The invention is applied in the therapy of brain and spinal cord tumors, degenerative, hypoxic, ischemic diseases and traumatic injuries of the central nervous system (CNS) and other diseases of humans and animals. Object of invention is to provide target delivery of signaling substance to the pathological area of an organism, triggering in due time and long-time support of active signaling intercellular action of specific therapeutic character of a healthy and well controlled stem cell (SC) onto controlling system of defective cells. The preparation of SC with reprogrammed cell signaling comprises the basic preparation of SC, the membrane, and/or nucleus, and/or cytoplasm of which contains implanted protein or pharmaceutical able to regulate signaling pathways of SC and cells of pathological focus in a mammal organism, provisionally encapsulated in nanocontainers of less than 100nm size, obtained from biodegradable material, intact for organelles and compartments of SC of the basic preparation. The material has a set biodegradation period in a mammal organism to provide programmed exit of protein or pharmaceutical in intra-or intercellular space thus reprogramming signal transduction of key genes in the desired therapeutic orientation of physiologic events in the cell cycle directly in the pathological area or tissue of an organism.