Identificação e anotação funcional de RNAs longos não codificadores associados à subtipos moleculares em tumores pancreáticos / Identification of long non coding RNAs associated to molecular subtypes in pancreatic tumors

O Adenocarcinoma Pancreático Ductal (Pancreatic Ductal Adenocarcinoma - PDAC) é a sé- tima causa de mortes por câncer no mundo, com uma taxa de sobrevida de apenas 6%. Embora alguns genes estejam recorrentemente mutados em grande parte dos tumores e sejam críticos para a oncogênese, a heterogeneidade das alterações moleculares tanto no tumor quanto em componentes do microambiente tumoral se reflete em diferentes características fenotípicas com comportamentos clínicos distintos e que têm sido associados a diferentes subtipos moleculares através da análise computacional de dados de alterações somáticas e transcricionais no PDAC. RNAs não codificadores longos (lncRNAs) têm sido reconhecidos como importantes reguladores da expressão gênica em doenças proliferativas mas sua associação com subtipos em PDAC e sua contribuição para o estabelecimento de diferentes fenótipos moleculares e clínicos da doença não foi explorada até o momento. Neste trabalho, foi implementada uma abordagem computacional com o objetivo de identificar e anotar funcionalmente lncRNAs associados a subtipos moleculares de PDAC. Inicialmente, a classificação não supervisionada por Fatoração Matricial Não Negativa (Non-Negative Matrix Factorization - NMF) de dados de expressão gê- nica global de amostras clínicas disponíveis publicamente (The Cancer Genome Atlas - TCGA) resultou na identificação de quatro subgrupos distintos de PDAC, que recapitulam os fenótipos Exócrino/Endócrino, Imunogênico, Escamoso e Progenitor descritos na literatura. Uma análise de expressão diferencial permitiu a identificação de assinaturas de expressão gênica características que incluem lncRNAs associados a cada subgrupo. Através da construção de redes de coexpressão de mRNAs e lncRNAs e a identificação de módulos da rede significativamente enriquecidos em genes que participam em vias moleculares conhecidas foi possível inferir possíveis funções biológicas à lncRNAs associados aos diferentes subtipos moleculares, tais como funções exócrinas/neuroendócrinas, imunogênicas, reparo de DNA/progressão do ciclo celular e progenitoras/morfogênicas. Entre ele, o subgrupo 3, enriquecido para fenótipo Escamoso e associado a hiper-expressão do supressor tumoral TP63, possui dois lncRNAS hiper-expressos neste subgrupo em relação aos outros subgrupos, sendo que o lncRNA antissenso FAM83A-AS1 tem a predição de interagir com as proteínas FGFR2, AXIN1, PTEN, BRAF, SMAD4, TGFBR2, TP53 e CDKN2A, que exercem funções importantes na transdução de sinal e supressão tumoral no câncer incluindo o de pâncreas. Entre os lncRNAs hipo-regulados no subgrupo 3 em relação ao outros subgrupos, alguns, como FLJ42875, LOC338651, C20orf56 e LOC38838 tem predição de interação com alta afinidade à proteína BRCA2, que está envolvida no reparo de DNA e participa de processos de resistência à quimioterápicos. As informações trazidas por este estudo permitem gerar hipóteses sobre a contribuição de lncRNAs para a definição de subtipos moleculares de PDAC e priorizar candidatos e experimentos para estudos funcionais de modo a contribuir para um melhor entendimento sobre os mecanismos de ação de lncRNAs na tumorigênese e agressividade do câncer de pâncreas

Pancreatic Ductal Adenocarcinoma (PDAC) is the seventh cause of worldwide cancer related deaths, with an overall survival rate of only 6%. Some genes might be recurrently mutated in a large number of tumors, and be critical for oncogenesis, molecular alteration heterogeneity both in the tumor as all as in the tumor microenvironment is reflected in diverse phenotypic features with distinct clinical outcomes, and this distinction in multiple molecular subtypes has been drawn through transcriptional and somatic alteration computational analysis within PDAC. Long Non Coding RNAs (lncRNAs) have been recognized as important gene expression regulators in proliferative diseases, but its association to molecular subtypes in PDAC and its contribution in the establishment of diverse molecular and clinical phenotypes hasnt been explored at length until the present. This work focused on the implementation of a computational approach with the objective of lncRNA identification and functional annotation associated to distinct molecular subtypes in PDAC. Initially, Non-negative Matrix Factorization (NMF), an unsupervised classification method, applied to global gene expression data from publicly available clinical samples (The Cancer Genome Atlas - TCGA) resulted in the identification of four distinct PDAC molecular subgroups reminiscent of Exocrine/Endocrine, Immunogenic, Squamous and Progenitor phenotypes. Differential expression analysis allowed a characteristic gene expression signature identification, including distinct molecular subtype associated lncRNAs. mRNA and lncRNA containing gene co-expression modules significantly enriched annotated pathways containing the molecular subtype associated lncRNAs allowed to designate possible molecular functions of the distinct molecular subtype associated lncRNAs, such as exocrine/neuroendocrine, immunogenic, DNA repair/cell cycle progression and progenitor/morphogenic functions. Subgroup 3, enriched with a Squamous phenotype and associated to TP63 over-expression contains two lncRNAs over-expressed compared to other subgroups; furthermore, the antisense lncRNA FAM83A-AS1 yielded a predicted lncRNA-protein interaction to FGFR2, AXIN1, PTEN, BRAF, SMAD4, TGFBR2, TP53 and CDKN2A, proteins that play important signal transduction and tumor suppressor roles in several cancer types, including pancreas. Among under-expressed lncRNAs in subgroup 3 compared to the other subgroups, some, such as FLJ42875, LOC338651, C20orf56 and LOC38838 yilded a high protein interaction prediction score with BRCA2, a protein involved in DNA repair and processes resuling in chemotherapy resistance. The information brought by this study allowed to generate hypothesis on lncRNA contribution to define PDAC molecular subtypes, helping prioritize candidates and experiments for functional studies, thus contributing to a better understanding on lncRNA mechanisms related to tumor progression and aggressiveness in pancreatic cancer

Dietary effect of green tea extract on hydration improvement and metabolism of free amino acid generation in epidermis of UV-irradiated hairless mice / 한국영양학회지

PURPOSE: Ultraviolet (UV) irradiation decreases epidermal hydration, which is maintained by reduction of natural moisturizing factors (NMFs). Among various NMFs, free amino acids (AA) are major constituents generated by filaggrin degradation. This experiment was conducted to determine whether or not dietary supplementation of green tea extract (GTE) in UV-irradiated mice can improve epidermal levels of hydration, filaggrin, free AAs, and peptidylarginine deiminase-3 (PAD3) expression (an enzyme involved in filaggrin degradation). METHODS: Hairless mice were fed a diet of 1% GTE for 10 weeks in parallel with UV irradiation (group UV+1%GTE). As controls, hairless mice were fed a control diet in parallel with (group UV+) or without (group UV-) UV irradiation. RESULTS: In group UV+, epidermal levels of hydration and filaggrin were lower than those in group UV-; these levels increased in group UV+1% GTE to levels similar to group UV-. Epidermal levels of PAD3 and major AAs of NMF, alanine, glycine and serine were similar in groups UV- and UV+, whereas these levels highly increased in group UV+1% GTE. CONCLUSION: Dietary GTE improves epidermal hydration by filaggrin generation and degradation into AAs.

Confocal Raman spectroscopy: determination of natural moisturizing factor profile related to skin hydration

INTRODUCTION: Skin health and skin care to reduce the effects of aging are the main interests of many researchers. The skin is very important because it protects the body from various effects of the external environment, and studies of the largest organ of the human body have been conducted since antiquity. In skin, aging effects are severe enough to promote changes in cell structure and biochemical composition. In this study, we quantitatively analyzed the water content and natural moisturizing factor of human facial skin in vivo and in real time by confocal Raman spectroscopy. This non-invasive technique is capable of providing detailed information on the biochemical composition at different depth profiles in the skin. METHODS: We studied 10 volunteers, phototype II (40 and 50 years old), using a confocal Raman system to examine the skin surface down to 25 µm. Raman spectra were obtained before product use (T0), and after 30 days of continuous use of cosmetics (T30). RESULTS: The results show a significant increase of 6.4% in water content in the surface layer of the facial skin after the cosmetic use. The amounts of natural moisturizing factor (NMF) compounds were also increased. Urocanic acid underwent a greater change in relation to carboxylic acid pyrrolidone, with a 38.5% increase in the stratum corneum. CONCLUSION: Confocal Raman spectroscopy identified changes in the biochemical composition of the superficial layers of the epidermis, which suggests the anti-aging efficacy of the formulation.

Deducing Isoform Abundance from Exon Junction Microarray

Alternative splicing (AS) is an important mechanism of producing transcriptome diversity and microarray techniques are being used increasingly to monitor the splice variants. There exist three types of microarrays interrogating AS events-junction, exon, and tiling arrays. Junction probes have the advantage of monitoring the splice site directly. Johnson et al., performed a genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays (Science 302:2141-2144, 2003), which monitored splicing at every known exon-exon junctions for more than 10,000 multi-exon human genes in 52 tissues and cell lines. Here, we describe an algorithm to deduce the relative concentration of isoforms from the junction array data. Non-negative Matrix Factorization (NMF) is applied to obtain the transcript structure inferred from the expression data. Then we choose the transcript models consistent with the ECgene model of alternative splicing which is based on mRNA and EST alignment. The probe-transcript matrix is constructed using the NMF-consistent ECgene transcripts, and the isoform abundance is deduced from the non-negative least squares (NNLS) fitting of experimental data. Our method can be easily extended to other types of microarrays with exon or junction probes.

Seasonal Variations of the Urinary N-Methylformamide Concentration among Workers at a Synthetic Leather Factory / 대한산업의학회지

OBJECTIVES: This study was carried out to identify seasonal variations of urinary concentrations of N-methylformamide (NMF) among workers employed at a synthetic leather factory. METHODS: Study subjects consisted of 16 male and 6 female workers who were involved in the direct treatment of dimethylformamide (DMF) in a synthetic leather factory. By using health examination data and the results of air measurements and biologic monitoring conducted in February and July, 2001, we identified seasonal variations of the DMF concentrations in the air and NMF concentrations in urine. RESULTS: 1) In winter and summer, average temperatures at the working sites were 3.2 degrees C and 26.5 degrees C, respectively and average humidities were 35.4 % and 84.5 %, respectively. 2) Airborne DMF concentrations were not significantly different between summer (13.78 ppm) and winter (11.55 ppm). 3) NMF concentrations in urine were found to be significantly higher in summer (96.09 mg/g creatinine) than in winter (31.23 mg/g creatinine) (p<0.001). CONCLUSIONS: The seasonal difference in the urinary excretion values of NMF may be due to increased dermal absorption of DMF with the higher ambient temperature and humidity in summer and the increased area of exposed skin.

Dry Skin

Though there is ambiguity in its medical definition, dry skin is a frequent skin problem of increasing importance these days. Generally "dry skin" denotes the status of skin showing erythema, roughness, scales, and itching resulted from low water content in the skin. Abnormalities in epidermal lipids, natural moisturizing factors, or corneocyte desquamation are regarded as important factors in its pathophysiology. It is not only accompanied with skin aging, but with various kinds of skin and systemic diseases(such as atopic dermatitis, ichthyosis, chronic renal failure, and diabetes mellitus). Important principles in the management or treatment of dry skin are preventing excessive washing and keeping moisture in the epidermis. For gentle cleansing, mild surfactants are better than the soap. Moisturizers are applied to the surface of skin to increase epidermal water content. Two different kinds of moisturizers are used as a mixture for the best result. Humectants are the material that draw water from the air or dermis. And emollients are the material that protects membrane by preventing water from evaporating from the epidermis. Though moisturizers are very helpful in management of dry skin, harmful result may happen by inadequate selection and wrong use.

A Study on the N-methylformamide Excretion Rate of Workers at Synthetic Leather Factories in Korea / 대한산업의학회지

This study was conducted to examine the excretion rate of dimethylformamide (DMF) from the workers exposed to DMF. The study was done at two synthetic leather factories located in Kyeonggi-do from the period of May 2 to 30, 1996. N-methyl- formamide (NMF) concentrations in urine were measured and compared by the three exposure level of DMF in air. The mean concentration of the Low (dry and winder part). Moderate (rinsing part) and High (mixing and coating part) exposure group were 3.99+/-3.54. 10.19 +/-5.69 and 32.10+/-7.87 mg/m3 during workshift of 8 hours, respectively. The mean concentration of urinary N-methylforinamide (NMF) were 2.13+/-2.58, 11.16+/-4.98 and 26.24 +/-7.35 mg/g creatinine, respectively. The concentration of NMIF in urine could reach to maximum in 3 hours and was reduced nearly to zero in about 18 hours after exposure to DMF.