Yang Lab

Reprogramming & Neurological Diseases

Research

nan yang mssm nueroscienceDr. Yang’s lab focuses on two interlocking areas of investigation:

  1. the understanding of genetic and epigenetic programs that control the development of distinct cell types
  2. the development of approaches using stem cells to advance our knowledge of the fundamental processes underlying human neural development and function.

Her research pioneered the direct cellular reprogramming from non-neuronal cells to neural lineages, which earned her a number of awards, including the Siebel Scholarship from Siebel Stem Cell Institute and the NARSAD Young Investigator award.

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Yang Laboratory
Nan Yang, PhD
Assistant Professor, Neuroscience
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Projects

Directing fate specification of human pluripotent stem cells

Overview: We have pioneered the transcription factor mediated (trans-)differentiation of non-neural human cells, including fibroblasts and pluripotent stem cells, into multiple neural lineages such as glutamatergic and GABAergic neurons, as well as oligodendrocyte progenitor cells. The ultimate goal is to be able to recreate the cellular diversity of the central nervous system.


Complex neural circuits consist of two main classes of neurons: excitatory long-range projection neurons and inhibitory interneurons that form local connections. Recent data support that perturbations in excitatory-inhibitory balance underlie multiple psychiatric conditions, such as schizophrenia, autism, and bipolar disorder. To achieve a mechanistic understanding of the contribution of individual cell types to different pathophysiological conditions, one must identify the specific cellular elements affected in each disease and understand how specific neural circuits might be altered. Thus, the generation of specific subtypes of human neurons is a critical and rate-limiting step toward the development of human cell models for neurological and neuropsychiatric disorders. Using the transcription factor mediated cell fate specification approach, we have shown that Ngn2 or Neurod1 could rapidly convert human iPS and ES cells into glutamatergic induced neuronal (iN) cells. In contrast, the proneuronal factor Ascl1 together with Dlx2 could induce the differentiation of human neurons with homogeneous GABAergic neurotransmitter specification. Currently, we are particularly interested in studying the specification of subclasses of GABAergic interneurons given that perturbation of the developmental programs utilized by specific interneuron populations can result in diseases.

Lab generated forebrain GABAergic neurons from human pluripotent stem cells labeled with the neuron-specific cytoskeletal protein Microtubule-associated protein 2 (MAP2) in green, and GABAergic neuron markers including GABA, DLX, GAD1/2, or interneuron subtype specific markers, such as Calbidin (CB), Calretinin (CR), Somatostatin (SST), and Parvalbumin (PV) in red. HuNu antibody stains the nuclei of human cells.

The genetic and epigenetic control of interneuron specifications

Overview: Cell type specific gene expression patterns arise as a consequence of the crosstalk between the genome and its signaling and cellular environment. This crosstalk is mediated by cis-regulatory elements, especially enhancers. Earlier discoveries have also attributed enhancer variation to several human diseases. We are interested in understanding how the regulatory activity encoded in enhancers is integrated with the transcriptional machinery to control the development and function of neurons.


In contrast to gene expression analysis that provides a snapshot of a neuron’s molecular activity at a single point in time, the epigenome maps reveal both the drivers of the expression program, such as transcriptional factor binding sites and enhancer marks, and downstream effects on the chromatin landscape, such as DNA methylation. Thus, the epigenomic information captures gene regulatory mechanisms, developmental origins, and potential future responses induced by neuronal activity. However, obtaining sufficient cell-type-specific DNA from tissues for epigenomic analysis is extremely challenging for complex tissues such as the brain. Luckily, induced neurons generated from human ES/iPS cells provide adequate cells for genomic and biochemical studies. We use epigenomic profiling technologies to annotate the regulatory elements in interneurons subclasses. The goal of this work is to identify transcription factors binding motifs, transcription factor regulatory networks via motif discovery, and eventually to build networks unique to different interneuron subtypes.

Given the importance of regulatory elements during development, the disruption of these sequences is likely to carry phenotypic consequences. It has been estimated that 40% of loci uncovered by GWASs are restricted to non-coding sequences, which points to a potential role for regulatory variation in common disease predisposition. Given that enhancers impact gene expression in a cell type-dependent manner, our work in mapping regulatory elements in interneurons provides the foundation to study how regulatory variants associated with neurological and neuropsychiatric disorders influence risk.

epigenomic landscapes human neurons

Modeling human diseases using pluripotent stem cells

Overview: The potential of human pluripotent stem cells in disease modeling is widely appreciated. We have a long-standing interest in using iPS and ES cells for modeling human disorders of the brain.


Recent genomic studies have identified many genomic variants associated with neurological and neuropsychiatric diseases. While genomic data provide significant correlations of genotype to phenotype, functional data supporting these correlations remain poor due to the lack of patient brain material and the tools to unequivocally identify the disease-relevant molecular phenotypes. The new advances in pluripotent stem cell biology and epigenetic reprogramming provide an important breakthrough as they allow the genetic modification and functional evaluation of human neurons. We study the function of disease-related mutations by generating human iPS cell lines with targeted mutagenesis using CRISPR/Cas9 system and/or AAV mediated homologous recombination. Human neurons are then generated using the transcription factor mediated differentiation approaches that we have developed for the functional interrogation of risk mutations and the study of their cell biological effects in human neurons.

Electrophysiological study revealed impaired synaptic transmission between neurons that carry a loss-of-function mutation in a disease associated gene. Patch-clamp configuration for postsynaptic recordings performed on day 28-30 old control or mutant human neurons. Left, bright field; Middle, EGFP-fluorescence view; and Right, both views merged. Rec, recording electrode. Sample traces shown are GABAR-mediated spontaneous inhibitory postsynaptic currents (IPSCs) recorded in cultures that contain control or mutant human neurons.

Publications

2017

Yang N, Chanda S, Marro S, Ng YH, Janas JA, Haag D, Ang CE, Tang Y, Flores Q, Mall M, Wapinski O, Li M, Ahlenius H, Rubenstein JL, Chang HY, Buylla AA, Südhof TC, Wernig M. Generation of pure GABAergic neurons by transcription factor programming. Nat Methods. 2017 Jun;14(6):621-628.

2014

Marro S, Yang N. Transdifferentiation of mouse fibroblasts and hepatocytes to functional neurons. Methods Mol Biol. 2014;1150:237-46 (book chapter)

2013

Yang N, Wernig M. Harnessing the stem cell potential: a case for neural stem cell therapy. Nat Med. 2013 Dec;19(12):1580-1.


Yang N, Zuchero JB, Ahlenius H, Marro S, Ng YH, Vierbuchen T, Hawkins JS, Geissler R, Barres BA, Wernig M. Generation of oligodendroglial cells by direct lineage conversion. Nat Biotechnol. 2013 May;31(5):434-9.

2011

(Review) Yang N, Ng YH, Pang ZP, Südhof TC, Wernig M. Induced neuronal cells: how to make and define a neuron. Cell Stem Cell. 2011 Dec 2;9(6):517-25.


Marro S, Pang ZP, Yang N, Tsai MC, Qu K, Chang HY, Südhof TC, Wernig M. Direct Lineage Conversion of Terminally Differentiated Hepatocytes to Functional Neurons. Cell Stem Cell. 2011 2011 Oct 4;9(4):374-82.


Pang ZP*, Yang N*, Vierbuchen T*, Ostermeier A, Fuentes DR, Yang TQ, Citri A, Sebastiano V, Marro S, Südhof TC, Wernig M. Induction of human neuronal cells by defined transcription factors. Nature. 2011 May 26;476(7359):220-3. (* Equal contribution)