A unified network systems approach uncovers a core novel program underlying T follicular helper cell differentiation

Introduction/Rationale: The complexity of T follicular helper (Tfh) cell populations and inconsistent findings across experimental systems have fueled ongoing debate regarding Tfh differentiation. Without a unified systems approach, it remains unclear whether these inconsistencies stem from technical artifacts or true biological differences between human and murine systems.

Methods: We adopted a novel multi-scale network approach that incorporates both regulatory and physical interactions. This systems approach elucidates circuits underlying Tfh differentiation by integrating data from ‘omic profiles. We then interrogate the circuits across data types, disease contexts and species to evaluate them and validate them in-vivo.

Results: We capture multi-level regulation of immune system organization and recapitulate known drivers. While components have been individually reported, the novel aspect lies in the discovery and connectivity of a core signature using an unbiased approach. We found a core Tfh set which is conserved across humans and mice addressing a fundamental open question in the field, as different systems (in-vitro, ex-vivo and in-vivo) have led to discovery of varying components. Further, we shed light on the scientific debate and demonstrate how IL-12 specifically blocks the differentiation of Tfh precursors into GC Tfh cells, in both humans and mice. Our in-vivo validation also demonstrated that at present, in-vitro systems fail to represent ex-vivo GC-Tfh, and combining high quality human cell analysis with murine experiments remains crucial for dissecting molecular mechanisms that are difficult to model in-vitro.

Conclusion: The gene sets identified in this analysis converge on a core regulatory network that is conserved across species, tissues, disease states, and experimental systems, an outcome only possible if the underlying biology is truly consistent. Notably, the necessity of IL-12 for Tfh differentiation has important implications for vaccine strategies that utilize IL-12 based adjuvants.