Soupir Alex C, Hayes Mitchell T, Peak Taylor C, Ospina Oscar, Chakiryan Nicholas H, Berglund Anders E, Stewart Paul A, Nguyen Jonathan, Segura Carlos Moran, Francis Natasha L, Echevarria Paola M Ramos, Chahoud Jad, Li Roger, Tsai Kenneth Y, Balasi Jodi A, Peres Yamila Caraballo, Dhillon Jasreman, Martinez Lindsey A, Gloria Warren E, Schurman Nathan, Kim Sean, Gregory Mark, Mulé James, Fridley Brooke L, Manley Brandon J
Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL 33612.
Department of Genitourinary Oncology, Moffitt Cancer Center, Tampa, FL 33612.
bioRxiv. 2023 Nov 17:2023.11.16.567457. doi: 10.1101/2023.11.16.567457.
Immunotherapy (IO) has improved survival for patients with advanced clear cell renal cell carcinoma (ccRCC), but resistance to therapy develops in most patients. We use cellular-resolution spatial transcriptomics in patients with IO naïve and IO exposed primary ccRCC tumors to better understand IO resistance. Spatial molecular imaging (SMI) was obtained for tumor and adjacent stroma samples. Spatial gene set enrichment analysis (GSEA) and autocorrelation (coupling with high expression) of ligand-receptor transcript pairs were assessed. Multiplex immunofluorescence (mIF) validation was used for significant autocorrelative findings and the cancer genome atlas (TCGA) and the clinical proteomic tumor analysis consortium (CPTAC) databases were queried to assess bulk RNA expression and proteomic correlates.
21 patient samples underwent SMI. Viable tumors following IO harbored more stromal CD8+ T cells and neutrophils than IO naïve tumors. was significantly upregulated in IO exposed tumor cells. The epithelial-mesenchymal transition pathway was enriched on spatial GSEA and the associated transcript pair had significantly higher autocorrelation in the stroma. Fibroblasts, tumor cells, and endothelium had the relative highest expression. More integrin αV+ cells were seen in IO exposed stroma on mIF validation. Compared to other cancers in TCGA, ccRCC tumors have the highest expression of both and . In CPTAC, collagen IV protein was more abundant in advanced stages of disease.
On spatial transcriptomics, and were more autocorrelated in IO-exposed stroma compared to IO-naïve tumors, with high expression amongst fibroblasts, tumor cells, and endothelium. Integrin represents a potential therapeutic target in IO treated ccRCC.
免疫疗法（IO）已改善了晚期透明细胞肾细胞癌（ccRCC）患者的生存率，但大多数患者会出现治疗耐药性。我们对未经IO治疗和接受过IO治疗的原发性ccRCC肿瘤患者进行细胞分辨率空间转录组学分析，以更好地了解IO耐药性。对肿瘤和相邻基质样本进行空间分子成像（SMI）。评估空间基因集富集分析（GSEA）以及配体-受体转录本对的自相关（与高表达耦合）。对显著的自相关结果进行多重免疫荧光（mIF）验证，并查询癌症基因组图谱（TCGA）和临床蛋白质组肿瘤分析联盟（CPTAC）数据库以评估整体RNA表达和蛋白质组相关性。
对21例患者样本进行了SMI。接受IO治疗后的存活肿瘤比未经IO治疗的肿瘤含有更多的基质CD8 + T细胞和中性粒细胞。 在接受IO治疗的肿瘤细胞中显著上调。上皮-间质转化途径在空间GSEA上富集，并且相关的转录本对在基质中具有显著更高的自相关性。成纤维细胞、肿瘤细胞和内皮细胞的表达相对最高。在mIF验证中，在接受IO治疗的基质中可见更多整合素αV +细胞。与TCGA中的其他癌症相比，ccRCC肿瘤中 和 的表达最高。在CPTAC中，胶原蛋白IV蛋白在疾病晚期更为丰富。
在空间转录组学上，与未经IO治疗的肿瘤相比，接受IO治疗的基质中 和 的自相关性更高，在成纤维细胞、肿瘤细胞和内皮细胞中高表达。整合素是IO治疗的ccRCC中的一个潜在治疗靶点。
