Single-cell and bulk transcriptome profiling reveals RNA-binding protein regulatory programs in cervical cancer
Abstract The aberrant expression of RNA binding proteins (RBPs) is linked to various diseases, including cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC). However, the single-cell landscape of RBPs in CESC remains unclear. We analyzed single-cell data from 2 HPV + and 2 HPV- C...
Saved in:
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2025-08-01
|
| Series: | Scientific Reports |
| Subjects: | |
| Online Access: | https://doi.org/10.1038/s41598-025-14823-1 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849333063727710208 |
|---|---|
| author | Shasha Yang Jingjing Zeng Yong Wang Yudi Tan Li Yu Jinkong Wei Yuying Wei Yuxuan Jin Junying Chen |
| author_facet | Shasha Yang Jingjing Zeng Yong Wang Yudi Tan Li Yu Jinkong Wei Yuying Wei Yuxuan Jin Junying Chen |
| author_sort | Shasha Yang |
| collection | DOAJ |
| description | Abstract The aberrant expression of RNA binding proteins (RBPs) is linked to various diseases, including cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC). However, the single-cell landscape of RBPs in CESC remains unclear. We analyzed single-cell data from 2 HPV + and 2 HPV- CESC samples to assess cell subtype composition and differential gene expression. Meanwhile, based on 2,141 reported RBPs, the expression patterns of different cell type-specific RBPs were further investigated. SUVA software was used to perform differential alternative splicing analysis on the TCGA CESC data. Finally, we did a lot of follow-up work and immunohistochemical studies to understand the true expression of RBP and its correlation with CESC prognosis. We observed a significant increase in the proportion of epithelial cells in the HPV + sample. The expression of RBP exhibited heterogeneity between HPV + and HPV- samples, with epithelial cells demonstrating the most diverse composition of RBP-expressing cell clusters. Results indicated that RNA splicing events were strongly associated with CESC progression. Covariation analysis identified 4 RBPs (CSTB, TIPARP, NDRG1, and NDRG2) correlated with 25 RNA alternative splicing events. Immunohistochemical experiments revealed that TIPARP expression was down-regulated in HPV + cervical cancer(p = 0.033). And the prognostic model that includes all RBPs, stage, and treatments may has have certain practical guiding significance for patients with CESC. Our study indicates that RBPs display specific expression patterns across HPV + and HPV- CESC. The regulatory checkpoints of these RBPs may serve as potential markers and therapeutic targets for the detection of HPV + CESC. |
| format | Article |
| id | doaj-art-3b6f363338eb4f5da3e6c945dce04048 |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj-art-3b6f363338eb4f5da3e6c945dce040482025-08-20T03:46:00ZengNature PortfolioScientific Reports2045-23222025-08-0115111510.1038/s41598-025-14823-1Single-cell and bulk transcriptome profiling reveals RNA-binding protein regulatory programs in cervical cancerShasha Yang0Jingjing Zeng1Yong Wang2Yudi Tan3Li Yu4Jinkong Wei5Yuying Wei6Yuxuan Jin7Junying Chen8Department of Obstetrics and Gynecology, First Affiliated Hospital of Guangxi Medical UniversityDepartment of Pathology, First Affiliated Hospital of Guangxi Medical UniversityDepartment of Obstetrics and Gynecology, First Affiliated Hospital of Guangxi Medical UniversityDepartment of Obstetrics and Gynecology, First Affiliated Hospital of Guangxi Medical UniversityDepartment of Obstetrics and Gynecology, First Affiliated Hospital of Guangxi Medical UniversityDepartment of Obstetrics and Gynecology, First Affiliated Hospital of Guangxi Medical UniversityDepartment of Obstetrics and Gynecology, First Affiliated Hospital of Guangxi Medical UniversityDepartment of Obstetrics and Gynecology, First Affiliated Hospital of Guangxi Medical UniversityDepartment of Obstetrics and Gynecology, First Affiliated Hospital of Guangxi Medical UniversityAbstract The aberrant expression of RNA binding proteins (RBPs) is linked to various diseases, including cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC). However, the single-cell landscape of RBPs in CESC remains unclear. We analyzed single-cell data from 2 HPV + and 2 HPV- CESC samples to assess cell subtype composition and differential gene expression. Meanwhile, based on 2,141 reported RBPs, the expression patterns of different cell type-specific RBPs were further investigated. SUVA software was used to perform differential alternative splicing analysis on the TCGA CESC data. Finally, we did a lot of follow-up work and immunohistochemical studies to understand the true expression of RBP and its correlation with CESC prognosis. We observed a significant increase in the proportion of epithelial cells in the HPV + sample. The expression of RBP exhibited heterogeneity between HPV + and HPV- samples, with epithelial cells demonstrating the most diverse composition of RBP-expressing cell clusters. Results indicated that RNA splicing events were strongly associated with CESC progression. Covariation analysis identified 4 RBPs (CSTB, TIPARP, NDRG1, and NDRG2) correlated with 25 RNA alternative splicing events. Immunohistochemical experiments revealed that TIPARP expression was down-regulated in HPV + cervical cancer(p = 0.033). And the prognostic model that includes all RBPs, stage, and treatments may has have certain practical guiding significance for patients with CESC. Our study indicates that RBPs display specific expression patterns across HPV + and HPV- CESC. The regulatory checkpoints of these RBPs may serve as potential markers and therapeutic targets for the detection of HPV + CESC.https://doi.org/10.1038/s41598-025-14823-1Alternative splicingCervical cancerEpithelial cellRNA binding proteinsScRNA-seq |
| spellingShingle | Shasha Yang Jingjing Zeng Yong Wang Yudi Tan Li Yu Jinkong Wei Yuying Wei Yuxuan Jin Junying Chen Single-cell and bulk transcriptome profiling reveals RNA-binding protein regulatory programs in cervical cancer Scientific Reports Alternative splicing Cervical cancer Epithelial cell RNA binding proteins ScRNA-seq |
| title | Single-cell and bulk transcriptome profiling reveals RNA-binding protein regulatory programs in cervical cancer |
| title_full | Single-cell and bulk transcriptome profiling reveals RNA-binding protein regulatory programs in cervical cancer |
| title_fullStr | Single-cell and bulk transcriptome profiling reveals RNA-binding protein regulatory programs in cervical cancer |
| title_full_unstemmed | Single-cell and bulk transcriptome profiling reveals RNA-binding protein regulatory programs in cervical cancer |
| title_short | Single-cell and bulk transcriptome profiling reveals RNA-binding protein regulatory programs in cervical cancer |
| title_sort | single cell and bulk transcriptome profiling reveals rna binding protein regulatory programs in cervical cancer |
| topic | Alternative splicing Cervical cancer Epithelial cell RNA binding proteins ScRNA-seq |
| url | https://doi.org/10.1038/s41598-025-14823-1 |
| work_keys_str_mv | AT shashayang singlecellandbulktranscriptomeprofilingrevealsrnabindingproteinregulatoryprogramsincervicalcancer AT jingjingzeng singlecellandbulktranscriptomeprofilingrevealsrnabindingproteinregulatoryprogramsincervicalcancer AT yongwang singlecellandbulktranscriptomeprofilingrevealsrnabindingproteinregulatoryprogramsincervicalcancer AT yuditan singlecellandbulktranscriptomeprofilingrevealsrnabindingproteinregulatoryprogramsincervicalcancer AT liyu singlecellandbulktranscriptomeprofilingrevealsrnabindingproteinregulatoryprogramsincervicalcancer AT jinkongwei singlecellandbulktranscriptomeprofilingrevealsrnabindingproteinregulatoryprogramsincervicalcancer AT yuyingwei singlecellandbulktranscriptomeprofilingrevealsrnabindingproteinregulatoryprogramsincervicalcancer AT yuxuanjin singlecellandbulktranscriptomeprofilingrevealsrnabindingproteinregulatoryprogramsincervicalcancer AT junyingchen singlecellandbulktranscriptomeprofilingrevealsrnabindingproteinregulatoryprogramsincervicalcancer |