Close-up of sample being place into microplate

His recent study based on a genome-wide functional genetic screen identified epigenetic circuitries that drive the mixed-lineage leukemias (Chen et al. 2015, Nature Medicine), and led the current research towards combinational epigenetic therapies in multiple types of hematopoietic malignancies.

Dr. Chen and his laboratory in the Department of Systems Biology will focus on dissecting the epigenetic mechanisms underlying the therapeutic resistance in cancers. He is skilled in high throughput CRISPR genetic screens for de novo therapeutic target discovery. He also utilizes next-generation sequencing for epigenomic and transcriptomic analyses (ChIPseq, ATACseq, RNAseq, etc). Additionally, Dr. Chen’s laboratory is involved in leading-edge technology development, including precision epigenome editing and transcriptional regulations.

Principal Investigator: Chun-Wei (David) Chen, Ph.D.

As an Associate Professor in the Department of Systems Biology, David Chen conducts research on epigenetic mechanisms for therapeutic resistance in cancers and therapeutic target discovery using high throughput genetic screens.

Full bio

Lab Members

Anthony Chan, Ph.D.

Staff Scientist

Research Focus Molecular cell biology and epigenetics in cancer research Therapeutic target discovery using high-throughput CRISPR genetic screens Drug discovery using a combination of in silico modeling, in vitro binding assays, and cell-based methods Full Bio

Shai Izraeli, M.D.

Research Professor

Research Focus Hematologic malignancies Cancer predisposition syndromes Centrosomal biology and chromosomal aneuploidy and its roles in developmental biology and cancer Full bio

Mingli Li, Ph.D.

Postdoctoral Fellow

Research Focus Molecular cell biology and biochemistry in cancer research Drug discovery using cell-based disease model screening Identification of novel therapeutic targets to eliminate cancer cells Full bio

Qiao Liu, M.S.

Postdoctoral Fellow

Research Focus CRISPR library screening identifying genes related to epigenetics in MLL-r leukemia Qiao Liu, M.S., obtained her M.Sc. degree from Fujian Medical University of Hematology in 2018. She is currently a Ph.D. student at Fujian Medical University, supervised by Professor Shaoyuan Wang. She joined Professor Chun-Wei (David) Chen’s laboratory in the Department of Systems Biology in February 2019 for further training. Her projects focus on high-throughput CRISPR library screening to validate the function of MLL-r related candidate genes and utilize the next-generation sequencing, including RNA-seq and ATAC-seq, to dissect the downstream mechanisms underlying these genes in MLL-r leukemia. Degrees 2015-2018, M.S., Hematology, Fujian Medical University, China 2010-2015, B.S., Clinical Medicine, Fujian Medical University, China Professional Experience 2021-present, Postdoctoral Fellow, Beckman Research Institute of City of Hope, Monrovia, CA 2019-2021, Visiting Graduate Researcher, Beckman Research Institute of City of Hope, Monrovia, CA Awards 2016, Outstanding graduate student of Fujian Medical University 2016, Scholarship of Fujian Medical University Memberships 2018-present, Anti-Cancer Association of China Publications Pan L, Li Y, Zhang HY, Liu XL, Hu Z, Wang Y, Wang J, Cai YH, Liu Q, Chen W, Guo Y, Huang YM, Qian F, Jin L, Wang J, Wang SY. DHX15 is associated with poor prognosis in acute myeloid leukemia (AML) and regulates cell apoptosis via the NF-kB signaling pathway. Oncotarget, 2017. Chen XL, Cai YH, Liu Q, Pan LL, Shi SL, Liu XL, Chen Y, Li JG, Wang J, Li Y, Li XF, Wang SY. ETS1 and SP1 drive DHX15 expression in acute lymphoblastic leukaemia. J. Cell. Mol. Med, 2017.

Wei Lu, M.S., Ph.D.

Postdoctoral Fellow

Research Focus Development of methods for designing and predicting drug-target binding and ligand binding areas Algorithms for cancer epigenetics-related information analysis Regulatory network analysis Wei Lu, Ph.D., M.S., is a postdoctoral fellow at the David Chen Lab in the Department of Systems Biology. He received his Ph.D. and M.S. degrees in informatics (computer science) at Kyoto University, Japan, and his B.S. in software engineering from Dalian Jiaotong University, China. Before joining the City of Hope, Dr. Lu worked as a research assistant developing novel methods for analyzing metabolic networks and predicting protein structures at Kyoto University. He also joined the research projects of traffic information systems supported by the Japanese government at the National Institute of Informatics, Japan. Currently, his research focuses on creating novel computational methods to support the development of diagnostics and therapeutics. Dr. Lu wants to develop cutting-edge computer technology to serve our patients. Degrees 2015, Ph.D., Informatics (Computer Science), Kyoto University, Kyoto, Japan 2011, M.S., Informatics (Computer Science), Kyoto University, Kyoto, Japan 2004, B.S., Software Engineering, Dalian Jiaotong University, Liaoning, China Professional Experience 2019-present, Postdoctoral Fellow, Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA 2015-2017, Postdoctoral Fellow, Digital Content and Media Sciences Research, National Institute of Informatics, Tokyo, Japan Publications Tamura T, Lu W, Song J, Akutsu T. Computing Minimum Reaction Modifications in a Boolean Metabolic Network. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2018; 15(6): 1853-62. Alegre-Sanahuja J, Lu W, Takasu A. Wavelet Transform Based Vehicle Detection from Sensors for Bridge Weigh-in-Motion. The 31st Annual ACM Symposium on Applied Computing (SAC2016). 2016; 935-940. Tamura T, Lu W, Akutsu T. Computational Methods for Modification of Metabolic Networks. Computational and Structural Biotechnology Journal. 2015; 13: 376-81. Lu W, Tamura T, Song J, Akutsu T. Computing Smallest Intervention Strategies for Multiple Metabolic Networks in a Boolean Model. Journal of Computational Biology. 2015; 22(2): 85-110. Lu W, Tamura T, Song J, Akutsu T. Integer programming-based method for designing synthetic metabolic networks by minimum reaction insertion in a Boolean model. PLoS ONE. 2014; 9: e92637.

Wei Lu, M.S., Ph.D.

Postdoctoral Fellow

Research Focus

Development of methods for designing and predicting drug-target binding and ligand binding areas
Algorithms for cancer epigenetics-related information analysis
Regulatory network analysis

Wei Lu, Ph.D., M.S., is a postdoctoral fellow at the David Chen Lab in the Department of Systems Biology. He received his Ph.D. and M.S. degrees in informatics (computer science) at Kyoto University, Japan, and his B.S. in software engineering from Dalian Jiaotong University, China. Before joining the City of Hope, Dr. Lu worked as a research assistant developing novel methods for analyzing metabolic networks and predicting protein structures at Kyoto University. He also joined the research projects of traffic information systems supported by the Japanese government at the National Institute of Informatics, Japan. Currently, his research focuses on creating novel computational methods to support the development of diagnostics and therapeutics. Dr. Lu wants to develop cutting-edge computer technology to serve our patients.

Degrees

2015, Ph.D., Informatics (Computer Science), Kyoto University, Kyoto, Japan
2011, M.S., Informatics (Computer Science), Kyoto University, Kyoto, Japan
2004, B.S., Software Engineering, Dalian Jiaotong University, Liaoning, China

Professional Experience

2019-present, Postdoctoral Fellow, Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA
2015-2017, Postdoctoral Fellow, Digital Content and Media Sciences Research, National Institute of Informatics, Tokyo, Japan

Publications

Tamura T, Lu W, Song J, Akutsu T. Computing Minimum Reaction Modifications in a Boolean Metabolic Network. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2018; 15(6): 1853-62.
Alegre-Sanahuja J, Lu W, Takasu A. Wavelet Transform Based Vehicle Detection from Sensors for Bridge Weigh-in-Motion. The 31st Annual ACM Symposium on Applied Computing (SAC2016). 2016; 935-940.
Tamura T, Lu W, Akutsu T. Computational Methods for Modification of Metabolic Networks. Computational and Structural Biotechnology Journal. 2015; 13: 376-81.
Lu W, Tamura T, Song J, Akutsu T. Computing Smallest Intervention Strategies for Multiple Metabolic Networks in a Boolean Model. Journal of Computational Biology. 2015; 22(2): 85-110.
Lu W, Tamura T, Song J, Akutsu T. Integer programming-based method for designing synthetic metabolic networks by minimum reaction insertion in a Boolean model. PLoS ONE. 2014; 9: e92637.

Nicole Mattson, B.S.

Graduate Student

Research Focus High throughput CRISPR screens for identification of essential surface proteins in breast cancer Nicole Mattson received her B.S. in biology with a focus in molecular biology and a minor in biotechnology from Santa Clara University in 2016. In June 2016, she joined the Vaccines Immunotherapy department at Pfizer in La Jolla, California, working on novel cancer therapeutics. In August 2018, Mattson started her graduate education at the Irell & Manella Graduate School of Biological Sciences at City of Hope. In July 2019, she joined the David Chen Lab in the Department of Systems Biology. Her research is focused on using high throughput CRISPR screens to identify essential genes on the surface of cancer cells. Her ultimate goal is to discover novel therapeutics to target identified genes. Degrees 2016, B.S. Biology, Minor Biotechnology, Santa Clara University, Santa Clara, CA

Sheela Pangeni Pokharel, M.S.

Research Associate II

Clinical Expertise Genotyping DNA/RNA/plasmid DNA extraction/preparation CRISPR library cloning Degrees 2015, M.S., Applied Microbiology and Biotechnology, University of Wolverhampton, England, United Kingdom 2009, B.S., Microbiology, Tribhuvan University, Kathmandu, Nepal Professional Experience 2017-present, Research Associate II, City of Hope Beckman Research Institute, Monrovia, CA 2016-2017, Research Technologist II, Northwestern University, Chicago, IL

Xiaobao Xu, Ph.D.

Postdoctoral Fellow

Research Focus Precision medical with single cell detection and imaging Investigation of epigenetics by using CRISPR-CAS9 Immunotherapy and mechanism of immune system respond to inflammation Dr. Xiaobao Xu obtained his Ph.D. degree from Zhejiang University, China. He is experienced in biomimicry drug self-delivery system based on red blood cells membrane, and immunotherapy based on combined checkpoint inhibitor with thermal therapy. Dr. Xu joined David Chen’s laboratory at the Department of Systems Biology in January 2019. His current projects focus on developing novel CRISPR-based systems for epigenome editing and cancer therapy. Degrees 2014 - 2018, Ph.D., Biomedical Engineering, Zhejiang University, Hangzhou, P. R. China 2009 - 2012, M.S. Bioengineering, Guizhou University, Guiyang, P. R. China 2005 - 2009, B.S. Bioengineering, Guizhou University, Guiyang, P. R. China Fellowship 2019 – Current, Department of Systems Biology, City of Hope Beckman Research Institute, Monrovia, CA Professional Experience 2019 – present, Postdoctoral Fellow, Department of Systems Biology, City of Hope Beckman Research Institute, Monrovia, CA 2016-2018, Visiting Scholar, Department of Biochemistry and Molecular Medicine, Medical Center, University of California, Davis, CA 2014-2018, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, P. R. China Publications Xu X, Yang G, Xue X, et al(2018). A polymer-free, biomimicry drug self-delivery system fabricated via a synergistic combination of bottom-up and top-down approaches[J]. Journal of Materials Chemistry B, 6(47): 7842-7853. XB. Xu, ed. Al. (2016) Metabolomic profile for the early detection of coronary artery disease by using UPLC-QTOF/MS.Journal of pharmaceutical and biomedical analysis, 129, 34-42. XB.Xu,TX.Wu,QL.Tang.(2016)ChangesinGastrodiatuber,EthanolExtracts During Grifola frondosa, Fermentation. Chemistry of Natural Compounds, 52(1):74-77. XD. Xue, Yee. Huang, RN. Bo, B. Jia, H. Wu, Y. Yuan, ZL. Wang, Z. Ma, D. Jing, XB. Xu, et al. (2018) Trojan Horse nanotheranostics with dual transformability and multifunctionality for highly effective cancer treatment. Nature Communications, DOI: 10.1038/s41467-018-06093-5. W. Zhu, XB. Xu, JK. Tian, et al.(2015) Proteomic Analysis of Lonicera japonica Thunb. Immature Flower Buds using Combinatorial Peptide Ligand Libraries and Polyethylene Glycol Fractionation. Journal of Proteome Research.

Xiaobao Xu, Ph.D.

Postdoctoral Fellow

Research Focus

Precision medical with single cell detection and imaging
Investigation of epigenetics by using CRISPR-CAS9
Immunotherapy and mechanism of immune system respond to inflammation

Dr. Xiaobao Xu obtained his Ph.D. degree from Zhejiang University, China. He is experienced in biomimicry drug self-delivery system based on red blood cells membrane, and immunotherapy based on combined checkpoint inhibitor with thermal therapy. Dr. Xu joined David Chen’s laboratory at the Department of Systems Biology in January 2019. His current projects focus on developing novel CRISPR-based systems for epigenome editing and cancer therapy.

Degrees

2014 - 2018, Ph.D., Biomedical Engineering, Zhejiang University, Hangzhou, P. R. China
2009 - 2012, M.S. Bioengineering, Guizhou University, Guiyang, P. R. China
2005 - 2009, B.S. Bioengineering, Guizhou University, Guiyang, P. R. China

Fellowship

2019 – Current, Department of Systems Biology, City of Hope Beckman Research Institute, Monrovia, CA

Professional Experience

2019 – present, Postdoctoral Fellow, Department of Systems Biology, City of Hope Beckman Research Institute, Monrovia, CA
2016-2018, Visiting Scholar, Department of Biochemistry and Molecular Medicine, Medical Center, University of California, Davis, CA
2014-2018, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, P. R. China

Publications

Xu X, Yang G, Xue X, et al(2018). A polymer-free, biomimicry drug self-delivery system fabricated via a synergistic combination of bottom-up and top-down approaches[J]. Journal of Materials Chemistry B, 6(47): 7842-7853.
XB. Xu, ed. Al. (2016) Metabolomic profile for the early detection of coronary artery disease by using UPLC-QTOF/MS.Journal of pharmaceutical and biomedical analysis, 129, 34-42.
XB.Xu,TX.Wu,QL.Tang.(2016)ChangesinGastrodiatuber,EthanolExtracts During Grifola frondosa, Fermentation. Chemistry of Natural Compounds, 52(1):74-77.
XD. Xue, Yee. Huang, RN. Bo, B. Jia, H. Wu, Y. Yuan, ZL. Wang, Z. Ma, D. Jing, XB. Xu, et al. (2018) Trojan Horse nanotheranostics with dual transformability and multifunctionality for highly effective cancer treatment. Nature Communications, DOI: 10.1038/s41467-018-06093-5.
W. Zhu, XB. Xu, JK. Tian, et al.(2015) Proteomic Analysis of Lonicera japonica Thunb. Immature Flower Buds using Combinatorial Peptide Ligand Libraries and Polyethylene Glycol Fractionation. Journal of Proteome Research.

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High-Resolution Characterization Of Gene Function Using Single-Cell CRISPR Tiling Screen. Nat Commun 12, 4063 (2021)

Yang, L., Chan, A., Miyashita, K, Delaney, C., Wang, X., Li, H., Pokharel, S., Li, S., Li, M., Xu, X., Lu, W., Liu, Q., Matthson, N., Chen, Wang, J., Yuan, Y.C., Horne, D., Rosen, S., Soto-Feliciano, Y., Feng, Z., Hoshii, T., Xio, G., Müschen, M., Chen, J., Armstrong, S.A. and Chen, C.W.

PLCG1 Is Required For AML1-ETO Leukemia Stem Cell Self-Renewal. Blood, blood.2021012778. Advance online publication.(2021)

Schnoeder, T.M., Schwarzer, A., Jayavelu, A.K., Hsu, C.J., Kirkpatrick, J., Döhner, K., Perner, F., Eifert, T., Huber, N., Arreba-Tutusaus, P., Dolnik, A., Assi, S.A., Nafria, M., Jiang, L., Dai, Y.T., Chen, Z., Chen, S.J., Kellaway, S.G., Ptasinska, A., Ng, E.S., Stanley, E.G., Elefanty, A.G., Buschbeck, M., Bierhoff, H., Brodt, S., Matziolis, G., Fischer, K.D., Hochhaus, A., Chen, C.W., Heidenreich, O., Mann, M., Lane, S.W., Bullinger, L., Ori, A., von Eyss, B., Bonifer, C., and Heidel, F.H.

3-Ketodihydrosphingosine Reductase Maintains ER Homeostasis And Unfolded Protein Response In Leukemia. Leukemia, 10.1038/s41375-021-01378-z. Advance online publication.

Liu, Q., Chan, A.K.N., Chang, W.H., Yang, L., Pokharel, S.P., Miyashita, K., Mattson, N., Xu, X., Li, M., Lu, W., Lin, R.J., Wang, S.Y. and Chen, C.W. (corresponding)

Generation And Validation Of CRISPR-Engineered Human Natural Killer Cell Lines For Research And Therapeutic Applications. STAR protocols, 2(4), 100874.

Kumar, A., Lee, S.J., Liu, Q., Chan, A., Pokharel, S.P., Yu, J., Chen, C.W. and Swaminathan, S.

Glycoproteome Remodeling In MLL-Rearranged B-Cell Precursor Acute Lymphoblastic Leukemia. Theranostics, 11(19), 9519–9537.

Oliveira, T., Zhang, M., Joo, E.J., Abdel-Azim, H., Chen, C.W., Yang, L., Chou, C.H., Qin, X., Chen, J., Alagesan, K., Almeida, A., Jacob, F., Packer, N.H., von Itzstein, M., Heisterkamp, N. and Kolarich, D.

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