bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intracellular Signaling triggered by engagement of PD-1 by PD-L1
Authors: Bu Xia , Bu Melissa , Hua Ping , Zhu Baogong , Sharpe Arlene H , Freeman Gordon J 
Published: January 2023

Abstract
Blockade of PD-1/PD-L1 is in effective anti-tumor immunotherapy. To further elucidate the mechanism by which PD-1/PD-L1 engagement causes T cell dysfunction, we investigated intracellular signaling triggered by PD-1/PD-L1 ligation in T cells. We describe a novel antibody that detects PD-1 signaling. This antibody detects phosphorylation of the immunotyrosine switch motif (ITSM) in the intracellular tail of both human and mouse PD-1 (phospho-PD-1). We first examined the expression of PD-1 and phosphorylated PD-1 in T cells from human PBMC. We found that without CD3 and CD28 mAb stimulation, PD-1 and phospho-PD-1 had minimal expression on CD3+CD4+ and CD3+CD8+ cell. Upon stimulation with CD3 and CD28 mAb, we observed increased expression of PD-1 and phospho PD-1 in both CD3+CD4+ and CD3+CD8+ cells. Furthermore, upon CD3 and CD28 mAb stimulation and PD-L1 recombinant protein treatment, the level of phospho PD-1 increased in CD3+CD4+ and CD3+CD8+ cells. Utilizing a co-culture system of Jurkat-hPD-1 and 300-hPD-L1, we mimicked the cell-cell interaction through molecular ligation of PD-1 and PD-L1. Upon stimulation with CD3 and CD28 mAb in this co-culture system, we detected increased phospho PD-1 signal and phospho SHP-2 signal by Western blot. When CD3 and CD28 mAb stimulated Jurkat-hPD-1 cells were treated with recombinant PD-L1 protein, we observed decreased IL-2 secretion which indicates PD-1/PD-L1 ligation suppresses T cell activation and corresponds with phospho PD-1 expression. This study examines the intrinsic intracellular signals upon PD-1/PD-L1 engagement, and the results may promote a better understanding of the mechanism of T cell dysfunction by PD-1/PD-L1 ligation.
Transforming growth factor beta induced PD-L1 expression promotes pro-fibrotic signaling
Authors: Jung Mi-Yeon , Kang Jeong-Han , Leof Edward B. 
Published: January 2023

Abstract
Immune checkpoint proteins such as programmed death-ligand 1 (PD-L1) retain general immune homeostasis and self-tolerance. PD-L1 binds to programmed cell death protein 1 (PD-1) and inhibits T cell activation or protects tumor cells from T cell-mediated killing. PD-L1 has recently been shown to be up-regulated in invasive lung fibroblasts by p53 and focal adhesion kinase (FAK), any potential role of transforming growth factor-beta (TGFβ) in PD-L1 action is unknown in fibrosis. TGFβ is a mysterious protein with various roles in healthy tissue homeostasis/development as well as the development or progression of cancer, fibrotic disorders, and immune modulation, et al. In the current study, we showed that TGFβ induces the expression of the immunoinhibitory molecule PD-L1 in human and murine fibroblasts in a Smad2/3- and YAP/TAZ-dependent manner. Furthermore, PD-L1 knockdown decreased the TGFβ-dependent induction of extracellular matrix proteins, including collagen Ia1 (colIa1) and alpha-smooth muscle actin (α-SMA), and cell migration/wound healing. In addition to an endogenous role for PD-L1 in profibrotic TGFβ signaling, TGFβ stimulated-human lung fibroblast-derived PD-L1 into extracellular vesicles (EVs) capable of inhibiting T-cell proliferation in response to T cell receptor stimulation and mediating fibroblast cell migration. These findings provide new insights and potential targets for a variety of fibrotic and malignant diseases.
IL-7 Receptor Alpha Chain Expression Identifies Human CD8+ Memory T Cell Subsets with Distinct Gene Expression Profiles and TCR Repertoire Compositions
Authors: Chiu Yen-Ling , Chang Shih-Chen , Chia Jean-San 
Published: January 2023

Abstract
Heterogeneity of CD8 T cell play crucial roles in cancer patients and reveals the co-evolution between tumor and immunity. While CD127 expression identifies memory precursor cells during acute infections, the role of CD127 expression in defining memory T cell heterogeneity is not investigated. Here, we analyzed the Vβ-CDR3 usage of human effector memory TEM and TEMRA cells accompanied by functional and gene expression patterns based on surface CD127 expression. We found that, CD127hi subsets are associated with higher level of TCR diversity regardless of their TEM or TEMRA phenotype. CD127lo populations are presented with relatively low TCR repertoire diversity. Moreover, there is a high correlation between CD127hi and CD127lo populations which imply possible differentiation tract between CD127hi and CD127lo T cells, but not between TEM and TEMRA cells. On the other hand, both TEM and TEMRA CD127lo populations showed higher expression of effector genes including perforin, granzyme B, granzyme H, and pan-inhibitory killer immunoglobulin-like receptors, exhibited lower phenotype plasticity upon TCR activation and cytokine-driven proliferation, when compared to their CD127hi counterparts. In other words, depending on the expression of CD127, T cells from either TEM or TEMRA are similar in their gene expression and functionality patterns. These results provide the first evidence that T cell repertoire and gene expression signature can be uncoupled based on distinct CD127-dependent phenotype expression patterns but are delicately balanced in the memory T cell pool.
Organ-specific isoform selection of fatty acid binding proteins in tissue-resident lymphocytes
Authors: Fonseca Raissa , Frizzell Hannah , Christo Susan , Evrard Maximilien , Park Simone L. , Freestone David , Mackay Laura K. 
Published: January 2023

Abstract
Tissue-resident memory T (TRM) cells exist throughout the body where they are poised to mediate local immune responses. Although studies have defined a common mechanism of residency independent of location, there is likely to be a level of specialization that adapts TRM cells to their given tissue of lodgment. It has been shown that TRM cells in the skin rely on the uptake of exogenous fatty acids for their survival and upregulate fatty acid binding proteins (FABP) 4 and FABP 5 as part of their transcriptional program. However, FABPs exist as a larger family of isoforms with different members selected in a tissue-specific fashion that is optimized for local fatty acid availability. Here we show that although TRM cells in a range of tissue widely express FABPs, they are not restricted to FABP 4 and 5. Instead, TRM cells show varying patterns of isoform usage that are determined by tissue-derived factors. These patterns are malleable since TRM cells relocated to different organs modify their FABP expression in line with their new location. As a consequence, these results argue for tissue-specific overlays to the TRM cell residency program, including FABP expression that is tailored to the particular tissue of TRM cell lodgment.
Inflammation-induced lactate leads to the rapid loss of hepatic tissue resident NK cells
Authors: Dodard Garvin , Tata Angela , Erick Timothy , Jaime Diego , Miah Shahjahan , Quatrini Linda , Escalière Bertrand , Ugolini Sophie , Vivier Eric , Brossay Laurent 
Published: January 2023

Abstract
The liver harbors two main innate lymphoid cell (ILC) populations, conventional NK (cNK) cells and tissue-resident NK (trNK) cells also called ILC1s. While the antiviral functions of cNK cells have been well established, trNK cell functions are only beginning to be uncovered. Using the MCMV model of infection, we found that in contrast to liver cNK cells, the trNK cell population initially undergoes a contraction phase prior to a recovery phase to homeostatic levels. The rapid contraction phase is due to apoptosis, while the recovery phase occurs via proliferation in situ. Liver trNK cell apoptosis is not mediated by fratricide, liver lymphocytes, or inflammatory cytokines. Instead, we found that liver trNK cell apoptosis is the consequence of an increased sensitivity to lactic acid. Interestingly, MCMV infection lead to an increase of lactate in the liver, which was supported by changes in lactate dehydrogenase expression. Mechanistic analysis indicates that trNK cell sensitivity to lactate is linked to impaired mitochondrial functions. These findings underscore the unique properties of the liver resident NK cell compartment.
Paneth cells regulate diet-induced obesity and trafficking of inflammatory immune cells into adipose tissues
Authors: Joldrichsen Marisa R , Kim Eunsoo , Cormet-Boyaka Estelle , Boyaka Prosper N 
Published: January 2023

Abstract
Paneth cells regulate many key aspects of gastrointestinal health through the antimicrobial products and cytokines they produce. Loss or defective Paneth cell functions leads to dysbiosis and is one of the causes of Inflammatory Bowel Disease (IBD). The prevalence of obesity is growing in the general population and among recently diagnosed IBD patients, leading to the speculation that obesity increases IBD incidence, but the underlying mechanisms remain to be elucidated. We addressed whether Paneth cells of the small intestine play a role in the development of obesity. For this purpose, control wild-type C57BL/6 and Sox9ΔIEC mice, which lack Paneth cells due to Sox9 gene deletion within the intestinal epithelium (Sox9ΔIEC mice), were fed a high fat diet for 13 weeks. Though the consumption of food was similar between the 2 groups, weekly measurement of body weight showed that Sox9ΔIEC mice gained weight much faster and ultimately became more obese than the wild-type mice. The Sox9ΔIEC mice also developed larger abdominal fats, which included increased numbers of inflammatory macrophages (p&lt;0.05) and neutrophils (p&lt;0.05). Interestingly, B cells were the most increased (p&lt;0.01) immune cells population in white fat tissues of Sox9ΔIEC mice. When compared to control mice, the Sox9ΔIEC mice displayed impaired glucose tolerance (p&lt;0.0001) indicating that these mice also developed a metabolic disorder. Finally, the in vivo FITC-dextran permeability assay showed that Sox9ΔIEC mice on high-fat diet have increased intestinal permeability (p&lt;0.05). These results suggest a new role for Paneth cells as regulators of diet-induced obesity via their impact on gut immune homeostasis and recruitment of immune cells into omental fat tissues.
miR-17-92 regulates MAIT cell development and function
Authors: Liu Tingting , Wang Jie , Zhou Li , Mi Qing-Sheng 
Published: January 2023

Abstract
Mucosal-associated invariant T (MAIT) cells are innate-like T cells that acquire an effector function and differentiate into MAIT1 (T-bet+) and MAIT17 (RORγt+) subsets prior to thymic export. Upon activation, MAIT cells quickly release IFN-γ and IL-17, which modulate a broad spectrum of diseases, including autoimmunity, infection, allergy and cancer. miRNAs are no-coding RNAs regulating immune cell development and function. A recent study indicated defective MAIT cell development in the miRNAs-deficient mice, but, the specific miRNAs that guide their development remain unclear. Previous studies indicated that miR-17-92 regulates different immune cell development and function, however, the role of miR-17-92 in the MAIT cell development remains unclear. Here, we generated T cell specific miR-17-92 knockout (KO) mice to test the role of miR-17-92 in MAIT cell development and function. We found that deletion of miR-17-92 led to a profound defect on the MAIT cells in the number and frequencies in the thymus and peripheral immune organs, including spleen, lymph nodes, and liver, as well as in the lung and peritoneal cavity (P&lt;0.05). The frequency of MAIT17 cells was dramatically reduced in miR-17-92 KO mice, while the frequency of MAIT1 cells was dramatically increased in thymic and peripheral immune organs, compared to wild-type (WT) controls. Furthermore, upon PMA/Ionomycin stimulation, we found a defect of IL-17 production, with significantly increased IFN-γ production by peripheral MAIT cells in miR-17-92 KO mice, compared to WT controls. The detailed miR-17-92 targeting pathway by RNA-Seq and Chip-Seq is under the investigation. Overall, our data indicated that miR-17-92 plays a pivotal role in MAIT cell development and function.
Intestinal intraepithelial lymphocyte repertoires are imprinted clonal structures selected for MHC reactivity
Authors: Schattgen Stefan A , Crawford Jeremy C , Van de Velde Lee-Ann , Chu Hiutung , Mazmanian Sarkis K , Bradley Phil , Thomas Paul G 
Published: January 2023

Abstract
The intestinal mucosa is an important barrier for maintaining homeostasis and immune tolerance. Residing in the gut mucosa are the intestinal intraepithelial lymphocytes (IELs), an unconventional T cell type expressing αβ T cell receptors (TCRs) thought to contribute in immune surveillance and mediate repair of damaged epithelium. IELs are in close contact with a stream of microbial, food, and self-antigens, and while TCR-antigen interaction is presumed the major mechanism governing their functions, little is known about the native TCRαβ-IEL repertoire or its specificity.
Previously, we developed a nearest-neighbor distance measurement (TCRdist) for quantifying convergence within TCR repertoires based on enriched features within their determinants of specificity. Here, we extended TCRdist to develop two novel tools for repertoire analysis: RepDist, for measuring similarity between repertoires, and TStar, for identifying repertoire-enriched features. We applied these to conduct a survey of the ‘normal’ TCR repertoires for three major subsets (CD8αα+, CD8, CD4) of IELs, under varying conditions of microbiome depletion, food antigen deprivation, MHC-deficiency, and combinations thereof. Surprisingly, the only perturbations that disrupted the IEL repertoire were deficiencies in Class I molecules or β2m. Food antigen and microbiome depletion had virtually no effect on the clonotypic composition of all three IEL subsets. MHC-substitution also had little effect, indicating that while Class I is required for CD8αα and CD8 IEL selection, it is haplotype-independent. Taken together, these data demonstrate the native IEL TCR repertoires are selected for self-reactivity, rather than specificity towards exogenous antigens.
BCG vaccination reduces the mortality of Mycobacterium tuberculosis-infected type 2 diabetes mellitus (T2DM) mice through the induction of CXCR3+ T-regulatory cells
Authors: Radhakrishnan Rajesh Kumar , Thandi Ramya Sivangala , Tripathi Deepak , Paidipally Padmaja , McAllister Madeline , Mulik Sachin , Samten Buka , Vankayalapati Ramakrishna 
Published: January 2023

Abstract
Diabetes is a significant risk factor for the development of active tuberculosis. In this study, we used mouse model of Streptozotocin/Nicotinamide (STZ/NA) induced non-obese type 2 diabetes mellitus (T2DM) to determine the effect of prior BCG vaccination on survival and immune responses to Mycobacterium tuberculosis (Mtb) infection. We found that at 6–7 months post-Mtb infection, 90% of the Mtb-infected T2DM mice died, whereas only 50% of BCG-vaccinated T2DM-Mtb-infected mice died. Moreover, 40% of the PBS-treated uninfected T2DM mice and 30% of the uninfected BCG-vaccinated T2DM mice died, whereas all uninfected and infected nondiabetic mice survived. BCG vaccination was less effective in reducing the lung bacterial burden of Mtb infected T2DM mice compared to Mtb-infected non-diabetic mice, however it reduced immunopathology of lung tissues. Further, we found increased survival of BCG vaccinated Mtb infected T2DM mice is associated with 2-fold expansion of IL-13 producing CXCR3+ T-regulatory cells as measured by flow cytometry, qRT-PCR and confocal microscopy. We also found that prior BCG vaccination restored the immunosuppressive function of T-regulatory cells of Mtb-infected T2DM mice and reduced inflammation. IL-13 producing T-regulatory cells of BCG vaccinated Mtb-infected T2DM mice converted proinflammatory M1 macrophages (iNOS) to anti-inflammatory M2 macrophage (Arg1) phenotype to suppress the inflammation. In contrast, anti-IL-13R antibody inhibited the conversion of macrophages from M1 to the M2 phenotype and enhanced the inflammatory cytokines (IL-6 and TNF-α) production. Our findings suggest a novel role for BCG in preventing excessive inflammation and mortality in T2DM mice infected with Mtb.
Identifying mechanisms that enhance the longevity of tissue-resident memory T cells in the lung
Authors: Lobby Jenna L , Uddback Ida , Cartwright Emily , Hayward Sarah L , Takamura Shiki , Thomsen Allan R , Christensen Jan , Kohlmeier Jacob E 
Published: January 2023

Abstract
Lung tissue-resident memory T cells (TRM) are crucial mediators of cellular immunity against influenza viruses, but the number of these cells in the lung tissue gradually declines in the months following influenza infection. Recently, we showed that intranasal immunization with a replication-deficient Adenovirus that expresses the nucleoprotein from influenza A virus (AdNP) results in long-term maintenance of lung CD8+ TRM for up to 1-year post-immunization. However, the mechanism(s) that promote this enhanced longevity of CD8+ lung TRM remain unknown. Using a combination of mouse infection models, flow cytometry, and RNA-sequencing, we compared CD8+ T cells from the airways, lung, and spleen from AdNP-immunized or influenza x31-infected mice. We found that CD8+ TRM in the lungs of AdNP-immunized mice show increased homeostatic turnover and encounter persistent antigen in the lung. In addition, parabiosis experiments suggest that the influenza-specific CD8+ lung TRM pool is maintained in AdNP-immunized mice by continual recruitment of circulating TEM into the lung TRM pool. RNA-sequencing analysis comparing CD8+ lung TRM from AdNP-immunized and x31-infected mice at 1-month and 1-year post-immunization showed only minor variations that did not fully explain the differences in lung TRM persistence. We are currently investigating how antigen is maintained in the lung following AdNP immunization using microscopy and Cre recombinase-expressing Adenovirus (AdCre) to identify antigen presenting cells harboring antigen long-term in the lung. The results of this study will identify mechanisms that improve the durability of cellular immunity, and will thus inform future design of cell-mediated influenza vaccines.
Dynamic local T cell responses underlie associations in disease severity during infant RSV infection
Authors: Connors Thomas , Dogra Pranay , Mertz Sara , Szabo Peter , Idzikowski Emma , Ramilo Octavio , Mejias Asuncion , Farber Donna L 
Published: January 2023

Abstract
Respiratory syncytial virus (RSV) infections are common throughout infancy, resulting in a wide range of clinical manifestations, with significant morbidity and mortality seen worldwide. The mechanisms leading to severe disease remain unknown. We sought to determine viral and immune mediated factors related to disease severity. Utilizing multi-parameter flow cytometry and single cell RNA sequencing, we correlated local T cell responses with dynamic changes to viral load in samples obtained from infants infected with RSV. Viral burden was highest at time of study enrollment and declined towards clearance in all subjects regardless of disease severity. Peak CD8 T cell response occurred several days after peak viral burden. Disease severity was associated with the accumulation of highly proliferative CD25+/Ki67+ CD8 T effector memory cells in the respiratory tract. Single cell RNA sequencing of T cells revealed distinct transcriptomic profiles of T cell populations. Respiratory tract CD8 T cells upregulated genes for granzyme, perforin, and tissue adhesion (CXCR6, CD49a) while CD4 T cells in the airway were enriched for regulatory T cell genes (FoxP3, CTLA4) compared to blood. Blood samples were defined primarily by gene signatures associated with naïve T cells and no significant upregulation of effector genes, emphasizing the compartmentalized nature of the immune response. Interestingly, clusters of gamma delta T cells upregulating AREG were found in airway samples, supporting a role for immune mediated tissue repair. These results show that disease severity during RSV infection in infancy is associated with localized immune responses and provide insights into how tissue repair may be mediated following severe disease.
Inducible epithelial resistance promotes survival of viral pneumonia by inactivating virus particles and preventing CD8+ T cell dependent immunopathology
Authors: Wali Shradha , Flores Jose , Goldblatt David , Tuvim Michael J , Dickey Burton , Evans Scott E 
Published: January 2023

Abstract
Respiratory viral infections cause significant morbidity and mortality worldwide, necessitating the development of novel strategies to prevent complications of respiratory infections. Our group has discovered the phenomenon of inducible epithelial resistance where mice treated with combination inhalation of Toll-like receptor (TLR) 2/6 and TLR9 agonists (Pam2-ODN) are protected against respiratory pathogens, including viruses. We investigated the mouse survival benefits of paramyxovirus, Sendai (SeV) infection and found that Pam2-ODN treatment one day prior to SeV challenge enhanced survival of mice. This protection was associated with reduced CD8+ T cell inflammation. Depletion of CD8+T cells prior to infection increased baseline virus susceptibility but did not affect protection afforded by Pam2-ODN. Depletion of CD8+T cells after viral burden waned but before peak mortality enhanced SeV pneumonia survival, even in the absence of Pam2-ODN pretreatment, revealing the profound role of CD8+ T cell mediated immunopathology in virus-induced mortality. We further demonstrated that Pam2-ODN treatment controls viral replication by inactivation of SeV prior to epithelial internalization. Epithelial generation of reactive oxygen species induced by Pam2-ODN treatment is necessary for SeV inactivation and preventing CD8+T cell mediated immunopathology. These findings highlight antiviral mechanisms of inducible epithelial resistance and may provide means to protect vulnerable immunocompromised patients against respiratory diseases.
Novel approach for the detection of antigen-specific CD8 T cell responses corresponding to treatment outcome in HPV+ cancer patients
Authors: Sierra Gloria , Ouerkaxi Wushouer , Daftarian Pirouz , Sastry Jagannadha K , George Marybeth , Delcommenne Marc 
Published: January 2023

Abstract
HPV cancer treatment outcome has been positively correlated to the presence of patient immunity against the virus. Six HPV strains account for over 75% of cervical cancer cases worldwide with HPVE6 & E7 protein integration into the host’s DNA being the driving factor in these cancers. However, the sequence of these proteins vary between strains resulting in high diversity in epitope presentation in patients with different HLA haplotypes. Therefore, using one tetramer gives an inaccurate read of a patient’s immunity to the virus. In this study, we set out to develop a method to obtain a more complete read-out of patient immunity to HPV by creating a more comprehensive tetramer staining panel. We first selected 29 in-silico predicted epitopes of both E6 and E7 oncogenic proteins in the 6 most common HPV strains for 3 HLA haplotypes (HLA-A*02:01, HLA-A*11:01 and *24:02). We then utilized a non-UV “peptide exchange MHC tetramer platform” to assess the binding of these peptides to corresponding MHC groove. Since the peptide exchange and affinity of peptides to the cleft of MHC are correlated, we used an algorithm to calculate the measure of the peptide exchange rate. We found that 3 of the 29 peptides showed poor or no binding to the matched MHC, while all others had rates over 81.78%. The MHC tetramers generated by this peptide exchange platform were then used alone or as part of a pool to stain HPV specific CD8+ T cell enriched PBMCs from an HPV positive host. Our results showed no significant difference in the detection of HPV+ CD8 T cells between our generated HPV16 E7 tetramer and the commercially available tetramer. This implies that the use of this peptide exchange tetramer platform can serve as an accurate tool for measuring HPV immunity in cancer patients.