bluuebunny/crossref_metadata_2025_split huggingface dataset:
Th2 immune responses induced by helminth infection reprogram multilineage progenitors to produce successive waves of neutrophils, basophils, and eosinophils
Authors: Ferchen Kyle , Song Baobao , Potter Crystal , Zhang Xuan , Chou Chih-Hsing , Khodoun Marat , Finkelman Fred D , Salomonis Nathan , Grimes H Leighton 
Published: August 2023

Abstract
Helminths are parasitic worm pathogens known to induce innate acquired type 2 immune responses that lead to the accumulation of granulocytes in peripheral tissues. N. brasiliensis is a natural rat nematode parasite used in mouse models to elicit this immune response. Infective larvae are injected into the skin, migrate to the lung within 24–48 hours, are coughed up at 48–72 hours, and mature in the intestines in 5–6 days. Though much is known about the cytokine signaling and recruitment of granulocytes, little is known about the source of these cells. Their short half-life suggests a role for multi-lineage progenitors in the bone marrow. To test this, we exploited CITE-seq, flow cytometry, and machine learning on mouse bone marrow to build a reference atlas of transcriptional and immunophenotypic states of hematopoietic stem and progenitor cells (HSPCs). We generated an InfinityFlow object from millions of HSPCs and integrated these values with CITE-seq ADT values to allow transfer of transcriptionally defined clusters to flow cytometry-defined immunophenotypes. This enabled the generation of unsupervised gating srategies for isolation and functional validation of transcriptionally defined developmental stages. We then applied scRNA-seq and flow cytometry along a time course of N. brasiliensis infection in mice to characterize bone marrow HSPC responses to Th2-mediated immune effectors. We identified a multilineage progenitor that expands and transcriptionally reprograms at 72 hrs after infection and leads to the production of successive waves of neutrophils, basophils, and eosinophils on days 3, 7, and 10, respectively. Thus, worm infection stimulates Th2 responses that call to the marrow to specify granulocyte production.
Easy 250 EasySep&[trade] Magnet: A Novel Magnetic Platform For Large-Volume CD34+ Hematopoietic Stem and Progenitor Cell Isolation from Leukapheresis Products
Authors: Morin Peter , Toombs Eric , MacDonald Neil , Eaves Allen C , Louis Sharon A , Kokaji Andy I , de Jong Susan 
Published: August 2023

Abstract
We have developed a novel magnetic platform for large-volume CD34+ hematopoietic stem and progenitor cell (HPSC) isolation from both mobilized and non-mobilized leukapheresis products. As the frequency of CD34+ cells is low, and cell quality and viability can be variable between samples, it takes great effort to isolate these cells with consistently high purities and yields. Working with large volume leukapheresis products can be challenging as the sample often needs to be split and processed in parallel, which can be both time-consuming and labor-intensive.
The Easy 250 EasySep™ Magnet simplifies cell isolation procedures when processing leukapheresis samples. It is based on column-free immunomagnetic EasySep™ cell isolation technology and can process sample volumes up to 225 mL. We have developed a negative selection protocol for the enrichment of CD34+ HPSCs (mean purity ± SD of 74.6 ± 10.5%; n = 8) from non-mobilized leukapheresis products. For mobilized leukapheresis products, an EasySep™ positive selection protocol has been optimized for the isolation of highly purified CD34+ HPSCs (mean purity ± SD of 92.0 ± 1.7%; n = 7).
Notably, these protocols can be completed in as little as 25 minutes, making the Easy 250 EasySep™ Magnet the fastest and simplest method for enriching highly purified HPSCs from large-volume leukapheresis products—critical for addressing the growing clinical demands for CD34+ cell-based therapies.
The role of TGF-β in the differentiation and lung specification of murine type 1 conventional dendritic cells
Authors: Romo-Perez Yuliana Maritza , Soysa Radika , Liudahl Shannon , Headley Mark 
Published: August 2023

Abstract
Lung-resident type 1 conventional dendritic cells (cDC1s) are critical for initiating immune responses against foreign respiratory viruses and endogenous assaults like cancer cells. Importantly, the cDCs of each tissue display unique phenotypes and functions dictated by the environment they populate. However, our understanding of the factors that regulate cDC1 development and function in the lung is minimal. The cytokines, FMS-like tyrosine kinase 3 ligand (FLT3L), and granulocyte-macrophage stimulating factor (GM-CSF) are essential for the development of tissue-resident cDC1, but in in vitro systems, these factors are insufficient to generate cDC1s with a lung-specific phenotype. RNAseq analysis of lung cDC1 identified a clear enrichment in genes associated with transforming growth factor beta (TGF-β) signaling, a factor also known to be enriched in the airspaces of the lung. TGF-β has been previously reported to maintain DC quiescence in the lung, however, our data suggested it may also play a role in differentiation and lung specification of these cells. Based on this, I hypothesized that adding TGF-β to in vitro bone marrow (BM) cultures alongside established cytokines FLT3L and GM-CSF would generate cDC1s phenotypically and functionally similar to in vivo lung cDC1s. The addition of TGF-β, but not GM-CSF, to optimized FLT3L-BMDC cultures resulted in development of cDC1 which highly resemble lung cDC1. The development of a high throughput in vitro system that differentiates functional lung cDC1s will not only inform the in vivo factors required for development of these cells but also provides a useful platform for interrogation of lung cDC1 function and a stepping-off point to begin models for human lung cDC1 production and study
Supported by grants from the University of Washington PREP program NIH (R25) and the Fred Hutchinson Cancer Center Diversity, Equity, and Inclusion Student Fellowship
Harnessing arginine metabolism overcomes hyperthermia-induced metabolic dysfunction of CAR T-cells
Authors: Kondo Taisuke , DuSold Justyn , Achar Sooraj , Adebola Serifat , Gonzalez-Menendez Pedro , Perrault Julie , Jess Jennifer , Yates Bonnie , Song Hannah , Fox Stephen , Xu Xia , Chan King , Abdelmaksoud Abdalla , Highfill Steven , Andresson Thorkell , Shah Nirali , Dardalhon Valerie , Altan-Bonnet Grégoire , Taylor Naomi 
Published: August 2023

Abstract
Chimeric antigen receptor (CAR) T-cells have shown remarkable success in the treatment of hematological malignancies, but many patients still relapse. One common adverse on-target effect of CAR T-cells is cytokine release syndrome. Importantly though, the impact of fever, a hallmark of this syndrome, on CAR T-cell function is not known. We find that exposure of CAR T-cells to hyperthermia (40°C) significantly decreased their subsequent cytotoxicity against NALM6 leukemic cells, both ex-vivo and in-vivo. This was associated with reduced secretion of IL-2, IFNg, and IL-8 by CAR T-cells and high dimensional analyses revealed the induction of a terminally differentiated T cell phenotype. Gene profiling assays highlighted a negative enrichment of mTORC1, glycolysis, and oxidative phosphorylation gene sets in CAR T-cells subjected to hyperthermia and metabolome analyses unveiled significant reductions in urea cycle metabolites. Notably, pharmacological supplementation of arginine markedly enhanced the ex-vivo and in-vivo cytotoxicity of hyperthermia-exposed CAR T-cells. Moreover, in the absence of hyperthermia, short-term arginine supplementation enhanced the metabolic fitness of CAR T-cells, augmenting their long-term in-vivo persistence and cytotoxicity. We identify arginine metabolism as a critical pathway in CAR T-cells rendered dysfunctional by exposure to hyperthermia and pharmacological arginine support will inform future iterations of CAR T-cell interventions.
Ketogenic diet influences the microbiome-immune axis with therapeutic potential in ASD
Authors: Yamamoto Brennan Y , Allan Nina , Kunihiro Braden P , Nunokawa Chandler K L , Umeda Lesley , Phankitnirundorn Krit , Peres Rafael , Maunakea Alika K 
Published: August 2023

Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder affecting social interaction and communication, associated with increased levels of inflammation and mitochondrial dysfunction. The ketogenic diet has neuroprotective affects and decreases the severity of inflammation related conditions. A cohort of 7 children aged 7 to 19 diagnosed with ASD have improved behavioral symptoms following the ketogenic diet. This study aims to identify changes to the gut microbiome and inflammatory markers that are associated with improved prognosis. Stool and plasma samples were collected before starting the diet and up to twelve months after starting the diet. Stool samples were sequenced for microbiome data and plasma samples were analyzed for inflammation factors, ketone bodies, and miRNA presence. Butyrate kinase (Buk) DNA and RNA levels were elevated in stool samples suggesting changes to the microbiome significantly affected butyrate kinase levels in the patient’s digestive tract. Metabolomic data identified the cohort had elevated butyrate levels following the ketogenic diet further characterizing the importance of butyrate kinase producing bacteria, including Roseburia. Changes to inflammatory factors identified a decrease in IL-1B, IL-12p70, and BDNF. Decreases in BDNF, an activator of the NF-kB pathway, identifies a potential pathway for decrease in IL-1B and IL-12p70. Correlation analysis identified that Roseburia species elevated Buk DNA and decreased inflammation. While limited in sample size, these findings provide important insight into key molecular changes in the microbiome-immune axis linked to brain function that could be targeted for treatment of ASD and warrants further investigation.
Supported by grants from NIH (P20GM113134)
Oral exposure to Escherichia coli toxin protects against lung allergen-induced inflammation
Authors: Salgado Caio Loureiro , Ayupe Marina Caçador , Rodrigues Juliana Falcão , Silva Luisa Menezes , De Castro Oliveira Bernardo , Moreira Francielly , Gonçalves Leonardo Mandu , da Silva Guilherme William , Ramirez Jofer Andree Zamame , De Souza Ferreira Luis Carlos , D’império-Lima Maria Regina , da Silva Henrique Borges , da Fonseca Denise Morais 
Published: August 2023

Abstract
Recent studies suggest that the intestinal microenvironment regulate lung immune cells. Conversely, changes in the lung can modulate the gut immune system. Yet, mucosal-associated immune responses have been studied in a compartmentalized manner, as if there is no communication between different organs. Thus, the role of the gut-lung axis in mucosal immune responses is poorly understood. Using enterotoxigenic Escherichia coli (ETEC), we established a model of intestine-localized infection without translocation to any other tissue. In response to ETEC, type 2 innate lymphoid cells (ILC2s) and eosinophils accumulated in the intestinal lamina propria, even after bacterial clearance. In addition, oral ETEC transiently increased the numbers of ILC2 and eosinophils in the lung parenchyma. To test if oral ETEC promote lung immune responses to allergen, we exposed mice that recently cleared ETEC to intranasal papain/ovalbumin allergy induction model. Unexpectedly, ETEC-exposed mice were significantly resistant to allergen-induced lung inflammation, with reduced number of ILC2, Type 2 effector CD4+ T cells (Th2) and eosinophils. Paradoxically, oral ETEC-induced protection against lung allergen exposure was dependent on IL-33: IL-33KO mice developed partial lung inflammation in this model, and no protection induced by ETEC exposure was observed. Importantly, protection from allergy was achieved with ETEC heat-labile toxin (LT) oral exposure; we also found that the toxicity domain of LT is needed for this protection. Our results indicate that gastrointestinal bacterial infection mediators (toxins) negatively regulate the onset of allergic inflammation and may provide a novel immunological basis for the “hygiene hypothesis”.
R01AI170649 FAPESP 2021/15185-2
Combination immunotherapy of ibrutinib, fludarabine, and pembrolizumab for high-risk CLL patients: clinical and immunological analysis of a pilot phase II study
Authors: Mu Rui , Ahn Inhye , Sun Clare , Chen Jonathon , Singh Komudi , Wiestner Adrian 
Published: August 2023

Abstract
Chronic lymphocytic leukemia (CLL) is due to clonal expansion of CD5+ B cells. Immunosuppression is a hallmark of CLL and includes impaired anti-tumor T cell responses. Exhaustion of PD-1+ CD8 T cells has been implicated in disease progression, providing a rationale to test checkpoint inhibitors in the clinic. However, single-agent anti-PD-1 antibodies lacked clinical efficacy. Here, we analyzed immunologic parameters in patients enrolled on a phase II study of ibrutinib (continuous administration), fludarabine (2 cycles) and pembrolizumab (for 18 cycles after fludarabine). 13 patients were enrolled, 10 patients were evaluable, 9 patients achieved partial response (90%) and 1 patient complete response (10%). Bulk RNA-seq of CLL and T cells revealed inhibition of B-cell receptor and NF-kB signaling in tumor cells, and increased proliferation and activation gene signatures in CD3+ T cells. The proportion of Ki-67+ CD8 T cells increased in 5 out of 13 patients (immune responders) 3 weeks after the first dose of pembrolizumab. Compared with immune non-responders, responders had a significantly higher percentage of CD45RO-CD27+ and CD45RO+CD27+ CD8 T cells. At 6 months, T cell proliferation in all patients was back to baseline and there was no change in TCR clonality at 12 months. In vitro stimulation with CD3 and CD28 antibodies upregulated activation markers on CD8 T cells in all patients, increases in Ki-67 were variable. Overall, responses in patients were weaker than in healthy controls. In summary, pembrolizumab in combination with ibrutinib transiently increased CD8 T cell proliferation in a subset of CLL patients but did not improve the clinical response over ibrutinib.
Antiviral vaccines for local immunotherapy against solid tumors
Authors: Cuburu Nicolas , Sethi Shiv , Bialkowski Lukasz , Thompson Cynthia , Pontejo Sergio M , Schiller John T 
Published: August 2023

Abstract
Local immunotherapy against solid tumors is considered a viable approach to stimulate the tumor immune microenvironment and anti-tumor immunity. Here, we interrogate whether preexisting anti-vaccine immunity induced by licensed subunit vaccines could be leveraged for local cancer immunotherapy in the syngeneic murine tumor models. We selected Shingrix, a VZV vaccine containing the glycoprotein E (gE) antigen and adjuvant AS01B, and Gardasil-9, a HPV vaccine containing the L1 virus-like particles and alum because of the CD4 and CD8 T cell responses they respectively induce.
Intratumoral injection of Shingrix alone or with immune checkpoint blockade (CTLA-4), in prevaccinated mice delayed tumor growth and often led to complete regression. These responses were associated with the induction of CD8+ T cell responses against tumor associated antigen, to tumor immune activation and alteration of the myeloid compartment. The injection of selected MHC-II-restricted gE minimal peptide epitopes combined with polyI:C also led to durable remission suggesting a contribution of gE-specific CD4 T cells. In contrast, Gardasil-9 i.t. injection did not delay tumor growth or cause tumor rejection which suggests inefficient class I cross-presentation of native VLP in the tumor cells. However, the injection of MHC-I-restricted L1 minimal peptide epitopes led to complete and durable remissions suggesting efficient tumor control by L1-specific CD8 T cells.
Our results suggest that anti-viral licensed vaccines can be leverage as a new class of immunotherapeutics for local cancer therapy and intrinsic immunogenicity properties of vaccines should be considered as these effects appeared to be vaccine specific.
NIH Intramural program.
Uncovering the role of the local environment in shaping antiviral immunity of the female reproductive tract
Authors: Segrist Elisha , Belkaid Yasmine 
Published: August 2023

Abstract
The female reproductive tract (FRT) is a unique barrier site. It tolerates foreign entities like sperm and the fetus for reproduction but must also be immunologically active enough to control pathogens, like viruses. Millions of women use antibiotics or anti-retrovirals, and these treatments alter the environment of the FRT by changing the microbiota or inhibiting endogenous retroviruses, but the impact of this on FRT immunity and function are understudied. Human cohort data has revealed that the vaginal microbiota profoundly influences risk of virus infection, but the mechanisms for this are not well understood. Endogenous retroviruses (ERV) are necessary for reproduction, as an ERV envelope protein is essential for placental formation, but how these elements shape immunity of the FRT is barely characterized. Preliminarily, I have found that both the microbiota and ERVs shape innate and adaptive immune cell populations and functions in the FRT. Additionally, I found that microbial derived ligands such as LPS are sufficient to induce ERV expression in the uterine epithelium. Therefore, the main hypothesis tested by my project is that the vaginal microbiota induces ERV expression in the epithelium of the reproductive tract which in turn activates host nucleic acid sensing pathways and interferon production in the epithelium and that this response promotes local antiviral protection.
Y.B. was supported by the Division of Intramural Research of the National Institute of Allergy and Infectious Diseases (NIAID; ZIAAI001115-09, ZIAAI001132-07, ZIAAI001133-08). E.S. was supported by the Training Office and OITE of the National Institute of Allergy and Infectious Diseases (Intramural AIDS Research Fellowship).
Molecular heterogeneity of antiviral resident memory CD8 T cell in the female reproductive tract
Authors: Hasan Mohammad H , Mithila Farha J , Lin Ying , Wallace Joselynn , Pacia Jessica , Zhang Nu , Beura Lalit K 
Published: August 2023

Abstract
Resident memory CD8 T cells (TRM) in the female reproductive tract (FRT) represent a primary defense mechanism against viruses. Presence of CD8 TRM in the reproductive mucosa is associated with accelerated viral control and rapid establishment of an antiviral state. However, little is known about the factors that control and maintain TRM in this important barrier organ. Here, using single-cell RNA-sequencing (scRNA-seq) and genetic methods, we characterized development of distinct FRT CD8 TRM subsets. Our scRNA-seq studies revealed that most FRT CD8 TRM belong to two transcriptionally distinct subsets that are marked by mutually exclusive surface expression of CD103 and Ly6C. CD103+ TRM were dependent on the cytokine TGF-b for development, as CD8 T cells lacking TGF-b receptors were significantly impaired at giving rise to CD103+ TRM. Local activation of TGF-b by av integrins was important for the maintenance of these FRT TRM. In comparison to the CD103+ TRM which resembled mature TRM, the Ly6C+ TRM exhibited features of effector cells. Ly6C+ TRM were regulated by the transcription factor T-bet and developed under distinct priming conditions compared to CD103+ TRM. Upon in vivo antigenic recall, the CD103+ subset elaborated greater cytotoxicity than the Ly6C+ subset. Taken together, our findings provide key insights into molecular and developmental heterogeneity of FRT CD8 TRM which has implications for improving vaccination and local immunotherapy approaches.
Supported by grants from NIH (P20GM121298)
SPHK1-S1P-S1PR1 signaling pathway is emerging as a potential therapeutic target in improving endothelial barrier function and prevent coronary artery disease
Authors: Alsiyaghy Jassam , Graefen Bahar , Aliyeva Leyla , Lnu Arina , Tauseef Mohammad , Fazal Nadeem 
Published: August 2023

Abstract
Sphingosine kinases (SPHKs) catalyze the formation of sphingosine 1 phosphate (S1P) from sphingosine. S1P, a lipid mediator, was shown to be one such factor promoting endothelial barrier function. S1P binds to S1P receptor-1 (S1PR1) in endothelial cells, leading to activation of heterotrimeric G proteins (Gi), and signals enhancement of endothelial barrier function by the activation of small GTPase Rac1. We hypothesized that SPHK1 via generation of S1P induces reannealing of adherens junctions and thereby prevents thrombin-induced endothelial permeability. To understand the role of SPHK1 pathway, we depleted SPHK1 protein in endothelial cells using SPHK1 specific small interference (si) RNA. Depletion of SPHK1 significantly disrupted the adherens junction, VE-cadherin and increased the gap formation of endothelial cells. Upon depletion of SPHK1 we found decrease cell proliferation and migration, but no change in the expression of Sphingosine 1 Phosphate Receptor 1 (S1PR1) expression in endothelial cells. To determine if in the absence of SPHK1, does S1P has any pharmacological role, we treated the cells with Sphingosine 1 Phosphate (S1P) at the dose of 1μM. We found that S1P re-anneal the adherens junctions and improve cell proliferation and migration in SPHK1 depleted endothelial cells. This indicates that SPHK1 via generation of S1P prevents endothelial permeability through S1PR1 receptor activation. Upon treatment with S1P in SPHK1 depleted endothelia showed completely recovery in barrier function. In conclusion, our study for the first time shows that SPHK1 maintains endothelial barrier function and reanneals adherens junctions, thus hastens the recovery process.
CTRE grant to Professor Nadeem Fazal, MD, PhD
Identification of p-eIF4E as a new regulator of regulatory T-cell activity
Authors: Santinon François , Papadopoulos Theodoros , Henderson-Berg Meagan-Helen , Gonçalves Christophe , Abrahams Madelyn , Gagnon Natascha , Gupta Vrinda , Chou Hsiang , Miller Wilson H , del Rincon Sonia Victoria 
Published: August 2023

Abstract

Objective
Phosphorylated Eukaryotic translation initiation factor 4E (p-eIF4E) is a critical regulator of protein synthesis and is phosphorylated by MNK1/2 to promote the translation of a mRNA subset. We have shown that blocking the eIF4E phosphorylation increased the anti-tumor immune response, especially the CD8 T cell activation. However, the role of p-eIF4E in CD4 T cell subsets, and in particular regulatory T cells (Tregs) is still unknown. The aim of this study was to explore the impact that the absence of p-eIF4E could have on the Treg activity as well as in an inflammatory context.

Methods
To investigate the role of p-eIF4E on Tregs activity, we used genetically modified mice expressing a non-phosphorylatable form of eIF4E (KI mice). First, we analyzed Treg activity in WT and KI mice and the same mice subjected to dextran sulfate sodium (DSS)-induced colitis. We also analyzed the colonic immune cell infiltration using spectral flow cytometry and CODEX technology.

Results
Using our mouse models, we observed that the p-eIF4E lack led to a decrease in Treg stability as well as a decrease in their ability to control the helper T cell (Th) proliferation. In the colitis context, we observed an increase in the disease severity in KI compared to WT mice characterized by an increase in colonic immune infiltration. Moreover, our mesenteric lymph node and colon immunophenotyping revealed a significant decrease in Treg, and an increase in Th expressing IFNγ in KI compared to WT mice. Finally, we observed a decrease in KI Treg ability to migrate to the lymph nodes.

Conclusion
These results demonstrate for the first time the preponderant role of p-eIF4E in the control of Treg stability and Treg migration but also in their ability to regulate inflammation.