Biogeographical distribution analysis of hydrocarbon degrading and biosurfactant producing genes suggests that near-equatorial biomes have higher abundance of genes with potential for bioremediation.

BACKGROUND: Bacterial and Archaeal communities have a complex, symbiotic role in crude oil bioremediation. Their biosurfactants and degradation enzymes have been in the spotlight, mainly due to the awareness of ecosystem pollution caused by crude oil accidents and their use. Initially, the scientific community studied the role of individual microbial species by characterizing and optimizing their biosurfactant and oil degradation genes, studying their individual distribution. However, with the advances in genomics, in particular with the use of New-Generation-Sequencing and Metagenomics, it is now possible to have a macro view of the complex pathways related to the symbiotic degradation of hydrocarbons and surfactant production. It is now possible, although more challenging, to obtain the DNA information of an entire microbial community before automatically characterizing it. By characterizing and understanding the interconnected role of microorganisms and the role of degradation and biosurfactant genes in an ecosystem, it becomes possible to develop new biotechnological approaches for bioremediation use. This paper analyzes 46 different metagenome samples, spanning 20 biomes from different geographies obtained from different research projects. RESULTS: A metagenomics bioinformatics pipeline, focused on the biodegradation and biosurfactant-production pathways, genes and organisms, was applied. Our main results show that: (1) surfactation and degradation are correlated events, and therefore should be studied together; (2) terrestrial biomes present more degradation genes, especially cyclic compounds, and less surfactation genes, when compared to water biomes; and (3) latitude has a significant influence on the diversity of genes involved in biodegradation and biosurfactant production. This suggests that microbiomes found near the equator are richer in genes that have a role in these processes and thus have a higher biotechnological potential. CONCLUSION: In this work we have focused on the biogeographical distribution of hydrocarbon degrading and biosurfactant producing genes. Our principle results can be seen as an important step forward in the application of bioremediation techniques, by considering the biostimulation, optimization or manipulation of a starting microbial consortia from the areas with higher degradation and biosurfactant producing genetic diversity.

Interleukin 10 (IL10) proximal promoter polymorphisms beyond clinical response in classical Hodgkin lymphoma: Exploring the basis for the genetic control of the tumor microenvironment.

Interleukin-10 (IL10) is an immune regulatory cytokine. Single nucleotide polymorphisms (SNPs) in IL10 promoter have been associated with prognosis in adult classical Hodgkin lymphoma (cHL). We analyzed IL10 SNPs -1082 and -592 in respect of therapy response, gene expression and tumor microenvironment (TME) composition in 98 pediatric patients with cHL. As confirmatory results, we found that -1082AA/AG; -592CC genotypes and ATA haplotype were associated with unfavourable prognosis: Progression-free survival (PFS) was shorter in -1082AA+AG (72.2%) than in GG patients (100%) (P = 0.024), and in -592AA (50%) and AC (74.2%) vs. CC patients (87.0%) (P = 0.009). In multivariate analysis, the -592CC genotype and the ATA haplotype retained prognostic impact (HR: 0.41, 95% CI 0.2-0.86; P = 0.018, and HR: 3.06 95% CI 1.03-9.12; P = 0.044, respectively). Our analysis further led to some new observations, namely: (1) Low IL10 mRNA expression was associated with -1082GG genotype (P = 0.014); (2) IL10 promoter polymorphisms influence TME composition;-1082GG/-592CC carriers showed low numbers of infiltrating cells expressing MAF transcription factor (20 vs. 78 and 49 vs. 108 cells/mm2, respectively; P< 0.05); while ATA haplotype (high expression) associated with high numbers of MAF+ cells (P = 0.005). Specifically, -1082GG patients exhibited low percentages of CD68+MAF+ (M2-like) intratumoral macrophages (15.04% vs. 47.26%, P = 0.017). Considering ours as an independent validation cohort, our results give support to the clinical importance of IL10 polymorphisms in the full spectrum of cHL, and advance the concept of genetic control of microenvironment composition as a basis for susceptibility and therapeutic response.

Relationship of Epstein-Barr virus and interleukin 10 promoter polymorphisms with the risk and clinical outcome of childhood Burkitt lymphoma.

Epstein-Barr virus (EBV) is an important environmental factor associated to the development of Burkitt lymphoma (BL) in endemic and intermediate risk regions. However, little is known about the contribution of genetic constitution to the development and clinical response of the disease. The aim of this work was to investigate the role of EBV and Interleukin 10 (IL10) single nucleotide polymorphisms (-1082A/G, -819C/T, -592C/A) and microsatellites (IL10.R and IL10.G) in susceptibility and clinical outcome in pediatric BL patients, in a region with intermediate EBV association frequency. The frequencies of IL10 promoter Single nucleotide polymorphisms -1082A/G, -819C/T, -592C/A, and IL10.R and IL10.G microsatellites were compared in 62 pediatric patients and 216 healthy donors. IL10 -1082GG and GCC/GCC genotypes were more frequent in patients than in controls, and associated to a higher risk of BL development (GG genotype OR 2.62, 95% CI, 1.25-5.51; P = 0.008; Pc = 0.024). EBV was detected in tumor samples by EBER-ISH in 54.1% of cases. EBV+ patients exhibited a better event free survival (EFS) (P = 0.019) than EBV- patients. Carriers of IL10 R3-GCC had worse EFS (P = 0.028). Our results suggest a risk effect and an independent prognostic value of IL10 polymorphisms and EBV in childhood BL patients.

Cell cycle characteristics and Epstein-Barr virus are differentially associated with aggressive and non-aggressive subsets of Hodgkin lymphoma in pediatric patients.

We investigated the correlation of tumor characteristics with clinico-biological markers of aggressive disease, evaluated by Ann Arbor stage, risk group, B-symptoms, number of involved anatomic areas, mediastinal mass, nodular sclerosis (NS) grade, and risk, in pediatric Hodgkin lymphoma (HL). Leukopenia and extranodal disease influenced event-free survival (p = 0.032 and p = 0.041). In multivariate analysis, extranodal disease was associated with high number of tumor-infiltrating eosinophils (p = 0.035) and Ki67 < 50% (p = 0.024); B-symptoms with Ki67 > or =75% (p = 0.027) and high LDH levels (p = 0.001); and mediastinal mass with leukopenia (p = 0.048), NS grade II (p = 0.025), and high-risk (p = 0.046). Furthermore, low stages correlated with Ki67 > or =50% (p = 0.005) and Epstein-Barr virus (EBV) (p = 0.065). Low-risk NS was associated with EBV (p = 0.014). Hierarchical cluster analysis identified two clusters, one composed of high-risk patients and cell cycle and apoptosis features, and the other including low-risk patients, EBV, and low-risk NS. Our results show the association of biological markers with disease aggressiveness in pediatric HL.

O papel dos polimorfismos do promotor proximal do gene da interleucina-10 na susceptibilidade e resposta terapêutica do linforma de burkitt pediátrico em uma região de associação intermediária com o vírus epstein-barr / [The role of polymorphisms of the dainterleukin-10 proximal promoter in the susceptibility and therapeutic response of pediatric Burkitt's lymphoma in a region of intermediate association with Epstein-Barr virus]

A citocina imunoregulatória interleucina-10 (IL-10) exerce função proliferativa em células B. Variações no promotor do gene da IL-10 regulam a expressão da proteína e a infecção com o vírus Epstein-Barr (EBV). Este trabalho objetivou investigar a associação dos polimorfismos da IL-10 com a susceptibilidade e resposta clínica no linfoma de Burkitt pediátrico (LB), de acordo com o status do EBV. Foi realizado um estudo caso-controle, incluindo 62 crianças com LB (2-16a) e 230 doadores saudáveis como grupo controle. O EBV foi detectado por EBER-ISH. Os SNPs -1082A/G e - 592A/C foram genotipados por PCR alelo específica (AS-PCR) e os haplótipos proximais por três AS-PCR cruzadas por caso. Iniciadores fluorescentes discriminaram alelos dos microssatélites IL10.G e IL10.R. A estatística incluiu testes não paramétricos para comparações caso-controle; regressão logística para cálculo de “odds ratios” (OR) com intervalos de confiança de 95% (IC 95%); e o método de Kaplan-Meier e comparações Log-rank para análise de sobrevida. As freqüências dos genótipos AA, AG e GG, do SNP -1082A/G, foram de 34,4%; 41%; 24,6% para pacientes e 46,5%; 43,9%; 9,6% para controles (Teste de Fisher, p=0,0017) com aumento do risco de desenvolvimento de LB na presença do genótipo GG (modelo recessivo) (OR 3,08; IC95% 1,49-6,4). As freqüências de CC, CA e AA, no SNP -592C/T, foram de 56,7%; 36,7%; 6,7% para pacientes e 42,9%; 44,7%; 12,4% para controles (Teste de Cochran- Armitage, p=0,045; OR=1,59; IC95% 1,01-2,51). A freqüência da combinação GCC/GCC mostrou diferenças nos pacientes vs. controles (25,4% vs. 10,1%; OR 3,02, IC95% 1,45-6,29, p=0,004). Não houve diferenças quanto às freqüências genotípicas dos polimorfismos de IL-10 entre os grupos EBV+ (n=33, 54,1%) e EBV- (n=28,45,9%). Foi observada uma estratificação etária no grupo de pacientes, com predominância do EBV no grupo 10 anos (HR 25,9; IC95% 3,13–214,5; p=0,03). Análise de sobrevida de 39 pacientes tratados uniformemente revelou que a presença do EBV foi associada a um desfecho favorável na sobrevida global (SG) (95,7% vs. 66,7%, p= 0,017), e livre de doença (SLD) (91,3% vs. 60%, p=0,021). Já a presença da família IL10.01 (R3-GCC) foi associada a pior SG (50% vs. 91,7%, p=0,005) e SLD (50% vs.83,3%, p=0,042). Tanto EBV quanto IL10.01 refletiram a SLD dos pacientes no grupo de risco avançado (GR3) (92,9% vs. 69,6%, p=0,097). A presença do alelo G12 também modificou a SLD dos pacientes no GR3 (33,3% vs. 81,3%, p=0,034). Um modelo de resposta terapêutica proposto a partir das variáveis independentes (EBV e IL10.01) para a SLD mostrou que pacientes EBV+/IL10.01- apresentaram 92,9% de SLD, comparados aos pacientes EBV-/IL10.01+, 25% (p=0,017). Em conclusão, variantes genéticas de IL-10 foram associadas ao risco desenvolvimento do LB com efeito de dose do haplótipo GCC...

The immunoregulatory cytokine Interleukin-10 (IL-10) exerts B cell proliferation functions. Genetic variations in the IL-10 gene promoter regulate the protein expression and Epstein-Barr virus (EBV) infection. We aimed to investigate whether IL-10 polymorphisms are associated to susceptibility and clinical outcome in pediatric Burkitt lymphoma (BL), according to EBV status. A case-control study including 62 children (2-16 y) with BL and a control group of 230 healthy donors was performed. EBV was detected by EBER-ISH. SNPs –1082A/G and –592C/T were genotyped by allelespecific (AS)-PCRs and the proximal haplotypes by three crossing PCRs by case. Fluorescent primers discriminated alleles of microsatellite IL10.G and IL10.R. The statistic included non-parametric tests for case-control analyses; logistic regression for the odds ratio (OR) with 95% confidence intervals (95% CI); and the Kaplan-Meier method and Log-Rank comparisons for survival analysis. Genotypes frequencies of AA, AG e GG of SNP -1082A/G were 34.4%; 41%; 24.6% for patients and 46.5%; 43.9%; 9.6% for controls (Fisher Test, p=0.0017) with a higher risk of BL development in the presence of GG genotype (recessive model) (OR 3.08; IC95% 1.49-6.4). The frequencies of CC, CA and AA genotypes of SNP -592C/T were 56.7%; 36.7%; 6.7% for patients and 42.9%; 44.7%; 12.4% for controls (Cochran-Armitage Test, p=0.045; OR=1.59; IC95% 1.01-2.51). The frequency of the haplotype combination GCC/GCC showed differences in patients vs. controls (25.4% vs. 10.1%; OR 3.02, IC95% 1.45- 6.29, p=0.004). Differences were not detected by comparing the genotype frequencies between EBV+ (n=33, 54.1%) and EBV- (n=28, 45.9%) groups. Age stratification was observed in the group of patients, in which EBV predominated in the age group 10y. (HR 25.9; IC95% 3.13–214.5; p=0.03). Survival analysis of 39 patients uniformly treated showed that presence of EBV was associated to a better overall survival (OS) (95.7% vs. 66.7%, p= 0.017), and disease free survival (DFS) (91.3% vs. 60%, p=0.021). Yet, the presence of IL10.01 family (R3-GCC) was associated to poor OS (50% vs. 91.7%, p=0.005) and DFS (50% vs. 83.3%, p=0.042). EBV and IL10.01 both reflected DFS of patients in the higher risk group (GR3) (92.9% vs. 69.6%, p=0.097). The presence of G12 allele also modified patients DFS at GR3 (33.3% vs. 81.3%, p=0.034). A therapeutic response model based on independent variables at DFS (EBV and IL10.01) showed that patients EBV+/IL10.01- presented 92.9% DFS, compared to patients EBV-/IL10.01+, 25% (p=0.017). In conclusion, IL-10 genetic variants were associated to higher BL risk development with a dose effect of GCC haplotype...