Applications of Microarray Technology to Acute Myelogenous Leukemia

Microarray technology is a powerful tool, which has been applied to further the understanding of gene expression changes in disease. Array technology has been applied to the diagnosis and prognosis of Acute Myelogenous Leukemia (AML). Arrays have also been used extensively in elucidating the mechanism of and predicting therapeutic response in AML, as well as to further define the mechanism of AML pathogenesis. In this review, we discuss the major paradigms of gene expression array analysis, and provide insights into the use of software tools to annotate the array dataset and elucidate deregulated pathways and gene interaction networks. We present the application of gene expression array technology to questions in acute myelogenous leukemia; specifically, disease diagnosis, treatment and prognosis, and disease pathogenesis. Finally, we discuss several new and emerging array technologies, and how they can be further utilized to improve our understanding of AML

mRNA transcript quantification in archival samples using multiplexed, color-coded probes

Background: A recently developed probe-based technology, the NanoString nCounter™ gene expression system, has been shown to allow accurate mRNA transcript quantification using low amounts of total RNA. We assessed the ability of this technology for mRNA expression quantification in archived formalin-fixed, paraffin-embedded (FFPE) oral carcinoma samples. Results: We measured the mRNA transcript abundance of 20 genes (COL3A1, COL4A1, COL5A1, COL5A2, CTHRC1, CXCL1, CXCL13, MMP1, P4HA2, PDPN, PLOD2, POSTN, SDHA, SERPINE1, SERPINE2, SERPINH1, THBS2, TNC, GAPDH, RPS18) in 38 samples (19 paired fresh-frozen and FFPE oral carcinoma tissues, archived from 1997-2008) by both NanoString and SYBR Green I fluorescent dye-based quantitative real-time PCR (RQ-PCR). We compared gene expression data obtained by NanoString vs. RQ-PCR in both fresh-frozen and FFPE samples. Fresh-frozen samples showed a good overall Pearson correlation of 0.78, and FFPE samples showed a lower overall correlation coefficient of 0.59, which is likely due to sample quality. We found a higher correlation coefficient between fresh-frozen and FFPE samples analyzed by NanoString (r = 0.90) compared to fresh-frozen and FFPE samples analyzed by RQ-PCR (r = 0.50). In addition, NanoString data showed a higher mean correlation (r = 0.94) between individual fresh-frozen and FFPE sample pairs compared to RQ-PCR (r = 0.53). Conclusions: Based on our results, we conclude that both technologies are useful for gene expression quantification in fresh-frozen or FFPE tissues; however, the probe-based NanoString method achieved superior gene expression quantification results when compared to RQ-PCR in archived FFPE samples. We believe that this newly developed technique is optimal for large-scale validation studies using total RNA isolated from archived, FFPE samples

Optimization and analysis of a quantitative real-time PCR-based technique to determine microRNA expression in formalin-fixed paraffin-embedded samples

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRs) are non-coding RNA molecules involved in post-transcriptional regulation, with diverse functions in tissue development, differentiation, cell proliferation and apoptosis. miRs may be less prone to degradation during formalin fixation, facilitating miR expression studies in formalin-fixed paraffin-embedded (FFPE) tissue.</p> <p>Results</p> <p>Our study demonstrates that the TaqMan Human MicroRNA Array v1.0 (Early Access) platform is suitable for miR expression analysis in FFPE tissue with a high reproducibility (correlation coefficients of 0.95 between duplicates, p < 0.00001) and outlines the optimal performance conditions of this platform using clinical FFPE samples. We also outline a method of data analysis looking at differences in miR abundance between FFPE and fresh-frozen samples. By dividing the profiled miR into abundance strata of high (Ct<30), medium (30≤Ct≤35), and low (Ct>35), we show that reproducibility between technical replicates, equivalent dilutions, and FFPE <it>vs</it>. frozen samples is best in the high abundance stratum. We also demonstrate that the miR expression profiles of FFPE samples are comparable to those of fresh-frozen samples, with a correlation of up to 0.87 (p < 0.001), when examining all miRs, regardless of RNA extraction method used. Examining correlation coefficients between FFPE and fresh-frozen samples in terms of miR abundance reveals correlation coefficients of up to 0.32 (low abundance), 0.70 (medium abundance) and up to 0.97 (high abundance).</p> <p>Conclusion</p> <p>Our study thus demonstrates the utility, reproducibility, and optimization steps needed in miR expression studies using FFPE samples on a high-throughput quantitative PCR-based miR platform, opening up a realm of research possibilities for retrospective studies.</p

Unveiling the mechanism of action of 7α-acetoxy-6β-hydroxyroyleanone on an mrsa/visa strain: Membrane and cell wall interactions

UIDB/00100/2020 PTDC/MED-QUI/29036/2017 CEECIND/03414/2018 UIDB/04378/2020 PTDC/BIA-MIC/31645/2017 UID/DTP/04138/2019 UID/DTP/04567/2019 CBIOS/PRUID/BI1/2017 UIDB/04567/2020 UID/AMB/50017 UIDP/50017/2020 UIDB/50017/2020The number of cases of failure in the treatment of infections associated with resistant bacteria is on the rise, due to the decreasing efficacy of current antibiotics. Notably, 7α-Acetoxy-6β-hydroxyroyleanone (AHR), a diterpene isolated from different Plectranthus species, showed antibacterial activity, namely against Methicillin-resistant Staphylococcus aureus (MRSA) strains. The high antibacterial activity and low cytotoxicity render this natural compound an interesting alternative against resistant bacteria. The aim of this study is to understand the mechanism of action of AHR on MRSA, using the MRSA/Vancomycin-intermediate S. aureus (VISA) strain CIP 106760, and to study the AHR effect on lipid bilayers and on the cell wall. Although AHR interacted with lipid bilayers, it did not have a significant effect on membrane passive permeability. Alternatively, bacteria treated with this royleanone displayed cell wall disruption, without revealing cell lysis. In conclusion, the results gathered so far point to a yet undescribed mode of action that needs further investigation.publishersversionpublishe

Epidemiology of COVID-19 in the State of Sergipe/Brazil and Its Relationship with Social Indicators

A pandemic is capable of generating a great impact, not only from the point of view of health, but also socioeconomically. In March 2020, the World Health Organization (WHO) declared that a new pandemic situation had arisen, due to the SARS-CoV-2 virus, whose probable origin was zoonotic. The largest number of cases of this disease is concentrated in the United States of America (USA), India, and Brazil. The mortality rate is estimated at 3.4%, but regional differences may exist, and places with a high demographic density have become true epicentres and may be related to higher rates of transmission. In addition to the above, lower human development indexes (HDI) can be related to worse outcomes, especially in the North and Northeast regions of Brazil since they are the least developed places. The Northeast region is the second-most-affected place in the number of COVID-19 cases in Brazil. An analytical observational study of an ecological type was carried out from April to October 2020 to assess the epidemiological situation of COVID-19 in the state of Sergipe and specifically to analyse the incidence of cases and deaths resulting from COVID-19 in the different health regions of the state of Sergipe, in relation to the values of the HDI and demographic density. During the study period, 84,325 cases of COVID-19 were identified, in which 2205 resulted in death. In most of the regions studied, there was a positive association between the number of cases and deaths and the greater the demographic density, but there was no increase in the risk of becoming ill, nor of dying the lower the HDI. Large and crowded cities are places of greatest vulnerability to illness, due to their greater capacity of transmitting the virus; however, further studies are needed to identify other factors that are decisive in the outcomes of this new disease.This research received no external funding.info:eu-repo/semantics/publishedVersio

Integration of miRNA and mRNA expression profles reveals microRNA-regulated networks during muscle wasting in cardiac cachexia

Cardiac cachexia (CC) is a common complication of heart failure (HF) associated with muscle wasting and poor patient prognosis. Although different mechanisms have been proposed to explain muscle wasting during CC, its pathogenesis is still not understood. Here, we described an integrative analysis between miRNA and mRNA expression profiles of muscle wasting during CC. Global gene expression profiling identified 1,281 genes and 19 miRNAs differentially expressed in muscle wasting during CC. Several of these deregulated genes are known or putative targets of the altered miRNAs, including miR-29a-3p, miR-29b-3p, miR-210-5p, miR-214, and miR-489. Gene ontology analysis on integrative mRNA/miRNA expression profiling data revealed miRNA interactions affecting genes that regulate extra-cellular matrix (ECM) organization, proteasome protein degradation, citric acid cycle and respiratory electron transport. We further identified 11 miRNAs, including miR-29a-3p and miR-29b-3p, which target 21 transcripts encoding the collagen proteins related to ECM organization. Integrative miRNA and mRNA global expression data allowed us to identify miRNA target genes involved in skeletal muscle wasting in CC. Our functional experiments in C2C12 cells confirmed that miR-29b down-regulates collagen genes and contributes to muscle cell atrophy. Collectively, our results suggest that key ECM-associated miRNAs and their target genes may contribute to CC in HF

Defining Metabolic Rewiring in Lung Squamous Cell Carcinoma

Metabolomics based on untargeted flow infusion electrospray ionization high-resolution mass spectrometry (FIE-HRMS) can provide a snap-shot of metabolism in living cells. Lung Squamous Cell Carcinoma (SCC) is one of the predominant subtypes of Non-Small Cell Lung Cancers (NSCLCs), which usually shows a poor prognosis. We analysed lung SCC samples and matched histologically normal lung tissues from eight patients. Metabolites were profiled by FIE-HRMS and assessed using t-test and principal component analysis (PCA). Differentially accumulating metabolites were mapped to pathways using the mummichog algorithm in R, and biologically meaningful patterns were indicated by Metabolite Set Enrichment Analysis (MSEA). We identified metabolic rewiring networks, including the suppression of the oxidative pentose pathway and found that the normal tricarboxylic acid (TCA) cycle were decoupled from increases in glycolysis and glutamine reductive carboxylation. Well-established associated effects on nucleotide, amino acid and thiol metabolism were also seen. Novel aspects in SCC tissue were increased in Vitamin B complex cofactors, serotonin and a reduction of &gamma;-aminobutyric acid (GABA). Our results show the value of FIE-HRMS as a high throughput screening method that could be exploited in clinical contexts

Task force on immigration and higher education in Central Massachusetts

In August 2007, the Colleges of Worcester Consortium, Inc. created a task force to examine the issue of immigration and higher education in Central Massachusetts. It has become increasingly clear from recent demographic and economic studies and projections that the population in the northeast, and certainly in Central Massachusetts, is showing minimal growth. There is evidence that a decline in the “native-born” population is caused by significant out-migration due to a number of factors, including the high cost of living, limited career opportunities and a declining birth rate. The limited population growth that is evident is due primarily to the recent influx of immigrants to this area, with the most significant numbers in Worcester coming from Ghana, Brazil, the Dominican Republic, Kenya, El Salvador, Albania and Liberia. It is also clear that the area’s economy is becoming more knowledge-based with an increasing percentage of all new jobs requiring some form of postsecondary education. According to the 2007 Massachusetts Department of Workforce Development’s Job Vacancy Survey, 38 percent of current job vacancies in Massachusetts require an associate’s degree or higher. This represents an increase from 30 percent in 2003. Consequently, the level of education that the immigrant population attains is of vital importance to everyone—not only to immigrant students and their families but also to the economic well-being of the entire region. The Task Force was charged with researching the barriers to higher education faced by this new wave of immigrants and suggesting recommendations to address those barriers. The 36-member Task Force was made up of representatives from Consortium member institutions; federal, state and local governments; community and faithbased organizations; the Worcester Public Schools; the Massachusetts Board of Higher Education; and the Massachusetts Immigrant and Refugee Advocacy (MIRA) Coalition. Meetings were held over six months, during which the Task Force identified three main barriers faced by immigrant communities in accessing higher education, and sub-committees were created to work on each of these. Speakers were invited to present on topics of interest. Two public hearings were held, the first of which was conducted at Worcester State College in October. It attracted community representatives, as well as college and high school faculty and administrators. The second hearing, held at the downtown branch of Quinsigamond Community College (QCC) in December, was attended by immigrants (English for Speakers of Other Languages – ESOL and GED) students as well as QCC staff.Published versio

Processamento auditivo: marcadores de tempo por habilidade auditiva

Model of study: descriptive study and cross. Purpose: to characterize the acquisition time of each hearing ability worked with children diagnosed with Disturbance of Central Auditory Processing, school age, from a speech therapy program pre-established, which lasted 20 sessions. Methods: participated in speech therapy 8 patients aged seven to nine years, school age, in a public school. For the analysis of the data set as a criterion for participation, the individual who completed at least 16 sessions of therapy, or one that reached the proposed objectives (adequacy of skills) in fewer sessions. For each session, which occurred weekly, lasting 40 minutes each, was conducted cursive record the child’s performance for each of the skills worked (location, discrimination, recognition, figure-ground/closing, comprehension e memory). Subsequently, we performed a descriptive content analysis of similarity between the skills. In the record was marked session considered the end of the activity, that is, the acquisition of skill. Results: the number of sessions held by the study subjects ranged from 10 to 20 sessions and the average length of sessions for each skill acquisition of auditory worked varied from three to 16 sessions. Conclusion: it was possible to observe adequacy in auditory skills in all subjects of the group, with a range of time worked for each skill. Studies with larger samples are essential to achieve time markers for the acquisition of auditory skills in this population segment.Modelo de estudo: estudo descritivo e transversal. Objetivo do estudo: caracterizar o tempo de aquisi- ção de cada habilidade auditiva trabalhada em crianças diagnosticadas com Distúrbio do Processamento Auditivo Central, em idade escolar, a partir de um programa de intervenção fonoaudiológica pré-estabelecido, com duração máxima de 20 sessões. Metodologia: foram selecionados, para a intervenção fonoaudiológica, 8 indivíduos na faixa etária de sete a nove anos, em idade escolar, de uma escola pública e que completasse, no mínimo, 16 sessões de terapia, ou, ainda, aquele que atingisse os objetivos propostos (adequação das habilidades) em menor número de sessões. Para cada sessão, que ocorreu semanalmente, com duração de 40 minutos, foi realizado registro cursivo do desempenho da crian- ça, para cada uma das habilidades trabalhadas (localização, discriminação, reconhecimento, figura-fundo/ fechamento, compreensão e memória). Posteriormente, foi realizada análise do conteúdo descritivo por semelhança entre as habilidades. No registro, foi assinalada a sessão considerada como término da atividade, isto é, a aquisição da habilidade. Resultados: o número de sessões realizadas pelos indivíduos do estudo variou de 10 a 20 sessões, sendo que o tempo médio de sessões para a aquisição de cada habilidade auditiva trabalhada oscilou entre três e 16 sessões. Conclusões: foi possível observar adequação das habilidades auditivas em todos os indivíduos do estudo, com variação de tempo para cada habilidade trabalhada. Estudos com maior casuística são fundamentais para que se alcancem marcadores de tempo para aquisição de habilidades auditivas, nesse segmento populacional