Bayesian Network Inference Modeling Identifies TRIB1 as a Novel Regulator of Cell-Cycle Progression and Survival in Cancer Cells.

Molecular networks governing responses to targeted therapies in cancer cells are complex dynamic systems that demonstrate nonintuitive behaviors. We applied a novel computational strategy to infer probabilistic causal relationships between network components based on gene expression. We constructed a model comprised of an ensemble of networks using multidimensional data from cell line models of cell-cycle arrest caused by inhibition of MEK1/2. Through simulation of a reverse-engineered Bayesian network model, we generated predictions of G1-S transition. The model identified known components of the cell-cycle machinery, such as CCND1, CCNE2, and CDC25A, as well as revealed novel regulators of G1-S transition, IER2, TRIB1, TRIM27. Experimental validation of model predictions confirmed 10 of 12 predicted genes to have a role in G1-S progression. Further analysis showed that TRIB1 regulated the cyclin D1 promoter via NFκB and AP-1 sites and sensitized cells to TRAIL-induced apoptosis. In clinical specimens of breast cancer, TRIB1 levels correlated with expression of NFκB and its target genes (IL8, CSF2), and TRIB1 copy number and expression were predictive of clinical outcome. Together, our results establish a critical role of TRIB1 in cell cycle and survival that is mediated via the modulation of NFκB signaling. Cancer Res; 77(7); 1575-85. ©2017 AACR.

[1]  Laura M. Heiser,et al.  Basal subtype and MAPK/ERK kinase (MEK)-phosphoinositide 3-kinase feedback signaling determine susceptibility of breast cancer cells to MEK inhibition. , 2009, Cancer research.

[2]  Jian Jin,et al.  Dynamic Reprogramming of the Kinome in Response to Targeted MEK Inhibition in Triple-Negative Breast Cancer , 2012, Cell.

[3]  W. Greene,et al.  p53 induces NF-kappaB activation by an IkappaB kinase-independent mechanism involving phosphorylation of p65 by ribosomal S6 kinase 1. , 2004, The Journal of biological chemistry.

[4]  Mark J. Smyth,et al.  The TRAIL apoptotic pathway in cancer onset, progression and therapy , 2008, Nature Reviews Cancer.

[5]  D. Crossman,et al.  Human Tribbles-1 Controls Proliferation and Chemotaxis of Smooth Muscle Cells via MAPK Signaling Pathways* , 2007, Journal of Biological Chemistry.

[6]  Y. Hosokawa,et al.  Mechanism of cyclin D1 (CCND1, PRAD1) overexpression in human cancer cells: Analysis of allele‐specific expression , 1998, Genes, chromosomes & cancer.

[7]  B. Aggarwal,et al.  NF-κB and cancer: how intimate is this relationship , 2010, Molecular and Cellular Biochemistry.

[8]  H Nojima,et al.  Cdc25A is a novel phosphatase functioning early in the cell cycle. , 1994, The EMBO journal.

[9]  D. Spandidos,et al.  Chemotherapeutic drugs sensitize cancer cells to TRAIL-mediated apoptosis: up-regulation of DR5 and inhibition of Yin Yang 1 , 2007, Molecular Cancer Therapeutics.

[10]  R. Assoian,et al.  Transcriptional regulation of the cyclin D1 gene at a glance , 2008, Journal of Cell Science.

[11]  P. Kaldis,et al.  Cdc2–cyclin E complexes regulate the G1/S phase transition , 2005, Nature Cell Biology.

[12]  M. Ermonval,et al.  Glycosylation-related genes are variably expressed depending on the differentiation state of a bioaminergic neuronal cell line: implication for the cellular prion protein , 2009, Glycoconjugate Journal.

[13]  N. Navaratnam,et al.  Regulation of ploidy and senescence by the AMPK‐related kinase NUAK1 , 2010, The EMBO journal.

[14]  Kevin A Janes,et al.  A biological approach to computational models of proteomic networks. , 2006, Current opinion in chemical biology.

[15]  K. Sachs,et al.  Causal Protein-Signaling Networks Derived from Multiparameter Single-Cell Data , 2005, Science.

[16]  L. Tierney,et al.  Accurate Approximations for Posterior Moments and Marginal Densities , 1986 .

[17]  S. Ghosh,et al.  The NF-kappaB family of transcription factors and its regulation. , 2009, Cold Spring Harbor perspectives in biology.

[18]  F. Markowetz,et al.  The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups , 2012, Nature.

[19]  Nir Friedman,et al.  Being Bayesian About Network Structure. A Bayesian Approach to Structure Discovery in Bayesian Networks , 2004, Machine Learning.

[20]  Juan Mata,et al.  Tribbles Coordinates Mitosis and Morphogenesis in Drosophila by Regulating String/CDC25 Proteolysis , 2000, Cell.

[21]  A. Blackburn,et al.  Abstract 3228: Dichloroacetate reverses the Warburg effect, inhibiting growth and sensitizing breast cancer cells towards apoptosis , 2012 .

[22]  M. Barbacid,et al.  Limited overlapping roles of P15INK4b and P18INK4c cell cycle inhibitors in proliferation and tumorigenesis , 2000, The EMBO journal.

[23]  Anja Schindler,et al.  A Direct Phenotypic Comparison of siRNA Pools and Multiple Individual Duplexes in a Functional Assay , 2009, PloS one.

[24]  M. Leptin,et al.  Tribbles, a cell-cycle brake that coordinates proliferation and morphogenesis during Drosophila gastrulation , 2000, Current Biology.

[25]  H. Ford,et al.  On the TRAIL to successful cancer therapy? Predicting and counteracting resistance against TRAIL-based therapeutics , 2013, Oncogene.

[26]  L. Pfeffer,et al.  NF-κB activation by tumour necrosis factor requires the Akt serine–threonine kinase , 1999, Nature.

[27]  S. Akira,et al.  Critical role of Trib1 in differentiation of tissue-resident M2-like macrophages , 2013, Nature.

[28]  Jeffrey L. Wrana,et al.  High throughput kinase inhibitor screens reveal TRB3 and MAPK-ERK/TGFβ pathways as fundamental Notch regulators in breast cancer , 2013, Proceedings of the National Academy of Sciences.

[29]  G. Sethi,et al.  Targeting transcription factor NF-kappaB to overcome chemoresistance and radioresistance in cancer therapy. , 2010, Biochimica et biophysica acta.

[30]  S. Blacklow,et al.  Differential ability of Tribbles family members to promote degradation of C/EBPalpha and induce acute myelogenous leukemia. , 2010, Blood.

[31]  Holger Fröhlich,et al.  Large scale statistical inference of signaling pathways from RNAi and microarray data , 2007, BMC Bioinformatics.

[32]  M. Pagano,et al.  Cyclin D1 is a nuclear protein required for cell cycle progression in G1. , 1993, Genes & development.

[33]  Wen-Lin Kuo,et al.  A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. , 2006, Cancer cell.

[34]  A. Thiel,et al.  The IκB Kinase Complex and NF-κB Actas Master Regulators of Lipopolysaccharide-Induced Gene Expressionand Control Subordinate Activation ofAP-1 , 2004, Molecular and Cellular Biology.

[35]  P. Krammer,et al.  Death receptors in chemotherapy and cancer , 2004, Oncogene.

[36]  Andrew D. Chisholm,et al.  Distinct Innate Immune Responses to Infection and Wounding in the C. elegans Epidermis , 2008, Current Biology.

[37]  P. LoRusso,et al.  Clinical experience of MEK inhibitors in cancer therapy. , 2007, Biochimica et biophysica acta.

[38]  J. Pouysségur,et al.  ERK implication in cell cycle regulation. , 2007, Biochimica et biophysica acta.

[39]  Michal Linial,et al.  Using Bayesian Networks to Analyze Expression Data , 2000, J. Comput. Biol..

[40]  Erik Willems,et al.  Standardization of real-time PCR gene expression data from independent biological replicates. , 2008, Analytical biochemistry.

[41]  E. Kiss-Toth,et al.  Regulation of expression and signalling modulator function of mammalian tribbles is cell-type specific. , 2006, Immunology letters.

[42]  Alan R. Saltiel,et al.  Blockade of the MAP kinase pathway suppresses growth of colon tumors in vivo , 1999, Nature Medicine.

[43]  D. Stacey.  Cyclin D1 serves as a cell cycle regulatory switch in actively proliferating cells. , 2003, Current opinion in cell biology.

[44]  S. Akira,et al.  Control of Adipose Tissue Inflammation Through TRB1 , 2010, Diabetes.

[45]  A. Thiel,et al.  The IkappaB kinase complex and NF-kappaB act as master regulators of lipopolysaccharide-induced gene expression and control subordinate activation of AP-1. , 2004, Molecular and cellular biology.

[46]  A. Adjei,et al.  Advances in Targeting the Ras/Raf/MEK/Erk Mitogen-Activated Protein Kinase Cascade with MEK Inhibitors for Cancer Therapy , 2008, Clinical Cancer Research.

[47]  W. Greene,et al.  p53 Induces NF-κB Activation by an IκB Kinase-independent Mechanism Involving Phosphorylation of p65 by Ribosomal S6 Kinase 1* , 2004, Journal of Biological Chemistry.

[48]  B. Bonavida,et al.  Mcl-1 and YY1 inhibition and induction of DR5 by the BH3-mimetic Obatoclax (GX15-070) contribute in the sensitization of B-NHL cells to TRAIL apoptosis , 2011, Cell cycle.

[49]  S. Dower,et al.  Human Tribbles, a Protein Family Controlling Mitogen-activated Protein Kinase Cascades* , 2004, Journal of Biological Chemistry.

[50]  Claus Scheidereit,et al.  NF-κB Function in Growth Control: Regulation of Cyclin D1 Expression and G0/G1-to-S-Phase Transition , 1999, Molecular and Cellular Biology.

[51]  F. McCormick,et al.  Beta-catenin regulates expression of cyclin D1 in colon carcinoma cells. , 1999, Nature.

[52]  Tanya Cashorali,et al.  Causal Modeling Using Network Ensemble Simulations of Genetic and Gene Expression Data Predicts Genes Involved in Rheumatoid Arthritis , 2011, PLoS Comput. Biol..

[53]  C. Lawrence,et al.  A statistical sampling algorithm for RNA secondary structure prediction. , 2003, Nucleic acids research.

[54]  M. McMahon,et al.  Pharmacologic inhibition of RAF-->MEK-->ERK signaling elicits pancreatic cancer cell cycle arrest through induced expression of p27Kip1. , 2005, Cancer research.

[55]  J. Baldassare,et al.  Sustained activation of extracellular-signal-regulated kinase 1 (ERK1) is required for the continued expression of cyclin D1 in G1 phase. , 1997, The Biochemical journal.

[56]  Terence P. Speed,et al.  Bayesian Inference of Signaling Network Topology in a Cancer Cell Line , 2012, Bioinform..

[57]  Carlotta Costa,et al.  MEK inhibition leads to PI3K/AKT activation by relieving a negative feedback on ERBB receptors. , 2012, Cancer research.