Coupling an EML4-ALK-centric interactome with RNA interference identifies sensitizers to ALK inhibitors.
Patients with lung cancers harboring anaplastic lymphoma kinase (ALK) gene fusions benefit from treatment with ALK inhibitors, but acquired resistance inevitably arises. A better understanding of proximal ALK signaling mechanisms may identify sensitizers to ALK inhibitors that disrupt the balance between prosurvival and proapoptotic effector signals. Using affinity purification coupled with mass spectrometry in an ALK fusion lung cancer cell line (H3122), we generated an ALK signaling network and investigated signaling activity using tyrosine phosphoproteomics. We identified a network of 464 proteins composed of subnetworks with differential response to ALK inhibitors. A small hairpin RNA screen targeting 407 proteins in this network revealed 64 and 9 proteins that when knocked down sensitized cells to crizotinib and alectinib, respectively. Among these, knocking down fibroblast growth factor receptor substrate 2 (FRS2) or coiled-coil and C2 domain-containing protein 1A (CC2D1A), both scaffolding proteins, sensitized multiple ALK fusion cell lines to the ALK inhibitors crizotinib and alectinib. Collectively, our data set provides a resource that enhances our understanding of signaling and drug resistance networks consequent to ALK fusions and identifies potential targets to improve the efficacy of ALK inhibitors in patients.
Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA.
Guolin
G
Zhang
Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
Hannah
H
Scarborough
Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
Jihye
J
Kim
Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
Andrii I
AI
Rozhok
Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA.
Yian Ann
YA
Chen
Department of Hematopathology and Laboratory Medicine, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA.
Xiaohui
X
Zhang
Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA.
Lanxi
L
Song
Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA.
Yun
Y
Bai
Proteomics Core Facility, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA.
Bin
B
Fang
Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA.
Richard Z
RZ
Liu
Department of Molecular Oncology Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA.
John
J
Koomen
Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
Aik Choon
AC
Tan
Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
James
J
Degregori
Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA. eric.haura@moffitt.org.
Eric B
EB
Haura
D048868:Adaptor Proteins, Signal Transducing / Q000235:genetics / Q000378:metabolism; D000077548:Anaplastic Lymphoma Kinase; D002227:Carbazoles / Q000494:pharmacology*; D018797:Cell Cycle Proteins / Q000235:genetics / Q000378:metabolism; D045744:Cell Line, Tumor; D000077547:Crizotinib; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D006801:Humans; D008175:Lung Neoplasms / Q000188:drug therapy / Q000235:genetics / Q000378:metabolism; D008565:Membrane Proteins / Q000235:genetics / Q000378:metabolism; D008869:Microtubule-Associated Proteins / Q000235:genetics / Q000378:metabolism; D010880:Piperidines / Q000494:pharmacology*; D011720:Pyrazoles / Q000494:pharmacology*; D011725:Pyridines / Q000494:pharmacology*; D034622:RNA Interference; D020794:Receptor Protein-Tyrosine Kinases / Q000037:antagonists & inhibitors / Q000235:genetics / Q000378:metabolism; D012697:Serine Endopeptidases / Q000235:genetics / Q000378:metabolism
D048868:Adaptor Proteins, Signal Transducing; C512283:CC2D1A protein, human; D002227:Carbazoles; D018797:Cell Cycle Proteins; D004268:DNA-Binding Proteins; C106534:FRS2 protein, human; D008565:Membrane Proteins; D008869:Microtubule-Associated Proteins; D010880:Piperidines; D011720:Pyrazoles; D011725:Pyridines; D000077547:Crizotinib; C000626173:ALK protein, human; D000077548:Anaplastic Lymphoma Kinase; D020794:Receptor Protein-Tyrosine Kinases; C415585:EML4 protein, human; D012697:Serine Endopeptidases; C582670:alectinib