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ANIMAL MODELS

Asxl1 deletion disrupts MYC and RNA polymerase II function in granulocyte progenitors

Leukemia volume 37, pages 478–487 (2023)Cite this article

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Abstract

Mutations in the gene Additional Sex-Combs Like 1 (ASXL1) are recurrent in myeloid malignancies as well as the pre-malignant condition clonal hematopoiesis, where they are universally associated with poor prognosis. However, the role of ASXL1 in myeloid lineage maturation is incompletely described. To define the role of ASXL1 in myelopoiesis, we employed single cell RNA sequencing and a murine model of hematopoietic-specific Asxl1 deletion. In granulocyte progenitors, Asxl1 deletion leads to hyperactivation of MYC and a quantitative decrease in neutrophil production. This loss of granulocyte production was not accompanied by significant changes in the landscape of covalent histone modifications. However, Asxl1 deletion results in a decrease in RNAPII promoter-proximal pausing in granulocyte progenitors, indicative of a global increase in productive transcription. These results suggest that ASXL1 inhibits productive transcription in granulocyte progenitors, identifying a new role for this epigenetic regulator in myeloid development.

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Fig. 1: Single cell RNA reveals a granulocyte maturation defect in Asxl1Δ/Δ mice at the point of cell cycle exit.
Fig. 2: Asxl1 deletion leads to hyperactivation of a Myc transcriptional signature in granulocyte progenitors.
Fig. 3: ASXL1 deletion does not substantially impact the landscape of covalent histone modifications in developing myeloid cells.
Fig. 4: ASXL1 deletion leads to an increase in RNAPII pause-release.

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Data availability

The datasets generated during this study are available at GEO under the accession number GSE158184.

References

  1. Gelsi-Boyer V, Brecqueville M, Devillier R, Murati A, Mozziconacci M-J, Birnbaum D. Mutations in ASXL1 are associated with poor prognosis across the spectrum of malignant myeloid diseases. J Hematol Oncol. 2012;5:12.

    Article  CAS  Google Scholar 

  2. Kim T, Tyndel MS, Zhang Z, Ahn J, Choi S, Szardenings M, et al. Exome sequencing reveals DNMT3A and ASXL1 variants associate with progression of chronic myeloid leukemia after tyrosine kinase inhibitor therapy. Leuk Res. 2017;59:142–8.

    Article  CAS  Google Scholar 

  3. Pratcorona M, Abbas S, Sanders MA, Koenders JE, Kavelaars FG, Erpelinck-Verschueren CAJ, et al. Acquired mutations in ASXL1 in acute myeloid leukemia: prevalence and prognostic value. Haematologica. 2012;97:388–92.

    Article  CAS  Google Scholar 

  4. Tefferi A, Guglielmelli P, Lasho TL, Rotunno G, Finke C, Mannarelli C, et al. CALR and ASXL1 mutations-based molecular prognostication in primary myelofibrosis: an international study of 570 patients. Leukemia. 2014;28:1494–500.

    Article  CAS  Google Scholar 

  5. Abelson S, Collord G, Ng SWK, Weissbrod O, Mendelson Cohen N, Niemeyer E, et al. Prediction of acute myeloid leukaemia risk in healthy individuals. Nature. 2018;559:400–4.

    Article  CAS  Google Scholar 

  6. Genovese G, Kähler AK, Handsaker RE, Lindberg J, Rose SA, Bakhoum SF, et al. Clonal hematopoiesis and blood-cancer risk inferred from blood DNA sequence. N Engl J Med. 2014;371:2477–87.

    Article  Google Scholar 

  7. Jaiswal S, Fontanillas P, Flannick J, Manning A, Grauman PV, Mar BG, et al. Age-related clonal hematopoiesis associated with adverse outcomes. N Engl J Med. 2014;371:2488–98.

    Article  Google Scholar 

  8. Abdel-Wahab O, Adli M, LaFave LM, Gao J, Hricik T, Shih AH, et al. ASXL1 mutations promote myeloid transformation through loss of PRC2-mediated gene repression. Cancer Cell. 2012;22:180–93.

    Article  CAS  Google Scholar 

  9. Abdel-Wahab O, Gao J, Adli M, Dey A, Trimarchi T, Chung YR, et al. Deletion of Asxl1 results in myelodysplasia and severe developmental defects in vivo. J Exp Med. 2013;210:2641–59.

    Article  CAS  Google Scholar 

  10. Zhang P, Chen Z, Li R, Guo Y, Shi H, Bai J, et al. Loss of ASXL1 in the bone marrow niche dysregulates hematopoietic stem and progenitor cell fates. Cell Discov. 2018;4:1–17.

    Article  Google Scholar 

  11. Izzo F, Lee SC, Poran A, Chaligne R, Gaiti F, Gross B, et al. DNA methylation disruption reshapes the hematopoietic differentiation landscape. Nat Genet. 2020;52:378–87.

    Article  CAS  Google Scholar 

  12. Viny AD, Bowman RL, Liu Y, Lavallée V-P, Eisman SE, Xiao W, et al. Cohesin members Stag1 and Stag2 display distinct roles in chromatin accessibility and topological control of HSC self-renewal and differentiation. Cell Stem Cell. 2019;25:682–96.e8.

    Article  CAS  Google Scholar 

  13. Stoeckius M, Hafemeister C, Stephenson W, Houck-Loomis B, Chattopadhyay PK, Swerdlow H, et al. Simultaneous epitope and transcriptome measurement in single cells. Nat Methods. 2017;14:865–8.

    Article  CAS  Google Scholar 

  14. Oguro H, Ding L, Morrison SJ. SLAM family markers resolve functionally distinct subpopulations of hematopoietic stem cells and multipotent progenitors. Cell Stem Cell. 2013;13:102–16.

    Article  CAS  Google Scholar 

  15. Pronk CJH, Rossi DJ, Månsson R, Attema JL, Norddahl GL, Chan CKF, et al. Elucidation of the phenotypic, functional, and molecular topography of a myeloerythroid progenitor cell hierarchy. Cell Stem Cell. 2007;1:428–42.

  16. Muench DE, Olsson A, Ferchen K, Pham G, Serafin RA, Chutipongtanate S, et al. Mouse models of neutropenia reveal progenitor-stage-specific defects. Nature. 2020;582:109–14.

    Article  CAS  Google Scholar 

  17. Gulati GS, Sikandar SS, Wesche DJ, Manjunath A, Bharadwaj A, Berger MJ, et al. Single-cell transcriptional diversity is a hallmark of developmental potential. Science. 2020;367:405–11.

    Article  CAS  Google Scholar 

  18. Babur Ö, Luna A, Korkut A, Durupinar F, Siper MC, Dogrusoz U et al. Causal interactions from proteomic profiles: molecular data meets pathway knowledge. Patterns. 2021;2:100257.

  19. Huang J, Ge M, Lu S, Shi J, Li X, Zhang J, et al. Mutations of ASXL1 and TET2 in aplastic anemia. Haematologica. 2015;100:e172–5.

    Article  Google Scholar 

  20. Mangaonkar AA, Gangat N, Al-Kali A, Elliott MA, Begna KH, Hanson CA, et al. Prognostic impact of ASXL1 mutations in patients with myelodysplastic syndromes and multilineage dysplasia with or without ring sideroblasts. Leuk Res. 2018;71:60–2.

    Article  CAS  Google Scholar 

  21. Kaya-Okur HS, Wu SJ, Codomo CA, Pledger ES, Bryson TD, Henikoff JG, et al. CUT&Tag for efficient epigenomic profiling of small samples and single cells. Nat Commun. 2019;10:1930.

    Article  Google Scholar 

  22. Kim M-H, Yang D, Kim M, Kim S-Y, Kim D, Kang S-J. A late-lineage murine neutrophil precursor population exhibits dynamic changes during demand-adapted granulopoiesis. Sci Rep. 2017;7:39804.

    Article  CAS  Google Scholar 

  23. Asada S, Goyama S, Inoue D, Shikata S, Takeda R, Fukushima T, et al. Mutant ASXL1 cooperates with BAP1 to promote myeloid leukaemogenesis. Nat Commun. 2018;9:2733.

    Article  Google Scholar 

  24. Eberhardy SR, Farnham PJ. Myc recruits P-TEFb to mediate the final step in the transcriptional activation of the cad promoter. J Biol Chem. 2002;277:40156–62.

    Article  CAS  Google Scholar 

  25. Price DH. Regulation of RNA polymerase II elongation by c-Myc. Cell. 2010;141:399–400.

    Article  CAS  Google Scholar 

  26. Nagase R, Inoue D, Pastore A, Fujino T, Hou H-A, Yamasaki N, et al. Expression of mutant Asxl1 perturbs hematopoiesis and promotes susceptibility to leukemic transformation. J Exp Med. 2018;215:1729–47.

    Article  CAS  Google Scholar 

  27. Olsson A, Venkatasubramanian M, Chaudhri VK, Aronow BJ, Salomonis N, Singh H, et al. Single-cell analysis of mixed-lineage states leading to a binary cell fate choice. Nature. 2016;537:698–702.

    Article  CAS  Google Scholar 

  28. Summers C, Rankin SM, Condliffe AM, Singh N, Peters AM, Chilvers ER. Neutrophil kinetics in health and disease. Trends Immunol. 2010;31:318–24.

    Article  CAS  Google Scholar 

  29. Zhang H, Wilmot B, Bottomly D, Dao K-HT, Stevens E, Eide CA, et al. Genomic landscape of neutrophilic leukemias of ambiguous diagnosis. Blood. 2019;134:867–79.

    Article  CAS  Google Scholar 

  30. Milne TA, Sinclair DA, Brock HW. The Additional sex combs gene of Drosophila is required for activation and repression of homeotic loci, and interacts specifically with Polycomb and super sex combs. Mol Gen Genet. 1999;261:753–61.

    Article  CAS  Google Scholar 

  31. Alharbi RA, Pettengell R, Pandha HS, Morgan R. The role of HOX genes in normal hematopoiesis and acute leukemia. Leukemia. 2013;27:1000–8.

    Article  CAS  Google Scholar 

  32. Ayton PM, Cleary ML. Transformation of myeloid progenitors by MLL oncoproteins is dependent on Hoxa7 and Hoxa9. Genes Dev. 2003;17:2298.

    Article  CAS  Google Scholar 

  33. Pineault N, Helgason CD, Lawrence HJ, Humphries RK. Differential expression of Hox, Meis1, and Pbx1 genes in primitive cells throughout murine hematopoietic ontogeny. Exp Hematol. 2002;30:49–57.

    Article  CAS  Google Scholar 

  34. Yang H, Kurtenbach S, Guo Y, Lohse I, Durante MA, Li J, et al. Gain of function of ASXL1 truncating protein in the pathogenesis of myeloid malignancies. Blood. 2018;131:328–41.

    Article  CAS  Google Scholar 

  35. Buenrostro JD, Corces R, Wu B, Schep AN, Lareau C, Majeti R et al. Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation. Cell. 2018;173:1535–1548.e16.

  36. Butler A, Hoffman P, Smibert P, Papalexi E, Satija R. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat Biotechnol. 2018;36:411–20.

    Article  CAS  Google Scholar 

  37. Stuart T, Butler A, Hoffman P, Hafemeister C, Papalexi E, Mauck WM, et al. Comprehensive Integration of Single-Cell Data. Cell. 2019;177:1888–902.e21.

    Article  CAS  Google Scholar 

  38. Choi J, Baldwin TM, Wong M, Bolden JE, Fairfax KA, Lucas EC, et al. Haemopedia RNA-seq: a database of gene expression during haematopoiesis in mice and humans. Nucleic Acids Res. 2019;47:D780–5.

    Article  Google Scholar 

  39. Qiu X, Mao Q, Tang Y, Wang L, Chawla R, Pliner HA, et al. Reversed graph embedding resolves complex single-cell trajectories. Nat Methods. 2017;14:979–82.

    Article  CAS  Google Scholar 

  40. Trapnell C, Cacchiarelli D, Grimsby J, Pokharel P, Li S, Morse M, et al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat Biotechnol. 2014;32:381–6.

    Article  CAS  Google Scholar 

  41. Balci H, Siper MC, Saleh N, Safarli I, Roy L, Kilicarslan M, et al. Newt: a comprehensive web-based tool for viewing, constructing and analyzing biological maps. Bioinformatics. 2021;37:1475–7.

    Article  CAS  Google Scholar 

  42. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.

    Article  CAS  Google Scholar 

  43. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29:15–21.

    Article  CAS  Google Scholar 

  44. Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.

    Article  Google Scholar 

  45. Kuleshov MV, Jones MR, Rouillard AD, Fernandez NF, Duan Q, Wang Z, et al. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res. 2016;44:W90–7.

    Article  CAS  Google Scholar 

  46. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–9.

    Article  CAS  Google Scholar 

  47. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25:2078–9.

    Article  Google Scholar 

  48. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9:R137.

    Article  Google Scholar 

  49. Ross-Innes CS, Stark R, Teschendorff AE, Holmes KA, Ali HR, Dunning MJ, et al. Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature. 2012;481:389–93.

    Article  CAS  Google Scholar 

  50. Ramírez F, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, Richter AS, et al. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 2016;44:W160–5.

    Article  Google Scholar 

  51. Fong N, Saldi T, Sheridan RM, Cortazar MA, Bentley DL. RNA Pol II dynamics modulate co-transcriptional chromatin modification, CTD phosphorylation, and transcriptional direction. Mol Cell. 2017;66:546–57.e3.

    Article  CAS  Google Scholar 

  52. Hauri S, Comoglio F, Seimiya M, Gerstung M, Glatter T, Hansen K, et al. A high-density map for navigating the human polycomb complexome. Cell Rep. 2016;17:583–95.

    Article  CAS  Google Scholar 

  53. Morgan MAJ, Rickels RA, Collings CK, He X, Cao K, Herz H-M, et al. A cryptic Tudor domain links BRWD2/PHIP to COMPASS-mediated histone H3K4 methylation. Genes Dev. 2017;31:2003–14.

    Article  CAS  Google Scholar 

  54. Savitsky P, Krojer T, Fujisawa T, Lambert J-P, Picaud S, Wang C-Y, et al. Multivalent histone and DNA engagement by a PHD/BRD/PWWP triple reader cassette recruits ZMYND8 to K14ac-Rich chromatin. Cell Rep. 2016;17:2724–37.

    Article  CAS  Google Scholar 

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Acknowledgements

We would like to thank Dr. Marilynn Chow-Castro for her thoughtful discussions and Hannah Manning for her contributions related to the Causal Path analysis; the OHSU Massively Parallel Sequencing Shared Resource for scRNA-seq library prep using their 10X Genomics Chromium Controller and performing short read sequencing assays. This project was supported by funding from the Cancer Early Detection and Research center (CEDAR) at Oregon Health and Science University’s Knight Cancer Institute, funding from the Edward P. Evans Foundation to TPB and R01HL157147 from the NCI to JEM.

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  1. These authors contributed equally: Theodore P. Braun, Joseph Estabrook.

Authors and Affiliations

  1. Knight Cancer Institute, Oregon Health & Science University, Portland, OR, 97239, USA

    Theodore P. Braun, Zachary Schonrock, Brittany M. Curtiss, Lucie Darmusey, Jommel Macaraeg, Cody Coblentz, Rowan Callahan, William Yashar, Akram Taherinasab, Daniel J. Coleman, Brian J. Druker, Emek Demir & Julia E. Maxson

  2. Division of Hematology & Medical Oncology, Oregon Health & Science University, Portland, OR, 97239, USA

    Theodore P. Braun & Brian J. Druker

  3. Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, OR, 97239, USA

    Joseph Estabrook, Trevor Enright, Hisham Mohammed, Emek Demir & Theresa A. Lusardi

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Contributions

Conceptualization, TPB, HM, BJD, TAL, JEM; Methodology TPB, TAL, JEM; Investigation, TPB, DJC, ZS, CC, BMS; Formal Analysis, TPB, JE, ZS, TE, RC, TAL; Writing—Original Draft, TPB, TAL; Writing—Reviewing and Editing, TPB, ZS, BJD, TAL, JEM; Funding Acquisition, TPB, HM, BJD, TAL, JEM.

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Correspondence to Theodore P. Braun, Theresa A. Lusardi or Julia E. Maxson.

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Competing interests

BJD potential competing interests-- SAB: Aileron Therapeutics, Therapy Architects (ALLCRON), Cepheid, Vivid Biosciences, Celgene, RUNX1 Research Program, Novartis, Gilead Sciences (inactive), Monojul (inactive); SAB & Stock: Aptose Biosciences, Blueprint Medicines, EnLiven Therapeutics, Iterion Therapeutics, Third Coast Therapeutics, GRAIL (SAB inactive); Scientific Founder: MolecularMD (inactive, acquired by ICON); Board of Directors & Stock: Amgen; Board of Directors: Burroughs Wellcome Fund, CureOne; Joint Steering Committee: Beat AML LLS; Founder: VB Therapeutics; Research Funding: EnLiven Therapeutics; Clinical Trial Funding: Novartis, Bristol-Myers Squibb, Pfizer; Royalties from Patent 6958335 (Novartis exclusive license) and OHSU and Dana-Farber Cancer Institute (one Merck exclusive license and one CytoImage, Inc. exclusive license). The remaining authors declare no competing interests.

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Braun, T.P., Estabrook, J., Schonrock, Z. et al. Asxl1 deletion disrupts MYC and RNA polymerase II function in granulocyte progenitors. Leukemia 37, 478–487 (2023). https://doi.org/10.1038/s41375-022-01792-x

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