Over-Generalizing About GC (Hypoxia): Pitfalls of Limiting Breadth of Experimental Systems and Analyses in Framing Informatics Conclusions

Accumulating evidence suggests that many immune responses are influenced by local nutrient concentrations in addition to the programming of intermediary metabolism within immune cells. Humoral immunity and germinal centers (GC) are settings in which these factors are under active investigation. Hypoxia is an example of how a particular nutrient is distributed in lymphoid follicles during an antibody response, and how oxygen sensors may impact the qualities of antibody output after immunization. Using exclusively a bio-informatic analysis of mRNA levels in GC and other B cells, recent work challenged the concept that there is any hypoxia or that it has any influence. To explore this proposition, we performed new analyses of published genomics data, explored potential sources of disparity, and elucidated aspects of the apparently conflicting conclusions. Specifically, replicability and variance among data sets derived from different naive as well as GC B cells were considered. The results highlight broader issues that merit consideration, especially at a time of heightened focus on scientific reports in the realm of immunity and antibody responses. Based on these analyses, a standard is proposed under which the relationship of new data sets should be compared to prior "fingerprints" of cell types and reported transparently to referees and readers. In light of independent evidence of diversity within and among GC elicited by protein immunization, avoidance of overly broad conclusions about germinal centers in general when experimental systems are subject to substantial constraints imposed by technical features also is warranted.