单细胞转录组测序 (scRNA-seq) 比批量 RNA-seq 能提供更高分辨率的细胞差异，从而能够解析甲状腺乳头状癌 (PTC) 中细胞类型对扰动的特异性反应。然而，细胞基因组特征高度异质，存在大量没有任何表达信号的基因，这阻碍了识别差异表达基因的统计能力，并可能产生许多假阳性结果。为了克服这一挑战，我们对两个 PTC scRNA-seq 数据集进行了综合分析，并交叉验证了一致的差异表达。通过结合两项研究中 32 种常见细胞类型的结果，我们确定了 7 种细胞类型中的 31 个一致差异表达基因 (DEG)，包括 B 细胞、内皮细胞、上皮细胞、单核细胞、NK 细胞、平滑肌细胞和 T 细胞。功能富集分析表明这些基因对于适应性免疫反应和自身免疫性甲状腺疾病很重要。额外的无病生存分析还证实，在大规模甲状腺癌队列中，这 31 个基因显着影响患者的生存时间。此外，我们通过实验验证了最一致的 DEG 之一作为 PTC 上皮细胞的潜在生物标志物基因 KRT7，它可能是 NF-κB 信号通路的上游基因。结果表明KRT7可能通过上皮间质转化和NF-κB信号通路促进甲状腺癌转移。总之，我们基于单细胞转录组整合的方法可以深入了解 NF-κB 在 PTC 基础生物学中的重要作用。© 2023 作者。

Single-cell transcriptome sequencing (scRNA-seq) provides a higher resolution of cellular differences than bulk RNA-seq, enabling the dissection of cell-type-specific responses to perturbations in papillary thyroid carcinoma (PTC). However, cellular genomic features are highly heterogeneous and have a large number of genes without any expression signals, which hinders the statistical power to identify differentially expressed genes and may generate many false-positive results. To overcome this challenge, we conducted an integrative analysis on two PTC scRNA-seq datasets and cross-validated consistent differential expression. By combining results from 32 common cell types in the two studies, we identified 31 consistently differentially expressed genes (DEGs) across seven cell types, including B cells, endothelial cells, epithelial cells, monocytes, NK cells, smooth muscle cells, and T cells. Functional enrichment analysis revealed that these genes are important for the adaptive immune response and autoimmune thyroid diseases. The additional disease-free survival analysis also confirmed that these 31 genes significantly affected patient survival time in large scale thyroid cancer cohort. Furthermore, we experimentally validated one of the top consistent DEGs as a potential biomarker gene of PTC epithelial cells, KRT7, which may be a upstream gene for the NF-κB signaling pathway. The result shows that KRT7 may promote thyroid cancer metastasis through the epithelial-mesenchymal transition and NF-κB signaling pathway. In summary, our single-cell transcriptome integration-based approach may provide insights into the important role of NF-κB in the underlying biology of the PTC.© 2023 The Authors.