Post-transcriptional knowledge in pathway analysis increases the accuracy of phenotypes classification

Motivation: Prediction of phenotypes from high-dimensional data is a crucial task in precision biology and medicine. Many technologies employ genomic biomarkers to characterize phenotypes. However, such elements are not sufficient to explain the underlying biology. To improve this, pathway analysis techniques have been proposed. Nevertheless, such methods have shown lack of accuracy in phenotypes classification. Results: Here we propose a novel methodology called MITHrIL (Mirna enrIched paTHway Impact anaLysis) for the analysis of signaling pathways, which has built on top of the work of Tarca et al., 2009. MITHrIL extends pathways by adding missing regulatory elements, such as microRNAs, and their interactions with genes. The method takes as input the expression values of genes and/or microRNAs and returns a list of pathways sorted according to their deregulation degree, together with the corresponding statistical significance (p-values). Our analysis shows that MITHrIL outperforms its competitors even in the worst case. In addition, our method is able to correctly classify sets of tumor samples drawn from TCGA. Availability: MITHrIL is freely available at the following URL: http://alpha.dmi.unict.it/mithril

Activation of the Erk8 Mitogen-activated Protein (MAP) Kinase by RET/PTC3, a Constitutively Active Form of the RET Proto-oncogene

Mitogen-activated protein (MAP) kinases have a central role in several biological functions, including cell adhesion and spreading, chemotaxis, cell cycle progression, differentiation, and apoptosis. Extracellular signal-regulated kinase 8 (Erk8) is a large MAP kinase whose activity is controlled by serum and the c-Src non-receptor tyrosine kinase. Here, we show that RET/PTC3, an activated form of the RET proto-oncogene, was able to activate Erk8, and we demon- strate that such MAP kinase participated in RET/PTC3-dependent stimulation of the c-jun promoter. By using RET/PTC3 molecules mutated in specific tyrosine autophosphorylation sites, we charac- terized Tyr981, a known binding site for c-Src, as a major determi- nant of RET/PTC3-induced Erk8 activation, although, surprisingly, the underlying mechanism did not strictly depend on the activity of Src. In contrast, we present evidence that RET/PTC3 acts on Erk8 through Tyr981-mediated activation of c-Abl. Furthermore, we localized the region responsible for the modulation of Erk8 activity by the RET/PTC3 and Abl oncogenes in the Erk8 C-terminal domain. Altogether, these results support a role for Erk8 as a novel effector of RET/PTC3 and, therefore, RET biological functions

The Platelet-derived Growth Factor Controls c-myc Expression through a JNK- and AP-1-dependent Signaling Pathway *

Pro-inflammatory cytokines, environmental stresses, as well as receptor tyrosine kinases regulate the activity of JNK. In turn, JNK phosphorylates Jun members of the AP-1 family of transcription factors, thereby controlling processes as different as cell growth, differentiation, and apoptosis. Still, very few targets of the JNK-Jun pathway have been identified. Here we show that JNK is required for the induction of c-myc expression by PDGF. Furthermore, we identify a phylogenetically conserved AP-1-responsive element in the promoter of the c-myc proto-oncogene that recruits in vivo the c-Jun and JunD AP-1 family members and controls the PDGF-dependent transactivation of the c-myc promoter. These findings suggest the existence of a novel biochemical route linking tyrosine kinase receptors, such as those for PDGF, and c-myc expression through JNK activation of AP-1 transcription factors. They also provide a novel potential mechanism by which both JNK and Jun proteins may exert either their proliferative or apoptotic potential by stimulating the expression of the c-myc proto-oncogene

Akt Regulates Drug-Induced Cell Death through Bcl-w Downregulation

Akt is a serine threonine kinase with a major role in transducing survival signals and regulating proteins involved in apoptosis. To find new interactors of Akt involved in cell survival, we performed a two-hybrid screening in yeast using human full-length Akt c-DNA as bait and a murine c-DNA library as prey. Among the 80 clones obtained, two were identified as Bcl-w. Bcl-w is a member of the Bcl-2 family that is essential for the regulation of cellular survival, and that is up-regulated in different human tumors, such as gastric and colorectal carcinomas. Direct interaction of Bcl-w with Akt was confirmed by immunoprecipitation assays. Subsequently, we addressed the function of this interaction: by interfering with the activity or amount of Akt, we have demonstrated that Akt modulates the amount of Bcl-w protein. We have found that inhibition of Akt activity may promote apoptosis through the downregulation of Bcl-w protein and the consequential reduction in interaction of Bcl-w with pro-apoptotic members of the Bcl-2 family. Our data provide evidence that Bcl-w is a new member of the Akt pathway and that Akt may induce anti-apoptotic signals at least in part through the regulation of the amount and activity of Bcl-w

Subaortic and mid-ventricular obstructive hypertrophic cardiomyopathy with an apical Aneurysm: a case report

BACKGROUND: Most patients with hypertrophic cardiomyopathy (HCM) have asymmetric septal hypertrophy and among them, 25% present dynamic subaortic obstruction. Apical HCM is unusual and mid-ventricular HCM is the most infrequent presentation, but both variants may be associated to an apical aneurysm. An even more rare presentation is the coexistece mid-ventricular and apical HCM. This case is a combination of obstructive HCM with mid-ventricular HCM and an apical aneurysm, which to date, has not been reported in the literature. CASE PRESENTATION: The patient is a 49 year-old lady who presents a combination of septal asymmetric hypertrophic cardiomyopathy (HCM) and midventricular HCM, a subaortic gradient of 65 mm Hg and a midventricular gradient of 20 mm Hg, plus an apical aneurysm. Her clinical presentation was an acute myocardial infarction in June 2005. One month after hospital discharge, the electrocardiogram (ECG) showed a right bundle branch block (RBBB) with no Q waves or ST segment elevation. Coronary angiography revealed normal coronary arteries, left ventricular hypertrophy and an apical aneurysm. CONCLUSION: This case is a rare example of an asymptomatic patient with subaortic and mid-ventricular hypertrophic cardiomyopathy, who presents a myocardial infarction and normal coronary arteries, and during the course of her disease develops an apical aneurysm

Prevalence of Early B-Cell Factor 1 Gene rs4704963 Single Nucleotide Polymorphism (T>C) in a Population of Type 2 Diabetic Patients with Obesity

Introducción: En estudios previos, se determinó para una población con agravamiento de la diabetes tipo 2 con obesidad (DBT+Ob) que sufría estrés una prevalencia del polimorfismo de nucleótido único (SNP) rs4704963 (T > C) del gen Early B-Cell Factor 1 (EBF1) del 16,5%. Objetivos: Determinar la prevalencia de este SNP en pacientes con DBT+ Ob que acuden al Hospital Ramos Mejía de la Ciudad Autónoma de Buenos .Aires y establecer si dicho polimorfismo se asocia con el estrés o la ocurrencia de eventos coronarios agudos. Material y métodos: Se llevó a cabo un estudio observacional, prospectivo, sobre prevalencia del polimorfismo en 53 pacientes con DBT+Ob e índice de masa corporal (IMC) entre 28 y 41, atendidos en el citado hospital en un período de 15 meses. A cada paciente se le computó una escala de estrés percibido, además de evaluarlo mediante la escala de acontecimientos vitales estresantes. Para el análisis estadístico, se realizaron las pruebas de Chi cuadrado y se calcularon los odds ratio (OR). Resultados: La población evaluada (53 pacientes) tuvo una media de edad de 60,2 ±9,77 años; 47,2% fueron hombres. De ellos, 8 individuos (15,1%) presentaron el SNP y todos fueron heterocigotas. Quince sujetos (28,3%) tuvieron síndrome isquémico agudo (SIA) y de estos solo uno (6,6%) tenía el SNP. No se halló relación estadísticamente significativa entre la presencia del SNP y la aparición de SIA (p = 0,282). Catorce pacientes (26,4%) presentaron estrés crónico moderado o grave, y no hubo relación entre este hallazgo y la presencia del SNP (p = 0,979). Conclusiones: La prevalencia del SNP rs4704963 (T > C) del gen EBF1 en la población de DBT+Ob estudiada fue del 15,1% y no se halló relación estadísticamente significativa del SNP con el estrés ni con el SIA.Background: Previous studies established that in a population with exacerbation of type 2 diabetes with obesity (DBT+Ob) suffering from stress, the prevalence of early B-Cell Factor 1 (EBF1) gene rs4704963 single nucleotide polymorphism (SNP) (T>C) is 16.5%. Objectives: The aim of this study was to determine the prevalence of this SNP in patients with DBT+Ob attending Hospital Ramos Mejía of the Autonomous City of Buenos Aires and to ascertain whether this polymorphism is associated with stress or acute coronary events. Methods: An observational, prospective study on the prevalence of rs4704963 SNP was performed in 53 patients with DBT+Ob and body mass index between 28 and 41, seen in Hospital Ramos Mejía for a period of 15 months. Each patient was evaluated with a stressful life events scale and a perceived stress scale. The chi-square test and odds ratio (OR) were used for statistical analysis. Results: A total of 53 patients were included in the study. Mean population age was 60.2±9.77 years and 47.2% were men. Among these patients, 8 (15.1%) presented SNP and all were heterozygous. Fifteen patients (28.3%) had acute ischemic syndrome (AIS), and among these, only one (6.6%) had SNP. No statistically significant relationship was found between the presence of SNP and AIS (p=0.282). Fourteen patients (26.4%) presented moderate or severe chronic stress, and there was no relationship between this finding and the presence of SNP (p=0.979). Conclusions: The prevalence of EBF1 gene rs4704963 SNP (T>C) in the DBT+Ob population was 15.1%. No statistically significant association was found between SNP and stress or AIS.Fil: Principato, Mario. Gobierno de la Ciudad de Buenos Aires. Hospital General de Agudos "Ramos Mejía"; ArgentinaFil: Castilla Lozano, Maria del Rocio. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Cardiológicas. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Cardiológicas; ArgentinaFil: Duarte, Alejandra Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Medicina Experimental. Academia Nacional de Medicina de Buenos Aires. Instituto de Medicina Experimental; ArgentinaFil: Bragagnolo, Julio César. Gobierno de la Ciudad de Buenos Aires. Hospital General de Agudos "Ramos Mejía"; ArgentinaFil: Ortensi, Graciela. Gobierno de la Ciudad de Buenos Aires. Hospital General de Agudos "Ramos Mejía"; ArgentinaFil: Von Wulffen, María Alejandra. Gobierno de la Ciudad de Buenos Aires. Hospital General de Agudos "Ramos Mejía"; ArgentinaFil: Carbajales, Justo. Gobierno de la Ciudad de Buenos Aires. Hospital General de Agudos "Ramos Mejía"; ArgentinaFil: Acunzo, Rafael Salvador. Gobierno de la Ciudad de Buenos Aires. Hospital General de Agudos "Ramos Mejía"; Argentin

A plasma miRNA-based classifier for small cell lung cancer diagnosis

IntroductionSmall cell lung cancer (SCLC) is characterized by poor prognosis and challenging diagnosis. Screening in high-risk smokers results in a reduction in lung cancer mortality, however, screening efforts are primarily focused on non-small cell lung cancer (NSCLC). SCLC diagnosis and surveillance remain significant challenges. The aberrant expression of circulating microRNAs (miRNAs/miRs) is reported in many tumors and can provide insights into the pathogenesis of tumor development and progression. Here, we conducted a comprehensive assessment of circulating miRNAs in SCLC with a goal of developing a miRNA-based classifier to assist in SCLC diagnoses.MethodsWe profiled deregulated circulating cell-free miRNAs in the plasma of SCLC patients. We tested selected miRNAs on a training cohort and created a classifier by integrating miRNA expression and patients’ clinical data. Finally, we applied the classifier on a validation dataset.ResultsWe determined that miR-375-3p can discriminate between SCLC and NSCLC patients, and between SCLC and Squamous Cell Carcinoma patients. Moreover, we found that a model comprising miR-375-3p, miR-320b, and miR-144-3p can be integrated with race and age to distinguish metastatic SCLC from a control group.DiscussionThis study proposes a miRNA-based biomarker classifier for SCLC that considers clinical demographics with specific cut offs to inform SCLC diagnosis

MicroRNA profiles discriminate among colon cancer metastasis

MicroRNAs are being exploited for diagnosis, prognosis and monitoring of cancer and other diseases. Their high tissue specificity and critical role in oncogenesis provide new biomarkers for the diagnosis and classification of cancer as well as predicting patients' outcomes. MicroRNAs signatures have been identified for many human tumors, including colorectal cancer (CRC). In most cases, metastatic disease is difficult to predict and to prevent with adequate therapies. The aim of our study was to identify a microRNA signature for metastatic CRC that could predict and differentiate metastatic target organ localization. Normal and cancer tissues of three different groups of CRC patients were analyzed. RNA microarray and TaqMan Array analysis were performed on 66 Italian patients with or without lymph nodes and/or liver recurrences. Data obtained with the two assays were analyzed separately and then intersected to identify a primary CRC metastatic signature. Five differentially expressed microRNAs (hsa-miR-21, -103, -93, -31 and -566) were validated by qRT-PCR on a second group of 16 American metastatic patients. In situ hybridization was performed on the 16 American patients as well as on three distinct commercial tissues microarray (TMA) containing normal adjacent colon, the primary adenocarcinoma, normal and metastatic lymph nodes and liver. Hsa-miRNA-21, -93, and -103 upregulation together with hsa-miR-566 downregulation defined the CRC metastatic signature, while in situ hybridization data identified a lymphonodal invasion profile. We provided the first microRNAs signature that could discriminate between colorectal recurrences to lymph nodes and liver and between colorectal liver metastasis and primary hepatic tumor