Our lab studies the mechanism of cell fate restriction. The approaches we take fall at the interface of several disciplines, including developmental biology, stem cell biology and epigenetics. Below is a brief summary of our work.
The hallmark of multicellular life is the presence of diverse cell types within a single organism, all bearing the same genome but disparate gene expression patterns. In mammals, as in many other taxa, this is accomplished via the progressive differentiation of pluripotent stem cells into a variety of specialized cell types. During this process, cells lose their potential for all but the lineage to which they have become committed. A longstanding but unresolved question in biology is: how is cell fate restricted during somatic differentiation? Furthermore, how is this restriction reversed during reproduction to reestablish pluripotency at the onset of development? Based on emerging data from the literature and our lab, we developed a conceptually simple model, dubbed the “gene occlusion” model, to account for cell fate restriction during somatic development and its reversal during reproduction.
The model makes three assertions: (1) A gene’s transcriptional potential can assume either the competent state wherein the gene is responsive to, and can be activated by, trans-acting factors in the cellular milieu, or the occluded state wherein the gene is blocked by cis-acting, chromatin-based mechanisms from responding to trans factors such that it remains silent irrespective of the presence of transcriptional activators. (2) As somatic differentiation proceeds, lineage-inappropriate genes shift progressively and irreversibly from competent to occluded state, thus restricting cell fate. (3) During reproduction, global deocclusion occurs in the germline and/or early zygotic cells to reset the genome to the competent state.
Monoallelic silencing such as X inactivation and imprinting is a clear example of occlusion. Here, the inactive state of the silent alleles can be causally attributed to cis (as opposed to trans) mechanisms given the presence of corresponding active alleles within the same trans environment of the cell. It was unclear, however, whether there are also many genes for which both alleles are occluded. We showed this to be the case using a cell fusion assay. Specifically, we fused two cell types and searched for genes with silent copies in one fusion partner but active copies in the other partner. The active copies served as a positive control for the presence of a transcriptionally supportive milieu, much like the active alleles of monoallelically silenced genes. With this control, the silent copies are identified as being occluded.
In the last few years, our lab has accumulated a substantial body of evidence supporting key predictions of the gene occlusion model in mammalian systems. We showed that occlusion is a prevalent phenomenon affecting a large number of genes in a variety of somatic cell types, including both terminally differentiated cells and somatic stem cells. We found that occluded genes in a given cell type include many master regulators of alternative lineages. We established a mechanistic link between DNA methylation and the maintenance of occlusion for at least some occluded genes, and showed that a variety of well-studied chromatin marks are likely not involved in occlusion. We uncovered functional evidence for a critical requirement of occlusion in cell fate restriction. Finally, we showed that embryonic stem cells are fundamentally distinct from somatic cells in that they have the capacity for genome-wide deocclusion. Collectively, these data establish the gene occlusion model as a simple and coherent conceptual framework for studying how the restriction of cell fate is brought about during development, erased during reproduction, and possibly subverted in disease.
Currently, we are continuing to study several aspects of the gene occlusion model. First, we are investigating the biochemical mechanism underlying the maintenance of occlusion in somatic cells. Second, we are probing the mechanism by which de novo occlusion is established during differentiation. Third, we are exploring the implications of gene occlusion in a variety of biological processes including stem cell differentiation, induction of iPS cells, cancer and aging.
Hydroxymethylation at gene regulatory regions directs stem/early progenitor cell commitment during erythropoiesis.
Madzo J, Liu H, Rodriguez A, Vasanthakumar A, Sundaravel S, Caces DBD, Looney TJ, Zhang L, Lepore JB, Macrae T, Duszynski R, Shih AH, Song CX, Yu M, Yu Y, Grossman R, Raumann B, Verma A, He C, Levine RL, Lavelle D, Lahn BT, Wickrema A, Godley LA. Hydroxymethylation at gene regulatory regions directs stem/early progenitor cell commitment during erythropoiesis. Cell Rep. 2014 Jan 16; 6(1):231-244.
Transcriptional Fingerprint of Hypomyelination in Zfp191null and Shiverer (Mbpshi) Mice.
Aaker JD, Elbaz B, Wu Y, Looney TJ, Zhang L, Lahn BT, Popko B. Transcriptional Fingerprint of Hypomyelination in Zfp191null and Shiverer (Mbpshi) Mice. ASN Neuro. 2016 Oct; 8(5).
TALEN-based generation of a cynomolgus monkey disease model for human microcephaly.
Ke Q, Li W, Lai X, Chen H, Huang L, Kang Z, Li K, Ren J, Lin X, Zheng H, Huang W, Ma Y, Xu D, Chen Z, Song X, Lin X, Zhuang M, Wang T, Zhuang F, Xi J, Mao FF, Xia H, Lahn BT, Zhou Q, Yang S, Xiang AP. TALEN-based generation of a cynomolgus monkey disease model for human microcephaly. Cell Res. 2016 09; 26(9):1048-61.
Distribution of the cytoskeletal protein, Nestin, in acute leukemia.
Du X, Yang XH, Wu YF, Liang J, Zhang J, Huang ZC, Zhu ZP, Lin W, Zou MX, Wen JY, Wu SJ, Guo R, Zhang XM, Lahn BT, He F, Xiang AP. Distribution of the cytoskeletal protein, Nestin, in acute leukemia. Biotech Histochem. 2015 Jul; 90(5):384-94.
Nestin(+) kidney resident mesenchymal stem cells for the treatment of acute kidney ischemia injury.
Jiang MH, Li G, Liu J, Liu L, Wu B, Huang W, He W, Deng C, Wang D, Li C, Lahn BT, Shi C, Xiang AP. Nestin(+) kidney resident mesenchymal stem cells for the treatment of acute kidney ischemia injury. Biomaterials. 2015 May; 50:56-66.
Characterization of Nestin-positive stem Leydig cells as a potential source for the treatment of testicular Leydig cell dysfunction.
Jiang MH, Cai B, Tuo Y, Wang J, Zang ZJ, Tu X, Gao Y, Su Z, Li W, Li G, Zhang M, Jiao J, Wan Z, Deng C, Lahn BT, Xiang AP. Characterization of Nestin-positive stem Leydig cells as a potential source for the treatment of testicular Leydig cell dysfunction. Cell Res. 2014 Dec; 24(12):1466-85.
Involvement of extracellular factors in maintaining self-renewal of neural stem cell by nestin.
Di CG, Xiang AP, Jia L, Liu JF, Lahn BT, Ma BF. Involvement of extracellular factors in maintaining self-renewal of neural stem cell by nestin. Neuroreport. 2014 Jul 09; 25(10):782-7.
Systematic mapping of occluded genes by cell fusion reveals prevalence and stability of cis-mediated silencing in somatic cells.
Looney TJ, Zhang L, Chen CH, Lee JH, Chari S, Mao FF, Pelizzola M, Zhang L, Lister R, Baker SW, Fernandes CJ, Gaetz J, Foshay KM, Clift KL, Zhang Z, Li WQ, Vallender EJ, Wagner U, Qin JY, Michelini KJ, Bugarija B, Park D, Aryee E, Stricker T, Zhou J, White KP, Ren B, Schroth GP, Ecker JR, Xiang AP, Lahn BT. Systematic mapping of occluded genes by cell fusion reveals prevalence and stability of cis-mediated silencing in somatic cells. Genome Res. 2014 Feb; 24(2):267-80.
Suicide gene-mediated ablation of tumor-initiating mouse pluripotent stem cells.
Chen F, Cai B, Gao Y, Yuan X, Cheng F, Wang T, Jiang M, Zhou Y, Lahn BT, Li W, Xiang AP. Suicide gene-mediated ablation of tumor-initiating mouse pluripotent stem cells. Biomaterials. 2013 Feb; 34(6):1701-11.
Truncated DNMT3B isoform DNMT3B7 suppresses growth, induces differentiation, and alters DNA methylation in human neuroblastoma.
Ostler KR, Yang Q, Looney TJ, Zhang L, Vasanthakumar A, Tian Y, Kocherginsky M, Raimondi SL, DeMaio JG, Salwen HR, Gu S, Chlenski A, Naranjo A, Gill A, Peddinti R, Lahn BT, Cohn SL, Godley LA. Truncated DNMT3B isoform DNMT3B7 suppresses growth, induces differentiation, and alters DNA methylation in human neuroblastoma. Cancer Res. 2012 Sep 15; 72(18):4714-23.