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RNA binding protein DDX5 directs tuft cell specification and function to regulate microbial repertoire and disease susceptibility in the intestine
  1. Tianyun Long1,
  2. Nazia Abbasi1,
  3. Juan E Hernandez1,
  4. Yuxin Li1,
  5. Ibrahim M Sayed2,
  6. Shengyun Ma1,
  7. Attilio Iemolo3,
  8. Brian A Yee1,
  9. Gene W Yeo1,
  10. Francesca Telese3,
  11. Pradipta Ghosh1,3,
  12. Soumita Das2,
  13. Wendy Jia Men Huang1
  1. 1 Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
  2. 2 Department of Pathology, University of California San Diego, La Jolla, California, USA
  3. 3 Department of Medicine, University of California, San Diego, La Jolla, California, USA
  1. Correspondence to Dr Wendy Jia Men Huang, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92093, USA; wjh003{at}ucsd.edu

Abstract

Objective Tuft cells residing in the intestinal epithelium have diverse functions. In the small intestine, they provide protection against inflammation, combat against helminth and protist infections, and serve as entry portals for enteroviruses. In the colon, they had been implicated in tumourigenesis. Commitment of intestinal progenitor cells to the tuft cell lineage requires Rho GTPase Cell Division Cycle 42 (CDC42), a Rho GTPase that acts downstream of the epidermal growth factor receptor and wingless-related integration site signalling cascades, and the master transcription factor POU class 2 homeobox 3 (POU2F3). This study investigates how this pathway is regulated by the DEAD box containing RNA binding protein DDX5 in vivo.

Design We assessed the role of DDX5 in tuft cell specification and function in control and epithelial cell-specific Ddx5 knockout mice (DDX5ΔIEC) using transcriptomic approaches.

Results DDX5ΔIEC mice harboured a loss of intestinal tuft cell populations, modified microbial repertoire, and altered susceptibilities to ileal inflammation and colonic tumourigenesis. Mechanistically, DDX5 promotes CDC42 protein synthesis through a post-transcriptional mechanism to license tuft cell specification. Importantly, the DDX5-CDC42 axis is parallel but distinct from the known interleukin-13 circuit implicated in tuft cell hyperplasia, and both pathways augment Pou2f3 expression in secretory lineage progenitors. In mature tuft cells, DDX5 not only promotes integrin signalling and microbial responses, it also represses gene programmes involved in membrane transport and lipid metabolism.

Conclusion RNA binding protein DDX5 directs tuft cell specification and function to regulate microbial repertoire and disease susceptibility in the intestine.

  • small intestine
  • colon carcinogenesis
  • gut inflammation
  • epithelial differentiation

Data availability statement

Data are available in a public, open access repository. Data are available on reasonable request. All data relevant to the study are included in the article or uploaded as online supplemental information. The authors confirm that the data supporting the findings of this study are available within the article (and/or) its online supplemental materials. eCLIPseq datasets discussed are available on GEO (Series GSE124023).All code and commands used to process eCLIP data is available and can be found here: https://github.com/yeolab/eclip. RNAseq datasets discussed are available on GEO (Series GSE123881). The spatial transcriptomic sequencing data reported in this paper is available on GEO (GSE184564). The tumour transcriptomic sequencing data reported in this paper is available on GEO (GSE146014).

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Data availability statement

Data are available in a public, open access repository. Data are available on reasonable request. All data relevant to the study are included in the article or uploaded as online supplemental information. The authors confirm that the data supporting the findings of this study are available within the article (and/or) its online supplemental materials. eCLIPseq datasets discussed are available on GEO (Series GSE124023).All code and commands used to process eCLIP data is available and can be found here: https://github.com/yeolab/eclip. RNAseq datasets discussed are available on GEO (Series GSE123881). The spatial transcriptomic sequencing data reported in this paper is available on GEO (GSE184564). The tumour transcriptomic sequencing data reported in this paper is available on GEO (GSE146014).

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Footnotes

  • Contributors TL and NA designed and performed the mouse studies. TL and IMS performed the small intestine and colon organoid assays. YL performed the bioinformatics analyses on the RNAseq datasets. JEH performed the crypt and goblet cell analyses. BAY completed the eCLIPseq analyses. GWY directed the eCLIPseq studies and edited the manuscript. PG and SD directed the organoid studies and edited the manuscript. SM initiated the spatial transcriptomic studies and TL completed the studies with help from AI. FT provided resources for the spatial transcriptomic and organoid imaging studies. TL wrote the manuscript with input from WJMH, NA and JEH. WJMH is the guarantor.

  • Funding TL, NA, YL, JE and WJMH are partially funded by the Edward Mallinckrodt, Jr. Foundation and the National Institutes of Health (R01-GM124494 to WJMH). PG and SD were funded by the National Institutes for Health (NIH) (R01-AI141630 to PG, DK107585 to SD and UG3TR003355, UG3TR002968 and R01-AI55696 to PG and SD). PG and SD were also supported by the Leona M. and Harry B. Helmsley Charitable Trust. G.W.Y. is partially supported by NIH grants HG004659 and HG009889. RNAseq was conducted at the IGM Genomics Center, University of California San Diego. We thank the UC San Diego Electron Microscopy Core, HUMANOID Core, and the Moores Cancer Center Histology Core supported by the National Cancer Institute (CCSG P30-CA23100).

  • Competing interests G.W.Y. is a co-founder, a member of the Board of Directors, a scientific advisor, an equity holder and a paid consultant for Locanabio and Eclipse BioInnovations. G.W.Y. is a visiting professor at the National University of Singapore. G.W.Y.’s interests have been reviewed and approved by the University of California San Diego, in accordance with its conflict-of-interest policies. The authors declare no other competing interests.

  • Provenance and peer review Not commissioned; externally peer reviewed.

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