Note: in the time since writing my answer, the paper in question has been retracted. Here's the text of the retraction notice provided by MDPI in collaboration with the authors:
The published article has been retracted. Following publication, the first author contacted the editorial office regarding an improper experimental design with the potential to significantly affect the integrity of the resultant experimental data.
Adhering to our complaint procedure, an investigation was conducted. Both the chosen construct of the spike plasmid that contained a C-terminal fused with 6xHis tag and use of a GFP reporter system under overexpression conditions in the protocol were identified as having the potential to introduce significant ambiguity regarding the nature of the reported observations. The reliability of the results and conclusions presented have therefore been undermined. Furthermore, statements regarding the effect of the spike protein on the adaptive immunity are misleading as in this article no experiments related to the adaptive immunity were performed, and the full-length spike-based vaccine was not studied. Therefore, conclusions related to vaccine safety are not validated and lacked experimental support. This article is retracted and shall be marked accordingly. This retraction was approved by the Editor-in-Chief of the journal Viruses.
While the linked paper presents interesting results, the conclusions must be interpreted in context of their in vitro methods and cannot be readily extrapolated to understand the in vivo effect of SARS-CoV-2 mRNA-LNP vaccines. Here is their important caveat:
Although no evidence has been published that SARS–CoV–2 can infect thymocytes or bone marrow lymphoid cells, our in vitro V(D)J reporter assay shows that the spike protein intensely impeded V(D)J recombination.
They show that spike protein expressed in human embryonic kidney cells (HEK293) can localize to the nucleus and inhibit non-homologous end-joining (NHEJ), which is a vital process in the generation of diversity in the antigen-binding regions of antibodies. However, the way the human adaptive immune system works is such that the cells responsible for generating antibody diversity never internalize the antigenic protein. Once injected, the mRNA-containing lipid nanoparticles are endocytosed by dendritic cells. The mRNA is then translated and the spike protein is presented to T- and B-cells in lymphoid tissues to elicit an immune response. These T- and B-cells are the cells that carry out V(D)J recombination, but they are not the cells that are engulfing the nanoparticle load.
Two good reviews that cover this process in-depth:
- Teijaro JR, Farber DL. COVID-19 vaccines: modes of immune activation and future challenges. Nat Rev Immunol. 2021 Apr;21(4):195-197.
- Angeli F, Spanevello A, Reboldi G, Visca D, Verdecchia P. SARS-CoV-2 vaccines: Lights and shadows. Eur J Intern Med. 2021 Jun;88:1-8.