Endothelial, epithelial, and fibroblast cells exhibit specific splicing programs independently of their tissue of origin.

Alternative splicing is the main mechanism of increasing the proteome diversity coded by a limited number of genes. It is well established that different tissues or organs express different splicing variants. However, organs are composed of common major cell types, including fibroblasts, epithelial, and endothelial cells. By analyzing large-scale data sets generated by The ENCODE Project Consortium and after extensive RT-PCR validation, we demonstrate that each of the three major cell types expresses a specific splicing program independently of its organ origin. Furthermore, by analyzing splicing factor expression across samples, publicly available splicing factor binding site data sets (CLIP-seq), and exon array data sets after splicing factor depletion, we identified several splicing factors, including ESRP1 and 2, MBNL1, NOVA1, PTBP1, and RBFOX2, that contribute to establishing these cell type-specific splicing programs. All of the analyzed data sets are freely available in a user-friendly web interface named FasterDB, which describes all known splicing variants of human and mouse genes and their splicing patterns across several dozens of normal and cancer cells as well as across tissues. Information regarding splicing factors that potentially contribute to individual exon regulation is also provided via a dedicated CLIP-seq and exon array data visualization interface. To the best of our knowledge, FasterDB is the first database integrating such a variety of large-scale data sets to enable functional genomics analyses at exon-level resolution.

The Ddx5 and Ddx17 RNA helicases are cornerstones in the complex regulatory array of steroid hormone-signaling pathways.

Estrogen and androgen receptors (ER and AR) play key roles in breast and prostate cancers, respectively, where they regulate the transcription of large arrays of genes. The activities of ER and AR are controlled by large networks of protein kinases and transcriptional coregulators, including Ddx5 and its highly related paralog Ddx17. The Ddx5 and Ddx17 RNA helicases are also splicing regulators. Here, we report that Ddx5 and Ddx17 are master regulators of the estrogen- and androgen-signaling pathways by controlling transcription and splicing both upstream and downstream of the receptors. First, Ddx5 and Ddx17 are required downstream of ER and AR for the transcriptional and splicing regulation of a large number of steroid hormone target genes. Second, Ddx5 and Ddx17 act upstream of ER and AR by controlling the expression, at the splicing level, of several key regulators of ER and AR activities. Of particular interest, we demonstrate that Ddx5 and Ddx17 control alternative splicing of the GSK3ß kinase, which impacts on both ER and AR protein stability. We also provide a freely available online resource which gives information regarding splicing variants of genes involved in the estrogen- and androgen-signaling pathways.

The RNA helicase DDX5/p68 is a key factor promoting c-fos expression at different levels from transcription to mRNA export.

It is widely accepted that pre-mRNA maturation, including splicing, is tightly coupled to both transcription and mRNA export, but factors linking the three processes are less understood. By analysing the estrogen-regulated expression of the c-fos mRNA that is processed during transcription, we show that the ddx5 RNA helicase, is required throughout the major nuclear steps of the expression of the c-fos gene, from transcription to mRNA export. Indeed, ddx5, whose recruitment on the c-fos gene was increased upon estrogen treatment, was required for the full transcriptional activation of the c-fos gene. In addition, ddx5 was required for c-fos co-transcriptional RNA splicing. When splicing occurred post-transcriptionally in the absence of ddx5, the c-fos mRNA was poorly exported into the cytosol because of inefficient recruitment of the TAP mRNA export receptor. Finally, ddx5 was present in the c-fos messenger ribonucleoprotein together with mRNA export factors, which further supports that ddx5 is a key operator in the c-fos 'mRNA factory'.

Outcome of children treated with haematopoietic-stem cell transplantations from donors expressing the rare C77G variant of the PTPRC (CD45) gene.

The uncommon C77G polymorphism of the Protein-Tyrosine Phosphatase (PTPRC) gene (PTPRC; previously termed CD45) could confer an increased risk of immunopathology. This study compared the outcome of children following human leucocyte antigen-matched unrelated haematopoïetic-stem cell transplantations (HSCT) from donors carrying (C77G cases: n = 8) or not (controls: n = 36) the PTPRC C77G polymorphism. Transmission of the PTPRC C77G polymorphism through the graft was suggested by unusual CD45RA phenotype in the donors and/or in the recipients after, but not before HSCT. Restriction-Fragment Length Polymorphism and sequencing confirmed the polymorphism. Overall survival rates were similar in C77G cases and controls (63% vs. 61%). Acute leukaemia relapse tended to be less frequent in C77G cases (0% vs. 32%; P = 0·09). Among recipients surviving ≥ 30 d, acute GVHD (aGVHD) ≥ grade 2 tended to be more frequent (100% vs. 58%; P = 0·07) and the rate of steroid-refractory or -dependant aGVHD higher (67% vs. 28%) in C77G cases. Finally, extensive chronic GVHD tended to occur more frequently (40% vs. 9%) in C77G cases. Recovery of lymphocyte subsets and virus-specific CD4 was similar in C77G cases and controls while interleukin 2 (IL2)-responses through CD3 stimulation were higher in C77G cases (P = 0·004). In conclusion, HSCT from PTPRC C77G donors could increase GVHD risk without compromising overall survival. Altered IL2-responses could be involved in this process.

Heparin and aspirin in pregnant Sudanese women with recurrent miscarriage associated with antiphospholipid antibodies.

This was a prospective clinical trial conducted at Khartoum Fertility Center, during the period June 2002 to February 2005 to investigate the efficacy of unfractionated heparin and low-dose aspirin as prophylaxis against pregnancy loss in 58 pregnant Sudanese women with recurrent (> or = 3) miscarriages associated with antiphospholipid syndrome (APS). Three (5.1%) patients had early miscarriages, three (5.1%) patients developed pre-eclamptic toxaemia and forty-seven (81%) of the 58 patients had cesarean delivery. Forty-seven (81%) women had live births and 8 (13.8%) had preterm deliveries. Eight (13.8%) of the neonates were admitted to the intensive care unit for various reasons. There were 6 (10.3%) perinatal deaths, all of them were due to prematurity. None of the patients developed thromboembolic episode. There was no maternal death. The rate of live birth in this study was consistent with the previous reports. This was a none controlled study; thus controlled clinical trials using low molecular weight heparin are urgently needed.

RNA helicases DDX5 and DDX17 dynamically orchestrate transcription, miRNA, and splicing programs in cell differentiation.

The RNA helicases DDX5 and DDX17 are members of a large family of highly conserved proteins that are involved in gene-expression regulation; however, their in vivo targets and activities in biological processes such as cell differentiation, which requires reprogramming of gene-expression programs at multiple levels, are not well characterized. Here, we uncovered a mechanism by which DDX5 and DDX17 cooperate with heterogeneous nuclear ribonucleoprotein (hnRNP) H/F splicing factors to define epithelial- and myoblast-specific splicing subprograms. We then observed that downregulation of DDX5 and DDX17 protein expression during myogenesis and epithelial-to-mesenchymal transdifferentiation contributes to the switching of splicing programs during these processes. Remarkably, this downregulation is mediated by the production of miRNAs induced upon differentiation in a DDX5/DDX17-dependent manner. Since DDX5 and DDX17 also function as coregulators of master transcriptional regulators of differentiation, we propose to name these proteins "master orchestrators" of differentiation that dynamically orchestrate several layers of gene expression.

Estrogen regulation and physiopathologic significance of alternative promoters in breast cancer.

Alternative promoters (AP) occur in >30% protein-coding genes and contribute to proteome diversity. However, large-scale analyses of AP regulation are lacking, and little is known about their potential physiopathologic significance. To better understand the transcriptomic effect of estrogens, which play a major role in breast cancer, we analyzed gene and AP regulation by estradiol in MCF7 cells using pan-genomic exon arrays. We thereby identified novel estrogen-regulated genes (ERG) and determined the regulation of AP-encoded transcripts in 150 regulated genes. In <30% cases, APs were regulated in a similar manner by estradiol, whereas in >70% cases, they were regulated differentially. The patterns of AP regulation correlated with the patterns of estrogen receptor alpha (ERalpha) and CCCTC-binding factor (CTCF) binding sites at regulated gene loci. Interestingly, among genes with differentially regulated (DR) APs, we identified cases where estradiol regulated APs in an opposite manner, sometimes without affecting global gene expression levels. This promoter switch was mediated by the DDX5/DDX17 family of ERalpha coregulators. Finally, genes with DR promoters were preferentially involved in specific processes (e.g., cell structure and motility, and cell cycle). We show, in particular, that isoforms encoded by the NET1 gene APs, which are inversely regulated by estradiol, play distinct roles in cell adhesion and cell cycle regulation and that their expression is differentially associated with prognosis in ER(+) breast cancer. Altogether, this study identifies the patterns of AP regulation in ERGs and shows the contribution of AP-encoded isoforms to the estradiol-regulated transcriptome as well as their physiopathologic significance in breast cancer.

Niveles de hormona estimulante de tiroides en niños obesos sin patología tiroidea / Levels of thyroid stimulating hormone in obese children without thyroid disease

OBJETIVO: Identificar los niveles de Hormona estimulante de tiroides en niños obesos sin patología tiroidea que acuden al consultorio externo de Endocrinología del Instituto Nacional Salud Niño durante el 2010. METODOLOGÍA: Se revisó 1199 historias clínicas, seleccionando 156 pacientes por cumplir con los requerimientos del estudio. Se recolectó en una ficha clínica datos como el sexo, peso, edad, talla, perímetro abdominal, índice de masa corporal, TSH, T4 libre, niveles de insulina, glucosa basal y anticuerpos antitiroideos. Se excluyó niños con obesidad endógena, aquellos que usaban corticoide o fármacos que alteren la función tiroidea. Se exploró las diferencias del IMC, perímetro abdominal y resistencia a la insulina entre los pacientes obesos que presentaron niveles normales de TSH con los pacientes que presentaron TSH elevados.RESULTADOS: De los 156 obesos estudiados, 55 (35.3%) presentaron niveles elevados de TSH. El 81.8% de ellos, tuvo resistencia a la insulina, 94.5% un perímetro abdominal aumentado y un índice de masa corporal mayor que aquellos pacientes con valores adecuados de TSH. El valor máximo de TSH fue de 8.44uiU/ml. CONCLUSIONES: Los pacientes obesos con TSH elevado presentaron un perímetro abdominal, Índice de masa corporal y resistencia a la insulina mayor que aquellos pacientes obesos con valores adecuados de TSH.

OBJETIVE: Identify levels of thyroid-stimulating hormone, in obese children without thyroid disease. The study subjects were seen as outpatients at the Instituto Nacional Salud Niño during 2010. METHODS: We did a retrospective review of 1199 medical records, using only 156 of them. We collected data about sex, age, weight, size, body mass index, abdominal circumference, TSH levels, free T4 levels, thyroid antibodies, insulin levels and glucose levels. Exclusion criteria included endogenous obesity, use of corticoids, and use of medications that can interfere with the thyroid function. We explored the difference between normal and elevated TSH levels according to body mass index, abdominal circumference and insulin resistance. RESULTS: From the 156 patients, 55 obese children (35.3%) had elevated TSH values. 81.8% of them had insulin resistance, 94.5% had a big abdominal circumference and a higher body mass index (minimum BMI was 21.76Kg/m2, maximum BMI was 40.02Kg/m2 vs minimum BMI was 19.34Kg/m2, maximum BMI was 37.4Kg/m2) in comparison to obese patients with normal TSH values. The maximum value of TSH was 8.44uiU/ml.CONCLUSIONS: Patients with elevated TSH values had a bigger abdominal circumference, insulin resistance and a higher body mass index in comparison to the obese patients that had a normal TSH value.

Uso indebido de antibióticos en pacientes con diarrea aguda acuosa macroscopicamente que acuden a la Unidad de Rehidratación Oral del Instituto Nacional de Salud del Niño en el mes de Abril y Mayo del 2010 / Misuse of antibiotics in patients with acute watery diarrhea macroscopically attending Oral Rehydration Unit of the National Institute of Child Health in April and May 2010

Introducción: Los Virus son la principal causa de diarrea aguda acuosa en países desarrollados y en vías de desarrollo, siendo el rotavirus una causa significativa de morbimortalidad en niños peruanos. Su evolución es autolimitada y su tratamiento sólo debe enfocarse al control de la sintomatología y sus consecuencias. El uso indebido de los antibióticos ha traído consigo la resistencia bacteriana, y a pesar de eso, son muchas las personas que ante una infección, sin saber su origen, se automedican con antibióticos e incluso los aconsejan familiares o amigos y/o farmacéuticos. Objetivos: Demostrar el uso indebido de antibióticos en pacientes con diarrea aguda acuosa macroscópicamente en la Unidad de Rehidratación Oral del Instituto Nacional de Salud del Niño en Abril y Mayo del 2010. Métodos: Descriptivo y prospectivo con una duración de dos meses y una muestra de 300 pacientes recién nacidos hasta los 17 años de edad con diagnóstico de diarrea acuosa. Se entrevistó mediante una ficha clínica al familiar responsable del paciente que se encuentren en la Unidad de Rehidratación Oral del Instituto Nacional de Salud del Niño durante el mes de Abril y Mayo del 2010. Para analizar datos se utilizó medidas descriptivas univariadas y bivariadas. Para procesamiento de datos se utilizó Software Estadístico SPSS 15.0. Los resultados fueron expresados mediante frecuencia, porcentajes, tablas doble entrada, gráficos, barras y circulares. Resultados: De un total de 300 pacientes, 128 (42.7 por ciento) hicieron uso indebido de antibióticos ante el cuadro de diarrea aguda acuosa y macroscópica...