CSPG4 RNA across sarcoma types with an expanded comparison of extraskeletal myxoid chondrosarcoma

Abstract

Background: Extraskeletal myxoid chondrosarcoma (EMC) is a rare soft-tissue sarcoma. Chondroitin sulfate proteoglycan 4 (CSPG4) is a cell-surface protein whose expression has been studied across sarcoma types. This study examined where EMC lies within a broader tissue RNA landscape and whether its differences from named sarcomas recur across datasets. Methods: An exploratory analysis of a curated 11-gene panel compared nine EMC specimens with 393 other specimens from 28 source-defined malignant tumor categories in one RNA-sequencing cohort. All 644 eligible specimens, including other tumor categories, remained in the descriptive atlas. Analysis used an exact rank-sum permutation test with Bonferroni correction for 11 genes, evaluated the array comparisons, and characterized additional public collections separately by source and measurement scale. Results: Median CSPG4 was 54.18 TPM in EMC and 11.87 TPM in the defined malignant reference. The probability of higher EMC expression, allowing half credit for ties, was 0.846; exact two-sided P=0.000130 and adjusted P=0.00143. CSPG4 was higher than low-grade fibromyxoid sarcoma in both RNA sequencing and arrays, with comparison scores of 0.966 and 1.000. Gastrointestinal stromal tumors and dermatofibrosarcoma protuberans had slightly higher medians than EMC in the same RNA-sequencing source. External collections expanded histologic context but supplied no additional explicitly labeled EMC comparison. Conclusions: These data place EMC toward the higher end of CSPG4 RNA expression within a defined sarcoma reference, with substantial overlap and comparator dependence. They support a broader comparative RNA account, without establishing diagnostic specificity, malignant-cell protein expression or therapeutic suitability.

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