
Jianjun Chen Lab
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.
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.



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.


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


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


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


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


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


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


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


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.


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


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


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


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.


Research Focus
- Identification and analysis DNA methylation in leukemia
- Screening and optimization of new targets for leukemia immunotherapeutic
Education
- 2007, M.D., Genetics, Henan University, China
- 2014, Ph.D., Genetics, Southeast University, China
Professional Experience
- 2021-present, Visiting Scholar, Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA
- 2014 -present, Resident, Central laboratory, Huai’an First People’s Hospital, Jiangsu, China
Awards
2021, Huai’an Science and Technology Star
Memberships
2021-present, Medical Genetics of Jiangsu Province
Publications
- Han, X., Zhang, C.*, & Ding, L.S.* PTIP Inhibits Cell Invasion in Esophageal Squamous Cell Carcinoma via Modulation of EphA2 Expression. Frontiers in oncology. 2021 Mar 23; 11: 629916.
- Zhang, C., et al. KDM6A promotes imatinib resistance through YY1-mediated transcriptional upregulation of TRKA independently of its demethylase activity in chronic myelogenous leukemia. Theranostics. 2021 Jan; 11(6):2691-2705.
- Zhang, C., et al. Drosophila UTX coordinates with p53 to regulate ku80 expression in response to DNA damage. PLoS One. 2013 Nov 12; 8(11):e78652.
Contact: 626-386-9339


Research Focus
- Exploring the interplay of epigenetic marks in chromatin configuration, and interaction of human genomes
- Studying the functions and mechanisms of RNA binding proteins and RNA modifications on RNAs with various high-throughput sequencing data
- Developing new bioinformatic methods for epigenetics and epitranscriptomics analysis


Research Focus
- The roles, mechanisms and therapeutic potential of m6A writers in solid tumors
We collaborate with organizations in progressing the development of new treatments in our specialized areas of research.

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