bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamics of adaptive natural killer cells in longitudinal analysis of CMV vaccine recipients
Authors: Gyurova Ivayla E , Schlums Heinrich , Bernstein David , Bryceson Yenan , Waggoner Stephen N 
Published: January 2023

Abstract
While cytomegalovirus (CMV) infection poses a considerable burden to public health, an efficacious vaccine is not yet available. Classical vaccine efforts focusing on the induction of B- and T-cell memory have proven ineffective and, therefore, CMV remains a significant public health threat. The incidence of recurrent, severe infections with cytomegalovirus (CMV) and other DNA viruses in patients lacking functional natural killer (NK) cells highlight the importance of these cells in viral control. Therefore, the marked expansion of phenotypically and functionally distinct subsets of NK cells during CMV infection may represent a component of immune control of CMV that should be replicated in vaccines. We interrogated blood leukocytes samples collected longitudinally during a CMV glycoprotein B vaccine trial to ascertain induction or accumulation of these unique CMV-associated subsets of NK cells. We observe tantalizing expansions of CMV-associated subsets of NK cells in some CMV-negative vaccine recipients, that are unexpectedly mirrored by similar expansions in placebo-recipients. Moreover, these subpopulations exhibit marked contractions or patterns of alternating expansion and contraction in other trial participants. Importantly, this unique longitudinal data in healthy CMV-seronegative individuals indicates that NK-cell subsets may react to unknown environmental or inflammatory cues and demonstrate greater flux that appreciated from past cross-sectional studies.
Quantifying the selection on influenza A virus imposed by CD8 T cells
Authors: Li Zheng-Rong Tiger , Zarnitsyna Veronika I , Lowen Anice C , Kohlmeier Jacob E , Antia Rustom 
Published: January 2023

Abstract
An essential question regarding the T cell-inducing influenza vaccine is whether the cellular immunity may drive the virus to rapidly evolve and escape. In our previous modeling study, we have shown an CD8 T cell escape-variant of influenza A virus (IAV) invades extremely slowly given empirical HLA allele frequencies and modest selection pressure. Guided by the model, we aim to quantify the selection from CD8 T cells using a novel digital droplet PCR system under different in vivo settings.
Mice were intranasally primed with HKx31 (H3N2) and challenged with a 1:1 mixture of wild-type and mutant PR8, which harbors an N370Q escaping mutation in its NP366–374 immunodominant epitope, on day 30 post-priming. The area under the in vivo viral growth curve (AUC) is used to measure the fitness of wild-type and mutant viruses. Based on the AUCs of C57BL/6 (H-2b/b) and CF1B6 (H-2b/d), the estimated selective advantage of this mutation is 0.28 [0.20, 0.36] and 0.21 [0.10, 0.34], respectively. Interestingly, although the intramuscularly primed C57BL/6 gave a similar estimate for the advantage (0.22 [0.16, 0.30]), the advantage became much more apparent on day 6 and 8 after PR8 challenge. This implies the lung resident memory CD8 T cells may be the source of selection during the initial stage of IAV infection.
In combination with the model prediction, an escape-variant of IAV that carries a mutant immunodominant epitope may need 100 to 500 generations (corresponding to 1 to 5 years if the infection period is assumed to be 4 days) to reach 50% of prevalence given the frequency of cognate HLA alleles is 20%. We concluded that the selection from CD8 T cells may not be sufficient to drive the CD8 T cell epitopes of IAV to evolve rapidly like the antibody epitopes.
Spatial Analysis of CD8+ T cell Activation After Local Viral Replication in the Skin
Authors: Malo Courtney Sarah , Reynoso Glennys V. , Hickman Heather D. 
Published: January 2023

Abstract
The generation of a robust CD8+ T cell response is critical for the elimination of virally infected cells and is dependent on presentation of viral antigen in the draining lymph node. Although we know much about antigen presentation in general, how antiviral T cell activation is precisely accomplished at the spatial level remains incompletely understood. Much of our knowledge of spatial details of viral antigen presentation derives from studies in which virus is subcutaneously injected, which likely differs greatly from presentation after virus replicates in the tissue and naturally drains to the regional lymph node. In order to better understand viral antigen presentation in the lymph node after viral replication in the skin and the impact on the initiation of CD8+ T cell responses, we infected mice in the ear pinna with vaccinia virus (VACV) epicutaneously using a bifurcated needle. VACV replicates to high titers in the skin, and viral antigen and genomes are detectable in the draining cervical lymph node by day 5 post infection, far beyond that after subcutaneous VACV injection. We are currently exploring the spatiotemporal dynamics of T cell activation as well as the antigen presenting cell subsets important for priming after epicutanous VACV infection. These findings are of significance for both our basic understanding of antiviral immunity and for the development of new T cell-based vaccination strategies, where optimization of CD8+ T cell responses is essential.
Protein kinase C-eta (PKCη) is dispensable for the activation and function of CD8+T cells
Authors: Liu Hsin Yu , Pedros Christophe , Canonigo Balancio Ann J , Altman Amnon 
Published: January 2023

Abstract
We previously reported that protein kinase C-eta (PKCη) forms a novel signaling complex with CTLA4 in regulatory T cells (Tregs) and this complex is required for the contact-dependent suppressive activity of Tregs. As a result, PKCη-deficient (Prkch−/−) Tregs fail to suppress anti-tumor immunity. However, given the ubiquitous expression of PKCη, it has remained unclear whether PKCη is also required for the effector functions of conventional T cells, particularly CD8+T cells that play a critical role in anti-tumor immunity. We therefore assessed the effect of genetic PKCη deletion on CD8+T cell-dependent immune functions. We found that Prkch−/− mouse or PRKCH knockdown human CD8+T cells displayed intact, and even enhanced, T cell activation in vitro as measured by proliferation and expression of TNFα, IFNγ, and granzyme B (GzmB) following anti-CD3 plus -CD28 costimulation. Next, we used the acute LCMV infection as an in vivo model to study the characteristics of virus-specific CD8+T cells, which were identified by specific staining with CD8 tetramers. Splenocytes from Prkch−/− mice showed similar frequencies of tetramer+CD8+T cells to those of wild-type (WT) mice, and these cells proliferated normally and expressed normal levels of TNFα and IFNγ. The LCMV-specific Prkch−/−CD8+T cells expressed normal or increased levels of GzmB, and the infected mice displayed greater viral clearance. We conclude that PKCη deficiency does not impact the activation and function of CD8+T cells. Taken together, the selective inhibition of the CTLA4-PKCη signaling pathway in cancer patients is a promising therapeutic strategy to inactivate tumor-promoting Tregs and, thus, enhance anti-tumor immunity, without having adverse effects on CD8+T cells.
Single-cell cloning of untreated HIV-specific natural killer cells in humans
Authors: Lucar Olivier Alexandre , Ghofrani Joshua , Goepfert Paul A , Jost Stephanie , Reeves R. Keith 
Published: January 2023

Abstract
Beyond their ability to eliminate infected cells without the need for prior sensitization, natural killer (NK) cells have been shown to exhibit adaptive immune functions. In particular, our lab demonstrated that antigen-specific memory NK cells responses against SIV can be induced by infection and vaccination in non-human primates. These data suggested that a subset of NK cells in humans may also mediate immunological memory responses to HIV.
To study human HIV-antigen-specific NK cells in more detail, we adapted limiting dilution assays to clonally expand individual peripheral blood NK cells (NKCL) from untreated HIV-infected individuals. Using a calcein acetoxymethyl ester cytotoxicity assay, the ability of each NKCL to lyse MHC-devoid K562 cell lines or autologous B-LCLs pulsed with a pool of MOG- (human self-peptide), HIV Gag- or HIV Env-derived overlapping peptides was assessed.
As expected, all tested NKCL could potently lyse K562 cells (median=56% killing) but did not kill B-LCL pulsed with the MOG control. Strikingly, 37.5% of NKCL displayed anti-HIV Gag cytotoxic activity up to 31% specific lysis (range: 1%–31%), while 25% of NKCL displayed anti-HIV Env cytotoxic activity up to 72% specific lysis (range: 1%–72%). Furthermore, pre-treatment with an anti-NKG2C blocking antibody decreased the specific lysis, thereby confirming the importance of NKG2C receptor in the function of antigen-specific NK cells.
Thus, we were able to isolate single NK cells displaying potent HIV-specific killing, within the range of robust cytotoxicity normally found against tumor cells. Together these data suggest that HIV-specific responses mediated by NK cells exist in humans and may have the potential to be harnessed for therapeutic modalities.
MicroRNA-21 is a critical regulator of the antiviral NK cell response
Authors: Geary Clair , Lau Colleen , Zawislak Carolyn , Santosa Endi K , Berrien-Elliott Melissa , Bezman Natalie , Lanier Lewis L , Fehniger Todd A , Sun Joseph Chai-Yuen 
Published: January 2023

Abstract
Natural killer (NK) cells are innate lymphocytes that possess adaptive features, including antigen-specific clonal expansion and memory responses. Global loss of microRNAs (miRNAs) leads to defects in NK cell homeostasis and antiviral responses; however, the role of individual miRNAs in these processes is poorly defined. Here, we investigated miR-21, a highly expressed miRNA in both human and mouse NK cells. While miR-21 was largely dispensable for NK cell development, miR-21-deficient NK cells failed to mediate significant host protection against mouse cytomegalovirus (MCMV) due to defective proliferation. Although activated NK cells upregulated miR-21 early after MCMV exposure, loss of miR-21 did not impact NK cell activation or effector molecule expression during viral infection. Transcriptome analysis of miR-21-deficient NK cells demonstrated dysregulation of cell cycle regulators, including several predicted targets of miR-21. Altogether, our findings demonstrate a novel role for miR-21 as a crucial regulator of adaptive NK cell responses during MCMV infection.
Reevaluating HLA-A2-restricted Lassa epitopes in human Lassa fever survivors
Authors: Sullivan Brian Martin , Sakabe Saori , Hartnett Jessica N , Nho Nhi , Goba Augustine , Momoh Mambu , Sandi John Demby , Kanneh Lansana , Cubitt Beatrice , Garcia Selma D , Ware Brian C , Kotliar Dylan , Robles-Sikisaka Refugio , Gangavarapu Karthik , de la Torre Juan Carlos , Sabeti Pardis C , Andersen Kristian G , Garry Robert F , Grant Donald S , Schieffelin John S , Oldstone Michael B 
Published: January 2023

Abstract
Many factors contribute to the selection of epitope-specific T cells. Often, candidate epitopes are generated through in silico prediction of various biological processes, mainly peptide generation and MHC binding, that are then tested in relevant biological assays. This is especially true of epitopes derived from BSL-4 pathogens or where relevant patient samples are difficult to obtain. Two previous studies identified CD8+ T cell epitopes from the Lassa virus glycoprotein through in silico prediction, experimental MHC binding assays, and epitope generation in HLA-A2 transgenic mice. Using samples from ten HLA-A*02:01 Lassa fever survivors, we tested whether these previously described epitope-specific CD8+ T cells were present and their relation to the broader Lassa virus-specific T cell response. Using overnight stimulation assays, we detected robust LASV-specific responses to the glycoprotein and nucleoprotein, but only one of the three epitopes (GP60–68)shown to be present and protective in mice made a substantial contribution to the overall LASV-specific response. Using a more sensitive proliferation assay, we detected the remaining two epitopes in some individuals at a very low frequency. Overall, this study shows the limitations of epitope discovery through in silico prediction, MHC binding and transgenic mouse models and highlights the complex nature of T cell selection during natural infection of humans.
Illuminating the Mechanism of MHC-I Folding and Antigen Repertoire Selection Using Deep Mutational Scanning and Biophysical Studies
Authors: Sgourakis Nikolaos , McShan Andrew C , Devlin Christine A , Morozov Giora , Procko Erik 
Published: January 2023

Abstract
Chaperones Tapasin and TAP-binding protein related (TAPBPR) perform the important functions of stabilizing nascent MHC-I molecules (chaperoning), and selecting high affinity peptide cargo in the MHC-I groove (editing). While X-ray and cryoEM snapshots of MHC-I molecules prepared in complex with TAPBPR and Tapasin, respectively, have provided important insights into the empty MHC-I groove structure, the molecular mechanism through which these chaperones influence the selection of specific amino acid sequences remains incompletely characterized. Of particular importance is a 16 aa loop region in TAPBPR (corresponding to 11 residues in the sequence of Tapasin), which has been suggested to actively compete with incoming peptides by forming direct contacts with the F-pocket of the empty MHC-I groove. Using a deep mutational scanning functional analysis of TAPBPR, we find that important residues for its chaperoning activity are located on the major interaction surfaces with nascent MHC-I molecules, excluding the loop. However, interactions with properly conformed molecules toward editing of their peptide cargo are influenced by loop mutations, in an MHC-I allele- and peptide-dependent manner, as shown in MHC-I tetramer staining experiments using a TAPBPR library expressed on the surface of yeast. Detailed biophysical characterization by NMR and ITC reveal that the loop does not interact with the empty MHC-I groove to compete with incoming peptides, but instead promotes peptide loading by acting as a kinetic “trap”. Our results suggest that, by utilizing a longer loop, TAPBPR lowers the affinity requirements for peptide selection relative to Tapasin to promote loading under conditions of reduced peptide concentration.
Single cell RNA sequence analysis reveals novel clusters unique to post-infectious myocarditis in the mouse model of Coxsackievirus infection
Authors: Lasrado Ninaad , Arumugam Rajkumar , Jayaraja Sabarirajan , Thibivilliers Sandra , Libault Marc , Starr Timothy K. , Reddy Jay 
Published: January 2023

Abstract
Myocarditis is a common occurrence in children and adolescents that can lead to dilated cardiomyopathy. Since it is difficult to identify the triggers of this complex disease, mechanistic understanding of DCM pathogenesis may create avenues to develop new treatment strategies. We have been engaged in delineating the autoimmune pathways underlying the development of DCM using various mouse models of myocarditis that resemble human disease. One such model is Coxsackievirus B3 (CVB)-induced myocarditis in A/J mice that show two distinct phases of disease, but occur in continuum. While, the acute, infectious phase (up to ~10 days post-infection) is marked by viremia and infiltrations in the hearts, infectious virions become undetected during the chronic phase (~beyond 18 days post-infection), and animals develop DCM. The latter phenotype can occur over a period of ~60 to 90 days, and hitherto, it has been a challenge to determine the underlying mechanisms. To dissect this complex nature of disease, we recently performed single cell RNA sequence analysis on heart infiltrates obtained from CVB-infected mice. Using panels of 15 to 30 marker genes for various immune and non-immune cells, we identified 18 and 26 clusters respectively in healthy and infected hearts that also include few unknown clusters unique for each group. Likewise, transcriptome analyses led us to identify a total of 14,051 genes to be differentially expressed, and of these, 206 and 345 transcripts were unique to healthy and CVB-infected groups, respectively. The data suggest that uniquely expressed genes in the CVB-infected hearts may have a role in the development of post-infectious myocarditis leading to DCM.
Microbiota-driven regulatory T cells suppress experimental autoimmune encephalomyelitis (EAE) in interleukin-17A deficient HLA class-II transgenic mice model of multiple sclerosis (MS)
Authors: Shahi Shailesh K , Freedman Samantha N , Murra Alexandra C , Cady Nicole , Gupta Arnav , Guseva Natalya V , Gibson-Corley Katherine N , Bossler Aaron D , Ganesan Sukirth M , Karandikar Nitin J , Mangalam Ashutosh K 
Published: January 2023

Abstract
Multiple sclerosis (MS) is an inflammatory demyelinating disease of the central nervous system. Despite IL-17A being linked to the immunopathogenesis of MS, the mechanism of IL-17A in disease development and maintenance is unclear. In the present study, we investigated the association of IL-17A and gut microbiota in disease development and severity, utilizing HLA-DR3 transgenic mice lacking IL-17A (IL-17A−/−). We found that HLA-DR3.IL-17A−/− mice had a higher frequency of CD4+CD25+FoxP3+ Treg cells and develop milder EAE compared to IL-17A suffcient HLA-DR3 mice. Utilizing 16S metagenocmic sequencing and analysis of gut microbiota we observed that HLA-DR3.IL-17A−/− mice had an increased abundance of regulatory T cells promoting bacteria in the gut such as Lactobacillus and Clostridia. Fecal transplantation followed by co-housing of HLA.DR3 mice with HLA-DR3.IL17A−/− resulted in development of milder EAE and an increase in CD4+CD25+FoxP3+ Treg cells in HLA-DR3 mice. Further whole-genome shotgun metagenomic analysis showed modulation of pathogen-associated molecular patterns (PAMPs) and O-antigen pathways linked with the host innate immune responses in HLA-DR3.IL-17A−/− mice. Thus our study suggests that gut microbiota changes due to the absence of IL17A induce regulatory T cells and suppresses disease in an animal model of MS by modulating the host-bacterial dynamics via PRR-PAMPS interactions.
Virus-mediated dysbiosis alters immune populations to promote type 1 diabetes onset
Authors: Morse Zachary J , Simister Rachel L , Crowe Sean A , Osborne Lisa C , Horwitz Marc S 
Published: January 2023

Abstract
In combination with genetic determinants, susceptibility to autoimmune diseases such as Type 1 Diabetes (T1D) is established by various environmental factors including infection, microbial dysbiosis, antibiotic use, and vitamin D deficiency. Studies have implicated infection with certain viruses such as coxsackievirus B (CVB) to be an important cofactor associated with diabetes development and pathogenesis. Infections may be an instigating factor to alter the microbiome and this microbial change may be sufficient to skew immune populations and promote autoimmunity. Mucosa-associated invariant T (MAIT) cell populations have been shown to be altered leading up to diabetes onset in patients and mice. These cells are activated by microbial products in the gut to promote intestinal integrity, but they can also take on a more inflammatory phenotype and participate in autoimmune responses in the pancreas. Ultimately, there exists a significant potential for cross-talk between CVB infection, the microbiome, and gut-resident immune cells impacting T1D susceptibility. We have found CVB infection not only promotes onset of T1D in non-obese diabetic (NOD) mice but also causes dysbiosis which resembles that of a spontaneously diabetic NOD mouse. Introducing this new infection-induced microbial composition into naïve mice through the use of fecal microbiome transfers (FMTs) can accelerate T1D onset and alter immune profiles in the gut as well as the pancreas. Furthermore, MAIT populations are altered by this “diabetogenic” microbiome and also respond directly to CVB infection. Together our data highlights the role of virus infection and its ability to affect the gut microbiome and immune homeostasis to contribute to T1D development.
Bacterially-derived indole modulates murine arthritis through alteration of B cell glycosylation enzymes
Authors: Chriswell Meagan , Jubair Widian , Tolbert Briana , Kuhn Kristine 
Published: January 2023

Abstract
Indole, a bacteria-derived immunomodulatory metabolite that binds the aryl hydrocarbon receptor (AhR), is produced by bacterial tryptophanase in the intestinal tract of both mice and humans. Our studies using the murine collagen-induced arthritis (CIA) model of inflammatory arthritis demonstrated that intestinal bacteria influence disease severity through modulation of autoantibody glycosylation, and indole significantly correlated with the development of disease (P&lt;0.0001). Therefore, we hypothesized that indole modulates CIA through modulation of B cell glycosylation enzymes via AhR signaling. Mice with CIA that were protected by treatment with broad-spectrum antibiotics at the time of booster injection (CIA+Abx), lost the protective effect of antibiotics when dosed with indole (arthritis score 3.6±0.75 CIA+Abx+Indole vs. 1±0.00 CIA+Abx, p&lt;0.001). Mice with CIA, compared to CIA+Abx, demonstrated significantly increased expression of β1,4-galactosyltransferase 1 (GalT) and β-galactoside α2, 6-sialyltransferase 1 (St6gal1), two enzymes important in mediating pathogenic antibody glycosylation; this effect was reversed in CIA+Abx+Indole. We further demonstrate that Ramos cells, a human B cell line, upregulate glycosylation enzymes and AhR expression in response to indole exposure, with a fold change expression of 3.315±0.92 of B4GALT5 in indole-treated cells as compared to untreated (p=0.05). While the requirement of AhR and the glycosylation status of antibodies in our studies need to be confirmed, these results suggest that microbiome changes in CIA result in indole signaling on B cells, affecting glycosylation enzymes that modulate autoantibody effector function towards a proinflammatory profile.
Prevotella histicola treatment reduces arthritic pain and partially normalizes gut microbiota and metabolites
Authors: Balakrishnan Baskar , Luckey David , Bodkhe Rahul , Taneja Veena 
Published: January 2023

Abstract
We have previously shown that treatment with a novel human commensal, Prevotella histicola, isolated from a duodenal biopsy, can protect HLA-DQ8 mice from collagen induced arthritis (CIA), a model for RA, by modulating the systemic immune response. The present study analyzed the functional and mechanistic impact of P. histicola by comparing pain, motor function, gut microbiota and metabolites in treated and non-treated arthritic DQ8 mice. P. histicola treatment reduced the arthritis-associated pain by improving the motor function when compared to control mice. Analysis of synovium showed that P. histicola treatment increased T regulatory cells and reduced the levels of IL6 in the synovium of arthritic mice which were associated with reduced pain. Treated mice showed P. histicola colonization in the duodenum, a niche from where it was isolated. Further, P. histicola treatment showed varied effects based on circadian rhythm. A longitudinal follow-up of the gut microbial profile in different gut sections suggested that dysbiosis caused due to arthritis in DQ8 is partly normalized to naïve profile after treatment with P. histicola. Treated mice showed an expansion of genus Allobaculum, a butyrate-producing Firmicutes in the guts of DQ8 arthritic mice as compared to pre-treatment. The post-treatment restoration was also reflected in short-chain fatty acids and glucose assimilation rates in T cells. The present study proposes that P. histicola treatment of arthritis in DQ8 mice leads to gut homeostasis. Normalized microbial diversity and metabolites lead to immune regulation resulting in reduced inflammation with improved physical function. The observations suggest P. histicola as a strong candidate for monoclonal bio-therapeutics.