bluuebunny/crossref_metadata_2025_split huggingface dataset:
M. tuberculosis Mce3C promotes mycobacterial mammalian cell entrance and enhances mycobactrial intracellular survival.
Authors: Liu Cui Hua , Li Jie , Li Bingxi , Wang Jing 
Published: January 2023

Abstract
It has been suggested that the mammalian cell entry (Mce) proteins are involved in the macrophage cell entry process and the subsequent intracellular survival of Mycobacterium tuberculosis during infection. However, relatively little is known about the specific roles of Mce3C in modulation of phagocytosis and host innate immune defenses. Here we demonstrate that Mce3C can promote the entry of mycobacteria into macrophage cells in a RGD motif-dependent manner. During our attempt to screen for potential Mce3C-interacting host proteins utilizing yeast two-hybrid assay, we found that Mce3C interacts with integrin β2 subunit, which renders it very likely that Mce3C binds β2 family of leukocyte integrins including αLβ2,αMβ2 and αXβ2 through its RGD motif, thus enhancing phagocytosis of mycobacteria by macrophage cells. Furthermore, Mce3C blocks the activation of ERK1/2 signaling pathway, leading to the suppression of Tnf and Il-1β expression, and the promotion of mycobacterial survival within macrophages. Finally, we discover that Mce3C undermines apoptosis of macrophage cells during the course of mycobacterial infection, which further facilitates the intracellular survival of mycobacteria. Thus, these results indicate that M. tuberculosis Mce3C not only strengthens the internalization of macrophage cells by mycobacteria via RGD-mediated interaction with β2 family of leukocyte integrins, but also enhances the intracellular survival of mycobacteria through inhibition of ERK1/2 signaling pathway and apoptosis in macrophage cells.
Recent Thymic Emigrants and Chronic Salmonellosis: How New T Cells Combat an Old Infection
Authors: Goggins J. Alan , Kurtz Jonathan R. , McLachlan James B 
Published: January 2023

Abstract
Typhoid fever, caused by infection with Salmonella bacteria affects approximately 21 million people annually, killing nearly 200,000 and yet the immunological response to this infection is poorly understood. Recent thymic emigrants (RTEs) are the youngest subset of peripheral T cells, which are known to differ in how they functionally contribute to the naïve T cell pool. This distinctive cell population is known to contribute to the maintenance of T cell receptor diversity in the peripheral T cell pool, but their involvement in combating chronic bacterial infections, such as typhoid fever, has not been explored. In the present study, we hypothesized that RTEs are essential contributors to the CD4 T cell response during persistent Salmonella Typhimurium (ST) infection, which predominantly relies on helper T cell immunity to control bacteria. Here, we show that thymectomy of adult mice prior to oral infection with ST leads to increased mortality in addition to significantly increased bacterial burdens in the spleen, mesenteric lymph nodes and liver 30 days post-infection compared to sham surgical controls, suggesting Salmonella-specific RTEs may contribute to bacterial clearance. Surprisingly, thymectomized animals also demonstrated expanded numbers of peripheral Salmonella-specific T cells, compared to control animals, implying that these existing cells are somehow incapable of controlling infection in the absence of RTEs. The results of this study provide insight into how new pathogen-specific T cells leaving the thymus participate in combatting a persistent bacterial infection.
Functional SLC11A1 (NRAMP1) enhances protection from Coxiella burnetii infection
Authors: Hedges Jodi F , Robison Amanda , Kimmel Emily , Jutila Mark A. 
Published: January 2023

Abstract
SLC11A1 is a divalent ion transporter formerly known as the natural resistance-associated macrophage protein (NRAMP1). Also known as the Bcg/Lsh/Ity locus, SLC11A1 was originally characterized as the resistance factor for Mycobacterium, Leshmania, and Salmonella infections. This protein is non-functional in C57BL/6 mice, thus, the susceptibility of this strain to these pathogens. We recently characterized the expression of SLC11A1 in the majority of γδ T cells and NK cells, which are primary sources of innate IFN-γ. Cells expressing SLC11A1 were more prone to activation. We hypothesized that SLC11A1 would have an important function in infections in which IFN-γ was a critical component. Only two genes have been described as potential susceptibility loci for Q fever caused by Coxiella burnetii infection, they are IFN-γ and SLC11A1 in humans. Thus, we assessed C. burnetii infection in congenic mice with and without functional SLC11A1. SLC11A1+ mice had improved disease symptoms, harbored fewer bacteria, and had increased expression of innate cytokines, including IFN-γ. The results indicate that mice expressing functional SLC11A1 were more resistant to infection with C. burnetii, suggesting an expanded role for this protein in innate immune protection.
Interleukin-17 are the major cytokine in chronic gastritis induced by Helicobacter pylori infection.
Authors: Rodrigues Denise Bertulucci , Silva Emerson Wood , Silva Natalia Jacomo , Fonseca Fernanda Machado , Sawan Monica , Ribeiro Betania Maria , Oliveira Adriana Gonçaves , Martins Ruchele Dias Nogueira , Pereira Sanivia Aparecida , Adad Sheila Jorge , Rodrigues Virmondes 
Published: January 2023

Abstract
Helicobacter pylori (H. pylori) is a highly prevalent bacteria directly involved in various diseases of the upper digestive tract such as gastritis, peptic ulcer and gastric cancer. In this study we analyze in situ immune response in gastric biopsies obtained during endoscopic procedures from 49 patients. Quantitative PCR were performed on cDNA copies of total RNA extracted from each biopsies. PCR were done using Taqman system to selected cytokines and cytokines transcriptions factor representative of Th1, Th2, Treg and Th17 lymphocytes. The relative number of mRNA copies were adjusted using the beta actin gene. The analysis were performed on samples grouped according to presence or absence of H. pylori infection. No significant difference was found in the expression of IFN-γ, IL-4 and IL-10 when comparisons were done between patients with and without H. pylori infection. Moreover, no difference was observed in the expression of T-bet, GATA-3 and FoxP3. On the other hand, the levels of IL-17 and ROR-gamma T were significantly higher in samples obtained from patients with H. pylori infection, compared with those from non infected. The results presented here suggest that IL-17 are involved in the chronic inflammatory process induced by H. pylori.
Nano-silver as effective intracellular bactericidal compound in human osteoclasts
Authors: Filgueira Luis , Schwartz Valerie , Kharoubi-Hess Solange , Walch Michael 
Published: January 2023

Abstract
Bone infections are difficult to treat, resulting usually in severe bone destruction. A variety of bacteria can be the cause of bone infections, including staphylococcus aureus. Osteoclasts, which belong to the macrophage family, are the key cells in bone infections, as they are not well equipped for killing bacteria, but rather enhance their bone resorbing function, when activated in the infection environment. In addition, newly recruited blood monocytes differentiate rather towards osteoclasts, instead of becoming effective macrophages. Silver has been known for centuries for its bactericidal activity. This project investigated the bactericidal effects of 80nm nanosilver particles in E. coli infected human osteoclasts, in vitro. Nano-silver was used at 10μg/ml, which was not toxic to the cells or to the bacteria, when applied directly. However, when bacteria-infected osteoclasts were exposed to nano-silver, intracellular bacterial survival was significantly reduced. Interestingly, ceftriaxone did not have any bactericidal effect on intracellular bacteria in osteoclasts. In conclusion, silver compounds should be considered in the future for the treatment of bacterial bone infections.
The role of neutrophils during Orientia infection.
Authors: Shelite Thomas R , Mendell Nicole L , Bouyer Donald H , Walker David Hughes , Soong Lynn 
Published: January 2023

Abstract
Scrub typhus is a seriously neglected disease with approximately one-third of the world’s population at risk of being infected with Orientia tsutsugamushi, and the occurrence of over one million scrub typhus cases annually illustrate its importance in global health. All scrub typhus case studies that report blood cell counts, describe neutrophilia during the course of infection. Patients with confirmed scrub typhus have significant increases in activated neutrophil proteins in serum, and the increase of neutrophil recruiting cytokines. We also observed neutrophilia as well as neutrophil recruitment to infected tissues in intravenously infected mice, suggesting key role for neutrophils in scrub typhus disease progression. To determine the role of neutrophils in this infection, female C57BL/6 mice were lethally challenged, and neutrophils were depleted one day prior to infection (D−1) or six (D+6) days post infection. The effects of neutrophil depletion were observed to be dependent on the time post infection. Animals depleted early (D-1) exhibited more severe pathology at an earlier time point and had disease progression similar to non-depleted animals but had greater survival. Animals depleted 6 dpi recovered weight, and signs of illness had resolved by 12 dpi. Histopathology demonstrated decreased cellular infiltrates when compared to infected, non-depleted animals. Depletion of neutrophils decreased mortality independent of when depleted, but only depletion 6 dpi resulted in amelioration of signs. These data suggest an important role of neutrophils in tissue pathology and disease progression during scrub typhus infection.
Exosomes: A possible mechanism for the development of Chlamydia-induced upper genital tract pathology
Authors: Russell Raedeen Sherilee , Igietseme Joseph U. , Eko Francis O. 
Published: January 2023

Abstract
It is estimated that 70% of chlamydial infections in women are asymptomatic and, if left untreated, can lead to severe irreversible complications including ectopic pregnancy and pelvic inflammatory disease. Chlamydia trachomatis infects cells in the cervix of the female genital tract and ascends to the upper genital tract (UGT) where it can cause diverse pathologies. It has been shown that Chlamydia-induced UGT pathology occurs even in the absence of live Chlamydia in the lower genital tract. The mechanism of ascending infection and disease is largely unknown. We hypothesize that the ascending infection leading to UGT pathology is mediated by exosomes. Exosomes are vesicles that can package intracellular molecules from donor cells and release their cargo into recipient cells thereby manipulating gene expression and cellular activity. To test our hypothesis, HeLa cells were infected with C. trachomatis serovar D and exosomes isolated from culture supernatants were characterized. Cytokines and chemokines from exosomes were assessed by a multiplex cytokine ELISA assay. Furthermore, purified exosomes were co-cultured with uninfected cells and the protein content of the lysed cells was examined. The results showed infected cells released higher concentrations of exosomes during early infection compared to uninfected cells and significantly higher levels of inflammatory cytokines were associated with these exosomes. Moreover, exosome recipient cells were found to contain chlamydial proteins. These results suggest exosomes could transport pathogenic chlamydial proteins from infected to uninfected cells with potential to stimulate inflammation in recipient cells and hence a possible mechanism for development of UGT pathology.
Commensal-dendritic-cell interaction specifies a unique protective skin immune signature.
Authors: Bouladoux Nicolas , Naik Shruti , Linehan Jonathan L , Han Seong-Ji , Harrison Oliver J , Tussiwand Roxanne , Murphy Kenneth M , Merad Miriam , Segre Julia A , Belkaid Yasmine 
Published: January 2023

Abstract
The skin represents the body’s primary interface with the environment, acting as the first line of physical and immunological defense. This organ is also home to trillions of microbes (bacteria, fungi and viruses) that play an important role in tissue homeostasis and local immunity. Skin microbial communities are highly diverse and can be remodeled over time or in response to environmental challenges. How in the context of this complexity, individual commensals may differentially modulate skin immunity and what the consequences of these responses for tissue physiology are remain unclear. Here, we demonstrate that defined commensals dominantly impact skin immunity and identify the cellular mediators involved in this specification. In particular, colonization with Staphylococcus epidermidis induces IL-17A+CD8+T cells that home to the epidermis, enhance innate barrier immunity and limit pathogen invasion. These commensal-specific T cell responses result from the coordinated action of skin resident dendritic cell subsets and are not associated with inflammation, revealing that tissue resident cells are poised to sense and respond to alterations in microbial communities. This dialogue may represent an evolutionary means by which the skin immune system uses fluctuating commensal clues to calibrate barrier immunity and provide heterologous protection against invasive pathogens. Altogether these findings reveal that the skin immune landscape is a highly dynamic environment that can be rapidly and specifically remodeled by encounters with defined commensals, findings that have profound implications for our understanding of tissue specific immunity and pathologies.
Imaging mass cytometry - elemental immunohistochemistry for multiparametric imaging and quantitation
Authors: Ornatsky Olga , Chag Qing , Swanson Eric , Closson Taunia , Bouzekri Alexandre , Loboda Alexander , Baranov Vladimir 
Published: January 2023

Abstract
Pathology assessment of tissue sections provides prognostic evaluation and helps select optimum treatment regimens. Digital pathology has made significant strides in the analysis of several markers. There is a growing understanding of cell heterogeneity within tumor tissue, role of microenvironment, and the impact of immune cells on cancer development. Sophisticated tools are needed to provide quantitative information for a large number of biomarkers, low-abundance small molecules and chemotherapeutic drugs, while retaining spatial resolution of cells and tissue architecture. Imaging mass cytometry (IMC) is a novel technology that can simultaneously detect and quantitatively measure more than 50 metal-containing reagents in tissue sections at 1 μm resolution. IMC combines laser ablation with the Helios CyTOF®. We will describe in detail technology, workflow, multiplexing protocols, image analysis and show representative data for human and mouse sections. We will demonstrate the use of metal-containing histological stains for tissue architecture, and endogenous element identification [iodine, platinum]. Combined detection of protein targets and transcripts within cells will be presented. Validation will be demonstrated on sequential tissue sections prepared by conventional immunohistochemistry.
Precision medicine is based on access to high-density data (proteomics and genomics) which provides accurate diagnosis and information on the best therapeutic approach. IMC is a highly multiparametric, quantitative method for phenotypic, signaling pathway, and cell state protein identification together with spatial information within tissue sections.
Identifying interactions between cytokine levels and clinical outcomes in influenza infection using a novel data-driven method for defining cytokine modules
Authors: Hertz Tomer , Fiore-Gartland Andrew , Panoskaltsis-Mortari Angela , Thomas Paul Glyndwr , Randolph Adrienne 
Published: January 2023

Abstract
Cytokines and chemokines are key signaling molecules of the immune system. Recent technological advances enable measurement of multiplexed cytokine profiles in blood as well as sites of infection such as the nasal and alveolar mucosa. These profiles can then be used to identify potential biomarkers of clinical outcomes following influenza infection, by comparing groups of individuals with different outcomes. Recently, several associations between single cytokines and mortality have been reported. However, single analyte association testing ignores context-dependent covariation in cytokine secretion and decreases statistical power due to multiple testing. We have developed a novel data-driven approach to analyze cytokine and chemokine profiles that uses unsupervised clustering to form functional modules. We applied this method to three cohorts of severely ill children infected with influenza. Innate profiles were assayed using a 42-plex Luminex panel at enrollment. Clinical outcomes were collected including hospitalization, septic shock, ALI/ARDS and death. Though many modules were consistent with the immunological literature, some of the modules included cytokines that have not previously been associated, generating novel hypotheses. Modules generated from blood were different than those generated at the site of infection. Furthermore, we found that the modules were significantly associated with clinical outcomes in all three cohorts, while individual cytokines were not statistically significant. Overall, our approach provides a novel method to characterize cytokine and chemokine profiles that both increases statistical power and provides novel hypotheses about context-specific innate signaling.
An optimized IFN-γ ELISpot assay using T-activated
® proteins for determination of CMV-specific cell-mediated immunity
Authors: Boeckl Katharina , Körber Nina , Barabas Sascha , Deml Ludwig , Bauer Tanja 
Published: January 2023

Abstract
In healthy individuals, Cytomegalovirus (CMV) infections are controlled by CMV-specific cell-mediated immunity (CMI). However, functional impairment of the CMI in immunocompromized individuals can lead to uncontrolled CMV-replication. Thus, monitoring CMV-specific CMI is highly relevant for the prognosis of CMV-associated diseases. Here we show the optimization and technical validation of a monitoring tool for the determination of CMV-specific CMI.
Phenotype, quantity and cytokine expression profile of T cells from 19 CMV-seropositive healthy donors reactivated by CMV (IE-1, pp65) -specific pools of overlapping 15mer peptides and the corresponding T-activated proteins® were compared using a 10-parameter flow cytometry-based intracellular cytokine staining assay. Subsequently, an IFN-g ELISpot protocol using T-activated proteins® was established and validated.
Pp65 peptide pool stimulation revealed significant higher CD8+ T-cell responses as the corresponding T-activated proteins® (p=0.006). CD4+ T-cell responses however were comparable. Testing of T-activated proteins® in seronegative donors revealed a specificity of 100%. Use of T-activated proteins® with the optimized IFN-g ELISpot resulted in coefficients of variation for inter-assay, inter-operator and inter-site variations of less than 22 %. A linear correlation between the amount of CMV protein-reactive cells and total PBMC counts was observed.
Given the natural antigen processing of T-activated proteins® along the cross-presentation pathway, reflecting the in vivo situation, these proteins in combination with the optimized IFN-g ELISpot serve as a valuable tool to monitor the CMV-specific CMI.
Unbiased High-Dimensional Identification of Lymphocytes in Mouse Uterus
Authors: Li Yan , Vazquez Jessica , Stanic-Kostic Aleksandar 
Published: January 2023

Abstract

Introduction
Uterine lymphocytes play an essential role at the maternal-fetal interface, contributing to vascular remodeling, fetal tolerance and protection against infection. Despite intense research interest, simultaneous population assessment of diverse immune cells has been limited by the use of few concurrent markers and difficulty in assigning unambiguous cell identity. We present the first comprehensive, unbiased identification of mouse uterine immune subsets by application of dimensionality reduction of highly-polychromatic flow cytometry.

Methods
Uterine specimens were dissected from C57BL/6 mice and mononuclear cells (MCs) were isolated by mechanical and enzymatic disruption. MCs labeled by flurochrome-conjugate antibodies. Data acquisition and analysis were performed using BD Fortessa flow cytometer in an 18 parameter, 5-laser configuration and Flowjo, respectively. Dimensionality reduction by Barnes-Hut modification of t-distributed Stochastic Neighbor Embedding (t-SNE) and density-based k-means clustering was performed using the open-source ACCENSE package.

Results
Analysis revealed uterine B-, T-, Dendritic, and Innate Lymphoid cell subsets. Analysis with ACCENSE allowed unbiased mapping of these subsets onto 2-dimensional scaffolds, without the necessity for expert manual gating.

Conclusion
We present the first comprehensive analysis of uterine immune cells, demonstrating a complex mixture of innate and adaptive immune mediators. The use of dimensionality reduction and population clustering allows allocation of uterine immune cell phenotype in an unambiguous fashion, enhancing reproducibility and functional analysis across studies.
LEARNING ABOUT HUMAN KIDNEY IMMUNOLOGY FROM THERAPEUTIC MONOCLONAL ANTIBODY-INDUCED KIDNEY INJURY: EFFECT OF PD1 BLOCKADE
Authors: Muczynski Kimberly , Anderson Susan , Torres Mark-Joseph 
Published: January 2023

Abstract
Human renal microvascular endothelial cells (RMEC) express high levels of MHC class II proteins under normal physiologic conditions. They are positioned to interact with circulating leukocytes. Yet, under normal conditions kidney inflammation does not occur.
Isolated RMEC can peptide presentation to influenza specific T cells. T cell proliferation and cytokine secretion are blocked by antibodies to CD40, CD58 and HLA-DR; and enhanced by antibodies to PDL1 (B7-H1,CD274). Using cytometry we find high levels of CD58 and CD274 on RMEC in normal human kidneys and CD40 on some RMEC of transplanted kidneys. We hypothesized that RMEC PDL1 interaction with T cell PD-1 (CD279) prevents T cell activation in human kidneys.
New PD-1 blocking monoclonal antibodies, such as nivolumab, are being used to treat advanced cancers by selectively blocking PD-1 interactions with ligands PD-L1 (CD274, B7H1) and PD-L2 (CD273, B7H2) present on tumor cells. We have identified four cases of acute kidney injury in patients receiving PD-1 pathway blockade. Biopsies revealed an intense interstitial nephritis in the area of the class II expressing RMEC.
Our interpretation of RMEC’s ability to activate T cells in a class II-peptide dependent manner, their high levels of PD-L1 (CD274) and now the development of interstitial inflammation in patients receiving anti-PD1 monoclonal therapy is that RMEC are poised to present peptide from circulating antigen as an immune surveillance system, with the PD1 pathway functioning to restrain T cell activation. Other human organs also express high levels of HLA class II on microvascular endothelial cells. Hence our hypothesis of a kidney capillary endothelium forming an immune surveillance system may also pertain to other organs.