TY - JOUR
T1 - Phosphoproteomic analysis identifies CLK1 as a novel therapeutic target in gastric cancer
AU - Babu, Niraj
AU - Pinto, Sneha M.
AU - Biswas, Manjusha
AU - Subbannayya, Tejaswini
AU - Rajappa, Manoj
AU - Mohan, Sonali V.
AU - Advani, Jayshree
AU - Rajagopalan, Pavithra
AU - Sathe, Gajanan
AU - Syed, Nazia
AU - Radhakrishna, Vinod D.
AU - Muthusamy, Oliyarasi
AU - Navani, Sanjay
AU - Kumar, Rekha V.
AU - Gopisetty, Gopal
AU - Rajkumar, Thangarajan
AU - Radhakrishnan, Padhma
AU - Thiyagarajan, Saravanan
AU - Pandey, Akhilesh
AU - Gowda, Harsha
AU - Majumder, Pradip
AU - Chatterjee, Aditi
N1 - Funding Information:
We thank the Department of Biotechnology (DBT), Government of India for research support to the Institute of Bioinformatics (IOB), Bangalore. IOB is supported by DBT Program Support on infrastructure for proteomic data analysis (BT/01/COE/08/05). NB is a recipient of the Senior Research Fellowship from the Council of Scientific and Industrial Research (CSIR), New Delhi, India.
Funding Information:
We thank the Department of Biotechnology (DBT), Government of India for research support to the Institute of Bioinformatics (IOB), Bangalore. IOB is supported by DBT Program Support on infrastructure for proteomic data analysis (BT/01/COE/08/05). NB is a recipient of the Senior Research Fellowship from the Council of Scientific and Industrial Research (CSIR), New Delhi, India.
Funding Information:
The project was funded with intramural funds of Institute of Bioinformatics and Mitra Biotech. Acknowledgements
Publisher Copyright:
© 2020, The International Gastric Cancer Association and The Japanese Gastric Cancer Association.
PY - 2020/9
Y1 - 2020/9
N2 - 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.
AB - 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.
KW - Biomarker
KW - PDX in vivo models
KW - Phosphoserine/threonine
KW - Spliceosome complex
KW - Targeted therapy
UR - http://www.scopus.com/inward/record.url?scp=85083861890&partnerID=8YFLogxK
U2 - 10.1007/s10120-020-01062-8
DO - 10.1007/s10120-020-01062-8
M3 - Article
C2 - 32333232
AN - SCOPUS:85083861890
SN - 1436-3291
VL - 23
SP - 796
EP - 810
JO - Gastric Cancer
JF - Gastric Cancer
IS - 5
ER -
