Alternative transcription initiation leads to expression of a novel ALK isoform in cancer

Abstract

Activation of oncogenes by mechanisms other than genetic aberrations such as mutations, translocations, or amplifications is largely undefined. Here we report a novel isoform of the anaplastic lymphoma kinase (ALK) that is expressed in ~ 11% of melanomas and sporadically in other human cancer types, but not in normal tissues. The novel ALK transcript initiates from a de novo alternative transcription initiation (ATI) site in ALK intron 19, and was termed ALKATI. In ALKATI-expressing tumours, the ATI site is enriched for H3K4me3 and RNA polymerase II, chromatin marks characteristic of active transcription initiation sites1. ALKATI is expressed from both ALK alleles, and no recurrent genetic aberrations are found at the ALK locus, indicating that the transcriptional activation is independent of genetic aberrations at the ALK locus. The ALKATI transcript encodes three proteins with molecular weights of 61.1, 60.8 and 58.7 kilodaltons, consisting primarily of the intracellular tyrosine kinase domain. ALKATI stimulates multiple oncogenic signalling pathways, drives growth-factor-independent cell proliferation in vitro, and promotes tumorigenesis in vivo in mouse models. ALK inhibitors can suppress the kinase activity of ALKATI, suggesting that patients with ALKATI-expressing tumours may benefit from ALK inhibitors. Our findings suggest a novel mechanism of oncogene activation in cancer through de novo alternative transcription initiation.

COP1/DET1/ETS axis regulates ERK transcriptome and sensitivity to MAPK inhibitors

“…Exome sequencing studies have shown that approximately 50% of resistant tumors harbor secondary mutations that reactivate the MAPK/ERK pathway (5,40). Nonmutational mechanisms that govern drug sensitivity are not fully understood and can involve reversible cellautonomous or microenvironment-mediated tuning of MAPK/ ERK pathway activity (8,9,(41)(42)(43). The strength of coupling between upstream MAPK/ERK signaling and the downstream transcriptional response can modulate the MAPK inhibitor response, as failure to turn off transcription in response to MAPK inhibition may increase drug tolerance.…”

The Truncated Isoform of the Receptor Tyrosine Kinase ALK Generated by Alternative Transcription Initiation (ALK^ATI) Induces Chromatin Structural Changes in the Nucleus in a Kinase Activity-Dependent Manner

“…1) Recently, the truncated isoform of ALK (ALK ATI ) was reported to localize to the nucleus as well as cytoplasm, but its nuclear role was not clarified. 13) Therefore, in the present study, we analyzed its role in the nucleus. We found that nuclear ALK ATI induces chromatin structural changes and heterochromatinization.…”

“…13) In order to confirm this finding, we transiently expressed ALK-FL and ALK ATI in HeLa S3 cells (Figs. 1A, B).…”

“…7) Given that the kinase domain of the full-length isoform of ALK localizes just under the plasma membrane, activation of ALK targets is expected to occur in the cytoplasm. The ALK ATI also predominantly localizes in the cytoplasm where it is involved in the activation of these three signaling pathways, 13) so its major targets are likely cytoplasmic proteins. However, unlike the full-length isoform, ALK ATI is reported to localize to the nucleus as well as the cytoplasm, and its nuclear role remains unclear.…”

“…12) Recently, ALK ATI , a truncated isoform of ALK, was identified in a variety of tumors. 13) This isoform is expressed from a transcript that is initiated from an alternative transcription initiation (ATI) site in ALK intron 19. ALK ATI , which consists of only the intracellular kinase domain, displays constitutive activation similar to EML4-ALK.…”