Abstract

Steadily accumulating evidence supports the concept that the outputs of immune responses are influenced by local nutrient and metabolite conditions or concentrations, as well as by the molecular programming of intermediary metabolism within immune cells. Humoral immunity and germinal center reactions are one setting in which these factors are under active investigation. Hypoxia has been highlighted as one example of how a particular nutrient is distributed in primary and secondary follicles during an antibody response, and how its sensors could impact the qualities of antibody output after immunization. Based on a bio-informatic analysis of mRNA levels in germinal center and other B cells, recently published work challenges the concept that there is any hypoxia or that it has any influence. In this perspective, we perform new analyses of published genomics data to explore potential sources of disparity and elucidate aspects of what on the surface might seem to be conflicting conclusions. In particular, the replicability and variance among data sets derived from different naive as well as germinal center B cells are considered. The results of the investigation highlight several broader issues that merit consideration, especially at a time of heightened focus on scientific reports in the realm of immunity and antibody responses. From one finding of this re-analysis, it is proposed that a standard should be expected in which the relationship of new data sets compared to prior "fingerprints" of cell types should be reported transparently to referees and readers. In light of the strong evidence for diversity in the constituencies within germinal centers elicited by protein immunization, it also is proposed that a core practice should be to avoid overly broad conclusions about germinal centers in general when experimental systems are subject to substantial constraints imposed by technical features.