bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lactation stage impacts the glycolytic function of CD4+ T cells during ex vivo activation
Authors: Eder Jordan M. , Gorden Patrick J. , Lippolis John D. , Reinhardt Timothy A. , Sacco Randy E. 
Published: January 2023

Abstract
Dairy cattle undergo dynamic physiological changes during pregnancy and lactation. The impact of these physiological changes on the immune system can, at times, leave the animal more susceptible to infection with specific pathogens. While research has shed light on periods of increased susceptibility to infection, the impact of the stage of lactation on immune cell function remains to be completely elucidated. We have examined the impact of stage of lactation on CD4+T cells. We focused on how their metabolic function may be altered during this period. During activation T lymphocytes increase the uptake of glucose and metabolically reprogram to support aerobic glycolysis instead of oxidative phosphorylation, the pathway favored during their resting state. Our ex vivo studies compare the effects of activation on metabolic function of CD4+T cells from dairy cattle across multiple stages of lactation. Results show dampened glycolytic function in early lactation stages. Glycolytic and mitochondrial function were analyzed using the Seahorse Extracellular Flux Analyzer. Cattle in early and mid-lactation, defined as 21–70 days in milk (DIM) and 71–150 DIM, respectively, have a decreased rate of glycolysis and reduced maximum glycolytic capacity in contrast to cattle in late lactation (151–330 DIM) and those that have been dried off and are pre-parturient. Mitochondrial results were comparable between the groups, suggesting no compensation of energy via the mitochondria in early and mid-lactation cows. CD4+T cells from dairy cattle in early and mid-lactation have decreased metabolic function as measured by glycolytic and mitochondrial respiration in contrast to those in late lactation or in the dry period.
The Florida manatee (Trichechus manatus latirostris) T cell receptor loci exhibit V segment locus synteny and chain-specific evolution
Authors: Breaux Breanna Laine , Hunter Margaret E. , Cruz-Schneider Maria Paula , Sena Leonardo , Bonde Robert K. , Criscitiello Michael F. 
Published: January 2023

Abstract
Manatees are a vulnerable, charismatic sentinel species from the evolutionarily divergent order Afrotheria. We have previously described the immunoglobulin heavy chain locus of the Florida manatee (Trichechus manatus latirostris) and found limited antigen receptor diversity in this humoral arm of the adaptive immune system. We therefore investigated the antigen receptor loci of the cellular arm: the T cell receptor. Manatees are the first species from either Afrotheria or Xenarthra, the most basal eutherian taxonomic groups, to have an in-depth characterization of all T cell receptor loci and expressed repertoires. We manually annotated the three TR loci on the T. m. latirostris genomic scaffolds using BLAST and RSSsite, and compared the segments and overall genomic organization to the human TR loci. We identified the human V segment subgroups that are conserved in T. m. latirostris and found that TRADV are most conserved, TRBV are moderately conserved, and TRGV are the least conserved. The V segment order in the TRAD and TRB loci also showed synteny between the two species. The TRAD locus had five V segment subgroup synteny blocks that showed long-range duplications in the T. m. latirostris locus. The TRB locus had three V segment subgroup synteny blocks that showed short-range duplications. The conservation of V segment sequence and order correlated to the locus complexity, emphasizing the role of genomic organization on gene evolution. We also identified evidence for a VHδ pseudogene for the first time in a eutherian mammal. These novel findings underline the value of including species within the basal radiation of eutherian evolution in comparative studies.
GITR/GITRL interaction in the lung provides signal 4 for T cell expansion and TRM formation
Authors: Chu Kuan Lun , Wang Kuan Chung , Batista Nathalia V. , Clouthier Derek , Zhou Angela C. , Watts Tania H. 
Published: January 2023

Abstract
Influenza remains an important global threat and it is important to identify key mechanisms by which the immune system handles the virus. TNFR family members can play a crucial role in determining the magnitude of T cell response against viral infections. Previous studies using TCR transgenic models showed that GITR, an NF-κB activating TNFR family member, is required on CD8 T cells for maximal response against influenza virus. However, it remains unknown how GITR affects the endogenous T cell response during influenza infection. Using competitive mixed bone marrow chimeras, we found that GITR is intrinsically required for the accumulation of effector CD4 and CD8 T cells in the lung and secondary lymphoid organs during influenza infection as well as for optimal lung Trm formation. GITR affected PA224–233-specific CD8 T cells more dramatically than NP366–374-specific CD8 T cells, which exhibited a compensatory increase in TCR affinity in the absence of GITR. GITRL expression was higher on inflammatory APCs compared to classical DCs with peak expression day 3 to day 5 post-infection in the lung. We observed peak GITR expression on CD4 T cells day 7 post-infection in the lung but earlier for CD8 T cells. The finding that both the receptor and the ligand are expressed in the lung raises the possibility that GITR costimulation plays an important role in the lung. Consistently, within the same mouse, lung GITR+/+OT-II had a higher level of pS6 (downstream of GITR signaling) than GITR−/− OT-II, providing evidence of GITR costimulation (signal 4) in the lung. In sum, GITR on CD4 and CD8 T cells plays an important role in their accumulation in the lung, likely through interaction with GITRL on inflammatory rather than classical DCs.
Funded by CIHR:MOP133443
IRF4-dependent DCs regulate T cell effector and memory responses in influenza virus infection
Authors: Ainsua-Enrich Erola , Hatipoglu Ibrahim , Kadel Sapana , Turner Sean , Paul Jinny , Singh Simar , Bagavant Harini , Kovats Susan 
Published: January 2023

Abstract
Dendritic cells (DCs) activate adaptive immune responses during respiratory virus infection. A number of transcription factors govern the development and function of tissue DCs, including IRF4. To determine the role of IRF4-dependent lung DCs in influenza virus infection, we studied CD11c-cre-Irf4f/f (KO) mice. In this KO, one lung resident CD11b+ DC subset is missing, and the other DC subsets lack IRF4. Upon infection with A/PuertoRico/8/34 virus, KO lung DCs contained increased IL-12 and reduced IL-10 RNA. This altered IL-12/IL-10 balance in KO mice led to increased numbers of T-bet+ IFNg+ influenza antigen-specific effector CD8+ and CD4+ T cells, yet reduced numbers of Foxp3+ T regulatory cells (Tregs) and CD8+ antigen-specific memory precursor effector cells (MPECs) at later stages of infection. The remaining MPECs in KO mice showed decreased expression of Foxo1 and Bcl6, key transcription factors important for T cell memory differentiation. This suggests that factors including IL-10 produced by IRF4-dependent DCs elicit a memory-biased transcriptional program in late CD8+ T cell effectors. Accordingly, KO lungs contained reduced numbers of resident CD8+ memory T cells (TRM) forty days post-infection. Upon rechallenge with heterosubtypic virus, KO mice showed deficient expansion of virus-specific IFNγ+ CD8+ T cells. Taken together, these data show that KO mice mount a stronger antiviral T cell response upon primary infection but then elaborate a weaker CD8+ T cell memory response to heterologous virus. Our data support the hypothesis that IRF4-dependent DCs normally act to promote the differentiation of CD8+ memory T cells during influenza virus infection.
SIV-specific CD8 T cells are largely excluded from B cell follicles during early SIV infection
Authors: Li Shengbin , Connick Elizabeth , Skinner Pamela J. 
Published: January 2023

Abstract
While HIV− and SIV-specific CD8 T cell responses are critical for suppression of virus producing cells, these cells fail to fully suppress viral replication. During chronic infection, one potential mechanism for this failure is relatively low levels of virus-specific CD8 T cells in B cell follicles, where virus is most concentrated, permitting ongoing virus replication. It is not known whether this phenomenon also occurs during early infection. Here, we determined the location, abundance, and phenotype of SIV-specific CD8 T cells in lymph nodes from SIV-infected rhesus macaques at 21 days post-infection. We found that levels of SIV-specific CD8 T cells in B cell follicles were significantly lower than in extrafollicular regions. Within follicles, SIV-specific CD8 T cells were largely excluded from germinal centers. A median of 62% of follicular SIV-specific CD8 T cells expressed PD-1. In addition, a median of 12% of follicular SIV-specific CD8 T cells were in direct contact with Foxp3+ cells, and 4% were themselves Foxp3+. Ki67 was expressed by a median of 41% of follicular SIV-specific CD8 T cells and 25% expressed high levels of perforin. These data suggest that during early stages of infection, low levels of follicular SIV-specific CD8 T cells may permit ongoing viral replication, similar to what we previously reported in chronic disease. Furthermore, these data suggest that follicular SIV-specific CD8 T cells are possibly exhausted, that subsets may be inhibited by Foxp3+ Tregs, that subsets are activated and dividing, and subsets express the effector molecule perforin suggesting cytolytic potential. These findings provide important insights into SIV immunopathogenesis and may help inform future cure strategies.
Profiling TCR affinity distribution in human CD8+ T cell subsets responding to a cytomegalovirus epitope
Authors: Williams Chad Manjeot , Ma Keyue , He Chenfeng , Sun Eric , Zhang Shuqi , Jiang Ning 
Published: January 2023

Abstract
CD8 T cell subsets have long been distinguished using phenotypic markers like CCR7, CD45RA, and IL-7Rα. These markers have allowed for the isolation of CD8 T cell populations with distinct functional and proliferative capacities as well as those that maintain better proliferative responses in vivo without antigenic stimulation thus contributing more to immunological memory. Although phenotypic analysis has allowed for the discerning of functional, proliferative, and homeostatic proliferative potential, there is still little known about the role TCR affinity plays in recruitment of various affinity TCRs into memory and effector phenotypes that generate long term immunological memory in human infection. Using the newly developed iTAST technique, CMV specific CD8 T cells were isolated from the blood and spleen of human patients seropositive for CMV. CMV specific T cells were split into memory and effector subsets using phenotypic markers CCR7, CD45RA, and IL-7Rα before isolation and quantification of 2D TCR affinity and sequence. A roughly 100-fold difference of 2D affinity was present in CMV specific cells within the immunological memory response; however, with an enrichment for high affinity TCRs across all phenotypes assessed. This is consistent with previous studies demonstrating high avidity TCR selection in CD8 T cell responses to CMV infection, coupled with a greater clonality observed in CMV specific TCRs within healthy older individuals infected with CMV. Overall the iTAST technique allows for quick and easy isolation of antigen specific populations, quantification of TCR affinity, and TCR sequence thus giving unique insight into immunological memory responses in individuals infected with human persistent viruses.
Comparative analysis of DR1 binding with H1N1 Hemagglutinin derived peptides
Authors: Osan Jaspreet Kaur , Kuhn Thomas 
Published: January 2023

Abstract
Binding of antigenic peptides to class II MHC molecules (MHCII) and the activity of the “editing” molecule HLA-DM (DM) on the resulting peptide-MHCII complexes are factors critical to the antigen presentation pathway. Different algorithms are available to predict peptide-MHC binding and identify CD4+ T-cell epitopes within pathogenic proteins. Fewer algorithms are focused on MHCII as compared to MHCI., and their reliability is also less solid. Possibly one reason for such difference lies in the greater complexity of peptide binding to MHCII, of which open-ended binding site features a larger flexibility and allows interaction with longer sequences. To validate algorithm predictions, we have compared the experimental IC50 of a library of overlapping 18-mers offset by 5 amino acids spanning the sequence of H1N1 influenza virus HA protein while interacting with HLA-DR1 with the one indicated by different prediction platforms online. The IC50 values for each peptide in the presence and absence of DM were measured using competition binding assay. The ex-vivo CD4+ T cell response to these sequences has already been published, on which basis they have been categorized into immunodominant, subdominant, weak and negative. Comparative analysis shows that measured IC50 is different from predictive IC50, with measured IC50 with DM showing immunodominant peptide as a top hit. Our data also shows that presence of DM reduced the affinity of all the peptides triggering the smaller CD4+ T cell response or negative, whereas the effect on the other peptides was less consistent. Thus, currently available algorithms are still inadequate to predict epitope for MHCII and DM is one important factor that should be considered when designing algorithms for MHCII.
Butyrophilin (BTN) molecules control γδ T cells in tissue epithelia
Authors: Rhodes David A. , McCarthy Neil , Trowsdale John , Eberl Matthias 
Published: January 2023

AbstractGammadelta (γδ) T cells are a lineage of innate-like T lymphocytes with potent cytotoxic, pro-inflammatory and regulatory properties. They express, as a defining feature, a T cell receptor (TCR) composed of a γ and δ chain heterodimer, both products of V(D)J recombination, which distinguishes them from conventional αβ T cells.Although restricted to anatomical locations including skin and intestinal epithelium, major sites of interaction with the microbiota and of autoimmune pathology, the role of γδ T cells in immune surveillance is poorly understood. It is now clear that butyrophilins (BTNs) are pivotal in the maintenance of immune homeostasis in tissue epithelium, by controlling activation of γδ T cells. Despite homology to B7 costimulatory receptors like CD80/86 and PD-L1, ligands for BTN molecules have remained elusive. Some data show a direct interaction of BTNs with the γδ TCR, although this remains to be confirmed.We aim to understand the function of BTNs in the regulation of γδ T cells and how their dysregulation contributes to disease. The model system we study is the human BTN3A proteins and their role in the activation of Vγ9/Vδ2 T cells, a prominent γδ T cell lineage in human blood and tissues. Since it is clear that specific BTN molecules control defined γδ T cell subsets, this work is relevant to other systems of γδ T cell activation. I will highlight how these new data on the molecular control of a major T cell compartment is relevant to human autoimmunity and cancer.
Targeted mass spectrometry identifies computationally predicted, public, leukemia associated minor histocompatibility antigens
Authors: Vincent Benjamin , Kirkpatrick christine , Lansford Jefferson , Wilkerson Emily , Herring Laura , Chai Shengjie , Hunsucker Sally , Armistead Paul 
Published: January 2023

Abstract

Background
Allogeneic stem cell transplantation (aSCT) remains the most effective form of immunotherapy for the treatment of high risk acute myeloid leukemia (AML). The alloreactivity that induces the so-called “graft versus leukemia” (GvL) effect is mediated by minor histocompatibility antigens (mHA) presented by recipient class I or II HLA that induce a donor derived T cell response.

Methods
To identify candidate GvL mHA, we mapped RNA-Seq data from HLA-A*02:01 transfected U937 cells to the human reference genome to identify high frequency SNPs that are expressed in hematopoietic tissue, leukemia or testis and not in GvHD target organs such as skin, colon or liver. All 8 to 11-mer amino acids containing identified SNPs were computationally evaluated for binding affinity to HLA-A*02:01, and we validated predictions using genotyping data from 101 AML patients who underwent aSCT. Peptides from highly expressed genes and with predicted high affinity to HLA-A*02:01 were synthesized. Targeted mass spectrometry using parallel reaction monitoring (PRM) compared the MS/MS spectra of a peptide epitope pool to those of the synthesized peptides.

Results
Our computational analysis predicted 63 candidate mHA, of which the 48 most promising candidates were selected for targeted MS based upon gene expression and predicted HLA-binding affinity. Of the 48 best candidates, 4 HLA-A*02:01 restricted peptide epitopes were identified by mass spectrometry: 3 different epitopes derived from CD33 and 1 derived from CD300a.

Conclusion
Combined computational prediction and targeted mass spectrometry is an efficient method for the identification of candidate GvL antigens that can be further tested for immunogenicity.
Chaperone-assisted peptide exchange on MHC-I is driven by a negative allostery release cycle: Implications for a role of peptide-editing Molecular Chaperones in scrutinizing the peptide repertoire
Authors: Sgourakis Nikolaos , McShan Andrew C. , Natarajan Kannan , Kumirov Vlad K. , Flores-Solis David , Jiang Jiansheng , Badstuebner Mareike , Kovrigin Evgenii L. , Margulies David H. 
Published: January 2023

Abstract
Molecular chaperones TAPBPR (TAP-binding protein related) and tapasin associate with major histocompatibility complex class I (MHC-I) to promote the loading of antigenic peptides through a poorly understood mechanism. Here, we use solution Nuclear Magnetic Resonance (NMR) spectroscopy to probe TAPBPR-induced changes on MHC-I. Dynamic motions present in the empty MHC groove become progressively dampened with increasing peptide occupancy, while allosteric communication between the A- and F-pockets regulates a conformational switch located near the TAPBPR binding site, which is crucial for chaperone release from the complex. Our analysis of NMR data recorded for a range of TAPBPR complexes prepared with both murine H2 and human HLA alleles complements the recent X-ray structures to provide atomic-resolution mechanistic insights into the selection of optimal peptide sequences for the displayed antigen repertoire. In particular, our results show that negative allosteric coupling between the MHC groove and chaperone binding sites allows TAPBPR to proofread MHC molecules containing a range of different peptides. Since the affinity of incoming peptides for the empty groove is greatly reduced in the chaperone complex, (micromolar range, relative to nanomolar for the free MHC), these interactions can provide a mechanism for optimizing the peptide repertoire, where only the highest-affinity peptides can drive chaperone release. Finally, our results suggest that TAPBPR may promote the dissociation of tightly bound peptides from MHC molecules, thereby further scrutinizing the displayed repertoire. These findings imply a similar mechanism for the specificity and editing function of tapasin in the peptide-loading complex.
Self-reactive T cells restricted by non-classical MHC Ib are associated with metabolic disease
Authors: Park Chansu , Guan Jian , Ding Tom , Gonzalez Federico , Shastri Nilabh 
Published: January 2023

Abstract
The normal peptide repertoire presented by classical and non-classical MHC class I molecules is regulated by ERAAP, the ER aminopeptidase associated with antigen processing. Loss of ERAAP’s peptide trimming function in cells causes dramatic changes in the peptide repertoire. The changes in the peptide repertoire enhance the immunogenicity of ERAAP-deficient cells and elicit potent immune responses in otherwise syngeneic wild-type mice. Normal ERAAP function is monitored by an unusual subset of semi-invariant CD8+ T cells that recognize the QFL ligand. The QFL ligand consists of a peptide encoded by the highly conserved FAM49a/b genes that is presented by Qa-1b, a non-classical MHC Ib molecule only on surface of ERAAP-deficient cells. We show that these QFL-specific CD8+ T cells (QFL-T cells) bear unique and semi-invariant αβ TCRs. Genetic manipulation of the expression of the self-QFL ligand and functional characteristics of QFL-T cells shows that in addition to monitoring ERAAP function, QFL-T cells may also regulate metabolic activity.
MHC class I expression by microglia is required for generating a complete antigen-specific CD8 T cell response in the CNS
Authors: Malo Courtney Sarah , Jin Fang , Hansen Michael J. , Fryer John D. , Pavelko Kevin D. , Johnson Aaron J. 
Published: January 2023

Abstract
Microglia are central nervous system (CNS) resident immune cells for which the impact of MHC class I antigen presentation is still being defined. To directly address if microglia contribute to CD8 T cell-mediated immunity of the CNS, we generated a novel tamoxifen inducible CX3CR1-creER H-2Kb MHC class I conditional knockout mouse. In this transgenic mouse, the H-2Kb MHC class I molecule is deleted on all CX3CR1-expressing cells following tamoxifen treatment. By two weeks post tamoxifen treatment, peripheral CX3CR1-expressing cells repopulate, restoring normal expressing of H-2Kb. This leaves only microglia as the sole MHC class I-deficient cell type. We hypothesized that deletion of H-2Kb on microglia would reduce CD8 T cell responses in the CNS. We challenged these animals and cre-negative littermates with intracranial picornavirus infection with Theiler’s murine encephalomyelitis virus expressing ovalbumin (TMEV-OVA). We also challenged mice with experimental GL261 gliomas. We found that microglia-specific H-2Kb deletion reduces the CD8 T cell response in the CNS and attenuates the activation status of brain-infiltrating CD8 T cells in both models of neuroinflammation. We conclude that microglia are functional antigen presenting cells, and are required for a complete antigen-specific CD8 T cell response in the brain. These findings are the first to definitively address the role of microglia-expressed MHC class I in CNS immunological challenges.