bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nucleosomal double-stranded DNA triggers APOL1 expression through the STINGTBK1-IRF3 pathway
Authors: Davis Shamara E , Khatua Atanu , Popik Waldemar 
Published: January 2023

Abstract
African Americans are four times more likely to develop kidney disease. Racial disparities in the frequency of nondiabetic kidney disease has led to the discovery of the apolipoprotein L1 (APOL1) gene variants, G1 and G2, which exist exclusively in individuals of recent African ancestry. The presence of these kidney risk alleles strongly correlates with several forms of nondiabetic kidney disease including lupus nephritis (LN). However, the mechanism by which APOL1 variants lead to a faster progression to LN in systemic lupus erythematosus (SLE) patients carrying APOL1 risk alleles is unclear. Increased levels of type I interferons (IFNs) and nucleosomal dsDNA fragments (nsDNA) in the blood is the hallmark of lupus erythematosus. We hypothesize that accumulation of dsDNA in the cytosol of podocytes that play a key role in maintenance of the filtration barrier in the kidney activates the DNA sensing pathways leading to expression of type I IFNs and proinflammatory cytokines damaging podocytes. Although type I IFNs stimulate APOL1 expression, it is unknown whether dsDNA induces APOL1 accumulation independently of IFN. Here we show that nsDNA triggers the expression of APOL1 through the activation of the cGAS/IFI16-STING-TBK1-IRF3 pathway. We have also shown that inhibition of type I IFN only partly inhibited APOL1 accumulation in podocytes, demonstrating that nsDNA directly activates expression of the APOL1 gene. We conclude that blocking type I IFN signaling and targeting elements of the nsDNA-induced pathway may represent a novel therapeutic approach to inhibit LN progression in African Americans SLE patients carrying APOL1 kidney risk alleles.
Proteomic profiling of autoinflammatory diseases, NOMID and CANDLE before and after treatment with interleukin-1 or with interferon blockade
Authors: Alehashemi Sara , Sawhney Megha , Sellers Brian , de Jesus Adriana , Cheung Foo , Biancotto Angélique , Goldbach-Mansky Raphaela 
Published: January 2023

Abstract
Systemic Autoinflammatory diseases (SAIDs) present with chronic sterile inflammation. NLRP3 mutation cause the IL-1 mediated SAID Neonatal-Onset Multisystem Inflammatory Disease (NOMID), that presents early in life with fever, rash, neutrophilic meningitis, hearing loss and eye inflammation. Chronic Atypical Neutrophilic Dermatosis, Lipodystrophy and Elevated Temperature (CANDLE) caused by additive loss-of-function mutations in proteasome genes including PSMB8, leads to chronic type 1 interferon signaling, characterized by early-onset fever, neutrophilic panniculitis, lipodystrophy, cytopenias, myositis and lymphocytic meningitis. IL-1 blocking treatments are approved for NOMID, and JAK-inhibitors show efficacy in CANDLE treatment.
We used proteomic analysis to compare differentially-regulated proteins in active NOMID and CANDLE compared to healthy children before and after treatment to identify inflammatory pathways that distinguish NOMID and CANDLE and are uniquely responsive to either IL-1 or IFN signaling blockade.
Serum samples from active NOMID (n=12) and CANDLE (n=7) before and after treatment and healthy controls (n=7) were subjected to proteomic profiling using SomaLogic platform (n=1129 proteins). Enriched pathways were identified in REACTOME and KEGG. Cytoscape was used for network extraction and visualization.
Differentially expressed proteins in NOMID vs CANDLE suggested endothelial cell function, coagulation and complement cascades and inflammation related pathways dysregulation. Distinct protein markers (i.e. cytokine and chemokines) are consisted the different immune dysregulation in NOMID and CANDLE; and uniquely respond to either IL-1 or IFN signaling blockade.
Regulation of GLI3 expression by TLR4 signaling
Authors: Matissek Stephan Josef , Elsawa Sherine F 
Published: January 2023

Abstract
While acute inflammation is an important host response to infections, chronic inflammation has emerged as a mechanism driving many diseases including autoimmune and malignant diseases. Monocytes are a subset of immune cells that secrete inflammatory cytokines in response to infections through toll-like receptor (TLR) signaling. The cross-talk between TLR signaling and other pathways has been shown to be important for downstream effector functions. We identify a novel role for the transcription factor GLI3, a negative regulator of Hedgehog signaling, in mediating TLR4-induced inflammation. Stimulation of monocytes with LPS increases GLI3 mRNA and protein expression. This occurred in a dose- and time-dependent manner. Investigation of the signaling mechanism suggests that LPS induced GLI3 occurs through the adaptor protein TRIF (but not MyD88). Targeting of transcription factors NFkb, AP-1 and IRF3 by pharmaceutical inhibitors suggests that TLR4-mediated GLI3 is regulated by IRF3. Transfection of our monocyte cell lines with shRNA targeting GLI3 suggests a regulatory role of transcription factor GLI3 in mRNA expression of essential cytokines involved in inflammation including IL-6 and CCL2. We generated conditional GLI3 knockout in mice myeloid cells using LysM-cre mediated recombination. IFA-elicited macrophages from mice with conditional GLI3 knockout driven by LysM-cre stimulated with LPS show reduced IL-6 and CCL2 secretion compared to macrophages from wild-type littermates. Taken together, these data suggest that GLI3 plays a role in innate immunity by regulating TLR4-induced inflammation.
Ligand-induced IFNγ down regulation calibrates myeloid cell IFNγ responsiveness
Authors: Crisler William J , Eshleman Emily , Lenz Laurel L 
Published: January 2023

Abstract
Inflammation triggers production of type II IFN (IFNγ), which induces expression of gamma-activated genes (GAGs) that enhance antigen presentation and antimicrobial activity associated with M1-type macrophage activation. Negative regulation of these responses is important to prevent excessive macrophage activity and inflammation. We report here that stimulation with IFNγ transiently reduces myeloid cell IFNGR to raise the threshold for STAT1 activation in response to subsequent IFNγ. IFNγ production contributed to reduced monocyte surface IFNGR during the first day after systemic Listeria monocytogenes (Lm) infection. IFNγ treatment also reduced IFNGR staining on cultured bone marrow derived macrophages (BMDM) and dendritic cells (BMDCs), and human monocytes. These reductions in IFNGR were independent of type I IFNs, the primary trigger for IFNGR reductions later after Lm infection. Reductions in IFNGR correlated with reduced macrophage ifngr1 transcript abundance but this was independent of effects on the proximal Ifngr1 promoter. IFNGR down regulation following a brief exposure to IFNγ was further observed to transiently reduce myeloid cell sensitivity to subsequent IFNγ, measured as induction of phosphorylated (p)STAT1. Prolonged or elevated IFNγ could overcome the suppression of pSTAT1 activation. These data suggest transient IFNγ production reduces IFNGR to calibrate M1-type myeloid cell activation.
IRF3 signaling in stromal cells contributes to sepsis pathogenesis
Authors: Walker Wendy , Harper Jourdan , Lopez Charlie , Nellikappallil Jose , Heipertz Erica L 
Published: January 2023

Abstract
Interferon regulatory factor 3 is a transcription factor that induces type 1 interferons and related inflammatory genes following activation of pattern recognition receptors. Our prior report demonstrates that IRF3-KO mice are substantially protected from sepsis in a lethal mouse model of cecal ligation and puncture (CLP). Here, we demonstrate that IRF3 remains relevant in the context of a CLP model incorporating clinical treatments (lactated ringer’s solution and antibiotics). 92.3% of IRF3-KO mice survived sepsis in this model, compared to 61.5% of wild-type mice. Septic IRF3-KO mice also had an improved disease score and lower levels of serum cytokines (IL-6 and IL-12), relative to wild-type counterparts. To examine if IRF3 exerts its effect within leukocytes, we generated bone marrow chimeras. We found that chimeras with IRF3-KO leukocytes did not exhibit a significant survival advantage over chimeras with wild-type leukocytes. However, chimeras with IRF3-KO stroma exhibited substantially improved survival relative to chimeras with wild-type stroma, paired with lower disease score and serum cytokines (IL-6 and IL-12). In vitro experiments with thioglycollate-elicited macrophages from IRF3-KO and wild-type mice demonstrate that IRF3 does not directly reduce the amount of IL-6 produced in response to cecal bacteria. However, wild-type monocytes that are adoptively transferred into septic hosts produce less IL-6 when the host is IRF3-KO vs wild-type. These experiments reveal the surprising finding that IRF3 exerts its major effect on sepsis pathogenesis through its presence in stromal cells, with indirect effects on leukocytes.
Assessment of the global chromatin landscape and transcriptome of peripheral iNKT cell subsets
Authors: Paynich Mallory L , Engel Isaac , Seumois Gregory , Liang Shu , de la Mata Sara Herrera , Sethi Ashu , Premlal Ashmitaa Logandha Ramamoorthy , Greenbaum Jason A , Vijayanand Pandurangan , Rao Anjana , Scott-Browne James , Kronenberg Mitchell 
Published: January 2023

Abstract
Vα14i invariant Natural Killer T (iNKT) cells are important modulators of immune responses. They differentiate into three effector cell subsets in the thymus, NKT1, NKT2, and NKT17, which resemble Th1, Th2, and Th17 CD4 T cells. After exiting the thymus, iNKT cells localize to tissues and do not recirculate, but the impact of tissue localization on the epigenetic landscape and transcriptome of each subset is not known. We assessed global chromatin accessibility and transcriptional activity using ATACseq and RNAseq in iNKT cell subsets isolated from the thymus, spleen, liver, and lung. By comparing iNKT cell subsets within each tissue, we found over 5,000 differentially accessible regions of chromatin. This is consistent with previous analyses showing great differences in the transcriptomes of the thymic iNKT cell subsets. Interestingly, relatively limited differences in the accessible chromatin or transcriptome were observed when comparing the same subset from different sites, e.g., NKT1 cells from different tissues. An exception is the unique set of accessible chromatin regions and transcripts identified in all iNKT cell subsets in the lung. Lung iNKT cells exhibited features of increased AP-1 transcription factor activity, which has been correlated with both activation and tissue residency, found in other lung lymphocyte populations. After antigen challenge, an iNKT cell subset with features similar to T follicular helper cells is abundant; these cells are highly different from the other subsets. Taken together, these data indicate that the epigenome and transcriptome of iNKT cells is highly impacted by subset decision, and much less by tissue localization, although dynamic changes occur after antigen exposure.
Sustained E protein activity selectively inhibits ILC2 development
Authors: Berrett Hannah R , Alberola-Ila Jose 
Published: January 2023

Abstract
Innate lymphoid cells (ILCs) are among the first cells to respond to invading pathogens. They coordinate the immune response through the use of effector programs, primed cell responses that cause release of specific cytokines. There are three ILC subsets, ILC1s, ILC2s, ILC3s. All three share a developmental requirement for Id2, a dominant negative inhibitor of the E protein family of transcription factors. To examine how E protein activity affects ILC subset development, we expressed ET-2 during ILC development in mice. ET-2 is a chimeric molecule which restores some E protein activity by competing with Id2 for E protein binding. We examined ILCs in their site of development, the bone marrow, and in a site of mature cells, the lungs. While we did not see changes in overall populations of ILC subsets between control and ET-2 mice, we did see a selective decrease in the percentage of ET-2-expressing ILC2s in ET-2 mice in both bone marrow and lungs. However, these ET-2-expressing ILC2s were still capable of secreting their effector program cytokines of IL-5 and IL-13. These results indicate that partially sustaining E protein activity negatively affects ILC2 development, but not that of ILC1s or ILC3s.
Interleukin-37 improves aging-associated declines in adaptive immunity leading to enhanced suppression of Ph+ leukemia
Authors: Henry Curtis J , Eisenmesser Elan , Dinarello Charles A , DeGregori James 
Published: January 2023

Abstract
Currently over 600 million people worldwide are over the age of 65. This number is predicted to reach 1.6 billion by 2050, representing a 17 percent increase in the world’s aged population. This amazing achievement also presents with concerns, notably our inability to effectively treat older patients with diseases of varying etiologies. Chronic inflammation, which commonly manifests in aged populations, has been shown to promote oncogenesis and compromise immunity. However, the relationship between these aging-associated manifestations are still unclear.
In preliminary studies we found that aging-associated inflammation promotes the expansion of inhibitory immune cells in the spleen, increases the surface expression of the inhibitory mediators PD1/PD-L1 on immune cells, and attenuates interferon-gamma (IFN-γ) production in both CD4+ and CD8+ T-cells. Surprisingly, we have discovered that the anti-inflammatory cytokine interleukin-37 (IL-37) significantly reduces inflammation in aged mice and restores IFN-γ production in both T-lymphocyte populations to almost youthful levels. Importantly, recombinant IL-37 (rIL-37) significantly extends the survival of aged mice with Ph+ leukemia. These observations suggest that chronic inflammation attenuates immunity in aged mice which can be rejuvenated by IL-37 exposure. Since attenuated immunity and increased disease prevalence are hallmarks of aging, our studies highlight the potential use of rIL-37 as a treatment strategy to improve immunity in aged populations to combat disease.
Keap1-Nrf2 system controls cellular metabolism to govern NKT cell homeostasis and effector functions
Authors: Pyaram Kalyani , Kumar Ajay , Chang Cheong-Hee 
Published: January 2023

Abstract
Kelch-like ECH-associated protein (Keap1) and nuclear factor (erythroid-derived 2)-like 2 (Nrf2) proteins work in concert as anti-oxidant system to regulate reactive oxygen species (ROS) levels. Additionally, Keap1-Nrf2 system has been shown to play a role in T cell-mediated inflammation but its role for maintenance and function of innate T cells is unclear. Using mice with T-cell specific deletion of Keap1 (KO) leading to higher Nrf2 activity, we recently reported that Keap1-Nrf2 system plays an essential role in the development and homeostasis of invariant natural killer T (NKT) cells. At steady state, KO NKT cells show increased rates of proliferation as well as apoptosis together with altered cell metabolism involving higher glucose uptake, glucose transporter-1 expression, mitochondrial mass and mitochondrial potential but lower ROS than WT NKT cells. Interestingly, upon activation with specific ligand a-GalCer, KO NKT cells proliferated lesser than WT NKT cells. Gene expression data indicated higher glycolysis and lower glutaminolysis in activated KO NKT than WT NKT cells. Further, unstimulated WT NKT cells were found to have elevated levels of glutamine and glutamate. NKT cells stimulated in the absence of glutamine survived and proliferated poorly but had no effect on cytokine production suggesting the importance of glutamine metabolism and keeping a check on glycolysis for the homeostasis and proliferation of NKT cells. Overall, our findings indicate that, via Nrf2, Keap1 positively regulates glutaminolysis and negatively regulates glycolysis to maintain NKT cell homeostasis and promote activation-driven proliferation. Here, we report a yet unknown role of Keap1-Nrf2 system in the cell metabolism of T cells.
Liver macrophages controls Mycobacterium tuberculosis growth by enhancing autophagy
Authors: Thandi Ramya Sivangala , Tripathi Deepak , Radhakrishnan Rajesh Kumar , Paidipally Padmaja , Vankayalapati Ramakrishna 
Published: January 2023

Abstract
Alveolar macrophages are the first cells to come in contact with TB pathogen in lung, but unable to eliminate Mycobacterium tuberculosis (M. tb) completely and serves as niche. In the current study, we compared M. tb growth and cytokine production by murine alveolar and liver macrophages. We found three-fold higher CFU in alveolar macrophages compared to liver macrophages (5 ± 1.7 × 106 vs. 1.776 ± 0.5 ×106 CFU) indicating that liver macrophages are more efficient in inhibiting M. tb growth. In contrast, M. tb H37Rv infected alveolar and liver macrophages produced equal amounts of TNF-α, IL-6, IL-10 & IL-1β. There is no significant difference in the apoptosis and M1/M2 paradigm of M. tb infected alveolar and liver macrophages. Flow cytometry analysis revealed the percentage of LC-3B+ M. tb infected liver macrophages were two-fold higher compared to percentage of LC-3B+ M. tb infected alveolar macrophage. This was confirmed by real time PCR. We also noted distinctly enhanced LC-3B puncta formation in infected liver macrophages as examined by confocal microscopy. We found significantly enhanced M. tb CFU in liver macrophages transfected with LC-3B, ATG-5, ATG-7 and Beclin-1 siRNA compared to liver macrophages transfected with control siRNA (p&lt;0.01; 0.006; 0.01&0.002) respectively. Our results suggest that autophagy is involved in better restriction of M. tb growth by liver macrophages. Studies are underway to compare metabolic changes of control and M. tb H37Rv infected alveolar and liver macrophages and in vivo relevance to our current findings using mouse model of M. tb infection.
Unrelated respiratory infections compromise established cellular immunity by promoting apoptosis of pre-existing lung-resident memory CD8 T cells
Authors: Hayward Sarah L , Li ZR Tiger , Lobby Jenna L , Eggert Joel O.P. , Kohlmeier Jacob E 
Published: January 2023

Abstract
Lung-resident memory T cells (lung TRM) are critical for protective heterosubtypic immunity against influenza viruses. However, the efficacy of cellular immunity against respiratory pathogens such as influenza wanes over time due to the gradual loss of flu-specific lung TRM. One possible mechanism for this decline is frequent exposure to environmental and biological insults resulting in localized inflammation that promotes the death of established lung TRM. We investigated whether unrelated infections could exacerbate the loss of pre-existing, flu-specific lung TRM and reduce the efficacy of cellular immunity to subsequent influenza challenge. Infection of influenza-immune mice with Sendai virus, an unrelated murine parainfluenza virus, resulted in significantly higher viral titers and greater morbidity following influenza challenge compared to PBS-treated controls. This loss of protective cellular immunity corresponded to a significant decrease in the number of pre-existing flu-specific lung CD8 TRM compared to PBS controls due to increased apoptosis. This loss of pre-existing lung TRM following Sendai infection was not due to competition for limited resources or tissue niches between flu- and Sendai-specific lung TRM. Sendai infection had no impact on the number of systemic flu-specific memory CD8 T cells in the spleen. The loss of lung TRM required a respiratory infection, as LCMV infection and intranasal delivery of TLR agonists did not significantly reduce the number of pre-existing flu-specific lung CD8 TRM. Together, these data suggest that tissue damage induced by unrelated respiratory infections can promote the loss of pre-existing lung TRM and compromise cellular immunity against respiratory pathogens.
Prior Bacillus Calmette-Guérin (BCG) vaccination ameliorates the pathogenesis of Type 2 diabetes mellitus mice infected with Mycobacterium tuberculosis
Authors: Radhakrishnan Rajesh Kumar , Tripathi Deepak , Thandi Ramya Sivangala , Paidipally Padmaja , Vankayalapati Ramakrishna 
Published: January 2023

Abstract
Previously, we found experimentally induced type 2 diabetes mellitus (T2DM) mice are highly susceptible to Mycobacterium tuberculosis (Mtb) infection. In the present study, we determined whether prior BCG vaccination has any effect on the susceptibility of T2DM mice infected with Mtb. C57BL/6 mice were vaccinated with BCG or treated with PBS, three months later some mice were induced with T2DM and after another month fifty percent of all groups of mice were challenged with Mtb. All Mtb infected T2DM mice and 40% of uninfected T2DM mice died within 10 months. In contrast, only 40% of Mtb infected BCG vaccinated T2DM mice and 20% of uninfected BCG vaccinated T2DM mice died. Lung bacterial burden was significantly less in Mtb infected BCG vaccinated T2DM mice compared to PBS treated Mtb infected mice. Pro and anti-inflammatory cytokine levels were significantly high in the lungs of Mtb infected BCG vaccinated T2DM mice compared to all other groups of vaccinated and PBS treated mice infected with Mtb. Our findings suggest that prior BCG vaccination protects Mtb infected mice from T2DM induced pathogenesis. Studies are underway to determine the BCG induced mechanism/s those protect T2DM mice challenged with Mtb.
Acetylcholine and Cholinergic Lymphocytes in the Immune Response to Influenza
Authors: Phillips Joy A , Horkowitz Alex , Feuer Ralph 
Published: January 2023

Abstract
Acetylcholine acts to control inflammation in part via binding to α7 nicotinic acetylcholine, receptors on inflammatory macrophages, inhibiting NF-κB nuclear translocation and down-regulating ongoing inflammatory cytokine synthesis. This pathway is presumed to function in the lungs, but the source of local acetylcholine in response to pulmonary inflammation is as yet unknown. We have found evidence that the airway acetylcholine concentration increases over the course of influenza infection, peaking 10 days after infection before rapidly decreasing. The kinetics of acetylcholine increase and loss is mirrored by the appearance and disappearance of cholinergic CD4 T cells in the lungs and airways during influenza illness and resolution. These CD4 T cells bind to influenza-specific tetramers, indicating antigen specificity. This is the first evidence for cholinergic lymphocyte participation in the response to respiratory viral infection. The role for acetylcholine during infleunza recovery is as yet unknown. Decreasing the airway acetylcholine concentration at the later stages of influenza infection leads to extended inflammation marked by increased expression of Allograft-inhibitory factor 1 (Aif-1, IBA1). Together, the results indicate that acetylcholine produced by cholinergic lymphocytes act to regulate pulmonary inflammation during viral infection.