Publications by authors named "Emilio Palumbo"

50 Publications

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

PLoS Genet 2020 12 28;16(12):e1009245. Epub 2020 Dec 28.

Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona (BIST), Catalonia, Spain.

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.
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http://dx.doi.org/10.1371/journal.pgen.1009245DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7793246PMC
December 2020

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

Sci Adv 2019 08 14;5(8):eaaw7965. Epub 2019 Aug 14.

IRB Barcelona, BIST, Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain.

The notable male predominance across many human cancer types remains unexplained. Here, we show that 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 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.
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http://dx.doi.org/10.1126/sciadv.aaw7965DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6693905PMC
August 2019

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

PLoS Comput Biol 2018 08 17;14(8):e1006360. Epub 2018 Aug 17.

Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.

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.
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http://dx.doi.org/10.1371/journal.pcbi.1006360DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6114895PMC
August 2018

The reference epigenome and regulatory chromatin landscape of chronic lymphocytic leukemia.

Nat Med 2018 06 21;24(6):868-880. Epub 2018 May 21.

Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.

Chronic lymphocytic leukemia (CLL) is a frequent hematological neoplasm in which underlying epigenetic alterations are only partially understood. Here, we analyze the reference epigenome of seven primary CLLs and the regulatory chromatin landscape of 107 primary cases in the context of normal B cell differentiation. We identify that the CLL chromatin landscape is largely influenced by distinct dynamics during normal B cell maturation. Beyond this, we define extensive catalogues of regulatory elements de novo reprogrammed in CLL as a whole and in its major clinico-biological subtypes classified by IGHV somatic hypermutation levels. We uncover that IGHV-unmutated CLLs harbor more active and open chromatin than IGHV-mutated cases. Furthermore, we show that de novo active regions in CLL are enriched for NFAT, FOX and TCF/LEF transcription factor family binding sites. Although most genetic alterations are not associated with consistent epigenetic profiles, CLLs with MYD88 mutations and trisomy 12 show distinct chromatin configurations. Furthermore, we observe that non-coding mutations in IGHV-mutated CLLs are enriched in H3K27ac-associated regulatory elements outside accessible chromatin. Overall, this study provides an integrative portrait of the CLL epigenome, identifies extensive networks of altered regulatory elements and sheds light on the relationship between the genetic and epigenetic architecture of the disease.
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http://dx.doi.org/10.1038/s41591-018-0028-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6363101PMC
June 2018

[Nextflow, an efficient tool to improve computation numerical stability in genomic analysis].

Biol Aujourdhui 2017 7;211(3):233-237. Epub 2018 Feb 7.

Comparative Bioinformatics Group, Bioinformatics and Genomics Programme, Center for Genomic Regulation (CRG), Dr Aiguader, 88, 08003 Barcelona, Spain - Universitat Pompeu Fabra (UPF), Barcelona, Spain.

Reproducing routine bioinformatics analysis is challenging owing to a combination of factors hard to control for. Nextflow is a flow management framework that uses container technology to insure efficient deployment and reproducibility of computational analysis pipelines. Third party pipelines can be ported into Nextflow with minimum re-coding. We used RNA-Seq quantification, genome annotation and phylogeny reconstruction examples to show how two seemingly irreproducible analyzes can be made stable across platforms when ported into Nextflow.
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http://dx.doi.org/10.1051/jbio/2017029DOI Listing
August 2018

Nextflow enables reproducible computational workflows.

Nat Biotechnol 2017 04;35(4):316-319

Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.

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http://dx.doi.org/10.1038/nbt.3820DOI Listing
April 2017

LncATLAS database for subcellular localization of long noncoding RNAs.

RNA 2017 07 6;23(7):1080-1087. Epub 2017 Apr 6.

Department of Clinical Research, University of Bern, 3008 Bern, Switzerland.

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.
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http://dx.doi.org/10.1261/rna.060814.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5473142PMC
July 2017

Brain Transcriptome Sequencing of a Natural Model of Alzheimer's Disease.

Front Aging Neurosci 2017 20;9:64. Epub 2017 Mar 20.

Laboratory of Molecular Neuropsychiatry, Institute of Cognitive and Translational Neuroscience (INCyT), INECO Foundation, Favaloro University, National Scientific and Technical Research CouncilBuenos Aires, Argentina; GeN.DDI LtdLondon, UK.

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http://dx.doi.org/10.3389/fnagi.2017.00064DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5357652PMC
March 2017

Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion.

PLoS Comput Biol 2017 03 2;13(3):e1005341. Epub 2017 Mar 2.

Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, Spain.

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.
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http://dx.doi.org/10.1371/journal.pcbi.1005341DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5333799PMC
March 2017

Discovery of Cancer Driver Long Noncoding RNAs across 1112 Tumour Genomes: New Candidates and Distinguishing Features.

Sci Rep 2017 01 27;7:41544. Epub 2017 Jan 27.

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain.

Long noncoding RNAs (lncRNAs) represent a vast unexplored genetic space that may hold missing drivers of tumourigenesis, but few such "driver lncRNAs" are known. Until now, they have been discovered through changes in expression, leading to problems in distinguishing between causative roles and passenger effects. We here present a different approach for driver lncRNA discovery using mutational patterns in tumour DNA. Our pipeline, ExInAtor, identifies genes with excess load of somatic single nucleotide variants (SNVs) across panels of tumour genomes. Heterogeneity in mutational signatures between cancer types and individuals is accounted for using a simple local trinucleotide background model, which yields high precision and low computational demands. We use ExInAtor to predict drivers from the GENCODE annotation across 1112 entire genomes from 23 cancer types. Using a stratified approach, we identify 15 high-confidence candidates: 9 novel and 6 known cancer-related genes, including MALAT1, NEAT1 and SAMMSON. Both known and novel driver lncRNAs are distinguished by elevated gene length, evolutionary conservation and expression. We have presented a first catalogue of mutated lncRNA genes driving cancer, which will grow and improve with the application of ExInAtor to future tumour genome projects.
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http://dx.doi.org/10.1038/srep41544DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5269722PMC
January 2017

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

BMC Genomics 2017 01 3;18(1). Epub 2017 Jan 3.

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.

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.
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http://dx.doi.org/10.1186/s12864-016-3404-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5209911PMC
January 2017

The impact of Docker containers on the performance of genomic pipelines.

PeerJ 2015 24;3:e1273. Epub 2015 Sep 24.

Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG) , Barcelona , Spain ; Universitat Pompeu Fabra (UPF) , Barcelona , Spain.

Genomic pipelines consist of several pieces of third party software and, because of their experimental nature, frequent changes and updates are commonly necessary thus raising serious deployment and reproducibility issues. Docker containers are emerging as a possible solution for many of these problems, as they allow the packaging of pipelines in an isolated and self-contained manner. This makes it easy to distribute and execute pipelines in a portable manner across a wide range of computing platforms. Thus, the question that arises is to what extent the use of Docker containers might affect the performance of these pipelines. Here we address this question and conclude that Docker containers have only a minor impact on the performance of common genomic pipelines, which is negligible when the executed jobs are long in terms of computational time.
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http://dx.doi.org/10.7717/peerj.1273DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4586803PMC
September 2015

Transcriptional diversity during lineage commitment of human blood progenitors.

Science 2014 Sep;345(6204):1251033

Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom.

Blood cells derive from hematopoietic stem cells through stepwise fating events. To characterize gene expression programs driving lineage choice, we sequenced RNA from eight primary human hematopoietic progenitor populations representing the major myeloid commitment stages and the main lymphoid stage. We identified extensive cell type-specific expression changes: 6711 genes and 10,724 transcripts, enriched in non-protein-coding elements at early stages of differentiation. In addition, we found 7881 novel splice junctions and 2301 differentially used alternative splicing events, enriched in genes involved in regulatory processes. We demonstrated experimentally cell-specific isoform usage, identifying nuclear factor I/B (NFIB) as a regulator of megakaryocyte maturation-the platelet precursor. Our data highlight the complexity of fating events in closely related progenitor populations, the understanding of which is essential for the advancement of transplantation and regenerative medicine.
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http://dx.doi.org/10.1126/science.1251033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4254742PMC
September 2014

[Recent advances in the diagnosis of vesicoureteral reflux in children].

Authors:
Emilio Palumbo

Recenti Prog Med 2013 Nov;104(11):585-9

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.
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http://dx.doi.org/10.1701/1370.15229DOI Listing
November 2013

[Kawasaki's syndrome: recent advances in diagnosis and therapy].

Authors:
Emilio Palumbo

Recenti Prog Med 2010 Sep;101(9):355-8

Reparto di Pediatria, Ospedale Civile, Sondrio.

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.
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September 2010

Pegylated interferon and ribavirin treatment for hepatitis C virus infection.

Authors:
Emilio Palumbo

Ther Adv Chronic Dis 2011 Jan;2(1):39-45

In patients affected by chronic hepatitis C (CHC) infection, viral eradication can be achieved by antiviral therapy based on the use of a combination of pegylated interferon α-2a or 2b and ribavirin that yields a sustained eradication in 40-50% of cases. The aim of this review is to evaluate the efficacy of pegylated interferon α-2a or α-2b plus ribavirin in the treatment of CHC infection. Treatment must be started in patients with detectable serum hepatitis C virus (HCV) RNA independently by serum alanine aminotransferase levels. In patients infected with genotype 1 or 4 HCV before treatment, a histological evaluation is required. These patients can be treated if stage is ≥2 according to the Knodell index. The treatment must be for 1 year duration and current guidelines allow treatment to be continued if patients remain HCV RNA positive at week 12 if a 2-log drop in viral load has been achieved. In patients with genotype 2 or 3 HCV, therapy must be prolonged for 6 months and histological evaluation pretreatment is not necessary.
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http://dx.doi.org/10.1177/2040622310384308DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3513870PMC
January 2011

Treatment strategies for mucocutaneous leishmaniasis.

Authors:
Emilio Palumbo

J Glob Infect Dis 2010 May;2(2):147-50

Department of Pediatric, Hospital of Sondrio, Italy.

Mucocutaneous is an infection caused by a single celled parasite transmitted by sand fly bites. There are about 20 species of Leishmania that may cause mucocutaneous leishmaniasis. Some Leishmania species are closely linked to humans and are therefore found in cities (L. tropica) whereas some others are more traditionally associated with animal species and therefore considered zoonoses (L. major). The evidence for optimal treatment of mucocutaneous 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.
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http://dx.doi.org/10.4103/0974-777X.62879DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889654PMC
May 2010

[Acute hemorrhagic syndrome by lupus anticoagulant].

Authors:
Emilio Palumbo

Recenti Prog Med 2010 May;101(5):199-201

Reparto di Pediatria e Patologia Neonatale, Ospedale Civile, San Benedetto del Tronto.

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.
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May 2010

[Dehydration in paediatric age: diagnosis and treatment].

Authors:
Emilio Palumbo

Recenti Prog Med 2009 Sep;100(9):414-6

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.
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September 2009

Diarrhoea in children: aetiology and clinical aspects.

Infez Med 2009 Jun;17(2):95-9

Clinica Pediatrica, Ospedale di Sondrio, Italy.

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.
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June 2009

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

Authors:
Emilio Palumbo

Am J Ther 2009 Nov-Dec;16(6):573-8

Clinic of Pediatric, Hospital of Sondrio, Italy.

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.
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http://dx.doi.org/10.1097/MJT.0b013e3181960819DOI Listing
February 2010

Current treatment for cutaneous leishmaniasis: a review.

Authors:
Emilio Palumbo

Am J Ther 2009 Mar-Apr;16(2):178-82

Department of Pediatric, Hospital of Sondrio, Foggia, Italy.

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.
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http://dx.doi.org/10.1097/MJT.0b013e3181822e90DOI Listing
May 2009

Treatment for chronic hepatitis C in children: a review.

Authors:
Emilio Palumbo

Am J Ther 2009 Sep-Oct;16(5):446-50

Department of Pediatric, Hospital of Sondrio, Sondrio, Italy.

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.
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http://dx.doi.org/10.1097/MJT.0b013e31818a88c5DOI Listing
February 2010

Lamivudine for chronic hepatitis B: a brief review.

Authors:
Emilio Palumbo

Braz J Infect Dis 2008 Oct;12(5):355-7

Pediatrics Department, Sondrio Hospital, Italy.

Until recently, the only generally approved treatment for chronic hepatitis B was alpha-interferon; however, it gives only moderate efficacy in terms of sustained response (biochemical, virological and histological). In fact, only 20% to 40% of treated patients respond to therapy, with lower percentages (~ 10%) among patients infected with precore-mutant strains of HBV (HBeAb HBV-DNA positive). The FDA of the USA approved the use of lamivudine in adult patients affected by chronic hepatitis B in 1998. In this review, we focused on the pharmacokinetic and pharmacodynamic properties and efficacy and tolerability of lamivudine in the treatment of chronic hepatitis B cases that are both HBeAg and anti-HBe-positive.
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http://dx.doi.org/10.1590/s1413-86702008000500002DOI Listing
October 2008

[Wilson's disease in paediatric age: diagnosis and treatment. Recent advances].

Authors:
Emilio Palumbo

Recenti Prog Med 2008 Nov;99(11):561-4

Reparto di Pediatria, Ospedale, Sondrio.

Wilson's disease is an autosomal-recessive disorder caused by mutation in the ATP7B gene, with resultant impairment of biliary excretion of copper. Subsequent copper accumulation, first in the liver but ultimately in the brain and other tissues, produces clinical manifestations that may include hepatic, neurological, psychiatric, ophthalmological, and other derangements. This article discusses the recent progress in diagnosis and treatment of this disease in paediatric age.
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November 2008

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

Authors:
Emilio Palumbo

Acta Biomed 2009 ;80(3):289-91

Department of Pediatrics, Hospital of Sondrio, Italy.

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.
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August 2010

Filariasis: diagnosis, treatment and prevention.

Authors:
Emilio Palumbo

Acta Biomed 2008 Aug;79(2):106-9

Department of Pediatrics, Hospital of Sondrio, Sondrio Italy.

Lymphatic filariasis caused by the mosquitoborne, lymphatic-dwelling nematodes Wuchereria bancrofti and Brigia malayi is still a common tropical parasitic disease and 120 million people are affected in the world, of which two-third in Asia. W. bancrofti is responsible for 90% of this disease, while B. malayi for the remaining 10%. Next to psychiatric illness, this is the leading cause for permanent and long-term disability. Some recent studies have evidenced new aspects in the diagnosis, management and in planning effective strategies for its global prevention. The aim of this up to date is to evidence clinical, diagnostic and therapeutic aspects of this very important infection.
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August 2008

[Mycoplasma pneumoniae encephalitis in immunocompetent child].

Recenti Prog Med 2008 Jun;99(6):306-8

Reparto di Pediatria, Ospedale Civile, Sondrio.

Mycoplasma pneumoniae is a common cause of community-acquired pneumonia, but this organism can also affect almost every organ system besides the lung. Neurological manifestations (meningitis, encephalitis, transverse myelitis, Guillain-Barrè syndrome) are the most frequent extrapulmonary complications of Mycoplasma pneumoniae. We report a case of a immunocompetent child affected by encephalitis caused by Mycoplasma pneumoniae.
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June 2008

Immune thrombocytopenic purpura as a complication of Bartonella henselae infection.

Infez Med 2008 Jun;16(2):99-102

Dipartimento di Pediatria, Ospedale di Sondrio, Sondrio, Italy.

Immune thrombocytopenic purpura is an infrequent yet well-recognized complication of viral infections, such as mumps, rubella, varicella, cytomegalovirus, parvovirus and infectious monunucleosis by Epstein-Barr virus. Some recent studies have described a possible association between Henoch-Schonlein purpura, a non-thrombocytopenic purpura, and seropositivity for Bartonella henselae, but in the literature only sporadic case reports have described a severe immune thrombocytopenic purpura as a complication of Bartonella henselae infection. We report a case of an immunocompetent child with clinical and serological evidence of Bartonella henselae infection presenting with purpura and cervical lymphoadenopathy and treated with intravenous immunoglobulin. The patient obtained a rapid and persistent increase in platelet count and a complete regression of purpura.
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June 2008

[Neonatal diagnosis of primary ciliary dyskinesia. Recent advances].

Authors:
Emilio Palumbo

Recenti Prog Med 2008 Apr;99(4):207-9

Primary ciliary dyskinesia is a rare, autosomal recessive genetic disease resulting of an abnormal ultrastructural morphology of cilia. Such disease is rarely recognized in neonatal period. Recently, unexplained neonatal respiratory distress has been found to be a common clinical presentation of patients with primary ciliary dyskinesia, indicating that this is an important symptom in early life for this condition. The diagnosis requires a high index of suspicion, but this disease must be considered in any newborn at term who develops unexplained respiratory distress, particularly when situs viscerum inversus is present.
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April 2008