Explore the vast range of titles available.

The small GTPase RAP1 is critical for platelet activation and thrombus formation. RAP1 activity in platelets is controlled by the GEF CalDAG-GEFI and an unknown regulator that operates downstream of the adenosine diphosphate (ADP) receptor, P2Y12, a target of antithrombotic therapy. Here, we provide evidence that the GAP, RASA3, inhibits platelet activation and provides a link between P2Y12 and activation of the RAP1 signaling pathway. In mice, reduced expression of RASA3 led to premature platelet activation and markedly reduced the life span of circulating platelets. The increased platelet turnover and the resulting thrombocytopenia were reversed by concomitant deletion of the gene encoding CalDAG-GEFI. Rasa3 mutant platelets were hyperresponsive to agonist stimulation, both in vitro and in vivo. Moreover, activation of Rasa3 mutant platelets occurred independently of ADP feedback signaling and was insensitive to inhibitors of P2Y12 or PI3 kinase. Together, our results indicate that RASA3 ensures that circulating platelets remain quiescent by restraining CalDAG-GEFI/RAP1 signaling and suggest that P2Y12 signaling is required to inhibit RASA3 and enable sustained RAP1-dependent platelet activation and thrombus formation at sites of vascular injury. These findings provide insight into the antithrombotic effect of P2Y12 inhibitors and may lead to improved diagnosis and treatment of platelet-related disorders.

Key Points Mice and humans share 99% of their genes, and so share common diseases. Most common human diseases are complex, or polygenic. Rapidly growing genomic resources in the mouse facilitate complex trait analysis Extensive phenotypic differences exist between inbred strains of mice, as catalogued by the Mouse Phenome Project, Eumorphia Empress and the German Mouse Clinic. Together, mouse genome and phenome advances have provided the resources that are required to rapidly and cost-effectively identify QTLs and narrow QTL confidence intervals. Establishment of the Collaborative Cross promises to add tremendously to our ability to identify genes that underlie QTLs in the future. The mouse is a powerful model for elucidating the genetic basis of complex human traits and diseases. One reason for this is the wealth of available resources for mouse genetics that has been built up over the past 100 years. The mouse has been a powerful force in elucidating the genetic basis of human physiology and pathophysiology. From its beginnings as the model organism for cancer research and transplantation biology to the present, when dissection of the genetic basis of complex disease is at the forefront of genomics research, an enormous and remarkable mouse resource infrastructure has accumulated. This review summarizes those resources and provides practical guidelines for their use, particularly in the analysis of quantitative traits.

Studies of the severely pancytopenic scat mouse model first demonstrated the crucial role of RASA3, a dual RAS and RAP GTPase activating protein (GAP), in hematopoiesis. RASA3 is required for survival in utero ; germline deletion is lethal at E12.5–13.5 due to severe hemorrhage. Here, conditional deletion in hematopoietic stem and progenitor cells (HSPCs) using Vav -i Cre recapitulates the null phenotype demonstrating that RASA3 is required at the stem and progenitor level to maintain blood vessel development and integrity and effective blood production. In adults, bone marrow blood cell production and spleen stress erythropoiesis are suppressed significantly upon induction of RASA3 deficiency, leading to pancytopenia and death within two weeks. Notably, RASA3 missense mutations in two mouse models, scat (G125V) and hlb381 (H794L), show dramatically different hematopoietic consequences specific to both genetic background and molecular variant. The mutation effect is mediated at least in part by differential effects on RAS and RAP activation. In addition, we show that the role of RASA3 is conserved during human terminal erythropoiesis, highlighting a potential function for the RASA3-RAS axis in disordered erythropoiesis in humans. Finally, global transcriptomic studies in scat suggest potential targets to ameliorate disease progression.

The transport and intracellular trafficking of heme biosynthesis intermediates are crucial for hemoglobin production, which is a critical process in developing red cells. Here, we profiled gene expression in terminally differentiating murine fetal liver-derived erythroid cells to identify regulators of heme metabolism. We determined that TMEM14C, an inner mitochondrial membrane protein that is enriched in vertebrate hematopoietic tissues, is essential for erythropoiesis and heme synthesis in vivo and in cultured erythroid cells. In mice, TMEM14C deficiency resulted in porphyrin accumulation in the fetal liver, erythroid maturation arrest, and embryonic lethality due to profound anemia. Protoporphyrin IX synthesis in TMEM14C-deficient erythroid cells was blocked, leading to an accumulation of porphyrin precursors. The heme synthesis defect in TMEM14C-deficient cells was ameliorated with a protoporphyrin IX analog, indicating that TMEM14C primarily functions in the terminal steps of the heme synthesis pathway. Together, our data demonstrate that TMEM14C facilitates the import of protoporphyrinogen IX into the mitochondrial matrix for heme synthesis and subsequent hemoglobin production. Furthermore, the identification of TMEM14C as a protoporphyrinogen IX importer provides a genetic tool for further exploring erythropoiesis and congenital anemias.

The spectrin membrane skeleton controls the disposition of selected membrane channels, receptors, and transporters. In the brain βIII spectrin binds directly to the excitatory amino acid transporter (EAAT4), the glutamate receptor delta, and other proteins. Mutations in βIII spectrin link strongly to human spinocerebellar ataxia type 5 (SCA5), correlating with alterations in EAAT4. We have explored the mechanistic basis of this phenotype by targeted gene disruption of Spnb3. Mice lacking intact βIII spectrin develop normally. By 6 months they display a mild nonprogressive ataxia. By 1 year most Spnb3⁻/⁻ animals develop a myoclonic seizure disorder with significant reductions of EAAT4, EAAT1, GluRδ, IP3R, and NCAM140. Other synaptic proteins are normal. The cerebellum displays increased dark Purkinje cells (PC), a thin molecular layer, fewer synapses, a loss of dendritic spines, and a 2-fold expansion of the PC dendrite diameter. Membrane and expanded Golgi profiles fill the PC dendrite and soma, and both regions accumulate EAAT4. Correlating with the seizure disorder are enhanced hippocampal levels of neuropeptide Y and EAAT3 and increased calpain proteolysis of αII spectrin. It appears that βIII spectrin disruption impairs synaptogenesis by disturbing the intracellular pathways selectively regulating protein trafficking to the synapse. The mislocalization of these proteins secondarily disrupts glutamate transport dynamics, leading to seizures, neuronal damage, and compensatory changes in EAAT3 and neuropeptide Y.

Systems genetics exploits natural genetic variation to associate molecular variation with complex traits. It is often impossible to measure complex traits and molecular intermediates on the same individuals and independent cohorts are used... Systems genetic analysis of complex traits involves the integrated analysis of genetic, genomic, and disease-related measures. However, these data are often collected separately across multiple study populations, rendering direct correlation of molecular features to complex traits impossible. Recent transcriptome-wide association studies (TWAS) have harnessed gene expression quantitative trait loci (eQTL) to associate unmeasured gene expression with a complex trait in genotyped individuals, but this approach relies primarily on strong eQTL. We propose a simple and powerful alternative strategy for correlating independently obtained sets of complex traits and molecular features. In contrast to TWAS, our approach gains precision by correlating complex traits through a common set of continuous phenotypes instead of genetic predictors, and can identify transcript–trait correlations for which the regulation is not genetic. In our approach, a set of multiple quantitative “reference” traits is measured across all individuals, while measures of the complex trait of interest and transcriptional profiles are obtained in disjoint subsamples. A conventional multivariate statistical method, canonical correlation analysis, is used to relate the reference traits and traits of interest to identify gene expression correlates. We evaluate power and sample size requirements of this methodology, as well as performance relative to other methods, via extensive simulation and analysis of a behavioral genetics experiment in 258 Diversity Outbred mice involving two independent sets of anxiety-related behaviors and hippocampal gene expression. After splitting the data set and hiding one set of anxiety-related traits in half the samples, we identified transcripts correlated with the hidden traits using the other set of anxiety-related traits and exploiting the highest canonical correlation (R = 0.69) between the trait data sets. We demonstrate that this approach outperforms TWAS in identifying associated transcripts. Together, these results demonstrate the validity, reliability, and power of reference trait analysis for identifying relations between complex traits and their molecular substrates.

Mouse genetics is a powerful approach for discovering genes and other genome features influencing human pain sensitivity. Genetic mapping studies have historically been limited by low mapping resolution of conventional mouse crosses, resulting in pain-related quantitative trait loci (QTL) spanning several megabases and containing hundreds of candidate genes. The recently developed Diversity Outbred (DO) population is derived from the same eight inbred founder strains as the Collaborative Cross, including three wild-derived strains. DO mice offer increased genetic heterozygosity and allelic diversity compared to crosses involving standard mouse strains. The high rate of recombinatorial precision afforded by DO mice makes them an ideal resource for high-resolution genetic mapping, allowing the circumvention of costly fine-mapping studies. We utilized a cohort of ~300 DO mice to map a 3.8 Mbp QTL on chromosome 8 associated with acute thermal pain sensitivity, which we have tentatively named Tpnr6. We used haplotype block partitioning to narrow Tpnr6 to a width of ~230 Kbp, reducing the number of putative candidate genes from 44 to 3. The plausibility of each candidate gene’s role in pain response was assessed using an integrative bioinformatics approach, combining data related to protein domain, biological annotation, gene expression pattern, and protein functional interaction. Our results reveal a novel, putative role for the protein-coding gene, Hydin, in thermal pain response, possibly through the gene’s role in ciliary motility in the choroid plexus–cerebrospinal fluid system of the brain. Real-time quantitative-PCR analysis showed no expression differences in Hydin transcript levels between pain-sensitive and pain-resistant mice, suggesting that Hydin may influence hot-plate behavior through other biological mechanisms.

Anemic Nan mice carry a mutation (E339D) in the second zinc finger of erythroid transcription factor KLF1. Nan-KLF1 fails to bind a subset of normal KLF1 targets and ectopically binds a large set of genes not normally engaged by KLF1, resulting in a corrupted fetal liver transcriptome. Here, we performed RNAseq using flow cytometric-sorted spleen erythroid precursors from adult Nan and WT littermates rendered anemic by phlebotomy to identify global transcriptome changes specific to the Nan Klf1 mutation as opposed to anemia generally. Mutant Nan-KLF1 leads to extensive and progressive transcriptome corruption in adult spleen erythroid precursors such that stress erythropoiesis is severely compromised. Terminal erythroid differentiation is defective in the bone marrow as well. Principle component analysis reveals two major patterns of differential gene expression predicting that defects in basic cellular processes including translation, cell cycle, and DNA repair could contribute to disordered erythropoiesis and anemia in Nan . Significant erythroid precursor stage specific changes were identified in some of these processes in Nan . Remarkably, however, despite expression changes in large numbers of associated genes, most basic cellular processes were intact in Nan indicating that developing red cells display significant physiological resiliency and establish new homeostatic set points in vivo .

Abstract The extracellular signal–regulated kinases 1 and 2 (ERK1/2) are phosphorylated after inhalation of asbestos. The effect of blocking this signaling pathway in lung epithelium is unclear. Asbestos-exposed transgenic mice expressing a dominant-negative mitogen-activated protein kinase kinase-1 (dnMEK1) (i.e., the upstream kinase necessary for phosphorylation of ERK1/2) targeted to lung epithelium exhibited morphologic and molecular changes in lung. Transgene-positive (Tg+) (i.e., dnMEK1) and transgene-negative (Tg−) littermates were exposed to crocidolite asbestos for 2, 4, 9, and 32 days or maintained in clean air (sham controls). Distal bronchiolar epithelium was isolated using laser capture microdissection and mRNA analyzed for molecular markers of proliferation and Clara cell secretory protein (CCSP). Lungs and bronchoalveolar lavage fluids were analyzed for inflammatory and proliferative changes and molecular markers of fibrogenesis. Distal bronchiolar epithelium of asbestos-exposed wild-type mice showed increased expression of c-fos at 2 days. Elevated mRNA levels of histone H3 and numbers of Ki-67–labeled proliferating bronchiolar epithelial cells were decreased at 4 days in asbestos-exposed Tg+ mice. At 32 days, distal bronchioles normally composed of Clara cells in asbestos-exposed Tg+ mouse lungs exhibited nonreplicating ciliated and mucin-secreting cells as well as decreased mRNA levels of CCSP. Gene expression (procollagen 3-a-1, procollagen 1-a-1, and IL-6) linked to fibrogenesis was also increased in lung homogenates of asbestos-exposed Tg− mice, but reduced in asbestos-exposed Tg+ mice. These results suggest a critical role of MEK1 signaling in epithelial cell proliferation and lung remodeling after toxic injury.

Activation of extracellular signal-regulated kinases (ERK) has been associated with the advent of asbestos-associated apoptosis and proliferation in mesothelial and alveolar epithelial cells and may be linked to the development of pulmonary fibrosis. The objective of studies here was to characterize the development of inflammation, cellular proliferation, and fibrosis in asbestos-exposed C57Bl/6 mice in relationship to patterns of ERK phosphorylation. Inflammation occurred after 10 and 20 days of asbestos exposure as evidenced by increases in total protein and neutrophils in bronchoalveolar lavage fluid. Increases in cell proliferation were observed at 30 days in bronchiolar epithelia and at 4, 14, and 30 days in the alveolar compartment of the lung. Trichrome-positive focal lesions of pulmonary fibrosis developed at 30 days in the absence of elevations in lung hydroxyproline or procollagen mRNA levels. Striking increases in ERK phosphorylation were observed within pulmonary epithelial cells at sites of developing fibrotic lesions after 14 and 30 days of inhalation. In addition to characterizing a murine inhalation model of asbestosis, we provide the first evidence showing activation of ERK signaling within lung epithelium in vivo, following inhalation of asbestos fibers.