RUNX1 deficiency cooperates with SRSF2 mutation to induce multilineage hematopoietic defects characteristic of MDS

Blood Advances - Tập 6 - Trang 6078-6092 - 2022
Yi-Jou Huang1,2, Jia-Yu Chen3, Ming Yan1, Amanda G. Davis1,2, Sayuri Miyauchi1, Liang Chen3, Yajing Hao3, Sigrid Katz1, Rafael Bejar1, Omar Abdel-Wahab4, Xiang-Dong Fu1,3, Dong-Er Zhang1,2,5
1Moores Cancer Center, UC San Diego (UCSD), La Jolla, CA
2Department of Molecular Biology, UCSD, La Jolla, CA
3Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA
4Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY
5Department of Pathology, UC San Diego, La Jolla, CA

Tóm tắt

Abstract

Myelodysplastic syndromes (MDSs) are a heterogeneous group of hematologic malignancies with a propensity to progress to acute myeloid leukemia. Causal mutations in multiple classes of genes have been identified in patients with MDS with some patients harboring more than 1 mutation. Interestingly, double mutations tend to occur in different classes rather than the same class of genes, as exemplified by frequent cooccurring mutations in the transcription factor RUNX1 and the splicing factor SRSF2. This prototypic double mutant provides an opportunity to understand how their divergent functions in transcription and posttranscriptional regulation may be altered to jointly promote MDS. Here, we report a mouse model in which Runx1 knockout was combined with the Srsf2 P95H mutation to cause multilineage hematopoietic defects. Besides their additive and synergistic effects, we also unexpectedly noted a degree of antagonizing activity of single mutations in specific hematopoietic progenitors. To uncover the mechanism, we further developed a cellular model using human K562 cells and performed parallel gene expression and splicing analyses in both human and murine contexts. Strikingly, although RUNX1 deficiency was responsible for altered transcription in both single and double mutants, it also induced dramatic changes in global splicing, as seen with mutant SRSF2, and only their combination induced missplicing of genes selectively enriched in the DNA damage response and cell cycle checkpoint pathways. Collectively, these data reveal the convergent impact of a prototypic MDS-associated double mutant on RNA processing and suggest that aberrant DNA damage repair and cell cycle regulation critically contribute to MDS development.


Tài liệu tham khảo

Gangat, 2016, Myelodysplastic syndromes: contemporary review and how we treat, Am J Hematol, 91, 76, 10.1002/ajh.24253 Haferlach, 2014, Landscape of genetic lesions in 944 patients with myelodysplastic syndromes, Leukemia, 28, 241, 10.1038/leu.2013.336 Papaemmanuil, 2013, Clinical and biological implications of driver mutations in myelodysplastic syndromes, Blood, 122, 3616, 10.1182/blood-2013-08-518886 Chen, 2007, RUNX1 gene mutation in primary myelodysplastic syndrome--the mutation can be detected early at diagnosis or acquired during disease progression and is associated with poor outcome, Br J Haematol, 139, 405, 10.1111/j.1365-2141.2007.06811.x Tsai, 2015, Biological activities of RUNX1 mutants predict secondary acute leukemia transformation from chronic myelomonocytic leukemia and myelodysplastic syndromes, Clin Cancer Res, 21, 3541, 10.1158/1078-0432.CCR-14-2203 Ito, 2015, The RUNX family: developmental regulators in cancer, Nat Rev Cancer, 15, 81, 10.1038/nrc3877 Sood, 2017, Role of RUNX1 in hematological malignancies, Blood, 129, 2070, 10.1182/blood-2016-10-687830 Chen, 2021, Splicing factor mutations in hematologic malignancies, Blood, 138, 599, 10.1182/blood.2019004260 Bejar, 2011, Clinical effect of point mutations in myelodysplastic syndromes, N Engl J Med, 364, 2496, 10.1056/NEJMoa1013343 Yoshida, 2011, Frequent pathway mutations of splicing machinery in myelodysplasia, Nature, 478, 64, 10.1038/nature10496 Papaemmanuil, 2011, Somatic SF3B1 mutation in myelodysplasia with ring sideroblasts, N Engl J Med, 365, 1384, 10.1056/NEJMoa1103283 Walter, 2012, Clonal architecture of secondary acute myeloid leukemia, N Engl J Med, 366, 1090, 10.1056/NEJMoa1106968 Sperling, 2017, The genetics of myelodysplastic syndrome: from clonal haematopoiesis to secondary leukaemia, Nat Rev Cancer, 17, 5, 10.1038/nrc.2016.112 Pellagatti, 2016, Targeted resequencing analysis of 31 genes commonly mutated in myeloid disorders in serial samples from myelodysplastic syndrome patients showing disease progression, Leukemia, 30, 247, 10.1038/leu.2015.129 Thol, 2012, Frequency and prognostic impact of mutations in SRSF2, U2AF1, and ZRSR2 in patients with myelodysplastic syndromes, Blood, 119, 3578, 10.1182/blood-2011-12-399337 Wu, 2012, The clinical implication of SRSF2 mutation in patients with myelodysplastic syndrome and its stability during disease evolution, Blood, 120, 3106, 10.1182/blood-2012-02-412296 Kim, 2015, SRSF2 mutations contribute to myelodysplasia by mutant-specific effects on exon recognition, Cancer Cell, 27, 617, 10.1016/j.ccell.2015.04.006 Komeno, 2015, SRSF2 is essential for hematopoiesis, and its myelodysplastic syndrome-related mutations dysregulate alternative pre-mRNA splicing, Mol Cell Biol, 35, 3071, 10.1128/MCB.00202-15 Smeets, 2018, Srsf2(P95H) initiates myeloid bias and myelodysplastic/myeloproliferative syndrome from hemopoietic stem cells, Blood, 132, 608, 10.1182/blood-2018-04-845602 Kon, 2018, Physiological Srsf2 P95H expression causes impaired hematopoietic stem cell functions and aberrant RNA splicing in mice, Blood, 131, 621, 10.1182/blood-2017-01-762393 Zhang, 2015, Disease-associated mutation in SRSF2 misregulates splicing by altering RNA-binding affinities, Proc Natl Acad Sci U S A, 112, E4726, 10.1073/pnas.1514105112 Damm, 2012, Mutations affecting mRNA splicing define distinct clinical phenotypes and correlate with patient outcome in myelodysplastic syndromes, Blood, 119, 3211, 10.1182/blood-2011-12-400994 Gaidzik, 2016, RUNX1 mutations in acute myeloid leukemia are associated with distinct clinico-pathologic and genetic features, Leukemia, 30, 2160, 10.1038/leu.2016.126 Ochi, 2020, Combined cohesin-RUNX1 deficiency synergistically perturbs chromatin looping and causes myelodysplastic syndromes, Cancer Discov, 10, 836, 10.1158/2159-8290.CD-19-0982 Growney, 2005, Loss of Runx1 perturbs adult hematopoiesis and is associated with a myeloproliferative phenotype, Blood, 106, 494, 10.1182/blood-2004-08-3280 Shastri, 2017, Stem and progenitor cell alterations in myelodysplastic syndromes, Blood, 129, 1586, 10.1182/blood-2016-10-696062 Ichikawa, 2004, AML-1 is required for megakaryocytic maturation and lymphocytic differentiation, but not for maintenance of hematopoietic stem cells in adult hematopoiesis, Nat Med, 10, 299, 10.1038/nm997 Pang, 2013, Hematopoietic stem cell and progenitor cell mechanisms in myelodysplastic syndromes, Proc Natl Acad Sci U S A, 110, 3011, 10.1073/pnas.1222861110 Pollyea, 2019, Myelodysplastic syndrome-associated spliceosome gene mutations enhance innate immune signaling, Haematologica, 104, e388, 10.3324/haematol.2018.214155 van Wijnen, 2004, Nomenclature for Runt-related (RUNX) proteins, Oncogene, 23, 4209, 10.1038/sj.onc.1207758 Mo, 2013, Unique role of SRSF2 in transcription activation and diverse functions of the SR and hnRNP proteins in gene expression regulation, Transcription, 4, 251, 10.4161/trns.26932 Ji, 2013, SR proteins collaborate with 7SK and promoter-associated nascent RNA to release paused polymerase, Cell, 153, 855, 10.1016/j.cell.2013.04.028 Yu, 2012, clusterProfiler: an R package for comparing biological themes among gene clusters, OMICS, 16, 284, 10.1089/omi.2011.0118 Wang, 2000, Requirement for ERK activation in cisplatin-induced apoptosis, J Biol Chem, 275, 39435, 10.1074/jbc.M004583200 Cagnol, 2010, ERK and cell death: mechanisms of ERK-induced cell death--apoptosis, autophagy and senescence, FEBS J, 277, 2, 10.1111/j.1742-4658.2009.07366.x Zhou, 2013, Myelodysplastic syndrome: an inability to appropriately respond to damaged DNA?, Exp Hematol, 41, 665, 10.1016/j.exphem.2013.04.008 Popp, 2017, Increase of DNA damage and alteration of the DNA damage response in myelodysplastic syndromes and acute myeloid leukemias, Leuk Res, 57, 112, 10.1016/j.leukres.2017.03.011 Ogawa, 2019, Genetics of MDS, Blood, 133, 1049, 10.1182/blood-2018-10-844621 Singh, 2020, SF3B1 mutations induce R-loop accumulation and DNA damage in MDS and leukemia cells with therapeutic implications, Leukemia, 34, 2525, 10.1038/s41375-020-0753-9 Nguyen, 2018, Spliceosome mutations induce R loop-associated sensitivity to ATR inhibition in myelodysplastic syndromes, Cancer Res, 78, 5363, 10.1158/0008-5472.CAN-17-3970 Cantor, 2001, BACH1, a novel helicase-like protein, interacts directly with BRCA1 and contributes to its DNA repair function, Cell, 105, 149, 10.1016/S0092-8674(01)00304-X Cantor, 2004, The BRCA1-associated protein BACH1 is a DNA helicase targeted by clinically relevant inactivating mutations, Proc Natl Acad Sci U S A, 101, 2357, 10.1073/pnas.0308717101 Seal, 2006, Truncating mutations in the Fanconi anemia J gene BRIP1 are low-penetrance breast cancer susceptibility alleles, Nat Genet, 38, 1239, 10.1038/ng1902 Levitus, 2005, The DNA helicase BRIP1 is defective in Fanconi anemia complementation group, J Nat Genet, 37, 934 Levran, 2005, The BRCA1-interacting helicase BRIP1 is deficient in Fanconi anemia, Nat Genet, 37, 931, 10.1038/ng1624 Wu, 2010, Fanconi anemia group J mutation abolishes its DNA repair function by uncoupling DNA translocation from helicase activity or disruption of protein-DNA complexes, Blood, 116, 3780, 10.1182/blood-2009-11-256016 Guo, 2014, Insight into the roles of helicase motif Ia by characterizing Fanconi anemia group J protein (FANCJ) patient mutations, J Biol Chem, 289, 10551, 10.1074/jbc.M113.538892 Huang, 2009, SOSS complexes participate in the maintenance of genomic stability, Mol Cell, 35, 384, 10.1016/j.molcel.2009.06.011 Li, 2009, HSSB1 and hSSB2 form similar multiprotein complexes that participate in DNA damage response, J Biol Chem, 284, 23525, 10.1074/jbc.C109.039586 Trujillo, 2012, On the role of FAN1 in Fanconi anemia, Blood, 120, 86, 10.1182/blood-2012-04-420604 Smogorzewska, 2010, A genetic screen identifies FAN1, a Fanconi anemia-associated nuclease necessary for DNA interstrand crosslink repair, Mol Cell, 39, 36, 10.1016/j.molcel.2010.06.023 Yoshikiyo, 2010, KIAA1018/FAN1 nuclease protects cells against genomic instability induced by interstrand cross-linking agents, Proc Natl Acad Sci U S A, 107, 21553, 10.1073/pnas.1011081107 Edwards, 1997, Human CPR (cell cycle progression restoration) genes impart a Far- phenotype on yeast cells, Genetics, 147, 1063, 10.1093/genetics/147.3.1063 Li, 2006, A novel histone deacetylase pathway regulates mitosis by modulating Aurora B kinase activity, Genes Dev, 20, 2566, 10.1101/gad.1455006 van Wijk, 2005, The energy-less red blood cell is lost: erythrocyte enzyme abnormalities of glycolysis, Blood, 106, 4034, 10.1182/blood-2005-04-1622 Garcia, 2009, Phosphofructo-1-kinase deficiency leads to a severe cardiac and hematological disorder in addition to skeletal muscle glycogenosis, PLoS Genet, 5, e1000615, 10.1371/journal.pgen.1000615 Mukherjee, 2002, The mammalian exosome mediates the efficient degradation of mRNAs that contain AU-rich elements, EMBO J, 21, 165, 10.1093/emboj/21.1.165 West, 2006, Adenylation and exosome-mediated degradation of cotranscriptionally cleaved pre-messenger RNA in human cells, Mol Cell, 21, 437, 10.1016/j.molcel.2005.12.008 van Dijk, 2007, Human cell growth requires a functional cytoplasmic exosome, which is involved in various mRNA decay pathways, RNA, 13, 1027, 10.1261/rna.575107 Sternberg, 2005, Evidence for reduced B-cell progenitors in early (low-risk) myelodysplastic syndrome, Blood, 106, 2982, 10.1182/blood-2005-04-1543 Yoshimi, 2019, Coordinated alterations in RNA splicing and epigenetic regulation drive leukaemogenesis, Nature, 574, 273, 10.1038/s41586-019-1618-0 Fei, 2018, Impaired hematopoiesis and leukemia development in mice with a conditional knock-in allele of a mutant splicing factor gene U2af1, Proc Natl Acad Sci U S A, 115, E10437, 10.1073/pnas.1812669115 Grinev, 2021, RUNX1/RUNX1T1 mediates alternative splicing and reorganises the transcriptional landscape in leukemia, Nat Commun, 12, 520, 10.1038/s41467-020-20848-z Barton, 2009, Characterization of RNA aptamers that disrupt the RUNX1-CBFbeta/DNA complex, Nucleic Acids Res, 37, 6818, 10.1093/nar/gkp728 Fukunaga, 2013, The Runt domain of AML1 (RUNX1) binds a sequence-conserved RNA motif that mimics a DNA element, RNA, 19, 927, 10.1261/rna.037879.112 Kornblihtt, 2004, Multiple links between transcription and splicing, RNA, 10, 1489, 10.1261/rna.7100104 Pandya-Jones, 2009, Co-transcriptional splicing of constitutive and alternative exons, RNA, 15, 1896, 10.1261/rna.1714509 Xu, 2022, Genome-wide screening identifies cell cycle control as a synthetic lethal pathway with SRSF2P95H mutation, Blood Adv, 6, 2092, 10.1182/bloodadvances.2021004571 Chen, 2018, The augmented R-loop is a unifying mechanism for myelodysplastic syndromes induced by high-risk splicing factor mutations, Mol Cell, 69, 412, 10.1016/j.molcel.2017.12.029 Bellissimo, 2017, RUNX1 mutations in inherited and sporadic leukemia, Front Cell Dev Biol, 5, 111, 10.3389/fcell.2017.00111 Samarakkody, 2020, Role of RUNX family transcription factors in DNA damage response, Mol Cells, 43, 99