bluuebunny/crossref_metadata_2025_split huggingface dataset:
Low-input chromatin profiling reveals inter- and intra-lineage differences across immune cell types
Authors:   Immunological Genome Consortium, Bale Michael J , Ahimovic Dughan J , Lee Juliana , Marunde Matthew R , Lin Carolina P , Maryanski Danielle N , Keogh Michael-Christopher , Josefowicz Steven Z 
Published: August 2023

Abstract
Transcriptional regulation in cells is governed by myriad traits that allow specific responses to ever-changing environments. Inclusive of these regulatory factors are the histone proteins that compact the genome while additionally being decorated with diverse post-translational modifications (PTM) suggested to direct the cellular machinery to express / repress lineage- and context-specific loci. Our consortium recently performed a detailed analysis of chromatin accessibility (ATACseq) across multiple mouse immunocyte populations, which advanced our understanding of how cis-regulatory elements (CRE) control transcriptional programs in rarer immune cell types. Understanding the role of histone PTMs in this process has remained elusive due to the high cell-input demands of the gold-standard assay: ChIPseq. To this end, we developed a streamlined CUT&RUN approach to support robust profiling at 10K cells per target in ~100 sorted mouse immunologic populations. We have used this to map histone PTM states characteristic of active (H3K4me1/3, H3K27ac, H3K36me3) or repressed (H3K27me3) chromatin and architectural factors associated with genome organization (H3.3, CTCF), in tandem with RNA- and ATAC-seq. We further dissected the effect of genomic variation by utilizing a B6xCast/EiJ F1 hybrid mouse to understand how CRE variation at each allele independently impacts transcriptional regulation. Taken together, our data provides a deeper understanding of transcriptional regulation in the mouse immune system across differentiation and perturbation states.
Defining TLR4-independent molecular pathways activated during endotoxemia
Authors: Hunat Junela Cecille Serrano , Calkins Phoebe , Salgado Cristal , Omodia Glory , Awan Hiba , Aaron Anique , Harberts Erin M 
Published: August 2023

Abstract
Sepsis is the leading cause of nosocomial mortality, accounting for almost 20% of annual global deaths. Patients who recover from septic shock maintain a significantly increased risk for mortality due to secondary infection. Toll-like receptor 4 (TLR4) recognizes Gram-negative bacterial lipopolysaccharides (LPS) and initiates robust immune activation that can be detrimental to the host. Towards the end of septicemia, cells self-regulate and remove surface TLR4 which contributes to immune ataxia. TLR4 deficient (TLR4−/−) C57BL6 mice are used as a model for the immune refractory period following septic shock and compared to wildtype (WT) mice. In the serum of both WT and TLR4−/− mice, 51 proteins were previously found to be dysregulated over the course of endotoxemia. We hypothesize that these 51 proteins represent TLR4 independent activation mechanisms. This study further investigates protein and mRNA distribution during endotoxemia. Liver, spleen, kidney, heart, and brain were collected at 0, 6, 12, and 18 hours post-intraperitoneal injection of 30 mg/kg E. coli LPS. Using qPCR and Western Blot to quantify gene and protein expression, we observed down regulation of genes involved with metabolism (Adsl, Mdh1) and erythrocyte cytoskeleton stabilization (Dmtn). In the same samples we observe activation of genes and proteins involved in T-cell function (Coro1a), and the complement cascades (Masp1, C1qb, Cfd, F5). These results further define TLR4 independent activation during endotoxemia as a model for immune ataxia that occurs after primary septic shock. This project could provide proof of principle to support the development of more targeted treatments to address immune activation during secondary infection after septic shock.
This project was supported by a Towson University FDRC grant to EMH and a Fisher College of Science and Mathematics undergraduate research award to JCH, HA, PC, and AA.
TGF-β promotes glycolysis through PFKL in activated macrophages and exacerbates sepsis by disrupting blood coagulation
Authors: Gauthier Thierry , Yao Chen , Jin Wenwen , Lim Yun-Ji , Patino Liliana C , Liu Na , Mitrovic Mladen , Tussiwand Roxane , O’Shea John J , Chen Wanjun 
Published: August 2023

Abstract
The metabolism of macrophages plays a key role in their immune responses, but the mechanisms by which the metabolism is regulated remain largely unknown. We show here that TGF-β induces a unique phenotype of macrophages and regulates the glycolysis of macrophages independently of inflammatory cytokine production. Specifically, TGF-β increased expression and activity of phosphofructokinase-1 liver type (PFKL) in macrophages and thus promoted their glycolysis during cell activation, yet paradoxically suppressed the production of proinflammatory cytokines in the same macrophages. The upregulation of glycolysis was mediated by an mTOR-c-MYC dependent pathway, whereas the inhibition of cytokines was ascribed to downregulated activation of the major pro-inflammatory transcription factors, namely AP-1, NFkB and STAT1. Importantly, we found that in LPS-induced sepsis model, TGF-β enhancement of macrophage glycolysis led to a decreased survival in mice by increasing blood coagulation. Analysis of cohorts of patients with sepsis and covid-19 revealed that the expression of PFKL, TGF-b receptors TGFBRI and coagulation factor F13A1 in monocytes positively correlated with the progression of the disease. Thus, TGF-β is emerging as a critical cytokine regulating macrophage metabolism and could serve as a therapeutic target in patients with sepsis and Covid-19.
AIM2 Promotes Epithelial Tuft Cell Development During Intestinal Type 2 Immune Responses
Authors: Wilson Justin E , Tribble Stephanie L , Verdugo Sydney A N , Reinartz Dakota M 
Published: August 2023

Abstract
The epithelium performs a growing list of immunologically relevant functions at mucosal sites. Specialized epithelial cells of the intestine interact with the microbiota and lamina propria immune cells to regulate host defense, yet we know little about the molecular regulators linking these interactions during different immunological insults. Here, we found that the DNA sensor Absent in Melanoma 2 (AIM2) promotes development of epithelial tuft cells, which initiate intestinal type 2 immunity. Aim2-deficient intestinal epithelial organoids displayed reduced tuft cell gene signatures and numbers during treatment with the tuft cell-promoting cytokines IL-4 and IL-13. Tuft cells respond to the microbial metabolite succinate, leading to IL-13 production by type 2 innate lymphoid cells (ILC2s) and tuft cell hyperplasia in vivo. Succinate-fed Aim2−/− mice displayed reduced tuft cells and IL13 expression compared to similarly treated wild type mice. Inflammasome-deficient Asc−/− mice and wild type mice displayed similar succinate-induced tuft cell profiles, suggesting AIM2 promotes tuft cell-ILC2 activation independently of its inflammasome function. RNA sequencing revealed Aim2−/− intestinal organoids displayed diminished expression of O-linked N-acetylglucosamine transferase (OGT), which is required for IL13/STAT6-induced tuft cell expansion. In line with these findings, Aim2−/− intestinal organoids and succinate-treated mice presented reduced OGT protein expression and STAT6 phosphorylation. These combined results reveal an novel role for AIM2 during type 2 intestinal inflammation in the intestine via promotion of tuft cell expansion, potentially through maintaining OGT-STAT6 signaling.
Supported by grants from NIH (K22 CA212030) and the AZ Dept. of Health Services (AZBRC New Investigator Award).
Non-canonical unfolded protein response transcription factor CREB3L2 regulates survival of long-lived plasma cells
Authors: Lau Louis C , Manakkat Vijay Godhev K , Hall David Reed , Singh Harinder 
Published: August 2023

Abstract
Differentiation of activated B cells into antibody-secreting cells (ASCs) involves extensive endoplasmic reticulum (ER) & Golgi biogenesis and remodeling that enable increased antibody synthesis and secretion. These processes are mediated by the unfolded protein response (UPR). Canonical UPR pathway genes are regulated by the transcription factors (TFs) XBP-1 and ATFs, which are activated upon ER or Golgi stress. Using scRNA-seq to analyze the generation of splenic and bone marrow (BM) plasma cells (PCs), we discovered that the Creb3l2 gene, encoding a non-canonical UPR TF, is specifically expressed in PCs, with highest levels in long-lived PCs (LLPCs). CREB3L2 has been shown to regulate transcription of genes encoding components critical to secretory cells of the pancreas and pituitary gland. To analyze the function of CREB3L2 in ASCs, we pursued a two-pronged strategy (i) using CRISPR/Cas9-RNP editing in the murine CH12 B lymphoma cell line to generate out-of-frame deletions in exon 2 of the Creb3l2 gene (Creb3l2−/−) and (ii) generating Creb3l2 B-cell conditional KO (cKO) mice carrying a floxed allele of the Creb3l2 gene by inserting loxp sites flanking exon 7 with a CD19-cre driver (Creb3l2fl/fl CD19cre/+). RNA-seq of Creb3l2−/− CH12 cells shows CREB3L2 positively regulated genes including Cd93 and Cd28 & its signaling adapter SLP-76 (Lcp2), that are involved in plasma cell survival in the BM niche. Expression of CD28/SLP-76 and CD93 proteins were strongly diminished in Creb3l2−/− CH12 cells. Consistent with these findings, Creb3l2 cKO mice had reduced NP-specific LLPCs (90 d.p.i) after NP-KLH immunization. Thus, CREB3L2 appears to selectively regulate the survival of LLPCs by controlling the expression of CD28/SLP-76 and CD93.
Supported by grants from NIAID (U01 AI141990, R01 AI145064).
Phenotypic Analysis of Fibrogenic Monocyte/Macrophage Subsets in Acute Inflammatory Exacerbations of Lung Disease Driven by Mutant Surfactant Protein-C Expression
Authors: Venosa Alessandro , Musci Teresa , Moos Philip 
Published: August 2023

Abstract
Acute inflammatory exacerbations (AIE) represent precipitous deteriorations of a number of chronic lung conditions, including pulmonary fibrosis (PF), COPD, and asthma. AIEs are marked by diffuse and persistent polycellular alveolitis that profoundly accelerate lung function decline and mortality. Excess monocyte mobilization during AIE, and their persistence in the lung are linked to poor disease outcome. Guided by clinical evidence, we have developed an inducible model of pulmonary fibrosis leveraging the PF-linked missense isoleucine to threonine mutation at position 73 [I73T] in the alveolar type-2 cell-restricted Surfactant Protein-C [SP-C] gene [SFTPC]. We have previously shown that ablation of CCR2+ monocytes was protective with respect to lung histopathology, mouse survival, and overall inflammation following SP-C mutant induction. Here we identify and phenotypically characterize resident and recruited monocytes/macrophages populations intervening during the initiation and progression of AIE-PF. Single cell sequencing shows pro-inflammatory and pro-fibrotic signatures originating from immature recruited clusters (itgax-itgam+ ccr2+ cx3cr1+) as well as activated macrophages (cd68+ itgax+ itgam+ arg1+) 14 d after SP-CI73T induction. Using CellChat Explorer database, these cells were predicted to coordinate intense tgfb1, fn1/fibronectin and spp1/osteopontin signaling. Together, these results provide a clear picture of the fibrogenic role of specific activated monocyte/macrophage subsets responding to alveolar epithelial stress.
NIEHS R01ES032553 (AV); ALSAM Foundation for Research Initiatives Grant (AV)
Randomized Clinical Trial of Intermittent Calorie Restriction in People with Multiple Sclerosis: Effects on Immunometabolic and Cognitive Measures
Authors: Tolentino Miguel , Ghezzi Laura , Tosti Valeria , Cantoni Claudia , Salter Amber , Lancia Samantha , Zhou Yanjiao , Obert Kathleen , Mikesell Robert , Sen Monokesh Kumer , Cross Anne , Naismith Robert , Piccio Laura 
Published: August 2023

Abstract

BACKGROUND
Intermittent calorie restriction (iCR) reduces inflammation in preclinical models and in people with Multiple Sclerosis (pwMS). Mechanisms could be related to changes in levels of adipose tissue-derived adipokines with reduced systemic inflammation and gut microbiota composition.

AIMS
Evaluate the effects of iCR on adipokines levels, metabolic and immune/inflammatory biomarkers compared to a control unrestricted diet (Ctr) in pwMS.

METHODS
PwMS (relapsing Remitting MS) were randomly assigned to the iCR or Ctr groups for 12 weeks. Blood was collected at baseline, 6 and 12 weeks. Leptin and adiponectin levels, peripheral blood metabolic and immunologic profiling, anthropometric and total body fat measures, and clinical and cognitive measures were evaluated. Differences between iCR and Ctr were examined using a linear, repeated measures mixed model and adjusted for baseline levels, age, sex and DMTs.

RESULTS
42 pwMS were randomized (iCR=22 and Ctr=20). 34 pwMS completed the study (iCR=17 and Ctr=17). PwMS on iCR showed a significant reduction of anthropometric (weight and BMI) and body adiposity measures (waist circumference and fat mass) over the 12 weeks. Leptin levels decreased and were significantly lower in the iCR group at 6 weeks and approaching significance at 12 weeks. Adiponectin increased from baseline in the iCR group at 6 and 12 weeks. The iCR group showed a significant decrease in Th1 cells and an increase in CD45RO+ regulatory T cells after 6 weeks. Cognitive testing using symbol digit modality test showed significantly greater improvement in the iCR group versus Ctr at 12 weeks.

CONCLUSIONS
Short term iCR is safe and feasible in pwMS, and it can ameliorate metabolic, immunologic, and cognitive profiles.

National Multiple Sclerosis Society # RG-1607-25158
Resistant starch supplementation alters the gut microbial consortium and attenuates kidney inflammation in an experimental model of autoimmune vasculitis
Authors: O’Sullivan Kim Maree , Snelson Matthew , Nguyen Jenny , Le Anne Cao , Coughlan Melinda 
Published: August 2023

Abstract
Anti-neutrophil cytoplasmic antibody (ANCA) associated vasculitis (AAV) is a rare autoimmune disease with suboptimal treatment options which contribute to morbidity and mortality. The characteristic pathological feature is severe inflammation induced by neutrophils which causes life threatening damage to the small blood vessels of the kidney. Neutrophil activity is influenced by microbial metabolites, including short chain fatty acids (SCFAs), produced from fermentation of non-digestible carbohydrates by gut microbiota. We utilised a well-established mouse model of AAV. Mice were randomised to receive either a control diet or a diet supplemented with 15% resistant starch (RS) (n=8 per group). At day 20, mice were culled and kidneys removed to assess injury. Glomerular neutrophil and macrophage infiltration were assessed by immunohistochemistry. Cecal contents were collected, DNA extracted and the V1-V2 hypervariable region amplified using 27F and 338R universal primers to assess the gut microbiota. The resistant starch intervention significantly reduced segmental necrosis in glomeruli (77.63 ± 7.2 % vs 25.59± 4.5 p/gcs, p &lt; 0.0001) and reduced neutrophil (1.3 ± 0.37per glomerular cross section (p/gcs) vs 0.4 ± 0.3p/gcs, p &lt; 0.0001) and macrophage (1.6± 0.3 p/gcs vs 0.4 ± 0.08 p/gcs, p &lt; 0.0001) infiltration into glomeruli. The resistant starch diet significantly altered the gut microbiota consortium and was associated with a substantial expansion of Bacteroidaceae and Muribaculaceae both SCFA producing bacteria. This is the first report of the therapeutic efficacy of a resistant starch supplemented diet in experimental AAV. This data represents a promising therapeutic avenue to limit autoimmune kidney injury in AAV.
Treatment with linsitinib, an IGF-1 receptor inhibitor, attenuates disease development and progression in an experimental model of Graves’ Orbitopathy
Authors: Gulbins Anne Renate Liselotte , Horstmann Mareike , Oeverhaus Michael , Banga J Paul , Floegel Ulrich , Daser Anke , Krause Gerd , Spencer Andrew , Zeidan Ryan , Hammer Gary Douglas , Bechrakis Nikolaos E , Philipp Svenja , Eckstein Anja , Goertz Gina-Eva 
Published: August 2023

Abstract

Study objective
The activity of linsitinib, a small molecule inhibitor of the insulin-like growth factor 1 receptor (IGF-1R), was assessed in a mouse model of Graves’ orbitopathy (GO). GO is the most common extra-thyroidal manifestation of Graves’ disease (GD), which is caused by autoantibodies against the thyroid stimulating hormone receptor (TSHR).

Methods
GD was induced in mice by immunization with a human TSHR A-subunit encoding plasmid. Linsitinib was administered orally for four weeks either in parallel to or after disease induction. Endocrine orbitopathy and inflammation were determined by histology and MRI.

Results
Immunization with the TSHR A-subunit induced hyperthyroidism, as well as CD3+ T-cell infiltration and macrophage infiltration into orbital muscle/adipose tissue. Linsitinib reduced these effects by up to 80% whether given prophylactically or after disease induction. In addition, linsitinib reduced the formation of brown adipose tissue in the orbit and displayed an additional effect on the immune system. An MRI using F19 imaging confirmed marked orbital inflammation, significant muscle edema and formation of brown fat in experimental GO, events that were abrogated upon application of linsitinib. Linsitinib’s pharmacologic effects were observed at a dose that did not impact the concentration of plasma glucose.

Conclusion
Linsitinib improved GO-related endpoints in a TSHR autoantibody dependent mouse model of Graves’ disease. Both prophylactic and therapeutic intervention with linsitinib improved clinically relevant endpoints in the orbita and thyroid gland. Our results are consistent with the therapeutic hypothesis being evaluated in an ongoing Phase 2b clinical study (NCT05276063).

This work was funded by Sling Therapeutics, Inc.
Profiling the gut microbiome unraveled signature bacterial groups in autoimmune diabetes which remain unperturbed regardless of the ionic strength of drinking water
Authors: Jayaraman Sundararajan , Babu Meghana , Aung Saw , Jayaraman Arathi 
Published: August 2023

Abstract
Type 1 diabetes is an autoimmune disease that occurs spontaneously in non-obese diabetic mice, and the gut microbiota has been implicated in disease manifestation. The simple dietary variable, acidified drinking water, exaggerated or reduced diabetes incidence in some studies but not in our investigation. To elucidate the underlying basis of these discrepancies, we profiled the gut microbiome of diabetic mice that were transitioned from acid to neutral water. Quantitative polymerase reactions using primers specific for 16S rRNA genes validated the relative abundance of bacterial taxa longitudinally from 6 weeks of age to adults that overtly manifested diabetes. Among the 15 representative bacterial groups examined, only Lactobacillus sp. remained low throughout the life of the mouse. The frequencies of the Firmicutes Ruminococcaceae and the Bactereoidetes phylum members Anaerophaga sp. and Paludibacter sp. increased during maturation. The level of mucin-degrading Akkermansia muciniphila, implicated in diabetes protection remained low throughout the life of the mouse. The segmented filamentous bacteria could be detected in the gut of young mice and remained abundant in adult mice that developed full blown diabetes. The drinking water’s pH neither impacted the relative abundance of these bacterial taxa investigated herein nor diabetes incidence. Thus, the combination of microbiome profiling and quantitative real-time polymerase chain reactions facilitated validation of the signature gut bacterial taxa in autoimmune diabetes, which remain unperturbed by the pH of the drinking water.
Supported by the University of Illinois at Chicago, Chicago.
Recombinant immune complexes (rICs) as a therapeutic for Multiple Sclerosis (MS): effect on myeloid cell activation
Authors: Wang Jin , Brown Kellie Nicole , Margaret Danehy Caroline , Rice Samuel Worcester , Thomas Fridtjof , Torgbe Kwame , Block David , Olsen Henrik , Strome Scott Eric , Fitzpatrick Elizabeth A 
Published: August 2023

Abstract
Monocyte recruitment into the central nervous system (CNS) is critical for driving pathology in neuroinflammatory diseases such as MS. The monocytic influx as well as activation of resident myeloid cells contribute to recruitment and subsequent re-activation of autoreactive T cells, ultimately leading to demyelinating lesions, axonal damage, and progressive paralysis. Using the murine model for MS, experimental autoimmune encephalitis (EAE) we tested a rIC, M019, to determine its efficacy in reducing myeloid cell activation and subsequently reducing disease severity. Four days following induction of EAE with MOG peptide, daily treatment with M019 inhibited clinical symptoms including weight loss and demyelination in a dose-dependent manner. M019 also delayed or prevented disease in the SJL model of relapsing remitting EAE demonstrating its effectiveness against several forms of EAE. Analysis of the immune cell infiltrate in the spinal cords of M019 and vehicle treated mice revealed that M019 significantly inhibits the infiltration of myeloid and lymphoid cells into the CNS. The myeloid cells that were present in the CNS of M019 treated mice had reduced levels of MHC II suggesting they are inefficient at antigen presentation to autoreactive T cells. Microglia in the M019 treated EAE mice did not upregulate MHC II expression compared to the vehicle treated mice suggesting M019 inhibits their activation. M019 binds directly to monocytes in the periphery via CD16 (FcγRIII) and CD32 (FcγRII) and we detected increased chemokines in the sera of M019 treated EAE mice compared to vehicle treated EAE mice. These results suggest that M019 blocks immune cell migration into the CNS, potentially via phenotypic and functional changes to monocytes.
Chimeric cytokine receptor provides IL-2 signaling for engineered regulatory T cell therapy
Authors: Cortez Jessica T , Ly Han , Trotta Eleonora , Matthaei James F , Kegler Peter , Phong Brian , Fiebiger Benjamin M , Torres Josue , Chase Jack , Mileur Trevor , Beilke Joshua N , Bluestone Jeffrey A , Ramsdell Fred , McKenzie Brent S , Van Gool Frédéric 
Published: August 2023

Abstract
Regulatory T cells (Tregs) are potent immune suppressors and critical to the maintenance of immunological tolerance. Interleukin 2 (IL-2) is essential for Treg survival, expansion, phenotypic stability, and suppressive function. However, Tregs do not produce IL-2 and are dependent on exogenous sources of IL-2. This poses a significant challenge for Treg cell therapies in tissues with no or limited IL-2 availability in the microenvironment. Therefore, we have developed engineered Treg cells containing a chimeric cytokine receptor that provides an IL-2 signal. The chimeric cytokine receptor, termed IL-9 tethered switch receptor (IL-9TSR), consists of interleukin 9 (IL-9) tethered to the extracellular domain of IL9RA paired with the intracellular domain of IL2RB. We have shown that Tregs expressing IL-9TSR can survive and expand in the absence of exogenous IL-2 in vitro and in vivo but require TCR stimulation for prolonged persistency. IL-9TSR Tregs have a stable FOXP3+HELIOS+ phenotype and superior suppressive function when compared to control Tregs. In conclusion, we have generated Treg cells engineered to survive and function in a low IL-2 environment. Treg cell therapies equipped with IL-2 signaling enable increased persistency and allow for potential use in more clinical indications than previously possible.