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ACUTE MYELOID LEUKEMIA

Control of focal adhesion kinase activation by RUNX1-regulated miRNAs in high-risk AML

Leukemia volume 37, pages 776–787 (2023)Cite this article

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Abstract

We recently described a 16-gene expression signature for improved risk stratification of acute myeloid leukemia (AML) patients called the AML Prognostic Score (APS). A subset of APS-high-risk AML patients showed increased levels of focal adhesion kinase (FAK), encoded by the Protein Tyrosine Kinase 2 (PTK2) gene, which was correlated with RUNX1 mutations. RUNX1 mutant cells are more sensitive to PTK2 inhibitors. As we were not able to detect RUNX1-binding sites in the PTK2 promoter, we hypothesized that RUNX1 might regulate micro(mi)RNAs that repress PTK2, such that loss-of-function RUNX1 mutations would result in reduced miRNA expression and derepression of PTK2. Examination of paired RNA-seq and miRNA-seq data from 301 AML cases revealed two miRNAs that positively correlated with RUNX1 expression, contained RUNX1-binding sites in their promoters and were predicted to target PTK2. We show that the hsa-let7a-2-3p and hsa-miR-135a-5p promoters are regulated by RUNX1, and that PTK2 is a direct target of both miRNAs. Even in the absence of RUNX1 mutations, hsa-let7a-2-3p and hsa-miR-135a-5p regulate PTK2 expression, and reduced expression of these two miRNAs sensitizes AML cells to PTK2 inhibition. These data explain how RUNX1 regulates PTK2, and identify potential miRNA biomarkers for targeting AML with PTK2 inhibitors.

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Fig. 1: APS differential expression analysis.
Fig. 2: miRNA:mRNA correlation.
Fig. 3: RUNX1 regulates the expression of miRNAs and PTK2.
Fig. 4: PTK2 is a direct target of both miRNAs.
Fig. 5: RUNX1 binds to miRNA promoters.
Fig. 6: Control of miRNA expression by RUNX1 is required for regulation of PTK2.
Fig. 7: Sensitivity of AML cells to PTK2 inhibitors upon knockdown of both miRNAs.

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References

  1. Fehlmann T, Backes C, Alles J, Fischer U, Hart M, Kern F, et al. A high-resolution map of the human small non-coding transcriptome. Bioinformatics. 2018;34:1621–8.

    CAS  PubMed  Google Scholar 

  2. Network CGAR. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med. 2013;368:2059–74.

    Google Scholar 

  3. Lim EL, Trinh DL, Ries RE, Wang J, Gerbing RB, Ma Y, et al. MicroRNA expression-based model indicates event-free survival in pediatric acute myeloid leukemia. J Clin Oncol. 2017;35:3964.

    CAS  PubMed  PubMed Central  Google Scholar 

  4. Robb T, Reid G, Blenkiron C. Exploiting microRNAs as cancer therapeutics. Target Oncol. 2017;12:163–78.

    PubMed  Google Scholar 

  5. Bracken CP, Scott HS, Goodall GJ. A network-biology perspective of microRNA function and dysfunction in cancer. Nat Rev Genet. 2016;17:719–32.

    CAS  PubMed  Google Scholar 

  6. Liu Y, Cheng Z, Pang Y, Cui L, Qian T, Quan L, et al. Role of microRNAs, circRNAs and long noncoding RNAs in acute myeloid leukemia. J Hematol Oncol. 2019;12:1–20.

    Google Scholar 

  7. Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J, Peck D, et al. MicroRNA expression profiles classify human cancers. Nature. 2005;435:834–8.

    CAS  PubMed  Google Scholar 

  8. Marcucci G, Radmacher MD, Maharry K, Mrózek K, Ruppert AS, Paschka P, et al. MicroRNA expression in cytogenetically normal acute myeloid leukemia. N Engl J Med. 2008;358:1919–28.

    CAS  PubMed  Google Scholar 

  9. Dhawan A, Scott JG, Harris AL, Buffa FM. Pan-cancer characterisation of microRNA across cancer hallmarks reveals microRNA-mediated downregulation of tumour suppressors. Nat Commun. 2018;9:1–13.

    Google Scholar 

  10. Starczynowski DT, Kuchenbauer F, Argiropoulos B, Sung S, Morin R, Muranyi A, et al. Identification of miR-145 and miR-146a as mediators of the 5q–syndrome phenotype. Nat Med. 2010;16:49–58.

    CAS  PubMed  Google Scholar 

  11. Li Z, Lu J, Sun M, Mi S, Zhang H, Luo RT, et al. Distinct microRNA expression profiles in acute myeloid leukemia with common translocations. Proc Natl Acad Sci USA. 2008;105:15535–40.

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Docking TR, Parker JDK, Jädersten M, Duns G, Chang L, Jiang J, et al. A clinical transcriptome approach to patient stratification and therapy selection in acute myeloid leukemia. Nat Commun. 2021;12:1–15.

    Google Scholar 

  13. Rossetti S, Sacchi N. RUNX1: a microRNA hub in normal and malignant hematopoiesis. Int J Mol Sci. 2013;14:1566–88.

    CAS  PubMed  PubMed Central  Google Scholar 

  14. Grants JM, Wegrzyn J, Hui T, O’Neill K, Shadbolt M, Knapp DJHF, et al. Altered microRNA expression links IL6 and TNF-induced inflammaging with myeloid malignancy in humans and mice. Blood. 2020;135:2235–51.

    PubMed  Google Scholar 

  15. Chu A, Robertson G, Brooks D, Mungall AJ, Birol I, Coope R, et al. Large-scale profiling of microRNAs for the cancer genome atlas. Nucleic Acids Res. 2016;44:e3–e3.

    PubMed  Google Scholar 

  16. Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:1–21.

    Google Scholar 

  17. Agarwal V, Bell GW, Nam J-W, Bartel DP. Predicting effective microRNA target sites in mammalian mRNAs. Elife. 2015;4:e05005.

    PubMed  PubMed Central  Google Scholar 

  18. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B. 1995;57:289–300.

    Google Scholar 

  19. Fabregat A, Jupe S, Matthews L, Sidiropoulos K, Gillespie M, Garapati P, et al. The reactome pathway knowledgebase. Nucleic Acids Res. 2018;46:D649–55.

    CAS  PubMed  Google Scholar 

  20. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA. 2005;102:15545–50.

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Tong Z, Cui Q, Wang J, Zhou Y. TransmiR v2. 0: an updated transcription factor-microRNA regulation database. Nucleic Acids Res. 2019;47:D253–8.

    CAS  PubMed  Google Scholar 

  22. Gheorghe M, Sandve GK, Khan A, Chèneby J, Ballester B, Mathelier A. A map of direct TF–DNA interactions in the human genome. Nucleic Acids Res. 2019;47:e21–e21.

    PubMed  Google Scholar 

  23. Yu G, Wang LG, Han Y, He QY. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012;16:284–7.

    CAS  PubMed  PubMed Central  Google Scholar 

  24. Tan SM, Lieberman J. Capture and identification of miRNA targets by biotin pulldown and RNA-seq. Methods Mol Biol. 2016;1358:211–28.

  25. Arun G, Akhade VS, Donakonda S, Rao MRS. mrhl RNA, a long noncoding RNA, negatively regulates Wnt signaling through its protein partner Ddx5/p68 in mouse spermatogonial cells. Mol Cell Biol. 2012;32:3140–52.

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Therneau TM, Lumley T. Package ‘survival’. R Top Doc. 2015;128:28–33.

    Google Scholar 

  27. Kassambara A, Kosinski M, Biecek P, Fabian S. Survminer: drawing survival curves using Ggplot2. 2021. R package version 0.4. 2021;9. https://CRAN.R-project.org/package=survminer.

  28. Alekhina O, Marchese A. β-Arrestin1 and Signal-transducing Adaptor Molecule 1 (STAM1) cooperate to promote focal adhesion kinase autophosphorylation and chemotaxis via the chemokine receptor CXCR4. J Biol Chem. 2016;291:26083–97.

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Wu H, Huang M, Cao P, Wang T, Shu Y, Liu P. MiR-135a targets JAK2 and inhibits gastric cancer cell proliferation. Cancer Biol Ther. 2012;13:281–8.

    CAS  PubMed  Google Scholar 

  30. Chen C-C, You J-Y, Lung J, Huang C-E, Chen Y-Y, Leu Y-W, et al. Aberrant let7a/HMGA2 signaling activity with unique clinical phenotype in JAK2-mutated myeloproliferative neoplasms. Haematologica. 2017;102:509.

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Kagoshima H, Shigesada K, Satake M, Ito Y, Miyoshi H, Ohki M, et al. The runt domain identifies a new family of heterometric transcriptional regulators. Trends Genet. 1993;9:338–41.

    CAS  PubMed  Google Scholar 

  32. Bravo J, Li Z, Speck NA, Warren AJ. The leukemia-associated AML1 (Runx1)–CBFβ complex functions as a DNA-induced molecular clamp. Nat Struct Biol. 2001;8:371–8.

    CAS  PubMed  Google Scholar 

  33. Bowers SR, Calero-Nieto FJ, Valeaux S, Fernandez-Fuentes N, Cockerill PN. Runx1 binds as a dimeric complex to overlapping Runx1 sites within a palindromic element in the human GM-CSF enhancer. Nucleic Acids Res. 2010;38:6124–34.

    CAS  PubMed  PubMed Central  Google Scholar 

  34. de Bruijn M, Dzierzak E. Runx transcription factors in the development and function of the definitive hematopoietic system. Blood. 2017;129:2061–9.

    PubMed  Google Scholar 

  35. Sood R, Kamikubo Y, Liu P. Role of RUNX1 in hematological malignancies. Blood. 2017;129:2070–82.

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Tober J, Maijenburg MW, Speck NA. Taking the leap: Runx1 in the formation of blood from endothelium. Curr Top Dev Biol. 2016;118:113–62.

    CAS  PubMed  Google Scholar 

  37. Tang J-L, Hou H-A, Chen C-Y, Liu C-Y, Chou W-C, Tseng M-H, et al. AML1/RUNX1 mutations in 470 adult patients with de novo acute myeloid leukemia: prognostic implication and interaction with other gene alterations. Blood. 2009;114:5352–61.

    CAS  PubMed  Google Scholar 

  38. Schnittger S, Dicker F, Kern W, Wendland N, Sundermann J, Alpermann T, et al. RUNX1 mutations are frequent in de novo AML with noncomplex karyotype and confer an unfavorable prognosis. Blood. 2011;117:2348–57.

    CAS  PubMed  Google Scholar 

  39. Mangan JK, Speck NA. RUNX1 mutations in clonal myeloid disorders: from conventional cytogenetics to next generation sequencing, a story 40 years in the making. Crit Rev Oncog. 2011;16:77–91.

    PubMed  PubMed Central  Google Scholar 

  40. Wallace JA, O’Connell RM. MicroRNAs and acute myeloid leukemia: therapeutic implications and emerging concepts. Blood. 2017;130:1290–301.

    CAS  PubMed  PubMed Central  Google Scholar 

  41. Grasedieck S, Sorrentino A, Langer C, Buske C, Döhner H, Mertens D, et al. Circulating microRNAs in hematological diseases: principles, challenges, and perspectives. Blood. 2013;121:4977–84.

    CAS  PubMed  Google Scholar 

  42. Mi S, Lu J, Sun M, Li Z, Zhang H, Neilly MB, et al. MicroRNA expression signatures accurately discriminate acute lymphoblastic leukemia from acute myeloid leukemia. Proc Natl Acad Sci USA. 2007;104:19971–6.

    CAS  PubMed  PubMed Central  Google Scholar 

  43. de Leeuw DC, van den Ancker W, Denkers F, de Menezes RX, Westers TM, Ossenkoppele GJ, et al. MicroRNA profiling can classify acute leukemias of ambiguous lineage as either acute myeloid leukemia or acute lymphoid leukemia. Clin Cancer Res. 2013;19:2187–96.

    PubMed  Google Scholar 

  44. Jiang X, Hu C, Arnovitz S, Bugno J, Yu M, Zuo Z, et al. miR-22 has a potent anti-tumour role with therapeutic potential in acute myeloid leukaemia. Nat Commun. 2016;7:1–15.

    Google Scholar 

  45. Dorrance AM, Neviani P, Ferenchak GJ, Huang X, Nicolet D, Maharry KS, et al. Targeting leukemia stem cells in vivo with antagomiR-126 nanoparticles in acute myeloid leukemia. Leukemia. 2015;29:2143–53.

    CAS  PubMed  PubMed Central  Google Scholar 

  46. Huang X, Schwind S, Yu B, Santhanam R, Wang H, Hoellerbauer P, et al. Targeted delivery of microRNA-29b by transferrin-conjugated anionic lipopolyplex nanoparticles: a novel therapeutic strategy in acute myeloid leukemia. Clin Cancer Res. 2013;19:2355–67.

    CAS  PubMed  PubMed Central  Google Scholar 

  47. Velu CS, Chaubey A, Phelan JD, Horman SR, Wunderlich M, Guzman ML, et al. Therapeutic antagonists of microRNAs deplete leukemia-initiating cell activity. J Clin Investig. 2014;124:222–36.

    CAS  PubMed  Google Scholar 

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Acknowledgements

We thank Dr. Mohamad Moustafa Ali from Uppsala University, Sweden for data analysis using the Synergy 3.0 tool. This work was supported by grants to AK from the Canadian Institutes of Health Research (Reference # PJT-166051, PJT-162131 and PJT-183924), the Terry Fox Research Institute (Project #1074), Genome BC (Grant # 121AML), the Leukemia and Lymphoma Society of Canada (Grant #619121), and the BC Cancer Foundation through the Leukemia and Myeloma Program (LaMP). VSA received funding from the Michael Smith Foundation for Health Research (Research Trainee Award, #18419). AK is the recipient of the BC Cancer Foundation John Auston Clinical Scientist Award and is a Tier 1 Canada Research Chair in Blood Cancers.

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  1. Department of Pathology & Laboratory Medicine, University of British Columbia, G105 - 2211 Wesbrook Mall, BC V6T 2B5, Vancouver, BC, Canada

    Vijay Suresh Akhade & Aly Karsan

  2. Canada’s Michael Smith Genome Sciences Centre, BC Cancer, 675 W10 Ave, BC V5Z 1L3, Vancouver, BC, Canada

    Vijay Suresh Akhade, Tian Liu, T. Roderick Docking, Jihong Jiang, Aparna Gopal & Aly Karsan

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AK conceived the project. VSA, TRD and AK designed and analyzed experiments and wrote the manuscript. VSA, JJ and AG performed experiments. TRD and TL carried out bioinformatic analyses.

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Correspondence to Aly Karsan.

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Akhade, V.S., Liu, T., Docking, T.R. et al. Control of focal adhesion kinase activation by RUNX1-regulated miRNAs in high-risk AML. Leukemia 37, 776–787 (2023). https://doi.org/10.1038/s41375-023-01841-z

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