The proximal signaling network of the BCR-ABL1 oncogene shows a modular organization

Abstract

BCR-ABL1 is a fusion tyrosine-kinase, which causes multiple types of leukemia. We used an integrated proteomic approach that includes label-free quantitative protein complex and phosphorylation profiling by mass spectrometry to systematically characterize the proximal signaling network of this oncogenic kinase. The proximal BCR-ABL1 signaling network shows a modular and layered organization with an inner core of three leukemia transformation-relevant adaptor protein complexes (Grb2/Gab2/Shc1 complex, CrkI complex, and Dok1/Dok2 complex). We introduced an “interaction directionality” analysis, which annotates static protein networks with information on the directionality of phosphorylation-dependent interactions. In this analysis, the observed network structure was consistent with a step-wise phosphorylation-dependent assembly of the Grb2/Gab2/Shc1 and the Dok1/Dok2 complexes on the BCR-ABL1 core. The CrkI complex demonstrated a different directionality, which supports a candidate assembly on the Nedd9 (Hef1, CasL) scaffold. Since adaptor protein family members can compensate for each other in leukemic transformation, we compared members of the Dok and Crk protein families and found both overlapping and differential binding patterns. We identified an additional level of regulation for the CrkII protein via binding to 14-3-3 proteins, which was independent from its inhibitory phosphorylation. We also identified novel components of the inner core complexes, including the kinases Pragmin (Sgk223) and Lrrk1 (Lrrk2 paralog). Pragmin was found as a component of the CrkI complex and is a potential link between BCR-ABL1/CrkI and RhoA signaling. Lrrk1 is an unusual kinase with a GTPase domain. We detected Lrrk1 as a component of the Grb2/Gab2/Shc1 complex and found that it functionally interacts with the regulator of small GTPases Arap1 (Centd2) and possibly participates in the MAP-kinase response to cellular stresses. This modular and phosphorylation-driven interaction network provides a framework for the integration of pleiotropic signaling effects of BCR-ABL1 towards leukemic transformation.

Oncogenic Tyrosine Kinases Target Dok-1 for Ubiquitin-Mediated Proteasomal Degradation To Promote Cell Transformation

“…For instance, Dok-1 levels remain unaltered upon expression of kinase-deficient mutants of p210 bcr-abl or Src, and treatment with the Abl kinase inhibitor STI571 prevents downregulation of Dok-1 in p210 bcr-abl -expressing cells. Given that Dok-1 is a substrate of both p210 bcr-abl and Src (6,13,77,80,84), a plausible scenario is that tyrosine phosphorylation of Dok-1 by these kinases creates a signal that is recognized by components of the ubiquitination machinery. PTK-elicited phosphorylation events have previously been shown to trigger protein degradation (35,47,96).…”

Studying post-translational modifications with protein interaction networks

“…Many studies have tackled interactomes of disease relevant single kinases such as BCR-ABL [32,33] or LRRK2 [34]. Providing a more global context for kinase function, two recent studies by Varjosalo et al presented proteomic analysis of complexes of a large number of human CMGC kinases [35 ] and of selected kinases from other major families [6].…”

From Hen House to Bedside: Tracing Hanafusa's Legacy from Avian Leukemia Viruses to SRC to ABL and Beyond

“…Adaptor molecules such as Grb2/Gab2/Shc, Dok1/ Dok2, and CrkI complexes orchestrate the activation of key signaling nodes. 57,58 Hanafusa's laboratory contributed many critical observations to this enormous compendium of data, such as elucidating the role of v-crk in activating the PI3K/ Akt signaling pathway. 59,60 CrkI was initially considered dispensable for lymphoid ABL transformation but proved in recent studies to be required for myeloid leukemia.…”