bluuebunny/crossref_metadata_2025_split huggingface dataset:
You too Brutus! Faculty fighting death-of-teaching in the classroom.
Authors: Fazal Nadeem , Graefen Bahar 
Published: November 2024

Abstract
In this study, we explored the hypothesis that active learning approaches to immunology improve comprehension and retention by increasing student engagement in class and their subsequent mastery of complex topics. What is “active learning”? Literature suggests that students participating in active learning “must do more than just listen: They must read, write, discuss, or be engaged in solving problems. The larger fear is that if this battle is lost it will change the battlefield forever. If faculty, classrooms, physical space of university, administration were to disappear physically if not virtually one can forecast a life-long learner, be of any age, be a student or teacher is positioned to stay amid machines. Pedagogical theory has taught us that students learn best by engaging with complicated questions and by thinking metacognitively about how to approach solutions. Building this skill set in today's students, who now hail from a broad demographic and who are accustomed to acquiring their knowledge from a variety of different media, requires a new set of teaching tools. A college-wide survey was sent to all the instructors and data was collected as per the requirements of IRB. To surmise faculty has lost motivation and enthusiasm for sustainability of classroom teaching methods and are testing unchartered water for teaching current sets of incoming professional students.
A novel method for inferring B cell clonal lineages from single-cell RNA sequencing data
Authors: Weber Leah , Reiman Derek , Roddur Mrinmoy , Qi Yuanyuan , El-Kebir Mohammed , Khan Aly 
Published: November 2024

Abstract
Understanding the adaptive and evolutionary mechanisms of B cells in response to specific stimuli remains a significant challenge in the field of immunology. We introduce a new method, TRIBAL, which aims to infer the evolutionary history of clonally related B cells from single-cell RNA equencing data (scRNA-seq). The key insight of TRIBAL is that inclusion of isotype data into the B cell lineage inference problem is valuable for reducing phylogenetic uncertainty that arises when only considering the receptor sequences. Consequently, TRIBAL inferred B cell lineage trees jointly capture the somatic mutations introduced to the B cell receptor during affinity maturation and isotype transitions during class switch recombination. In addition, TRIBAL infers isotype transition probabilities that are valuable for gaining insight into the dynamics of class switching.
We validated our method on simulated data, demonstrating more accurate reconstruction than existing methods. Using experimental scRNA-seq datasets, we show that TRIBAL recapitulates expected biological trends in a model affinity maturation system. Furthermore, the B cell lineage trees inferred by TRIBAL were equally plausible for the BCR sequences as those inferred by competing methods but yielded lower entropic partitions for the isotypes of the sequenced B cell. TRIBAL holds the potential to advance our understanding of vaccine responses, disease progression, and the identification of therapeutic antibodies.
The Igh distal enhancers modulate locus topology and repertoire diversity in pro-B cells
Authors: Drake Ellen , Priyadarshi Saurabh , Naiyer Sarah , Kenter Amy 
Published: November 2024

Abstract
The Igh locus undergoes large-scale locus contraction prior to V(D)J recombination in pro B cells. Our Hi-C analyses have identified chromatin loops anchored by a series of distal VH enhancers, EVH1-4 and Pax5-activated intergenic repeat 4 (PAIR4) implying that these interactions contribute to Igh locus contraction. Indeed, EVH1 modulates Igh locus spatial organization and VH gene usage in VDJ recombination linking Igh locus conformation with function (Nat Comm. 14:1225). Loop extrusion is a process that forms chromatin loops by extruding chromatin through cohesin’s ring structure and is a critical regulator of distal V(D)J recombination. However, the relationship between chromatin looping and loop extrusion remains incompletely understood. We posit that EVHs and PAIR4 provide structure independent of loop extrusion which then interacts with loop extrusion to shape higher order locus architecture. Wings apart-like protein (Wapl) is a cohesin release factor. Acute WAPL-depletion increases loop extrusion, enabling us to directly test the relationship between Igh regulatory elements and loop extrusion in Abelson transformed (Abl-t) pro-B cell lines. We show that EVH4 and PAIR4 deletion reduce distal Igh locus interactions despite increased loop extrusion. Our studies support a model in which cis regulatory elements modulate loop extrusion to shape Igh locus architecture and consequently direct VH gene usage.
Uterine Tissue-Resident Natural Killer Cells Derived from Conventional Natural Killer Cells are Regulated by Progesterone
Authors: Sojka Dorothy , Tatematsu Bruna 
Published: November 2024

Abstract
Innate lymphoid cells (ILCs) respond to pathogen-induced tissue distress and maintain tissue homeostasis. The uterus contains three subsets of ILCs: ILC1, conventional natural killer (cNK) cells, and tissue-resident NK (trNK) cells. ILC1s and cNK cells seed the uterus before puberty. In contrast, trNK cells emerge at the onset of puberty and persist with varied frequency throughout the estrous cycle. Here, we considered the origin of uterine trNK cells and the potential influence of hormones on their differentiation in the uterus. We intravascularly labeled immune cells to distinguish cells in the vasculature by flow cytometry of ovariectomized (OVX) mice supplemented with hormones, intact and parabiosed mice. We found that mice OVX at three weeks of age and analyzed as adults did not have trNK cells in the uterine tissue unless progesterone (P4) was administered. In parabiosed mice, we identified cNK-derived trNK cells in estrous cycling but not in the noncycling parabionts. Delivery of P4 to OVX or intact mice induced the expansion of cNK-derived trNK cells which was abrogated if RU486 was administered. Uterine ILCs from Nfil3-/- mice, that lack cNK cells, did not expand in response to P4. Finally, sorted cNK cells transferred into OVX mice supplemented with P4 differentiated into trNK cells in the uterus, but not the spleen. Taken together, we identified a novel differentiation pathway for uterine trNK cells tightly regulated by P4 in the uterine tissue.
Stabilization of β-Catenin directs HEB to limit Thymic Selection
Authors: Tousinas Georgios , Emmanuel Akinola Olumide , Tracy Melissa , Arnovitz Stephen , Friedman David , Khazaie Khashayarsha , Gounari Fotini 
Published: November 2024

Abstract
Activation of β-catenin in CD4+CD8+ (DP) thymocytes stalls progression through thymic selection and predisposes to transformation. Leukemogenesis but not the developmental block depends on Tcf-1, β-catenin’s DNA binding partner. Here we show that β-catenin deregulation directs the DNA-binding protein HEB to stall thymocyte development at the thymic selection stage. Conditional loss of HEB along with β-catenin activation restores the frequency of TCRβ+/CCR7+ DP thymocytes, with reduced CXCR4 expression indicating their potential to migrate to the thymic medulla. It also restores the emergence of TCRβ+/CD69+ DPs and enhances the overall CD69+DP expression profile that were diminished by activating β-catenin, indicating a functional response to TCR stimulation. β-Catenin stabilization redirects the binding of HEB to ~11,000 novel DNA sites throughout the genome. A major fraction of these sites occupy promoter regions of genes associated with cell cycle regulation and mitotic processes. HEB binding to those regions corelates with downregulation of the associated genes, and HEB inactivation restores their expression to physiologic levels. These findings highlight the complex molecular interplay between HEB and β-catenin in impairing thymic development.
The role of TCR in regulating T cell function in acute and chronic infections and cancer
Authors: Krause Jenny , Gavil Noah , Rollins Meagan , Wijeyesinghe Sathi , Matson Courtney , Künzli Marco , O'Flanagan Stephen , Smith Olivia , Quarnstrom Clare , Weyu Eyob , Yu Yun , Webber Beau , Vezys Vaiva , Masopust David 
Published: November 2024

Abstract
In contrast to naive T cells, memory T cells do not require TCR stimulation to survive and are maintained by cytokines to undergo homeostatic proliferation. However, permanent TCR stimulation of T cells by persistent antigen in chronic infections and cancer causes a dysfunctional state, termed T cell exhaustion (TEX). Yet, how TCR signaling influences the location, maintenance, and function of T cell subsets remains incompletely understood.
Using an inducible TCR knockout model (UBC-CreERT2 x Trac flox/flox), longevity of tissue resident memory T cells (TRM) and persistent CD69 expression after TCR deletion was shown. However, this model was limited due to the polyclonal memory T cell population used.
To study the role of TCR in the regulation of TRM and TEX in infections and cancer, we designed a rAAV6 vector construct that encodes the floxed P14 TCRa and TCRb to the endogenous TRAC locus using CRISPR/Cas9. We validated the construct in vitro by transfecting UBC-CreERT2 cells, adoptively transferred into CD45.1 mice and infected with LCMV Armstrong before TCR deletion after tamoxifen treatment. We next generated UBC-CreERT2 x P14a flox mice using the same approach, and confirmed the expression by PCR and H-2Db/gp33 MHC I tetramer stain by flow cytometry.
We will use this model to understand how TCR signaling influences T cell differentiation, residence and exhaustion by inducing TCR ablation at the effector, contraction, memory and exhaustion state.
Exportin 1 (XPO1) blockade regulates immunosuppressive function of tumor myeloid derived suppressor cells
Authors: Daneshmandi Saeed , Yan Qi , Choi Jee Eun , Katsuta Eriko , MacDonald Cameron , Goruganthu Mounika , Roberts Nathan , Repasky Elizabeth , Singh Prashant , Attwood Kristopher , Wang Jianmin , Landesman Yosef , McCarthy Philip , Mohammadpour Hemn 
Published: November 2024

Abstract
Myeloid-derived suppressor cells (MDSCs) are key regulators of immune responses in the tumor microenvironment (TME). Here we report the pivotal role played by Exportin 1 (XPO1) in shaping the phenotype and suppressive function of tumor associated MDSCs, thereby influencing tumor progression. Using the EL-4 murine tumor model, we demonstrated that tumor MDSCs exhibit elevated levels of XPO1, that drive their immunosuppressive activity. We showed that the XPO1 inhibition can effectively remodel MDSCs phenotype and functions, resulting in enhanced anti-tumor responses and the suppression of tumor growth. We showed that depletion of MDSC by anti-Ly6C antibody, restore tumor growth post XPO1 blockade. Unbiased proteomic analysis revealed that nuclear export of ERK1/2 by XPO1 is pivotal for IL-6 mediated MAPK signaling, which underpins MDSC immunosuppressive functions. Importantly, our data confirm that blockade of XPO1 function by Selinexor (an XPO1 inhibitor), sequesters ERK1/2 in the MDSC nucleus. This results in the suppression of IL-6 mediated MAPK signaling, a shift in transcriptional profiles toward the induction of neutrophil-like immunostimulatory cells. Our study demonstrates that XPO1 inhibition transforms tumor MDSCs into immune-stimulating neutrophil-like cells, reducing tumor growth and prolonging survival in pre-clinical tumor models. These results reveal novel targets for MDSC reprogramming to enhance cancer treatment outcomes in clinical practice.
Differential proteomic signatures of host responses following COVID-19 vaccination in individuals with or without prior SARS-CoV-2 infection
Authors: Echeverri Tribin Felipe , Williams Erin , Carreno Juan , Krammer Florian , Hoffer Michael , Pallikkuth Suresh , Pahwa Savita 
Published: November 2024

Abstract
The goal of this study is to characterize how proteomic signatures differ following COVID-19 vaccination in individuals naïve to SARS-CoV-2 infection (CoV-N) and those with a prior history of infection (CoV-P) to better understand the influence of pre-infection on host responses to vaccination. A subset of individuals (n = 63) enrolled in our IRB-approved, longitudinal cohort (COVID-19 Immunity Study [CITY]) were included in this study. Serum samples collected at baseline and ≤ 14 days following two doses of primary vaccination (PV) were analyzed with the proteomic aptamer-based SomaScan assay across 1500 targets. Significant (α ≤ 0.05) differentially expressed proteins (DEPs) were those with ≥ 2.5 log2-adjusted fold changes following PV among both CoV-P and CoV-N. Proteins identified in both groups were utilized in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis to elucidate biological regulation following PV. Twenty DEPs were identified in the CoV-P group and 91 DEPs in the CoV-N group. CoV-P displayed downregulation of fibrinogen, the active compound in fibrin clot synthesis. CoV-N displayed increased activation of C3, the essential activator of the alternative complement pathway, and downregulation of alternate pathway inhibitors CR1 and complement decay acceleration factor. The significant activation of complement pathways in CoV-N indicates an enhanced innate immunoprotected effect following vaccination not observed in CoV-P individuals.
Keap1-Nrf2 regulate nutrient metabolism to direct CD4+ T-cell activation and inflammatory functions.
Authors: Pyaram Kalyani , Tripathi Aprajita , Dasgupta Debolina , Pant Anil , Bugbee Ashlyn 
Published: November 2024

Abstract
CD4+T-cells are critical orchestrators of antigen-specific adaptive immunity. Here we elucidate the role of nuclear factor erythroid 2–related factor2 (Nrf2), negatively regulated by Kelch-like ECH-associated protein (Keap1), beyond the traditional oxidative stress regulation, in modulating the effector responses of CD4+ T-cells by influencing their nutrient metabolism. We noted that in CD4+ T-cells, Nrf2 protein levels increase during early activation but decrease during their expansion. With the objective of identifying the effect of T-cell intrinsic Nrf2, we used T-cell specific knockout (KO) mice of Keap1 or Nrf2. In vitro CD4+ T-cell activation and Th subset differentiation assays were performed, and the findings were validated in vivo. Constitutively high Nrf2 in activated CD4+ T-cells lead to increased proliferation as well as apoptosis, increased expression of early activation markers and augmented TCR signaling in addition to dampened Th1 differentiation yet elevated Foxp3+Treg generation. Further, Nrf2-high Keap1-KO CD4+ T-cells caused a milder disease in mouse models of inflammatory bowel disease than WT or Nrf2-KO cells. Mechanistically, Nrf2 drives glutaminolysis to support increased proliferative capacity but inhibits glycolysis in CD4+ T-cells. Overall, our data uncover a novel role of Nrf2 as a metabolic modulator of activation driven expansion and inflammatory function of CD4+ T-cells, thus providing a framework for improving Nrf2-targeting drugs.
Dynamic recruitment of inhibitory complexes by CD25 controls B-cell development and selection
Authors: Sun Ruifeng , Lee Jaewoong , Robinson Mark , Kume Kohei , Ma Ning , Cosgun Kadriye Nehir , Chan Lai , Antoshkina Irina , Khanduja Dhruv , Leveille Etienne , Katz Samuel , Vaidehi Nagarajan , Müschen Markus 
Published: November 2024

Abstract
Initiation of BCR signaling, and subsequent antigen-encounter in germinal centers are both marked by sharp increases of CD25 surface-expression. While CD25 is known as an IL2-receptor chain on T- and NK-cells, the significance of its expression on B cells was unclear.
Our genetic studies revealed that, rather than functioning as an IL2-receptor chain, CD25 expressed on B-cells assembled an inhibitory complex including PKCd, ITIM-bearing receptors and inhibitory phosphatases for feedback control of BCR-signaling. Conditional CD25-deletion resulted in clonal expansion and autoimmunity.
Mechanistic studies revealed that BCR engagement induced PKCd-mediated phosphorylation of CD25, which anchored CD25 on cell surface in proximity to the BCR complex. Moreover, CD25 recruited inhibitory receptors CD22, that bear ITIM-motifs for the activation of inhibitory phosphatases (e.g., SHP1). The positively charged tail of CD25 engages negatively charged residues in the cytoplasmic tails of the BCR signaling chain CD79B and the inhibitory CD22-ITIM. Molecular dynamics simulations, Co-IP and TIRF microscopy results revealed that the ternary complex between CD25, CD79B and CD22 enables recruitment and activation of the phosphatase SHP1 within reach of its substrate. Thereby, the SH2-domain of SHP1 engages the CD22-ITIM motif, while its phosphatase domain interacts with the CD79B-ITAM to terminate BCR-signaling. This complex, while engaging and activating SHP1, is held together by CD25.
Determining the natural time course of immune response
Authors: Zeng Wei-ping , Zhou Baohua 
Published: November 2024

Abstract
Given the dynamic nature of immune response, it is important to study and medically interfere the molecular events in lymphocytes in accordance with the kinetics of the immune response. However, unlike in laboratory settings, in clinical settings the time of antigen exposure is usually uncertain. We found that the natural time course of immune response can be tracked by the dynamic changes of the intracellular pH of the lymphocytes. Therefore, the stage of immune response at a given time can be determined without the knowledge of the time of initial antigen exposure.
The Transcription Factor ELF4 Restrains the Inflammatory Potential of CD4+ T Cells
Authors: Bender Mackenzie , Olyha Sam , Bucklin Molly , Siddapureddy Sindhura , Attanasio John , Pan Jie , Muise Aleixo , Lucas Carrie 
Published: November 2024

Abstract
ELF4 is a member of the ETS family of transcription factors, known to be involved in the regulation and development of immune cells. Yet, the primary function of ELF4 was unknown prior to our discovery of patients with loss-of-function mutations in ELF4 that cause the monogenic autoinflammatory disease Deficiency in ELF4, X-linked (DEX), driven by aberrant inflammation. While it has been demonstrated by our lab that global loss of ELF4 results in hyper-cytokine release in macrophages and restrains Th17 differentiation in mice, the breadth and mechanisms of CD4+ T cell regulation by ELF4 remain enigmatic. Here, we show that loss of T cell-intrinsic ELF4 leads to enhanced interferon gamma and IL-17A production upon activation of naïve CD4+ T cells and demonstrate modulation of CD4+ T cell cytokine production by ELF4 is independent of its presence during T cell development as well as extrinsic signaling in vivo. Further, absence of T cell-intrinsic ELF4 leads to decreased expression of ATF4, a master regulator of the integrated stress response demonstrated to be crucial in restraining cytokine release upon initial activation of naïve T cells. Notably, we found ELF4 binds to the promoter region of ATF4, and expression of ATF4-induced genes is significantly reduced in CD4+ T cells in the absence of ELF4 post-activation. Thus, we elucidate an essential mechanism for restraining CD4+ T cell inflammatory potential dependent on regulation of the integrated stress response by ELF4.
Vasculopathy Leading to Stroke in Adult Onset Still’s Disorder
Authors: Qiu Esther , Kaddouh Firas 
Published: November 2024

Abstract
Background
Rheumatological disorders may predispose patients to hypercoagulability and/or vasculopathy increasing stroke risk. Adult-Onset Still’s Disease (AOSD) is not usually associated with either, with only two reported cases in the literature to have had strokes. We present a case of AOSD with acute stroke manifesting as lateral medullary syndrome. We hypothesize that vasculopathy and thrombocytosis may have contributed to stroke occurrence. We further explore the possible underlying pathomechanism in this patient population.
Case Presentation
A 35-year-old woman with AOSD on methotrexate, tocilizumab and daily prednisone presented with vertigo and numbness involving her right face and left arm. She was found to have an ischemic stroke in the lateral medulla with vertebral artery thrombotic changes. No recent trauma. Investigation of other underlying stroke etiologies was unyielding with negative lupus anticoagulants, ANCAs and normal ESR and CRP.
Discussion & Conclusion
Our case marks the third report of stroke occurrence in AOSD in the literature. While our patient had no elevated inflammatory markers, she still developed stroke due to ongoing endothelial inflammation and thrombotic changes in the vertebral artery. The presence of vascular involvement leading to stroke may provide initial insight into the nature of this event. Further research should thus be done to investigate the exact mechanism of stroke and vasculopathy in AOSD patients.
Metabolic pathways in T cells are modulated by CCR7 and IL-7R to facilitate T cell motility.
Authors: Morrissey Kimberly , Gridley Rebekah , Byrum Janie , Cannon Judy 
Published: November 2024

Abstract
T cells play an essential role in eliminating infections by migrating through tissues and interacting with antigen-presenting dendritic cells within lymph nodes, leading to activation. A continuous supply of energy is required for T cell movement to enable scanning of dendritic cells. Many studies have established that signaling through chemokine receptor CCR7 facilitates rapid movement, however, how CCR7 signaling induces T cell metabolism remains poorly understood. IL-7 signaling regulates glycolysis to promote T cell survival, but how signaling through the IL-7R affects T cell movement is unexplored. This study investigates the roles of CCR7 and IL-7R in metabolism to drive naïve T cell movement. Utilizing Seahorse analysis, we observe that CCL21 signaling to CCR7 has no effect on glycolysis, yet decreases cellular respiration. Conversely, IL-7 has no effect on respiration but promotes glycolysis. We then determined whether oxidative phosphorylation and glycolysis play a role in CCL21 and IL-7 driven T cell movement. We employ inhibitors of oxidative phosphorylation such as rotenone to examine the influence of different metabolic pathways on T cell mobility. Our findings provide new insights into the intersection of metabolism and motility, suggesting potential differential mechanisms of ATP production that drive interactions.
Flow cytometry-based FRET to monitor β2 integrins activation
Authors: Wang Yan 
Published: November 2024

Abstract
β2 integrins is very important for leukocyte arrest, rolling and transmigration. Neutrophils mainly express two β2 integrins, αLβ2 and αMβ2. Neutrophil arrest is triggered by rapid conformational change of β2 integrins from bent and low affinity to open and high affinity. Recent studies have reported a new conformation of β2 integrins bent high affinity (PMID: 27578049, PMID: 30605669). This conformation is very difficult to monitor. By dynamic molecular simulation, we found that bent high affinity conformation of integrin is close enough to membrane, less than 10nm. Förster resonance energy transfer (FRET) is a powerful technology to interrogate close association between two fluorescent molecules. Importantly, FRET requires a distance of 10nm or less. Using real-time flow cytometry-based FRET, we can not only detect bent high affinity conformation but also the dynamic conformational change of β2 integrins along time. Interestingly, the FRET signal was detected between bent high affinity β2 integrins and cell membrane using conformational antibody mAb24 and membrane dye octadecyl rhodamine B (ORB). We developed an easy and efficient way to monitor the bent high affinity conformation of β2 integrins.