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For the first time it was shown that complement factors can be detected and are altered within mouse jejunum mucus after experimental sepsis. Complement anaphylatoxins C3a and C5a levels vary distinctively in mucus collected from proximal to distal jejunum. Even basal levels of such complement activation can be detected in control mouse mucus, which vary spatially, and the levels of C3a but not C5a are significantly enhanced 24 to 72 hours after CLP-sepsis. Unlike serum complement factors, the levels of complement in the mucus were very low and corresponded with low in vitro complement activity measured at the level of C3 activation. CLP-sepsis mice mucus had reduced in vitro complement activation levels indicating putative complement consumption in the intestinal lumen. However, like serum, this complement activation in mucus can be reduced though not inhibited with EDTA. Classical complement activity in vitro could not be detected in mucus. Furthermore, when tested for concomitant digestive pancreatic protease activity, a decreasing gradient of global protease activity was found in control mouse mucus from proximal to distal jejunum. CLP-sepsis further enhanced this activity only in the proximal portion of the jejunum due to chymotrypsin and elastase activities. In vitro cleavage assays showed that pancreatic proteases can cleave C3 and C5 into activation products C3a and C5a. Conclusively, this study alludes to a functional role of complement activation within the small intestinal lumen, altered pronouncedly during experimental sepsis, and may not involve interference by the local digestive proteases.