New Insights into Dyskerin-CypA Interaction: Implications for X-Linked Dyskeratosis Congenita and Beyond

The highly conserved family of cyclophilins comprises multifunctional chaperones that interact with proteins and RNAs, facilitating the dynamic assembly of multimolecular complexes involved in various cellular processes. Cyclophilin A (CypA), the predominant member of this family, exhibits peptidyl-prolyl cis-trans isomerase activity. This enzymatic function aids with the folding and activation of protein structures and often serves as a molecular regulatory switch for large multimolecular complexes, ensuring appropriate inter- and intra-molecular interactions. Here, we investigated the involvement of CypA in the nucleus, where it plays a crucial role in supporting the assembly and trafficking of heterogeneous ribonucleoproteins (RNPs). We reveal that CypA is enriched in the nucleolus, where it colocalizes with the pseudouridine synthase dyskerin, the catalytic component of the multifunctional H/ACA RNPs involved in the modification of cellular RNAs and telomere stability. We show that dyskerin, whose mutations cause the X-linked dyskeratosis (X-DC) and the Hoyeraal-Hreidarsson congenital ribosomopathies, can directly interact with CypA. These findings, together with the remark that substitution of four dyskerin prolines are known to cause X-DC pathogenic mutations, lead us to indicate this protein as a CypA client. The data presented here suggest that this chaperone can modulate dyskerin activity influencing all its partecipated RNPs.

Better quality of life and reduced fecal incontinence in rectal cancer patients with the watch-and-wait follow-up strategy

INTRODUCTION

The watch-and-wait (WW) strategy is an alternative to anterior resection in patients with rectal cancer (RC) that have had a complete clinical response to neoadjuvant treatment. Few reports describe the quality of life and functional anorectal disorders (FADs) in that population.

AIM

To analyze and compare the FADs and quality of life in patients with locally advanced adenocarcinoma of the rectum treated with neoadjuvant therapy, divided into two different strategy groups: group 1 (G1), WW; and group 2 (G2), anterior resection.

MATERIALS AND METHODS

Thirty patients (G1: n = 20 and G2: n = 10) that had finished neoadjuvant therapy at least 12 months prior were included. Mean patient age was 59.5 years (range: 41-79) and 15 of the patients were men. The FADs were evaluated through: a) clinical history, b) 21-day bowel diary, c) Jorge and Wexner fecal incontinence scale, d) anorectal manometry (ARM), and fecal incontinence quality of life scale (FIQL).

RESULTS

Bowel diary: fecal incontinence (40%) and urge to defecate (45%) in G1 vs. fecal incontinence (60%) and urge to defecate (30%) in G2, with no significant differences (p = NS). Fecal incontinence scale: fecal incontinence in G1 was significantly less severe than that in G2 (median 6.5 points vs. 13 points [p = 0.0142]). ARM: no differences between the two groups. Quality of life: significantly different between the two groups (FIQL/G1: 3.7 vs. FIQL/G2: 2.8; p < 0.03).

CONCLUSIONS

The WW follow-up strategy in patients with locally advanced rectal cancer was associated with better quality of life and reduced fecal incontinence.

Better quality of life and reduced fecal incontinence in rectal cancer patients with the watch-and-wait follow-up strategy

INTRODUCTION

The watch-and-wait (WW) strategy is an alternative to anterior resection in patients with rectal cancer (RC) that have had a complete clinical response to neoadjuvant treatment. Few reports describe the quality of life and functional anorectal disorders (FADs) in that population.

AIM

To analyze and compare the FADs and quality of life in patients with locally advanced adenocarcinoma of the rectum treated with neoadjuvant therapy, divided into two different strategy groups: group 1 (G1), WW; and group 2 (G2), anterior resection.

MATERIALS AND METHODS

Thirty patients (G1: n = 20 and G2: n = 10) that had finished neoadjuvant therapy at least 12 months prior were included. Mean patient age was 59.5 years (range: 41-79) and 15 of the patients were men. The FADs were evaluated through: a) clinical history, b) 21-day bowel diary, c) Jorge and Wexner fecal incontinence scale, d) anorectal manometry (ARM), and fecal incontinence quality of life scale (FIQL).

RESULTS

Bowel diary: fecal incontinence (40%) and urge to defecate (45%) in G1 vs. fecal incontinence (60%) and urge to defecate (30%) in G2, with no significant differences (p = NS). Fecal incontinence scale: fecal incontinence in G1 was significantly less severe than that in G2 (median 6.5 points vs. 13 points [p = 0.0142]). ARM: no differences between the two groups. Quality of life: significantly different between the two groups (FIQL/G1: 3.7 vs. FIQL/G2: 2.8; p < 0.03).

CONCLUSIONS

The WW follow-up strategy in patients with locally advanced rectal cancer was associated with better quality of life and reduced fecal incontinence.

Triple blockade of EGFR, MEK and PD-L1 has antitumor activity in colorectal cancer models with constitutive activation of MAPK signaling and PD-L1 overexpression

BACKGROUND

Molecular mechanisms driving acquired resistance to anti-EGFR therapies in metastatic colorectal cancer (mCRC) are complex but generally involve the activation of the downstream RAS-RAF-MEK-MAPK pathway. Nevertheless, even if inhibition of EGFR and MEK could be a strategy for overcoming anti-EGFR resistance, its use is limited by the development of MEK inhibitor (MEKi) resistance.

METHODS

We have generated in vitro and in vivo different CRC models in order to underline the mechanisms of MEKi resistance.

RESULTS

The three different in vitro MEKi resistant models, two generated by human CRC cells quadruple wild type for KRAS, NRAS, BRAF, PI3KCA genes (SW48-MR and LIM1215-MR) and one by human CRC cells harboring KRAS mutation (HCT116-MR) showed features related to the gene signature of colorectal cancer CMS4 with up-regulation of immune pathway as confirmed by microarray and western blot analysis. In particular, the MEKi phenotype was associated with the loss of epithelial features and acquisition of mesenchymal markers and morphology. The change in morphology was accompanied by up-regulation of PD-L1 expression and activation of EGFR and its downstream pathway, independently to RAS mutation status. To extend these in vitro findings, we have obtained mouse colon cancer MC38- and CT26-MEKi resistant syngeneic models (MC38-MR and CT26-MR). Combined treatment with MEKi, EGFR inhibitor (EGFRi) and PD-L1 inhibitor (PD-L1i) resulted in a marked inhibition of tumor growth in both models.

CONCLUSIONS

These results suggest a strategy to potentially improve the efficacy of MEK inhibition by co-treatment with EGFR and PD-L1 inhibitors via modulation of host immune responses.

Receptor tyrosine kinase-dependent PI3K activation is an escape mechanism to vertical suppression of the EGFR/RAS/MAPK pathway in KRAS-mutated human colorectal cancer cell lines

Background

Previous studies showed that the combination of an anti-Epidermal growth factor (EGFR) and a MEK-inhibitor is able to prevent the onset of resistance to anti-EGFR monoclonal antibodies in KRAS-wild type colorectal cancer (CRC), while the same combination reverts anti-EGFR primary resistance in KRAS mutated CRC cell lines. However, rapid onset of resistance is a limit to combination therapies in KRAS mutated CRC.

Methods

We generated four different KRAS mutated CRC cell lines resistant to a combination of cetuximab (an anti-EGFR antibody) and refametinib (a selective MEK-inhibitor) after continuous exposure to increasing concentration of the drugs. We characterized these resistant cell lines by evaluating the expression and activation status of a panel of receptor tyrosine kinases (RTKs) and intracellular transducers by immunoblot and qRT-PCR. Oncomine comprehensive assay and microarray analysis were carried out to investigate new acquired mutations or transcriptomic adaptation, respectively, in the resistant cell lines. Immunofluorescence assay was used to show the localization of RTKs in resistant and parental clones.

Results

We found that PI3K-AKT pathway activation acts as an escape mechanism in cell lines with acquired resistance to combined inhibition of EGFR and MEK. AKT pathway activation is coupled to the activation of multiple RTKs such as HER2, HER3 and IGF1R, though its pharmacological inhibition is not sufficient to revert the resistant phenotype. PI3K pathway activation is mediated by autocrine loops and by heterodimerization of multiple receptors.

Conclusions

PI3K activation plays a central role in the acquired resistance to the combination of anti-EGFR and MEK-inhibitor in KRAS mutated colorectal cancer cell lines. PI3K activation is cooperatively achieved through the activation of multiple RTKs such as HER2, HER3 and IGF1R.

A functional connection between dyskerin and energy metabolism

The human DKC1 gene encodes dyskerin, an evolutionarily conserved nuclear protein whose overexpression represents a common trait of many types of aggressive sporadic cancers. As a crucial component of the nuclear H/ACA snoRNP complexes, dyskerin is involved in a variety of essential processes, including telomere maintenance, splicing efficiency, ribosome biogenesis, snoRNAs stabilization and stress response. Although multiple minor dyskerin splicing isoforms have been identified, their functions remain to be defined. Considering that low-abundance splice variants could contribute to the wide functional repertoire attributed to dyskerin, possibly having more specialized tasks or playing significant roles in changing cell status, we investigated in more detail the biological roles of a truncated dyskerin isoform that lacks the C-terminal nuclear localization signal and shows a prevalent cytoplasmic localization. Here we show that this dyskerin variant can boost energy metabolism and improve respiration, ultimately conferring a ROS adaptive response and a growth advantage to cells. These results reveal an unexpected involvement of DKC1 in energy metabolism, highlighting a previously underscored role in the regulation of metabolic cell homeostasis.

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Human dyskerin is an evolutionary conserved component of nuclear H/ACA snoRNPs.

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The functional role of a truncated dyskerin isoform (Iso3) is analyzed.

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Iso3 overexpression boosts energy metabolism and induces a ROS adaptive response.

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Iso3 connects dyskerin with mitochondrial functionality and redox homeostasis.

A new role for human dyskerin in vesicular trafficking

Dyskerin is an essential, conserved, multifunctional protein found in the nucleolus, whose loss of function causes the rare genetic diseases X‐linked dyskeratosis congenita and Hoyeraal‐Hreidarsson syndrome. To further investigate the wide range of dyskerin's biological roles, we set up stable cell lines able to trigger inducible protein knockdown and allow a detailed analysis of the cascade of events occurring within a short time frame. We report that dyskerin depletion quickly induces cytoskeleton remodeling and significant alterations in endocytic Ras‐related protein Rab‐5A/Rab11 trafficking. These effects arise in different cell lines well before the onset of telomere shortening, which is widely considered the main cause of dyskerin‐related diseases. Given that vesicular trafficking affects many homeostatic and differentiative processes, these findings add novel insights into the molecular mechanisms underlining the pleiotropic manifestation of the dyskerin loss‐of‐function phenotype.

Chlorpyrifos exposure affects fgf8, sox9, and bmp4 expression required for cranial neural crest morphogenesis and chondrogenesis in Xenopus laevis embryos

Chlorpyrifos (CPF) is an organophosphate insecticide used primarily to control foliage and soil-borne insect pests on a variety of food and feed crops. In mammals, maternal exposure to CPF has been reported to induce dose-related abnormalities such as slower brain growth and cerebral cortex thinning. In lower vertebrates, for example, fish and amphibians, teratogenic activity of this compound is correlated with several anatomical alterations. Little is known about the effects of CPF on mRNA expression of genes involved in early development of the anatomical structures appearing abnormal in embryos. This study investigated the effects of exposure to different CPF concentrations (10, 15 and 20 mg/L) on Xenopus laevis embryos from stage 4/8 to stage 46. Some of the morphological changes we detected in CPF-exposed embryos included cranial neural crest cell (NCC)-derived structures. For this reason, we analyzed the expression of select genes involved in hindbrain patterning (egr2), cranial neural crest chondrogenesis, and craniofacial development (fgf8, bmp4, sox9, hoxa2 and hoxb2). We found that CPF exposure induced a reduction in transcription of all the genes involved in NCC-dependent chondrogenesis, with largest reductions in fgf8 and sox9; whereas, in hindbrain, we did not find any alterations in egr2 expression. Changes in the expression of fgf8, bmp4, and sox9, which are master regulators of several developmental pathways, have important implications. If these changes are confirmed to belong to a general pattern of alterations in vertebrates prenatally exposed to OP, they might be useful to assess damage during vertebrate embryo development. Environ. Mol. Mutagen. 57:589-604, 2016. © 2016 Wiley Periodicals, Inc.

Unusual Novel SnoRNA-Like RNAs in Drosophila melanogaster

A computational screen for novel small nucleolar RNAs in Drosophila melanogaster uncovered 15 novel snoRNAs and snoRNA-like long non-coding RNAs. In contrast to earlier surverys, the novel sequences are mostly poorly conserved and originate from unusual genomic locations. The majority derive from precurors antisense to well-known protein-coding genes, and four of the candidates are produced from exon-coding regions. Only a minority of the new sequences appears to have canonical target sites in ribosomal or small nuclear RNAs. Taken together, these evolutionary young, poorly conserved, and genomically atypical sequences point at a class of snoRNA-like transcripts with predominantly regulatory functions in the fruit fly genome.

Developmentally regulated expression and expression strategies of Drosophila snoRNAs

Small nucleolar RNAs constitute a significant portion of the eukaryotic small ncRNA transcriptome and guide site-specific methylation or pseudouridylation of target RNAs. In addition, they can play diverse regulatory roles on gene expression, acting as precursors of smaller fragments able to modulate alternative splicing or operate as microRNAs. Defining their expression strategies and the full repertory of their biological functions is a critical, but still ongoing, process in most organisms. Considering that Drosophila melanogaster is one of the most advantageous model organism for genetic, functional and developmental studies, we analysed the whole genomic organization of its annotated snoRNAs - whose vast majority is known to be embedded in an intronic context - and show by GO term enrichment analysis that protein-coding genes involved in cell division and cytoskeleton organization are those mostly preferred as hosts. This finding was unexpected, and delineates an unpredicted link between snoRNA host genes and cell proliferation that might be of general relevance. We also defined by quantitative RT-PCR the expression of a representative subset of annotated specimens throughout the life cycle, providing a first overview on developmental profiling of the fly snoRNA transcriptome. We found that most of the tested specimens, rather than acting as housekeeping genes with uniform expression, exhibit dynamic developmental expression patterns; moreover, intronic snoRNAs harboured by the same host gene often exhibit distinct temporal profiles, indicating that they can be expressed uncoordinatedly. In addition to provide an updated outline of the fly snoRNA transcriptome, our data highlight that expression of these versatile ncRNAs can be finely regulated.

Human dyskerin: beyond telomeres

Human dyskerin is an evolutively conserved protein that participates in diverse nuclear complexes: the H/ACA snoRNPs, that control ribosome biogenesis, RNA pseudouridylation, and stability of H/ACA snoRNAs; the scaRNPs, that control pseudouridylation of snRNAs; and the telomerase active holoenzyme, which safeguards telomere integrity. The biological importance of dyskerin is further outlined by the fact that its deficiency causes the X-linked dyskeratosis congenita disease, while its over-expression characterizes several types of cancers and has been proposed as prognostic marker. The role of dyskerin in telomere maintenance has widely been discussed, while its functions as H/ACA sno/scaRNP component has been so far mostly overlooked and represent the main goal of this review. Here we summarize how increasing evidence indicates that the snoRNA/microRNA pathways can be interlaced, and that dyskerin-dependent RNA pseudouridylation represents a flexible mechanism able to modulate RNA function in different ways, including modulation of splicing, change of mRNA coding properties, and selective regulation of IRES-dependent translation. We also propose a speculative model that suggests that the dynamics of pre-assembly and nuclear import of H/ACA RNPs are crucial regulatory steps that can be finely controlled in the cytoplasm in response to developmental, differentiative and stress stimuli.

Intron retention: a human DKC1 gene common splicing event

Identification of alternatively spliced transcripts produced by a gene is a crucial step in deciphering the bulk of its biological roles and the overall processes that regulate its activity. By using a combination of bioinformatic and molecular approaches we identified, cloned, and characterized 3 novel alternative splice isoforms derived from human dyskeratosis congenita 1 (hDKC1), an essential human gene causative of the X-linked dyskeratosis congenita disease and involved in multiple functions related to cell growth, proliferation, and telomere maintenance. Expression of the new isoforms, all characterized by intron retention, was confirmed by RT-PCR in a panel of diverse cell lines and normal human tissues, and despite the presence of premature termination codons, was not down-regulated by the mechanism of nonsense-mediated decay. Accumulation of these transcripts fluctuated distinctly in the diverse tissues and during in vitro differentiation of Caco2 cells, suggesting that their ratio may contribute to the gene functional diversity across different cell types. Intriguingly, the structure of one isoform leads to exonize an intronically encoded small nucleolar RNA (snoRNA), highlighting an additional layer of complexity that can contribute to overall gene regulation.

[Functional dyspepsia and the satiety test: its usefulness in clinical practice]

INTRODUCTION

According to the Rome III Criteria, functional dyspepsia (FD) is classified as postprandial distress syndrome (PDS) and epigastric pain syndrome (EPS). On the other hand, the satiety test (ST) has been used to evaluate gastric accommodation and emptying, distinguishing healthy individuals from those with dyspepsia.

AIMS

To determine whether the ST can distinguish dyspeptic individuals from healthy ones and to evaluate its usefulness in differentiating the two FD subtypes.

METHODS

Adults with FD were consecutively enrolled in a cross-sectional study within the time frame of August 2011 and October 2012. Healthy subjects participated as controls. The ST consisted of the intake of a nutritional supplement (Fortisip®, Nutricia Bagó®) at a constant speed; satiety was graded at 5-minute intervals (1 to 5 points). Intake was suspended when the maximum score was reported. The total ingested volume and caloric intake was recorded and the Mann-Whitney U test was used in the statistical analysis.

RESULTS

The study included 39 dyspeptic patients and 20 control individuals. The patients were predominantly women (84.6 vs. 25%; p < 0.0001) and they were similar in age (39.59 ± 13.53 vs. 34.70 ± 9.85 years) and BMI (24.32 ± 3.52 vs. 25.82 ± 3.34 kg/m2) with respect to the controls. The FD subtype percentages were PDS: 61%, EPS: 31%, and Mixed syndrome: 8%. There was a lower ingested volume and caloric intake on the part of the dyspeptic patients (185 vs. 300 ml and 277 vs. 520 Kcal, respectively. Both: P<.001). No differences in the ST were observed between the two pure dyspepsia subtypes.

CONCLUSIONS

There was a difference in the ST between healthy individuals and those with dyspepsia, but the ingested volume and caloric intake in the two FD subtypes were similar.

Laser microdissection applied to gene expression profiling of subset of cells from the Drosophila wing disc

Heterogeneous nature of tissues has proven to be a limiting factor in the amount of information that can be generated from biological samples, compromising downstream analyses. Considering the complex and dynamic cellular associations existing within many tissues, in order to recapitulate the in vivo interactions thorough molecular analysis one must be able to analyze specific cell populations within their native context. Laser-mediated microdissection can achieve this goal, allowing unambiguous identification and successful harvest of cells of interest under direct microscopic visualization while maintaining molecular integrity. We have applied this technology to analyse gene expression within defined areas of the developing Drosophila wing disc, which represents an advantageous model system to study growth control, cell differentiation and organogenesis. Larval imaginal discs are precociously subdivided into anterior and posterior, dorsal and ventral compartments by lineage restriction boundaries. Making use of the inducible GAL4-UAS binary expression system, each of these compartments can be specifically labelled in transgenic flies expressing an UAS-GFP transgene under the control of the appropriate GAL4-driver construct. In the transgenic discs, gene expression profiling of discrete subsets of cells can precisely be determined after laser-mediated microdissection, using the fluorescent GFP signal to guide laser cut. Among the variety of downstream applications, we focused on RNA transcript profiling after localised RNA interference (RNAi). With the advent of RNAi technology, GFP labelling can be coupled with localised knockdown of a given gene, allowing to determinate the transcriptional response of a discrete cell population to the specific gene silencing. To validate this approach, we dissected equivalent areas of the disc from the posterior (labelled by GFP expression), and the anterior (unlabelled) compartment upon regional silencing in the P compartment of an otherwise ubiquitously expressed gene. RNA was extracted from microdissected silenced and unsilenced areas and comparative gene expression profiling determined by quantitative real-time RT-PCR. We show that this method can effectively be applied for accurate transcriptomics of subsets of cells within the Drosophila imaginal discs. Indeed, while massive disc preparation as source of RNA generally assumes cell homogeneity, it is well known that transcriptional expression can vary greatly within these structures in consequence of positional information. Using localized fluorescent GFP signal to guide laser cut, more accurate transcriptional analyses can be performed and profitably applied to disparate applications, including transcript profiling of distinct cell lineages within their native context.

A novel Drosophila antisense scaRNA with a predicted guide function

A significant portion of eukaryotic small ncRNA transcriptome is composed by small nucleolar RNAs. From archaeal to mammalian cells, these molecules act as guides in the site-specific pseudouridylation or methylation of target RNAs. We used a bioinformatics search program to detect Drosophila putative orthologues of U79, one out of ten snoRNAs produced by GAS5, a human ncRNA involved in apoptosis, susceptibility to cancer and autoimmune diseases. This search led to the definition of a list of U79-related fly snoRNAs whose genomic organization, evolution and expression strategy are discussed here. We report that an intriguing novel specimen, named Dm46E3, is transcribed as a longer, unspliced precursor from the reverse strand of eiger, a fly regulatory gene that plays a key role in cell differentiation, apoptosis and immune response. Expression of Dm46E3 was found significantly up-regulated in a mutant strain in which eiger transcription is greatly reduced, suggesting that these two sense-antisense genes may be mutually regulated. Relevant to its function, Dm46E3 concentrated specifically in the Cajal bodies, followed a dynamic spatial expression profile during embryogenesis and displayed a degenerate antisense element that enables it to target U1b, a developmentally regulated isoform of the U1 spliceosomal snRNA that is particularly abundant in embryos.

A computational search for box C/D snoRNA genes in the Drosophila melanogaster genome

MOTIVATION

In eukaryotes, the family of non-coding RNA genes includes a number of genes encoding small nucleolar RNAs (mainly C/D and H/ACA snoRNAs), which act as guides in the maturation or post-transcriptional modifications of target RNA molecules. Since in Drosophila melanogaster (Dm) only few examples of snoRNAs have been identified so far by cDNA libraries screening, integration of the molecular data with in silico identification of these types of genes could throw light on their organization in the Dm genome.

RESULTS

We have performed a computational screening of the Dm genome for C/D snoRNA genes, followed by experimental validation of the putative candidates. Few of the 26 confirmed snoRNAs had been recognized by cDNA library analysis. Organization of the Dm genome was also found to be more variegated than previously suspected, with snoRNA genes nested in both the introns and exons of protein-coding genes. This finding suggests that the presence of additional mechanisms of snoRNA biogenesis based on the alternative production of overlapping mRNA/snoRNA molecules.

AVAILABILITY

Additional information is available at http://www.bioinformatica.unito.it/bioinformatics/snoRNAs.

The clot gene of Drosophila melanogaster encodes a conserved member of the thioredoxin-like protein superfamily

The conversion of pyruvoyl-H(4)-pterin to pyrimidodiazepine (PDA), which is an essential step in the biosynthesis of the red components of Drosophila eye pigments known as drosopterins, requires the products of the genes sepia and clot. While the product of sepia has been shown to correspond to the enzyme PDA-synthase, the role of clot remains unknown, although the clot(1) allele was one of the first eye-color mutants to be isolated in Drosophila melanogaster,and much genetic and biochemical data has become available since. Here we report the cloning of the clot gene, describe its molecular organization and characterize the sequence alterations associated with the alleles cl(1) and cl(2). The coding properties of the gene show that it encodes a protein related to the Glutaredoxin class of the Thioredoxin-like enzyme superfamily, conserved members of which are found in human, mouse and plants. We suggest that the Clot protein is an essential component of a glutathione redox system required for the final step in the biosynthetic pathway for drosopterins.

RNAi triggered by symmetrically transcribed transgenes in Drosophila melanogaster

Specific silencing of target genes can be induced in a variety of organisms by providing homologous double-stranded RNA molecules. In vivo, these molecules can be generated either by transcription of sequences having an inverted-repeat (IR) configuration or by simultaneous transcription of sense-antisense strands. Since IR constructs are difficult to prepare and can stimulate genomic rearrangements, we investigated the silencing potential of symmetrically transcribed sequences. We report that Drosophila transgenes whose sense-antisense transcription was driven by two convergent arrays of Gal4-dependent UAS sequences can induce specific, dominant, and heritable repression of target genes. This effect is not dependent on a mechanism based on homology-dependent DNA/DNA interactions, but is directly triggered by transcriptional activation and is accompanied by specific depletion of the endogenous target RNA. Tissue-specific induction of these transgenes restricts the target gene silencing to selected body domains, and spreading phenomena described in other cases of post-transcriptional gene silencing (PTGS) were not observed. In addition to providing an additional tool useful for Drosophila functional genomic analysis, these results add further strength to the view that events of sense-antisense transcription may readily account for some, if not all, PTGS-cosuppression phenomena and can potentially play a relevant role in gene regulation.

Functional analysis of regulatory elements controlling the expression of the ecdysone-regulated Drosophila ng-1 gene

The steroid hormone ecdysone controls multiple aspects of insect development, including larval moults and metamorphosis, and can induce specific genetic responses in different tissues. The definition of the molecular mechanisms able to mediate this tissue-specific responsiveness may greatly contribute to understanding how such an accurate genetic response is achieved. In this work we have identified, by transgenic analysis, the regulatory elements directing the expression of ng-1, an ecdysone-regulated Drosophila gene showing a highly specific developmental expression profile. Our results show that an ecdysone-responsive element located within the ng-1 coding region is necessary for high-level gene expression, whereas the gene's spatial and temporal expression profile is fully controlled by a distinct upstream regulatory region. This region binds a set of transcriptional factors, including the FKH regulatory protein, which can potentially modulate the ecdysone genetic regulated response.

minifly, a Drosophila gene required for ribosome biogenesis

We report here the genetic, molecular, and functional characterization of the Drosophila melanogaster minifly (mfl) gene. Genetic analysis shows that mfl is essential for Drosophila viability and fertility. While P-element induced total loss-of-function mutations cause lethality, mfl partial loss-of-function mutations cause pleiotropic defects, such as extreme reduction of body size, developmental delay, hatched abdominal cuticle, and reduced female fertility. Morphological abnormalities characteristic of apoptosis are found in the ovaries, and a proportion of eggs laid by mfl mutant females degenerates during embryogenesis. We show that mfl encodes an ubiquitous nucleolar protein that plays a central role in ribosomal RNA processing and pseudouridylation, whose known eukaryotic homologues are yeast Cfb5p, rat NAP57 and human dyskerin, encoded by the gene responsible for the X-linked dyskeratosis congenita disease. mfl genetic analysis represents the first in vivo functional characterization of a member of this highly conserved gene family from higher eukaryotes. In addition, we report that mfl hosts an intron encoded box H/ACA snoRNA gene, the first member of this class of snoRNAs identified so far from Drosophila.

Cross-talking among Drosophila nuclear receptors at the promiscuous response element of the ng-1 and ng-2 intermolt genes

In Drosophila, peaks of the titer of the steroid hormone ecdysone act as molecular signals that trigger all the major developmental transitions occurring along the life cycle. The EcR/USP heterodimer, known to constitute the functional ecdysone receptor, binds with high affinity to specific target sequences, the ecdysone response elements (EcREs), whose repertoire still remains to be fully characterized at both the molecular and functional levels. In order to investigate the properties of EcREs composed of directly repeated half-sites (DRs), we have analysed the binding properties of the ng-EcRE, a DR element located within the coding region of ng-1 and ng-2, two highly homologous genes mapping at the ecdysone-regulated 3C intermolt puff. We report here that the ng-EcRE contacts the ecdysone receptor through its directly repeated half-sites spaced by 12 bp, and that this element may interact efficiently with at least three Drosophila orphan receptors, namely DHR38, DHR39 and beta FTZ-F1. Interestingly, DHR38 is bound alone or in combination with USP, providing the first evidence that the EcR-USP and DHR38-USP may directly compete for binding to a common response element. These results suggest that EcREs composed of widely spaced DRs may contribute to the establishment of extensive nuclear receptors cross-talking along the development, a mechanism that might play a relevant role in determining the temporal and spatial specificity of the ecdysone response. Finally, we show that the ng-EcRE can promote functional interactions in vitro as well as in vivo, acting as a transcriptional enhancer able to confer a specific developmental expression profile to a minimal promoter in transgenic flies.

Tosca: a Drosophila gene encoding a nuclease specifically expressed in the female germline

We describe here a Drosophila gene, tosca (tos), that is specifically expressed in the female germline. tos mRNA accumulates selectively within the pro-oocyte in germarial region 2 and persists throughout oogenesis. In the early embryo, the maternally supplied tos mRNA is evenly distributed at the syncytial blastoderm stage, but is excluded from the forming cells when cellularization begins. tos product is the first Drosophila member of the RAD2 protein family, a group of related DNA repair nucleases conserved from yeast to humans. Within the family, Tos is more closely related to ExoI, a Schizosaccharomyces pombe 5'-->3' double-stranded DNA exonuclease specifically induced in meiotic prophase I. The definite oocyte localization of tos transcript during meiosis and its ubiquitous distribution in early embryos suggest that tos may play a role in mismatch repair during genetic recombination and early cleavage divisions.

The moulting hormone ecdysone is able to recognize target elements composed of direct repeats

In Drosophila melanogaster, three temporally distinct ecdysone-responsive puff sets, the so-called intermoult, early and late puffs, have been described on the salivary gland polytene chromosomes. We have analyzed in detail a DNA segment of the 3C polytene region, from which the originates one of the most prominent intermoult puffs, with the aim of identifying ecdysone response elements (EcREs). Here we report that two putative EcREs of identical sequence are located at this puff site. Interestingly, these elements display a novel structural feature, being composed of directly repeated half-sites. Our results show that the EcR/USP heterodimer known to constitute the ecdysone functional receptor complex is able to bind to and transactivate through target elements composed of directly repeated half-sites. In addition, we show that these elements are also able to bind efficiently USP alone, suggesting that USP and EcR/USP could compete for their binding to DNA.

The role of the BR-C locus on the expression of genes located at the ecdysone-regulated 3C puff of Drosophila melanogaster

During the third larval instar, the steroid moulting hormone ecdysone activates three temporally distinct puff sets on the D. melanogaster salivary gland polytene chromosome: the so-called intermoult, early and late puffs. Hormonal regulation of intermoult puffs is quite complex and, so far, largely not understood. In order to further investigate this aspect, we have analysed the effects of mutations in a key regulator of the ecdysone response at the onset of metamorphosis, the Broad-Complex (BR-C) locus, on the expression of genes mapping at the 3C intermoult puff. On the basis of an accurate examination of 3C intermoult gene activity in single, carefully staged, third instar larvae of wild-type and BR-C mutant strains, we were able to subdivide these genes into two groups. Each group is characterised by a different temporal expression profile, so that at the beginning of the wandering stage the transcription of the first group declines as group II transcription is induced. Interestingly, the BR-C locus appears to play a regulatory role in establishing this transcriptional switch. By using mutants of each of the three lethal complementation groups, we precisely defined the role of BR-C functions in this developmental transition and we show that this locus also plays an essential role in the early pre-metamorphic hormonal response.

Dense cluster of genes is located at the ecdysone-regulated 3C puff of Drosophila melanogaster

The 3C11-12 polytene bands of the Drosophila melanogaster X chromosome give rise to a prominent puff, whose regression is triggered by the increase in the titre of the steroid hormone 20-hydroxyecdysone occurring before the metamorphosis. Here, we report the molecular characterization of three genes, named ng-2, ng-3 and ng-4, which we found to be closely linked to each other and to Sgs-4, Pig-1 and ng-1, three other genes previously mapped at this polytene region. All six genes are, in fact, arranged in a tightly linked cluster spanning a DNA segment of only 11 kb. With the exception of ng-4, all the clustered genes are highly expressed only during the larval life and share the same tissue-specificity, being mainly transcribed within the salivary glands. In addition, two members of the cluster, ng-1 and ng-2, show a very high degree of sequence homology, clearly indicating that they are related to each other by means of a duplication event. Interestingly to note, the entire cluster shows a peculiar genomic location, extending across two introns of the memory gene dunce, a large gene of Drosophila whose organization has proved to be remarkably complex.

A cDNA clone representative of a novel splicing pattern of the D. melanogaster dunce gene

The D. melanogaster dunce gene is involved in both the learning and memory processes of the fly. The gene encodes for a cAMP-specific phosphodiesterase, a function playing a central role in the regulation of the intracellular cAMP level. Molecular cloning of dunce has so far not been completely achieved, although it is known that the gene encodes a large set of RNAs and has a complex organization, extending for more than 140 kilobases and containing several genes within its introns. Here we report the isolation and the characterization of 21/7, a cDNA clone representative of a novel dunce splicing pattern. The nucleotide sequence of this clone led to the identification of a dunce exon included in at least one transcript so far uncharacterized.

Opa-like repeats in the genome of the Medfly Ceratitis capitata

The sequence determination of several genomic clones isolated from the Mediterranean fruitfly Ceratitis capitata identified the existence of opa-like repeats, often more than one being clustered in small chromosomal segments. These repeats have previously been shown to consist of stretches of tandemly reiterated glutamine-encoding residues, and they are found in multiple genes of several organisms. Most of the repeats described here are flanked or interrupted by stop codons in all reading frames and, thus, could not possibly be part of protein-coding sequences. Furthermore, these repeats, of which there are several hundred in the genome of the Medfly, can be used effectively for the determination of sequence polymorphisms, providing a convenient approach to obtain additional landmarks for the construction of genomic maps of this economically important insect.

Molecular characterization of a Drosophila melanogaster variant strain defective in the Sgs-4 gene dosage compensation

The X-linked Sgs-4 gene of Drosophila melanogaster encodes a salivary glue protein. Here we report the molecular characterization of a non-dosage compensated variant strain, named Karsnas, in which males accumulate only about half of the Sgs-4 polypeptide amount as do females. The results obtained show that significant nucleotide sequence alterations are accumulated within the Sgs-4 coding and 3' untranslated region of the variant strain, thus suggesting a possible role of these sequences in the Sgs-4 dosage compensation.

Effect of ecd1 mutation on the expression of genes mapped at the Drosophila melanogaster 3C11-12 intermoult puff

The Drosophila melanogaster ecd1 mutation causes a severe temperature-sensitive deficiency in the titre of the steroid hormone ecdysone. This mutation was used to investigate the role of ecdysone in both the transcription of the genes mapped at the 3C11-12 intermoult puff region and the puff formation. Thoroughly synchronized ecd1 larvae were shifted to the non-permissive temperature at various times of the development; after 24 or 48 h, the levels of the transcripts derived from Sgs-4, Pig-1 and ng-1, the three genes located at the 3C11-12 polytene bands, were determined. The results showed that the levels of the transcripts encoded by Pig-1 and ng-1 are unaffected by the drop in the ecdysone titre occurring in non-permissive conditions whereas the amount of Sgs-4 mRNA is greatly reduced. These data clearly indicate that transcription of the three genes mapped within the puff region is affected differently by the hormone. Furthermore, ecd1 larvae cultured at the non-permissive temperature show a prominent puff at the 3C11-12 polytene bands, indicating that ecdysone is not essential for puff induction and that puff size is not simply correlated with high-level Sgs-4 transcription.

Molecular organization of the Drosophila melanogaster Pig-1 gene

The Pre-intermoult gene-1 (Pig-1) of Drosophila melanogaster maps on the X chromosome, at polytene bands 3C11-12, and is nested within the 79 kb intron of the dunce gene. Pig-1 has so far been characterized only preliminarily and its function is still unknown. We analysed the molecular organization of the gene by cDNA clone isolation and sequencing as well as S1 mapping and primer extension analyses. The results obtained reveal that the gene is colinear with its genomic sequence and define the usage of both 5' and 3' alternative sites for Pig-1 transcription; two continuous open reading frames (ORFs) are fully contained within the Pig-1 transcribed region, although several lines of evidence suggest that only the longer ORF is likely to be translated. We also report that the level of Pig-1 transcript is nearly fourfold reduced in a variant strain carrying a deletion within the Pig-1 upstream sequence, thus identifying a regulatory element required for high level gene expression.

Bone mineral metabolism in juvenile chronic arthritis: the influence of steroids

Calciotropic hormone assays and bone mineral density (BMD) evaluations were carried out on a group of 36 children affected with juvenile chronic arthritis (JCA) (13 with pauciarticular, 8 with polyarticular and 15 with systemic onset subtype) and in a matched control group. The plasma levels of calcium, phosphate and alkaline phosphatase were normal in all the groups. Basal 25-OH D plasma levels were significantly decreased both in the polyarticular and in the systemic groups; the latter showed a further decrease after 1 year. There was a significant decrease in both the basal and the 1-year plasma levels of 1-25-OH D only in the systemic group. The BMD was decreased in the systemic group alone and the percentage increase after 1 year was significantly inferior to that in the other groups and in the controls. There was a clear relationship between the decrease in hormones and the cumulative dose of steroids administered, as well as between the BMD decrease and the physical activity of the patients (according to Steinbrocker's classification).

A new gene nested within the dunce genetic unit of Drosophila melanogaster

The molecular organization of the dunce gene of Drosophila melanogaster has proved to be particularly complex, with two divergently transcribed genes, Sgs-4 and Pig-1, nested within its 79 kb intron (1). Here we report the identification and the molecular characterization of a third gene nested within the transcription unit of dunce. This newly identified gene is located nearly 6 kb downstream Pig-1, within a more upstream dunce intron. The gene is developmentally regulated and transcribed with the same polarity of dunce; several lines of evidence indicate that it might encode for a salivary gland secreted (Sgs) protein.

[Pars plana phacoemulsification. Technics, indications and results]

Pars plana phacoemulsification allows cataract extraction through a 3 mm posterior sclerotomy. The indications of these technics are the combined cataract-vitrectomy, the cataracts on vitrectomised eyes and cataracts on eyes filled with silicone oil. The alteration of corneal endothelium is very reduced with the endocapsular pars plana phacoemulsification. After the emulsification, the capsular bag is extracted with a microforceps through the pars plana. It is also possible to save the anterior capsule to reduce corneal alteration during endocular surgery. We present the indications and the advantages of these technics.