Bio

Bio

Ning Deng is a Senior Research Scientist in the Department of Genetics at Stanford University. She graduated with a Ph.D. in Biochemistry and Molecular Biology from the laboratory of Dr. Lin Li at the Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, where her research focused on the Wnt signal pathway regulation and phosphoproteomics study. In 2008, Dr. Deng joined the research laboratory of Dr. Stanley N. Cohen at Stanford University, Genetics Department studying cancer drug-resistant gene Txr1 function. Later, she focused on the transcription elongation factor Supt4, which is required for certain expanded nucleotide repeats transcription such as CAG repeats in htt gene which causes Huntington's Disease. She set up and led a high-throughput screening for small molecules to interrupt transcription elongation complex and testing small molecules effect on lowering htt gene expression in iPSCs from Huntington's Disease patients. Now her interests expand to 1) exploration of global effects from Supt4 gene deficiency with NGS technologies; 2) Supt4's regulation on other nucleotide repeat diseases; 3) using microvesicles to deliver macromolecules to target cells.

Current Role at Stanford

Senior Research Scientist

Lab Manager

Supervisors

Education & Certifications

  • Ph.D., Institute of Biochemistry and Cell Biology, Shanghai institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China, Biochemistry and Molecular Biology (2007)
  • BS, School of Life Science, Wuhan University, Wuhan, China, Biochemistry (2001)

Patents

  • Stanley N. Cohen, Ning Deng. "United States Patent 10882821 Enantiomeric compound for the reduction of the deleterious activity of extended nucleotide repeat containing genes", THE BOARD OF TRUSTEES OF THE LELAND STANFORD JUNIOR UNIVERSITY, Jan 5, 2021
  • Stanley N. Cohen,Ning Deng,Yanan Feng,Tzu-Hao Cheng,Thomas W. Sun. "United States Patent US20200147069A1 Compounds for The Reduction of The Deleterious Activity of Extended Nucleotide Repeat Containing Genes", Leland Stanford Junior University, Jun 19, 2018
  • Stanley N. Cohen, Ning Deng, Yanan Feng, Tzu-Hao Cheng, Yun-Yun Wu, Wen-Chieh Hsieh. "United States Patent US10675293B2 Nucleoside agents for the reduction of the deleterious activity of extended nucleotide repeat containing genes", National Yang Ming University, Leland Stanford Junior University, May 18, 2016
  • Lin Li?Xiaoqing Gan, Zhihai Ma, Ning Deng, Jiyong Wang. "China P.Rep. Patent CN100519743C New use of G protein coupled acceptor kinase", Shanghai institutes for Biological Sciences, Chinese Academy of Sciences, Jul 29, 2009

Contact

    • Tel: (650) 723-5317

Publications

All Publications

  • Spt4 selectively regulates the expression of C9orf72 sense and antisense mutant transcripts. Science Kramer, N. J., Carlomagno, Y., Zhang, Y., Almeida, S., Cook, C. N., Gendron, T. F., Prudencio, M., van Blitterswijk, M., Belzil, V., Couthouis, J., Paul, J. W., Goodman, L. D., Daughrity, L., Chew, J., Garrett, A., Pregent, L., Jansen-West, K., Tabassian, L. J., Rademakers, R., Boylan, K., Graff-Radford, N. R., Josephs, K. A., Parisi, J. E., Knopman, D. S., Petersen, R. C., Boeve, B. F., Deng, N., Feng, Y., Cheng, T., Dickson, D. W., Cohen, S. N., Bonini, N. M., Link, C. D., Gao, F., Petrucelli, L., Gitler, A. D. 2016; 353 (6300): 708-712

    Abstract

    An expanded hexanucleotide repeat in C9orf72 causes amyotrophic lateral sclerosis and frontotemporal dementia (c9FTD/ALS). Therapeutics are being developed to target RNAs containing the expanded repeat sequence (GGGGCC); however, this approach is complicated by the presence of antisense strand transcription of expanded GGCCCC repeats. We found that targeting the transcription elongation factor Spt4 selectively decreased production of both sense and antisense expanded transcripts, as well as their translated dipeptide repeat (DPR) products, and also mitigated degeneration in animal models. Knockdown of SUPT4H1, the human Spt4 ortholog, similarly decreased production of sense and antisense RNA foci, as well as DPR proteins, in patient cells. Therapeutic targeting of a single factor to eliminate c9FTD/ALS pathological features offers advantages over approaches that require targeting sense and antisense repeats separately.

    View details for DOI 10.1126/science.aaf7791

    View details for PubMedID 27516603

  • Effects on murine behavior and lifespan of selectively decreasing expression of mutant huntingtin allele by supt4h knockdown. PLoS genetics Cheng, H., Chern, Y., Chen, I., Liu, C., Li, S., Chun, S. J., Rigo, F., Bennett, C. F., Deng, N., Feng, Y., Lin, C., Yan, Y., Cohen, S. N., Cheng, T. 2015; 11 (3)

    Abstract

    Production of protein containing lengthy stretches of polyglutamine encoded by multiple repeats of the trinucleotide CAG is a hallmark of Huntington's disease (HD) and of a variety of other inherited degenerative neurological and neuromuscular disorders. Earlier work has shown that interference with production of the transcription elongation protein SUPT4H results in decreased cellular capacity to transcribe mutant huntingtin gene (Htt) alleles containing long CAG expansions, but has little effect on expression of genes containing short CAG stretches. zQ175 and R6/2 are genetically engineered mouse strains whose genomes contain human HTT alleles that include greatly expanded CAG repeats and which are used as animal models for HD. Here we show that reduction of SUPT4H expression in brains of zQ175 mice by intracerebroventricular bolus injection of antisense 2'-O-methoxyethyl oligonucleotides (ASOs) directed against Supt4h, or in R6/2 mice by deletion of one copy of the Supt4h gene, results in a decrease in mRNA and protein encoded specifically by mutant Htt alleles. We further show that reduction of SUPT4H in mouse brains is associated with decreased HTT protein aggregation, and in R6/2 mice, also with prolonged lifespan and delay of the motor impairment that normally develops in these animals. Our findings support the view that targeting of SUPT4H function may be useful as a therapeutic countermeasure against HD.

    View details for DOI 10.1371/journal.pgen.1005043

    View details for PubMedID 25760041

  • Spt4 Is Selectively Required for Transcription of Extended Trinucleotide Repeats CELL Liu, C., Chang, C., Chern, Y., Wang, T., Hsieh, W., Shen, W., Chang, C., Chu, I., Deng, N., Cohen, S. N., Cheng, T. 2012; 148 (4): 690-701

    Abstract

    Lengthy trinucleotide repeats encoding polyglutamine (polyQ) stretches characterize the variant proteins of Huntington's disease and certain other inherited neurological disorders. Using a phenotypic screen to identify events that restore functionality to polyQ proteins in S. cerevisiae, we discovered that transcription elongation factor Spt4 is required to transcribe long trinucleotide repeats located either in ORFs or nonprotein-coding regions of DNA templates. Mutation of SPT4 selectively decreased synthesis of and restored enzymatic activity to expanded polyQ protein without affecting protein lacking long-polyQ stretches. RNA-seq analysis revealed limited effects of Spt4 on overall gene expression. Inhibition of Supt4h, the mammalian ortholog of Spt4, reduced mutant huntingtin protein in neuronal cells and decreased its aggregation and toxicity while not altering overall cellular mRNA synthesis. Our findings identify a cellular mechanism for transcription through repeated trinucleotides and a potential target for countermeasures against neurological disorders attributable to expanded trinucleotide regions.

    View details for DOI 10.1016/j.cell.2011.12.032

    View details for Web of Science ID 000300622400011

    View details for PubMedID 22341442

  • Dishevelled interacts with p65 and acts as a repressor of NF-?B-mediated transcription. Cell research Deng, N., Ye, Y., Wang, W., Li, L. 2010; 20 (10): 1117?27

    Abstract

    Dishevelled (Dvl) is a highly conserved protein family that plays an important role in mediating Wnt signaling from membrane to cytoplasm. Recently we reported that Dvl also functions in the nucleus by stabilizing the ?-catenin/TCFs transcriptional complex. Here we describe that Dvl may function as a repressor of NF-?B. Our data show that Dvl directly binds to p65 and their interaction occurs in the nucleus. Dvl expression inhibits p65-mediated or TNF-?-stimulated activation of the NF-?B dependent reporter. This action of Dvl, however, is not dependent on Wnt or its downstream effector ?-catenin. Chromatin immunoprecipitation assay shows that recruitment of p65 to the promoters of NF-?B target genes is significantly enhanced when expression of Dvl is knocked down. Consistently, the expression level of a subset of NF-?B target genes is also increased after knock-down of Dvl. Moreover, our data suggest that Dvl may relieve the anti-apoptotic effect of NF-?B, thus play a role in promoting apoptosis. Therefore, this work demonstrates a novel function of Dvl in modulating NF-?B-regulated gene transcription.

    View details for DOI 10.1038/cr.2010.108

    View details for PubMedID 20628365

  • Quantitative phosphoproteome profiling of Wnt3a-mediated signaling network: indicating the involvement of ribonucleoside-diphosphate reductase M2 subunit phosphorylation at residue serine 20 in canonical Wnt signal transduction. Molecular & cellular proteomics : MCP Tang, L. Y., Deng, N., Wang, L. S., Dai, J., Wang, Z. L., Jiang, X. S., Li, S. J., Li, L., Sheng, Q. H., Wu, D. Q., Li, L., Zeng, R. 2007; 6 (11): 1952?67

    Abstract

    The complexity of canonical Wnt signaling comes not only from the numerous components but also from multiple post-translational modifications. Protein phosphorylation is one of the most common modifications that propagates signals from extracellular stimuli to downstream effectors. To investigate the global phosphorylation regulation and uncover novel phosphoproteins at the early stages of canonical Wnt signaling, HEK293 cells were metabolically labeled with two stable isotopic forms of lysine and were stimulated for 0, 1, or 30 min with purified Wnt3a. After phosphoprotein enrichment and LC-MS/MS analysis, 1057 proteins were identified in all three time points. In total 287 proteins showed a 1.5-fold or greater change in at least one time point. In addition to many known Wnt signaling transducers, other phosphoproteins were identified and quantitated, implicating their involvement in canonical Wnt signaling. k-Means clustering analysis showed dynamic patterns for the differential phosphoproteins. Profile pattern and interaction network analysis of the differential phosphoproteins implicated the possible roles for those unreported components in Wnt signaling. Moreover 100 unique phosphorylation sites were identified, and 54 of them were quantitated in the three time points. Site-specific phosphopeptide quantitation revealed that Ser-20 phosphorylation on RRM2 increased upon 30-min Wnt3a stimulation. Further studies with mutagenesis, the Wnt reporter gene assay, and RNA interference indicated that RRM2 functioned downstream of beta-catenin as an inhibitor of Wnt signaling and that Ser-20 phosphorylation of RRM2 counteracted its inhibition effect. Our systematic profiling of dynamic phosphorylation changes responding to Wnt3a stimulation not only presented a comprehensive phosphorylation network regulated by canonical Wnt signaling but also found novel molecules and phosphorylation involved in Wnt signaling.

    View details for DOI 10.1074/mcp.M700120-MCP200

    View details for PubMedID 17693683

  • Regulation of PTEN by Rho small GTPases. Nature cell biology Li, Z., Dong, X., Wang, Z., Liu, W., Deng, N., Ding, Y., Tang, L., Hla, T., Zeng, R., Li, L., Wu, D. 2005; 7 (4): 399?404

    Abstract

    PTEN (phosphatase and tensin homologue) is a phosphatase that dephosphorylates both protein and phosphoinositide substrates. It is mutated in a variety of human tumours and has important roles in a diverse range of biological processes, including cell migration and chemotaxis. PTEN's intracellular localization and presumably activity are regulated by chemoattractants in Dictyostelium and mouse neutrophils. However, the mechanisms for its regulation remain elusive. Here we show that RhoA and Cdc42, members of the Rho family of small GTPases, regulate the intracellular localization of PTEN in leukocytes and human transfected embryonic kidney cells. In addition, active RhoA is able to stimulate the phospholipid phosphatase activity of PTEN in human embryonic kidney cells and leukocytes, and this regulation seems to require RhoA's downstream effector, RhoA-associated kinase (Rock). Furthermore, we have identified key residues on PTEN that are required for its regulation by the small GTPase, and show that small GTPase-mediated regulation of PTEN has a significant role in the regulation of chemotaxis.

    View details for DOI 10.1038/ncb1236

    View details for PubMedID 15793569

  • Involvement of the C-terminal proline-rich motif of G protein-coupled receptor kinases in recognition of activated rhodopsin. The Journal of biological chemistry Gan, X., Ma, Z., Deng, N., Wang, J., Ding, J., Li, L. 2004; 279 (48): 49741?46

    Abstract

    G protein-coupled receptor kinases (GRKs) are a family of serine/threonine kinases that phosphorylate many activated G protein-coupled receptors (GPCRs) and play an important role in GPCR desensitization. Our previous work has demonstrated that the C-terminal conserved region (CC) of GRK-2 participates in interaction with rhodopsin and that this interaction is necessary for GRK-2-mediated receptor phosphorylation (Gan, X. Q., Wang, J. Y., Yang, Q. H., Li, Z., Liu, F., Pei, G., and Li, L. (2000) J. Biol. Chem. 275, 8469-8474). In this report, we further investigated whether the CC of other GRKs had the same functions and defined the specific sequences in CC that are required for the functions. The CC regions of GRK-1, GRK-2, and GRK-5, representatives of the three subfamilies of GRKs, could bind rhodopsin in vitro and inhibit GRK-2-mediated phosphorylation of rhodopsin, but not a peptide GRK substrate. Through a series of mutagenesis analyses, a proline-rich motif in the CC was identified as the key element involved in the interaction between the CC region and rhodopsin. Point mutations of this motif not only disrupted the interaction of GRK-2 with rhodopsin but also abolished the ability of GRK-2 to phosphorylate rhodopsin. The findings that the CC region of GRKs interact only with the light-activated but not the non-activated rhodopsin and that the N-terminal domain of GRK-2 interacts with rhodopsin in a light-independent manner suggest that the CC region is responsible for the recognition of activated GPCRs in the canonical model.

    View details for DOI 10.1074/jbc.M407570200

    View details for PubMedID 15375171

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