bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of naturally acquired immune responses against the Plasmodium falciparum malaria vaccine candidate PF3D7_1136200
Authors: Garza Rolando , Reers Ashley , Reyes Raphael , Ssewanyana Isaac , Greenhouse Bryan , Bol Sebastiaan , Bunnik Evelien 
Published: August 2023

Abstract
Humoral immunity is critical for protection against Plasmodium falciparum malaria. In endemic areas, individuals acquire protective immunity against malaria through repeated exposure to P. falciparum parasites. Understanding these naturally acquired immune responses would be highly informative for the development of improved vaccination strategies against malaria. Antibody responses against the uncharacterized protein PF3D7_1136200 correlate with protection from malaria, however, the development of these antibody responses over time and their role in protecting against malaria remain unknown. Here, we compared PF3D7_1136200-specific antibody and B cell responses to that of other P. falciparum antigens in Ugandan individuals with different immune status: immune adults (n=24) and children with high (n=10) or low (n=8) susceptibility to malaria. In all groups, serum antibody reactivity against MSP1, MSP3, AMA1, VFT, Pf41, and Pf113 was dominated by IgG. In contrast, serum IgG antibody reactivity against PF3D7_1136200 was much lower, while IgM reactivity was at a similar or higher level compared to these antigens. In line with the low serum IgG reactivity against PF3D7_1136200 among adults, we exclusively observed IgM+ memory B cells (MBCs) against PF3D7_1136200, while IgG+ MBCs were more abundant than IgM+ MBCs for all other antigens. These results indicate that PF3D7_1136200 has a low antigenic profile, similar to that of other favorable P. falciparum vaccine candidates, and suggest potential shielding of antigen from the host immune system. Together with the genetic conservation of PF3D7_1136200, these characteristics highlight that Pf3D7_1136200 has potential as a novel vaccine candidate against malaria.
Supported by grants from NIH (R01 AI153425, P30 CA054174-20)
Memory phenotype Tfh cells are homeostatically maintained and are important for the development of germinal centers and B cell responses to virus infection
Authors: Wang Ping , Symonds Alistair , Li Suling 
Published: August 2023

Abstract
Memory phenotype (MP) CD4 T cells that develop in the absence of overt antigen stimulation are important for both innate and adaptive immune responses. Although pathogen specific MP CD4 T cells have been found to function effectively against infection, it is not known if MP Tfh cells can also be developed in the absence of overt antigen stimulation. Here, we demonstrate that MP Tfh cells develop in the absence of overt antigen stimulation. In addition to FR4+, a mark found in pathogen induced memory Tfh cells, MP Tfh expressed high levels of Egr2. The development of MP Tfh are defective in CD2-Egr2/3−/− mice. MP Tfh cells share similar features in phenotypes and epigenetics with antigen induced memory Tfh cells and can effectively induce germinal center formation and B cells responses. Thus, MP Tfh cells regulated by Egr2/3 pathway are important component of adaptive immunity.
Medical Research Council UK (MR/N00096X/1), Barts Charity (MGU0463)
Prevention of thymus involution rescues old mice from fatal Toxoplasma gondii infection
Authors: Morales-Sanchez Abigail , Cowan Jennifer , Vacchio Melanie , Zhao Yongge , Jankovic Dragana , Sen Ranjan , Bosselut Remy , Bhandoola Avinash 
Published: August 2023

Abstract
Thymic epithelial cells (TEC) make up the thymic microenvironments that support the generation of a functionally competent and self-tolerant T-cell repertoire. Infections, starvation, and aging, among other factors, cause thymus involution with loss of T-cell generation and decreased frequency of naive T-cells in secondary lymphoid organs. However, the causes and consequences of thymus involution are not clearly understood. Since thymus function declines with involution, we need a better understanding how the thymus controls T cell development. We found that constitutive overexpression of Myc (cMycTg) in TEC prevents thymus involution, causing a dramatic increase in thymus size in adult mice (Cowan et al, 2019). In addition, cMycTg mice restored frequencies of CD4+ and CD8+ naive T-cell populations to the levels observed in young adult mice. In unpublished work, we have found that prevention of thymus involution rescues aging mice from lethal Toxoplasma gondii infection. During the acute infection, old mice showed a significantly decreased frequency of parasite-specific T-cells and increased serum levels of IFNγ, IL6 and TNFα. Furthermore, antibody depletion of T-cells in aging mice challenged with Toxoplasma gondii prolonged their survival. These findings identify a role for thymic involution in the age-associated mortality of Toxoplasma gondii infection. We are now investigating the mechanisms responsible for the pathogenic immune responses seen in aged individuals to understand how improved thymic function modifies immune responses.
AMS is supported by the patronage of the Children’s Hospital of Mexico.
SCS, JEC and AB are supported by the NIH Intramural Cancer Research Training Award to post-doctoral fellows.
Identification of immunosuppressive and tumor-promoting neutrophils in bone marrow of human and human immune system mice
Authors: Li Yan , Liu Wei , Che Keying , Lu Chun , Wei Jia 
Published: August 2023

Abstract
Neutrophils in cancer patients were identified as a specialized heterogeneous population that suppress anti-tumor responses and accelerate tumor progression. However, the developmental stage and the source of this population remain elusive. To address this issue, we defined human neutrophil development based on previous publications and demonstrated that immature neutrophils predominate tumor tissues of patients. On the quest to identify the origin of immature neutrophils, we unexpectedly discovered that immature neutrophils collected from bone marrow of healthy people and human immune system (HIS) mice are naturally immunosuppressive and tumor promoting, whereas the mouse counterpart is not. To further investigate the linkage between peripheral and bone marrow immature neutrophils, we created a NCG-Gfi1−/− strain, which overcomes the issue of poor human neutrophil engraftment in periphery. NCG-Gfi1−/− HIS mice manifest similar kinetics of immature neutrophil expansion as cancer patients both in bone marrow and periphery after tumor cell inoculation. Single cell analysis of immature neutrophils cross human tumor, bone marrow and HIS mouse bone marrow samples revealed FCN1 as a common marker for this heterogeneous population. Finally, we proved that elimination of bone marrow immature neutrophils with Flt3L treatment reduced tumor associated neutrophils and delays tumor growth in NCG-Gfi1−/− HIS mice. In summary, human immunosuppressive and tumor-promoting neutrophils are predominantly immature neutrophils and targeting this population in bone marrow may represent a novel strategy for cancer immunotherapy
This study was supported by grants from the National Key Research and Development Program of China (2019YFA0802900), and National Natural Science Foundation of China (32070942, 32122035, 32000669).
Breast cancer remodels the bone marrow immune microenvironment to favor bone metastasis
Authors: Teijeiro Ana , Belkaid Yasmine 
Published: August 2023

Abstract
Bone is the most common site of breast cancer (BC) metastasis, occurring in 70% of patients, and an indication of short-term prognosis. Understanding the environmental and host factors involved in the induction of metastasis is essential to develop therapies that extend patient’s lifespan. Bone colonization by cancer cells is a stepwise process that relies on interactions between cancer cells and the cells that comprise the bone microenvironment, such as osteoclasts, osteoblasts, hematopoietic cells, immune cells, and adipocytes. Calcium, growth factors, and chemokines facilitate bone metastasis. However, the role of immune cells in bone metastasis remains poorly understood. Further, how physiological stressors such as nutrition contribute to pro- or anti-metastatic bone immunity remains unclear. Using mouse models of BC, we found that BC profoundly transforms the bone marrow (BM) immune microenvironment to support metastasis. BC induces bone lymphoid cell loss, with significant reduction in B cells, T cells and NK cells. On the other hand, mammary tumors are associated with enhanced monocytes and eosinophils within the BM. These results support the idea that BC cells crosstalk with the bone and remodel the immune microenvironment to favor tumor cell colonization. We have previously showed that caloric restriction (CR) induces T cell migration to the BM and remodels the bone microenvironment, favoring T cell function and a protective environment. Of note, CR-mediated targeting of the bone microenvironment restores the immune homeostatic pool and contributes to an anti-tumor bone immunity. Thus, nutritional interventions my represent potential therapeutic strategies to target bone metastasis.
This work was supported in part by intramural funds of NIAID, NIH. A.T. is supported by the EMBO Postdoctoral Fellowship Programme (ALTF 1014-2021).
Mass cytometry analysis of mouse nonclassical monocyte heterogeneity in breast tumors
Authors: Valentin-Guillama Gabriel A , Alkan Fulya , Alkan Hilmi , Alimadadi Ahmad , Korkaya Hasan , Hedrick Catherine C 
Published: August 2023

Abstract
Monocytes have emerged as important regulators of cancer progression. Our previous studies demonstrated the importance of nonclassical Ly6Clo monocytes in regulating cancer metastasis in mouse models. Here, we aimed to study monocyte heterogeneity in two different breast cancer tumors in mice using either 4T1 or EMT6 cells. 4T1 tumors exhibit an increased ability to metastasize in the lung in a BALB/c mouse breast cancer model compared to the less aggressive EMT6 tumor model. We evaluated 35 surface markers of tumor-infiltrated monocytes and dendritic cells in tumors isolated from each model using CyTOF mass cytometry. Analysis of monocytes and dendritic cells in the tumors using the Seurat package and the FlowSom algorithm identified 12 cell subsets. Significant differences were discovered between the two tumor types in frequencies of four of 12 identified subsets. However, only one of these subsets, a nonclassical monocyte subset, was higher in the less metastatic EMT6 tumors. This subset was 5-fold higher in EMT6 tumors versus more aggressive 4T1 tumors. This Ly6Clo nonclassical monocyte subset showed high expression of CD169 and CX3CR1, CD86 and CD80. These differentially expressed markers suggest a functional importance in this subset in migration to the tumor and antigen presentation, both of which are anti-tumoral functions. Ongoing studies are aimed towards understanding the role of this non-classical monocyte population in regulating breast cancer metastasis.
This work was supported by NIH R01 CA202987, and P01 HL136275
Blood monocyte-derived CD169+ macrophages contribute to antitumor immunity against glioblastoma
Authors: Kim Hyun-Jin , Park Jang Hyun , Kim Hyeon Cheol , Kim Chae Won , Kang In , Lee Heung Kyu 
Published: August 2023

Abstract
Infiltrating tumor-associated macrophages (TAM) are known to impede immunotherapy against glioblastoma (GBM), however, TAMs are heterogeneous, and there are no clear markers to distinguish immunosuppressive and potentially immune-activating populations. Here we identify a subset of CD169+ macrophages promoting an anti-tumoral microenvironment in GBM. Using single-cell transcriptome analysis, we find that CD169+ macrophages in human and mouse gliomas produce pro-inflammatory chemokines, leading to the accumulation of T cells and NK cells. CD169 expression on macrophages facilitates phagocytosis of apoptotic glioma cells and hence tumor-specific T cell responses. Depletion of CD169+ macrophages leads to functionally impaired antitumor lymphocytes and poorer survival of glioma-bearing mice. We show that NK-cell-derived IFN-γ is critical for the accumulation of blood monocyte-derived CD169+ macrophages in gliomas. Our work thus identifies a well-distinguished TAM subset promoting antitumor immunity against GBM, and identifies key factors that might shift the balance from immunosuppressive to anti-tumor TAM.
This work was supported by Samsung Science and Technology Foundation (SSTF-BA1902-05), Republic of Korea. This work was also supported by the National Research Foundation of Korea grant (NRF-2021M3A9H3015688).
1,25-Dihydroxy Vitamin D Enhances the Differentiation of Intestinal Stem Cells Ex Vivo and In Vivo
Authors: Shaikh Nisar Ali F N U , Liu Chenfan , Yin Yue , Zhang Xiao-Bing , Baylink David J , Galea Dan , Das Bhaskar , Tang Xiaolei 
Published: August 2023

Abstract
Inflammatory bowel disease (IBD) is a chronic inflammatory disorder in the intestines. Current therapies aim at suppressing inflammation to prevent further damage. However, healing already damaged intestinal epithelia is still an unmet medical need. In this regard, epithelial healing is achieved via intestinal stem cells (ISCs) that are located in the intestinal crypts. Considering the literature reports that the active vitamin D (1,25[OH]2D) is essential for the maintenance of Lgr5+ ISCs, the active proliferating ISCs, we recently proposed to deliver locally high 1,25(OH)2D concentrations to the proximity of intestinal crypts to promote intestinal stem cell functions. This local delivery was devised to avoid potential side effects associated with systemically high 1,25(OH)2D concentrations. Using 5-Bromo-20-deoxyuridine (BrdU) to label the actively proliferating ISCs, our previous data indicated that the locally delivered 1,25(OH)2D enhanced the migration and differentiation of Lgr5+ ISCs. However, although sparse in the crypts, other proliferating cells may be labeled with BrdU. This current study used a unique mouse strain to precisely trace Lgr5+ ISCs and consolidated our previous finding that the locally delivered 1,25(OH)2D augmented ISC differentiation. Besides, we generated pure Lgr5+ ISC lines that could be induced to differentiate on demand. Our data showed that, in vitro, 1,25(OH)2D enhanced the differentiation of Lgr5+ ISCs. Moreover, by knocking down the vitamin D receptor (VDR), we demonstrated that the 1,25(OH)2D functions in ISCs are mediated through VDR. Accordingly, our findings suggest that locally high 1,25(OH)2D concentrations are a promising strategy for intestinal epithelial healing.
This study was partially supported by the National Institute of Health (NIH, USA) grant (1R21AI142170); the US Army Medical Research and Materiel Command grant (W81XWH-15-0240); and the GI Foundation of Loma Linda University Innovation grant (RIG-GI 681207-2967).
A computational pipeline for drug discovery in immunometabolism against autoimmune diseases
Authors: Puniya Bhanwar Lal , Bessell Brandt , Zhao Zhongyuan , Loecker Josh , Aghamiri Sara Sadat , Mohanty Sabyasachi , Amin Rada , Helikar Tomas 
Published: August 2023

Abstract
We developed a computational pipeline to study immunometabolism for drug discovery in immune mediated diseases. Our pipeline integrates RNA-seq and proteomics data to build genome scale metabolic models and integrate these models with external drug databases and patient data to perform metabolic flux analyses for identifying drug targets and repurposing. We applied our pipeline to explore the metabolism of B cells in the context of rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE). We constructed metabolic models of B cells, performed enzymatic inhibition of targets of existing drugs and compounds, and integrated the model’s results with differentially expressed genes in RA and SLE patients. Using a computational scoring method, we ranked the inhibited targets based on their ability to stimulate the reactions of differentially expressed genes in diseases to have metabolic flux in opposite directions of their up and down-regulation. As a result, we identified 25 B cell drug targets against RA and 23 B cell drug targets against SLE. We validated these targets by comparing them against the current treatment options for these diseases. For RA, five of the identified targets are genes that are already targeted by existing drugs used to treat RA. Our top-ranked targets for RA are adenine phosphoribosyltransferase, galactosidase beta 1, and aldehyde dehydrogenase 5 family member A1. For SLE, the top-ranked new targets are geranylgeranyl diphosphate synthase 1, glutathione-disulfide reductase, and galactosidase beta 1. Our pipeline provides a streamlined approach for identifying drug targets and predicting repurposable drugs and can facilitate the investigation of novel indications for diseases to improve global health.
Supported by Layman Seed grant from University of Nebraska Foundation, and NIH grant R35GM119770.
In vitro assay development to assess successful removal of T and B cell epitopes through Seismic’s IMPACT platform
Authors: Newton Andita P , Pellerin Alex , Anderson Jordan , Rollins Nathan , Hollfelder Melissa , Peckner Ryan , Higginson-Scott Nathan , Otipoby Kevin , Mascanfroni Ivan 
Published: August 2023

Abstract
Proteases derived from human pathogens can specifically cleave IgG into F(ab’)2 and Fc fragments. IdeS, an IgG cleaving enzyme derived from Streptococcus pyogenes, has shown clinical proof of concept, and is approved for use before kidney transplantation. Due to the immunogenic nature of these proteases, dosing is limited by high prevalence of pre-existing antibodies and the induction of anti-drug antibodies after dosing. Therefore, to mitigate the impact of the immune system on our enzyme, we identify and remove putative T and B cell epitopes using Seismic’s IMPACT platform leveraging machine learning.
To experimentally validate in silico predictions, we developed two complementary in vitro assays using intravenous immunoglobulin (IVIg) to assess removal of B cell epitopes. First, we assess how mutating the wild type (WT) protease sequence impacts pre-existing antibodies in a competitive binding assay followed by evaluating global binding of pre-existing antibodies to our protease. Additionally, we developed an in vitro PBMC proliferation assay to determine the success of T cell epitope removal. Using flow cytometry, we quantitively assess CD4 proliferation via bromodeoxyuridine (BrdU) incorporation.
We demonstrate examples of molecules designed through our IMPACT platform to reduce both T and B cell epitopes. The B cell epitope assays show a decrease in competition as compared to the WT protease while achieving a reduction in IVIg binding. These data suggest that these in vitro assays can be used to screen for successful invisibilization of molecules of interest.
PPARd restricts intratumoral Treg function through negatively regulating the CIITA-MHCII axis
Authors: Yang Qiyuan , Liang Yuqiong , Zheng Ye 
Published: August 2023

Abstract
Regulatory T cells (Treg) have been associated with poor clinical prognosis of multiple types of cancers due to their suppression of anti-tumor immunity. Although Treg depletion can lead to the rejuvenation of the patient’s immune response to tumors, systemic Treg depletion induces autoimmune diseases such as type-1 diabetes and inflammatory bowel disease. Therefore, understanding how Treg cells adapt to the tumor microenvironment (TME) and how they suppress anti-tumor immunity is critical for the development of novel Treg-based cancer treatment. Peroxisome proliferator activated receptor δ (PPARd) is a member of the nuclear hormone receptor family, and plays a crucial regulatory role in fatty acids metabolism. Here, we uncover that ablation of PPARd in Treg leads to accelerated tumor growth with a more immuno-suppressive TME. Mechanistically, the loss of PPARd in Treg leads to upregulation of a set of genes involved in the antigen presentation pathway, including CIITA and MHCII. Deleting CIITA in PPARd deficient Tregs boosts anti-tumor immunity and inhibits tumor growth, indicating CIITA is a key regulator downstream of PPARd in Tregs. Moreover, overexpressing CIITA in Treg enhances its suppressive function, while knocking out MHCII reduces Treg suppressive function. Our study demonstrated that PPARd restrains tumor Treg function by downregulating the CIITA-MHCII pathway, and identified a previously unrecognized MHCII+ tumor Treg subset as a potent suppressor of anti-tumor immunity. Targeting this Treg subset could open a new avenue for boosting anti-tumor immunity while mitigating autoimmunity risk.
Q.Y. was supported by a NOMIS fellowship.
Y.Z. was supported by the NOMIS Foundation and the National Institutes of Health (R01-AI107027, R01-AI1511123, R21-AI154919, and P30-CA014195).
CRISPR-Cas9 screen identifies potential novel regulators of CD8+ T cell dysfunction
Authors: Holcomb Erin A , Jiang Long , Tate Akshay , Pearson Ashley N , Wang Zhuwen , Jungles Kassidy Mikala , James Jadyn , Huber Amanda , Green Michael 
Published: August 2023

Abstract
CD8+ T cells directly target and kill cancer cells and are required for effective antitumor immunity and response to immunotherapy. However, CD8+ T cells may become dysfunctional and exhausted when exposed to chronic antigen stimulation during cancer. Dysfunction is characterized by increased expression of inhibitory receptors as well as impaired effector function, yet the genetic mechanisms controlling dysfunction remain poorly understood. To address this gap, we have developed an ex vivo restimulation model that recapitulates features of CD8+ T cell dysfunction seen within the tumor microenvironment. By coupling this system with genome-wide CRISPR-Cas9 loss of function screening, we have identified genetic factors which may play a novel role in the progression of CD8+ T cells to a dysfunctional state. Deletion of select factors restored CD8+ T cell survival and effector function during chronic restimulation conditions in vitro, including tumor cell killing capability. Future studies will focus on further characterizing the phenotypic and functional roles of these regulators, as well as translating this model to primary human CD8+ T cells. In summary, we have uncovered novel potential regulators of CD8+ T cell dysfunction and targeting these genes may improve antitumor immunity and immunotherapy efficacy.