bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterizing the role of Lactobacillus spp. in systemic lupus erythematosus
Authors: Puig Xavier Cabana , Mu Qinghui , Swartwout Brianna , Abdelhamid Leila , Prakash Meeta B. , Reilly Christopher M. , Luo Xin M. 
Published: January 2023

Abstract
Systemic lupus erythematosus (SLE) is a multi-system autoimmune disease with no known cure. The role of gut microbiota and its interaction with the immune system can direct tolerance induction to self-antigens not only in the intestinal mucosa but also at the systemic level. Our lab previously showed differences between the gut microbiota in lupus-prone MRL/Mp-Faslpr (lpr) mice compared to healthy controls, with lower Lactobacillaceae levels in lpr mice. Restoring the microbiota with a mix of 5 different Lactobacillus strains, L. reuteri, L. oris, L. johnsonii, L. gasseri, and L. rhamnosus significantly attenuated lupus-liked disease in lpr mice, by increasing regulatory T cells and balancing T helper-17 cells. Interestingly, we found L. reuteri and an uncultured Lactobacillus spp. were present based on 16S rRNA sequencing. To evaluate the effect of the main candidate L. reuteri in attenuating lupus, we treated lpr mice with the single bacterial strain. Surprisingly, L. reuteri did not reproduce the same results as the Lactobacillus mixture. Thus, we tested the remaining strains individually but none was able to recapitulate the effect of the 5 strains. Additionally, we treated lpr mice with the supernatant of the 5 strains containing secreted metabolites, which did not significantly attenuate lupus. These results suggest that communications among different strains of lactobacilli may be required in ameliorating the disease. Probiotic Lactobacillus spp. may be an alternative treatment against SLE, but further investigations are warranted to delineate the mechanisms of how multiple strains of lactobacilli can exert a beneficial effect as a community.
Analysis of the nonobese diabetic mouse islet MHC-II peptidome reveals posttranslationally modified autoantigens
Authors: Lichti Cheryl , Vomund Anthony N. , Peterson Orion J. , Wan Xiaoxiao , Unanue Emil R 
Published: January 2023

Abstract
Autoimmune diabetes results from the destruction of insulin-producing beta cells, a process initiated by CD4 T cells recognizing MHC-II bound beta cell-derived peptides. We identified MHC-II bound peptides in the islets and throughout the peripheral lymphatic system in order to better understand diabetes initiation and progression. Toward this end, we performed unbiased nanoflow liquid chromatography-tandem mass spectrometry (nLC-MS/MS) analysis to obtain sequence information for MHC-II peptides isolated from islets, pancreatic lymph nodes and spleens of nonobese diabetic (NOD) mice. Peptides derived from beta cell proteins were further examined for their relative I-Ag7 binding strength and CD4 T cell autoreactivity. For a discussion of the major immunogenic peptides derived from the B chain of insulin and from C peptide, see the abstract of Wan et al.
Herein we discuss the finding of a deamidated C peptide fragment and our search for fused peptides. We identified the deamidated insulin-1 C peptide fragment Ins1C:51–61, LQTLALEVARE. Evidence in the literature supports this C-terminal deamidation as being spontaneous rather than enzyme-mediated. Deamidation improved I-Ag7 binding compared to the wild type peptide and increased its immunogenicity, demonstrating the biological importance of this modification. The homologous peptide from insulin-2 was not identified, indicating a possible sequence bias for spontaneous deamidation. We identified only one fused peptide bound to I-Ag7, an insulin C peptide-islet amyloid polypeptide hybrid insulin peptide (HIP) that matches the previously reported HIP6.9. We also identified several free fused peptides in crinosomes and posit this as the probable site of their formation.
Toll-like Receptor 2 induces pathogenicity in Th17 cells
Authors: Marks Kathryne E , Flaherty Stephanie , Reynolds Joseph M 
Published: January 2023

Abstract
CD4+ T cells, especially Th17 cells, are instrumental in the development and progression of autoimmune diseases, such as multiple sclerosis (MS), psoriasis, and rheumatoid arthritis. While pathogenic Th17 cells drive inflammation in autoimmunity, the molecular programming underlying their pathogenicity remains insufficiently understood. Furthermore, very little is known regarding the role of the pattern recognition receptor TLR2 in Th17 pathogenicity. We have previously shown that activation of TLR2 with PAM3CSK4 during Th17 differentiation results in increased production of IL-17A and IL-17F and significantly increases the proliferation of Th17 cells in vitro. Herein, we show that TLR2 induces pathogenicity in Th17 cells, similar to what has been shown for IL-23. TLR2 signaling results in increased encephalitogenic migration of Th17 cells, in addition to increased cytokine production. To further investigate the effect of TLR2 activation on Th17 cells, we utilized RNA sequencing and found 390 genes that are upregulated and 355 genes that are downregulated following TLR2 signaling in Th17 cells. Several of these genes we have identified are important regulators that either increase or restrain the inflammatory potential of Th17 cells. We further address the role of TLR2 in Th17-mediated autoimmune disease using experimental autoimmune encephalomyelitis (EAE), a mouse model of MS. We show that encephalitogenic Th17 cells expanded with a TLR2 agonist induced EAE disease to the same extent as those expanded with IL-23. Altogether, this study establishes TLR2 signaling as crucial for induction of pathogenic Th17 cells in autoimmune disease.
Genetic Interactions of the Transcription Factor Ets1 and IL17RA Signaling in Autoimmunity and Immunodeficiency
Authors: Battaglia Michael , Sunshine Alex , Luo Wei , Jin Richard M , Garis Matthew , Stith Alifa , Lindemann Matthew , Miller Lloyd S , Sinha Satrajit , Wohlfert Elizabeth A , Garrett-Sinha Lee Ann 
Published: January 2023

Abstract
Ets1 is a lineage-specific transcription factor that regulates B and T cell functions in development and disease. Mice that lack Ets1 (Ets1 KO) develop spontaneous autoimmune disease with high levels of autoantibodies. Naïve CD4+ T cells isolated from Ets1 KO mice differentiate more readily to Th17 cells that secrete IL17, a cytokine extensively implicated in autoimmune disease pathogenesis. To determine if increased IL17 production contributes to the development of autoimmunity in Ets1 KO mice, we crossed Ets1 KO mice to mice lacking the IL17 receptor A subunit (IL17RA KO) to generate double knock out (DKO) mice. We found that the absence of IL17RA signaling did not prevent or ameliorate the autoimmune phenotype of Ets1 KO mice, but rather that DKO animals exhibited worse symptoms with significant increases in activated B cells and secreted autoantibodies. This was correlated with a prominent increase in the numbers of T helper 2 (Th2) and T follicular helper (Tfh) cells. In addition to the autoimmune phenotype, DKO mice also showed aspects of immunodeficiency and developed spontaneous skin lesions colonized by Staphylococcal species. When DKO mice were experimentally infected with Staphylococcus aureus they were unable to clear the bacteria, despite a robust anti-staphylococcal antibody response. Persistent skin infection results in increased immune cell activation and likely contributes to the enhanced autoimmune symptoms of DKO versus Ets1 KO mice. Our studies suggest that targeting IL17RA signaling in autoimmune diseases might in some cases result in increased autoimmunity or to increased susceptibility to opportunistic infections.
GM-CSF mediates development of eosinophil-dominant autoimmune uveitis in the absence of both IFN-γ and IL-17A
Authors: Horai Reiko , Bing So Jin , Silver Phyllis B. , Jittayasothorn Yingyos , Chan Chi-Chao , Caspi Rachel R 
Published: January 2023

Abstract
Autoimmune uveitis is a group of blinding diseases triggered by activated retina-specific T cells. Studies in uveitis patients and experiments in animal models of experimental autoimmune uveitis (EAU) support the notion that Th1 and Th17 cells are both pathogenic effectors and each can elicit ocular autoimmunity independently of the other. Since absence of IFN-γ or IL-17A individually failed to abolish pathology of EAU, we examined EAU development in the absence of both cytokines. Ifng−/−Il17a−/− mice were fully susceptible to EAU and displayed eosinophil-dominant ocular infiltrates, as opposed to mononuclear infiltrates in WT mice. EAU was ameliorated in double-deficient mice when eosinophils were genetically absent or their migration was blocked, supporting a pathogenic role of eosinophils in the absence of both IFN-γ and IL-17A. In Ifng−/−Il17a−/− mice immunized for EAU, ocular infiltrates contained increased GM-CSF-producing CD4 T cells, and supernatants of antigen-recalled splenocytes contained enhanced levels of GM-CSF that contributed to activation and migration of eosinophils in vitro. Systemic or local blockade of GM-CSF ameliorated EAU in Ifng−/−Il17a−/− mice. Neutralization of GM-CSF during the induction phase of EAU decreased eosinophil infiltration to the eye and eosinophil peroxidase levels in the eye and in the serum. These results support the interpretation that, in the concurrent absence of IFN-γ and IL-17A, GM-CSF takes on a major role as a pathogenic effector cytokine and induces an eosinophil-dominant pathology. This may impact therapeutic strategies aiming to target IFN-γ and IL-17A in autoimmune uveitis.
Regulation of necroptosis by targeting tumor suppressor death-associated protein kinase 1
Authors: Lai Ming-Zong , Wu Yung-Hsuan , Chou Ting-Fang , Young Leslie , Hsieh Fu-Yi , Pan Hsuan-Yin , Mo Shu-Ting , Brown Shani Bialik , Chen Ruey-Hwa , Kimchi Adi 
Published: January 2023

Abstract
Death-associated protein kinase 1 (DAPK1, DAPk, DAPK) is known for its involvement in apoptosis and autophagy-associated cell death. Here, we identified an unexpected function of DAPK1 in suppressing necroptosis. DAPK1-deficiency renders macrophages and dendritic cells susceptible to necroptotic induction by different stimuli. We also observed an inhibitory role for DAPK1 in necroptosis in HT-29 cells, since knockdown or knockout of DAPK1 in such cells increased their sensitivity to necroptosis. Increased necroptosis was associated with enhanced formation of the RIPK1-RIPK3-MLKL complex in these DAPK1-deficient cells. We further found that DAPK1-deficiency led to decreased MAPK activated kinase 2 (MK2) activation and reduced RIPK1 S321 phosphorylation, with this latter representing a critical step controlling necrosome formation. Most TNF signaling pathways, including ERK, JNK and AKT, were not regulated by DAPK. In contrast, DAPK selectively promoted MKK3-induced p38 MAPK activation, resulting in enhanced MK2 phosphrylation. Our results reveal a novel role for DAPK1 in inhibiting necroptosis and illustrate an unexpected selectivity for DAPK1 in promoting p38 MAPK-MK2 activation. Importantly, our study suggests that modulation of necroptosis and p38/MK2-mediated inflammation may be achieved by targeting DAPK1.
Gamma subunit of complement component 8 is an innate immune suppressor in brain
Authors: Suk Kyoungho 
Published: January 2023

Abstract
The complement system is a part of the innate immune system, which comprises several small proteins activated by sequential cleavages. The majority of these complement components, such as components 3a (C3a) and C5a, are chemotactic and pro-inflammatory. However, in this study, we revealed an inhibitory role of complement component 8 gamma (C8G) in neuroinflammation. Novel findings show that the expression level of C8G increases in inflamed brain, and C8G is mainly localized to brain astrocytes. Experiments using recombinant C8G protein and shRNA-mediated knockdown showed that C8G inhibits microglial activation and neuroinflammation. In acute and chronic animal models of Alzheimer’s disease (AD), which exhibit strong neuroinflammation, C8G attenuated cognitive decline and glial hyperactivation. In these animals and patients with AD, we found higher C8G levels in brain tissue, cerebrospinal fluid, and plasma. Additionally, we identified sphingosine-1-phosphate receptor 2 (S1PR2) as a novel interaction protein of C8G and demonstrated that astrocyte-derived C8G interacts with S1PR2 to antagonize the pro-inflammatory action of S1P in microglia. Taken together, our results reveal a previously unrecognized role of C8G as a neuroinflammation inhibitor and indicate that C8G can be used therapeutically for the containment of neuroinflammation and treatment of related neurological diseases, such as AD.
IEX-1 deficiency in hematopoietic cells mitigates high fat diet-induced obesity and glucose intolerance
Authors: Shahid Mohd , Loya Egwin , Wen Shuguang , Wu Mei X 
Published: January 2023

Abstract
We previously showed that IEX-1 paucity in mice inhibited high fat diet (HFD)-induced obesity and insulin resistance. IEX-1 deficiency induced browning of white adipose tissue (WAT) by promoting alternative activation of macrophages (AAMs), increasing energy expenditure. We now hypothesize that IEX-1 deficiency in macrophages promotes alternative activation of adipose tissue macrophages (ATM) and induces browning to inhibit obesity. We performed reciprocal bone marrow (BM) transplantation between IEX-1 knockout (KO) and wild-type (WT) mice to generate four types of chimeras. We fed these mice with HFD for 20 weeks and monitored their body weight, glucose disposal, and determined ATM phenotype using flow cytometry. While WT+WT-BM control mice (WT mice received WT bone marrow) gained ~80% body weight on HFD, WT+KO-BM mice (WT mice received KO bone marrow) increased their body weight only by 50% (p&lt;0.01). Conversely, KO+WT-BM mice (KO mice received WT bone marrow) exhibited increased weight gain on HFD as compared to KO+KO-BM control mice that remained lean (p&lt;0.05). Likewise, WT+KO-BM mice displayed greater glucose disposal as compared to WT control, and KO+WT-BM mice became glucose intolerant as compared to KO control as determined by glucose tolerance test. Analysis of ATM phenotype in mice fed with HFD for 5 weeks showed that HFD increased the percentage of classically activated macrophages (CAMs) by 3–4-folds (p&lt;0.01), and decreased AAMs by ~30% (P&lt;0.05) in epidydmal and inguinal WAT of WT+WT-BM mice. However, these effects were markedly suppressed in WT+KO-BM mice. Collectively, these data suggest that IEX-1 in hematopoietic cells contributes to HFD-induced obesity and glucose intolerance via inhibiting AAMs polarization.
Phosphatase SHP2-mediated mitochondrial homeostasis for the resolution of inflammation
Authors: Xu Qiang , Guo Wenjie , Wu Xingxin , Sun Yang 
Published: January 2023

Abstract
The negative regulation of inflammation is very important for the resolution of inflammatory diseases. Although many components and mediators in inflammation have been identified, how inflammation is finely regulated remains lack of evidence. Here we show that Src homology-2 domain containing protein tyrosine phosphatase-2 (SHP2) translocates to mitochondria in the early time of inflammatory stimulation. The RRWFH motif in SH2 domain is essential for the translocation of SHP2. This phosphatase localizes in the mitochondrial matrix with the help of Tom20/Tom40 in outer membrane and Tim23 in inner membrane. Then SHP2 interacts with ANT1, a central molecule controlling mitochondrial permeability transition. This mechanism prevents the collapse of mitochondrial membrane potential, mtDNA release and ROS production, and thus inhibits the hyperactivation of NLRP3 inflammasome. Ablation or inhibition of SHP2 in macrophage causes intensified NLRP3 inflammasome activation, production of IL-1β and IL-18, and increased sensitivity to peritonitis. We are also engaged in seeking the activator of SHP2. We have found that the natural products fusaruside and trichomides A can increase the phosphorylation of SHP2 and some of synthesized compounds can directly activate the phosphatase. These SHP2 activators show a significant anti-inflammatory activity in various disease models. Collectively, our data highlight that SHP2 orchestrates an intrinsic regulatory loop for the mitochondrial homeostasis to limit excessive NLRP3 inflammasome activation, suggesting a possibility to treat inflammatory diseases via maintaining mitochondrial homeostasis.
Role of myeloid derived suppressor cells in regulating herpes stromal keratitis
Authors: Sarkar Roman , Sehrawat Sharvan 
Published: January 2023

Abstract
Myeloid derived suppressor cells (MDSCs) are heterogeneous subsets of immature myeloid cells. Phenotypically such cells are identified as CD11b+Gr1lo-int cells in mice and CD33+CD11+LIN−HLA-DR− cells in humans. That MDSCs expand and modify the disease outcome in cancers and some infections is known. In this study, we investigated the role of MDSCs during HSV1 induced herpes stromal keratitis (HSK), an immunoblinding disease of the cornea. MDSCs are expanded during the progression of HSK and effected immune suppression. MDSCs generated from bone marrow precursor cells using IL-6, IL-4 and GM-CSF inhibited CD4+ T cell activation in a contact dependent manner. Adoptive transfer of in vitro generated MDSCs in mice reduced the severity of HSK and recipient mice expressed reduction in PMNs and T effector cells in cornea. CD4+ T cells isolated from lymphoid organs of MDSCs recipient mice expressed higher levels of CD62L suggesting their hampered emigration. Pro inflammatory TH17 cells are also reduced in MDSCs recipient animals but the magnitude of regulatory T cells were increased. The promotion of foxp3+ regulatory T cells was achieved by both the conversion of non-Tregs into Tregs and stabilization of foxp3 in already committed regulatory T cells. Insights into the molecular mechanisms obtained by transcriptomic profile of two populations will be discussed.
The growth regulator human proliferation-associated 2G4 (PA2G4) protein interacts with NLRP7 which is involved in recurrent hydatidiform molar pregnancy
Authors: So Matthew , Lupfer Christopher R 
Published: January 2023

Abstract
Recurrent hydatidiform molar pregnancies are characterized by uncontrolled proliferation of trophoblasts resulting in the failure of the embryo and placenta to develop properly. Previous studies genetically mapped a mutation in NLRP7 as a cause for recurrent molar pregnancies. The goal of this study is to identify human proteins that interact with NLRP7, especially those that are involved in DNA acetylation and methylation, which could lead to the development of molar pregnancies. A yeast two-hybrid system using a human cDNA library was used to screen for interacting proteins, and protein interactions were verified by co-immunoprecipitation in HEK 239T cells. Additional experiments are planned to determine the functional significance of such interactions. Yeast screening results indicated several proteins that interact with NLRP7, however further testing will be focused on the interaction with Human proliferation-associated 2G4 (PA2G4), a human protein involved in growth regulation. Having potentially identified a protein involved in development through acetylation/deacetylation that interacts with NLRP7, we hope to shed more light on the molecular pathways that lead to the formation of recurrent molar pregnancies.
Connecting GWAS SNPs to Target Genes in primary human immune cell types
Authors: Chandra Vivek , Bhattacharyya Sourya , Schmiedel Benjamin J. , Madrigal Ariel , Gonzalez-Colin Cristian , Fotsing Stephanie , Kronenberg Mitchell , Peters Bjoern , Ay Ferhat , Vijayanand Pandurangan 
Published: January 2023

Abstract
Expression quantitative trait loci (eQTLs) studies have provided associations with gene expression for many non-coding genetic variants associated with human disease and evolution. However, they fail to pinpoint the functionally important eQTLs or provide mechanistic insights. Also, most eQTL discovery studies restrict analysis to SNPs within ±1 Mb of the TSS of the gene tested to minimize corrections for multiple association tests. Using proximity ligation-assisted H3K27ac ChIP-seq (HiChIP) assays, here we mapped eQTLs that overlap active cis-regulatory elements and interact with their target gene promoters (promoter-interacting eQTLs, pieQTLs) in five common immune cell types. This allowed us to narrow down functionally important eQTLs and show mechanisms that explain their cell type restriction. A subset of the identified pieQTLs overlapped non-transcribed promoters, which interact with their target gene promoters and function as enhancers as validated by CRISPRi. In addition, we devised a novel approach to eQTL discovery that relied on HiChIP-based promoter interaction maps as a structural framework for deciding what SNPs to test for association with gene expression. We discovered ultralong distance pieQTLs (&gt;1Mb from target gene), including several disease-risk variants and new eGenes such as FHIT for which we validated the role of an ultralong distance pieQTL by CRISPRi. Our study provides insights into cell-specific gene regulatory mechanisms and highlights the potentially functional non-coding variants (pieQTLs) linked to human diseases.
Regulatory T cells suppress novel skeletal muscle macrophages identified by single-cell RNA sequencing
Authors: COULIS Gerald , Kastenschmidt Jenna , Mannaa Ali , Nguyen Quy , Pervolarakis Nicholas , Duarte Jorge , Emami Melissa , Yang Catherine , Kessenbrock Kai , VILLALTA Armando 
Published: January 2023

Abstract
Duchenne muscular dystrophy (DMD) is a lethal X-linked disorder that results from mutations in the dystrophin gene causing necrosis, inflammation and ultimately fibrosis. In DMD, muscle macrophages are multifaceted effector immune cells that regulate multiple pathogenic processes, including myofiber injury, inflammation and fibrosis, but also promote regeneration. Previously, we demonstrated that regulatory T cells (Tregs) ameliorated the severity of muscular dystrophy by regulating M1-like and M2-like macrophage activation, and more recently, a subset of undefined macrophages. Herein, we used single-cell RNA sequencing (scRNAseq) approaches to define the phenotypic complexity and transcriptional profile of muscle macrophages in healthy and dystrophic muscle. A T-distributed Stochastic Neighbor Embedding (t-SNE) analysis of gene expression data revealed that muscle macrophages clustered into six novel populations defined by unique transcriptional programs. We observed that a population expressing high levels of galectin-3 was absent in wildtype and dystrophic muscle before the onset of disease, but was increased at the onset of acute pathology and further expanded when Tregs were depleted in the mdx mouse model of DMD. In light of emerging evidence in the literature suggesting a role for galectin-3 and Tregs in fibrosis, we performed in vivo functional assays to underscore the role of the Treg-Macrophages axis in the control of fibrosis in DMD. Our data support a new paradigm, in which unique transcriptional programs define novel macrophage populations likely adapted to the diseased muscle milieu, and suggest that therapies focused on augmenting Tregs function in dystrophic muscle may be beneficial to treat fibrosis.