bluuebunny/crossref_metadata_2025_split huggingface dataset:
The fate and function of NK cells in the suppressive tumor microenvironment
Authors: Liu Xia , Ma Feiya , Zhang Yuanqin , Tao Yan , Hoft Daniel F , Peng Guangyong 
Published: January 2023

Abstract
Natural killer (NK) cells are an important cell subset of the innate immune system. Accumulating evidence indicates that NK cells are dysfunctional in the tumor microenvironment during cancer development. However, the dynamic changes in phenotypes and functional interactions within the tumor microenvironment during tumor development and progression are unknown. Here, we used both the mouse E0771 breast cancer and B16F0 melanoma tumor models to mimic different clinical stages of human cancers and characterized the dynamic distributions and qualities of NK cells in different organs and tumors associated with tumor progression. We found that NK cells are dynamically involved in the immune responses to cancer with different distributions and phenotypic profiles in tumor sites and other peripheral organs during the course of tumor development and progression. In the early stages of tumor development, NK cells exhibit effector properties. In the later cancer stages, NK cells have impaired cytotoxic capacities and dysfunctional states. Importantly, we found that melanoma and breast cancer cells promote NK cells to become senescent NK cells in vitro and in vivo in tumor microenvironments. These studies provide a better understanding of the dynamic and functional role of NK cells in anti-tumor immunity, which may facilitate the development of novel immunotherapies targeting NK cells for cancer treatment.
the Melanoma Research Alliance, American Cancer Society, and the National Institutes of Health.
Isolation of alpaca-derived single-domain antibodies against zika virus non-structural proteins to interrogate viral replication
Authors: Weinstein Jules B , Tafesse Fikadu G 
Published: January 2023

Abstract
Zika virus (ZIKV) is a re-emergent flavivirus that triggered a global health emergency from 2015 to 2017. ZIKV and other impactful flaviviruses, including dengue virus, lack the antiviral treatments and vaccines needed to diminish their threat to communities world-wide. This is in part due to gaps in our understanding of the flavivirus lifecycle; despite numerous investigations into flavivirus non-structural (NS) protein function. I hope to forge a deeper understanding of crucial NS protein functions and interactions throughout the ZIKV replication cycle. I will use alpaca-derived variable heavy-chain-only (VHH) antibody fragments, isolated from an alpaca immunized with ZIKV NS proteins, to perturb the replication cycle and therefore identify key NS protein epitopes used during replication. I individually purified NS1, NS2b, NS3, NS4b, NS5 for use in alpaca immunization, phage display panning, and enzyme-linked immunosorbent assays (ELISAs). From the alpaca peripheral blood I isolated RNA and amplified VHH genes, enriched for NS-protein binders with iterative phage display, and screened potential high binders via ELISA. I have isolated VHH sequences that interact with the ZIKV helicase, NS3, and the RNA-dependent RNA polymerase, NS5. I plan to purify each VHH and express them in ZIKA-permissive A549 cells as stable lines. Using purified VHH, I will analyze their binding ability in-vitro by ELISA and bio layer interferometry, and quantify in-vitro inhibition of NS3 protease and helicase activity for NS3 binders, and NS5 polymerase and methyltransferase activity. With the stable cells lines I will investigate each VHHs ability to impede ZIKV virus production and formation of replication complexes in infected cell lines.
Support from training grant “Interactions at the Microbe-Host Interface” T32AI007472
RhCMV/SIV tropism modulation programs unconventional CD8+ T cell priming and vaccine efficacy
Authors: Hancock Meaghan , Hansen Scott , Malouli Daniel , Marshall Emily , Hughes Collette , Randall Kurt T , Morrow David , Ford Julia , Gilbride Roxanne , Selseth Andrea , Trethewy Renee Espinosa , Bishop Lindsey , Oswald Kelli , Shoemaker Rebecca , Berkemeier Brian , Bosche William , Hull Michael , Nekorchuk Michael , Busman-Sahay Kathleen , Estes Jacob , Axthelm Michael , Smedley Jeremy , Shao Danica , Edlefsen Paul , Lifson Jeffrey , Fruh Klaus , Nelson Jay , Picker Louis J 
Published: January 2023

Abstract
Strain 68-1 rhesus cytomegalovirus (RhCMV) vectors expressing simian immunodeficiency virus (SIV) antigens demonstrate a vaccine efficacy where 50–60% of vaccinated rhesus macaques are protected from SIV challenge. Intriguingly, RhCMV/SIV vectors elicit CD8+ T cells recognizing epitopes presented by MHC-II and MHC-E instead of MHC-Ia. We are studying how these unconventional T cell responses are elicited and contribute to the efficacy against SIV challenge. Here we utilize host microRNA (miRNA)-mediated vector tropism restriction to show that MHC-II- and MHC-E-restricted responses are primed by directly infected, non-overlapping cell types in rhesus macaques. Targeting essential RhCMV genes with myeloid cell-selective miR-142-3p eliminated MHC-E-restricted CD8+ T cell priming, yielding an exclusively MHC-II-restricted response, whereas endothelial cell-selective miR-126-3p targeting eliminated MHC-II-restricted CD8+ T cell priming, yielding an exclusively MHC-E-restricted response. Incorporation of both restriction elements reverts CD8+ T cell responses back to conventional MHC-Ia restriction. Using these otherwise isogenic vectors we show that although they demonstrate similar overall immunogenicity, only the vectors programmed to elicit MHC-E-restricted CD8+ T cell responses provided protection against SIV challenge. The MHC-E-only RhCMV/SIV vaccine efficacy did not exceed that of the parental 68-1 RhCMV/SIV vectors (that elicits both MHC-II and MHC-E responses) indicating that while the MHC-II-restricted CD8+ T cell responses are neutral to overall vaccine efficacy, an additional component of 68-1 RhCMV/SIV-induced immunity contributes to overall vaccine efficacy.
This work was supported by the National Institute of Allergy and Infectious Diseases (NIAID) grants UM1 AI124377 and U19 AI128741 to LJP; the Oregon National Primate Research Center Core grant from the National Institutes of Health, Office of the Director (P51 OD011092); contracts from the National Cancer Institute (# HHSN261200800001E) to JDL; and the Bill and Melinda Gates Foundation grant OPP1107409.
T cell programming by the cytomegalovirus MHC class I homologue UL18
Authors: Taher Husam , Malouli Daniel , Hansen Scott G , Mansouri Mandana , Iyer Ravi , Papen Courtney , Schell John B , Cleveland-Rubeor Hillary , McArdle Matthew R , Hughes Colette M , Randall Kurt T , McNett Alisha , Picker Louis J , Früh Klaus 
Published: January 2023

Abstract
Rhesus cytomegalovirus (RhCMV) strain 68-1 vectored vaccines elicit MHC-II-and MHC-E-, but not classical, MHC-Ia-restricted CD8+ T cell responses. This is due to the presence of a viral MHC-E ligand encoded by Rh67 (UL40 in HCMV) and the combined deletion or inactivation of Rh157.5/.4 (UL128/UL130 in HCMV) and Rh158–Rh161 (members of the UL146 family of CXC chemokines). Importantly, the ability to elicit MHC-E-restricted CD8+ T cell responses correlates with the efficacy of RhCMV-vectored vaccines to control and clear infection by highly virulent simian immunodeficiency virus (SIV). To investigate whether HCMV encodes additional modulators of unconventional CD8+ T-cell priming that are not conserved in non-human primate CMVs, we inserted non-conserved HCMV genes into 68-1 and monitored the induction of the unconventional CD8+ T cells. This screen revealed that the UL18 protein of HCMV prevented the induction of MHC-II and MHC-E restricted CD8+ T cells resulting in a classical, MHC-Ia-targeted T cell response. UL18 is a MHC-Ia homolog and associates with cellular β2 microglobulin and peptides. However, unlike host MHC-Ia, this trimeric complex does not engage with the T cell receptor, but binds with high affinity to the inhibitory receptor LIR-1 widely expressed on leukocytes. Indeed, 68-1 recombinants expressing UL18 mutants lacking LIR-1-binding no longer interfered with the induction of MHC-II and MHC-E restricted CD8+ T cells. Thus, HCMV UL18 appears to prevent unconventional T cell priming by binding to LIR-1. In the event that this mechanism is conserved in the human host, UL18 could interfere with HCMV/HIV vaccine efficacy as the ability to elicit MHC-E-restricted CD8+ T cells is likely required for protection against HIV.
Bead-based Multiplex Assay Panels for Quantifying COVID-19 Vaccine-induced Serological Response, Neutralizing Antibodies and Cytokines
Authors: Zhao Amy , Zhao Jessica , Webster Edvelyn , Wheat Cassandra , Sun Binggang , Ni Jessie 
Published: January 2023

Abstract
The COVID-19 pandemic, caused by SARS-CoV-2 virus infection, has resulted in more than 5 million deaths and triggered severe social and economic disruptions worldwide. The emergence of multiple variants of the virus (Alpha, Beta, Gamma, Delta, and Omicron) has further made the pandemic to be one of the most dangerous in history. In order to enable biomedical researchers to understand the disease and develop advanced vaccines and treatments, BioLegend has developed a series of bead-based multiplex panels including SARS-CoV-2 serological IgA, IgM and IgG Panel, Variants Neutralization Antibody, and COVID-19 Cytokine Storm Panels. These panels can quantify simultaneously either various isotype of antibodies, functional antibodies or cytokines in one sample using commonly available flow cytometers. Highly specific antibodies were used in order to ensure assay specificities and robust performance. In addition, these multiplex assay panels are validated in biological samples (serum and plasma) obtained from donors before and after vaccination. Our preliminary data indicate that three types of vaccines induced different antibody responses and cytokine profiles. The experimental data demonstrated that these panels can be reliable, convenient and cost-effective tools for vaccine developers and COVID-19 research.
Proteomic analysis of plasma exosomes as biomarkers of response to MVP-S based immunotherapy
Authors: Smith Pascal , Teh Evelyn , Chisholm Ken , Penny Susanne , Pinto Devanand , Patterson Kelcey , Dirk Brennan , Bydoun Moamen , Fiset Stephan , Bramhecha Yogesh , Hirsch Heather , Hrytsenko Olga , Graff Jeremy 
Published: January 2023

Abstract
Ovarian cancer is a deadly gynaecological disease owing to its late-stage diagnosis. Recurrence and chemo-resistance develop despite initial treatment success. Maveropepimut-S (MVP-S), formerly DPX-Survivac, is a DPX-based immune educating therapy that elicits robust, targeted and, sustained specific anti-tumor T- and B-cell responses in advanced ovarian cancer patients.
Exosomes are a subtype of extracellular vesicles (EVs) secreted by cells involved in intercellular communication. They contain bioactive molecules that can influence the tumor, the immune system, and the extracellular environment. Hence, circulating exosomes could provide real time assessment of disease evolution making them ideal minimally invasive biomarkers for monitoring response to immunotherapies.
Plasma exosomes were isolated from advanced ovarian cancer patients (n=22) at pre- and on-treatment with MVP-S based therapy (DeCidE1 trial, NCT02785250). Subjects with clinical benefit (&gt;10% tumor shrinkage) to therapy displayed a lower overall total EV protein concentration. Untargeted proteomic profiling by liquid chromatography tandem mass spectrometry identified 227 proteins in exosomes. Of these, 95 (42%) were likely from non-tumor exosomes and involved in immune modulation such as regulation of humoral response and B-cell immunity. When compared to the plasma proteome, 128 (56%) proteins were found to be exclusive to exosomes. Functional annotations of these proteins suggest their role in modulating immune pathways related to Fc receptor mediated signaling and T-cell migration.
The results highlight the potential value of plasma exosome assays for monitoring disease and as a potential surrogate response biomarker.
Supported by -IMV inc. -NRC-IRAP R&D Certificate Program.
Harnessing the unique immune biology of cytomegalovirus for cancer immunotherapy
Authors: Iyer L Ravi F , Verweij Marieke C , Nair Sujit , Morrow David , Mansouri Mandana , Beechwood Teresa , Meyer Christine , Chakravarty Dimple , Uebelhoer Luke , Ventura Abigail , Lauron Elvin J , Selseth Andrea , Axthelm Michael , Lind Evan F , Saultz Jennifer , Douglas Janet , Korman Alan , Bhardwaj Nina , Tewari Ashutosh K , Hansen Scott G , Malouli Daniel , Picker Louis J , Fruh Klaus 
Published: January 2023

Abstract
Pre-clinical models in non-human primates demonstrate that cytomegalovirus (CMV)-vectored vaccines are unique in their ability to elicit and indefinitely maintain high frequencies of polyfunctional effector memory T cells to heterologous pathogen antigens, including in animals that are already chronically CMV infected. By introducing defined genetic modifications into the CMV backbone it is possible to program CD8+ T cell responses that are either directed to MHC-I, MHC-II or the non-classical MHC-I molecule MHC-E. In progress clinical studies are evaluating CMV-based vaccine immunity in humans as potential vaccines against HIV. To see if the pre-clinical findings could be extended to cancer antigens we inserted known tumor associated antigens (TAA) or viral TAA into genetically modified rhesus CMV (RhCMV) and characterized the T cell response in rhesus macaques. We found T cell responses to all TAA that were comparable to pathogen antigen-specific responses in frequency, duration, phenotype, epitope density and MHC-restriction. Since many of these TAA are expressed in healthy tissue, this suggests that CMV-vectored cancer vaccines are well-suited to overcome immunological tolerance. As such, CMV-based vectors expressing TAAs could be a powerful new tool for cancer immunotherapy. We show that TAA-specific, MHC-E restricted CD8+ T cells from RhCMV/TAA-immunized RM are stimulated by TAA-expressing cancer tissues and cell lines, indicating that cancer cells can present TAA-derived peptides via MHC-E. Since MHC-E is often upregulated in cancer cells to engage the inhibitory NKG2A receptor on tumor-infiltrating T and NK cells, these results suggest that MHC-E could be used as a novel target for T cell-based immunotherapies.
Combination of NKG2A and PD-1 Blockade Improves Radiotherapy Response in Radioresistant Tumors
Authors: Battaglia Nicholas G , Murphy Joseph D , Uccello Taylor P , Hughson Angela , Gavras Nicholas W , Caldon Johnathan J , Gerber Scott A , Lord Edith M 
Published: January 2023

Abstract
Radiotherapy (RT) is commonly employed to treat solid tumors. Immune checkpoint blockade of programmed cell death protein 1 (PD-1) and CTLA-4 improves survival in RT patients, yet many fail to respond to combination therapy. Natural killer group 2 (NKG2) family receptors, particularly inhibitory NKG2A and activating NKG2D, have emerged as promising therapeutic targets to improve antitumor T cell responses; thus, we examined how these receptors and their ligands (Qa-1b and retinoic acid early inducible 1 [Rae-1], respectively) regulate the RT response in C57BL/6 mice bearing syngeneic B16F10 melanoma and MC38 colorectal adenocarcinoma tumors. RT (15 Gy) transiently reduced B16F10 tumor burden, whereas MC38 tumors exhibited durable response to RT. Intratumoral NK and CD8 T cells expressed NKG2A and NKG2D in both models, which was unaltered by RT. In vitro/in vivo RT increased tumor/stromal cell Qa-1b and Rae-1 expression in both models, especially B16F10 tumors, but IFN-γ stimulation induced both Qa-1b and Rae-1 only in B16F10 tumors. NKG2A/Qa-1b inhibition alone did not improve RT response in either model, but combined RT and NKG2A/PD-1 blockade improved survival in the B16F10 model. Depletion experiments indicate that the triple therapy efficacy is CD8 T cell–dependent with negligible NK cell contribution. RNA sequencing of CD8 T cells from triple therapy–treated B16F10 tumors showed increased proliferative capacity compared with RT and PD-1 blockade alone. Our work demonstrates that RT modulates NKG2A ligand expression, which inhibits RT-induced T cell responses in tumors that fail to respond to combined RT and PD-1 blockade. These results provide a rationale for combining NKG2A blockade with immune checkpoint blockade therapies and RT to improve clinical response.
A Rapid Translational Immune Response Program in CD8 Memory T Lymphocytes
Authors: Salloum Darin , Singh Kamini , Davidson Natalie R , Cao Linlin , Kuo David , Sanghvi Viraj R , Jiang Man , Lafoz Maria Tello , Viale Agnes , Ratsch Gunnar , Wendel Hans-Guido 
Published: January 2023

Abstract
The activation of memory T cells is a very rapid and concerted cellular response that requires coordination between cellular processes in different compartments and on different time scales. In this study, we use ribosome profiling and deep RNA sequencing to define the acute mRNA translation changes in CD8 memory T cells following initial activation events. We find that initial translation enables subsequent events of human and mouse T cell activation and expansion. Briefly, early events in the activation of Ag-experienced CD8 T cells are insensitive to transcriptional blockade with actinomycin D, and instead depend on the translation of pre-existing mRNAs and are blocked by cycloheximide. Ribosome profiling identifies ∼92 mRNAs that are recruited into ribosomes following CD8 T cell stimulation. These mRNAs typically have structured GC and pyrimidine-rich 5′ untranslated regions and they encode key regulators of T cell activation and proliferation such as Notch1, Ifngr1, Il2rb, and serine metabolism enzymes Psat1 and Shmt2 (serine hydroxymethyltransferase 2), as well as translation factors eEF1a1 (eukaryotic elongation factor α1) and eEF2 (eukaryotic elongation factor 2). The increased production of receptors of IL-2 and IFN-γ precedes the activation of gene expression and augments cellular signals and T cell activation. Taken together, we identify an early RNA translation program that acts in a feed-forward manner to enable the rapid and dramatic process of CD8 memory T cell expansion and activation.
A Baseline Cellular Antiviral State Is Maintained by cGAS and Its Most Frequent Naturally Occurring Variant rs610913
Authors: Kazmierski Julia , Elsner Carina , Döhner Katinka , Xu Shuting , Ducroux Aurélie , Pott Fabian , Jansen Jenny , Thorball Christian W , Zeymer Ole , Zhou Xiaoyi , Fedorov Roman , Fellay Jacques , Löffler Markus W , Weber Alexander N R , Sodeik Beate , Goffinet Christine 
Published: January 2023

Abstract
Upon recognition of aberrantly located DNA, the innate immune sensor cyclic GMP-AMP synthase (cGAS) activates stimulator of IFN genes (STING)/IFN regulatory factor (IRF)3–driven antiviral responses. In this study, we characterized the ability of a specific variant of the human cGAS-encoding gene MB21D1, rs610913, to alter cGAS-mediated DNA sensing and viral infection. rs610913 is a frequent G&gt;T polymorphism resulting in a P261H exchange in the cGAS protein. Data from the International Collaboration for the Genomics of HIV suggested that rs610913 nominally associates with HIV-1 acquisition in vivo. Molecular modeling of cGAS(P261H) hinted toward the possibility for an additional binding site for a potential cellular cofactor in cGAS dimers. However, cGAS(wild-type [WT]) or cGAS(P261H)-reconstituted THP-1 cGAS knockout cells shared steady-state expression of IFN-stimulated genes, as opposed to cells expressing the enzymatically inactive cGAS(G212A/S213A). Accordingly, cGAS(WT) and cGAS(P261H) cells were less susceptible to lentiviral transduction and infection with HIV-1, HSV-1, and Chikungunya virus as compared with cGAS knockout or cGAS(G212A/S213A) cells. Upon DNA challenge, innate immune activation appeared to be mildly reduced upon expression of cGAS(P261H) compared with cGAS(WT). Finally, DNA challenge of PBMCs from donors homozygously expressing rs610913 provoked a trend toward a slightly reduced type I IFN response as compared with PBMCs from GG donors. Taken together, the steady-state activity of cGAS maintains a baseline antiviral state rendering cells more refractory to IFN-stimulated gene–sensitive viral infections. rs610913 failed to grossly differ phenotypically from the WT gene, suggesting that cGAS(P261H) and WT cGAS share a similar ability to sense viral infections in vivo.
Ornithine Decarboxylase in Gastric Epithelial Cells Promotes the Immunopathogenesis of Helicobacter pylori Infection
Authors: Latour Yvonne L , Sierra Johanna C , McNamara Kara M , Smith Thaddeus M , Luis Paula B , Schneider Claus , Delgado Alberto G , Barry Daniel P , Allaman Margaret M , Calcutt M Wade , Schey Kevin L , Piazuelo M Blanca , Gobert Alain P , Wilson Keith T 
Published: January 2023

Abstract
Colonization by Helicobacter pylori is associated with gastric diseases, ranging from superficial gastritis to more severe pathologies, including intestinal metaplasia and adenocarcinoma. The interplay of the host response and the pathogen affect the outcome of disease. One major component of the mucosal response to H. pylori is the activation of a strong but inefficient immune response that fails to control the infection and frequently causes tissue damage. We have shown that polyamines can regulate H. pylori–induced inflammation. Chemical inhibition of ornithine decarboxylase (ODC), which generates the polyamine putrescine from l-ornithine, reduces gastritis in mice and adenocarcinoma incidence in gerbils infected with H. pylori. However, we have also demonstrated that Odc deletion in myeloid cells enhances M1 macrophage activation and gastritis. Here we used a genetic approach to assess the specific role of gastric epithelial ODC during H. pylori infection. Specific deletion of the gene encoding for ODC in gastric epithelial cells reduces gastritis, attenuates epithelial proliferation, alters the metabolome, and downregulates the expression of immune mediators induced by H. pylori. Inhibition of ODC activity or ODC knockdown in human gastric epithelial cells dampens H. pylori–induced NF-κB activation, CXCL8 mRNA expression, and IL-8 production. Chronic inflammation is a major risk factor for the progression to more severe pathologies associated with H. pylori infection, and we now show that epithelial ODC plays an important role in mediating this inflammatory response.