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The pathogenesis of the amyloid deposition diseases is poorly understood. The CE/J mouse, which is naturally protected from amyloid A (AA) protein amyloidosis, has provided a tool to study mechanisms that may be implicated in amyloid deposition diseases by means of comparison of findings with those in an AA-susceptible mouse strain. We have compared proteoglycan/glycosaminoglycan accumulationin vivoin amyloid-protected CE/J mouse strain and in AA-susceptible CBA/J mouse strain in homeostasis and when injected with amyloid-inducing agents. Results indicate that there is an overall increase in[35S]proteoglycan/glycosaminoglycan accumulation in the spleens of both strains of mice, but with a specific increase in heparan sulfate in only CBA/J mouse spleens that are rich in amyloid. Further, we report the absence of heparan sulfate in the splenic perifollicular areas of amyloid-free CE/J mouse, whereas in the amyloid-laden CBA/J mouse there is co-localization of heparan sulfate with the AA deposits. We have also examined the glycosaminoglycan disaccharide products in both these strains of mice for their sulfation positions and found no differences in the disaccharide composition of chondroitin/dermatan sulfate and heparan sulfate isolated from the control CBA/J and control CE/J mice. There were no differences in chondroitin/dermatan sulfate in both strains after experimental induction. However, analysis of the heparan sulfate disaccharides by means of capillary high-performance liquid chromatography linked to microelectrospray ionization time-of-flight mass spectrometry indicated that the disaccharide composition of the splenic heparan sulfate obtained from the treated CBA/J mice that had developed amyloid was markedly different from that obtained from the control CBA/J mice and the treated amyloid-resistant CE/J mice. These findings suggest that unique heparan sulfates play a fundamental role in the pathogenesis of amyloid. [ABSTRACT FROM AUTHOR]