bluuebunny/crossref_metadata_2025_split huggingface dataset:
A potential candidate for Zika virus vaccine
Authors: Chen Wei-Yu , Chen Pei-Kai , Sung Kuan-Wei , Ku Chia-Chi 
Published: November 2024

Abstract
Zika virus (ZIKV) caused a large outbreak in Brazil during 2015-2016 and sporadic cases globally. In light of the potential for the virus to reemerge, developing a potent Zika vaccine is crucial. In this study, we aimed to enhance the immunogenicity of ZIKV by isolating a single clone from clinical human isolates. Initial vaccination of Balb/c mice with inactivated clinical ZIKV (ZIKV-P0) failed to generate neutralizing antibodies. We turned to adapt the Virus in cell culture by serial passages in Vero cells and isolated a single clone by plaque purification. ZIKV-1_PP4, one of the purified clones, exhibited high titer and homogeneous morphology. Prime-boost immunization with inactivated ZIKV-1_PP4 antigen induced significant neutralizing antibody responses in Balb/c mice. Notably, when challenged with ZIKV, mice immunized with ZIKV-1_PP4 showed reduced susceptibility compared to those immunized with ZIKV-1_P0. Additionally, ZIKV-1_PP4 infection showed enhanced recruitment of innate immune cells, including neutrophils, monocytes, and DCs. Furthermore, DCs from ZIKV-1_PP4 infected mice expressed higher levels of costimulatory molecules, with elevated levels of IL-12, IFN-γ, IL-1β, and TNF-α. In summary, our study demonstrated that plaque-purified ZIKV-1_PP4 significantly triggered heightened activation of innate immune responses and improved the generation of neutralizing antibodies. These findings underscore the effectiveness of this vaccine candidate against ZIKV.
Prime-boost vaccination combining rF1-V subunit and novel live attenuated bacterial strains protects mice from virulent aerosolized nonencapsulated Yersinia pestis
Authors: Davies Michael , Biryukov Sergei , Rill Nathaniel , Klimko Christopher , Hunter Melissa , Dankmeyer Jennifer , Shoe Jennifer , Mlynek Kevin , Talyansky Yuli , Toothman Ronald , Qiu Ju , Bozue Joel , Cote Christopher 
Published: November 2024

Abstract
Yersinia pestis (Yp) is a security concern since it can be aerosolized and cause pneumonic plague, a rapidly progressing illness that is fatal if not treated promptly with antibiotics. There are no FDA-approved vaccines, and candidate vaccines are less effective against pneumonic than bubonic plague. The major protective vaccine antigen has been the F1 capsule protein; protection against nonencapsulated strains has been elusive. We constructed two novel live attenuated vaccine (LAV) strains on the pgm-pPst- background, which is excluded from the CDC select agent list due to established safety. These strains, Δcaf1 and ΔyopD/Δcaf1, lack F1 and may be more effective at inducing immunity against nonencapsulated strains like C12. Female BALB/c mice were immunized with a heterologous prime-boost strategy combining one subcutaneous injection of novel LAV and one of recombinant F1-V (rF1-V) subunit, then challenged with aerosolized virulent Yp C12 and monitored for survival, bacterial load, and immunological factors. Priming with rF1-V and boosting with LAV was more protective than the reverse strategy. Protection was accompanied by high antibody titers against rF1-V and rV. rF1-V prime and LAV boost also led to a higher IgG2a/IgG1 antibody ratio than the reverse, suggesting a balanced Th1/Th2 response. These data support rF1-V prime and pgm-pPst-Δcaf1 LAV boost as a promising strategy for a safe and effective vaccine against both encapsulated and nonencapsulated Yp.
Lipid nanoparticle encapsulation enhances the immunogenicty of a SARS-CoV-2 Delta variant-based DNA vaccine and enables protection against heterologous omicron subvariants
Authors: Tamming Levi , Duque Diana , Lansdell Casey , Raman Sathya , Wang Lisheng , Tran Anh , Johnston Michael , Li Xuguang 
Published: November 2024

Abstract
mRNA vaccines were instrumental in limiting the extent of the COVID-19 pandemic. Despite being presented as an alternative to mRNA vaccines, DNA vaccines have not achieved similar levels of clinical success. We evaluated the immunogenicity and protective efficacy of a CD40L-adjuvanted Spike DNA vaccine based on the B.1.617.2 (Delta) variant when encapsulated in lipid nanoparticle formulations, created using DLin-KC2-DMA and SM-102 ionizable lipids. Syrian hamsters were vaccinated twice intramuscularly with unformulated or LNP-encapsulated DNA vaccines before being challenged with homologous or heterologous BA.5 (Omicron) strains of SARS-CoV-2. LNP encapsulation enhanced immune responses following one and two doses, increasing binding and neutralizing antibody titers. LNP encapsulation also enabled the neutralization of multiple omicron sub variants. LNP encapsulation also provided greater protection from challenge with both Delta and Omicron strains of SARS-CoV-2, reducing weight loss and suppressing viral replication in the upper and lower respiratory tract. This reduced viral burden coincided with the prevention of lung pathology. These results highlight the increased effectiveness of DNA vaccines afforded using similar delivery vehicles as those found in commercial mRNA vaccine formulations. Further studies are required to fully understand the safety and tolerability of this approach, as well as to directly compare the DNA formulations with mRNA vaccines.
Nanoparticle immunoadjuvant complexes augment antigen-specific germinal center responses to enhance humoral immunity
Authors: Tursi Nicholas , Kannan Toshitha , Londregan Jennifer , Lederer Katlyn , Helble Michaela , Gary Ebony , Bedanova Nicole , Maillard Ivan , Allman David , Escolano Amelia , Kossenkov Andrew , Kulp Daniel , Weiner David 
Published: November 2024

Abstract
An alluring strategy for improving protective humoral immunity against infectious diseases would be to directly target the germinal center (GC). Robust GC responses are associated with high titer and high affinity antibody responses. Despite advances in formulation strategies and vaccine design, there remains a critical need for next generation approaches to elicit potent humoral immunity. Multimeric nanoparticles offer enhanced immunogenicity compared with monomeric antigen partially due to potent B cell activation and increased antigen density on the nanoparticle. Here, we investigated whether GC cytokine IL-21 could be displayed on nanoparticles to further enhance immune responses. We designed a chimeric nanoparticle using the GT8-60mer, a germline targeting HIV immunogen, as a model to scaffold IL-21. GT8 and IL-21 scaffolded nanoparticles, termed GT8 IL-21 nanoparticle immunoadjuvant complexes (GT8 IL-21 NIC), increased antigen-specific GC B cells, functional Tfh cell responses, and serum antibody titers relative to the antigen-only GT8-60mer. Additionally, GT8 IL-21 NICs reorganized antigen-specific GC B cell responses to the light zone (LZ) of the GC, the canonical site of antigen-driven selection. Single-cell RNA sequencing of antigen-specific GC B cells from GT8 IL-21 NIC immunized mice demonstrated upregulation of selection-associated gene signatures and a shift in the clonal repertoire. Thus, GC targeting NICs may provide value to drive improved humoral immunity.
SARS-CoV-2 WA1 induces distinct immune transcriptome profiles in human and deer primary respiratory epithelial cells
Authors: Nelli Rahul , Sarlo Davila Kaitlyn , Phadke Kruttika , Ruden Rachel , Bellaire Bryan , Sang Yongming , Giménez-Lirola Luis , Miller Laura 
Published: November 2024

Abstract
The ability of SARS-CoV-2 to infect animals, especially white-tailed deer (WTD), is a public health and economic concern. Humans experience varied clinical outcomes, while WTD are usually asymptomatic carriers. The immune factors responsible for these differences have yet to be studied. A comparative transcriptomic analysis in primary respiratory epithelial cells of humans (HRECs) and WTD (Deer-RECs) infected with SARS-CoV-2 WA1 was assessed throughout 48 hours post-inoculation (hpi). Both HRECs and Deer-RECs were susceptible to SARS-CoV-2, with significantly (P &lt; 0.001) lower virus replication in Deer-RECs. The number of differentially expressed genes (DEG) gradually increased in Deer-RECs but decreased in HRECs throughout the infection. The ingenuity pathway analysis of DEGs further identified that genes commonly altered during SARS-CoV-2 infection mainly belong to cytokine/chemokine response pathways mediated via IL-17 and NF-κB signaling pathways. SARS-CoV-2 activated AP-1/JUN transcription factor in both HRECs and Deer-RECs. Deer-RECs showed delayed upregulation of genes related to wound repair, including CXCL8, MAP4K4, p21, VEGFA, and HBEGF. The early inhibition of the NF-κB signaling in Deer-RECs predicted at 6 hpi may have contributed to the comparatively less proinflammation observed in Deer-RECs than HRECs. These findings may partly explain differences in WTD and human responses to SARS-CoV-2 WA1 infection.
The proteomic landscape of interferon signaling in primary T cells
Authors: Gordon David , Beusch Christian , Monaco Christopher , Swaldi Hailey 
Published: November 2024

Abstract
Interferon signaling has a central role in host defense against pathogens and modulation of inflammation, and it also impacts angiogenesis, carcinogenesis, and response to cancer therapeutics. Despite the physiological importance of interferon, the diverse molecular pathways mediating interferon signaling remain poorly defined, complicating understanding and treatment of interferon-mediated pathology. To address this knowledge gap, we applied mass-spectrometry based proteomics to map the phosphorylation pathways downstream of type-I interferon treatment in primary human T cells. Through time-course analysis of our phosphoproteomic data, we observe profound and rapid changes across over 1,300 phosphosites, revealing a dramatic rewiring of the proteome caused by interferon treatment. Clustering analysis of our phosphoproteomic data highlights numerous immunity-associated proteins, many of which have not previously been associated with interferon signaling, co-clustering with canonical STAT phosphosites (e.g. STAT1-Y701, STAT3-Y705, and STAT4-Y693). This rich dataset highlights the complexity of interferon signaling, and forms the basis for a drastically improved understanding of interferon-regulated pathways. In follow up work, we are also applying experimental genetics paired with phosphoproteomic analysis, as well as proteome-wide interaction studies, to delineate the network architecture of type-I interferon signaling.
Chikungunya-virus-specific CD4+ T cells are associated with chronic chikungunya viral arthritic disease in humans
Authors: Agarwal Rimjhim , Chang James , Cortes Fernanda , Ha Calvin , Villalpando John , Castillo Izabella , Galvez Rosa , Grifoni Alba , Sette Alessandro , Romero-Vivas Claudia , Heise Mark , Premkumar Lakshmanane , Falconar Andrew , Weiskopf Daniela 
Published: November 2024

Abstract
Chikungunya virus (CHIKV) is a mosquito-borne Alphavirus that causes recurrent outbreaks in tropical and subtropical regions of the world. In the first 2-7 days of infection, most individuals experience high fever, skin rash and joint pain and swelling. However, about 30-60% of the infected individuals, primarily middle-age females, develop debilitating chronic arthritis-like symptoms such as joint pain, muscle aches and edema. Despite ongoing treatment and vaccine development efforts, the immune responses to CHIKV in humans remain largely understudied. In this study, we tested peripheral blood mononuclear cells (PBMCs) collected from a cohort of 39 individuals diagnosed with CHIKV disease during the 2014-2015 epidemic in Colombia against pools of overlapping sequentially spanning the entire CHIKV genome. Using high-resolution spectral flow cytometry, we detected robust CHIKV-specific CD4+ T cell responses, but not CD8+ T cell responses in the periphery. Patients experiencing chronic symptoms displayed a significantly higher abundance of CHIKV-specific memory CD4+ T cells, compared to their recovered counterparts. Furthermore, these CD4+ T cells displayed a significantly lower Th1 phenotype but were enriched in the Th17 phenotype, with the predominant production of TNFɑ. Overall, our work demonstrates that CD4+ T cells play a pivotal role in the pathogenesis of CHIKV and provides insight into possible therapeutic options.
RSV-induced Epigenetic regulation of DC via H3K4 demethylase KDM5b
Authors: Mire Mohamed , Cortes Ashley , Morris Susan , Rasky Andrew , Lukacs Nicholas , Ptaschinski Catherine 
Published: November 2024

Abstract
Immune regulation by epigenetic mechanisms has become an intense area of research. The concept that our immune system responses are influenced by environmental factors including microorganisms, pollution, and pathogen exposure is important as a backdrop for understanding disease progression. We previously observed an upregulation of KDM5B, an H3K4 demethylase, following RSV infection of DCs that regulates key innate cytokines, Type I IFN and TNF. As H3K4 tri-methylation is an activating mark, this demethylase should act as a transcriptional repressor to specific gene targets. Our in vitro and transcriptomic data shows genomic ablation of KDM5B in DC leads to greater antiviral response following RSV or TLR stimulation. This includes upregulation of type I IFN and downstream elements such as Cxcl10, Oasl1, and Mx2 genes. While more than 500 genes appear to be regulated in the KDM5b KO DC after RSV infection compared to WT DC, specific transcriptional regulation linked to type I responses were indicated. Utilizing the transcription factor prediction tool BART reveals IRF3, IRF7, and STAT1 as regulatory factors for the differentially expressed genes following TLR re-stimulation of RSV infected KDM5B-KO DC. To further extend these findings to an in vivo setting, KDM5b-CD11c-CRE+ mice were infected by RSV and, after 3 weeks, re-infected with RSV. Compared to KDM5b sufficient mice, there was a reduction in secondary RSV infection induced pathology and altered immune mediators.
Age influences CMV-specific NK and CD8 T cell memory fates
Authors: Jensen Isaac , Redenti Benjamin , Gray Joshua , Caron Daniel , Farber Donna 
Published: November 2024

Abstract
Cytomegalovirus (CMV), a prevalent persistent infection often unnoticed in healthy adults, is the most common congenital infection of neonates/ infants. NK cells and CD8 T cells control CMV via cytolysis of infected cells; yet their coordinate response to CMV remains uncharacterized, particularly in infants. We interrogated how NK and CD8 T cell responses differed between adults and infants in a murine CMV (MCMV) infection model. Infant mice had higher viral burden and delayed viral clearance in multiple tissues. T cell depletion enhanced infant MCMV-induced morbidity; yet, co-adoptive transfer of adult and infant OT-I CD8 T cells followed by MCMV-OVA infection revealed phenotypic and transcriptional limits in infant T cell capacity to form memory precursors and subsequent memory. This impairment was age-dependent, co-transfer of OT-I cells from sequentially aged mice had increasing memory formation, overall infant CD8 T cells are effector biased with limited memory potential. To reconcile how infants bridge this gap in T cell immunity we interrogated NK cell responses. Unlike adult mice, infant Ly49H+ (MCMV-specific) NK cells potently responded to infection, adopting an effector-memory (KLRG1+CD62L+) phenotype. Notably, loss of memory NK cells with age coincided with the increasing OT-I memory potential. Our data suggest discrete roles for NK cells and CD8 T cells in MCMV infection during infancy with NK cells as key responders prior to T cell ability to acquire memory.
Neurotropic viral infections induce priming and maintenance of a novel antigen-specific CD8 T cell population within the bone marrow that dysregulates the stem cell niche upon reactivation
Authors: Reesman Rachael , Wolf Delaney , Tritz Zachariah , Pfaller Christian , Hoyt-Miggelbrink Alexandra , Hansen Michael , Fain Cori , Johnson Aaron , Ayasoufi Katayoun 
Published: November 2024

Abstract
Bone marrow (BM) is the primary immune organ responsible for stem cell maintenance. Neurotropic infections elicit sequestration of T cells within the BM. Changes of the BM niche during brain viral infections are unknown. Intracranial infection with the neurotropic Theiler’s Murine Encephalomyelitis Virus (TMEV) in C57BL/6 mouse is cleared by 30 days due to generation of an antigen-specific CD8 T cell response. We determined that 1-10% of CD8 T cells present in the sternal, femoral, and cranial BM were virus antigen-specific 7 days post intracranial infection. Over 70% of these CD8 T cells were tissue resident. We determined antigen-specific CD8 T cells were generated in the BM within 4 days of infection, a timeline similar to lymph nodes. Continuous treatment with FTY720, which sequesters T cells outside of the blood, did not eliminate antigen-specific CD8 T cells in any BM compartment. CD8 T cells in the BM established durable memory populations and were reactivated upon antigen reencounter. Both acute infection and reactivation caused an increase in lineage-, Sca-1+, ckit+ (LSK) cells in the BM. This LSK dysregulation was abrogated upon CD8 T cell depletion and was limited to the intracranial routes of infection. We conclude that brain viral infections induce in situ effector and memory T cell responses within the BM and cause stem cell dysregulation. Our data paves the way for crucial studies of BM resident antigen-specific CD8 T cells in health and disease.
Loss of myeloid-KLF2 mediates LPS-induced mortality in neonatal pups by NLRP3 inflammasome signaling and altered neutrophil aging
Authors: Satyavolu Sriram , Mukherjee Devashis , Thomas Asha , Nayak Lalitha 
Published: November 2024

Abstract
Preterm neonates have disrupted myeloid cell activation and aging. KLF2 inhibits myeloid cell activation by repressing NF-kB, which controls NLRP3 transcription. In our myeloid-KLF2 deleted (MKO) murine model, postnatal day (P) 4 pups have higher LPS-induced mortality than controls but 100% survival in both groups after LPS at P12. P4 and P12 reflect preterm and term physiology, respectively. We aimed to to determine the role of neutrophil-NLRP3 and neutrophil aging in LPS-induced mortality in P4 MKO pups. Serum IL-1β was measured 4h post-LPS injection. BM neutrophils were treated with LPS and nigericin for NLRP3 protein expression in lysate and IL-1b levels in the supernatant. Daily MCC950 injections (P1-P4) were used to inhibit NLRP3 before LPS injection on P4. BM neutrophils were treated with LPS ex vivo and flow-sorted to examine CXCR4/CD62L expression. MKO pups have increased serum IL-1β, neutrophil-NLRP3 expression, and IL-1b release, P4&gt;P12. In vivo NLRP3 inhibition rescued survival in P4 MKO and controls. P4 MKO have reduced BM and higher circulating neutrophils. MKO BM neutrophils are more aged (CD62Llo), but CXCR4lo, affecting aged neutrophil homing to the BM. Myeloid-KLF2 loss increases LPS mortality via NLRP3 activation in P4 pups. It accelerates neutrophil aging, but leads to persistence of aged neutrophils in the circulation by reducing CXCR4 expression. Future mechanistic studies will focus on KLF2's regulation of NLRP3 and CXCR4 expression at P4 and P12.
P120 catenin enhances macrophage efferocytosis and facilitates resolution of lung inflammatory injury
Authors: Wang Jianguo , Kanmani Paulraj , Hu Guochang 
Published: November 2024

Abstract
Efficient clearance of apoptotic neutrophils (PMNs) (efferocytosis) after sepsis plays a crucial role in facilitating tissue repair, resolving inflammation, and maintaining immune system balance. Here, we identified p120 catenin (p120) as a pivotal regulator in efferocytosis and subsequent recovery from inflammatory lung injury. We found that specific macrophage p120 deletion had a profound delay in the resolution of PMN infiltration, extracellular protein accumulation, and lung edema and injury following LPS challenge. p120 deletion increased the levels of TNF-α and IL-6, and reduced the levels of TGF-β1 and IL-10. Depletion of p120 also led to a marked decrease in the phagocytosis of apoptotic PMNs by macrophages. The number of p120-depleted alveolar macrophages containing apoptotic PMNs in bronchoalveolar lavage fluid was significantly lower. p120 deficiency caused a reduction in the expression of key efferocytosis-related molecules, namely AXL and CD36. p120-depleted macrophages exhibited a shift in polarization towards the M1 phenotype. Apoptotic cells triggered the association and co-localization of p120 and PPAR, and p120 deletion decreased the activity of PPARgamma in response to apoptotic PMNs. Inhibition of PPAR abolished p120-mediated efferocytosis and the resolution of lung inflammation. These findings underscore the critical role of p120 in facilitating the resolution of lung inflammation through modulation of macrophage polarization and PPAR signaling pathway.
Deciphering the role of Klf2 in CD8 T cell differentiation and exhaustion during chronic infection
Authors: Shen Jian , Brown Ryan , Kharel Arjun , Zhang Yuqi , Brown Ashley , Lin Siying , Cui Weiguo 
Published: November 2024

Abstract
T cell exhaustion, a state of dysfunction occurring during chronic infections and cancer, is marked by a progressive loss of effector functions and increased expression of inhibitory receptors. In chronic infection, CD8 T cells differentiate into TCF1+ progenitor (TPRO), CX3CR1+ effector (TEFF), and terminally exhausted (TEXH) subsets. The differentiation pathways are governed by complex transcription factor (TF) networks. Employing regulon analysis enabled by single-cell RNA+ATAC multiome sequencing, we dissected the TF networks orchestrating the fate of exhausted CD8 T cell populations. Our integrative analysis, complemented by single-cell CRISPR screening, highlighted Krüppel-like factor 2 (KLF2) as a pivotal TF necessary for maintaining TPRO cells and generating TEFF cells. Our research also revealed that KLF2 regulates the distinct distribution patterns of CD8 T cell subsets across organs. More intriguingly, multiomic analysis uncovered a novel function of Klf2 in limiting T cell exhaustion. Klf2-deficient CD8 T cells exhibited a marked increase in exhaustion signature genes. ATAC-seq and CUT&TAG assays further revealed different chromatin accessibility and histone modifications within Klf2 and its enhancers across CD8 T cell subsets. These insights underscore the differential transcriptional and epigenetic regulation of Klf2, presenting a novel mechanism that influences the cell fate decision of CD8 T cells during chronic infections.