In parallel with the expansion of RNA interference (RNAi) techniques, accumulating evidence indicates that RNAi analyses might be seriously biased due to the off-target effects of gene-specific short hairpin RNAs (shRNAs). Our findings indicated that off-target effects of non-targeting shRNA comprise another source of misinterpreted shRNA-based data. We found that SHC016, which is one of two non-targeting shRNA controls for the MISSION (commercialized TRC) library, exerts deleterious effects that lead to elimination of the shRNA-coding cassette from the genomes of cultured murine and human cells. Here, we used a lentiviral vector with inducible SHC016 expression to confirm that this shRNA induces apoptosis in murine cells and senescence or mitotic catastrophe depending on the p53 status in human tumor cells. We identified the core spliceosomal protein, small nuclear ribonucleoprotein Sm D3 (SNRPD3), as a major SHC016 target in several cell lines and confirmed that CRISPRi knockdown of SNRPD3 mimics the effects of SHC016 expression in A549 and U251 cells. The overexpression of SNRPD3 rescued U251 cells from SHC016-induced mitotic catastrophe. Our findings disqualified non-targeting SHC016 shRNA and added a new premise to the discussion about the sources of uncertainty in RNAi results.

In parallel with the expansion of RNA interference techniques evidence has been accumulating that RNAi analyses may be seriously biased due to off-target effects of gene-specific shRNAs. Our work points to another possible source of misinterpretations of shRNA-based data – off-target effects of non-targeting shRNA. We found that one such control for the MISSION® library (commercialized TRC library), SHC016, is cytotoxic. Using a lentiviral vector with inducible expression of SHC016 we proved that this shRNA induces apoptosis in murine cells and, depending on p53 status, senescence or mitotic catastrophe in human tumor cell lines. We identified SNRPD3, a core spliceosomal protein, as a major SHC016 target in several cell lines and confirmed in A549 and U251 cell lines that CRISPRi-knockdown of SNRPD3 mimics the effects of SHC016 expression. Our finding disqualifies non-targeting SHC016 shRNA and adds a new premise to the discussion about the sources of uncertainty of RNAi results.

RNA interference is one of the common methods of studying protein functions. In recent years critical reports have emerged indicating that off-target effects may have a much greater impact on RNAi-based analysis than previously assumed. We studied the influence of Adam10 and Adam17 silencing on MC38CEA cell response to proinflammatory stimuli. Eight lentiviral vector-encoded shRNAs that reduced ADAM10 expression, including two specific towards ADAM17, caused inhibition of cytokine-induced Nos2 expression presumably via off-target effects. ADAM10 silencing was not responsible for this effect because: (i) CRISPR/Cas9 knockdown of ADAM10 did not affect Nos2 levels; (ii) ADAM10 inhibitor increased rather than decreased Nos2 expression; (iii) overexpression of ADAM10 in the cells with shRNA-silenced Adam10 did not reverse the effect induced by shRNA; (iv) shRNA targeting ADAM10 resulted in decrease of Nos2 expression even in ADAM10-deficient cells. The studied shRNAs influenced transcription of Nos2 rather than stability of Nos2 mRNA. They also affected stimulation of Ccl2 and Ccl7 expression. Additionally, we used vectors with doxycycline-inducible expression of chosen shRNAs and observed reduced activation of NF-κB and, to a lesser extent, AP-1 transcription factors. We discuss the requirements of strict controls and verification of results with complementary methods for reliable conclusions of shRNA-based experiments.

Funding Acknowledgements Type of funding sources: Public grant(s) – National budget only. Main funding source(s): Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Young scientists grant MNS9/2021 Polish National Science Centre PRELUDIUM grant 2019/33/N/NZ1/03066 Introduction Although gene therapy has become a feasible alternative to regular treatment in numerous disorders, efficient targeting of human heart still seems out of reach. So far, adeno-associated viral vectors (AAVs) have been the most promising transgene carriers in in vivo applications. Transduction with AAVs relies on serotype-specific binding to the glycan residues on the cell surface. While AAV serotype 9 (AAV9) - binding galactose - was successfully used for delivery of therapeutic genes to cardiac muscle in murine models, its effect was underwhelming in large animals. Switching the serotype to AAV1 or AAV6 – binding sialic acids – enabled transduction of porcine hearts, and cardiomyocytes derived from human induced pluripotent stem cells (hiPSC) in 2D in vitro culture. But, as evidenced in clinical trials where less than 1% of heart cells contained delivered transgene, such strategy was not suitable for in vivo application in humans. Purpose Taking into account differences in glycosylation patterns between humans and other mammals, we aimed to investigate the role of surface glycans in AAV6 and AAV9 transduction mechanism in 2D and 3D cultures of human cardiomyocytes. Methods We generated hiPSC- derived cardiomyocytes (hiPSC-CMs) and epicardial fibroblasts (hiPSC-CFs). Cells were cultured in regular 2D conditions or 3D co-cultures (as spheroids), since direct cells interaction may influence the availability of terminal sugar residues. Surface glycans were stained with lectins and imaged using confocal microscope. Results While in 2D conditions AAV6 transduces hiPSC-CMs very efficiently, it is significantly less potent in 3D culture. Conversely, AAV9 maintains most of its functionality in 3D model. Our data collected from spheroids, indicate that cells in such 3D cultures undergo significant changes in terminal glycosylation pattern. While the level of galactose (AAV9 receptor) increased from day 1 to day 7, the signal from sialic acids attached to galactose (AAV6 receptor) decreased. This effect was accompanied by the upregulation of sialidase-3 expression, that regulates availability of galactose residues on the cell surface. As a result, transduction efficiency was improved in spheroids exposed to AAV9 on day 7 of 3D culture, in comparison to those transduced on day 1. Inhibition of sialidases activity with NADNA reduced the level of terminal galactose in both, hiPSC-CMs and hiPSC-CFs, and was associated with more efficient transduction of cardiomyocytes with AAV6, and less efficient transduction with AAV9. Additionally, we observed that galactosylation of collagen can be another factor that influences cell-vector interaction in 2D and 3D culture. Conclusions Our results demonstrate that the availability of terminal sugar residues is a key factor regulating transduction of hiPSC-CMs with AAV vectors, and underline the need for development of appropriate models for testing of AAV functionality in preclinical studies.