Sohyoung Kim

The Systems Biology Graphical Notation

Circuit diagrams and Unified Modeling Language diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity, removing ambiguity and enabling software tool support for communication of complex information. Ironically, despite having one of the highest ratios of graphical to textual information, biology still lacks standard graphical notations. The recent deluge of biological knowledge makes addressing this deficit a pressing concern. Toward this goal, we present the Systems Biology Graphical Notation (SBGN), a visual language developed by a community of biochemists, modelers and computer scientists. SBGN consists of three complementary languages: process diagram, entity relationship diagram and activity flow diagram. Together they enable scientists to represent networks of biochemical interactions in a standard, unambiguous way. We believe that SBGN will foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling.

Depicting combinatorial complexity with the molecular interaction map notation

To help us understand how bioregulatory networks operate, we need a standard notation for diagrams analogous to electronic circuit diagrams. Such diagrams must surmount the difficulties posed by complex patterns of protein modifications and multiprotein complexes. To meet that challenge, we have designed the molecular interaction map (MIM) notation (http://discover.nci.nih.gov/mim/). Here we show the advantages of the MIM notation for three important types of diagrams: (1) explicit diagrams that define specific pathway models for computer simulation; (2) heuristic maps that organize the available information about molecular interactions and encompass the possible processes or pathways; and (3) diagrams of combinatorially complex models. We focus on signaling from the epidermal growth factor receptor family (EGFR, ErbB), a network that reflects the major challenges of representing in a compact manner the combinatorial complexity of multimolecular complexes. By comparing MIMs with other diagrams of this network that have recently been published, we show the utility of the MIM notation. These comparisons may help cell and systems biologists adopt a graphical language that is unambiguous and generally understood.

Predicted Functions of MdmX in Fine-Tuning the Response of p53 to DNA Damage

Tumor suppressor protein p53 is regulated by two structurally homologous proteins, Mdm2 and MdmX. In contrast to Mdm2, MdmX lacks ubiquitin ligase activity. Although the essential interactions of MdmX are known, it is not clear how they function to regulate p53. The regulation of tumor suppressor p53 by Mdm2 and MdmX in response to DNA damage was investigated by mathematical modeling of a simplified network. The simplified network model was derived from a detailed molecular interaction map (MIM) that exhibited four coherent DNA damage response pathways. The results suggest that MdmX may amplify or stabilize DNA damage-induced p53 responses via non-enzymatic interactions. Transient effects of MdmX are mediated by reservoirs of p53∶MdmX and Mdm2∶MdmX heterodimers, with MdmX buffering the concentrations of p53 and/or Mdm2. A survey of kinetic parameter space disclosed regions of switch-like behavior stemming from such reservoir-based transients. During an early response to DNA damage, MdmX positively or negatively regulated p53 activity, depending on the level of Mdm2; this led to amplification of p53 activity and switch-like response. During a late response to DNA damage, MdmX could dampen oscillations of p53 activity. A possible role of MdmX may be to dampen such oscillations that otherwise could produce erratic cell behavior. Our study suggests how MdmX may participate in the response of p53 to DNA damage either by increasing dependency of p53 on Mdm2 or by dampening oscillations of p53 activity and presents a model for experimental investigation.

Abstract 4782: Genome-wide chromatin profiling in bladder and prostate cancers

Mutations in a few driver genes can cause cancer, and a main goal of cancer genome analysis has been the identification of these cancer genes. Recent findings, however, indicate that deregulation of enhancers can play a major role in carcinogenesis. In this study, we aim to understand how enhancer networks evolve during cancer initiation and progression and to identify epigenetic states that are predictive of cancer stage and drug response. We surveyed 15 bladder cell lines, including the T24 lineage (T24, T24T, FL, and SL) and the UMUC3 lineage (UMUC3 and LUL2), and 10 prostate cancer cell lines including BPH1, DU145 and LNCap. These cell lines display different tumorigenic and metastatic potentials, and thus present a model for cancer progression and development of castration-resistance. DNase-seq was performed to map genome-wide regulatory profiles in these cells. The enhancers detected as DNase I hypersensitivity sites (DHSs) showed large-scale changes in the chromatin accessibility landscape during the acquisition of tumorigenic and metastatic phenotypes. Selective sets of gained or lost DHSs were identified. Among the changes during the T24 to T24T transition, the loss of DHSs was remarkable. Some of these DHSs were found near genes that are in the downstream response to HDACs. Induction of expression by the HDAC inhibitor, Na butyrate, was correlated with DNase-seq signal for these genes. Gene Ontology (GO) enrichment analysis also indentified a set of genes neighboring lost DHSs that belong to the focal adhesion class in GO category. This study identified a set of DHSs that were associated with cancer progression in bladder and prostate cancer, and the potential clinical application of the identified DHSs will be discussed. Citation Format: Sohyoung Kim, Lyuba Varticovski, Qizong Lao, Songjoon Baek, Myong-Hee Sung, Lars Grontved, Michael L. Nickerson, Bethtrice Thompson, Dan Theodorescu, Michael Dean, Gordon H. Hager. Genome-wide chromatin profiling in bladder and prostate cancers. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4782. doi:10.1158/1538-7445.AM2015-4782

Abstract 4783: Novel molecular markers of bladder cancer progression identified by global chromatin profiling

Bladder cancer (BCa) is the 5th most prevalent cancer in the US, and the metastatic disease has very poor prognosis with 150,000 deaths per year worldwide. The use of molecular markers to predict disease progression has been largely unsuccessful, with only few therapeutically approachable mutations. Over 2,300 alterations in the coding sequences have been described in high-grade bladder cancer, encompassing frequent alterations in genes involving chromatin modifiers. Thus, chromatin organization may play a critical role in this tumor type. The development of tumor progression models from transitional carcinoma samples that are poorly tumorigenic and non-metastatic to highly metastatic to the lung or liver by serial in vivo passaging allows analysis of the mechanisms associated with tumor progression. We examined whole exome sequencing to identify mutations, gene expression, and DNase I hypersensitivity followed by deep sequencing to identify sites of chromatin modification during tumor progression. Bioinformatic analysis of was performed using algorithms developed at LRBGE. Comparative analysis combining multiple data sets was performed using Ingenuity Pathways. Mutations in several previously identified genes associated with bladder cancer: TP53, RAS and TERT, and mutations/deletions in several chromatin modifiers KDM6A and MLL2/3 were found in parental cells. Only few additional mutations, none identifiable as cancer driver mutations marked the progression to metastatic phenotype. Changes in gene expression were already evident in progression to tumorigenic state, with high score in cells in cell-to-cell interaction pathway marked by a decrease in cell adhesion, increase in genes associated with EMT and genes associated with cancer. Changes in global chromatin landscape occurred at many known genes correlated with pathways detected by expression analysis, but many were in novel sites distant to promoters, suggestive of novel distant enhancer and confirm massive reprogramming of regulatory networks. Many of these sites were unique for each stage of tumor progression and have potential clinical application. Specific chromatin modifications were found in NFkB and inflammatory pathways. Thus, in the tumorigenic stage, these cells acquired not only the capacity for tumor formation, but also some of the characteristics associated with metastasis. Combination of exome sequencing with the gene expression and unbiased analysis of global chromatin landscape provided valuable new information on bladder cancer biology and tumor progression. Citation Format: Lyuba Varticovski, Sohyoung Kim, Michael L. Nickerson, Bethtrice Thompson, Qizong Lao, Lars Grontved, Songjoon Baek, Myong-Hee Sung, Dan Theodorescu, Michael Dean, Gordon L. Hager. Novel molecular markers of bladder cancer progression identified by global chromatin profiling. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4783. doi:10.1158/1538-7445.AM2015-4783

Abstract 474: Changes in global chromatin landscape identify bladder cancer progression

Bladder cancer is the 4th most common cancer in men in the US and metastatic disease has a poor prognosis. To date, only few mutations in cancer driving genes have been identified in this tumor. Altered gene expression involving an estimate of >2,300 coding sequences is reported in high-grade bladder cancer. In addition to previously reported mutations in KRAS, FGFR3 and TPp53, recent data showed frequent deletions and mutations in genes involving several chromatin modifiers, such as UTX (KDM6A). These data indicate that chromatin organization may play an important role in bladder cancer development and progression. The process of in vivo passaging of a poorly tumorigenic bladder cells (T24) with subsequent injection into mice and selection for tumorigenic and metastatic phenotype specifically to the lung and liver, provides a unique opportunity for analysis of mechanisms associated with tumor development and progression. We compared whole exome sequencing and mRNA expression with analysis of DNase I hypersensitivity combined with deep sequencing (DHS-seq) on multiple cell lines developed by in vivo selection. Bioinformatics of DHS-seq was performed using algorithms developed at LRBGE. Analysis of microarray expression was performed using Ingenuity Pathways (IPA). Mutations in several genes, including TP53, RAS, TERT and chromatin remodeler UTX (KDM6A), were detected in parent cell line, T24. Only few additional mutations marked the progression to the metastatic phenotype. Changes in gene expression were already evident in progression from parental cells that were weakly tumorigenic (T24) to cells that were capable to form tumors in mice, but rarely formed metastasis (T24T). The highest score was assigned to genes involved in Cell-to-Cell interaction. Prominent changes included genes involved in cell adhesion and genes associated with EMT, followed by changes in genes associated with cancer. Thus, during the progression from weakly tumorigenic to fully tumorigenic but weakly metastatic cell type, bladder cancer cells acquired gene expression and chromatin landscape changes associated with tumor formation and metastasis. Gene expression profile for most genes correlated with nearby chromatin remodeling of regulatory regions. In addition, DHS analysis identified many novel areas of changes, termed “hot spots” which were located in upstream or downstream enhancer regions. Some of these changes were unique for each stage of tumor progression. Genome-wide analysis of DHS showed large-scale changes in chromatin landscape during tumorigenesis indicating massive reprogramming of regulatory networks during cancer development and progression. Thus, combination of exome sequencing with microarray gene expression and analysis of global unbiased chromatin landscape provides valuable new information on bladder cancer biology and tumor progression. Citation Format: Sohyoung Kim, Lyuba Varticovski, Lars Grontved, Songjoon Baek, Bethrice Thompson, Michael Dean, Daniel Theodoresco, Michael L. Nickerson, Gordon L. Hager. Changes in global chromatin landscape identify bladder cancer progression. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 474. doi:10.1158/1538-7445.AM2014-474