Oncogenic Kinases in Cancer

Tsintarakis, Antonis; Zafiropoulos, Alexandros

doi:10.1002/9780470015902.a0006051.pub3

Cited by 2 publications

(1 citation statement)

References 20 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Among the 538 known kinase genes in humans, there are numerous relevant targets. Specifically, mutations have been observed in kinases serving as growth factor receptors [4], cell cycle regulators [5,6], nuclear signaling [7], and apoptosis regulators [8]. In melanomas, BRAF is most commonly mutated, along with other kinases including NRAS and NF1.…”

Section: Introductionmentioning

confidence: 99%

Characterization and clustering of kinase isoform expression in metastatic melanoma

et al. 2022

View full text Add to dashboard Cite

Mutations to the human kinome are known to play causal roles in cancer. The kinome regulates numerous cell processes including growth, proliferation, differentiation, and apoptosis. In addition to aberrant expression, aberrant alternative splicing of cancer-driver genes is receiving increased attention as it could lead to loss or gain of functional domains, altering a kinase’s downstream impact. The present study quantifies changes in gene expression and isoform ratios in the kinome of metastatic melanoma cells relative to primary tumors. We contrast 538 total kinases and 3,040 known kinase isoforms between 103 primary tumor and 367 metastatic samples from The Cancer Genome Atlas (TCGA). We find strong evidence of differential expression (DE) at the gene level in 123 kinases (23%). Additionally, of the 468 kinases with alternative isoforms, 60 (13%) had significant difference in isoform ratios (DIR). Notably, DE and DIR have little correlation; for instance, although DE highlights enrichment in receptor tyrosine kinases (RTKs), DIR identifies altered splicing in non-receptor tyrosine kinases (nRTKs). Using exon junction mapping, we identify five examples of splicing events favored in metastatic samples. We demonstrate differential apoptosis and protein localization between SLK isoforms in metastatic melanoma. We cluster isoform expression data and identify subgroups that correlate with genomic subtypes and anatomic tumor locations. Notably, distinct DE and DIR patterns separate samples with BRAF hotspot mutations and (N/K/H)RAS hotspot mutations, the latter of which lacks effective kinase inhibitor treatments. DE in RAS mutants concentrates in CMGC kinases (a group including cell cycle and splicing regulators) rather than RTKs as in BRAF mutants. Furthermore, isoforms in the RAS kinase subgroup show enrichment for cancer-related processes such as angiogenesis and cell migration. Our results reveal a new approach to therapeutic target identification and demonstrate how different mutational subtypes may respond differently to treatments highlighting possible new driver events in cancer.

show abstract

Section: Introductionmentioning

confidence: 99%

Characterization and clustering of kinase isoform expression in metastatic melanoma

et al. 2022

View full text Add to dashboard Cite

show abstract

Characterization and clustering of kinase isoform expression in metastatic melanoma

Holland

Gotea

Fedkenheuer

et al. 2021

Preprint

View full text Add to dashboard Cite

Mutations to the human kinome are known to play causal roles in cancer. The kinome regulates numerous cell processes including growth, proliferation, differentiation, and apoptosis. In addition to aberrant expression, aberrant alternative splicing of cancer-driver genes is receiving increased attention as it could create loss or gain of functional domains, altering a kinase’s downstream effects.The present study quantifies changes in gene expression and isoform ratios in the kinome of metastatic melanoma cells relative to primary tumors. We contrast 538 total kinases and 3042 known kinase isoforms between 103 primary tumor and 367 metastatic samples from The Cancer Genome Atlas (TCGA). We find strong evidence of differential expression (DE) at the gene level in 123 genes (23%). Additionally, of the 468 genes with alternative isoforms, 60 (13%) had differential isoform ratios (DIR). Notably, DE and DIR have little correlation; for instance, although DE highlights enrichment in receptor tyrosine kinases (RTKs), DIR identifies altered splicing in non-receptor tyrosine kinases (nRTKs). Using exon junction mapping, we identify five examples of splicing events favored in metastatic samples.We cluster isoform expression data and identify subgroups that correlate with genomic subtypes and anatomic tumor locations. Notably, distinct DE and DIR patterns separate samples with BRAF hotspot mutations and (N/K/H)RAS hotspot mutations, the latter of which lacks effective kinase inhibitor treatments. DE in RAS mutants concentrates in CMGC kinases (a group including cell cycle and splicing regulators) rather than RTKs as in BRAF mutants. Furthermore, isoforms in the RAS kinase subgroup show enrichment for cancer-related processes such as angiogenesis and cell migration. Our results reveal a new approach to therapeutic target identification and demonstrate how different mutational subtypes may respond differently to treatments highlighting possible new driver events in cancer.

show abstract

Oncogenic Kinases in Cancer

Cited by 2 publications

References 20 publications

Characterization and clustering of kinase isoform expression in metastatic melanoma

Characterization and clustering of kinase isoform expression in metastatic melanoma

Characterization and clustering of kinase isoform expression in metastatic melanoma

Contact Info

Product

Resources

About