NK cells. NKTR-255 could form soluble complexes with IL-15Rα; binding to murine IL-15Rα generated superagonists that preferentially stimulated NK cells, showing that conversion to IL-15Rß agonist biases the response toward NK cells. These findings highlight the ability of NKTR-255 to utilize IL-15Rα for cis presentation and act as an IL-15Rαß agonist on CD8+ T cells.


Subject(s)
CD8-Positive T-Lymphocytes/drug effects , Interleukin-15/pharmacology , Killer Cells, Natural/drug effects , Animals , CD8-Positive T-Lymphocytes/immunology , Female , Immunologic Memory , Interleukin-15/chemistry , Interleukin-15 Receptor alpha Subunit/physiology , Interleukin-2 Receptor beta Subunit/agonists , Killer Cells, Natural/immunology , Male , Mice , Mice, Inbred BALB C , Mice, Inbred C57BL , Polyethylene Glycols/chemistry
12.
Cell ; 184(18): 4713-4733.e22, 2021 09 02.
Article in English | MEDLINE | ID: mdl-34352228

ABSTRACT

SARS-CoV-2 infection can cause severe respiratory COVID-19. However, many individuals present with isolated upper respiratory symptoms, suggesting potential to constrain viral pathology to the nasopharynx. Which cells SARS-CoV-2 primarily targets and how infection influences the respiratory epithelium remains incompletely understood. We performed scRNA-seq on nasopharyngeal swabs from 58 healthy and COVID-19 participants. During COVID-19, we observe expansion of secretory, loss of ciliated, and epithelial cell repopulation via deuterosomal cell expansion. In mild and moderate COVID-19, epithelial cells express anti-viral/interferon-responsive genes, while cells in severe COVID-19 have muted anti-viral responses despite equivalent viral loads. SARS-CoV-2 RNA+ host-target cells are highly heterogenous, including developing ciliated, interferon-responsive ciliated, AZGP1high goblet, and KRT13+ "hillock"-like cells, and we identify genes associated with susceptibility, resistance, or infection response. Our study defines protective and detrimental responses to SARS-CoV-2, the direct viral targets of infection, and suggests that failed nasal epithelial anti-viral immunity may underlie and precede severe COVID-19.


Subject(s)
COVID-19/immunology , COVID-19/virology , Immunity , SARS-CoV-2/physiology , Severity of Illness Index , Adult , Aged , Bystander Effect , COVID-19/genetics , Cohort Studies , Female , Humans , Male , Middle Aged , Nasopharynx/pathology , Nasopharynx/virology , RNA, Viral/analysis , RNA, Viral/genetics , Respiratory Mucosa/pathology , Respiratory Mucosa/virology , Transcription, Genetic , Viral Load
13.
Gut Microbes ; 13(1): 1-15, 2021.
Article in English | MEDLINE | ID: mdl-34100340

ABSTRACT

To investigate the relationship between intestinal microbiota and SARS-CoV-2-mediated pathogenicity in a United States, majority African American cohort. We prospectively collected fecal samples from 50 SARS-CoV-2 infected patients, 9 SARS-CoV-2 recovered patients, and 34 uninfected subjects seen by the hospital with unrelated respiratory medical conditions (controls). 16S rRNA sequencing and qPCR analysis was performed on fecal DNA/RNA. The fecal microbial composition was found to be significantly different between SARS-CoV-2 patients and controls (PERMANOVA FDR-P = .004), independent of antibiotic exposure. Peptoniphilus, Corynebacterium and Campylobacter were identified as the three most significantly enriched genera in COVID-19 patients compared to controls. Actively infected patients were also found to have a different gut microbiota than recovered patients (PERMANOVA FDR-P = .003), and the most enriched genus in infected patients was Campylobacter, with Agathobacter and Faecalibacterium being enriched in the recovered patients. No difference in microbial community structure between recovered patients and uninfected controls was observed, nor a difference in alpha diversity between the three groups. 24 of the 50 COVID-19 patients (48%) tested positive via RT-qPCR for fecal SARS-CoV-2 RNA. A significant difference in gut microbial composition between SARS-CoV-2 positive and negative samples was observed, with Klebsiella and Agathobacter being enriched in the positive cohort. No significant associations between microbiome composition and disease severity was found. The intestinal microbiota is sensitive to the presence of SARS-CoV-2, with increased relative abundance of genera (Campylobacter, Klebsiella) associated with gastrointestinal (GI) disease. Further studies are needed to investigate the functional impact of SARS-CoV-2 on GI health.


Subject(s)
COVID-19/microbiology , Gastrointestinal Microbiome , Aged , Bacteria/classification , Bacteria/genetics , Bacteria/isolation & purification , COVID-19/diagnosis , COVID-19/virology , Cohort Studies , Feces/microbiology , Feces/virology , Female , Humans , Male , Middle Aged , RNA, Ribosomal, 16S/genetics , RNA, Viral/genetics , SARS-CoV-2/isolation & purification , SARS-CoV-2/pathogenicity , Severity of Illness Index , United States/epidemiology
14.
Am J Gastroenterol ; 116(8): 1638-1645, 2021 08 01.
Article in English | MEDLINE | ID: mdl-34047305

ABSTRACT

INTRODUCTION: Proton pump inhibitor (PPI) use was recently reported to be associated with increased severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and worse clinical outcomes. The underlying mechanism(s) for this association are unclear. METHODS: We performed a prospective study of hospitalized coronavirus disease 2019 (COVID-19) patients and COVID-negative controls to understand how PPI use may affect angiotensin-converting enzyme 2 (ACE2) expression and stool SARS-CoV-2 RNA. Analysis of a retrospective cohort of hospitalized patients with COVID-19 from March 15, 2020 to August 15, 2020 in 6 hospitals was performed to evaluate the association of PPI use and mortality. Covariates with clinical relevance to COVID-19 outcomes were included to determine predictors of in-hospital mortality. RESULTS: Control PPI users had higher salivary ACE2 mRNA levels than nonusers, 2.39 ± 1.15 vs 1.22 ± 0.92 (P = 0.02), respectively. Salivary ACE2 levels and stool SARS-CoV-2 RNA detection rates were comparable between users and nonusers of PPI. In 694 hospitalized patients with COVID-19 (age = 58 years, 46% men, and 65% black), mortality rate in PPI users and nonusers was 30% (68/227) vs 12.1% (53/439), respectively. Predictors of mortality by logistic regression were PPI use (adjusted odds ratio [aOR] = 2.72, P < 0.001), age (aOR = 1.66 per decade, P < 0.001), race (aOR = 3.03, P = 0.002), cancer (aOR = 2.22, P = 0.008), and diabetes (aOR = 1.95, P = 0.003). The PPI-associated mortality risk was higher in black patients (aOR = 4.16, 95% confidence interval: 2.28-7.59) than others (aOR = 1.62, 95% confidence interval: 0.82-3.19, P = 0.04 for interaction). DISCUSSION: COVID-negative PPI users had higher salivary ACE2 expression. PPI use was associated with increased mortality risk in patients with COVID-19, particularly African Americans.


Subject(s)
Angiotensin-Converting Enzyme 2/blood , COVID-19/blood , COVID-19/mortality , Proton Pump Inhibitors/adverse effects , Adult , Aged , Female , Humans , Male , Middle Aged , Prospective Studies , Retrospective Studies , Risk Assessment
15.
J Allergy Clin Immunol ; 148(3): 813-821.e7, 2021 09.
Article in English | MEDLINE | ID: mdl-33865872

ABSTRACT

BACKGROUND: Hereditary alpha-tryptasemia (HαT) is characterized by elevated basal serum tryptase due to increased copies of the TPSAB1 gene. Individuals with HαT frequently present with multisystem complaints, including anaphylaxis and seemingly functional gastrointestinal (GI) symptoms. OBJECTIVE: We sought to determine the prevalence of HαT in an irritable bowel syndrome cohort and associated immunologic characteristics that may distinguish patients with HαT from patients without HαT. METHODS: Tryptase genotyping by droplet digital PCR, flow cytometry, cytometry by time-of-flight, immunohistochemistry, and other molecular biology techniques was used. RESULTS: HαT prevalence in a large irritable bowel syndrome cohort was 5% (N = 8/158). Immunophenotyping of HαT PBMCs (N ≥ 27) revealed increased total and class-switched memory B cells. In the small bowel, expansion of tissue mast cells with expression of CD203c, HLA-DR, and FcεRI, higher intestinal epithelial cell pyroptosis, and increased class-switched memory B cells were observed. IgG profiles in sera from individuals with HαT (N = 21) significantly differed from those in individuals with quiescent Crohn disease (N = 20) and non-HαT controls (N = 19), with increased antibodies directed against GI-associated proteins identified in individuals with HαT. CONCLUSIONS: Increased mast cell number and intestinal epithelial cell pyroptosis in the small intestine, and class-switched memory B cells in both the gut and peripheral blood associated with IgG reactive to GI-related proteins, distinguish HαT from functional GI disease. These innate and adaptive immunologic findings identified in association with HαT are suggestive of subclinical intestinal inflammation in symptomatic individuals.


Subject(s)
Gastrointestinal Diseases , Genetic Diseases, Inborn , Immunoglobulin G/immunology , Intestine, Small/immunology , Mastocytosis , Tryptases , Adult , Epithelial Cells/immunology , Female , Gastrointestinal Diseases/blood , Gastrointestinal Diseases/genetics , Gastrointestinal Diseases/immunology , Gastrointestinal Diseases/pathology , Genetic Diseases, Inborn/blood , Genetic Diseases, Inborn/genetics , Genetic Diseases, Inborn/immunology , Genetic Diseases, Inborn/pathology , Genotype , Humans , Immunoglobulin G/blood , Intestine, Small/cytology , Intestine, Small/pathology , Male , Mast Cells/immunology , Mastocytosis/blood , Mastocytosis/genetics , Mastocytosis/immunology , Mastocytosis/pathology , Middle Aged , Pyroptosis , Tryptases/blood , Tryptases/genetics , Young Adult
16.
bioRxiv ; 2021 Feb 20.
Article in English | MEDLINE | ID: mdl-33619488

ABSTRACT

Infection with SARS-CoV-2, the virus that causes COVID-19, can lead to severe lower respiratory illness including pneumonia and acute respiratory distress syndrome, which can result in profound morbidity and mortality. However, many infected individuals are either asymptomatic or have isolated upper respiratory symptoms, which suggests that the upper airways represent the initial site of viral infection, and that some individuals are able to largely constrain viral pathology to the nasal and oropharyngeal tissues. Which cell types in the human nasopharynx are the primary targets of SARS-CoV-2 infection, and how infection influences the cellular organization of the respiratory epithelium remains incompletely understood. Here, we present nasopharyngeal samples from a cohort of 35 individuals with COVID-19, representing a wide spectrum of disease states from ambulatory to critically ill, as well as 23 healthy and intubated patients without COVID-19. Using standard nasopharyngeal swabs, we collected viable cells and performed single-cell RNA-sequencing (scRNA-seq), simultaneously profiling both host and viral RNA. We find that following infection with SARS-CoV-2, the upper respiratory epithelium undergoes massive reorganization: secretory cells diversify and expand, and mature epithelial cells are preferentially lost. Further, we observe evidence for deuterosomal cell and immature ciliated cell expansion, potentially representing active repopulation of lost ciliated cells through coupled secretory cell differentiation. Epithelial cells from participants with mild/moderate COVID-19 show extensive induction of genes associated with anti-viral and type I interferon responses. In contrast, cells from participants with severe lower respiratory symptoms appear globally muted in their anti-viral capacity, despite substantially higher local inflammatory myeloid populations and equivalent nasal viral loads. This suggests an essential role for intrinsic, local epithelial immunity in curbing and constraining viral-induced pathology. Using a custom computational pipeline, we characterized cell-associated SARS-CoV-2 RNA and identified rare cells with RNA intermediates strongly suggestive of active replication. Both within and across individuals, we find remarkable diversity and heterogeneity among SARS-CoV-2 RNA+ host cells, including developing/immature and interferon-responsive ciliated cells, KRT13+ "hillock"-like cells, and unique subsets of secretory, goblet, and squamous cells. Finally, SARS-CoV-2 RNA+ cells, as compared to uninfected bystanders, are enriched for genes involved in susceptibility (e.g., CTSL, TMPRSS2) or response (e.g., MX1, IFITM3, EIF2AK2) to infection. Together, this work defines both protective and detrimental host responses to SARS-CoV-2, determines the direct viral targets of infection, and suggests that failed anti-viral epithelial immunity in the nasal mucosa may underlie the progression to severe COVID-19.

17.
Virology ; 516: 21-29, 2018 03.
Article in English | MEDLINE | ID: mdl-29324358

ABSTRACT

During chronic HIV-1 infection, regulatory CD4 T cells (Tregs) frequently represent the largest subpopulation of CD4 T cell subsets, implying relative resistant to HIV-1. When HIV-1 infection of CD4 T cells was explored in vitro and ex vivo from patient samples, Tregs possessed lower levels of HIV-1 DNA and RNA in comparison with conventional effector and memory CD4 T cells. Moreover, Tregs suppressed HIV-1 expression in other CD4 T cells in an in vitro co-culture system. This suppression was mediated in part via multiple inhibitory surface proteins expressed on Tregs. Antibody blockade of CTLA-4, PD-1, and GARP on Tregs resulted in increased HIV-1 DNA integration and mRNA expression in neighboring CD4 T cells. Moreover, antibody blockade of Tregs inhibitory proteins resulted in increased HIV-1 LTR transcription in co-cultured CD4 T cells. Thus, Tregs inhibit HIV-1 infection of other CD4 T cell subsets via interactions with inhibitory cell surface proteins.


Subject(s)
CD4-Positive T-Lymphocytes/immunology , HIV Infections/immunology , HIV-1/genetics , T-Lymphocyte Subsets/immunology , CD4-Positive T-Lymphocytes/virology , CTLA-4 Antigen/genetics , CTLA-4 Antigen/immunology , Gene Expression Regulation, Viral , HIV Infections/virology , HIV Long Terminal Repeat , HIV-1/physiology , Humans , Programmed Cell Death 1 Receptor/genetics , Programmed Cell Death 1 Receptor/immunology , T-Lymphocyte Subsets/virology , T-Lymphocytes, Regulatory/immunology , T-Lymphocytes, Regulatory/virology , Virus Replication
18.
Curr Protoc Immunol ; 118: 14.3.1-14.3.14, 2017 Aug 01.
Article in English | MEDLINE | ID: mdl-28762485

ABSTRACT

Monocytes and macrophages play fundamental roles in defense against microbes, clearance of senescent and dead cells, and immunoregulation. Although blood monocytes are the source of intestinal macrophages in the developed mucosal immune system, blood monocytes and intestinal macrophages from healthy human subjects display distinct phenotypic and functional differences. Blood monocytes can be induced to polarize into M1 and M2 macrophages, whereas intestinal macrophages appear to be terminally differentiated and are unable to undergo such inducible polarization. Nevertheless, in response to local conditions, monocytes differentiated into intestinal macrophages display phenotypic and functional characteristics that enhance their capacity to provide non-inflammatory host defense and participate in local immunoregulation. Using the protocols described here, this unit presents the key phenotypic and functional differences between human blood monocytes and intestinal macrophages, as well as between mouse and human intestinal macrophages. © 2017 by John Wiley & Sons, Inc.


Subject(s)
Intestines/cytology , Macrophages , Monocytes , Animals , Humans , Macrophages/cytology , Macrophages/immunology , Macrophages/metabolism , Mice , Monocytes/cytology , Monocytes/immunology , Monocytes/metabolism , Phenotype , Receptors, Cell Surface/immunology , Receptors, Cell Surface/metabolism
19.
Immunol Lett ; 190: 159-168, 2017 10.
Article in English | MEDLINE | ID: mdl-28823521

ABSTRACT

This review provides an in-depth description of the preclinical and clinical studies demonstrating the effectiveness and limitations of IL-15 and IL-15 analogs given as an exogenous immuno-oncology agent. IL-15 is a cytokine that primarily stimulates the proliferation and cytotoxic functions of CD8T cells and NK cells leading to enhanced anti-tumor responses. While initially showing promise as a cancer therapeutic, the efficacy of IL-15 was limited by its short in vivo half-life. More recently, various approaches have been developed to improve the in vivo half-life and efficacy of IL-15, largely by generating IL-15/IL-15Rα conjugates. These new IL-15 based agents renew the prospect of IL-15 as a cancer immunotherapeutic agent. While having some efficacy in inducing tumor regression as a monotherapy, IL-15 agents also show great potential in being used in combination with other immuno-oncological therapies. Indeed, IL-15 used in combination therapy yields even better anti-tumor responses and prolongs survival than IL-15 treatment alone in numerous murine cancer models. The promising results from these preclinical studies have led to the implementation of several clinical trials to test the safety and efficacy of IL-15-based agents as a stand-alone treatment or in conjunction with other therapies to treat both advanced solid tumors and hematological malignancies.


Subject(s)
CD8-Positive T-Lymphocytes/immunology , Immunotherapy/methods , Interleukin-15/therapeutic use , Killer Cells, Natural/immunology , Neoplasms/therapy , Animals , Cell Proliferation , Clinical Trials as Topic , Cytotoxicity, Immunologic , Humans , Neoplasms/immunology , Protein Stability , Receptors, Interleukin-15/metabolism
20.
Virology ; 504: 79-87, 2017 04.
Article in English | MEDLINE | ID: mdl-28157548

ABSTRACT

Previous in vitro studies have shown that the HIV-1 virus can alter the cytokine/chemokine profile of polarized macrophages which may lead to their increased susceptibility to viral infection. Here, we found that M2 monocyte derived macrophages (MDM) were significantly more permissive to productive infection by R5-tropic HIV-1 strains, including transmitted founder (T/F) viruses, than M1 MDM. Previous in vitro studies by our lab showed that regulatory T cells (Tregs) suppress HIV-1 infection in non-Treg CD4 T cells. Here, we investigated potential inhibitory effects of Tregs on HIV-1 infection of polarized MDM. We found that Tregs significantly increased HIV-1 infection in M1 and M2 MDM via a mechanism that was cell contact dependent. These findings suggest a potential role for Tregs in HIV-1 infection of tissue resident macrophages of M1 and M2 phenotype, which may contribute to the establishment and pathogenesis of HIV-1 disease.


Subject(s)
HIV Infections/immunology , HIV-1/metabolism , Macrophages/immunology , Macrophages/virology , T-Lymphocytes, Regulatory/immunology , Adult , Cell Differentiation/immunology , Cells, Cultured , Cytokines/metabolism , HIV Infections/virology , Humans , Macrophages/cytology , Receptors, CCR5/metabolism , Virus Replication
SELECTION OF CITATIONS
SEARCH DETAIL
...