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Research Lab Overview

The Chen laboratory is interested in discovering novel genetic/epigenetic regulations and the associated molecular mechanisms of both protein-coding genes and noncoding RNAs (e.g., microRNAs) in normal developmental processes (e.g., hematopoiesis) and tumorigenesis (e.g., leukemogenesis). In recent years, Chen and colleagues have been focusing on both basic and translational research associated with RNA/DNA epigenetics, especially RNA methylation/demethylation related to the N6 methyladenosine (m6A) machinery and DNA demethylation related to the TET1/2/3 family, and have developed several small-molecule compound inhibitors to selectively target cancer-related RNA/DNA epigenetic modifiers that hold therapeutic potential. The ultimate goal of the lab is to translate the laboratory discoveries into the development of effective novel therapeutic strategies to treat cancers, especially acute leukemia, in the clinic.

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Principal Investigator: Jianjun Chen, Ph.D.

Professor and Chair of the Department of Systems Biology, Jianjun Chen conducts research that focuses on systems biology. He received his Ph.D. from Shanghai Institute of Biochemistry, Chinese Academy of Sciences, Shanghai, China, and then conducted postdoctorate training with Dr. Janet D. Rowley at University of Chicago, Department of Medicine where he launched his independent laboratory in 2009.

Full bio

Lab Members

Meiling Chen

Visiting Scholar

Research Focus Epitranscriptomic dysregulation in leukemogenesis Education 2020-present, Ph.D. candidate, Hematology, Fujian Medical University, Fuzhou, Fujian, China 2014, B.S. and M.D., Clinical Medicine, Fujian Medical University, Fuzhou, Fujian, China Professional Experience 2021-present, Visiting Scholar, Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 2018-present, Attending Physician, Department of Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian, China Awards 2014, Outstanding Graduate Student of Fujian Medical University 2012, National Scholarship for Graduate Students Memberships 2020-present, Secretary of the Youth Committee of the Hematology Physician of Fujian Medical Association Publications The effect of interfering TGF-β receptor ǁ expression on NB4 cells proliferation and different response to ATRA and ATO. Chin J Pathol. 2018, 34(10): 1729-1735. Chen M, Zhang S, Chen Y, Guo Y, Wu Y. Expression and role of granulocyte macrophage colony-stimulating factor receptor (GM-CSFR) and granulocyte colony-stimulating factor receptor(G-CSFR) on Ph-positive acute B lymphoblastic leukemia. Hematology. 2018, 23(8): 439-447. Tan M, Chen M, Chen Y, Wu Y.

Zhen-Hua Chen, Ph.D.

Postdoctoral Fellow, Department of Systems Biology

Research Focus Identification and analysis of RNA epigenetics Investigation of leukemia and other cancers Contact Email: zhenhchen@coh.org

Xiaolan Deng

Assistant Research Professor, Department of Systems Biology

Research Focus New cancer therapy targeting methyltransferse Role of m6A modification in acute myeloid leukemia Contact Email: xideng@coh.org Full bio

Lei Dong, Ph.D.

Staff Scientist, Department of Systems Biology

Research Focus Developing a manually extracted database of experimentally supported database of RNA deregulation in various cancers Systematic analysis of epigenetic regulation of RNA expression in gastric cancer Identifying SNP INDEL SV and CNV in cancer cells by using single cell sequence Analyzing the results of ChIP and next-generation sequencing, developing innovative algorithms for high-throughput data Contact Email: ledong@coh.org

Li Han

Postdoctoral Fellow, Department of Systems Biology

Research Focus RNA/DNA epigenetics, especially RNA methylation/demethylation Small molecule compound inhibitors to treat cancers Identification of new RNA methylation “writer” Contact Email: lihan@coh.org

Keith Leung

Research Associate II

Research Focus DNA/RNA epigenetics Investigation of small molecules and compound inhibitors that show therapeutic potential for treating cancers Genotyping

Wei Li, Ph.D.

Postdoctoral Fellow, Department of Systems Biology

Research Focus Functional analysis of DNA/RNA regulators during leukemogenesis and normal hematopoietic differentiation Screening and optimization of new targets for leukemia immmunotherapeutics Contact Email: weili2@coh.org

Xi (Iris) Qin, M.S.

Graduate Student, Department of Systems Biology

Research Focus Epigenetic regulation in acute lymphoblastic leukemia Contact Email: xqin@coh.org

Ying Qing, M.D., Ph.D.

Postdoctoral Fellow

Ying Qing received her M.D. from Shandong University, China, and her Ph.D. from the Irell & Manella Graduate School of Biological Sciences at City of Hope. She joined the Jianjun Chen lab in 2017. Her current research is focused on (1) deciphering the common epitranscriptomic mechanism underlying obesity and cancer and (2) comparing the different roles of TET1 protein in leukemia and solid tumors and identifying the different regulatory pathways. Her long-term research interests involve developing a comprehensive understanding of the mechanisms, especially epigenetic or epitranscriptomic mechanism, underlying cancer initiation, promotion, and progression, and how to develop novel effective anti-cancer therapies based on that knowledge. Research Focus Uncovering the common epitranscriptomic signaling pathway that mediates the development of obesity and cancer induced by Western lifestyle Different roles of TET1 in leukemia and solid tumors Degrees 2021, Ph.D., Biological Sciences, Irell & Manella Graduate School of Biological Sciences at City of Hope, Duarte, CA 2015, M.D., Clinical Medicine (Internal Medicine), Shandong University, Jinan, China Professional Experience 2021-present, Postdoctoral Fellow, Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA Publications Qing, Y.*, Dong, L.*, Gao, L.*, Li, C., Li, Y., Han, L., Prince, E., Tan, B., Deng, X., Wetzel, C., Shen, C., Gao, M., Chen, Z., Li, W., Zhang, B., Braas, D., Hoeve, J.T., Sanchez, G.J., Chen, H., Chan, L.N., Chen, C.W., Ann, D., Jiang, L., Müschen, M., Marcucci, G., Plas, D., Li, Z., Su, R., & Chen, J. R-2-hydroxyglutarate attenuates aerobic glycolysis in leukemia by targeting the FTO/m6A/PFKP/LDHB axis. Molecular Cell. 2021;81(5):922-39. doi: 10.1016/j.molcel.2020.12.026, 2021. PubMed PMID: 33434505. (*Co-first authors) Qing, Y., Su, R., & Chen, J. RNA modifications in hematopoietic malignancies: A new research frontier. Blood. 2021;138(8):637-648. doi: 10.1182/blood.2019004263. PubMed PMID: 34157073. Qing, Y., Gao, L., Han, L., Su, R., & Chen, J. Evaluation of glycolytic rates in human hematopoietic stem/progenitor cells after target gene depletion. STAR Protoc. 2021;2(2):100603. doi: 10.1016/j.xpro.2021.100603. PubMed PMID: 34169295. Su, R.*, Qing, Y.*, & Chen, J. Targeting Differentiation Blockade in AML: New Hope from Cell Surface-based CRISPR Screens. Cell Stem Cell. 2021;28(4):585-7. doi: 10.1016/j.stem.2021.03.006. PubMed PMID: 33798415. (*Co-first authors) Qing, Y., Tian, Z., Bi, Y., Wang, Y., Long, J., Song, C.X., & Diao, J. Quantitation and mapping of the epigenetic marker 5-hydroxymethylcytosine. Bioessays. 2017;39(5):1700010. doi: 10.1002/bies.201700010. Review. PubMed PMID: 28332209. Qing, Y., Wang, M., Lin, Y.M., Wu, D., Zhu, J.Y., Gao, L., Liu, Y.Y., & Yin, T.F. Correlation between Helicobacter pylori-associated gastric diseases and colorectal neoplasia. World J Gastroenterol. 2016;22(18):4576-84. doi: 10.3748/wjg.v22.i18.4576. PubMed PMID: 27182167.

Ying Qing, M.D., Ph.D.

Postdoctoral Fellow

Research Focus

Uncovering the common epitranscriptomic signaling pathway that mediates the development of obesity and cancer induced by Western lifestyle
Different roles of TET1 in leukemia and solid tumors

Degrees

2021, Ph.D., Biological Sciences, Irell & Manella Graduate School of Biological Sciences at City of Hope, Duarte, CA
2015, M.D., Clinical Medicine (Internal Medicine), Shandong University, Jinan, China

Professional Experience

2021-present, Postdoctoral Fellow, Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA

Publications

Qing, Y.*, Dong, L.*, Gao, L.*, Li, C., Li, Y., Han, L., Prince, E., Tan, B., Deng, X., Wetzel, C., Shen, C., Gao, M., Chen, Z., Li, W., Zhang, B., Braas, D., Hoeve, J.T., Sanchez, G.J., Chen, H., Chan, L.N., Chen, C.W., Ann, D., Jiang, L., Müschen, M., Marcucci, G., Plas, D., Li, Z., Su, R., & Chen, J. R-2-hydroxyglutarate attenuates aerobic glycolysis in leukemia by targeting the FTO/m6A/PFKP/LDHB axis. Molecular Cell. 2021;81(5):922-39. doi: 10.1016/j.molcel.2020.12.026, 2021. PubMed PMID: 33434505. (*Co-first authors)
Qing, Y., Su, R., & Chen, J. RNA modifications in hematopoietic malignancies: A new research frontier. Blood. 2021;138(8):637-648. doi: 10.1182/blood.2019004263. PubMed PMID: 34157073.
Qing, Y., Gao, L., Han, L., Su, R., & Chen, J. Evaluation of glycolytic rates in human hematopoietic stem/progenitor cells after target gene depletion. STAR Protoc. 2021;2(2):100603. doi: 10.1016/j.xpro.2021.100603. PubMed PMID: 34169295.
Su, R.*, Qing, Y.*, & Chen, J. Targeting Differentiation Blockade in AML: New Hope from Cell Surface-based CRISPR Screens. Cell Stem Cell. 2021;28(4):585-7. doi: 10.1016/j.stem.2021.03.006. PubMed PMID: 33798415. (*Co-first authors)
Qing, Y., Tian, Z., Bi, Y., Wang, Y., Long, J., Song, C.X., & Diao, J. Quantitation and mapping of the epigenetic marker 5-hydroxymethylcytosine. Bioessays. 2017;39(5):1700010. doi: 10.1002/bies.201700010. Review. PubMed PMID: 28332209.
Qing, Y., Wang, M., Lin, Y.M., Wu, D., Zhu, J.Y., Gao, L., Liu, Y.Y., & Yin, T.F. Correlation between Helicobacter pylori-associated gastric diseases and colorectal neoplasia. World J Gastroenterol. 2016;22(18):4576-84. doi: 10.3748/wjg.v22.i18.4576. PubMed PMID: 27182167.

Chao Shen, Ph.D.

Postdoctoral Fellow, Department of Systems Biology

Research Focus Role of DNA and RNA modifiers in leukemia Therapeutic value of small compounds targeting cancer-related RNA/DNA epigenetic modifiers Contact Email: chashen@coh.org

Lu Yang, Ph.D.

Assistant Research Professor, Department of Systems Biology

Research Focus Functional analysis of tiling CRISPR screen in cancer research, to further dissect functional protein domain or novel domain. Single cell transcriptomic analysis, in conjugation with single cell CRISPR screen. Integrating systems biology, clinical science, sequencing techniques and bioinformatics to improve cancer research, diagnosis and treatment. Appointments Assistant Research Professor, Department of Systems Biology

Kitty Wang

Research Associate II

Research Focus Role of DNA and RNA modifiers in leukemia Therapeutic value of small compounds targeting cancer-related RNA/DNA epigenetic modifiers

Dong Wu, Ph.D.

Postdoctoral Fellow

Research Focus Association between metabolic disorder and cancer development Degrees 2013-2018, Ph.D., Shandong University, Jinan, China 2016-2018, visiting Ph.D. student, University of Cincinnati, OH 2008-2013, M.D., Shandong University, Jinan, China Fellowship 2020-2022, Fellowship in Pancreatic Surgery, Qilu Hospital of Shandong University, Jinan, China Residency 2018-2020, Residency in General Surgery, Qilu Hospital of Shandong University, Jinan, China Professional Experience 2022-present, Postdoctoral fellow, Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA Awards 2019, First prize of Shandong Province Science and Technology Progress Award (11/12) 2014, Outstanding Graduate Students of Shandong University 2012, National Scholarship 2009, National Endeavor Scholarship Publications Wu, D., Cheng, Y.G., Huang, X., Zhong, M.W., Liu, S.Z., & Hu, S.Y. Downregulation of lncRNA MALAT1 contributes to renal functional improvement after duodenal-jejunal bypass in a diabetic rat model. J Physiol Biochem. 2018 Aug;74(3):431-439. doi: 10.1007/s13105-018-0636-y. Epub 2018 May 21. PMID: 29781038. Wu, D.*, Yan, Z.B.*, Cheng, Y.G., Zhong, M.W., Liu, S.Z., Zhang, G.Y., & Hu, S.Y. Deactivation of the NLRP3 inflammasome in infiltrating macrophages by duodenal-jejunal bypass surgery mediates improvement of beta cell function in type 2 diabetes. Metabolism. 2018 Apr;81:1-12. doi: 10.1016/j.metabol.2017.10.015. Epub 2017 Nov 10. PMID: 29129820. Zhan, H.X., Xu, J.W., Wu, D., Wu, Z.Y., Wang, L., Hu, S.Y., & Zhang, G.Y. Neoadjuvant therapy in pancreatic cancer: a systematic review and meta-analysis of prospective studies. Cancer Med. 2017 Jun;6(6):1201-1219. doi: 10.1002/cam4.1071. Epub 2017 May 23. PMID: 28544758; PMCID: PMC5463082.

Dong Wu, Ph.D.

Postdoctoral Fellow

Research Focus

Association between metabolic disorder and cancer development

Degrees

2013-2018, Ph.D., Shandong University, Jinan, China
2016-2018, visiting Ph.D. student, University of Cincinnati, OH
2008-2013, M.D., Shandong University, Jinan, China

Fellowship

2020-2022, Fellowship in Pancreatic Surgery, Qilu Hospital of Shandong University, Jinan, China

Residency

2018-2020, Residency in General Surgery, Qilu Hospital of Shandong University, Jinan, China

Professional Experience

2022-present, Postdoctoral fellow, Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA

Awards

2019, First prize of Shandong Province Science and Technology Progress Award (11/12)
2014, Outstanding Graduate Students of Shandong University
2012, National Scholarship
2009, National Endeavor Scholarship

Publications

Wu, D., Cheng, Y.G., Huang, X., Zhong, M.W., Liu, S.Z., & Hu, S.Y. Downregulation of lncRNA MALAT1 contributes to renal functional improvement after duodenal-jejunal bypass in a diabetic rat model. J Physiol Biochem. 2018 Aug;74(3):431-439. doi: 10.1007/s13105-018-0636-y. Epub 2018 May 21. PMID: 29781038.
Wu, D.*, Yan, Z.B.*, Cheng, Y.G., Zhong, M.W., Liu, S.Z., Zhang, G.Y., & Hu, S.Y. Deactivation of the NLRP3 inflammasome in infiltrating macrophages by duodenal-jejunal bypass surgery mediates improvement of beta cell function in type 2 diabetes. Metabolism. 2018 Apr;81:1-12. doi: 10.1016/j.metabol.2017.10.015. Epub 2017 Nov 10. PMID: 29129820.
Zhan, H.X., Xu, J.W., Wu, D., Wu, Z.Y., Wang, L., Hu, S.Y., & Zhang, G.Y. Neoadjuvant therapy in pancreatic cancer: a systematic review and meta-analysis of prospective studies. Cancer Med. 2017 Jun;6(6):1201-1219. doi: 10.1002/cam4.1071. Epub 2017 May 23. PMID: 28544758; PMCID: PMC5463082.