bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gut commensal Lactobacillus reuteri exacerbates CNS autoimmunity in a dietary tryptophan-dependent manner.
Authors: Montgomery Theresa L , Eckstrom Korin , Künstner Axel , Kennedy Josephine J. , Busch Hauke , Krementsov Dimitry 
Published: February 2023

Abstract
Gut commensal bacteria exert profound effects on the immune system of the mammalian host. In particular, Lactobacillus species have a long-standing history as putative probiotics, generally being characterized as safe and/or beneficial for the mammalian host. Despite this fact, current literature points to both pro- and anti-inflammatory roles for this genus, with little consensus as to the mechanisms governing these divergent outcomes. Using mouse models, we and others have previously shown that, unexpectedly, stable commensal colonization with Lactobacillus reuteri (L. reuteri) is correlated with, and sufficient to enhance host susceptibility to experimental autoimmune encephalomyelitis (EAE), in association with alterations in tryptophan derived metabolites in host circulation. To identify the underlying mechanisms, we characterized the genomes of commensal L. reuteri isolates, along with two other representative Lactobacillus species, L. murinus and L. johnsonii. Whole genome sequencing revealed an enrichment in the enzymatic machinery necessary to catabolize dietary tryptophan into immunomodulatory indole derivatives in L. reuteri. Mechanistically, supplementation with high dietary tryptophan sustained an L. reuteri-dependent exacerbation of EAE and augmented inflammatory T cell populations, while depletion of dietary tryptophan profoundly suppressed EAE in a microbiome-specific manner. Taken together, our data reveal considerable variation in the genetic landscape of commensal Lactobacilli, and demonstrate mechanisms responsible for differential modulation of autoimmunity by gut microbiota, including an unexpected disease-promoting role for catabolism of host dietary tryptophan.
Germinal center checkpoint restrains anti-insulin B lymphocytes in type 1 diabetes-prone mice
Authors: McNitt Dudley H , Joose Bryan A , Thomas James W , Bonami Rachel H 
Published: February 2023

Abstract
Anti-insulin B lymphocytes (AIBCs) are key drivers of the autoimmune attack in type 1 diabetes (T1D) but their exact functions in T1D pathogenesis, and the point(s) during their development where tolerance is lost, are unknown. In the class-switch-competent anti-insulin B cell receptor transgenic non-obese diabetic (VH125SD.NOD) mice, 1–2% of B lymphocytes are insulin-specific, which accelerates diabetes development despite limited insulin autoantibody (IAA) production. Here we used VH125SD.NOD mice to determine where immune tolerance is lost throughout AIBC class-switch, germinal center entry, and antibody-secreting cell differentiation. We find an increased percentage of AIBCs enter germinal centers relative to non-insulin binding B lymphocytes in the same mice. In addition, an increased percentage of AIBCs are found within the pancreas, class-switch to IgG1, and proliferate relative to non-insulin binding B lymphocytes. We also find that AIBCs are activated in the gut to a greater extent than non-insulin binding B lymphocytes. These data suggest that AIBCs escape anergy and are able to class-switch, enter GCs, and proliferate, but maintain functional silencing preventing spontaneous IAA-production. Moreover, the escape from anergy may occur within the pancreas and/or the gastrointestinal tract. Our data has implications in immunotherapy treatments for T1D, as these GC checkpoints may provide an opportunity for T1D intervention.
Simultaneous Measurement of 67 Non-Human Primate Immunological, Metabolic and Hormonal Biomarkers using Luminex® xMAP® Technology
Authors: Keith Robert H , Luo Hong , Raeber Tina , Kornmeier Christine , Gilliam Brooke , Xiao Qiang 
Published: February 2023

Abstract
Immunology, metabolic, and pituitary biomarker research in non-human primates (NHP) is essential for the study of several diseases and biological regulation. To meet this need, we developed three NHP MILLIPLEX® multiplex panels: 12-plex NHP Metabolic Hormone, 7-plex NHP Pituitary Panel 1, and our new 48-plex NHP Cytokine/Chemokine Panel A for the simultaneous measurement of picogram levels of 67 immune, metabolic and hormone factors, in small volumes of serum, plasma or cell culture samples using Luminex® xMAP® technology. Serum from in vivo LPS-challenged animals (n=2 cynomolgus, n=2 rhesus) demonstrated increased levels of 19 cytokines/chemokines with peak elevated levels at 1 hr for 4 analytes (e.g. IL-10, TNFα), at 3 hr for 11 analytes (e.g. IL-6, IFNγ) and at 8 hr (e.g. Fractalkine, I-TAC). Metabolic markers, GIP and GLP-1 (active) in rhesus, also increased significantly at 8 hr and 3 hr, respectively (p&lt;0.02). Significant differences between fasted and fed serum sample values (n=5 cynomolgus, n=5 rhesus) were found for several metabolic markers, including C-peptide, GIP, Insulin and PP, which increased with feeding (P&lt;0.05). In cynomolgus, I-TAC and IP-10 significantly increased after feeding (P&lt;0.003). Testing healthy serum samples from three additional NHP species (African green monkey (n=5), baboon (n=5), chimpanzee (n=5)) exhibited overall sample detectability of 89%, 77%, and 64% for the MILLIPLEX®Cytokine/Chemokine Panel A, Pituitary, and Metabolic multiplex panels, respectively. Thus, the MILLIPLEX®NHP Metabolic Hormone, NHP Pituitary Panel 1 and our latest and largest NHP panel, the 48-plex NHP Cytokine/Chemokine Panel A, are valuable tools for profiling 67 biomarkers in 5 NHP species for disease research.
Type I interferon-induced β-catenin promotes hematopoietic stem cell activation in persistent viral infection in mice
Authors: NGUYEN TRIEU HAI , KWARTENG EDWARD , LAULHE XAVIER , CHARTRAND KARINE , LAMARRE ALAIN , HEINONEN KRISTA 
Published: February 2023

Abstract
Quiescent hematopoietic stem cells (HSCs) become activated and exit their bone marrow niches in response to infections or sterile inflammation to initiate extramedullary hematopoiesis at peripheral sites. While these processes have been described in acute infections, the impact of persistent viral infections on HSC activation and mobilization remains less clear. Our results demonstrate that an active persistent lymphocytic choriomeningitis virus (LCMV) clone 13 infection resulted in type I interferon-dependent stabilization of β-catenin in HSCs, promoting their activation, mobilization and functional exhaustion that was sustained in time and could be seen even after transfer to uninfected hosts. To further examine the functional role of β-catenin in HSC activation, we generated bone marrow chimeras to follow β-catenin-deficient (Ctnnb1−/−) and wild type HSC response to LCMV Cl13 in the same environment. Ctnnb1−/− HSCs and multipotent progenitor cells failed to expand in response to the infection, while still retaining their ability to reconstitute secondary hosts. Moreover, through the course of the infection, Ctnnb1−/− cells produced myeloid progeny at a similar level to the wild type. These findings lead us to propose that β-catenin is required for HSC activation by interferons in the early phase of the infection; however, it appears dispensable for LCMV-induced emergency myelopoiesis.
Fetal liver hematopoietic stem cells possess the mast cell repopulation ability within a limited time window
Authors: Kobayashi Michihiro , Kosters Astrid , Ghosn Eliver Eid Bou , Yoshimoto Momoko 
Published: February 2023

Abstract
Recent progress in developmental immunology has revealed the hematopoietic stem cell (HSC)-independent ontogeny for the various hematopoietic lineages, including mast cells (MC). Adult bone marrow (BM) HSCs fail to generate MC in both lineage tracing and transplantation assays. However, it is unclear whether fetal liver (FL) HSCs can generate MC in vivo. We investigated the MC potential of HSCs from FL and the aorta-gonad-mesonephros (AGM) in lineage tracing and transplantation assays. We employed different genetic mouse models that allowed us to identify the Tomato+ progeny of hematopoietic precursors (Runx1mer-cre-mer), endothelial cells (EC, Cdh5ERT2Cre) and HSCs (Fgd5ERT2Cre) by injecting tamoxifen (TAM) at different embryonic days starting at E7.5. TdTomato (Tom)+ HSCs and MCs were quantified after birth. In addition, we transplanted HSCs from AGM (11.5), FL (E12.5 and E15.5), and adult BM (&gt;6 wks) into irradiated mice.

Results:
The EC-labeling at E7.5 efficiently generated Tomato+ MC, but not HSCs (similar results were obtained for the Runx1mer-cre-mer model). EC-labeling at E9.5 made equivalent Tom+ labeling efficiency in MC and HSCs (~85%). However, E11.5 EC mostly failed to mark MC, but still generated Tom+ HSCs (~25%). HSC-labeling at E14 or postnatal day 2 efficiently marked HSCs, but not MC. Collectively, our results indicate that active MC production terminates before E12 and that HSCs after E14 lack MC potential. Our transplantation study also shows lack of MC repopulation by HSCs after E15. However, E11.5 AGM and E12.5 FL HSCs repopulated MC, revealing a transient MC production potential of HSCs.

Conclusion:
MC production by hemogenic ECs terminates before E12 and early HSCs produce MC within a limited time window.
Genomic Tools and Models for Investigating the Role of Germline Diversity in Mouse Antibody Repertoire Development
Authors: Kos Justin T , Watson Corey T 
Published: February 2023

Abstract
In mouse, the immunoglobulin (IG) loci span several Mb of the genome and contain hundreds of repeated, highly homologous sets of variable (V), diversity (D), and joining (J) genes that recombine in B cells to produce an individual’s expressed Ab repertoire. Similar to what has been reported in humans, recent data has shown significant levels of haplotype variation in the IG loci between commonly used inbred mouse strains, challenging the assumption that the IG loci are conserved across all strains of mice. We are using this intra-strain diversity to develop new models for studying the role of IG germline variation on Ab repertoire dynamics and function, questions that remain difficult to address in outbred human populations and pre-existing animal models.
Given the diversity and complexity within the IG loci, the development of effective mouse models first requires the characterization of intra-strain differences and the construction of high-quality reference assemblies for the IG loci in several representative strains. To address this problem, we are using the Pacific Biosciences SMRT sequencing to sequence BAC clones spanning the IGH, IGK, and IGL loci in NOD/ShiLtJ and BALB/cByJ strains. We are also gaining additional insight on intra-strain diversity by profiling the expressed IGM, IGK, and IGL repertoires of 18 commonly used laboratory mouse strains. We have used this data to guide the construction of congenic lines on the C57BL/6 background, carrying divergent IGH or IGK loci from BALB/cByJ or NOD/ShiLtJ, respectively. Together, our data show significant germline diversity in our new IG assemblies, as well as divergent Ab repertoires in common lab mouse strains.
Splenic B-1 Cells Shows Diversified IgM Repertoire in Aged Atherosclerotic Mice.
Authors: Srikakulapu Prasad , Upadhye Aditi , Marshall Melissa A , Holodick Nichol , Rothstein Thomas L , McNamara Coleen A 
Published: February 2023

Abstract
B-1 cell derived IgM attenuates chronic inflammatory diseases like atherosclerosis. The spleen is a major lymphoid tissue where B-1 cells (both B-1a and B-1b) produce natural IgM. B-1 derived natural IgM has long been thought to contain restricted predominantly germline encoded V-D-J gene segments with low number of non-template encoded nucleotide (N)-additions, which are added at the junctions between V-D and D-J segments. However, differences in VDJ gene usage and N-addition frequency between peritoneal cavity (PerC) and spleen B-1 cells in aged atherosclerotic mice are unknown. B-1a and B-1b cells were single-cell sorted from PerC and spleen of 100-week-old, chow-fed ApoE−/− mice. Single cell sequencing of the immunoglobulin heavy chain variable region was performed. Splenic B-1 cells displayed increased diversity at the V-D and D-J junctions, as evidenced by increased average number of N-additions. Sequences containing &gt;1 N-additions at both V-D and D-J junctions were 2% and 27% for PerC B-1a and B-1b sequences as compared to 44% and 44% of sequences in splenic B-1a and B-1b respectively. B-1 cells from PerC and spleen showed marked differences in VH, D and JH gene segment usage. Importantly, the most commonly expressed heavy chain complementarity determining region 3 (CDR-H3) amino acid sequence in spleen B-1a (AREVTTMYYFDY) and B-1b (AREDYYGSSYYFDY) cells was different from PerC B-1a (AGDYDGYWYFDV) and B-1b (AGDRDGYWYFDV) cells. Results provide clear evidence of a diversified IgM repertoire expressed by spleen B-1 cells compared to PerC B-1 cells during advanced atherosclerosis. The CDR-H3 sequences of splenic B-1 cells suggest underlying differences in antigen specificity which could further regulate disease progression.
mCherry-expressing Mycobacterium tuberculosis gives insight into host cell tropism and immune pressure at the single bacterium level in macaques with tuberculosis
Authors: Mattila Joshua T , Pisu Davide , Junecko Beth A. , Flynn JoAnne L , Russell David G. 
Published: February 2023

Abstract
Tuberculosis is caused by Mycobacterium tuberculosis (Mtb) and is associated with granuloma formation in the lungs and other tissues. These lesions can limit bacterial replication but also contain host cells for Mtb and support bacterial persistence and dissemination in poorly controlled disease. Macrophages are often viewed as primary host cells for Mtb but work in mice demonstrates that other cell types host Mtb in acute infection. Less is known about host cell tropism in human TB, especially in the early stages of infection but these early interactions may have implications for later stages of disease. To identify which cells are infected in early and established TB, we infected two cynomolgus macaques with an mCherry-expressing Mtb strain and used flow cytometry and microscopy to identify and phenotype the infected cells at four- and ten-weeks post infection. This approach also allowed us to compare bacterial mCherry expression and size to determine if granulomas exert different levels of pressure on Mtb that vary by timepoint or lesion type. We found that granulomas contained numerous Mtb-infected neutrophils and macrophages at four weeks post infection but fewer infected neutrophils at ten weeks post infection. When the fluorescence and size of individual bacteria were compared across granulomas and timepoints, we found that bacteria in high Mtb burden granulomas were more fluorescent than bacteria in granulomas that contained fewer bacteria, and the bacteria in the four-week granulomas were longer, suggesting that early granulomas are better at supporting Mtb growth than granulomas in established disease. These results provide new insights into Mtb-host cell dynamics in a nonhuman primate model that replicates human TB.
Lactate production by Staphylococcus aureus biofilm inhibits HDAC11 to reprogram the host immune response during persistent infection
Authors: Heim Cortney , Bosch Megan E , Yamada Kelsey J , Aldrich Amy L , Chaudhari Sujata S , Klinkebiel David , Gries Casey M , Alqarzaee Abdulelah A , Li Yixuan , Thomas Vinai C , Seto Edward , Kielian Tammy 
Published: February 2023

Abstract
Staphylococcus aureus (S. aureus) is a leading cause of prosthetic joint infection (PJI) typified by biofilm formation. Our laboratory has identified preferential myeloid-derived suppressor cell (MDSC) recruitment as a critical mechanism for biofilm persistence, as MDSCs are a main source of IL-10. We screened the Nebraska Transposon Mutant Library to identify S. aureus mutants impaired in their ability to trigger MDSC IL-10 production. Significant hits in lactate biosynthesis were identified. A S. aureus Δddh/ldh1/ldh2 mutant, defective in both D- and L-lactate production, decreased leukocyte IL-10 expression and biofilm-associated monocytes were reprogrammed to a pro-inflammatory state, resulting in reduced biofilm burden. Histone acetylation plays a central role in regulating gene expression and histone deacetylase (HDAC) activity was significantly increased in leukocytes recovered from mice infected with Δddh/ldh1/ldh2 compared to WT, resulting in decreased global histone 3 (H3) acetylation at the IL-10 promoter in MDSCs from Δddh/ldh1/ldh2-infected mice. Lactate inhibited HDAC11, resulting in unchecked activity of HDAC6, a positive regulator of Il-10 transcription, and increased IL-10 production. MDSCs and macrophages produced significantly less IL-10 when treated with HDAC6 inhibitor tubastatin A during co-culture with WT but not Δddh/ldh1/ldh2 biofilm. D-lactate was elevated in synovial fluid of patients with PJI compared to aseptic controls and lactate promoted IL-10 production by human monocyte-derived macrophages. Collectively, S. aureus lactate-mediated inhibition of HDAC11 plays a critical role during biofilm infection, leading to epigenetic changes that reprogram the host immune response.
Uncovering the role of CBLB for innate immune responses regulating systemic dissemination during a Non-Tuberculous Mycobacterial infection
Authors: Sharma Jaishree , Mudalagiriyappa Srinivasu , Abdelaal Hazem F.M. , Kelly Thomas C. , Choi Woosuk , Vieson Miranda D. , Talaat Adel M. , Nanjappa Som Gowda 
Published: February 2023

Abstract
Non-Tuberculous Mycobacteria (NTM) are ubiquitous and cause chronic lung infections to fatal disseminated diseases in immunocompromised individuals. The incidence and prevalence of NTM infections are increasing globally, mainly due to the surging numbers of immunocompromised patients. The diagnosis is often misleading, and the emergence of multi-drug resistant NTM has deprived the treatment options. Innate immune responses, dictated by immune regulators, shape the clinical outcomes of NTM infections. Here, we describe the role of an E3 ubiquitin ligase, CBLB, for innate immunity against an NTM infection. We found that the absence of CBLB, under T-cell deficiency, enhanced the bacterial burden and dissemination following both intravenous and intratracheal infections. Strikingly, CBLB fostered an early induction of granulomatous inflammation, which thwarts the dissemination. CBLB-deficiency caused a significant reduction of NK cell numbers, but not their intrinsic functions. Further, we found that CBLB was required to augment the numbers of inflammatory monocytes and conventional dendritic cells, the latter, additionally, for their activation. Thus, our findings suggest that CBLB plays an essential role in eliciting protective innate immune responses to control the growth and dissemination of NTM during T-cell deficiency.
Diminished monocyte response in severe COVID-19 patients.
Authors: Davis-Gardner Meredith E , Edara Venkata , Lai Lilin , Jin Fengzhi , Floyd Katharine , Nyhoff Lindsay , Mantus Grace , Adelman Max , Pellegrini Kathryn , Chirkova Tatiana , Kissick Haydn , Bosinger Steven , Anderson Larry , Rouphael Nadine , Ahmed Rafi , Wrammert Jens , Grakoui Arash , Suthar Mehul S 
Published: February 2023

Abstract
The COVID-19 pandemic has caused a global public health crisis of unprecedented proportions. SARS-CoV-2, the etiological agent of COVID-19, primarily infects the respiratory tract, leading to a range of symptoms including dry cough, fever, and shortness of breath. While many cases remain mild or asymptomatic, a subset progress to acute respiratory distress syndrome (ARDS) requiring ICU admission and ventilation support. Rapid progress has been made to understand the pathogenesis and immune response to SARS-CoV-2 infection; however, there remain a number of unanswered questions.
Recent evidence has indicated that mild cases of COVID-19 are controlled by an effective innate immune response. However, in moderate and severe cases, the immune response to infection appears to be dysfunctional leading to low levels of interferon and high inflammatory responses.
Here, we examined a cohort of patients admitted to the Emory University Hospital with severe COVID-19. Patients had variable neutralization titers measured by FRNT assay, which did not correlate age or disease severity. Flow cytometry immune subset analysis, cytokine and chemokine quantification, and single cell RNA sequencing (scRNAseq) revealed an inflammatory phenotype including a significant shift in the myeloid compartment compared to healthy donors. Numbers of pDCs and non-classical (CD14−CD16+) monocytes in the blood were decreased, while intermediate monocytes (CD14+CD16+) cells were increased. Additionally, stimulated CD14+ cells from healthy donors were able to limit SARS-CoV-2 infection in a human airway epithelial culture system. This suggests a role for monocytes to combat infection by SARS-CoV-2 that may be dysregulated in severe patients.
Constitutive immune surveillance of the nasal mucosa by neutrophils
Authors: Gonzalez Rodrigo J. , Alvarez David , Mazo Irina B , Matysyak Colette , Garg Rohit , Helble Jennifer , Starnbach Michael N , von Andrian Ulrich H 
Published: February 2023

Abstract
The nasal mucosa is a versatile tissue where functions such as olfaction and conditioning of air take place. A particularly relevant and less explored function of this tissue relates to its capacity to respond to insult. Air-borne pathogens can use the nasal mucosa as a portal of entry to further disseminate into deeper tissues and little is known about the immune cell populations these pathogens encounter upon infection. We asked what immune cell populations are present in the murine nasal mucosa and unexpectedly found extravascular neutrophils to be a constitutive and prominent population in the steady state. These neutrophils were found in comparable numbers in conventional vs. germ-free mice and can be divided into three well-defined populations based on the expression of specific cell surface markers and mRNA transcript profiles. One of the populations was traced to nasal mucosa-associated pockets of bone marrow and determined to contribute to the nasal mucosa neutrophil extravascular pool. A second population was found to preferentially phagocytose bacteria during infection. In the absence of infection, this population differentiates into a third population, which interacts with other cells of the nasal mucosa in a manner that resembles trogocytosis. Lastly, we found extravascular granulocyte hematopoietic precursors in the nasal mucosa that likely contribute to the extravascular neutrophil pool. Thus, the nasal mucosa encompasses a constitutive population of extravascular neutrophils that show diverse origins and specialization of function. These findings contribute to our understanding of the composition and development of the microenvironment that air-borne pathogens encounter upon infection in the nasal mucosa.