Phosphoproteomic analysis identifies CLK1 as a novel therapeutic target in gastric cancer

Niraj Babu, Sneha M. Pinto, Manjusha Biswas, Tejaswini Subbannayya, Manoj Rajappa, Sonali V. Mohan, Jayshree Advani, Pavithra Rajagopalan, Gajanan Sathe, Nazia Syed, Vinod D. Radhakrishna, Oliyarasi Muthusamy, Sanjay Navani, Rekha V. Kumar, Gopal Gopisetty, Thangarajan Rajkumar, Padhma Radhakrishnan, Saravanan Thiyagarajan, Akhilesh Pandey, Harsha GowdaPradip Majumder (Lead / Corresponding author), Aditi Chatterjee (Lead / Corresponding author)

Research output: Contribution to journalArticlepeer-review

29 Citations (Scopus)


Background: Phosphorylation is an important regulatory mechanism of protein activity in cells. Studies in various cancers have reported perturbations in kinases resulting in aberrant phosphorylation of oncoproteins and tumor suppressor proteins.

Methods: In this study, we carried out quantitative phosphoproteomic analysis of gastric cancer tissues and corresponding xenograft samples. Using these data, we employed bioinformatics analysis to identify aberrant signaling pathways. We further performed molecular inhibition and silencing of the upstream regulatory kinase in gastric cancer cell lines and validated its effect on cellular phenotype. Through an ex vivo technology utilizing patient tumor and blood sample, we sought to understand the therapeutic potential of the kinase by recreating the tumor microenvironment.

Results: Using mass spectrometry-based high-throughput analysis, we identified 1,344 phosphosites and 848 phosphoproteins, including differential phosphorylation of 177 proteins (fold change cut-off ≥ 1.5). Our data showed that a subset of differentially phosphorylated proteins belonged to splicing machinery. Pathway analysis highlighted Cdc2-like kinase (CLK1) as upstream kinase. Inhibition of CLK1 using TG003 and CLK1 siRNA resulted in a decreased cell viability, proliferation, invasion and migration as well as modulation in the phosphorylation of SRSF2. Ex vivo experiments which utilizes patient’s own tumor and blood to recreate the tumor microenvironment validated the use of CLK1 as a potential target for gastric cancer treatment.

Conclusions: Our data indicates that CLK1 plays a crucial role in the regulation of splicing process in gastric cancer and that CLK1 can act as a novel therapeutic target in gastric cancer.

Original languageEnglish
Pages (from-to)796-810
Number of pages15
JournalGastric Cancer
Issue number5
Early online date24 Apr 2020
Publication statusPublished - Sept 2020


  • Biomarker
  • PDX in vivo models
  • Phosphoserine/threonine
  • Spliceosome complex
  • Targeted therapy

ASJC Scopus subject areas

  • Oncology
  • Gastroenterology
  • Cancer Research


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