The Wang Lab Integrative RNA Biology
Intro Heading link
MicroRNAs (miRNAs) are a family of small non-coding RNAs, and each miRNA can regulate the expression of hundreds of gene targets. By broadly controlling the functions of thousands of genes, miRNAs play important regulatory roles in almost all known molecular pathways. Our main research interests include: computational and experimental identification of miRNA targets; development of bioinformatics tools for miRNA and gene expression research; identification of miRNA-related biomarkers for human cancers; functional characterization of miRNA in cancer development and progression; and development of miRNA therapeutics for human cancers.
We have developed multiple bioinformatics tools and experimental methods to facilitate miRNA studies. For example, we have developed an online database, miRDB for miRNA target prediction and functional analysis. miRDB has quickly become a widely-used bioinformatics tool for miRNA research and has been referenced by thousands of publications. Besides tools related to miRNA, our lab has also developed other popular bioinformatics tools for gene expression studies.
Several prominent examples are:
- PrimerBank database for real-time PCR studies, which has been referenced by thousands of publications;
- siOligo program for siRNA design, which is currently used by Life Technologies to design the siRNA products they have been distributing to hundreds of labs throughout the world;
- WU-CRISPR, a recently developed tool for the design of CRISPR/Cas9 assays.
Our lab is also very interested in translational cancer research. We have identified prognostic biomarkers to stratify patients based on the risk of failure to standard therapies. The lab has performed gene expression profiling studies and established multiple miRNA-based prognostic models for robust prediction of a variety of human cancers. In particular, we have focused on cervical and oropharyngeal cancers, both of which are closely associated with human papillomavirus (HPV) infection. Besides miRNA biomarkers, we have also functionally characterized the interactions between miRNA and HPV during the development of HPV-induced cancers. We are currently collaborating with Radiation Oncologists to validate the clinical utility of the identified prognostic biomarkers to guide treatment decisions.
Principal Investigator
Xiaowei Wang
Professor
xwang317@uic.edu
Dr. Wang received his BS in Biochemistry from Nankai University (1993) and PhD in Biochemistry from Tufts University School of Medicine (2000). He then worked as a Bioinformatics Specialist at Massachusetts General Hospital and later as a Bioinformatics Manager at Applied Biosystems. In 2007, Dr. Wang joined Washington University to start a lab focusing on microRNA and translational cancer research. In 2020, Dr. wang joined the University of Illinois at Chicago in the department of Pharmacology.
Wang Heading link
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Team Members
Staff
- Xinyi Liu
Research Assistant Professor
xinyiliu@uic.edu
Xinyi completed her PhD in bioinformatics at Harbin Medical University, China. She studied human endogenous retroviruses involved in autoimmune disease and the relationships between small molecules and miRNAs. Her project here is focused on identification of miRNA biomarkers in HPV-induced cancers. - Yuanxiang Li
Research Instructor
yli345@uic.edu
Yuanxiang joined the Wang lab in 2021. She achieved her PhD in marine biology from the Chinese Academy of Sciences. She studied the physiological and transcriptomic response under high light stress in Dunaliella salina. She also studied the effects of red and blue light on the expression of carotenoid biosynthesis genes.
Students
- Yuhao Chen
PhD Candidate – Electrical and Systems Engineering
chen.yuhao@wustl.edu
Yuhao Chen joined the Department of Electrical and System Engineering at WUSTL in 2015. He earned his Bachelor of Engineering degree in information engineering at the Beijing Institute of Technology in 2014. He joined the Wang lab to pursue his PhD in Bioinformatics. - Gongyu Tang
PhD Candidate – Mechanical Engineering
gongyutang@wustl.edu
Gongyu is a PhD student in mechanical engineering and joined the Wang lab in August 2018. He received his M.S. in mechanical engineering at WUSTL in 2017 and his B.S in mechanical engineering at Huazhong Agriculture University in 2015. He previously researched computational fluid dynamics and is now working on bioinformatics research. - Minsu Cho
PhD Student – Biomedical Engineering (Bioinformatics)
mcho43@uic.edu
Minsu is a PhD student in bioinformatics and joined the lab in August 2020. He started his Ph.D.in August 2021 at UIC. He received his M.S. in bioinformatics at Northeastern University in 2020 and his B.S in Biotechnology at the University of Massachusetts Lowell in 2018. - Dan-Ho Tran
PhD Student – Graduate Education in Biomedical Science
dtran36@uic.edu
Dan-Ho is a Ph.D. student in the Graduate Education in Biomedical Sciences program and joined the Wang lab in August 2021. He received his B.S in molecular genetics at The Ohio State University in 2018.
- Xinyi Liu
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Publications
Below are some main publications:
Below are some main publications:
- Chen Y and Wang X (2022) Evaluation of efficiency prediction algorithms and development of ensemble model for CRISPR/Cas9 gRNA selection. Bioinformatics. 38(23):5175–5181.
- Tang G, Cho M, Wang X (2022) OncoDB: an interactive online database for analysis of gene expression and viral infection in cancer, Nucleic Acids Research.50(D1):D1334-D1339
- Huang X, Tang G, Ismail N, Wang X (2022) Developing RT-LAMP assays for rapid diagnosis of SARS-CoV-2 in saliva.EBioMedicine.75:103736
- Liu X, Liu P, Chernock RD, Lang Kuhs KA, Lewis JS Jr, Li H, Gay HA, Thorstad WL, Wang X (2022). Impact of human papillomavirus on the tumor microenvironment in oropharyngeal squamous cell carcinoma. Int J Cancer.1;150(3):521-531
- Liu X, Liu P, Chernock, RD, Yang Z, Kuhs KA, Lewis Jr. JS, Luo J, Li H, Gay HA, Thorstad, WL, Wang X (2021) A microRNA expression signature as prognostic marker for oropharyngeal squamous cell carcinoma. JNCI: Journal of the National Cancer Institute.113(6):752-759.
- Liu X, Liu P, Chernock, RD, Kuhs KA, Lewis Jr. JS, Luo J, Gay HA, Thorstad, WL, Wang X (2020) A prognostic gene expression signature for oropharyngeal squamous cell carcinoma. EBioMedicine.2020;61:102805.
- Tong F, Andress A, Tang G, Liu P, Wang X (2020) Comprehensive profiling of extracellular RNA in HPV-induced cancers using an improved pipeline for small RNA-seq analysis. Scientific Reports. 10(1):19450.
- Hiranniramol K, Chen Y, Liu W, Wang X (2020) Generalizable sgRNA design for improved CRISPR/Cas9 editing efficiency. Bioinformatics. 36(9):2684-2689.
- Hiranniramol K, Chen Y, Wang X (2020) CRISPR/Cas9 Guide RNA Design Rules for Predicting Activity. Methods in Molecular Biology. 2115:351-364.
- Cosper PF, McNair C, Ivan Gonzalez, Wong N, Knudsen KE, Chen JJ, Markovina S, Schwarz JK, Grigsby PW, Wang X (2020) Decreased local immune response and retained HPV gene expression during chemoradiotherapy are associated with treatment resistance and death from cervical cancer. International Journal of Cancer. 146(7):2047–2058.
- Chen Y and Wang X (2020) miRDB: an online database for prediction of functional microRNA targets. Nucleic Acids Research. 48(D1):D127-D131.
- Liu W, Wang X (2019) Prediction of functional microRNA targets by integrative modeling of microRNA binding and target expression data. Genome Biology. 20:18 1-10.
- Wong N, Chen Y, Chen S, Wang X (2018) OncomiR: An online resource for exploring pan-cancer microRNA dysregulation. Bioinformatics. 34(4):713-715.
- Liu W, Chen H, Wong N, Haynes W, Baker CM, Wang X (2017) Pseudohypoxia induced by miR-126 deactivation promotes migration and therapeutic resistance in renal cell carcinoma. Cancer Letters. 394:65-75.
- Wang X (2016) Improving microRNA target prediction by modeling with unambiguously identified microRNA-target pairs from CLIP-Ligation studies. Bioinformatics. 32(9):1316-1322.
- Khwaja SS, Baker C, Haynes W, Spencer CR, Gay H, Thorstad W, Adkins DR, Nussenbaum B, Chernock RD, Lewis Jr. JS, Wang X (2016) High E6 gene expression predicts for distant metastasis and poor survival in patients with HPV-positive oropharyngeal squamous cell carcinoma. Int J Radiat Oncol Biol Phys. 95(4): 1132-1141.
Publications
- Wong N, Khwaja SS, Baker CM, Gay HA, Thorstad WL, Daly MD, Lewis JS Jr, Wang X (2016) Prognostic microRNA signatures derived from The Cancer Genome Atlas for head and neck squamous cell carcinomas. Cancer Medicine. 5(7):1619-1628.
- Wong N, Liu W, Wang X (2015) WU-CRISPR: characteristics of functional guide RNAs for the CRISPR/Cas9 system. Genome Biology. 16(1):218 1-8.
- Wong N, Wang X (2015) miRDB: an online resource for microRNA target prediction and functional annotations. Nucleic Acids Research. 43(D1):D146-152.
- Liu W, Gao G, Hu X, Wang Y, Schwarz JK, Chen JJ, Grigsby PW, Wang X (2014) Activation of miR-9 by human papillomavirus in cervical cancer. Oncotarget. 5(22):11620-11630.
- Wang X (2014) Composition of seed sequence is a major determinant of microRNA targeting patterns. Bioinformatics 30(10):1377-1383.
- Jiang Z, Liu W, Wang Y, Gao Z, Gao G, Wang X (2013) Rational design of microRNA-siRNA chimeras for multi-functional target suppression. RNA 19(12):1745-1754.
- Gao G, Gay HA, Chernock RD, Zhang TR, Luo J, Thorstad WL, Lewis JS, Wang X (2013) A microRNA expression signature for the prognosis of oropharyngeal squamous cell carcinoma. Cancer 119(1):72-80.
- Gao G, Chernock RD, Gay HA, Thorstad WL, Zhang TR, Wang H, Ma XJ, Luo Y, Lewis JS, Wang X (2013) A novel RT-PCR method for quantification of human papillomavirus transcripts in archived tissues and its application in oropharyngeal cancer prognosis. International Journal of Cancer 132(4):882-90.
- Wang X, Spandidos A, Wang H, Seed B (2012) PrimerBank: a PCR primer database for quantitative gene expression analysis, 2012 update. Nucleic Acids Research 40(1):D1144-1149.
- Nelson PT, Wang WX, Mao G, Wilfred BR, Xie K, Jennings MH, Gao Z, Wang X (2011) Specific sequence determinants of miR-15/107 microRNA gene group targets. Nucleic Acids Research 39(18):8163-8172.
- Hu X, Schwarz JK, Lewis JS., Huettner PC, Rader JS, Deasy JO, Grigsby PW, Wang X (2010) A microRNA expression signature for cervical cancer prognosis. Cancer Research 70(4):1441-1448.
- Wang X (2010) Computational prediction of microRNA targets. Methods in Molecular Biology 667:283-295.
- Wang X, Wang XH, Varma RK, Beauchamp L, Magdaleno S, Sendera TJ (2009) Selection of hyperfunctional siRNAs with improved potency and specificity. Nucleic Acids Research 37(22):e152 1-9.
- Hu X, Macdonald DM, Huettner PC, Feng Z, El Naqa IM, Schwarz JK, Mutch DG, Grigsby PW, Powell SN, Wang X (2009) A miR-200 microRNA cluster as prognostic marker in advanced ovarian cancer. Gynecologic Oncology 114(3):457-464.
- Wang X (2009) A PCR-based platform for microRNA expression profiling studies. RNA 15(4):716-723.
- Wang X (2008) miRDB: a microRNA target prediction and functional annotation database with a wiki interface. RNA 14(6):1012-1017.
- Wang X and El Naqa IM (2008) Prediction of both conserved and nonconserved microRNA targets in animals. Bioinformatics 24(3):325-332.
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Resources
CRISPRDB
CRISPRDB is an online database for genome-wide CRISPR/Cas9 gRNA design. All the gRNAs in CRISPRDB were pre-designed and predicted by a gRNA efficiency prediction model, ensemble_ridge, which was developed by assembling five high-performing gRNA design algorithms using stacking ensemble method. CRISPRDB hosts pre-designed gRNAs in two species: human, and mouse. There are three options for users to input the target gene: GenBank Accession, NCBI Gene ID or Gene Symbol. Example inputs of these three options are provided. Users could do gRNA search using our pre-designed gRNA database based on their input genes. Besides gRNA search function, users may also provide their own genomic target sequences for gRNA design using the updated prediction algorithm.
miRDB
miRDB is an online database for miRNA target prediction and functional annotations. All the targets in miRDB were predicted by the bioinformatics tool MirTarget, which was developed through the analysis of thousands of miRNA-target interactions from high-throughput sequencing experiments. Common features associated with miRNA target binding have been identified and used to predict miRNA targets with machine learning methods. miRDB hosts predicted miRNA targets in five species: human, mouse, rat, dog, and chicken. As a recent update, users may provide their own sequences for customized target prediction. In addition, through combined computational analyses and literature mining, functionally active miRNAs in humans and mice have been identified. These miRNAs, as well as associated functional annotations, are presented in the FuncMir Collection in miRDB.
WU-CRISPR
The CRISPR/Cas9 system lacks robust bioinformatics tools for the design of single guide RNA (sgRNA), which determines the efficacy and specificity of genome editing. We have analyzed CRISPR RNA-seq data and identified many novel features that are characteristic of highly potent sgRNAs. These features were used to develop a bioinformatics tool for genome-wide design of sgRNAs with improved efficiency. These sgRNAs as well as the design tool are freely accessible via a web server, WU-CRISPR.
OncomiR
OncomiR is an online resource for exploring miRNA dysregulation in cancer. Using OncomiR, miRNAs can be queried for association with:
- Tumor stage and grade
- Cancer patient survival
- Gene targets
On-the-fly analysis can be conducted to examine:
- miRNA-based survival signatures
- Cancer type clustering by miRNA expression profile
PrimerBank
PrimerBank is a public resource for PCR primers, containing over 306,800 primers covering most human and mouse genes. These primers are designed for gene expression detection or quantification. The primer design algorithm has been extensively tested by real-time PCR experiments for specificity and efficiency, with a design success rate of 82.6%, based on agarose gel electrophoresis.
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Research Positions
Multiple openings for various research positions available. We are looking for talented researchers at all levels, from junior-level research technicians to senior-level postdoctoral scientists. We are especially interested in candidates who have experience in genomics and computational biology.
Student Rotation Projects
Students interested in pursuing PhD degrees in our lab are encouraged to contact Prof. Xiaowei Wang. We’d love to discuss potential rotation projects with students from all backgrounds. We do both computational and experimental studies.