Research Papers:

Constructing Bayesian networks by integrating gene expression and copy number data identifies NLGN4Y as a novel regulator of prostate cancer progression

Yixuan Gong, Li Wang, Uma Chippada-Venkata, Xudong Dai, William K. Oh and Jun Zhu _

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Oncotarget. 2016; 7:68688-68707. https://doi.org/10.18632/oncotarget.11925

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Yixuan Gong1,*, Li Wang2,3,*, Uma Chippada-Venkata1, Xudong Dai2,3, William K. Oh1, Jun Zhu1,2,3

1The Tisch Cancer Institute, Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA

2Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA

3Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA

*These authors have contributed equally to this work

Correspondence to:

Jun Zhu, email: [email protected]

William K. Oh, email: [email protected]

Keywords: Bayesian networks, NLGN4Y, prostate cancer, negative regulator, gene expression

Received: April 15, 2016     Accepted: August 24, 2016     Published: September 10, 2016


To understand the heterogeneity of prostate cancer (PCa) and identify novel underlying drivers, we constructed integrative molecular Bayesian networks (IMBNs) for PCa by integrating gene expression and copy number alteration data from published datasets. After demonstrating such IMBNs with superior network accuracy, we identified multiple sub-networks within IMBNs related to biochemical recurrence (BCR) of PCa and inferred the corresponding key drivers. The key drivers regulated a set of common effectors including genes preferentially expressed in neuronal cells. NLGN4Y—a protein involved in synaptic adhesion in neurons—was ranked as the top gene closely linked to key drivers of myogenesis subnetworks. Lower expression of NLGN4Y was associated with higher grade PCa and an increased risk of BCR. We show that restoration of the protein expression of NLGN4Y in PC-3 cells leads to decreased cell proliferation, migration and inflammatory cytokine expression. Our results suggest that NLGN4Y is an important negative regulator in prostate cancer progression. More importantly, it highlights the value of IMBNs in generating biologically and clinically relevant hypotheses about prostate cancer that can be validated by independent studies.

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