TrxT and dhd are dispensable for Drosophila brain development but essential for l(3)mbt brain tumour growth.

Expression of the Drosophila cancer-germline (CG), X-linked, head-to-head gene pair TrxT and dhd is normally germline-specific but becomes upregulated in brain tumours caused by mutation in l(3)mbt. Here, we show that TrxT and dhd play a major synergistic role in the emergence of l(3)mbt tumour-linked transcriptomic signatures and tumour development, which is remarkable, taking into account that these two genes are never expressed together under normal conditions. We also show that TrxT, but not dhd, is crucial for the growth of l(3)mbt allografts, hence suggesting that the initial stages of tumour development and long-term tumour growth may depend on different molecular pathways. In humans, head-to-head inverted gene pairs are abundant among CG genes that map to the X chromosome. Our results identify a first example of an X-linked, head-to-head CG gene pair in Drosophila, underpinning the potential of such CG genes, dispensable for normal development and homoeostasis of somatic tissue, as targets to curtail malignant growth with minimal impact on overall health.

RNAget: an API to securely retrieve RNA quantifications.

SUMMARY: Large-scale sharing of genomic quantification data requires standardized access interfaces. In this Global Alliance for Genomics and Health project, we developed RNAget, an API for secure access to genomic quantification data in matrix form. RNAget provides for slicing matrices to extract desired subsets of data and is applicable to all expression matrix-format data, including RNA sequencing and microarrays. Further, it generalizes to quantification matrices of other sequence-based genomics such as ATAC-seq and ChIP-seq. AVAILABILITY AND IMPLEMENTATION: https://ga4gh-rnaseq.github.io/schema/docs/index.html.

bsAS, an antisense long non-coding RNA, essential for correct wing development through regulation of blistered/DSRF isoform usage.

Natural Antisense Transcripts (NATs) are long non-coding RNAs (lncRNAs) that overlap coding genes in the opposite strand. NATs roles have been related to gene regulation through different mechanisms, including post-transcriptional RNA processing. With the aim to identify NATs with potential regulatory function during fly development, we generated RNA-Seq data in Drosophila developing tissues and found bsAS, one of the most highly expressed lncRNAs in the fly wing. bsAS is antisense to bs/DSRF, a gene involved in wing development and neural processes. bsAS plays a crucial role in the tissue specific regulation of the expression of the bs/DSRF isoforms. This regulation is essential for the correct determination of cell fate during Drosophila development, as bsAS knockouts show highly aberrant phenotypes. Regulation of bs isoform usage by bsAS is mediated by specific physical interactions between the promoters of these two genes, which suggests a regulatory mechanism involving the collision of RNA polymerases transcribing in opposite directions. Evolutionary analysis suggests that bsAS NAT emerged simultaneously to the long-short isoform structure of bs, preceding the emergence of wings in insects.

LncATLAS database for subcellular localization of long noncoding RNAs.

The subcellular localization of long noncoding RNAs (lncRNAs) holds valuable clues to their molecular function. However, measuring localization of newly discovered lncRNAs involves time-consuming and costly experimental methods. We have created "lncATLAS," a comprehensive resource of lncRNA localization in human cells based on RNA-sequencing data sets. Altogether, 6768 GENCODE-annotated lncRNAs are represented across various compartments of 15 cell lines. We introduce relative concentration index (RCI) as a useful measure of localization derived from ensemble RNA-seq measurements. LncATLAS is accessible through an intuitive and informative webserver, from which lncRNAs of interest are accessed using identifiers or names. Localization is presented across cell types and organelles, and may be compared to the distribution of all other genes. Publication-quality figures and raw data tables are automatically generated with each query, and the entire data set is also available to download. LncATLAS makes lncRNA subcellular localization data available to the widest possible number of researchers. It is available at lncatlas.crg.eu.

ggsashimi: Sashimi plot revised for browser- and annotation-independent splicing visualization.

We present ggsashimi, a command-line tool for the visualization of splicing events across multiple samples. Given a specified genomic region, ggsashimi creates sashimi plots for individual RNA-seq experiments as well as aggregated plots for groups of experiments, a feature unique to this software. Compared to the existing versions of programs generating sashimi plots, it uses popular bioinformatics file formats, it is annotation-independent, and allows the visualization of splicing events even for large genomic regions by scaling down the genomic segments between splice sites. ggsashimi is freely available at https://github.com/guigolab/ggsashimi. It is implemented in python, and internally generates R code for plotting.

Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion.

CRISPR-Cas9 technology can be used to engineer precise genomic deletions with pairs of single guide RNAs (sgRNAs). This approach has been widely adopted for diverse applications, from disease modelling of individual loci, to parallelized loss-of-function screens of thousands of regulatory elements. However, no solution has been presented for the unique bioinformatic design requirements of CRISPR deletion. We here present CRISPETa, a pipeline for flexible and scalable paired sgRNA design based on an empirical scoring model. Multiple sgRNA pairs are returned for each target, and any number of targets can be analyzed in parallel, making CRISPETa equally useful for focussed or high-throughput studies. Fast run-times are achieved using a pre-computed off-target database. sgRNA pair designs are output in a convenient format for visualisation and oligonucleotide ordering. We present pre-designed, high-coverage library designs for entire classes of protein-coding and non-coding elements in human, mouse, zebrafish, Drosophila melanogaster and Caenorhabditis elegans. In human cells, we reproducibly observe deletion efficiencies of ≥50% for CRISPETa designs targeting an enhancer and exonic fragment of the MALAT1 oncogene. In the latter case, deletion results in production of desired, truncated RNA. CRISPETa will be useful for researchers seeking to harness CRISPR for targeted genomic deletion, in a variety of model organisms, from single-target to high-throughput scales.

ChimPipe: accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data.

BACKGROUND: Chimeric transcripts are commonly defined as transcripts linking two or more different genes in the genome, and can be explained by various biological mechanisms such as genomic rearrangement, read-through or trans-splicing, but also by technical or biological artefacts. Several studies have shown their importance in cancer, cell pluripotency and motility. Many programs have recently been developed to identify chimeras from Illumina RNA-seq data (mostly fusion genes in cancer). However outputs of different programs on the same dataset can be widely inconsistent, and tend to include many false positives. Other issues relate to simulated datasets restricted to fusion genes, real datasets with limited numbers of validated cases, result inconsistencies between simulated and real datasets, and gene rather than junction level assessment. RESULTS: Here we present ChimPipe, a modular and easy-to-use method to reliably identify fusion genes and transcription-induced chimeras from paired-end Illumina RNA-seq data. We have also produced realistic simulated datasets for three different read lengths, and enhanced two gold-standard cancer datasets by associating exact junction points to validated gene fusions. Benchmarking ChimPipe together with four other state-of-the-art tools on this data showed ChimPipe to be the top program at identifying exact junction coordinates for both kinds of datasets, and the one showing the best trade-off between sensitivity and precision. Applied to 106 ENCODE human RNA-seq datasets, ChimPipe identified 137 high confidence chimeras connecting the protein coding sequence of their parent genes. In subsequent experiments, three out of four predicted chimeras, two of which recurrently expressed in a large majority of the samples, could be validated. Cloning and sequencing of the three cases revealed several new chimeric transcript structures, 3 of which with the potential to encode a chimeric protein for which we hypothesized a new role. Applying ChimPipe to human and mouse ENCODE RNA-seq data led to the identification of 131 recurrent chimeras common to both species, and therefore potentially conserved. CONCLUSIONS: ChimPipe combines discordant paired-end reads and split-reads to detect any kind of chimeras, including those originating from polymerase read-through, and shows an excellent trade-off between sensitivity and precision. The chimeras found by ChimPipe can be validated in-vitro with high accuracy.

CapTrap-seq: a platform-agnostic and quantitative approach for high-fidelity full-length RNA sequencing.

Long-read RNA sequencing is essential to produce accurate and exhaustive annotation of eukaryotic genomes. Despite advancements in throughput and accuracy, achieving reliable end-to-end identification of RNA transcripts remains a challenge for long-read sequencing methods. To address this limitation, we develop CapTrap-seq, a cDNA library preparation method, which combines the Cap-trapping strategy with oligo(dT) priming to detect 5' capped, full-length transcripts. In our study, we evaluate the performance of CapTrap-seq alongside other widely used RNA-seq library preparation protocols in human and mouse tissues, employing both ONT and PacBio sequencing technologies. To explore the quantitative capabilities of CapTrap-seq and its accuracy in reconstructing full-length RNA molecules, we implement a capping strategy for synthetic RNA spike-in sequences that mimics the natural 5'cap formation. Our benchmarks, incorporating the Long-read RNA-seq Genome Annotation Assessment Project (LRGASP) data, demonstrate that CapTrap-seq is a competitive, platform-agnostic RNA library preparation method for generating full-length transcript sequences.

[Recent advances in the diagnosis of vesicoureteral reflux in children]. / Diagnosi di reflusso vescico-ureterale in età pediatrica.

Primary vesicoureteral reflux is a common congenital urinary tract abnormality in children. There is considerable controversy regarding its management. Preservation of kidney function is the main goal treatment, which necessitates identification of patients requiring early intervention. The aim of this review is to evidence the recent advances in the diagnosis of this congenital abnormality and to indicate the guidelines for its diagnostic management.

CapTrap-Seq: A platform-agnostic and quantitative approach for high-fidelity full-length RNA transcript sequencing.

Long-read RNA sequencing is essential to produce accurate and exhaustive annotation of eukaryotic genomes. Despite advancements in throughput and accuracy, achieving reliable end-to-end identification of RNA transcripts remains a challenge for long-read sequencing methods. To address this limitation, we developed CapTrap-seq, a cDNA library preparation method, which combines the Cap-trapping strategy with oligo(dT) priming to detect 5'capped, full-length transcripts, together with the data processing pipeline LyRic. We benchmarked CapTrap-seq and other popular RNA-seq library preparation protocols in a number of human tissues using both ONT and PacBio sequencing. To assess the accuracy of the transcript models produced, we introduced a capping strategy for synthetic RNA spike-in sequences that mimics the natural 5'cap formation in RNA spike-in molecules. We found that the vast majority (up to 90%) of transcript models that LyRic derives from CapTrap-seq reads are full-length. This makes it possible to produce highly accurate annotations with minimal human intervention.

Brain transcriptomic profiling reveals common alterations across neurodegenerative and psychiatric disorders.

Neurodegenerative and neuropsychiatric disorders (ND-NPs) are multifactorial, polygenic and complex behavioral phenotypes caused by brain abnormalities. Large-scale collaborative efforts have tried to identify the genetic architecture of these conditions. However, the specific and shared underlying molecular pathobiology of brain illnesses is not clear. Here, we examine transcriptome-wide characterization of eight conditions, using a total of 2,633 post-mortem brain samples from patients with Alzheimer's disease (AD), Parkinson's disease (PD), Progressive Supranuclear Palsy (PSP), Pathological Aging (PA), Autism Spectrum Disorder (ASD), Schizophrenia (Scz), Major Depressive Disorder (MDD), and Bipolar Disorder (BP)-in comparison with 2,078 brain samples from matched control subjects. Similar transcriptome alterations were observed between NDs and NPs with the top correlations obtained between Scz-BP, ASD-PD, AD-PD, and Scz-ASD. Region-specific comparisons also revealed shared transcriptome alterations in frontal and temporal lobes across NPs and NDs. Co-expression network analysis identified coordinated dysregulations of cell-type-specific modules across NDs and NPs. This study provides a transcriptomic framework to understand the molecular alterations of NPs and NDs through their shared- and specific gene expression in the brain.

[Kawasaki's syndrome: recent advances in diagnosis and therapy]. / La sindrome di Kawasaki: recenti progressi nella diagnosi e nella terapia.

Kawasaki disease is an autoimmune disease that manifests as a multisystemic necrotizing medium vessel vasculitis that is largely seen in children under 5 years of age. It affects many organs, including the skin, lymph nodes, and blood vessel walls, but the most serious effect is on the heart where it can cause severe aneurysmal dilations in untreated children. The aim of this paper is to evidence the recent advances in the diagnosis and therapy of this disease.

[Acute hemorrhagic syndrome by lupus anticoagulant]. / Sindrome emorragica acuta da lupus anticoagulant.

Antiphospholipid antibodies are correlated to antiphospholipid syndrome, that is characterized by one or more thrombotic episodes and obstetric complications. Some recent studies have evidenced as antiphospholipid antibodies can be correlated to an transitory hemorrhagic syndrome with prolonged aPTT. This syndrome compares 7-10 days after a bacterial or viral infection and it is characterized by a spontaneous regression into a period of three months. The aim of this paper is to evidence the pathogenesis and the clinical aspects of this syndrome.

Current treatment for cutaneous leishmaniasis: a review.

Cutaneous leishmaniasis is the most common form of leishmaniasis. It is a skin infection caused by a single-celled parasite that is transmitted by sand fly bites. There are about 20 species of Leishmania that may cause cutaneous leishmaniasis. Some Leishmania species are closely linked to humans and are therefore found in cities (Leishmania tropica), whereas some are more traditionally associated with animal species and are therefore considered zoonoses (Leishmania major). The evidence for optimal treatment of cutaneous leishmaniasis is patchy. Although the cutaneous form of the disease is often self-limiting, it does result in significant scarring and can spread to more invasive, mucocutaneous disease. Therefore, treatment may be considered to prevent these complications. Drugs for systemic and topical treatment are presented and discussed with regard to their application, use, and adverse effects.

PEG-interferon in acute and chronic hepatitis C: a review.

In patients affected by chronic hepatitis, prevention of hepatitis C virus (HCV) infection complications can be achieved by antiviral therapy based on the use of a combination of pegylated interferon (PEG-IFN) alfa-2b and ribavirin, which yields a sustained eradication of infection in 40% to 50% of cases. The aim of this review is to evaluate the efficacy of PEG-IFN alpha in the treatment of acute and chronic HCV-related hepatitis. In patients affected by acute hepatitis C, the treatment is represented by PEG-IFN alpha-2b monotherapy, and combination therapy with ribavirin produces a similar response to that with interferon monotherapy. Treatment must be started within 3 months of onset of infection (at the first evidence of HCV RNA positivity) and must be prolonged for 3 months for patients affected by genotypes 2 and 3 and for 6 months for patients with genotype 1 or 4. For patients affected by chronic hepatitis C, the first line of therapy is the combination PEG-IFN alpha-2a or alpha-2b and ribavirin. Treatment must be started only for patients with detectable serum HCV RNA and an alanine aminotransferase (ALT) value >80 IU/L (normal value, 40 UI/L); if serum HCV RNA is detectable but the ALT value is normal or <80 IU/L, the patient must be monitored every 6 months. In patients infected by genotypes 1 or 4, before treatment a histological evaluation is needed only for those aged >50 years. These patients can be treated if the infection stage is >/=2 according to the Knodell index. In patients aged <50 years, in my opinion, histological evaluation is not needed, because treatment must be started also for patients with stage 1 infection. The treatment must be prolonged for 1 year, but if after 3 months of therapy the patient is positive for serum HCV RNA, then therapy must be stopped and the patient is considered a nonresponder. In patients affected by genotypes 2 and 3, therapy must be prolonged for 6 months and a histological evaluation before treatment is not needed.

Treatment for chronic hepatitis C in children: a review.

The aim of this review was to evidence the actual treatment used for chronic hepatitis C virus (HCV) in children. A review of the use of interferon (IFN) as monotherapy in children demonstrates a sustained virological response (SVR) of 33%-45%. This is significantly better than the SVR rate for IFN monotherapy observed for adults. When the data are further scrutinized, the SVR for genotype 1 is 26% and 70% for other genotypes. The higher response rate observed in children might be the result of the earlier stage of the disease, higher relative IFN dosage, or lack of comorbid conditions. The use of IFN-alpha2b in combination with ribavirin was reported by Gonzalez-Peralta et al and has led to Food and Drug Administration approval of this therapy for children with a SVR significantly higher in children with HCV genotype 2/3 (84%) than in those with HCV genotype 1 (36%). About the use of pegylated IFN in combination with ribavirin, the first-line treatment in adult patients affected by chronic hepatitis C, there are few experiences. These preliminary experiences evidenced that combination treatment of PEG-IFN-alpha2b with ribavirin shows encouraging results and was well tolerated in children and adolescents with chronic hepatitis C.

Diagnosis of Henoch-Schonlein purpura in a child presenting with bilateral acute scrotum.

Schonlein-Henoch syndrome (HSP) is one of the manifestations of acute systemic vasculitis related to circulating immune complexes including IgA. It usually involves the kidney, gastrointestinal tract, joints and skin. Except for rare cases that progress to renal failure, it is a disease which heals without complications. The first case of male genital involvement in this syndrome was reported by Allen et al in 1960. Since then, several reports of this condition with an incidence of scrotal involvement varying from 2 to 38% have been described. The involvement of the male genitalia presenting as the only initial manifestation of SHS is so unusual that the diagnosis can easily be missed. In literature rare cases have been reported in which acute scrotum was the initial presenting symptom in patients affected by HSP. We report a case of HSP presenting as acute scrotum in a 5-year-old boy hospitalized for fever and viral bronchopneumonia.

Diarrhoea in children: aetiology and clinical aspects.

To determine the aetiology of diarrhoea in children younger than 5 years hospitalised for acute enteritis and to evidence the chief clinical aspects in correlation with different aetiological agents, a total of 402 children with acute diarrhoea were examined between February 2003 and December 2006 in the Paediatric Department of Sondrio Hospital. Faecal samples were collected and processed by routine microbiological and biochemical tests. For all patients the clinical signs and symptoms on admission were evidenced. Most of the patients (310/402, 77.1%) were infected by rotavirus, while of the remaining 82 (22.9%) 40 were infected by salmonella species. In 42 patients, no bacterial agent was evidenced by microbiological tests. Clinical signs of mild dehydration were observed in 13 children during the hospital stay (all infected by rotavirus), while no case of metabolic acidosis, hypoglycaemia or hypovolaemic shock was documented. Elevated serum levels of uric acid were evidenced in 13/302 (4.3%) of patients with rotavirus infection, while only 1/82 (1.2%) rotavirus-negative children presented a minimal increase in serum uric acid level. Our retrospective study confirms the epidemiological and clinical importance of rotavirus as the main aetiological agent in hospitalised children younger than 5 years affected by acute diarrhoea. There also emerged a possible correlation between rotavirus infection and hyperuricaemia, probably connected with dehydration.

[Dehydration in paediatric age: diagnosis and treatment]. / Disidratazione in età pediatrica: diagnosi e terapia.

Dehydration is the most common cause of hospitalization in paediatric age. The aim of this review is to evidence some parameters for a correct diagnosis and an effective treatment of dehydration in children.

The histone code reader PHD finger protein 7 controls sex-linked disparities in gene expression and malignancy in Drosophila.

The notable male predominance across many human cancer types remains unexplained. Here, we show that Drosophila l(3)mbt brain tumors are more invasive and develop as malignant neoplasms more often in males than in females. By quantitative proteomics, we have identified a signature of proteins that are differentially expressed between male and female tumor samples. Prominent among them is the conserved chromatin reader PHD finger protein 7 (Phf7). We show that Phf7 depletion reduces sex-dependent differences in gene expression and suppresses the enhanced malignant traits of male tumors. Our results identify potential regulators of sex-linked tumor dimorphism and show that these genes may serve as targets to suppress sex-linked malignant traits.