Autofluorescence: A potential pitfall in immunofluorescence-based inflammation grading

Immunofluorescence (IF) staining of paraffin-embedded tissues is a frequently used method to answer research questions or even detect the abundance of a certain protein for diagnostic use. However, the signal originating from specific antibody-staining might be distorted by autofluorescence (AF) of the assessed tissue. Although the AF phenomenon is well known, its presence is often neglected by insufficient staining controls. In this study, we describe the existence of cellular AF in paraffin-embedded healthy and inflamed human and murine colonic tissues and present ways to reduce AF. The AF signal is detectable at emission spectra from 425 nm–738 nm, upon excitation from 403.6–638.7 nm and appears more pronounced in inflamed tissues. Most signals are located subepithelially in the tissue and in blood vessels. Previous studies have shown that the AF signals are caused by lipofuscin, which accumulates in lamina propria immune cells. In murine small intestine AF signals are present in granules in the Paneth cell zone. For alleviation of the AF signal, sudan black b (SBB) or copper sulfate was used. Incubation of the tissue slices with either one of the substances reduced AF. In conclusion, AF appears as an intrinsic biomarker for colonic inflammation. The dominant existence of AF in immune cells of IBD tissue elucidates the importance of negative controls and the limitation of IF staining for potential diagnostic purposes. •Human and murine intestinal tissues show strong autofluorescence signals.•Autofluorescence appears as an intrinsic biomarker for colonic inflammation.•Immune cells in IBD tissue accumulate lipofuscin and emit fluorescence.•Specificity of IF antibody staining requires proper negative control stainings.