Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

A coordinated function of lncRNA HOTTIP and miRNA-196b underpinning leukemogenesis by targeting FAS signaling

Oncogene volume 41, pages 718–731 (2022)Cite this article

Subjects

Abstract

MicroRNAs (miRNAs) may modulate more than 60% of human coding genes and act as negative regulators, whereas long noncoding RNAs (lncRNAs) regulate gene expression on multiple levels by interacting with chromatin, functional proteins, and RNAs such as mRNAs and microRNAs. However, the crosstalk between HOTTIP lncRNA and miRNAs in leukemogenesis remains elusive. Using combined integrated analyses of global miRNA expression profiling and state-of-the-art genomic analyses of chromatin such as ChIRP-seq (HOTTIP binding in genomewide), ChIP-seq, and ATAC-seq, we found that some miRNA genes are directly controlled by HOTTIP. Specifically, the HOX cluster miRNAs (miR-196a, miR-196b, miR-10a, and miR-10b), located cis and trans, were most dramatically regulated and significantly decreased in HOTTIP−/− AML cells. HOTTIP bound to the miR-196b promoter and HOTTIP deletion reduced chromatin accessibility and enrichment of active histone modifications at HOX cluster-associated miRNAs in AML cells, whereas reactivation of HOTTIP restored miR gene expression and chromatin accessibility in the CTCF-boundary-attenuated AML cells. Inactivation of HOTTIP or miR-196b promotes apoptosis by altering the chromatin signature at the FAS promoter and increasing FAS expression. Transplantation of miR-196b knockdown MOLM13 cells in NSG mice increased overall survival of mice compared to wild-type cells transplanted into mice. Thus, HOTTIP remodels the chromatin architecture around miRNAs to promote their transcription and consequently represses tumor suppressors and promotes leukemogenesis.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: LncRNA HOTTIP regulates miRNAs target genes control leukemogenic program in AML cells.
Fig. 2: HOTTIP−/− perturbs HOX cluster miRNAs, mediate oncogenic program.
Fig. 3: HOTTIP controls the epigenetic modifications of HOX cluster miRNAs.
Fig. 4: CBS7/9 boundary regulates HOX cluster miRNAs chromatin neighborhood.
Fig. 5: Inhibition of miR-196b induced apoptosis in MOLM13 cells.
Fig. 6: HOTTIP targets FAS and CBS7/9 boundary play a role in maintaining the HOTTIP targets chromatin neighborhood.
Fig. 7: Inhibition of miR-196b inhibits in vivo leukemogenesis.

Similar content being viewed by others

References

  1. He RZ, Luo DX, Mo YY. Emerging roles of lncRNAs in the post-transcriptional regulation in cancer. Genes Dis. 2019;6:6–15.

    Article  CAS  Google Scholar 

  2. Dey BK, Mueller AC, Dutta A. Long non-coding RNAs as emerging regulators of differentiation, development, and disease. Transcription. 2014;5:e944014.

    Article  Google Scholar 

  3. Lambert M, Alioui M, Jambon S, Depauw S, Van Seuningen I, David-Cordonnier MH. Direct and indirect targeting of HOXA9 transcription factor in acute myeloid leukemia. Cancers (Basel). 2019;11:837.

  4. Collins CT, Hess JL. Deregulation of the HOXA9/MEIS1 axis in acute leukemia. Curr Opin Hematol. 2016;23:354–61.

    Article  CAS  Google Scholar 

  5. De Kumar B, Krumlauf R. HOXs and lincRNAs: two sides of the same coin. Sci Adv. 2016;2:e1501402.

    Article  Google Scholar 

  6. Long Y, Wang X, Youmans DT, Cech TR. How do lncRNAs regulate transcription. Sci Adv. 2017;3:eaao2110.

    Article  Google Scholar 

  7. Grossi E, Raimondi I, Goni E, Gonzalez J, Marchese FP, Chapaprieta V, et al. A lncRNA-SWI/SNF complex crosstalk controls transcriptional activation at specific promoter regions. Nat Commun. 2020;11:936.

    Article  CAS  Google Scholar 

  8. Singh AP, Archer TK. Analysis of the SWI/SNF chromatin-remodeling complex during early heart development and BAF250a repression cardiac gene transcription during P19 cell differentiation. Nucleic Acids Res. 2014;42:2958–75.

    Article  CAS  Google Scholar 

  9. Singh AP, Foley JF, Rubino M, Boyle MC, Tandon A, Shah R, et al. Brg1 enables rapid growth of the early embryo by suppressing genes that regulate apoptosis and cell growth arrest. Mol Cell Biol. 2016;36:1990–2010.

    Article  CAS  Google Scholar 

  10. Singh AP, Foley J, Tandon A, Phadke D, Karimi Kinyamu H, Archer TK. A role for BRG1 in the regulation of genes required for development of the lymphatic system. Oncotarget. 2017;8:54925–38.

    Article  Google Scholar 

  11. Basta JM, Singh A, Robbins L, Stout L, Pherson M, Rauchman M. The core SWI/SNF catalytic subunit Brg1 regulates nephron progenitor cell proliferation and differentiation. Dev Biol. 2020;464:176–87.

    Article  CAS  Google Scholar 

  12. Luo H, Zhu G, Xu J, Lai Q, Yan B, Guo Y, et al. HOTTIP lncRNA promotes hematopoietic stem cell self-renewal leading to AML-like disease in mice. Cancer Cell. 2019;36:645–59 e648.

    Article  CAS  Google Scholar 

  13. Singh AP, Hung YH, Shanahan MT, Kanke M, Bonfini A, Dame MK, et al. Enteroendocrine progenitor cell-enriched miR-7 regulates intestinal epithelial proliferation in an Xiap-dependent manner. Cell Mol Gastroenterol Hepatol. 2020;9:447–64.

    Article  Google Scholar 

  14. Fernandes JCR, Acuna SM, Aoki JI, Floeter-Winter LM, Muxel SM. Long non-coding RNAs in the regulation of gene expression: physiology and disease. Noncoding RNA. 2019;5:17.

    PubMed Central  Google Scholar 

  15. Furio-Tari P, Tarazona S, Gabaldon T, Enright AJ, Conesa A. spongeScan: a web for detecting microRNA binding elements in lncRNA sequences. Nucleic Acids Res. 2016;44:W176–180.

    Article  CAS  Google Scholar 

  16. Dykes IM, Emanueli C. Transcriptional and post-transcriptional gene regulation by long non-coding RNA. Genomics Proteomics Bioinformatics. 2017;15:177–86.

    Article  Google Scholar 

  17. Jonas S, Izaurralde E. Towards a molecular understanding of microRNA-mediated gene silencing. Nat Rev Genet. 2015;16:421–33.

    Article  CAS  Google Scholar 

  18. Yendamuri S, Calin GA. The role of microRNA in human leukemia: a review. Leukemia. 2009;23:1257–63.

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  20. Garzon R, Pichiorri F, Palumbo T, Iuliano R, Cimmino A, Aqeilan R, et al. MicroRNA fingerprints during human megakaryocytopoiesis. Proc Natl Acad Sci USA. 2006;103:5078–83.

    Article  CAS  Google Scholar 

  21. Tan Y, Zhang B, Wu T, Skogerbo G, Zhu X, Guo X, et al. Transcriptional inhibiton of Hoxd4 expression by miRNA-10a in human breast cancer cells. BMC Mol Biol. 2009;10:12.

    Article  Google Scholar 

  22. Weiss FU, Marques IJ, Woltering JM, Vlecken DH, Aghdassi A, Partecke LI, et al. Retinoic acid receptor antagonists inhibit miR-10a expression and block metastatic behavior of pancreatic cancer. Gastroenterology. 2009;137:2136–45. e2131-2137

    Article  CAS  Google Scholar 

  23. Stadthagen G, Tehler D, Hoyland-Kroghsbo NM, Wen J, Krogh A, Jensen KT, et al. Loss of miR-10a activates lpo and collaborates with activated Wnt signaling in inducing intestinal neoplasia in female mice. PLoS Genet. 2013;9:e1003913.

    Article  Google Scholar 

  24. Neijts R, Amin S, van Rooijen C, Tan S, Creyghton MP, de Laat W, et al. Polarized regulatory landscape and Wnt responsiveness underlie Hox activation in embryos. Genes Dev. 2016;30:1937–42.

    Article  CAS  Google Scholar 

  25. Rodrigues AR, Yakushiji-Kaminatsui N, Atsuta Y, Andrey G, Schorderet P, Duboule D, et al. Integration of Shh and Fgf signaling in controlling Hox gene expression in cultured limb cells. Proc Natl Acad Sci USA. 2017;114:3139–44.

    Article  CAS  Google Scholar 

  26. Denans N, Iimura T, Pourquie O. Hox genes control vertebrate body elongation by collinear Wnt repression. Elife. 2015;4:e04379.

    Article  Google Scholar 

  27. Takacs-Vellai K, Vellai T, Chen EB, Zhang Y, Guerry F, Stern MJ, et al. Transcriptional control of Notch signaling by a HOX and a PBX/EXD protein during vulval development in C. elegans. Dev Biol. 2007;302:661–9.

    Article  CAS  Google Scholar 

  28. Li Z, Huang H, Chen P, He M, Li Y, Arnovitz S, et al. miR-196b directly targets both HOXA9/MEIS1 oncogenes and FAS tumour suppressor in MLL-rearranged leukaemia. Nat Commun. 2012;3:688.

    Article  Google Scholar 

  29. Mo JS, Alam KJ, Kang IH, Park WC, Seo GS, Choi SC, et al. MicroRNA 196B regulates FAS-mediated apoptosis in colorectal cancer cells. Oncotarget. 2015;6:2843–55.

    Article  Google Scholar 

  30. Luo H, Wang F, Zha J, Li H, Yan B, Du Q, et al. CTCF boundary remodels chromatin domain and drives aberrant HOX gene transcription in acute myeloid leukemia. Blood. 2018;132:837–48.

    Article  CAS  Google Scholar 

  31. Qiu Y, Xu M, Huang S. Long noncoding RNAs: emerging regulators of normal and malignant hematopoiesis. Blood. 2021;blood.2021011992.

  32. Yamamura S, Imai-Sumida M, Tanaka Y, Dahiya R. Interaction and cross-talk between non-coding RNAs. Cell Mol Life Sci. 2018;75:467–84.

    Article  CAS  Google Scholar 

  33. Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, et al. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature. 2011;472:120–4.

    Article  CAS  Google Scholar 

  34. de Boer J, Walf-Vorderwulbecke V, Williams O. In focus: MLL-rearranged leukemia. Leukemia. 2013;27:1224–8.

    Article  Google Scholar 

  35. 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 

  36. Chou CH, Shrestha S, Yang CD, Chang NW, Lin YL, Liao KW, et al. miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions. Nucleic Acids Res. 2018;46:D296–D302.

    Article  CAS  Google Scholar 

  37. Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, et al. Integrative genomics viewer. Nat Biotechnol. 2011;29:24–26.

    Article  CAS  Google Scholar 

  38. Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010;38:576–89.

    Article  CAS  Google Scholar 

  39. Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4:44–57.

    Article  CAS  Google Scholar 

  40. McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, et al. GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol. 2010;28:495–501.

    Article  CAS  Google Scholar 

  41. 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 

  42. Schep AN, Wu BJ, Buenrostro JD, Greenleaf WJ. chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data. Nat Methods. 2017;14:975–+.

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We are grateful to the Penn State College of Medicine Genome Science Facility for illumine sequencing core and the Flow Cytometry & Cell Sorting Core. We are grateful for helpful discussions from Dr. Yi Qiu (Penn State College of Medicine). We thank Dr. Sachin Singh (Center for Cellular and Molecular Biology, India) for helping the data analysis from the TCGA dataset. This work was supported by the grants from National Institutes of Health (S.H., R01DK110108, R01CA204044, and R01HL141950).

Author information

Author notes

  1. These authors contributed equally: Ajeet P. Singh, Huacheng Luo.

Authors and Affiliations

  1. Division of Pediatric Hematology/Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA

    Ajeet P. Singh, Huacheng Luo, Meghana Matur, Melanie A. Eshelman, Karina Hamamoto, Julia Lesperance & Suming Huang

  2. Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA

    Ajeet P. Singh

  3. Thoracic Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA

    Ajeet P. Singh

  4. Penn State Cancer Institute, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA

    Huacheng Luo, Arati Sharma & Suming Huang

  5. Division of Hematology and Oncology, Department of Medicine, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA

    Arati Sharma

  6. Department of Pharmacology, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA

    Arati Sharma

Authors
  1. Ajeet P. Singh
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Huacheng Luo
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Meghana Matur
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Melanie A. Eshelman
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Karina Hamamoto
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Arati Sharma
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Julia Lesperance
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Suming Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Conceptualization, study design and direction, performed overall experiments, data analysis, result interpretation, writing original draft and editing of the manuscript, and project administration: APS, HL, MM, ME, KH, and SH. Data curation: HL, MM, ME KH, and AS. Manuscript review, editing, and data visualization: HL, ME, and SH. Project administration: SH. All authors reviewed and approved the final manuscript.

Corresponding authors

Correspondence to Ajeet P. Singh, Huacheng Luo or Suming Huang.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Singh, A.P., Luo, H., Matur, M. et al. A coordinated function of lncRNA HOTTIP and miRNA-196b underpinning leukemogenesis by targeting FAS signaling. Oncogene 41, 718–731 (2022). https://doi.org/10.1038/s41388-021-02127-3

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41388-021-02127-3

This article is cited by

Search

Advanced search

Quick links