CRISPR/Cas9-based discovery of ccRCC therapeutic opportunities through molecular mechanism and immune microenvironment analysis
IntroductionClear cell renal cell carcinoma is a common and aggressive form of renal cell carcinoma. Its incidence continues to rise, and metastatic recurrence leads to poor clinical outcomes. Current prognostic biomarkers lack reliability. We integrated multi-omics data to discover key ccRCC genes...
Saved in:
| Main Authors: | , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2025-07-01
|
| Series: | Frontiers in Immunology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fimmu.2025.1619361/full |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849428032662536192 |
|---|---|
| author | Bo Han Weiyang Liu Wanhui Wang Zhuolun Li Bosen You Dongze Liu Yunfeng Nan Tiankai Ding Zhou Dai Yantong Zhang Wei Zhang Qing Liu Xuedong Li |
| author_facet | Bo Han Weiyang Liu Wanhui Wang Zhuolun Li Bosen You Dongze Liu Yunfeng Nan Tiankai Ding Zhou Dai Yantong Zhang Wei Zhang Qing Liu Xuedong Li |
| author_sort | Bo Han |
| collection | DOAJ |
| description | IntroductionClear cell renal cell carcinoma is a common and aggressive form of renal cell carcinoma. Its incidence continues to rise, and metastatic recurrence leads to poor clinical outcomes. Current prognostic biomarkers lack reliability. We integrated multi-omics data to discover key ccRCC genes and build a prognostic model to improve risk prediction and guide treatment decisions.MethodsOur study integrated genome-wide CRISPR screening data from DepMap and transcriptomic profiles from TCGA to identify key genes associated with ccRCC pathogenesis. Initial screening identified 11 candidate genes through differential expression analysis and CRISPR functional validation. Using LASSO and Cox regression, we selected five key genes (GGT6, HAO2, SLPI, MELK, and EIF4A1) for model construction. The functional role of MELK was tested by knockdown experiments. Additional analyses included tumor mutation burden, immune microenvironment assessment, and drug response prediction.ResultsThe model stratified patients into high-risk and low-risk groups with distinct survival outcomes. High-risk cases showed higher mutation loads, immunosuppressive features, and activated cytokine pathways, whereas low-risk cases displayed metabolic pathway activity. MELK knockdown reduced cancer cell proliferation and migration. High-risk patients exhibited better responses to targeted drugs such as pazopanib and sunitinib.DiscussionOur study demonstrates the pivotal role of MELK in ccRCC progression. This multi-omics-driven model elucidates MELK-mediated mechanisms and their interactions with the tumor microenvironment, providing novel strategies for risk stratification and targeted therapy. Future studies will validate these findings in independent cohorts and investigate the regulatory networks of MELK to identify potential therapeutic targets. |
| format | Article |
| id | doaj-art-86fefec0b49f4ba3b06b07ced8a538f5 |
| institution | Kabale University |
| issn | 1664-3224 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Immunology |
| spelling | doaj-art-86fefec0b49f4ba3b06b07ced8a538f52025-08-20T03:28:50ZengFrontiers Media S.A.Frontiers in Immunology1664-32242025-07-011610.3389/fimmu.2025.16193611619361CRISPR/Cas9-based discovery of ccRCC therapeutic opportunities through molecular mechanism and immune microenvironment analysisBo HanWeiyang LiuWanhui WangZhuolun LiBosen YouDongze LiuYunfeng NanTiankai DingZhou DaiYantong ZhangWei ZhangQing LiuXuedong LiIntroductionClear cell renal cell carcinoma is a common and aggressive form of renal cell carcinoma. Its incidence continues to rise, and metastatic recurrence leads to poor clinical outcomes. Current prognostic biomarkers lack reliability. We integrated multi-omics data to discover key ccRCC genes and build a prognostic model to improve risk prediction and guide treatment decisions.MethodsOur study integrated genome-wide CRISPR screening data from DepMap and transcriptomic profiles from TCGA to identify key genes associated with ccRCC pathogenesis. Initial screening identified 11 candidate genes through differential expression analysis and CRISPR functional validation. Using LASSO and Cox regression, we selected five key genes (GGT6, HAO2, SLPI, MELK, and EIF4A1) for model construction. The functional role of MELK was tested by knockdown experiments. Additional analyses included tumor mutation burden, immune microenvironment assessment, and drug response prediction.ResultsThe model stratified patients into high-risk and low-risk groups with distinct survival outcomes. High-risk cases showed higher mutation loads, immunosuppressive features, and activated cytokine pathways, whereas low-risk cases displayed metabolic pathway activity. MELK knockdown reduced cancer cell proliferation and migration. High-risk patients exhibited better responses to targeted drugs such as pazopanib and sunitinib.DiscussionOur study demonstrates the pivotal role of MELK in ccRCC progression. This multi-omics-driven model elucidates MELK-mediated mechanisms and their interactions with the tumor microenvironment, providing novel strategies for risk stratification and targeted therapy. Future studies will validate these findings in independent cohorts and investigate the regulatory networks of MELK to identify potential therapeutic targets.https://www.frontiersin.org/articles/10.3389/fimmu.2025.1619361/fullCRISPR-Cas9 screeningccRCCprognostic modelMELKimmunotherapy |
| spellingShingle | Bo Han Weiyang Liu Wanhui Wang Zhuolun Li Bosen You Dongze Liu Yunfeng Nan Tiankai Ding Zhou Dai Yantong Zhang Wei Zhang Qing Liu Xuedong Li CRISPR/Cas9-based discovery of ccRCC therapeutic opportunities through molecular mechanism and immune microenvironment analysis Frontiers in Immunology CRISPR-Cas9 screening ccRCC prognostic model MELK immunotherapy |
| title | CRISPR/Cas9-based discovery of ccRCC therapeutic opportunities through molecular mechanism and immune microenvironment analysis |
| title_full | CRISPR/Cas9-based discovery of ccRCC therapeutic opportunities through molecular mechanism and immune microenvironment analysis |
| title_fullStr | CRISPR/Cas9-based discovery of ccRCC therapeutic opportunities through molecular mechanism and immune microenvironment analysis |
| title_full_unstemmed | CRISPR/Cas9-based discovery of ccRCC therapeutic opportunities through molecular mechanism and immune microenvironment analysis |
| title_short | CRISPR/Cas9-based discovery of ccRCC therapeutic opportunities through molecular mechanism and immune microenvironment analysis |
| title_sort | crispr cas9 based discovery of ccrcc therapeutic opportunities through molecular mechanism and immune microenvironment analysis |
| topic | CRISPR-Cas9 screening ccRCC prognostic model MELK immunotherapy |
| url | https://www.frontiersin.org/articles/10.3389/fimmu.2025.1619361/full |
| work_keys_str_mv | AT bohan crisprcas9baseddiscoveryofccrcctherapeuticopportunitiesthroughmolecularmechanismandimmunemicroenvironmentanalysis AT weiyangliu crisprcas9baseddiscoveryofccrcctherapeuticopportunitiesthroughmolecularmechanismandimmunemicroenvironmentanalysis AT wanhuiwang crisprcas9baseddiscoveryofccrcctherapeuticopportunitiesthroughmolecularmechanismandimmunemicroenvironmentanalysis AT zhuolunli crisprcas9baseddiscoveryofccrcctherapeuticopportunitiesthroughmolecularmechanismandimmunemicroenvironmentanalysis AT bosenyou crisprcas9baseddiscoveryofccrcctherapeuticopportunitiesthroughmolecularmechanismandimmunemicroenvironmentanalysis AT dongzeliu crisprcas9baseddiscoveryofccrcctherapeuticopportunitiesthroughmolecularmechanismandimmunemicroenvironmentanalysis AT yunfengnan crisprcas9baseddiscoveryofccrcctherapeuticopportunitiesthroughmolecularmechanismandimmunemicroenvironmentanalysis AT tiankaiding crisprcas9baseddiscoveryofccrcctherapeuticopportunitiesthroughmolecularmechanismandimmunemicroenvironmentanalysis AT zhoudai crisprcas9baseddiscoveryofccrcctherapeuticopportunitiesthroughmolecularmechanismandimmunemicroenvironmentanalysis AT yantongzhang crisprcas9baseddiscoveryofccrcctherapeuticopportunitiesthroughmolecularmechanismandimmunemicroenvironmentanalysis AT weizhang crisprcas9baseddiscoveryofccrcctherapeuticopportunitiesthroughmolecularmechanismandimmunemicroenvironmentanalysis AT qingliu crisprcas9baseddiscoveryofccrcctherapeuticopportunitiesthroughmolecularmechanismandimmunemicroenvironmentanalysis AT xuedongli crisprcas9baseddiscoveryofccrcctherapeuticopportunitiesthroughmolecularmechanismandimmunemicroenvironmentanalysis |