Combinational usage of next generation sequencing and qPCR for the analysis of tumor samples.

The combination of multiple techniques especially those adding complementary information have proven to be beneficial in terms of data consistency. The employment of quantitative PCR (qPCR) prior to next generation sequencing (NGS) methods such as RNA-Seq and mutational analysis presented here does not only enhance data in terms of CNV integration and sample choice, but also allows a faster and more efficient workflow. Correct analysis of libraries prior to sequencing has proven to be a vital step for specific assumption and to some extent for a more parallel testing. By illustrating the combination of qPCR and NGS in oncological examples, the potential of this approach is presented.

Chemokine receptor Ccr5 deficiency induces alternative macrophage activation and improves long-term renal allograft outcome.

The chemokine (C-C motif) receptor 5 (CCR5) has been implicated in experimental and clinical allograft rejection. To dissect the function of CCR5 in acute and chronic renal allograft rejection, bilaterally nephrectomized WT and Ccr5-/- C57BL/6 mice were used as recipients of WT BALB/c renal allografts and analyzed 7 and 42 days after transplantation. Lesion scores (glomerular damage, vascular rejection, tubulointerstitial inflammation) and numbers of CD4+, CD8+, CD11c+ and alpha smooth muscle actin (alphaSMA)+ cells were reduced in allografts from Ccr5-/- recipients during the chronic phase. Increasing creatinine levels indicated deterioration of allograft function over time. While mRNA expression of Th1-associated markers decreased between 7 and 42 days, Th2-associated markers increased. Markers for alternatively activated macrophages (arginase 1, chitinase 3-like 3, resistin-like alpha, mannose receptor, C type 1), were strongly upregulated (mRNA and/or protein level) only in allografts from Ccr5-/- recipients at 42 days. Ccr5 deficiency shifted intragraft immune responses during the chronic phase towards the Th2 type and led to accumulation of alternatively activated macrophages. Additionally, splenocytes from unchallenged Ccr5-/- mice showed significantly increased arginase 1 and mannose receptor 1 mRNA levels, suggesting constitutive alternative activation of splenic macrophages. We conclude that Ccr5 deficiency favors alternative macrophage activation. This finding may be relevant for other inflammatory diseases that involve macrophage activation and may also influence future therapeutic strategies targeting CCR5.