bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inflammation perturbs NK cell phenotype and function in chronic myeloid leukemia (CML)
Authors: Kuznetsova Valeriya , Costa Amanda , Patel Sweta , Luca Francesca , Franceski Alana , Goel Paran , Crown Brittany , Camacho Virginia , Matkins Victoria , Welner Robert 
Published: August 2023

Abstract
Natural killer (NK) cells have the capacity to recognize and clear cancer cells by releasing cytotoxic granules. In fact, NK cells’ mature phenotype and abundance are associated with prolonged treatment-free remission in chronic myeloid leukemia (CML). However, NK cell anti-leukemic activity is suppressed during the disease, and the environmental triggers of this impairment are not fully characterized. Given the role of inflammatory cytokines in the progression of myeloid malignancies, we define their impact on NK cell function in a BCR-ABL1+ CML chimeric mouse model. Consistent with clinical observations, NK cells are reduced in counts in leukemic mice, display immature phenotype, low degranulation rate, and altered expression of activating and inhibitory receptors. Single-cell RNAseq analysis confirmed these observations at the transcriptional level, and revealed enrichment in genes and pathways associated with inflammatory cytokine response (e.g., GM-CSF, LTα/β, XCL1, IL-6st, IL-2Ra, SOCS1/2/3, CIS; IL-6/STAT3 and TNFa/NF-kB pathways) in CML-exposed NK cells. To validate the clinical relevance of our findings, we characterized NK cells from CML patients. As expected, NK cell frequencies are reduced in our cohort and display diminished K562-targeted degranulation. Mirroring mouse scRNAseq data, patient NK cells possess a pro-inflammatory gene signature with the activation of JAK-STAT, TNFa/NF-kB, and PI3K-Akt signaling pathways. As this is likely triggered by leukemic cytokines, we found that leukemic serum dampens ex vivo NK cell degranulation capacity. Thus, we speculate that NK cells are sensitive to CML-associated cytokines and that inflammation represents an optimal target for NK-boosting immunotherapies.
γδ T cells are significantly suppressed in glioma patients but retain their cytotoxic potential
Authors: Lehman Natalia , Mazurek Marek , Mrozowska Karolina , Michalski Adam , Rola Radosław , Bojarska-Junak Agnieszka , Zarobkiewicz Michał 
Published: August 2023

Abstract
Complex interactions between tumor and immune cells influence γδ T cells in the course of glioma. The study aimed to characterise the γδ T cells in glioma patients and assess their potential for γδ T-based immunotherapy. Peripheral blood from 52 glioma patients and 30 healthy controls was collected. γδ T cells and their subsets were assessed by flow cytometry and compared between stages i.e. LGG and HGG. Cytokine expression and cytotoxicity against U251MG was tested on Vδ2 in vitro cultures. The co-culture of healthy donors PBMC with glioma patient plasma or 4 hours stimulations with U251MG were performed.
Both total γδ T and Vδ1 cells were significantly expanded in glioma patients. While stimulatory molecules (CD226 and NKG2D) were downregulated, co-inhibitory molecules (PD-1, CTLA-4, TIGIT, TIM-3, LAG-3) were overexpressed. Suppression of γδ T cells seems to be promoted by circulating cytokines as PD-1, TIGIT, TIM-3, LAG-3 were upregulated in cultures with patient plasma. Healthy volunteer γδ T cells are usually significantly activated by U251MG as was demonstrated by an increase in CD69 and CD107a expression after short-term co-culture. Importantly, glioma patient-derived Vδ2 cells retained their cytotoxic potential against glioblastoma cells, even though they overexpressed anti-inflammatory cytokines (IL-10, TGF-β, IL-17).
The results highlight the profoundly immunosuppressive peripheral blood environment in gliomas. Most importantly, this may significantly affect the general fitness of γδ T cells, lowering their potential for immunotherapy. On the other hand, those changes seem to be at least partially reversible as patient-derived γδ T cells retain their cytotoxic potential after in-vitro activation and culture.
Supported by grant from Medical University of Lublin MG 25/2022.
Identification and characterization of selective FcγRIIb binders and their potential of IMPACTing immune-mediated diseases
Authors: Lutz Stephen , Cianci Mike , Grebinoski Stephanie J , Borah Minasri , Stanlie Andre , Goydel Rebecca , Visweswaraiah Jyothsna , Higginson-Scott Nathan , Otipoby Kevin , Cipolletta Daniela 
Published: August 2023

Abstract
Biologics targeting multiple pathways and/or multiple cell types simultaneously have the potential to restore normal immune homeostasis. Inhibitory checkpoint receptor agonism by antibodies benefits from higher order clustering for strong activation, which can be achieved by antibody Fc binding to Fc gamma receptors (FcγRs). However, many of the current agonist antibodies non discriminately bind activating FcγRs. This has the potential to trigger inflammatory cytokines by antigen presenting cells (APCs) or cause antibody dependent cellular cytotoxicity (ADCC).
Clustering by Fc binding to the inhibitory Fc receptor, FcγRIIb has the potential to provide superior clustering by avoiding inflammatory cytokine responses and limiting APC activation. However, FcγRIIb is 93% homologous to the activating receptor FcγRIIa, and designing molecules that specifically bind FcγRIIb presents a challenge that our IMPACT platform can address. Using integrated machine learning, structural biology and traditional antibody campaigns, we have identified selective FcγRIIb binding molecules, and characterized their potential for IMPACTing immune-mediated diseases.
The promise of machine learning: using Seismic’s IMPACT platform to design IgG cleaving enzymes for chronic treatment of autoimmune diseases
Authors: Pellerin Alex , Anderson Jordan , Rollins Nathan , Sanmarco Liliana , Newton Andita , Le Nam , Shin June , Hoel Chris , Cianci Michael , Hoyt Emily , Mojta Shanell , Hollfelder Melissa , Cipoletta Daniela , 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. This unique trait suggests a novel opportunity to use these molecules to treat auto antibody mediated disease. IdeS, an IgG cleaving enzyme derived from Streptococcus pyogenes has shown clinical proof of concept and is approved for use before kidney transplant. Due to the immunogenic nature of these proteases, the dosing regimen is impacted by pre-existing antibodies and the induction of anti-drug antibodies after dosing.
To mitigate the impact of the immune system on our novel enzyme, we employed our IMPACT platform leveraging machine learning to reduce T and B cell epitopes and to ensure that our molecule exhibits desirable drug like properties while maintaining enzymatic activity. To extend the pharmacokinetics (PK) of our molecule, we fused it with a Fc domain. To evaluate IgG protease PK and pharmacodynamics (PD), intravenous immunoglobulin (IVIg) was injected at different time points after protease treatment and IgG levels were quantified by MSD. As expected, the addition of the Fc increased the molecule’s half-life that resulted in a PD effect at later time points than observed with a control enzyme without a Fc. Taken together, our IMPACT platform leveraging machine learning demonstrates that we can optimize drug-like properties and reduce the immunogenicity of a molecule while maintaining function, resulting in a potential novel treatment for chronic autoimmune diseases.
Ineffective polarization characterizes CD4 T cell responses to persistent Borrelia burgdorferi infection
Authors: Hammond Elizabeth M , Tucker Inglis , Olsen Kimberly , Shah Priya , Baumgarth Nicole 
Published: August 2023

Abstract
Borrelia burgdorferi (Bb), the spirochetal agent of Lyme disease, evades immune clearance in infected mice and humans, suggesting ongoing immune suppression. Here we explored the functionality of Bb-induced CD4 T cell responses in infected mice, which are considered Th1 polarized. Surprisingly, in vitro restimulation of CD4 T cells from mice infected for 12 days failed to induce secretion of the hallmark Th1 cytokine IFNg. Consistent with that data, flow cytometry and RNAseq of CD4 T cells from lymph nodes (LNs) of Bb-infected mice at 6, 10, 14, and 21 days post infection (dpi) showed a transient Th1 and Th17 polarization that peaked at 10 dpi before declining, confirmed also by RT-PCR. While Th1 and Th17 gene expression profiles returned to baseline by 14 dpi, increased frequencies of CXCR4+ CXCR5+ PD-1hi ICOS+ BCL6+ T follicular helper (Tfh) cells emerged at that time, concomitant with germinal center induction. The lack of CD4 T cell effector polarization was noted also in the skin, an effector site after Bb infection, as well as in antigen-specific T cells, which were identified using a new MHCII tetramer to the Bb surface antigen arthritis related protein (Arp). Together, our results indicate a failure to sustain effector CD4 T cell polarization after Bb infection, identifying CD4 T cells as a potential target of Bb-mediated immune suppression.
This work was supported by grants from the Global Lyme Alliance, the Stephen & Alexander Cohen Foundation, NIH R01AI157007 (NB) and T32 AI060555 (EMH).
This work was supported by grants from the Global Lyme Alliance, the Stephen & Alexander Cohen Foundation, NIH R01AI157007 (NB) and T32 AI060555 (EMH).
IL-21 from IFN-g+ IL-21+ hybrid T cells promotes germinal center B cell proliferation
Authors: Gbedande Komi , Domingo Nadia N , Puebla-Clark Lucinda , Weinstein Jason D , Stephens Robin 
Published: August 2023

Abstract
Clearance of infection with Plasmodium spp. requires both antibody and Th1-type responses. While Th1-like cells control the peak in P. chabaudi infection, however specific IgG is delayed. Both Tfh and GC-Tfh can promote specific antibodies and long-lived plasma cells to fully clear infection. GC-Tfh numbers remain stable throughout P. chabaudi infection, while Th1/Tfh hybrid (IFN-g+/IL-21+CXCR5int) cells expand. Testing if triple cytokine reporter mice (Il21-Kat Il4-GFP Ifng/Thy1.1 Knock-In) report Tfh functionality accurately, we confirmed that Tfh-like Il-21+ Ifng− cells were enriched for GC Tfh (CXCR5hi PD-1hi CXCR6−) while the majority of Ifng+ Il21+ cells were CXCR5int CXCR6+. GC-Tfh appear functional sooner than Ifng+ Il21+ with expression of CCR7int and Il4+ as early as day 5p.i. Transfer of cytokine-expressing subsets from triple reporter and Il21−/− Ifng-Thy1.1 KI mice into T cell deficient recipients, which are then infected with P. chabaudi, also shows that Il21+ Ifng− Tfh-like cells from day 8 of P. chabaudi infection are functional. Il21+ Ifng− cell recipients generated more GC B cells, larger GCs and more parasite-specific IgG compared to other groups. Il21+ Ifng+ hybrid T cells, also promoted GCs, but Th1-like Ifng+ T cells from WT or Il21−/− mice did not. As GCs were larger, but not more numerous, in Il21+ Ifng− recipient spleens, we hypothesized that B cell proliferation was increased. Indeed, there were more BrdU+ dark zone (CXCR4+ CD86−) GCB cells in recipients of Il21+ Ifng− cells than other groups, particularly recipients of Ifng+ T cells from IL-21 KO. Combined, this data suggests that IL-21 from hybrid Th1/Tfh promotes GCB cells in vivo, though less than Il21+ Ifng− T cells.
R01AI13506101
Modeling phagocytosis resistance in Escherichia coli using Dictyostelium discoideum
Authors: Riddick Terra , Riaz Tahreem , Perez-Vazquez Marta , Snyder Michelle 
Published: August 2023

Abstract
Pathogenic Escherichia coli are responsible for morbidity and mortality around the world, especially in young children in developing countries. Though some strains of E. coli are not harmful, other strains are responsible for diarrhea, intestinal diseases, and urinary infections. E. coli and other bacteria have acquired virulence factors which have led to increased resistance to phagocytosis and other immune system mechanisms. Although sequencing has assisted in the determination of some genes and virulence factors associated with E. coli, many genes remain uncharacterized. Dictyostelium discoideum is a social amoeba that feeds on bacteria using phagocytosis. Its phagocytic mechanisms are conserved in mammalian immune cells like macrophages. D. discoideum is a good model to study host pathogen interactions because it is cost effective, easy to cultivate, and it has previously been used to identify virulence factors in bacteria. We hypothesize that D. discoideum can be used as a model organism to identify E. coli genes involved in resistance to phagocytosis. The aims of my project are to identify and characterize potential virulence genes granting resistance to D. discoideum grazing and phagocytic killing. Results show that extraintestinal pathogenic E. coli strains are more grazing resistant than intestinal pathogenic strains. We are currently working to characterize gipA (growth in Peyer’s patches gene), a gene found in strains of E. coli resistant to D. discoideum grazing. By identifying genes associated with phagocytosis resistance, our research can lead to better targeting of pathogenic bacteria and the development of more effective treatments for bacterial infections.
Supported by grants from NIH NIGMS R25 GM119970 & T32 GM146694
Association between the dynamics of the gut microbiota and responsiveness to mental health therapy
Authors: Zhou Xin , Ganz Ariel B , Lu Xinrui , Li Yizhou , Snyder Michael 
Published: August 2023

Abstract
Growing evidence suggests that the intestinal microbiota may influence brain activity through metabolites and/or inflammation, but it is unclear whether the impact of psychological interventions such as meditation is connected to the dynamics of gut microbiota. In the presented study, we collected gut microbiota and plasma cytokine, chemokine, and growth factor data from a longitudinal cohort of 52 people (142 multi-omics samples) before, during, and after a nine-day meditation. We identified a strong relationship between the mental health status and the composition of gut microbiota. High level of bacteria genus Prevotella is correlated with improved meditation effects in stressed persons. In addition, a number of inflammatory cytokines, such as GROA, are significantly reduced in the Prevotella-dominating individuals. Following nine days of meditation, there is a decrease in pro-inflammatory cytokines, an increase in relative abundance of Prevotella, and an improvement in individual’s mental health measurements. Our study provides a novel link towards the possibility that the gut microbiota affects the level of stress through regulating cytokines.
The role of immune cells in Chlamydia spread to the gastrointestinal tract following reproductive tract infection
Authors: Latifi Flutur , Hyseni Besmir , Konjufca Vjollca 
Published: August 2023

Abstract
Chlamydia trachomatis is the main cause of sexually transmitted disease and preventable blindness worldwide. In both animals and humans, Chlamydia spp. infect not only the female reproductive tract (FRT), but also the gastrointestinal tract (GIT), where it persists for long periods, without causing obvious pathology. In the murine model, following FRT infection, Chlamydia spreads to the GIT in stages and relies on carriage by host cells. After initial infection of epithelial cells in the FRT, lamina propria DCs internalize Chlamydia, which triggers their migration (and thus Chlamydia carriage) to the FRT-draining iliac lymph nodes. In the ILNs, Chlamydia infects other cells, which, then guided by the sphingosine 1-phosphate (S1P) gradient, enter the circulation, and carry Chlamydia to the spleen and the GIT. Selective depletion of either CD8 T cells, or monocytes/macrophages significantly lowers Chlamydia burden in the spleen and the GIT. In contrast, depletion of CD4 T cells significantly increases Chlamydia burden in the iliac lymph nodes and the GIT. While it takes about one week for FRT to GIT Chlamydia spread, ceca of CD4 depleted mice become positive for Chlamydia by day 3 of infection. It remains to be determined whether T cells and monocytes/macrophages become infected and actively transport Chlamydia to the GIT, or simply limit (or allow) its growth at different stages of infection and thus affect Chlamydia spread. Delineating the interactions of Chlamydia with specific host cells in vivo and identifying the cells and chemokines that mediate Chlamydia spread will shed light on Chlamydia pathogenesis, and on regulation of host cell migration during Chlamydia infection.
Supported by grant from NIH (1 R21 AI159743-01)
CD8+ T cell recognition of neuronal cysts during chronic Toxoplasma gondii infection
Authors: Bunkofske Molly , Eberhard Julia , Hunter Christopher A 
Published: August 2023

Abstract
The parasite Toxoplasma gondii establishes persistent infection within neurons by forming cysts that harbor latent form bradyzoites. The ability to form cysts is dependent on the parasite transcription factor BFD1 and, given the presence of a thick cyst wall, it was previously thought that cysts were protected from immune recognition. However, the generation of a BAG1-OVA parasite line, in which OVA protein expression is restricted to bradyzoites, revealed that in vivo infection elicited the activation and expansion of OVA-specific OT-I CD8+ T cells. To determine whether endogenous CD8+ T cells can recognize natural cyst-derived antigens and potentially participate in cyst control, in vitro T cell recognition assays were performed using a BFD1-inducible line of parasites that form in vitro cysts. In these assays, CD8+ T cells isolated from T. gondii-infected mice recognized both infected murine fibroblasts and neurons containing cysts. These studies indicate that cyst-specific T cells are present during infection and future studies will explore if any parasite antigens transported beyond the cyst wall can be presented by neurons for T cell recognition.
Supported by NIH grant R01 AI157247-01
Plasmodium-infected mosquito bite elicits an immune response at the bite site
Authors: Rabinovich-Ernst Orna , Hopp Christine , Kanatani Sachie , Archer Nathan K , Sinnis Photini 
Published: August 2023

Abstract
To induce long-lasting immunity, the host’s immune system must recognize and respond to an invading pathogen upon first encounter. Plasmodium sporozoites, the infective stage of the malaria parasite, are inoculated into the skin by infected mosquitoes as they probe for blood. Only 20% of sporozoites reach the liver, while the rest either reach the draining lymph nodes (dLN) or remain in the infected area for at least 6 hours, shedding an abundant amount of their major surface protein, the circumsporozoite protein (CSP). Yet, sterile immunity against sporozoites or CSP does not occur, despite the presence of the foreign antigens in the skin and the dLN, and repeated exposures, suggesting that Plasmodium sporozoites may modulate the host immune response. In this study we investigate the immune response elicited by P. berghei-infected mosquito bite at the bite site in-vivo. Using intravital imaging of sporozoites inoculation by a mosquito bite to a LysM-CRE GFP expressing mouse, we can observe neutrophil recruitment to the bite site in real time. When investigating the expression of pro- and anti-inflammatory genes in the skin, we find a specific expression patten that is elevated in response to a P. berghei-infected mosquito bite, when compared to a bite of an uninfected mosquito. Here we show fast immune cells recruitment as well as specific immune response to Plasmodium infection, suggesting a quick recognition of infection by the immune system. Nonetheless, gene expression analysis suggests a mechanism by which Plasmodium sporozoites may suppress the immune response to their presence.
Kindly supported by grants from NIH (R01 AI132359) and JHMRI.
T-cell derived interferon gamma is required for restriction of Mycobacterium tuberculosis in the murine lung: A reappraisal of conflicting models
Authors: Maciag Karolina , Cohen Sara , Plumlee Courtney , Urdahl Kevin 
Published: August 2023

Abstract
An effective vaccine for Mycobacterium tuberculosis (Mtb) is urgently needed, yet its development has been hampered by incomplete understanding of immunity to Mtb. While vaccine candidates are routinely assessed by their ability to induce CD4+ T cell-derived interferon gamma (IFNγ), this marker has been unreliable in predicting vaccine protection against TB. Furthermore, T cell adoptive transfer studies in RAG1−/− mice have suggested that lung T cell-derived IFNγ only plays a minor role in pulmonary immunity against Mtb. In contrast with prior results, our experiments using IFNγ−/− T cell chimeric mice, and with TCRβ−/− δ−/− mice receiving adoptively transferred IFNγ−/− T cells, demonstrate that control of lung Mtb burden is in fact dependent on T cell-derived IFNγ. We show that this discrepancy is partially due to the confounding effects of RAG−/− vs. the more specific TCRβ−/− δ−/− hosts. Flow cytometry and RNA-seq analysis of lung cells in WT, IFNγ−/−, and TCRβ−/− δ−/− T cell-chimeric mice reveal that absence of T cell-derived IFNγ decreases recruitment of monocyte-derived macrophages to the infected lung, skews infected and bystander macrophages to an alternative M2 phenotype, and promotes neutrophil and eosinophil influx. Together, these results reassert and characterize the role of T cell-derived IFNγ in protection against pulmonary Mtb.
Supported by grants from NIH (T32 AI007044, U19 AI135976) and the Firland Foundation (Northrop-Park Fellowship).
Establishing an immunological profile of 96 cytokines, chemokines, and growth factors in human biofluids via MILLIPLEX® multiplex immunoassay
Authors: Steiner Harold L , Williams Sasha , Banerjee Munmun , Saporita Anthony , Gilliam Brooke , Qiang Xiao 
Published: August 2023

Abstract
Multiplex immunoassays are well-established research tools enabling the simultaneous measurement of several proteins in biological samples. In the field of immunology, these immunoassay kits have been critically important for profiling the expression of a wide array of immunomodulatory proteins, including cytokines, chemokines, and growth factors. To this end, we recently developed two MILLIPLEX® multiplex immunoassay kits, each capable of the simultaneous measurement of 48 unique proteins in human samples. In this study, our objective was to profile the relative abundance of 96 cytokines, chemokines, and growth factors in a diverse collection of human biofluids, including serum, plasma, cerebrospinal fluid, saliva, sputum, urine, tears, milk, synovial fluid, and bronchoalveolar lavage (BAL). For each analyte, the fold increase in the average sample measurement relative to the limit of detection was determined. Some biofluids were generally rich in these immunological factors, such as BAL samples, whereas others were sparse, as noted in milk samples. Additionally, the reagent compatibility of the two immunoassay kits used to interrogate the sample cohort was examined to define opportunities for developing novel custom multiplex immunoassays containing analytes from each of the parent kits. The result of this effort was the generation of a set of rules guiding the acceptable combinations amongst the 96 proteins as well as the identification of mutually exclusive protein targets.