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Rothenberg lab research
Research Interests 2007-8
Initiation of T-cell development depends on Notch/Delta signaling, and beyond that, it also requires the staged upregulation of a variety of other transcription factors: GATA-3, TCF-1, specific forms of the bHLH transcription factor HEB, and other factors. One set of projects in the lab is to understand exactly how each of these regulatory molecules contributes to the onset of T-cell gene expression. Even as these T-lineage associated factors are being induced, the cells preserve a stem-cell-like pluripotency through many cell divisions into the beginning of their T-cell program. Throughout this period, the cells also continue to express a surprisingly broad range of regulatory factors inherited from hematopoietic stem cells. What eventually "locks down" the T-cell identity in these cells, then, appears to be a separate mechanism dominated by repression: repression of regulatory genes like PU.1, which play positive roles in stem cells before T-lineage differentiation but also can actively maintain access to non-T developmental options. In a second major interest of the lab, we are now closing in on the identification of the key repressors that terminate PU.1 expression.
Some take-home lessons have emerged about the nature of T-lineage specification process as a whole. It is not a simple command cascade of dedicated regulators, such as appear to drive differentiation of other blood-cell types. Instead, many if not all of the critical T-lineage regulatory genes are used for other pathways as well and can even push early T-lineage cells to alternative fates under certain circumstances. Their essential roles in T-cell development are completely context-dependent and dose-dependent. This is true not only of factors like PU.1, which plays only a transient positive role in T-cell development, but also of GATA-3, which is used repeatedly throughout T-cell development. Thus, the regulatory network context gives these factors their T-lineage promoting impact, and solving its structure is a major goal of the lab. This year, we have shown that Notch/Delta signaling plays a sustained role in this regulatory context long after it initiates the whole T-lineage differentiation process, transforming the net impact of the other regulatory factors, and protecting the cells from lineage diversion through at least two different mechanisms. Another insight that has emerged is how close in regulatory terms developing T-cell precursors remain to cells of the "innate immune system", such as dendritic cells, macrophages, and mast cells. A major new enterprise for the group is a collaboration with Dr. Hamid Bolouri and his team to model the gene regulatory network that accounts for all aspects of these lineage choices.
Recently, Dr. Mary Yui in our group has shown that the earliest checkpoints that normally provide "quality control" for newly committed T-lineage cells are altered in function in mice that are genetically susceptible to autoimmune diabetes. The checkpoints affected are complex, including a life vs. death threshold as well as a less-understood developmental branch point between alph beta and gamma delta lineage T cells, which develop using somewhat different transcriptional programs. The identification of the checkpoint alteration in autoimmunity-prone mice provides an exciting opportunity because autoimmune diabetes is a multigene disease that has been difficult to dissect into discrete "component phenotypes". Dr. Yui is now leading a project to map the genetic defects that contribute to this alteration and to determine its molecular basis. The goal is to reveal in detail how subtle early developmental defects may result in a mature T-cell population with key failures in self-restraint mechanisms.
In exploring the evolutionary origins of the complex lymphocyte developmental program, we focus on the interface between the conventional B- and T-lymphocyte based immune systems of jawed vertebrates and the lymphocyte-independent innate immune systems of all invertebrates. The discontinuity between these systems is represented by the lamprey, a jawless vertebrate with lymphocytes that recognize antigen using highly polymorphic receptors, but receptors of a completely different structural type than the B- and T-cell receptors of all jawed vertebrates. The lamprey lymphocytes cannot be clearly identified as more T-like or more B-like, and the animal lacks any recognizable thymus in which a specialized T-cell program could be induced through Notch/Notch ligand interaction. Thus it is of some interest to understand the regulatory signature of the lamprey lymphocytes, as a clue to what the ancestral immune-cell developmental program might have been. To do this, we are starting from the known lamprey lymphocyte receptor genes and using their regulatory sequences to determine what kinds of factors control their expression, with the goal of understanding this truly ancient family connection in the near future.
