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Systems Genetic Analysis of Osteoblast-Lineage Cells Systems Genetic Analysis of Osteoblast-Lineage Cells Gina Calabrese1, Brian J. Bennett2, Luz Orozco3, Hyun M. Kang4, Eleazar Eskin5, Carlos Dombret6, Olivier De Backer6, Aldons J. Lusis3,7,8, Charles R. Farber1,9,10* 1 Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America, 2 Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America, 3 Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America, 4 Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, United States of America, 5 Department of Computer Science, University of California Los Angeles, Los Angeles, California, United States of America, 6 Unite´ de Recherche en Physiologie Mole´culaire (URPHYM), Namur Research Institute for Life Sciences (NARILIS), FUNDP School of Medicine, University of Namur, Namur, Belgium, 7 Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America, 8 Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, California, United States of America, 9 Department of Medicine, Division of Cardiovascular Medicine, University of Virginia, Charlottesville, Virginia, United States of America, 10 Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, United States of America Abstract The osteoblast-lineage consists of cells at various stages of maturation that are essential for skeletal development, growth, and maintenance. Over the past decade, many of the signaling cascades that regulate this lineage have been elucidated; however, little is known of the networks that coordinate, modulate, and transmit these signals. Here, we identify a gene network specific to the osteoblast-lineage through the reconstruction of a bone co-expression network using microarray profiles collected on 96 Hybrid Mouse Diversity Panel (HMDP) inbred strains. Of the 21 modules that comprised the bone network, module 9 (M9) contained genes that were highly correlated with prototypical osteoblast maker genes and were more highly expressed in osteoblasts relative to other bone cells. In addition, the M9 contained many of the key genes that define the osteoblast-lineage, which together suggested that it was specific to this lineage. To use the M9 to identify novel osteoblast genes and highlight its biological relevance, we knocked-down the expression of its two most connected ‘‘hub’’ genes, Maged1 and Pard6g. Their perturbation altered both osteoblast proliferation and differentiation. Furthermore, we demonstrated the mice deficient in Maged1 had decreased bone mineral density (BMD). It was also discovered that a local expression quantitative trait locus (eQTL) regulating the Wnt signaling antagonist Sfrp1 was a key driver of the M9. We also show that the M9 is associated with BMD in the HMDP and is enriched for genes implicated in the regulation of human BMD through genome-wide association studies. In conclusion, we have identified a physiologically relevant gene network and used it to discover novel genes and regulatory mechanisms involved in the function of osteoblast-lineage cells. Our results highlight the power of harnessing natural genetic variation to generate co-expression networks that can be used to gain insight into the function of specific cell-types. Citation: Calabrese G, Bennett BJ, Orozco L, Kang HM, Eskin E, et al. (2012) Systems Genetic Analysis of Osteoblast-Lineage Cells. PLoS Genet 8(12): e1003150. doi:10.1371/journal.pgen.1003150 Editor: Takashi Gojobori, National Institute of Genetics, Japan Received May 12, 2012; Accepted October 23, 2012; Published December 27, 2012 Copyright: ß 2012 Calabrese et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: The project described was supported in part by grant number R01 AR057759 to CRF, P01 HL30568 to AJL, and P01 HL28481 AJL. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: [email protected] Introduction mineral metabolism [7] and bone resorption [8,9]. Therefore, the development of a more comprehensive understanding of the The osteoblast-lineage consists of a spectrum of cells beginning molecular networks operative in osteoblast-lineage cells will have with osteoprogenitors derived from mesenchymal stem cells that important implications not only for osteoporosis, but many other then differentiate to form mature bone-forming osteoblasts and common complex diseases. bone-lining cells. The final stage in the life-cycle of the lineage Genetic, molecular and biochemical approaches have been used occurs when a subset of mature osteoblasts become entombed in over the last decade to identify many of the key genes that are bone as mechanosensitive osteocytes [1]. As the only known bone- required for osteoblast progenitor commitment, proliferation, forming cell, osteoblasts are essential for skeletal development, differentiation and apoptosis as well as mature osteoblast and growth and maintenance [1]. In addition to their critical role in osteocyte activity [1]. An example of this has been the discovery the skeleton, osteoblast-lineage cell have been shown to be that the Wnt signaling pathway plays a central role in many important for other physiological systems. Osteoprogenitors can functional aspects of the osteoblast lineage [10]. However, these support and modulate erythropoiesis [2] and mature osteoblasts investigations have been reductionist in nature and therefore have are responsible for many of the endocrine functions of bone, not provided information on how key signaling genes interact in including the regulation of energy expenditure [3–5] and male complex cellular networks, which is critical to fully understand the fertility [6]. Furthermore, osteocytes play important roles in molecular mechanisms that underlie cellular processes and disease. PLOS Genetics | www.plosgenetics.org 1 December 2012 | Volume 8 | Issue 12 | e1003150 Osteoblast Co-Expression Network Author Summary predictive of survival in a human brain co-expression module associated with glioblastoma [23]. Recently, we demonstrated that The osteoblast-lineage consists of a range of cells from in a co-expression module associated with Bone Mineral Density osteogenic precursors that mature into bone-forming (BMD) in humans, hub genes were more likely to be genetically osteoblasts to osteocytes that are entombed in bone. associated with BMD than non-hub genes [24]. We have also Each cell in the lineage serves a number of distinct and shown that hubs within a chrondrocyte co-expression network play critical roles in the growth and maintenance of the key roles in chrondrocyte differentiation [20]. skeleton, as well as many extra-skeletal functions. Over In this study, we reconstructed a bone co-expression network the last decade, many of the major regulatory pathways using Weighted Gene Co-expression Network Analysis (WGCNA) governing the differentiation and activity of these cells and gene expression microarray profiles from femur samples have been discovered. In contrast, little is known regarding collected from 96 Hybrid Mouse Diversity Panel (HMDP) strains. the composition or function of gene networks within the The resulting network was used to identify a core module of genes lineage. The goal of this study was to increase our understanding of how genes are organized into networks (module 9; M9) specific to cells of the osteoblast-lineage. We then in osteoblasts. Towards this goal, we used microarray gene demonstrated that the top two M9 hub genes were regulators of expression profiles from bone to identify a group of genes osteoblast function and one was a regulator of BMD in vivo.In that formed a network specific to the osteoblast-lineage. addition, we showed that a local eQTL regulating the expression We used the knowledge of this network to identify novel of secreted frizzled-related protein 1 (Sfrp1), orchestrated the genes that are important for regulating various aspects of transcriptional behavior of the M9. Notably, Sfrp1 is an antagonist osteoblast function. These data improve our understand- of Wnt signaling, which is a major pro-osteoblastic signal, and Sfrp1 ing of the gene networks operative in cells of the transgenic and knockout mice display alterations in BMD and osteoblast-lineage. osteoblast functions [25,26]. We further demonstrated the physiologically relevant nature of the M9 by identifying a strong non-linear relationship between the M9 and BMD in the HMDP In many cases, the insight gained regarding how genes interact in and that the M9 is enriched for genes implicated in the regulation networks goes well beyond what can be learned about a process of human BMD through genome-wide association studies. In using only traditional approaches [11]. summary, our results begin to clarify the composition and role of Systems genetics is an emerging approach that provides a cellular networks in the osteoblast cell lineage. systems-level perspective of the role
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