bluuebunny/crossref_metadata_2025_split huggingface dataset:
Capsule-dependent metabolic immunosuppression of host cells by Francisella tularensis
Authors: Stromberg Kaitlin A , Jessop Forrest , Schwarz Benjamin , Wehrly Tara , Bosio Catharine M 
Published: February 2023

Abstract
Francisella tularensis subsp. tularensis (Ftt) is a highly pathogenic, intracellular bacterium capable of replicating while avoiding detection by the host immune system. An O-antigen polysaccharide capsule has been identified as an important virulence factor involved in suppressing the immune response. Previous studies have shown that Ftt capsule limits the metabolic shift from oxidative phosphorylation to glycolysis needed for activation of host defense mechanisms. The specific mechanism by which Ftt capsule alters host metabolism is not fully understood but involves improvement of mitochondrial function. In this study, central metabolism in primary cell culture was mapped using targeted metabolomics following TLR stimulation and capsule treatment. Consistent with previous findings, capsule stimulated TCA cycle activity to increase mitochondrial respiration. Ftt capsule treatment did not inhibit increased glycolytic flux associated with TLR-induced metabolic activation. However, capsule limited accumulation of lactate and depletion of acetyl-CoA pools associated with TLR-driven uncoupling of glycolysis and the TCA cycle. These data point to capsule-dependent manipulation of pyruvate dehydrogenase, the enzyme responsible for converting pyruvate made during glycolysis into acetyl-CoA for utilization within the TCA-cycle. Together, these results demonstrate a novel mechanism by which a bacterial capsule can limit inflammation by maintaining coupling of central metabolic pathways.
Functional CFTR channel is essential for effective antimicrobial activities of neutrophils
Authors: Avila Frank Hanz Robledo , Kopp Benjamin T , Partida-Sanchez Santiago 
Published: February 2023

Abstract
Patients with Cystic Fibrosis (CF) are highly susceptible to infections caused by opportunistic pathogens including Burkholderia cenocepacia. In response to infection, CF neutrophils are deficient in clearing bacteria and release inflammatory molecules that contributes to aggravated lung-tissue damage in people with CF (PWCF). Although CF has no cure, novel therapeutic drugs have emerged targeting defective CFTR channel (CFTR modulators). However, it is unknown whether CFTR modulators may restore the basic antimicrobial functions of phagocytes in PWCF.
Here, we first evaluated the expression and subcellular localization of CFTR. Neutrophils from PWCF and non-CF donors were treated in vitro with CF modulators, before infection with B. cenocepacia, and then, CFTR cellular localization was evaluated by confocal microscopy followed by the analysis of antimicrobial killing, and the production of Neutrophil Extracellular Traps (NETs). Furthermore, CFTR-mediated currents were measured by patch-clamp in non-CF and CF neutrophils after treatment with the CFTR modulators.
We found that CFTR modulators increased the expression of functional CFTR channel at the plasma membrane, and also potentiated CFTR-mediated channel activity in CF and non-CF neutrophils, as recorded by whole-cell patch clamp. The production of NETs was also increased in both CF and non-CF neutrophils treated with CFTR modulators, those changes were comparable to cells stimulated with B. cenocepacia or PMA. Finally, CF neutrophils treated with the CFTR modulators restored their antimicrobial killing against B. cenocepacia. Together, these data indicate that functional CFTR channel is essential for regulating the antimicrobial mechanisms of neutrophils.
Maternal high fat diet interacts with the maternal microbiome to expand IL-17 producing type 3 innate lymphoid cells in offspring.
Authors: Mirpuri Julie , Lu Dongmei , Niu Xinying , Mahendroo Mala 
Published: February 2023

Abstract
Introduction: Previously, we demonstrated that maternal high fat diet (mHFD) exposure results in a unique pattern of microbial colonization in offspring and subsequent expansion of IL-17 producing type 3 innate lymphoid cells (ILC3). We hypothesized that in utero mechanisms involving the maternal microbiome were responsible for the phenotype in offspring.

Methods:
To assess if the maternal microbiome was responsible for altering the mHFD offspring phenotype, we delivered mHFD and regular diet (RD)-exposed pups at birth by C-section (CS) and exposed mHFD mothers to broad-spectrum antibiotics (ABX) throughout pregnancy. We cross-fostered the offspring to RD mothers at birth. Microbial colonization in 2-week-old offspring was determined by 16s-based rRNA analysis, intestinal cytokines were quantified by qRT-PCR and lamina propria cells (LP) were profiled by flow cytometry. To determine if innate immunity is altered prenatally by maternal diet, we delivered mHFD and RD offspring by CS and examined the small intestine (SI) at birth for cytokine expression, TLR signaling and LP profiling. Global MyD88 KO mice on mHFD or RD were also examined for the same endpoints.

Results:
mHFD offspring at 2-weeks showed an expansion of Firmicutes and IL-17 producing ILC3, independent of the mode of delivery. ABX in mHFD mothers ameliorated the mHFD offspring phenotype, with microbial colonization and ILC3 similar to controls. mHFD offspring had altered TLR signaling at birth in SI. ILC3 were expanded at birth in mHFD offspring (14.2% vs 9.5%). MyD88−/− offspring exposed to mHFD did not have an expansion of ILC3.

Conclusion:
mHFD prenatally alters the offspring microbiome and ILC3 and this effect is dependent on the maternal microbiome and TLR signaling.
B cells in the mesenteric fat contribute to Crohn’s disease
Authors: Erlich Emma , Czepielewski Rafael Sanguinetti , Kumar Shashi , Andhey Prabhakar Sairam , Artyomov Maxim N. , Ellebedy Ali H. , Randolph Gwendalyn J 
Published: February 2023

Abstract
Crohn’s disease [CD] is one of the two common forms of inflammatory bowel disease and it affects over half a million Americans. Like many other diseases marked by chronic inflammation, some patients with CD develop tertiary lymphoid organs [TLO] in regions of the gut with active disease. TLOs are organized clusters of adaptive immune cells, similar in function and structure to secondary lymphoid organs. Recently, we found B cell rich lymphoid aggregates in the mesenteric fat of CD patients positioned along dramatically remodeled lymphatic vessels, but their function, specifically of the B cells within these aggregates, is completely unknown. Using complementary imaging, flow cytometry, and single cell RNA sequencing approaches, we analyzed B cells present in the mesenteric fat from CD patients. Whereas B cells were essentially not present in the mesentery under homeostatic conditions, they were significantly increased in the inflamed mesenteric fat of CD patients. Single cell RNA sequencing data revealed differences in B cell populations in the mesenteric fat that potentially implicate B cells as contributing to lymphangiogenesis associated with TLOs. Simultaneously, we used a murine model of ileal inflammation to probe mechanism. Imaging and flow cytometry showed that the B cells in TLOs from TNFΔARE/+mice were comparable to the B cells from CD patients. Additionally, TNFΔARE/+/μMT mice, which lack B cells, further revealed that B cells may be required for the lymphatic remodeling seen in the mesentery.
Cross-neutralizing antibody recognition of sarbecoviruses
Authors: Liu Hejun , Yuan Meng , Lee Chang-Chun D. , Wu Nicholas C. , Wilson Ian A. 
Published: February 2023

Abstract
The ongoing COVID-19 pandemic has been devasting to public health and global economy, with more than 82 million confirmed cases and 1.8 million deaths in 2020. Vaccines and antibody therapies are currently under emergency use authorization and provide hope to slow down and eventually stop the spread of SARS-CoV-2 infection. However, the continued identification of SARS-CoV-2 mutants as well as reciprocal transmission between human and farmed mink raise concerns on antigenic drift of SARS-CoV-2 and potential escape from current vaccines. Despite potent and versatile antibody responses to the receptor binding site of the SARS-CoV-2 spike protein, cross-neutralizing antibodies isolated from COVID-19 patients are relatively rare. We have been characterizing these rare cross-neutralizing antibodies using high-resolution X-ray crystallography, as well as other biophysical methods. These antibodies neutralize SARS-CoV-2 and SARS-CoV pseudotyped viruses and are cross-reactive with the receptor binding domain of several sarbecoviruses tested. Our structures have revealed the location of the conserved epitopes that lead to cross-neutralization and the different neutralization mechanisms used by these antibodies. Our findings provide insights for developing more universal SARS-like coronavirus vaccines and therapies to combat antigenic drift in SARS-CoV-2 as well as potential epidemics of other zoonotic coronaviruses.
Glycan-reactive natural antibodies mediate blockade of endogenous retroviruses emergence
Authors: Yang Yexin , Treger Rebecca S. , Hernandez-Bird Juan , Iwasaki Akiko 
Published: February 2023

Abstract
Endogenous retroviruses (ERVs), comprising a substantial portion of the vertebrate genome, are remnants of ancient genetic invaders. Although multiple layers of cell-intrinsic control are utilized to prevent retroviral reactivation, ERVs with intact coding potential are able to reactivate in immunodeficient mice. While previous studies have indicated that B cells are indispensable for preventing ERV reactivation, it is not yet clear which B cell population mediates the blockade of ERV emergence to prevent subsequent damage in the host. Here, we employed direct labeling of B cells reactive with emerged ERV particles to characterize the B cell population and clonal repertoire responsible for recognition of ERV, and to study the mechanism by which B cells provide protection against ERV emergence. We found that ERV-reactive B cells are enriched in innate-like B-1 cell compartment that predominantly reside in peritoneal and pleural cavities. B-1 cells specificity is biased toward conserved epitopes shared by bacterial- and self-antigens due to distinct developmental pathways in fetal haematopoiesis. We identified ERV-reactive antibodies in unimmunized mice, the level of which further increases upon innate sensor stimulation. B cell receptor repertoire profiling of ERV-reactive B-1 cells revealed increased usage of Igh VH genes that give rise to glycan-specific antibodies targeting glycan structures exhibited by bacterial and viral antigens. We demonstrated that these glycan-specific natural antibodies engage complement pathway to facilitate clearance of reactivated ERV particles. In conclusion, we elucidated the role of glycan-specific B-1 cells and secreted natural antibodies in mediating blockade of ERV emergence.
Epitope-resolved profiling of the SARS-CoV-2 antibody response identifies cross-reactivity with endemic human coronaviruses
Authors: Altin John , Ladner Jason T , Kainov Denis , Shiryaev Sergey , Henson Sierra , Boyle Annalee , Rahee Fatima , Engelbrektson Anna 
Published: February 2023

Abstract
The SARS-CoV-2 proteome shares regions of conservation with endemic human Coronaviruses (CoVs), but it remains unknown to what extent these may be cross-recognized by the antibody response. Here, we study cross-reactivity using a highly-multiplexed peptide assay (‘PepSeq’) to generate an epitope-resolved view of IgG reactivity across all human CoVs in both COVID-19 convalescent and negative donors. PepSeq resolves epitopes across the SARS-CoV-2 Spike and Nucleocapsid proteins that are commonly targeted in convalescent donors, including several sites also recognized in some uninfected controls. By comparing patterns of homologous reactivity between CoVs and using targeted antibody-depletion experiments, we demonstrate that SARS-CoV-2 elicits antibodies that cross-recognize pandemic and endemic CoV antigens at two Spike S2 subunit epitopes. We further show that these cross-reactive antibodies preferentially bind endemic homologs. Our findings highlight sites at which the SARS-CoV-2 response appears to be shaped by previous CoV exposures and which have potential to raise broadly-neutralizing responses.
IgG Antibodies against SARS-CoV-2 Correlate with Days from Symptom Onset, Viral Load and IL-10
Authors: Young Mary K , Kornmeier Christine , Carpenter Rebecca , Natale Nick , Sasson Jennifer , Solga Michael , Mathers Amy , Poulter Mendy , Qiang Xiao , Petri William A. 
Published: February 2023

Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in a pandemic of coronavirus disease 2019 (COVID-19). Antibody testing is essential to identify persons exposed to the virus and potentially predicting immunity. 183 COVID-19 patients (68 mechanically ventilated) and 41 controls were tested for plasma IgG, IgA and IgM against the SARS-CoV-2 S1, S2, receptor binding domain (RBD) and N proteins using the MILLIPLEX® SARS-CoV-2 Antigen Panels. COVID-19 positive patients had high levels of IgG, IgA and IgM anti-SARS-CoV-2 antibodies against viral proteins. Sensitivity of anti-S1 IgG increased from 60% to 93% one week after symptom onset. S1-IgG and S1-IgA had specificities of 98%. Ventilated COVID-19 patients had higher antibody levels than the COVID-19 patients who were not ventilated. IgG antibody levels against S1 protein had the strongest correlation to days from symptom onset. We found that patients with the highest IgG levels had the lowest viral load. Finally, there was a correlation of high plasma IL-10 with low anti-SARS-CoV-2 IgG.
ScRNA-seq of Rashes Shows Recurrent Downregulation of the RNA-binding protein ZFP36L2, Revealing Its Role In Mediating Human T cell Cytokine Repression
Authors: Cheng Jeffrey , Liu Yale , Cook Christopher , Cho Raymond 
Published: February 2023

Abstract
The mechanisms driving inflammatory disease are incompletely understood. We performed single-cell RNA-seq on immune cells isolated from 24 human inflammatory skin disease samples of atopic dermatitis, psoriasis, and lichen planus and identified the RNA-binding protein ZFP36L2 as a recurrently repressed transcript in T cells (log FC = −0.85; adjPval &lt; 0.001). CRISPR/Cas9-mediated disruption of ZFP36L2 in unstimulated primary human T cells resulted in a greater than 5-fold induction of inflammatory cytokines (e.g. TNF-α (p = 0.008), GM-CSF, (p = 0.002), IFN-γ (p = 0.030), and IL-13 (p = 0.044)), with minimal effect in stimulated T cells. This greater effect prior to stimulation suggests a role for ZFP36L2 in repressing the onset of inflammation. Consistent with this, temporal analysis of ZFP36L2 and cytokine T cell response to inflammatory stimuli displays ZFP36L2 transcript downregulation prior to induction of cytokine transcripts. These results reveal a previously unknown early, central regulatory role for ZFP36L2 in human inflammation and cutaneous disease, suggesting a potential target for therapeutic exploitation.
Respiratory exposure to putative Gulf War toxins induces phenotypic and transcriptional alterations with effector dysfunction in alveolar macrophages
Authors: Powers Amy A , Jones Katherine E , Eisenberg Seth H , Rigatti Lora H , Luketich James D , Lotze Michael T. , LaRue Amanda C , Dhupar Rajeev , Soloff Adam C 
Published: February 2023

Abstract
Respiratory disorders including chronic obstructive pulmonary disease, asthma, and increased susceptibility to lung infections are a prominent component of Gulf War Illness (GWI). Although the mechanisms of GWI are unknown, chronic immune dysfunction is a consistent factor of this multi-symptomatic disorder. Alveolar macrophages (AMs) represent the predominant mononuclear phagocytes of the pulmonary mucosa, orchestrating the host response to pathogens and environmental stimuli via balanced induction of inflammatory, anti-inflammatory, and pro-resolution mediators. Utilizing commercially available instrumentation, we evaluated the effect of aerosolized exposure to two putative GW toxins, the pesticide malathion and diesel exhaust particulate (DEP), on the immune composition and inflammatory response of the lung in FVB/N mice. Toxin exposure resulted in gross lung pathology with variable increases in protein, lactose dehydrogenase, and cytokines in bronchoalveolar lavage (BAL). Aerosolized toxin exposure reduced AMs in the lung and BAL, associated with a shift to wound-healing phenotypes and concomitant influx of monocyte-derived progenitors from the circulation. Exposure to DEP and malathion, either alone or in combination, induced varying levels of dysfunction in flow-sorted AMs ex vivo as determined by inhibited migration, cytokine production, and phagocytosis. Toxin-induced alterations were associated with unique transcriptional profiles following RNA sequencing analysis. Collectively, these findings suggest that respiratory toxin-induced macrophage dysfunction may establish a state of frustrated immune resolution underlying the chronic immunopathology of respiratory GWI.
The Impact of Aging on Antiviral Pathways and Consequences for Immune Function
Authors: Connors Jennifer R , Kutzler Michele A. , Haddad Elias 
Published: February 2023

Abstract
It is known that aging leads to increased morbidity and mortality, however, this has become more of a concern as the world population shifts to an increased percentage of older adults (&gt;65) especially for COVID-19. These deaths may be from immunosenescence, a condition of chronic increased level of basal inflammation which can also result in diminished vaccine responses and immune system dysregulation, leading to COVID-19 complications. Current research shows a decrease in pro-inflammatory cytokines but the downstream signaling pathways in the context of aging have yet to be evaluated. Two critical pathway points in the production of type I IFN are the phosphorylation of pIRF7 in the TLR 7/8 pathway and of pTBK-1 in the RIG-I and cGAS-STING pathways. We show a decrease in pIRF7 and pTBK-1 in cDC1s, cDC2s, and CD14dimCD16+vascular patrolling monocytes from older adults (n=12) following stimulation with pathway specific agonists in comparison with healthy controls (n=12). This decrease correlates with decreased phagocytosis in the same cell subsets. These data support our previous reports of a delayed and decreased pro-inflammatory output following stimulation and demonstrate potential targets of antiviral pathways that can resolve dysfunctions of the aging immune system for an effective vaccination response. Therefore, we further hypothesize that cDC1, cDC2, and CD14dimCD16+ from older adults will have reduced antigen presentation and ability to cross-present viral peptides. We will utilize COVID-19 patient samples (n=110) to assess antigen-specificity of DCs and T cells in older COVID-19 pos. patients vs healthy controls (n=12).
CD40 intracellular TRAF binding domains modulate B cell activation and experimental autoimmune encephalomyelitis development
Authors: Xu Max , Lu Ying , Zhang Ray , Chiang Jeffrey , Hodes Richard J. 
Published: February 2023

Abstract
CD40 is a costimulatory surface protein expressed on multiple immune cells, including B cells, where it is required for their full activation. Upon interacting with CD40 ligand, CD40 initiates downstream signaling that culminates in activation of naïve B cells. Previous work from our lab revealed that cell autonomous expression of CD40 on B cells regulates their activity, including germinal center development and antibody class switching. Intracellular (IC) domains of the CD40 protein are crucial for signaling. Several of these domains are known to be associated with TNF receptor associated factor proteins (TRAFs) which facilitate further downstream signaling. These include a TRAF6 binding domain and a TRAF2/3 binding domain. We analyzed the CD40 IC domain requirements for CD40 signaling in B cells and for induction of experimental autoimmune encephalomyelitis (EAE). To do so, multiple mouse strains were generated with elimination of the putative TRAF6 or TRAF2/3 domains by CRISPR technology. Whereas eliminating the putative TRAF6 binding site (Domain 1) had little to no effect on B cell viability and in vitro activation by anti-CD40 antibody, eliminating the putative TRAF2/3 binding site (Domain 2) impaired both these functions. Similarly, generation of high affinity IgG in vivo was also dependent on Domain 2 but not Domain 1. In contrast, both Domain 1 and Domain 2 were required for full development of EAE. Interestingly, mixed BM chimeras revealed that the ameliorating effect of CD40 mutations on EAE was mediated by hematopoietic derived non-B cells. Our results indicate that the CD40 TRAF2/3 binding Domain 2 is critical for CD40 dependent B cell function, while both Domain 1 and Domain 2 expression by other APCs function in EAE induction.
Complement Factor H regulates kidney function by modulating macrophages
Authors: Alexander Jessy John , Okamura Kazuki , Jacob Alexander , Chaves Lee Daniel 
Published: February 2023

Abstract
The complement system is a powerful arm of the innate immune system. Complement factor H (CFH) is a critical regulator of the complement system and CFH abnormalities have been implicated in diseases such as dense deposit disease, atypical hemolytic syndrome and age related macular degeneration. Earlier studies from our lab showed that absence of CFH rendered the, normally resistant, C57BL6 mouse susceptible to immune complex mediated glomerulonephritis. CFH knockout mice developed proliferative glomerulonephritis with endocapillary F4/80+ macrophage (Mϕs) infiltration. Nanostring assessment of wild type (WT) and CFHKO kidneys using mouse myeloid panel and stringent analysis revealed that of the 754 genes on the array, 18 macrophage related genes were decreased with at least 1.5 fold change and p&lt;0.05. We therefore studied the role of Mϕs in this setting. Depletion of Mϕs with liposomal clodronate was protective from disease pathology as assessed by BUN, histology, and reduced expression of laminin. For the first time, our studies show that Mϕs isolated from WT mice and grown in culture express intrinsic CFH. Therefore to understand whether the changes are induced by intrinsic Mϕ CFH or CFH in circulation, we have grown bone marrow derived Mϕs from CFH KO and WT mice. Metabolic bioenergetics was markedly impaired in Mϕs deficient in CFH. Since oxidative phosphorylation enables repolarization, our results suggest that modulation of mitochondrial function by complement and thereby reprogramming of inflammatory Mϕs could be a therapeutic avenue in this setting.