Are Anti-Ro52 Antibodies Associated with Pulmonary Involvement in Scleroderma?

Abstract Introduction: The presence of anti-Ro52 antibodies has been reported in a wide variety of autoimmune diseases, particularly in myositis, scleroderma and autoimmune liver diseases. Clinical significance of anti-Ro52 antibodies remains controversial. Studies are lacking in clarifying the association of anti-Ro52 with pulmonary involvement in scleroderma. Objectives: To determine if anti-Ro52 antibodies are associated with pulmonary involvement (interstitial, indirect pulmonary hypertension, or both) in scleroderma. Methods: Single center, retrospective study based on immunoblotting panel analysis and patients clinical records. Pulmonary manifestations were sub-grouped in: 1) interstitial (alveolitis and/or fibrosis), 2) pulmonary artery systolic pressure (PASP) ≥40 mmHg plus interstitial pulmonary disease, and 3) isolated PASP≥40 mmHg (purely vascular). Results: Our scleroderma cohort included 200 patients, of which 137 had immunoblotting panels with anti-Ro52 reactivity analysis. The search was conducted between January 2010 and July 2011. The frequency of pulmonary manifestations in patients with positive anti-Ro52 antibodies was 67.7% (n=31), and 60% (n=24) in the negative anti-Ro52 group, showing no significant differences between groups (p=0.621). Still no significant differences were found when pulmonary manifestations were evaluated according to the subgroups (p=0.525). Sensitivity, specificity, positive and negative predictive values of anti-Ro52 reactivity for determining pulmonary involvement in scleroderma were low. Conclusion: No association was found between positive anti-Ro52 antibodies and pulmonary involvement in scleroderma

AVALIAÇÂO DE UMA NOVA TÉCNICA DE QUIMIOLUMINESCÊNCIA PARA DETERMINAÇÃO DE ANTICORPOS ANTI-DSDNA

Introdução A determinação dos anticorpos anti-dsDNA é um teste de grande importância para o diagnóstico e monitorização de doentes com Lúpus Eritematoso Sistémico (LES), fazendo parte dos critérios de classificação de LES do ACR. (American College of Rheumathology). Existem actualmente vários métodos laboratoriais disponíveis, que respondem de forma desigual na determinação destes anticorpos nos doentes, em diferentes fases de evolução da patologia. Objectivo Avaliar o desempenho do novo método automatizado de determinação dos anticorpos anti-dsDNA por técnica de quimioluminescência (CLIA), Zenit RA dsDNA (Menarini), comparando-o com os métodos de imunofluorescência indirecta (IFI) e fluoroimunoensaio (FEIA), utilizados na rotina assistencial no Serviço de Imunologia do CHP. Material e Métodos A população estudada incluiu 151 amostras seriadas de doentes com LES, 33 doentes com doença infecciosa, 28 doentes com outras patologias com envolvimento autoimune e 38 indivíduos saudáveis. Realizou-se a determinação dos anticorpos anti-dsDNA por técnica CLIA no equipamento ZENIT RA (Menarini), por técnica FEIA no equipamento ImmunoCAP 250 (Phadia) e por IFI em lâminas de Crithidia luciliae (BioRad) processadas no aparelho PhD (BioRad). Resultados Todos os testes apresentaram uma baixa sensibilidade nos doentes com LES (33,1% a 44,4%), traduzindo o facto de um grande número de doentes se encontrar em tratamento e com fraca actividade da doença. O teste CLIA apresentou uma especificidade semelhante à da IFI (93,9% vs. 95,6%), superior à observada no FEIA (85,9%). Conclusões O teste dsDNA ZENIT RA revelou uma sensibilidade inferior ao FEIA mas uma melhor especificidade e valor preditivo positivo, semelhantes aos observados na técnica de IFI. Sendo um teste totalmente automatizado e sem a subjectividade da IFI, será agora importante a sua avaliação numa população com critérios de actividade bem definidos

Influence of soil and organic residue management on biomass and biodiversity of understory vegetation in a Eucalyptus globulus Labill. plantation

The objective of this study was to assess the effect of different options of soil preparation and management of harvesting debris on biodiversity and biomass of understory vegetation in plantations of Eucalyptus globulus of Central Portugal. The experiment consisted of six treatments in a replanted area and four treatments in a coppice area with five replicates, following a randomised block design. Surveys of vegetation were performed for 6 years. The proportion of soil cover by plant specieswas estimated and the Shannon–Wiener diversity and equitability indexes determined for each treatment and year. After the 2nd year, the understory vegetation was randomly sampled for above-ground biomass determination.Within the planted area, the removal of slash without soil preparation induced the highest number of species during the experimental period. A similar trend was observed in the coppice area, but less regularly. Significant differences in the proportion of soil cover only occurred within the planted area in the first year, when slash removal without soil preparation induced the highest understory cover. Species diversity was not clearly affected by treatments: significant differences only occurred occasionally and were apparently related to differences in the number of species. Therefore, differences in the equitability index between treatments never were significant. Removal of slash without soil disturbance and broadcast of slash over the soil usually shared the highest biodiversity. Differences between treatments in the amount of understory biomass were never statistically significant during the experimental period. Tendency for a negative influence of soil mobilisation on the amount of understory biomass was observed within the planted area, as well as a similar effect of the treatments consisting of broadcast of slash over the soil surface in the coppice area. In parallel to tree development and canopy closure biomass of that vegetation along the study period was reduced, especially in the planted area

Species richness and biomass of understory vegetation in a Eucalyptus globulus Labill. coppice as affected by slash management

The aim of this study was to assess the effect of different slash management practices on understory biodiversity and biomass in Eucalyptus globulus coppices in Central Portugal. The experiment consisted of four treatments: (a) removal of slash (R), (b) broadcast over the soil (S), (c) as in S but concentrating woody residues between tree rows (W) and (d) incorporation of slash into soil by harrowing (I). Understory vegetation was surveyed during 1–6, 9, and 10 years, the proportion of soil cover by plant species estimated, and diversity and equitability indexes determined. Above ground understory biomass was sampled in years 2–6, 9, and 10. The highest number of species in most years occurred in plots where slash was removed. Differences between treatments in the proportion of plant soil cover were never significant, whereas differences in diversity index were only occasionally significant and apparently related to the number of species. Thus, differences in the equitability index were not significant. Understory biomass did not decrease during the rotation period, and was usually highest in R and I, and lowest in S, but not significantly different. At the end of the rotation period, understory biodiversity indices and biomass were apparently independent of slash treatment

Cyclin D mediates tolerance of genome-doubling in cancers with functional p53

BACKGROUND: Aneuploidy and chromosomal instability (CIN) are common features of human malignancy that fuel genetic heterogeneity. Although tolerance to tetraploidization, an intermediate state that further exacerbates CIN, is frequently mediated by TP53 dysfunction, we find that some genome-doubled tumours retain wild-type TP53. We sought to understand how tetraploid cells with a functional p53/p21-axis tolerate genome-doubling events. METHOD: We performed quantitative proteomics in a diploid/tetraploid pair within a system of multiple independently derived TP53 wild-type tetraploid clones arising spontaneously from a diploid progenitor. We characterized adapted and acute tetraploidization in a variety of flow cytometry and biochemical assays and tested our findings against human tumours through bioinformatics analysis of the TCGA dataset. RESULTS: Cyclin D1 was found to be specifically overexpressed in early but not late passage tetraploid clones, and this overexpression was sufficient to promote tolerance to spontaneous and pharmacologically induced tetraploidy. We provide evidence that this role extends to D-type cyclins and their overexpression confers specific proliferative advantage to tetraploid cells. We demonstrate that tetraploid clones exhibit elevated levels of functional p53 and p21 but override the p53/p21 checkpoint by elevated expression of cyclin D1, via a stoichiometry-dependent and CDK activity-independent mechanism. Tetraploid cells do not exhibit increased sensitivity to abemaciclib, suggesting that cyclin D-overexpressing tumours might not be specifically amenable to treatment with CDK4/6 inhibitors. CONCLUSION: Our study suggests that D-type cyclin overexpression is an acute event, permissive for rapid adaptation to a genome-doubled state in TP53 wild-type tumours and that its overexpression is dispensable in later stages of tumour progression

Both SEPT2 and MLL are down-regulated in MLL-SEPT2 therapy-related myeloid neoplasia

<p>Abstract</p> <p>Background</p> <p>A relevant role of septins in leukemogenesis has been uncovered by their involvement as fusion partners in <it>MLL</it>-related leukemia. Recently, we have established the <it>MLL-SEPT2 </it>gene fusion as the molecular abnormality subjacent to the translocation t(2;11)(q37;q23) in therapy-related acute myeloid leukemia. In this work we quantified <it>MLL </it>and <it>SEPT2 </it>gene expression in 58 acute myeloid leukemia patients selected to represent the major AML genetic subgroups, as well as in all three cases of <it>MLL-SEPT2</it>-associated myeloid neoplasms so far described in the literature.</p> <p>Methods</p> <p>Cytogenetics, fluorescence in situ hybridization (FISH) and molecular studies (RT-PCR, qRT-PCR and qMSP) were used to characterize 58 acute myeloid leukemia patients (AML) at diagnosis selected to represent the major AML genetic subgroups: <it>CBFB-MYH11 </it>(n = 13), <it>PML-RARA </it>(n = 12); <it>RUNX1-RUNX1T1 </it>(n = 12), normal karyotype (n = 11), and <it>MLL </it>gene fusions other than <it>MLL-SEPT2 </it>(n = 10). We also studied all three <it>MLL-SEPT2 </it>myeloid neoplasia cases reported in the literature, namely two AML patients and a t-MDS patient.</p> <p>Results</p> <p>When compared with normal controls, we found a 12.8-fold reduction of wild-type <it>SEPT2 </it>and <it>MLL-SEPT2 </it>combined expression in cases with the <it>MLL-SEPT2 </it>gene fusion (p = 0.007), which is accompanied by a 12.4-fold down-regulation of wild-type <it>MLL </it>and <it>MLL-SEPT2 </it>combined expression (p = 0.028). The down-regulation of <it>SEPT2 </it>in <it>MLL-SEPT2 </it>myeloid neoplasias was statistically significant when compared with all other leukemia genetic subgroups (including those with other <it>MLL </it>gene fusions). In addition, <it>MLL </it>expression was also down-regulated in the group of <it>MLL </it>fusions other than <it>MLL-SEPT2</it>, when compared with the normal control group (p = 0.023)</p> <p>Conclusion</p> <p>We found a significant down-regulation of both <it>SEPT2 </it>and <it>MLL </it>in <it>MLL-SEPT2 </it>myeloid neoplasias. In addition, we also found that <it>MLL </it>is under-expressed in AML patients with <it>MLL </it>fusions other than <it>MLL-SEPT2</it>.</p

FusorSV: an algorithm for optimally combining data from multiple structural variation detection methods.

Comprehensive and accurate identification of structural variations (SVs) from next generation sequencing data remains a major challenge. We develop FusorSV, which uses a data mining approach to assess performance and merge callsets from an ensemble of SV-calling algorithms. It includes a fusion model built using analysis of 27 deep-coverage human genomes from the 1000 Genomes Project. We identify 843 novel SV calls that were not reported by the 1000 Genomes Project for these 27 samples. Experimental validation of a subset of these calls yields a validation rate of 86.7%. FusorSV is available at https://github.com/TheJacksonLaboratory/SVE . Genome Biol 2018 Mar 20; 19(1):38

High-resolution deconstruction of evolution induced by chemotherapy treatments in breast cancer xenografts.

The processes by which tumors evolve are essential to the efficacy of treatment, but quantitative understanding of intratumoral dynamics has been limited. Although intratumoral heterogeneity is common, quantification of evolution is difficult from clinical samples because treatment replicates cannot be performed and because matched serial samples are infrequently available. To circumvent these problems we derived and assayed large sets of human triple-negative breast cancer xenografts and cell cultures from two patients, including 86 xenografts from cyclophosphamide, doxorubicin, cisplatin, docetaxel, or vehicle treatment cohorts as well as 45 related cell cultures. We assayed these samples via exome-seq and/or high-resolution droplet digital PCR, allowing us to distinguish complex therapy-induced selection and drift processes among endogenous cancer subclones with cellularity uncertaint