bluuebunny/crossref_metadata_2025_split huggingface dataset:
T cell receptor repertoire in Kenyan HIV exposed but uninfected infants at birth: evidence of in utero clonal expansions
Authors: Gabriel Benjamin , Bosire Rose , Mbori-Ngacha Dorothy , Farquhar Carey , John-Stewart Grace , Overbaugh Julie , Richardson Barbra , Payne Barbara Lohman 
Published: January 2023

Abstract
With the expansion of global strategies to prevent mother to child transmission of HIV, the number of perinatal HIV infections had dropped dramatically. This public health achievement has created a population of HIV exposed but uninfected (HEU) infants with substantially more morbidity and mortality than their HIV unexposed (HU) peers. We hypothesize that in utero exposure to maternal HIV induces a premature activation and expansion of fetal T cells, potentially leading to infant immune dysregulation (Th1 polarization/immune exhaustion) upon exposure to pathogens after birth.
We selected pre-ARV era cord blood samples from 17 HEU infants born to viremic Kenyan women and 17 cord blood samples from HIV unexposed infants born to Kenyan women with similar sociodemographics. Next generation technology including addition of unique molecular identifiers was used to generate amplicon libraries for sequencing (MiSeq, Illumina). We calculated the Simpson Diversity Index for the 100 most frequent clones per TRB family. The median Ds for HU cord blood samples was 0.1, representing near maximal diversity of the TCR repertoire. Overall, HEU samples displayed a 30% reduction in diversity compared to the samples from HU infants, indicative of fetal T cell clonal expansion. Of note, the median diversity of Kenyan HEU samples located closer to the diversity of American adult peripheral blood than to the diversity of American cord blood.
Although the antigen specificity of these cells is unknown, these results support the hypothesis that HIV exposure in utero stimulates fetal immune responses and point towards the existence of specific features of the immune system of newborn HEU infants which might be linked to their poor morbidity and mortality rates.
The contribution of CD8 T cells targeting Cryptic Epitopes on viral evolution during acute HIV-1 infection.
Authors: Peng Binghao J , Carlson Jonathan M , Hunter Eric , Bansal Anju , Goepfert Paul A 
Published: January 2023

Abstract
Alternative reading frames (ARF) of HIV, in both sense and antisense directions, have been shown to produce polypeptides of unknown functions. These peptides, known as cryptic epitopes (CE), commonly induce CD8 T cell responses in HIV; however, their role in controlling HIV-1 infection remains unclear.
We hypothesized that CD8 T-cells target CE shortly following acute HIV infection and force viral escape. Such a finding would indicate that CE may serve as viable immunogens for inclusion in preventative HIV-1 vaccines. Using an HLA-I binding prediction algorithm applied to fixed mutations in ARF during the first two years of infection in a Zambian patient cohort, we predicted 66 CD8 T-cell escape mutations within gag, pol, and nef, which we further tested for immunogenicity.
8/32 chronic patient samples responded to at least one predicted CE as shown by IFNγ ELISpot. Furthermore, all ten immunogenic CE identified in the study were derived from a single antisense reading frame within the coding region of pol. Longitudinal studies failed to show any evidence of early viral escape to CE, as evaluation of these CE-specific CD8 T-cells following acute infection was not temporally associated with the occurrence of potential escape mutations. Our data suggest that although T-cell responses to CE can be detected during early HIV infections, they rarely establish HIV-1 escape mutations. As such their contribution to viral control is likely limited. Potential reasons for their limitations in forcing escape mutations include their infrequent expression and the weak magnitude of T-cell responses generated. Nevertheless, these data indicate that cryptic epitopes are not optimal targets for a preventative HIV vaccine.
Activation of intrahepatic mucosal associated invariant T cells resolves with antiviral therapy for hepatitis C
Authors: Bolte Fabian J , O’Keefe Ashley C. , Webb Lauren M , Serti Elisavet , Rivera Elenita , Liang Jake , Ghany Marc , Rehermann Barbara 
Published: January 2023

Abstract

BACKGROUND
Chronic hepatitis profoundly affects the phenotype of innate and adaptive immune cells. Mucosal associated invariant T (MAIT) cells are innate-like T cells that are enriched in the intestine and the liver. They can be activated by cytokines and by bacteria translocated from the gut. The relative roles of cytokines and bacteria in MAIT cell activation and function are unknown in chronic hepatitis.

METHODS
MAIT cells and monocytes were studied in liver and blood of 37 patients with chronic hepatitis C prior to and after Sofosbuvir/Velpatasvir-induced viral clearance.

RESULTS
MAIT cells were more frequent and showed a more activated and cytotoxic phenotype in the liver than in the blood. The frequency of intrahepatic MAIT cells correlated inversely with liver inflammation. The amelioration of liver inflammation by week 4 of antiviral therapy was associated with a significant decrease in MAIT cell activation and cytotoxicity. MAIT cell activation correlated with the frequency of intermediate/pro-inflammatory monocytes and the quality of MAIT cell effector responses was dependent on monocyte-derived IL-18. MAIT cell responses to T cell receptor-dependent (E. coli) and -independent (IL-12/IL-18) stimulation were not different before and after antiviral therapy and were not impaired compared to uninfected controls.

CONCLUSIONS
MAIT cells are activated by monocyte-derived cytokines in chronic HCV infection. They are reduced in number but maintain their response to cytokines and bacteria. MAIT cell activation rapidly declines during antiviral therapy and their frequency increases in the liver.
Neonatal mouse model to study Zika virus pathogenesis: Host immune response determines ZIKV tropism and outcome of disease.
Authors: Manangeeswaran Mohanraj , Ireland Derek D.C. , Sykes Jacob , McWilliams Ian , Verthelyi Daniela 
Published: January 2023

Abstract
Zika virus (ZIKV) is a mosquito-borne flavivirus that has spread to more than 70 countries and has infected more than 2 million people worldwide. The recent ZIKV outbreak has resulted in CNS complications including microcephaly, Guillain Barre and polyneuropathy. Current ZIKV infection models use interferon (IFN) deficient mice that develop high viral loads systemically and die within a week. Establishing an Immunocompetent animal model that replicates ZIKV neurotropism is critical to understand ZIKV pathology and testing of immunotherapies. We developed an immunocompetent neonatal mouse model in wild type C57BL/6 mice by challenging 1 day old mice with contemporary ZIKV isolate PRVABC59. Infected mice developed unsteady gait, loss of balance, kinetic tremors, severe ataxia and seizures beginning 13 days post infection (dpi) that resolved by 28 dpi. Following challenge the mice developed a systemic infection with high virus titers in spleen, liver and kidney that was cleared by 10 dpi. In the Central Nervous System (CNS) and the eye, the virus was detected starting 6 dpi, peaked at 9–15 dpi, and then decreased over 6 weeks. Unlike IFN deficient that have a significant increase in mRNA expression of complement (C3), Cox2, Il1a, Il1b, and Il6, the CNS of infected B6 mice showed increased expression of genes associated with T cell responses including CD3, CD4, CD8, MHC-II, CD80, IFNg, perforin and granzyme B., Despite the absence of clinical disease in convalescent B6wt mice, there remain increased expression of inflammatory and T cell associated genes that suggest that the virus could have long-term effects on the CNS. Further investigation including behavioral studies is needed to explore possible long term CNS sequelae of ZIKV infection.
T cell infiltration associated with neurodegeneration and Zika virus control in the CNS of immunocompetent, neonatal mice.
Authors: Ireland Derek D.C. , Manangeeswaran Mohanraj , Miller-Novak Leia , Sykes Jacob , Verthelyi Daniela 
Published: January 2023

Abstract
The recent spread of Zika virus (ZIKV) and its association with neurological disorders as well as congenital defects has created an urgent need to develop animal models that allow the elucidation of pathogenesis following ZIKV infection and to develop and test therapeutic agents that will prevent or eliminate CNS disease. We have developed a novel model of ZIKV infection in mice, using B6 WT, neonatal mice that are susceptible to contemporary ZIKV (PRVABC59) CNS infection following peripheral, subcutaneous inoculation at P1. Immunocompetent B6 WT mice develop a discrete neurological disease that includes: unsteady gait, kinetic tremors, severe ataxia and seizures by 12–15 dpi that gradually resolve. Gene expression and immunohistochemistry demonstrate inflammation in the CNS of ZIKV infected B6 WT mice starting after 9 dpi and infiltration of immune cells into the parenchyma of the CNS beginning concomitantly. At the peak of disease (15 dpi), immune cell infiltrates in the CNS consisted primarily of T cells, particularly CD8+ T cells. Gene expression analysis indicated an upregulation of genes consistent with this infiltration. Immunohistochemistry of the CNS indicates a concomitant increase in apoptosis and neurodegeneration after 9 dpi in the CNS particularly in the granular and Purkinje cell layers of the cerebellum. The role of T cells in the control of ZIKV infection in the CNS and the periphery will be explored.
Differential susceptibility to granzymes drives delayed apoptosis of HIV-infected macrophages and promotes CTL pro-inflammatory cytokine release
Authors: Clayton Kiera , Collins David , Dotiwala Farokh , Lieberman Judy , Walker Bruce D 
Published: January 2023

Abstract
Although CD4+ T cells represent the main target cell for HIV/SIV infection, macrophages also contribute to viral reservoirs. Given CD8+ cytotoxic T lymphocytes (CTL) are essential for controlling viral replication, characterizing how they interact with HIV-infected targets will provide insights into mechanisms of reservoir persistence and cure strategies. CTL killing of SIV-infected macrophages is less efficient than CD4+ T cells, but the mechanism of this differential killing and whether this applies to HIV is not known. Here, we demonstrate that in contrast to infected CD4+ T cells, HIV-infected macrophages are intrinsically resistant to ex vivo CTL-mediated killing, resulting in inefficient suppression of viral infection. However, when macrophages are killed, apoptosis is delayed and caspase-3-dependent versus CD4+ T cell apoptosis, which is rapid and caspase-independent. Induction of these separate apoptosis pathways is a result of differential sensitivity to granzymes, specifically granzyme B, which is poorly expressed by ex vivo HIV-specific CTLs. Differential killing is not a consequence of poor recognition. On the contrary, CTL interaction with antigen-loaded macrophages is associated with longer effector-target contact time and increased CTL production of IFN-γ. This excess IFN-γ induces production of macrophage pro-inflammatory chemokines, CXCL9 and CXCL10, which recruit activated CD4+ T cell targets. These results suggest that inefficient CTL killing of HIV-infected macrophages may contribute to reservoir persistence, chronic inflammation, and recruitment of CD4+ T cells to sites of infection.
Systematic analysis of T cell responses specific to the Epstein-Barr virus proteome using ATLAS™
Authors: Kaufmann Johanna K , Liu Biao , Jacques Judy , Wu Ning , Yan Zheng , Alami Aula , Kelley Christine , O’Keeffe Michael S , Hoover Maegan E , McManus Margaret M , Henderson Jennifer , Ghamsari Lila , Olivieri Kevin C , Flechtner Jessica B , Broom Wendy , Flano Emilio , Luzuriaga Katherine 
Published: January 2023

Abstract
Epstein-Barr virus (EBV) is a human herpesvirus infecting 95% of the world population. Primary infection can cause acute infectious mononucleosis (AIM), mainly when EBV is acquired later in life. In addition, EBV establishes latency and has been associated with several cancers. To date, efforts to develop vaccines for prevention of infection or disease by induction of gp350-specific neutralizing antibody responses have failed. To improve antigen selection for future vaccines, we utilized ATLAS™, a screening platform that can characterize the specificity of CD4+ and CD8+ T cell recall responses to the entire EBV proteome without bias of immunodominance.
Firstly, we measured antigen-specific T cell activation in 15 AIM patients longitudinally during and 6 weeks after the symptomatic disease phase. For both T cell subsets, the breadth of response significantly decreased with resolution of disease, likely in parallel to the contraction of the CD8+ T cell compartment associated with AIM clearance. Notably, we detected a substantial overlap in antigen specificity between T cell responses in samples collected during AIM and in convalescence.
Secondly, we identified EBV antigens that elicit T cell responses in both seropositive and seronegative but possibly exposed adolescents. Interim analysis revealed that ATLAS™ not only confirmed several previously described CD4+ and CD8+ T cell targets in latently infected individuals, but also identified novel T cell antigens independently of serostatus. Ongoing comparative analyses will focus on differences in the memory T cell repertoire between cohorts and on antigens overrepresented in exposed seronegative individuals that may be protective and therefore of value for vaccine development.
Cognate epitope is dispensable in maintenance of PD-1 expression on tissue-resident CD8+ cells
Authors: Shwetank  , Frost Elizabeth L. , Abdelsamed Hossam Aly , Mockus Taryn , Maru Saumya , Youngblood Ben A , Lukacher Aron 
Published: January 2023

Abstract
Persistent CNS infection by mouse polyomavirus (MuPyV) establishes a tissue-resident memory (TRM) CD8+ T cell population possessing higher TCR affinity than the memory cells in spleen. This necessitates a mechanism to regulate the functions of a non-replenished TRM population. Here, we report that virus-specific CD8+ T cells express PD-1 during acute infection and remain PD-1hion brain-infiltrating T cells. In contrast, antiviral memory CD8+ T cells in the spleen downregulate PD-1 expression during persistent infection, despite having similar viral load as the brain. The Pdcd1 promoter was found to be partially remethylated following its downregulation in the splenic population while the locus remained unmethylated in the brain-resident cells. Antiviral TRM cells purified from infected brain when transferred into a naïve mouse via intracerebral route, remained PD-1hi. Thus, epitope as well as inflammation are dispensable for maintenance of PD-1 expression. Absence of PD-1 signaling in an in vitro peptide stimulation assay resulted in augmented IFN-γ production and in vivo absence of PD-1 or PD-L1 resulted in increased IFN-γ-dependent microglial activation, indicating that PD-1 operates to limit CD8+ T cell-dependent neuroinflammation. PD-L1 was found to be expressed on infiltrating myeloid cells and astrocytes; astrocytes were also found to support productive MuPyV infection. PD-L1−/− mice had fewer anti-MuPyV brain-TRM cells, but increased proportion of the cells that were CD103hi, an αE integrin expressed by TRM cells. In summary, our data shows that PD-1 plays an important role in maintenance of antiviral CD8+ TRM cells in the brain and its expression is independent of the cognate epitope.
CD11c+ MHCIIint bone marrow-derived dendritic cells as adjuvants for neoepitope – based cancer immunotherapy
Authors: Ebrahimi-Nik Hakimeh , Corwin William L. , Yamamoto Ryo , Srivastava Pramod K 
Published: January 2023

Abstract
Total splenocytes, macrophage and bone-marrow-derived dendritic cells (BMDCs) were compared for adjuvanticity in a tumor rejection assay, where a neoepitope of the BALB/c Meth-fibrosarcoma, was the immunogen. BMDCs showed the highest activity, providing 100% tumor protection. BMDCs were sorted into various sub-populations, each of which was tested individually in parallel in the same assay. The CD11c+, MCHIIint, CD11bhi, CD86−, CD40−, CD24− BMDCs provided the highest tumor protection. The high adjuvanticity of BMDCs was not MHC I-dependent, as the neoepitope-pulsed BMDCs from C57BL/6 or BALB/c mice provided roughly equivalent protection. These data show that as adjuvants, BMDCs function as antigen reservoirs, facilitating cross-presentation by endogenous antigen presenting cells. These results have obvious implications for neoepitope-based human cancer immunotherapy.
Tumor Lysate Loaded Dendritic Cells Induce a T cell Specific Antitumor Response Against Gallbladder Cancer
Authors: Rojas-Sepúlveda Daniel Alberto , Gleisner Mª Alejandra , Pereda Cristian , López Mercedes , Salazar-Onfray Flavio 
Published: January 2023

Abstract

Introduction
Although infrequent, Gallbladder cancer (GBC) has high incidence rates in South America. In fact, Chile has the highest GBC incidence and mortality worldwide. Currently, surgery is the only effective treatment, and the five-year survival rate is less than 10%. Previously, we demonstrated that allogeneic melanoma cell lysates-loaded dendritic cells (DCs) provide a standardized, applicable tumor-specific vaccine; capable to induce a cell mediated immune response in melanoma patients, improving survival. Here, we investigated the effect of tumor lysates derived from gallbladder cancer cell (GCC) lines on immature DCs and their capacity to induce a T cell mediated anti GBC responses in vitro.

Material and Methods
DCs were stimulated with GCC lysates and analyzed by flow cytometry for a panel of surface markers. Autologous CD3+ T cells were co-cultured with these DCs for 14 days. CD4+ and CD8+ T cells were analyzed by flow cytometry for activation and chemokine receptor expression. CD8+ T cells were isolated and co-cultured with GCC lines GBd1, TGBC-2TKB and melanoma cell line Mel1 for 16hrs. IFN-γ secretion was measured by ELISPOT.

Results
All GCC lysates induced DCs maturation, increasing surface expression of MHC-I, MHC-II, CD80, CD83, CD86, CCR7. DCs maturated with GCC lysate induced CD3+ T cells activation, increasing expression of CD25, CD69, CXCR3, CXCR4 in both CD4+ and CD8+ T cells compared with non-stimulated lymphocytes. Additionally, CD8+ T cells co-cultured with GBC-loaded DCs, released higher amounts of IFN-γ than controls.

Discussion
Based on these results, DCs maturated with GCC lysates are capable to induce specific T cells activation against GBC and can be considered for future immunotherapy approaches.
Activation of the TLR2-MyD88 pathway is required for in-vivo efficacy of Lipid Nanoparticle based vaccine formulation
Authors: Swaminathan Gokul , Lin Shu-An , Patel ManishKumar , DiFelice Katie , Smith Jeffrey , Gindy Marian , Mahne Ashley , Cua Daniel , Casimiro Danilo , Espeseth Amy , Bett Andrew 
Published: January 2023

Abstract
Emerging evidence suggests that bioengineered nanoparticles can be used as immunomodulatory agents. Using murine and non-human primate vaccination models, we have identified novel cationic lipid nanoparticles (LNPs) that significantly enhance antigen-specific B-cell, CD4+T cell, and most notably, CD8+ T-cell responses. Importantly, we found that LNP-containing vaccine formulations resulted in protective efficacy in a virus challenge model, as well as, in syngeneic murine tumor models. In-vivo imaging and immunophenotyping studies showed that LNPs prolong antigen retention at the injection site and enhance antigen migration to the lymph nodes. Unbiased screening of LNPs ability to activate innate immune sensors showed that LNPs selectively activate Toll-Like Receptor-2 (TLR2). Using genetic ablation, and antibody mediated blockade, we uncovered that TLR2-MyD88 pathway is required for LNPs ability to boost immune responses in-vivo. Ex-vivo and in-vitro studies using dendritic cells (DC) showed that neutralization of TLR2 does not impact the LNP mediated increase in antigen uptake. However, LNP dependent enhancement of DC maturation, antigen processing & presentation, and chemokine production, were significantly reduced when TLR2 was neutralized. Pharmacological inhibition TIRAP, and CD14-MD2, further confirmed the need for the activation of TLR2-MyD88 pathway in LNP’s functionality. Future studies are aimed at utilizing chosen Merck chemical inhibitors of innate immune kinases to further interrogate the TLR2-MyD88 pathway’s involvement in LNP functionality. Such detailed knowledge of LNP’s mode of action will significantly influence the future design of LNPs for vaccines and immune oncology applications.
Targeting adenosine A2A receptors to improve vaccine efficacy
Authors: Cekic Caglar , Savas Ali Can , Kayhan Merve , Koyas Altay , Akdemir Imran 
Published: January 2023

Abstract
Activation of immune cells is associated with increased expression of adenosine receptors. Extracellular adenosine is present in primary and secondary lymphoid organs and limit the amplitude of immune responses suggesting that antagonists for adenosine receptors can be targeted to improve the efficacy of vaccines. Here we showed that vaccine adjuvant Monophosphoryl Lipid A (MPLA) strongly increased adenosine A2A and adenosine A2B receptor expression in primary macrophages and dendritic cells. Adenosine A2A but not adenosine A2B receptor blockade significantly increased both numbers and percentages of antigen specific endogenous T cells in both spleen and draining lymph nodes after primary immunizations with MPLA and ovalbumin. We observed a similar increase in both endogenous or adoptively transferred T cells in mice with myeloid-specific deletion of A2A receptors after primary immunization. Adenosine receptor blockade significantly increased the total IgG titers and IgG2c/IgG1 ratio after rechallenge with ovalbumin. These results suggest that adenosine A2A receptor blockade potentially improve vaccine efficacy by promoting both cellular and humoral immune responses and promoting Th1 type immunity. Our results also suggest that A2ARs on antigen presenting cells are important targets to improve vaccine efficacy by adenosine A2A receptor blockade. These findings have important implications for the design of novel and more efficacious vaccine formulations.