bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modulation of Epidermal γδ T Cell Functionality by Obesity due to Acute versus Chronic TNF-α Reception
Authors: Jameson Julie M , Ahmed Jasmine , Rhoiney Mikaela , Matthews Carolyn 
Published: January 2023

Abstract
Epidermal γδ T cells exhibit functional plasticity with roles varying from wound healing to tumor cell lysis. Activation of epidermal γδ T cells occurs via the γδ TCR along with costimulation, suggesting that costimulatory ligand expression regulates functional outcome. Data from our lab indicates that the cytokine milieu adds an additional pressure on epidermal γδ T cells to mediate or inhibit a particular functionality. Previous work from our lab shows that obesity impairs epidermal γδ T cell wound repair function in a TNF-α dependent manner. Here we identify TNF-α as a modulator of epidermal γδ T cell function in wound repair or cellular lysis depending on reception of acute or chronic signals. TNF-α signals through two receptors, tumor necrosis factor receptor 1 and 2 (TNFR1 and TNFR2), thus the signaling dynamics are complex and induce varied responses including apoptosis, survival and inflammation. We show that epidermal γδ T cells exhibit low TNFR1 and TNFR2 expression prior to TCR activation. Even with low TNFR expression epidermal γδ T cells produce cytokines and chemokines involved in inflammation and macrophage recruitment in response to acute TNF-α signals without TCR activation. During TCR activation or IL-2 stimulation epidermal γδ T cells to upregulate TNFR2 indicating a reliance on TNFR2 signaling during activation. Alternatively, chronic TNF-α stimulation, similar to levels in obese patients, induces a reduction in epidermal γδ T cell cytotoxicity, proliferation and viability. Normal function is restored with IL-2 addition suggesting the inhibition is not permanent, but instead can be modulated. These studies provide potential targets for regulating epidermal γδ T cell functions such as wound repair and tumor lysis.
Selenoprotein I is important for phosphatidylethanolamine synthesis and autophagy during T cell activation
Authors: Avery Joseph , Ma Chi , Hoffmann FuKun , Hoffmann Peter 
Published: January 2023

Abstract
Selenoprotein I (SELENOI) is a type I CDP-alcohol phosphatidyltransferase that synthesizes phosphatidylethanolamine (PE) in the final reaction of the Kennedy pathway. We have found that SELENOI deletion in the whole animal is embryonic lethal, which emphasizes the key role PE synthesis plays in cellular division and development. One important role for PE in cells is the role it plays as a ligand for the conversion of LC3I to the lipidated LC3II molecule, which in turn allows the progression of early autophagosomes to proceed to later stage autophagosomes. Using a T cell-specific knockout (KO) model of SELENOI, we investigated SELENOI loss-of-function studies in these immune cells. In particular, SELENOI KO T cells were stimulated with STING-dependent and STING-independent agonists to test the importance of this selenoenzyme in autophagy and downstream signaling events that depend on efficient autophagy. Our results found that PE levels were lower in TCR-activated T cells lacking SELENOI compared to wild-type (WT) controls. LC3I to LC3II conversion was impaired in SELENOI KO T compared to controls, and STING-dependent autophagosome formation was particularly decreased in the absence of SELENOI. Using bone marrow-derived macrophages (BMDMs) from a doxycycline-inducible transgenic mouse that expresses a short hairpin RNA (shRNA) that lowers SELENOI &lt;50%, we found impaired LC3I to LC3II conversion as well as reduced autophagosome formation but not to the extent of that found with the KO T cell model. Our data suggest that SELENOI is an important enzyme for proper lipidation of LC3-I and autophagosome formation within immune cells.
Cytoskeletal control of the developing and mature B cell antigen receptor repertoire
Authors: Gupta Neetu , Labib Christina , Giudicelli Veronique , Aouinti Safa , Lefranc Marie-Paul , Kossida Sofia 
Published: January 2023

Abstract
The existence of diverse B cell antigen receptor (BCR) specificities is essential for development of protective antibody responses against a wide variety of pathogens. In developing B cells, the BCR repertoire is crafted through sequential rearrangements of heavy and light chain genes, and involves both combinatorial and junctional diversification catalyzed by recombinases and nucleases. Mature B cells undergo further diversification in peripheral lymphoid organs through isotype switching and somatic hypermutations in response to foreign antigens; although these events are not known to alter BCR antigen specificity. Cytoskeletal proteins modulate BCR signal strength and thereby antibody responses, but it is not known if they play a role in the generation of BCR diversity. Using next generation sequencing, and iRepertoire, Inc and ImMunoGeneTics (IMGT) software platforms we examined BCR repertoires in developing and mature B cells that lack the expression of Ezrin, a prominent cytoskeletal regulator of BCR organization, signaling and activation. We show that Ezrin deficiency impacts the generation of BCR repertoire diversity during B cell development, as well as the mature BCR repertoire. Our analysis provides a window into the major processes involved in diversifying the B cell repertoire in control and Ezrin-deficient B cells, including V gene usage, number, frequency and length of unique CDR3s, nucleotide additions and trimming, and shared and unique clonotypes. Our data suggest that the Ezrin cytoskeleton in B cells impacts humoral immunity not only through modulation of B cell activation upon foreign antigen encounter, but also through qualitative and quantitative modulation of the available BCR repertoire.
Co-expression network analysis identified cell cycle signaling hub genes associated with progression and prognosis of multiple myeloma
Authors: Adebayo Olayinka Omoyitola , Dammer Eric , Singh Rajesh , Sanjay Jain , Boise Lawrence , Lillard James W 
Published: January 2023

Abstract
There is a gap in understanding the molecular mechanisms behind early multiple myeloma (MM) progression in the newly diagnosed patient on standard treatment, i.e., lenalidomide, bortezomib, and dexamethasone (RVD). As a result, the relatively high percentage of patients that progress after early treatment with RVD is significant. Therefore, identification of clinically relevant clusters of co-expressed genes or related biomarkers for MM progression, while on RVD, would help identify new molecular mechanisms and drug targets. The objective of this study is to use weighted gene co-expression network analysis (WGCNA) to identify gene-signaling networks associated with early MM progression. Therefore, we performed a novel WGCNA to determine module-trait correlations. We next examined the overrepresentation of upregulators and signal pathway networks from MM patients in the MMRF CoMMpass dataset (n = 175). WGCNA constructed 45 modules based on the correlations between patients on RVD and death using 30,598 gene transcripts. We are using death as a biomarker for MM progression and two years as cut off for treatment. One of the highest modules identified; Pink module has HDAC8, HSPG2, LILRB4, CDC and FOXM1 genes and other 595 genes that are co-expressed together, that are significantly and positively correlated (p &lt; 3.6 × 10-8, R2 =0.38) with overall survival of &lt; 2 years following initial treatment with RVD. These genes are associated with cell cycle signaling, and Jak-Stat signaling pathways and their biological process is largely significant for proliferation and tumorigenesis. In future, connectivity mapping will be used to identify drug signatures that can target any of the hub genes. This study is expected to improve MM’s relapse.
Human B cells respond more strongly to membrane-associated antigen than soluble antigen with the help of mechanosensors
Authors: Kwak Kihyuck , Karell Paul , Yom Jina , Sohn Haewon , Manzella-Lapeira Javier , Pierce Susan K 
Published: January 2023

Abstract
Unlike T cells that recognize peptide-MHC complexes, B cells recognize native antigen in both soluble and membrane-associated forms. It is well established that foreign antigen can be presented in membrane-bound form and induce B cell activation but it remains unclear how mildly autoreactive B cells retained within the repertoire after central tolerance are prevented from inducing humoral autoimmunity despite the presence of their cognate antigen in serum. Here, we demonstrate that membrane-associated antigen provides superior affinity discrimination than soluble antigen. We also show that B cells express various mechanosensors, PIEZO-1, PIEZO-2, TRPA1, and TRPV5, which play an important role in robust B cell activation and in induction of the key B cell regulator gene, Myc, when B cells encounter membrane-associated antigen. We speculate that the mechanisms at play in conferring distinct sensitivity to different forms of antigen helps to explain B cell tolerance and activation in response to auto- and foreign antigens, respectively.
Mechanisms of Activation-Induced Chromatin Decondensation in the Lymphoid Lineage
Authors: Rawlings Jason S , Hurst Madison , Rahn Cassidy , Stuart Sara , Johnson Jamila 
Published: January 2023

Abstract
During an immune response, αβ T cells undergo a dramatic change in chromatin configuration, from a very condensed organization seen in naïve cells to a decondensed state in activated cells. It has previously been demonstrated that this change in chromatin architecture is required for αβ T cell proliferation. Since B cells and γδ T cells share the same lineage as αβ T cells, originating from a common lymphoid progenitor, we hypothesized that chromatin status could regulate their proliferation as well. To test this hypothesis, we analyzed chromatin status as a function of activation and found that in their basal (naïve) state, both B cells and Thy1.2hi (naïve) γδ T cells possess condensed chromatin, similar to αβ T cells, whereas Thy1.2lo (activated/memory) γδ T cells have a more open chromatin configuration. Upon exposure to activation stimuli, all three cell types decondense chromatin, but to different extents that correlate with their known ability to proliferate in response to activation stimuli. To investigate the signaling mechanisms controlling chromatin decondensation in these cells, we selectively activated the IP3 and DAG pathways, demonstrating that activation of either pathway can induce the decondensation of chromatin. Investigating the IP3 pathway further, we show that in B cells, the flux of intracellular calcium is required for the proper decondensation of chromatin, similar to previously published data on αβ T cells. Future studies will investigate if intracellular calcium is sufficient for chromatin decondensation in γδ T cells, establishing a conserved mechanism to control proliferation of cells of the lymphoid lineage during an immune response.
Activation-dependent post-transcriptional regulation of CD40L mediates B cell development and survival in germinal centers
Authors: De Maio Diego Javier Prado , Narayanan Bitha , La Porta James , Xie Ping , Covey Lori R 
Published: January 2023

Abstract
We have previously described a post-transcriptional pathway of induced mRNA stability that occurs at late times of T cell activation and is engaged by the binding of polypyrimidine tract-binding protein (PTBP1) complex to the 3′ UTR of the CD40L transcript. We recently explored the in vivo role of this pathway by generating a genetically modified mouse (CD40LΔ5) bearing a deletion of the PTBP1 stability element. We found that the CD40LΔ5 mice display a dysfunctional germinal center (GC) response including significantly decreased levels of isotype switched antibodies, antibody-secreting cells, memory B cells and GL7+ GC B cells. To extend our earlier findings we measured affinity maturation of antibodies in response to the hapten NP and found a loss of high affinity binding that corresponded to reduced numbers of targeted VH mutations known to be associated with high affinity binding. However, there were no discernible differences in the overall number of mutations across the VH segment, suggesting that the CD40LΔ5 pathway may have a greater effect on the selection and/or expansion of high-affinity B cells rather than on the somatic hypermutation (SHM) in general.
To identify how the CD40L mRNA stability pathway impacted B cells during an immune response, CD19+ B cells from immunized mice were transcriptionally profiled using RNAseq. Expression of genes associated with cell survival and proliferation were found to be down-regulated and apoptotic genes up-regulated in CD40LΔ5 B cells compared to WT cells. Together these finding are consistent with the Δ5 stability element playing a critical role in the proliferation and cell survival of high affinity GC B cells through a pathway of enhanced expression of CD40L in CD4 T cells.
Expression of microglia-specific transcriptional signatures correlates with the severity of behavioral deficits in systemic lupus erythematosus
Authors: Makinde Hadijat M , MIke Elise V , Putterman Chaim , Winter Deborah R , Cuda Carla M 
Published: January 2023

Abstract
Systemic lupus erythematosus (SLE) is a complex autoimmune disease affecting multiple organs, including the brain. Though 50% of patients may experience neuropsychiatric symptoms (NPSLE), disease mechanisms remain largely unknown. Microglia are the resident innate immune cell of the brain and suggested to act as drivers of neurological conditions ranging from neurodevelopmental (autism) to neurodegenerative (Alzheimer’s disease) disorders. The majority of investigations into microglia, particularly the recently discovered disease-associated microglia (DAM) subset, have occurred in models of neurodegenerative disease. However, few studies have examined microglia, particularly DAM, in NPSLE. We performed RNA-seq on microglia isolated from two NPSLE-prone mouse strains to correlate gene signatures with behavioral deficits. Similar to patients, both NPSLE models exhibit cognitive impairment. Of the significantly upregulated genes found in NPSLE microglia compared to their respective controls, a common 18-gene ‘NPSLE signature’ is shared and enriched for genes associated with lipid metabolism, scavenger receptor activity and downregulating inflammatory responses and cell chemotaxis processes. NPSLE microglia are also enriched for DAM-associated genes and expression of ‘NPSLE’ and ‘DAM’ signatures significantly correlates with the severity of behavioral deficits. The discovery of our novel ‘NPSLE signature’ and enrichment of the ‘DAM signature’ represents the first to connect microglia-specific transcriptional signatures with clinical outcomes. In future studies, we will assess the penetrance of these signatures to further interrogate how defective microglial function may incite NPSLE.
Protein tyrosine phosphatase SHP-1 modulates microtubule organization in later stages of mast cell activation
Authors: DRABER Pavel , Klebanovych Anastasiya , Sladkova Vladimira , Sulimenko Tetyana , Vosecka Vera , Rubikova Zuzana , Draberova Eduarda , Sulimenko Vadym 
Published: January 2023

Abstract
Antigen-mediated activation of mast cells initiates signaling events leading to degranulation and release of inflammatory mediators. Although rapid and transient microtubule reorganization during activation has been described, the molecular mechanisms that control their rearrangement are largely unknown. Important role in microtubule nucleation from centrosomes play γ-tubulin complexes. Here we report on the regulation of microtubule organization in bone marrow-derived mast cells (BMMCs) by Src homology 2 (SH2) domain-containing protein tyrosine phosphatase 1 (SHP-1). Reciprocal immunoprecipitation experiments revealed that SHP-1 is present in complexes containing γ-tubulin complex proteins and protein tyrosine kinase Syk. Pull-down experiments with truncated forms of γ-tubulin and SHP-1 unveiled corresponding interaction domains. When compared to controls, activated BMMCs without SHP-1 had more protrusions containing microtubules, higher level of tyrosine phosphorylation, enhanced activity of Syk kinase, as well as increased expression of cytokines and prostaglandins. Intracellular calcium mobilization and degranulation also increased. Microtubule regrowth experiments in cells lacking SHP-1 revealed stimulation of microtubule nucleation, and phenotypic rescue experiments confirmed that SHP-1 represents a negative regulator of microtubule nucleation in BMMCs. Moreover, inhibition of the SHP-1 activity by inhibitors TPI-1 and NSC87877 also augmented microtubule nucleation. The regulation was due to changes of γ-tubulin accumulation in centrosomes. Our data suggest a novel SHP-1 dependent mechanism for the suppression of microtubule formation in later stages of mast cell activation.
Electrophilic properties of itaconate regulating macrophage activation
Authors: Bambouskova Monika , Gorvel Laurent , Lampropoulou Vicky , Sergushichev Alexey , Loginicheva Ekaterina , Jovanovic Marko , Klechevsky Eynav , Stewart Kelly M. , Randolph Gwendalyn J. , Artyomov Maxim N. 
Published: January 2023

Abstract
Metabolic regulation has been recognized as a powerful principle guiding immune responses. Inflammatory macrophages undergo extensive metabolic rewiring marked by the production of substantial amounts of itaconate, which has recently been described as an immunoregulatory metabolite. Itaconate and its membrane-permeable derivative dimethyl itaconate (DI) selectively inhibit a subset of cytokines, including IL-6 and IL-12 but not TNF. The major effects of itaconate on cellular metabolism during macrophage activation have been attributed to the inhibition of succinate dehydrogenase, yet this inhibition alone is not sufficient to account for the pronounced immunoregulatory effects observed in the case of DI. Furthermore, the regulatory pathway responsible for such selective effects of itaconate and DI on the inflammatory program has not been defined. Here we show that itaconate and DI induce electrophilic stress, react with glutathione and subsequently induce both Nrf2 (also known as NFE2L2)-dependent and -independent responses. We find that electrophilic stress can selectively regulate secondary, but not primary, transcriptional responses to toll-like receptor stimulation via inhibition of IκBζ protein induction. The regulation of IκBζ is independent of Nrf2, and we identify ATF3 as its key mediator. The inhibitory effect is conserved across species and cell types, and the in vivo administration of DI can ameliorate IL-17-IκBζ-driven skin pathology in a mouse model of psoriasis, highlighting the therapeutic potential of this regulatory pathway. Our results demonstrate that targeting the DI-IκBζ regulatory axis could be an important new strategy for the treatment of IL-17-IκBζ-mediated autoimmune diseases.
Immune Tolerance Induction by the Exopolysaccharide from the Probiotic Bacillus subtilis
Authors: Zamora-Pineda Jesus Bernabe , Knight Katherine L. 
Published: January 2023

Abstract
Intestinal microbiota can lessen the severity of inflammatory diseases, although the mechanisms by which this occurs are poorly understood. We showed that exopolysaccharide (EPS) from the probiotic Bacillus subtilis induces anti-inflammatory macrophages and protects mice from enteric infection and sepsis. Here, we examined the molecular mechanisms by which EPS induces an anti-inflammatory response. In co-cultures of OVA-loaded bone marrow-derived dendritic cells (BMDC) and OT-II T cells, EPS inhibits T cell activation in a TLR4-dependent manner. We hypothesize that EPS engages TLR4 and activates the noncanonical NF-κB signaling pathway, which up-regulates the expression of indoleamine 2,3-dioxygenase (IDO). IDO degrades the essential amino acid tryptophan into kynurenine. The subsequent tryptophan depletion leads to suppression of T-cell activation and induction of tolerance. Western blot analysis of BMDC treated with EPS showed nuclear translocation of the transcriptional factor RelB, which is central to the noncanonical pathway. Current studies are testing if IDO expression is also induced by EPS treatment of BMDC, and if this is the mechanism by which EPS induces anti-inflammatory responses.
Distinct Changes in the Chromatin Landscape Regulate Maturation of the Alveolar Macrophage Immune Response In Vivo
Authors: Yamamura Asami , Hoeksema Marten A. , Sakai Mashito , Lund Sean J. , Butcher Lindsay D. , Lakhdari Omar , Oppong-Nonterah Gertrude O. , Sajti Eniko , Glass Christopher K. , Prince Lawrence S. 
Published: January 2023

Abstract
Alveolar macrophages (AMs) perform specialized functions in the lung including protection against inhaled microbes and repair following injury. Neonates are particularly susceptible to lung infection and injury, suggesting immaturity of AM function. In mice, AMs differentiate from fetal myeloid precursors within the first week following birth. To measure the molecular and functional differences between neonatal and adult AMs, we performed RNA-seq and ATAC-seq on sorted AMs. Based on RNA-seq data, adult AMs expressed higher levels of genes associated with fatty acid metabolism (Fabp1 and Abcg1), while neonatal AMs expressed higher levels of proinflammatory genes (including Il1b, Il6, Tnf, and S100a8). Consistent with higher proinflammatory gene expression in neonatal AMs, ATAC-seq revealed enrichment of accessible AP1, NF-kB, and IRF binding motifs. In contrast, adult AMs contained open chromatin enriched in motifs for KLF, AR, and STAT. To test if these differences contributed to differential innate immune function, we treated both neonatal and adult mice in vivo with inhaled LPS. LPS-exposed AMs demonstrated robust innate immune responses in both neonatal and adult mice. Interestingly, many of the LPS-induced genes in neonatal AMs had higher basal levels of expression, suggesting constitutive innate immune activation in the neonatal lung. These differences appeared to be driven by the lung microenvironment, as isolating and culturing AMs resulted in rapid loss of differences in gene expression between neonatal and adult cells. Our data therefore suggest the developing environment of the neonatal lung drives unique molecular and functional differences in AM mediated innate immunity.
Antigen Receptor Specificity and Cell Location Influence the Diversification and Selection of the B-1a Cell Pool with Age
Authors: Holodick Nichol E , Tsuji Naomi , Rothstein Thomas L. 
Published: January 2023

Abstract
B-1a cells provide immediate and essential protection from infection through production of natural immunoglobulin, which is germline-like due to minimal insertion of N-region additions. We have previously demonstrated peritoneal B-1a cell derived phosphorylcholine (PC)-specific and total IgM moves away from germline (as evidenced by an increase in N-additions) with age as a result of selection. In young mice, anti-phosphatidylcholine (PtC) antibodies, like anti-PC antibodies, contain few N-additions, and have been shown to be essential in protection from bacterial sepsis. Herein, we demonstrate the germline-like status of PtC specific peritoneal B-1a cell IgM does not change with age. In direct contrast, the splenic PtC-binding B-1a cell population does not preserve its IgM germline status in the aged. Furthermore, splenic PtC-binding B-1a cells displayed more diverse VH use in both the young and aged as compared to peritoneal PtC-binding B-1a cells. While both peritoneal and splenic PtC-binding populations increase VH12 use with age, differential use of VH11 and VH2 is observed between these populations with age. These results suggest disparate selection pressures occur with age upon B-1a cells expressing different specificities in distinct locations. Overall, these results illuminate the need to further elucidate how B-1a cells are influenced over time in terms of production and selection, both of which contribute to the actual and available natural IgM repertoire with increasing age. Such studies would aid in the development of more effective vaccination and therapeutic strategies in the aged population.