Stem Cell Systems Biology

What makes a cell become a neuron or macrophage or cardiomyocyte? Each one of a human's 100 trillion cells has a developmental story to tell. This story originates in the zygote, passes through the pluripotent embryonic stem cells and proceeds down a differentiation path that ends in one of the more than 200 cell types that form our body.

At the phenotypic level, stem cells are defined by two unique properties: their self renewal property, i.e., their ability to divide indefinitely to create more stem cells, and their potency, i.e., their ability to differentiate into any number of cell types. In order to understand what combination of extracellular cues and intracellular changes determine the differentiation pathways from stem cells to terminally differentiated cells, scientists are attempting to map the wiring diagram of the stem cell's regulatory circuit. Recent, fascinating work has started to crack some of these circuits. It appears that human embryonic stem cells are defined, at the intracellular level, by the activation of several transcription factors that form the core regulatory network that ensures the maintenance of pluripotency and the suppression of genes that lead to differentiation.

The signals that lead to a reprogramming of cells to an embryonic-like state are also being intensely investigated. It has been recently shown that the four transcription factors (OCT4, SOX2, NANOG, and LIN28) are sufficient to reprogram human somatic cells to pluripotent embryonic stem cells. Such induced pluripotent human cell lines have obvious applications in medicine, once technical limitations are eliminated.

To unravel the molecular circuits that will eventually lead to a deep understanding of cellular development and the manipulation of differentiated cells into pluripotent cells, it is necessary to integrate genomics, proteomics, gene expression profiling, SNP genotyping, DNA methylation and other high information content approaches. In this meeting, three leading stem cell researchers will discuss how the tools of systems biology can be used to create cellular models to guide our exploration of the biological complexity in the processes of development.

Organizer: Gustavo Stolovitzky, IBM Research

Speakers: Ihor Lemischka, Mount Sinai School of Medicine; Jeanne Loring, The Scripps Research Institute; Raju Chaganti, Memorial Sloan-Kettering Cancer Center

Abstracts

The Secret Lives of Stem Cells: Unraveling the Molecular Basis of Pluripotence
Jeanne Loring, The Scripps Research Institute

Human pluripotent stem cells possess a unique combination of two qualities: self-renewal and the ability to differentiate into virtually any cell type. Pluripotence is a characteristic of cells derived from blastocyst-stage embryos and germ cell tumors, and, remarkably, the pluripotent state can be induced in cultured adult cells by a relatively simple genetic engineering process. We are learning about the extraordinary abilities of these cells by looking for common features among pluripotent cell types, using high-throughput molecular tools to globally map expression of genes and regulatory noncoding RNAs, profiles of DNA methylation, and copy-number variations that arise in culture. Every kind of analysis confirms that pluripotent cells are unlike any other cell type ever studied, and we propose that our systems biology approach will help us understand how stem cells maintain pluripotence and choose their pathways of differentiation.

Analysis of Stem Cell and Differentiation-Specific Transcription Factor Networks in Germ Cell Tumors and Embryonic Stem Cells Using Systems Biology Approaches
Raju Chaganti, Memorial Sloan-Kettering Cancer Center

Human male germ cell tumors (GCTs), derived from germ cells, are pluripotent and display embryonic and extraembryonic lineage differentiation. The subset embryonal carcinoma (EC) is considered to be analogous to embryonic stem cells (ES) in terms of pluripotency and ability to differentiate in vivo as well as in vitro, the latter in response to morphogens such as all-trans retinoic acid (ATRA) and bone morphogenetic protein 2 (BMP2). We have performed gene expression profiling (GEP) of over 140 GCT biopsies and in vitro differentiation of EC cells into neuronal, epidermal, and endodermal lineages using Affymetrix U133 arrays. These GEP data were analyzed using ARACNe and Master Regulator Analysis (MRA) algorithms to identify transcription factor networks involved in regulation of pluripotency and lineage differentiation. The GEP data from the tumor cohort allowed the generation of a GCT interactome comprising over 1000 transcription factor nodes representing the multiple developmental lineages present in the tumor samples. A combined analysis of the interactome and in vitro differentiation GEP data by MRA allowed the identification of novel master regulatory transcription factors. Targets of multiple transcription factors, including the core transcription factors that regulate pluripotency, OCT4, SOX2, and NANOG, were identified for validation. The systems biology approach provides powerful methods to analyze pluripotency and differentiation.