bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative single-cell transcriptome analysis informs early innate immune response in severe human burns
Authors: Dinh Huy , Hou Yiran , Khatri Parth , Rindy Julie , Gao Anqi , Gibson Angela , Huttenlocher Anna 
Published: August 2023

Abstract
Proper wound healing requires a coordinated time-dependent balance of immune pathways to prevent irreversible systemic damage. Given that innate immune cells are first to mobilize to sites of injury, we hypothesize that neutrophils, macrophages, and their interactions are associated with burn severity. To test this, we employed systems immunology and bioinformatics approaches utilizing single-cell transcriptome (scRNA-Seq) in model organisms and large-scale bulk transcriptome of human burns. To this end, we generated the first to-date scRNA-Seq atlas of 6,671 neutrophils and 12,560 macrophages from a time-course zebrafish tail burn model. Our data unveiled transcriptionally distinct subsets that present different dynamics during the wound healing process. We identified the granularity of IL6-IL6R interactions between macrophages and neutrophils, which impair neutrophil recruitment to sterile thermal injury, making the area vulnerable to microbial invasion and subsequent infection. Furthermore, we generated a comprehensive cross-species reference of neutrophils and macrophages in injury models by integrating publicly available mice scRNA-Seq with our zebrafish data. This reference allows us to deconvolute bulk transcriptome data from different published human cohorts and discover signatures of early innate immune cells associated with burn severity in humans. Our discovery demonstrates the power of using comparative bioinformatics approach to better understand the innate immune system during wound healing. In the future, these advances will guide interventional genomics approaches to identify druggable pathways to optimize burn wound healing in human patients.
The Serological Sciences Network (SeroNet); the U.S. government’s effort to boost testing capacity and escalate standardized research on immune responses to SARS-CoV-2
Authors: Roche Nancy V , Hickey Tom , Freund Elaine , Breads Patrick , Hempel Heidi , Berny-Lang Michelle , Klemm Juli , Finstad Samantha , Cherry Jim , Pinto Ligia , Singer Dinah V 
Published: August 2023

Abstract
In April 2020, the National Cancer Institute (NCI) and the Frederick National Laboratory for Cancer Research (FNLCR) built the Serological Sciences Network(SeroNet) on the foundation of the HPV Serology program to develop serology technologies to better understand the immune response to infection and vaccines. SeroNet members (steering committee, investigators, working groups) are funded by NCI (through The Paycheck Protection Program and Healthcare Enhancement Act) to characterize immune responses elicited by SARS-CoV-2 and the modifiers and mechanisms driving these responses, the serological correlates of disease pathogenesis/protection, and the barriers to SARS-CoV-2 serological testing. Studies were conducted by 8 Centers of Excellence and 13 Research Projects, with reference material development and longitudinal vaccine response studies conducted at FNLCR and 4 subcontracted Capacity Building Centers (CBCs). CBC testing capacity has reached &gt;5,000 tests/week and has collected &gt;8000 aliquots of serum/peripheral blood mononuclear cells (PBMC) samples and ~3000 healthy control/immunocompromised patients (serum, PBMC’s, clinical/follow up data) for use by SeroNet. SeroNet has produced 332 papers on correlates of protection and characterization of the immune response. Study level data for 87 papers is found in the Immunology Database and Analysis Portal (ImmPort). SeroNet has produced study design templates, standard operating procedures, common data elements, and well-characterized SARS-CoV-2 serology standards, such as the first US SARS-CoV-2 serology standard, which is calibrated against the WHO International Standard and evaluation panels to facility assay development and validation.
National Cancer Institute
Clonal dynamics of SARS-CoV-2 specific CD4 T cells in lymph nodes after vaccination
Authors: Bartolo Laurent , Pan Yi-Gen , Afroz Sumbul , Su Laura 
Published: August 2023

Abstract
The ongoing COVID-19 pandemic highlight the importance of vaccination. Past studies have surveyed SARS-CoV-2 specific B cell response in the lymph node (LN) of vaccinated patient, but the quality, the dynamics, and the specificity of the T helper response following mRNA vaccination remains incompletely understood. We address this question in healthy individuals receiving mRNA vaccine (BNT162b or mRNA-1273). We collected axillary draining LN using fine needle aspiration following vaccination and analyzed CD4+ T cells by single cell transcriptome, proteome analysis and TCR sequencing. We observed an accumulation T cell having characteristic signature of activated T follicular helper cell (Tfh), through the course of the 6 months, as well as an increase expansion of Tfh clones. Using TCR sequences to track progenies of same T cell over time, we observed that some Tfh cells in the 6 months’ time point were already detectable after the first vaccine dose. We then generated a library of SARS-CoV-2 specific TCR sequences by performing TCR sequencing on cells that proliferated in response to a spike peptide pool. The majority of these TCR sequences mapped to cells with a strong Tfh signature on the transcriptomic level and accumulated after 6 months. In conclusion, we observed an expansion of SARS-CoV-2 specific Tfh clones after the first dose of vaccine, some of which persisted after 6 months. We hypothesize that, in a protective SARS-CoV-2 response, short-lived clones are progressively replaced by long-lasting SARS-CoV-2 specific Tfh clones. We plan to test this hypothesis by analyzing clonal dynamics at other time points and by using aggregate TCR sequences from the publicly available sequences from individuals with mild or severe COVID-19.
NIH R01AO66358
Spike protein vaccine triggers systemic Th2 and Th17 inflammatory responses and pulmonary immunopathology following SARS-CoV-2 breakthrough infection
Authors: Zhang Tianyi , Magazine Nicholas , McGee Michael C , Babawale Pius , Upshaw Sarah , Carossino Mariano , Kousoulas Konstantin G , August Avery , Huang Weishan 
Published: August 2023

Abstract
Vaccines have shown remarkable protection against COVID-19, but vaccination-enhanced respiratory disease (VAERD) following breakthrough infections poses safety concerns. SARS-CoV-2 Spike (SARS-2 S) protein subunit vaccines induced VAERD in hamsters, where aluminum adjuvant primed a Th2-biased immunization, resulting in elevated type 2 pulmonary inflammation in animals with breakthrough infections. To further understand the potential risks and immunopathogenesis of VAERD, we immunized K18-hACE2 mice with SARS-2 S protein in the presence of aluminum and CpG ODN adjuvants and infected them with a lethal dose of SARS-2. The vaccine induced robust antibody and T cell responses, significantly reducing viral titers and increasing host survival. However, following breakthrough infection, vaccinated animals exhibited severe airway immunopathology, with a dramatic increase of eosinophils and CD4+ T cells, and elevated Th2/Th17 cytokines in the lungs. Intracellular flow cytometric analysis showed a systemic Th2/Th17 inflammatory response, prominently in the lungs. Our data show that the aluminum/ODN adjuvants elicit strong protection against COVID-19 but prime a robust Th2/Th17 inflammatory response that may contribute to rapid onset of T cell-mediated pulmonary immunopathology following breakthrough infection. Our results highlight the need for additional studies to elucidate COVID-19-associated VAERD and to further improve vaccine formulations for broad protection and maximal safety.
This research was supported in part by grants from the National Institutes of Health (P20 GM130555-6610 and R01 AI151139).
Memory CD4 T cell recall following Influenza A Virus infection is unaltered by the pregnancy environment
Authors: Malavet Valeria Flores , Prokop Emily , Strutt Tara M 
Published: August 2023

Abstract
The risk of severe influenza A virus (IAV) infection increases during pregnancy. A widely accepted paradigm suggests that this increased severity is resultant from immunity that is shifted towards Th2- versus Th1-immune responses, the latter of which is essential for control of virus. While this concept is accepted for primary immune responses, whether memory T cell responses are similarly shifted during pregnancy is unclear. Using a reductionist murine model, here we explore whether and how adoptively transferred, Th1-polarized IAV-specific memory CD4 T cells responding against IAV are impacted by pregnancy. Following infection, we find that donor cell migration to the lung, surface marker phenotype, T-BET transcription factor expression, multi-cytokine production capacity in terms of IFN-γ, TNF, and IL-2, and ability to control virus in the lung are comparable between non-gravid and gravid hosts. A significant increase in donor CD4 T cell Th2-associated GATA-3 transcription factor expression and cytokine production following IAV infection was not observed in gravid hosts. Enhancement of Th2-associated IL-4, IL-5, and IL-13 cytokine production was only observed in infected hosts when IAV-specific Th2-polarized CD4 T cells already poised to produce these cytokines were adoptively transferred. These findings suggest that in context of an IAV infection during pregnancy, preexisting Th1-polarized IAV-specific memory cells retain their protective recall potential. Furthermore, they support that employment of vaccination strategies that induce universal T cell immunity prior to pregnancy are a potential means to protect the vulnerable pregnant population from severe seasonal as well as pandemic IAV infection.
The Solomon Klotz Excellence in Immunology Award Florida Education Fund McKnight Doctoral Fellowship Supported by grants from the NIH Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD) (5R21HD093948-02)
Clonal replacement sustains long-lived germinal centers primed by respiratory viruses
Authors: de Carvalho Renan , Ersching Jonatan , Barbulescu Alexandru , Mesin Luka , Victora Gabriel 
Published: August 2023

Abstract
Germinal centers (GCs) form in secondary lymphoid organs in response to infection and immunization and are the source of affinity-matured B cells. The duration of GC reactions spans a wide range, and long-lasting GCs (LLGCs) are potentially a source of highly mutated B cells. We show that, rather than consisting of continuously evolving B cell clones, LLGCs elicited by influenza virus or SARS-CoV-2 infection in mice are sustained by progressive replacement of founder clones by naïve-derived invader B cells that do not detectably bind viral antigens. Rare founder clones that resist replacement for long periods are enriched in clones with heavily mutated immunoglobulins, including some with very high affinity for antigen, that can be recalled by boosting. Our findings reveal underappreciated aspects of the biology of LLGCs generated by respiratory virus infection and identify clonal replacement as a potential constraint on the development of highly mutated antibodies within these structures (de Carvalho et al, Cell, 2023).
NIH/NIAID grants R01AI119006, R01AI139117, and R01AI157137. Additional support by NIH grant DP1AI144248 (Pioneer award) and the Robertson Foundation.
The Interconnection Between Periodontitis and Inflammatory Bowel Disease
Authors: Tanwar Himanshi , Gnanasekaran Jeba Mercy , Allison Devon , Das Amitabh , Yesupatham Sathish , Dilshad Yasir , Kear Bernice , Wang Sheng , Wang Xiaobei , Chung Man-Kyo , Scott Alison , Rasko David , Ernst Robert , Raufman Jean-Pierre , Math Vivek Thumbigere 
Published: August 2023

Abstract

Objective
Periodontitis, an oral infection affecting ~50% of Americans, is associated with the pathogenesis of inflammatory bowel disease (IBD), however, the contributory mechanisms remain ill defined. Previous GWAS studies have identified SNPs in the Interferon Regulatory Factor 8 (IRF8) gene as risk factors for IBD. The objective of this study was to explore the relationship between periodontitis and IBD using Irf8 knockout (KO) mice.

Methods
Periodontitis was induced in wild-type (WT) and Irf8 KO mice using the well-established oral ligature-induced periodontitis (LIP) model. The effects of LIP on oral bacterial colonization in the mouth and gut were measured by 16S rRNA and shotgun metagenomics sequencing. The influence of LIP on oral bacteria-mediated immune cell infiltration in the colonic mucosa was measured by flow cytometry, RT-qPCR, and ELISA.

Results
LIP promoted expansion of native oral pathogens and accumulation of the same species in the mouth and gut of Irf8 KO mice, which was associated with colitis development in Irf8 KO mice when compared to WT mice. LIP Irf8 KO mice exhibited ~2-fold increased infiltration of Th17 cells and ~2–4-fold decrease infiltration of Th1 and Treg cells in the colonic mucosa, which led to over production of IL17 and decreased production of IFN-γ and IL10. Similarly, IL-1β-producing cells were found to be higher in the colonic mucosa of LIP Irf8 KO vs WT mice. Resolution of periodontitis correlated with reduced intestinal load of oral bacteria and reversal of colitis in Irf8 KO mice.

Conclusion
Our study provides new perspectives on the pathophysiology of IBD. Irf8 deficiency along with dysbiotic oral and gut microbiota promote colitis in mice by activating IL17 and IL-1β signaling pathways.
Cell-autonomous complement C3 maintains prostate epithelial cell homeostasis and prevents malignant transformation
Authors: Kunz Natalia , West Erin E , Yamamoto Hidekazu , Tajmul Md , Loetscher Jonas , Kellerhals Tamara , Kolev Martin , Balmer Maria L , Chandra Ash , Seymour Len , Klos Andreas , Hess Christoph , Afzali Ben , Kazemian Majid , Dasgupta Prokar , Kemper Claudia 
Published: August 2023

Abstract
Intracellularly active complement C3 and C3a emerged as central regulators of normal immune cell function and proliferation via control of mTOR and glycolysis. Because increased glycolysis is a hallmark of many cancer cells, we hypothesized that augmented cell-intrinsic C3 activity may contribute to epithelial cell malignancy.
However, while benign prostate epithelial cells (PECs) harbored expected intracellular C3/C3a storages, cancerous PECs, surprisingly, exhibited loss of C3/C3a. Further, C3/C3a reduction levels in PECs correlated inversely with worsening Gleason scores in patients, silencing of C3 in healthy PECs induced uncontrolled proliferation, and reconstitution of intracellular C3a in prostate cancer cell line DU145 normalized their hyper-proliferation. In line with an unexpected anti-proliferative role for C3a in PECs, C3ar−/− mice developed spontaneous hyperplasia of prostate tubular cells with age, treatment of DU145 tumors, implanted subcutaneously into the flanks of athymic mice, with C3a-expressing adenovirus significantly reduced tumor growth in vivo, and augmented C3 levels are associated with a better prognosis in patients with prostate and other types of epithelial cell cancers. RNA-sequencing of C3 or C3aR-deficient human PECs identified intrinsic C3a as novel controller of several known PEC oncogenes, likely via up-stream impact on the c-MYC pathway.
In sum, while intracellular C3 drives proliferation in immune cells, in (prostate) epithelial cells, cell-autonomous C3/C3a is a negative regulator of growths and, thus, represses oncogenic transformation. Such cell-specific intracellular C3/C3a activities should be taken into consideration when targeting this system therapeutically.
PD1 blockade promotes IFN-γ production by progenitor exhausted PD1-expressing T cells in atherosclerotic plaques
Authors: Mulholland Megan , Yu Yinda , Lin Shiying , Jakobsson Gabriel , Schiopu Alexandru , Björkbacka Harry , Lichtman Andrew H , Gisterå Anton , Engelbertsen Daniel 
Published: August 2023

Abstract

Objective
Interferon-γ (IFN-γ) is a key cytokine regulating the development of atherosclerosis, but little is known regarding the phenotype and regulation of T cells producing IFN-γ in plaques.

Methods
To identify and characterize IFN-γ-producing T cells in the development atherosclerosis, we utilized IFN-γ-YFP and Nur77-GFP reporter mice crossed onto an atherosclerotic background (Apoe−/− IFN-γYFP/YFP; Apoe−/−Nur77GFP/wt), adoptive transfer of transgenic ApoB-reactive T-cells into mice containing humanized ApoB100 (HuBL mice), and treatment with immune checkpoint inhibitors in atherosclerotic mice.

Results
Aortic CD4+ and CD8+ T cells producing IFN-γ were a complex set of cells comprised predominantly of “progenitor exhausted” PD1-intermediate (PD1int) SLAMF6+ IL7R+ T cells and a minor population of “terminally exhausted” PD1hi TOX+ T cells. However, both PD1int and PD1hi plaque T cells were Ki67+ and displayed elevated levels of recent TCR signaling (Nur77-GFP+). ApoB-specific transgenic CD4+ T cells adoptively transferred to a hypercholesterolemic HuBL mice showed sign of early exhaustion, upregulating PD1, TOX, and Tim3. Finally, PD1 blockade in mice with advanced atherosclerosis resulted in increased levels of IFN-γ production of plaque-infiltrating CD4+ and CD8+ T cells.

Conclusion
IFN-γ-producing T cells in the atherosclerotic plaque display markers classically associated with an exhausted T cell phenotype but still produce cytokines, proliferate, and are responsive to anti-PD1 treatment. Our study suggests that PD1 signaling regulates T cell IFN-γ production in plaques and reveals a potential mechanism by which immune checkpoint blockade therapy aggravates cardiovascular disease.

Supported by grants from Swedish Heart-Lung Foundation (#20200522, #20190449) sourced by Daniel Engelbertsen.
The functional role of Helios in CD4+ T cells
Authors: Yang Neil X , Tison Kole , Penna Vinay , Oguz Cihan , Lack Justin , Shevach Ethan M , Thornton Angela M 
Published: August 2023

Abstract
The transcription factor Helios is expressed in the majority of Foxp3+ Regulatory T cells (Treg), where it plays an essential role in Treg function. Loss of Helios in the Treg population induces systemic autoimmunity, marked by CD4 and CD8 hyperproliferation, enhanced germinal center formation, and systemic immune activation. Helios is also expressed in a small subset of conventional CD4+ T cells. However, when Helios is deleted in all CD4 cells, conventional and Treg, by crossing the mice to CD4Cre, this phenotype is abrogated, indicating that Helios must also play a significant role in the function of conventional CD4+ T cells.
In order to examine specific subsets of CD4+ memory cells, we performed single cell transcriptome analysis of CD44hi memory cells from WT mice and mice with the CD4 specific deletion of Helios. Characterization of the CD44hi Helios+ population showed that Helios expression changed dramatically with age, so cells from young (5–6 weeks) and old (5–6 months) mice were included in the analysis. Both longitudinal (young vs old) and cross-sectional (WT vs KO) comparisons were made, with emphasis placed on cross-sectional comparisons at old age. The sequencing results indicated significant transcriptomic and numeric shifts in multiple subpopulations of the analyzed splenocytes, including the almost complete loss of one cluster in both the young and old Helios deficient mice. Taken together, the observed transcriptomic and clustering changes may explain the role Helios plays in the abrogation of autoimmunity in our model and may provide a starting point for us to analyze its function in other biological pathways.
This work was supported by the Intramural Research Program of NIAID, NIH
This work was supported by the Intramural Research Program of NIAID, NIH
Paternal cadmium exposure decreases DMNT2 expression and increases obesity in male offspring
Authors: McCall Jamie L , Martinez Ivan , Barnett John B 
Published: August 2023

Abstract
Prenatal exposure to toxic agents, including cadmium (Cd), can alter offspring immune cell development and function. As Cd does not readily cross the placenta, it is hypothesized that prenatal Cd alters the epigenetic programming of genes including non-coding RNAs (ncRNAs). We found that prenatal Cd exposure increases CD4+ T cell proliferation following activation and that this phenotype is dependent on the upregulation of an oncogenic long non-coding RNA (lncRNA) known as small nucleolar RNA host gene 7 (lncSnhg7). In our previous studies, both parents were exposed. To determine the contribution of paternal exposure, we treated male mice with 10 ppm Cd in their drinking water for 7 days and then mated them with unexposed females. The male offspring of these mice were significantly larger than control mice at one year of age (p&lt;0.001). The offspring had increased fat mass (p=0.04) and reduced lean mass (p=0.03) as compared to controls as well as increased macrophages within the visceral adipose tissue. We hypothesized that sperm epigenetic alterations contribute to the phenotypes observed in the offspring. Cd exposure has been reported to alter sperm DNA methylation patterns in mice. Furthermore, DMNT2, a tRNA methyltransferase, has been reported to mediate intergenerational transmission of paternally acquired metabolic disorders by altering sperm small non-coding RNAs. We measured DNMT1, DNMT2, DNMT3a, and DNMT3b RNA expression in the sperm of Cd-exposed mice. The DNA methyltransferases (1, 3a, and 3b) were unaffected, but DNMT2 was significantly reduced in the sperm of Cd-exposed males. Thus, acute paternal exposure to Cd prior to conception alters DNMT2 expression which may lead to obesity and increased inflammation in the offspring.
Supported by grants from NIH/NIGMS (R01 ES023845, 2U54 GM104942-03, P20 GM103434, U54 GM-104942) and NSF (NSF/1920920, NSF/1761792).
MR1-deficiency in neonatal mice renders protection from necrotizing enterocolitis
Authors: Liu Jianyun , Hunter Chelsea , Manohar Krishna , Mesfin Fikir , Shelley William Christopher , Brokaw John , Markel Troy 
Published: August 2023

Abstract
Necrotizing enterocolitis (NEC) is a life-threatening disease that affects ~ 7% of premature neonates. NEC maintains high morbidity/mortality and there are long term sequelae including short bowel syndrome. The risk factors of developing NEC include prematurity, very low birth weight, microbial dysbiosis and infections. Mucosal-associated invariant T (MAIT) cells are innate T cells that have both innate and adaptive immune cell characteristics and are enriched in mucosal tissues, such as intestines. MR1 is the antigen presenting molecule for MAIT cells. Therefore, MR1-knockout (MR1 KO) mice lack MAIT cells. We hypothesized that MR1/MAIT cells play a key role in the development of NEC. To test the hypothesis, NEC was induced in 5-day old B6 wild type (WT) and MR1 KO mouse pups with gavage formula feeds supplemented with LPS as well as exposure to intermittent hypoxia and hypothermia. Pups were assessed daily for clinical sickness scores. Animals were euthanized on postnatal day 9. Intestine segments were harvested and assessed for histological NEC and cytokines were measured using multiplex assay. Compared to WT mice, we found MR1 KO pups did not develop typical NEC symptoms. When compared to WT mice with NEC, MR1 KO mice undergoing the treatment for NEC, had lower clinical scores (WT=4 [3–4]; MR1 KO=0 [0–0], p&lt;0.05) and intestinal histology scores (WT=1.5 [1–2.375]; MR1 KO=0 [0–0.3745], p&lt;0.05). The cytokine profile of the intestines in MR1 KO NEC mice, when compared to those in WT NEC mice, showed significant differences in IL-6 and IL-10 levels. In conclusion, deletion of MR1 in mice appears to be protective in experimental NEC. Future work will focus on studying the role MR1/MAIT cells in NEC disease development.