bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epigenetic reprogramming of CD8+ T cell populations drives exhaustion in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)
Authors: Iu David , Maya Jessica , Vu Luyen , Fogarty Elizabeth , Munn Paul , Grenier Jennifer , Hanson Maureen , Grimson Andrew 
Published: November 2024

Abstract
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a severe, debilitating disease with striking similarities to long-COVID/PASC, but its etiology remains unclear. Mounting evidence implicates immune dysfunction as a potential cause for ME/CFS. We previously reported metabolic changes in ME/CFS CD8+ T cells, including increased fatty acid oxidation, decreased glycolysis, and reduced mitochondrial membrane potential - features commonly found in exhausted T cells. To comprehensively characterize the gene regulatory state underlying potential transcriptional dysregulation, we first re-analyzed a single cell transcriptomic atlas of ME/CFS by reclassifying CD8+ T cells, where we found that various clusters upregulated exhaustion-associated genes. We then generated high resolution profiles of gene expression and chromatin accessibility in effector memory (TEM) and naïve CD8+ T cells by RNA-seq and ATAC-seq at baseline and further analyzed different CD8+ subsets following symptom provocation. We observed in ME/CFS TEM upregulation of key transcription factors associated with exhaustion and downregulation of genes controlling key metabolic activities, as well as an altered chromatin landscape consistent with exhaustion programs, while ME/CFS TN displayed a potential loss of naïve identity. Our dataset serves as an important resource for understanding ME/CFS pathology and supports a novel state of immune dysregulation in ME/CFS which may offer new treatment options.
Investigating biomarkers and therapeutic approaches in mouse models of SARS-CoV2 induced Long COVID with neuroinflammation and cognitive deficits.
Authors: Lu Peiwen , Fernández-Castañeda Anthony , Geraghty Anna C , Song Eric , Monje Michelle , Iwasaki Akiko 
Published: November 2024

Abstract
Survivors of COVID-19 frequently experience lingering neurological symptoms including cognitive impairment. However, the absence of suitable animal models presents a significant challenge in comprehensively understanding the post-acute sequelae of SARS-CoV-2 (PASC) or Long COVID. Utilizing a mild SARS-CoV2 infection mouse model, we explored neuroinflammation caused by respiratory SARS-CoV2 infection in mouse with AAV-hACE2 delivery in lower respiratory system only and found white matter selective microglial reactivity. After subjecting mice to mild SARS-CoV-2 infection for 7 weeks, we observed persistently impaired hippocampal neurogenesis, decreased oligodendrocytes, and myelin loss along with increased CCL11 in cerebrospinal fluid (CSF). Notably, individuals experiencing lasting cognitive symptoms post-COVID exhibited elevated CCL11 levels, suggesting its potential as a biomarker for Long COVID. Concurrently, we developed a model of moderate mortality SARS-CoV-2 infection in K18-hACE2 transgenic mice by modifying the infection route, allowing us to study the development of neuropathology and simulate Long COVID patients with a history of hospitalization at the acute SARS-CoV-2 infection stage. To address neuroinflammation in the mild respiratory COVID and moderate mortality COVID mouse model, we are targeting reactive microglia for therapeutic intervention, evaluating various approaches.
Role of mTOR and HIF-1α in LMP2A-mediated increase in ATP production
Authors: Swanson-Mungerson Michelle , Devitt Grace , Braich Kamiljit , Salimian Melody , Monroy Del Toro Rosalinda , Incrocci Ryan 
Published: November 2024

Abstract
Numerous studies indicate that latency proteins from Epstein-Barr virus contribute not only to the development, but also the survival of B cell lymphomas. Our laboratory has demonstrated that LMP2A promotes B cell lymphoma survival by inducing the activation of STAT3. More recently, pathways that link STAT3 activation with increased cellular metabolism suggested that LMP2A may increase B cell lymphoma ATP production via the mTOR-dependent activation of STAT3. Using LMP2A-negative and -positive B cell lymphoma cell lines, our data suggest that LMP2A increases ATP production in an mTOR-dependent pathway. However, the addition of the STAT3 inhibitor, STATTIC, did not impact the LMP2A-mediated increase in ATP production. Further investigation indicated that LMP2A-mediated activation of mTOR results in increases in HIF-1α protein, but not RNA, that are required for the enhancements in ATP production. Finally, our data demonstrate that LMP2A requires the activation of phosphorylated p70 ribosomal s6 kinase and 4E-BP1 to increase protein levels of HIF-1α that are required to increase ATP levels in LMP2A-expressing cell lines. Taken together, our data suggest that LMP2A gives lymphoma cells a competitive advantage to produce more ATP through increases in HIF-1α that are mTOR and p70s6K/4E-BP-1 dependent.
Amelioration of lung inflammation induced with viral infectious stimulation by a high-molecular weight sulfated polysaccharide compound, Fucoidan mix-AG
Authors: Miyazaki Yoshiyuki , Nakano Hayato , Takeuchi Shugo , Takeuchi Hideaki , Tachikawa Daisuke 
Published: November 2024

Abstract
Fucoidan, viscous components in brown algae, has been reported to possess the effect enhancing cellular immune responses against cancer and viral infections. In contrast, it is also known to contribute to the alleviation of pathology in some inflammatory diseases, and almost certainly be effective in maintaining mucosal immune homeostasis. In this study, we evaluated the mitigating effect of fucoidan on pneumonia in aggravated upper airway infection. Consequently, C57BL/6J mice were orally administered 30 mg of Fucoidan mix-AG (Fm-AG) daily for 2 weeks, and then a solution of TLR ligands (TLR3-L: 62 µg Poly(I:C), TLR4-L: 25 µg rSARS-CoV-2 spike protein, TLR7-L: 5 µg Gardiquimod) were injected via oropharyngeal aspiration to simulate lung inflammation in viral infections. As a result, enhanced cellular infiltration into bronchoalveolar lavage (BAL) fluid were observed after the treatment with TLR ligands, but the expression of class II MHC molecules on the leukocytes was reduced in the Fm-AG-administrated mice as compared with the control mice. In addition, the markedly augmented production of inflammatory cytokine IL-6 in the model mice were significantly lowered by administration of Fm-AG both in BAL fluid and plasma. However, no reduction in the level of anti-viral IFNs were observed in the mice administrated Fm-AG. These results suggested that continuous intake of Fm-AG would prevent the severe complications (pneumonia and cytokine storm) during upper airway infections.
Autism-related CHD8 is required for maintaining Treg cell fitness
Authors: Yang Junqi , Zheng Yi , Guo Fukun 
Published: November 2024

Abstract
CHD8 is an adenosine triphosphate (ATP)-dependent chromatin remodeler, the mutations of which define a subtype of autism spectrum disorders. CHD8 has recently been found to be important for hematopoietic stem cell survival and erythroblast cytokinesis. It remains unclear whether CHD8 plays a role in regulatory T (Treg) cells that suppress effector T cells such as CD4+ Th1/Th2/Th17 cells and CD8+ cytotoxic T cells to maintain immune tolerance. In this study we have generated Treg cell-specific CHD8-deficient mice. We found that CHD8 deletion led to early, fatal systemic inflammatory disorders. The autoimmune responses came from an increase in activated CD4+ and CD8+ T cells and in effector T cells including Th1, Th2 and Th17 cells. The immune activation was due to increased Treg cell plasticity as evidenced by increased effector T cell cytokine expression in Treg cells. Paradoxically, CHD8 deletion upregulated Treg cell functional markers such as CTLA-4, PD-1, GITR and ICOS, indicative of functional exhaustion. RNA-seq revealed that CHD8 deletion upregulated a number of hallmark pathways including inflammatory response, p53 pathway, apoptosis, G2M checkpoint, mTORC1 signaling, glycolysis, oxidative phosphorylation, and reactive oxygen species pathway. Collectively, our findings suggest that CHD8 is required for maintaining Treg cell fitness and function by modulating p53-mediated cell survival and cell cycle progression, and mTOR-mediated mitochondrial metabolism.
Mechanisms of pTreg development from anergic precursors
Authors: Ristin Svetlana , Nivelo Luis , Stelekati Erietta , Villarino Alejandro 
Published: November 2024

Abstract
Regulatory T cells (Tregs) are generated either in the thymus or periphery. While factors governing ‘natural’ thymus-derived Treg (nTreg) development are well described, there is limited understanding of those directing peripheral regulatory T cell (pTreg) differentiation. Using a mouse model of oral tolerance, we demonstrate that T cells must first enter a state of anergy prior to becoming pTreg, suggesting a two-stage process. Stage 1 is characterized by T cell anergy with prominent induction of ‘checkpoint’ inhibitory receptors, most notably PD-1 and CD200. Stage 2 then follows with pTreg conversion or, alternatively, adoption of a ‘deep’ anergic state. Given this induction of inhibitory receptors, we assessed the impact of PD-1 deficiency and found that T cells proliferate more and convert less to pTreg. Intriguingly, we also find that PD-1 expression distinguishes pTreg derived from anergic precursors from those derived from non-anergic precursors. Based on scRNAseq data showing that IL-2-STAT5 signaling is highly active in pTreg, we also assessed the role of IL-2Ra and STAT5 and found that both are strictly required for induction of pTreg, suggesting that this pathway drives transition from Stage 1 to Stage 2 tolerance. Taken together, our data shows that transition from Treg-independent (Stage 1) to Treg-dependent (Stage 2) tolerance is driven by cell extrinsic signals provided by inhibitory receptors and IL-2-STAT5 signaling which combine to induce pTreg development.
IL-8 Reprograms Monocyte-derived Macrophages into M2-like States in Human Glioblastoma
Authors: Medina Stephanie , Hayes Madeline , Brockman Asa , Ihrie Rebecca , Irish Jonathan 
Published: November 2024

Abstract
Glioblastoma (GBM), the most common primary brain tumor in adults, remains incurable and has not yet benefitted from immunotherapies. Microglial and hematopoietic macrophages are the most abundant immune cells in GBM and play contrasting roles in the disease. Our prior studies revealed a signature of CD32 and HLA-DR protein expression and STAT3 signaling in hematopoietic macrophages associated with poor GBM patient survival and neural stem cell niche contact (PMC10371245). We hypothesized that GBM cells may secrete factors to remodel the cellular microenvironment and generate this signature macrophage subset from myeloid cells. In a series of experiments, 1) IL-8 was the primary cytokine expressed in vivo and ex vivo by human GBM cells (immunohistochemistry, cytokine arrays), 2) IL-8 was sufficient to instruct healthy monocytes to adopt the CD32+ HLA-DR+ signature of in vivo GBM macrophages (spectral flow cytometry, mass cytometry), and 3) IL-8 was required for primary GBM cell supernatant to polarize healthy macrophages into CD163+ CD206+ CD32+ HLA-DR+ M2-like cells in ex vivo 6-day cultures (α-IL-8 blocking antibodies, spectral flow cytometry). This ex vivo system will now be used to test the function of the GBM signature macrophages and to explore targeting of IL-8 to improve GBM therapy.
Novel Oral Treatment for Atopic Dermatitis: Allosteric Modulation of GABAA Receptor Signaling
Authors: Meyer Michelle , Webb Daniel , Lee Majia , Kowalczyk Ethan , Stafford Douglas , Arnold Leggy 
Published: November 2024

Abstract
Background: This study explores the development of a groundbreaking oral treatment for atopic dermatitis (AD) by investigating the effects of allosteric modulators targeting the gamma-aminobutyric acid type A (GABAA) receptor outside the brain.
Methods: To induce the AD phenotype, mice strains including Swiss Webster, Balb/c, and C57/BL6 received Calcipotriol (MC903) applied to both ears. The experimental groups were treated with either the novel GABAA receptor ligands, vehicle, or positive control compounds. Over a seventeen-day period, various parameters such as animal weight, ear thickness, and scratching behavior were monitored. Post-study, mice were euthanized, and gene expression and histology of their ears were examined. Statistical analysis employed a 2-way ANOVA.
Results: Our findings indicate a significant reduction in the induction of inflammatory genes especially for the thymic stromal lymphopoietin (TSLP) in response to the MC903-induced AD phenotype when treated with GABAA receptor ligands. A notable reduction in scratching behavior was observed, especially when treated after the establishment of the AD phenotype.
Conclusion: The administration of GABAA receptor ligands demonstrated a substantial reduction in ear inflammation, ear thickness, and ear scratching in the murine model for AD. This research provides promising insights into the development of a novel and effective oral treatment for AD.
IL-10 mitigates inflammation within the CNS during West Nile virus neuroinvasive disease
Authors: Halasah Nadeem , Kallingal Isha , Durrant Douglas 
Published: November 2024

Abstract
West Nile virus (WNV) causes a severe CNS infection in humans, primarily in the elderly and immunocompromised. Prior studies revealed that IL-10, primarily through the suppression of antiviral and proinflammatory cytokine production, predominately has a negative role in WNV immunity. However, in the absence of a critical DC-subset, IL-10-expressing lymphocyte infiltration was reduced in the WNV-infected CNS and excessive inflammation and immunopathology caused increased susceptibility to WNND. These results suggest a neuroprotective role of IL-10. Preliminary findings demonstrate CD8+ T cells as major IL-10 producers at day 12 post-infection compared with animals deficient in CD8a+DEC-205+ DCs. We intend to validate these observations by assessing IL-10 production in infiltrating cells expressing CD4, CD11b, and CD11c. Additionally, we will administer anti-IL-10 monoclonal antibody (mAb) post-WNV infection to neutralize IL-10's effects within the CNS. Monitoring survival and viral burden after intracranial injection of aIL-10 mAb or control IgG, our study seeks to elucidate IL-10's protective role in WNND by mitigating inflammation.
The molecular program of CD4+ regulatory and effector T cell expansion in vitro
Authors: Moro Alejandro , Yu Aixin , Nivelo Luis , Villarino Alejandro , Malek Thomas 
Published: November 2024

Abstract
Adoptive Treg therapy is being advanced to treat autoimmunity. To discern the molecular pathways underlying Treg expansion in vitro, we evaluated the chromatin landscape and gene expression profiles of Treg and Teff cells in response to TCR/CD28/IL-2 priming followed by IL-2 expansion over 12-days. Although initially similar over the first 6 days, Tregs showed somewhat higher STAT5 activation and chromatin opening, leading to optimal expansion on day 6, which was 2-fold greater than Teff cells. After day 6, Tregs, but not Teff cells, showed substantial reduction in expansion. At day 9 and 12, more marked changes in gene expression and chromatin accessibility at promoter regions were seen between Treg and Teff cells. PCA revealed for RNAseq and ATACseq a clockwise movement, where the day 12 cells expressed a profile that reverts toward the input populations. Temporal integration of differentially expressed genes and chromatin accessibility revealed 6 patterns of responses, 4 of which were similar between Treg and Teff cells. The glycolytic activity in Treg and Teff cells during expansion until day 6 was similar but then they declined more rapidly in Tregs. Hence, these differences in gene accessibility and expression and glycolysis likely contribute to the more rapid decay in Treg expansion in response to IL-2. Thus, Tregs are programmed temporally for more limited expansion in vitro that may reflect a mechanism to finely tune Treg numbers to maintain homeostasis in vivo.
Umbilical Cord Mesenchymal Stromal/Stem Cells Interplay with Th-17 Cell Response Pathway
Authors: Alsabri Sami , Najar Mehdi , Rahmani Saida , Faour Wissam , Lombard Catherine , Fayyad-Kazan Hussein , Sokal Etienne , Merimi Makram , Fahmi Hassan 
Published: November 2024

Abstract
Umbilical cord derived mesenchymal stromal/stem cells (UC-MSCs) were assessed, as an immunomodulatory therapeutics, for their dynamic interaction with the Th-17 immune response pathway. UC-MSCs were able to modulate lymphocyte response by promoting a Th-17-like profile. Such modulation depended on the cell ratio of the co-cultures as well as the presence of an inflammatory setting. UC-MSCs significantly increased the expression of IL-17A and RORγt but differentially modulated IL-23R expression by T cells. In parallel, the secretion profile of the fifteen factors (1β, IL-4, IL-6, IL-10, IL-17A, IL-17F, IL-22, IL-21, IL-23, IL-25, IL-31, IL-33, INF-γ, sCD40, and TNF-α) involved in the Th-17 immune response pathway was substantially altered during these co-cultures. Upregulation of cytokines and regulatory mediators demonstrates the capacity of UC-MSCs to sense and actively respond to tissue challenges. Protein network and functional enrichment analysis indicated that several biological processes, molecular functions and cellular components linked to distinct Th-17 signaling interactions are involved in several trophic, inflammatory and immune network responses. These immunological changes and interactions with the Th-17 pathway are likely critical to tissue healing and may help to identify molecular targets that will improve therapeutic strategies involving UC-MSCs.
Label-free single cell metabolic imaging of neutrophil activation
Authors: Datta Rupsa , Miskolci Veronika , Britt Emily , Fan Jing , Huttenlocher Anna , Skala Melissa 
Published: November 2024

Abstract
Upon activation, neutrophils combat infiltrating pathogens through a variety of effector functions, including oxidative burst, phagocytosis, and neutrophil extracellular traps (NETs). Metabolic pathways within neutrophils can be pharmacologically affected to modify immune outcomes. However, there is a lack of techniques to assess neutrophil metabolism in a label-free, non-destructive manner at single cell level. To address this, human neutrophil metabolism was investigated using two-photon microscopy of intrinsic fluorophores reduced nicotinamide adenine dinucleotide (phosphate), NAD(P)H, and flavin adenine dinucleotide, FAD. We image the optical redox ratio (ORR), [NAD(P)H / (NAD(P)H + FAD)] and the fluorescence lifetimes of NAD(P)H. Single-cell metabolic profiles of neutrophils were generated using an automatic cell segmentation pipeline. We found that activation of neutrophils either pharmacologically or by pathogen infection induced a significant metabolic change characterized by an increase in ORR and decrease in NAD(P)H lifetime, indicating an increase of the NAD(P)H pool, which suggests increases in glycolysis and the pentose phosphate pathway. Neutrophil activation was confirmed by measuring effector functions including oxidative burst. Importantly, identical metabolic changes were detected in the neutrophils of transgenic zebrafish larvae following activation, confirming the validity of these findings in vivo.
Deficiency of Myeloid PP4 in mice exacerbates Neutrophil Hyperactivation during Sepsis
Authors: Yang Feng-Ming 
Published: November 2024

Abstract
We previously demonstrated that serine/threonine phosphatase PP4 functions as a negative regulator of innate immunity, prevents hyperactivation of Toll-like receptors (TLRs) signaling in sepsis. Because the recruitment of monocytes to sites of inflammation is critical for host defense, we then explored the role of PP4 in myeloid lineage cells. Mice without PP4 only in myeloid cells were more susceptible to sepsis due to serious tissue damage. Importantly, CLP induced myeloid PP4 deficiency mice produced significantly more proinflammatory cytokines and chemokines, which contributed to dysregulated neutrophil recruitment. Neutrophils isolated from mice without PP4 showed an increase in NETs formation in response to subsequent RANTES stimulation. Mechanistically, PP4 regulated RANTES production via TBK1/IRF3 axis in macrophages. Finally, RNA-seq analysis of the livers obtained from myeloid PP4 deficiency mice relative to wildtype controls identified 1849 differentially expressed genes. Of these, 628 were upregulated and 1221 were downregulated. Moreover, 25 significantly enriched GO terms and 1 significantly enriched KEGG pathways were identified, involving multicellular organismal homeostasis, regulation of phosphorylation and inflammation response, and cytokine-cytokine receptor interaction, which might also play roles in the process of sepsis. Thus, our data provide a remarkable new resource of regulatory pathways for understanding PP4 function at the organism level.
Proteostasis maintenance by macrophage trogocytosis
Authors: Kimura Yoshitaka , Philip Naomi , Chavan Arun , Medzhitov Ruslan 
Published: November 2024

Abstract
Cells are frequently exposed to a wide variety of stresses that perturb cellular fitness. Stressed cells autonomously drive the defense mechanism to maintain their homeostasis, such as DNA repair program upon DNA damage and chaperone induction and protein degradation pathway upon protein misfolding. However, how cell-to-cell interaction contributes to the maintenance of cellular fitness has been elusive. Here, we show that macrophages interact with proteotoxically stressed cells and promote their proteostasis. Cells undergoing protein aggregate accumulation are detected by macrophages, and a part of their body is taken up via trogocytosis. In this process, protein aggregates in stressed cells are transferred to macrophages, leading to the reduction of protein aggregate load in stressed cells. Mechanistically, the macrophage detection and uptake of protein aggregates requires the stressed cells to express membrane-associated isoform of a macrophage growth factor CSF1 (mCSF1), which is upregulated by endoplasmic reticulum stress response pathways. The analysis of mCSF1-deficient mice in systemic proteotoxicity model reveals mCSF1 suppresses cellular damage in tissues, suggesting the trogocytosis-mediated removal of protein aggregates contributes to cellular homeostasis in vivo. These findings point to the fundamental cellular stress responses to induce full-blown proteostasis through the communication to immune cells in cooperation with autonomous responses.