Gene expression profiling of S. purpuratus coelomocytes
While immune cell repertoires of humans and mice have been well characterized in terms of cell types and their distinct gene expression patterns (under resting and activated conditions), almost nothing is know about the gene expression in sea urchin coelomocytes.  Four different coelomocyte types (phagocytic cells, vibratile cells, red spherule cells, and colorless spherule cells) can be readily identified based on their morphology, but only aggregate RNAseq data is publicly available.  We have generated RNAseq datasets for three populations that can be separated by density gradient centrifugation and are currently pursuing single-cell RNAseq approaches to characterize the immune cell repertoire of coelomocytes freely floating in the coelomic cavity of adult S. purpuratus.  Our goal is to expand these studies (1) to include gene expression profiles in activated cells during immune responses, and (2) towards tissue-resident immune cells (and their progenitors).  We anticipate to obtain a comprehensive database of S. purpuratus immune cell types, their expression profiles, and based on that information to start develop models for the evolutionary trajectory of immune cells across metazoans.  

Immune receptor signaling in S. purpuratus
Innate immune responses are initiated by recognition of pathogen-associated molecular patterns by sensor molecules, the information is subsequently transmitted via a signaling cascade, until finally effector molecules are produced to directly act on the pathogen, to recruit suitable immune cells, and to orchestrate a synergistic response of many innate immune components.  One central family of innate immune sensors in vertebrates are the Toll-like receptors (TLRs) and their specificity, signaling pathways, and effector mechanisms are well understood.  In contrast very little is known about the role of TLRs in immune signaling in most invertebrates including S. purpuratus, which shows a surprising dramatic expansion of TLR genes (>200 compared to ten human TLRs) and putative signaling components (more than five S. purp. MyD88 genes compared to one in humans), and a lack of genes encoding the TRIF/IRF3/IFN pathway that is downstream of viral recognition by TLRs in vertebrates.  We are thus trying to identify and characterize the central components of the S. purpuratus TLR immune signaling system including the unknown ligands that trigger this conserved innate response axis.   

Are inflammatory responses conserved in invertebrates ?
Inflammation is the manifestation of an innate immune response that has been well characterized in vertebrates (in particular in mice and humans) and plays a key role in the etiology of many human health conditions including infections, cancer, and aging.  At the mechanistic level, molecular sensors recognize stress (in case of infection a pathogen), induce the formation of inflammasomes that involve the clustering and activation of Caspase-1, and ultimately lead to the secretion of pro-inflammatory cytokines (including IL1β) and in some cases pyroptotic cell death.  The molecular players in inflammation in invertebrates remain largely unknown, and hence our goal is to delineate the central players of this signaling cascade in our S. purpuratus model.  Our current focus is on classifying the >30 predicted caspases in this organism to identify homologs of the inflammatory caspases that are essential for activating all downstream effectors of inflammation. 

Does RNA-editing lead to the divorce of a symbiotic relationship ?
Dinoflagellates of the genus Symbiodinium are endosymbionts of cnidarians, in particular corals and sea anemones.  A rapid increase in ocean temperature leads to the eviction of these symbionts from the host cells, a phenomenon known as coral bleaching.  The molecular mechanism of this process is poorly understood, and a recent study observed an increase in RNA editing in Symbiodinium cultures upon heat (and cold) stress.  RNA editing rapidly but only transiently alters the proteome, and thus might be responsible for the rejection by the coral.  We now study RNA editing in both the sea anemone Exaiptasia pallida and its symbiont S. minutum when heat stress is applied to this host-symbiont system using sophisticated next-generation sequencing approaches, and try to discover how this stress response pathway contributes to coral bleaching.  

Geographic isolation and the evolution of immunity
The Formosan land-locked salmon (Oncorhynchus masou formosanus) is an iconic fish species in Taiwan that was once called the rarest fish on earth with a total of as few as 300 individuals.  Recent breeding efforts led to an increase of the overall population but inbreeding may have resulted in a dramatic loss of allelic variation across the genome.  As MHC genes are the most polymorphic genes in vertebrate genomes, we are now genotyping the MHC loci of more than 30 individuals to assess their genetic diversity.  In the future we will obtain a complete genome sequence of Oncorhynchus masou formosanus and its close Japanese relatives the Amago salmo (Oncorhynchus masou ishikawae) and the Biwa trout (Oncorhynchus masou subsp "Biwa") .  This will allow us to assess how fast immune genes adapt to changes in life style as the Oncorhynchus masou formosanus stopped migrating and remained in cold mountain streams once lowland rivers got to warm after the last glacial period 15000 years ago.