bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbiome methods in experimental autoimmune encephalomyelitis.
Authors: Hoffman Kristina R , Daberkow David P , Kohl Hannah M , Long Tyrel , Kirby Trevor O , Ochoa-Reparaz Javier 
Published: January 2023

Abstract
Multiple Sclerosis (MS) is an autoimmune disease that affects the central nervous system (CNS) via neuroinflammation and demyelination. The exact triggers, subsets and effector mechanisms that contribute to disease progression are still largely unknown. Recent studies of healthy vs MS human stool samples indicated an altered microbiome, dysbiosis, which could lead to inflammation and disease. Experimental autoimmune encephalomyelitis (EAE) is a model used for the study of MS and can be induced in multiple non-rodent and rodent species. It is critical to control the environment of both the animal facility and experimental housing conditions in microbiome studies. We compared commercial vendors, Envigo and Jackson Laboratory, C57BL/6 female mice. Fecal samples were collected at Day 0, 14, and 21 for DNA extraction and sequencing of the ribosomal DNA (rDNA) to analyze the gut microbiome composition prior to and after induction of EAE. There was a significant difference between sources with Jackson Laboratory mice having an increased severity index compared to Envigo mice (p &lt; 0.01) and a decreased survival rate of 20% when compared to 85% for Envigo mice. Our results suggest different sources of EAE mouse models have critical impacts on microbiome composition and levels of disease severity. Furthermore, this highlights the importance of consistent and controlled conditions from the animal model source, and throughout the experiment, when inducing EAE in mice and other animal models of disease.
This project was sponsored by NIH grant R15 NS107743.
T cell intrinsic role for NOD2 in Blau Syndrome
Authors: Napier Ruth J , Vance Emily E , Koney Kylie V , Lee Ellen J , Davey Michael M , Rosenzweig Holly L 
Published: January 2023

Abstract
Children with mutations in the nucleotide binding domain of NOD2 cause the monogenetic inflammatory disease Blau Syndrome, which is characterized by dermatitis, arthritis and uveitis. NOD2 is a well-known microbial sensor important in anti-bacterial immunity. However, the mechanism by which mutated NOD2 causes non-infectious inflammation in Blau is unknown. We recently reported a novel function of Nod2 as a central regulator of T cell homeostasis and as a negative regulator of autoreactive Th17 responses in experimental autoimmune uveitis (EAU) and arthritis. Here, we examined the effect of Blau mutations on T cell function and EAU using Blau knock-in mice carrying the most common Blau-mutation R314Q (corresponding to R334Q in humans) and Blau patient cells. We found that CD4+ T cells from Blau patients and Blau mice, produced increased IL-17 but decreased IFNγ following in vitro TCR-activation compared to control patients and WT mice, respectively. Blau mice developed worsened EAU compared to WT controls, which was accompanied by increased autoreactive (retina-specific) Th17 cells within the eye. Lymphocyte-deplete Rag1−/− mice reconstituted with Blau CD4+ T cells developed worse EAU than WT T cell recipients, indicating that CD4+ T cells expressing Blau-specific Nod2 mutations are sufficient to cause exacerbated EAU. Cumulatively, these data reveal a previously unconsidered role for Th17 cells in Blau Syndrome, and provide new T cell-targeted therapeutic avenues to treat this disease.
Supported by grants from VA (CDA-2 IK2BX004523 and Merit I01BX002180) and NIH (R01 EY025250).
Leveraging genetic correlation across immune-mediated disease to gain insights into underpowered studies of rare conditions
Authors: Molineros Julio , Elliott Katherine , Truong Dongnhu T , Fang Hai , Hart Amy , Li Shuwei , Waterworth Dawn , Knight Julian C , Black Mary Helen 
Published: January 2023

Abstract
Prevalence of immune mediated disease (IMD) within N. European populations varies from common (atopic dermatitis AD=10%) to rarer (giant cell arteritis-GCA=0.02%; hidradenitis suppurativa-HS=0.77%). This directly affects statistical power to detect genomewide SNP associations and to identify “causal” genes.

Objective
Leverage genetic correlations between differently powered IMD cohorts to study the genetic mechanisms underlying multiple immune-mediated diseases.
We used UK Biobank clinical data to create 18 IMD cohorts and a control set of individuals without any history of autoimmune disease (N=50,136). Using whole genome sequencing data from ~140K participants of the UKB, we performed SNP-level GWAS with REGENIE v2, and prioritized the associated genes using association statistics, in silico annotation, and eQTL information, as implemented in the Priority Index (Pi) algorithm. We used k-means clustering across relative gene rank distances optimized with the elbow method to group IMDs according to similar genetic architectures.

Result
IMD cohort size ranged from 196 to 3,411 cases and were each compared with a common set of controls. Optimal clustering yielded 4 groups, each with 6,5,4 or 3 IMD’s respectively. One cluster of interest contained HS, AD, vitiligo, GCA and Sjogren’s syndrome. This cluster reflects similarity in common “pathogenic” genes across IMD and highlights new candidate genes for further investigation that would otherwise go unnoticed in poorly powered studies of GCA and HS.
In conclusion, our proposed use of genetic associations and clustering of their relative ranks across multiple disease phenotypes identified pathogenic genes in understudied IMDs that would otherwise not have been elucidated.
Supported by Janssen Research & Development
Genes associated with Multiple Organ Dysfunction Syndrome during severe pediatric influenza
Authors: Novak Tanya , Crawford Jeremy Chase , Lange Christoph , Hahn Georg , Randolph Adrienne G 
Published: January 2023

Abstract
Influenza remains a global pathogen that causes significant morbidity and mortality even in previously healthy children. Multiple Organ Dysfunction Syndrome (MODS) is a potential complication developed during severe infection. This multi-site, national study investigated which genes are associated with resolving, developing, or predicting prolonged MODS in children admitted to ICU with severe influenza. PAXgene whole blood RNA from 216 influenza positive patients (median age 6.7 years, IQR: 2.6, 11.2) was extracted and hybridized to 469 NanoString nCounter® mRNA probes including positive/negative controls. Absolute mRNA molecules were quantified, normalized to 5 reference genes, and analyzed using linear models controlling for age, bacteria co-infections and type I error via FDR. Children who developed MODS had significantly higher levels of the antimicrobial Lactotransferrin (LTF) mRNA expression than those that never had MODS (p=0.04) whilst the latter group showed significantly higher expression of Transforming Growth Factor β1 (TGFBI) (p=0.04). In children with prolonged MODS, nine neutrophil degranulation genes were upregulated including TCN1, RETN, and LCN2 (p&lt;0.001) which have previously been implicated in sepsis-related ARDS and mortality, and as biomarkers for severe influenza in adults. This study highlighted a panel of genes that are associated with MODS during severe pediatric influenza and could potentially be used for predicting and managing this complication.
Supported by grants from NIH/Department of Health and Human Services 1R21HD095228-01
Targeted transcriptomic signature for monitoring anti-tuberculosis treatment response
Authors: Manneh Ismaila L , Darboe Fatoumatta , Owolabi Olumuyiwa , Dockrell Hazel M , Sutherland Jayne S 
Published: January 2023

Abstract
The long duration of anti-tuberculosis treatment is associated with poor adherence and treatment outcomes leading to higher relapse rates. Shortening treatment duration has been suggested to improve treatment outcome by increasing adherence. Sputum conversion, the gold standard for monitoring treatment, has low sensitivity and specificity for predicting relapse. Better markers are therefore needed and blood-based biomarkers have been suggested as potential alternatives. The aim of this study was to identify transcriptional signatures to predict anti-tuberculosis treatment outcomes, relapse, and treatment failure. We extracted RNA from whole blood PAXgene samples from 37 confirmed TB cases at diagnosis (baseline), 14 days and two months of treatment and measured gene expression using targeted sequencing on the NanoString nCounter MAX platform using the 799-gene host response panel. To identify genes that predict treatment response and relapse, we identified differentially expressed genes (DEGs) at Day 14 and two months of treatment and compared expression between fast (sputum converters by 2 months) and slow responders (sputum converters after 2 months). Using a cut-off of 1.5-fold change and a p value of 0.05, we observed 58 DEGs at Day 14 and 175 DEGs at two months relative to baseline. When we compared slow and fast responders, 14 genes were differentially expressed but these were not significant when adjusted for multiple comparisons. We have shown that DEGs can identify different stages of disease or treatment. Further analysis is ongoing to include other treatment timepoints (four months and six months) and importantly to include participants with known relapse.
SARS-CoV-2 induced oxidative stress promotes HMGB1 secretion to induce inflammation
Authors: Hosakote Yashoda Madaiah , Rayavara Kempaiah , Corri Levine B , McLellan Susan , Weaver Scott C , Chopra Ashok , Tseng Chein-Te K 
Published: January 2023

Abstract
The coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is a major ongoing pandemic, which results in life-threatening pneumonia and multiple-organ failure. Although the molecular mechanisms by which SARS-CoV-2 lead to various disease sequalae remain elusive, exaggerated inflammatory and immune responses can lead to the debilitating and lethal outcomes of this disease. Understanding how immune mechanisms contribute to the development of severe symptoms is essential for designing effective countermeasures against SARS-CoV-2. Our studies show that SARS-CoV-2 induces increased extracellular secretion of high-mobility group box 1 (HMGB1), a prominent damage-associated molecular pattern family member that alerts the immune system to potential damage and triggers immediate response. The goal of this study is to dissect the molecular mechanisms that promotes the release of HMGB1 and its associated cellular signaling in response to SARS-CoV-2 infection. Studies were conducted in human lung epithelial cells including A549-ACE2 and Calu-3/2B4 cells, mice, and COVID-19 patient samples. HMGB1 levels and oxidative stress markers were measured by an immune assay, Western blot, and qRT-PCR. SARS-CoV-2 infection induced severe oxidative stress, leading to enhanced extracellular release of HMGB1 and subsequent activation of signaling cascades to promote inflammation. Therefore, modulation of HMGB1’s proinflammatory signaling may reduce SARS-CoV-2-induced inflammation by controlling oxidative and inflammatory stress in COVID-19 disease.
This study was supported by a Young Clinical Scientist Award from the Flight Attendant Medical Research Institute (FAMRI) to YMH (grant I.D. number 123385), NIH/NIAID R21 AI35619 to YMH, and Rapid Response Pilot grant from NIEHS P30 Center Grant ES030285 to YMH. Additional support was from the Institute for Translational Science at UTMB, supported by a Clinical and Translational Science Award Mentored Career Development (KL2 Award; KL2TR001441), and Pilot grant (85393) from Institute for Human Infections & Immunity at UTMB, supported by Sealy & Smith Foundation to YMH.
Molecular mechanisms of dexamethasone-mediated modulation of inflammatory and interferon responses in severe COVID-19 patients.
Authors: Chimote Ameet A , Alshwimi Abdulaziz , Chirra Martina , Gawali Vaibhavkumar S , Hudock Kristin M , Powers-Fletcher Margaret V , Conforti Laura 
Published: January 2023

Abstract
Severe COVID-19 is characterized by cytokine storm, an excessive production of pro-inflammatory cytokines, which results in acute lung damage and death. Dexamethasone (Dex), a corticosteroid administered as a standard of care for severe COVID-19, has been shown to reduce the onset of severe complications in these patients. However, the mechanisms underlying the beneficial effects of Dex are poorly understood. We conducted a transcriptomic analysis (NanoString) of peripheral blood mononuclear cells (PBMCs) from COVID-19 patients with mild (no hospitalization) and severe (on ventilator in the ICU) disease. The latter group included patients ± Dex. Treatment of severe COVID-19 patients with Dex inhibited pro-inflammatory pathways, circulating cytotoxic and Th1 cells, interferon (IFN) signaling and the genes involved in cytokine storm (IL-1, IL-6 and IFN-γ), which were altered in severe vs mild disease. Pro-inflammatory immune cell functions are regulated by calcium signaling, which in turn is under the control of Kv1.3 potassium channels, but their role in the complications associated with COVID-19 remains elusive. RT-qPCR experiments in PBMCs from COVID-19 patient cohorts showed an increase in Kv1.3 expression in severe patients that was significantly reduced by Dex treatment. In agreement with these findings, in vitro treatment with Dex reduced Kv1.3 protein abundance in CD3+, CD4+, CD8+ T cell and CD56dim NK cells in healthy donor (HD) PBMC, while NanoString showed inhibition of pro-inflammatory genes and cytokines. Functional studies showed that Dex significantly reduced Kv1.3 activity and IFN-γ in HD T cells. Thus, our findings suggest that Kv1.3 inhibition contributes to the immunosuppression by Dex.
This work was supported by Senior Pilot Grant, University of Cincinnati, Department of Internal Medicine to LC, NIH (R38HL155775 to MC) and Biospecimens and associated data were provided by the Cincinnati COVID-19 Repository at the University of Cincinnati and Cincinnati Children’s Hospital Medical Center.
A surprising pathogenic role of B cells in mice with Alzheimer’s disease
Authors: Biragyn Arya , Kim Ki , Wang Xin , Ragonnaud Emeline , Bodogai Monica , McDevitt Ross A , Okun Eitan 
Published: January 2023

Abstract
The role of adaptive immune cells in Alzheimer’s disease (AD), a progressive neurodegenerative disease that associates with impaired clearance of toxic amyloid-b (Ab) peptide aggregates from the brain parenchyma, is rarely explored and mostly assumed to be beneficial. Here, using three, widely utilized transgenic AD mouse models (3xTgAD, APP/PS1, and 5xFAD mice), we provide counterintuitive evidence that the manifestation of AD requires B cells. Despite expression of the AD-fostering transgenes, the genetic loss of B cells or antibody-mediated depletion of circulating B cells at the onset of the disease is sufficient to reverse Aβ plaque burden and disease-associated microglia in the brains. The B-cell loss also ameliorates behavioral and memory deficits in AD mice. Mechanistically, AD we linked to infiltration of B cells into the brain parenchyma and production of immunoglobulins and pro-inflammatory factors. These results warrant a new look to B cells as important, pathogenic players of AD. As such, it underscores therapeutic value of B-cell inactivation in control AD progression 1.
This work was supported by the Intramural Research Program, NIA/NIH.
Inhibition of LRRK2 Kinase Activity in the Treatment of Crohn’s Disease
Authors: Deloer Sharmina , Fuss Ivan , Suebsuwong Chalada , Kumar Kunal , Devita Robert J , Peter Inga , Strober Warren 
Published: January 2023

Abstract
The leucine-rich repeat kinase 2 (LRRK2) gene is a genetic hotspot for gain-of-function mutations associated with various diseases such as Crohn’s and Parkinson’s disease. These mutations enhance LRRK2 kinase activity and, consequently, various inhibitors of this activity are currently being tested as treatment modalities. Here, we report studies of two novel kinase inhibitors (Termed CS-190 and CS-82) with LRRK2 inhibition activity. In vitro studies disclosed that the two inhibitors suppress LRRK2 phosphorylation as well as its ability to phosphorylate the LRRK2 targets, Rab 10 and 12; in addition, they suppress human dendritic cell production of TNFa stimulated by several known LRRK2 activators including the Dectin-1-ligand, zymosan-depleted S. cerevisiae extract. Finally, the inhibitors exhibited powerful suppression of the ability of LRRK2 to mediate NLRC4 inflammasome production of IL-1beta. These in vitro finding correlated with in vivo studies showing that IP administration of one of the kinase inhibitors (CS-82) ameliorates colitis in the DSS-colitis model as evaluated by weight loss and inflammation scores. These findings suggest that these newly developed inhibitors are potential agents for treatment of Crohn’s disease.
Contrasting roles for neutrophils and macrophages during experimental pyelonephritis
Authors: de Dios Ruiz Rosado Juan , Cortado Hanna , Robledo-Avila Frank , Spencer John David , Becknell Brian , Partida-Sanchez Santiago 
Published: January 2023

Abstract

Background
Urinary tract infections (UTIs) account for 7 million annual office visits and over $1.6 billion in health care spending in the United States. Uropathogenic Escherichia coli (UPEC) initiates over 80% of UTIs. When UPEC ascends from the bladder to the kidneys, the resulting pyelonephritis can lead to renal scarring and end-stage renal disease.

Objective
We determined the specific roles of monocytes and neutrophils in bacterial clearance and the development of kidney fibrosis during pyelonephritis.

Methods
Female C3H/HeOuJ mice were treated with neutrophil depleting or monocyte depleting antibodies (monoclonal). After cell depletion, the animals were transurethrally infected with UPEC (CFT073 strain). The progression of UTI was assessed via biophotonic imaging and quantification of bacterial burden in the urinary tract. Transcriptomic analyses were performed using customized TaqMan Arrays. Histopathological scores were performed by H&E and Sirius-Red stainings. The renal function was assessed by measuring blood levels of waste products and electrolytes.

Results
Monocytes and neutrophils function in a synchronized manner, while neutrophils engulf and eliminate UPEC in the urinary tract, monocytes differentiate into macrophages and promote inflammation in the bladder and kidney to boost the recruitment of neutrophils. However, the absence of neutrophils results in increased macrophage infiltration and exaggerated inflammatory responses in the urinary tract. Macrophage-dependent inflammation leads to renal scarring and renal dysfunction during UTI.

Conclusions
Our findings uncover a detrimental role for the neutrophil-macrophage imbalance in promoting renal scarring during pyelonephritis.
Supported by grants from NIH (K01 DK128379-01)
The role of phosphatidylserine receptor-mediated phagocytosis of amyloid-β by microglia in Alzheimer’s Disease.
Authors: Bauchle Casey Jordan , Owlett Laura , Karaahmet Berke , Olschowka John , O’Banion Kerry , Elliott Michael Rusty 
Published: January 2023

Abstract
The phagocytosis of apoptotic cells and cellular debris by microglia critically regulates immune homeostasis in the brain. In Alzheimer’s Disease (AD), microglial phagocytosis of amyloid-β (Aβ) aggregates is thought to play a protective role in AD pathogenesis, but the mechanisms by which this occurs are not well understood. Recent work has suggested that phosphatidylserine (PtdSer)-sensing receptors may induce Aβ plaque engulfment, and data from our lab and others’ supports this idea. To better understand the role of PtdSer-sensing receptors in Aβ clearance, we utilized immortalized cell lines and isolated primary microglia to examine PtdSer-mediated phagocytosis of Aβ aggregate targets in vitro and compared this to phagocytosis of apoptotic cells, as well as to phagocytosis by Fcγ receptors and complement receptors. Phagocytosis was measured by live-cell imaging and flow cytometry, and revealed distinct kinetics between the different forms of phagocytosis. We further investigated the role of specific PtdSer receptors using genetic and pharmacologic blocking approaches. In vivo results using the APP/PS1 AD mouse model support a role for the PtdSer binding protein Gas6 in mediating Aβ plaque clearance. Our work supports a model in which the effective clearance of Aβ by microglia occurs via a combination of phagocytic mechanisms.
mTOR-associated Mitochondrial Energy Metabolism Limits Mycobacterium ESX-1-induced Cytotoxicity
Authors: Pagán Antonio J , Lee Lauren J , Edwards-Hicks Joy , Moens Cecilia B , Tobin David M , Pearce Erika L , Busch-Nentwich Elisabeth , Ramakrishnan Lalita 
Published: January 2023

Abstract
Necrosis of macrophages in the tuberculous granuloma represents a major pathogenic event in tuberculosis. Through a zebrafish forward genetic screen, we identified the mTOR kinase, a master regulator of metabolism, as an early host resistance factor in tuberculosis. We found that mTOR protects macrophages from mycobacterium-induced death by enabling infection-induced increases in mitochondrial energy metabolism fueled by glycolysis. These metabolic adaptations were required to prevent mitochondrial damage and death caused specifically by the mycobacterial ESX-1 secretion system. Our finding that the host can effectively counter this early critical mycobacterial virulence mechanism simply by regulating energy metabolism may help explain why Mycobacterium tuberculosis, albeit humanity’s most lethal pathogen, only causes disease in a minority of infected individuals.
This work was supported by a Wellcome Trust Principal Research Fellowship (103950/Z/14) and an NIH MERIT award (R37 AI054503) (L.R.).
The role of ERK2 in dendritic cell function
Authors: Abdul-Baki Nawal Samer , Negron Austin , Forsthuber Thomas 
Published: January 2023

Abstract
Dendritic cells (DCs) are an important link between the innate and adaptive immune systems, specifically by serving as key regulators of T cell-dependent (TD) immune responses. In DCs, several processes critical for initiating TD immune responses, such as migration, provision of costimulatory signals, and antigen uptake and presentation, utilize the mitogen-activated protein kinase (MAPK) signaling pathway. The dysregulation of these processes can result in the aberrant activation of autoreactive CD4+ T cells, resulting in autoimmune disease. Extracellular signal-regulated kinase 1 and 2 (ERK1/2) are key effectors of the MAPK pathway, and while ERK1 has been shown to be a critical regulator of DC migration and TLR-induced IL-10 secretion, the function of ERK2 remains unknown. Preliminary data has shown that Erk2Δ bone marrow-derived DCs (BMDCs), as well as Erk2Δ splenic DCs, exhibit altered expression of surface markers associated with T cell costimulation, antigen presentation, and migration compared with DCs from littermate control. Taken together, this suggests that ERK2 plays a unique role in the regulation of several DC functions, potentially opening a new approach to treating CD4+ T cell-mediated autoimmune diseases.
Supported by grant R21AI44731 from the NIH/NIAID (TGF)