We will recall using the CBA × DBA/2, CBA × BALB/c system the paradigms of immunotrophism, Th1/TH2 balance, and the role of complement. We will then recall inflammation in implantation and discuss the “IL-15, IL-18,NK” tripod. We will then introduce T regs mediated regulation, and discuss TWEAK, IL-23 IL-27, IL-35 and Th17/IL-17. Thus, finally we will as an example study early pregnancy loss using a large scale microarray analysis and discuss the impact of the breeding environment of the mice on the decidual gene related expression. Both mating combinations showed a very important inflammatory-like cytokines up-regulation in the immediate post-coitum and pre-implantation days. However, amongst those cytokines expressed in those early steps, the expression level of genes classically considered to be markers of abortion or even causative of such early pregnancy loss in the post implantation period (Ifn-g, Tnf-a, Il-10) did not significantly differ in the CBA x DBA/2 mating from the CBA × BALB/c combination. Yet, significant differences in the transcriptome between the abortion prone combination compared to the control one were detected during the periimplantation period (3.5–7.5 dpc), ranging from 14 to 254 differentially expressed genes (DEG) while the highest number of DEG was detected at 0.5 day post-coitum (n = 486). Moreover, few DEG has appeared to be common between two days of pregnancy. The relation of these genes to what is now known of the early determination of abortion will be discussed. In the controlled pathogen free environment, important differences appear at the transcriptome level between the two murine strains as early as the preimplantation process. Our data mining analyses of the DEG have shown a dramatic impact on the inflammation process from which a selection of genes is currently investigated.
