Patients
TFPI2 levels were measured in patients with RCC and healthy volunteers at a single-center (Yokohama City University Hospital). All patients with RCC underwent radical nephrectomy between 2001 and 2023 for suspected renal masses and were diagnosed with renal malignancies based on pathological findings. Healthy voluntary samples were collected anonymously by the Tosoh Corporation (Tokyo, Japan) or the Biobank at Yokohama City University. This study was performed in accordance with the Declaration of Helsinki and the Ethical Guidelines for Medical and Health Research Involving Human Subjects, after approval by the Institutional Ethics Committee of Yokohama City University (B181100031, B200800009, and B210300038).
Measurement of serum TFPI2 values in patients with RCC and healthy volunteers
Preoperative serum samples were obtained and stored for the analysis of TFPI2 serum concentration. To compare the preoperative and postoperative values of TFPI2, some patients were prospectively enrolled and blood sampling was performed preoperatively.
Blood samples were drawn within one month of surgery and collected in Venoject II serum separator tubes (VPAS109K60, Terumo, Tokyo, Japan). The tubes were stored for 2–3 h at 4 °C or 30 min at room temperature, and then centrifuged at 1000–1500g for 10 min. Serum aliquots were stored between −40 to 80 °C. TFPI2 concentrations in each serum sample were measured at the Department of Clinical Laboratory at Yokohama City University Hospital or Tosoh Corporation using reagents provided by the Tosoh Diagnostics Product Division (Tosoh Corporation, Tokyo, Japan). The measurements were performed by clinical laboratory technologists who were blinded to the sample information. TFPI2 concentration was measured by the direct assay method using an automated immunoassay analyzer system (Tosoh Corporation), as described in our previous study [7].
Expression analysis of TFPI2 in renal tumor tissue and generation of Kaplan-Meier survival curves derived from the publicly available databases
The UCSC Xena database (https://xena.ucsc.edu/) provided the bulk RNA-seq data. For comparison of TFPI2 gene expression levels in normal tissues and renal CCC tissues, "GDC TCGA Kidney Clear Cell Carcinoma (KIRC)" from the UCSC Xena was used. TFPI2 expression in normal tissues (72 samples) and primary tumors (534 samples) was compared.
The UCSC Xena data was also used to perform prognostic analysis according to the expression levels of TFPI2 in TCGA database. “GDC TCGA Kidney Clear Cell Carcinoma (KIRC)”, ”GDC TCGA Kidney Papillary Cell Carcinoma (KIRP)”, and ”GDC TCGA Kidney Chromophobe (KICH)” were used for clear cell, papillary, and chromophobe RCCs, respectively.
The primary tumors in each dataset were analyzed. The samples were divided into two groups based on median TFPI2 expression levels.
Identification of RNA expression of TFPI2 using single-cell RNA sequencing
We previously performed single-cell RNA sequencing of twelve surgically resected specimens from seven patients, including one Birt-Hogg-Dubé (BHD)-associated hybrid oncocytic chromophobe tumor (HOCT), one BHD-associated chromophobe RCC, one primary lesion, one lymph node metastasis from hereditary leiomyomatosis and renal cell cancer (HLRCC)-associated kidney cancer, two von Hippel-Lindau (VHL)-associated kidney cancers, one sporadic renal CCC, three intratumoral samples from a second sporadic renal CCC, and two normal kidney tissues [10]. We obtained the single-cell transcriptomes of 108,342 cells from these 12 tissues and divided them into 46,890 immune and 61,452 nonimmune cells using CD45, an immune cell marker. Nonimmune cells were annotated into cell clusters using previously reported marker genes for intercalated or principal cells of the collecting duct, distal tubules, loops of Henle, proximal tubules, glomerulus/vascular, and kidney cancers.
We analyzed this dataset following the methodology used in previous studies [10]. A total of 61,452 nonimmune cells were analyzed using the R package “Seurat” (version 3.1.2) [11]. The FindNeighbors (dims = 1:10) and FindClusters functions (resolution = 0.8) were used as parameters, and default settings were used for all other parameters. Each cluster was annotated based on the expression of existing marker genes as described in previous studies. Finally, the expression of the TFPI2 in each cluster was visualized using UMAP and violin plots.
Statistical analyses
Continuous variables were reported as means and standard deviations. Comparisons between two groups were performed using Student’s t, chi-square, or Welch's tests. For multiple comparisons of TFPI2, the Kruskal-Wallis H test was used. To compare survival curves, a log-rank test was performed between the two groups. The selection thresholds were as follows: log-rank P value<0.05 (two-sided) and hazard ratio (HR) within the 95% confidence interval (CI). Spearman’s coefficient values were used for the correlation analysis. All statistical analyses were two-sided, and statistical significance was set at P<0.05. All analyses were performed using SPSS software (version 28.0, Armonk, NY, IBM Corp.).