Analysis of genomic heterogeneity and the mutational landscape in cutaneous squamous cell carcinoma through multi-patient-targeted single-cell DNA sequencing
Abstract Background Cutaneous squamous cell carcinoma (CSCC) is a prevalent skin cancer with aggressive progression that poses significant challenges, especially in metastatic cases. Single-cell DNA sequencing (scDNA-seq) has become an advanced technology for elucidating tumor heterogeneity and clon...
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BMC
2025-08-01
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| Online Access: | https://doi.org/10.1186/s12885-025-14585-z |
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| author | Wen Chen Jiawei Xu Chengdong Yu Meng Zhou Yong Ai Wenbing Rao Qingchuan Wang Siyi Xu Lei Tang Si Gong Jun Rao |
| author_facet | Wen Chen Jiawei Xu Chengdong Yu Meng Zhou Yong Ai Wenbing Rao Qingchuan Wang Siyi Xu Lei Tang Si Gong Jun Rao |
| author_sort | Wen Chen |
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| description | Abstract Background Cutaneous squamous cell carcinoma (CSCC) is a prevalent skin cancer with aggressive progression that poses significant challenges, especially in metastatic cases. Single-cell DNA sequencing (scDNA-seq) has become an advanced technology for elucidating tumor heterogeneity and clonal evolution. However, comprehensive scDNA-seq studies and tailored mutation panels for CSCC are lacking. Methods We analyzed the genomic landscape of Chinese CSCC patients via a Multi-Patient-Targeted (MPT) scDNA-seq approach. This method combined bulk exome sequencing with Tapestri scDNA-seq. Mutations identified through bulk sequencing were used to design a targeted panel for scDNA-seq. Comparative analysis was conducted to explore the associations between specific gene mutations and clinical characteristics such as tumor stage and patient sex. Clonal evolution analysis was performed to understand the evolutionary trajectories of the tumors. Results Bulk sequencing revealed a diverse spectrum of somatic mutations in CSCC tumors, with missense mutations being predominant. The top tumor mutations, such as those in NOTCH1, TP53, NOTCH2, TTN, MUC16, RYR2, PRUNE2, DMD, HRAS, and CDKN2A, presented similar frequencies to those reported in studies in Korean and Caucasian populations. However, the mutation frequencies of HRAS, TTN, MUC16 and MUC4 were significantly different from the Korean and Caucasian populations. Comparative analysis revealed associations between specific gene mutations and clinical characteristics such as tumor stage and patient sex. Clonal evolution analysis via scDNA-seq revealed distinct evolutionary trajectories and their potential correlation with tumor development and patient prognosis. Furthermore, scDNA-seq identified two low-frequency mutation clones, NLRP5 and HMMR, which play important roles in the clonal evolution of CSCC. Conclusions Our study introduced a novel MPT sequencing approach for CSCC, providing insights into tumor heterogeneity and clonal evolution. We identified novel mutations and their potential associations with patient survival and tumor characteristics. Overall, our study layed the groundwork for personalized treatment strategies and provides a reference for future applications of the MPT panel in CSCC patients. |
| format | Article |
| id | doaj-art-dfdfe1ec7d6840ee8f4c86119466b132 |
| institution | Kabale University |
| issn | 1471-2407 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Cancer |
| spelling | doaj-art-dfdfe1ec7d6840ee8f4c86119466b1322025-08-24T11:34:32ZengBMCBMC Cancer1471-24072025-08-0125111510.1186/s12885-025-14585-zAnalysis of genomic heterogeneity and the mutational landscape in cutaneous squamous cell carcinoma through multi-patient-targeted single-cell DNA sequencingWen Chen0Jiawei Xu1Chengdong Yu2Meng Zhou3Yong Ai4Wenbing Rao5Qingchuan Wang6Siyi Xu7Lei Tang8Si Gong9Jun Rao10Department of Breast Surgery, Jiangxi Cancer Hospital, The Second Affiliated Hospital of Nanchang Medical College, Jiangxi Cancer InstituteDepartment of Breast Surgery, Jiangxi Cancer Hospital, The Second Affiliated Hospital of Nanchang Medical College, Jiangxi Cancer InstituteDepartment of Breast Surgery, Jiangxi Cancer Hospital, The Second Affiliated Hospital of Nanchang Medical College, Jiangxi Cancer InstituteDepartment of Breast Surgery, Jiangxi Cancer Hospital, The Second Affiliated Hospital of Nanchang Medical College, Jiangxi Cancer InstituteDepartment of Dermatologic Surgery, Dermatology Hospital of Jiangxi ProvinceDepartment of Dermatologic Surgery, Dermatology Hospital of Jiangxi ProvinceDepartment of Breast Surgery, Jiangxi Cancer Hospital, The Second Affiliated Hospital of Nanchang Medical College, Jiangxi Cancer InstituteDepartment of Breast Surgery, Jiangxi Cancer Hospital, The Second Affiliated Hospital of Nanchang Medical College, Jiangxi Cancer InstituteDepartment of Breast Surgery, Jiangxi Cancer Hospital, The Second Affiliated Hospital of Nanchang Medical College, Jiangxi Cancer InstituteJiangxi Cancer Hospital, The Second Affiliated Hospital of Nanchang Medical College, Jiangxi Cancer Institute, Jiangxi Clinical Research Center for CancerJiangxi Cancer Hospital, The Second Affiliated Hospital of Nanchang Medical College, Jiangxi Cancer Institute, Jiangxi Clinical Research Center for CancerAbstract Background Cutaneous squamous cell carcinoma (CSCC) is a prevalent skin cancer with aggressive progression that poses significant challenges, especially in metastatic cases. Single-cell DNA sequencing (scDNA-seq) has become an advanced technology for elucidating tumor heterogeneity and clonal evolution. However, comprehensive scDNA-seq studies and tailored mutation panels for CSCC are lacking. Methods We analyzed the genomic landscape of Chinese CSCC patients via a Multi-Patient-Targeted (MPT) scDNA-seq approach. This method combined bulk exome sequencing with Tapestri scDNA-seq. Mutations identified through bulk sequencing were used to design a targeted panel for scDNA-seq. Comparative analysis was conducted to explore the associations between specific gene mutations and clinical characteristics such as tumor stage and patient sex. Clonal evolution analysis was performed to understand the evolutionary trajectories of the tumors. Results Bulk sequencing revealed a diverse spectrum of somatic mutations in CSCC tumors, with missense mutations being predominant. The top tumor mutations, such as those in NOTCH1, TP53, NOTCH2, TTN, MUC16, RYR2, PRUNE2, DMD, HRAS, and CDKN2A, presented similar frequencies to those reported in studies in Korean and Caucasian populations. However, the mutation frequencies of HRAS, TTN, MUC16 and MUC4 were significantly different from the Korean and Caucasian populations. Comparative analysis revealed associations between specific gene mutations and clinical characteristics such as tumor stage and patient sex. Clonal evolution analysis via scDNA-seq revealed distinct evolutionary trajectories and their potential correlation with tumor development and patient prognosis. Furthermore, scDNA-seq identified two low-frequency mutation clones, NLRP5 and HMMR, which play important roles in the clonal evolution of CSCC. Conclusions Our study introduced a novel MPT sequencing approach for CSCC, providing insights into tumor heterogeneity and clonal evolution. We identified novel mutations and their potential associations with patient survival and tumor characteristics. Overall, our study layed the groundwork for personalized treatment strategies and provides a reference for future applications of the MPT panel in CSCC patients.https://doi.org/10.1186/s12885-025-14585-zCutaneous squamous cell carcinoma (CSCC)Genomic heterogeneityMutational landscapeEvolutionary dynamics |
| spellingShingle | Wen Chen Jiawei Xu Chengdong Yu Meng Zhou Yong Ai Wenbing Rao Qingchuan Wang Siyi Xu Lei Tang Si Gong Jun Rao Analysis of genomic heterogeneity and the mutational landscape in cutaneous squamous cell carcinoma through multi-patient-targeted single-cell DNA sequencing BMC Cancer Cutaneous squamous cell carcinoma (CSCC) Genomic heterogeneity Mutational landscape Evolutionary dynamics |
| title | Analysis of genomic heterogeneity and the mutational landscape in cutaneous squamous cell carcinoma through multi-patient-targeted single-cell DNA sequencing |
| title_full | Analysis of genomic heterogeneity and the mutational landscape in cutaneous squamous cell carcinoma through multi-patient-targeted single-cell DNA sequencing |
| title_fullStr | Analysis of genomic heterogeneity and the mutational landscape in cutaneous squamous cell carcinoma through multi-patient-targeted single-cell DNA sequencing |
| title_full_unstemmed | Analysis of genomic heterogeneity and the mutational landscape in cutaneous squamous cell carcinoma through multi-patient-targeted single-cell DNA sequencing |
| title_short | Analysis of genomic heterogeneity and the mutational landscape in cutaneous squamous cell carcinoma through multi-patient-targeted single-cell DNA sequencing |
| title_sort | analysis of genomic heterogeneity and the mutational landscape in cutaneous squamous cell carcinoma through multi patient targeted single cell dna sequencing |
| topic | Cutaneous squamous cell carcinoma (CSCC) Genomic heterogeneity Mutational landscape Evolutionary dynamics |
| url | https://doi.org/10.1186/s12885-025-14585-z |
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