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Comprehensive pan-cancer analysis reveals CCDC58 as a carcinogenic factor related to immune infiltration

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CCDC58, a member of the CCDC protein family, has been primarily associated with the malignant progression of hepatocellular carcinoma (HCC) and breast cancer, with limited research conducted on its involvement in other tumor types. We aimed to assess the significance of CCDC58 in pan-cancer. We utilized the TCGA, GTEx, and UALCAN databases to perform the differential expression of CCDC58 at both mRNA and protein levels. Prognostic value was evaluated through univariate Cox regression and Kaplan–Meier methods. Mutation and methylation analyses were conducted using the cBioPortal and SMART databases. We identified genes interacting with and correlated to CCDC58 through STRING and GEPIA2, respectively. Subsequently, we performed GO and KEGG enrichment analyses. To gain insights into the functional status of CCDC58 at the single-cell level, we utilized CancerSEA. We explored the correlation between CCDC58 and immune infiltration as well as immunotherapy using the ESTIMATE package, TIMER2.0, TISIDB, TIDE, TIMSO, and TCIA. We examined the relationship between CCDC58 and tumor heterogeneity, stemness, DNA methyltransferases, and MMR genes. Lastly, we constructed a nomogram based on CCDC58 in HCC and investigated its association with drug sensitivity. CCDC58 expression was significantly upregulated and correlated with poor prognosis across various tumor types. The mutation frequency of CCDC58 was found to be increased in 25 tumors. We observed a negative correlation between CCDC58 expression and the methylation sites in the majority of tumors. CCDC58 showed negative correlations with immune and stromal scores, as well as with NK T cells, Tregs, CAFs, endothelial cells, and immunomodulators. Its value in immunotherapy was comparable to that of tumor mutational burden. CCDC58 exhibited positive correlations with tumor heterogeneity, stemness, DNA methyltransferase genes, and MMR genes. In HCC, CCDC58 was identified as an independent risk factor and demonstrated potential associations with multiple drugs. CCDC58 demonstrates significant clinical value as a prognostic marker and indicator of immune response across various tumor types. Its comprehensive analysis provides insights into its potential implications in pan-cancer research.

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Data availability

The data are available from the corresponding author for reasonable requests.



Adrenocortical carcinoma


Area under the curve


Bladder urothelial carcinoma


Biological process


Breast invasive carcinoma


Cancer-associated fibroblasts


Cellular component


Coiled-coil domain containing 58


Cervical squamous cell carcinoma and endocervical adenocarcinoma




Copy number alteration


Copy number variants


Colon adenocarcinoma


Colon adenocarcinoma/rectum adenocarcinoma


Disease-free interval


Lymphoid neoplasm diffuse large B-cell lymphoma


Disease-specific survival


Esophageal carcinoma


Glioblastoma multiforme




Gene ontology


Gene set enrichment analysis


Hepatocellular carcinoma


Head and neck squamous cell carcinoma


Homologous recombination deficiency


Half-maximal inhibitory concentration


Immune checkpoint blockade


Immune phenotype scores


Kyoto encyclopedia of genes and genomes


Kidney chromophobe


Pan-kidney cohort (KICH + KIRC + KIRP)


Kidney renal clear cell carcinoma


Kidney renal papillary cell carcinoma




Acute myeloid leukemia


Brain lower grade glioma


Liver hepatocellular carcinoma


Loss of heterozygosity


Lung adenocarcinoma


Lung squamous cell carcinoma


Mutational and clonal intratumoral heterogeneity


Myeloid-derived suppressor cells




Molecular function


Mismatch repair


Microsatellite instability


Neoantigen load


Overall survival


Ovarian serous cystadenocarcinoma


Pancreatic adenocarcinoma


Pheochromocytoma and paraganglioma


Progression-free interval


Protein–protein interaction


Prostate adenocarcinoma


Rectum adenocarcinoma


Receiver operating characteristic




Skin cutaneous melanoma


Single nucleotide variants


Stomach adenocarcinoma


Stomach and esophageal carcinoma


Testicular germ cell tumors


Thyroid carcinoma




Tumor-infiltrating lymphocytes


Tumor mutational burden


Tumor microenvironment


Triple-negative breast cancer


Uterine corpus endometrial carcinoma


Uterine carcinosarcoma


Uveal melanoma


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HW, QG, WS, and CQ participated in the conception, design, acquisition of data, analysis, and interpretation. All authors participated in drafting the article and gave final approval.

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Correspondence to Wenxiang Shi or Chenjie Qiu.

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Wu, H., Geng, Q., Shi, W. et al. Comprehensive pan-cancer analysis reveals CCDC58 as a carcinogenic factor related to immune infiltration. Apoptosis 29, 536–555 (2024).

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