Cross talk between the liver microbiome and epigenome in patients with metabolic dysfunction-associated steatotic liver disease

BACKGROUND

The pathogenesis of MASLD (metabolic dysfunction-associated steatotic liver disease), including its severe clinical forms, involves complex processes at all levels of biological organization. This study examined the potential link between the liver microbiome profile and epigenetic factors.

METHODS

Liver microbial DNA composition was analysed using high throughput 16S rRNA gene sequencing in 116 individuals, with 55% being female, across the spectrum of liver disease severity. Total activity of histone deacetylases (HDACs) and acetyltransferases (HATs) was assayed in nuclear extracts from fresh liver samples. In addition, we measured the global 5-hydroxymethylcytosine (5-hmC) levels of liver DNA.

FINDINGS

Patients with MASLD showed a 2.07-fold increase (p = 0.013) in liver total HAT activity. Moreover, a correlation was observed between liver total HAT activity and the score for histological steatosis (Spearman's R = 0.60, p = 1.0E-3) and disease severity (R = 0.40, p = 2.0E-2). Liver HAT and HDAC activities also showed associations with the abundance of several liver bacterial DNAs. Additionally, liver global levels of 5-hmC showed negative correlation with the read number of Bacteroidetes (R = -0.62, p = 9.3E-4) and Gammaproteobacteria (R = -0.43, p = 3.2E-2), while it was positively correlated with the abundance of Acidobacteria (R = 0.42, p = 4.1E-2) and Actinobacteria (R = 0.47, p = 1.8E-2).

INTERPRETATION

The host liver epigenome, including the activity of enzymes involved in maintaining the balance between protein acetylation and deacetylation and the global DNA hydroxy-methylation status, may be the target of microbial signals.

FUNDING

Agencia Nacional de Promoción Científica y Tecnológica, FonCyT.

The influence of host genetics on liver microbiome composition in patients with NAFLD

Background

Human body microbiotas are influenced by several factors, including the interaction of the host with the environment and dietary preferences. The role of host genetics in modulating the liver microbiota in the context of NAFLD remains unknown. To address this gap, we examined the interplay between the liver metataxonomic profile and host genetics.

Methods

We obtained 16S rRNA gene sequences from liver biopsies and genotypes by Taqman-assays in 116 individuals. We compared taxon abundance at the genus level across host genotypes using dominant models of inheritance. We focused the analysis on variants influencing the risk/ protection against NAFLD-histological severity (PNPLA3-rs738409, TM6SF2-rs58542926, MBOAT7-rs641738, and HSD17B13-rs72613567) and a variant influencing macronutrient intake (FGF21-rs838133). We also explored the variants' combined effect via a polygenic risk score (PRS).

Findings

We identified at least 18 bacterial taxa associated with variants in the selected loci. Members of the Gammaproteobacteria class were significantly enriched in carriers of the rs738409 and rs58542926 risk-alleles, including Enterobacter (fold change [FC]=6.2) and Pseudoalteromonas (FC=2) genera, respectively. Lawsonella (1.6-FC), Prevotella_9 (FC=1.5), and Staphylococcus (FC=1.3) genera were enriched in rs838133-minor allele carriers, which is linked to sugar consumption and carbohydrate intake. Tyzzerella abundance (FC=2.64) exhibited the strongest association (p = 0.0019) with high PRS values (>4 risk alleles). The percentage of genus-level taxa variation explained by the PRS was ∼7.4%, independently of liver steatosis score and obesity.

Interpretation

We provided evidence that genetic variation may influence the liver microbial DNA composition. These observations may represent potentially actionable mechanisms of disease.

Computational Pipeline for Next-Generation Sequencing (NGS) Studies in Genetics of NASH

High-throughput sequencing (HTS) technologies have contributed to expand current knowledge of the biology of complex diseases, including nonalcoholic fatty liver disease (NAFLD). Genome-wide association studies, whole exome sequencing, and sequencing of entire genes are used to identify variants and/or mutations that predispose to the disease pathogenesis. Here, we present a tutorial that may guide readers to manage high volume of genetics data in the context of Next-Generation Sequencing (NGS) studies.

Pleiotropy within gene variants associated with nonalcoholic fatty liver disease and traits of the hematopoietic system

Genome-wide association studies of complex diseases, including nonalcoholic fatty liver disease (NAFLD), have demonstrated that a large number of variants are implicated in the susceptibility of multiple traits — a phenomenon known as pleiotropy that is increasingly being explored through phenome-wide association studies. We focused on the analysis of pleiotropy within variants associated with hematologic traits and NAFLD. We used information retrieved from large public National Health and Nutrition Examination Surveys, Genome-wide association studies, and phenome-wide association studies based on the general population and explored whether variants associated with NAFLD also present associations with blood cell-related traits. Next, we applied systems biology approaches to assess the potential biological connection/s between genes that predispose affected individuals to NAFLD and nonalcoholic steatohepatitis, and genes that modulate hematological-related traits—specifically platelet count. We reasoned that this analysis would allow the identification of potential molecular mediators that link NAFLD with platelets. Genes associated with platelet count are most highly expressed in the liver, followed by the pancreas, heart, and muscle. Conversely, genes associated with NAFLD presented high expression levels in the brain, lung, spleen, and colon. Functional mapping, gene prioritization, and functional analysis of the most significant loci (P < 1 × 10^-8) revealed that loci involved in the genetic modulation of platelet count presented significant enrichment in metabolic and energy balance pathways. In conclusion, variants in genes influencing NAFLD exhibit pleiotropic associations with hematologic traits, particularly platelet count. Likewise, significant enrichment of related genes with variants influencing platelet traits was noted in metabolic-related pathways. Hence, this approach yields novel mechanistic insights into NAFLD pathogenesis.

Intrahepatic bacterial metataxonomic signature in non-alcoholic fatty liver disease

OBJECTIVE

We aimed to characterise the liver tissue bacterial metataxonomic signature in two independent cohorts of patients with biopsy-proven non-alcoholic fatty liver disease (NAFLD) diagnosis, as differences in the host phenotypic features-from moderate to severe obesity-may be associated with significant changes in the microbial DNA profile.

DESIGN AND METHODS

Liver tissue samples from 116 individuals, comprising of 47 NAFLD overweight or moderately obese patients, 50 NAFLD morbidly obese patients elected for bariatric surgery and 19 controls, were analysed using high-throughput 16S rRNA gene sequencing.

RESULTS

Liver bacterial DNA profile significantly differs between morbidly obese and non-morbidly obese patients with NAFLD. Bacteroidetes (p=1.8e-18) and Firmicutes (p=0.0044) were over-represented in morbidly obese patients and Proteobacteria (p=5.2e-10)-specifically Gammaproteobacteria and Alphaproteobacteria, and Deinococcus-Thermus (p=0.00012)-were over-represented in the non-morbidly obese cohort. Cohort-specific analysis of liver microbial DNA signatures shows patterns linked to obesity. The imbalance in Proteobacteria (Alpha or Gamma) among non-morbidly obese patients, and Peptostreptococcaceae, Verrucomicrobia, Actinobacteria and Gamma Proteobacteria DNA among morbidly obese patients was associated with histological severity. Decreased amounts of bacterial DNA from the Lachnospiraceae family were associated with more severe histological features. Proteobacteria DNA was consistently associated with lobular and portal inflammation scores. Microbial DNA composition corresponded to predicted functional differences.

CONCLUSION

This is the first comprehensive study showing that the liver tissue of NAFLD patients contains a diverse repertoire of bacterial DNA (up to 2.5×10⁴ read counts). The liver metataxonomic signature may explain differences in the NAFLD pathogenic mechanisms as well as physiological functions of the host.

Isolated and combined effects of elevated CO2 and high temperature on the whole-plant biomass and the chemical composition of soybean seeds

Soybean plants of the variety 'MG/BR Conquista' were grown in open top chambers, simulating elevated CO2 concentration ([CO2]) and high temperature under the following treatments: 1) ambient [CO2] and ambient temperature (Amb); 2) elevated [CO2] (eCO2) and ambient temperature (Elev); 3) ambient [CO2] and high temperature (Amb/Temp); 4) elevated CO2 and high temperature (Elev/Temp). The aim was to evaluate responses to elevated [CO2] and high temperature, with focus on plant development and seed yield, and composition. Elev stimulated grain yield and Amb/Temp had opposite effect. Several biochemical parameters were affected by Amb/Temp, most of them reversed by simultaneous application of Elev. The oil obtained with Elev/Temp had lower degree of unsaturation. A network of relationships among biochemical parameters of grains at three developmental stages revealed that Amb/Temp and Elev/Temp affect significantly both carbohydrate and lipid metabolisms. No significant difference was obtained comparing networks corresponding to Amb and Elev/Temp.

Comparative chemistry of propolis from eight brazilian localities

Propolis is a complex honeybee product with resinous aspect, containing plant exudates and beeswax. Their color, texture, and chemical composition vary, depending on the location of the hives and local flora. The most studied Brazilian propolis is the green (alecrim-do-campo) type, which contains mainly prenylated phenylpropanoids and caffeoylquinic acids. Other types of propolis are produced in Brazil, some with red color, others brown, grey, or black. The aim of the present work was to determine the chemical profiles of alcohol and chloroform extracts of eight samples of propolis, corresponding to six Brazilian regions. Methanol and chloroform extracts were obtained and analyzed by HPLC/DAD/ESI/MS and GC/MS. Two chemical profiles were recognized among the samples analyzed: (1) black Brazilian propolis, characterized chiefly by flavanones and glycosyl flavones, stemming from Picos (Piauí state) and Pirenópolis (Goiás state); (2) green Brazilian propolis, characterized by prenylated phenylpropanoids and caffeoylquinic acids, stemming from Cabo Verde (Bahia state), Lavras and Mira Bela (Minas Gerais state), Pariquera-Açu and Bauru (São Paulo state), and Ponta Grossa (Paraná state). The present work represents the first report of prenylated flavonoids in Brazilian propolis and schaftoside (apigenin-8-C-glucosyl-6-C-arabinose) in green propolis.

Psidium guajava 'Paluma' (the guava plant) as a new bio-indicator of ozone in the tropics

Psidium guajava 'Paluma' saplings were exposed to carbon filtered air (CF), ambient non-filtered air (NF), and ambient non-filtered air+40ppb ozone (NF+O(3)) 8h per day during two months. The AOT40 values at the end of the experiment were 48, 910 and 12 895ppbh(-1), respectively for the three treatments. After 5 days of exposure (AOT40=1497ppbh(-1)), interveinal red stippling appeared in plants in the NF+O(3) chamber. In the NF chamber, symptoms were observed only after 40 days of exposure (AOT40=880ppbh(-1)). After 60 days, injured leaves per plant corresponded to 86% in NF+O(3) and 25% in the NF treatment, and the average leaf area injured was 45% in NF+O(3) and 5% in the NF treatment. The extent of leaf area injured (leaf injury index) was explained mainly by the accumulated exposure of ozone (r(2)=0.91; p<0.05).

Flavonoids of Lavoisiera, Microlicia and Trembleya (Melastomataceae) and their taxonomic meaning

Leaves of species of three closely related genera of Melastomataceae, Lavoisiera, Microlicia and Trembleya were analyzed for their flavonoid composition. A total of 116 compounds were obtained, comprising 69 flavonol and 47 flavone glycosides. The common occurrence of flavones, including 6-oxygenated derivatives, characterize Lavoisiera (which often yielded methoxylated flavonols and flavones). Flavonols predominate in species of Microlicia. The flavonoid patterns of Trembleya are rather confusing, some species being akin to Lavoisiera, others to Microlicia. UPGMA analysis using the flavonoid aglycones as characters and the samples analyzed as OTUs gives no complete resolution for the three genera, but provides clusters combining exclusively or preferentially species of either Lavoisiera and Microlicia. Species of Trembleya emerge from the phenogram interspersed among species of the other genera. The data suggest the recognition of Lavoisiera and Microlicia and the lumping of species of Trembleya with either of these genera. If greater flavone diversity is viewed as indicative of further evolutionary advancement, shrubby habits in Microliceae (Lavoisiera and Trembleya) should be regarded as derived from herbaceous ones (Microlicia).

Monomer composition of polysaccharides of seed cell walls and the taxonomy of the Vochysiaceae

The distribution of polysaccharides from the seed cell walls of 57 samples of Vochysiaceae native to Brazil were studied, comprising 16 species distributed among the genera Callisthene, Qualea, Salvertia and Vochysia. The polysaccharides were extracted with hot water, then hydrolyzed with the resulting monomers analyzed by HPLC. All samples yielded arabinose, galactose, glucose. mannose and rhamnose, the relative amounts of each monomer, however, varying from one sample to another. Arabinose was always the predominant component, which implies that it might possibly be used as a marker of the Vochysiaceae. The quantitative distribution of monosaccharides was similar between the species of Qualea and Callisthene, characterized by the predominance of arabinose and mannose, and between the species of Salvertia and Vochysia, which contained higher amounts of arabinose and galactose. Such results are consistent with affinities inferred from floral morphology, wood anatomy and molecular data. Substantial intraspecific variation was observed for some species. UPGMA analysis based on the distribution of the monosaccharides reveals two main clusters, according to the links commented above. The resultant phenogram is not coherent with the current sectional classification of the Vochysiaceae, but the differences in the monosaccharides distribution between the two clusters are strongly supported by ANOVA.

Major constituents of the foliar epicuticular waxes of species from the Caatinga and Cerrado

The epicuticular waxes of leaves of four species (Aspidosperma pyrifolium, Capparis yco, Maytenus rigida and Ziziphus joazeiro) from the Caatinga, (a semi-arid ecosystem of Northeast Brazil) and four species (Aristolochia esperanzae, Didymopanax vinosum, Strychnos pseudoquina and Tocoyena formosa) from the Cerrado, (a savanna ecosystem covering one third of the Brazilian territory), were analyzed. Six species contained a high content (above 60 microg x cm(-2)) of wax, four of them from the Caatinga. Triterpenoids and n-alkanes were the most frequent and abundant constituents found in the species from both habitats. The distribution of n-alkanes predominated by homologues with 27, 29, 31 and 33 carbon atoms, displayed no consistent differences between species from the two habitats. Lupeol, beta-amyrin, epifriedelinol and ursolic acid were the triterpenoids found. Triterpenoids clearly predominate over alkanes in the waxes from the Cerrado species. The waxes of two evergreen species from the Caatinga yielded n-alkanes as predominant constituents. A comparison of foliar epicuticular waxes of native plants from ecosystems with different hydric constraints is discussed.

Effect of ursolic acid from epicuticular waxes of Jacaranda decurrens on Schizaphis graminum

Ursolic acid from Jacaranda decurrens showed toxicity and feeding deterrency towards the greenbug Schizaphis graminum. Biological activity was determined by analyzing ursolic acid effects on the survival, reproductive index, and population growth rate of the greenbug. Survival and reproductive index decreased in direct proportion to ursolic acid content in the diet. The population growth rate decreased markedly when the aphids were fed on barley leaves sprayed with ursolic acid dissolved in DMSO, in comparison to leaves sprayed only with DMSO. The feeding behavior of the greenbug was also affected by ursolic acid. Ingestion time on diet with 0.1 mM was reduced about 30% in relation to the ingestion time on control diet.

[The treatment of spontaneous pneumothorax. A report on 160 cases]

The results achieved in the treatment of 160 cases of spontaneous pneumothorax in 1976-1986 are examined. Pleural aspiration drainage was practised in 141 cases and produced a permanent cure. 5 cases were surgically treated. Hospitalisation time was less than 16 days in 110 cases.

[Comparison of endoscopic aspects and cytohistological patterns in primary lung neoplasia]

Four-hundred and thirty-six patients recognized affected by primitive lung neoplasia have been examined to prove possible correlation between the endoscopic aspects, histologic type and central or peripheral localization of the neoplasia. The diagnostic sensibility of the different cytohistological techniques used in fiberoptic bronchoscopy have been valued too. For the peripheral localizations the diagnosis has been obtained in most cases by using fine needle percutaneous aspiration.