Regulation of Apoptosis by XIAP Ubiquitin- Ligase Activity

Virtually all animal cells have the known ability to self-destruct by undergoing apoptosis, a morphologically distinct form of programmed cell death. The proper regulation of apoptosis is critical for both development and tissue homeostasis, and inhibition of apoptosis contributes to the development and progression of cancer. Inhibitor of Apoptosis Proteins (IAPs) can bind to and inhibit caspases, the key executioners of apoptosis. Because IAPs are frequently over-expressed in human tumors, they have become major pharmacological targets for developing new cancer therapeutics. Many IAPs contain RING domains that function as E3 ubiquitin-ligases to regulate the abundance of IAPs themselves and their binding partners by engaging the ubiquitin system. The precise physiological function of individual mammalian IAPs and their role as E3- ubiquitin ligases in situ remain largely obscure. Here, we investigated the function of XIAP ubiquitin-ligase activity by deleting the RING motif via gene targeting in the mouse. Mice expressing XIAP ΔRING were fertile, born in expected proportions, and were not obviously prone to disease in a pathogen-free environment. Removing the RING finger motif stabilized XIAP protein in apoptotic thymocytes, demonstrating that XIAP ubiquitin-ligase activity is a major determinant of XIAP protein stability. However, consistent with earlier reports on XIAP-null mice, we found no detectable abnormalities in apoptosis of mutant thymocytes. On the other hand, ΔRING embryonic stem cells and fibroblasts had elevated caspase-3 enzyme activity and impaired ubiquitination of active caspase-3 during apoptosis. Furthermore, XIAP ΔRING embryonic fibroblasts were strongly sensitized to TNF-α-induced apoptosis. Similar results were obtained with XIAP-null mice. Finally, deletion of the RING also improved the survival of mice in the Eμ-Myc lymphoma model. The improved prognosis corresponded to increased apoptosis and decreased abundance of proliferating B-cells in the bone marrow, and a curtailed incidence of leukemia. This demonstrates a physiological requirement of XIAP E3 ubiquitin-ligase activity for the inhibition of apoptosis and for tumor suppression in vivo

Protein coding variation in the J:ARC and J:DO outbred laboratory mouse stocks provides a molecular basis for distinct research applications.

Outbred laboratory mice (Mus musculus) are readily available and have high fecundity, making them a popular choice in biomedical research, especially toxicological and pharmacological applications. Direct high throughput genome sequencing (HTS) of these widely used research animals is an important genetic quality control measure that enhances research reproducibility. HTS data have been used to confirm the common origin of outbred stocks and to molecularly define distinct outbred populations. But these data have also revealed unexpected population structure and homozygosity in some populations; genetic features that emerge when outbred stocks are not properly maintained. We used exome sequencing to discover and interrogate protein-coding variation in a newly established population of Swiss-derived outbred stock (J:ARC) that is closely related to other, commonly used CD-1 outbred populations. We used these data to describe the genetic architecture of the J:ARC population including heterozygosity, minor allele frequency, LD decay, and we defined novel, protein-coding sequence variation. These data reveal the expected genetic architecture for a properly maintained outbred stock and provide a basis for the on-going genetic quality control. We also compared these data to protein-coding variation found in a multiparent outbred stock, the Diversity Outbred (J:DO). We found that the more recently derived, multiparent outbred stock has significantly higher interindividual variability, greater overall genetic variation, higher heterozygosity, and fewer novel variants than the Swiss-derived J:ARC stock. However, among the novel variants found in the J:DO stock, significantly more are predicted to be protein-damaging. The fact that individuals from this population can tolerate a higher load of potentially damaging variants highlights the buffering effects of allelic diversity and the differing selective pressures in these stocks. While both outbred stocks offer significant individual heterozygosity, our data provide a molecular basis for their intended applications, where the J:DO are best suited for studies requiring maximum, population-level genetic diversity and power for mapping, while the J:ARC are best suited as a general-purpose outbred stock with robust fecundity, relatively low allelic diversity, and less potential for extreme phenotypic variability

Molecular mechanisms of cell death: recommendations of the Nomenclature Committee on Cell Death 2018.

Over the past decade, the Nomenclature Committee on Cell Death (NCCD) has formulated guidelines for the definition and interpretation of cell death from morphological, biochemical, and functional perspectives. Since the field continues to expand and novel mechanisms that orchestrate multiple cell death pathways are unveiled, we propose an updated classification of cell death subroutines focusing on mechanistic and essential (as opposed to correlative and dispensable) aspects of the process. As we provide molecularly oriented definitions of terms including intrinsic apoptosis, extrinsic apoptosis, mitochondrial permeability transition (MPT)-driven necrosis, necroptosis, ferroptosis, pyroptosis, parthanatos, entotic cell death, NETotic cell death, lysosome-dependent cell death, autophagy-dependent cell death, immunogenic cell death, cellular senescence, and mitotic catastrophe, we discuss the utility of neologisms that refer to highly specialized instances of these processes. The mission of the NCCD is to provide a widely accepted nomenclature on cell death in support of the continued development of the field

Genetic and pharmacologic models for type 1 diabetes.

Curr Protocol Mouse Biol 2013; 3:9-19

Comparison of Two New Mouse Models of Polygenic Type 2 Diabetes at the Jackson Laboratory, NONcNZO10Lt/J and TALLYHO/JngJ

This review compares two novel polygenic mouse models of type 2 diabetes (T2D), TALLYHO/JngJ and NONcNZO10/LtJ, and contrasts both with the well-known C57BLKS/J-Leprdb (db/db) monogenic diabesity model. We posit that the new polygenic models are more representative of the “garden variety” obesity underlying human T2D in terms of their polygenetic rather than monogenic etiology. Moreover, the clinical phenotypes in these new models are less extreme, for example, more moderated development of obesity coupled with less extreme endocrine disturbances. The more progressive development of obesity produces a maturity-onset development of hyperglycemia in contrast to the juvenile-onset diabetes observed in the morbidly obese db/db model. Unlike the leptin receptor-deficient db/db models with central leptin resistance, the new models develop a progressive peripheral leptin resistance and are able to maintain reproductive function. Although the T2D pathophysiology in both TALLYHO/JngJ and NONcNZO10/LtJ is remarkably similar, their genetic etiologies are clearly different, underscoring the genetic heterogeneity underlying T2D in humans

Dataset: Mangrove, tidal wetland and seagrass soil carbon stocks along latitudinal gradients

Coastal and marine ecosystems have the potential to produce and sequester organic carbon at rates that exceed tropical and temperate forests. Recent recognition of the value of these ecosystems as significant carbon sinks has strengthened worldwide interest in their management, conservation, and restoration for the purpose of climate change mitigation. However, many gaps in understanding carbon sequestration in coastal ecosystems remain, creating challenges for the application coastal ecosystem carbon research at local, regional and global scales. A major limitation is the fact that most research on this topic has been conducted in relatively few temperate and tropical ecosystems, despite a tremendous amount of spatial variability in carbon stocks across gradients of climate, hydrology, geomorphology, and tide range. Additionally, a standardized protocol has not been widely utilized, which would enable more rigorous comparison across ecosystems and climates. The main objective of this research was to apply a standardized method for documenting carbon storage in vegetated coastal ecosystems along latitudinal gradients, including mangroves, tidal wetlands, and seagrass beds. Field sites were located in Twin Cays, Belize, three islands in Bocas del Toro, Panama, the Indian River Lagoon, Florida, Wachapreague, Virginia, three sites in San Francisco Bay, California, and three sites in Kachemak Bay, Alaska. At each mangrove and tidal wetland site, six deep soil cores were retrieved using an open faced gouge corer, ranging in depth from 70 to 496 cm and subsampled at set depth ranges. At each seagrass site, a one meter long piston corer was used to retrieve the core and subsampled using syringes. All samples were dried to a constant weight to determine dry bulk density. Samples were ground with a ball grinder and subsamples were burned in a muffle furnace to determine loss on ignition (LOI). For all seagrass samples, organic carbon was determined by differencing the percent carbon from ashed and unashed samples analyzed with an elemental analyzer. A subset of mangrove and tidal wetland samples were analyzed in an elemental analyzer to determine organic carbon and a relationship between LOI and percent carbon was determined and applied to the remaining samples. Total organic carbon was quantified with depth and summed for each core

Sept4/ARTS is required for stem cell apoptosis and tumor suppression

Inhibitor of Apoptosis Proteins (IAPs) are frequently overexpressed in tumors and have become promising targets for developing anti-cancer drugs. IAPs can be inhibited by natural antagonists, but a physiological requirement of mammalian IAP antagonists remains to be established. Here we show that deletion of the mouse Sept4 gene, which encodes the IAP antagonist ARTS, promotes tumor development. Sept4-null mice have increased numbers of hematopoietic stem and progenitor cells, elevated XIAP protein, increased resistance to cell death, and accelerated tumor development in an Eμ-Myc background. These phenotypes are partially suppressed by inactivation of XIAP. Our results suggest that apoptosis plays an important role as a frontline defense against cancer by restricting the number of normal stem cells