The clear cell sarcoma functional genomic landscape

Clear cell sarcoma (CCS) is a deadly malignancy affecting adolescents and young adults. It is characterized by reciprocal translocations resulting in expression of the chimeric EWSR1-ATF1 or EWSR1-CREB1 fusion proteins, driving sarcomagenesis. Besides these characteristics, CCS has remained genomically uncharacterized. Copy number analysis of human CCSs showed frequent amplifications of the MITF locus and chromosomes 7 and 8. Few alterations were shared with Ewing sarcoma or desmoplastic, small round cell tumors, which are other EWSR1-rearranged tumors. Exome sequencing in mouse tumors generated by expression of EWSR1-ATF1 from the Rosa26 locus demonstrated no other repeated pathogenic variants. Additionally, we generated a new CCS mouse by Cre-loxP-induced chromosomal translocation between Ewsr1 and Atf1, resulting in copy number loss of chromosome 6 and chromosome 15 instability, including amplification of a portion syntenic to human chromosome 8, surrounding Myc. Additional experiments in the Rosa26 conditional model demonstrated that Mitf or Myc can contribute to sarcomagenesis. Copy number observations in human tumors and genetic experiments in mice rendered, for the first time to our knowledge, a functional landscape of the CCS genome. These data advance efforts to understand the biology of CCS using innovative models that will eventually allow us to validate preclinical therapies necessary to achieve longer and better survival for young patients with this disease.

A Microglia Sublineage Protects from Sex-Linked Anxiety Symptoms and Obsessive Compulsion

Aberrant microglia activity is associated with many neurological and psychiatric disorders, yet our knowledge about the pathological mechanisms is incomplete. Here, we describe a genetically defined microglia sublineage in mice which has the ability to suppress obsessive compulsion and anxiety symptoms. These microglia derive from precursors expressing the transcription factor Hoxb8. Selective ablation of Hoxb8-lineage microglia or the Hoxb8 gene revealed that dysfunction in this cell type causes severe over-grooming and anxiety-like behavior and stress responses. Moreover, we show that the severity of the pathology is set by female sex hormones. Together, our findings reveal that different microglia lineages have distinct functions. In addition, our data suggest a mechanistic link between biological sex and genetics, two major risk factors for developing anxiety and related disorders in humans.

Two distinct ontogenies confer heterogeneity to mouse brain microglia

Hoxb8 mutant mice show compulsive behavior similar to trichotillomania, a human obsessive-compulsive-spectrum disorder. The only Hoxb8 lineage-labeled cells in the brains of mice are microglia, suggesting that defective Hoxb8 microglia caused the disorder. What is the source of the Hoxb8 microglia? It has been posited that all microglia progenitors arise at embryonic day (E) 7.5 during yolk sac hematopoiesis, and colonize the brain at E9.5. In contrast, we show the presence of two microglia subpopulations: canonical, non-Hoxb8 microglia and Hoxb8 microglia. Unlike non-Hoxb8 microglia, Hoxb8 microglia progenitors appear to be generated during the second wave of yolk sac hematopoiesis, then detected in the aorto-gonad-mesonephros (AGM) and fetal liver, where they are greatly expanded, prior to infiltrating the E12.5 brain. Further, we demonstrate that Hoxb8 hematopoietic progenitor cells taken from fetal liver are competent to give rise to microglia in vivo Although the two microglial subpopulations are very similar molecularly, and in their response to brain injury and participation in synaptic pruning, they show distinct brain distributions which might contribute to pathological specificity. Non-Hoxb8 microglia significantly outnumber Hoxb8 microglia, but they cannot compensate for the loss of Hoxb8 function in Hoxb8 microglia, suggesting further crucial differences between the two subpopulations.

(CA/GT)(n) microsatellites affect homologous recombination during yeast meiosis

One of the most common microsatellites in eukaryotes consists of tandem arrays of the dinucleotide GT. Although the study of the instability of such repetitive DNA has been extremely fruitful over the last decade, no biological function has been demonstrated for these sequences. We investigated the genetic behavior of a region of the yeast Saccharomyces cerevisiae genome containing a 39-CA/GT dinucleotide repeat sequence. When the microsatellite sequence was present at the ARG4 locus on homologous chromosomes, diploid cells undergoing meiosis generated an excess of tetrads containing a conversion of the region restricted to the region of the microsatellite close to the recombination-initiation double-strand break. Moreover, whereas the repetitive sequence had no effect on the frequency of single crossover, its presence strongly stimulated the formation of multiple crossovers. The combined data strongly suggest that numerous recombination events are restricted to the initiation side of the microsatellite as though progression of the strand exchange initiated at the ARG4 promoter locus was impaired by the repetitive sequence. This observation corroborates in vitro experiments that demonstrated that RecA-promoted strand exchange is inhibited by CA/GT dinucleotide tracts. Surprisingly, meiotic instability of the microsatellite was very high (>0.1 alterations per tetrad) in all the spores with parental and recombinant chromosomes.

Increase of spontaneous intrachromosomal homologous recombination in mammalian cells expressing a mutant p53 protein

Homologous recombination plays an essential role in processes involved in genome stability/instability, such as molecular evolution, gene diversification, meiotic chromosome segregation, DNA repair and chromosomal rearrangements. p53 devoid cells exhibit predisposition to neoplasia, defects in G1 checkpoint and high genetic instability but a normal rate of point mutations. We investigated the effect of a p53 mutation, on spontaneous homologous recombination between intrachromosomal direct repeat sequences, in mouse L cells. In these cells, wild type for the p53 gene, we have overexpressed the mutant p53(175(Arg>His)) protein leading to a p53 mutant phenotype, as verified by the absence of a G1 arrest after gamma-irradiation. We show that the rate of spontaneous recombination is increased from five- to 20-fold in the mutant p53 lines. Moreover, this increase is observed in gene conversion as well as in deletion events. Our results provide new insights into the molecular mechanisms of genetic instability due to a defect of p53.

Monoclonal antibody-based methods for quantitation of hemoglobins: application to evaluating patients with sickle cell anemia treated with hydroxyurea

High-titer monoclonal antibodies (mAb) were raised against chromatographically purified human hemoglobin (Hb) species. These mAb were specific for either Hb A, Hb F, Hb S or Hb C. Based on these antibodies, which were directly conjugated with either fluorochromes or an enzyme (horseradish peroxidase), we developed immunoassays for determining the Hb profile in the peripheral blood; an enzyme-linked immunosorbent assay (ELISA) for determining the absolute and relative quantities of various Hb species and one-step immunolabeling for fluorescence microscopic and flow cytometric analyses of the distribution of RBC with respect to their Hb types. We utilized these methods for monitoring the Hb F level and the percentage of Hb F-containing cells in patients with sickle cell anemia undergoing treatment with hydroxyurea.

Respiratory symptoms and bronchial reactivity among pig and dairy farmers

OBJECTIVES

This study assessed the prevalence of respiratory manifestations among French pig and dairy farmers and determined the relationship between bronchial reactivity and respiratory manifestations.

METHODS

The pig farmers included 102 men working more than half-time inside swine confinement buildings. There were 51 male dairy farmers and 81 male referents. The demographic characteristics of the three groups were similar except for more smokers among the referents. Each subject completed a standardized questionnaire. Pulmonary function tests were performed before and after a methacholine challenge (cumulative doses 80, 240, and 560 micrograms). Airborne dust, ammonia, and carbon dioxide were measured inside 28 swine confinement buildings.

RESULTS

The pig farmers were exposed to a total dust level of 2.41 mg.m-3. The respirable particle concentration was low. The pig and dairy farmers had a significantly higher prevalence of cough and morning phlegm than the referents. Before the methacholine challenge, the dairy farmers had nonsignificantly lower mean lung function values than the other groups. Among the subjects with no history of asthma, nonspecific bronchial hyperreactivity was significantly higher among the pig and dairy farmers than among the referents. There was a fall in the forced expiratory volume in 1 s (FEV 1.0) that was greater than 10% in 6.7% of the referents, 17.9% of the swine workers, and 35.6% of the dairy farmers. This result was unchanged after adjustment for the initial FEV1.0.

CONCLUSIONS

The prevalence of respiratory symptoms was significantly higher among the pig farmers without base-line lung function impairment. However, both the pig and the dairy farmers had increased bronchial reactivity.

QRI8, a novel ubiquitin-conjugating enzyme in Saccharomyces cerevisiae

We have cloned and sequenced the gene encoding a novel ubiquitin-conjugating enzyme in Saccharomyces cerevisiae. Disruption of this gene shows that it is not essential for cell viability.

Possible involvement of the yeast POLIII DNA polymerase in induced gene conversion

In Saccharomyces cerevisiae, three different DNA polymerase complexes, POLI, POLII and POLIII, are known to be involved in DNA replication. The catalytic subunit of POLIII is encoded by the essential CDC2 gene. The existence of different thermosensitive noncomplementing mutants of CDC2 offers the possibility of using a genetic approach to investigate the involvement of POLIII in induced gene conversion. When cdc2 heteroallelic cells were irradiated and incubated under restrictive conditions, almost no induction of thermoresistant cells could be detected, suggesting an essential role for POLIII in mitotic gene conversion events.

The absence of introns in yeast mitochondria does not abolish mitochondrial recombination

The respiratory competency of a yeast strain devoid of mitochondrial introns is quite normal. However, it may be asked whether intron-encoded proteins participate in metabolisms other than those of mitochondrial introns. Using strains without mitochondrial introns we have answered two questions. The first was: does the absence of intron-encoded proteins abolish mitochondrial recombination? The second was: do mitochondrial introns and intron-encoded proteins play a part in mitochondrial DNA rearrangements induced by ethidium bromide (rho- production)? We have shown that the introns and intron-encoded proteins are not essential components of either phenomenon.

Structure and function of the Saccharomyces cerevisiae CDC2 gene encoding the large subunit of DNA polymerase III

Saccharomyces cerevisiae cdc2 mutants arrest in the S-phase of the cell cycle when grown at the non-permissive temperature, implicating this gene product as essential for DNA synthesis. The CDC2 gene has been cloned from a yeast genomic library in vector YEp13 by complementation of a cdc2 mutation. An open reading frame coding for a 1093 amino acid long protein with a calculated mol. wt of 124,518 was determined from the sequence. This putative protein shows significant homology with a class of eukaryotic DNA polymerases exemplified by human DNA polymerase alpha and herpes simplex virus DNA polymerase. Fractionation of extracts from cdc2 strains showed that these mutants lacked both the polymerase and proofreading 3'-5' exonuclease activity of DNA polymerase III, the yeast analog of mammalian DNA polymerase delta. These studies indicate that DNA polymerase III is an essential component of the DNA replication machinery.

Mitochondrial introns aI1 and/or aI2 are needed for the in vivo deletion of intervening sequences

Some pet- (or mit-) mutations impeding the splicing of one or several intron(s) of the yeast mitochondrial pre-mRNA(s) are suppressed in vivo by the DNA deletion of these introns. We have genetically demonstrated that introns aI1 and/or aI2 of the cytochrome c oxidase subunit 1 gene are necessary for this deletion process. The facts that adjacent introns are simultaneously deleted and that, in the pet- (or mit-) mutants which easily revert by intron deletion, the splicing of the introns they affect is only partially blocked, suggest that the intron encoded proteins aI1 and/or aI2 could intervene by means of their putative reverse transcriptase activity.

Mitochondrial splicing requires a protein from a novel helicase family

Proteins involved in mitochondrial splicing but encoded by nuclear genes have been characterized in Saccharomyces and Neurospora. The role in splicing of these proteins is largely unknown. Here we report that mutations in the nuclear gene MSS116 directly affect the splicing of several introns of the cytochrome b (cob) and cytochrome c oxidase subunit I (cox1) primary transcripts. This implies that the MSS116 protein (pMSS116) is an important component of the mitochondrial splicing machinery. The sequence of the cloned MSS116 gene shows that its protein product is homologous to the translation eIF-4A factor and the human nuclear protein p68. We show further that these proteins share several conserved amino-acid blocks with DNA helicases and related proteins. This suggests that pMSS116 has an RNA helicase activity. RNA helicases may be involved in many different processes including translation and splicing.

Construction of a yeast strain devoid of mitochondrial introns and its use to screen nuclear genes involved in mitochondrial splicing

We have constructed a respiring yeast strain devoid of mitochondrial introns to screen nuclear pet- mutants for those that play a direct role in mitochondrial intron excision. Intron-less mitochondria are introduced by cytoduction into pet- strains that have been made rho0; cytoductants therefrom recover respiratory competency if the original pet- mutation is required only for mitochondrial splicing. By this means, we have identified 11 complementation groups of such genes. Their total number may be estimated as about 18.

Allergenicity and cross-reactivity of rye grass pollen extracts revealed by monoclonal antibodies

Using monoclonal antibodies the immunogenic and allergenic characteristics of rye Group I were redefined by SDS-PAGE analysis and immunoblotting. The purified rye Group I from NIH possesses a major component of approximately 34000 Da against which most of the sera from grass-sensitive patients and none from non-atopic volunteers contain specific IgE antibodies. Monoclonal antibodies to rye Group I were raised and used to purify the antigen and to verify the cross-reactivity between grass extracts. The 3 monoclonal antibodies studied recognized different components of timothy grass and 2 of them recognized kentucky june grass but none recognized components of ragweed extracts.

Development of a reverse enzymoallergosorbent test (REAST) to detect timothy-specific IgE antibodies. Comparison with RAST

Radioallergosorbent test (RAST) for the measurement of IgE antibodies has been introduced more than 15 years ago and a number of technical modifications have since improved its sensitivity and reproducibility. The test has been applied to the diagnosis of allergy and to determine changes in the levels of IgE antibodies following immunotherapy. However, specific IgG antibodies are raised during such a therapy and can interfere with the RAST. We have developed a reverse enzymoallergosorbent test (REAST) where microtiter plates are first coated with a purified polyclonal anti-IgE antibody, then with the serum to test and finally with peroxidase-labeled antigen. This assay is antigen specific as shown by the significant inhibition of binding of the labeled antigen in presence of unlabeled specific antigen (greater than 95%) and the absence of inhibition in presence of irrelevant antigens. The values found in atopic patients (85 subjects) were significantly higher than in the non-atopic donors (35 subjects) (1.14 U +/- 1.20 vs. 0.01 U +/- 0.02, P less than 0.0005) and there was a good correlation with the Pharmacia RAST (P less than 0.0005). The levels of specific IgE by both REAST and RAST correlated well with the clinical symptomatology.

Gene conversion at different points in the mitotic cycle of Saccharomyces cerevisiae

In the Saccharomyces cerevisiae mitotic cycle, the timing of radiation-induced gene conversion has been studied using thermosensitive cell division cycle mutants. The cells were found to perform conversion at different G1 or post-replication steps. A lower yield in induction is found during the G2 phase and is explained by the competition for recombinational repair between sister chromatids and homologous chromosomes. The results are discussed in relation to repair.

[Demonstration of maturation promoting factor activity in Saccharomyces cerevisiae]

Microinjection of a crude yeast extract into fully grown immature Xenopus laevis oocytes induces the reinitiation of meiotic maturation as does Xenopus laevis oocyte MPF (Maturation Promoting Factor) by itself. Using several strains of yeast exhibiting temperature sensitive cell cycle block (cdc), it was observed that yeast extract exhibits MPF activity only when obtained during the time interval from the G2 period to the metaphase. This observation stresses eucaryotic ubiquity of MPF.