bluuebunny/crossref_metadata_2025_split huggingface dataset:
Natural infection with SARS-CoV-2 generates durable Spike S1 Receptor-Binding-Domain-specific memory B cell and neutralizing antibody responses.
Authors: Mishra Pankaj Kumar , Bruiners Natalie , Ukey Rahul , Datta Pratik , Onyuka Alberta , Handler Deborah , Singh Sukhwinder , Honnen William , Chang Theresa Li-Yun , Pinter Abraham , Gennaro Maria L 
Published: February 2023

Abstract
Since human infection with coronavirus SARS-CoV-2 was first detected in December 2019, we are still developing an understanding of the nature and duration of protection against this infection. Most neutralizing antibodies, which are a key component of the protective response against SARS-CoV-2 infection, target the Receptor Binding Domain (RBD) of the Spike glycoprotein and critically prevent binding of the virus to the host cell receptor, and viral entry. Thus, it is of vital importance to monitor the presence of neutralizing antibodies and RBD-specific B cells that are key for rapid production of protective antibodies upon reinfection with SARS-COV2 infection. In this study, we developed a multicolor flow cytometric assay to enumerate the RBD-specific memory B cell and memory B cell subsets. We collected peripheral blood cells and plasma from 22 subjects 1–2 months since COVID-19 diagnosis (early time point - ET) and then again after 5–7 months (late time point – LT). Comparing the data collected from these two time points, we observed a significant decrease in plasma blasts and double-negative memory B cell and an increase in the IgG+ switched-memory B cells and decrease in the IgM+ switched-memory B cells at LT relative to ET. We concurrently observed a trend toward decreased anti-RBD IgG titers over time. When we tested plasma neutralizing activity employing ACE2-expressing HeLa cell lines infected with mNeonGreen(mNG)SARS-CoV-2, we also observed reduced neutralizing antibody titers over time. Thus, a correlation exists between titers of RBD-specific IgG antibody and neutralizing titers. In addition, the presence of RBD-specific B-cell memory in circulating blood is a strong indication of a durable protective response.
Anti-pseudomonas antibodies contribute to lung disease in cystic fibrosis.
Authors: Lu Shiping , Bomberger Jennifer , Kolls Jay K 
Published: February 2023

Abstract
Cystic fibrosis (CF) is an inherited lethal disease caused by mutations in CFTR. Approximately 60% of patients have homozygous F508del mutation, but their lung function is quite variable. Gene modifier studies identified I MHC II alleles are associated with the age of first Pseudomonas aeruginosa (PA) infection and lung function. Thus, we assessed serological responses to PA among CF subjects with poor lung function (FEV1&lt;70%) versus good lung function (FEV1&gt;90%). Immunoprecipitation-proteomics using outer membrane proteins (OMPs) from PA and human serum identified OprI as a potential important B cell antigen. We found increased anti-mucoid PA antibodies in CF and higher titers against OMPs and recombinant OprI in patients with poor lung function. Mice that were immunized with either recombinant OprI or inactivated whole PA subcutaneously developed high IgG titers in serum. Immunized mice that were challenged with mucoid PA had more weight loss and more severe lung pathology compared to unimmunized controls. There was minimal weight loss in PA immunized Rag2KO mice (impaired T and B cells), suggesting a role of adaptive immunity in the pathology. We observed more sensitive responses in FABP-hCFTR mice (CFTR knockout except GI tract) that OprI-immunized group exhibited the highest anti-OprI IgG titer and the most significant weight loss after challenge. These data suggest that one mechanism by which class II MHC is a modifier gene in CF is through antigen presentation and determining the types of anti-PA antibodies are generated in CF. Anti-PA antibodies may contribute to CF lung disease that we are conducting systems serology studies to understand which antibody functions are exacerbating disease.
Screening immunotherapy cancer drugs in a scalable, physiologically relevant 3D in vitro tumor microenvironment model
Authors: Chiovaro Francesca , Strebel Silvan , Wolf Armin , Moritz Wolfgang , Agarkova Irina 
Published: February 2023

Abstract
Interaction of tumor cells with surrounding stromal and immune cells, secreted cytokines, and extracellular matrix proteins, collectively known as the tumor microenvironment (TME), is crucial for cancer progression and metastasis. Here, we present a novel 3D in vitro TME model to assess candidate drugs for cancer therapy.
For this study, we prepared lung carcinoma spheroids from GFP-A549 cells co-cultured with cancer-associated fibroblasts (CAFs) and PBMCs. To simulate a pro-inflammatory tumor microenvironment, we activated PBMCs with cytokines and/or anti-CD3/CD28. We assessed the effect of PD-1 inhibitors in combination with cytokines for potential synergistic anti-cancer effects. We then developed a tumor model using melanoma PDX cells labeled with CellTracker to monitor tumor cell viability after exposure to activated PBMCs. We evaluated killing activity and effector function of T cells by measuring tumor microtissue size by automatic stage fluorescence microscopy and release of IL-6, TNFa, IFNγ and GM-CSF with a MAGPIXTM Luminex system over time. Immune cell infiltration and its effects on tumor were assessed by histological analysis using tumor, immune cell and apoptosis markers.
Our results show combination treatment with cytokines and anti-PD-1 antibody led to higher secretion of IL-6/TNFa/IFNγ/GM-CSF, reduced tumor size, increased infiltration of the model by CD8+ T cells, stronger expression of Granzyme B resulting in enhanced tumor apoptosis and killing. This confirms our novel 3D in vitro TME model is a promising tool for studying cell-cell interactions and allows for HCS of novel candidates for anti-cancer drugs.
The clinical considerations for early cancer detection using ctDNA within the Pacific setting
Authors: Sika-Paotonu Dianne , Walton Mischa , Finau Eseta , Faavae Sepola , Vaimoli Jessica , Guilford Parry 
Published: February 2023

Abstract
Pacific Peoples living in Aotearoa/New Zealand and in the Pacific Region, remain disproportionately affected by some cancers. In addition to ensuring effective treatments and therapies are available and continue to improve, continued early cancer diagnostic efforts are also critical for supporting better health outcomes for Pacific Peoples within the cancer setting. A novel and promising early cancer detection method known as circulating tumour DNA (ctDNA) analyses small fragments of tumour DNA found in the blood circulation to provide information about a tumour. This approach is more commonly associated with and utilised for monitoring patients being treated for their cancers and is being adapted to support early cancer detection efforts. To support the possible acceptability of this approach for early cancer diagnosis for Pacific Peoples, it is imperative to better understand the clinical considerations relevant to the Pacific setting. To identify the clinical considerations needed for early cancer detection with ctDNA approaches within the Pacific setting for Pacific Peoples living in Aotearoa/New Zealand, researchers and Pacific Health Professionals were consulted. Relevant considerations included the immediate need to support early cancer diagnostic efforts to avoid late presentations, better understanding of the cultural context for Pacific Peoples within the healthcare setting more broadly, with strong support expressed for a simple approach for early cancer detection such as that being proposed with ctDNA technology. These findings highlight the critical need to consider the clinical context within the cancer setting for Pacific Peoples.
Health Research Council of New Zealand
Control of antigen-mediated proliferation and activation of CD4+ T cells by the RNA binding protein HuR
Authors: Ellis Jason S , Fattahi Fatemeh , Atasoy Ulus 
Published: February 2023

Abstract
The RNA binding protein HuR (elavl1) stabilizes target mRNAs and aids in their transport to the heavy polysomes, ultimately resulting in increased protein expression. We have previously shown that HuR plays a critical role in T helper cell fate decisions, with HuR deficient mice having significant impairment in Th2 differentiation. Interestingly, HuR deficiency also leads to large increases in IL-2 production. We hypothesized that HuR is important for normal T cell activation and expansion. To investigate this, we used mouse models in which HuR was conditionally ablated during T cell development either early at the double positive stage (CD4-Cre ROSA HuRfl/fl) or late (distal Lck-Cre ROSA HuRfl/fl). Upon activation in vitro, HuR KO T cells had significant reductions in CD25 (IL-2Ra) protein and RNA. An in vivo OVA challenge model was used to determine ascertain the effects of HuR KO on airway inflammation. Despite only half of CD4+ T cells in dLck-Cre HuR KO mice lacking HuR, there was a significant decrease in total inflammation, with essentially no T cell infiltrate. These mice also had significantly reduced BAL IL-13. Furthermore, mice were immunized with either OVA or KLH, boosted 10 days later, and antigen specific proliferative responses measured in vitro. T cells lacking HuR had profound proliferation defects compared to control cells, regardless of the antigen system employed. Interestingly, non-specific CD3/CD28 stimulation only partially restored these proliferative defects. RNA-Seq analysis of activated HuR deficient T cells indicated altered expression in multiple genes associated with T cell activation and function. We conclude HuR function is vital for normal antigen-specific activation and proliferation in CD4+ T cells.
Profiling CIS progression and stability using RNA-seq single-cell analysis in peripheral blood mononuclear cells
Authors: Giarraputo James , Jain Vaibhav , Arvai Stephanie , Smilek Dawn E , Harris Kristina M , Gregory Simon 
Published: February 2023

Abstract

Objective:
To use single-cell mRNA analyses to identify immune cell profiles in CIS patients associated with a higher risk of developing an MS relapse or new central nervous system (CNS) disease activity on brain MRI.

Methods:
Cryopreserved peripheral blood mononuclear cells were collected at study entry and six months from six CIS participants in the ITN020AI STAyCIS trial of atorvastatin. Three participants met the primary endpoint defined as ≥ 3 new T2 lesions on MRI or an MS relapse within 12 months, while the other three did not. RNA from about 10,000 PBMC per sample were identified at the single-cell level using the 10X Genomics Chromium platform and analyzed using Cell Ranger software. Seurat R software package was used for downstream analysis.

Results:
31 clusters of differentially expressed genes were assigned as specific cell types; baseline frequencies of clusters enriched &gt;2-fold for macrophage, NK, NKT, CD4+ T cell, and B cell markers were associated with disparate outcomes at six months. Several clusters of B cells, CD4+ and CD8+ T cells were expanded from baseline at six months in participants with CNS disease activity at that time point, while no notable changes were observed in those with stable disease.

Conclusion:
Our results show varied frequencies of innate and adaptive leukocyte populations in participants with disparate clinical outcomes, suggesting a predictive biomarker for aggressive early intervention. Expanded clusters of CD4+ and CD8+ T cells and B cells in blood at the time of disease activity may identify biomarkers leading to acute demyelination. Follow-up studies are underway to increase sample size and incorporate protein data to better define cell subtypes associated with disparate outcomes in the STAyCIS trial.
Analysis of immunogenic cell death in the tumor microenvironment of tumor spheroids
Authors: Demuynck Robin , Efimova Iuliia , Krysko Olga , Declercq Heidi , Krysko Dmitri 
Published: February 2023

Abstract
The failure of drug efficacy in clinical trials remains a big issue in cancer research. This is largely due to the limitations of two-dimensional (2D) cell cultures, the most used tool in drug screening. Nowadays, three-dimensional (3D) cultures, including spheroids, are acknowledged to be a better model of the in vivo environment. Immunogenic cell death (ICD) has the potential to be exploited in immunotherapy by activating the host’s own immune system against the cancerous cells, but analysis of ICD induction (including ferroptosis) in 3D cultures has not been performed so far. In this work, we have optimized cell death induction in tumor spheroids. Our cell death analysis method (3DELTA) uses Sytox dyes as a cell death marker and Triton X-100, which efficiently permeabilizes all cells in spheroids, was used to establish 100% cell death. The 3DELTA method was able to detect cell death type without the need to disaggregate spheroids. Moreover, in this work we also demonstrated that 2D experiments cannot be extrapolated to 3D cultures as 3D cultures are less sensitive to cell death induction. Ferroptotic cell death induction in spheroids lead to 50% of cell death whereas in 2D cultures, this caused 90% of cell death. The tumor microenvironment is an important factor that can affect the outcome of anti-cancer therapy. By adding endothelial cells (EC) to cancer cells (CC) in an optimized ratio (EC:CC), we were able to form vascularized spheroids. In conclusion, these spheroids will be a more relevant model for in vivo tumors by analyzing interactions between the different cell types and can be further used for analysis of their immunogenic potential.
IL-33 activates mTOCR1 and modulates glycolytic metabolism in CD8+ T cells
Authors: Wang Xiaofang , liang Yuejin , Sun Jiaren 
Published: February 2023

Abstract
Interleukin (IL)-33, a member of cytokines in the IL-1 family, plays a central role in innate and adaptive immunity. However, the underlying mechanism of IL-33-mediated T cell regulation and the associated downstream signals remain elusive. In this study, we found the increased IL-33 expression in T cells following cell activation. However, extracellular, but not nuclear IL-33 contribute to effector CD8+ T cell activation and proliferation. IL-33 not only induced its receptor ST2 expression, but also up-regulated GATA3 and T-bet levels in CD8+ T cells. Importantly, IL-33 induced mTORC1 activation in CD8+ T cells as evidenced by increased p-S6 levels both in vitro and in vivo. Meanwhile, this IL-33-induced T cell activation was suppressed by mTORC1 inhibitor rapamycin. Move over, IL-33 elevated glucose uptake and lactate production in CD8+ T cells in a dose- and time-dependent manners. Our mechanistic study further revealed that IL-33 was capable of promoting the expression of glucose transporter and glycolytic enzymes via mTORC1, leading to accelerated aerobic glucose metabolism and increased effector T cell activation. Together, our data provide a new insight into IL-33-mediated regulation of T cells, and might be beneficial for therapeutic strategies of inflammatory and infectious diseases in future.
Tropomyosins are critical mediators of CD8+ T cell synaptic actomyosin organization.
Authors: Schrock Dillon C 
Published: February 2023

Abstract
CD8+ T cells are a critical arm of the adaptive immune system because they kill virally-infected and transformed cells. Their function is critically dependent on their ability to form stable interactions with antigen-presenting cells (APCs). These interactions are mediated by a highly-organized structure at the T cell: APC interface termed the immunological synapse (IS). The IS itself is organized largely by the underlying actin cytoskeleton. Perturbation of either the Arp2/3-dependent branched network of the distal region or of the formin-derived arc network of the peripheral region dampens TCR signaling and impairs subsequent T cell activation. Tropomyosins are actin-binding proteins that form head-to-tail polymers along the actin filament. Several tropomyosin isoforms associate preferentially with linear formin-generated filaments, such as those in the peripheral region of the IS, where they promote the recruitment and activation of myosin 2 and thwart cofilin-mediated severing. We have found that mouse CD8+ T cells express two prominent tropomyosin isoforms (Tpm3.1 and Tpm4.2) and that these isoforms are strongly upregulated following naïve cell activation. Interestingly, both of these isoforms have been associated with human pathology in proteomics experiments. Fluorescent-tagged versions of these tropomyosins colocalize with pSMAC actomyosin arcs and migrate toward the center of the IS. Importantly, treatment with an inhibitor of Tpm3.1, ATM3507, severely impacts the organization of T cell synaptic actin structures. Our aim is to examine the role that tropomyosins play in the organization of T cell synaptic actin and actomyosin structures and to determine their importance for effector function.
Determining the impact of HLA type and chronic viral infection on peripheral T-cell receptor sharing between unrelated individuals
Authors: Johnson Sarah , Seale Spencer , Gittelman Rachel M , Sanders Catherine M , Robins Harlan , Fields Paul 
Published: February 2023

Abstract
T cells generate highly diverse T-cell receptors (TCRs) to recognize antigens, most of which are private to a given individual. TCRs with low junctional complexity have a higher likelihood of being generated and thus shared across multiple individuals. Additional factors that may further limit diversity and increase the likelihood that particular TCRs are public include: (a) thymus selection for maturation of TCRs that bind antigens presented by an individual’s human leukocyte antigen (HLA) proteins, and (b) T-cell proliferation upon exposure to cognate antigens, which remain within the periphery as memory T cells. Numerous public TCRs have been associated with particular HLA restrictions and antigen specificities1,2. Chowell et al. also recently showed that HLA diversity is important for mounting an effective T-cell response against solid tumors3. However, little is known about the overall impact of these forces on the diversity of the T-cell repertoire and the expected TCR sharing across individuals. Here, we leverage the TCR repertoires of 666 healthy individuals sequenced with the immunoSEQ® Assay (Adaptive Biotechnologies, Seattle, WA) to address these questions. We investigate (a) how the similarity of HLA alleles between individuals impacts the number of TCRs shared between individuals and (b) the impact of shared antigen exposure by determining how age and CMV status impacts clone sharing between individuals. These data show that HLA type, age, and CMV exposure shape the immune repertoire and influence the sharing of clones between unrelated individuals.
Tlr3 interacts with ESCRT-I components Tsg101 and Hcrp1 in mouse astrocyte cell line
Authors: Mielcarska Matylda Barbara , Struzik Justyna , Toka Felix Ngosa 
Published: February 2023

Abstract
It is established now that ESCRT (endosomal sorting complex required for transport) complexes participate in the trafficking of endosomal Toll-like receptors (TLRs), which are relevant in the regulation of the TLR-mediated immune response. TLR3 plays a vital role in the innate immune control of herpes simplex type 1 virus (HSV-1) infection in the brain, however, the process of TLR3 delivery to the ligand recognition site and fate as endosomal cargo including the receptor degradation await explication. Proximity ligation assays in TLR3 agonist, poly(I:C) stimulated or unstimulated murine astrocytes, confirmed the association of Tlr3 with Tsg101 and Hcrp1, ESCRT-I subunits essential for the lysosomal sorting of ubiquitinated membrane receptors. The interaction of Tlr3 and ESCRT-I components was prominent in the first hour and 24 h after poly(I:C) addition. TLR3 was highly ubiquitinated in cells at all studied times, while the interaction of Hrs, a core component of ESCRT-0 and ESCRT-I, and Tlr3, as well as Hrs and Tsg101, and Hrs and Hcrp1, increased in the first hour of stimulation, but 24 h following stimulation returned to levels observed in unstimulated cells. Results suggest a possible role of ESCRT-I in prolongation of TLR3 signaling and/or receptor degradation, prompting investigation whether Tsg101 and Hcrp1 influence Tlr3 transportation in cells of the central nervous system, which would portray ESCRT-I as a possible modulation target regarding TLR3-mediated antiviral response in the brain.
The leaked mitochondrial C1QBP inhibits activation of the DNA sensor cGAS
Authors: Song Kun , Wu Yakun , Fu Bishi , Wang Lingyan , Hao Wenzhuo , Hua Fang , Sun Yiwen , Dorf Martin E , Li Shitao 
Published: February 2023

Abstract
Cytosolic DNA released from microbial pathogens triggers the activation of DNA sensor cyclic GMP-AMP synthase (cGAS) which catalyzes the synthesis of the cyclic GMP-AMP (cGAMP), a second messenger that triggers a signaling cascade leading to type I interferon (IFN) production. The cGAS cannot discriminate the origin and sequence of dsDNA; thus, it is also activated by self-DNA leaked from the nucleus or the mitochondria. Recent studies have shown that DNA virus infection triggers mitochondrial stress, leading to the release of mtDNA to the cytosol and activation of cGAS; however, the regulatory mechanism of the mtDNA-mediated cGAS activation is not well elucidated. To seek potential regulators for cGAS, we used proteomics to map the protein interactome of cGAS in macrophages and found C1QBP as a novel binding partner of cGAS. C1QBP is predominantly localized in the mitochondria matrix and leaked to the cytosol upon DNA virus infection. C1QBP binds to the NTase domain of cGAS and inhibits the cGAS activity in cells and in vitro. Overexpression of the cytosolic form of C1QBP inhibited the cytosolic DNA-induced immune response and facilitated HSV-1 infection. By contrast, deficiency of C1QBP leads to elevated innate immune responses and impaired HSV-1 infection. Taken together, our study suggests that C1QBP is a cGAS inhibitor hidden in the mitochondria.
Distinct type I interferon (IFN) signaling is involved in damage and fungal clearance during Aspergillus pulmonary infection
Authors: Shepardson Kelly , Roemer Julia , Robinson Ema , Johns Laura L , Hall Monica , Rynda-Apple Agnieszka 
Published: February 2023

Abstract
Human fungal infections with Aspergillus fumigatus (Af) are becoming more prevalent. Over 4 million cases of Af occur globally, with 300,000 cases/year due to invasive pulmonary aspergillosis in immune suppressed patients. Recent increases in number/severity of cases of influenza and SARS-CoV-2-infected patients acquiring Af suggests that viral infections create suppressed immune environments permissive to fungal infection. Influenza infection was also shown to increase Af susceptibility in mice and was associated with anti-viral type I interferon (IFN) signaling. Importantly, we found that type I IFN signaling, via IFNAR2 of the IFNAR1/2 receptor, contributes to regulation of susceptibility to and damage from influenza in mice, while others have found that IFNAR2 expression correlates with SARS-CoV-2 infection severity. As clinical outcome to Af is associated with host tissue damage, this suggested involvement of IFNAR2 signaling in Af susceptibility. We found that absence of IFNAR2 (Ifnar2−/− mice) resulted in increased damage in the lungs (from myeloid and epithelial/endothelial cells), morbidity, and inflammation in response to Af, while absence of IFNAR1 (Ifnar1−/− mice) did not. We also found that Ifnar2−/− mice developed invasive disease with increased hyphal growth compared to Ifnar1−/− and WT mice and this was associated with epithelial/endothelial damage. Our results also indicate that altered myeloid cell function in Ifnar2−/− mice, rather than differences in cell recruitment, may enhance damage responses and fungal growth. Together, our results begin to establish IFNAR2’s role in regulating host damage responses to Af and suggest that aberrant type I IFN signaling contributes to an Af permissive environment.