Hepatic Proteomics Analysis of Nonalcoholic Fatty Liver Disease Obese Rat Model After Short- and Long-Term Soy Protein Isolate Feeding.

To identify possible mechanisms involved in the development and progression of nonalcoholic fatty liver disease (NAFLD), we conducted shotgun proteomics analysis on liver of obese Zucker rats fed either casein (CAS) or soy protein isolate (SPI) for 8 and 16 weeks. Rats (7 weeks old, n = 8-9/group) were randomly assigned to either a CAS-based or an SPI-based diet. Rats were killed after 8 or 16 weeks of feeding and livers were stored at -80°C. Ingenuity Pathway Analysis (IPA) software was used to facilitate interpretation of proteomics data. Predictions of activation or inhibition of molecules in the data were made based on activation z-score and P value of overlap (P < .05). Activation z-scores ≥2.0 indicate that a molecule is predicted to be activated, whereas activation z-scores of less than or equal to -2.0 indicate that a target molecule is predicted to be inhibited. Upstream regulator analysis with IPA revealed Neuregulin 1 (NRG1) to be the top activated protein in (z-score = 2.48, P < .05), and MKNK1 as the top inhibited protein (z-score = -2.83, P < .05) in SPI diet compared with CAS diet after both 8 and 16 weeks of SPI feeding. Regulator effects analysis also predicted that some proteins would be participating, directly or indirectly, in the inhibition of immune response functions (such as leukocyte migration) and lipid metabolism (such as synthesis of lipids) in SPI-fed rats relative to CAS-fed rats. Our results suggest that SPI diet modifies the expression of proteins that could be involved in the reduction of NAFLD.

Effects of Short- and Long-Term Soy Protein Feeding on Hepatic Cytochrome P450 Expression in Obese Nonalcoholic Fatty Liver Disease Rat Model.

Obesity can lead to chronic health complications such as nonalcoholic fatty liver disease (NAFLD). NAFLD is characterized by lipid aggregation in the hepatocytes and inflammation of the liver tissue as a consequence that can contribute to the development of cirrhosis and hepatocellular carcinoma (HCC). Previously, we reported that feeding obese Zucker rats with soy protein isolate (SPI) can reduce liver steatosis when compared with a casein (CAS) diet as a control. However, the effects of SPI on cytochrome P450 (CYP) in an obese rat model are less known. In addition, there is a lack of information concerning the consumption of soy protein in adolescents and its effect in reducing the early onset of NAFLD in this group. Our main goal was to understand if the SPI diet had any impact on the hepatic CYP gene expression when compared with the CAS diet. For this purpose, we used the transcriptomic data obtained in a previous study in which liver samples were collected from obese rats after short-term (eight-week) and long-term (16-week) feeding of SPI (n = 8 per group). To analyze this RNAseq data, we used Ingenuity Pathway Analysis (IPA) software. Comparing short- vs long-term feeding revealed an increase in the number of downregulated CYP genes from three at 8 weeks of SPI diet to five at 16 weeks of the same diet (P ≤ 0.05). On the other hand, upregulated CYP gene numbers showed a small increase in the long-term SPI diet compared to the short-term SPI diet, from 14 genes at 8 weeks to 17 genes at 16 weeks (P ≤ 0.05). The observed changes may have an important role in the attenuation of liver steatosis.

Effects of obesity and 10 weeks metformin treatment on liver steatosis.

Non-alcoholic fatty liver disease (NAFLD) is the leading cause of liver disease in adolescents and adults, and the risk of developing NAFLD increases with obesity. In the present study, it was shown that obesity increased fatty liver (steatosis) using an obese Zucker rat model. Metformin is an oral anti-hyperglycemic agent approved by the FDA for treatment of type 2 diabetes in adults and children >10 years of age. There is insufficient evidence regarding the effects of metformin on pediatric liver steatosis. Thus, in the present study, the effects of 10 weeks metformin treatment on liver steatosis and related serum markers for liver damage was assessed. Lean and obese (n=16 per group) 5-week old female Zucker rats were provided an AIN-93 G diet for 8 weeks to induce NAFLD, and then rats were randomly assigned to 4 groups (8 rats/group): i) lean without metformin (LC), ii) lean + metformin (LM), iii) obese without metformin (OC), and iv) obese + metformin (OM). Rats were provided ad libitum access to the diet containing metformin (1 g metformin per kg of food). Rats were weighed twice weekly and were sacrificed 10 weeks later. Serum was collected to measure the levels of aspartate aminotransferase (AST), alanine aminotransferase (ALT), leptin and adiponectin. Livers were collected for histological analysis. The results showed that obese rats gained significantly more weight than lean rats in both the control and metformin treatment groups (P<0.001). OM treated rats exhibited a lower degree of liver steatosis compared with the OC rats (P<0.04). There were no significant differences in serum ALT levels between the groups. However, obesity significantly increased serum AST levels in both the control and metformin treatment groups (P=0.01). The ratio of leptin to adiponectin was increased in obese compared with the lean rats in both the control and metformin treatment groups (P<0.0001). There was no effect of metformin on serum biomarkers. In summary, short-term metformin treatment decreased liver steatosis but did not affect the serum markers of liver steatosis.

A Comparison of Short- and Long-Term Soy Protein Isolate Intake and Its Ability to Reduce Liver Steatosis in Obese Zucker Rats Through Modifications of Genes Involved in Inflammation and Lipid Transport.

Obesity can lead to several health disorders including nonalcoholic fatty liver disease (NAFLD), the aggregation of lipids within hepatocytes, and consequent inflammation of the liver tissue. Previously, we reported that feeding obese Zucker rats with soy protein isolate (SPI) can reduce liver steatosis. To understand how SPI reduced liver steatosis, we conducted global gene expression analysis on liver samples obtained from these rats after short- (8 weeks) and long-term SPI feeding (16 weeks). We compared and contrasted these data using Ingenuity Pathway Analysis (IPA) software. This study focused mainly on target molecules that could be participating in inflammation processes and lipid metabolism that are well-known components of NAFLD. Inflammatory response was predicted to be inhibited in animals fed the SPI diet at both 8 and 16 weeks of experiment. This general prediction was based on negative activation z scores obtained through IPA (z score < -2.0, P < .00001) for eight aspects of immune function/inflammatory response. Lipid metabolism was predicted to be strongly enhanced in rats fed the SPI diet for 16 weeks than for 8 weeks. This prediction was based on positive activation z scores (z scores >2.0, P < .00001) of eight functions involved in lipid transport and metabolism. We observed that the longer the rats were fed the SPI diet, the more beneficial it resulted against NAFLD. Based on our findings, the predicted reductions in inflammatory mechanisms while enhancing lipid transport out of the liver could be the reasons behind the reduction of liver steatosis.

Long-Term Soy Protein Isolate Consumption Reduces Liver Steatosis Through Changes in Global Transcriptomics in Obese Zucker Rats.

To determine how soy protein isolate (SPI) ameliorated liver steatosis in male obese Zucker rats, we conducted global transcriptomic expression (RNAseq) analysis on liver samples of male rats fed either the SPI or a control casein (CAS)-based diet (n = 8 per group) for 16 weeks. Liver transcriptomics were analyzed using an Ilumina HiSeq system with 2 × 100 base pair paired-end reads method. Bioinformatics was conducted using Ingenuity Pathway Analysis (IPA) software (Qiagen, CA) with P < 0.05 and 1.3-fold differential expression cutoff values. Regression analysis between RNAseq data and targeted mRNA expression analysis of 12 top differentially expressed genes (from the IPA program) using quantitative PCR (qPCR) revealed a significant regression analysis (r 2 = 0.69, P = 0.0008). In addition, all qPCR values had qualitatively similar direction of up- or down-regulation compared to the RNAseq transcriptomic data. Diseases and function analyses that were based on differentially expressed target molecules in the dataset predicted that lipid metabolism would be enhanced whereas inflammation was predicted to be inhibited in SPI-fed compared to CAS-fed rats at 16 weeks. Combining upstream regulator and regulator effects functions in IPA facilitates the prediction of upstream regulators (e.g., transcription regulators) that could play important roles in attenuating or promoting liver steatosis due to SPI or CAS diets. Upstream regulators that were predicted to be activated (from expression of down-stream targets) linked to increased conversion of lipid and transport of lipid in SPI-fed rats included hepatocyte nuclear factor 4 alpha (HNF4A) and aryl hydrocarbon receptor (AHR). Upstream regulators that were predicted to be activated in CAS-fed rats linked to activation of phagocytosis and neutrophil chemotaxis included colony stimulating factor 2 and tumor necrosis factor. The results provide clear indication that long-term SPI-fed rats exhibited diminished inflammatory response and increased lipid transport in liver compared to CAS-fed rats that likely would contribute to reduced liver steatosis in this obese Zucker rat model.

Comparison of liver gene expression by RNAseq and PCR analysis after 8 weeks of feeding soy protein isolate- or casein-based diets in an obese liver steatosis rat model.

Previously, we reported that feeding soy protein isolate (SPI) reduced liver steatosis in obese rats compared to those fed a casein (CAS)-based diet; however, the mechanism for this protection is unknown. To gain insight into the ability of SPI to ameliorate liver steatosis, we conducted transcriptomic (RNAseq) analysis on liver samples from obese rats fed either the SPI- or CAS-based diets (n = 8 per group) for 8 weeks using an Ilumina HiSeq with 100 base paired end reads for sequencing. Data were analyzed by Ingenuity Pathway Analysis (IPA) software using a P < 0.05 and 1.3-fold differential expression cutoff values between the SPI- and CAS-based groups. To independently validate the RNAseq data, we conducted targeted mRNA expression analysis using quantitative PCR (qPCR) on a subset of differently expressed genes. The results indicate that mRNA expression by qPCR concurred with RNAseq for NPTX2, GPT, INMT, and HAL that were up-regulated in SPI-fed rats (P < 0.05) and PRSS8, AJUBA, CSF2RB, and Cyp2c12 that were down-regulated (P < 0.05) in SPI-fed rats compared to CAS-fed rats. Our findings may shed light on understanding mechanisms enabling SPI diet to reduce liver steatosis in this obese Zucker rat model.

Diversity, distribution and dynamics of full-length Copia and Gypsy LTR retroelements in Solanum lycopersicum.

Transposable elements are the most abundant components of plant genomes and can dramatically induce genetic changes and impact genome evolution. In the recently sequenced genome of tomato (Solanum lycopersicum), the estimated fraction of elements corresponding to retrotransposons is nearly 62%. Given that tomato is one of the most important vegetable crop cultivated and consumed worldwide, understanding retrotransposon dynamics can provide insight into its evolution and domestication processes. In this study, we performed a genome-wide in silico search of full-length LTR retroelements in the tomato nuclear genome and annotated 736 full-length Gypsy and Copia retroelements. The dispersion level across the 12 chromosomes, the diversity and tissue-specific expression of those elements were estimated. Phylogenetic analysis based on the retrotranscriptase region revealed the presence of 12 major lineages of LTR retroelements in the tomato genome. We identified 97 families, of which 77 and 20 belong to the superfamilies Copia and Gypsy, respectively. Each retroelement family was characterized according to their element size, relative frequencies and insertion time. These analyses represent a valuable resource for comparative genomics within the Solanaceae, transposon-tagging and for the design of cultivar-specific molecular markers in tomato.

Limited mitogenomic degradation in response to a parasitic lifestyle in Orobanchaceae.

In parasitic plants, the reduction in plastid genome (plastome) size and content is driven predominantly by the loss of photosynthetic genes. The first completed mitochondrial genomes (mitogenomes) from parasitic mistletoes also exhibit significant degradation, but the generality of this observation for other parasitic plants is unclear. We sequenced the complete mitogenome and plastome of the hemiparasite Castilleja paramensis (Orobanchaceae) and compared them with additional holoparasitic, hemiparasitic and nonparasitic species from Orobanchaceae. Comparative mitogenomic analysis revealed minimal gene loss among the seven Orobanchaceae species, indicating the retention of typical mitochondrial function among Orobanchaceae species. Phylogenetic analysis demonstrated that the mobile cox1 intron was acquired vertically from a nonparasitic ancestor, arguing against a role for Orobanchaceae parasites in the horizontal acquisition or distribution of this intron. The C. paramensis plastome has retained nearly all genes except for the recent pseudogenization of four subunits of the NAD(P)H dehydrogenase complex, indicating a very early stage of plastome degradation. These results lend support to the notion that loss of ndh gene function is the first step of plastome degradation in the transition to a parasitic lifestyle.