An enhanced triple fluorescence flow-cytometry-based assay shows differential activation of the Notch signaling pathway by human papillomavirus E6 proteins

Human papillomaviruses are DNA tumor viruses. A persistent infection with high-risk HPV types is the necessary risk factor for the development of anogenital carcinoma. The E6 protein is a viral oncoprotein that directly interacts with different cellular regulatory proteins mainly affecting the cell cycle, cellular differentiation and polarization of epithelial cells. In dependency of the phylogenetic classification of HPV different interaction partners of E6 have been described. The Notch pathway seems to be one common target of HPV, which can be up or down regulated by different E6 proteins. Our novel triple fluorescence flow-cytometry-based assay allows a semi-quantitative comparison of the E6 proteins´ effect on the Notch pathway using a Notch-responsive reporter plasmid. As a result, all E6 proteins of beta-HPV repressed the Notch reporter expression, of which HPV38 E6 showed the greatest repression potential. In contrast, alpha-HPV E6 of HPV16, activates the reporter expression most significantly, whereas E6 of HPV31 and low-risk HPV6b showed significant activation only in a p53-null cell line. Interestingly, HPV18 E6, with the second highest carcinogenic risk, shows no effect. This high divergence within different genus of HPV is important for targeting the Notch pathway regarding a potential HPV therapy.

. Scheme of the Notch signaling pathway. The Notch receptor is cleaved at S2 cleavage site by ADAM 10 protease upon binding to Notch ligand, Jagged from neighboring cells. Thus, releasing Notch extracellular domain (NECD) for receptor endocytosis. Cleavage of Notch intracellular domain (NICD) at S3 cleavage site by γ secretase leads to the translocation of NICD into nucleus. NICD then recruits MAML1, p300, CSL and other co-activators to activate the expression of Notch target gene, HES1. Beta HPV E6 protein associates with MAML1 and inhibits Notch Signaling. Adapted from "Notch Signaling Pathway", by BioRender.com (2020). Retrieved from https:// app. biore nder. com/ biore nder-templ ates. www.nature.com/scientificreports/ types of human papillomaviruses (HPV), of which only some repress the Notch pathway. Types of the beta genus interfere with Notch signaling via the interaction of the viral protein E6 with proteins of the transcription initiation complex for Notch-responsive expression as of HES1 12,[14][15][16] . In contrast, it has been reported, that HPV16 found in 50% of all cervical cancer 17 , shows an upregulation of HES1 and Notch in cervical cancer cells 3,[18][19][20] . This indicates, that E6 proteins of different HPV types can either up-or downregulate the Notch signaling pathway. E6 proteins of different HPV types are conserved in their amino acid sequence and structure. However, it has been shown, that the E6 proteins of different HPVs differ in their intracellular level 21 . A comparison of the modulatory effect of the individual E6 proteins on the Notch signaling necessitates information about its intracellular protein amount on a single-cell level. However, this cannot be achieved by commonly employed dual luciferase-based assays measuring luciferase expression controlled by the Notch-responsive HES1-promotor.
To overcome this, we developed a flow-cytometry-based assay to analyze P-HES1 activity using three different fluorescent proteins reporting (I) the transfection of the activator plasmid, human Notch 1 intracellular domain by EGFP co-expression (here NICD), (II) the intracellular amount of the modulator (here E6) by N-terminal fusion of mTagBFP2 and (III) the promotor activity (here of P-HES1) by DsRed2 expression (Fig. 2). This allows us to monitor HES1-activation on a single cell level and consider only cells which are triple positive. By this, we can reduce the background and, additionally account for different protein expression levels (Fig. 3). Using this strategy, we assess the activating or repressing potential of E6 proteins of different genera, species and types of HPV (Table 1) on the Notch signaling pathway with a semi-quantitative approach.

Results
Exogenous activation of Notch signaling pathway in C33A and H1299 cells. To verify, that the cell systems activate Notch signaling in response to exogenous NICD, we co-transfected the reporter plasmid and the control plasmid encoding for mTagBFP2 further with and without the activator plasmid and gated for Figure 2. Constructs of triple fluorescence flow-cytometry-based assay to analyze P-HES1 activity. Three plasmids are co-transfected: (I) activator plasmid with two open reading frames encoding the Notch intracellular domain (NICD) as the activator of the Notch pathway and the EGFP as transfection control for the activator plasmid. (II) the modulator plasmid, encoding the modulator protein of interest E6, which is N-terminally fused to mTagBFP2 to monitor E6 expression. (III) the reporter plasmid encoding for the reporter DsRed2. The expression of DsRed2 is under control of the HES1 promotor which is regulated by the Notch pathway. Picture was created with CorelDRAW X7, version 17.5.0.907. Living cells are first identified by FSC/SSC gating followed by specific inclusions of cells that are transfected with the activator plasmid (EGFP + cells). Next step is to gate on EGFP/ mTagBFP2 to only monitor cells that have been transfected with the activator and the modulator (EGFP + / mTagBFP2 + cells). Then, Notch-activation is assessed in this population by measuring the DsRed2 expression (EGFP + /mTagBFP2 + /DsRed2 + cells). Picture was created with BioRender.com. www.nature.com/scientificreports/ DsRed2 positive cells (Fig. 4). Without the activator plasmid, C33A and H1299 cells showed less than 0.2 ± 0.06% and 0.02 ± 0.003% DsRed2 expressing cell population, respectively (Fig. 4), indicating that the constitutive and endogenous Notch signaling is low and thereby not triggering P-HES1 regulated reporter expression sufficiently. Additionally, the co-expression of neither mTagBFP2 nor EGFP affected the signal of DsRed2. Conversely, C33A and H1299 cells co-transfected with the activator plasmid showed a significant increase in the DsRed2 expressing cell population, which was at least tenfold above the background signal of DsRed2 expressing cell population without exogenous NICD. Hence, both cell lines clearly show an activation of the Notch pathway by exogenous NICD with very low background of endogenous P-HES1-activity ( Fig. 4b and c).

Scientific
Triple gating strategy-proof of concept. As the excitation and emission spectra of fluorescent proteins EGFP, mTagBFP2, DsRed2 overlap partially, it is important to carefully control for crosstalk in the three applied channels and compensate accordingly. As a control, we transfected cells individually with plasmids each encoding for EGFP, mTagBFP2 or DsRed2. Gates were set for each protein such as there is no crosstalk (< 0.5%) in the other channels (Fig. 5). By this, we were able to gate specifically for triple positive viable cells (P1/EGFP/mTag-BFP2/DsRed2) showing EGFP (activator transfected), mTagBFP2 (modulator protein) and DsRed2 (Notchresponsive reporter) expression. It had been shown previously that Notch signaling is activated when the NICD translocate into the nucleus and forms a Notch initiation complex with other cellular proteins. However, E6 proteins localize into the nucleus to interfere with formation of the Notch initiation complex. Thus, it would be interesting to know if mTagBFP2-E6s fusion retain ability to localize into the nucleus. Hence, we first analyze the mTagBFP2-E6s fusion constructs, of which all accumulated in the nucleus (Supplementary information SI1 -SI3).
To examine the P-HES1 reporter activity with our triple gating strategy, an exemplary triple gating is shown for C33A co-transfected with P-HES1 reporter plasmid, NICD activator plasmid and mTagBFP2-E6 modulator plasmid for 16E6 and 8E6 (Fig. 6). Finally, ~ 66.0 ± 1.6% cells for 16E6 and ~ 18.7 ± 4.5% cells for the E6 of the HPV8 (8E6) were DsRed2 positive in the triple gated cell population. Compared with our control (46.6 ± 4.7% cells), where we co-transfected mTagBFP2 instead of the fusion construct mTagBFP2-E6, 16E6 clearly shows an activation, while 8E6 clearly shows a repression of the P-HES1 activity.
In parallel, we validated the results by Western Blot analysis (Fig. 7). This shows, that EGFP, mTagBFP2, mTagBFP2-E6 and DsRed2 are expressed. In accordance with the flow cytometric analyses, the P-HES1 regulated expression of DsRed2 is activated by co-transfection of the activator plasmid (NICD), decreased for 8E6 and increased for 16E6.

Modulation of Notch signaling pathway by different HPV E6 proteins.
We analyzed the effect on the Notch signaling pathway of seven different E6 proteins derived from HPVs of different genus, species and carcinogenic potential ( Table 1). E6 proteins interfere with p53, especially HPV types of high-risk directly degrade p53 21 . Since there is a crosstalk between p53 and the Notch pathway, we performed the same experiments in two different cell lines: the HPV-negative cervix carcinoma cell line C33A and the p53 null lung cancer cell line H1299. Applying our triple gating strategy, we analyzed the data considering the percentage of DsRed2 positive cells and the mean fluorescence intensity (MFI) (Fig. 8). Assessing MFI considers the intracellular expression level of DsRed2 produced upon activation of P-HES1. Analyzing the % of DsRed2 positive cells does not account for the individual single-cell level of DsRed2 expression, but rather focuses on changes on cell population levels. Nevertheless, both, % cells and MFI should change accordingly in case of repression or activation.
The E6 proteins of beta HPV 5, 8 and 38 showed a significant repression of DsRed2 + % cells and MFI in C33A and H1299 cells. In H1299 cells, repression was so potent, that the total cell numbers in the final triplegated DsRed2 + population was below 500 cells. In contrast, the alpha-7 HPV 16E6 showed a highly significant activation of reporter expression in both cell lines.
The E6 of alpha-7 HPV 31 and alpha-10 HPV 6b show a low activation of P-HES1 activity in C33A cells, in which activation by HPV 31 is not significant for the MFI of the DsRed2. In the p53-null H1299 cells the activation of Notch pathway by 31E6 and 6bE6 seems increased, especially for 31E6. Regarding the effect of alpha-7 HPV 18E6, in % cell-signal 18E6 shows a slight repression, whereas this effect was less clear and not significant for the MFI of the DsRed2 in both cell lines. Altogether, our triple gating strategy is suitable to monitor the modulation of the Notch signaling pathway by different E6, which show repression for all beta-HPV E6, activation for HPV16, cell-line dependent activation for HPV31 and 6b and rather no effect for HPV18.
Semi-quantitative analysis of E6 activities. Both signals of mTagBFP2-E6 for % cells and MFI, , vary between the different E6 proteins ( Fig. 9) indicating that the intracellular protein amount of the mTagBFP2-E6 variants differs between the different HPV types. Principally, the MFI per cell of a FP is equivalent to the amount of the respective FP per cell. Thereby, the MFI of mTagBFP2 equals to the amount of the modulator mTagBFP2-E6 and the MFI of DsRed2 equals the amount of DsRed2 as the reporter of P-HES1 activity.   , c). Three independent biological replicates were conducted. A significant cell population of DsRed2 positive cells was detected in C33A (b) and H1299 (c), respectively in presence of exogenous NICD (P-HES1-DsRed2 + mTagBFP2 + NICD). In contrast, the endogenous NICD does not activate P-HES1-DsRed2 expression sufficiently (P-HES1-DsRed2 + mTagBFP2), independent of the co-transfection of EGFP control plasmid (P-HES1-DsRed2 + mTagBFP2 + EGFP). The mean % cells of DsRed2 expressing cell populations as gated for each sample is stated above each bar and the error bars plotted indicate the standard deviation of the mean from the three independent biological replicates. P-values were calculated using One-Way ANOVA with Fischer's LSD test by comparing the mean of each sample with mean of P-HES1-DsRed2 + mTagBFP2. **** = P ≤ 0.0001, ns = P > 0.05. www.nature.com/scientificreports/ Assuming no effect of unfused mTagBFP2, its DsRed2 MFI was set to zero. Subsequently, as expected, normalized MFI < 0 show repression, whereas MFI > 0 show activation of P-HES1. We then calculated the ratio of normalized MFI DsRed2 to the MFI of mTagBFP2-E6 including triple positive cells only. This ratio then resembles the specific activity of each E6 protein in this assay (Fig. 10) accounting for the different E6 expression levels ( Fig. 9). A step to step analysis guide can be found in Supplementary information SI 5. As a result, the repressing activities of the beta-HPV 5E6 and 8E6 proteins are comparable, whereas 38E6 shows a 2-times and 4-times higher potential in repressing P-HES1 regulated transcription of DsRed2 in H1299 and C33A cells, respectively. 16E6 shows a 5-7-times higher activation potential than the other E6 proteins of alpha-HPV 6bE6, 31E6, 18E6, which showed no significant impact on P-HES1 activity in C33A cells. Surprisingly, a higher and more significant activation of the Notch pathway was observed in the p53-null H1299 cells for E6 of HPV 31 and 6b. Here the activity of 31E6 is even similar to the activity of 16E6. In principle, the trend of these semi-quantitative results www.nature.com/scientificreports/ is in line with the results above (Fig. 8). An additional accounting for the different E6 expression shows, that the individual activities of E6 proteins diverge largely in modulating the Notch pathway and are cell line dependent.

Discussion
Notch signaling pathway plays an important role in cell fate determination and cell proliferation 1 . Dysregulation of Notch signaling is often observed in the progression of carcinoma 2,3 . Hence, it is extensively studied as a potential drug target to counter for treatment of its associated diseases. Numerous studies have shown the dysregulation of Notch signaling in HPV associated cancer progression by employing dual-luciferase assay [14][15][16] . However, the disadvantages of this luciferase reporter assay include the needs of the expensive commercial dual luciferase kit containing exogeneous substrates and cell lysis, disrupting the compartmentation of cells. The main limitation of luciferase assays is the comparison of the effect of different modulators on the reporter gene expression based on the expression of these modulatory proteins. To overcome these drawbacks, we established a triple fluorescence flow-cytometry-based reporter assay to analyze the effect of different HPV E6 proteins on Notch signaling pathway. The advantage of this flow-cytometry-based reporter assay is the triple gating strategy, which allows to monitor exclusively living cells that express the modulatory protein as well as the reporter and the activator. Reducing the background is especially advantageous if potential modulatory proteins show low transfection efficiencies and/or low steady-state expression levels. In addition to that, fluorescently labeled Concerning the background of endogenous Notch signaling, which is tenfold lower than of the exogenously activated cells (Fig. 4). We expected that the E6 proteins also modulate the endogenous NICD. Indeed, we conducted experiments by co-transfecting C33A and H1299 cells with only P-HES1-DsRed2 reporter plasmid and mTagBFP2-E6 or mTagBFP2 (control) to examine the modulation effect of P-HES1 activity by HPV16 and 8 E6 with endogenous NICD. In this case, a double fluorescence gating strategy was applied whereby the viable cells were gated for mTagBFP2 followed by DsRed2 (P1 > P1/mTagBFP2 > P1/mTagBFP2/DsRed2). Despite a similar overall trend, without heterologous expression of NICD, the % cells expressing DsRed2 in mTagBFP2-E6 cell population are too low to find a statistically relevant population to quantify differences (Supplementary information SI 6).
The effect of modulatory proteins on gene regulation can be influenced by protein activity (the more active the protein, the higher the effect) and the protein amount (the more protein, the higher the effect). In our assay, the expression level of mTagBFP2-E6 varies among the different HPV types. Different intracellular levels of E6 have been reported previously 21 affecting the gene regulation by different E6 amounts. The expression levels of E6 are unknown in its native environment, during infection or cell transformation. Of course, the assay conditions do not fully resemble the native environment, especially with regard to the levels of E6, NICD and P-HES1. Nevertheless, and therefore allows a comparison of their activity this assay provides information about the specific activity of individual E6 proteins, which allow a comparison of each E6 protein potential in the context of dysregulating the Notch signaling pathway by HPVs. Our semi-quantitative analysis allows the comparison of different modulatory proteins, e.g. the different HPV E6 proteins, or mutants accounting for their individual variations in their expression levels. Overall, the triple fluorescence assay can be easily transferred to other genes of interest or signaling pathways by cloning the respective promotor, activator and modulatory protein into respective plasmids. Further it can be used to screen specific inhibitors of the modulatory proteins, here the HPV E6 proteins, and monitor their efficiency on the target gene expression in a fast way as well as in medium throughput.
Concerning the HPV E6 proteins and their biological functions, we could show that E6 proteins of different genus differentially manipulate the Notch signaling pathway. (I) all tested E6 proteins of beta-HPV repress the Notch pathway. This is in line with their reported interaction with MAML1 as a co-factor of the initiation complex of HES1 transcription 2,12,14-16 . The repression potential is highest for 38E6, and lower for 5E6 and 8E6. 5E6 and 8E6 show a similar repression potential. HPV 38 belongs to beta-2 HPV, whereas HPV 5 and 8 belong to beta-1 HPV, indicating an association between function and phylogeny. (II) E6 of alpha-HPV do marginally interact with MAML1 and do not repress Notch signaling, as previously proposed for e.g. 16E6 12,14 . Indeed, the activity of the tested alpha-HPV E6 proteins is highly divergent. In C33A only 16E6 showed a clear activation. Higher levels of Notch signaling were previously reported for HPV16-positive keratinocytes and high-grade lesions 19,20,[22][23][24] . 18E6, 31E6 and 6bE6 showed no significant impact in C33A cells. (III) It is known, that E6 proteins of high-risk alpha-HPV 16, 18 and 31 lead to the degradation of the tumor suppressor p53 [25][26][27][28][29] . Since there is a crosstalk between p53 and the Notch pathway 30,31 we applied the same experiment in H1299 cells, which are p53 deficient. Here, the overall trend looks similar, beta-HPV E6 proteins repress and 16E6 activates the activity of the P-HES1 reporter. Remarkably, the repressing effect in H1299 was so strong, that the triple positive cell population consisted of less than 500 cells. Nevertheless, the repressing effect of beta-HPV is clear and the tendency of the potentials of the different beta-HPV E6 proteins resembles the results measured in C33A. Whereas 18E6 again shows no effect on Notch signaling. H1299 31E6 and 6bE6 show a clear tendency to activate the Notch pathway in the p53-null cell line. Especially HPV 31E6, a high-risk type of the same species as 16E6, shows a strong activation similar to the activity of 16E6 and over two-fold stronger than the low-risk HPV 6bE6.  www.nature.com/scientificreports/ Why 31E6 is more active in the p53-null cell line H1299 than in C33A, whereas the activity of the closely related 16E6 seems similar in both cell lines, is unknown. Both cell lines certainly differ in more than just the presence of p53. However, a speculative relation might be the lower potential of 31E6 interacting with 32 and degrading p53 21 than 16E6. E6 of HPV18, as the second most carcinogenic HPV type, surprisingly shows no significant effect on the Notch signaling in both cell lines. However, this approach focused only on the P-HES1 promotor which is downstream of the Notch signaling pathway. To our knowledge, the effect of HPV18 on Notch signaling pathway has not been investigated so far. One speculation might be that HPV18 E6 is interfering with Notch signaling in a different way. Besides, to dysregulate cell proliferation many options exist despite Notch signaling. It was previously reported that the HPV-related activation of the Notch pathway is driven by the transcription factor NFX123 22 , which is upregulated by 16E6. Presumably, the activation observed here depends on NICD downstream of gamma-secretase cleavage and impacts the formation of the transcription initiation complex (Fig. 1) directly or indirectly.
In conclusion, the triple fluorescence flow-cytometry-based assay is a novel suitable method to investigate the influence of exogenous proteins on the Notch pathway utilizing a Notch-responsive reporter plasmid. The possibility for semi-quantification allows a comparison of multiple modulatory proteins. Here, we utilized the assay to establish the differential regulation of the Notch-pathway by different HPV E6 proteins. In line with previous data, beta-1-HPV 5, 8 and beta-2-HPV 38 E6 proteins repress Notch, with 38E6 being the most potent repressor. Alpha-7 (16, 31) and alpha-10 (6b) HPV E6 proteins seem to activate the Notch pathway. Especially in the p53null H1299 cell line both high-risk alpha-7 HPV 16E6 and 31E6 show a strong activation on P-HES1 activity. E6 www.nature.com/scientificreports/ of alpha-9 HPV18, which is the second most carcinogenic HPV after HPV16, had no effect on the Notch pathway.
In summary the potency of the E6 proteins of HPV influencing the Notch pathway is highly variable even within the same genera but also between high-risk HPV types. Targeting the Notch pathway for HPV therapy requires an HPV-typing and individual adaption with respect to the HPV type.   . E6 activity on P-HES1 regulated genes. The ratio of mean fluorescence intensity (MFI) of DsRed2 and mTagBFP2 were calculated for each mTagBFP2-E6 based on the triple gating strategy as described in Fig. 6 and normalized to the control mTagBFP2, which has no effect on P-HES1 controlled DsRed2 expression (ratio set to zero). The more negative or positive the value the higher the repressing or activating activity of the respective E6. Data are derived from the average of three independent biological replicates with the mean value labelled above each bar. The error bars plotted are the standard deviation of the mean from the three independent biological replicates. P value were calculated using One-Way ANOVA with Fischer's LSD test by comparing the mean of each activation and repression sample with the control activation sample where * = P ≤ 0.05, ** = P ≤ 0.01, *** = P ≤ 0.005, **** = P ≤ 0.0001, ns = P > 0.05.