SARS-CoV-2-reactive tissue-resident memory T cells in healthy and cancer subjects

项目摘要 这个多PI提案题为“SARS-CoV-2-reactive 受试者”是针对“RFA-CA-20-039”编写的- 健康和癌症中的组织驻留记忆T细胞 SARS-CoV-2血清学研究项目。 最近的研究表明，对SARS-CoV-2感染的抗体应答随时间迅速下降，这意味着 缺乏持久的保护性体液（B细胞）免疫。这是否也适用于细胞免疫（例如，不 细胞）知之甚少。已经确定，CD 8 + TRM细胞是病毒感染的第一道防线 在粘膜/屏障部位。它们还已知可保护宿主免受同源或异源再感染。 我们的研究小组是第一个证明TRM细胞在驱动有效的抗肿瘤免疫反应中起关键作用的人。 TRM细胞是抗PD 1治疗的主要细胞靶点。这些主要发现是 这是因为Vijayanand博士、Ay博士和Ottensmeier博士（多PI）之间正在进行的合作。 该团队汇集了T细胞免疫学、单细胞基因组学、生物信息学和癌症方面的经验 免疫学我们的Multi-PI团队最近进行了第一个也是最大的单细胞RNA-seq和TCR-seq 分析来自COVID-19患者的SARS-CoV-2反应性CD 8+和CD 4 + T细胞（约30万个单细胞）。在这里， 为了了解TRM对SARS-CoV-2的反应，我们将利用癌症（n=100）和非癌症队列 （n=100）例患者，将提供过量气道（鼻、口咽、喉）、肺和肿瘤组织标本 在常规手术中获得。在AIM 1中，我们将定义SARS-CoV-2反应性TRM细胞的特性， 有或无SARS-CoV-2感染史的癌症和非癌症患者。我们将结合 气道（鼻、口咽）、肺和肿瘤中CD 8 + TRM细胞的单细胞RNA-seq和TCR-seq分析 组织.同时，通过用SARS-CoV-2肽库刺激PBMC，我们将确定转录组学， 和SARS-CoV-2反应性T细胞的TCR序列。我们将利用该TCR序列信息来定义 粘膜和肿瘤组织中SARS-CoV-2反应性TRM细胞的数量和性质。最近的研究在非 暴露个体（COVID-19大流行前）表明预先存在的循环CD 8 + T细胞， 冠状病毒交叉反应性。在这里，我们将测量预先存在的SARS-CoV-2交叉感染的数量和质量， 无既往SARS-CoV-2感染临床或血清学证据的受试者的反应性TRM应答。在 目的2，我们将评估SARS-CoV-2感染对抗肿瘤和其他抗病毒TRM反应的影响。我们 将用靶向（i）常见呼吸道RNA病毒的肽库刺激匹配的PBMC（如上所述 （流感病毒（FLU）、RSV），（ii）持久性DNA病毒（CMV、EBV），和（iii）肿瘤驱动病毒（HPV），以定义 相应的病毒特异性和肿瘤（HPV）特异性CD 8 + T细胞的TCR序列;我们将利用TCR序列 确定粘膜和肿瘤中其他病毒/肿瘤反应性TRM细胞的频率和特性的信息- 组织细胞

PROJECT SUMMARY This multi-PI proposal titled “SARS-CoV-2-reactive subjects” is written in response to ‘RFA-CA-20-039’ - tissue-resident memory T cells in healthy and cancer Research projects in SARS-CoV-2 Serological Sciences. Recent studies have shown that antibody responses to SARS-CoV-2 infection decline rapidly over time, implying a lack of durable protective humoral (B cell) immunity. Whether this is also true for cellular immunity (e.g., T cells) is poorly understood. It is well established that CD8+ TRM cells are the first line of defense in viral infections at mucosal/barrier sites. They are also known to protect hosts against homologous or heterologous re-infections. Our group was the first to show that TRM cells are pivotal players in driving effective anti-tumor immune responses in lung cancer, and that TRM cells are the primary cellular targets of anti-PD1 therapies. These key findings were possible because of the ongoing collaboration between Dr. Vijayanand, Dr. Ay, and Dr. Ottensmeier (Multi-PI). This team brings together experience in T cell immunology, single-cell genomics, bioinformatics, and cancer immunology. Our Multi-PI team has recently performed the first and largest single-cell RNA-seq and TCR-seq analysis of SARS-CoV-2-reactive CD8+ and CD4+ T cells (~300,000 single-cells) from COVID-19 patients. Here, to understand TRM responses to SARS-CoV-2, we will capitalize on a cohort of cancer (n=100) and non-cancer (n=100) patients, who will provide excess airway (nasal, oropharynx, larynx), lung and tumor tissue specimens obtained during routine surgery. In AIM 1, we will define the properties of SARS-CoV-2 reactive TRM cells from cancer and non-cancer patients with or without previous SARS-CoV-2 infection. We will perform combined single-cell RNA-seq and TCR-seq analysis of CD8+ TRM cells in the airways (nasal, oropharynx), lung, and tumor tissue. In parallel, by stimulating PBMCs with SARS-CoV-2 peptide pool, we will determine the transcriptomic and TCR sequence of SARS-CoV-2 reactive T cells. We will utilize this TCR sequence information to define the numbers and properties of SARS-CoV-2 reactive-TRM cells in mucosal and tumor tissues. Recent studies in non- exposed individuals (pre-COVID-19 pandemic) indicate pre-existing, circulating CD8+ T cells, with human coronavirus cross-reactivity. Here, we will measure the quantity and quality of pre-existing SARS-CoV-2 cross- reactive TRM responses in subjects without clinical or serological evidence of previous SARS-CoV-2 infection. In AIM 2, we will assess the impact of SARS-CoV-2 infection on anti-tumor and other anti-viral TRM responses. We will stimulate matched PBMCs (as above) with peptide pools targeting (i) common respiratory RNA viruses (influenza (FLU), RSV), (ii) persistent DNA viruses (CMV, EBV), and (iii) a tumor-driving virus (HPV) to define the TCR sequence of the respective virus-specific and tumor(HPV)-specific CD8+ T cells; we will utilize the TCR information to determine frequency and properties of other virus/tumor-reactive TRM cells in mucosal and tumor- tissue cells.