bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure-guided design of the TIL1383I T cell receptor
Authors: Alonso Jesus A , Singh Nishant K , Devancaze Lauren , Devlin Jason , Baker Brian M 
Published: January 2023

Abstract
T cell therapy is an exciting form of cancer immunotherapy in which T cells are engineered to target specific tumor antigens. We employed a structure-guided design approach with the goal of engineering a safer and more effective variant of the TIL1383I T cell receptor (TCR) currently under study in clinical trials for malignant melanoma. Using our unpublished structure of TIL1383I we are in process of designing a panel of TCR variants with the goal of identifying candidates that improve “focus” towards the tyrosinase antigen presented on the MHC class I molecule HLA-A2. Structural analysis of TIL1383I revealed key residues, particularly beta-chain residues E97, G101, L102, responsible for engaging the tyrosinase peptide bound to HLA-A2. The crystal structure of TIL1383I in complex with tyrosinase-HLA-A2 also highlighted its uncharacteristic binding geometry and we therefore hypothesize that this binding orientation is associated with the observed CD8 co-receptor independence of TIL1383I. Indeed, functional analysis with TIL1383I-transduced CD8-positive and CD8-negative T cells, transduced T cells expressing a truncated CD8 lacking the intracellular LCK signaling domain, and tyrosinase peptide variants presented by HLA-A2 mutants outline this co-receptor independence. Combined with our interrogation of tyrosinase peptide cross-reactivity via a peptide positional scanning library approach, structure-guided design resulted in the identification of TIL1383I variants with improved binding affinities to the tyrosinase peptide as well as an understanding of structural characteristics that may contribute to TIL1383I’s co-receptor independence.
LAG3 mediates its inhibitory function by associating with the TCR:CD3 complex and inducing co-receptor:p56lck dissociation
Authors: Workman Creg , Guy Cliff , Mitrea Diana , Chou Po-Chien , Temirov Jamshid , Vignali Kate , Liu Xueyan , Zhang Hui , Kriwacki Richard , Bruchez Marcel , Watkins Simon , Vignali Dario 
Published: January 2023

Abstract
Lymphocyte activation gene 3 (LAG3) is an inhibitory receptor that is highly expressed on exhausted T cells in the tumor microenvironment. Despite over ten LAG3-targeting immunotherapeutics in clinical trials, we still do not know how LAG3 mediates its inhibitory activity. We show that LAG3 can function in the absence of MHC class II ligation and that in the absence of LAG3 there is a 2–3 fold increase in T cell receptor signaling resulting in increased proliferation. We show that both murine and human LAG3 molecules track to the immunological synapse (IS) by close association with the T cell receptor (TCR):CD3 complex. A phylogenetically conserved, acidic tandem glutamic acid–proline repeat in the LAG3 cytoplasmic tail can lower local pH at the IS and chelate Zn2+, limiting T cell activating signals by causing the dissociation of CD4:p56lck, which interact via a di-cystine:Zn2+ complex. This in turn causes a loss of co-receptor:TCR signaling. This novel inhibitory pH-mediated, Zn2+-displacement mechanism highlights LAG3 as a “signal disruptor” that can function in an MHC class II independent manner, providing critical insight into the mechanism of action of LAG3-targeting immunotherapies.
Therapeutic manipulation of memory T cell homeostasis in vivo
Authors: Wolf Gideon S , Singh Nevil J 
Published: January 2023

Abstract
After a primary immune response, a cohort of antigen-specific memory T cells are retained in vivo conferring long term protection against that specific pathogen. Over a lifetime, the accumulation of a memory T cell repertoire with specificities to multiple pathogens, collectively keeps the host safe against prevalent environmental threats. Other than booster vaccinations which narrowly increase the frequency of a single antigen-specific cohort, there are no viable strategies available to globally alter the total memory T cell population in vivo. Since memory T cells are thought be maintained by trophic signals from cytokines or self-MHC- both of which are available from endogenous antigen-presenting cells (APC)- we hypothesized that enhancing APC numbers in vivo can be a viable strategy to amplify memory T cells. Towards this end we treated mice with FMS-like tyrosine kinase 3 ligand (Flt3l) or specific self-peptides known to increase the peripheral survival of cohorts of CD4 T cells. After an acute expansion of dendritic cells (DCs) following Flt3l treatment, we observed an increase in effector memory CD4s and CD8s, but not in naïve T cells. Over the short term, this increase was independent of alterations in the thymus. On cessation of Flt3l treatment, the increase in DCs was not sustained, and the population of memory T cells also returned to steady state, suggesting restoration of competitive homeostasis. In contrast to this global effect, administering an endogenous self-peptide used by a small subset of peripheral T cells did not significantly alter the overall number or distribution of the memory repertoire. Taken together, these data suggest new options to manipulate memory T cell populations in clinically relevant situations.
Naive brain harbors resident memory T cells that respond to neurological insults prior to infiltration of antigen specific T cells
Authors: Ayasoufi Katayoun , Namen Shelby L , Goddery Emma , Tritz Zachariah Peter , Yokanovich Lila T , Fain Cori , Jin Fang , Hansen Michael , Johnson Aaron J 
Published: January 2023

Abstract
Brain resident memory T cells (TRM) have recently been phenotypically characterized. However, the function of these cells in the brain, and their changes during neurological insults, is not well understood. Using the described phenotype of brain TRMs (TCRB+, CD69+, CD4 or CD8+, CD103−, CD44+), we evaluated cellular responses of this population in the naïve brain and upon various neurological insults. We found that numbers of brain TRMs increased as a function of age. Additionally, TRM cells in the naïve brain produce TNFα constitutively, setting them apart from TRMs in other organs. Parabiosis studies revealed that circulating pools of memory T cells contributes to maintenance of TRM cells in the naïve brain. During neurological injury, we observed an increase in numbers of TRMs as early as 24 hours following physical insult induced by intracranial injection of PBS. During brain infection with Theiler’s Murine Encephalomyelitis virus, brain TRMs increased in number prior to detection of any virus-specific CD8 T cells. This implies TRMs respond to CNS viral infections prior to generation of virus antigen specific responses. This response is due to proliferation of TRM cells in the brain, as treatment with FTY720 did not inhibit TRM proliferation 24 hours post infection. In short, naïve brains harbor populations of TNFα producing TRM cells. And TRMs rapidly respond to neurological injuries through proliferation in an antigen independent manner. Understanding brain TRMs is crucial in investigating their role in neurodegenerative disorders or targeting this potent population of brain resident T cells in cancers of the CNS.
Characterization of macrophages in the liver of total body irradiated mice
Authors: Okamoto Norio , Asai Akira , Matsui Masahiro , Yasuoka Hidetaka , Nishikawa Tomohiro , Yokohama Keisuke , Nakamura Ken , Ohama Hideko , Tsuchimoto Yusuke , Fukunishi Shinya , Tsuda Yasuhiro , Higuchi Kazuhide 
Published: January 2023

Abstract
Two hepatic macrophage (MΦ) populations have been described in the inflamed liver: F4/80+CD11b+ cells and F4/80+CD68+ cells. In normal conditions, hepatic F4/80+CD11b+ cells are involved in host antibacterial resistance. However, these cells in total body irradiated mice (TBI mice) are unfunctional for the elimination of bacteria translocated from intestinal tracts. In this study, the properties of hepatic MΦ populations in TBI mice were characterized. Normal mice and mice 7 days after exposure to 4 Gy of X-rays were infected i.v. with 107 CFU/mouse of Enterococcus faecalis (E. faecalis). Three day after infection, F4/80+CD11b+ cells and F4/80+CD68+ cells isolated from the liver of these mice were cultured for 24 hrs, and culture fluids were assayed for IL-12, IL-10 and CCL1 by ELISA. NSG mice were inoculated i.v. with these MΦ preparations (2 × 105 cells/mouse), then infected i.v. with 5 × 104 CFU/mouse of E. faecalis. In the results, all TBI mice died within 2 weeks, while all normal mice survived. IL-12 was produced by F4/80+CD11b+ cells from normal mice, but not by both MΦ preparations from TBI mice. IL-10 was produced by F4/80+CD68+ cells from TBI mice (529.9 ± 272.6 pg/ml) and normal mice (445.8 ± 147.7 pg/ml). Large amounts of IL-10 (912.1 ± 103.7 pg/ml) was produced by F4/80+CD11b+ cells from TBI mice, and these cells produced CCL1 (327.5 ± 9.1 pg/ml), while other MΦ preparations did not. NSG mice inoculated with F4/80+CD11b+ cells from normal mice were resistant to infection; however, NSG mice inoculated with F4/80+CD11b+ cells from TBI mice did not. These results indicate hepatic F4/80+CD11b+ cells are polarized to M2bMΦ in response to total body irradiation, and these MΦ are involved in the decreased host antibacterial resistance in TBI mice.
Circulating memory is sufficient for protective immunity to infection with Chlamydia muridarum
Authors: Labuda Jasmine C , McSorley Stephen J 
Published: January 2023

Abstract
Chlamydia trachomatis is the most prevalent bacterial sexually transmitted infection worldwide and yet no vaccine currently exists to protect the public from this reproductive tract pathogen. Recent reports suggest that CD4 tissue resident memory cells (TRM) are essential for vaccine-induced protection against Chlamydia trachomatis in a mouse infection model. Additionally, CD4 TRM in the female reproductive tract (FRT) have been shown to co-localize with APCs in memory lymphocyte clusters (MLCs) to enhance secondary adaptive immunity to reproductive tract infections. Here, we examine a requirement for CD4 TRM and MLCs in protective immunity against infection with Chlamydia muridarum (Cm). Using parabiosis of naïve and Chlamydia-immune mice, we demonstrate that although CD4 TRM form in the FRT after primary Cm infection, they are not required for protection. Furthermore, histological analysis of FRT tissue from parabionts revealed that circulating memory is sufficient for protection against intravaginal challenge with Cm in the absence of CD4 TRM or MLCs in the reproductive tract. Moreover, this protective circulating memory can be induced through intravaginal or intranasal challenge with Chlamydia, indicating that a strong mucosal immunization can generate circulating protection in a vaccine setting. Ongoing work using adoptive transfers and antibody depletions of CD4 T cells and B cells will reveal which memory lymphocytes are responsible for the observed circulating protection.
GM-CSF+ Tc17 cells mediate vaccine-immunity, but not immunopathology, against lethal fungal pneumonia under CD4+ T-cell lymphopenia
Authors: Mudalagiriyappa Srinivasu , Vieson Miranda , Nanjappa Som G 
Published: January 2023

Abstract
Although opportunistic fungal infections are rising at alarming rates in immunocompromised individuals, there is no licensed vaccine available nor the clear understanding of the protective host responses. In a mouse model of fungal vaccine-immunity in CD4+ T-cell lymphopenia, we have previously shown that vaccine-induced IL-17A producing CD8+ T (Tc17) cells are necessary for controlling lethal fungal pneumonia. However, we found a significant number of Tc17 cells that co-expressed GM-CSF (&gt;50%), but their role has been implicated as ‘pathogenic’ in autoimmune disorders. In this study, using state-of-the-art approaches, we found that GM-CSF +Tc17 cells are essential for vaccine-immunity against lethal fungal pneumonia without precipitating an adverse immunopathology. Induction of GM-CSF+Tc17 cells, following vaccination, required signaling from cytokines, IL-1 and IL-23, that promoted differentiation and proliferation of effectors. However, memory homeostasis of GM-CSF+Tc17 cells was mostly independent of IL-23. Following the lethal challenge by the pulmonary route, IL-23 was required for the GM-CSF+Tc17 cells responses, but not for their re-differentiation, and was necessary to mitigate the immunopathology of the lungs. Collectively, GM-CSF+Tc17 cells are required for vaccine-mediated immunity against lethal fungal pneumonia.
Regions of mouse chromosomes 2 and 11 in SJL mice contain critical alleles for resistance to Cryptococcus neoformans
Authors: Davis Michael J , Rodriguez-Gil Jorge , Hoke Liz , Pinheiro Giovana , Chang Yun , Khillan Jaspal , Paven William , Kwon-Chung June 
Published: January 2023

Abstract
Cryptococcus neoformans (Cn) remains a leading cause of deadly mycosis. While previous studies have elucidated some of the host immune processes, little is known about the fundamental host factors that determine the outcome of Cn infection. Unfortunately, all commonly used inbred mice (including the common C57BL/6) are highly susceptible to virulent Cn strains, whereas humans are resistant to Cn unless immunocompromised. Thus, we sought a murine Cn infection system that more closely models humans. Testing the susceptibility of about 20 inbred strains of mice, we found that the SJL strain is, by far, the most Cn resistant inbred mouse strain in contrast to the closely related FVB strain being completely susceptible. While the early stages of Cn infection seem similar, SJL mice eventually cleared Cn and resolved pulmonary pathology, with little CNS dissemination. In contrast, susceptible mice showed significant and increasing fungal loads in both lungs and brains with associated pathology and death. F1 mice from FVB × SJL crosses were highly resistant to Cn suggesting that the resistant phenotype is dominant. Twenty percent of N2 mice (FVB × SJL F1 mice backcrossed to FVB) survived infection suggesting the involvement of multiple loci. Gene mapping uncovered two areas of genetic linkage to Cn resistance. These areas of interest were in portions of chromosomes 2 and 11. Genomic analysis found several candidate genes which are currently under evaluation. Mapping these cryptococcal resistance gene alleles may illuminate pathways of natural resistance which could be utilized for improved therapeutic options or to identify human populations at risk for cryptococcosis, making SJL mice an important tool for understanding cryptococcosis.
Dietary Antigens Drive Protective Innate-like CD4 T Cell Immunity at the Mucosal Barrier of the Small Intestine
Authors: Chen Angeline , Thiault Nicolas , Verstichel Greet , Iwaya Hitoshi , Cheroutre Hilde 
Published: January 2023

Abstract
CD4 T helper (Th) cells reprogram to cytotoxic T lymphocytes (CTLs) in the intestinal epithelium during steady state. The unique localization of mucosal CD4 CTLs, in the absence of a pathogenic threat, suggests local non-pathogen antigens and organ-specific properties direct the CTL conversion.
Similar to myeloid antigen presenting cells, intestinal epithelial cells (IECs) constitutively express MHC class II (MHCII), indicating crosstalk with nearby CD4 T cells. IECs constantly absorb and process luminal digested proteins and present these dietary antigens to neighboring CD4 T cells on their basolateral side. We have generated solid evidence with murine conditional knock-out and bone marrow chimera models that MHCII+ IECs and the dietary epitopes they present are instrumental in the development of small intestinal CD4 CTLs in a homeostatic, non-inflammatory environment.
These dietary antigen-specific CD4 CTLs accumulate over time as innate-like protective cells that fortify the epithelium with a pre-existing protective arm. As fully differentiated and functional resident T cells, CD4 CTLs are aptly designed to rapidly respond, independent of pathogen specificity, and contain infections. Using Salmonella as an enteric pathogen model, the data show that dietary antigen-specific CD4 CTLs have the capacity to rapidly and effectively kill infected epithelial cells, thereby preserving the integrity of the barrier and blocking systemic spreading of the pathogen. The double-pronged ability for CD4 CTLs to protect against invaders while also mitigating immunopathology, by differentiating inflammatory CD4 T cells into excellently trained CD4 CTLs, reveal previously unknown mechanisms of mucosal lymphocyte biology.
Indole metabolites are altered in maternal high fat diet exposed offspring and can modulate type 3 innate lymphoid cell function
Authors: Mirpuri Julie , Jaleel Sana , Niu Xinying 
Published: January 2023

Abstract

Background
We have shown that maternal high fat diet exposure (mHFD) results in a microbiota-dependent expansion of IL-17 producing type 3 innate lymphoid cells (ILC3) in offspring. We hypothesized that the unique mHFD microbiome in offspring would result in an altered metabolite profile that could potentiate Ahr signaling and ILC3 function.

Methods
Murine offspring exposed to 60% mHFD were examined at 2-weeks old. Stool was examined by high-throughput, non-targeted mass spectroscopy-based metabolic analysis. Microbial colonization was examined by next generation sequencing. 2-week-old small intestine (SI) from regular diet (RD) offspring was exposed to selected indole metabolites for 24 hours and supernatant examined by ELISA. For in vivo experiments, bacteria was gavaged to RD offspring beginning at 5 days old. Flow cytometry of SI lamina propria cells was used to examine ILC3.

Results
mHFD offspring had a differential pattern of colonization and metabolite composition. mHFD offspring had a consistent expansion of Lactobacillus murinus. In vivo exposure to L. murinus resulted in a 30% increase in IL-17 producing ILC3 not seen with exposure to L. rhamnosus. Metabolomics of stool from mHFD offspring showed a decrease in indole-3-acetate and 3-methyldiozyindole (p&lt;0.00001). SI stimulated with indole metabolites showed a 50% decrease in production of IL-17 (p&lt;0.05) and IL-22 (p&lt;0.05).

Conclusion
L. murinus is specifically expanded in mHFD offspring and can increase IL-17 producing ILC3. L. murinus may expand ILC3 by differential metabolism of indole metabolites. Metabolism of indole metabolites by L. murinus and their role on Ahr signaling need to be further examined as a mechanism of modulating ILC3 response in offspring.
Ingested microplastics pose a potentially serious risk to the gastrointestinal microenvironment
Authors: Castillo Eliseo F 
Published: January 2023

Abstract

BACKGROUND
Plastic pollution has increased exponentially over the past 70 years. Slow breakdown of plastic materials primarily leads to smaller and smaller microplastic particles (MP), but not actual degradation of the material. We now face extensive MP contamination of our food and water sources, raising ecological and public health concerns. MP ingestion by humans is now an inevitable consequence of global plastic pollution, and we are only now becoming aware of this burgeoning crisis. Given this crisis, there is also an important gap in knowledge regarding how MP affect the major direct organ of contact, the gastrointestinal tract. We provide compelling evidence that MP affect both intestinal epithelium and macrophages.

DESIGN
We utilized human colonic organoids and colonic cell lines to examine the effects of MP on intestinal permeability and wound healing. Additionally, we examined the effects of microplastics on macrophage function and metabolism. Lastly, we examined the in vivo response to microplastics in animal models.

RESULTS
Regarding the intestinal barrier, we show MP impede wound healing and affects intestinal permeability. In macrophages, phagocytosis of MP leads to the upregulation of costimulatory molecules and induces metabolic shift towards glycolysis. In vivo MP ingestion affects the weight and microbiota composition of mice.

CONCLUSION
In summary, our findings indicate MP ingestion may pose a serious human health hazard by disrupting both intestinal epithelial barrier and macrophage function subsequently causing intestinal permeability, dysbiosis, and an inflammatory state that could lead to intestinal and systemic inflammation.
Viable bacterial colonization is limited in the human intestine in utero
Authors: Rackaityte Elze , Halkias Joanna , Fukui Elle M , Mendoza Ventura F , Hayzelden Clive , Crawford Emily D , Fujimura Kei E , Burt Trevor D , Lynch Susan V 
Published: January 2023

Abstract
Mucosal immunity develops in the human fetal intestine by 11–14 weeks gestation, yet whether viable microbes exist in utero and interact with intestinal immunity is unknown. Structures consistent with coccoid bacterial morphology, embedded in fetal meconium were evident before mid-gestation by high-resolution scanning electron microscopy (n=4). Molecular methods indicated extremely low bacterial burden and simple profiles in fetal meconium (n=40 of 50) compared to controls (n=87). A subset of Micrococcaceae-dominated (n=9) meconium associated with proportions of lamina propria PLZF+ CD161+ CD4+ T cells and divergent intestinal epithelial transcriptomes. Fetal Micrococcus luteus was isolated only in the presence of a monocyte feeder cell line. This strain grew on placental hormones, remained viable within fetal antigen presenting cells, exhibited species-specific immunomodulatory capacity and genomic features indicating fetal adaptation. Thus, viable bacteria are highly limited and inconsistently detectable in human fetal meconium at mid-gestation.
HY209 alleviates inflammation in colitis mice through NLRP3 inflammasome inhibition
Authors: ZOU YUNYUN , Seong Seung-Yong 
Published: January 2023

Abstract
The anti-inflammatory effects of HY209 have been identified in sepsis. However, the anti-inflammatory potential of HY209 in colitis has not yet been investigated. In here, we evaluated the therapy efficacy of HY209 in an acute colitis mice model which induced by using dextran sulfate sodium (DSS). Compare to vehicle mice, HY209 treated mice showed significantly less body weight loss, lower disease activity index, longer colon length, as well as a lower histology disease scores. Meanwhile, the expression of pro-inflammatory cytokines (TNF-α, IL-1ß, IL-6) were reduced in colon tissue after HY209 treatment. Furthermore, HY209 treated mice significantly reduced inflammatory macrophage, but increased anti-inflammatory macrophage in lamina propria. In vitro, HY209 showed a strong inhibition to LPS and ATP/BzATP activated NLRP3 inflammasome formation in the bone marrow derived macrophages (BMDMs). In summary, our findings demonstrated that HY209 alleviates inflammation in colitis mice through NLRP3 inflammasome inhibition, discovery the potential of HY209 as a therapeutic option for colitis.