An Effective Model of the Retinoic Acid Induced HL-60 Differentiation Program

Ryan Tasseff,Johanna Congleton,Rodica P Bunaciu,Jeffrey D Varner,David Dai,Adithya Sagar,Andrew Yen,Holly A Jensen,Katharine V Rogers

doi:10.1038/s41598-017-14523-5

Abstract

In this study, we present an effective model All-Trans Retinoic Acid (ATRA)-induced differentiation of HL-60 cells. The model describes reinforcing feedback between an ATRA-inducible signalsome complex involving many proteins including Vav1, a guanine nucleotide exchange factor, and the activation of the mitogen activated protein kinase (MAPK) cascade. We decomposed the effective model into three modules; a signal initiation module that sensed and transformed an ATRA signal into program activation signals; a signal integration module that controlled the expression of upstream transcription factors; and a phenotype module which encoded the expression of functional differentiation markers from the ATRA-inducible transcription factors. We identified an ensemble of effective model parameters using measurements taken from ATRA-induced HL-60 cells. Using these parameters, model analysis predicted that MAPK activation was bistable as a function of ATRA exposure. Conformational experiments supported ATRA-induced bistability. Additionally, the model captured intermediate and phenotypic gene expression data. Knockout analysis suggested Gfi-1 and PPARg were critical to the ATRAinduced differentiation program. These findings, combined with other literature evidence, suggested that reinforcing feedback is central to hyperactive signaling in a diversity of cell fate programs.

Highlights

Sustained mitogen-activated protein kinase (MAPK) pathway activation is a defining feature of All-Trans Retinoic Acid (ATRA)-induced HL-60 differentiation
We constructed an effective model of ATRA-induced HL-60 differentiation which described signaling and gene expression events following the addition of ATRA (Fig. 1)
We decomposed the ATRA program into three modules; a signal initiation module that sensed and transformed the ATRA signal into activated cRaf-pS621 and the ATRA-retinoic acid receptor (RAR)/retinoid X receptor (RXR) (Trigger) signals (Fig. 1A); a signal integration module that controlled the expression of upstream transcription factors given cRaf-pS621 and activated Trigger signals (Fig. 1B); and a phenotype module which encoded the expression of functional differentiation markers from the ATRA-inducible transcription factors (Fig. 1C)

Summary

Introduction

Sustained mitogen-activated protein kinase (MAPK) pathway activation is a defining feature of ATRA-induced HL-60 differentiation. A previous computational study of ATRA-induced differentiation of HL-60 cells suggested that the BLR1-MAPK positive feedback circuit was sufficient to explain ATRA-induced sustained MAPK activation, and the expression of a limited number of functional differentiation markers[27]. Model analysis suggested that Raf was the most distinct of the MAPK proteins This previous study developed and analyzed a complex model, leaving open the critical question of what is the minimal positive feedback circuit required to drive ATRA-induced differentiation. We showed through immunoprecipitation and inhibitor studies, that the guanine nucleotide exchange factor Vav[1] is potentially a new ATRA-inducible member of the signalsome complex functioning as a regulator that contributes to signal amplification in the signalsome Taken together, these findings when combined with other literature evidence, suggested that reinforcing feedback was central to differentiation programs generally, and necessary for ATRA-induced differentiation. The model answers a biologically important question that is not experimentally attacked, namely given the complexity of the signaling machine and the pathways it embodies, is there a critical small suite of molecules that are the action elements seminal to eliciting ATRA-induced cell differentiation and G0 arrest

Methods

Results

Conclusion