Enhanced Preprints

The lncRNA Malat1 Inhibits miR-15/16 to Enhance Cytotoxic T Cell Activation and Memory Cell Formation

  1. Benjamin D Wheeler
  2. John D Gagnon
  3. Wandi S Zhu
  4. Priscila Muñoz-Sandoval
  5. Simon K Wong
  6. Dimitre R Simeonov
  7. Zhongmei Li
  8. Rachel Debarge
  9. Matthew H Spitzer
  10. Alexander Marson
  11. K Mark Ansel author has email address
  1. Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA 94143, USA
  2. Sandler Asthma Basic Research Program, University of California, San Francisco, San Francisco, CA, USA
  3. Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
  4. Department of Otolaryngology-Head and Neck Surgery, University of California San Francisco, San Francisco, CA 94143, USA
  5. Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129
  6. Chan Zuckerberg Biohub, San Francisco, CA 94158
  7. Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA

Editors

  • Reviewing Editor
    Howard Chang
    Stanford University, Stanford, United States of America
  • Senior Editor
    Carla Rothlin
    Yale University, New Haven, United States of America

Reviewer #1 (Public Review):

Wheeler et al. have discovered a new RNA circuit that regulates T-cell function. They found that the long non-coding RNA Malat1 sponges miR-15/16, which controls many genes related to T cell activation, survival, and memory. This suggests that Malat1 indirectly regulates T-cell function. They used CRISPR to mutate the miR-15/16 binding site in Malat1 and observed that this disrupted the RNA circuit and impaired cytotoxic T-cell responses. While this study presents a novel molecular mechanism of T-cell regulation by Malat1-miR-15/16, the effects of Malat1 are weaker compared to miR-15/16. This could be due to several reasons, including higher levels of miR-15/16 compared to Malat1 or Malat1 expression being mostly restricted to the nucleus. Although the role of miR15/16 in T-cell activation has been previously published, if the authors can demonstrate that miR15/16 and/or Malat1 affect the clearance of Listeria or LCMV, this will significantly add to the current findings and provide physiological context to the study.

Reviewer #2 (Public Review):

This study connects prior findings on MicroRNA15/16 and Malat1 to demonstrate a functional interaction that is consequential for T cell activation and cell fate.

The study uses mice (Malat1scr/scr) with a precise genetic modification of Malat1 to specifically excise the sites of interaction with the microRNA, but sparing all other sequences, and mice with T-cell specific deletion of miR-15/16. The effects of genetic modification on in vivo T-cell responses are detected using specific mutations and shown to be T-cell intrinsic.

It is not known where in the cell the consequential interactions between MicroRNA15/16 and Malat1 take place. The authors depict in the graphical abstract Malat1 to be a nuclear lncRNA. Malat 1 is very abundant, but it is unclear if it can shuttle between the nucleus and cytoplasm. As the authors discuss future work defining where in the cell the relevant interactions take place will be important.

In addition to showing physiological phenotypic effects, the mouse models prove to be very helpful when the effects measured are small and sometimes hard to quantitate in the context of considerable variation between biological replicates (for example the results in Figure 4D).

The impact of the genetic modification on the CD28-IL2- Bcl2 axis is quantitatively small at the level of expression of individual proteins and there are likely to be additional components to this circuitry.

  1. Howard Hughes Medical Institute
  2. Wellcome Trust
  3. Max-Planck-Gesellschaft
  4. Knut and Alice Wallenberg Foundation