bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential gene expression of the B Cell Receptor (BCR) signaling pathway during pregnancy in mice
Authors: Valeff Natalin Jimena , Muzzio Damian , Abba Martin , Zygmunt Marek , Jensen Federico 
Published: January 2023

Abstract
The aim of this work was to characterize BCR signaling pathway gene expression in B cells during pregnancy. B-cell receptor (BCR) signaling regulates critical cell-fate decisions in B cells like activation, proliferation, expression of costimulatory molecules and cytokine receptors. Changes on the dynamic of BCR signaling pathway during pregnancy might have an impact on the way how the immune system fight against infections or regulate autoimmunity during this critical period of time.
We performed a genome-wide transcriptome profile (GeneChip™ Mouse Gene 1.0 ST Array, Affymetrix) on pure splenic B cells isolated from pregnant and non-pregnant mice. Results were analyzed and significant gene expression regulation was confirmed by qPCR.
In silico analysis showed that genes associated with B cell receptor signaling pathway were significantly down-regulated in B cells from pregnant mice compared to non-pregnant animals (≈1.5–2 fold changes, Limma eBayes test, p&lt;0.0001, n=4). Further qPCR analysis showed that genes of the BCR pathway involved in B cell activation, proliferation and antibodies production were down-regulated (Unpaired t test, one-tailed, *p&lt;0.05, n=8) in B cell from pregnant mice as compared to non-pregnant females. In contrast, genes of the BCR pathway that inhibits B cells activation presented no significant differences.
We showed here that genes associated with BCR signaling leading to B cell activation and proliferation were significantly down-regulated during pregnancy. These results might help to understand why pregnant women are more susceptible to infections as well as some B cell associated autoimmune diseases experience a significant improvement in the symptoms during pregnancy.
Human plasma cells

switch on

and

turn off

antibody secretion
Authors: Nguyen Doan C , Saney Celia , Ley Ariel , Sanz Iñaki , Lee F. Eun-Hyung 
Published: January 2023

Abstract
Long-lived plasma cells (LLPC) are terminally-differentiated, non-dividing cells that reside in a protected and supportive bone marrow (BM) microenvironment. After terminal differentiation, antibody (Ab)-secreting cells (ASC) or plasma cells (PC) are believed to constitutively secrete Ab for a life-time. Recently, by integrated bioinformatics and using a novel in vitro cell-free BM microniche system, we demonstrated that protein factors such as fibronectin, YWHAZ, GAPDH, HSPD1, and hnRNPA1 are required for human ASC/PC survival. Specific blockade or inhibition of GAPDH, HSPD1, or hnRNPA1 resulted in loss of human ASC/PC IgG ELISpot frequencies. To understand whether ASC/PC secretion or survival was affected, we sequentially removed the inhibitors and replated the previously-treated ASC/PC in fresh conditions. Upon removal of the inhibitors, the inhibitory effects of Ab secretion were reversed, suggesting a functional recovery of Ab secretion of the inhibited ASC/PC. No evidence of additional ASC/PC proliferation was observed by BrdU uptake. Given the physiological functions of GAPDH, HSPD1, and hnRNPA1, it appeared that mechanisms involved in glucose or mitochondrial metabolism, or protein synthesis, can modulate Ab secretion of human ASC/PC. Together, these data suggest that human ASC/PC do not produce Ab constitutively, but can actually modulate Ab secretion based on their local microenvironment. Moreover, Ab secretion is not linked to survival. In essence, human ASC/PC switch on or turn off Ab secretion, but the exact mechanisms require further validation.
The bona fide structure of IgM pentamer and its binding mode with AIM/CD5L molecule
Authors: Miyazaki Toru , Hiramoto Emiri , Arai Satoko 
Published: January 2023

Abstract
Soluble IgM forms a predominantly pentameric complex that also contains a small polypeptide J chain. While the IgM pentamer has various immune functions to defend against foreign pathogens, it also behaves as a carrier of the circulating apoptosis inhibitor of macrophage (AIM, also called CD5L). The binding to IgM pentamer protects AIM from renal excretion, leading to high serum AIM levels. When AIM dissociates from IgM, it becomes functionally active and facilitates the repair of a variety of diseases including acute kidney injury and hepatocellular carcinoma. Since the precise manner of AIM-IgM pentamer binding remains unknown, we examined the structure using a latest single-particle negative-stain electron microscopy. Surprisingly, the IgM pentamer shapes “one-piece missing” hexagon containing one large gap, which is markedly different from the textbook prediction of a symmetric pentagon model. A single AIM molecule stably fits into the gap, cross-bridging two IgM-Fc through a disulfide bond and a charge-based interaction. We also found that the association of AIM with IgM pentamer not only inactivates AIM but also progresses inflammatory immune-complex formation in certain autoimmune diseases such as IgA nephropathy. Thus, our current findings of the bona fide structure of the AIM/IgM pentamer complex provides an important insight into the releasing mechanism of AIM from IgM, which could be the basis for the development of new therapeutic strategies against multiple diseases, via the increase of active AIM as well as the disruption of immune-complex formation.
Effects of antiorthostatic suspension, tetanus toxoid, and CpG on the bone marrow antibody repertoire in C57BL/6 mice
Authors: Rettig Trisha A , Nishiyama Nina C , Pecaut Michael J , Chapes Stephen K 
Published: January 2023

Abstract
Each B cell produces an antibody composed of two heavy chains paired with two light chains. During development, B cells rearrange V-, D- (heavy chain only), and J-gene segments. These rearrangements along with the imprecisions in recombination and mutations create diversity in the antibody repertoire.
The physical and psychological stressors of spaceflight are known to affect both the innate and adaptive immune systems. We used a ground-based model, antiorthostatic suspension (AOS), to analyze the impact of spaceflight environmental stressors on the antibody repertoire. Eight-week-old female C57BL/6J mice were suspended for two weeks and immunized via ip injection with saline, tetanus toxoid (TT) and/or CpG, and resuspended. Two weeks after immunization, animals were sacrificed, and bone marrow was collected. RNA was extracted and sequenced using MiSeq 2×300bp. Resulting sequences were analyzed using ImMunoGeneTic’s High-V quest program to identify antibody characteristics.
We identified significant variations in VH, Vκ, D, JH, and Jκ-gene segment usage and CDR3 length due to AOS, TT, and CpG treatment. Changes were also detected in the class-switched repertoire for VH-gene segment usage. We also focused our analysis on the loaded saline, loaded TT+CpG, and AOS+TT+CpG treatment groups to isolate the TT-specific antibody response. Statistically significant changes were detected in VH-gene segment usage and gene segment combinations among treatment groups. These results demonstrate that treatment with a physiological model of spaceflight leads to alterations in the development of the TT-specific antibody repertoire in the bone marrow.
Epigenetic priming underpins enhanced memory B cell differentiation
Authors: Price Madeline J , Scharer Christopher D. , Kania Anna K , Mi Tian , Hicks Sakeenah L , Randall Troy D , Boss Jeremy 
Published: January 2023

Abstract
Immunological memory is a hallmark of the adaptive immune response. Memory B cells (MBC) have increased affinity, expression of costimulatory molecules, and capacity to proliferate and differentiate than their naïve counterparts; however, the epigenetic mechanisms that control enhanced MBC functions are currently unknown. Using a murine model of influenza infection, nucleoprotein (NP)-specific MBC and follicular naïve B cells (nB) were isolated and the chromatin accessibility and transcriptional landscape determined by ATAC and RNA-seq, respectively. MBC displayed distinct gene expression profiles from nB, including an upregulation of plasma cell (PC) signature genes and significant overall increases in total mRNA content. Furthermore, MBC display an open and primed chromatin conformation in gene regulatory regions that map to transcription factors controlling either PC (Prdm1 and Irf4), germinal center (Aicda), or MBC (Zbtb32) fates. These data reveal additional novel MBC-specific transcription factor networks and describe an epigenetic “antigen experience” signature that correlates with enhanced MBC function. To confirm the importance of these molecular changes, naïve and memory mice were challenged with a heterosubtypic influenza infection or isolated and cultured with CD40L, IL-4, and IL-5. In vivo, MBC form germinal centers earlier and to a higher frequency than nB. MBC also form significantly more NP+IgG+ PCs by flow cytometry and ELISPOT, corroborating the open chromatin signature. Ex vivo, MBCs upregulated primed transcription factors earlier than nB, validating the enhanced formation of CD138+ PCs. These data describe an epigenetic basis for enhanced the differentiation capacity and function of MBC.
Transcriptional regulation of IL-10 in T helper cells
Authors: Zhang Huiyuan , Madi Asaf , Yosef Nir , Chihara Norio , Awasthi Amit , Pot Caroline , Apetoh Lionel , Srivastava Amitabh , Wang Chao , Regev Aviv , Kuchroo Vijay 
Published: January 2023

Abstract
IL-10 produced by CD4 T cells plays an essential role in limiting inflammation and autoimmunity. All T help cell subsets can co-produce IL-10 to mitigate unwanted immunopathology but naïve CD4 T cells can also be directly polarized to IL-10 producing Type 1 regulatory (Tr1) cells by the immunoregulatory cytokine, IL-27. Although several transcription factors (TFs) have been shown to regulate IL-10 expression in different contexts, a comprehensive transcriptional network that induce and maintain IL-10 in various CD4 T cells is lacking.
Here we utilized two complementary approaches to systemically study the transcriptional mechanisms driving IL-10 production in T helper cells: 1) We combined novel computational tools with transcriptomic profiling of in-vitro Tr1 cell differentiation at high temporal resolution to build a comprehensive and dynamic transcriptional network that regulates IL-10 production in CD4 T cells. We identified four transcription waves that govern Tr1 differentiation: dynamic early phase, stable early phase, induction phase and maintenance phase. Based on the network analysis, we computationally predicted 78 TFs that regulate different waves and experimentally validated 24 of them using knock-out mice. 2) To identify TFs associated with IL-10 production across T helper cell subsets, we compared RNA-seq data of IL-10+ versus IL-10− compartments of in-vitro differentiated Th1, Th2 and Th17 cells. Using a comprehensive ranking scheme, we identified two TFs that regulates IL-10 production in all helper T cell subsets. Conditional deletion of both the TFs but not either alone with CD4-Cre abolishes IL-10 production from Tr1 cells in vitro and leads to spontaneous colitis in vivo.
Lymph node-fibroblastic reticular cells regulate differentiation of CD4+ T cells through CD25
Authors: Kim Tae Woo , Kim Dong-Eon 
Published: January 2023

Abstract
Lymph node-fibroblastic reticular cells (LN-FRCs) provide functional structure to LNs and play important roles in interactions between T cells and antigen-presenting cells. However, the direct impacts of LN-FRCs on naïve CD4+ T cell differentiation have not been explored. Here, we show that FRCs in T cell zones of LNs express CD25 (IL-2 receptor α chain (IL-2Rα) of the IL-2R hetero-trimer). LN-FRCs trans-presented IL-2 to naïve CD4+ T cells through CD25, thereby facilitating early IL-2-mediated signaling. CD25-deficient LN-FRCs attenuated STAT5 phosphorylation of naïve CD4+ T cells during CD4+ T cell lineage differentiation, promoted T helper 17 (Th17) cell differentiation, and induced Th17 immune response-related gene expression. In an experimental autoimmune encephalomyelitis (EAE) disease model, Th17 cell-mediated EAE severity was elevated in mice lacking CD25 in LN-FRCs. Therefore, our results suggest that CD25 expression in LN-FRCs regulates CD4+ T cell differentiation by modulating early IL-2 signaling of neighboring naive CD4+ T cells, influencing immune responses.
Helios predisposes human fetal CD4+ naive T cells towards regulatory T cell differentiation
Authors: Ng Melissa , Roth Theodore , Mendoza Ventura , Marson Alexander , Burt Trevor 
Published: January 2023

Abstract
Activation of naïve CD4+ T cells by T cell receptor (TCR) stimulation and cytokine cues lead to differentiation into effector T cell populations with distinct pro-inflammatory or regulatory functions. Unlike adult naïve T cells, human fetal naïve CD4+ T cells uniquely differentiate into FOXP3+ regulatory T (Treg) cells upon TCR activation independent of exogenous cytokine signalling. This facility for Treg differentiation is crucial for generating tolerance in utero; however, the mechanisms underlying this ability in fetal naïve cells are largely unknown. Here, we reveal FOXP3-independent transcriptional and epigenetic programs shared between fetal naive T cells and committed adult Treg cells that are inactive in adult naive T cells. We show that a subset of adult Treg-specific super-enhancers is active within fetal naive T cells, including two super-enhancers at Helios, a thymic Treg gene. Helios is expressed in fetal naive T cells, but not in adult naïve T cells, and only fetal-derived induced Treg (iTreg) cells continue to express Helios. Fetal, but not adult iTreg cells, have suppressed IL-2 production, which is regulated by Helios in committed Treg cells. CRISPR-Cas9 ablation of Helios in fetal naive T cells then resulted in increased IL-2 production in fetal iTreg cells. Crucially, the loss of Helios expression in fetal naïve T cells impaired their differentiation into Treg cells upon TCR stimulation, indicating Helios as a critical contributor to the cell-intrinsic predisposition of fetal naive T cells for Treg cell differentiation. Treg-biased transcriptional and epigenetic programs within fetal naive T cells identified here could be utilized to engineer enhanced adult iTreg populations for adoptive cellular therapies.
DNA Methylation impairs monocyte function in tuberculosis leading to disease progression
Authors: Frantz Fabiani G , Castro Ricardo Cardoso , Fontanari Caroline , Bollela Valdes Roberto , Zambuzi Fabiana Albani 
Published: January 2023

Abstract
Despite treatment and cure, Tuberculosis (TB) is still considered a world health public problem. It is known that interaction between bacteria and host immune mechanisms results in changes in gene expression, which could be a result of epigenetic changes, as DNA methylation. Recent studies suggest that alterations in host epigenome could be promoted by Mtb infection and influence immune cells function. In this context, we aimed to determine the methylation profile of monocytes from tuberculosis patients and correlate with immune function of these cells. Monocytes were isolated from active TB patients (APTB) with treatment-time less than one month (n=10) and non-disease controls (CTRL) (n=16) - Ethics Committee approval FMRP-USP (Protocol #6481/2013). The monocytes were used to evaluate the global DNA methylation content and immune function, through cytokine and ROS production after heat killed Mtb challenge. When we evaluated the group of tuberculosis patients according to their lung injury degree, we found an increased methylation in those with more severe disease. Also, it was possible to observe that monocytes from patients with increased methylation profile, presented a reduction in secretion of anti-inflammatory cytokine, IL-10 and increased pro-inflammatory IL-12, indicating impairment in monocytes ability to regulate the excess of inflammation, which mediates the lung injury often observed in these patients. Hence, we suggested that global DNA methylation content might act as a clinic prognostic toll for active tuberculosis disease.
Macropinocytosis of amino acids regulates T cell growth by promoting the sustained activation of mTORC1
Authors: Charpentier John , Lapinski Philip E. , Turner Jackson , Grigorova Irina , Swanson Joel A. , King Philip D 
Published: January 2023

Abstract
Macropinocytosis, a non-selective form of bulk endocytosis, has been associated with diverse processes in mammalian cells, including antigen presentation and regulation of receptor density. In Ras-transformed tumor cells, macropinocytosis of protein regulates growth when amino acids are limiting in the extracellular space. A requirement of macropinocytosis for the growth of non-transformed cells has not been described previously. Here we show that primary mouse and human T cells engage in constitutive macropinocytosis that is enhanced approximately three-fold in response to CD3/CD28 antibody stimulation. We further show that macropinocytosis is essential for the growth of CD3/CD28 antibody-stimulated T cells during the G1 phase of the cell cycle, even under amino acid-replete conditions. Macropinocytosis in activated T cells provides a means of access of extracellular amino acids to an endolysosomal compartment necessary for sustained activation of the mechanistic target of rapamycin complex 1 (mTORC1), which in part explains its function in G1 growth. In addition, macropinocytosis promotes activated T cell growth by means other than activation of mTORC1, possibly by furnishing bulk substrates for anabolism and anaplerosis. Regulation of mammalian cell growth by macropinocytosis, therefore, is not limited to Ras-transformed tumor cells but may instead represent a more general means of promoting sustained mTORC1 activation in highly proliferative cells. These findings provide important new information upon the mechanisms by which T cells acquire nutrients for growth and suggest means by which T cell growth might be manipulated for therapeutic benefit.
A ‘sweet spot’ for complement receptor CD46 activity via direct regulation of glycolytic vs. moonlighting functions of GAPDH
Authors: Kunz Natalia , Le Friec Gaelle , Singh Parul , Lavender Paul , Kazemian Majid , Hess Christoph , Kemper Claudia 
Published: January 2023

Abstract
Autocrine engagement of the complement receptor CD46, driven by T cell receptor (TCR) activation on human CD4+ T cells, is critical for human Th1 induction: Processing of the intracellular CD46 domains by γ-secretase and their nuclear translocation mediates the expression of nutrient transporters GLUT1 and LAT1, increases glycolysis and oxidative phosphorylation, and enables metabolic reprogramming required for cell growth, expansion and effector function. How, at the molecular level, CYT-1 enables this fundamental cellular adaptation remains unknown. To probe for CYT-1 interacting proteins we generated antibodies against cleaved CYT-1 and performed co-immunoprecipitation experiments. Unexpectedly, mass spectrometry revealed association of CYT-1 with several glycolytic enzymes, including glyceraldehyde 3-phosphate dehydrogenase (GAPDH). Although ELISA and MST-based experiments confirmed a strong, dose-dependent CYT-1/GAPDH interaction, glycolytic activity was hardly affected by CYT-1. Rather, CYT-1 modulated the activity of a key ‘moonlighting function’ of GAPDH, namely the posttranscriptional regulation of mRNA stability/translation: CYT-1 binding fostered desoligomerization of glycolytically active GAPDH tetramers to monomers with altered mRNA binding abilities – particularly for mRNAs encoding metabolic enzymes. These data identify CD46 as a ‘shape-shifter’ of GAPDH activity, critically balancing its canonical (glycolysis) versus non-canonical (posttranscriptional regulation) activity – further substantiating the notion that autocrine complement is a critical regulator of normal cell physiology.
Regulation of IL-10-producing T cells by polyunsaturated fatty acids
Authors: Escalante Jaileene Hernandez , Jones Albert , Sedletsky Victoria Volfson , Dooms Hans 
Published: January 2023

Abstract
The modern day western diet has led to an increase of n-6 polyunsaturated fatty acid (n-6 PUFA) intake and is considered an environmental factor resulting in negative health outcomes in different disease settings. In relation to the immune system, it is not well understood how changes in dietary factors like n-6 PUFAs can influence immune responses, for example during autoimmune disease. PUFAs have a variety of roles within cells such as being used as an energy source, incorporation in cell membranes, and conversion into lipid mediators that influence cell signaling and gene expression. We initially sought to understand how n-6 PUFAs influence the phenotype and function of T cell subsets from the Type 1 Diabetes mouse model (NOD) and non-diabetic control mouse model (B6.NOD). By treating splenocytes from these mouse models in vitro with n-6 PUFA linoleic acid we discovered by flow cytometry a dose response inhibition of interleukin 10 (IL-10), an anti-inflammatory cytokine, in both CD4+ and CD8+ T cell subsets. To the contrary, interferon γ production was not diminished after linoleic acid treatment. While IL-10 inhibition was not strain-specific, further studies by gene expression analysis displayed a decrease of IL-10 mRNA expression and of transcription factors involved in regulation of IL-10 (c-maf, IRF4, and Bhlhe40) after linoleic acid treatment. These results demonstrate that dietary n-6 PUFAs regulate T cell cytokine production and can influence the balance of pro- and anti-inflammatory cytokines. Further studies will provide more insight into the regulation of T cell subsets by fatty acids present in the organismal environment, with potential implications for the development of new therapeutics to modulate autoimmune responses.
Serum Amyloid P Component Bound to Fungal Functional Amyloid Is Anti-Phagocytic and Anti-inflammatory
Authors: Bradley Nicole Elizabeth , Lipke Peter N , Pilling Darrell , Gomer Richard H , Klotz Stephen A 
Published: January 2023

Abstract
Invasive fungal disease is often characterized by a sparse cellular inflammatory response, and we have proposed that deposition of serum amyloid P component (SAP, also called PTX2) on fungal surfaces dampens the innate immune response. Binding of SAP to fungi was dependent upon fungal expression of cell surface functional amyloid, with 92% of Candida albicans yeast cells binding SAP, whereas only 18% of yeasts of an amyloid-depleted strain of Saccharomyces cerevisiae bound SAP. Furthermore, SAP bound to 40% of S. cerevisiae cells expressing the amyloidogenic C. albicans adhesin Als5pWT, but only 19% of cells expressing a non-amyloidogenic single site mutant, Als5pV326N. Macrophages phagocytosed fungi in proportion to expression of surface amyloid: C. albicans &gt; S. cerevisiae expressing Als5pWT &gt;&gt;&gt;S. cerevisiae expressing Als5pV326N or S. cerevisiae. Macrophages incubated with C. albicans yeasts secreted significantly increased amounts of IFNγ, IL-6, TNFα and IL-10. Pre-treatment of macrophages with SAP or yeasts with SAP reduced C. albicans phagocytosis by more than 80% within 30 minutes, and led to reductions of IFNγ, IL-6, TNFα, but to an increase in the secretion of the anti-inflammatory cytokine IL-10. The structurally similar pentraxin, C-reactive protein, demonstrated negligible binding to Candida (7% on flow cytometry) and slightly increased macrophage phagocytosis of yeasts. Thus SAP, whether added exogenously to macrophages or coating fungi, rapidly dampened the host cellular immune response. These findings support the hypothesis that amyloid-dependent SAP binding diminishes cellular innate immunity in invasive candidiasis in humans.