The present invention provides, among other things, methods of treatment of donor and/or host subjects prior to, during, and/or after transplantation of donor tissue into the host subject with nanoparticle compositions encapsulating tissue components to usefully manage immune responses associated with transplantation. In some embodiments, methods include administering to a recipient organism who has received or will receive a transplant of one or more heterologous tissue components from a donor organism a composition including encapsulated donor organism tissue components. In some embodiments, methods include administering to a donor organism from which one or more donor tissue components are to be transplanted into a recipient organism a composition including one or more encapsulated recipient tissue components. In some embodiments, methods include administering to the recipient organism into which one or more donor tissue components are to be transplanted from the donor organism one or more encapsulated MHC proteins.
