bluuebunny/crossref_metadata_2025_split huggingface dataset:
Maintenance of the naive T cell population during malnutrition is associated with residency in the bone marrow
Authors: Foster Takesha R , Dadzie Kwesi A , Moore Lindsay , Saravanan Rithanya , Adams Olivia , Washington Aja , Gubbels Bupp Melanie R 
Published: August 2023

Abstract
In mammals, T cell migration is under circadian control, likely to anticipate daily rhythms in infection risk. Glucocorticoids control this process, and malnutrition is associated with increased glucocorticoid levels. Therefore, we evaluated whether malnutrition disrupts the circadian migratory patterns of T cells. Malnutrition did not impact circadian patterns of T cell residency of lymphoid tissues; indicating that fluctuations, rather than specific concentrations, of glucocorticoids are a key circadian signal. Additionally, the total number of CD4+ and CD8+ T cells in the lymph nodes and blood were lower in malnourished as compared to well-nourished mice. However, the percentage and total number of naïve T cells was maintained in the lymph nodes, blood, and spleen of malnourished mice, suggesting preferential preservation of naïve T cells. Interestingly, the percentage and total number of CD4+ and CD8+ T cells in the bone marrow was elevated significantly in mice on a malnourished diet. Additionally, malnourished CD4+ and CD8+ T cells in the bone marrow showed significantly high CCR7 expression and CCL21 expression was increased in malnourished bone marrow compared to control. CCR7 and its chemokine, CCL21, may be responsible for trafficking malnourished T cells to the bone marrow during malnutrition. Overall, these findings suggest that the bone marrow may contribute to naïve T cell preservation during malnutrition.
NSF-MRI [DBI- 1920116] NSF -RUI [IOS-1951881]
Plasticity of clonal memory CD8 T cell differentiation
Authors: Hiam-Gálvez Kamir , Black Mollie , Raposo Colin J , Satpathy Ansuman T 
Published: August 2023

Abstract
Memory CD8 T cells provide highly specific and long-lasting protection against previously experienced pathogens. This potent protection is mediated by hundreds to thousands of unique clones with distinct T cell receptors (TCRs). Higher T cell clonal diversity and recognition of a wider range of pathogen antigens are associated with improved host protection. Therefore, understanding how clonal responses are organized is important for improving T cell function in a range of diseases. To comprehensively test the range of clonal memory T cell differentiation capacity, we deeply profiled polyclonal mouse memory CD8 T cells from acute lymphocytic choriomeningitis virus (LCMV) infection before and after viral rechallenge by paired single cell RNA and TCR sequencing. We found that individual memory T cell clone expansion and differentiation at the peak of the rechallenge response is highly variable. Clones are spread across various patterns of unique phenotypes ranging from highly cytotoxic to stem-like memory states. To quantify clonal differentiation plasticity, we transferred memory T cells into multiple new congenic recipients. Clonal progeny in different hosts acquired highly similar differentiation states suggesting that emergent memory clone behavior is imprinted by events during the primary infection. Indeed, transcriptional state of clones prior to rechallenge was sufficient to predict clone behavior upon rechallenge. This work provides a platform for understanding the mechanisms by which memory T cells make decisions and future studies will aim to perturb clones to elicit specific functions during a memory response.
Supported by grants from the Burroughs Wellcome Fund (Career Award for Medical Scientists [ATS]), Cancer Research Institute (Technology Impact Award, Lloyd J. Old STAR Award [ATS]), American Society of Hematology (ASH Scholar Award [ATS]), Parker Institute for Cancer Immunotherapy (ATS), Stanford School of Medicine (Propel Postdoctoral Scholarship [KHG]), National Institutes of Health (5T32AI007290-38 [CJR])
The age-related changes in lymph node stromal cells underlie defects in peripheral T cell maintenance and immune function decline in old mice
Authors: Sonar Sandip Ashok , Bhat Ruchika , Coplen Christopher P , Nikolich-Zugich Janko 
Published: August 2023

Abstract
Older adults are more vulnerable to infection and cancer, and poorly respond to vaccination. The structural stromal cells in the lymph nodes (LN) are essential regulators of T cell homeostasis and immune response. However, how does aging of LN stromal cells contribute to T cell maintenance defects and functional immunity is incompletely understood. Here we used single cell RNA-Seq of purified stromal cells from adult (3mo) and old (21mo) peripheral LN of C57BL/6 mice to characterize the age-related transcriptional differences in major stromal cell subsets. Our data revealed the enrichment of CCL19hi and CCL19low while diminution of Nr4a1+ and Inmt+ FRC in old LN. The enriched FRC in old LN exhibited a gene signature of cellular and oxidative stress response, mitochondrial defects, and negative regulation of immunity. The ex vivo functional characterization revealed that old LN stromal cells exhibit elevated mitochondrial reactive oxygen species coupled with increased mitochondrial mass and reduced membrane potential, indicative of mitochondrial defects during the senescence. Interestingly, these defects are observed in older but not mid-age LN. Furthermore, in vitro co-culture of LN stromal cells and purified naive T (TN) cells showed that old LN stromal cells poorly support CD8 TN cell survival. Finally, boosting the function of old LN stromal cells using agonistic anti-LTbR or mitigating oxidative stress using N-Acetyl Cysteine reversed this effect, via stabilization of BCL2 in TN cells. Thus, these results suggest that age-related adverse changes in LN stromal cells contribute to defects in maintenance of TN cells, and highlight that these defects could be reversed to restore TN cell homeostasis and functional immunity.
This work is supported by grants from NIH (P01 AG052359 and R37 AG020719) to Dr. Janko Nikolich-Zugich.
Uncovering the role of STAT5 in CD8+ T cell fate
Authors: Chanda Monica Kasturi , Gu Zehui , Piper Taylor L , Shudde Claire E , Courtney Adam H 
Published: August 2023

Abstract
Long-term protection against infection and disease requires long-lived memory CD8+ T cells. The development of these memory CD8+ T cells requires a differentiation process influenced by cytokines – such as IL-2, IL-7, and IL-15 – that are known to mediate the balance between effector and memory populations. Interestingly, these cytokines act through the common activation of STAT5, however, the mechanisms by which STAT5 dictates CD8+ T cell fate is poorly understood. To elucidate how STAT5 affects CD8+ T cell differentiation, we have developed a strategy to activate endogenous STAT5 in the absence of cytokine. We compared CD8+ T cells cultured in IL-2, a cytokine known to promote effector CD8+ T cells, to those where STAT5 was directly activated. We found that direct activation of STAT5 resulted in decreased IFNγ production in comparison to IL-2 treatment. This observation led us to evaluate the expression of transcription factors and proteins related to effector, memory, and exhausted states. Our results demonstrate that CD8+ T cells that experience direct activation of STAT5 have higher levels of TCF1 and lower levels of granzyme B compared to CD8+ T cells cultured in IL-2. To gain an understanding of phenotypic changes and differentiation state, we performed bulk RNA sequencing to assess global changes in gene expression. Our RNA sequencing results indicate that when compared to CD8+ T cells cultured in IL-2, direct STAT5 activation causes increased expression of genes related to a memory phenotype and a corresponding decrease in those related to an effector or exhausted phenotype. Our findings suggest that STAT5 activation is critical to a memory-like phenotype and could be harnessed for therapeutic benefit in CD8+ T cell-based treatments.
Supported by grants from the V Foundation and the Concern Foundation
Identification of novel genes that regulate B-1 cells
Authors: Rosero Sara , Luo Zheng , Loyd Kent , Baumgarth Nicole 
Published: August 2023

Abstract
IgM is the first antibody produced in ontogeny and in response to an initial antigen exposure. It plays an important role in effective immune protection, and is required for maximal antigen-specific IgG responses. In mice, most circulating serum IgM is generated by fetal-derived B-1 cells in spleen and bone marrow. How B-1 cells preferentially develop into natural IgM secreting cells is incompletely understood. To identify candidate genes critical for B-1 cells development and/or maintenance we generated parts of a larger immunophenotyping database Knock Out Mouse Project (KOMP) providing results of the flow cytometric evaluation of spleen cells from 641 mouse strains, each containing a single-gene deletion as well as 200 individual congenic control mice, identifying 58 distinct leukocyte subsets for each spleen. We generated and curated a complete list of each gene found to be associated with B-1 cell changes. Seven genes were identified that significantly reduced frequencies of CD5+ B-1 cells in males and/or females, of which three were uniquely altering the B-1 cell subset. None of these genes have been associated with B-1 cell regulation previously. Using qRT-PCR we found that 4 showed B-1 cell intrinsic gene expression. Ongoing work is to determine the impact of each gene on serum antibody levels and immune protection to influenza virus challenge.
This work was supported by NIH UM1 OD023221 (KCKL), R0AI148652 (NB), and the Graduate Student Support Program UC Davis (SR).
Aberrant expansion of spontaneous splenic germinal centers induced by hallmark genetic lesions of aggressive lymphoma
Authors: Muppidi Jagan R , Pindzola Grace M , Razzaghi Raud , Tavory Rachel N , Nguyen Hang , Morris Vivian , Darbha Sriranjani 
Published: August 2023

Abstract
Diffuse large B cell lymphoma (DLBCL) is an aggressive heterogeneous clinical entity that is thought to be derived from germinal center (GC) B cells or cells that have recently passed through the GC. Unique molecular vulnerabilities have been identified in the aggressive MCD/C5 genetic subclass of DLBCL. However, the pre-malignant cell-of-origin exhibiting MCD-like dependencies remains elusive. In this study, we examined animals carrying up to four hallmark genetic lesions found in MCD consisting of gain-of-function mutations in Myd88 and Cd79b, loss of Prdm1 and overexpression of BCL2. We discovered that expression of combinations of these alleles in vivo promoted a cell-intrinsic accumulation of B cells in spontaneous splenic GCs. Like MCD, these pre-malignant B cells were enriched for B-cell receptors (BCRs) with evidence of self-reactivity, showed a de novo dependence on Tlr9 and were more sensitive to inhibition of BTK. Mutant spontaneous splenic GC B cells (GCB) showed increased proliferation and IRF4 expression. Mice carrying all four genetic lesions showed a greater than 50-fold expansion of spontaneous splenic GCs exhibiting aberrant histologic features with a dark zone immunophenotype and went on to develop DLBCL in the spleen with age. Thus, by combining multiple hallmark genetic alterations associated with MCD, our study identifies aberrant spontaneous splenic GCB as a likely cell-of-origin for this aggressive genetic subtype of lymphoma.
This research was supported by the Intramural Research Program of the NIH, CCR, NCI.
Borrelia burgdorferi c-di-AMP induces type I IFN response in macrophage through the activation of STING signaling pathway
Authors: Priya Raj , Raghunandanan Sajith , Alanazi Fuad , Yang Frank 
Published: August 2023

Abstract
Lyme disease (LD) which is caused by the spirochete Borrelia burgdorferi (Bb) poses a global health threat. Bb infection induces type I IFN response that is associated with arthritis and other symptoms. However, the ligands, PAMPs, and signaling pathways associated with type I IFN production by Bb are poorly characterized. Stimulator of Interferon Genes (STING) signaling pathway is an intracellular surveillance pathway that detects c-di-nucleotides (CDNs) produced by pathogens through STING and induces type I IFN production. Bb produces CDNs and hence it has the potential to activate the STING signaling pathway. In this study, the role of c-di-AMP in the elicitation of type I IFN response to Bb infection was elucidated. The RAW cell line was infected with Bb and activation of STING signaling was measured by detecting the activation of downstream proteins (pSTING, pTBK1, pIRF3 & pNF-κB), proinflammatory cytokines (IL6, TNF-α) and Type I IFN (IFN-β) response using ELISA, western blotting, immunostaining, and Luciferase Reporter assay. Bb infection to macrophage results in c-di-AMP mediated elicitation of type I IFN response. The induction level of type I IFN response was dependent on the level of c-di-AMP as the Bb mutant strain producing higher c-di-AMP level induced higher cytokine production. Interestingly, c-di-AMP released into the BSK-II medium during the culture of Bb could also stimulate the production of type I IFN response. The induction of type I IFN by c-di-AMP was dependent on STING protein as the RAW STING KO cell line showed a reduction in the level of IFN-β. In conclusion, our results show that Bb-produced c-di-AMP is a major PAMP that triggers type I interferon production in macrophage by activation of the STING signaling pathway.
Removal of the spleen abrogates the long-term hydrosalpinx pathology following Chlamydia genital infection
Authors: Konjufca Vjollca H , Essmyer Zana , Shillova Nita , Hyseni Besmir , Howe Savannah 
Published: August 2023

Abstract
C. trachomatis infections in women may cause pelvic inflammatory disease, chronic pelvic pain, and infertility. In the mouse model, genital Chlamydia disseminates systemically to infect the spleen. Removal of the spleen (splenectomy) abrogates hydrosalpinx pathology in the female reproductive tract (FRT), although it does not affect FRT Chlamydia clearance. Ascension of Chlamydia to the upper FRT (uteri, ovaries, oviducts) is critical for the development of hydrosalpinx. Over the course of genital infection, splenectomized mice exhibit significantly lower Chlamydia burden in the upper FRT and the GI tract compared to controls. Based on the report that Chlamydia-specific IgA secreted in the FRT protects against genital Chlamydia challenge, we hypothesized that splenectomy induces IgA secretion in the FRT. Examination of vaginal washes revealed that unlike controls, splenectomized mice exhibit Chlamydia-specific IgA by 4 weeks post-infection (wpi). However, the presence of IgA at this time did not explain the significant reduction in Chlamydia ascension observed by 2 wpi. Unlike controls, splenectomized mice additionally exhibit Chlamydia-specific IgM antibodies in vaginal secretions as early as 2 wpi. Naïve mice infected with Chlamydia pre-incubated with vaginal washes of splenectomized mice collected at 2 or 6 wpi exhibited reduced Chlamydia burden in the FRT, ILNs, spleen, and the GI tract at 3 and 7 days post-infection compared to controls. Secreted IgM and IgA thus neutralize Chlamydia, diminish its ascension in the upper FRT and thus abrogate the long-term hydrosalpinx pathology. This work reveals a previously unknown role that the spleen plays in the regulation of antibody secretion in the FRT mucosa.
Supported by a grant from NIH (1 R21 AI159743-01)
AIM2-mediated Immunity to Plasmodium Infection in Hepatocytes
Authors: Kurup Samarchith P 
Published: August 2023

Abstract
Malaria, caused by Plasmodium parasites is a severe disease affecting millions of people around the world. Plasmodium undergoes obligatory development and replication in the hepatocytes, before initiating the life-threatening clinical disease of blood-stage malaria. Although the innate immune responses that control Plasmodium infection and development in the liver are known to limit clinical malaria and transmission, the mechanism of such responses remain relatively unknown. Here we demonstrate that the DNA of Plasmodium is sensed by AIM2 (absent in melanoma 2) receptors in the infected hepatocytes, resulting in Caspase-1 activation. However, we observed that Caspase-1 undergoes an unconventional and incomplete proteolytic processing in such hepatocytes, resulting in the activation of the membrane pore-forming protein, Gasdermin D (GSDMD), without the concurrent activation of the inflammasome-associated pro-inflammatory cytokines such as interleukin (IL)-1 and IL-18. Nevertheless, the AIM2-mediated Caspase-1 activation pathway induced the elimination of Plasmodium-infected hepatocytes and a resultant control of malaria in the liver.
Supported by grants from NIH (R01 AI168307)
Induction of protective interferon-β responses in murine osteoblasts following S. aureus infection and the use of nucleic acid nanoparticles to enhance bacterial killing
Authors: Johnson Morgan B , Afonin Kirill , Marriott Ian 
Published: August 2023

Abstract
Staphylococcus aureus is the primary causative agent of osteomyelitis, a severe inflammatory bone infection. Treatment for osteomyelitis includes long-term antibiotic treatment, surgical debridement of necrotic bone, or even amputation. Treatment is challenging due to an inability of antibiotics to penetrate bone tissue and resident bone cells that harbor intracellular bacteria, and the increased incidence of infections associated with antibiotic-resistant S. aureus strains. Following S. aureus infection, resident bone cells including osteoblasts produce immune mediators and bone regulatory factors. While type I interferons (IFNs) are best known for their antiviral effects, it is becoming apparent that they impact susceptibility to many pathogens. Here, we report elevated IFN-β levels in infected femurs in a mouse model of osteomyelitis. RNA Tag-Seq analysis of S. aureus infected osteoblasts showed elevated expression of mRNA encoding IFN-β and ISGs. We confirmed rapid and robust release of IFN-β protein production by osteoblasts following S. aureus challenge. Furthermore, we showed increased protein expression of ISGs by infected osteoblasts and demonstrate that this occurs secondary to the release of IFN-β by these cells. Importantly, we have determined that exposure of S. aureus-infected osteoblasts to IFN-β markedly reduces the viable bacteria harbored by these cells. Finally, we have demonstrated delivery of immunomodulatory nucleic acid nanoparticle (NANPs) scaffolds using lipid-based carriers to murine osteoblasts. These NANPs are promising agents that could induce protective IFNs during S. aureus infection of bone tissue and be further functionalized with antimicrobials to kill intracellular S. aureus.
This work was supported by grant 1R01AI170012-01 to IM and MBJ from the National Institute for Arthritis and Musculoskeletal and Skin Diseases.
Immune recognition of latent neuronal Toxoplasma gondii infection
Authors: Eberhard Julia N , Bunkofske Molly , Shallberg Lindsey , Hunter Christopher A 
Published: August 2023

Abstract
Toxoplasma gondii is a neurotropic parasite with high mortality rates in immunocompromised individuals. Successful therapies have been developed against the acute tachyzoite stage, but no treatment options exist to target the latent form of the parasite – bradyzoites that form cysts within neurons. It is thought that residence of cysts in neurons shelters T. gondii from immune recognition and clearance. However, a decline in cyst numbers over time suggests the presence of anti-cyst immunity. Additionally, neuronal deletion of STAT1 results in increased cyst size and number, but no change in tachyzoite replication, providing evidence for IFN-γ-mediated cyst control. T cells are a major source of IFN-γ and are crucial for parasite control in the CNS, but it remains unclear if T cells directly target cyst-infected neurons. The use of transgenic parasites with bradyzoite-restricted OVA expression (BagOVA) reveals that cyst-derived antigen can induce OT-I CD8+ T cell responses in the brains of chronically infected mice. These cyst-specific OT-Is have distinct effector phenotypes and cytokine production when compared to T cells responding to antigen expressed by both tachyzoites and bradyzoites (ptubOVA). To determine whether neurons directly present cyst antigen to induce CD8+ T cell responses in BagOVA infection, mice with neuronal-specific loss of MHCI were generated. Infection of these mice showed no significant change in the magnitude of T cell responses or parasite burden in the CNS. Together these findings reveal that T cell responses can be mounted against cyst antigens, but another cell type likely mediates cross presentation of cyst derived antigens.
Supported by grants from NIH (R01 580-5803-4-580697-XXXX-2000-3000)
Pulmonary Immunopathogenesis of Granulibacter bethesdensis
Authors: Sharma Atul , Chauhan Arun , Ramesh Ashwin , Mishra Bibhuti B , Sharma Jyotika 
Published: August 2023

Abstract
Granulibacter bethesdensis (Gb) is a Gram negative bacterial pathogen reported to cause disease exclusively in patients with Chronic Granulomatous Disease harboring mutations in one of the five subunits of NADPH oxidase complex. The pathogen has been shown to cause chronic as well as recurrent infections in CGD patients that can be fatal. Although systemic and septic infection have been reported, the pathogenesis of Gb in respiratory microenvironment is completely unknown. Here we compared the disease progression and infection outcome of wild-type (WT) and murine CGD model Gp91−/− mice following intranasal infection with a clinical isolate of Gb. We found that compared to the WT mice, Gp91−/− CGD mice are highly susceptible to respiratory infection with Gb. While the WT mice displayed transient increase in inflammatory cytokines and moderate leukocyte infiltration characteristic of a mild, resolving infection, CGD mice displayed hypercytokinemia but attenuated antimicrobial function of phagocytic cells. A significant upregulation of Type 2 inflammatory cytokine IFN-γ in lungs Gb infected gp91−/− prompted investigation the its role in GB pathogenesis. Neutralization of this cytokine mitigated the inflammatory response and reduced bacterial burden in infected Gp91−/− CGD mice resulting in significantly improved overall survival. Mechanistically, IFN-γ neutralization improved antimicrobial function of neutrophils. Taken together, our findings suggest that in the absence of a functional superoxide production machinery, G. bethesdensis is capable of causing a chronic respiratory infection with fulminant sepsis and IFN-γ produced during the infection has a detrimental effect on the bacterial clearance.