bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tissue-resident memory T cells mediate melanoma surveillance and are targets of immunotherapy
Authors: Park Simone L , Buzzai Anthony , Hor Jyh Liang , Effern Maike , Christo Susan N , Mueller Scott N , Holzel Michael , Waithman Jason , Mackay Laura K , Gebhardt Thomas 
Published: January 2023

Abstract
Non-recirculating tissue-resident memory T (TRM) cells reside permanently in epithelial tissues where they are known to protect against infection. TRM cells have now been identified in various human cancers where they correlate with improved patient outcomes, but the mechanisms through which they may mediate protective tumour immunity remain unclear. Using a novel mouse model of transplantable cutaneous melanoma, we show that tumour-specific TRM cells form spontaneously in the epithelial tumour microenvironment where they protect against cancer development independently of circulating memory T cells. A proportion of epicutaneously inoculated mice remained free of macroscopic tumours long after inoculation, and intravital imaging revealed that these mice harboured dormant melanoma cells in their skin that were dynamically surveyed by tumour-specific TRM cells. Depletion of TRM cells from these mice triggered melanoma escape, indicating that TRM cells suppress tumour progression by promoting cancer-immune equilibrium. Further, we found that pre-activated T cells transferred to tumour-bearing mice in a model of adoptive cell therapy gave rise to TRM cells that inhibited the growth of established melanoma. These tumour-specific TRM cells retained their capacity to execute effector functions and protect against tumour growth despite expression of various inhibitory molecules typically associated with T cell dysfunction. Combined, our findings reveal TRM cells to be durable mediators of anti-tumour immunity and suggest that targeting TRM cell responses could serve as a novel immunotherapeutic strategy to drive elimination of solid tumours.
Novel approaches for studying cell-mediated immune responses to influenza vaccination in humans
Authors: Cao Weiping , Mishina Margarita , Ende Zachary , Mboko Wadzanai P , Batra Dhwani , Bohannon Caitlin , Carney Paul , Chang Jessie , Ranjan Priya , Kumar Amrita , Amoah Samuel , Gangappa Shivaprakash , Mittal Suresh , Sheth Mili , Pohl Jan , Stevens James , Sambhara Suryaprakash 
Published: January 2023

Abstract
Vaccination is the most cost-effective public health intervention strategy in the prevention of the spread of infectious diseases. Unfortunately, each year, a substantial proportion of individuals do not respond or respond poorly to vaccination due to age, nutrition, pre-existing medical conditions, vaccine mismatch, or other unknown reasons. To investigate this further, we propose studying the mechanisms and molecular signatures associated with immunogenicity and the efficacy of influenza vaccination in different populations.
The priming environment, induced by the innate immune system is crucial for initiating and fine-tuning antigen-specific adaptive immune responses. Comprehensive antibody panels have been developed to identify the new paradigms in the innate priming environment, focusing on NK, innate lymphoid cells and γδ T cells by flow cytometry in PBMC from vaccine recipients. The specific functions of these cells are then analyzed using single cell sorting and high-throughput transcriptomic and proteomics analysis. To further probe the adaptive response, we have successfully developed receptor binding site mutant HA (H1, H3, B) and HA stem (group 1 and 2) probes that are conjugated to fluorochromes to enumerate and characterize HA-specific B cells. M2e antigen probes are under development. Combining cell sorting, single cell molecular analyses, and the Illumina MiSeq system, paired heavy and light chains of B cell receptors (BCR) from isolated antigen specific B cells are sequenced to dissect antibody diversity.
Through these novel approaches, we aim to identify and characterize critical host factors that can be exploited to develop as novel adjuvants and strategies for more effective influenza vaccines.
Neuraminidase expressed on virus-like particles is superior to inactivated split virus vaccine in conferring cross protection via humoral and cellular immunity
Authors: Kim Ki-Hye , Lee Young-Tae , Park Soojin , Jung Yu-Jin , Kim Yu-Jin , Lee Youri , Kang Sang-Moo 
Published: January 2023

Abstract
Neuraminidase (NA) is the second major surface antigen on influenza virus but often ignored as a vaccine component. In this study, we developed N1 virus-like particles (N1 VLP) containing NA derived from 2009 pandemic H1N1 influenza virus (2009H1N1), and compared with inactivated split virus vaccine in the immune mechanisms of cross protection. Intramuscular immunization of mice with N1 VLP induced IgG antibody responses to 2009H1N1 virus and NA inhibition activity. Mice immunized with N1 VLP induced superior cross protection against lethal infection compared to a current vaccine platform, split virus vaccine (1934H1N1), as determined by body weight changes, lung viral titers, infiltrating innate immune cells, cytokines, and histopathology. Furthermore, N1 VLP immunized mice induced higher levels of IFN-γ effector CD4 T cells, plasma cells, and germinal center B cell (GL7+B220+IgD−CD19+) and plasma cells (CD138+B220+/− IgD-CD19+) than split virus vaccine mice. Also, N1 VLP immune sera provided heterosubtypic cross-protection against H3N2 virus in naïve mice. Therefore, these results suggest that N1 NA-presenting VLP can be developed as an effective cross-protective vaccine candidate standalone or in combination of current influenza vaccination in a supplemented vaccine platform.
Mucosal delivery of nanofiber booster vaccine enhances generation of antigen-specific memory T cells in the lung parenchyma
Authors: Files Megan A , Bharaj Preeti , Saito Tais B , Rudra Jai , Endsley Janice J 
Published: January 2023

Abstract
Tuberculosis (TB) infection caused by Mycobacterium tuberculosis (Mtb) is a serious threat to global health with 10 million new infections each year and 1–2 million deaths. The only licensed vaccine approved for human use, Mycobacterium bovis Bacille Calmette-Guerin (BCG), has been administered to 4 billion people despite variable efficacy. Heterologous vaccine regimens that boost T cell memory generated through BCG priming, however, may be an effective immunization strategy. Our lab previously demonstrated efficacy of a nanofiber (NF) vaccine platform containing co-assembled CD8+ and CD4+ epitopes as evidenced by the generation of polyfunctional CD8+ T cells and protection from aerosol challenge with Mtb. In recent investigations, we observed that boosting BCG-primed mice through a pulmonary route with the NF-based vaccine bearing Ag85B CD4+T cells epitopes generated increased frequency of Mtb antigen-specific T cells in the lung parenchyma as indicated by number of tetramer (I-Ab:Ag85B) positive CD4+T cells. The frequency of Mtb-specific CD4+T cells was further increased by adoptive transfer of dendritic cells pulsed with Ag85B-bearing NF. The Ag85B-specific T cells were further characterized as tissue resident memory (Trm) and effector memory (Tem) T cells based on the surface marker phenotypes (I-Ab:Ag85B+ CD69+/− CCR7− CD44+ CD62Llo). In memory recall experiments, splenocytes from vaccinated mice also expressed polyfunctional cytokines that have been associated with protective immunity. These results suggest that protective immunity following vaccination with a NF subunit vaccine in a prime/boost strategy with BCG is associated with expansion of Trm CD4+T cells in lung parenchyma that recognize the Ag85B epitope.
Natural gene-encoded affinity for cognate antigen facilitates vaccine-amplification of broadly neutralizing antibodies against influenza virus
Authors: Lingwood Daniel 
Published: January 2023

Abstract
B cell receptors display V gene-encoded CDRs and hypervariable CDR3, where the former may harbor innate-like antigen recognition characteristics. To test this in vivo, we deployed transgenic mice containing full human CDRH3 diversity but were constrained to single human VH genes: IGHV1-69*01, a human VH reproducibly used to generate broadly neutralizing antibodies (bnAbs) targeting hemagglutinin stalk of Group 1 influenza A viruses or irrelevant IGHV1-2*02. With this system, we could experimentally evaluate the contribution of V gene encoded CDRs to forming the antibody paratope following immune challenge. Exposure to virus or hemagglutinin vaccine-nanoparticles elicited primary antibody responses targeting the bnAb epitope, but only in IGHV1-69 animals. Repeated exposure amplified off-target responses, however, prime/boost with stalk-only nanoparticle (SS-np) refocused serum antibodies to the target-epitope, expanding the human IGHV1-69 bnAb lineage to elicit prototypic IGHV1-69 Group 1 bnAbs. The bnAb pathway was expanded from a genetically endowed but low frequency population of on target germline B cell precursors (&lt;0.3% of the repertoire). IGHV1-69 therefore endows natural cognate anti-influenza targeting affinity which can be exploited through rational vaccine design to redirect antibodies against an otherwise immunologically silent ‘universal’ flu vaccine target. Remarkably, similar on-target germline B cell levels were seen in human PBMC, suggesting SS-np may elicit bnAbs in humans.
Generation of tissue-restricted CD4 effectors (TFH and ThCTL) requires signals from local antigen & infection during the effector phase
Authors: Devarajan Priyadharshini , Vong Allen M , Castonguay Catherine H , Bautista Bianca L , Swain Susan L 
Published: January 2023

Abstract
Key specialized tissue-restricted CD4 effector subsets such as T helper cytotoxic cells (ThCTL) in the infected tissue and T follicular helper cells (TFH) in secondary lymphoid organs arise after other CD4 effectors (Th1, Th17) peak. In an influenza A virus (IAV) infection model, we find that generation of ThCTL and TFH require that CD4 effectors recognize specific Ag/MHC Class II, 5–7 days after initial infection. We restrict Ag presentation to specific APC subsets and add various APC via different routes, to study which APC and infection conditions drive TFH vs. ThCTL generation at the checkpoint. We find most MHC Class II-expressing APC subsets, including dendritic cells and B cells, are able to drive TFH and ThCTL generation. However, local Ag presentation is crucial. Strikingly, we find that continuing infection, even at this late effector phase, is needed for optimal generation of both subsets. This contrasts with CD4 memory generation, which in our previous studies, was not dependent on infection at this checkpoint. Thus, at the effector checkpoint, Ag presentation in the local tissue drives both optimal specialized effector and most memory generation, whilst signals from infection are required for optimum tissue-restricted effector differentiation. The infection signal can be provided by multiple PRR pathways. We suggest that vaccines will need to be designed to provide additional Ag presentation and the signals associated with infection at the effector checkpoint to induce optimum protective immune responses: to promote strong CD4 memory for broad, heterosubtypic protection and indirectly strong B cell response and memory leading to long-term humoral protection.
CD4+ T cells Promote Humoral Immunity and Viral Control during Zika Virus Infection
Authors: Ngono Annie Elong , Young Matthew P , Bunz Maximilian , Xu Zhigang , Hattakam Sararat , Vizcarra Edward , Regla-Nava Jose Angel , Tang William W , Yamabhai Montarop , Wen Jinsheng , Shresta Sujan 
Published: January 2023

Abstract
Several Zika virus (ZIKV) vaccines designed to elicit protective antibody (Ab) responses are currently under rapid development, but the underlying mechanisms that control the magnitude and quality of the Ab response remain unclear. Here, we investigated the CD4+ T cell response to primary intravenous and intravaginal infection with ZIKV. Using the LysMCre+Ifnar1fl/fl (myeloid type I IFN receptor-deficient) C57BL/6 mouse models, we identified six I-Ab-restricted ZIKV epitopes that stimulated CD4+ T cells with a predominantly cytotoxic Th1 phenotype in mice primed with ZIKV. Intravenous and intravaginal infection with ZIKV effectively induced follicular helper and regulatory CD4+ T cells. Treatment of mice with a CD4+ T cell-depleting Ab reduced the plasma cell, germinal center B cell, and IgG responses to ZIKV without affecting the CD8+ T cell response. CD4+ T cells were required to protect mice from a lethal dose of ZIKV after infection intravaginally, but not intravenously. However, adoptive transfer and peptide immunization experiments showed a role for memory CD4+ T cells in ZIKV clearance in mice challenged intravenously. These results demonstrate that CD4+ T cells are required mainly for the generation of a ZIKV-specific humoral response but not for an efficient CD8+ T cell response. Thus, CD4+ T cells could be important mediators of protection against ZIKV, depending on the infection or vaccination context.
Evaluation of HIV-Specific T-Cell Responses in HIV-Infected Aging Patients with Controlled Viremia on Long-term Antiretroviral Therapy
Authors: Bradley Nicole Elizabeth , Wertheimer Anne , Klotz Stephen A , Ahmad Nafees 
Published: January 2023

Abstract
While long-term antiretroviral therapy (ART) has helped many human immunodeficiency virus type 1 (HIV-1) infected aging patients to achieve controlled viremia and restored CD4 T-cell counts, the role of HIV-specific T-cell responses in these patients is not clearly understood. We have investigated HIV-specific CD4 and CD8 T-cell responses in 100 HIV-infected patients (HIV+) who have aged on long-term antiretroviral therapy (ART) with controlled viremia and restored CD4 T-cell counts. We show the median circulating HIV-specific CD4+ and CD8+IFN-γ T-cells in HIV+ were higher than uninfected controls (HIV−), including increased levels of HIV-specific CD4+IFN-γ T-cells and decreased levels of CD8+IFN-γ T-cells with increasing CD4T-cell counts in HIV+. In addition, HIV-specific CD8+TNF-α T-cells were higher in HIV+ than HIV−, including decreasing levels were seen with increasing CD4T-cell counts of HIV+. Furthermore, the CD8+ T-cell mediators, Granzyme B and CD107a, were higher in HIV+ than HIV−, however these mediators decreased with increasing CD4 T-cell counts in HIV+. More importantly, HIV-specific CD4+ and CD8+ T-cells produced higher levels of IFN-γ and CD8+ T-cells TNF-α, Granzyme B and CD107a with increasing age of HIV+ probably to counter residual HIV and reduced immunity in older individuals. In conclusion, while HIV-infected patients with controlled viremia and improved CD4 T-cell counts showed reduced CD8 T-cell responses, the CD8 T-cell responses were higher in HIV+ with lower CD4 T-cell counts as well as in HIV+ patients with increasing age.
PSGL-1 is a negative regulator of effector and memory T cells
Authors: Tinoco Roberto , Bradley Linda M 
Published: January 2023

Abstract
Effective T cell responses depend on adhesion mechanisms that guide T cells to sites of infection and inflammation. P-selectin glycoprotein ligand-1 (PSGL-1) has been shown to impact T cell migration; however, its role in the differentiation of responding T cells has not been investigated. Since PSGL-1 is highly expressed on naïve, effector, and memory T cells with varying degrees of glycosylation that impact ligand binding, we hypothesized that PSGL-1 may regulate T cell fates. Using mice deficient in PSGL-1 and we found that PSGL-1 limited the magnitude of the ensuing T cell response. PSGL-1-deficient mice had an increased accumulation of anti-viral CD4+ and CD8+ T cells after acute LCMV infection. Virus-specific PSGL-1-deficient T cells had enhanced survival and were not hyper proliferative. Furthermore, PSGL-1-deficient T cells had superior effector function, downregulation of PD-1 and other inhibitory receptors and changes in their transcriptional signature. After viral clearance, more CD4+ and CD8+ PSGL-1-deficient T cells survived to form memory cells. Interestingly, memory T cells from PSGL-1-deficient mice sustained PD-1 downregulation implying that PSGL-1 may regulate inhibitory receptors in memory T cells. Our findings highlight a previously unrecognized role for PSGL-1 in negatively regulating T cell differentiation during acute viral infection.
The pleiotropic effects of PTPN22 and its pro-autoimmune alternative allele on the antiviral immune response and T cell exhaustion
Authors: Orozco Robin C , Marquardt Kristi , Mowen Kerri A , Pratumchai Isaraphorn , Teijaro John R , Sherman Linda A 
Published: January 2023

Abstract
A major alternative allele of the tyrosine phosphatase, PTPN22 1858T, is present in 5–10% of the North American population and is strongly associated with numerous autoimmune diseases. Extensive work understanding this allele in the context of autoimmune disorders has defined a role for PTPN22 in TCR and BCR signaling, toll-like receptor activation, and cytokine production. However, despite the importance of these inflammatory factors in controlling viral infection and promoting T cell exhaustion, very little work has been done to understand how PTPN22 affects these processes. Using mice deficient in expression of PTPN22, our lab previously identified a role for this gene in promoting T cell exhaustion during chronic viral infection. Yet, the mechanism by which it is acting and how the alternative allele effects T cell exhaustion remains unknown. To examine these questions, we used CRISPR/Cas9 to generate mice expressing the human-relevant PTPN22 alternative allele (PTPN22 R619W). Using the well-established LCMV-cl13 infection model in our mice, we tested the hypothesis that pleiotropic effects of PTPN22 contributes to T cell exhaustion and chronic viral infection. We address this through examining R619W expression in various immune cells contributing to viral clearance. Importantly, we determine T cells expressing R619W have increased antigen specific activation during viral infection. Additionally, we show that expression of R619W in CD8α-conventional dendritic cells reduces PD-L1 expression during viral infection and elucidate the underlying mechanism. Results of this study provide a new mechanism through which PTPN22 tempers the immune response that may be applicable to other diseases beyond chronic viral infection.
Small GTPase Rab8 plays a critical role in B cell antigen presentation
Authors: Mattila Pieta K , Vainio Marika , Perez Sara Hernandez , Sustar Vid , Rajala Johanna 
Published: January 2023

Abstract
Upon recognition of specific antigens, B cells commit to receptor-mediated endocytosis and subsequent processing of antigen into peptides for presentation on MHC class II (MHCII) molecules. This highly specific and efficient antigen presentation is a prerequisite for B cells to be able to receive T cell help and initiate high-affinity antibody responses. The intracellular vesicle trafficking and the identity of the compartments vital for antigen processing and peptide-MHCII presentation remain poorly known. We set to characterize the vesicular pathway of internalized antigen in B cells via extensive co-localization analysis using various different markers. Our data reveal involvement of both classical endosomal markers and more specialized vesicular regulators. It appears that B cells process antigen in atypical endosomes that share both early (EEA1+, Rab5+) and late (Rab7+, Rab9+, LAMP1+) endosomal markers together with Cathepsin-S, required for proteolytic processing. Interestingly, a small GTPase Rab8, linked to specialized protein secretion pathways in the literature, strongly colocalizes with antigen throughout different stages of vesicle transport. To investigate the functional role of Rab8 on B cell antigen processing, we went on to generate Rab8-deficient B cell lines by CRISPR/Cas9. Notably, we detected a dramatic loss of antigen presentation in the cells deficient in Rab8. Our preliminary data points towards a role for Rab8 both in the transport of antigen as well as MHCII.
Peptide editing and MHC binding mechanisms of Tapasin and TAP binding protein related, TAPBPR
Authors: Kim Ellen J , Natarajan Kannan , Boyd Lisa F , Jiang Jiansheng , Mage Michael G , Margulies David H 
Published: January 2023

Abstract
Cell surface major histocompatibility complex class I (MHC-I) molecules play a crucial role in immunity to microbes and tumors by presenting intracellular peptides for recognition by CD8+ T cells. Since the repertoire of bound peptides is crucial to MHC-I stability as well as to T cell and NK cell recognition, the molecular mechanism by which peptides are selectively loaded onto MHC-I molecules is of considerable interest. A key role is played by the well-characterized chaperone tapasin as indicated by reduced cell surface MHC-I levels and altered peptide repertoires in tapasin deficient cell lines and mice. Despite extensive studies of the functional role of tapasin in shaping peptide repertoires, direct structural information on its interaction with MHC-I is lacking. Following the recent biochemical and crystallographic studies of the interaction of the tapasin homolog, TAPBPR, with MHC-I, we have engineered soluble versions of tapasin for comparison with TAPBPR. Using surface plasmon resonance assays of purified, untethered proteins, we observe that tapasin binds directly to an MHC-I molecule loaded with truncated peptides but with lower apparent affinity than TAPBPR. Similarly, using fluorescence polarization, we find that tapasin facilitates peptide exchange onto MHC-I with a lower efficiency than TAPBPR. These experiments permit direct comparisons of tapasin/MHC-I and TAPBPR/MHC-I interactions and help elucidate the functional relationship of these two distinct chaperones in shaping the MHC-I peptide repertoire.
Self-adjuvanting properties of peptide nanofiber vaccines are dependent on autophagy
Authors: Rudra Jai S , Khan Arshad , Endsley Janice J , Zloza Andrew , Jagannath Chinnaswamy 
Published: January 2023

Abstract
A crucial challenge in subunit vaccine development is to minimize adjuvant-associated toxicity and balance immunogenicity with safety. Due to the chemical heterogeneity and toxicity associated with most plant- or pathogen-derived adjuvants, those clinically approved in the U.S. are limited to alum and AS04 (alum combined with MPLA). Therefore, there is a compelling clinical need for new adjuvant strategies that potentiate strong immune responses and are chemically defined and minimally toxic. We have previously demonstrated that supramolecular peptide nanofibers are potent adjuvants that elicit protective antibody and cellular immune responses in animal models of infectious diseases, cancer, and addiction. Critically, the adjuvant potential was non-inflammatory and the exact mechanism of action was unknown. Here, we report that self-assembling peptide nanofibers bearing CD4+ or CD8+T cell epitopes are processed through mechanisms of autophagy in antigen presenting cells (APCs). Using in vitro antigen presentation assays, we confirmed loss and gain of adjuvant function using pharmacological modulators of autophagy and APCs deficient in multiple autophagy proteins. Incorporation of microtubule associated protein 1A/1B-light chain 3 (LC3-II) into the autophagosomal membrane, a key biological marker for autophagy, was confirmed using microscopy. Our findings indicate that autophagy plays an essential role in the mechanism of adjuvant action of supramolecular peptide nanofibers.