bluuebunny/crossref_metadata_2025_split huggingface dataset:
LAIV vaccination prior to pregnancy protects against lethal influenza infection and prevents infection-associated outcomes in offspring
Authors: Strutt Tara M , Satchmei Ali R. 
Published: January 2023

Abstract
Influenza is a highly contagious respiratory infection of public health concern. Pregnant women are among those at greater risk of suffering from serious influenza A virus (IAV) infection. Compromised cell-mediated immune responses, low inactivated vaccine efficacy, and poor vaccine uptake all increase the likelihood that exposure to the virus during pregnancy will result in infection-associated maternal and gestational complications such as stillbirths, preterm delivery, and low birthweights. The protective potential of IAV-specific immunological T cell memory induced by vaccination with a cold adapted live attenuated influenza vaccine (LAIV) during pregnancy has not been described; this immunity has the potential to mediate universal protection against influenza. Here, we investigated how LAIV priming before pregnancy and subsequent heterosubtypic IAV challenge during pregnancy impacts maternal and fetal outcomes in mice. LAIV priming prior to pregnancy completely protects pregnant dams against the morbidity and mortality of infection that is lethal to unprimed mice and primed dams go on to drop average sized litters. Pups born to unprimed dams are significantly smaller in terms of weight on days 3, 7, 14, and 21 when compared to pups born to LAIV primed dams. In contrast, morphological development determined by crown-rump length and skeletal measurements, while initially hindered, does not significantly differ between pups born to unprimed and primed dams after the first week following birth. LAIV priming prior to pregnancy thus appears to prevent adverse maternal and fetal IAV-associated outcomes. These data support that LAIV has potential for use as a universal vaccine to protect pregnant females against pandemic IAV.
Respiratory Syncytial Virus Induces a Functional tRNA-derived Fragment to Promote Infection by Targeting SYNE2
Authors: Chen Yu , Bao Xiaoyong 
Published: January 2023

Abstract
RSV is the most common cause of lower respiratory tract infection, such as pneumonia and bronchiolitis, in infants. RSV also leads to significant outpatient visits. However the host-virus interaction is still poorly understood. The tRNA-derived RNA fragments (tRFs) is a recently discovered family of small non-coding RNAs. They are significantly induced by RSV and some have been demonstrated to play a role in mediating virus replication and host responses. However, the mechanisms used by most tRFs for the regulation are not clear. Previously, we have shown that an RSV-induced tRF derived from the 5′-end of mature tRNAs decoding GlyCCC (named as tRF5-GlyCCC) promotes RSV replication and has a regulatory function in gene expression. To identify target(s) of tRF5-GlyGCC, we first investigated tRF5-GlyCC-associated mRNAs by HIgh-Throughput Sequencing of RNAs Associated with Biotinylated tRF (HITS-ABt). The targets were prioritized by identifying common mRNAs whose expression is suppressed by RSV and predicted free energy for the interaction of tRF5-GlyCCC and targets. SYNE-2 is one of the most likely target genes for tRF5-GlyCCC. Our experiments confirmed that SYNE-2 was downregulated by RSV infection. In addition, we found that antisense oligonucleotides of tRF5-GlyCCC reversed the SYNE-2 downregulation by RSV. We also found that SYNE2 is not involved in the replication of RSV, but important in RSV-regulated innate cellular response. Two immune mediators MIP-1β and IP-10 are selectively regulated by tRF5-GlyGCC, possibly through controlling the activation of transcription factor p50. In summary, this study provides accumulative evidence that tRFs induced by RSV are not degraded byproducts, but functional molecules.
Sodium pyruvate reduces immune signaling during influenza A virus infection in macrophages
Authors: Reel Jessica Morgan , Abysalamah Hazzar M. , Lupfer Christopher R 
Published: January 2023

Abstract
Pyruvate is a key metabolite for energy synthesis. After the production of pyruvate through glycolysis, the molecule is shuttled into the mitochondria. Once there, it is modified for use in the TCA cycle and the energy derived from pyruvate is eventually converted into ATP. While pyruvate is a key metabolite, it also appears to have anti-inflammatory properties. In models of sterile inflammation, like ischemia, pyruvate limits inflammation. We observed that infecting murine bone marrow derived macrophages (BMDM) with influenza A virus (IAV) and treating those macrophages with sodium pyruvate results in lower inflammasome activation and reactive oxygen species (ROS) production. However, this was specific to IAV infection as inflammasome activation and ROS were not affected by sodium pyruvate during E. coli infection or lipopolysaccharide (LPS) and ATP treatment of BMDMs. Our results show that IAV induces a potent and unique metabolic reprograming of infected cells. The addition of sodium pyruvate facilitates ATP production, which correlates with less mitochondrial damage and reduced inflammasome activation. Thus, pyruvate deserves additional examination as an anti-inflammatory treatment in diseases where mitochondrial metabolic stress is a factor.
MLKL-independent RIPK3 signaling alters adaptive immune responses to IAV pneumonia
Authors: Riegler Ashleigh Nichole , Jenkins Meagan M , Ballesteros-Tato Andre , Orihuela Carlos J 
Published: January 2023

Abstract
Necroptosis, a programmed form of lytic cell death, is initiated by various viral and bacterial pathogens as result of irreparable ion dysregulation and energy depletion. This cellular damage results in the activation of the kinases RIPK1 and RIPK3, then the activation and membrane targeting of MLKL, resulting in cell lysis. We demonstrated that necroptosis of airway epithelial cells (AECs) is key in the development of the adaptive immune response to the bacterial pathogen, Streptococcus pneumoniae. Here we examined the role of necroptosis in the generation of an adaptive immune response to influenza A virus (IAV), a pathogen also shown to induce necroptosis of AECs. Wildtype (WT), RIPK3 KO, and MLKL KO mice were challenged intranasally with IAV strain A/Puerto Rico/8/1934 (i.e. PR8). Weight loss was monitored as a measure of disease severity. Compared to WT and MLKL KO, RIPK3 KO mice experienced the most severe weight loss, independent of viral titers, as they were equivalent. The lungs of RIPK3 KO mice showed a significant increase in IAV-specific CD8+ T cells compared to those of WT and MLKL KO. In vitro we observed increased IL-8 production by IAV-infected RIPK3 deficient AECs. IAV-specific germinal center B cells in RIPK3 KO and MLKL KO mice were decreased compared to WT. No differences were observed in IAV specific lymph node and lung regulatory, follicular helper, central, effector, or tissue resident memory T cells. These results suggest fundamental differences in the roles of RIPK3 and MLKL in the development of adaptive immunity against IAV infection. Ongoing studies are focused on determining the contribution of MLKL-independent RIPK3 responses in AECs and immune cells in IAV infection and pathology.
NMP4 regulates innate immune responses to influenza A virus infection
Authors: Yang Shuangshuang , Adaway Michele , Sun Jie , Huang Shengping , Bidwell Joseph , Zhou Baohua 
Published: January 2023

Abstract
Severe influenza A virus infection typically triggers excessive and detrimental lung inflammation with massive cell infiltration and hyper-production of cytokines and chemokines. Defining research models to alleviate lung damage without compromising viral control is critical. We identified a novel function for nuclear matrix protein 4 (NMP4), a zinc-finger-containing transcription factor in regulating lung inflammation and antiviral innate immune responses. Nmp4-deficient mice are protected from H1N1 influenza infection, losing less body weight compared to the wild-type mice. Nmp4-deficiency does not affect viral clearance or adaptive immune responses, but significantly reduces the accumulation of neutrophils and monocytes in the lungs and the early inflammation. Consistent with fewer innate cells in the airways, infected Nmp4-deficient mice show decreased expression of chemokine genes Ccl2 and Cxcl1 as well as pro-inflammatory cytokine genes Il1b and Il6. We further reveal that NMP4 binds to the promoters and/or conserved non-coding sequences (CNS) of Ccl2 and Cxcl1 in mouse lung epithelial cells. Besides, the knockdown of NMP4 by CRISPR/Cas9 or siRNA significantly lessens the luciferase activities of Ccl2 and Cxcl1 promoters and/or CNS. Taken together, our data suggest that NMP4 regulates monocyte- and neutrophil-attracting chemokine expression in airway epithelial cells upon influenza infection, resulting in exaggerated innate inflammation and lung tissue damage.
CD8+ T cell intrinsic MAVS promotes antigen-specific responses and mitochondrial metabolism during West Nile Virus neuroinvasive disease
Authors: Vanderheiden Abigail , Aguilar-Valenzuela Renan , Verkerke Hans , Price Madeline , Boss Jeremy M , Grakoui Arash , Suthar Mehul S 
Published: January 2023

Abstract
West Nile Virus (WNV) is an arbovirus of the Flaviviridae family that causes annual outbreaks of encephalitis across North America. RIG-I like receptor (RLR) signaling through the central adaptor Mitochondrial antiviral signaling protein (MAVS) is essential for promoting immunity against WNV infection. While MAVS has been associated with type I interferon (IFN) induction during virus infection, here we describe a novel, cell-intrinsic role for MAVS in regulating antigen-specific CD8+ T cell responses. MAVS is expressed in CD8+ T cells and remains constant during the differentiation of CD8+ T cells. Generation of an effective CD8+ T cell response against WNV is essential for limiting virus replication in neurons, mitigating pathology in the brain, and protecting against lethal outcome. To understand how MAVS impacts CD8+ T cell responses during WNV infection, we utilized the WNV mouse model and adoptively co-transferred WT and Mavs−/− CD8+ T cells into congenically marked WT mice. We found that compared to WT cells, Mavs−/− antigen-specific CD8+ T cells displayed reduced accumulation of antigen-specific CD8+ T cells, reduced IFN-γ production and reduced formation of memory precursor cells during virus infection. At the peak of brain infection, Mavs−/− antigen-specific CD8+ T cells displayed highly divergent transcriptomes, including altered metabolic profiles, compared to WT CD8+ T cells. Further mechanistic studies found that after TCR stimulation of CD8+ T cells, MAVS promotes oxidative respiration and remodeling of mitochondrial morphology. Our findings identify a novel, non-canonical role for MAVS in the regulation of antigen-specific CD8+ T cell responses and mitochondrial function during neuroinvasive viral infection.
Abundance, diversity and functionality of cytomegalovirus-specific T cells depends on HLA genotype of the donor and hierarchy of the immunodominant epitopes
Authors: Maleeva Alexandra Vladimirovna , Zornikova Ksenia Victorovna , Kiryukhin Dmitry Olegovych , Shakirova Naina Talgatovna , Shmarov Vyacheslav Anatolevich , Efimov Grigory Alexandrovich 
Published: January 2023

Abstract
Cytomegalovirus (CMV)-specific T-cells from healthy donor are used as a treatment of CMV infection in patients receiving immunosuppressive therapy following transplantation. To choose the optimal donor and to select the best isolation method (MHC-tetramer or IFNy secretion assay) CMV-specific T-cells should be characterized by specificity and functionality.
We compared the antigen specificity, diversity and functionality of T-cell responding to CMV pp65 and to three pp65-derived immunodominant epitopes: NLV restricted by HLA-A*02, TPR and RPH restricted by HLA-B*07.
87 healthy donors were divided into 4 groups according to the presence of HLA-A*02 and/or HLA-B*07. CMV-specific response was analyzed by flow cytometry. For 6 donors antigen-specific cells were isolated by MHC-tetramer staining and pp65 IFNγ secretion assay followed by FACS. cDNA libraries of T-cell receptor β-chains were prepared and sequenced by NGS.
We found that pp65-specific T-cell response (IFNy-producing T-cell after stimulation with pp65 CMV) was strongly focused on pp65-derived epitopes NLV, TPR and RPH in fixed hierarchy. NLV-specific clones constituted most pp65-specific cells in presence of HLA-A*02 but not when HLA-B*07 was also present.
NLV-specific fraction consisted of few large clones, TPR− and RPH-specific cells were more diverse. Many MHC-tetramer+ clones were non-functional as they were not detected in IFNy+ fraction after pp65 stimulation.
In summary, HLA-genotype significantly affects magnitude and structure of pp65-specific T-cell response. It should be taken into consideration for choosing a donor of CMV-specific T cells. IFNy secretion assay produces more diverse and more functional cell product.
Stochastic modelling of the T cell repertoire with epitope affinity
Authors: Duque Daniel F Luque , Molina-Paris Carmen , Lythe Grant , Garcia Martin Lopez , Thomas Paul Glyndwr , Gaevert Jessica 
Published: January 2023

Abstract
Mathematical models devised to simulate competition of species for a survival resource can also be used to model the competition of T cell clonotypes for stimulus from self-pMHC complexes. A clonotype is analogous to a species that receives survival stimuli from different self-pMHC with different strengths. Thus, we can describe the T cell repertoire as a set of naive clones that are crossreactive. By studying this model we obtain informative statistics such as the mean time to extinction of a clonotype, which depends on the starting number of cells per clone and the number of self-pMHC that it can recognise. Next, we introduce viral peptides into the model, as survival resources that provide stimuli orders of magnitude stronger to that provided by self-pMHC, simulating the immune response to foreign antigens. With this addition to the model we study the effect of such perturbations on the distribution of clonal sizes. The model will be updated to include naive, effector and memory compartments of T cells, so that changes in the repertoire can be studied over the course of more than one infection. An application of this model is in the study of Influenza A viruses, where research is being done on immune response to a second exposure to a different strain.
Priming by lung-mDCs in the spleen initiates CD8+ T cell responses during influenza infection
Authors: Jenkins Meagan M , Bachus Holly , Botta Davide , Leon-Ruiz Beatriz , Ballesteros-Tato Andre 
Published: January 2023

Abstract
Initiation of CD8+ T cell responses to influenza virus requires the trafficking of activated lung-migratory dendritic cells (mDCs) from the lung into the lung-draining mediastinal LN (mLN) in response to influenza virus infection in the lungs. As such, when mDCs are absent or are unable to migrate into the mLN, T cell responses are severely compromised, and the mortality rate increases in mouse models of influenza infection. Importantly, it is generally considered that mDCs die shortly after reaching the mLN. Thus, the current paradigm suggests that priming of influenza-specific T cell responses by lung-mDC takes place entirely in the mLN. Recent reports have suggested that CD8+ T cell responses may also be initiated in the spleen, although influenza derived antigens to not freely reach the spleen or blood circulation. Together, these data and recent reports highlight a gap in knowledge of basic antigen trafficking. We show here, that a fraction of the lung mDCs egress the mLN, enter the blood circulation, and subsequently traffic to the spleen, where they prime influenza-specific CD8+ T cell responses. Mechanistically, the exit of mDCs from the mLN is controlled by Sphingosine-1-Phosphate Receptors (S1PRs) expressed by lung-mDCs, and when these receptors are blocked, CD8+ T cell activation is conjointly blocked. Collectively, our results demonstrate a novel DC trafficking pathway and support a new paradigm for the initiation of CD8+ T cell responses, where a portion of the total response, including the memory response, is primed in the spleen instead of only the mLN.
Moving in for the kill: natural killer cell immunoregulation requires CXCR3
Authors: Ali Ayad , Moran Michael T , Tuazon Jasmine , Rajaram Sanjeeth , Waggoner Stephen N 
Published: January 2023

Abstract
Natural killer (NK) cells dictate the pathogenic outcomes of infection via both direct killing of virus-infected cells and indirect immunoregulatory killing of antiviral T cells. The latter involves a perforin-dependent mechanism targeting activated CD4 T cells during the first three days of infection. Given that perforin-dependent killing involves cell-cell contact, we speculated that NK cells must re-locate proximal to recently activated T cells within the white pulp (WP) follicles of secondary lymphoid tissue during this critical temporal window of immunoregulatory activity. As expected, virus infection prompted a gradual accumulation of NK cells within T cell rich regions of splenic WP that peaked by the third day of infection. NK cells deficient in the chemokine receptor CXCR3 exhibited impaired localization to the WP and a markedly diminished capacity to suppress antiviral T-cell and germinal center B-cell responses. Our results reveal a critical role for CXCR3 in properly positioning NK cells to prune developing antiviral T cell responses, which potentially explains loss of tolerance and enhanced immune-mediated organ damage in absence of CXCR3. Strategies to curtail localization of NK cells in the WP during immunization may be an effective means to enhance vaccine-elicited immune responses.
CD8+ T cells mediate an NS3-based vaccine protection against Zika virus
Authors: Ngono Annie Elong , Syed Thasneem , Nguyen Anh-Viet , Nava Jose Regla , Susantono Mercylia , Spasova Darina , Aguilar Allison , West Melissa , Sparks Jessica , Gonzalez Andrew , Branche Emilie , DeHart Jason L. , Kamrud Kurt , Aliahmad Parinaz , Wang Nathaniel , Shresta Sujan 
Published: January 2023

Abstract
Zika virus (ZIKV), a member of the flaviviridae family, is associated with severe congenital malformations in infants born to infected mothers, and with neurological disorders, such as Guillain–Barré syndrome, in infected adults. To date, the development of anti-flavivirus vaccines has focused predominantly on the induction of neutralizing antibodies. Paradoxically, a suboptimal antibody response may enhance disease severity upon subsequent flaviviral infection through a phenomenon known as antibody-dependent enhancement. Thus, alternative approaches to ZIKV vaccine design are necessary. Here, we report induction of a protective anti-ZIKV CD8+ T cell response in the HLA-B*0702 Ifnar1−/− transgenic mouse model using an alphavirus-based replicon RNA vaccine expressing ZIKV nonstructural protein NS3, a potent T cell antigen. The NS3 vaccine did not induce an antibody response, but elicited polyfunctional CD8+ T cells that were necessary and sufficient for controlling viral burden and preventing death in lethally infected adult mice. In addition, the NS3 vaccine prevented fetal growth restriction and death in infected pregnant mice. These data identify CD8+ T cells as the major mediators of the ZIKV NS3 vaccine-induced protection and suggest a new strategy to develop safe and effective anti-flavivirus vaccines that avoid inadvertent antibody-dependent enhancement.
Phosphoproteomic landscaping of HIV-1 in vitro identified phosphorylated epitopes capable of eliciting CD8+ cytotoxic T cell (CTL) responses in patient samples ex vivo
Authors: Chowdhury Fatema Z , Maddali Shivaali , Szucs Matthew J , Ahmad Rushdy , Carr Steven A , Lichterfeld Mathias , Yu Xu G 
Published: January 2023

Abstract
Significant progress has been made in recent years in our abilities to simultaneously detect proteome and posttranslational modifications (PTMs), including phosphorylation responsible for regulating protein functions. We have an incomplete understanding of the role of phosphorylation in host-pathogen interaction. The objective of this study was to fine-map phosphorylation of HIV-1 proteins and subsequently study the consequences of these PTMs. Using mass-spectrometry, we identified over 30 unique phosphorylated sites on HIV-1 proteins detected in infected primary CD4+ T cells and in cell-free virus, with the majority being present on the viral proteins Gag, Pol, and Rev proteins. Interestingly, many of these phosphorylated sites were within previously identified optimal CTL epitopes. While CTL responses to phospho-neoepitopes is subject to recent research in cancer immunology, we lack any understanding of how phosphorylation of virus affects antiviral immune responses. We stimulated PBMCs from HIV-1 infected patients ex vivo in the presence of HIV-1 epitopes with or without phosphorylation, followed by assessment of IFN-γ, TNF-α, MIP1β, and CD107a expressions by flowcytometry. Two Gag-derived phospho-epitopes were able to elicit immune responses in CTLs, potentially indicating the genesis and functional responses to such modified epitopes in vivo in HIV-1 infected patients. Moreover, CTL clones of HLA B*5701 background responded with significantly more cytotoxic marker without any effector cytokine expression, suggesting that phospho-epitopes can modulate the quality of CTL responses. Taken together, our studies shed light on a new way of evaluating host-pathogen interaction with potential for vaccine research.
HIV-infected macrophages evade NK cell-mediated killing while driving inflammation
Authors: Clayton Kiera , Stuart Heather , Mylvaganam Geetha , Ocando Alonso Villasmil , Maus Marcela , Walker Bruce D 
Published: January 2023

Abstract
The primary targets for HIV infection are CD4 T cells, however macrophages (MΦ) are also infected and persist despite antiretroviral therapy, suggesting evasion of immune responses. Our previous work shows that while HIV-infected MΦ are recognized by cytolytic CD8 T lymphocytes (CTL), killing is inefficient and causes hypersecretion of CTL cytokines that propagate inflammation, emphasizing the need for rapid killing to limit inflammation. Thus, we hypothesized that NK cells would be able to rapidly kill HIV-infected MΦ while limiting inflammation. To test this hypothesis, innate interactions between NK cells and HIV-infected MΦ or CD4 T cells were assessed via flow cytometry-based recognition/killing assays. To characterize the potential for antibody-dependent cellular cytotoxicity (ADCC), HIV envelope expression on MΦ was characterized by flow cytometry and HIV-specific CAR T cells. Finally, ADCC responses against infected CD4 T cells and MΦ were assessed via flow cytometry. Despite similar levels of recognition of HIV-infected CD4 T cells and MΦ (degranulation and TNF-α production), NK responses to MΦ were significantly skewed towards non-cytolytic, cytokine production (p&lt;0.0001), which was associated with poor elimination (p&lt;0.0001). Surface HIV envelope is equally accessible on both MΦ and CD4 T cells, as determined by CAR T cell recognition. While ADCC enhanced NK cell responses to both cell types, responses to MΦ were significantly lower compared to that of CD4 T cells (p&lt;0.05). Together, these data suggest HIV-infected MΦ employ a unique mechanism to evade cytolytic NK cell recognition while preserving inflammatory cytokine responses, emphasizing the need to develop alternative strategies to eliminate infected MΦ.