技术资料

Despite the growing knowledge of T cell responses in COVID-19 patients,there is a lack of detailed characterizations for T cell-antigen interactions and T cell functions. Here,with a predicted peptide library from SARS-CoV-2 S and N proteins,we found that specific CD8+ T cell responses were identified in over 75% of COVID-19 convalescent patients (15/20) and an epitope from the N protein,N361-369 (KTFPPTEPK),was the most dominant epitope from our selected peptide library. Importantly,we discovered 2 N361-369-specific T cell receptors (TCRs) with high functional avidity that were independent of the CD8 co-receptor. These TCRs exhibited complementary cross-reactivity to several presently reported N361-369 mutant variants,as to the wild-type epitope. Further,the natural functions of these TCRs in the cytotoxic immunity against SARS-CoV-2 were determined with dendritic cells (DCs) and the lung organoid model. We found that the N361-369 epitope could be normally processed and endogenously presented by these different types of antigen presenting cells,to elicit successful activation and effective cytotoxicity of CD8+ T cells ex vivo. Our study evidenced potential mechanisms of cellular immunity to SARS-CoV-2,and illuminated potential ways of viral clearance in COVID-19 patients. These results indicate that utilizing CD8-independent TCRs against SARS-CoV-2-associated antigens may provide functional superiority that is beneficial for the adoptive cell immunotherapies based on natural or genetically engineered T cells. Additionally,this information is highly relevant for the development of the next-generation vaccines with protections against continuously emerged SARS-CoV-2 mutant strains. View Publication

Proton export is often considered a detoxifying process in animal cells,with monocarboxylate symporters coexporting excessive lactate and protons during glycolysis or the Warburg effect. We report a novel mechanism by which lactate/H+ export is sufficient to induce cell growth. Increased intracellular pH selectively activates catalysis by key metabolic gatekeeper enzymes HK1/PKM2/G6PDH,thereby enhancing glycolytic and pentose phosphate pathway carbon flux. The result is increased nucleotide levels,NADPH/NADP+ ratio,and cell proliferation. Simply increasing the lactate/proton symporter monocarboxylate transporter 4 (MCT4) or the sodium-proton antiporter NHE1 was sufficient to increase intracellular pH and give normal hematopoietic cells a significant competitive growth advantage in vivo. This process does not require additional cytokine triggers and is exploited in malignancy,where leukemogenic mutations epigenetically increase MCT4. Inhibiting MCT4 decreased intracellular pH and carbon flux and eliminated acute myeloid leukemia-initiating cells in mice without cytotoxic chemotherapy. Intracellular alkalization is a primitive mechanism by which proton partitioning can directly reprogram carbon metabolism for cell growth. View Publication

Extracellular vesicles (EVs) have potential as minimally invasive biomarkers. However,the methods most commonly used for EV retrieval rely on ultracentrifugation,are time-consuming,and unrealistic to translate to standard-of-care. We sought a method suitable for EV separation from blood that could be used in patient care. Sera from breast cancer patients and age-matched controls (n = 27 patients; n = 36 controls) were analysed to compare 6 proposed EV separation methods. The EVs were then characterised on 8 parameters. The selected method was subsequently applied to independent cohorts of sera (n = 20 patients; n = 20 controls),as proof-of-principle,investigating EVs' gremlin-1 cargo. Three independent runs with each method were very reproducible,within each given method. All isolates contained EVs,although they varied in quantity and purity. Methods that require ultracentrifugation were not superior for low volumes of sera typically available in routine standard-of-care. A CD63/CD81/CD9-coated immunobead-based method was most suitable based on EV markers' detection and minimal albumin and lipoprotein contamination. Applying this method to independent sera cohorts,EVs and their gremlin-1 cargo were at significantly higher amounts for breast cancer patients compared to controls. In conclusion,CD63/CD81/CD9-coated immunobeads may enable clinical utility of blood-based EVs as biomarkers. View Publication

Asthma and its heterogeneity change with age. Increased airspace neutrophil numbers contribute to severe steroid-resistant asthma exacerbation in the elderly,which correlates with the changes seen in adults with asthma. However,whether that resembles the same disease mechanism and pathophysiology in aged and adults is poorly understood. Here,we sought to address the underlying molecular mechanism of steroid-resistant airway inflammation development and response to corticosteroid (Dex) therapy in aged mice. To study the changes in inflammatory mechanism,we used a clinically relevant treatment model of house-dust mite (HDM)-induced allergic asthma and investigated lung adaptive immune response in adult (20-22 wk old) and aged (80-82 wk old) mice. Our result indicates an age-dependent increase in airway hyperresponsiveness (AHR),mixed granulomatous airway inflammation comprising eosinophils and neutrophils,and Th1/Th17 immune response with progressive decrease in frequencies and numbers of HDM-bearing dendritic cells (DC) accumulation in the draining lymph node (DLn) of aged mice as compared with adult mice. RNA-Seq experiments of the aged lung revealed short palate,lung,and nasal epithelial clone 1 (SPLUNC1) as one of the steroid-responsive genes,which progressively declined with age and further by HDM-induced inflammation. Moreover,we found increased glycolytic reprogramming,maturation/activation of DCs,the proliferation of OT-II cells,and Th2 cytokine secretion with recombinant SPLUNC1 (rSPLUNC1) treatment. Our results indicate a novel immunomodulatory role of SPLUNC1 regulating metabolic adaptation/maturation of DC. An age-dependent decline in the SPLUNC1 level may be involved in developing steroid-resistant airway inflammation and asthma heterogeneity. View Publication

CD8+ memory T (TM) cells play a critical role in immune defense against infection. Two common $\gamma$-chain family cytokines,IL-2 and IL-7,although triggering the same mTORC1-S6K pathway,distinctly induce effector T (TE) cells and TM cells,respectively,but the underlying mechanism(s) remains elusive. In this study,we generated IL-7R-/and AMPK$\alpha$1-knockout (KO)/OTI mice. By using genetic and pharmaceutical tools,we demonstrate that IL-7 deficiency represses expression of FOXO1,TCF1,p-AMPK$\alpha$1 (T172),and p-ULK1 (S555) and abolishes T cell memory differentiation in IL-7R KO T cells after Listeria monocytogenesis rLmOVA infection. IL-2- and IL-7-stimulated strong and weak S6K (IL-2/S6Kstrong and IL-7/S6Kweak) signals control short-lived IL-7R-CD62L-KLRG1+ TE and long-term IL-7R+CD62L+KLRG1- TM cell formations,respectively. To assess underlying molecular pathway(s),we performed flow cytometry,Western blotting,confocal microscopy,and Seahorse assay analyses by using the IL-7/S6Kweak-stimulated TM (IL-7/TM) and the control IL-2/S6Kstrong-stimulated TE (IL-2/TE) cells. We determine that the IL-7/S6Kweak signal activates transcriptional FOXO1,TCF1,and Id3 and metabolic p-AMPK$\alpha$1,p-ULK1,and ATG7 molecules in IL-7/TM cells. IL-7/TM cells upregulate IL-7R and CD62L,promote mitochondria biogenesis and fatty acid oxidation metabolism,and show long-term cell survival and functional recall responses. Interestingly,AMPK$\alpha$1 deficiency abolishes the AMPK$\alpha$1 but maintains the FOXO1 pathway and induces a metabolic switch from fatty acid oxidation to glycolysis in AMPK$\alpha$1 KO IL-7/TM cells,leading to loss of cell survival and recall responses. Taken together,our data demonstrate that IL-7-stimulated weak strength of mTORC1-S6K signaling controls T cell memory via activation of transcriptional FOXO1-TCF1-Id3 and metabolic AMPK$\alpha$1-ULK1-ATG7 pathways. This (to our knowledge) novel finding provides a new mechanism for a distinct IL-2/IL-7 stimulation model in T cell memory and greatly impacts vaccine development. View Publication

Background: Immunotherapy efficacy in esophageal squamous cell carcinoma (ESCC) is often limited by an immunosuppressive tumor microenvironment (TME). NLRC5,a key regulator of MHC-I antigen presentation,exhibits context-dependent roles in tumor immunity; however,its function in ESCC remains unclear. This study aimed to systematically investigate the expression pattern,prognostic value,and immunological role of NLRC5 in ESCC. Methods: An integrated analysis of bulk RNA sequencing and single-cell RNA sequencing (scRNA-seq) data was performed using multiple cohorts,including The Cancer Genome Atlas,Gene Expression Omnibus,and an in-house ESCC cohort. Differential expression,survival analysis,immune infiltration estimation,and functional enrichment analyses were conducted to elucidate the role of NLRC5 in the tumor microenvironment. Results: NLRC5 was significantly upregulated in ESCC and its high expression independently predicted poor patient survival. Although NLRC5 expression was associated with increased CD8+ T cell infiltration,it was paradoxically accompanied by features of T-cell exhaustion and elevated expression of multiple immune checkpoints. Moreover,NLRC5-high tumors were enriched in transcriptional programs related to PANoptosis,indicating an additional immunosuppressive mechanism within the TME. Conclusions: NLRC5 is not only a prognostic biomarker but also a key modulator of an immune-active yet functionally suppressed tumor microenvironment in ESCC. These findings highlight NLRC5 as a potential therapeutic target for restoring effective antitumor immunity. View Publication

Cryptococcus gattii is an emerging fungal pathogen that is acquired through the respiratory tract and causes invasive infections in both immunocompromised and otherwise healthy people. Many of these apparently immunocompetent patients are subsequently found to have autoantibodies against the pleiotropic cytokine GM-CSF. In this study,we investigated the potential role of GM-CSF (or CSF2) in the host response to C. gattii using a murine model of infection. Interestingly,infected Csf2-/- mice were found to have significantly improved survival and decreased lung fungal burden compared to wild type (WT) mice. We determined that during C. gattii infection,GM-CSF promotes the differentiation of monocytes into alveolar and interstitial macrophages. When these macrophages are ablated in CCR2-DTR+ mice,there is a corresponding improvement in survival with decreased lung fungal burden,thus phenocopying Csf2-/- mice. WT bone-marrow derived macrophages challenged with C. gattii and interstitial and alveolar macrophages from infected WT mice are unable to undergo M1 polarization,suggesting that monocyte-derived macrophages (moMacs) are rendered permissive for fungal proliferation. Therefore,GM-CSF and moMacs mediate immune responses that are harmful to the host. We further found that GM-CSF and moMacs preferentially promote the influx of eosinophils over neutrophils into the infected lung which is associated with substantial inflammatory lung pathology. Ablation of neutrophils using Mrp8cretg iDTR+ mice significantly increased C. gattii burden in the lungs,indicating that GM-CSF and moMacs block the entry of these beneficial,fungal-clearing granulocytes during infection. Altogether,our results show that GM-CSF plays a key role in impeding host anti-fungal responses to C. gattii by coordinating monocyte-derived macrophages and granulocyte activity and crosstalk. Author summaryCryptococcus gattii is an environmental fungus that can cause severe lung and brain infections after inhalation through the respiratory tract. C. gattii causes disease in patients with known immune deficits but also in individuals that are apparently healthy. Studies on otherwise healthy people who become infected with C. gattii suggest that they may have a previously unrecognized problem involving granulocyte macrophage-colony stimulating factor (GM-CSF),a cytokine,or messenger protein,that is an important part of the immune system. Here,we investigate the role of GM-CSF in the immune response to C. gattii using a mouse model of infection. We find that C. gattii increases GM-CSF in the lungs,leading to the influx of immune cells,including monocyte-derived macrophages and eosinophils,while inhibiting the entry of neutrophils. The macrophages and eosinophils allow the fungus to proliferate and cause inflammatory damage to the lungs,which is ultimately fatal. The absence of neutrophils also contributes to fungal growth,as these immune cells would otherwise be able to help kill the fungus. Our study provides new insight into how GM-CSF regulates immunity to C. gattii and has important implications as to the mechanisms that govern susceptibility to this infection. View Publication

Multi-kilobase knock-ins (KIs) are a necessary,yet challenging type of genome editing to create and characterize in cell lines and animals. The combination of rAAV donor transduction and electroporation of single-cell mouse embryos with Cas9/gRNA ribonucleoprotein complex enables highly efficient KI,but the insert size is limited by the viral packaging capacity. Here,we report the creation of up to 6.7 kb precise KI achieved in one step by using three rAAVs designed to insert one after the other. To fully characterize the edited genome with large KIs,we developed LOCK-seq (LOng-read sequencing of Captured Kilo-base targets),where relevant genomic regions are enriched via hybridization,achieving over 100-fold greater coverage compared with other long-read methods with enrichment. LOCK-seq simultaneously detects the presence of precise KI alleles,imprecision in the insert and donor concatenation,genotypes of non-KI alleles,and more importantly,uniquely identifies and localizes random integration of the full or partial donor(s). Additionally,the multi-rAAV donor approach is successfully applied to cell lines,including lines intolerant of plasmid DNA,whereas LOCK-seq reliably and efficiently screens for KI clones. Together,the two approaches significantly improve the creation and precision of knock-in models. View Publication

Teratoma formation is a critical obstacle to safe clinical translation of human embryonic stem (ES) cell-based therapies in the future. As current methods of isolation are unable to yield 100% pure population of differentiated cells from a pluripotent donor source,potential development of these tumors is a significant concern. Here we used non-invasive reporter gene imaging to investigate the relationship between human ES cell number and teratoma formation in a xenogenic model of ES cell transplantation. Human ES cells (H9 line) were stably transduced with a double fusion (DF) reporter construct containing firefly luciferase and enhanced green fluorescent protein (Fluc- eGFP) driven by a human ubiquitin promoter. Immunodeficient mice received intramyocardial (n = 35) or skeletal muscle (n = 35) injection of 1 × 102,1 × 103,1 × 104,1 × 105 or 1 × 106 DF positive ES cells suspended in saline for myocardium and Matrigel for skeletal muscle. Cell survival and proliferation were monitored via bioluminescence imaging (BLI) for an 8 week period following transplantation. Mice negative for Fluc signal after 8 weeks were followed out to day 365 to confirm tumor absence. Significantly,in this study,a minimum of 1 × 105 ES cells in the myocardium and 1 × 104 cells in the skeletal muscle was observed to be requisite for teratoma development,suggesting that human ES cell number may be a critical factor in teratoma formation. Engraftment and tumor occurrence were also observed to be highly dependent on ES cell number. We anticipate these results should yield useful insights to the safe and reliable application of human ES cell derivatives in the clinic. Keywords View Publication

Fetal liver,the major site of hematopoiesis during embryonic development,acquires additional various metabolic functions near birth. Although liver development has been characterized biologically as consisting of several distinct steps,the molecular events accompanying this process are just beginning to be characterized. In this study,we have established a novel culture system of fetal murine hepatocytes and investigated factors required for development of hepatocytes. We found that oncostatin M (OSM),an interleukin-6 family cytokine,in combination with glucocorticoid,induced maturation of hepatocytes as evidenced by morphological changes that closely resemble more differentiated hepatocytes,expression of hepatic differentiation markers and intracellular glycogen accumulation. Consistent with these in vitro observations,livers from mice deficient for gp130,an OSM receptor subunit,display defects in maturation of hepatocytes. Interestingly,OSM is expressed in CD45(+) hematopoietic cells in the developing liver,whereas the OSM receptor is expressed predominantly in hepatocytes. These results suggest a paracrine mechanism of hepatogenesis; blood cells,transiently expanding in the fetal liver,produce OSM to promote development of hepatocytes in vivo. View Publication

A novel homology model of the kinase domain of Janus kinase (JAK) 3 was used for the structure-based design of dimethoxyquinazoline compounds with potent and specific inhibitory activity against JAK3. The active site of JAK3 in this homology model measures roughly 8 A x 11 A x 20 A,with a volume of approximately 530 A3 available for inhibitor binding. Modeling studies indicated that 4-(phenyl)-amino-6,7-dimethoxyquinazoline (parent compound WHI-258) would likely fit into the catalytic site of JAK3 and that derivatives of this compound that contain an OH group at the 4' position of the phenyl ring would more strongly bind to JAK3 because of added interactions with Asp-967,a key residue in the catalytic site of JAK3. These predictions were consistent with docking studies indicating that compounds containing a 4'-OH group,WHI-P131 [4-(4'-hydroxyphenyl)-amino-6,7-dimethoxyquinazoline],WHI-P154 [4-(3'-bromo-4'-hydroxylphenyl)-amino-6,7-dimethoxyquinazoline],and WHI-P97 [4-(3',5'-dibromo-4'-hydroxylphenyl)-amino-6,7-dimethoxyquinazolin e],were likely to bind favorably to JAK3,with estimated K(i)s ranging from 0.6 to 2.3 microM. These compounds inhibited JAK3 in immune complex kinase assays in a dose-dependent fashion. In contrast,compounds lacking the 4'-OH group,WHI-P79 [4-(3'-bromophenyl)-amino-6,7-dimethoxyquinazoline],WHI-P111 [4-(3'-bromo-4'-methylphenyl)-amino-6,7-dimethoxyquinazoline],WHI-P112 [4-(2',5'-dibromophenyl)-amino-6,7-dimethoxyquinazoline],WHI-P132 [4-(2'-hydroxylphenyl)-amino-6,7-dimethoxyquinazoline],and WHI-P258 [4-(phenyl)-amino-6,7-dimethoxyquinazoline],were predicted to bind less strongly,with estimated K(i)s ranging from 28 to 72 microM. These compounds did not show any significant JAK3 inhibition in kinase assays. Furthermore,the lead dimethoxyquinazoline compound,WHI-P131,which showed potent JAK3-inhibitory activity (IC50 of 78 microM),did not inhibit JAK1 and JAK2,the ZAP/SYK family tyrosine kinase SYK,the TEC family tyrosine kinase BTK,the SRC family tyrosine kinase LYN,or the receptor family tyrosine kinase insulin receptor kinase,even at concentrations as high as 350 microM. WHI-P131 induced apoptosis in JAK3-expressing human leukemia cell lines NALM-6 and LC1;19 but not in melanoma (M24-MET) or squamous carcinoma (SQ20B) cells. Leukemia cells were not killed by dimethoxyquinazoline compounds that were inactive against JAK3. WHI-P131 inhibited the clonogenic growth of JAK3-positive leukemia cell lines DAUDI,RAMOS,LC1;19,NALM-6,MOLT-3,and HL-60 (but not JAK3-negative BT-20 breast cancer,M24-MET melanoma,or SQ20B squamous carcinoma cell lines) in a concentration-dependent fashion. Potent and specific inhibitors of JAK3 such as WHI-P131 may provide the basis for the design of new treatment strategies against acute lymphoblastic leukemia,the most common form of childhood cancer. View Publication

In this report,we sought to optimize gene transfer into primitive human umbilical cord blood (UCB) cells. Initially,we found that fresh UCB isolated with the CD34brCD38 CD33 phenotype were highly enriched for hematopoietic progenitors detected in extended long-term cultures (8-week LTCs). In addition,following ex vivo gene transfer,this population possessed virtually all the 8-week LTC activity of the cultured cells. A multiparameter FACS assay was developed to efficiently screen the effects of alternative retroviral vector gene transfer procedures on the transduction efficiency and maintenance of CD34brCD38 CD33 cells. Proliferation of the CD34brCD38 CD33 cells was found to be a prerequisite for efficient transduction. However,in all conditions tested,proliferation of the CD34brCD38 CD33 cells was associated with a progressive loss of primitive cell properties including a reduction in CD34 expression,an increase in CD38/CD33 expression,and a decline in the ability to sustain 8-week LTCs. These observations indicate that it will be necessary to define conditions that more effectively support the self-renewal capacity of CD34brCD38 CD33 cells to optimize retroviral vector gene transfer in these cells. Evaluating these conditions and reagents will be facilitated by the multiparameter FACS assay described in this report. View Publication