bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global evaluation of the role of ubiquitin in MHC Class I-restricted antigen processing. (106.35)
Authors: Goodenough Elliot , Eisenlohr Laurence 
Published: January 2023

Abstract
The multicatalytic proteasome plays an indispensable role in cellular proteolysis and in the production of most MHC class I-restricted antigenic peptides. Although ubiquitinylation was originally considered to be necessary for directing substrates to proteasomal destruction, growing evidence supports a role for ubiquitin-independent degradation as a substantial portion of intracellular proteolysis. To explore the importance of ubiquitin in MHC class I-restricted antigen processing, we have employed an inducible vaccinia virus system to overexpress wild-type and dominant-negative lysineless forms of ubiquitin (Ub) in mammalian cells. We have previously shown that abrogation of polyubiquitination in this manner inhibited epitope presentation from endoplasmic reticulum-targeted model antigens but had little impact on antigen presentation from cytosolic proteins. We are now seeking to elucidate the selective role of ubiquitin in MHC class I antigen processing by global evaluation of MHC class I-associated peptide display in the presence or absence of polyubiquitination, using mass spectrometric identification of peptides and comparative analysis of parent protein families.
Phenotypic and functional characterization of human blood BDCA3+ subsets (106.4)
Authors: Shih Tiffany , Dai Jihong , Fitzgerald-Bocarsly Patricia 
Published: January 2023

Abstract
There has been a recent focus on human blood DCs expressing BDCA3 (CD141). However, these cells are not fully characterized. Our study aimed to understand whether they constitute a homogeneous population or if they are related to two other DC subsets: plasmacytoid DCs (BDCA2+) and myeloid DCs (BDCA1+). We constructed multi-color panels for surface phenotyping of blood BDCA3+ DCs by flow cytometric analysis. We observed that lineage- PBMC heterogeneously distribute into BDCA3hi and BDCA3int subsets, with the latter subset expressing higher levels of CCR5 and CXCR4. Surface phenotyping of lineage- PBMC for the BDCA2 (found on pDC) and BDCA3 surface antigens yielded a subset of BDCA2+/BDCA3int cells, representing 15-30% of BDCA2+/lin- pDC. To assess functional significance of this population, we stimulated PBMC with TLR9 agonists CpGA or HSV-1 and stained for intracellular IFN-α and TNF-α in cells expressing BDCA2 and/or BDCA3. The BDCA2+/BDCA3int subpopulation produced IFN-α and TNF-α and upregulated the transcription factor IRF-7 more strongly than the BDCA2+/BDCA3- subpopulation, while the BDCA2-/BDCA3+ subpopulation constitutively expressed the lowest level of IRF-7 and barely produced IFN-α. However, similarly lower levels of TNF-α were found in the BDCA2-/BDCA3+ and BDCA2+/BDCA3- subpopulations when compared to the BDCA2+/BDCA3int subpopulation. These results suggest that the BDCA2+/BDCA3int subset has major functions associated with classical pDCs.
Describing the Peptide Binding Specificity of HLA-C (106.41)
Authors: Rasmussen Michael , Harndahl Mikkel , Nielsen Morten , Buus Søren , Stryhn Anette 
Published: January 2023

Abstract
Human leukocyte antigen (HLA) presents peptides to T-cells for immune scrutiny. Whereas HLA-A and -B have been described in great detail, HLA-C has received much less attention. Here, to increase the coverage of HLA-C and the accuracy of the corresponding tools, we have generated HLA-C molecules; peptide-binding assays, data and predictors; and tetramers; representing the most prevalent HLA-C molecules. We have combined positional scanning combinatorial peptide library (PSCPL) with a homogenous high-throughput dissociation assay and generated specificity matrices for 11 different HLA-C molecules. We find preference for hydrophobic residues at the peptide C-terminus for all HLA-C molecules. Most molecules were found to have an additional strong anchor at P2 or P3, with auxiliary anchor observed at P1, P2, P3, and P7. The binding affinity is measured for peptides fitting the specificity matrix for 5 HLA-C molecules and for all, but one, molecule we find a high frequency of binders, &gt;70%, among these peptides. To extend the examined peptide space, we use bioinformatic prediction tools to search for additional binders. Finally, we update our prediction tool, NetMHCpan, with the HLA-C affinity data and show that the predictive performance for HLA-C molecules now is increased to a level comparable withthat of HLA-A and -B. These novel HLA-C molecules and predictors are successfully used to generate HLA-C tetramers and validate HLA-C-restricted T cell responses.
MHC Class II immunoproteomic analysis of Chlamydia trachomatis and C. muridarum infected murine dendritic cells reveals overlapping immunodominant epitopes (106.7)
Authors: Karunakaran Karuna , Yu Hong , Jiang Xiaozhou , Moon Kyung-Mee , Shen Caixia , Foster Leonard , Brunham Robert 
Published: January 2023

Abstract
Protective immunity to Chlamydia is T cell-mediated, requiring MHC class II presented antigens. Immunodominant T cell antigens are potential human Chlamydia vaccine candidates. An immunoproteomic approach was undertaken in which Chlamydia-derived peptides presented by MHC class II molecules on the surface of infected murine dendritic cells (DCs) were identified by tandem mass spectrometry. DCs from both Balb/c and C57BL/6 mice were infected with C. muridarum and DCs from C57BL/6 were infected with C. trachomatis and C. muridarum. DCs from Balb/c infected with C. muridarum yielded 14 MHC class II binding peptides from 11 different C. muridarum proteins. Only one of the 11 proteins was shared in common with 16 C. muridarum proteins that generated MHC class II binding peptides using DCs from C57BL/6 mice. However, C57BL/6 DCs infected with C. trachomatis serovar D yielded 60 MHC class II binding peptides derived from 27 proteins, 10 of which were shared between the C. muridarum and C. trachomatis proteome. Among the 10 overlapping proteins six were tested for protective immunity and all conferred protection in mice against C. muridarum genital tract infection using DDA/MPL adjuvant. Three of the protective proteins belonged to the polymorphic membrane family of proteins, which generated MHC binding epitopes at distinct sequences within the proteins. We conclude that T cell immunodominance is determined by both MHC allelic selection and inherent properties of pathogen proteins.
Autophagy in dendritic cells modulates CD4+ T cell response during RSV infection (106.9)
Authors: Reed Michelle , Morris Susan , Lukacs Nicholas 
Published: January 2023

Abstract
Severe respiratory syncytial virus (RSV) infections cause significant morbidity among susceptible individuals, especially infants. During viral infection, dendritic cells (DC) prime appropriate adaptive immune responses through antigen presentation, cytokine production and costimulation of T cells. Previous studies suggest that macroautophagy, an intracellular process delivering cytoplasmic constituents to endosomes for degradation, functions in intracellular pathogen surveillance and antigen delivery for presentation by DC. RSV infection of bone marrow-derived dendritic cells (BMDC) stimulates autophagosome formation, while siRNA knockdown of LC3 prior to RSV infection reduces innate cytokine production. Pulmonary DCs from RSV-infected LC3b-deficient mice show dysregulated maturation through altered MHC class II and costimulatory molecule expression. BMDC cultured from LC3b-deficient mice skew primary and secondary T cell responses toward Th17, while decreasing expression of IFNγ and Th2 cytokines. These results suggest that virally-induced autophagy in DC modulates the host response to RSV infection through altered activation of CD4+ T cells.
MAP kinase phosphatase 5 regulates innate immune response to influenza via type I interferon (108.14)
Authors: Zhang Yongliang , Teh Hong Ying , Flavell Richard , Dong Chen 
Published: January 2023

Abstract
MAP kinase phosphatases (MKP), also known as dual specificity phosphatases, are major negative regulators of MAP kinases and play important roles in immunity. Previously, we have shown that MAP kinase phosphatase 5 (MKP5), one member of MKP protein family, plays critical roles in both innate and adaptive immune responses. However, the role of this protein in anti-viral immune responses has not been well studied. To investigate the role of MKP5 in innate immune response against influenza, wild-type (WT) and MKP5 knockout (KO) mice were infected with A/Putero Rico/8/34 (PR8, H1N1) viruses. We found that viral titers in the lung of MKP5 KO mice are significantly lower on day 3 and day 5 post-infection than those in the lung of WT mice, which is associated with increased expression of IFN-beta in the lung and IFN-beta concentrations in the BAL from KO mice compared with those from WT mice. Overexpression of MKP5 in macrophages inhibits IFN-beta promoter activity as well as its expression. Macrophages from MKP5 KO mice produced significantly higher amount of IFN-alpha and IFN-beta in response to PR8 virus infection than cells from WT mice. The regulation of type I interferon by MKP5 was further investigated. Our study demonstrated that MKP5-regulated signaling plays an important role in regulating type I interferon and innate immune responses against virus infection.
CCR5-deficiency abrogates microglial activation and neuronal injury in HIV gp120-transgenic mice. (108.5)
Authors: Kaul Marcus , Maung Ricky , Sejbuk Natalia , Medders Kathryn , Desai Maya , Russo Rossella , Williams Roy 
Published: January 2023

Abstract
AIDS patients and mice expressing the envelope glycoprotein gp120 of human immunodeficiency virus-1 (HIV-1) as transgene in the brain (gp120tg) share key features of viral neuropathology, such as a decrease of neurites and synapses, pronounced astrocytosis, and activated microglia and macrophages. Virus-associated or soluble HIV-1 gp120 interacts with CD4 and co-receptors CCR5 and CXCR4 leading to infection and/or cellular signaling. In the present study we crossed HIVgp120tg with CCR5KO mice. Microarray analysis of brain tissue from 6 month-old mice showed that HIV-1 gp120 affected the expression of about 800 genes in the presence of CCR5 but of only 51 genes in the absence of the co-receptor. Differentially expressed genes in CCR5 wild type (wt)/gp120tg mice compared to non-transgenic controls primarily belong in the nervous and immune systems. CCR5KO/gp120tg mice and non-transgenic CCR5KO controls differed mostly in expression of an astrocytic protein and factors of the innate immune system. Using quantitative fluorescence and deconvolution microscopy, we assessed neuronal injury and glial cell activation in brain sections. CCR5wt/gp120tg mice displayed a significant reduction in neuronal dendrites and pre-synaptic terminals besides microglial activation (increased Iba1 immuno-reactivity) in comparison to all of the three other genotypes. Thus, in our model CCR5 is required for HIV-1 gp120 to activate microglia and to cause damage to neuronal processes and synapses.
Aging-associated alterations in IL-7 receptor signaling and inflammation promote declining B-lymphopoiesis and increased leukemogenesis (109.9)
Authors: Henry Curtis , Marusyk Andriy , Zaberezhnyy Vadym , Casas Matias , Adane Biniam , Merz Andrea , Serkova Natalie , DeGregori James 
Published: January 2023

Abstract
The accumulation of oncogenic mutations over time is thought drive increased cancer incidence with age. Alternatively, we hypothesize that aging reduces cellular fitness in stem and progenitor pools, leading to increased selection for oncogenic mutations and increased cancers. We have explored how aging affects the fitness of B-progenitor cells and leukemogenesis. The fitness of B-progenitors declines with age, as defined by competitive transplantation assays. Analyses of aged B-progenitors revealed increased expression of inflammatory genes, and decreased expression of genes involved in B-lineage determination, B-cell signaling, nucleotide synthesis, and other metabolic pathways. These changes correlated with decreased interleukin-7 receptor (IL-7R) mediated signaling, reduced production of ATP and other nucleotides, and perturbations in the TCA cycle in aged B-progenitors. Decreasing IL-7R signaling and inducing inflammation in young mice impaired B-lymphopoiesis, accompanied by aging-like gene expression profiles. Importantly, neutralization of IL-7 significantly increased selection for the Bcr-Abl oncogene in B-progenitor pools, coinciding with restored signaling. Similarly, Bcr-Abl is adaptive within B-progenitor pools from aged but not young mice. These studies reveal roles for IL-7R signaling and inflammation in declining B-lymphopoiesis in old age, and demonstrate how the selection for Bcr-Abl in aged lymphopoietic backgrounds can drive leukemogenesis.
MiR-155 modulates effector and memory CD8 T cell differentiation in response to murine γ herpes virus. (110.13)
Authors: Tsai Ching-Yi , Zhang Weijun , Allie S. , Usherwood Edward 
Published: January 2023

Abstract
MicroRNAs (miRNAs) have emerged as a major regulatory network with profound effects on many physiological processes. They are particularly important for determining cell fate decisions. Several processes mediate CD8 T cell differentiation. While many studies have revealed the importance of transcriptional and epigenetic regulation, it is likely that miRNAs also contribute to this programming. miRNAs are critical in determining B and CD4 T cell lineage, yet little is known about their effect on CD8 T cell differentiation. Studies with in vitro skewed central memory CD8 T cells show a down regulation of miR-155 relative to skewed effector memory cells. Using murine gammaherpesvirus 68 as a model, we examined the influence of miR-155 on CD8 differentiation in vivo. Our results showed lowered CD8 responses in the absence of miR-155 accompanied by a phenotypic skewing towards a memory precursor phenotype at the acute phase, which resulted in more central memory cells. The resulting memory cells in the absence of miR-155 were as functionally competent as their wild type counterparts, as revealed by their ability to recall to the same antigen. Our data indicate the importance of mIR-155 in effector differentiation, which may be a critical piece of the puzzle in CD8 differentiation giving useful information for vaccine research.
Itk and antigen specific CD8+ T cell memory differentiation (110.8)
Authors: Huang Fei , Huang Weishan , Bai Yuting , Chew Tina , Briggs Jessica , August Avery 
Published: January 2023

Abstract
It has been shown that Itk, a Tec kinase family member, is important for T cell development and differentiation. CD4+ and CD8+ T cells in Itk-/- mice display innate memory phenotype. Since Itk-/- CD8+ T cells preferentially develop into innate memory T cells in thymus, we aimed to determine whether naïve Itk-/- CD8+ T cells also preferentially differentiate into memory T cells after primary response to foreign antigens. To study the intrinsic and extrinsic effects of Itk in naïve CD8+ T cell differentiation into memory T cells, we used an OVA-Listeria monocytogenes infection model in which naïve OTI Rag1-/- T cells or OTI Itk-/- Rag1-/- T cells were adoptively transferred into Itk-/- or WT recipient mice. We found that naïve OTI ITK-/- Rag1-/- T cells have comparable ability to WT OTI Rag-/- T cells in memory T cell differentiation after a 5-week infection in WT hosts. In contrast, WT OTI Rag1-/- T cells are deficient in differentiating into memory T cells when placed in Itk-/- hosts. Although Itk affects the CD8+ T cell development in the thymus, its absence does not affect antigen specific CD8+ memory T cell differentiation. However, Itk-/- mice have an impaired environment for naïve CD8+ T cells differentiation into memory T cells during L. monocytogenes infection. These results suggest that Itk expression in cells other than CD8+ T cells is critical for supporting the antigen specific CD8+ T cell memory differentiation.
Immune ontogeny of CD4 T cells (111.28)
Authors: dela Pena Myra Grace , Rao Kalyan , Abel Kristina 
Published: January 2023

Abstract
The knowledge of immune ontogeny is limited. Our goal is to define molecular mechanisms that underlie the T helper 2-biased response of infant CD4 T cells. Age-dependent differences in cytokine signaling were determined by (i) measuring the cytokine profile of CD4 T cells after PMA/ionomycin stimulation, (ii) quantitation of cytokine receptors on CD4 T cells, and (iii) Phosflow analysis of cytokine-specific transcription factors using human cord (n=5) and adult (n=5) blood samples and longitudinal samples of infant rhesus macaques from birth to 1 year of age (n=20). Antigen-experienced T cells increased throughout the first year. Despite apparent phenotypic maturation, infant compared to adult CD4 T cells continued to show reduced cytokine responsiveness. In particular, IL-2 and TNF-α producing CD4 T cells were detectable as early as 1 week, but IFN-γ producing CD4 T cells remained rare. Lower IFN-γ production was associated with fewer IFN-γ receptors on infant compared to adult CD4 T cells. Furthermore, only 1.00%±1.66% of infant, but 15.00%±10.09% of adult CD4 T cells responded with STAT1 phosphorylation to IFN-γ stimulation (P&lt;0.003). Similar results were obtained for STAT5 after IL-2 stimulation (P&lt; 0.0001). In contrast, there was no difference in the activation of STAT6 in response to IL-4, consistent with similar levels of IL-4Rα on infant and adult CD4 T cells. Thus, distinct molecular mechanisms in cytokine signaling contribute to the Th2-biased response in infants.
Notch ligands control the human αβ/γδ lineage choice through receptor-specific induction of differential Notch signal strength. (111.29)
Authors: Taghon Tom , Van de Walle Inge , Waegemans Els , De Medts Jelle , De Smet Greet , De Smedt Magda , Vandekerckhove Bart , Kerre Tessa , Leclercq Georges , Wang Tao , Plum Jean 
Published: January 2023

Abstract
Differential Notch signal strength influences the αβ versus γδ T-cell lineage decision in both mouse and human. Here, we show that the Notch ligands Delta-like-4, Jagged1 and Jagged2, differentially impact this lineage decision in human. Whereas Delta-like-4 supports both αβ and γδ T-cell development, Jagged1 induces αβ-lineage differentiation and Jagged2 primarily γδ T-cell development. Jagged2 induces the strongest Notch signal in human thymocytes as a result of interactions with both Notch1 and Notch3, whereas Delta-like-4 only binds Notch1. In agreement, Notch3 is a stronger activator of Notch target genes and only supports γδ-lineage development, whereas Notch1 is a weaker activator supporting both αβ and γδ T cell development. Blockage of Notch3 activation in Jagged2 cocultures rescues αβ-lineage differentiation, showing the importance of this interaction for driving γδ-lineage differentiation. Further analysis revealed that Jagged2-mediated Notch3 activation blocks αβ-lineage differentiation as a result of inhibition of TCR-β chain expression. Consistently, TCR-αβ T cell development is restored in Jagged2 cocultures by providing immature human T cell progenitors with a TCR-β chain. Our results show that Notch ligands control the human αβ/γδ lineage choice through receptor-specific induction of differential Notch signal strength and that Jagged2-mediated Notch3 activation drives human γδ-lineage differentiation as a result of inhibition of αβ-lineage differentiation.
Homing of hematopoietic progenitors to the thymus is profoundly reduced after irradiation (111.32)
Authors: Zhang Shirley , Manna Sugata , Zlotoff Daniel , Bhandoola Avinash 
Published: January 2023

Abstract
After bone marrow transplantation (BMT), T cells are among the last of the hematopoietic lineages to recover, but the reasons for this delay are poorly understood. Previous work on T lineage reconstitution after BMT assumed progenitor supply to the thymus was not limiting; therefore research focused on intrathymic defects as potentially underlying delayed T cell recovery. We have recently discovered that delivery of progenitors to the thymus is limiting for T cell reconstitution after BMT. We have developed an assay that directly measures settling of intravenously injected progenitors within the thymus. Using this short-term settling assay, we have found that irradiated mice exhibit dramatically reduced thymic settling by intravenously injected progenitors. Directed irradiation of the thymus alone also showed reduced thymic settling. We suggest that one defect in T cell reconstitution after BMT is due to defective progenitor homing to the thymus, as survival of progenitors in the post-irradiation environment appears intact.
Methyl-CpG binding by the Mi-2/NuRD complex is required for transcriptional repression in B cells. (111.33)
Authors: Dege Carissa , Ramirez Julita , Hagman James 
Published: January 2023

Abstract
We demonstrated previously that the mb-1 (Igα; Cd79a) promoter is demethylated progressively during its activation in early B cell development. Demethylation of promoter CpGs is initiated by binding of the transcription factor, Early B Cell Factor 1 (EBF1). EBF1 activates the accessibility and demethylation of mb-1 promoter DNA, which allows for binding by Pax5 prior to transcription. This process is inhibited by Mi-2/NuRD chromatin remodeling complexes. This was evidenced by knockdown of the ATPase subunit of Mi-2/NuRD, Mi-2β (CHD4), which potentiated effects of EBF1 and Pax5. Recent work in the laboratory has focused on other components of the Mi-2/NuRD complex to assess its association with methylated DNA. The Mi-2/NuRD complex contains the Methyl Binding Domain proteins 2 or 3 (MBD2 or MBD3). MBD2 has the ability to bind methylated cytosines, while MBD3 binds hydroxymethylated cytosines. Similar to depletion of Mi-2β, knockdown of MBD2 using shRNA potentiated mb-1 transcriptional activation in the presence of EBF1 and Pax5. This increased activation was similar to that obtained using 5-azacytidine, which reduces cytosine methylation by inhibiting DNA methyltransferases. In contrast, depletion of MBD3 had no effect on EBF1/Pax5-dependent promoter transcription. Our data suggest that methyl-cytosine binding by Mi-2/NuRD complexes containing MBD2 is important for transcriptional attenuation of the mb-1 gene in B cells.
Defective Flt3L driven DC development in the absence of Ikaros (111.35)
Authors: Brugmann William , Winandy Susan 
Published: January 2023

Abstract
Ikaros null (Ik-) mice have impaired dendritic cell (DC) development. This defect is recapitulated when Ik- bone marrow (BM) is cultured with Flt3L, a DC growth factor. Ik- BM cultures generate significantly fewer DCs than their wild type (WT) counterparts. This phenotype is specific to Flt3L-driven DC developments as Ik- GM-CSF cultures generate normal numbers of DCs. Time course gene expression analyses of Flt3L-cultures show that genes important for DC development such as Irf4, Irf8 and Spib are variably under-expressed in both Ik- progenitors and mature DCs, with Spib being the most affected. These data demonstrate that low expression of DC genes is not solely due to decreased DC differentiation and suggest that Ikaros may regulate their expression, which we are now exploring. The DCs that develop in Ik- Flt3L cultures are also qualitatively different from their WT counterparts. They have an activated phenotype, implicating Ikaros in regulation of DC function as well. Enforced expression of full-length Ikaros (Ik1) in Ik- BM cannot restore Flt3L-driven DC development, suggesting a different Ikaros isoform may be needed for DC rescue. Studies now underway will define Ikaros isoform expression during DC development and determine if enforced expression of discrete Ikaros isoforms or the Flt3 receptor itself can restore Flt3L-driven DC development in Ik- BM. These studies will place Ikaros relative to Flt3 signals during DC development and define its molecular role.