Oct4 and Its Pseudogenes Confuse Stem Cell Research.
Authors: Liedtke Stefanie , Enczmann Jürgen , Waclawczyk Simon , Wernet Peter , Kögler Gesine 
Published: April 2020

Abstract
Octamer-binding transcription factor 4 (Oct4) encodes a nuclear protein that belongs to a family of transcription factors containing the POU DNA binding domain. It is specifically expressed in embryonic stem cells but can also be detected in adult stem cells such as bone marrow-derived mesenchymal stem cells. The expression of Oct4 is down-regulated coincident with stem cell differentiation and loss of expression leading to differentiation. It plays a critical role for maintaining pluripotency and self-renewal of embryonic stem cells. However, the usefulness of Oct4 as a pluripotency marker was challenged recently. More and more data seem to support that Oct4 is expressed on a variety of differentiated cells, including peripheral blood mononuclear cells. Taking into account that RT-PCR can potentially generate experimental artifacts due to pseudogene transcripts, the existence of Oct4 pseudogenes should be investigated further here. Suo et al. were able to detect transcription of some Oct4 pseudogenes in cancer cell lines as well as cancer tissues. These results show that some of the known Oct4 pseudogenes are transcribed in vivo and therefore could lead to RT-PCR artifacts. However this known problem was not seriously taken into consideration in recent publications on adult stem cells and tissue analysis referring to Oct4. We started with an initial alignment of Oct4 compared to its alternative splice variants as well as its pseudogenes. This alignment served as a prerequisite for an exact primer design. First the sequence and organization of the functional human Oct4 gene were clarified to allow comparison to the pseudogenes and alternatively spliced transcripts. The NCBI human EST database was searched and the UniGene cluster for Oct4 (NM_002701) examined. This yielded 13 mRNA sequences and 129 EST sequences. An additional BLASTn search of the human genome using single exons of Oct4 revealed several other highly similar sequences. All these hits encoded complete or partial Oct4 sequences and could therefore represent either functional members of an Oct4 gene family or pseudogenes. The fact that so many homologous sequences resemble the original Oct4 transcript makes an RT-PCR analysis difficult, because a lot of artifacts can arise during amplification. Therefore primers were designed which are able to exclude amplification of all unwanted transcripts. To conclude, based on the fact that the expression of Oct4 has been reported in adult stem cells as well as in a variety of differentiated cells the possibility cannot be excluded that the detected Oct4 signal came from alternatively spliced or Oct4 pseudogene transcripts. As shown here, an exact design of Oct4-specific primers is an inevitable prerequisite for appropriate RT-PCR analysis. In addition, a careful comparison of quantitative differences to human embryonic stem cells should be present too, before cells are described as embryonic like cells. We hope that our findings will help other stem cell researchers to find their appropriate tools especially for RT-PCR analysis and give an example how later problematic artifacts can be ruled out from the beginning by a detailed alignment as a prerequisite for designing appropriate primers.