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Mobilization of jumping genes in pluripotent stem cells may affect safety of stem cell-based therapies

Reprogramming of human cells into induced pluripotent stem cells (hiPSCs) activates normally repressed, endogenous mobile DNA (retrotransposons; jumping genes), which can result in new insertions in the stem cell genome. The function of differentiated cells derived from such stem cells could be hampered by these mutations. Moreover, these retrotransposon insertions can affect genes relevant to tumor development. These findings raise questions regarding the biosafety of hiPSC-derived therapeutic cells. Nature Communications reports these findings in its online issue from 8th January 2016.

01 / 2016

Human induced pluripotent stem cells (hiPSCs) hold substantial promise for biomedical applications because they have the potential to give rise to every cell type of the human body. Amongst other applications, hiPSCs have the potential to be applied in regenerative medicine for autologous cell therapies. To this end, patients’ somatic cells are reprogrammed into hiPSCs, differentiated into the favored, therapeutically relevant cell type, and finally administered to the patient. However, during reprogramming and hiPSC cultivation, genetic and epigenetic aberrations occur.

An international research team headed by Dr Gerald Schumann, Division of Medical Biotechnology, Paul-Ehrlich-Institut, demonstrated in collaboration with the research groups of Drs. Geoffrey Faulkner (Mater Research Institute-University of Queensland, Australia) and Jose Garcia-Perez (Pfizer/University of Granada and Andalusian Regional Government Center for Genomics and Oncology, Spain) that both during reprogramming and subsequent cultivation of newly generated hiPSC lines, mobilization of endogenous transposable elements occurs in the stem cell genome resulting in new additional insertions. These mobile genetic elements include LINE-1 (L1), Alu and SVA retrotransposons, which are also termed 'jumping genes', because they duplicate and spread throughout the genome via a copy & paste mechanism. By applying a novel high-throughput sequencing approach termed ‘Retrotransposon Capture Sequencing’ (RC-Seq), the researchers compared the genomes of 8 hiPSC lines with those of their differentiated parental cells from which the hiPSC lines were derived by reprogramming.

Human induced pluripotent stem cell colony expressing endogenous LINE-1 proteins (red) which lead to the mobilization of transposable elements in the stem cell genome. Cell nuclei are cyan stained. Human induced pluripotent stem cell colony expressing endogenous LINE-1 proteins (red) which lead to the mobilization of transposable elements in the stem cell genome. Cell nuclei are cyan stained.Human induced pluripotent stem cell colony expressing endogenous LINE-1 proteins (red) which lead to the mobilization of transposable elements in the stem cell genome. Cell nuclei are cyan stained. Source: Klawitter S et al.: Nature Communications

The scientists uncovered that mobilization and resulting new insertions of endogenous jumping genes occurred in the genomes of 4 out of 8 analyzed hiPSC lines both during reprogramming and subsequent hiPSC cultivation. Mobilization of jumping genes occurred at a frequency of ~1 retro­transposition event per hiPSC. Mobilization of preexisting endogenous L1 elements also generated new functional L1 copies which again are able to spread throughout the genome and give rise to new gene mutations. Jumping of endogenous transposable elements causes new, potentially mutagenic insertions that can influence the function of the host cell and participate in the process of transformation to a tumor cell. "Genomic integrity of pluripotent stem cells can be impaired by the mobilization of endogenous transposable elements which is mediated by endogenous L1 activity. This raises the question to what extent the safety of cellular therapies is affected if differentiated cells derived from such hiPSCs are applied", said Dr Schumann explaining the significance of their findings. The research group will address these questions as a next step. From a regulatory point of view, testing the safety of these cells before they are applied in a potentially therapeutic setting would reduce the risk associated with these cells.

Background – Induced pluripotent stem cells in Biomedicine

Human induced pluripotent stem cells (hiPSCs) hold substantial promise for regenerative medicine. hiPSCs are capable of unlimited proliferation and can differentiate in vitro to generate derivatives of the three primary germ layers. hiPSC applications include disease modeling, study of cell development and function, in vitro screening of drug candidates on healthy and diseased cells. hiPSCs are a cell source of potential future substitutive and regenerative autologous cell therapies where patient cells are reprogrammed to pluripotent stem cells and subsequently differentiated into the favoured therapeutic cell type. Unlike organ transplants and human embryonic stem cells, hiPSCs are a source of autologous cells compatible with the immune system of transplant recipients.

Original Publication

Klawitter S, Fuchs NV, Upton KR, Muñoz-Lopez M, Shukla R, Wang J, Garcia-Canadas M, Lopez-Ruiz C, Gerhardt DJ, Sebe A, Grabundzija I, Merkert S, Gerdes P, Pulgarin JA, Bock A, Held U, Witthuhn A, Haase A, Sarkadi B, Löwer J, Wolvetang EJ, Martin U, Ivics Z, Izsvák Z, Garcia-Perez JL, Faulkner GJ, Schumann GG (2016): Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells.
Nat Commun Jan 8 [Epub ahead of print].
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