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author:

Lin, X. (Lin, X..) [1] | Ma, Q. (Ma, Q..) [2] | Chen, L. (Chen, L..) [3] | Guo, W. (Guo, W..) [4] | Huang, Z. (Huang, Z..) [5] | Huang, T. (Huang, T..) [6] | Cai, Y.-D. (Cai, Y.-D..) [7]

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Abstract:

Background: Targeted therapy has revolutionized cancer treatment, greatly improving patient outcomes and quality of life. Lung cancer, specifically non-small cell lung cancer, is frequently driven by the G12C mutation at the KRAS locus. The development of KRAS inhibitors has been a breakthrough in the field of cancer research, given the crucial role of KRAS mutations in driving tumor growth and progression. However, over half of patients with cancer bypass inhibition show limited response to treatment. The mechanisms underlying tumor cell resistance to this treatment remain poorly understood. Methods: To address above gap in knowledge, we conducted a study aimed to elucidate the differences between tumor cells that respond positively to KRAS (G12C) inhibitor therapy and those that do not. Specifically, we analyzed single-cell gene expression profiles from KRAS G12C-mutant tumor cell models (H358, H2122, and SW1573) treated with KRAS G12C (ARS-1620) inhibitor, which contained 4297 cells that continued to proliferate under treatment and 3315 cells that became quiescent. Each cell was represented by the expression levels on 8687 genes. We then designed an innovative machine learning based framework, incorporating seven feature ranking algorithms and four classification algorithms to identify essential genes and establish quantitative rules. Results: Our analysis identified some top-ranked genes, including H2AFZ, CKS1B, TUBA1B, RRM2, and BIRC5, that are known to be associated with the progression of multiple cancers. Conclusion: Above genes were relevant to tumor cell resistance to targeted therapy. This study provides important insights into the molecular mechanisms underlying tumor cell resistance to KRAS inhibitor treatment. © 2023 Elsevier B.V.

Keyword:

cancer KRAS Machine learning Single-cell gene expression Tumor cell

Community:

  • [ 1 ] [Lin X.]Laboratory of Radiation Oncology and Radiobiology, Clinical Oncology School of Fujian Medical University and Fujian Cancer Hospital, Fuzhou, 350014, China
  • [ 2 ] [Ma Q.]School of Life Sciences, Shanghai University, Shanghai, 200444, China
  • [ 3 ] [Chen L.]College of Information Engineering, Shanghai Maritime University, Shanghai, 201306, China
  • [ 4 ] [Guo W.]Key Laboratory of Stem Cell Biology, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, 200030, China
  • [ 5 ] [Huang Z.]College of Chemistry, Fuzhou University, Fuzhou, 350000, China
  • [ 6 ] [Huang T.]Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
  • [ 7 ] [Huang T.]CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
  • [ 8 ] [Cai Y.-D.]School of Life Sciences, Shanghai University, Shanghai, 200444, China

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Source :

Biochimica et Biophysica Acta - General Subjects

ISSN: 0304-4165

Year: 2023

Issue: 12

Volume: 1867

2 . 8

JCR@2023

2 . 8 0 0

JCR@2023

JCR Journal Grade:2

CAS Journal Grade:3

Cited Count:

WoS CC Cited Count:

SCOPUS Cited Count:

ESI Highly Cited Papers on the List: 0 Unfold All

WanFang Cited Count:

Chinese Cited Count:

30 Days PV: 3

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