bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Atlas of the Complement System in Developing and Adult Mouse Brains
Authors: Zhang Yingying , Moffitt Jeffrey , Carroll Michael 
Published: February 2023

Abstract
The complement system is traditionally known as a key pathway of peripheral innate immunity. Recent studies reveal distinct functions of the complement system in normal development of mammalian central nervous system (CNS). Over activation of the complement system has been associated with increased risks for Schizophrenia in humans by causing excessive synapse pruning. However, the source of complement and its regulation in the CNS remains largely unknown. To this end, we applied MERFISH (Multiplexed Error Robust Fluorescent in &lt;underline&gt;s&lt;/underline&gt;itu Hybridization), a novel spatial transcriptomic approach, to establish a brain atlas of the complement system during development. We found that most components of the complement pathway are locally expressed in the brain. They are expressed by particular types of cells in the brain with distinct spatial and temporal distribution. Notably, the lectin pathway showed striking age-dependent differences in expression level and spatial heterogeneity in the brain. Moreover, suggesting an active role of complement in brain development, we found the spatial distribution of a subset of complement regulatory genes coincides with that of neural development-related genes in the cerebral cortex. To further investigate this hypothesis, we are currently studying the effect of complement inactivation on CNS development by comparing neuronal populations from wild type mice to those with C3 or C4 deficiency. Ultimately, we aim to use our approach to understand molecular changes and abnormalities in CNS development caused by overactivation of the complement cascade, and how these changes increase risks for developing Schizophrenia. This work is supported by the Conte Center Grant NIH 1P50MH112491.
Single-cell transcriptome analysis reveals CNS innate immune landscape plasticity in diet-induced obesity and type 2 diabetes
Authors: Yu I-Chen Ivorine , Paraiso Hallel C. , Kuo Ping-Chang , Scofield Barbara A. , Chang Fen-Lei , Yen Jui-Hung 
Published: February 2023

Abstract
Midlife obesity and type 2 diabetes are strong risk factors for late-life cognitive impairment and dementia. Previous studies show that obesity is associated with a heightened state of neuroinflammation, indicating that systemic factors profoundly influence brain innate immunity. Here, we reported that the diversity and plasticity of brain myeloid cells are reshaped in middle-aged mice fed with a high-fat diet (HFD). Using single-cell RNA sequencing, we revealed the heterogeneity of brain-resident myeloid cells, including microglia (MG, Tmem119/P2ry12/Hexb) and border-associated macrophages (BAMs, Mrc1/Ms4a7/Pf4). MG from HFD-fed mice exhibited changes of genes involved in oxidative phosphorylation and lipoprotein metabolism, suggesting a modulated cellular metabolism in MG responding to HFD. A subset of MG displayed induced disease-associated MG (DAM) gene signature during HFD feeding. We found that Apoe was predominantly expressed in BAM clusters and up-regulated in HFD-fed MG clusters. Several distinct subsets of BAMs enriched in MHC-II (H2-Eb1, H2-Aa, and Cd74), or leukocyte adhesion and migration (Clec4n, Ccl7, Vcam1) genes, displayed the increased cell proportion in HFD-fed mice. In addition, HFD feeding led to the IL-10 downregulation in MHC-II-expressing BAMs. These data suggested that pro-inflammatory BAMs might incorporate T cell immunity to potentiate cerebrovascular inflammation during chronic HFD consumption. Overall, our results highlighted the heterogeneity and plasticity of the brain myeloid cells in middle-aged obesity. The identified BAM subsets provide insights into crosstalk between CNS innate immune cells and T cells to feature neuroinflammation in obesity-associated cognitive decline.
The transcription factor Bach1 plays an important role in regulating macrophage ferroptosis upon iron supplementation
Authors: Aberman Kate , Fisher Logan , Oland Sandra , Sher Alan , Amaral Eduardo P. 
Published: February 2023

Abstract
Ferroptosis is a novel iron-mediated necrotic cell death pathway associated with accumulation of lipid peroxidation, reduced levels of glutathione (GSH) and glutathione peroxidase-4 (Gpx4). This form of cell death has been implicated in different diseases, including tuberculosis. Our group previously described that Mtb-induced macrophage necrosis is associated with hallmarks of ferroptosis, facilitating bacterial spread extracellularly. Nevertheless, the mechanisms underlying the effect of iron in modulating cell death remain poorly delineated. In this study, we used an iron overload model of ferroptosis on bone-marrow derived macrophages (BMDMs) to investigate molecular mediators of antioxidant generation and lipid peroxidation, and their role in modulating ferroptotic cell death. Our findings showed that BMDMs deficient in Nrf2, a transcription factor that regulates many antioxidant genes, were highly susceptible to iron-mediated ferroptosis. In the opposite direction, BMDMs deficient in lipoxygenase-5 (5-LO) as well as in Bach1, a Nrf2 suppressor, displayed enhanced resistance to the cytotoxic effects of iron overload. Interestingly, ~50% of the ferroptotic death triggered by iron supplementation was blocked by 5-LO deficiency while in Bach1-/- macrophage cultures this suppression reached ~94%. Together, these findings indicate that 5-LO plays a partial role in lipid peroxidation driven by iron overload and reveal Bach1 as a master regulator of ferroptosis in macrophages. This study additionally provides a conceptual basis for further investigation of the role of ferroptosis-induced cellular and tissue damage in Mtb infection.
SHIP-1 Inhibitors improve human microglial-like cell function
Authors: Ramakrishnan Gautham S , Humphrey Mary Beth 
Published: February 2023

Abstract
Alzheimer’s disease (AD) is associated with progressive formation of Aβ plaques and neuronal cell death in the brain. Microglia maintain brain homeostasis and their dysfunction is implicated in AD pathology. Triggering receptor expressed on myeloid cells #2 (TREM2) promotes phagocytosis, migration, and metabolic fitness of microglia. TREM2 signaling is inhibited by src-homology 2(SH2) domain containing inositol phosphatase 1 (SHIP-1), encoded by INPP5D, in macrophages and osteoclasts, and the rs669 SNP is associated with increased brain SHIP-1 expression and confers AD risk. We hypothesize that overexpression of SHIP-1 leads to reduced TREM2 signaling and subsequent microglial dysfunction. To test this hypothesis, we treated human microglial like (HMC3) cells, expressing endogenous TREM2, SHIP-1, Iba-1, and CD68, with small molecule inhibitors of SHIP-1 (SHIPi) (3AC) and its paralog SHIP-2 (K161). Treatment with SHIPi significantly increases the surface expression of TREM2 and CD68 as detected by flow cytometry, while not changing Iba-1 expression. Additionally, we demonstrate that treatment of HMC3 cells with SHIPi significantly improves their ability to phagocytose fluorescently tagged Aβ. At concentrations that promote phagocytosis, SHIPi were non-toxic at 72 hours. Together, these data have given us early evidence that SHIPi can promote human microglia-like cell phagocytosis. Further studies are underway to determine the effect of SHIPi on metabolic fitness. SHIPi are safe and effective in mouse models of metabolic dysfunction and obesity and could be an ideal treatment for AD alone or in combination with stimulating TREM2 antibodies.
Interferon-Lambda: A Key Cytokine for Dendritic Cell Development?
Authors: Baffit Mariam , Pang Ee Shan , Wright Mark , O’Keeffe Meredith , Hertzog Paul 
Published: February 2023

Abstract
In light of the current pandemic, COVID-19, our understanding of how the immune system combats viral infection has become more important than ever. Interferons (IFNs) are an integral component of the immune system’s anti-viral response. While the functions of Type I Interferons have been extensively studied, the newest member of the Interferon family, Interferon-Lambda (IFN-λ), is yet to be fully investigated. Currently, it is believed that the canonical signalling pathway of the IFN-λ receptor (R, defined as IFN-λR1 and IL-10Rb) is shared with Type I IFN-αR signalling and leads to the transcription of Interferon Stimulated Genes (ISGs), key genes involved in antiviral immunity. However, there is a growing body of evidence that indicates that IFN-λR1 is involved in signalling pathways that differ to IFN-αR. Notably amongst this evidence is IFN-λR1’s restricted expression to epithelial and some haematopoietic cells as well as non-redundant roles being discovered at mucosal barriers. Building on novel preliminary data, this project seeks to differentiate IFN-λR1 signalling from this canonical pathway and determine whether other receptor chains are involved. Dendritic Cells (DCs), key mediators linking innate and adaptive immunity, are the focus of this project as they are major producers of IFN-λ and are also one of the few haematopoietic cells which express IFN-λR1. Using DCs, this project will investigate the signalling pathways regulated by IFN-λR1 and other potential pathways instigated by the interaction between IFN-λR1 and other receptors. Additionally, this work will focus on how IFN-λ signalling contributes to cellular function in the context of DC differentiation and development.
Innate immune profiling discriminates between liver regeneration and liver failure following partial hepatectomy
Authors: Navarro-Alvarez Nalu , Huang Christene A. , Kovacs Elizabeth J , Yang Yong-Guang 
Published: February 2023

Abstract
Post-hepatectomy liver failure is a major complication following liver resection and while the basic mechanisms are not well understood, limited regeneration of the remnant tissue contributes to its development. Using an established murine model of 70% partial hepatectomy, we studied the innate immunological profile associated with liver regeneration and liver failure. Following partial hepatectomy, there is a significant increase in circulating CD11b+ myeloid derived cells from (52±10 to 70±12 p&gt;0.01). Further characterization of the CD11b+ cells revealed three different subpopulations: Gr-1hiF4/80, Gr-1hiF4/80+, and Gr-1loF4/80+. Liver failure was accompanying with markedly prolonged and increased mobilization and liver infiltration of activated CD11b+ cells (6±2% on day 0 to 55±12% on day 1 p&gt;0.001). Specifically, the CD11b+Gr-1hiF4/80− cells identified as neutrophils were predominantly increased in these mice from (25±5% to 80±10% p&gt;0.001) on day 1. And persistently remained high until day 7. We also found high IL-6 serum levels in these mice (300±150pg/mL) on day 1. The other CD11b+ cell populations, including Gr-1hiF4/80+ and Gr-1loF4/80+ cells, were markedly reduced in peripheral blood of mice with impaired liver regeneration. In contrast, all CD11b+ populations rapidly recovered to normal levels within 2 days in mice showing normal liver regeneration. In conclusion, following partial hepatectomy, significantly prolonged infiltration of CD11b+ neutrophils and marked reduction of other CD11b+ populations are a hallmark of liver failure. Thus, controlling neutrophil infiltration/activation may help ease recovery from the surgical procedure and improve liver regeneration after partial liver resection.
Activation of stimulator of interferon genes in dendritic cells induces interferon-lambda and subset- and species-specific dendritic cell death
Authors: Pang Ee Shan , Daraj Ghazal , Macri Christophe , Balka Katherine , de Nardo Dominic , Hochrein Hubertus , Masterman Kelly-Anne , Zhan Yifan , Kile Benjamin , Lawlor Kate , Radford Kristen , Wright Mark , O’Keeffe Meredith 
Published: February 2023

Abstract
Stimulator of Interferon (IFN) Genes (STING), a cytosolic DNA sensor that recognises cyclic dinucleotides (CDNs), has been an adjuvant target in many cancer immunotherapies. Activation of STING results in the production of Type I IFN through the phosphorylation of TANK-binding kinase 1 (TBK1) and IFN regulatory factor 3 (IRF3) and it is thought this enhances cross-presentation of tumour antigens by dendritic cells (DCs). However, DCs interrogated in many of these studies use in vitro-generated DCs instead of putative ex vivo DCs, and the direct effects of STING activation on different DC subsets are not completely understood. Here, we report that mouse and humanised mouse splenic DC subsets as well as human blood DCs are activated by CDN stimulation and produce Type III IFN (IFN-lambda) but only type 2 conventional DCs (cDC2s) and plasmacytoid DCs (pDCs) produce Type I IFN in response to CDN stimulation. However, only mouse pDCs aberrantly express extremely high levels of CD86 and CD80 and are ablated rapidly after STING activation. Some DC death was also observed in mouse and human cDC2s, but not in human pDCs. This ablation is STING-dependent and occurs via a cell-intrinsic mechanism involving intrinsic apoptosis. These observations demonstrate the differential effects STING activation has on DC subsets as well as highlight a discordance amongst mouse and human DCs during activation, which serve as an important consideration in the translation of animal cancer models and the use of STING ligands as adjuvants in cancer immunotherapy.
Till cell death do us part: The protective role of inflammasome-mediated pyroptosis and genomic DNA recognition during brucellosis
Authors: Tupik Juselyn D , Coutermarsh-Ott Sheryl L , Benton Angela H , King Kellie A , Kiryluk Hanna D , Caswell Clayton C , Allen Irving C 
Published: February 2023

Abstract
Brucellosis, a zoonotic disease instigated by the bacteria Brucella, results in chronic inflammatory symptoms. Despite mechanisms utilized by Brucella for immune evasion, some pattern recognition receptors, specifically NOD-like receptors (NLRs), sense Brucella pathogen-associated molecular patterns (PAMPS) and form a multi-protein complex termed the inflammasome. The inflammasome attenuates Brucella pathogenesis through caspase-1 (canonical) or caspase-11 (non-canonical) mediated cleavage of pro-inflammatory cytokines IL-18 & IL-1β. It can also activate inflammatory cell death known as pyroptosis, a mechanism rarely implicated with canonical inflammasome activation in brucellosis. Here, we evaluated in vivo canonical (Asc−/−) and non-canonical (Caspase-11−/−) inflammasome mouse models infected with Brucella abortus and determined that wildtype mice displayed increased survival and recruitment of WBCs with decreased bacteria load in comparison with Asc−/− mice. This indicates that the canonical inflammasome plays a necessary, defensive role against Brucella. Conducting in vitro B. abortus infections in Asc−/− macrophages, we further determined this protective mechanism of canonical inflammasome activation results from the activation of pyroptosis. We also found that the Brucella PAMP genomic (g)DNA instigated a high inflammatory response in wildtype macrophages that was suppressed in Asc−/− and amplified in anti-inflammatory NLR knockouts. This suggests that NLR activation occurs through sensing gDNA and may involve mechanisms of interaction among NLRs. Ultimately, these results suggest a greater importance and continued exploration of pyroptosis and the recognition of gDNA during brucellosis.
MicroRNA and periodontal pathogen interaction in shaping innate immune response
Authors: Valverde Araceli Maria , Schaller Samantha , Naqvi Afsar Raza 
Published: February 2023

Abstract
MicroRNA (miR) play a critical role in the pathogenesis of immune-mediated diseases, however, their role in periodontal disease (PD) remain poorly studied. We hypothesize that periopathogens (P. gingivalis [Pg] and A. actinomycemtemcomitans [Aa]) impair host immune response by perturbing miR expression. Naïve CD14+ monocytes were isolated from human PBMC and differentiated to M1 MΦ or M2 MΦ in presence of GM-CSF or M-CSF for 7 days. Cells were challenged with Pg or Aa (both 100 MOI) for 4 h and 24 h. Total RNA was isolated to quantitate expression of pro- and anti-inflammatory miRNAs, cell lysate was prepared for protein expression of NFκB, PU.1 and CEBP/β by western blot and supernatants were collected to analyze cytokine profiles. We observed that expression of pro-inflammatory miRNAs viz., miR-125a and miR-155a are increased in M1-MΦ and M2-MΦ challenged with Pg and Aa. Surprisingly, the expression of anti-inflammatory miR-146a was differentially expressed in both MΦ, but miR-511 expression was reduced. miR-142-3p expression in response to Pg and Aa challenge was decreased suggesting its possible anti-inflammatory function. To examine the impact of miR-142-3p on Pg and Aa-mediated immune responses, we examined PU.1 levels, a known TF regulating miR-142 expression, and noticed a significant decrease in PU.1 and it correlates with mature miR-142-3p levels. miR-142-3p transfected MΦ challenged with Pg or Aa exhibit altered secretion of inflammatory cytokines. In conclusion, periopathogen-mediated activation of NFκB and miR-155 augments inflammatory signaling by suppressing expression of anti-inflammatory miR-142-3p by decreasing PU.1 levels. Perturbation of miR by periodontal bacteria is central to the pathogenesis of PD.
Priming of microvascular endothelium by microbiota-derived metabolites regulates neutrophil trafficking to the liver during sepsis
Authors: Zucoloto Amanda , Yu Katrina , McCoy Kathy , McDonald Braedon 
Published: February 2023

Abstract
During systemic bacterial infections and sepsis, neutrophils are recruited en mass into the microcirculation of the liver and lungs as part of a coordinated intravascular response to defend the bloodstream against bacterial pathogens. The mechanisms that program this response have not been elucidated. The gut microbiota regulates immune cell development and function. In extra-intestinal organs, the microbiota conducts long-distance communication with immune cells through the release of metabolites into the bloodstream. While gut microbes augment granulopoiesis in the bone marrow, the role the microbiota and commensal-derived metabolites on neutrophil trafficking is poorly understood. Using confocal intravital microscopy, we observed that germ-free (GF) mice had impaired neutrophil recruitment to the liver, but not the lungs, during sepsis. Analysis of microbial metabolites in the gut, portal circulation (between gut and liver), and systemic circulation revealed that commensal-derived D-lactate levels are high in the gut and portal circulation, but nearly absent in the systemic circulation. Reconstitution of gut-to-liver D-lactate signalling by enteral administration restored neutrophil trafficking to the liver. In contrast, D-lactate did not impact neutrophil infiltration to the lungs, systemic levels of pro-inflammatory mediators or granulopoiesis. Instead, commensal D-lactate primed liver endothelium to express adhesion molecules required for neutrophil adhesion and crawling. Taken together, we show that compartmentalized molecular communication between gut microbes and the liver primes the microvascular endothelium for neutrophil recruitment in response to systemic bacterial infection and sepsis.
hRSV nonstructural protein 1 (NS1) binds chromatin at regulatory regions of immune response genes.
Authors: Beri Nina , Pei Jingjing , Amarasinghe Gaya , Leung Daisy , Payton Jacqueline 
Published: February 2023

Abstract
Human respiratory syncytial virus (hRSV) causes severe acute respiratory tract infections in infants, elderly and immunocompromised people worldwide and few effective treatments are available. The hRSV nonstructural protein NS1 is known to inhibit host interferon responses in the cytoplasm. We and others have used in vitro interactome studies to identify host proteins that interact with NS1. Among these is the Mediator complex, a transcriptional coactivator localized in the nucleus, suggesting that NS1 may have a more direct role in modulating IFN-stimulated gene expression. We performed chromatin immunoprecipitation of NS1 or Mediator followed by sequencing (ChIP-seq) to map the genomic localization of hRSV NS1 or Mediator in A549 cells infected with hRSV or exogenously expressing hRSV-NS1. We identified 1756 NS1 binding sites, of which 82% (1442) of these are located within 10 KB of at least one gene. 42% (739 / 1756) of NS1 binding sites coincide with Mediator binding sites identified in the same cells, and 73% (1277 / 1756) overlap a known enhancer element (Enhancer Atlas). Moreover, NS1 binding sites often coincide with transcription factor binding sites in A549 cells (ENCODE). Comparison of RNA-seq from hRSV infected cells showed that nearly one-fourth of NS1 binding sites are located near genes significantly up- or down-regulated by hRSV infection. Moreover, these genes are enriched for IFN response genes. Finally, expression of NS1 reduced reporter gene expression when regulated by NS1-bound genetic elements. Together, our findings suggest that NS1 partially suppresses the expression of IFN immune response genes via directly interfering with transcriptional mechanisms, thereby contributing to immune evasion by hRSV.
Interferon-gamma receptor (IFN-γR) signaling is critical for bacterial containment during Staphylococcus aureus craniotomy infection
Authors: Kak Gunjan , Horn Christopher M. , Heim Cortney E. , Kielian Tammy 
Published: February 2023

Abstract
Neurosurgery for brain tumor or epilepsy resection requires a craniotomy to access the brain. Infectious complications occur at a frequency of 1–3%, with approximately half caused by Staphylococcus aureus (S. aureus) that forms a biofilm on the bone flap. Our recent scRNA-seq study revealed the transcriptional heterogeneity of infiltrating leukocyte populations during S. aureus craniotomy infection, several of which were enriched for IFN-γ-regulated genes. In the current report, we examined the functional importance of IFN-γ signaling during S. aureus craniotomy infection in IFN-γR knockout (KO) mice. Bacterial burden was significantly increased in the subcutaneous galea of IFN-γR KO compared to WT mice throughout the 28 day time course, whereas titers in the brain and bone flap were similar, highlighting a compartmentalized immune response. Leukocyte infiltrates in the galea were equivalent in IFN-γR KO and WT animals, which led us to utilize scRNA-seq to interrogate alterations in leukocyte activation following IFN-γR loss. Bioinformatics revealed the predominance of granulocyte-myeloid-derived suppressor cell (G-MDSC)-like subsets in the galea of both IFN-γR KO and WT mice. Hallmark pathway analysis identified a significant reduction in not only the IFN-γ pathway in G-MDSC-like subsets, but also a decrease in IFN-α and inflammatory (IL-1β, IL-18, and PLAUR) pathways in IFN-γR KO mice. Collectively, these results demonstrate the importance of IFN-γR signaling in preventing S. aureus outgrowth in the galea and a likely synergism between Type I and Type II IFN pathways in controlling craniotomy infection.