bluuebunny/crossref_metadata_2025_split huggingface dataset:
Amplified STAT3 increases expression of the CD39 ectoenzyme and impairs function of CD8+ T cells.
Authors: Campos Duran Jose , Sayed Samir , Knight Montana , Dalalo Megan , Conrey Peyton , Hay Ceire , Schmitt Erica , Thelin Martin , Mauracher Andrea , Forbes Lisa , Holland Steven , Bergerson Jenna , Su Helen , Romberg Neil , Freeman Alexandra , Leiding Jennifer , Anderson Mark 
Published: November 2024

Abstract
Regulation of T cell signaling is paramount to mount an appropriate immune response and protect the host from pathophysiology. Here, we study the impact on CD8+ T cells in monogenic inborn error of immunity patients exhibiting dysregulated signal 3 (cytokine signaling) pathways resulting from STAT3 gain- or loss-of-function variants (STAT3 GOF and STAT3 LOF). Using high dimensional immune profiling, we demonstrate increased expression of the ectoenzyme, CD39, which hydrolyzes extracellular ATP, on STAT3 GOF patient CD8+ T cells. Moreover, CD8+ T cells from two mouse models of STAT3 GOF (STAT3+/G421R and NOD-STAT3+/K392R) recapitulated this increase in CD39. In vitro, STAT3-activating cytokines (e.g., IL-6, IL-21, IL-27, IL-10) augment CD39 induction in a TCR-dependent manner in healthy donor and in STAT3 GOF CD8+ T cells. In contrast, STAT3 LOF patients show diminished CD39 induction. We find a positive correlation between CD39 induction and phosphorylated STAT3 levels while STAT3 inhibition prevents this cytokine-driven augmentation of CD39. Finally, acutely activated, and sorted CD39+CD8+ T cells from healthy donors inhibit bystander CD8+ T cell cytokine production (e.g., IFN-g). Pharmacologic inhibition of CD39 enzymatic activity or genetic ablation via CRISPR/Cas9 editing reversed decreases in cytokine production. Together, our data demonstrate a mechanistic connection between amplified STAT3 signaling and CD39 levels which is capable of impairing CD8+ T cell function.
Spatial Molecular Profiling of the Kidney of Children with Lupus Nephritis
Authors: Rodriguez-Alcazar Juan , Balaji Uthra , Troncoso Leanna , Reid Amanda , Hamon Pauline , Houghton Sean , Walters Lynnette , Smitherman Cynthia , Baisch Jeanine , Santos Marina , Larosiliere Owen , Robinson Lauren , Wright Tracey , Merad Miriam , Caielli Simone , Gu Jinghua , Pascual Virginia 
Published: November 2024

Abstract
Childhood-onset lupus nephritis (cLN) affects 80% of pediatric systemic lupus erythematosus patients. Classified based on histological renal features, cLN is treated with immunosuppressive agents that trigger side effects. Despite the need for targeted therapies, little is known on the molecular pathways causing cLN and their variability across patients. We employ spatial transcriptomics and proteomics approaches to profile kidney biopsies of cLN patients and define cellular and molecular endotypes across clinical traits. We found that distinct spatial organization of the renal immune compartment classified cLN biopsies according to histological classification. Myeloid cells with phagocytic and highly inflammatory transcriptional programs, including the expression of S100A9, infiltrate glomeruli of proliferative cLN. A subset of these patients also presents glomerular inflammasome-competent myeloid cells expressing IL-1β. Tubulointerstitial and periglomerular immune hubs characterize a subgroup of membranous and mixed cLN. Immune hubs’ cell composition varies across patients and tissue lesions and can be skewed towards specific lymphoid populations, including T, B, or plasma cells with different isotype specificity. Our results highlight the importance of understanding the spatial organization and heterogeneity of the renal immune compartment in cLN. The prognostic value of these findings and their relevance to target disease is being currently explored.
Cell-intrinsic Tim-3 is Required for an Optimal Acute CD8+ T Cell Response
Authors: Manandhar Priyanka , Landy Emily , Cardona Eddie , Kane Lawrence 
Published: November 2024

Abstract
Tim-3, or transmembrane immunoglobulin and mucin domain-3, is a type I membrane protein expressed by various immune cells, best known as a negative regulator of anti-tumor immunity. However, Tim-3 also has a co-stimulatory role in T cells under some conditions, via enhancement of PI3K signaling. We hypothesize that Tim-3 signaling enhances CD8+ T cell activation during acute infection and contributes to enhanced CD8+ effector function.
To test this hypothesis, we used LCMV-specific TCR transgenic (P14) mice expressing a truncated, non-signaling, allele of Tim-3 or CD8-specific deletion of Tim-3 and used LCMV Armstrong as an acute infection model. At the effector stage, endogenous Tim-3+ T cells had increased expression of effector markers, and cytokine production compared with Tim-3- cells. Tim-3 knockout mice also showed a significantly lower number of LCMV-specific T cells. Bulk RNA sequencing and TCR sequencing revealed that Tim-3-expressing effector CD8+ T cells had a distinct pattern of effector gene upregulation, with increased expansion of a subset of TCR clones. Mechanistically, Tim-3 signals enhances phosphorylation of Foxo1, inhibiting its entry into the nucleus, conferring enhanced effector function. Thus, Tim-3 signaling contributes positively to an effective CD8+ T cell response during acute infection. These findings may lead to a better understanding of CD8+ T cell function in different settings, including in tumors.
Investigating neuroinflammation in the human brain tumor microenvironment using the new RNAscopeTM Multiomic assay
Authors: Wakhloo Debia , Dikshit Anushka , Kim Ge-Ah , Yu Julia , Deshpande Sonali , Wang Li-Chong , Srinivasan Maithreyan 
Published: November 2024

Abstract
Glioblastomas are one of the most aggressive forms of brain tumors characterized by distinct genetic and molecular signatures. Compared to other solid tumors, role of immune cells in progression, invasion and prognosis is not well studies for CNS tumors. Here, we demonstrate a novel RNAscope Multiomic Assay that enables detection of multiple RNA and protein markers simultaneously.
With this novel TSA amplification-based co-detection assay we visualized a few combinations of 3 RNA and 3 protein marker panels on human FFPE normal brain and brain tumor tissues. Antibodies targeting key immune cell markers and morphology markers such as CD8, IBA1 ,CD68, S100B and GFAP were used. RNA probes targeting chemokines and cytokines such as CXCL10, IFNG, TNFA, CXCL2. IL-6 were also used in the panels.
Immune cells infiltrating the brain tumor tissues were characterized by studying co-expression of key RNA and protein markers. The tumors demonstrated infiltration of immune cells such as T cells, microglia and macrophages. Expression of key cytokines indicated that some populations within these cells were activated. Distinct differences in neuroinflammation signatures were also observed between the normal and tumor brain tissues.
The multiomic assay offers a powerful technique for visualizing target RNA biomarkers in specific cell-types identified by cell-marker protein expression.
Synthetic saponin derivatives act as functional subunit vaccine adjuvants through an NLRP3-inflammasome-independent mechanism
Authors: Santhin Austin , Ghorai Jayanta , Hartwig Stacey , Miller Ann , Almounajed Leila , Nguyen Dr Hien , Varga Dr Steven 
Published: November 2024

Abstract
Quillaja saponaria 21 (QS-21) is a saponin compound extracted from the bark of a South American evergreen tree. The ability of QS-21 to induce robust cellular and humoral immunity as an adjuvant led to it being evaluated in multiple clinical vaccine trials. However, mechanistic and toxicity questions following its purification hinder its potential use and led to the search for suitable alternative adjuvants. A group of 14 novel synthetic compounds have been chemically derived from a less toxic saponin, lablaboside F, to be tested as suitable alternatives to QS-21. When administered with an OVA peptide antigen intramuscularly into C57BL/6 mice using a prime-boost strategy, compound JG-151 elicited increased production of OVA-specific total IgG antibodies 2 weeks post-boost compared to control mice. When analyzed in vitro, JG-151 displayed decreased cellular toxicity 24 hrs post-treatment compared to QS-21. However, JG-151 neither activated NF-kB alone nor induced significant production of the pro-inflammatory cytokine IL-1ß with MPLA 24 hrs post-treatment. These results indicate JG-151 does not activate the NLRP3 inflammasome, in contrast to QS-21. Our results demonstrate that novel saponin derivatives, such as JG-151, safely elicit humoral immunity through an NLRP3 inflammasome-independent mechanism and could serve as suitable subunit vaccine adjuvant alternatives to QS-21.
Using Non-Human Primate to Investigate the Generation of Liver Immunity in Malaria
Authors: Osii Rowland , Kirtley Payton , Aleshnick Maya , Boggey Gregory Boggey , Marrow David , Mutai Koko , Beebe Roxanne , Tonelli Rachael , Smedley Jeremy , Fisher Miranda , Feltham Shana , Ojha Sohita , Bimber Benjamin , Wilder Brandon 
Published: November 2024

Abstract
Malaria is still a global health issue that afects more than half of the worlds population. While a number of malaria vaccines are currently under development. The most potent and long-lived vaccine have been whole sporozoite vaccines that use live-attenuated sporozoites to generate both antibodies and liver resident memory T cells capable of blocking infection. This vaccine has a higher efficacy in a malaria naïve population (up to 100%), but this efficacy drops in a malaria endemic population (0-30%). It has been hypothesized that the immune profile of people living in malaria endemic regions is altered in a way that negatively affects vaccine induced immunity, but a better understanding of how this occurs is required to generate optimal vaccine strategies. Yet to understand how the parasite alters the immune system, thus causing vaccine hyporesponsive in endemic regions, requires detailed information on previous parasite exposure and access to tissue resident cells that reside in the liver and other lymphoid organs—both limiting our ability to study this phenomenon in humans. To overcome this, we used a non-human primate model of malaria that enables us to access tissues before and after infection and vaccination via minimally invasive biopsies. Here, we present ongoing analysis that shows the longitudinal changes in the immune landscape after infection, vaccination and infection after vaccination using flow cytometry and single cell transcriptomics.
Transcriptomic Analyses of B Cells Infected In Vitro with Transmitted/Founder HIV-1 of R5 Phenotype (HIV-R5) Reveal Downregulation of IGLL1 Gene in Persistent Infection.
Authors: Vyas Girish , Bozzini Randall , Nix Matthew , Sanchez Claudia , Santos Yale , Vashishtha Anshu , Wiita Arun , Chiu Charles , Lowell Clifford 
Published: November 2024

Abstract
HIV-neutralizing antibodies against T cell-dependent antigens of HIVenv permit persistent infection. Conceivably, B cell repertoire has a clone capable of eliciting antibodies to eliminate any HIV. Receptors for T cell-independent conformational antigens (TiCA) of the trimeric envelope glycoprotein subunits (TEGS) of HIV permit persistent infection of that clone. To test this concept, a human B cell line (CA46, ATCC) was chosen for in vitro infection with HIV-X4 or HIV-R5. Both infected cell lines continued to produce infectious virions. Transcriptomic analyses of uninfected and HIV-infected cells was done, and data analyzed by the Edge R and Surpi software. Differential gene expression data for paired analyses of B cells infected with HIV-R5 versus uninfected cells showed that 108 genes were upregulated, while 148 genes were downregulated. Notably, the IGLL1 gene that determines surface expression of Ig-receptors on B cells, was down-regulated in cells infected with HIV-R5 (logFC= 3.30). Such a difference was not seen in B cells infected with HIV-X4. Heatmaps showing RNA-Seq data for pathway analysis revealed distinct patterns of gene expression in B cells infected with HIV-R5 versus HIV-X4. These data are in accord with HIV-R5 initiating all persistent HIV infections worldwide. We conclude 1) HIV-R5 infects B cells to establish persistent infection, 2) Studies with CD19+ normal B cells would enable synthesis of antibodies against TiCA and TEGSs for immune prevention of HIV.
Is AIDS an Actinopathy? HIV Inhibition of ARP2/3 is Reminiscent of Primary Immunodeficiencies in Normal Progressors but Absent in A Subset of HIV Controllers.
Authors: Furler O'Brien Robert , Kovacs Colin 
Published: November 2024

Abstract
HIV-1 infection disrupts the cortical actin network, leading to morphological and migratory changes in CD4+ T cells. We utilized time-lapse and ultrastructural microscopy to observe primary CD4+ T cells infected with wild-type HIV-1 and Nef-deleted (ΔNef) virus to assess cytoskeletal cytopathicity. Furthermore, we investigated the link between HIV-1-mediated actin disruption and primary immunodeficiencies that affect the ARP2/3 complex to cytopathicities found in HIV infection.
Of the five aberrant phenotypes observed, we identified two novel pathological morphologies unique to HIV-1 infected CD4+ T cells. The observed morphologies mirror those seen in migrating cells containing genetic determinants of primary immunodeficiencies affecting ARP2/3 complex. Nef-deleted virus partially ameliorated the cytopathicity in infected cells. In contrast to normal progressors and healthy controls, two-thirds of HIV-1 controllers tested retained cortical actin stability in the presence of WT infection.
The link between these cellular pathologies and disease progression provides insights into HIV-1 induced immune dysfunction. Additionally, we observed that certain HIV-1 controllers lack these cellular pathologies, possibly indicating a protective mechanism against viral replication and immune response. Restoring ARP2/3 function and cortical actin integrity in HIV-1-infected individuals may present a promising avenue for eradicating infected cells from the body.
Tissue resident memory CD8 T cells limit respiratory virus transmission by IFN-γ production and activation of nasal cavity epithelial cells
Authors: Michalets Sarah , Saha Ananya , Jimenez Ariana , Uddbäck Ida , Williams M Elliott , Mattingly Cameron , Kost Kirsten , Hicks Sakeenah , Lowen Anice , Scharer Christopher , Antia Rustom , Kohlmeier Jacob 
Published: November 2024

Abstract
Many vaccines against respiratory viruses have proven suboptimal in generating long-lasting sterilizing immunity and preventing transmission among populations. It is well established that respiratory tract resident memory CD8 T cells (TRM) induced by vaccination can reduce viral burdens and limit immunopathology upon direct inoculation of respiratory viruses. However, the ability of respiratory tract CD8 TRM to limit viral transmission has remained elusive. We developed a murine model to investigate the role of respiratory tract CD8 TRM in viral transmission using Sendai virus, which naturally transmits among mice. Contact mice were first immunized to generate Sendai virus-specific CD8 TRM and challenged by co-housing with a Sendai virus-infected index mouse. We demonstrated that CD8 TRM can limit viral transmission and decrease viral burdens, even in the absence of B cell responses, CD4 T cells, and circulating effector memory T cells. We evaluated multiple CD8 T cell effector mechanisms for their importance in limiting viral transmission and determined that IFN-γ secretion was critical. Upon IFN-γ signaling, nasal cavity epithelial cells adopted an anti-viral program. Furthermore, CD8 TRM in the nasal cavity alone were sufficient to limit respiratory virus transmission. These findings suggest that respiratory tract CD8 TRM, particularly those within the upper respiratory tract, are a promising vaccine target to prevent respiratory virus transmission among populations.
Quality Assessment of Metabolic Fitness during T Cell and NK Cell Expansion
Authors: Wang Guoxiao , Swain Pamela , McGarrigle Ryan , Romero Natalia 
Published: November 2024

Abstract
CAR-T cells have revolutionized cancer treatment, and other cell types like CAR-NK cells are also showing promising results. Engineered cells generally need to be expanded ex vivo before being transfused into patients. Growth conditions, including expansion platform, cell culture media, and cytokine composition, time of expansion, etc., can have a strong effect on the characteristics of the final products and need to be monitored to establish the appropriate development process.
Recent developments highlight the significance of cell metabolism in influencing immune responses and the anti-tumor efficacy of cell therapies. In the present study, we utilized Seahorse XF technology and assays to characterize T cell and NK cell metabolic fitness during cell expansion. We cultured human T cells and NK cells under different expansion conditions including culture media, culture devices, and cytokine combinations, and sampled cells at different time points for quality assessment of metabolic fitness. Using the new Seahorse XF assay alongside immunophenotypic characterization using Novocyte Flow Cytometry, we obtained robust information on mitochondrial and glycolytic energy production, metabolic poise, and the bioenergetic capacity of the expanded cells, allowing us to identify conditions that resulted in increased metabolic fitness of the cell population that can contribute to defining cell expansion conditions during immunotherapy development.
High throughput Targeted Transcriptome Sequencing of Bone Marrow Mononuclear Cells identifies a Rare Leukemia-Specific T Cell Subset.
Authors: Papalexi Efthymia , Hariadi Bryan , Kim Grace , Suyama Alexa , Roco Charles , Rosenberg Alexander 
Published: November 2024

Abstract
Many applications of scRNA-seq are focused on cell type identification, gene regulatory networks, or biomarker discovery. These applications often do not require surveying the whole transcriptome (WT), but rather require the interrogation of specific sets of well-characterized genes. In these cases, sequencing the entire transcriptome may be adding unnecessary costs. To increase throughput and minimize sequencing costs, the development of a targeted gene enrichment method is required.
Here, we demonstrate an approach to combine split-pool combinatorial barcoding with enrichment of 1000 genes (Immune1000 panel) representing immune cell markers and pathways. We use this gene panel to characterize 730,000 human bone marrow mononuclear cells (BMMCs) from four leukemia and four healthy donors. We found that enrichment with the Immune1000 Panel enabled the characterization of all major immune cell types at low sequencing depth and allowed for the detection of known leukemia-associated shifts in cell type proportions. Moreover, our targeted sequencing method enabled the detection of a rare (~0.35%), leukemia-specific T cell population that showed highly proliferative and cytotoxic potential.
Overall, we demonstrate our modular enrichment strategy preserves biological structure and allows for deep characterization of rare disease-relevant cell types and gene signatures with less sequencing.
Decoding mucosal immunity: A unique natural killer cell profile in vaginal tissue.
Authors: Vick Sarah , Domenjo-Vila Eva , Hughes Sean , Kirby Anna , Fialkow Michael , Hladik Florian , Prlic Martin , Lund Jennifer 
Published: November 2024

Abstract
Mucosal immunity in the vaginal tract (VT) remains poorly characterized despite its critical role in protecting from sexually transmitted infections. NK cells, critical for resolving infections, are found in the VT in significant numbers yet it is unknown how the immune system in the VT differs from that in circulation. To address this important question, vaginal tissue and autologous blood were collected from healthy donors and NK cells were profiled using high-parameter flow cytometry (n=10) and scRNA-seq (n=4) to define differences between NK cells from blood and tissue. The scRNA-seq data revealed a unique gene signature in tissue NK cells with a downregulation in genes related to cytotoxicity. We confirmed this data utilizing a 28-color flow cytometry panel. The frequency of markers expressed on blood and tissue NK cells were analyzed using a paired t-test. We found that NK cells in the VT express increased tissue residency markers CD69 and CD103 (p=0.0001, p=0.0009) when compared to NK cells from the blood. The NK cells from the VT displayed a decrease in maturation markers and cytotoxic molecule Granzyme B (p=0.0002). Despite the quiescent nature of NK cells in the VT, these cells produce increased levels of IFNg upon stimulation with cytokines (p=0.0021). This suggests NK cells in the VT may be regulated to limit tissue damage but are poised to robustly respond to inflammatory stimuli. In sum, I demonstrate how NK cells are phenotypically unique in mucosal tissue.
Unraveling the early transcriptional signature of peripheral blood NK cell transition to uterine residency
Authors: Greene Morgan , Asiimwe Rebecca , Bell Markayla , Wright Emma , Knott Brittney , Yates Stefani , Epstein Daniel , Little Shawn , Locke Jayme , Freud Aharon , Richter Holly , Porrett Paige 
Published: November 2024

Abstract
Tissue-resident uterine NK cells are essential for successful pregnancy, yet the molecular mechanisms guiding their tissue residency programming early after infiltration of blood-based precursors remain unknown. We examined the transition of CD56+ peripheral blood NK cells to a uterine resident state by performing scRNA-seq on enriched CD56+ cells from a matched peripheral blood (pb) and endometrial (e) biopsy taken during the secretory phase. Our integrated analysis comparing eNK vs pbNK cells identified a tissue adaptation signature. Key components of this signature included NR4A2 (94% vs 0%, p=9.46e-22), FOS (90% vs 9%, p=9.05e-14), and JUNB (77% vs 16%, p=3.15e-07) respectively. This signature also mirrored genes previously identified in activated murine intestinal CD8+ TRM cells early after LCMV infection. This signature was found in all endometrial CD56+ cells, including CD56bright CD16- eNKs, NKTs, and conventional eNKs (CD56dimCD16+). Pathway analysis implicated IL-17 and IL-18 cytokines, along with NFAT and VEGF signals in tissue residency programming. In conclusion, these data expand our understanding of early transcriptional programs in lymphocyte tissue adaptation, revealing the involvement of cytokines beyond TGF-β. Our data further indicate that signals associated with early tissue adaptation are conserved across species and cell types independent of an antigen receptor.
IL-12 induces a B cell-intrinsic IL-12/IFNg feed-forward loop promoting extrafollicular B cell responses
Authors: Elsner Rebecca , Shlomchik Mark , Smita Shuchi 
Published: November 2024

Abstract
While some infections elicit germinal centers (GC), others produce only extrafollicular (EF) responses. The mechanisms controlling these dichotomous fates are poorly understood. We identify IL-12 as a cytokine switch, acting directly on B cells to promote EF and suppress GC responses. IL-12 initiates a B cell intrinsic feed-forward loop between IL-12 and IFNg, amplifying IFNg production, which promotes proliferation and plasmablast (PB) differentiation, in synergy with IL-12. IL-12 sustains the expression of a portion of IFNg-inducible genes. Together, they also induce unique gene changes, reflecting both IFNg-amplification and cooperative effects between both cytokines. In vivo, cells lacking both IL-12 and IFNg receptors are more impaired in PB production than those lacking either receptor alone. Further, B cell-derived IL-12 enhances both PB responses and TH1 commitment. Thus, B cell-derived IL-12, acting on T and B cells, determines the immune response mode, with implications for vaccines, pathogen protection and autoimmunity.