Physical interaction between MYCN oncogene and polycomb repressive complex 2 (PRC2) in neuroblastoma: Functional and therapeutic implications

This article is made available through the Brunel Open Access Publishing Fund. © 2013 by The American Society for Biochemistry and Molecular Biology, Inc.CLU (clusterin) is a tumor suppressor gene that we have previously shown to be negatively modulated by the MYCN proto-oncogene, but the mechanism of repression was unclear. Here, we show that MYCN inhibits the expression of CLU by direct interaction with the non-canonical E box sequence CACGCG in the 5′-flanking region. Binding of MYCN to the CLU gene induces bivalent epigenetic marks and recruitment of repressive proteins such as histone deacetylases and Polycomb members. MYCN physically binds in vitro and in vivo to EZH2, a component of the Polycomb repressive complex 2, required to repress CLU. Notably, EZH2 interacts with the Myc box domain 3, a segment of MYC known to be essential for its transforming effects. The expression of CLU can be restored in MYCN-amplified cells by epigenetic drugs with therapeutic results. Importantly, the anticancer effects of the drugs are ablated if CLU expression is blunted by RNA interference. Our study implies that MYC tumorigenesis can be effectively antagonized by epigenetic drugs that interfere with the recruitment of chromatin modifiers at repressive E boxes of tumor suppressor genes such as CLU.SPARKS, The Neuroblastoma Society, a Wellcome Trust grant (to A. S.), and the Italian Association for Cancer Research

Heterologous RNA silencing suppressors from both plant- and animal-infecting viruses support Plum pox virus infection

[EN] HCPro, the RNA silencing suppressor (RSS) of viruses belonging to the Potyvirus genus in the Potyviridae family, is a multifunctional protein presumably involved in all essential steps of the viral infection cycle. Recent studies have shown that Plum pox potyvirus (PPV) HCPro can be successfully replaced by Cucumber vein yellowing ipomovirus P1b, a sequence unrelated RSS from a virus of the same family. In order to gain insight into the requirement of a particular RSS to establish a successful potyviral infection, we tested the ability of different heterologous RSSs from both plant- and animal-infecting viruses to substitute HCPro. Making use of engineered PPV chimeras, we show that PPV HCPro can be functionally replaced by some, but not all, unrelated RSSs, including the NS1 protein of the mammalian-infecting Influenza A virus. Interestingly, the capacity of a particular RSS to replace HCPro does not strictly correlate with its RNA silencing suppression strength. Altogether, our results suggest that not all suppression strategies are equally suitable for an efficient escape of PPV from the RNA silencing machinery. The approach followed here based on using PPV chimeras in which an under-consideration RSS substitutes for HCPro could further help to study the function of diverse RSSs in a ¿highly-sensitive¿ RNA silencing context, such as that taking place in plant cells during the process of a viral infection.We are especially grateful to those people who sent us plasmids containing the DNA sequence of different viral proteins. We thank Veronique Ziegler-Graff for providing BWYV P0, Ana Giner and Juan Jose Lopez-Moya for providing SPMMV P1, Joel Milner for providing CaMV P6, Maria Rosa Lopez-Huertas and Jose Alcami for providing HIV Tat, Jan Kreuze for providing SPCSV RNase3, and M. Taliansky for providing GRV ORF3. We thank Herman Scholthof and Ariel Rodriguez for providing anti-P19 and anti-NS1 serum, respectively. We are also grateful to David Baulcombe for providing the GFP expression vector and TBSV P19-containing plasmid, and Mark Curtis for providing the pMDC32 destination vector. This work was supported by grants from Spanish MICINN (BIO2010-18541) and the European Union (KBBE-204429). M. C. was the recipient of an 13P fellowship from CSIC-Fondo Social Europeo.Maliogka, VI.; Calvo, M.; Carbonell, A.; Garcia, JA.; Valli, A. (2012). Heterologous RNA silencing suppressors from both plant- and animal-infecting viruses support Plum pox virus infection. Journal of General Virology. 93(7):1601-1611. https://doi.org/10.1099/vir.0.042168-0S16011611937Ala-Poikela, M., Goytia, E., Haikonen, T., Rajamäki, M.-L., & Valkonen, J. P. T. (2011). Helper Component Proteinase of the Genus Potyvirus Is an Interaction Partner of Translation Initiation Factors eIF(iso)4E and eIF4E and Contains a 4E Binding Motif. Journal of Virology, 85(13), 6784-6794. doi:10.1128/jvi.00485-11Ambros, V., & Chen, X. (2007). 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Boson-exchange parquet solver for dual fermions

We present and implement a parquet approximation within the dual-fermion formalism based on a partial bosonization of the dual vertex function which substantially reduces the computational cost of the calculation. The method relies on splitting the vertex exactly into single-boson exchange contributions and a residual four-fermion vertex, which physically embody, respectively, long- and short-range spatial correlations. After recasting the parquet equations in terms of the residual vertex, these are solved using the truncated-unity method of Eckhardt et al. [Phys. Rev. B 101, 155104 (2020)2469-995010.1103/PhysRevB.101.155104], which allows for a rapid convergence with the number of form factors in different regimes. While our numerical treatment of the parquet equations can be restricted to only a few Matsubara frequencies, reminiscent of Astretsov et al. [Phys. Rev. B 101, 075109 (2020)2469-995010.1103/PhysRevB.101.075109], the one- and two-particle spectral information is fully retained. In applications to the two-dimensional Hubbard model the method agrees quantitatively with a stochastic summation of diagrams over a wide range of parameters

Canopy uptake dominates nighttime carbonyl sulfide fluxes in a boreal forest

Nighttime vegetative uptake of carbonyl sulfide (COS) can exist due to the incomplete closure of stomata and the light independence of the enzyme carbonic anhydrase, which complicates the use of COS as a tracer for gross primary productivity (GPP). In this study we derived nighttime COS fluxes in a boreal forest (the SMEAR II station in Hyytiälä, Finland; 61°51′ N, 24°17′ E; 181 m a.s.l.) from June to November 2015 using two different methods: eddy-covariance (EC) measurements (FCOS-EC) and the radon-tracer method (FCOS-Rn). The total nighttime COS fluxes averaged over the whole measurement period were −6.8 ± 2.2 and −7.9 ± 3.8 pmol m−2 s−1 for FCOS-Rn and FCOS-EC, respectively, which is 33–38 % of the average daytime fluxes and 21 % of the total daily COS uptake. The correlation of 222Rn (of which the source is the soil) with COS (average R2  =  0.58) was lower than with CO2 (0.70), suggesting that the main sink of COS is not located at the ground. These observations are supported by soil chamber measurements that show that soil contributes to only 34–40 % of the total nighttime COS uptake. We found a decrease in COS uptake with decreasing nighttime stomatal conductance and increasing vapor-pressure deficit and air temperature, driven by stomatal closure in response to a warm and dry period in August. We also discuss the effect that canopy layer mixing can have on the radon-tracer method and the sensitivity of (FCOS-EC) to atmospheric turbulence. Our results suggest that the nighttime uptake of COS is mainly driven by the tree foliage and is significant in a boreal forest, such that it needs to be taken into account when using COS as a tracer for GPP

Counteracting the Common Shwachman–Diamond Syndrome-Causing SBDS c.258+2T>C Mutation by RNA Therapeutics and Base/Prime Editing

Shwachman-Diamond syndrome (SDS) represents one of the most common inherited bone marrow failure syndromes and is mainly caused by SBDS gene mutations. Only supportive treatments are available, with hematopoietic cell transplantation required when marrow failure occurs. Among all causative mutations, the SBDS c.258+2T>C variant at the 5 ' splice site (ss) of exon 2 is one of the most frequent. Here, we investigated the molecular mechanisms underlying aberrant SBDS splicing and showed that SBDS exon 2 is dense in splicing regulatory elements and cryptic splice sites, complicating proper 5 ' ss selection. Studies ex vivo and in vitro demonstrated that the mutation alters splicing, but it is also compatible with tiny amounts of correct transcripts, which would explain the survival of SDS patients. Moreover, for the first time for SDS, we explored a panel of correction approaches at the RNA and DNA levels and provided experimental evidence that the mutation effect can be partially counteracted by engineered U1snRNA, trans-splicing, and base/prime editors, ultimately leading to correctly spliced transcripts (from barely detectable to 2.5-5.5%). Among them, we propose DNA editors that, by stably reverting the mutation and potentially conferring positive selection to bone-marrow cells, could lead to the development of an innovative SDS therapy

Incidence and clinicopathologic features of gastrointestinal stromal tumors. A population-based study.

BACKGROUND: Although the diagnostic criteria and pathogenesis of gastrointestinal stromal tumors (GIST) have recently been elucidated, knowledge of the epidemiology of this malignancy is still limited. This study examined the incidence of GIST in the province of Modena, including pathologic features and clinical outcome. METHODS: Gastrointestinal mesenchymal tumors identified by the Modena Cancer Registry between 1991 and 2004 were analyzed with an immunohistochemical panel that included staining for CD-117 and PDGFRalpha. Size, mitotic rate, and other pathologic parameters were recorded. Each tumor was categorized into National Institutes of Health risk categories (very low, low, intermediate, and high risk). RESULTS: One hundred twenty-four cases were classified as GIST. The age-adjusted incidence rate was 6.6 per million. Seventy-five percent of patients were symptomatic; 34% had a previous or concomitant history of cancer. High-risk features were present in 47% of cases. Seventy-eight percent were submitted to radical surgery. After complete resection, the 5-year disease-free survival rates were 94%, 92%, 100%, and 40% for patients at very low, low, intermediate, and high risk, respectively. In multivariate analysis, high risk was the main predictor of recurrence. CONCLUSION: This population-based study shows that the incidence of GIST in Northern Italy is comparable to that reported in other European countries. Survival was favorable in lower risk categories and in most of the resected cases. In our study, resected patients at very low, low, and intermediate risk had a similar outcome. Our data support the need to consider high-risk patients after complete surgical resection for treatment with the best available approach

Elemental characterization of PM10, PM2.5 and PM1 in the town of Genoa (Italy)

The particulate matter (PM) concentration and composition, the PM10, PM2.5, PM1 fractions, were studied in the urban area of Genoa, a coastal town in the northwest of Italy. Two instruments, the continuous monitor TEOM and the sequential sampler PARTISOL, were operated almost continuously on the same site from July 2001 to September 2004. Samples collected by PARTISOL were weighted to obtain PM concentration and then analysed by PIXE (particle induced X-ray emission) and by ED-XRF (energy dispersion X-ray fluorescence), obtaining concentrations for elements from Na to Pb. Some of the filters used in the TEOM microbalance were analysed by ED-XRF to calculate Pb concentration values averaged over 7\u201330 d periods

Patterns of practice of regional nodal irradiation in breast cancer: results of the European Organization for Research and Treatment of Cancer (EORTC) NOdal Radiotherapy (NORA) survey†

Predicting breast cancer outcome based on SLN node status without ALND is currently an area of uncertainty in SLN+ patients. These uncertainties influence the decision-making of adjuvant nodal irradiation. The NORA Survey was designed to examine the patterns of RNI practice in Europe to provide a basis for designing future trials in areas of equipoise in clinical decision-making concerning RN

Case Report: Heterozygous Germline Variant in EIF6 Additional to Biallelic SBDS Pathogenic Variants in a Patient With Ribosomopathy Shwachman–Diamond Syndrome

Background: Shwachman-Diamond syndrome (SDS) is a rare autosomal recessive ribosomopathy mainly characterized by exocrine pancreatic insufficiency, skeletal alterations, neutropenia, and a relevant risk of hematological transformation. At least 90% of SDS patients have pathogenic variants in SBDS, the first gene associated with the disease with very low allelic heterogeneity; three variants, derived from events of genetic conversion between SBDS and its pseudogene, SBDSP1, provided the alleles observed in about 62% of SDS patients.Methods: We performed a reanalysis of the available WES files of a group of SDS patients with biallelic SBDS pathogenic variants, studying the results by next bioinformatic and protein structural analysis. Parallelly, careful clinical attention was given to the patient focused in this study.Results: We found and confirmed in one SDS patient a germline heterozygous missense variant (c.100T>C; p.Phe34Leu) in the EIF6 gene. This variant, inherited from his mother, has a very low frequency, and it is predicted as pathogenic, according to several in silico prediction tools. The protein structural analysis also envisages the variant could reduce the binding to the nascent 60S ribosomal.Conclusion: This study focused on the hypothesis that the EIF6 germline variant mimics the effect of somatic deletions of chromosome 20, always including the locus of this gene, and similarly may rescue the ribosomal stress and ribosomal dysfunction due to SBDS mutations. It is likely that this rescue may contribute to the stable and not severe hematological status of the proband, but a definite answer on the role of this EIF6 variant can be obtained only by adding a functional layer of evidence. In the future, these results are likely to be useful for selected cases in personalized medicine and therapy

Severe peripheral joint laxity is a distinctive clinical feature of spondylodysplastic-ehlers-danlos syndrome (Eds)-b4galt7 and spondylodysplastic-eds-b3galt6

Variations in genes encoding for the enzymes responsible for synthesizing the linker region of proteoglycans may result in recessive conditions known as “linkeropathies”. The two phenotypes related to mutations in genes B4GALT7 and B3GALT6 (encoding for galactosyltransferase I and II respectively) are similar, characterized by short stature, hypotonia, joint hypermobility, skeletal features and a suggestive face with prominent forehead, thin soft tissue and prominent eyes. The most outstanding feature of these disorders is the combination of severe connective tissue involvement, often manifesting in newborns and infants, and skeletal dysplasia that becomes apparent during childhood. Here, we intend to more accurately define some of the clinical features of B4GALT7 and B3GALT6-related conditions and underline the extreme hypermobility of distal joints and the soft, doughy skin on the hands and feet as features that may be useful as the first clues for a correct diagnosis