bluuebunny/crossref_metadata_2025_split huggingface dataset:
Escalating Dose Immunization Regimen in Non-Human Primates to Improve Immunogen-Specific Responses
Authors: Carson Audrey , Cheng Cheng , Biju Andrea , Changela Anita , Duan Hongying , Foulds Kathryn , Irvine Darrell , Kwong Peter , Koup Richard , Pierson Theodore 
Published: November 2024

Abstract
HIV-1 remains a major health threat, highlighting the need for a vaccine that induces broadly neutralizing antibodies. Epitope-based vaccine designs that focus humoral responses to vulnerable sites on the HIV-1 Env trimer protein are promising approaches, including those targeting the HIV-1 fusion peptide (FP). Escalating dose (ED) immunizations are a strategy to increase immunogen uptake into germinal centers and boost affinity maturation of the antiviral antibody response. In this study, we tested the impact of an ED immunization scheme on enhancing the FP-directed humoral response. Five groups of non-human primates were immunized: four received an ED immunization of either FP or a cocktail of FP+trimer, and one control group was dosed with a bolus FP+trimer cocktail. Two ED groups were adjuvanted with SMNP. The remaining groups used 3M052/alum. Fourteen weeks post-immunization, all ED groups had higher anti-FP IgG titers compared to the control, with the cocktail ED group adjuvanted with 3M052/alum characterized by 14.5-fold higher titers than the bolus control. While the ED cocktail and bolus groups had similar anti-trimer IgG titers, the ED groups had a higher non-base trimer response, shown by an 8.6-fold IgG increase between the 3M052/alum cocktail ED group and its bolus control. ED prime seems promising in raising anti-immunogen titers and lowering responses to the artificial trimer base, and further boosts will be administered to elicit serum neutralizing activity.
Validation of a Microbiome Dependent Colitis Model via Fecal Microbial Transplant in Germ-Free IL-10 Deficient Mice
Authors: Parello Caitlin , Van Dam Brett , McKim Andrew , Knights Mathew , Durrant Jessica , Panwell Kristin , Van Engelenburg Alex , Dube Philip , Lyng Gregory , Sonis Stephen 
Published: November 2024

Abstract
Inflammatory Bowel Diseases (IBD) are immune-mediated intestinal tract diseases with undefined etiologies. Proposed pathogenic mechanisms include abnormal inflammatory response to the intestinal microbiome. Mice deficient in IL-10, a critical cytokine for mucosal immune homeostasis, spontaneously develop enterocolitis; phenotypes are microbiome-sensitive. To establish a microbiome-dependent colitis model with improved construct validity and translational clinical relevance, we assessed colitis development in Germ-Free IL-10 knockout mice (GF IL-10 KO; Taconic Biosciences) following inoculation with fecal microbial transplant (FMT) from wild-type C57BL/6NTac mice at the Murine Pathogen Free™ (MPF™) health standard and assessed clinical responses to anti-IL-12/23p40 (anti-p40). Compared to control GF IL-10 KO mice, FMT-inoculated mice demonstrated reduced weight gain, elevated levels of fecal lipocalin 2 and calprotectin, and increased colon weight:length ratio at 8 weeks following FMT. FMT-inoculated mice also showed elevated histopathology scores, increased colonic CD3+ T cells and CD4+ TH cells, and epithelial hyperplasia by Ki-67 immunolabeling. Several colon cytokines were elevated in FMT-inoculated mice. Anti-p40 treatment significantly reduced all of these disease indicators with the exception of colon weight:length. These data provide a validated colitis model with relevant mechanisms for assessing the role of the microbiome and response to therapeutics in IBD.
Next-generation B cell ImmunoSpot™ assays permit in-depth assessment of the B cell response elicited by SARS-CoV-2 infection and/or COVID-19 mRNA vaccination
Authors: Kirchenbaum Greg , Lehmann Paul , Becza Noemi , Chepke Jack , Yao Lingling , Valente Alexis , Liu Zhigang 
Published: November 2024

Abstract
The affinity distribution of antigen-specific Bmem in the body is a critical variable that defines an individual’s ability to rapidly generate protective antibody specificities. Moreover, defining the Ig class/subclass usage of such antigen-specific Bmem is also critical since it forecasts the anamnestic response to be engaged upon antigen re-encounter. Here, we leveraged multiplexed ImmunoSpot to comprehensively define the magnitude and Ig class/subclass usage of the SARS-CoV-2 S-specific Bmem following infection and/or multiple COVID-19 mRNA vaccinations. Beyond evidencing past SARS-CoV-2 infection more reliably than assessment of plasma IgG reactivity against the nucleocapsid protein, direct assessment of Bmem provided insights into their affinity distribution and cross-reactivity profiles against emerging variants such as Delta and Omicron. Following stimulation of PBMC to transition resting Bmem into antibody-secreting cells, our studies entailed tracking of the S-specific Bmem compartment in subjects as their immune histories became increasingly more complex. Of note, our next-generation ImmunoSpot assay approaches evidenced improved functional affinity at single-cell resolution. Collectively, such B cell ImmunoSpot assays offer tremendous value for future B cell immune monitoring efforts owing to their ease of implementation, applicability to essentially any antigenic system, economy of PBMC utilization and suitability for regulated testing.
Regulation of NK cell effector function by Acly
Authors: Sohn Stacey , Cooper Megan , Kolicheski Ana , Laurent Jennifer , Saucier Nermina , Trammel Kelsey , Tobin Joshua 
Published: November 2024

Abstract
Natural Killer (NK) cells, crucial for viral immunity and tumor clearance, are influenced by metabolism. A prior study revealed that cytokine stimulation boosts the citrate-malate shuttle and cytosolic acetyl-CoA through ATP citrate lyase (ACLY) in NK cells. Acetyl-CoA is vital for fatty acid synthesis and protein acetylation, including histones. To explore the role of ACLY in NK cell function, we generated an inducible NK-specific Acly knockout mouse model. ACLY loss in NKp46+ NK cells did not alter maturation or IFN-γ production in naïve NK cells. However, ACLY-deficient NK cells exhibited notable proliferation defects in homeostatic and IL-15-stimulated conditions, associated with impaired glycolysis. The stimulation and priming of NK cells through IL-15 is an important mechanism for enhancing effector and anti-tumor functions. In addition to proliferation defect, IL-15-primed ACLY-deficient NK cells showed reduced IFN-γ responses to DAP12-associated activating receptors, specifically NKG2D, Ly49H, and Ly49D. RNA-seq revealed ACLY-deficient NK cells failed to upregulate DAP12 expression with IL-15 stimulation, confirmed at the protein level. These findings suggest the importance of ACLY in NK cell proliferation and potentially DAP12-driven effector functions. Ongoing experiments are focused on investigating how ACLY and cytosolic acetyl-CoA are linked to DAP12 expression, and the effects of this during in vivo effector functions.
Impaired Early Interferon Responses to Influenza Virus Infection in Aged Mice are Associated With Increased Pulmonary Inflammation
Authors: Metcalf Jordan , Alexander Jeremy , Booth J Leland , Miller Craig , Drevets Douglas , Wu Wenxin 
Published: November 2024

Abstract
Background: Seventy to ninety percent of seasonal influenza deaths occur in those aged 65 or older. Methods: To determine the innate immune responses to influenza A virus (IAV) infection, young (12-week) and old (70-week) C57BL/6J mice were infected intranasally (i.n.) with IAV PR8. Immune responses and viral replication were determined by qRT-PCR. Lung inflammation and injury were evaluated by histology and bronchoalveolar lavage (BAL) and lung to body weight ratio respectively.
Results: Comparing young and old mice at the times indicated there were no differences in weight loss percentages, lung-to-body weight ratios and total immune cells in BALF after IAV infection. However, aged mice had significantly higher viral loads and lower type I interferon (IFN) expression in the lung at day 3 p.i. In contrast, at this time point, aged mice had significantly higher amounts of type III IFN expression, which correlated with higher viral loads. Histopathology revealed that IAV infection in aged mice resulted in lower pathological scores early (day 5) and higher lung pathological scores later (day 7) of disease than in young mice.
Conclusion: Our models demonstrated that aging dysregulates early IFN responses to influenza infection resulting in enhanced viral replication. These altered IFN responses in aged mice also result in enhanced lung inflammation late after infection and may also be a cause of the increased incidence of secondary bacterial infections seen in the aged.
Single cell transcriptomes from fetuses exposed to HCMV during gestation reveals a distinct subset of memory-like NKG2C+ fetal NK cells
Authors: Khalil Mohamed , Terhune Scott , Malarkannan Subramaniam 
Published: November 2024

Abstract
Congenital cytomegalovirus (cCMV) infection is the most common cause of intrauterine infection in the USA, impacting 1 in 100 live births. Although most infected newborns are asymptomatic, 10% display severe congenital anomalies, including microcephaly, sensorineural hearing loss, cerebral palsy, growth restriction, and perinatal mortality. Natural killer (NK) cells are the first lymphocytes to develop during gestation and are required to manage CMV infections. The role of fetal NK cells during cCMV is limited and their development and functions within the umbilical cord has not yet been explored. To investigate this, four sets of umbilical cord blood (UCB) and matching umbilical cord tissues were collected from 2 CMV seropositive (CMV+) and 2 CMV seronegative (CMV-) fetuses that did not experience any complications during gestation. We were able to successfully sort and capture over 5,000 fetal NK cells and perform single-cell RNA-sequencing (scRNA-seq). Using scRNA-seq, we observed and characterized 5 unique fetal NK cell subsets in the UCB and 4 subsets in the corresponding tissue. Interestingly, we identified a distinct subset of NKG2C+ memory fetal NK cells displaying elevated expression levels of NKG2C, CD52, CD2, CD16, and CD3E. Here, we demonstrate that cCMV can induce the formation of memory-like NKG2C+ NK cells that display a unique transcriptional profile. These findings have the potential to influence the future application of fetal memory NK cells.
The role of CX3CR1+ FALC-associated macrophages in health and inflammation
Authors: Dominguez Joseph , Kim Jiseon , Kim Seung Hyeon , Adams Hannah , Ludewig Burkhard , Kim Ki-wook 
Published: November 2024

Abstract
The omentum is a visceral adipose tissue that contains fat-associated lymphoid clusters (FALC) to aid in peritoneal immunity. These clusters consist of large aggregates of lymphocytes, dendritic cells, macrophages, and innate lymphoid cells that participate in the clearance of pathogens. Tissue-resident macrophages (TRM) are immune cells found in every tissue and can be defined by their origins, consisting of subsets maintained either by embryonic precursors or by bone-marrow progenitors. A recent study found embryonically derived TRM express at least one marker amongst Tim4, LYVE1, FOLR2 while bone marrow derived macrophages maintain CCR2 expression. Previous publications have shown the existence of LYVE1+ macrophages surrounding each cluster, here we study an unexamined subset of FALC-associated macrophages that are imbedded within the lymphoid structures. Using confocal imaging, flow cytometry analysis with reporter/ conditional knock-out mice, we have characterized this TRM subset as CX3CR1+ Tim4- LYVE1lo/- and CCR2 dependent. In addition, we examined the interaction between CX3CR1+ macrophages and CCL19+ fibroblastic reticular cells by generating CCL19-driven Csf1 depleted mice and found CX3CR1+ macrophages were partially depleted. Lastly, we looked at the role of tissue-resident macrophages in the omentum in early ovarian tumor burden and found omental/peritoneal TRM macrophage depletion by Wt1-driven Csf1 depletion led to increased tumor burden.
Single-cell transcriptomics of CD8 T cells in autoimmune diabetes after anti-CD3 monoclonal antibody treatment
Authors: Wu Ying , Spurrell Maxwell , Deng Songyan , Herold Kevan 
Published: November 2024

Abstract
The FcR non-binding anti-CD3 mAb, teplizumab is the first drug approved by FDA to delay Type 1 diabetes (T1D) by modulating the immune mediated destruction of insulin-producing β cells. However, we and others have observed that after remission is induced in diabetic NOD mice that are treated with F(ab’)2 fragments of mAb 145-2C11, insulitis remains. To understand how the antibody induces long-term tolerance, we performed single-cell RNA-seq and TCR-seq on T cells from the islets and pancreas-draining lymph nodes (pLN) of long-term remitted NOD mice treated by anti-CD3 mAb or pre-diabetic NOD mice with insulitis. In the islets, CD8 T cells of remitted NOD had higher expressions of TCF-1 and EOMES, than their counterparts from pre-diabetic control. Notably, CD8 T cells from islets of remitted NOD had increased expressions of TOX and EOMES while with no difference in TCF-1, compared to their counterparts from paired pLN. In contrast, islet-infiltrating CD8 T cells of pre-diabetic NOD had decreased expressions of EOMES and TCF-1 but with no difference in TOX, compared to their pLN counterparts. Moreover, islet-infiltrating CD8 T cells of remitted NOD had higher median TCR entropy indicating a more diverse TCR repertoire than their counterparts from pre-diabetic NOD. These results suggest that anti-CD3 modulates the terminal differentiation of islet-infiltrating CD8 T cells. Tolerance is maintained by cells with stem-like and exhaustion features and a more diverse TCR repertoire.
Hyaluronidase 2 induces pathogenicity in Th17 cells
Authors: Adhikari Laxmi Prasad , Woodman Kaitlyn , Reynolds Joseph 
Published: November 2024

Abstract
Autoreactive Th17 cells express high levels of inflammatory cytokine IL-17A promoting the development and progression of autoimmune diseases. Previous studies show that differentiation of Th17 cells with IL-1 and IL-23 or TLR2 activation drives their aggressive proliferation, making them pathogenic to induce experimental autoimmune encephalomyelitis (EAE). We aim to study a previously undefined role of hyaluronic acid (HA) and its modulation in influencing inflammatory potential and pathogenicity of Th17 cells in autoimmune diseases. Our in vitro differentiation experiments with HA and its modifying enzymes show that a baseline level of HA is essential for the normal differentiation and proliferation of Th17 cells. The overexpression of hyaluronidase 2 (Hyal2) that cleaves HA in Th17 cells decreases IL-17A production but increases cell proliferation in vitro, and adoptive transfer of these cells is sufficient to induce EAE in mice. Furthermore, flow cytometric analysis of infiltrated CD4+ T cells in the CNS of EAE mice indicates lower levels of inflammatory cytokines. Our findings suggest that Hyal2 itself exhibits a level of pathogenicity challenging the prevailing paradigm that these cells can induce the disease only when producing higher levels of encephalitogenic cytokines. Future experiments will delve into the regulation and mechanisms underlying the impact of HA on pathogenic Th17 cells, potentially identifying target molecules to treat autoimmune disorders.
Single-cell RNA sequencing reveals an immunomodulatory population of double negative T-cells in the diabetic NOD mouse
Authors: Robben Michael , Luber Jacob , Kostic Aleksander 
Published: November 2024

Abstract
NOD mice are a widely used model of type 1 diabetes, an inflammatory autoimmune condition characterized by autoreactive T-cells that target insulin producing beta cells of the pancreatic islets. While T cell biology in the context of this disease is important it is unclear why autoreactive T-cells develop in this model or what they do within the islets themselves. We have designed a single cell sequencing experiment where enriched T-cells taken from diabetic and non-diabetic NOD mice are sequenced for mRNA expression and TCR sequence concurrently. The resulting sequencing data shows abnormal representation of Double Negative (DN) T-cells in all tissues and conditions (~30%). We have observed that like CD8+ and CD4+ T-cells, this population displays normal maturation phenotypes, but experience reduced exhaustion of effector subsets after infiltration of the pancreatic islets. Looking at clonal subpopulations of T-cells we have discovered a subset of CD8+ T-cells that have high expression of GzmA even after loss of the survival signal marker, IL7r. Through investigation of these aberrant T-cell populations, we have found that the diabetic NOD mouse pancreatic is highly immunosuppresive and expression of T-cell co-receptors may have a significant impact on diabetic onset.
Unraveling the Role of CD137 in Treg-Mediated Suppression of Type 1 Diabetes: Insights from Treg-Specific CD137 Knockout Mice
Authors: Nabi Rabia , Ciecko Ashley , Lin Chien , Chen Yi-Guang 
Published: November 2024

Abstract
CD137, encoded by Tnfrsf9, acts as a costimulatory molecule on activated T cells. Conversely, soluble CD137 exerts immunosuppression by binding to CD137L on T cells, inhibiting activation. In the NOD mouse model of Type 1 Diabetes (T1D), CD137 expression in Foxp3+ regulatory CD4 T cells (Tregs) inhibits T1D, but the underlying mechanism remains elusive. To investigate the role of CD137 in Treg-mediated T1D suppression, we generated Treg-specific CD137 knockout mice (NOD.Treg-Tnfrsf9-/-). While no systemic inflammation was observed, these mice developed accelerated T1D compared to wildtype control. Reduced serum-soluble CD137 in these mice indicated Tregs are its main producers. scRNA-seq revealed phenotypic alterations of Tregs isolated from pancreatic islets of NOD.Treg-Tnfrsf9-/- mice, showing lower activation and clonal expansion than wildtype counterparts. Reduced Treg activity in these mice was associated with increased frequencies of islet-activated CD8 T cell subsets and their clonal expansion. MHC class I tetramer staining revealed a higher frequency of β-cell antigen IGRP206-214 specific CD8 T cells in NOD.Treg-Tnfrsf9-/- mice. No discernible differences in the initial expansion and activation of β-cell autoreactive CD8 T cells in pancreatic lymph nodes were observed. Our results suggest CD137 expression in Tregs is critical for restraining ongoing autoimmune inflammation in islets of NOD mice but dispensable for controlling autoreactive T cells in lymphoid tissues.
Chitinase 3-Like-1/BRP-39 regulates extracellular matrix remodeling during allergic fungal asthma
Authors: Ellis Diandra , Makullah Mgayya , Jones Mary Jane , Godfried Jarrett , Rokicki Ellie , Cheung Suki , Steele Chad 
Published: November 2024

Abstract
We previously reported that fungal-sensitized human asthmatics had higher levels of the chitinase-like protein YKL-40 in sputum than non-fungal sensitized asthmatics. Unexpectedly, we found that mice deficient in BRP-39 (Chi3l1-/- mice; the murine ortholog of human YKL-40) had increased airway hyperreactivity (AHR) during experimental allergic fungal asthma, despite no correlation with classic drivers of AHR (type 2 and eosinophilic responses). BRP-39 has been reported to bind lectins and complex carbohydrates and is involved in non-immune processes such as cell proliferation, angiogenesis and tissue remodeling. The extracellular matrix (ECM) of the lung is mainly comprised of collagen and elastin that provides elasticity and resilience to compressive and expanding forces. We found that Chi3l1-/- mice subjected to allergic fungal asthma demonstrated restrictions in lung mechanics due to increased elastic stiffness in the conducting airways and the alveolar/parenchymal compartment. This correlated with increased levels of collagen and elastin in mutant mice. ECM enzymes involved in matrix remodeling of collagen and elastin, such as matrix metalloproteinases (MMPs) 2, 3, 9, and 12, were reduced in mutant mice. We further identified BRP-39 dependent differences in MMP secretion by stimulating primary lung fibroblasts. Ultimately, these findings highlight BRP-39 as a crucial regulator of MMPs needed to turnover lung ECM proteins during the progression of allergic fungal asthma.
An engineered viral protein rewires signaling pathways to overcome T cell suppression.
Authors: Zheng Yating , Gu Zehui , Shudde Claire , Piper Taylor , Wang Xinyu , Aleck Grace , Zhou Jiajia , Chanda Monica , Trinch Lilliana , Zou Weiping , Courtney Adam 
Published: November 2024

Abstract
Cancer can evade destruction by depriving T cells of cytokines, such as IL-2, that cause JAK-STAT signaling required for T cell functionality. We hypothesized that the direct activation of STAT proteins in a cytokine-independent manner could restore the signals needed by T cells. Because STATs are regulated by phosphorylation, we predicted that enforced recruitment of kinase activity to STATs could activate them directly in the absence of cytokine. Tyrosine-protein kinase-interacting protein (TIP), expressed by Herpesvirus saimiri, co-opts LCK kinase by recruiting LCK to non-canonical substrates, including STATs. We evaluated whether a minimal region of TIP could be isolated from the full-length viral protein and combined with STAT binding sites derived from cytokine receptors. Using this platform, we demonstrate that LCK kinase activity can be recruited to targeted STAT proteins to activate them. We determined that a STAT5 activator (aSTAT5) allowed CD8+ T cells to remain viable in the absence of IL-2 and retained their capacity to produce IFNg and kill cancer cells ex vivo. We therefore incorporated aSTAT5 into tumor-specific T cells (TST) and transferred them into tumor-bearing mice. We determined that aSTAT5 TST caused potent tumor regression and reduced tumor outgrowth due to improved T cell persistence and functionality. Our findings highlight that T cells can be improved to resist the miscommunication that cancer causes by targeting intracellular signaling pathways.
Immune experiences alter tolerance in T cell-mediated autoimmunity.
Authors: Rollins Meagan , Bhela Siddheshvar , Weyu Eyob , Nelson Christine , Quarnstrom Clare , O'Flanagan Stephen , Smith Olivia , Sofianou Xenia , Seelig Davis , Fife Brain , Masopust David , Vezys Vaiva 
Published: November 2024

Abstract
Autoimmune diseases afflict &gt;20M Americans and alarmingly the incidence of autoimmune diseases is increasing particularly in children. The hygiene hypothesis (HH) proposes that there is an inverse correlation between microbial exposure and subsequent development of autoimmunity, i.e., the “cleaner” the environment, the higher the probability that autoimmunity develops. Critically, how microbial exposures and infections alter self-antigen (Ag), a critical component of immune tolerance, is unknown. Our data show that immune-experienced mice have decreased self-specific CD8 T cell priming and organ pathology mediated by resident cells in lymph nodes (LN). Resident Ag-bearing LN stromal cells isolated from immune-experienced mice induced less self-specific CD8 T cell proliferation in vitro indicating changes in self-Ag. The HH determines that environmental stressors are important drivers of autoimmunity, yet the human immune experience is poorly modeled in SPF models of tolerance and autoimmunity. Therefore, we used mice exposed to natural mouse pathogens, "dirty" mice showed a decrease in T cell activity to self-Ag. The cohousing of NOD mice with pet shop mice resulted in zero mice developing autoimmune diabetes. Overall, our data suggest novel mechanisms by which self-antigen is altered in lymph nodes due to previous immune experiences addressing a critical mechanism behind the hygiene hypothesis, intersecting TCR reactivity with environmental impact.