Cellular hierarchy framework based on single-cell and bulk RNA sequencing reveals fatty acid metabolic biomarker MYDGF as a therapeutic target for ccRCC

Background Fatty acid metabolism (FAM) reprogramming is a prominent feature of clear cell renal cell carcinoma (ccRCC). Nevertheless, the effect of FAM reprogramming on the heterogeneity and prognosis of ccRCC individuals remains insufficiently understood. Methods We utilized single-cell sequencing and spatial transcriptomics to investigate the heterogeneity of FAM in ccRCC comprehensively. Functional enrichment algorithms, including AUCell, UCell, singscore, ssGSEA, and AddModuleScore, along with hdWGCNA analysis, were used to identify hub genes influencing high FAM of ccRCC. Machine learning methods were then applied to pinpoint the optimal feature gene. The function of the selected genes in FAM was validated through clinical samples and cellular functional experiments. Results The results revealed significant upregulation of FAM in malignant epithelial cells. Through five distinct enrichment scoring methods and hdWGCNA analysis, we redefined a gene set related to increased FAM at the single-cell level. By the integration of this gene set with bulk transcriptomic data and the application of machine-learning algorithms, we found four candidate genes—MYDGF, ZNHIT1, HMGN3, and ARL6IP4—that were linked to ccRCC progression. Bulk RNA sequencing validated their increased expression in ccRCC individuals, underscoring their diagnostic and prognostic potential. Single-cell analysis further revealed that these genes were primarily upregulated in malignant epithelial cells, emphasizing their cell-specific roles in ccRCC. It was verified that MYDGF could promote cell proliferation, migration and invasion while inhibiting cell apoptosis. Functional experiments further confirmed that MYDGF is a key FAM-related biomarker that enhances lipid deposition by suppressing fatty acid oxidation, thereby accelerating tumor progression. Conclusions MYDGF was identified as a FAM-related oncogenic biomarker that promotes ccRCC progression by inhibiting fatty acid oxidation. Our findings elucidated the cellular hierarchy of ccRCC from the perspective of FAM reprogramming and may offer new insights and therapeutic targets for future ccRCC treatments.