Shuo Gu, Ph.D.
Dr. Gu’s research focuses on the mechanisms of RNA interference and microRNA pathways, and their applications in cancer treatment. MiRNAs play essential roles in gene regulation networks, human diseases and cancer. Research in the Gu lab aims to unveil the mechanisms of miRNA biogenesis, post-transcriptional modifications, and biological functions in mammalian systems. This information will then be used to test novel RNA-based approaches designed to alter gene expression with improved safety, off-targeting, and potency profiles, which can then be used as tools for biological discovery and therapeutics.
1) RNAi, 2) miRNA, 3) non-coding RNA, 4) gene therapy, 5) RNA biology
Research in the Gu lab aims to unveil the roles of non-coding RNAs in gene regulation and to develop new therapeutic approaches for cancer treatment. MicroRNA (miRNA), as a small non-coding RNA, plays an essential role in gene regulation networks, human diseases and cancer. We are interested in understanding the mechanisms of miRNA biogenesis, post-transcriptional modifications, and biological functions in mammalian systems. This information will then be used to test novel RNA-based approaches designed to alter gene expression with improved safety, off-targeting, and potency profiles, which can then be used as tools for biological discovery and therapeutics.
Fidelity of miRNA biogenesis. Enormous efforts have focused on studying the alteration in miRNA expression levels during development and disease. However, imprecise biogenesis or post-maturation modification alters miRNA function by changing the sequence of the final product rather than its abundance. The biological importance of these changes in normal and disease states is not well defined. We are interested in unveiling the molecular mechanism controlling the fidelity of miRNA biogenesis and its effects on miRNA function. Recent advances in sequencing technology are making it possible to reveal such information in living cells. Together with applying classical biochemical approaches and reporter-based functional assays, we established a "loop-counting" rule governing the preciseness of Dicer processing, which is critical for miRNA biogenesis and function. We will extend our efforts to study other events in miRNA biogenesis to develop a more complete picture of how the ends of miRNA are generated, which can then serve as a reference point in investigating post-maturation modification of miRNAs.
In vivo study of RISC assembly. MicroRNAs and siRNAs interact with target sequences, inducing gene repression through the RNA-induced silencing complex (RISC) that consists of one of four mammalian Argonaute (Ago) proteins. Despite its importance, our understanding of RISC assembly is limited. The majority of the knowledge about this process is drawn from experiments performed within cell-free or reconstituted systems. During the past few years, we have developed a cell-based assay to specifically measure the RISC assembly process of cleaving Ago (Ago2) and non-cleaving Agos (Ago1/3/4) in vivo. Applying such a system, we are interested in studying how miRNA isoforms, which are generated by non-precise processing during biogenesis, affect RISC assembly and function in normal and disease states.
Novel design of potent DNA-directed RNAi (shRNA) with minimal off-target effects. DNA-directed RNAi (shRNA expressed from plasmids) is more desirable than traditional synthetic siRNAs in many applications. It is preferred or required in genetic screens and specific RNAi approaches in gene therapy settings. However, the application of ddRNAi is hampered due to unwanted off-target effects. Currently, attempts in reducing off-target effects are mainly based on empirical approaches with limited success.
We are interested in achieving such a goal through rational design based on the knowledge gained in the mechanistic studies outlined above. Our finding on Dicer processing has established the loop-counting rule, which laid the groundwork in designing Pol III-driven pre-miRNA-like shRNAs free of the off-target effects resulting from heterogeneous processing. We are currently working on transferring such a design into the Pol II system. In addition, based on the recent findings of how RISC interacts with its target mRNA on a molecular level, we are developing a novel strategy for designing shRNA with minimal off-target effects originating from the miRNA-like pathway.
Selected Recent Publications
- Mol Cell. May 25: 2019. [ Journal Article ]
Structural Differences between Pri-miRNA Paralogs Promote Alternative Drosha Cleavage and Expand Target Repertoires.Cell reports. 26: 447-459, 2019. [ Journal Article ]
- Bioinformatics. 2018. [ Journal Article ]
- Nucleic Acids Res. 2016 Dec 1;44(21): Epub 10454-10466, 2016. [ Journal Article ]
- Methods. 2016 Jul 1;103: Epub 157-166, 2016. [ Journal Article ]
Shuo Gu received his B.A. in Tsinghua University, CHINA in 1998. He completed his Ph.D. training in the laboratory of Dr. John Rossi at Beckman Research Institute, City of Hope, Los Angeles. Shuo Gu undertook his postdoctoral training in the laboratory of Dr. Mark Kay at Stanford University Medical School, Palo Alto. Both his Ph.D. and postdoctoral research focused on the mechanisms of RNA interference and microRNA pathways, and their applications in gene therapy. He Joined the Gene Regulation and Chromosome Biology Laboratory in 2013.
|Xavier Bofill de Ros Ph.D.||Postdoctoral Fellow (Visiting)|
|Lisheng Dai Ph.D.||Postdoctoral Fellow (Visiting)|
|Lillian F. Hallmark||Postbaccalaureate Fellow (CRTA)|
|Chuanjiang Lian Ph.D.||Special Volunteer|
|Acong Yang Ph.D.||Research Fellow|
Gene-regulating microRNAs gain control over hundreds of new genes with common sequence modification
miRNAs, lncRNAs and circRNAs are newfound types of non-coding RNAs that are shedding light on the regulation of gene expression.
Photo courtesy of the NIH IRP
MicroRNAs have an enormous influence over what happens inside cells. By blocking the activity of specific sets of genes, they help control virtually every known biological pathway and process. Disruptions in microRNAs have been linked to many diseases, and understanding how these molecules function, which genes they control and how they themselves are regulated are high priorities in cancer research.
New research from Shuo Gu, Ph.D., Investigator in the RNA Biology Laboratory, shows that when a microRNA undergoes a common modification called uridylation, its genetic targets change. A single microRNA can regulate hundreds of different genes, but when a microRNA is uridylated, the team found, even more genes come under its control.
Modifications to microRNAs that either clip off or add to their short sequences are widespread, but it has not been know what effect these modifications have on microRNA function. Until the new study, reported June 6, 2019, in Molecular Cell, there were few clues to suggest that uridylation might alter the way a microRNA interacts with its targets.
2019 CCR Excellence in Postdoctoral Transition Award
Xavier Bofill de Ros Visiting Fellow; mapping the miRNA maturation defects that lead to malignancy.
Outstanding Poster Award at the 2019 Spring Research Festival
Richard Ma (intern) - Gene Therapy Genome Editing, and Genetics
Congratulations to our Postbac Poster Day 2019 recipient
Ben Birkenfeld CRTA - Outstanding Poster Award
Congratulations to our NCI Director's Innovation Award recipients -
2020 Xavier Bofill de Ros Visiting Fellow
2018 Acong Yang Research Fellow
2017 Xavier Bofill de Ros Visiting Fellow