Myelodysplastic Syndromes (MDS) are chronic hematopoietic disorders characterized by dysplasia, inefficient hematopoiesis, and the propensity to transform into acute myeloid leukemia (AML). Recent advances in genomic sequencing revealed a large number of mutations associated with the disease, which can be roughly grouped into three classes: (1) genes involved in signaling (i.e. FLT3, JAK2, KRAS), (2) genes functioning at the levels of chromatin and pre-mRNA splicing (i.e. RUNX1, ASXL1, SRSF2, U2AF1), and (3) genes responsible for establishing/maintaining the genome methylome (i.e. DNMT3a, TET2, IDH1/2). Given MDS is highly heterogeneous in its clinical features, a fundamental question is whether individual mutations cause the disease via distinct mechanisms or whether many mutations function in some converging pathways. Support of the latter possibility is the co-occurrence of many of these causal mutations in MDS patients. As disease-oriented (Zhang) and mechanism-central (Fu) labs, we have been taking advantage of our combined expertise to work together under this funded R01 to attack some pressing questions in the field, focusing on RUNX1 and SRSF2. In the past funding cycle (9/2013-present), we have made two conceptual breakthroughs. First, by linking specific mutations to splicing responses in MDS patients, we found that non- overlapping responses induced by splicing factor mutations are converged to the common pathways of cell cycle and DNA damage response. Second, we unexpectedly uncovered that, besides their traditional roles in splicing, all causal mutations in key splicing factors trigger excessive R-loop formation, leading to replication stress and cell cycle checkpoint activation. These findings point to dysregulation of the DNA damage response as a common ground for MDS etiology. Importantly, such elucidated common ground has laid a critical foundation for our next phase of investigation, which is to understand the contribution of individual mutations to MDS and potential synergy among them, despite their diverse roles in regulating gene expression. Building upon both our published and unpublished results, we propose to pursue the following specific aims in the next phase:
Aim 1. Function of RUNX1 and its synergy with SRSF2 in preventing DNA damage;
Aim 2. Mutant SRSF2 and epigenetic regulators to synergistically drive aberrant gene expression;
Aim 3. Potential mechanism for bypassing R-loop-induced cell cycle checkpoint activation.

Public Health Relevance

Myelodyplastic syndrome (MDS) is a class of bone marrow cell failure and multi-lineage dysfunction disease, which affects the quality of life for many people in the world. Recent efforts in genomic sequencing led to the identification of major gene mutations associated with MDS. The aim of this application is to provide molecular insights of how such mutations lead to the disease in order to develop novel and effective treatments of related disorders.

National Institute of Health (NIH)
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)
Research Project (R01)
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Molecular and Cellular Hematology Study Section (MCH)
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Roy, Cindy
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University of California, San Diego
Schools of Medicine
La Jolla
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Zhang, Kai; Zhang, Xiaorong; Cai, Zhiqiang et al. (2018) A novel class of microRNA-recognition elements that function only within open reading frames. Nat Struct Mol Biol 25:1019-1027
Chen, Liang; Chen, Jia-Yu; Huang, Yi-Jou et al. (2018) The Augmented R-Loop Is a Unifying Mechanism for Myelodysplastic Syndromes Induced by High-Risk Splicing Factor Mutations. Mol Cell 69:412-425.e6
Chen, Liang; Chen, Jia-Yu; Zhang, Xuan et al. (2017) R-ChIP Using Inactive RNase H Reveals Dynamic Coupling of R-loops with Transcriptional Pausing at Gene Promoters. Mol Cell 68:745-757.e5
Li, Xiao; Zhou, Bing; Chen, Liang et al. (2017) GRID-seq reveals the global RNA-chromatin interactome. Nat Biotechnol 35:940-950
Fu, Xiang-Dong (2017) Exploiting the Hidden Treasure of Detained Introns. Cancer Cell 32:393-395
Lam, K; Muselman, A; Du, R et al. (2016) Loss of RUNX1 function results in enhanced granulocyte-colony-stimulating factor-mediated mobilization. Blood Cancer J 6:e407
Qiu, Jinsong; Zhou, Bing; Thol, Felicitas et al. (2016) Distinct splicing signatures affect converged pathways in myelodysplastic syndrome patients carrying mutations in different splicing regulators. RNA 22:1535-49
Wu, Tongbin; Fu, Xiang-Dong (2015) Genomic functions of U2AF in constitutive and regulated splicing. RNA Biol 12:479-85
Komeno, Yukiko; Huang, Yi-Jou; Qiu, Jinsong et al. (2015) SRSF2 Is Essential for Hematopoiesis, and Its Myelodysplastic Syndrome-Related Mutations Dysregulate Alternative Pre-mRNA Splicing. Mol Cell Biol 35:3071-82
Lam, Kentson; Muselman, Alexander; Du, Randal et al. (2014) Hmga2 is a direct target gene of RUNX1 and regulates expansion of myeloid progenitors in mice. Blood 124:2203-12

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