PO.BCS01.01 · 生物信息与计算
空间转录组学揭示小细胞肺癌中转录重编程与免疫逃逸的模式
Spatial transcriptomics uncovers patterns of transcriptional reprogramming and immune evasion in small cell lung cancer
作者与单位 Authors & Affiliations
摘要 Abstract
中文摘要
从非小细胞肺癌(NSCLC)向小细胞肺癌(SCLC)的组织学转化是治疗耐药的主要机制之一,然而支配这一表型转换的空间和分子程序仍不甚明确。本研究采用10X Xenium In Situ空间转录组学技术,对16例发生SCLC转化患者的22个原发及转移性肺肿瘤生成亚细胞分辨率的转录组图谱,细胞总数超过1000万个。配套的单细胞RNA测序实现了对转录状态的整合分析,并作为一种互补手段支持空间学发现。采用涵盖神经内分泌(NE)、上皮、干性、免疫和基质程序的389基因panel进行空间分析,揭示出30种不同的细胞类型,以及肺腺癌(LUAD)、鳞状细胞癌(LUSC)和小细胞肺癌亚型(ASCL1+:SCLC-A和NEUROD1+:SCLC-N)之间显著的肿瘤间和肿瘤内异质性。肿瘤呈现出几种典型的结构模式:(1)离散的亚型区室化;(2)斑点状NE转化;(3)自成体系的多层亚型组织结构。一例发生SCLC转化的淋巴结转移灶的代表性切除标本显示出两个独立的肿瘤区域,每个区域均呈现出显著的放射状排列。在第一个区域中,混杂的LUAD和NOTCH1- SCLC-A构成肿瘤核心,随后是NOTCH1+ SCLC-A和SCLC-N的同心层,免疫细胞位于外周。鉴于Notch信号通路在SCLC亚型转换中已确立的作用,以及我们观察到相邻肿瘤亚型间存在抑制性的DLL3-NOTCH1相互作用,这些调控关系可能促成了肿瘤亚型的空间区室化。第二个肿瘤区域缺乏LUAD和NOTCH1+ SCLC-A细胞群,而是由被SCLC-N包裹的NOTCH1- SCLC-A核心构成,同样被免疫区所包围。对两个区域Xenium数据的拟时序分析也重现了从LUAD到SCLC-A再到SCLC-N的轨迹。这两项发现,结合此前将SCLC-N表征为缺乏免疫浸润的“免疫冷”肿瘤的研究,提示这种空间模式以及亚型间的相互作用可能是在恶劣环境中免疫逃逸和进展的一个重要机制。由于队列内细胞数量和样本面积的不平衡,空间比较被限制在较小的感兴趣区域(ROI)。对ROI细胞-细胞邻接矩阵进行聚类,揭示出与特定肿瘤亚型及微环境状态(如坏死或免疫浸润)相关的反复出现的空间相互作用模式。这些分析凸显了神经内分泌转化的不同结构模式,并强调了空间背景在耐药过程中塑造表型演化中的作用。
查看英文原文 English abstract
Histologic transformation from non-small cell lung cancer (NSCLC) to small cell lung cancer (SCLC) is a major mechanism of therapeutic resistance, yet the spatial and molecular programs governing this phenotypic switch remain poorly defined. 10X Xenium In Situ spatial transcriptomics was used to generate subcellular-resolution transcriptomic maps of 22 primary and metastatic lung tumors across 16 patients with SCLC transformation, totaling >10 million cells. Matched single-cell RNA sequencing enabled integrated analysis of transcriptional states and served as a complementary modality to support spatial findings. Spatial profiling with a 389-gene panel encompassing neuroendocrine (NE), epithelial, stemness, immune, and stromal programs revealed 30 distinct cell types and marked inter- and intra-tumoral heterogeneity across lung adenocarcinoma (LUAD), squamous cell carcinoma (LUSC), and small cell lung cancer subtypes (ASCL1+: SCLC-A and NEUROD1+: SCLC-N). Tumors organized into several canonical structural patterns: (1) discrete subtype compartmentalization, (2) speckled NE transformation, and (3) self-contained, multilayered subtype organization.A representative resection of a lymph-node metastasis with SCLC transformation displayed two separate tumor regions, each with a striking radial arrangement. In the first region, admixed LUAD and NOTCH1- SCLC-A formed the tumor core, followed by concentric layers of NOTCH1+ SCLC-A and SCLC-N, with immune cells at the periphery. Given the established role of Notch signaling in SCLC subtype switching, and our observation of inhibitory DLL3-NOTCH1 interactions across neighboring tumor subtypes, these regulatory relationships may contribute to the spatial compartmentalization of tumor subtypes. The second tumor region lacks the LUAD and NOTCH1+ SCLC-A populations, instead composed of a NOTCH1- SCLC-A core encased by SCLC-N, again surrounded by immune zones. Pseudotime analysis of the Xenium data across both regions also recapitulated a trajectory from LUAD to SCLC-A to SCLC-N. These two findings, combined with previous studies characterizing SCLC-N as an “immune-cold” tumor devoid of immune infiltrate, suggest that this spatial patterning and interplay between subtypes may be an important mechanism for immune evasion and progression in a hostile environment.Due to imbalance in cell number and sample area within the cohort, spatial comparisons were constrained to smaller regions of interest (ROIs). Clustering ROI cell-cell adjacency matrices uncovered recurring spatial interaction patterns associated with specific tumor subtypes and microenvironmental states, such as necrosis or immune infiltration. These analyses highlight distinct architectural modes of neuroendocrine transformation and underscore the role of spatial context in shaping phenotypic evolution during resistance.
利益披露 Disclosure
E. S. Spanos, None.