Laboratory of Jiaqian Wu, Ph.D.

Wu laboratory combines neuroscience, stem cell biology and systems-based approaches involving genomics, bioinformatics and functional assays to unravel gene transcription and regulatory mechanisms. We have carried out unprecedented transcriptome profiling for eight types of highly purified neuron, glia and vascular cells from brain by RNA-Seq. We identified many novel long noncoding RNAs (lncRNAs), and our functional and genetic experiments substantiated the role of lncRNA in oligodendrocyte precursor cell (OPC) formation for the first time.

One major focus of our group is investigating the mechanisms and developing effective and safe treatment for spinal cord injury and neurological diseases. We have published protein coding and lncRNA gene expression in multiple acute and chronic spinal cord injury phases in mouse and rat models. We provided unprecedented data source and a powerful analysis framework for functional investigations of lncRNAs in CNS cell types. We also have deposited the complete datasets of purified brain cell types and spinal cord injury in databases displayed using an interactive web browser for analyzing and comparing protein-coding, lncRNA gene transcription as well as alternative splicing profiles. It serves as a widely used data source for the research community.

The other area of our research interest lies in the studies of the regulatory networks of stem and progenitor cell self-renewal and differentiation using integrated genomic and proteomic approaches. Our goal is to identify and modulate key regulators as therapeutic targets.

About Dr. Wu

Dr. Jiaqian Wu is an Associate Professor with Tenure in the Vivian L. Smith Department of Neurosurgery and Center for Stem Cell and Regenerative Medicine at McGovern Medical School at UTHealth.. Dr. Wu earned her doctorate in molecular and human genetics at Baylor College of Medicine in Houston, where her research focused on novel mammalian gene discovery and the characterization of transcriptome complexity. Dr. Wu led the NIH Mammalian Gene Collection effort and cloned thousands of mammalian genes which are publicly available through GE Dharmacon now. During her postdoctoral training at Yale University and Stanford University, Dr. Wu employed interdisciplinary approaches including molecular and cellular biology and genomics to study gene expression, transcription factor regulation, and regulatory networks of stem cell self-renewal and differentiation. She was one of the first using RNA-Seq to characterize stem cell neural differentiation process. Dr. Wu’s work has been recognized with prestigious honors and awards, including the National Institutes of Health Ruth L. Kirschstein National Research Service Award for Individual Postdoctoral Fellows, and the International Society for Stem Cell Research (ISSCR) Annual Meeting Travel Award, the National Institute of Health Pathway to Independence (PI) Award (K99/R00), R01 and the Senator Lloyd and B.A. Bentsen Investigator Award. A reviewer for NIH, New York State Department of Health-Spinal Cord Injury Research Board, MRC, ANR, and various journals such as Nature Communications, Nature Biotechnology, Cell Reports and Cell Systems, Dr. Wu has presented invited talks and lectures at national and international conferences, universities and institutions. She has developed a patent, authored two books, and wrote many articles that have appeared in PNAS, the Journal of Neuroscience, Stem Cell Reports, Plos Genetics, Genome Research, Genome Biology, Nature Materials and Nature, among others.

Research Projects

  • Investigate gene expression and regulatory mechanisms during stem cell differentiation
  • Characterize molecular signatures and identify therapeutic targets for spinal cord injury and neurological diseases
  • Pinpoint key transcription factors and regulatory RNAs, and modulate key regulators to steer the direction of stem cell differentiation and improve efficiency
  • Determine the molecular switch of precursor cell self-renewal and differentiation
  • Network analysis of stem cell differentiation and global network integration of multiple types of omic data

Team Members

Haichao Wei, Ph.D., Postdoctoral Fellow
Xizi Wu, M.D., Postdoctoral Fellow
Xu li, Ph.D., Postdoctoral Fellow
Vy Hong, Undergraduate Student
Eyad Shihabeddin, Rotation Student

Contact the Lab

Email: Jiaqian.Wu@uth.tmc.edu
Office Phone: (713) 500-3421

Recent Publications (SELECTED)

    1. Wu, J. Q., Habegger, L., Noisa, P., Szekely, A., Qiu, C., Hutchison, S., Raha, D., Lin, H., Egholm, M., Weissman, S., Cui, W., Gerstein, M., and Snyder, M. (2010). Dynamic Transcriptomes during Neural Differentiation of Human Embryonic Stem Cells Revealed by Integrating Short, Long, and Paired-end Sequencing. PNAS. 107: 5254-5259.
    2. Wu, J. Q., Seay, M., Schulz, V., Hariharan, M., Tuck, D., Lian, J., Du, J., Shi, M., Ye, Z. J., Gerstein, M., Snyder, M., and Weissman, S. (2012). Tcf7 is a key regulator of the self-renewal and differentiation switch in a multipotential hematopoietic cell line. PLoS Genet 8(3): e1002565. PMC3297581
    3. Zhang, Y., Chen, K., Sloan, S., Bennett, M., Scholze, A., O’Keeffe, S., Phatnani, H., Guarnieri, P., Caneda, C., Ruderisch, N., Deng, S., Liddelow, S., Zhang, C., Daneman, R., Maniatis, T., Barres, B., Wu, J.Q. (2014) An RNA-Seq transcriptome and splicing database of neurons, glia and vascular cells of the cerebral cortex. J. Neurosci., 34(36): 11929-11947. PMID:25186741
    4. Yan, Q., Weyn-Vanhentenryck, S. M., Wu, J., Sloan, S., Zhang, Y., Chen, K.,Wu, J. Q., Barres, B., Zhang, C. (2015) Systematic discovery of regulated and conserved alternative exons in the mammalian brain reveals NMD modulating chromatin regulators. PNAS. Mar 17;112(11):3445-50
    5. Building an RNA-sequencing transciptome of the nervous system. Dong, X., You, Y. and Wu, JQ. The Neuroscientist. 2015 Oct 13. PMID:26463470
    6. Comprehensive Identification of Long Non-coding RNAs in Purified Cell Types from the Brain Reveals Functional LncRNA in OPC Fate Determination. Dong, X., Chen, KN, Duran, R., You, Y. Sloan, S., Ye, Z., Zong, S., Cao, Q., Barres, B., and Wu, JQ. PLoS Genet. 2015 Dec 18;11(12):e1005669.
    7. The Systematic analysis of coding and long non-coding RNAs in the sub-chronic and chronic stages of spinal cord injury. Cuevas-Diaz Duran, R., Yan, H., Zheng, Y., Huang,  X., Grill, R., Kim, D.H., Cao, Q., and Wu, JQ. Sci Rep.  Jan 20;7:41008. doi: 10.1038/srep41008. 2017
    8. Cuevas-Diaz Duran R, Wang CY, Zheng H, Deneen B, Wu JQ. Brain Region-Specific Gene Signatures Revealed by Distinct Astrocyte Subpopulations Unveil Links to Glioma and Neurodegenerative Diseases. eNeuro. 2019 Apr 2;6(2). doi: 10.1523/ENEURO.0288-18.2019. PMID:30957015.
    9. He, L., Zhou, J., Chen, M., Lin, C., Kim, S. G., Zhou, Y., Xiang, L., Xie, M., Bai, H., Yao, H., Shi, C., Coelho, P. G., Bromage, T. G., Hu, B., Tovar, N., Witek, L., Wu, J., Chen, K., Gu, W., Jinxuan Zheng, J., Christopher L. Ricupero, C.L., Sheu, T., Zhong, J., Wen, J., Niu, Y., Cheng, B., Gong, Q., Owens, D. M., Stanislauskas, M., Pei, J., Chotkowski, G., Wang, S., Yang, G., Shelanski, M., Zegarelli, D.J., Zheng, Y., Shi, X., Finkel, M., Zhang, W., Li, J., Cheng, J., Tarnow, D.P., Zhou, X., Wang, Z., Jiang, X., Romanov, A., Wang, S., Ye, L., Ling, J., Mao, J. J. Parenchymal and Stromal Tissue Regeneration of Tooth Organ by Pivotal Signals Reinstated in Decellularized Matrix. Nature Materials. 2019 Jun;18(6):627-637. doi: 10.1038/s41563-019-0368-6. PMID:31114073
    10. Kobayashi, M., Tarnawsky, S.P., Wei, H., Mishra, A., Azevedo Portilho, N., Wenzel, P., Davis, B., Wu, J., Hadland, B. and Yoshimoto, M. Hemogenic Endothelial Cells Can Transition to Hematopoietic Stem Cells through a B-1 Lymphocyte-Biased State during Maturation in the Mouse Embryo. Stem cell reports. 2019 Jun 10. pii: S2213-6711(19)30193-6. doi: 10.1016/j.stemcr.2019.05.025. PMID:31231025

Complete List of Published Work in My Bibliography