bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dissecting the roles of CD91 in heat shock protein-mediated cancer immunosurveillance
Authors: Harkness James F , Binder Robert J 
Published: August 2023

Abstract
Our lab has shown that cancer immunosurveillance is dependent on CD91, a receptor for heat shock proteins (HSPs), which is expressed on antigen-presenting cells (APCs). HSP-chaperoned tumor antigens are cross-presented following endocytosis by CD91. Binding of HSPs to CD91 also initiates an intracellular signaling pathway that is poorly understood. Two tyrosine residues on the intracellular domain (β-chain) of CD91 become phosphorylated following HSP binding, leading to downstream activation of NF-kB and STAT1. We found that the immunogenic HSPs differentially utilize these two phosphorylation sites on CD91 for downstream signaling resulting in unique cytokine profiles and co-stimulation capacity. We investigate here the CD91-interacting adaptor proteins and kinases by crosslinking and co-immunoprecipitation of CD91 and its signaling complex following stimulation with each immunogenic HSP (gp96, calreticulin or hsp70). Mass spectrometry studies with gp96 identified the adaptor protein Shc and two other receptor tyrosine kinase associated with CD91. Inhibition of these kinases leads to a significant decrease in gp96-mediated cytokine production. Further work is being done to elucidate the remainder of this signaling network for each HSP and examine any differences between APC types. This project will aid in better understanding of how CD91-mediated signaling differentially activates effector cytokine profiles in APCs. This knowledge can be used in the development of new therapeutic approaches to enhance immunosurveillance of cancers and to better eradicate established disease.
A multiscale mechanistic model of human dendritic cells for in-silico investigation of immune responses and novel therapeutics discovery
Authors: Amin Rada , Aghamiri Sara Sadat , Puniya Bhanwar Lal , Helikar Tomáš 
Published: August 2023

Abstract
Given the critical role of dendritic cells (DCs) in shaping immunity, they present an attractive avenue as a therapeutic target to program the immune system and reverse immune disease disorders. DC-mediated immune response grows into a complex continuum of molecular and cellular networks where each scale decides to be later translated into a seamless phenotype. Computational models open novel frontiers in research by integrating large-scale interaction to interrogate the influence of complex biological behavior across scales. The ability of modeling to digest large amounts of biological networks will likely pave the way to understanding any complex system in more approachable ways. We developed a logical and predictive model of DC function that integrates the heterogeneity of DCs population, APC function, and cell-cell interaction, spanning molecular to population levels. We provided three sample use cases to apply the model in the context of studying cell dynamics and disease environments. First, we characterized the DC molecular response to Sars-Cov-2 and influenza by comparing single to co-infection conditions. The second example presents simulations to predict the crosstalk between DCs and T cells in a cancer microenvironment. Finally, for the third example, we used the Kyoto Encyclopedia of Genes and Genomes enrichment analysis against the model’s components to identify 45 diseases and 24 molecular pathways that the DC model can address. This study presents a resource to decode the complex dynamics underlying DC-derived APC communication and provides a platform for researchers to perform in-silico experiments on human DC for vaccine design, drug discovery, and immunotherapies.
The work was supported by an NIH grant R35GM119770 to Tomáš Helikar
Decrypting pMHCI Diversity Through Noncanonical Translation Initiation
Authors: Rodriguez Jesus Contreras , Esteban Adrian Martin , Peske J David , Shastri Nilabh , Sadegh-Nasseri Scheherazade 
Published: August 2023

Abstract
CD8+ T-cells rely on MHCI to surveil the proteomic state of cells in the form of peptide-MHCI (pMHCI). We previously uncovered a set of ATG-like translation initiation codons that can define noncanonical open reading frames (ORFs) of cryptic peptides presented by MHCI. The model cryptic codon CTG shares key translation initiation requirements with canonical ATG initiation, yet incorporates N-terminal Methionine (nMet) or Leucine (nLeu). We aim to characterize the activity and peptide products of the remaining cryptic codons to understand how cryptic ORFs contribute to the peptidome accessible to MHCI. Therefore, we make use of the subfemtomole sensitivity of the hyperB3Z reporter T-cell hybridoma to interrogate the identity of a modified OVA peptide (SIINFEHL;[SHL8]) reporter in a fixed cryptic initiation context, while retaining information on the residue incorporated during translation initiation. Following transfection of mammalian model cell lines with reporter, purified peptides from total cell extracts are RP-HPLC fractionated to differentiate N-terminally extended and trimmed [SHL8] intermediates. We found that nMet is incorporated by CTG and ACG initiation, while nLeu was absent under CTG initiation despite coexpression of the H2-Db allotype known to protect N-terminally extended [SHL8]. Peptide reporters with a P-2 residue derived from a codon satisfying the optimal (CACCxxx G) Kozak sequence (i.e. G, D) revealed that bulky P-2 residues enhance recovery of total reporter suggesting cryptic ORF peptide stability largely depends on P-2. Thus, by understanding the products of cryptic ORFs we expand the definition of immune-self while exposing new sources of pMHCI unique to autoimmunity and viral pathogens.
Supported by grants from NIH (R01-AI130210, R01-AI121174, R37-AI060040)
Cryptic MHC-E epitope from influenza elicits a potent cytolytic T cell response
Authors: Hogan Michael J , Maheshwari Nikita , Begg Bridget E , Nicastri Annalisa , Muramatsu Hiromi , Pardi Norbert , Miller Michael A , Reilly Shanelle P , Brossay Laurent , Lynch Kristen W , Ternette Nicola , Eisenlohr Laurence C 
Published: August 2023

Abstract
Non-classically-restricted T cells have shown remarkable therapeutic activity in a variety of disease settings; most notably, CD8 T cells restricted to MHC-E (Qa-1 in mice; HLA-E in humans) have proven capable of eliminating a primate lentivirus infection. Here, we used mass spectrometry to identify a Qa-1-restricted 9-mer peptide, named M-SL9, that elicits a strong CD8 T cell response in mice infected with influenza A virus. The M-SL9 specificity accounted for roughly 5–10% of all lung CD8 T cells, approaching the frequency of classically restricted CD8 T cell responses to flu. A broad investigation of the M-SL9-specific T cells showed that they are generally similar in phenotype to classically restricted CD8 T cells, including strong co-expression of type 1-associated cytokines (polyfunctionality) and cytolytic markers; however, M-SL9-specific T cells were unique in that they were anatomically restricted to the lungs and were not present in blood and spleen like other specificities. Intriguingly, the M-SL9 epitope derives from a previously unknown translation product encoded by the +1 alternative reading frame of the matrix 1 (M1) protein-coding sequence. Presentation and immunogenicity of M-SL9 were completely dependent on ribosomal initiation at the second AUG codon of the matrix gene segment. Analysis of potential precursors suggests that M-SL9 is processed from a novel 16-mer peptide that is not required for viral replication in mice. These discoveries imply that unconventional epitopes may drive a large fraction of physiologically relevant T cell responses, and M-SL9 presents a highly tractable system in which to dissect the mechanisms governing MHC-E-restricted T cell responses and their protective effects.
Supported by Cancer Research Institute Irvington Fellowship, Roy and Diana Vagelos Molecular Life Sciences Program and College Alumni Society Research Grant from the Univ. of Pennsylvania, and NIH grants R01 AI146101, R01 AI153064, R01 AI046709-18S1, R01 AI046709, R01 AI125524, and R21 AI153978.
Human versus mouse Beta 2 microglobulin alters TCR antigen recognition kinetics with mouse MHCI
Authors: Rase Viva Jeanne , Kolawole Elizabeth M , Liu Baoyu , Ayres Cory M , Rogers Jhordan , Salaita Khalid , Baker Brian M , Evavold Brian D 
Published: August 2023

Abstract
There are three isoforms of Beta2 microglobulin (B2m) identified in mice and they differ by a single amino acid residue. To study how B2m can modify the peptide binding pocket of MHCI we turned to the comparison of mouse (mB2m) and human (hB2m). It is known that hB2m forms more stable with mouse MHCI heavy chain as compared to mb2m and hB2m is often the choice for most pMHCI tetramer production. Analysis of mB2m and hB2m tetramer (GP33 41M) following LCMV infection revealed no difference in percentage of tetramer positive cells but an increase was observed in staining intensity (MFI) of hB2m. Using steered molecular dynamics we found that there were allosteric effects with mB2m displaying more movement within the binding pocket than hB2m. Consistent with this we saw increased 2D affinity for antigen MHC Db and Kb hB2m complexes for OT1 and P14 TCRs, respectively. We also measured the force effects on bond lifetime between TCR and pMHC using biomembrane force probe (BFP) and DNA tension sensor. For OTI, we found that mB2m complexes had a longer bond lifetime measured by both methods. We observed signaling and functional effects consistent with the 2D affinity and bond lifetime measurements in mouse verses human B2m. For example, mB2m leads to increased levels of activated LCK (pY394/505) in OT1 T cells. Therefore, alterations in B2m effect the distal peptide binding domain of MHCI and suggests dynamic allostery may influence antigen recognition by TCR.
5T32NS115664-03 5R01AI147641-03
4-1BB costimulation following mRNA vaccination improves CD8 T cell responses
Authors: Sanchez Sarah , Penaloza-MacMaster Pablo 
Published: August 2023

Abstract
mRNA vaccines have received full FDA approval to prevent COVID-19, and are being explored for multiple infectious diseases as well as cancer. While they have shown high efficacy at preventing severe disease caused by SARS-CoV-2, waning immunity has motivated the development of improved mRNA vaccine regimens. 4-1BB (also known as CD137) is a costimulatory receptor that has been shown to be important for T cell responses following viral infections and cancer. We asked whether triggering 4-1BB costimulation with agonistic antibodies could improve immune responses elicited by mRNA vaccines in C57BL/6 mice. Here, we show that triggering 4-1BB costimulation at the time of mRNA vaccination impairs CD8 T cell responses, whereas triggering 4-1BB costimulation after day 4 of mRNA vaccination improves CD8 T cell immune responses. These data demonstrate time-dependent effects of 4-1BB costimulation on cellular responses elicited by mRNA vaccines, and suggest that delayed provision of 4-1BB costimulation could offer immunologic benefits following mRNA vaccination.
This work was supported by a DP2 New Innovator Award to P.P.M.
This work was supported by a DP2 New Innovator Award to P.P.M.
Calibrating T cell help by antigen cross-linking as a universal vaccine platform against rapidly evolving pathogenic viruses
Authors: Mallajosyula Vamsee , Chakraborty Saborni , Sola Elsa , Gao Fei , Wang Taia , Davis Mark M 
Published: August 2023

Abstract
The effectiveness of influenza vaccine is limited by the heterogeneous immune response it elicits. Factors such as age, sex, and pre-existing antibody titers only partially explain this heterogeneity. Using a novel deconvolution analysis we find subtype-specific bias as a major source of this inter-individual variation. Since the 1940’s it has been proposed that this phenomenon is due to prior strain exposure, referred to as “Original Antigenic Sin”. But our analysis of flu vaccine responses in a monozygotic twin cohort showed that antigenic imprinting from past exposures can only partially explain strain preference (r2=0.25, p=4.7×10−5). Thus, we hypothesized that host genetics may play a major role in subtype-bias. Consistent with this is our finding that strain-preferences are evident after vaccination in an influenza naïve infant cohort indicating that prior exposure is not essential. We determined the source of this genetic component to the wide variation in influenza hemagglutinin peptide presentation by different HLA class-II alleles resulting in an imbalanced, subtype-specific CD4+ T follicular help after vaccination. To address this, we developed a tunable, plug-and-play vaccine platform to better calibrate T cell help. In a human tonsil organoid system, we demonstrated that engineered, cross-linked HA induces a significantly higher response against multiple influenza subtypes in comparison to the inactivated influenza vaccine. In summary, we have developed an effective strategy to overcome response bias in a population with diverse genetic backgrounds and pre-existing immunity. Furthermore, we successfully adapted this platform to generate a pan-coronavirus vaccine.
Supported by grants from NIH to MMD (5U19AI090019, 5U19AI057229). Additional support was provided by ITI-YIA to VM.
Therapeutic anti-glycan antibodies against antibiotic resistant Staphylococcus aureus
Authors: Nagy Kenna K , Kain Lisa , Stanfield Robyn , Grimes Catherine , Wilson Ian A , Savage Paul B , Finn M G , Teyton Luc 
Published: August 2023

Abstract
Antibiotic resistance threatens clinical control of bacterial infections while the genetic adaptability of microbes continues to outpace small-molecule development. The combinatorial diversity of antibodies offers a solution to this problem. However, under normal circumstances the polymeric glycans of bacterial surfaces avoid adaptive recognition by not binding to MHC molecules. Thus, they are T cell independent antigens and targeted only by low affinity IgM responses. Glycoconjugate vaccines have been developed to provide bystander T cell help to overcome this limitation but have failed to elicit protective responses against antibiotic resistant Staphylococcus aureus in clinical trials. To address limitations in current conjugate vaccine approaches, we optimized anti-glycan B cell help through three convergent prongs: exploiting cognate T cell help, using a B cell-centric adjuvant, and using synthetic minimal glycans. This prototype next generation conjugate vaccine was used to produce nanomolar affinity anti-glycan responses in proof-of-concept studies. Focusing on antibiotic resistant Staphylococcus aureus three glycan targets of the cell wall and bacterial capsule have been selected and used to produce monoclonal antibodies. These antibodies were characterized structurally, biophysically, and by B cell sequencing to confirm high affinity, maturation, and specificity towards the intended targets. The potential therapeutic benefits are currently being tested in three preclinical mouse models: skin, lung, and systemic infection, using passive and active immunization. Preliminary studies have shown therapeutic efficacy in both a preventative and interventional model for some of these antibodies.
Kenna Nagy supported by: NIH TL1TR002551 For this project P.I. Luc Teyton supported by: NIH U01 AI160338, NIH R01 AI139748
Phenotypic analysis of HIV-1 resistance to CD4 binding site broadly-neutralizing antibodies
Authors: Shrader Hannah , Hait Sabrina Helmold , Lovelace Sarah , Kilner Meaghan , Shen Chen-Hsiang , Coates Emily , Gaudinski Martin , Rothwell Ro Shauna , Donaghy Eileen , Roa Jhoanna , Fichtenbaum Carl , Santana Jorge , Presti Rachel M , Bhatnager Anjali , Lynch Rebecca , Tebas Pablo , Ledgerwood Julie , Mascola John , Koup Richard , Pegu Amarendra 
Published: August 2023

Abstract
Broadly neutralizing antibodies (bNAbs) show strong immunotherapy potential by targeting conserved regions of the HIV-1 envelope. Single bNAb use in viremic individuals quickly results in the emergence of escape variants, likely originating from existing quasispecies. An ex vivo assay was developed to predict bNAb efficacy in viremic individuals. The development of a predictive bNAb efficacy model may assist with the planning of future clinical trials.
The ex vivo assay used pre-infusion CD4+ T cells from participants enrolled in the VRC 607/ACTG A5378 phase I study of the CD4 binding site (CD4bs) bNAbs’ VRC01LS (n=7) or VRC07-523LS (n=9). From these assays, the escape variant signatures of outgrowth viruses that replicated in presence of CD4bs bNAbs, were identified. We found that these escape variants contained key changes to the ß23-V5 region of the gp120 envelope, including charge changes, glycan loss, and/or glycan shifts. Outgrowth viruses from each participant had similar escape mutation patterns. Resistance mutations of the viral env sequences were confirmed in pseudovirus-based neutralization assays.
We found complementary escape profiles from 3 CD4bs bNAbs (1–18LS, N6LS, and VRC01v23) with ex vivo and neutralization assays showing suppression by 1 or 2 but not all 3 bNAbs, supporting the potential for combination bNAb therapy. Our data suggest that the simultaneous use of multiple CD4 binding site bNAbs together could aid in limiting viral escape.
Supported by intramural funds from NIH.
Modulating Innate Immune Responses for Improved Vaccine Tolerability and Durability
Authors: Esser-Kahn Aaron P , Rosenberger Matthew Glenn , Kim Jeremiah 
Published: August 2023

Abstract
Stimulation of the innate immune system is crucial in both effective vaccinations and immunotherapies. This is often achieved through adjuvants, molecules that usually activate pattern recognition receptors (PRRs) and stimulate two innate immune signaling pathways: the nuclear factor kappa-light-chain-enhancer of activated B-cells pathway (NF-κB) and the interferon regulatory factors pathway (IRF). Here, we demonstrate the ability to alter and improve adjuvant activity via the addition of small molecule “immunomodulators”. By modulating signaling activity instead of receptor binding, these molecules allow the customization of select innate responses. We demonstrate both inhibition and enhancement of the products of the NF-κB and IRF pathways by several orders of magnitude. Some modulators apply generally across many receptors, while others focus specifically on individual receptors. Modulators boost correlates of a protective immune responses in a commercial flu vaccine model and reduced correlates of reactogenicity in a typhoid vaccine model. These modulators have a range of applications: from adjuvanticity in prophylactics to enhancement of immunotherapy.
NIH 75N93019C00041
Innate Immune Memory for Improved Vaccine Response
Authors: Esser-Kahn Aaron P 
Published: August 2023

Abstract
Emerging diseases require generating new vaccines, which can often be time-consuming. An alternate method to boost host defense is by inducing nonspecific innate immune memory, called trained immunity, to develop novel prophylactics. Many molecules, most notably β-glucan, induce trained immunity, but their effects are often short-lived and uncontrolled. This lack of temporal control limits both the therapeutic ability of training and provides fundamental questions about its nature. To improve on the capabilities of β-glucan, we developed a method for temporal control of trained immunity and examined its use both as a prophylactic and as an additive for improve vaccine outcomes. We engineered controlled release nanoparticles encapsulating only 3.5% the standard dose of β-glucan to attain sustained release over a month. Nanoparticle trained mice exhibited prolonged training effects and improved resistance to a B16F10 tumor challenge compared to mice that received an equivalent amount of free β-glucan. We also showed that trained mice exhibited higher antibody responses upon vaccination. These results demonstrate that dosing and temporal control can substantially alter the trained response to unanticipated levels. As such, this approach using sustained release platforms might lead to a novel prophylactic strategy for improved disease resistance against a wide variety of diseases.
HDTRA11810052
Intranasal delivery of adenovirus-vectored vaccine confers protective mucosal immunity against SARS-CoV-2
Authors: Jung Hi Eun , Ku Keun Bon , Kang Byeong Hoon , Kim Kyun-Do , Lee Heung Kyu 
Published: August 2023

Abstract
The ongoing pandemic of COVID-19, caused by SARS-CoV-2 infection, has threatened the global health. Since the first case of infection was reported in December 2019, SARS-CoV-2 has rapidly spread all over the world and caused millions of deaths. As vaccination is the best way to protect the host from invading pathogens, several vaccines have been developed to prevent the infection of SARS-CoV-2 and saved huge numbers of lives so far. However, SARS-CoV-2 constantly change their antigens resulting in the escape from vaccine-induced protection, and the persistence of immunity induced by vaccine becomes an issue. Further, traditional intramuscular COVID-19 vaccines are insufficient to evoke mucosal specific immune response. Because the respiratory tract is the primary route of SARS-CoV-2 entry, the need for mucosal vaccine has been strongly suggested. Using adenoviral (Ad) vector platform, we generated recombinant COVID-19 vaccines that encode modified-spike antigen, and evaluated the vaccine efficacy in murine models. We found that intranasal delivery of Ad-vectored vaccines elicited both systemic as well as mucosal immune responses, and rescued mice from lethal SARS-CoV-2 infection. Further, we revealed that intranasal vaccination of Ad-vectored vaccines changed transcriptional landscape of lung. These results indicate that our recombinant Ad-vectored vaccine has the potential to confer protective immunity against SARS-CoV-2.
This study was supported by the National Research Foundation of Korea (NRF-2021M3A9D3026428 and NRF-2021M3A9H3015688) funded by the Ministry of Science and ICT of Korea. This work was also supported by Mobile Clinic Module Project funded by KAIST and the 2020 Joint Research Project of Institutes of Science and Technology. H.E. Jung was supported by Basic Science Research Program through the NRF funded by the Ministry of Education (2022R1I1A1A01071399)
Booster mRNA vaccination post-SARS-CoV-2 infection enhances functional qualities of T cell immunity
Authors: Cai Curtis , Gao Yu , Olsson Annika , Sette Alessandro , Wherry E John , Aleman Soo , Buggert Marcus 
Published: August 2023

Abstract
T cells are critical to generate protection from severe respiratory viral disease. Whether repeated SARS-CoV-2 antigen exposure through vaccination causes T cell exhaustion or gain of functions remains debated. In this study, we sampled SARS-CoV-2 convalescent donors before and after vaccination to determine the functional consequences of hybrid immunity. Donors were sampled at 6 months and 18 months convalescence and divided according to their history of mild or severe/hospitalized disease (n = 44 and 45 respectively). In between the two sampling timepoints, donors also received mRNA vaccination through the national COVID-19 vaccination program. Using activation-induced marker assays, intracellular cytokine staining, single-cell transcriptomics and single-cell T-cell receptor sequencing analyses, we show that spike-specific T cells increase in magnitude but, importantly, also gain highly functional characteristics. By contrast, T cell responses to non-spike proteins were diminished or remained unchanged. Elevated interferon-gamma expression was a common hallmark of CD4+ and CD8+ T cells post-mRNA-vaccination. These responses were founded on both pre-expanded and newly detected CD8+ T cell clones after vaccination. Collectively, these data demonstrate the cumulative benefits of booster vaccinations, leading to increased quantity and quality of cell-mediated immunity.
Supported by a grant from Karolinska Institutet Research foundation grants (2022-01708)