An interaction between my viral protein of interest and a host protein is observed in HEK 293T cells but not in HFF1 cells.
There could be many reasons. But, we need more information pertaining to your specific experiment.
Is the host protein of interest endogenous or exogenous? Presumably the viral protein is expressed exogenously using transfection or viral transduction. If both proteins are being supplied exogenously, you may be running into an expression issue in HFF1 cells. Be sure that both exogenous proteins are being expressed in the HFF1 cells. If the host protein is endogenous, the HFF1 cells may simply not express it to a high level naturally. You can measure expression of the proteins using western blot of your input lysates. If you are not getting good expression of exogenous constructs in HFF1, then you may turn to alternative methods of supplying the trans-gene (like viral transduction).
HEK-293-T have a high transfection efficiency, so you may be getting more of both proteins expressed and are therefore able to see an interaction. Generally, an interaction in HEK-293-T cells is considered biologically relevant. That being said, these cells lack many components that other cell lines have.
Aside from this technical consideration, there are many other reasons an interaction may occur in one cell line and not another. Different cell lines will have different global protein expression as well as post-translational modifications (PTMs). So, if your host protein is endogenous, check baseline levels in both cell lines. Also check for differences in the banding pattern between cell lines to spot PTMs. For instance, the endogenous host protein may be cleaved or phosphorylated in HFF1.
As an additional consideration, cell lines may respond differently to the method of trans-gene delivery. For instance, the HFF1 cells may have more intact innate immune signaling pathways than the HEK-293-T cells, including ones for foreign DNA sensing. When you supply the trans-gene using transfection, the HFF1 cell components are able to identify the foreign DNA as a threat and carry out an inflammatory signaling pathway. This type of signaling can alter host proteins (via PTMs or gene expression/repression) and may lead to loss of a protein-protein interaction in that cell type.
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