Cell-type diversity and regionalized gene expression in the planarian intestine

Abstract

Proper function and repair of the digestive system are vital to most animals. Deciphering the mechanisms involved in these processes requires an atlas of gene expression and cell types. Here, we applied laser-capture microdissection (LCM) and RNA-seq to characterize the intestinal transcriptome of Schmidtea mediterranea, a planarian flatworm that can regenerate all organs, including the gut. We identified hundreds of genes with intestinal expression undetected by previous approaches. Systematic analyses revealed extensive conservation of digestive physiology and cell types with other animals, including humans. Furthermore, spatial LCM enabled us to uncover previously unappreciated regionalization of gene expression in the planarian intestine along the medio-lateral axis, especially among intestinal goblet cells. Finally, we identified two intestine-enriched transcription factors that specifically regulate regeneration (hedgehog signaling effector gli-1) or maintenance (RREB2) of goblet cells. Altogether, this work provides resources for further investigation of mechanisms involved in gastrointestinal function, repair and regeneration.

Transcriptomic analysis of early stages of intestinal regeneration in Holothuria glaberrima

“…Sea cucumbers have been particularly attractive for intestinal regeneration studies because of their innate capacity of expelling their digestive tract in a process known as evisceration, which is then followed by its regeneration. Research relating regeneration of the whole digestive system is scarce among regenerating competent organisms, where in addition to sea cucumbers, other studies include planarians 15,16 .…”

Intestine-enriched apolipoprotein b orthologs are required for stem cell differentiation and regeneration in planarians

“…dsRNA synthesis and RNAi experiments were conducted as described (Rouhana et al, 2013; Forsthoefel et al, 2020) by mixing one μg of in vitro-synthesized dsRNA with 8-9 μl of 1:10 food coloring:water mix, and 40 μl of 2:1 liver:water homogenate. For nkx2.2 RNAi, animals were fed only once; RNA was extracted for RNA-Seq after seven days.…”

“…For nkx2.2(RNAi) , quality control and read mapping were conducted with FastQC (v0.11.5) (Andrews, 2010), BBDuk (v35.66) (https://sourceforge.net/projects/bbmap/), Bowtie2 c(v2.3.1) (Langmead and Salzberg, 2012), and Samtools (v1.3) (Li et al, 2009) to unique transcripts in dd_Smed_v6 (Brandl et al, 2016) as previously described (Forsthoefel et al, 2020). Similar methods were used for apob(RNAi) reads, with several exceptions as follows.…”

Identification of rare transient somatic cell states induced by injury and required for whole-body regeneration

“…Several types of support and stem cells important for tissue maintenance and injury repair have been identified, including rare or transient cell states that only respond to particular types of injuries (15,17,64,65). The planarian intestine contains three distinct cells types: secretory goblet cells, absorptive phagocytes/enterocytes, and recently identified 'outer' or 'basal' intestinal cells (32,66). We found three different amputation-specific cell states within the planarian intestine -intestinal cluster 1 (IC1), 9 (IC9), and 12 (IC12) ( Fig.…”