Single-cell atlas of lung tissue-resident memory T cells reactive to upper and lower respiratory tract pathogens

对上呼吸道和下呼吸道病原体有反应的肺组织驻留记忆T细胞的单细胞图谱

• 批准号: 10419455
• 负责人: Pandurangan Vijayanand
• 金额: $ 58.47万
• 依托单位: LA JOLLA INSTITUTE FOR IMMUNOLOGY
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-06-15 至 2027-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10419455
• 关键词: 2019-nCoV; ATAC-seq; Animal Model; Aspergillus; Atlases; Automobile Driving; Biological Assay; Blood; Bronchoalveolar Lavage; Bronchoscopy; CD4 Positive T Lymphocytes; CD8-Positive T-Lymphocytes; COVID-19 patient; COVID-19 vaccine; Candida; Catalogs; Cells; Clinical; Common Cold; Communicable Diseases; Coronavirus; Enhancers; Epitopes; Excision; Genetic Transcription; Genus Mycobacterium; Goals; Health; Human; Human Characteristics; Hypersensitivity; Immune; Immunology; Infection; Influenza; Link; Living Donors; Lower respiratory tract structure; Lung; Malignant Neoplasms; Malignant neoplasm of lung; Molecular; Mucous Membrane; Nature; Operative Surgical Procedures; Peptides; Peripheral Blood Mononuclear Cell; Pertussis; Pertussis Vaccine; Phenotype; Pneumococcal vaccine; Pneumovirus; Property; Research; Respiratory Tract Diseases; Respiratory Tract Infections; Respiratory syncytial virus; Sampling; Science; Severity of illness; Specificity; Streptococcus pneumoniae; Structure of parenchyma of lung; Subgroup; T memory cell; T-Cell Receptor; T-Lymphocyte; T-cell receptor repertoire; Tissue Sample; Tissues; Vaccinated; Vaccination; Vaccines; Viral; Virus Diseases; anti-PD1 therapy; anti-tumor immune response; antigen-specific T cells; cancer type; cellular targeting; cohort; epigenome; epigenomics; flu; influenza virus vaccine; insight; mouse model; novel; pathogen; pathogenic bacteria; pathogenic fungus; pathogenic virus; programs; prospective; recruit; respiratory pathogen; response; single cell analysis; single-cell RNA sequencing; synergism; transcription factor; transcriptome; transcriptomics; vaccine evaluation; vaccine response

PROJECT SUMMARY La Jolla HIPC team will focus on common pathogens causing infectious diseases of the respiratory tract. Here in Project 3, we will determine the molecular properties of lung tissue-resident memory T cells (TRM cells) that are specific to a wide-range of viral, bacterial and fungal pathogens. Our goal is to establish a single-cell atlas of the transcriptome, epigenome and T cell receptor (TCR) repertoire of pathogen-reactive lung TRM cells. In Aim 1, we will perform single-cell RNA-seq, ATAC-seq, and TCR-seq analysis of T cells isolated from lung tissue and bronchoalveolar lavage (BAL) of 100 living donors, who undergo surgical resection for suspected early-stage lung cancer (TARGET Lung study). We will utilize their TCR sequences to determine the pathogen- specificity of lung TRM cells. To achieve this goal, we will generate a catalogue of experimentally-validated TCR sequences that are specific to different pathogen epitopes and HLA-typed donors; we will achieve this goal by stimulating PBMCs of matched donors with peptide pools targeting specific pathogens that infects the lungs such as: viral (Influenza, respiratory syncytial virus, para influenza, meta pneumovirus, SARS-CoV-2, common cold corona virus), bacterial (pneumococcus, pertussis, mycobacterium) and fungal (aspergillus and candida) pathogens, and retrieve TCR sequences of responding T cells. Longitudinal assessments: To assess persistence and plasticity of pathogen-specific lung TRM cells, in a subgroup of donors (n~25-50), we will obtain BAL samples 1 year after initial assessments and perform single-cell analysis as above. In Aim 2, we will define the molecular properties of human lung T cells responding to vaccination (n=100). In 100 donors (TARGET Lung study), we will assess effects of 4 different vaccines (n=25/vaccine cohort): (i) inactivated influenza vaccine, (ii) pneumococcal vaccine (PPSV23), (iii) SARS-CoV-2 vaccine, (iv) Pertussis vaccine (Boostrix-IPV). We will compare the molecular features of circulating and lung T cells (TRM cells) that respond to vaccines targeting different pathogens. In addition, we will determine if vaccine-responding T cells in the blood truly reflect TRM responses in the lung tissue. Longitudinal assessments: We will also collect repeat blood and BAL samples, obtained by research bronchoscopy, 12 months after vaccination. We will determine the magnitude and phenotype of vaccine-responsive T cells in the blood and lungs to assess their persistence and plasticity. We have extensive synergies with Project 1 and 2, especially the focus on generating immune signatures of various respiratory pathogen-specific T cells.

项目摘要 拉霍亚重债穷国小组将重点关注引起呼吸道传染病的常见病原体。 在项目3中，我们将确定肺组织驻留记忆T细胞（TRM细胞）的分子特性。 它们对各种病毒、细菌和真菌病原体都有特异性。我们的目标是建立一个单细胞 病原体反应性肺TRM细胞的转录组、表观基因组和T细胞受体（TCR）库图谱。 在目标1中，我们将对从肺中分离的T细胞进行单细胞RNA-seq、ATAC-seq和TCR-seq分析。 组织和支气管肺泡灌洗（BAL）的100名活体供体，谁接受手术切除的怀疑 早期肺癌（TARGET Lung研究）。我们将利用他们的TCR序列来确定病原体- 肺TRM细胞的特异性。为了实现这一目标，我们将生成一个经过实验验证的TCR目录 特异性针对不同病原体表位和HLA型供体的序列;我们将通过以下方式实现这一目标： 用靶向感染肺部的特定病原体的肽库刺激匹配供体的PBMC， 作为：病毒（流感、呼吸道合胞病毒、帕拉流感、Meta肺病毒、SARS-CoV-2、普通感冒 冠状病毒）、细菌（肺炎球菌、百日咳、分枝杆菌）和真菌（曲霉菌和念珠菌） 病原体，并检索应答T细胞的TCR序列。纵向评估：评估 病原体特异性肺TRM细胞的持久性和可塑性，在供体亚组（n~25-50）中，我们将获得 在初始评估后1年采集BAL样本，并如上所述进行单细胞分析。在目标2中，我们定义 人肺T细胞对疫苗接种应答的分子特性（n=100）。在100名供体中（靶肺 研究），我们将评估4种不同疫苗（n=25/疫苗队列）的效果：（i）灭活流感疫苗，（ii） 肺炎球菌疫苗（PPSV 23），（iii）SARS-CoV-2疫苗，（iv）百日咳疫苗（Boostrix-IPV）。我们将 比较循环和肺T细胞（TRM细胞）的分子特征， 不同的病原体此外，我们还将确定血液中的疫苗应答T细胞是否真正反映了TRM 肺组织的反应。纵向评估：我们还将收集重复血液和BAL样本， 接种后12个月，通过支气管镜检查获得。我们将确定其大小， 在血液和肺中检测疫苗应答性T细胞的表型，以评估其持久性和可塑性。我们 与项目1和2有广泛的协同作用，特别是专注于产生各种免疫特征， 呼吸道病原体特异性T细胞。