Detection of rare and novel EGFR mutations in NSCLC patients: Implications for treatment-decision.

OBJECTIVES: Mutations in the gene that encodes epidermal growth factor receptor (EGFR) are biomarkers that predict how non-small cell lung cancer (NSCLC) patients respond to EGFR-targeted therapies collectively known as tyrosine kinase inhibitors (TKIs). Thus, EGFR genotyping provides crucial information for treatment decision. Both Sanger sequencing and real-time PCR methodologies are used for EGFR genotyping. However, methods based on real-time PCR have limitations, as they may not detect rare or novel mutations. The aim of this study was to determine the prevalence of rare mutations in the tyrosine kinase domain (exons 18-21) of the EGFR gene not targeted by the most frequently used real-time PCR approaches, i.e., the cobas® EGFR Mutation Test, and the Idylla™ EGFR Mutation Assay. METHODS: A total of 1228 NSCLC patients were screened for mutations in exons 18-21 of the EGFR gene using Sanger sequencing. RESULTS: We observed that 252 patients (∼20%) had at least one mutation in the EGFR gene, and 38 (∼3%) carried uncommon genetic alterations that would not be identified by the cobas® or the Idylla™ tests. We further found six new single mutations and seven previously unreported compound mutations. Clinical information and patient outcome are presented for these cases. CONCLUSIONS: This study highlights the value of sequencing-based approaches to identify rare mutations. Our results add to the inventory of known EGFR mutations, thus contributing to improved lung cancer precision treatment.

TAL1/SCL is downregulated upon histone deacetylase inhibition in T-cell acute lymphoblastic leukemia cells.

The transcription factor T-cell acute lymphocytic leukemia (TAL)-1 is a major T-cell oncogene associated with poor prognosis in T-cell acute lymphoblastic leukemia (T-ALL). TAL1 binds histone deacetylase 1 and incubation with histone deacetylase inhibitors (HDACis) promotes apoptosis of leukemia cells obtained from TAL1 transgenic mice. Here, we show for the first time that TAL1 protein expression is strikingly downregulated upon histone deacetylase inhibition in T-ALL cells. This is due to decreased TAL1 gene transcription in cells with native TAL1 promoter, and due to impaired TAL1 mRNA translation in cells that harbor the TAL1(d) microdeletion and consequently express TAL1 under the control of the SCL/TAL1 interrupting locus (SIL) promoter. Notably, HDACi-triggered apoptosis of T-ALL cells is significantly reversed by TAL1 forced overexpression. Our results indicate that the HDACi-mediated apoptotic program in T-ALL cells is partially dependent on their capacity to downregulate TAL1 and provide support for the therapeutic use of HDACi in T-ALL.

Inflammatory cell infiltrate and RANKL/OPG expression in rheumatoid synovium: comparison with other inflammatory arthropathies and correlation with outcome.

OBJECTIVES: To evaluate if the immunofluorescence analysis of synovial tissue (ST) using antibodies against RANKL/OPG, conjugated with the immunophenotyping of lymphocytes and macrophages, could be of diagnostic and prognostic value in rheumatoid arthritis (RA) patients. METHODS: 3-year prospective study of 103 consecutive patients submitted to closed needle biopsy for diagnostic purposes. ST was analyzed with routine histologic techniques and immunofluorescence, using monoclonal antibodies against RANKL, OPG, CD163, CD68, CD4, CD8, interferon-gamma and CD19. Patients were prospectively evaluated with a clinical, laboratorial and radiological protocol. At the end of the follow-up patients were divided according to the final diagnosis. Results of the initial histologic evaluation were compared between the main diagnostic groups and in RA patients histologic data was correlated with clinical and radiologic outcome measures. RESULTS: The RANKL/OPG ratio and the inflammatory infiltrate were significatively higher in RA (n = 25) as compared to the same ratio observed in other inflammatory joint diseases (OIJD, n = 48) and in osteoarthritis (n = 17). The difference between RA and OIJD was specifically confirmed when the comparison involved spondyloarthropathy (n = 26). Final HAQ score and radiologic outcome were correlated with the density of intimal CD68+ macrophages. Radiologic progression was correlated with subintimal CD4+ lymphocytes and CD68+ macrophages and intimal CD68 and CD163+ macrophages. CONCLUSION: The quantification of the RANKL/OPG ratio and of the number of lymphocytes in the ST might be useful to differentiate RA from other inflammatory joint diseases. The ST number of CD4+ lymphocytes and macrophages are probable predictors of radiologic progression in RA patients.

[Corpus callosum agenesis]. / Agenesia del cuerpo calloso.

BACKGROUND: Corpus callosum agenesis (CCA) is an uncommon entity, which can be diagnosed in utero. Uncertain prognosis makes prenatal counseling difficult. AIM. We have tried to establish a positive correlation between clinical history and imaging findings in patients with CCA. PATIENTS AND METHODS: We retrospectively reviewed clinical data and imaging findings of patients with callosal agenesis diagnosed at our institution between December 1995 and September 2002. RESULTS: Eight patients with CCA were found, five males and three females. Mean age at last clinical follow up was six years and six months, ranging from three months to 20 years. All diagnoses except for one were post natal. All patients underwent, at least, one magnetic resonance (MR) of the brain. Abnormal pregnancy was reported in three patients. Family history was unremarkable in all patients. Three patients were diagnosed with isolated CCA. One of these patients was asymptomatic at three months. Another had a slight language delay at seventeen months. The other patient had a mild developmental delay at five years. All other five patients had non isolated CCA and all were symptomatic, with variable clinical pictures: psicomotor developmental delay (4), epilepsy (4), hemiparesis (1), ocular apraxia (1), macrocephaly (2). CONCLUSION: Non isolated CCA is likely to have a worse prognosis. This may be of significant value in prenatal counseling.

[Subdural empyema secondary to sinusitis: four pediatric cases]. / Empiema subdural secundario a sinusitis: cuatro casos pediátricos.

INTRODUCTION: Perinasal sinus infections is a common and benign condition in most pediatric cases. Because of the widespread use of antibiotics, intracranial extension of sinusitis is rarely seen today. Nevertheless, the clinician must be aware of the gravity of this condition, because late recognition and delay in treatment can increase mortality and morbidity. The authors made a retrospective study of pediatric patients admitted to Garcia de Orta Hospital between 1996 and 2001 with the diagnosis of subdural empyema and sinusitis. CASE REPORTS: Four patients were identified, with ages between 9 and 13 years. Prodromal manifestations of sinusitis were present in all, followed several days later by headaches, fever, vomiting and neurological abnormalities. Two patients presented in the emergency department with an acute confusional state and a non convulsive status epilepticus. The other two patients had a longer duration of disease, severe deterioration of consciousness and focal neurologic signs. Medical treatment was started in all cases at admission, but none improved significantly before being submitted to surgical intervention, which was repeated several times in two patients. Streptococcus milleri and anaerobic organisms were isolated. There was no mortality and global evolution was favorable, with a median follow up of 32 months. CONCLUSIONS: Clinical presentation of subdural empyema can be relatively inespecific, requiring a high degree of suspicion. Facing a young adolescent with fever of unknown origin associated with any neurological abnormality and previous history of sinusitis, neuroradiological investigation shoul be asked. Early diagnosis and treatment are the mainstays of successful outcome.

[Herpetic encephalitis in childhood: a diagnosis which should not be forgotten]. / Encefalitis herpética en la edad pediátrica: un diagnóstico que no hay que olvidar.

INTRODUCTION: Herpes simplex encephalitis is a serious infection of the nervous system, causing death or considerable neurological morbidity in infants and children. Rapid diagnosis and prompt institution of antiviral therapy is essential. Prodromal manifestations (fever, headache, and behavioural disturbances) can be quite unspecific. Focal neurological signs, seizures (focal or generalised) and coma appear subsequently. Electrophysiologic studies and neuroimaging can be normal or show non specific changes, particularly in this age group. After the 1990 s polymerase chain reaction (PCR) examination of the LCR has become the gold standard for diagnosing herpes simplex encephalitis, virtually replacing cerebral biopsy with high sensitivity and specificity. The authors present the acute presentation and follow up of four children aged 3 months 12 years, admitted between 1997 and 2000 with the diagnosis of herpes simplex encephalitis. Clinical presentation, electroencephalogram and neuroimaging studies are discussed. Diagnostic confirmation was obtained with serologic methods in one child and with PCR in the remaining three. Evolution was severe, with a movement disorder that responded dramatically to tetrabenazine in one child, severe neurological sequel with refractory epilepsy in two children and one death with cerebral hemorrhage during the acute stage of disease.

Chromosomal G-dark bands determine the spatial organization of centromeric heterochromatin in the nucleus.

Gene expression can be silenced by proximity to heterochromatin blocks containing centromeric alpha-satellite DNA. This has been shown experimentally through cis-acting chromosome rearrangements resulting in linear genomic proximity, or through trans-acting changes resulting in intranuclear spatial proximity. Although it has long been been established that centromeres are nonrandomly distributed during interphase, little is known of what determines the three-dimensional organization of these silencing domains in the nucleus. Here, we propose a model that predicts the intranuclear positioning of centromeric heterochromatin for each individual chromosome. With the use of fluorescence in situ hybridization and confocal microscopy, we show that the distribution of centromeric alpha-satellite DNA in human lymphoid cells synchronized at G(0)/G(1) is unique for most individual chromosomes. Regression analysis reveals a tight correlation between nuclear distribution of centromeric alpha-satellite DNA and the presence of G-dark bands in the corresponding chromosome. Centromeres surrounded by G-dark bands are preferentially located at the nuclear periphery, whereas centromeres of chromosomes with a lower content of G-dark bands tend to be localized at the nucleolus. Consistent with the model, a t(11; 14) translocation that removes G-dark bands from chromosome 11 causes a repositioning of the centromere, which becomes less frequently localized at the nuclear periphery and more frequently associated with the nucleolus. The data suggest that "chromosomal environment" plays a key role in the intranuclear organization of centromeric heterochromatin. Our model further predicts that facultative heterochromatinization of distinct genomic regions may contribute to cell-type specific patterns of centromere localization.

Triplet repeats, RNA secondary structure and toxic gain-of-function models for pathogenesis.

Ten years after the discovery of human diseases caused by trinucleotide repeat expansions, searching for mechanistic links between gene mutation and pathological phenotype remains a fundamental and unsolved issue. Evidence accumulated so far indicates that the pathogenesis of repeat disorders is complex and multi-factorial. Diseases caused by CAG expansions coding for polyglutamine tracts have been extensively studied, and in most cases a toxic gain-of-function of the mutant protein was demonstrated. Most recently, tracking the effects of repeats along the pathway of gene expression is providing additional clues to understand how a triplet repeat expansion can cause disease. Expanded repeats form DNA secondary structures that confer genetic instability, and most likely contribute to alter the local chromatin configuration leading to transcriptional silencing. At the level of RNA, the expanded repeat may either interfere with processing of the primary transcript, resulting in deficit of the corresponding protein, or interact with RNA-binding proteins altering their normal activity. The latter mechanism, termed RNA gain-of-function, has no precedents in human genetics. Recent evidence suggests that expanded RNAs and associated RNA-binding proteins are potential contributors to the pathogenesis of several triplet repeat diseases.

Precursor RNAs harboring nonsense codons accumulate near the site of transcription.

Messenger RNAs containing premature termination codons (PTCs) are selectively eliminated by nonsense-mediated mRNA decay (NMD). Paradoxically, although cytoplasmic ribosomes are the only known species capable of PTC recognition, in mammals many PTC-containing mRNAs are apparently eliminated prior to release from the nucleus. To determine whether PTCs can influence events within the nucleus proper, we studied the immunoglobulin (Ig)-mu and T cell receptor (TCR)-beta genes using fluorescent in situ hybridization (FISH). Alleles containing PTCs, but not those containing a missense mutation or a frameshift followed by frame-correcting mutations, exhibited elevated levels of pre-mRNA, which accumulated at or near the site of transcription. Our data indicate that mRNA reading frame can influence events at or near the site of gene transcription.

The rules and roles of nucleocytoplasmic shuttling proteins.

The spatial separation of mRNA synthesis from translation, while providing eukaryotes with the possibility to achieve higher complexity through a more elaborate regulation of gene expression, has set the need for transport mechanisms through the nuclear envelope. In a simplistic view of nucleocytoplasmic transport, nuclear proteins are imported into the nucleus while RNAs are exported to the cytoplasm. The reality is, however, that transport of either proteins or RNAs across the nuclear envelope can be bi-directional. During the past years, an increasing number of proteins have been identified that shuttle continuously back and forth between the nucleus and the cytoplasm. The emerging picture is that shuttling proteins are key factors in conveying information on nuclear and cytoplasmic activities within the cell.

Transcription-dependent nucleocytoplasmic distribution of hnRNP A1 protein in early mouse embryos.

A unique feature of certain members of the heterogeneous nuclear ribonucleoprotein (hnRNP) family of proteins is that they shuttle continuously between nucleus and cytoplasm and their accumulation in the nucleus is transcription-dependent. An extensively characterised protein of this group is hnRNP A1. To date, most studies addressing the transcription-dependent transport of hnRNP A1 have been performed on cultured cell lines treated with transcription inhibitors. Here we have analysed the nucleocytoplasmic distribution of hnRNP A1 in early mouse embryos, where the haploid pronuclei remain transcriptionally inactive for a period of several hours. Consistent with its small molecular size (36 kDa), the hnRNP A1 protein diffuses passively through the nuclear pores and equilibrates between the nucleus and the cytoplasm of transcriptionally inactive embryos. In contrast, following transcriptional activation the A1 protein becomes accumulated in the nucleus. This accumulation of the A1 protein in the nucleus is blocked by the lectin wheat germ agglutinin (WGA), which binds to nuclear pore proteins and prevents translocation of receptor-cargo complexes through the pores. This indicates that a carrier-mediated transport pathway is required for the concentration of A1 in transcriptionally active nuclei. To further analyse how transcription is coupled to nucleocytoplasmic transport, we transplanted transcriptionally inactive pronuclei into the cytoplasm of transcriptionally active embryos. The results show that the presence of newly synthesised RNAs in the cytoplasm is not sufficient to induce the accumulation of hnRNP A1 in the nucleus. Rather, the appearance of nascent transcripts in the nucleus appears to be the crucial event. Since hnRNP A1 is a shuttling protein, an increase in its steady state nuclear concentration could be the result of either faster nuclear import or slower export to the cytoplasm. We propose that binding of A1 to nascent transcripts retards its export to the cytoplasm and therefore contributes to its concentration in the nucleus.

REF proteins mediate the export of spliced and unspliced mRNAs from the nucleus.

The REF family of evolutionarily conserved heterogeneous ribonucleoprotein (hnRNP)-like proteins consists of one central RNP-type RNA binding domain flanked by Arg-Gly-rich regions of variable length. Members of this protein family bind directly to RNA and the mRNA export factor TAP/Mex67p, and it has been suggested that they facilitate the recruitment of TAP/Mex67p to cellular mRNPs. We show that the variable regions are necessary for binding of REFs to RNA and to TAP. Antibodies specific to REFs prevent their interaction with RNA in vitro. After microinjection into Xenopus oocytes, these antibodies inhibit mRNA nuclear export. This inhibition of export is observed whether or not the mRNAs are generated by splicing. The antibodies do not interfere with pre-mRNA splicing or with the nuclear export of constitutive transport element (CTE)-containing RNAs (directly mediated by TAP), so REF proteins must play a critical role in mRNA nuclear export, acting downstream of splicing and upstream of TAP/Mex67p. We also show that recombinant REFs stimulate directly the export of mRNAs that are otherwise exported inefficiently. Together, our data indicate that REFs are directly implicated in the export of mRNAs from the nucleus. More generally, we show that spliced and unspliced mRNAs use common export factors to reach the cytoplasm.

Quality control of gene expression in the nucleus.

Proteins are responsible for most cellular and extra-cellular functions. If altered, proteins can loose their normal activity and/or gain new properties. Either way the consequences may be deleterious for the cell and lead to disease at the organism level. Not surprisingly, eukaryotes have evolved mechanisms to recognize abnormal messenger RNAs and prevent them from producing faulty proteins. Protein-encoding genes are transcribed in the nucleus by RNA polymerase II as precursor RNAs that undergo extensive processing before being translocated to the cytoplasm for translation by the ribosomes. This spatial and temporal separation between RNA and protein synthesis offers an immense opportunity for control and regulation. Here we review recent studies that are beginning to unravel how the coupling between transcription, processing and transport of mRNAs contributes to control the quality of gene expression in the nucleus.

Nucleocytoplasmic shuttling of heterodimeric splicing factor U2AF.

The U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) is a heterodimeric splicing factor composed of 65-kDa (U2AF(65)) and 35-kDa (U2AF(35)) subunits. The large subunit of U2AF recognizes the intronic polypyrimidine tract, a sequence located adjacent to the 3' splice site that serves as an important signal for both constitutive and regulated pre-mRNA splicing. The small subunit U2AF(35) interacts with the 3' splice site dinucleotide AG and is essential for regulated splicing. Like several other proteins involved in constitutive and regulated splicing, both U2AF(65) and U2AF(35) contain an arginine/serine-rich (RS) domain. In the present study we determined the role of RS domains in the subcellular localization of U2AF. Both U2AF(65) and U2AF(35) are shown to shuttle continuously between the nucleus and the cytoplasm by a mechanism that involves carrier receptors and is independent from binding to mRNA. The RS domain on either U2AF(65) or U2AF(35) acts as a nuclear localization signal and is sufficient to target a heterologous protein to the nuclear speckles. Furthermore, the results suggest that the presence of an RS domain in either U2AF subunit is sufficient to trigger the nucleocytoplasmic import of the heterodimeric complex. Shuttling of U2AF between nucleus and cytoplasm possibly represents a means to control the availability of this factor to initiate spliceosome assembly and therefore contribute to regulate splicing.

Vesicular stomatitis virus matrix protein inhibits host cell gene expression by targeting the nucleoporin Nup98.

Vesicular stomatitis virus matrix protein (VSV M) has been shown to inhibit both transcription and nucleocytoplasmic transport. We have isolated a mutant form of M, termed M(D), lacking both inhibitory activities. HeLa cells expressing M, but not M(D), accumulate polyadenylated RNAs within the nucleus. Concomitantly, a fraction of M, but not of the M(D) mutant, localizes at the nuclear rim. Additionally, the nucleoporin Nup98 specifically interacts with M but not with M(D). In Nup98(-/-) cells, both the levels of M at the nuclear envelope and its inhibitory effects on host cell-directed expression of reporter genes were significantly reduced. Together, our data demonstrate that VSV M inhibits host cell gene expression by targeting a nucleoporin and primarily blocking nuclear export.

Histology of the synovial tissue: value of semiquantitative analysis for the prediction of joint erosions in rheumatoid arthritis.

OBJECTIVE: Routine histologic techniques are still the main procedure in the study of the synovial biopsy. The relationship between the typical histological changes of rheumatoid synovium and clinical manifestations has not been studied in detail. METHODS: With the aim of determining whether a simple semiquantitative method of evaluating the changes in closed synovial biopsies was of clinical value in assessing both the diagnosis and prognosis of rheumatoid arthritis (RA) patients, we evaluated retrospectively 72 synovial biopsy specimens (26 RA patients, 30 patients with other inflammatory diseases and 16 osteoarthritis patients). Scores (0-10) were assigned to each biopsy specimen for each of 6 histologic features: synoviocyte hyperplasia; fibrosis in the subsynovial layer; proliferating blood vessels; perivascular infiltrates of lymphocytes; focal aggregates of lymphocytes; and diffuse infiltrates of lymphocytes. Scores were compared between the 3 groups and also between the RA subgroups with early and late disease; positive and negative rheumatoid factor; with and without joint erosions; and with and without systemic disease. RESULTS: Significant differences in the mean global score (mean of the 6 scores) were found both between RA and osteoarthritis and between other inflammatory diseases and osteoarthritis (p < 0.01). The mean global score for RA was higher than the mean global score obtained for the other inflammatory diseases, but the difference was not significant. We found a significantly higher mean global score in the RA patients with erosions in comparison to the RA patients without erosions, this difference being particularly evident for the lymphocyte perivascular infiltrate (p < 0.05). There were no significant differences between the other RA subgroups. CONCLUSION: In this study we have identified differences, using routine histologic techniques, between the rheumatoid synovial membrane of patients with and without erosions. Based on our present observations we suggest that the intensity of inflammatory histological features and, in particular, a high percentage of vessels with perivascular lymphocyte infiltrate might be of prognostic value in RA.

TAP (NXF1) belongs to a multigene family of putative RNA export factors with a conserved modular architecture.

Vertebrate TAP (also called NXF1) and its yeast orthologue, Mex67p, have been implicated in the export of mRNAs from the nucleus. The TAP protein includes a noncanonical RNP-type RNA binding domain, four leucine-rich repeats, an NTF2-like domain that allows heterodimerization with p15 (also called NXT1), and a ubiquitin-associated domain that mediates the interaction with nucleoporins. Here we show that TAP belongs to an evolutionarily conserved family of proteins that has more than one member in higher eukaryotes. Not only the overall domain organization but also residues important for p15 and nucleoporin interaction are conserved in most family members. We characterize two of four human TAP homologues and show that one of them, NXF2, binds RNA, localizes to the nuclear envelope, and exhibits RNA export activity. NXF3, which does not bind RNA or localize to the nuclear rim, has no RNA export activity. Database searches revealed that although only one p15 (nxt) gene is present in the Drosophila melanogaster and Caenorhabditis elegans genomes, there is at least one additional p15 homologue (p15-2 [also called NXT2]) encoded by the human genome. Both human p15 homologues bind TAP, NXF2, and NXF3. Together, our results indicate that the TAP-p15 mRNA export pathway has diversified in higher eukaryotes compared to yeast, perhaps reflecting a greater substrate complexity.

Molecular mechanisms involved in cisplatin cytotoxicity.

cis-diamminedichloroplatinum(II) or cisplatin is a DNA-damaging agent that is widely used in cancer chemotherapy. Cisplatin cross-links to DNA, forming intra- and interstrand adducts, which bend and unwind the duplex and attract high-mobility-group domain and other proteins. Presumably due to a shielding effect caused by these proteins, the cisplatin-modified DNA is poorly repaired. The resulting DNA damage triggers cell-cycle arrest and apoptosis. Although it is still debatable whether the clinical success of cisplatin relies primarily on its ability to trigger apoptosis, at least two distinct pathways have been proposed to contribute to cisplatin-induced apoptosis in vitro. One involves the tumour-suppressor protein p53, the other is mediated by the p53-related protein p73. Coupling cisplatin damage to apoptosis requires mismatch repair activity, and recent observations further suggest involvement of the homologous recombinatorial repair system. At present it is generally accepted that abortive attempts to repair the DNA lesions play a key role in the cytotoxicity of the drug, and loss of the mismatch repair activity is known to cause cisplatin resistance, a major problem in antineoplastic therapy. Clearly, a better understanding of the signalling networks involved in cisplatin toxicity should provide a rational basis for the development of new therapeutic strategies.

Identification of two novel RanGTP-binding proteins belonging to the importin beta superfamily.

Nucleo-cytoplasmic transport comprises a large number of distinct pathways, many of which are defined by members of the importin beta superfamily of nuclear transport receptors. These transport receptors all directly interact with RanGTP to modulate the compartment-specific binding of their transport substrates. To identify new members of the importin beta family, we used affinity chromatography on immobilized RanGTP and isolated Ran-binding protein (RanBP) 16 from HeLa cell extracts. RanBP16 and its close human homologue, RanBP17, are distant members of the importin beta family. Like the other members of the transport receptor superfamily, RanBP16 interacts with the nuclear pore complex and is able to enter the nucleus independent of energy and additional nuclear transport receptors.