Faculty Bibliography

IRE1 mediates the Unfolded Protein Response (UPR) in part by regulating XBP1 mRNA splicing in response to endoplasmic reticulum (ER) stress. In cultured metazoan cells, IRE1 also exhibits XBP1-independent biochemical activities. IRE1 and XBP1 are developmentally essential genes in Drosophila and mammals, but the source of the physiological ER stress and the relative contributions of XBP1 activation versus other IRE1 functions to development remain unknown. Here, employed Drosophila to address this question. Specifically, we find that specific regions of the developing alimentary canal, fat body and the male reproductive organ are the sources of physiological stress that requires ire1 and xbp1 for resolution. In particular, the developmental lethality associated with xbp1 nulls was rescued by transgenic expression of xbp1 in the alimentary canal. IRE1's domains involved in detecting unfolded proteins, cleaving RNAs and activating XBP1 splicing were all essential for development. The earlier onset of developmental defects of ire1 mutant larvae compared to xbp1-null flies supports a developmental role for XBP1-independent IRE1 RNase activity while challenging the importance of RNase-independent effector mechanisms of Drosophila IRE1 function.

Glioblastoma (GBM) stem cells (GSCs) reside in both hypoxic and vascular microenvironments within tumors. The molecular mechanisms that allow GSCs to occupy such contrasting niches are not understood. We used patient-derived GBM cultures to identify GSC subtypes with differential activation of Notch signaling, which co-exist in tumors but occupy distinct niches and match their metabolism accordingly. Multipotent GSCs with Notch pathway activation reside in perivascular niches, and are unable to entrain anaerobic glycolysis during hypoxia. In contrast, most CD133-expressing GSCs do not depend on canonical Notch signaling, populate tumors regardless of local vascularity and selectively utilize anaerobic glycolysis to expand in hypoxia. Ectopic activation of Notch signaling in CD133-expressing GSCs is sufficient to suppress anaerobic glycolysis and resistance to hypoxia. These findings demonstrate a novel role for Notch signaling in regulating GSC metabolism and suggest intratumoral GSC heterogeneity ensures metabolic adaptations to support tumor growth in diverse tumor microenvironments.

Abnormal skin scarring causes functional impairment, psychological stress, and high socioeconomic cost. Evidence shows that altered mechanotransduction pathways have been linked to both inflammation and fibrosis, and that focal adhesion kinase (FAK) is a key mediator of these processes. We investigated the importance of keratinocyte FAK at the single cell level in key fibrogenic pathways critical for scar formation. Keratinocytes were isolated from wildtype and keratinocyte-specific FAK-deleted mice, cultured, and sorted into single cells. Keratinocytes were evaluated using a microfluidic-based platform for high-resolution transcriptional analysis. Partitive clustering, gene enrichment analysis, and network modeling were applied to characterize the significance of FAK on regulating keratinocyte subpopulations and fibrogenic pathways important for scar formation. Considerable transcriptional heterogeneity was observed within the keratinocyte populations. FAK-deleted keratinocytes demonstrated increased expression of genes integral to mechanotransduction and extracellular matrix production, including Igtbl, Mmpla, and Col4a1. Transcriptional activities upon FAK deletion were not identical across all single keratinocytes, resulting in higher frequency of a minor subpopulation characterized by a matrix-remodeling profile compared to wildtype keratinocyte population. The importance of keratinocyte FAK signaling gene expression was revealed. A minor subpopulation of keratinocytes characterized by a matrix-modulating profile may be a keratinocyte subset important for mechanotransduction and scar formation.

The migration of primordial germ cells (PGCs) from their place of origin to the embryonic gonad is an essential reproductive feature in many animal species. In Drosophila melanogaster, a single G protein-coupled receptor, Trapped in endoderm 1 (Tre1), mediates germ cell polarization at the onset of active migration and directs subsequent migration of PGCs through the midgut primordium. How these different aspects of cell behavior are coordinated through a single receptor is not known. We demonstrate that two highly conserved domains, the E/N/DRY and NPxxY motifs, have overlapping and unique functions in Tre1. The Tre1-NRY domain via G protein signaling is required for reading and responding to guidance and survival cues controlled by the lipid phosphate phosphatases Wunen and Wunen2. In contrast, the Tre1-NPIIY domain has a separate role in Rho1- and E-cadherin-mediated polarization at the initiation stage independent of G protein signaling. We propose that this bifurcation of the Tre1 G protein-coupled receptor signaling response via G protein-dependent and independent branches enables distinct spatiotemporal regulation of germ cell migration.

Atlantic tomcod in the Hudson River Estuary bioaccumulate high hepatic burdens of environmental toxicants. Previously, we demonstrated that Hudson River tomcod developed resistance to TCDD and PCB toxicity probably through strong natural selection during their early life-stages for a variant of the Aryl Hydrocarbon Receptor2 (AHR2). Here, we evaluated the genomic consequences of the resistant genotype by comparing global gene expression in larval tomcod from the Hudson River with expression in larvae from a nearby sensitive population (Shinnecock Bay). We developed an annotated draft tomcod genome to explore the effects of multigenerational exposure to toxicants and a functionally impaired AHR2 on the transcriptome. We used the tomcod genome as a reference in RNA-Seq to compare global gene expression in tomcod larvae from the Hudson River and Shinnecock Bay after experimental exposure of larvae to graded doses of TCDD. We found dramatic differences between offspring from the two populations in the number of genes that were differentially expressed at all doses (0.01, 0.1, and 1 ppb) and even in the vehicle controls. At the two lowest TCDD doses, 250 and 1,141 genes were differentially expressed in Shinnecock Bay larvae compared with 14 and 12, respectively, in Hudson River larvae. At the highest dose (1.0 ppb), 934 genes were differentially expressed in Shinnecock Bay larvae and 173 in Hudson River larvae, but only 28 (16%) of affected genes were shared among both populations. Given the large difference between the two populations in the number and identity of differentially expressed genes, it is likely that the AHR2 pathway interacts directly or indirectly with many genes beyond those known in the AHR2 battery and that other regulatory systems may also respond to TCDD exposure. The effects of chronic multi-generational exposure to environmental toxicants on the genome of Hudson River tomcod are much greater than previously expected.