Long noncoding RNA CCDC144NL-AS1 knockdown induces naïve-like state conversion of human pluripotent stem cells

Abstract

Background Human naïve pluripotency state cells can be derived from direct isolation of inner cell mass or primed-to-naïve resetting of human embryonic stem cells (hESCs) through different combinations of transcription factors, small molecular inhibitors, and growth factors. Long noncoding RNAs (lncRNAs) have been identified to be crucial in diverse biological processes, including pluripotency regulatory circuit of mouse pluripotent stem cells (PSCs), but few are involved in human PSCs’ regulation of pluripotency and naïve pluripotency derivation. This study initially planned to discover more lncRNAs possibly playing significant roles in the regulation of human PSCs’ pluripotency, but accidently identified a lncRNA whose knockdown in human PSCs induced naïve-like pluripotency conversion. Methods Candidate lncRNAs tightly correlated with human pluripotency were screened from 55 RNA-seq data containing human ESC, human induced pluripotent stem cell (iPSC), and somatic tissue samples. Then loss-of-function experiments in human PSCs were performed to investigate the function of these candidate lncRNAs. The naïve-like pluripotency conversion caused by CCDC144NL-AS1 knockdown (KD) was characterized by quantitative real-time PCR, immunofluorescence staining, western blotting, differentiation of hESCs in vitro and in vivo, RNA-seq, and chromatin immunoprecipitation. Finally, the signaling pathways in CCDC144NL-AS1-KD human PSCs were examined through western blotting and analysis of RNA-seq data. Results The results indicated that knockdown of CCDC144NL-AS1 induces naïve-like state conversion of human PSCs in the absence of additional transcription factors or small molecular inhibitors. CCDC144NL-AS1-KD human PSCs reveal naïve-like pluripotency features, such as elevated expression of naïve pluripotency-associated genes, increased developmental capacity, analogous transcriptional profiles to human naïve PSCs, and global reduction of repressive chromatin modification marks. Furthermore, CCDC144NL-AS1-KD human PSCs display inhibition of MAPK (ERK), accumulation of active β-catenin, and upregulation of some LIF/STAT3 target genes, and all of these are concordant with previously reported traits of human naïve PSCs. Conclusions Our study unveils an unexpected role of a lncRNA, CCDC144NL-AS1 , in the naïve-like state conversion of human PSCs, providing a new perspective to further understand the regulation process of human early pluripotency states conversion. It is suggested that CCDC144NL-AS1 can be potentially valuable for future research on deriving higher quality naïve state human PSCs and promoting their therapeutic applications. Electronic supplementary material The online version of this article (10.1186/s13287-019-1323-9) contains supplementary material, which is available to authorized users.

Balanced Reciprocal Translocation t(17;22)(p11.2;q11.2) and 10q23.31 Microduplication in a Infertility Male Suffering from Teratospermia

“…The destruction of UBB (Ubiquitin B) gene was related to the low expression of many proteins involving in spermatogenesis and the reducing of germ cell number (29). UBB gene knockout mice were infertility, because of the structure destruction in gonad and reproductive organ, resulting in unformed gametes (30). Some other genes, such as CCDC144NL-AS1, LLGL1, FLII, TOP3A and ULK2, were involved in important functions like cell proliferation (31), embryonic development(32)(33) (34) and autophagy (35).…”

Case Report: Balanced Reciprocal Translocation t (17; 22) (p11.2; q11.2) and 10q23.31 Microduplication in an Infertile Male Patient Suffering From Teratozoospermia

“…UBB-knockout mice are infertile because of structural destruction of the gonads and reproductive organs, which results in unformed gametes (Ryu et al, 2008). Some other genes, such as coiled coil domain containing 144NL antisense RNA 1(CCDC144NL-AS1), FLII actin remodeling protein (FLII), and unc-51 like autophagy activating kinase 2 (ULK2), are involved in important functions, such as cell proliferation (Wang et al, 2019), embryonic development (Jossin et al, 2017) (Yang et al, 2021), and autophagy (Chan et al, 2009). Genes exhibit multiple physiological and pathological functions depending on the tissue and/or cell type where they are expressed (Priyanka and Yenugu, 2021).…”

Lnc‐ing pluripotency maintenance and early differentiation in human pluripotent stem cells

“…CCDC144NL-AS1-deficient ESCs showed naïvelike pluripotency with greater capacity to differentiate into the three germ layers. 12 In addition to regulating pluripotency gene expression, lncRNAs have important roles in X chromosome inactivation in different pluripotent states, 13 such as the XIST 14 and XACT lncRNAs. 15 These studies show that lncRNAs not only can serve as hallmarks of naïve pluripotency, but can also play essential regulatory roles in the core pluripotent gene circuitry ( Figure 1 and Table 1).…”

“…Moreover, a study screening for candidate pluripotency‐associated lncRNAs in 55 human ESC RNA‐seq samples identified a lncRNA named CCDC144NL‐AS1 , a repressor of naïve pluripotency. CCDC144NL‐AS1 ‐deficient ESCs showed naïve‐like pluripotency with greater capacity to differentiate into the three germ layers 12 . In addition to regulating pluripotency gene expression, lncRNAs have important roles in X chromosome inactivation in different pluripotent states, 13 such as the XIST 14 and XACT lncRNAs 15 .…”