Deciphering the tumour microenvironment of clear cell renal cell carcinoma: Prognostic insights from programmed death genes using machine learning.

Journal: Journal of cellular and molecular medicine
PMID: 39011666

Abstract

Clear cell renal cell carcinoma (ccRCC), a prevalent kidney cancer form characterised by its invasiveness and heterogeneity, presents challenges in late-stage prognosis and treatment outcomes. Programmed cell death mechanisms, crucial in eliminating cancer cells, offer substantial insights into malignant tumour diagnosis, treatment and prognosis. This study aims to provide a model based on 15 types of Programmed Cell Death-Related Genes (PCDRGs) for evaluating immune microenvironment and prognosis in ccRCC patients. ccRCC patients from the TCGA and arrayexpress cohorts were grouped based on PCDRGs. A combination model using Lasso and SuperPC was constructed to identify prognostic gene features. The arrayexpress cohort validated the model, confirming its robustness. Immune microenvironment analysis, facilitated by PCDRGs, employed various methods, including CIBERSORT. Drug sensitivity analysis guided clinical treatment decisions. Single-cell data enabled Programmed Cell Death-Related scoring, subsequent pseudo-temporal and cell-cell communication analyses. A PCDRGs signature was established using TCGA-KIRC data. External validation in the arrayexpress cohort underscored the model's superiority over traditional clinical features. Furthermore, our single-cell analysis unveiled the roles of PCDRG-based single-cell subgroups in ccRCC, both in pseudo-temporal progression and intercellular communication. Finally, we performed CCK-8 assay and other experiments to investigate csf2. In conclusion, these findings reveal that csf2 inhibit the growth, infiltration and movement of cells associated with renal clear cell carcinoma. This study introduces a PCDRGs prognostic model benefiting ccRCC patients while shedding light on the pivotal role of programmed cell death genes in shaping the immune microenvironment of ccRCC patients.

Authors

  • Hongtao Tu
    Department of Urology, Dazhou Central Hospital, Dazhou, Sichuan, China.
  • Qingwen Hu
    Clinical Medical College, Southwest Medical University, Luzhou, China.
  • Yuying Ma
    Three Gorges Hospital, Chongqing University, Chongqing, China.
  • Jinbang Huang
    School of Clinical Medicine, The Affiliated Hospital, Southwest Medical University, Luzhou, China.
  • Honghao Luo
    Department of Ultrasound, West China Hospital of Sichuan University, Chengdu, 610041, China.
  • Lai Jiang
  • Shengke Zhang
    Clinical Medical College, Southwest Medical University, Luzhou, China.
  • Chenglu Jiang
    School of Clinical Medicine, The Affiliated Hospital, Southwest Medical University, Luzhou, China.
  • Haotian Lai
    Clinical Medical College, Southwest Medical University, Luzhou, China.
  • Jie Liu
    School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China.
  • Jianyou Chen
    Department of Urology, Dazhou Integrated Traditional Chinese Medicine and Western Medicine Hospital, Dazhou, Sichuan, China.
  • Liwei Guo
    Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
  • Guanhu Yang
    Department of Specialty Medicine, Ohio University, Athens, OH, United States.
  • Ke Xu
    Mechatronics Engineering of University of Electronic Science and Technology of China, Chengdu, 611731, China.
  • Hao Chi
    University of Chinese Academy of Sciences , Beijing, China.
  • Haiqing Chen
    Clinical Medical College, Southwest Medical University, Luzhou, China.

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