Zeng Zhen, Zhang Tianbei, Zhang Jiajia, Li Shuai, Connor Sydney, Zhang Boyang, Zhao Yimin, Wilson Jordan, Singh Dipika, Kulikauskas Rima, Church Candice D, Pulliam Thomas H, Jani Saumya, Nghiem Paul, Topalian Suzanne L, Forde Patrick M, Pardoll Drew M, Ji Hongkai, Smith Kellie N
Bloomberg~Kimmel Institute for Cancer Immunotherapy, Baltimore, MD, US.
Mark Center for Advanced Genomics and Imaging, Baltimore, MD, US.
Nat Commun. 2025 Feb 3;16(1):1070. doi: 10.1038/s41467-024-55059-3.
Identifying tumor-specific T cell clones that mediate immunotherapy responses remains challenging. Mutation-associated neoantigen (MANA) -specific CD8+ tumor-infiltrating lymphocytes (TIL) have been shown to express high levels of CXCL13 and CD39 (ENTPD1), and low IL-7 receptor (IL7R) levels in many cancer types, but their collective relevance to T cell functionality has not been established. Here we present an integrative tool to identify MANA-specific TIL using weighted expression levels of these three genes in lung cancer and melanoma single-cell RNAseq datasets. Our three-gene "MANAscore" algorithm outperforms other RNAseq-based algorithms in identifying validated neoantigen-specific CD8+ clones, and accurately identifies TILs that recognize other classes of tumor antigens, including cancer testis antigens, endogenous retroviruses and viral oncogenes. Most of these TIL are characterized by a tissue resident memory gene expression program. Putative tumor-reactive cells (pTRC) identified via MANAscore in anti-PD-1-treated lung tumors had higher expression of checkpoint and cytotoxicity-related genes relative to putative non-tumor-reactive cells. pTRC in pathologically responding tumors showed distinguished gene expression patterns and trajectories. Collectively, we show that MANAscore is a robust tool that can greatly enrich candidate tumor-specific T cells and be used to understand the functional programming of tumor-reactive TIL.
识别介导免疫治疗反应的肿瘤特异性T细胞克隆仍然具有挑战性。在许多癌症类型中，与突变相关的新抗原（MANA）特异性CD8+肿瘤浸润淋巴细胞（TIL）已被证明高表达CXCL13和CD39（ENTPD1），而低表达白细胞介素-7受体（IL7R），但它们与T细胞功能的整体相关性尚未确立。在这里，我们提出了一种整合工具，利用肺癌和黑色素瘤单细胞RNA测序数据集中这三个基因的加权表达水平来识别MANA特异性TIL。我们的三基因“MANA评分”算法在识别经过验证的新抗原特异性CD8+克隆方面优于其他基于RNA测序的算法，并且能够准确识别识别其他类型肿瘤抗原的TIL，包括癌睾丸抗原、内源性逆转录病毒和病毒癌基因。这些TIL大多具有组织驻留记忆基因表达程序的特征。在抗程序性死亡蛋白1（PD-1）治疗的肺癌中，通过MANA评分鉴定出的推定肿瘤反应性细胞（pTRC）相对于推定的非肿瘤反应性细胞，具有更高的检查点和细胞毒性相关基因表达。病理反应性肿瘤中的pTRC表现出独特的基因表达模式和轨迹。总体而言，我们表明MANA评分是一种强大的工具，可以极大地富集候选肿瘤特异性T细胞，并用于了解肿瘤反应性TIL的功能编程。
