To determine whether the Sjögren's syndrome autoantigens alpha-fodrin and the type 3 muscarinic acetylcholine receptor (M3R) are cleaved during cytotoxic lymphocyte granule-induced death, to yield novel fragments. Primary salivary gland epithelial cells, human salivary gland cells, and HeLa cells were incubated with granule contents. The susceptibility to cleavage and the generation of novel fragments of Sjögren's syndrome autoantigens in this form of apoptosis was assessed by immunoblotting. Cleavage of M3R was further characterized by assays performed on the M3R molecule generated by in vitro translation. This study demonstrated that alpha-fodrin was uniquely cleaved during cytotoxic lymphocyte granule-induced cell death, generating a 155-kd fragment distinct from those generated by caspase 3 in other forms of apoptosis. The study also demonstrates that M3R (which is restricted in expression to the peripheral autonomic organs) was efficiently cleaved by granzyme B (but not by caspases) at several sites, both in vitro and in intact cells. This is the first description of cleavage of a transmembrane autoantigen by granzyme B. The observation that both ubiquitously expressed autoantigens (e.g., alpha-fodrin, La, and nuclear mitotic apparatus protein) and tissue-restricted autoantigens (e.g., M3R) targeted in Sjögren's syndrome are specifically cleaved by granzyme B, generating unique fragments, strongly suggests that a common biochemical event (novel autoantigen cleavage during granule-induced epithelial cell death) is responsible for selecting this apparently unconnected group of molecules for a high-titer autoantibody response. The data focus attention on the role of cytotoxic lymphocytes in the initiation and propagation of Sjögren's syndrome.