Transcriptomic Profile of Canine Mammary Ductal Carcinoma.

Dogs can be excellent models for spontaneous studies about breast cancers, presenting similarities in clinical behavior and molecular pathways of the disease. Thus, analyses of the canine transcriptome can identify deregulated genes and pathways, contributing to the identification of biomarkers and new therapeutic targets, benefiting humans and animals. In this context, this study aimed to determine the transcriptional profile of canine mammary ductal carcinoma and contribute to the clarification of the importance of deregulated molecules in the molecular pathways involved in the disease. Therefore, we used mammary ductal carcinoma tissue samples and non-tumor mammary tissue from the radical mastectomy of six female dogs. Sequencing was performed on the NextSeq-500 System platform. A comparison of carcinoma tissue and normal tissue revealed 633 downregulated and 573 upregulated genes, which were able to differentiate the groups by principal component analysis. Gene ontology analysis indicated that inflammatory, cell differentiation and adhesion, and extracellular matrix maintenance pathways were mainly deregulated in this series. The main differentially expressed genes observed in this research can indicate greater disease aggressiveness and worse prognosis. Finally, the study of the canine transcriptome indicates that it is an excellent model to generate information relevant to oncology in both species.

Differential Plasma Metabolites between High- and Low-Grade Meningioma Cases.

Meningiomas (MGMs) are currently classified into grades I, II, and III. High-grade tumors are correlated with decreased survival rates and increased recurrence rates. The current grading classification is based on histological criteria and determined only after surgical tumor sampling. This study aimed to identify plasma metabolic alterations in meningiomas of different grades, which would aid surgeons in predefining the ideal surgical strategy. Plasma samples were collected from 51 patients with meningioma and classified into low-grade (LG) (grade I; n = 43), and high-grade (HG) samples (grade II, n = 5; grade III, n = 3). An untargeted metabolomic approach was used to analyze plasma metabolites. Statistical analyses were performed to select differential biomarkers among HG and LG groups. Metabolites were identified using tandem mass spectrometry along with database verification. Five and four differential biomarkers were identified for HG and LG meningiomas, respectively. To evaluate the potential of HG MGM metabolites to differentiate between HG and LG tumors, a receiving operating characteristic curve was constructed, which revealed an area under the curve of 95.7%. This indicates that the five HG MGM metabolites represent metabolic alterations that can differentiate between LG and HG meningiomas. These metabolites may indicate tumor grade even before the appearance of histological features.

Hepatitis D infection in Brazil: Prevalence and geographical distribution of anti-Delta antibody.

In Brazil, the Amazon Basin is endemic for hepatitis D virus (HDV) infection; however, studies in other regions of the country are scarce. This study aims to map the seroepidemiological situation of anti-Delta antibodies in chronic hepatitis B carriers in all five Brazilian geographic regions. Serum samples from 1240 HBsAg positive individuals (55.4% men; mean age 43.1 ± 13.4 years) from 24 of 26 Brazilian states were tested for the presence of anti-Delta antibodies using a commercial immunoassay. Anti-Delta antibodies were detected in 40 samples (3.2%; 52.5% female; mean age of 38.1 ± 13.8 years). Age less than 20 years was significantly associated with anti-HDV positivity (P < 0.001). The distribution of anti-Delta differed markedly in the diverse regions of the country. The highest prevalence of anti-HDV was found in the North (8.5%; P < 0.001), followed by Central West (2.5%), Southeast (1.7%), Northeast (0.8%), and South (0.0%). Anti-Delta antibodies were detected in 12 states, but more than 60% of the positive cases were observed in two states, Amazonas and Acre, located in the western portion of the Amazon region. The overall HDV prevalence of 3.2% emphasizes that HDV is far from being a disease under control in Brazil. Despite the low HDV prevalence in non-endemic regions, this infection persists as a major concern in two states (Acre and Amazonas) in the north of the country, indicating that a continuous epidemiological surveillance program should be implemented in all Brazilian regions.

Nationwide overview of the distribution of hepatitis B virus genotypes in Brazil: a 1000-sample multicentre study.

The influence of hepatitis B virus (HBV) genotypes in the natural history of the disease and its response to antiviral treatment have been addressed in many studies. In Brazil, studies on HBV genotype circulation have been restricted to specific population groups and states. Here, we have conducted a nationwide multicentre study with an unprecedented sample size representing all Brazilian regions in an effort to better understand the viral variants of HBV circulating among chronic carriers. Seven HBV genotypes were found circulating in Brazil. Overall, HBV/A was the most prevalent, identified in 589 (58.7 %) samples, followed by HBV/D (23.4 %) and HBV/F (11.3 %). Genotypes E, G, C and B were found in a minor proportion. The distribution of the genotypes differed markedly from the north to the south of the country. While HBV/A was the most prevalent in the North (71.6 %) and Northeast (65.0 %) regions, HBV/D was found in 78.9 % of the specimens analysed in the South region. HBV/F was the second most prevalent genotype in the Northeast region (23.5 %). It was detected in low proportions (7 to 10 %) in the North, Central-West and Southeast regions, and in only one sample in the South region. HBV/E was detected in all regions except in the South, while monoinfection with HBV/G was found countrywide, with the exception of Central-West states. Our sampling covered 24 of the 26 Brazilian states and the Federal District and is the first report of genotype distribution in seven states. This nationwide study provides the most complete overview of HBV genotype distribution in Brazil to date and reflects the origin and plurality of the Brazilian population.

Circulation of HDV Genotypes in Brazil: Identification of a Putative Novel HDV-8 Subgenotype.

Hepatitis D virus (HDV) is classified into 8 genotypes (1 to 8) and several subgenotypes. In Brazil, HDV-3 and HDV-1 predominate; however, most of the diagnosis efforts and molecular studies are directed to the area of endemicity of the Amazon Basin. Here, we determined the molecular epidemiological profile of circulating HDV in Brazilian HBsAg-positive patients between 2013 and 2015 in areas of endemicity and non-areas of endemicity. From 38 anti-HDV-positive individuals, 13 (34.2%) had detectable HDV-RNA and 11 (28.9%) were successfully sequenced. Partial HDAg (~320 nt) sequencing followed by phylogenetic analysis with reference sequences resulted in the identification of HDV-3 (9/11; 81.8%), HDV-5 (1/11; 9.1%), and HDV-8 (1/11; 9.1%). Most HDV-3 samples (8/9; 88.9%) were found in the endemic North region, while one was found in Central-West Brazil, a non-area of endemicity. HDV-5 and 8, genotypes native from African countries, were found in São Paulo, a cosmopolitan city from Southeast Brazil with a high circulation of immigrants. Phylogenetic analysis of HDV-8 strains indicated that the sample determined in our study, along with previously reported sequences from Brazil, formed a highly supported monophyletic clade, likely representing a putative novel HDV-8 subgenotype. IMPORTANCE Considered a neglected pathogen until the last 2 decades, an increase in the availability of genetic data of hepatitis D virus (HDV) strains around the world has been noticed recently, resulting in the proposition of different classifications. Our study aimed to determine the molecular epidemiological profile of HDV isolates circulating in areas of endemicity and non-areas of endemicity in Brazil. Based on the analyzed fragment, HDV-8 sequences clustered out of the clades formed by subgenotypes 8a and 8b might suggest the identification of a novel subgenotype, putatively designated subgenotype 8c. Our findings demonstrate the importance of continuous epidemiological surveillance to map HDV spread pathways and the introduction of imported variants. It also reinforces that as the amount of HDV genomes generated and reported increases, we will have changes in viral classification and, consequently, in our understanding of the dynamics of variability of this viral agent.

Large-scale transcriptome analyses reveal new genetic marker candidates of head, neck, and thyroid cancer.

A detailed genome mapping analysis of 213,636 expressed sequence tags (EST) derived from nontumor and tumor tissues of the oral cavity, larynx, pharynx, and thyroid was done. Transcripts matching known human genes were identified; potential new splice variants were flagged and subjected to manual curation, pointing to 788 putatively new alternative splicing isoforms, the majority (75%) being insertion events. A subset of 34 new splicing isoforms (5% of 788 events) was selected and 23 (68%) were confirmed by reverse transcription-PCR and DNA sequencing. Putative new genes were revealed, including six transcripts mapped to well-studied chromosomes such as 22, as well as transcripts that mapped to 253 intergenic regions. In addition, 2,251 noncoding intronic RNAs, eventually involved in transcriptional regulation, were found. A set of 250 candidate markers for loss of heterozygosis or gene amplification was selected by identifying transcripts that mapped to genomic regions previously known to be frequently amplified or deleted in head, neck, and thyroid tumors. Three of these markers were evaluated by quantitative reverse transcription-PCR in an independent set of individual samples. Along with detailed clinical data about tumor origin, the information reported here is now publicly available on a dedicated Web site as a resource for further biological investigation. This first in silico reconstruction of the head, neck, and thyroid transcriptomes points to a wealth of new candidate markers that can be used for future studies on the molecular basis of these tumors. Similar analysis is warranted for a number of other tumors for which large EST data sets are available.

Identification and complete sequencing of novel human transcripts through the use of mouse orthologs and testis cDNA sequences.

The correct identification of all human genes, and their derived transcripts, has not yet been achieved, and it remains one of the major aims of the worldwide genomics community. Computational programs suggest the existence of 30,000 to 40,000 human genes. However, definitive gene identification can only be achieved by experimental approaches. We used two distinct methodologies, one based on the alignment of mouse orthologous sequences to the human genome, and another based on the construction of a high-quality human testis cDNA library, in an attempt to identify new human transcripts within the human genome sequence. We generated 47 complete human transcript sequences, comprising 27 unannotated and 20 annotated sequences. Eight of these transcripts are variants of previously known genes. These transcripts were characterized according to size, number of exons, and chromosomal localization, and a search for protein domains was undertaken based on their putative open reading frames. In silico expression analysis suggests that some of these transcripts are expressed at low levels and in a restricted set of tissues.

Lower levels of oxidative DNA damage and apoptosis in lymphocytes from patients undergoing surgery with propofol anesthesia.

Propofol, which is widely used as an intravenous anesthetic, has a phenolic structure similar to that of α-tocopherol with antioxidant properties that could prevent genotoxicity and cytotoxicity in lymphocytes of anesthetized patients. The aims of this study were to evaluate oxidative DNA damage and apoptosis in lymphocytes and the expression of DNA repair genes in blood cells from patients undergoing elective surgery under anesthesia with propofol. Twenty healthy adults of both genders (18-50 years old) who were scheduled for otorhinological surgery were enrolled in this study. Blood samples were collected before anesthesia induction (T1-baseline), 120 min after anesthesia induction (T2), and on the first postoperative day (T3). Oxidative DNA damage in peripheral lymphocytes was assessed using the comet assay. Lymphocytes were phenotyped as T helper or cytotoxic T cells, and apoptosis was evaluated using flow cytometry. The expression of DNA repair genes (hOGG1 and XRCC1) was assessed by quantitative polymerase chain reaction. A reduction in the level of oxidized purines in DNA (P < 0.01) was observed 120 min after anesthesia induction, and reduced apoptosis of T helper cells was observed 120 min after anesthesia induction and on the first postoperative day. Down-regulation of hOGG1 and XRCC1 gene expression was observed on the first postoperative day. In conclusion, patients undergoing non-invasive surgery under propofol anesthesia presented lower levels of oxidized purines and apoptosis of T helper lymphocytes. Furthermore, anesthesia with propofol did not directly influence the expression of the DNA repair genes hOGG1 and XRCC1 in blood cells.

Detecção do rearranjo da proteína BCL2/JH em carcinomas epidermoides de boca e faringe / Detection of protein BCL2/JH rearrangement in epidermoid carcinomas of mouth and pharynx

Introdução: A proteína BCL2 encontrada na membrana mitocondrial interna, regula a apoptose inibindo a morte celular programada. A translocação (14;18), detectada em 70 a 85% dos linfomas foliculares, leva a superexpressão da proteína BCL2, pela justaposição do gene BCL2 ao segmento JH do gene da cadeia pesada da imunoglobulina. Porém, os achados da expressão da BCL2 em carcinoma de cabeça e pescoço são contraditórios. Objetivo: Investigar a presença da translocação (14;18) do gene BCL2 em carcinomas de cabeça e pescoço. Método: Foram examinadas 16 amostras de DNA, sendo 13 de carcinomas de células escamosas (CCE) e 3 de epidermoide (CE), por meio da reação em cadeia da polimerase (PCR). Resultados: O rearranjo BCL2/JH foi encontrado em 2 (15%) dos 13 casos de CCE e em nenhum dos 3 casos de CE. A média de frequência de moléculas com rearranjo foi de 46,44 x 107. Não foi observada associação entre a presença de rearranjo e a exposição ao tabaco e álcool (p=0,6545). Conclusão: Diferente dos resultados encontrados em linfomas foliculares a presença da translocação (14;18) em carcinomas de cabeça e pescoço não é comum e, quando ocorre, pode ser uma mutação ocasional não associada a exposição ao tabaco e álcool.

Introduction: The BCL2 protein found in the internal mothocondrial membrana regulates the apoptosis preventing the programmed cell death. The translocation (14:18), detected in 70 to 85% of the follicular lymphoma, lead the super expression of BCL2 protein, by juxtaposition of BCL2 gene to the JH segment of the immunoglobulins' heavy chain gene. However, the found of the BCL2 expression in head and neck carcinoma are contradictious. Objective: To investigate the presence of the translocation (14:18) of the BCL2 gene in head and neck carcinoma. Method: Sixteen DNA samplers were examinated being 13 of squamous cells carcinoma (SCC) and 3 of epidermoid (CE), y means of chain reaction of the polymerase (PCR). Results: The BCL2/JH rearrangement in 2 (15%) of the CCE 13 cases and in none of the 3 cases of CE. The average of the frequency of molecules with rearrangement was 46,44x107. Was not observed association between the rearrangement presence and the exhibition to tobacco and alcohol (p=0, 6545). Conclusion: Different from the results found in follicular lymphoma, the presence of the translocation (14; 18) in head and neck carcinomas is not common and, when it occurs, it can be an occasional mutation not associated to exhibition to the tobacco and alcohol.

Methylation status of the SOCS 1 and JUNB genes in chronic myeloid leukemia patients / Padrão de metilação dos genes SOCS 1 e JUNB em pacientes com leucemia mieloide crônica

Alterations in the methylation status of genes may contribute to the progression of Chronic Myeloid Leukemia (CML). In this study, the methylation status in exon2 of SOCS- 1 and promoter regions of both SOCS- 1 and JUNB were evaluated in CML patients. The methylation status of these genes was analyzed using methylation- specific Polymerase Chain Reaction (MSP) in 30 samples from CML patients, 30 samples from these same patients after hematopoietic stem cell transplantation (HSCT) and 30 samples from healthy controls. The samples of CML patients presented methylation as follows: JUNB gene (3.3 percent), promoter region of the SOCS- 1 gene (6.6 percent) and exon2 of the SOCS- 1 gene (46.6 percent). The samples of the healthy individuals presented methylation (10 percent, P = 0.002) only in exon 2 of the SOCS- 1 gene. After transplantation, patients presented alterations in the methylation status of the promoter region of the SOCS- 1 gene (6.6 percent), exon2 of SOCS- 1 (46.6 percent) and the promoter region of the JUNB gene (16.6 percent). Methylation of the promoter regions of the SOCS- 1 gene and the JUNB gene is not a frequent event in CML. In contrast, SOCS- 1 gene methylation in exon2 is a frequent event, susceptible to alterations in status after HSCT with possible implications for the progression of this disease.

Alteração no padrão de metilação gênica pode contribuir para a progressão da leucemia mielóide crônica (LMC). Neste estudo, o padrão de metilação no exon 2 do gene SOCS- 1 e região promotora de ambos SOCS- 1 e JUNB foram avaliadas em pacientes com LMC. O padrão de metilação desses genes foi analisado usando a técnica " methylation- specific polymerase chain reaction (MSP)" em 30 amostras de pacientes com LMC, 30 amostras desses mesmos pacientes após transplante de medula óssea (TMO) e 30 amostras controle de indivíduos saudáveis. As amostras de pacientes com LMC apresentaram o seguinte padrão de metilação: gene JUNB (3.3 por cento), região promotora do gene SOCS- 1 (6.6 por cento) e exon2 do gene SOCS- 1 (46.6 por cento). Amostras dos indivíduos saudáveis apresentaram metilação somente no exon 2 do gene SOCS- 1 (10 por cento, P = 0.002). Após o transplante, os pacientes apresentaram alterações no padrão de metilação da região promotora do gene SOCS- 1 (6.6 por cento), no exon2 do gene SOCS- 1 (46.6 por cento) e na região promotora do gene JUNB (16.6 por cento). Metilação das regiões promotoras dos genes SOCS- 1 e JUNB não é um evento frequente em LMC. Em contraste, metilação no exon 2 do gene SOCS- 1 apresenta- se como um evento frequente, suscetível a alterações no padrão de metilação após TMO.

Extração de DNA de materiais de arquivo e fontes escassas para utilização em reação de polimerização em cadeia (PCR) / Methods of DNA extraction from archived materials and rare sources for utilization in polymer chain reaction

Este trabalho visou a comparação de cinco métodos diferentes de extração de DNA de materiais de arquivo (tecidos incluídos em parafina, esfregaços de sangue periférico - corados e não corados com Leishman, lâminas com mielogramas, gotas de sangue em Guthrie Card) e de fontes escassas (células bucais, um e três bulbos capilares e 2 mL de urina), para que fossem avaliadas a facilidade de aplicação e a facilidade de amplificação deste DNA pela técnica da reação de polimerização em cadeia (PCR). Os métodos incluíram digestão por proteinase K, seguida ou não por purificação com fenol/clorofórmio; Chelex 100® (BioRad); Insta Gene® (BioRad) e fervura em água estéril. O DNA obtido foi testado para amplificação de três fragmentos gênicos: Brain-derived neutrophic factor (764 pb), Factor V Leiden (220 pb) e Abelson (106 pb). De acordo com o comprimento do fragmento gênico estudado, da fonte potencial de DNA e do método de extração utilizado, os resultados caracterizaram o melhor caminho para padronização de procedimentos técnicos a serem incluídos no manual de Procedimentos Operacionais Padrão do Laboratório de Biologia Molecular do Hemocentro - HC - Unesp - Botucatu.

The present work aimed at comparing five different methods ofDNA extraction of samples from archived materials (paraffinembeddedtissues, peripheral blood smears - stained or not withLeishman, aspired bone marrow smears and Guthrie cardbloodspots) and from rare sources (oral cells, one and threecapillary bulbs, 2 mL of urine), to evaluate the ease of applicationand the possibility of amplification of this DNA by thepolymerization chain reaction (PCR) technique. The methodsincluded proteinase K digestion - followed or not by phenol/chloroform purification, Chelex 100® (BioRad), InstaGene®(BioRad) and boiling in the sterile water. The DNA obtained wastested for amplification of three genic fragments: the brain-derivedneutrophic factor gene (764 bp), the Factor V Leiden gene (220bp) and the Abelson gene (106 bp). According to the gene fragmentlength studied, the DNA potential source and the extraction methodused, the results characterized the best way to standardizetechnical procedures to be included in the Standard OperationalProcedure Manual of the Molecular Biology Laboratory of theBlood Center in the Medicine School of Unesp, Botucatu, Brazil.

Identification and complete sequencing of novel human transcripts through the use of mouse orthologs and testis cDNA sequences

The correct identification of all human genes, and their derived transcripts, has not yet been achieved, and it remains one of the major aims of the worldwide genomics community. Computational programs suggest the existence of 30,000 to 40,000 human genes. However, definitive gene identification can only be achieved by experimental approaches. We used two distinct methodologies, one based on the alignment of mouse orthologous sequences to the human genome, and another based on the construction of a high-quality human testis cDNA library, in an attempt to identify new human transcripts within the human genome sequence. We generated 47 complete human transcript sequences, comprising 27 unannotated and 20 annotated sequences. Eight of these transcripts are variants of previously known genes. These transcripts were characterized according to size, number of exons, and chromosomal localization, and a search for protein domains was undertaken based on their putative open reading frames. In silico expression analysis suggests that some of these transcripts are expressed at low levels and in a restricted set of tissues.

Detecçäo de mRNAs quiméricos BCR/ABL em pacientes portadores de leucemia mielóide crônica, leucemia linfóide aguda/mielóide aguda pela reaçäo de polimerizaçäo em cadeia (PCR) / Detection of BCR/ABL chimeric mRNAs in patients with chronic myeloid leukemia, acute lymphocytic leukemia/ acute myeloid by polimerase chain reaction (PCR)

A leucemia mielóide crônica (LMC) é uma doença caracterizada pela proliferaçao e acumulaçao de células mielóides e seus precursores, induzida pela transformaçao neoplásica de uma célula hematopoética pluripotente, a stem-cell. Esse clone possui uma anormalidade citogenética que se caracteriza pela translocaçao recíproca entre os cromossomos 9 e 22 [t(9;22) (q34;q11)], resultando na formaçao do cromossomo Philadelphia (Ph1). O resultado dessa translocaçao é a justaposiçao do gene BCR com o protooncogene ABL, originando um gene híbrido que codifica uma proteína anormal com atividade tirosina quinase exacerbada. A reaçao de polimerizaçao em cadeia (PCR) baseada na amplificaçao do cDNA híbrido BCR/ABL tem sido considerada um meio altamente sensível e específico para detecçao dessa patologia, em nível molecular. O RNA total foi extraído pelo método de isocianato de guanidina, de leucócitos de sangue periférico e (ou) medula óssea. A primeira fita (cDNA) foi sintetizada utilizando primer complementar à regiao 3' do mRNA quimérico BCR/ABL, transcriptase reversa (Super Script II - Gibco-BRL) segundo sugestao do fabricante. A reaçao de PCR foi realizada em duas etapas: a primeira utilizando primers complementares à regiao BCR e ABL, num total de 25 ciclos com temperatura de 94 graus Celsius, 49 graus Celsius e 72 graus Celsius para desnaturaçao, anelamento e extensao, respectivamente; na segunda etapa foram utilizados primers internos aos primeiros (Nested-PCR) num total de 35 ciclos com temperatura de anelamento de 60 graus Celsius (primers sintetizados pela Genomic - Engenharia Molecular, SP). O controle de todo o procedimento técnico foi realizado pela amplificaçao de uma regiao do gene ABL. A presença de bandas características da LMC foram visualizadas após eletroforese em gel de poliacrilamida 6 por cento e coloraçao por brometo de etídio. O método foi considerado extremamente sensível e rápido para a detecçao da t(9;22) quando comparada com a citogenética convencional.