Summary 1.One of the most exciting recent discoveries in the field of ecological immunology has been that insects employ the help of heritable symbionts as a defence against parasitoids and pathogens. Aphids commonly harbour the facultative bacterial endosymbiont Hamiltonella defensa, which is known to increase their resistance to parasitoids. It is unknown how this resistance develops during the aphids' ontogeny, following the transmission bottleneck between mother and offspring, and how specific symbiont-conferred defences are. 2. We addressed these issues in the black bean aphid, Aphis fabae, by exposing aphids of different age classes to the parasitoid Lysiphlebus fabarum. The susceptibility of aphids that were either naturally or experimentally infected with H. defensa was compared with that of uninfected aphids. 3. Susceptibility to parasitoids decreased with aphid age, but aphids harbouring H. defensa showed an earlier and ⁄ or steeper decline to lower levels of susceptibility than aphids without this symbiont. This is consistent with the hypothesis that during aphid development, symbiontconferred resistance builds up with bacterial population growth, which we documented using quantitative polymerase chain reaction (qPCR). 4. Parasitoids that successfully overcame the symbiont-conferred resistance still suffered from sublethal effects of H. defensa. They exhibited lower emergence, delayed development and reduced size compared with parasitoids developing in aphids without H. defensa. 5. The most striking result was a strong interaction on the rates of parasitism between aphid sublines infected with different isolates of H. defensa and the parasitoid lines they were exposed to, suggesting a high specificity of symbiont-conferred resistance. 6. Based on these results, we conclude that when faced with hosts possessing H. defensa, aphid parasitoids are under selection to preferentially attack the youngest host stages and ⁄ or to discriminate against symbiont-protected aphids. Furthermore, the specificity induced by H. defensa in the interaction between host and parasitoid is likely to have important consequences for coevolution. It may result in negative frequency-dependent selection and thus promote genotypic variation.

Formalin-fixed, paraffin-embedded (FFPE), biobanked tissue samples offer an invaluable resource for clinical and biomarker research. Here, we developed a pressure cycling technology (PCT)-SWATH mass spectrometry workflow to analyze FFPE tissue proteomes and applied it to the stratification of prostate cancer (PCa) and diffuse large B-cell lymphoma (DLBCL) samples. We show that the proteome patterns of FFPE PCa tissue samples and their analogous fresh-frozen (FF) counterparts have a high degree of similarity and we confirmed multiple proteins consistently regulated in PCa tissues in an independent sample cohort. We further demonstrate temporal stability of proteome patterns from FFPE samples that were stored Abbreviations BPH, benign prostatic hyperplasia; CRYAB, crystallin alpha Bbetween 1 and 15 years in a biobank and show a high degree of the proteome pattern similarity between two types of histological regions in small FFPE samples, that is, punched tissue biopsies and thin tissue sections of micrometer thickness, despite the existence of a certain degree of biological variations. Applying the method to two independent DLBCL cohorts, we identified myeloperoxidase, a peroxidase enzyme, as a novel prognostic marker. In summary, this study presents a robust proteomic method to analyze bulk and biopsy FFPE tissues and reports the first systematic comparison of proteome maps generated from FFPE and FF samples. Our data demonstrate the practicality and superiority of FFPE over FF samples for proteome in biomarker discovery. Promising biomarker candidates for PCa and DLBCL have been discovered.

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