Mass spectrometric identification of immunogenic SARS-CoV-2 epitopes and cognate TCRs.
Mass spectrometric identification of immunogenic SARS-CoV-2 epitopes and cognate TCRs.
复制标题
DOI：
10.1073/pnas.2111815118
复制
发表时间：
2021-11-16
影响因子：
11.1
通讯作者：
Yee C
中科院分区：
文献类型：
--
作者：
Pan K;Chiu Y;Huang E;Chen M;Wang J;Lai I;Singh S;Shaw RM;MacCoss MJ;Yee C
通过对严重急性呼吸综合征冠状病毒 2 (SARS-CoV-2) 和新出现的 SARS-CoV-2 变种产生强大的 T 细胞反应，可以实现针对 COVID-19 感染的持久保护；对于感染者来说，迫切需要有效的治疗。为了使这些策略取得成功，T 细胞表位的准确识别至关重要。在本研究中，我们使用主要组织相容性复合物免疫沉淀、酸洗脱和串联质谱来定义膜糖蛋白（MGP）和非结构蛋白的 SARS-CoV-2 免疫肽组。此外，利用高度稳健的内源性 T 细胞工作流程，我们通过体外生成 MGP 和 NSP13 肽特异性 T 细胞来验证这些 MS 定义的肽的免疫原性，并确认 T 细胞对 MGP 或 NSP13 内源表达细胞系的识别。严重急性呼吸综合征冠状病毒 2 (SARS-CoV-2) 感染会引发体液和细胞免疫反应。对于预防和治疗由 SARS-CoV-2 引起的疾病 COVID-19，越来越明显的是，T 细胞反应在介导恢复和免疫保护方面与体液反应同样重要，甚至更重要。开发基于 T 细胞的传染病和恶性疾病疗法的一大挑战是鉴定能够引发有意义的 T 细胞反应的免疫原性表位。传统上，这是通过使用复杂的计算机方法来预测从结合亲和力推导出的推定表位来实现的。我们的研究发现，与目前的惯例相反，通过这种计算机方法定义的“免疫显性”SARS-CoV-2 肽通常无法引发识别自然存在的 SARS-CoV-2 表位的 T 细胞反应。我们假设，通过直接分析从自然加工的肽-主要组织相容性复合物 (MHC) 中洗脱的肽，然后通过确定此类肽是否可以引发识别 SARS-CoV-2 抗原表达细胞的 T 细胞来验证免疫原性，最好根据经验确定 SARS-CoV-2 的免疫原性表位。使用串联质谱方法，我们鉴定了来自 SARS-CoV-2 毒株高度保守区域的结构基因和非结构基因的表位，包括最近识别的变体。最后，尚无报道的 T 细胞受体工程 T 细胞技术可以重定向 T 细胞特异性以识别和杀死 SARS-CoV-2 靶细胞。我们在这里报告了通过 MHC 洗脱肽的质谱分析定义的几个 SARS-CoV-2 表位，为其免疫原性提供经验证据，并证明了工程化的 TCR 重定向杀伤。
Durable protection against COVID-19 infection may be achieved by generating robust T cell responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and emerging SARS-CoV-2 variants; for those infected, effective treatments are urgently needed. For these strategies to be successful, accurate identification of T cell epitopes is critical. In this study, we used major histocompatibility complex immune precipitation, acid elution, and tandem mass spectrometry to define the SARS-CoV-2 immunopeptidome for membrane glycoprotein (MGP) and the nonstructural protein. Furthermore, taking advantage of a highly robust endogenous T cell workflow, we verify the immunogenicity of these MS-defined peptides by in vitro generation of MGP and NSP13 peptide-specific T cells and confirm T cell recognition of MGP or NSP13 endogenously expressing cell lines. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections elicit both humoral and cellular immune responses. For the prevention and treatment of COVID-19, the disease caused by SARS-CoV-2, it has become increasingly apparent that T cell responses are equally if not more important than humoral responses in mediating recovery and immune protection. One major challenge in developing T cell–based therapies for infectious and malignant diseases has been the identification of immunogenic epitopes that can elicit a meaningful T cell response. Traditionally, this has been achieved using sophisticated in silico methods to predict putative epitopes deduced from binding affinities. Our studies find that, in contrast to current convention, “immunodominant” SARS-CoV-2 peptides defined by such in silico methods often fail to elicit T cell responses recognizing naturally presented SARS-CoV-2 epitopes. We postulated that immunogenic epitopes for SARS-CoV-2 are best defined empirically by directly analyzing peptides eluted from the naturally processed peptide–major histocompatibility complex (MHC) and then validating immunogenicity by determining whether such peptides can elicit T cells recognizing SARS-CoV-2 antigen-expressing cells. Using a tandem mass spectrometry approach, we identified epitopes derived from not only structural but also nonstructural genes in regions highly conserved among SARS-CoV-2 strains, including recently recognized variants. Finally, there are no reported T cell receptor–engineered T cell technology that can redirect T cell specificity to recognize and kill SARS-CoV-2 target cells. We report here several SARS-CoV-2 epitopes defined by mass spectrometric analysis of MHC-eluted peptides, provide empiric evidence for their immunogenicity, and demonstrate engineered TCR-redirected killing.
登录
查看更多内容
影响因子：
11.8
作者：
Gallais F;Velay A;Nazon C;Wendling MJ;Partisani M;Sibilia J;Candon S;Fafi-Kremer S
通讯作者：
Fafi-Kremer S
影响因子：
5.5
作者：
Safavi A;Kefayat A;Mahdevar E;Abiri A;Ghahremani F
通讯作者：
Ghahremani F
DOI：
10.1016/s0140-6736(20)32137-1
发表时间：
2020-11-14
期刊：
Lancet (London, England)
影响因子：
--
作者：
Poland GA;Ovsyannikova IG;Kennedy RB
通讯作者：
Kennedy RB
影响因子：
2.7
作者：
Kessler, JH;Mommaas, B;Drijfhout, JW
通讯作者：
Drijfhout, JW
影响因子：
7.8
作者：
Olvera A;Noguera-Julian M;Kilpelainen A;Romero-Martín L;Prado JG;Brander C
通讯作者：
Brander C