The present invention relates to a pharmaceutical composition with an active principle that includes membrane vesicle conjugates of Neisseria meningitidis and the GM3 ganglioside in a conjugation proportion with a protein excess, with special features regarding the size, surface charge and morphology associated with nanoparticle systems that confer advantageous properties as an immunomodulator, since it induces a convenient and significant reduction of myeloid-derived suppressor cells, with an impact on lymphocyte T response and the survival of tumour patients. The invention further relates to the use of the disclosed pharmaceutical composition for the treatment of cancer, in particular those types of cancer with an increase of myeloid-derived suppressor cells (MDSC); and to a method for treating cancer patients with this composition and to a method for selecting the patients receiving this treatment.