Paraiso KD et al. (2019), Morpholinos Do Not Elicit an Innate Immune Resp...

XB-ART-55969

Dev Cell 2019 May 20;494:643-650.e3. doi: 10.1016/j.devcel.2019.04.019.

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Morpholinos Do Not Elicit an Innate Immune Response during Early Xenopus Embryogenesis.

Paraiso KD , Blitz IL , Zhou JJ , Cho KWY .

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It has recently been reported that a common side effect of translation-blocking morpholino antisense oligonucleotides is the induction of a set of innate immune response genes in Xenopus embryos and that splicing-blocking morpholinos lead to unexpected off-target mis-splicing events. Here, we present an analysis of all publicly available Xenopus RNA sequencing (RNA-seq) data in a reexamination of the effects of translation-blocking morpholinos on the innate immune response. Our analysis does not support the authors' general conclusion, which was based on a limited number of RNA-seq datasets. Moreover, the strong induction of an immune response appears to be specific to the tbxt/tbxt2 morpholinos. The more comprehensive study presented here indicates that using morpholinos for targeted gene knockdowns remains of considerable value for the rapid identification of gene function.

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Species referenced: Xenopus laevis
Genes referenced: ascl1 c1s c3ar1 c5 cdx1 cdx2 cdx4 crx ctnnb1 exosc9 foxh1 foxn4 gsc lhx1 mov10 otx2 ptafr ptbp1 rab7b rfx2 riok3 ripk2 socs3 tbxt tbxt.2 tcf21 tcf3 tp53 tp53inp1 tra2b wnt8a
GO keywords: innate immune response
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	Figure 1. Expression of Innate Immune Response Genes in X. tropicalis and X. laevis RNA-Seq Datasets (A) Fold change in induction caused by the tbxt/tbxt2 MOs and the control MOs. (B) Fold change caused by control MO in biological replicates at stages 10 and 36 using RT-qPCR. (C and D) Fold-change induction of innate immune response genes in X. tropicalis (C) and X. laevis (D) datasets.
	Figure 2. Expression of GO-Identified Innate Immune Response Genes in X. tropicalis and X. laevis RNA-Seq Datasets (A–C) Fold-change expression of innate immune response genes across 29 datasets in X. tropicalis (A), across 13 datasets in X. laevis (B), and in 12 of the tbxt/t2 MO datasets (C). The gray region indicates fold change of <1.5×. Green asterisk (∗) indicates a t test p value of <0.01.
	Figure 3. Expression of Literature-Identified Innate Immune Response Genes in X. tropicalis and X. laevis RNA-Seq Datasets (A–C) Fold-change expression of innate immune response genes across 29 datasets in X. tropicalis (A), 13 datasets in X. laevis (B), and in 12 of the tbxt/t2 MO datasets (C). Gray region indicates fold change of < 1.5×. Green asterisk (∗) indicates a t test p value of < 0.01.
	Figure 4. Specific Induction of Innate Immune Response Genes (A and B) Fold-change expression of genes, which were identified to be significantly activated in the X. tropicalis datasets in both the GO-identified (A) and the literature-identified (B) cohort of genes. (C–E) Fold-change expression of X. laevis genes ptafr.L/gene13059 (C), socs3.L/gene3766 (D), and socs3.S/gene50103 (E), which were identified to be significantly activated. We used the criteria p value < 0.01 and fold change > 1.5 to define significant.

References [+] :

Ashburner, Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. 2000, Pubmed