Integration of scRNA and bulk RNA-sequence to construct the 5-gene molecular prognostic model based on the heterogeneity of thyroid carcinoma endothelial cell
Thyroid cancer (TC) is a kind of cancer with high heterogeneity, which leads to significant difference in prognosis. The prognostic molecular processes are not well understood. Cancer cells and tumor microenvironment (TME) cells jointly determine the heterogeneity. However, quite a little attention...
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
China Science Publishing & Media Ltd.
2024-01-01
|
| Series: | Acta Biochimica et Biophysica Sinica |
| Subjects: | |
| Online Access: | https://www.sciengine.com/doi/10.3724/abbs.2023254 |
| _version_ | 1797294005316222976 |
|---|---|
| author | Ni Zhaoxian Cong Shan Li Hongchang Liu Jiazhe Zhang Qing Wei Chuanchao Pan Gaofeng He Hui Liu Weiyan Mao Anwei |
| author_facet | Ni Zhaoxian Cong Shan Li Hongchang Liu Jiazhe Zhang Qing Wei Chuanchao Pan Gaofeng He Hui Liu Weiyan Mao Anwei |
| author_sort | Ni Zhaoxian |
| collection | DOAJ |
| description | Thyroid cancer (TC) is a kind of cancer with high heterogeneity, which leads to significant difference in prognosis. The prognostic molecular processes are not well understood. Cancer cells and tumor microenvironment (TME) cells jointly determine the heterogeneity. However, quite a little attention was paid to cells in the TME in the past years. In this study, we not only reveal that endothelial cells (ECs) are strongly associated with the progress of papillary thyroid cancer (PTC) using single-cell RNA-seq (scRNA-seq) data downloaded from Gene Expression Omnibus (GEO) and WGCNA, but also screen 5 crucial genes of ECs: CLDN5, ABCG2, NOTCH4, PLAT, and TMEM47. Furthermore, the 5-gene molecular prognostic model is constructed, which can predict how well a patient will do on PD-L1 blockade immunotherapy for TC and evaluate prognosis. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis demonstrates that PLAT is decreased in TC and the increase of PLAT can restrain the migratory capacity of TC cells. Meanwhile, in TC cells, PLAT suppresses VEGFa/VEGFR2-mediated human umbilical vascular endothelial cell (HUVEC) proliferation and tube formation. Totally, we construct the 5-gene molecular prognostic model from the perspective of EC and provide a new idea for immunotherapy of TC. |
| first_indexed | 2024-03-07T21:23:58Z |
| format | Article |
| id | doaj.art-74518eea52054cd0b50d04738d15d599 |
| institution | Directory Open Access Journal |
| issn | 1672-9145 |
| language | English |
| last_indexed | 2024-03-07T21:23:58Z |
| publishDate | 2024-01-01 |
| publisher | China Science Publishing & Media Ltd. |
| record_format | Article |
| series | Acta Biochimica et Biophysica Sinica |
| spelling | doaj.art-74518eea52054cd0b50d04738d15d5992024-02-27T07:34:46ZengChina Science Publishing & Media Ltd.Acta Biochimica et Biophysica Sinica1672-91452024-01-015625526910.3724/abbs.202325420d259ccIntegration of scRNA and bulk RNA-sequence to construct the 5-gene molecular prognostic model based on the heterogeneity of thyroid carcinoma endothelial cellNi Zhaoxian0Cong Shan1Li Hongchang2Liu Jiazhe3Zhang Qing4Wei Chuanchao5Pan Gaofeng6He Hui7Liu Weiyan8Mao Anwei9["Department of General Surgery, Minhang Hospital, Fudan University, Shanghai 201199, China","Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China","Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China"]["Department of Laparoscopic Surgery, the First Affiliated Hospital of Dalian Medical University, Dalian 116000, China"]["Department of General Surgery, Minhang Hospital, Fudan University, Shanghai 201199, China"]["Department of General Surgery, Minhang Hospital, Fudan University, Shanghai 201199, China"]["Department of General Surgery, Minhang Hospital, Fudan University, Shanghai 201199, China"]["Department of General Surgery, Minhang Hospital, Fudan University, Shanghai 201199, China"]["Department of General Surgery, Minhang Hospital, Fudan University, Shanghai 201199, China"]["Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China","Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China","Department of Laparoscopic Surgery, the First Affiliated Hospital of Dalian Medical University, Dalian 116000, China"]["Department of General Surgery, Minhang Hospital, Fudan University, Shanghai 201199, China"]["Department of General Surgery, Minhang Hospital, Fudan University, Shanghai 201199, China"]Thyroid cancer (TC) is a kind of cancer with high heterogeneity, which leads to significant difference in prognosis. The prognostic molecular processes are not well understood. Cancer cells and tumor microenvironment (TME) cells jointly determine the heterogeneity. However, quite a little attention was paid to cells in the TME in the past years. In this study, we not only reveal that endothelial cells (ECs) are strongly associated with the progress of papillary thyroid cancer (PTC) using single-cell RNA-seq (scRNA-seq) data downloaded from Gene Expression Omnibus (GEO) and WGCNA, but also screen 5 crucial genes of ECs: CLDN5, ABCG2, NOTCH4, PLAT, and TMEM47. Furthermore, the 5-gene molecular prognostic model is constructed, which can predict how well a patient will do on PD-L1 blockade immunotherapy for TC and evaluate prognosis. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis demonstrates that PLAT is decreased in TC and the increase of PLAT can restrain the migratory capacity of TC cells. Meanwhile, in TC cells, PLAT suppresses VEGFa/VEGFR2-mediated human umbilical vascular endothelial cell (HUVEC) proliferation and tube formation. Totally, we construct the 5-gene molecular prognostic model from the perspective of EC and provide a new idea for immunotherapy of TC.https://www.sciengine.com/doi/10.3724/abbs.2023254thyroid cancersingle-cell RNA-seqbiomarkerprognosis module |
| spellingShingle | Ni Zhaoxian Cong Shan Li Hongchang Liu Jiazhe Zhang Qing Wei Chuanchao Pan Gaofeng He Hui Liu Weiyan Mao Anwei Integration of scRNA and bulk RNA-sequence to construct the 5-gene molecular prognostic model based on the heterogeneity of thyroid carcinoma endothelial cell Acta Biochimica et Biophysica Sinica thyroid cancer single-cell RNA-seq biomarker prognosis module |
| title | Integration of scRNA and bulk RNA-sequence to construct the 5-gene molecular prognostic model based on the heterogeneity of thyroid carcinoma endothelial cell |
| title_full | Integration of scRNA and bulk RNA-sequence to construct the 5-gene molecular prognostic model based on the heterogeneity of thyroid carcinoma endothelial cell |
| title_fullStr | Integration of scRNA and bulk RNA-sequence to construct the 5-gene molecular prognostic model based on the heterogeneity of thyroid carcinoma endothelial cell |
| title_full_unstemmed | Integration of scRNA and bulk RNA-sequence to construct the 5-gene molecular prognostic model based on the heterogeneity of thyroid carcinoma endothelial cell |
| title_short | Integration of scRNA and bulk RNA-sequence to construct the 5-gene molecular prognostic model based on the heterogeneity of thyroid carcinoma endothelial cell |
| title_sort | integration of scrna and bulk rna sequence to construct the 5 gene molecular prognostic model based on the heterogeneity of thyroid carcinoma endothelial cell |
| topic | thyroid cancer single-cell RNA-seq biomarker prognosis module |
| url | https://www.sciengine.com/doi/10.3724/abbs.2023254 |
| work_keys_str_mv | AT nizhaoxian integrationofscrnaandbulkrnasequencetoconstructthe5genemolecularprognosticmodelbasedontheheterogeneityofthyroidcarcinomaendothelialcell AT congshan integrationofscrnaandbulkrnasequencetoconstructthe5genemolecularprognosticmodelbasedontheheterogeneityofthyroidcarcinomaendothelialcell AT lihongchang integrationofscrnaandbulkrnasequencetoconstructthe5genemolecularprognosticmodelbasedontheheterogeneityofthyroidcarcinomaendothelialcell AT liujiazhe integrationofscrnaandbulkrnasequencetoconstructthe5genemolecularprognosticmodelbasedontheheterogeneityofthyroidcarcinomaendothelialcell AT zhangqing integrationofscrnaandbulkrnasequencetoconstructthe5genemolecularprognosticmodelbasedontheheterogeneityofthyroidcarcinomaendothelialcell AT weichuanchao integrationofscrnaandbulkrnasequencetoconstructthe5genemolecularprognosticmodelbasedontheheterogeneityofthyroidcarcinomaendothelialcell AT pangaofeng integrationofscrnaandbulkrnasequencetoconstructthe5genemolecularprognosticmodelbasedontheheterogeneityofthyroidcarcinomaendothelialcell AT hehui integrationofscrnaandbulkrnasequencetoconstructthe5genemolecularprognosticmodelbasedontheheterogeneityofthyroidcarcinomaendothelialcell AT liuweiyan integrationofscrnaandbulkrnasequencetoconstructthe5genemolecularprognosticmodelbasedontheheterogeneityofthyroidcarcinomaendothelialcell AT maoanwei integrationofscrnaandbulkrnasequencetoconstructthe5genemolecularprognosticmodelbasedontheheterogeneityofthyroidcarcinomaendothelialcell |