The present invention relates to compositions and methods for diagnosing, monitoring and/or treating disease (e.g., autoimmune or chronic inflammatory disease, heart disease and/or stroke). In particular, the present invention provides methods for diagnosing, monitoring and treating disease based upon detecting or altering (e.g., altering expression or methylation status of) disease proteins (e.g., CD70, CD40L, and/or KIR). The present invention also provides kits for detecting methylation status of disease proteins (e.g., CD70, CD40L, and/or KIR) and for diagnosing, monitoring and/or treating diseases (e.g., autoimmune or chronic inflammatory disease, heart disease and/or stroke).