ArticleBriefings in bioinformatics2018
Kinase impact assessment in the landscape of fusion genes that retain kinase domains: a pan-cancer study.
Article in Briefings in bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 34 citations in OpenAlex.
- Out-of-frame CBX3::ALK fusion drives ALK activation and therapy response.Cell reports. Medicine · 2026Article
- Review
- CCDC6-RET fusion protein regulates Ras/MAPK signaling through the fusion- GRB2-SHC1 signal niche.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- FusionNW, a potential clinical impact assessment of kinases in pan-cancer fusion gene network.Briefings in bioinformatics · 2024Article
- FusionPDB: a knowledgebase of human fusion proteins.Nucleic acids research · 2024Article
- Review
- [Drug Resistance Mechanism and Therapeutic Strategy of Targeted Therapy of Non-small Cell Lung Cancer with MET Alterations].Zhongguo fei ai za zhi = Chinese journal of lung cancer · 2023Article
- Decoding Oncofusions: Unveiling Mechanisms, Clinical Impact, and Prospects for Personalized Cancer Therapies.Cancers · 2023Review
- Overview of Molecular Detection Technologies forCancers · 2023Review
- Molecular and clinical features of papillary thyroid cancer in adult patients with a non-classical phenotype.Frontiers in endocrinology · 2023Article
- NTRK-fusions in pediatric thyroid tumors: Current state and future perspectives.Cancer genetics · 2022Review
- FusionGDB 2.0: fusion gene annotation updates aided by deep learning.Nucleic acids research · 2022Article
- Identification of RET fusions in a Chinese multicancer retrospective analysis by next-generation sequencing.Cancer science · 2022Article
- Clinically relevant fusion oncogenes: detection and practical implications.Therapeutic advances in medical oncology · 2022Review
- Article
- Landscape of drug-resistance mutations in kinase regulatory hotspots.Briefings in bioinformatics · 2021Article
- Genomically Complex Human Angiosarcoma and Canine Hemangiosarcoma Establish Convergent Angiogenic Transcriptional Programs Driven by Novel Gene Fusions.Molecular cancer research : MCR · 2021Article
- Deep generative neural network for accurate drug response imputation.Nature communications · 2021Article
- Mining potentially actionable kinase gene fusions in cancer cell lines with the KuNG FU database.Scientific data · 2020Article
- MET-dependent solid tumours - molecular diagnosis and targeted therapy.Nature reviews. Clinical oncology · 2020Review
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3 authors at 1 institution in 1 country.
Funding
Abstract
Assessing the impact of kinase in gene fusion is essential for both identifying driver fusion genes (FGs) and developing molecular targeted therapies. Kinase domain retention is a crucial factor in kinase fusion genes (KFGs), but such a systematic investigation has not been done yet. To this end, we analyzed kinase domain retention (KDR) status in chimeric protein sequences of 914 KFGs covering 312 kinases across 13 major cancer types. Based on 171 kinase domain-retained KFGs including 101 kinases, we studied their recurrence, kinase groups, fusion partners, exon-based expression depth, short DNA motifs around the break points and networks. Our results, such as more KDR than 5'-kinase fusion genes, combinatorial effects between 3'-KDR kinases and their 5'-partners and a signal transduction-specific DNA sequence motif in the break point intronic sequences, supported positive selection on 3'-kinase fusion genes in cancer. We introduced a degree-of-frequency (DoF) score to measure the possible number of KFGs of a kinase. Interestingly, kinases with high DoF scores tended to undergo strong gene expression alteration at the break points. Furthermore, our KDR gene fusion network analysis revealed six of the seven kinases with the highest DoF scores (ALK, BRAF, MET, NTRK1, NTRK3 and RET) were all observed in thyroid carcinoma. Finally, we summarized common features of 'effective' (highly recurrent) kinases in gene fusions such as expression alteration at break point, redundant usage in multiple cancer types and 3'-location tendency. Collectively, our findings are useful for prioritizing driver kinases and FGs and provided insights into KFGs' clinical implications.
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