Patients and materials
This study was conducted in accordance with the principles of the Declaration of Helsinki. It was also approved by the Ethics Committee of Kyushu University (Nos. 29-429, 29-625) and consent was obtained from patients who donated tissue. A total of 51 UPS cases, diagnosed as malignant fibrous histiocytoma or UPS, were retrieved from among soft-tissue tumors registered at the Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan, from 1998 to 2019.
To collect definitive UPS samples, secondary sarcomas, radiation-associated sarcomas, myxofibrosarcomas, dedifferentiated liposarcomas, and other sarcomas were excluded (Ishihara et al. 2020). A total of 48 tumors were the same as in this previous study, while three were newly retrieved. Four tumors that had been used in the previous study were not used in this study because the formalin-fixed, paraffin-embedded (FFPE) samples had been used up (Ishihara et al. 2020).
Immunohistochemistry
FFPE tissue was sliced into sections at a thickness of 3 μm. Antigen retrieval was performed by boiling the slides in 10 mM sodium citrate (pH 6.0) or Target Retrieval Solution (Dako). The immunoperoxidase polymer method (EnVision-kit and EnVision Flex-kit; Dako) was used. We used the following primary antibodies: anti-PD-L1 (rabbit, polyclonal, 28-8, 1:400; Abcam) and anti-CMTM6 (rabbit, polyclonal, SAB270119, 1:100; Sigma-Aldrich). We stained PD-L1 and CMTM6 using the EnVision Flex-kit and EnVision-kit, respectively.
PD-L1 was assessed by determining the proportion of membranous staining-positive tumor cells relative to all tumor cells, as described previously (Ishihara et al. 2020). CMTM6 evaluation was performed in a manner similar to that used for estrogen and progesterone receptor evaluation in breast cancer using the Allred score. Proportion score (PS) was assessed by determining the proportion of tumor cells revealing cytoplasmic positivity for staining relative to all tumor cells on the slide. PS of CMTM6 was defined as follows: PS 0: no positive cells, PS 1: > 0% and < 1% positive tumor cells, PS 2: ≥ 1% and < 10%, PS 3: ≥ 10% and < 33%, PS 4: ≥ 33% and < 66%, and PS 5: ≥ 66% and ≤ 100%. Intensity score (IS) was assessed using the intensity of the staining as follows: IS 0: negative, not stained, IS 1: weak cytoplasmic staining and no membranous staining, and IS 2: strong cytoplasmic and strong membranous staining. In the Allred scoring system, IS is classified into four groups: “negative,” “weak,” “intermediate,” and “strong.” However, in this study, cases were classified into three groups to maintain reproducibility, because it was difficult to distinguish between “intermediate” and “strong”. We set the cut-offs of PS and IS of CMTM6 immunostaining for statistical analysis by drawing ROC curves.
Copy number assay
Copy number assay was conducted using TaqMan quantitative PCR (Thermo Fisher Scientific Inc.). We used the following primers: CMTM6 (catalog number: 4400291; Thermo Fisher Scientific Inc.) and RNase P (catalog number: 4403326; Thermo Fisher Scientific Inc.). For the copy number assay, 13 frozen samples and 14 FFPE samples were used. The copy number assay was not conducted for some cases because the sample volume was small or little sample was left. A normal tissue sample of a UPS case was also tested as a control. Finally, DNA was extracted in 28 cases. PCR was performed with THUNDERBIRD Probe qPCR Mix (TOYOBO), using the following protocol on a Step One Plus Real Time PCR System (Thermo Fisher Scientific Inc.): pre-denaturing at 95 °C for 10 min; and then 45 cycles of denaturing at 98 °C for 15 s, annealing at 60 °C for 15 s, and extension at 68 °C for 30 s. The obtained relative quantities were processed using CopyCaller (Thermo Fisher Scientific Inc.) and copy numbers were determined.
Subgrouping in accordance with PD-L1, CMTM6, and tumor-infiltrating lymphocytes
We divided the UPS cases into subgroups according to the PD-L1 expression, the level of CD8-positive TILs, and the CMTM6 expression. In this subgrouping, the cut-off of PD-L1 was set as 1% because this is the threshold for administering anti-PD-1 therapy for many cancers. We counted CD8-positive TILs in UPS in five randomly chosen high-power fields, as previously described (Ishihara et al. 2020). Cases were classified as TILs-high or TILs-low according to the cut-off, which was determined by drawing ROC curves (Supplementary Figure 1). If either PS or IS of CMTM6 was evaluated as high, CMTM6 expression was considered to be positive.
DNA copy number and mRNA expression profiling using TCGA data
DNA copy number data and mRNA expression data of 50 UPS cases in TCGA (https://www.cancer.gov/tcga) were analyzed using the cBio Cancer Genomics Portal (cBioPortal), an open platform for evaluating genomic data (http://www.cbioportal.org/) (Gao et al. 2014; Cerami et al. 2017).
Statistics
The relationship between the immune expression of CMTM6 and PD-L1 was analyzed by Fisher’s exact test. Steel’s multiple comparison test was used to analyze the correlation between CMTM6 mRNA and DNA copy number in TCGA data using cBioPortal. The relationship between immunohistochemistry (IHC) data and DNA copy number of CMTM6 was analyzed using the Mann–Whitney U test. Survival curves were constructed using the Kaplan–Meier method. Overall survival and disease-free survival curves were analyzed using the log-rank test. Multivariate analysis was conducted using Cox’s proportional hazard model. We used the JMP statistical software package (version 14; SAS Institute) for analysis. A p-value of < 0.05 was considered significant in the statistical analysis.