bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel role of the Type I CRISPR-Cas system in impairing host immunity by targeting endogenous genes
Authors: Wu Min , Li Rongpeng 
Published: January 2023

Abstract
The CRISPR-Cas9 of bacterial adaptive immune systems has garnered intense interests due to its potent and flexible ability to edit genes. However, the role and mechanism of CRISPR-Cas function in bacterial invasion of hosts have remained elusive. We demonstrate that the type I CRISPR-Cas system mediates evasion from host defense via targeting and regulation of bacterial endogenous genes. Our work shows that the CRISPR-cas type I has such a function in Pseudomonas aeruginosa (PA14 strain). The type I CRISPR-Cas system of PA14 modulates quorum-sensing mast regulator LasR to dampen host immunity and inflammatory responses by evading TLR4 recognition. These findings provide insight into the role of Type I CRISPR-Cas system of pathogenic bacteria in the evasion of host immune response, reducing inflammatory response and less resistance to infection. Because we observed a similar evasion mechanism of host defense in other bacteria such as Klebsiella pneumoniae and Escherchia coli, we reasoned that this phenomenon of “self-priming (endogenous target regulation)” is likely applicable other in pathogenic bacteria. Since the type I CRISPR-Cas system and quorum sensing system ubiquitously exist in a variety of bacteria, our findings indicate a potentially common strategy employed by bacteria to evade host immune function, which may have potential therapeutic interest.
Bait and Switch: A strategy to avoid host defense by the ticks
Authors: Bakshi Mariam , Kim Tae , Radulovic Zeljko , Porter Lindsay , Mwangi Waithaka , Mulenga Albert 
Published: January 2023

Abstract
Ticks are obligate haematophagous ectoparasites of animals and humans. In the livestock industry, economic losses due to ticks and tick borne diseases (TBD) amount to million of dollars. In public health, ticks are second to mosquitoes in terms of impact of human diseases. CDC has listed 14 TBD causative agents of which, 9 are transmitted by Amblyomma americanum and Ixodes scapularis. With few exceptions, the transmission of TBD agents requires successful tick feeding. Thus understanding tick-feeding mechanism is a critical step in developing novel methods to stop TBD agent transmission. We know that ticks secrete numerous tick saliva proteins that suppress host immunity to facilitate feeding and disease agent colonization. However, mechanisms of how the tick suppresses host immunity remain unanswered. We investigated the effect of 15 A. americanum and I. scapularis recombinant tick saliva proteins (rTSPs) on murine macrophage function as revealed by expression of pro-inflammatory co-stimulatory markers (CD40, C80, and CD86). Additionally, the effect of rTSP on macrophage secretion of pro- and anti-inflammatory cytokines (TNFa, IL1, IL6, IL-10, TGF beta) was also investigated. Our analysis identified five pro-inflammatory and two anti-inflammatory tick saliva proteins. The two anti-inflammatory proteins appear to reverse the expression of co-stimulatory markers activated by LPS and rTSPs. These data collectively demonstrate the presence of a “bait and switch” mechanism through which the tick may evade host immunity. We propose that ticks secrete two types of immune-modulating proteins: those that stimulate host immune cells and those that dampen the activated cells.
Wnt5a signaling antagonizes Leishmania donovani infection.
Authors: Chakraborty Arijit , Roy Syamal , Sundar Shyam , Sen Malini 
Published: January 2023

Abstract
Leishmania donovani, the causative agent for visceral leishmaniasis creates a niche within host immune cells to sustain itself. In light of the fact that Wnt5a utilizes a Rac1–NFκB circuitry for sustaining immune homeostasis in macrophages and alters actin assembly (Naskar.et.al 2014, Witze et.al 2008) we deciphered whether there is any influence of Wnt5a signaling on L. donovani infection. Upon infection of macrophages with L.donovani, we noted significant decrease in Wnt5a protein levels. Infection with both SAG sensitive and SAG resistant parasite strains yielded similar results. Interestingly, upon treatment of macrophages with recombinant Wnt5a prior to infection separately with SAG senstive and SAG resistant L.donovani, there was significant decrease in the intracellular load of both strains of parasite, as judged by microscopic analysis and expression of Leishmania specific genes (Amastin and G6PDH). Depleting Wnt5a from the macrophages by si-RNA in-vitro or by use of Inhibitor of Wnt Production (IWP2) in-vivo, on the other hand, led to an increase in parasite load. Using specific inhibitors of the Wnt5a signaling intermediates Rac1 and NFκB, we demonstrated that Wnt5a induced reduction in parasite load is due to Wnt5a dependent Rac1 activity but not NFκB signalling. In light of the known involvement of Rac1 in actin organization, the altered actin assembly of Wnt5a pre-treated macrophages, as evident from flow cytometric analysis corroborated the observed Rac1 mediated inhibition of L.donovani infection. Taken together, our results indicate that (i) Wnt5a signaling is detrimental to L. donovani infection and (ii) the parasite evades host immune response at least partly through obliteration of Wnt5a signaling.
Gene expression profile changes in NB4 cells induced by Retinoic Acid and pathogenic bacteria
Authors: Lin Lin , Wang Amy , Bai Ray 
Published: January 2023

Abstract
For several years, we have been developing a cellular immunotherapy based on differentiation of NB4 to neutrophils to treat neutropenia fungal and bacterial infection in neutropenia patients. Here, we report the study of gene expression profiles changed in activated NB4 cells and to elucidate the molecular level associated with retinoic acid (RA) and lethal bacteria. The total RNA was isolated from following samples for cDNA microarray: NB4 cells, induced mature neutrophils from NB4 cells (NB4-PMN), NB4-PMN+Acinetobacter baumannii (AB), NB4-PMN+Staphylococcus aureus (LAC), NB4+AB and NB4+LAC. The analysis of gene expression profiles indicated that after the treatment of RA, RA+AB and RA+LAC, 2 genes were dramatically up-regulated and the other 2 gene were significantly down-regulated; these genes may be related to the differentiation of NB4 cells induced by RA plus pathogenic bacteria and help us improve the NB4 cells differentiation. In addition, this can help us understand the molecular mechanism of activated NB4 cells on how it protects against lethal bacterial infection. Finally, we found that the RA+AB treatment’s result showed similar gene expression when compared to RA’s induction. In contrast, RA+LAC treatment’s result showed different gene expression when compared to the RA’s induction. However, AB and LAC stimulation by themselves didn’t change inactivated NB gene expression profiles.
Nox2-derived oxidative stress results in inefficacy of antibiotics against post-influenza S. aureus pneumonia.
Authors: Sun Keer , Yajjala Vijaya Kumar , Bauer Christopher , Talmon Geoffrey A , Fischer Karl K , Kielian Tammy L , Metzger Dennis W 
Published: January 2023

Abstract
Clinical post-influenza S. aureus pneumonia is characterized by extensive lung inflammation, associated with severe morbidity and mortality even after appropriate antibiotic treatment. In this study, we found that antibiotics rescue NADPH oxidase 2 (Nox2)-deficient mice but fail to fully protect WT animals from influenza and S. aureus coinfection. Further studies indicate that the inefficacy of antibiotics against coinfection is attributable to oxidative stress-associated inflammatory lung injury. However, Nox2-induced lung damage during coinfection was not associated with aggravated inflammatory cytokine response or cell infiltration but rather due to reduced survival of myeloid cells. Specifically, oxidative stress increased necrotic death of inflammatory cells, thereby resulting in lethal damage to surrounding tissue. Collectively, our results demonstrate that influenza infection disrupts the delicate balance between Nox2-dependent antibacterial immunity and inflammation. This disruption not only leads to increased susceptibility to S. aureus infection but also extensive lung damage. Importantly, we show that combination treatment of antibiotic and NADPH oxidase inhibitor significantly improved animal survival from coinfection. These findings suggest that treatment strategies that target both bacteria and oxidative stress will significantly benefit patients with influenza-complicated S. aureus pneumonia.
Innate Immune Response to Respiratory Syncytial Virus-like Particles: Comparison with the Parental Virus
Authors: Walpita Pramila 
Published: January 2023

Abstract
Respiratory Syncytia Virus (RSV) virus-like particles (VLPs) composed of of the two surface glycoproteins G, and F, and M protein self-assemble into VLPs. Both morphologically and immunologically, and are seen by the host cell as the real virus. RSV VLPs with adjuvant showed protection of the the lung and nose while RSV without adjuvant no protection in either site, while RSV without adjuvant provided to no protection in either site. To unravel the mystery behind the poor protection, we evaluated RSV VLPs-induced innate immunity and characterized RSV VLP-mediated cytokine response using human monocytic THP-1 cell line. Using PCR array we tested innate immune gene expression. We show that both the virus and the VLPs induced IFN-1β, pSTAT2 and interferon-stimulated genes (ISGs), namely ISG-15, ISG-56, IP-10 OAS-1 and MxA, suggesting the antiviral state in both cases. RSV-mediated induction of IFN-1β and ISG-15 seemed partially dependent on TLR-4, whereas RSV VLP-mediated induction of IFN-1β and the same ISGs was entirely dependent on TLR-4. Array data demonstrated that RSV signaled through MYD88 while RSV VLPs signaled through IRAK2, inducing NFKB activation. Furthermore, both RSV VLPs and RSV induced a Th1-biased cytokine response; however the RSV-induced responses were much weaker. Taken together, these findings suggest that RSV VLPs have several intrinsic properties that would make an effective and safe vaccine candidate when formulated with adjuvants.
Functional characterization of T cells that recognize modified epitopes in patients with type 1 diabetes
Authors: Nguyen Hai T , Arribas-Layton David , Chow I-Ting , Greenbaum Carla , Marre Meghan L. , Piganelli Jon D , Kwok William , James Eddie A 
Published: January 2023

Abstract
Selective recognition of self-proteins that have undergone enzymatic post-translational modification (PTM) by CD4+ T cells is increasingly implicated as a means of potentiating the loss of tolerance in autoimmune diseases such as type 1 diabetes (T1D). In particular, enzymatic deamidation and citrullination of beta cell derived peptides at HLA anchor residues enhances their presentation by high risk alleles (DR4 and DQ8). Modification of residues outside of binding pockets alter T cell recognition, resulting in enhanced proliferation and increased cytokine production. Our work demonstrates that CD4+ T cells specific for PTM epitopes are present in the peripheral blood of patients with T1D at significantly higher ex vivo frequencies than in HLA matched controls. Upon re-activation, PTM specific T cells from T1D patients produce elevated levels of effector cytokines, most notably interferon gamma. Among T1D patients, we observed heterogeneous frequencies of PTM specific T cells with a range of functional profiles. This led us to hypothesize that activation of a PTM specific T cell response is of particular significance in a subset of T1D patients. To test this hypothesis we compared the ex vivo frequency and functional profiles of PTM specific T cells in a cross sectional cohort of patients selected to include diverse levels of residual c-peptide. Our findings implicate a mechanistic role for PTMs in exacerbating autoreactive T cell responses in T1D.
Dual regulatory role of c-Rel O-GlcNAcylation in T cell function and Type 1 Diabetes
Authors: Tomalka Jeffrey Alan , Ramakrishnan Parameswaran 
Published: January 2023

Abstract
O-GlcNAcylation is a post-translational protein modification involving the addition of N-acetylglucosamine (GlcNAc) to serine and threonine residues on target proteins. Global O-GlcNAcylation levels rise under hyperglycemia such as that caused by Type 1 Diabetes (T1D). We found that hyperglycemia induces O-GlcNAcylation of the NF-kappaB protein c-Rel at a single serine residue, S350. O-GlcNAcylation of c-Rel enhances its DNA binding and the transcription of c-Rel-dependent pro-autoimmune Th1 cytokines in T cells. This direct link between hyperglycemia and augmented Th1 function imply a key regulatory role for c-Rel O-GlcNAcylation in the pathology of T1D. Interestingly, our recent results show that O-GlcNAcylation inhibits binding of c-Rel to the FOXP3 promoter, leading to reduced FOXP3 expression. Together, these data suggest that c-Rel O-GlcNAcylation has a novel, dual regulatory role in controlling T cell function by: 1) Enhancing pro-autoimmune T cell function and 2) Suppressing Treg function. This creates an immune environment prone to heightened inflammation and autoimmunity that may exacerbate the frequency of autoimmunity in Western countries. Our current work focuses on defining the molecular mechanisms by which c-Rel O-GlcNAcylation regulates transcriptional activation in T cells and Treg cells. We are studying the non-obese diabetic (NOD) mouse model of spontaneous diabetes to examine the pathophysiological role of c-Rel O-GlcNAcylation. Knowledge on the regulation of autoimmunity by c-Rel O-GlcNAcylation will enhance our understanding of the etiology immune-mediated pathologies in diabetes and reveal a new therapeutic target to treat autoimmune diabetes.
HIGH-DIMENSIONAL ANALYSIS OF HUMAN REGULATORY T CELLS USING MASS CYTOMETRY
Authors: Dawson Nicholas , Cook Laura , Pesenacker Anne , Hoeppli Romy , Morishita Kimberly , Broady Raewyn , Levings Megan K 
Published: January 2023

Abstract
Regulatory T cells (Tregs) are critical for maintenance of peripheral tolerance in a variety of tissues. Evidence that Tregs seem to be a phenotypically diverse population that varies between individuals and tissues suggests that there may be functionally-specialized subsets of Tregs which vary depending on location and/or disease state. We developed a new mass cytometry-based method to measure FOXP3 in combination with 20 other parameters to characterize the phenotype of human Tregs in different tissues, and to enable analysis of antigen-specific cells. We first developed a protocol to detect FOXP3, the Treg lineage-defining transcription factor, via mass cytometry. We found this optimized protocol is more sensitive than commercially-available methodology to detect FOXP3 by mass cytometry and is compatible with staining of other intracellular targets such as cytokines and other transcription factors. To ask how Treg populations differ depending on location and disease state, we stained mononuclear cells from adult peripheral blood, pediatric thymus and cord blood, as well as synovial fluid from pediatric subjects with juvenile idiopathic arthritis with our Treg-specific mass cytometry panel. The resulting data were analyzed using several bioinformatics approaches including viSNE and revealed diversity in the heterogeneity and phenotype of Tregs depending on their origin. The ability to stain FOXP3 using mass cytometry will facilitate the further characterization of Tregs in health versus disease and help us understand how Tregs are functionally specialized in the context of different tissues and disease.
Loss of SOCS1 in dendritic cells increases dendritic cell maturation and decreases the CD8 T cell response to Listeria monocytogenes.
Authors: Alice Alejandro , Kramer Gwen , Crittenden Marka R , Bahjat Keith , Gough Michael J 
Published: January 2023

Abstract
The suppressor of cytokine signaling (SOCS) family is a group of structurally related proteins characterized by a central SH2 domain that targets the SOCS proteins to specific molecules within the JAK-STAT pathway, and a SOCS-box domain that promotes degradation of the cytokine-receptor complex. SOCS-1 is induced by cellular activation and serves as a negative feedback mechanism for a range of cytokines. It has been described that silencing SOCS-1 in dendritic cells (DC) enhances antigen presentation, T cell priming, and anti-tumor immunity. Therefore, inhibition of SOCS-1 could profoundly augment the potency of the L. monocytogenes (Lm) based cancer vaccines that we are testing in clinical studies. We questioned the role of SOCS-1 in dendritic cells in vivo during intracellular infection, a scenario where antigen-specific T cells are required for microbial clearance. To test this we characterized the infection and immune response to Lm in CD11c-Cre × SOCS1fl/fl mice that have a SOCS1 deficiency in DC. DC lacking SOCS1 showed increased maturation in vivo at baseline, but showed equivalent responses to vaccination with DC-targeted antigens combined with α-CD40. We found that Lm can be recovered from spleens and livers from mice with SOCS1-deficient DC at similar levels to that of the wild type animals. However, mice with SOCS1-deficient DC showed a dramatic defect in the specific-CD8+ T cell response while the specific-CD4+ T cells response was not affected. The lack of CD8+ T cells response correlated with low levels of IFN-γ and MCP-1 in serum during the first days of infection and decreased NK maturation. Our results demonstrate that SOCS1 expression in DC is critical to generate a strong CD8 T cell response to Lm.
The Nrf2 activator, tBHQ, inhibits IL-2 production by human T cells in a largely Nrf2-independent manner
Authors: Zagorski Joseph Ward , Turley Alexandra E , Maser Tyler P , Rockwell Cheryl Elizabeth 
Published: January 2023

Abstract
Nrf2 is a transcription factor that is activated by cell stress, such as oxidative insult and exposure to xenobiotics. Upon activation, Nrf2 translocates to the nucleus, where it upregulates its target genes, many of which arecytoprotective in function. Nrf2 has been shown to modulate immune function; Nrf2-null mice are more sensitive to many models of inflammatory disease, including experimental autoimmune encephalitis and sepsis induced by cecal ligation and puncture. We have previously shown that activation of Nrf2 in primary mouse CD4 T cells promotes Th2 differentiation, which may have implications on the development of allergy and asthma. However, the role of Nrf2 in human CD4 T cell function remains uncharacterized. Thus, the purpose of the present studies was to determine the role of Nrf2 in the early events following CD4 T cell activation. Primary human CD4 T cells from peripheral blood were treated with varying concentrations of tBHQ (a known Nrf2 activator) prior to activation with anti-CD3/anti-CD28. Although treatment of human T cells with tBHQ suppressed the production of early cytokines, such as IL-2, the model fell short in determining whether these effects were Nrf2-dependent. Toward that end, Nrf2-null T cells were generated by implementation of CRISPR-CAS9 gene editing, in human Jurkat T cells. Treatment of Nrf2-null and Wild-type Jurkat T cells demonstrated that the effects of tBHQ upon cytokine production are largely independent of Nrf2. In contrast, suppression of CD25 expression by tBHQ is partially Nrf2-dependent. The current studies demonstrate that many of the effects of tBHQ on early events following CD4 T cell activation are independent of Nrf2. (This work was funded by NIH grants ES018885 and GM092715)
ADAMTS5: A critical enzyme for the maintenance of influenza-specific CD8+ T cell memory
Authors: McMahon Meagan K , McCulloch Daniel , Stambas John 
Published: January 2023

Abstract
Extracellular matrix (ECM) enzymes, such as the ADAMTS (A disintegrin-like and metalloproteinase with thrombospondin-1 motifs) family, play a significant role in ECM remodelling. ECM remodelling facilitates immune cell migration and adhesion. ADAMTS5, a member of the ADAMTS family, cleaves ECM proteoglycans, such as aggrecan and versican, and has a well-characterised role in osteoarthritis and embryogenesis. However, ADAMTS5 has an un-identified role throughout the immune response. Our previous studies indicated that ADAMTS5 expression is required to mediate T cell migration during acute influenza virus infection. In this current study, we analysed secondary acute responses (day 7) and primary memory (day 30) following influenza infection of Adamts5−/− mice. Here, we primed Adamts5−/− mice with PR8 influenza virus (1.5×107 pfu/mouse) and challenged 8 weeks later with X31 influenza virus (104 pfu/mouse). Following secondary infection, Adamts5−/− mice displayed greater weight loss and expressed fewer IFNγ+NP366-372+CD8+T cells. Critically, we observed a reduced number of influenza-specific CD8+ memory cells (CD62LhiCD44lo) in Adamts5−/− mice after primary infection, which may result in the lower number of IFNγ+NP366-372+CD8+T cells observed in secondary acute infection. We therefore hypothesize that the ADAMTS5 enzyme, through its ECM remodelling capabilities, is essential for the maintenance of memory and recall of functional immunity following secondary infection.
Specific patterns of self-antigen expression determine the mechanisms by which polyclonal self-reactive CD4+ T cells are tolerized.
Authors: Malhotra Deepali , Linehan Jonathan L , Dileepan Thamotharampillai , Lee You Jeong , Purtha Whitney E , Lu Jennifer V , Nelson Ryan W , Fife Brian T , Orr Harry T , Anderson Mark S , Hogquist Kristin A , Jenkins Marc K 
Published: January 2023

Abstract
Understanding how self-tolerance is maintained requires the ability to track rare, self-reactive T cells of known specificity in normal individuals. However, due to technical limitations much of our knowledge has relied on the study of T cell receptor transgenic cells that recognize model antigens. While this work has identified numerous modes of tolerance, it is unclear which mechanisms operate in normally diverse repertoires and how this decision is made. We studied polyclonal CD4+ T cells specific for an epitope from green fluorescent protein (GFP) in fourteen different mouse strains that express GFP under the control of tissue-specific promoters. We found that clonal deletion was the key tolerance mechanism for self-antigens that were uniformly expressed by thymic antigen-presenting cells. In contrast, self-antigens that were absent from the thymus were ignored. A more complex form of tolerance regulated CD4+ T cells specific for self-antigens with limited expression by thymic antigen-presenting cells. These populations showed partial clonal deletion and impaired effector T cell potential but enhanced regulatory T cell potential of remaining cells. Furthermore, these tolerance mechanisms were also found to regulate CD4+ T cells specific for endogenously expressed self-antigens. Thus, self-antigen expression patterns dictate the tolerance mechanisms by which self-reactive polyclonal CD4+ T cells are regulated.
Tissue-specific antigens induce dual complementary T cell tolerance mechanisms
Authors: Martinez Ryan J , Blanchfield Lori , Barwick Benjamin , Martinez Hunter , Reid Hugh , Evavold Brian D 
Published: January 2023

Abstract
To understand tolerance mechanisms to tissue-specific antigens, we probed the development of polyclonal T cells specific for myelin oligodendrocyte glycoprotein (MOG), a myelin antigen targeted during autoimmune demyelinating disease. We find T cell tolerance occurs via two thymocyte selection processes. First, the presence of tissue-specific antigen intrinsically broadens the TCR repertoire to lower overall reactivity of effector T cells. Second, expression of MOG extrinsically induces a higher frequency of more efficacious antigen-specific Foxp3+ regulatory T cell population that prevents autoimmunity. Interestingly, clonal deletion mediated by thymocyte negative selection of high-affinity T cells was not apparent. Thus, cooperative tolerance exists to prevent autoimmunity towards tissue-specific antigens.