bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating plasma antibody repertoires in breast cancer patients with progesterone receptor positive and negative tumors
Authors: Chapoval Andrei I , Podlesnykh Stepan V , Kolosova Eugenia A , Koltysheva Polina I , Tishchenko Ekaterina D , Shoikhet Yakov N , Lazarev Aleksandr F , Johnston Stephen Albert 
Published: January 2023

Abstract
Breast cancer is the most frequently diagnosed cancer and the leading cause of cancer death in females worldwide. Early cancer detection and tumors molecular characterization are the key measures for effective therapy. Molecular changes associated with tumor development are detected by the immune system and reflected with specific antibody production. We used microarrays containing 120K of peptides with random amino acid sequences to analyze the repertoire of circulating antibodies in the blood plasma of patients with early stages of breast cancer (BC). Previously we have shown that healthy donors and BC patients have distinct circulating antibody repertoires. Further analysis reviled that BC patients with various progesterone receptor (PR) expression levels also have circulating antibodies reacting with different peptides (mimotopes) on microarrays. In this study we selected 61 peptides from 120K peptides presented on microarrays that show statistically significant difference for the interaction with the circulating antibodies of blood plasma from PR+ and PR- BC patients. Peptides interacting with PR+ and PR- patients plasma have common amino acid motifs suggesting that patients with tumors expressing different PR levels mount specific immune response reflecting molecular changes associated with various tumor subtype. Therefore, the panel of peptides that specifically interact with the immunoglobulins of patients with different PR expression can be used for the development of non-invasive test systems. Thus, peptide microarrays can be used to create a new tool for studying the repertoire of circulating antibodies for different diseases evaluation. Supported by grant FZMW-2020-0007.
Supported by grants from the Ministry of Science and Higher Education of the Russian Federation (FZMW-2020-0007)
Analysis of expression and function of LLT1 (CLEC2D) in Ewing sarcoma
Authors: Mathew Stephen O , Buller Casey W 
Published: January 2023

Abstract
Ewing Sarcoma (EWS) is a pediatric bone cancer that is characterized by a chromosomal translocation giving rise to a neomorphic gene fusion. Although treatment of EWS has a 5-year incident free survival rate of 66%, treatment has plateaued since the 1980’s. Natural killer (NK) cells are an important innate immune cell due to their ability to recognize and lyse virally infected and cancerous cells. Cancerous cells often employ strategies such as the downregulation of major histocompatibility complex (MHC) I, or upregulation of inhibitory ligands enabling the escape of T-cells and NK cell mediated killing. Previously, we showed that LLT1 is an inhibitory ligand that is expressed on triple negative breast cancer (TNBC) and prostate cancer cell lines. The expression of LLT1 and its function in Ewing Sarcoma (EWS) cell lines has yet to be performed. Our results have demonstrated a higher expression of LLT1 on EWS cell lines. We have shown that blocking LLT1 and NKRP1A interaction with anti-LLT1 antibodies increases NK cell cytotoxicity against EWS target cells. These results indicate that LLT1 is a potential immunotherapy target that needs to be further evaluated in an in vivo model.
Supported by intramural funds from UNT Health Science Center
CD4 T cell memory restoration upon antiretroviral initiation in people living with HIV.
Authors: Sponaugle Alexis Thieme , Abad-Ferenandez Maria , Clutton Genevieve , Weideman Ann Marie K , Hudgens Michael G , Davy-Mendez Thibaut , Adimora Adaora A , Ramirez Catalina , Floris-Moore Michelle , Kuruc JoAnn , Margolis David M , Gay Cynthia , Eron Jospeh J , Goonetilleke Nilu 
Published: January 2023

Abstract
HIV infection depletes CD4 T cells and dysregulates formation of long-lived memory CD4 T cells. Studies show that antiretroviral therapy (ART) in people with HIV (PWH) more effectively restores CD4 T cell memory phenotypes when initiated early (&lt; Fiebig V). We used a 31 marker mass cytometry panel to assess CD4 T cell phenotype in PWH treated in acute infection (AHI) (median 2.3 years post ART initiation) and chronic infection (CHI) (median 5.8 years post ART initiation) compared to healthy donors (HD) (n=10 per group). Markers of activation (HLA-DR, CD25), exhaustion (PD-1), survival (Bcl-2) and memory (CD127) were examined. CD4 T cell memory phenotypes of AHI clustered closely with HD whereas CHI had fewer central memory CD4 T cells. We also examined IL-7 signaling in CD4 T cells, measuring STAT5 phosphorylation (pSTAT5) in response to IL-7. CHI exhibited significantly lower pSTAT5 than HD in contrast to AHI who exhibited restored IL-7 signaling. This suggests ongoing and underappreciated functional defects in CD4 T cells in CHI. To examine this further, we are completing detailed analysis of CHI before and after ART initiation (pre-ART, day 2, 7, 10, 14, 28, month 5, 9 and 18). Data will be compared to our recent work showing that CD4 T cell memory subsets, activation and exhaustion markers are highly stable in durably suppressed CHI on ART over 19–27 months. New work is examining CD4 T cell function in immunological non-responders (INR) who fail to restore CD4 counts following ART. Altogether these studies will inform how HIV impacts formation of both CD4 memory and the HIV reservoir (which is largely harbored in long lived memory CD4 T cells) following ART initiation, potentially identifying novel therapeutic targets to accelerate HIV cure in CHI.
This work was made possible by the National Institute of Allergy and Infectious Diseases U01 AI131310, Collaboratory of AIDS Researchers for Eradication (UM1 AI164567) and UNC WIHS (U01 AI103390).
Altered cytokine and chemokine profiles in the lungs of vitamin A deficient mice with respiratory syncytial virus infection
Authors: Hong Suyeon , McGill Jodi L 
Published: January 2023

Abstract
Human respiratory syncytial virus (RSV) is a leading cause of severe acute lower respiratory tract disease worldwide in infants and young children. Epidemiologically, low levels of vitamin A (VA) are known to increase susceptibility to severe respiratory infection. However, little is known regarding how VA impacts lung immune function, specifically during RSV infection. Here, we investigated the impact of VA deficiency (VAD) on innate immunity in the lungs following RSV infection using a BALB/c mouse model. Groups of VA sufficient (VAS) and VAD, 6 to 8-week-old mice were intranasally infected with RSV, and lung tissues were collected at 3, 4, and 8 days post-infection for evaluation of vitamin A status, flow cytometry for innate immune populations, and Luminex bead-based multiplex assays for inflammatory cytokines. Acute RSV infection negatively impacted lung VA status in vitamin-replete mice. Although no differences in morbidity were observed between treatment groups, VAD mice had more neutrophils recruited to the lungs. VAD also altered the phenotype of γδ T cell populations in the lung, resulting in significantly increased frequencies of CD27+ γδ T cells, and fewer CD27 negative γδ T cells compared to VAS mice. Moreover, cytokine and chemokine production was altered in the lung of VAD animals after RSV infection, with reduced production of IL-1β, IL-6, IL-17, and KC (CXCL1). These results suggest that VAD alters the inflammatory environment in the lung, which may contribute to disease susceptibility. Future experiments will focus on further changes to the innate and adaptive immune systems in the lungs during VAD after RSV infection.
Supported by Roy J. Carver Charitable Trust Grant #20-5306
Bclaf1 promotes hematopoietic stem cell repopulating capacity and self-renewal
Authors: Crowley Stephanie , White Lynn S , Li Yanan , Yang Wei , Magee Jeffrey A , Bednarski Jeffrey J 
Published: January 2023

Abstract
Hematopoietic stem cells (HSC) balance differentiation and self-renewal to promote maintenance of mature blood cell lineages. The mechanisms that regulate HSC expansion during fetal hematopoietic development and adult HSC maintenance remain significant knowledge gaps. BCLAF1 (Bcl2-associated factor 1), a transcriptional regulator, is highly expressed in hematopoietic cells. We recently defined its function as a modulator of ETS-family transcription factor activity in developing B cells. Our objective in this study is to determine the molecular mechanism of BCLAF1 in regulation of fetal and adult HSCs. We used mouse models with selective deletion of Bclaf1 in hematopoietic cells to test whether BCLAF1 regulates HSC development and function. We find that loss of Bclaf1 results in significantly reduced numbers of fetal HSCs. The reduced HSC numbers persist in adult mice; but there is no additional decline or development of bone marrow failure with aging. In competitive transplant experiments, Bclaf1-deficient fetal and adult HSCs have defective repopulation and self-renewal capacity resulting in reduced reconstitution of all hematopoietic populations. Bclaf1-deficient HSCs do not have abnormalities in emergence, proliferation, cell death, or homing activity. Using single cell RNA-sequencing of fetal HSCs, we find that loss of BCLAF1 results in reduction of a subpopulation of HSCs and upregulation of the early response genes Jun, Fos, and Egr1. Collectively, these findings suggest BCLAF1 restrains activity of immediate early genes to preserve HSC self-renewal capacity and promote HSC expansion during both fetal development and repopulation of hematopoiesis after HSC transplant.
Supported by grants from Children’s Discovery Institute, St. Louis Children’s Hospital Foundation, Siteman Cancer Center, and NIH (T32 AI007163).
Discovery of Antigen Specific CD4+ T cells in anti-3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGCR) Immune Mediated Necrotizing Myopathy (IMNM)
Authors: Tiniakou Eleni , Mammen Andrew , Darrah Erika 
Published: January 2023

Abstract
Anti-HMGCR+ IMNM is characterized by IgG antibodies against HMGCR and a strong association with HLA-DRB1* 11:01. Although this implicates HMGCR-specific CD4+ T cells in disease pathogenesis, no such cells have been identified thus far.
Monocyte derived dendritic cells from 6 anti-HMGCR+ IMNM patients were incubated with HMGCR protein and presented peptides were identified using a natural antigen processing assay (NAPA). Briefly, HLA-DR/peptide complexes were isolated by immunoprecipitation and bound peptides were sequenced by mass spectrometry. HMGCR peptides corresponding to putative T cell epitopes were synthesized and used to stimulate peripheral blood mononuclear cells from: 10 anti-HMGCR+ IMNM patients, 10 dermatomyositis patients (DM), 5 HLA-DRB1* 11:01+ healthy controls (HC). HMGCR-reactive CD4+ T cells were identified by flow cytometry based on CD154 upregulation.
A total of 7 different naturally processed HMGCR peptides were identified. The number of distinct peptides presented per patient ranged from 1 to 5, with 5 being presented by at least 2 patients. All HMGCR peptides elicited robust CD4+ T cell responses in 9/10 anti-HMGCR+ IMNM patients, compared to 4/10 DM patients (p=0.017), 1/5 of HC (p=0.0119). The anti-HMGCR+ IMNM patients responded to more epitopes (p=0.0163) and had higher total number of positive CD4+ T cell cells (p= 0.0001).
Our findings represent the first report of antigen-specific CD4+ T cells in anti-HMGCR+ IMNM. Leveraging NAPA, we defined a core set of naturally presented HMGCR peptides defining precise immunologically relevant CD4+ T cell epitopes. Definition of these epitopes is key in understanding disease pathogenesis and will aid in the development of antigen-specific therapeutic tools.
Supported by grants from Rheumatology Research Foundation and the Buck Foundation.
Comparison of salt-soluble wheat allergens in a mouse model vs. known human wheat allergens: evidence from durum and ancient wheats
Authors: Jorgensen Rick Dean , Gao Haoran , Raghunath Rajsri , Chandra Shivam , Noble Amanda , Olson Eric , Ng Perry K W , Gangur Venugopal 
Published: January 2023

Abstract
Wheat allergies are among the major types of food allergies that are potentially life-threatening because of anaphylaxis. Monitoring changes to wheat allergens in novel wheat lines/genotypes is critical to prevent inadvertent introduction of potentially hyper-allergenic varieties from genetic modification. Nonetheless, validated methods for this purpose are unavailable at present. We have previously described a mouse model of wheat allergy using salt-soluble protein extract (SSPE) from durum wheat. As a proof-of-concept study, here we tested the hypothesis that wheat allergens in this mouse model will be identical to those reported for human wheat allergy. We created a mini plasma bank using hyper-IgE immune plasma obtained from Balb/cJ female mice (n=20) that had been sensitized with durum-SSPE along with alum adjuvant followed by repeated booster intraperitoneal injections with SSPE alone. Using hyper-IgE plasma we optimized an IgE-Western Blot (IgEWB) method to identify allergens present in SSPEs from durum wheat and an ancient tauschii wheat. The IgE-binding allergenic bands present in raw and boiled/reduced SSPEs from durum and tauschii wheats were sequenced using LC-MS/MS method. The most abundant allergens were identified and compared with a human wheat allergen database. There were 13 allergens present in durum-SSPE, of which 6 were present only in raw extract, 2 were present only in boiled/reduced extract, and 5 were present in both. There were 10 allergens present in tauschii-SSPE, of which 7 were present only in raw extract, and 3 were present in both raw and boiled/reduced extract. Between durum and tauschii wheats, 14 allergens were present in this mouse model, of which 10 are human wheat allergens.
Supported by USDA/NIFA, MSU
TFR-derived IL-4 is required for antigen-specific IgE but not antigen-specific IgG1 production in a peanut allergy model
Authors: Chen Qiang , Dent Alexander 
Published: January 2023

Abstract
T follicular regulatory cells (TFR) have been shown to regulate antibody production in germinal centers. Cytokine IL-4 controls the class-switching of IgG1 and IgE and is associated with the type II immune response. Though T follicular help cells (TFH) have been identified as a source of IL-4, whether and how IL-4 from TFR cells regulate antibodies including IgE remains unknown. Utilizing a food allergy model in which mice are sensitized using peanut extract and cholera toxin through oral gavage, we found that peanut-specific IgE but not IgG1 is absent with in vivo anti-IL-4Rα antibody treatment, while total IgE is also affected. This differential requirement for IL-4 is further validated using Il4-heterzygous mice, suggesting that IL-4 haploinsufficiency only impairs IgE production. Additionally, the number of germinal center B cells were not reduced in both models. To determine the role of IL-4 from TFR cells specifically, bone marrow chimera mice were constructed in which IL-4 is deficient in TFH and/or TFR cells. Both peanut-specific IgG1 and IgE were impaired when IL-4 is deficient in both TFH and TFR cells, while only peanut-specific IgE is almost absent when IL-4 is deficient in TFR cells. In another mouse model, where mice are immunized with OVA plus alum, the differential roles of IL-4 in IgE and IgG1 production are recapitulated. In conclusion, switching to IgE requires a stronger IL-4 signal compared to IgG1, and TFR cell-derived IL-4 plays a critical role in switching to IgE but not to IgG1.
Supported by grants from NIH (R01AI132771)
Brain mast cell accumulation and activation in an asymptomatic mouse model of cow’s milk allergy
Authors: La Mae Germundson Danielle , Nagamoto-Combs Kumi 
Published: January 2023

Abstract
Mast cells (MCs) are best known as the effector cells of allergy. Due to their presence in the brain and production of potent inflammatory mediators, MCs have been implicated in the pathogenesis of neuroinflammatory disorders. Previously, we showed that acutely challenging allergically sensitized mice increased the numbers of brain MCs. However, the consequences and mechanism of MC recruitment and activation within the brain are still unclear. We hypothesized that MCs increase in the brain due to allergen infiltration into the central nervous system, which subsequently activates MCs that release histamine, increasing blood-brain barrier (BBB) permeability and neuroinflammation. C57BL6/J mice were sensitized to a bovine whey allergen β-lactoglobulin (BLG) and placed on a whey-containing diet for two weeks to simulate prolonged allergen consumption. Although no overt allergic symptoms were observed, BLG-sensitized mice exhibited depression-like behavior after the allergen consumption period. Serum BLG-specific IgE and histamine were also significantly elevated, validating their hypersensitivity status. In the brains of sensitized mice, MC numbers and histamine levels were increased. IgG extravasation and perivascular astrogliosis were also detected, indicating BBB impairment and neuroinflammation, respectively. Furthermore, myelin staining revealed demyelination in select cortical regions of BLG-sensitized mice, suggesting a potential action of MC-derived proteases. Together, our findings support the involvement of MCs in peripheral-to-central communication during a chronic allergic response. MC stabilization or allergen avoidance may be useful to treat neuroinflammation in susceptible individuals.
Supported by grants from the NIH/NIGMS (P20GM103442), UND Host-Pathogen CoBRE Pilot Grant (P20GM113123) and funds from the University of North Dakota SMHS Department of Biomedical Sciences
Psychological Stress of aged mice has long-term impact on Mycobacterium tuberculosis infection by altering composition of lung T cell populations
Authors: Lafuse William P , Sunkum Shrayes , Kumar Naresh , Ahumada Omar Santiagonunez , Turner Joanne , Rajaram Murugesan V S 
Published: January 2023

Abstract
Aging is a major risk factor for chronic infections, including tuberculosis (TB). Elderly TB patients also suffer from elevated levels of psychological stress. It is not known how psychological stress impacts TB pathogenesis. To study the effects of stress on Mycobacterium tuberculosis (M.tb) we used a social disruption stress (SDR) model which involves repeated social defeat in subordinate mice. Young (3 month) and Old (18 month) C57BL/6 mice were subjected to SDR and infected with M.tb. Mice were sacrificed at 30 and 60 days post infection and M.tb burden analyzed by CFU assay and lung pathology by HE staining of lung sections. At day 30, M.tb burden was lower in control old mice compared to young mice and SDR did not significantly alter M.tb burden. However, at day 60, SDR in old mice significantly increased M.tb burden compared to SDR in young mice, indicating that SDR in old mice has a detrimental effect on the ability to control the infection. Our gene expression analysis revealed that T cell genes (JAK3 and LCP2) in the lungs of old SDR infected mice were increased but not in young SDR mice, suggesting that SDR in old mice increased T cell recruitment in the lung. Additionally, we found that Tbet (Th1) and GATA3 (Th2) gene expression were unchanged by SDR, in contrast the expression of RORγT (Th17) was increased by SDR in old mice at day 60. Also, mRNA levels of IL-10 at day 60 were increased by SDR in old mice, but not in young mice, while SDR decreased IFN-γ in both young and old mice. To further define T cell populations, we are analyzing lung sections by confocal microscopy. In conclusion, our studies suggest that psychological stress prior to M.tb prior to infection has long-term impact by altering composition of T cell populations in the lung.
Supported by NIH grants (PO1-AG051428, AI146252 and AI146690)
Bacteria load and hypoxia contribute to glucose uptake by macrophages and T cells in cynomolgus macaque granulomas
Authors: Mattila Joshua T , Gould Victoria A , Junecko Beth A , Bellavia Michael C , Borish H Jacob , White Alexander G , Maiello Pauline , Nyiranshuti Lea , Lin Philana Ling , Scanga Charles A , Anderson Carolyn J , Flynn JoAnne L 
Published: January 2023

Abstract
Granulomas form during tuberculosis (TB) and restrain bacterial dissemination but are also sites of mycobacterial replication and persistence. The immunometabolic state of cells in granulomas has immunologic and diagnostic relevance and PET-CT with the glucose analog FDG demonstrates that granuloma glucose uptake is dynamic and heterogenous within a host. Basic details on glucose uptake, including the cells responsible for FDG PET signal, have not been resolved and filling these gaps will improve interpretation of PET data in TB. Our objective was to identify relationships between glucose (FDG) uptake and granuloma composition and to identify factors that drive this process in M. tuberculosis-infected cynomolgus macaques. We used glucose transporter 1 (GLUT1) to identity cells that may be using glucose as an energy source in granulomas, and compared these data with the cell’s microenvironment, and the granuloma’s bacteria load and FDG PET data to determine how these factors influence GLUT1 expression. We found that GLUT1 was strongly expressed by myeloid cell subsets in specific granuloma microenvironments and this pattern was conserved in granulomas from different organs. We also identified macrophage subsets and T cells that may be important contributors to a granuloma’s potential glucose (FDG) uptake when their GLUT1 expression and population sizes were considered. We also correlated granuloma bacteria loads and hypoxia with GLUT1 expression, suggesting that bacterial antigens and hypoxic conditions drive a granuloma’s glucose uptake. Taken together, our data suggest that granuloma glycolysis and FDG uptake are driven, in part, by cell subset-specific responses to a granuloma’s microbial and microenvironmental milieu.
This work was supported by NIH grants AI134183 and AI118195.
C. elegans host defense pathways protect against microbiota cryptic virulence
Authors: Gonzalez Xavier , Wollenberg Amanda , Irazoqui Javier 
Published: January 2023

Abstract
Animals are colonized by diverse communities that provide essential functions to the superorganism. At homeostasis, such microbiota communities are thought to benefit the healthy host. In contrast, dysbiosis can be both pathogenic and a consequence of disease. Establishing causal relationships among microbiota composition, host immune status, and disease is essential for fundamental understanding of many diseases and for their therapeutic targeting. Here we took a reductionist approach to address the potential for normal microbiota bacteria to cause disease in the immunodeficient host (i.e., the cryptic virulence of pathobionts) using C. elegans. C. elegans are known to rely on several host defense pathways to counteract intestinal infections. Although these pathways are known to play pivotal roles in defense against various human pathogenic bacteria, it is not clear what roles these pathways play for interactions with the native microbiota. To address this gap in knowledge, we determined the functional significance of p38, Wnt, and TFEB pathways in terms of gene expression and host survival of monocolonization by individual members of the C. elegans microbiota. We find that distinct host defense pathways are necessary for normal survival of animals colonized with distinct microbiota members. Our results suggest that specific microbiota members trigger specific host defense pathways, which are necessary for the host to defend against their cryptic virulence. The new insights provide the necessary foundation to characterize the molecular mechanisms by which microbiota members trigger host defense pathways specifically, including potentially novel bacterial metabolites with useful therapeutic properties in mammals.
Supported by gran from NIH (R01GM101056-10) Supported by grant from NIH (Innate Immunity Training Grant (T32 AI095213))