Introduction
With the development and improvement of high-throughput sequencing technologies, the acquisition and processing approaches of various biological omics data on different levels are becoming more mature. Despite several new disease-associated factors have been discovered based on single omics data analysis, identification of disease targets by integrative analysis of multi-omics data is still growing. Since life is a complex regulatory system in which the regulation of gene mutations, epigenetic alterations, abnormal gene expression as well as anomalous variations in signal pathway are related with the occurrence and development of diseases, it is obvious that finding therapeutic factors using single omics data analysis has its limitation. Systematical studies of clinical and pathological mechanisms and identification of optimal therapeutic targets through integrative analysis of multi-omics data from different levels and resources have become an important research direction of precision medicine, which would provide innovative perspectives on disease study and new theoretical basis for early diagnosis, personalized treatment and medicine guide.
Erythroid differentiation is an excellent example of the complex changes in temporal, developmental, and differentiation stage-specific gene expression exhibited by a single cell type. Previous studies indicated that erythroid differentiation is finely regulated by multiple factors: trans-factors, cis-elements, non-coding RNAs and chromatin conformation. Using multiple technologies including DNase I-Seq, histone ChIP-seq, chromatin conformation capture (3C-Seq), mRNA-seq, and miRNA-seq, we preliminary grasp the epigenetic and transcriptional dynamic profiles during erythroid differentiation and development. Integrative analyses on these data will help us to screen more candidates that may play key role in erythroid differentiation. We aim to identify and confirm key factors in erythroid differentiation for further clinical use.
Melanoma is characterized by genetic heterogeneity, high malignancy, and poor prognosis. Melanoma is one of the successful models for the study of tumor molecular typing and targeted drug development. The scientists from Europe and United States had developed BRAF inhibitor and anti-PD-1 for precision treatment by utilizing large-scale biologic databases, omics methods, functional assays, and computational tools. However, Caucasian melanoma patients have shown different in clinical features and gene mutation spectrum with Chinese population. Thus, efforts are still needed to improve the ways we anticipate, prevent, diagnose, and treat melanoma in China. Basically, analyzing more melanoma genomes and functional confirming of key genes/factors are needed to achieve deeper understanding of melanoma initiation and development in Chinese population.
Group Leader
Dr. FANG Xiangdong is currently a professor of Beijing Institute for Genomics, Chinese Academy of Sciences (CAS). Dr. FANG started his scientific career since 1992 when he received his M.D. degree from Nanfang Medical University in Guangzhou, China. After 5-years professional training at the State Key Laboratory of Molecular Biology leaded by Dr. CHI Chengwu, the Academician of CAS, in the Institute of Biochemistry and Cell Biology in CAS in Shanghai, Dr. FANG received his Master degree in Immunology in 1995 and Ph.D. degree in Anatomy and Histology and Embryology in 1999.
Dr. FANG continued his postdoctoral research in the Division of Medical Genetics in the Medical School at University of Washington (Seattle, WA, USA) from 2000 to 2003. He was promoted to Instructor in 2003 and Research Assistant Professor in Medicine in 2007. When he worked in the Dr. George Stamatoyannopoulos’s lab, Dr. FANG developed the methods named chromatin immunoprecipitation (ChIP) and chromatin conformation capture (3C) assay by adapting the real-time PCR method. These quantitative methods are two of the most important epigenetic techniques to study protein-DNA and protein-protein interactions in vivo.
Dr. FANG’s works focus on the epigenetic regulation in the eukaryocyte and high-throughput epigenetic techniques based on next-generation sequencing platform. Dr. FANG’s works had provided major insights about the role of some important trans-factors and cis-elements in globin gene regulation. The mutations impair recruitment of TBP, TFIIB, and Pol II in adult splenic erythroblasts, but not in embryonic erythroid cells (PNAS, 2002 & 2004; J Biol Chem, 2004; Nucleic Acids Res, 2006). High-level transcription of the globin genes requires the enhancement of a distant enhancer, locus control region (LCR) (Blood, 2002; Mol Cell Biol, 2005; J Mol Biol, 2007;J Mol Biol, 2009).
The focus of our current research is to dissect the molecular mechanism controlling stem cell differentiation, hematopoiesis and tumor metastasis. With next-generation sequencing, the biological data deluge imminent both in size and complexity. Meanwhile, a large body of clinical and pharmaceutical data has been accumulated and is urgent to be truly enhanced with molecular pathology, which provides us big opportunities and challenges to achieve our research goals. We will construct the system of biomedical big data standardization, integration, processing and utilization to make the data analysis faster and more accurate, and most importantly to discover clinical biomarkers. By interpreting various omics and clinical data of massive normal and disease samples, we are trying to construct essential interaction networks related to diseases which consist of trans-factors, cis-elements, coding and non-coding RNAs, methylated DNA, post-translational histones, as well as chromatin conformation. Appropriate cell lines and animal models will be used to confirm the hypothesis. Erythroid differentiation of stem cells is chose as normal lineage developmental model for its distinctive stage specificity. Melanoma is chose as carcinoma model for its highly malignant property.
1. Identification of the Novel Regulatory Factors and Their Networks in Human Erythroid Differentiation and Development
We focus on how erythroid differentiation is precisely regulated to make sure sufficient qualified red blood cells produced. By RNA-seq, DNase I-seq, and histone modification ChIP-seq, we presented a global and dynamic view of gene expression and chromatin activity during erythroid differentiation. Comprehensive analyses of DNase I and histone modification data, as well as experimental validation identified novel enhancers and erythroid specific enhancers. RNA-seq data provided dynamic expression patterns of genes and non-coding RNAs. Integrative analyses suggested several potential erythroid regulating proteins and non-coding RNAs. Taking advantage of induced erythroid differentiation cell lines and zebrafish as model, our studies indicated that transcriptional factor FOXO3 and KLF3, non-coding RNA miR-218, and miR-200a play an important role in erythroid differentiation. We are trying to investigate erythroid differentiation by study chromatin itself and chromatin products to achieve a comprehensive understanding. Our efforts in erythroid differentiation involved with explorations at genomic, epigenomic, and transcription. Our current achievements provide novel regulator of erythroid differentiation and our study strategies enrich perspectives of the field.
Additionally, we pay attentions on erythroid disease, especially the Diamond-Blackfan anemia (DBA). To identify the DBA pathogenesis (why ribosomal gene mutation cause DBA and is there any novel gene mutation able to cause DBA?), we performed RNA-seq and miRNA-seq of DBA patient samples. Preliminary results show that several differentially expressed genes, one fusion gene, and expression of pseudo-genes of pathogenic genes (e.g. ribosomal gene) may play a role in DBA development. To get a further insight on how mutations of ribosomal genes lead to DBA, we applied zebrafish as model. Comprehensive analyses of experimental and sequencing results illustrated the molecular mechanism of RPL5, RPL11, RPS19, and RPS24 causing DBA respectively. Our studies provide valuable data and practical study model for DBA research.
2. Delineation of the Molecular Mechanism of Carcinoma Development and Metastasis
Carcinomas threat human health and wellbeing severely. Multiple Omics data do provide substantial information about tumors, however, experimental and clinical validation are still needed to achieve precision medicine. Melanoma is one of the malignant cancers with most rising morbidity and most lethality in skin tumor. The morbidity rate of melanoma is 3-5% per year. Even in China where morbidity rate is lower than Europe and North America, new cases of melanoma are increasing very fast which are more than 20,000 every year and number of fatality is also increasing. Locations of melanoma between Chinese and white people are quite different, since acral lentiginous melanomas are common among Chinese population and superficial spreading melanoma are among white population. The different locations of melanoma indicate that molecular mechanism will be various in these tumors. So we focus on melanoma to figure out its molecular mechanism of malignant and metastasis, and find genes and miRNAs that are involved in these progressions. To do this, we compared two cancer cell lines which are A375 and A2058 representing low metastatic melanoma and high metastatic melanoma respectively with a normal cell line which is HEMn-LP representing melanocyte. By analyzing RNA-seq data of these three cell lines, we provided a global and dynamic gene and miRNA differential expression pattern during melanoma developing. We focused on the genes and miRNAs which are involved in Epithelial-mesenchymal transition (EMT) and cancer stem cell (CSC), and then identified IGFBP5, MAGEA1, CTGF, Twist1 and miR-219 as candidates that may play a role during melanoma process. Through in vitro and in vivo examination, IGFBP5 was proved to act as an inhibit factor of melanoma, which can decrease the ability of migration, invasion in cancer cell, depress EMT and cancer stem cell markers. MiR-219 is a microRNA which target twist1, an oncogene in melanoma. This microRNA can inhibit melanoma migration and invasion in vitro. Our studies suggest that MAGEA1 and CTGF can both promote melanoma migration and invasion in vitro, and are associated with EMT. Migration and invasion of melanoma cell lines will be decreased by shRNAs which target MAGEA1 and CTGF. By functional biological studies in the cell lines and mouse models, we confirmed these candidates play a vital role in melanoma and revealed their molecular mechanisms. Our studies provided a helpful model and strategy as well as valuable omics data sets for melanoma and other carcinoma researches.
Taken together, our findings highlight the advantages of high-throughput based omics techniques are powerful tools to identify molecular biomarkers for disease diagnosis and therapy.
3. Construction of the Biological Knowledge Bases for Multiple Omics Data
Publicly-accessible resources have promoted the advance of scientific discovery. The era of genomics and big data has brought the need for collaboration and data sharing in order to make effective use of this new knowledge. To improve omics data management situation in China, we participate in construction of Genome Sequence Archive (GSA), a data repository for genome, transcriptome and other omics primitive sequencing data. GSA archives raw sequence data produced from a wide variety of sequencing platforms. For domestic researchers, GSA provides important and necessary support for effectively and expediently manage, access, and use omics data. To obtain a macroscopic and comprehensive view of life processing, we collected sets of genomic, transcriptomic, and epigenomic data. These data involved in several types of malignant tumors and (mimic) normal lineage differentiation. We developed a serial of analyses pipe lines and data storage criterions to investigate these omics data. These pipe lines and criterions will improve data utilization efficiency, and promote application of biomedical big data in near future.
Publications
1. Li Y#, Zhang Q#, Du Z#, Lu Z, Liu S, Zhang L, Ding N, Bao B, Yang Y, Xiong Q, Wang H, Zhang Z, Qu H, Jia H*, Fang X*. Hsa-miR-200a inhibits erythroid differentiation by targeting PDCD4 and THRB. Brit J Haematol 2017; 176(1): 50-64
2. Wang J#, Ding N#, Li Y#, Cheng H#, Wang D, Yang Q, Deng Y, Yang Y, Li Y, Ruan X, Xie F, Zhao H*, Fang X*. Insulin-like growth factor binding protein 5 (IGFBP5) functions as a tumor suppressor in human melanoma cells. Oncotarget 2015; 6(24): 20636-20649
3. Wang H#, Li Y#, Wang S#, Zhang Q, Zheng J, Yang Y, Qi H, Qu H, Zhang Z, Liu F*, Fang X*. Knockdown of transcription factor forkhead box O3 (FOXO3) suppresses erythroid differentiation in human cells and zebrafish. Biochem Biophys Res Commun 2015; 460(4): 923-930
4. Li Y#, Liu S#, Sun H#, Yang Y, Qi H, Ding N, Zheng J, Dong X, Qu H, Zhang Z, Fang X*. Regulation of ALAS2 by miR-218 during iron metabolism and erythroid differentiation. Int J Mol Sci 2015; 16: 28156-28168
5. Song B#, Zhang Q#, Zhang Z, Wan Y, Jia Q, Wang X, Zhu X, Leung AY, Cheng T, Fang X*, Yuan W*, Jia H*. Systematic transcriptome analysis of the zebrafish model of Diamond-Blackfan anemia induced by RPS24 deficiency. BMC Genomics 2014; 15: 759
6. Zhao H#, Li Y#, Wang S#, Yang Y, Wang J, Ruan X, Yang Y, Cai K, Zhang B, Cui P, Yan J, Zhao Y, Wakeland EK, Li Q, Hu S*, Fang X*. Whole transcriptome RNA-seq analysis: the tumorigenesis and metastasis of melanoma. Gene 2014; 548(2): 234-243
7. Zhang Z#, Jia H#, Zhang Q, Wan Y, Zhou Y, Jia Q, Zhang W, Yuan W, Cheng T, Zhu X*, Fang X*. Assessment of hematopoietic failure due to RPL11 deficiency in a zebrafish model of Diamond-Blackfan anemia by deep sequencing. BMC Genomics 2013; 14: 896
8. Yang Y#, Wang H#, Chang KH#, Qu H, Zhang Z, Xiong Q, Qi H, Cui P, Lin Q, Ruan X, Yang Y, Li Y, Shu C, Li Q, Wakeland EK, Yan J, Hu S*, Fang X*. Transcriptome dynamics during human erythroid differentiation and development. Genomics 2013; 102(5-6): 431-441
9. Wang Y#, Zhang Z#, Chi Y, Zhang Q, Xu F, Yang Z, Meng L, Yang S, Yan S, Mao A, Zhang J, Yang Y, Wang S, Cui J, Liang L, Ji Y, Han ZB*, Fang X*, Han Z*. Long-term cultured mesenchymal stem cells frequently develop genomic mutations but do not undergo malignant transformation. Cell Death Dis 2013; 4: e950
10. Chang KH#, Fang X#, Wang H, Huang A, Cao H, Yang Y, Bonig H, Stamatoyannopoulos JA, Papayannopoulou T*. Epigenetic modifications and chromosome conformations of the beta-globin locus throughout development. Stem Cell Rev 2013; 9(4): 397-407
11. Xiong Q#, Zhang Z#, Chang KH#, Qu H, Wang H, Qi H, Li Y, Ruan X, Yang Y, Yang Y, Li Y, Sandstrom R, Sabo PJ, Li Q, Stamatoyannopoulos G, Stamatoyannopoulos JA*, Fang X*. Comprehensive characterization of erythroid-specific enhancers in the genomic regions of human Krüppel-like factors. BMC Genomics 2013; 14: 587
12. Wang H#, Hu H#, Zhang Q, Yang Y, Li Y, Hu Y, Ruan X, Yang Y, Zhang Z, Shu C, Yan J, Wakeland EK, Li Q, Hu S*, Fang X*. Dynamic transcriptomes of human myeloid leukemia cells. Genomics 2013; 102(4): 250-256
13. Su RJ#, Yang Y#, Neises A, Payne KJ, Wang J, Viswanathan K, Wakeland EK, Fang X*, Zhang XB*. Few de novo single nucleotide variations in exomes of human cord blood induced pluripotent stem cells. PLoS One 2013; 8(4): e59908
14. Li Y#, Wang H#, Yang B#, Yang J, Ruan X, Yang Y, Wakeland EK, Li Q*, Fang X*. Influence of carbon monoxide on growth and apoptosis of human umbilical artery smooth muscle cells and vein endothelial cells. Int J Biol Sci 2012; 8(10): 1431-1446
15. Fang X, Yin W, Xiang P, Han H, Stamatoyannopoulos G*, Li Q*. The higher structure of chromatin in the LCR of the beta-globin locus changes during development. J Mol Biol 2009; 394(2): 197-208
16. Fang X, Xiang P, Yin W, Stamatoyannopoulos G, Li Q*. Cooperativeness of the higher chromatin structure of the beta-globin locus revealed by the deletion mutations of HS3 of the LCR. J Mol Biol 2007; 365(1): 31-37
17. Fang X, Sun J, Xiang P, Yu M, Navas PA, Peterson KR, Stamatoyannopoulos G, Li Q*. Synergistic and additive properties of the beta-globin LCR revealed by 5'HS3 deletion mutations: Implication for LCR chromatin architecture. Mol Cell Biol 2005; 25(16): 7033-7041
18. Fang X, Han H, Stamatoyannopoulos G, Li Q*. Developmentally specific role of the CCAAT box in regulation of human gamma-globin gene expression. J Biol Chem 2004; 279(7): 5444-5449
19. Fang X, Peterson KR, Li Q, Stamatoyannopoulos G*. Locus control regions. In: Makrides SC, ed. Gene Transfer And Expression In Mammalian Cells. St. Louis: Elsevier Science B.V.; 2003. pp. 397-409
20. Duan ZJ#, Fang X#, Rohde A, Han H, Stamatoyannopoulos G, Li Q*. Developmental specificity of recruitment of TBP to the TATA box of the human gamma-globin gene. Proc Natl Acad Sci USA 2002; 99(8): 5509-5514
Group Members
Staff
FANG Xiangdong (Principal Investigator) e-mail: fangxd@big.ac.cn
RUAN Xiuyan (Research Assistant) e-mail: ruanxy@big.ac.cn
QU Hongzhu (Associate Professor) e-mail: quhongzhu@big.ac.cn
ZHANG Zhaojun (Associate Professor) e-mail: zhangzhaojun@big.ac.cn
LI Yongjun (Assistant Professor) e-mail: yjli@big.ac.cn
LI Yanming (Assistant Professor) e-mail: liym@big.ac.cn
ZHANG Qian (Assistant Professor) e-mail: zhangqian@big.ac.cn
Graduate Students
2011 YANG Qiong
2013 XIE Bingbing
2014 SHI Jian, PENG Sie, REN Lan, ZHANG Lu
2015 YANG Yadong, WANG Chen, LI Pin, HE Ning
2016 XIAO Rudan, ZHU Junwei, ZHAO Xuetong, REN Yunxiao
Contact
Tel: +86-10-84097495
