RNA editing of the apolipoprotein B gene A mechanism to regulate the atherogenic potential of intestinal lipoproteins?

RNA Editing in Glioma as a Sexually Dimorphic Prognostic Factor That Affects mRNA Abundance in Fatty Acid Metabolism and Inflammation Pathways

RNA editing alters the nucleotide sequence and has been associated with cancer progression. However, little is known about its prognostic and regulatory roles in glioma, one of the most common types of primary brain tumors. We characterized and analyzed RNA editomes of glioblastoma and isocitrate dehydrogenase mutated (IDH-MUT) gliomas from The Cancer Genome Atlas and the Chinese Glioma Genome Atlas (CGGA). We showed that editing change during glioma progression was another layer of molecular alterations and that editing profiles predicted the prognosis of glioblastoma and IDH-MUT gliomas in a sex-dependent manner. Hyper-editing was associated with poor survival in females but better survival in males. Moreover, noncoding editing events impacted mRNA abundance of the host genes. Genes associated with inflammatory response (e.g., EIF2AK2, a key mediator of innate immunity) and fatty acid oxidation (e.g., acyl-CoA oxidase 1, the rate-limiting enzyme in fatty acid β-oxidation) were editing-regulated and associated with glioma progression. The above findings were further validated in CGGA samples. Establishment of the prognostic and regulatory roles of RNA editing in glioma holds promise for developing editing-based therapeutic strategies against glioma progression. Furthermore, sexual dimorphism at the epitranscriptional level highlights the importance of developing sex-specific treatments for glioma.

Accurate Prediction of Protein Sequences for Proteogenomics Data Integration

This book chapter discusses proteogenomics data integration and provides an overview into the different omics layer involved in defining the proteome of a living organism. Various aspects of genome variability affecting either the sequence or abundance level of proteins are discussed in this book chapter, such as the effect of single-nucleotide variants or larger genomic structural variants on the proteome. Next, various sequencing technologies are introduced and discussed from a proteogenomics data integration perspective such as those providing short- and long-read sequencing and listing their respective advantages and shortcomings for accurate protein variant prediction using genomic/transcriptomics sequencing data. Finally, the various bioinformatics tools used to process and analyze DNA/RNA sequencing data are discussed with the ultimate goal of obtaining accurately predicted sample-specific protein sequences that can be used as a drop-in replacement in existing approaches for peptide and protein identification using popular database search engines such as MSFragger, SearchGUI/PeptideShaker.

Genomic determinants of long-term cardiometabolic complications in childhood acute lymphoblastic leukemia survivors

BACKGROUND

While cure rates for childhood acute lymphoblastic leukemia (cALL) now exceed 80%, over 60% of survivors will face treatment-related long-term sequelae, including cardiometabolic complications such as obesity, insulin resistance, dyslipidemia and hypertension. Although genetic susceptibility contributes to the development of these problems, there are very few studies that have so far addressed this issue in a cALL survivorship context.

METHODS

In this study, we aimed at evaluating the associations between common and rare genetic variants and long-term cardiometabolic complications in survivors of cALL. We examined the cardiometabolic profile and performed whole-exome sequencing in 209 cALL survivors from the PETALE cohort. Variants associated with cardiometabolic outcomes were identified using PLINK (common) or SKAT (common and rare) and a logistic regression was used to evaluate their impact in multivariate models.

RESULTS

Our results showed that rare and common variants in the BAD and FCRL3 genes were associated (p<0.05) with an extreme cardiometabolic phenotype (3 or more cardiometabolic risk factors). Common variants in OGFOD3 and APOB as well as rare and common BAD variants were significantly (p<0.05) associated with dyslipidemia. Common BAD and SERPINA6 variants were associated (p<0.05) with obesity and insulin resistance, respectively.

CONCLUSIONS

In summary, we identified genetic susceptibility loci as contributing factors to the development of late treatment-related cardiometabolic complications in cALL survivors. These biomarkers could be used as early detection strategies to identify susceptible individuals and implement appropriate measures and follow-up to prevent the development of risk factors in this high-risk population.

Recent discoveries on absorption of dietary fat: Presence, synthesis, and metabolism of cytoplasmic lipid droplets within enterocytes

Dietary fat provides essential nutrients, contributes to energy balance, and regulates blood lipid concentrations. These functions are important to health, but can also become dysregulated and contribute to diseases such as obesity, diabetes, cardiovascular disease, and cancer. Within enterocytes, the digestive products of dietary fat are re-synthesized into triacylglycerol, which is either secreted on chylomicrons or stored within cytoplasmic lipid droplets (CLDs). CLDs were originally thought to be inert stores of neutral lipids, but are now recognized as dynamic organelles that function in multiple cellular processes in addition to lipid metabolism. This review will highlight recent discoveries related to dietary fat absorption with an emphasis on the presence, synthesis, and metabolism of CLDs within this process.

Multiple functions of microsomal triglyceride transfer protein

Microsomal triglyceride transfer protein (MTP) was first identified as a major cellular protein capable of transferring neutral lipids between membrane vesicles. Its role as an essential chaperone for the biosynthesis of apolipoprotein B (apoB)-containing triglyceride-rich lipoproteins was established after the realization that abetalipoproteinemia patients carry mutations in the MTTP gene resulting in the loss of its lipid transfer activity. Now it is known that it also plays a role in the biosynthesis of CD1, glycolipid presenting molecules, as well as in the regulation of cholesterol ester biosynthesis. In this review, we will provide a historical perspective about the identification, purification and characterization of MTP, describe methods used to measure its lipid transfer activity, and discuss tissue expression and function. Finally, we will review the role MTP plays in the assembly of apoB-lipoprotein, the regulation of cholesterol ester synthesis, biosynthesis of CD1 proteins and propagation of hepatitis C virus. We will also provide a brief overview about the clinical potentials of MTP inhibition.

A proposed model for the assembly of chylomicrons

The intestine synthesizes very low density lipoproteins (VLDL) and chylomicrons (CM) to transport fat and fat-soluble vitamins into the blood. VLDL assembly occurs constitutively whereas CM assembly is a characteristic property of the enterocytes during the postprandial state. The secretion of CM is specifically inhibited by Pluronic L81. CM are very heterogeneously-sized particles that consist of a core of triglycerides (TG) and cholesterol esters and a monolayer of phospholipids (PL), cholesterol and proteins. The fatty acid composition of TG, but not PL, in CM mirrors the fatty acid composition of fat in the diet. CM assembly is deficient in abetalipoproteinemia and CM retention disease. Abetalipoproteinemia results due to mutation in the mttp gene and is characterized by the virtual absence of apoB-containing lipoproteins in the plasma. Patients suffer from neurologic disorders, visual impairment, and exhibit acanthocytosis. CM retention disease, an inherited recessive disorder, is characterized by chronic diarrhea with steatorrhea in infancy, abdominal distention and failure to thrive. It is caused by a specific defect in the secretion of intestinal lipoproteins; secretion of lipoproteins by the liver is not affected. Besides human disorders, mice that do not assemble intestinal lipoproteins have been developed. These mice are normal at birth, but defective in fat and fat-soluble vitamin absorption, and fail to thrive. Thus, fat and fat-soluble vitamin transport by the intestinal lipoproteins is essential for proper growth and development of neonates. Recently, differentiated Caco-2 cells and rabbit primary enterocytes have been described that synthesize and secrete CM. These cells can be valuable in distinguishing between the two different models proposed for the assembly of CM. In the first model, the assembly of VLDL and CM is proposed to occur by two 'independent' pathways. Second, CM assembly is proposed to be a product of 'core expansion' that results in the synthesis of lipoproteins of different sizes. According to this model, intestinal lipoprotein assembly begins with the synthesis of 'primordial' lipoprotein particles and involves release of the nascent apoB with PL derived from the endoplasmic reticulum (ER) membrane. In addition, TG-rich 'lipid droplets' of different sizes are formed independent of apoB synthesis. The fusion of lipid droplets and primordial lipoproteins results in the formation of different size lipoproteins due to the 'core expansion' of the primordial lipoproteins.

Insights into apolipoprotein B biology from transgenic and gene-targeted mice

Over the past five years, several laboratories have used transgenic and gene-targeted mice to study apolipoprotein (apo) B biology. Genetically modified mice have proven useful for investigating the genetic and environmental factors affecting atherogenesis, for defining apoB structure/function relationships, for understanding the regulation of the apoB gene expression in the intestine, for defining the "physiologic rationale" for the existence of the two different forms of apoB (apoB48 and apoB100) in mammalian metabolism and for providing mechanistic insights into the human apoB deficiency syndrome, familial hypobetalipoproteinemia. This review will provide several examples of how genetically modified mice have contributed to our understanding of apoB biology, including our new discovery that human heart myocytes secrete nascent apoB-containing lipoproteins.

A gene-targeted mouse model for familial hypobetalipoproteinemia. Low levels of apolipoprotein B mRNA in association with a nonsense mutation in exon 26 of the apolipoprotein B gene

Familial hypobetalipoproteinemia, a syndrome characterized by abnormally low plasma levels of low density lipoprotein cholesterol, is caused by mutations in the apolipoprotein (apo) B gene that interfere with the synthesis of a full-length apoB100. In many cases of familial hypobetalipoproteinemia, nonsense or frameshift mutations result in the synthesis of a truncated apoB protein. To understand why these mutations result in low plasma cholesterol levels, we used gene targeting in mouse embryonic stem cells to introduce a nonsense mutation (N1785Stop) into exon 26 of the mouse Apob gene. The sole product of this mutant Apob allele was a truncated apoB, apoB39. Mice homozygous for this "apoB39-only" (Apob39) allele had low plasma levels of apoB39 and markedly reduced plasma levels of very low density lipoprotein and low density lipoprotein cholesterol when fed a high fat diet. Analysis of liver and intestinal RNA from heterozygous apoB39-only mice revealed that the Apob39 mRNA levels were 60-70% lower than those from the wild-type allele. Interestingly, apoB39 was not cleared as rapidly from the plasma as apoB48. The apoB39-only mice provide new insights into the mechanisms of familial hypobetalipoproteinemia and the structural features of apoB that are important for lipoprotein metabolism.

Hepatic gene expression of apolipoprotein B100 during early lactation in underfed, high producing dairy cows

The hepatic gene expression of apolipoprotein B, the major protein of very low density lipoproteins in plasma, was studied using 8 Holstein x Friesian cows during the first 12 wk of lactation. Cows were fattened during gestation and were underfed just after parturition to increase fat mobilization and subsequent hepatic steatosis. Intracellular concentrations of apolipoprotein B and apolipoprotein B mRNA and control parameters (albumin, total lipids, RNA, and proteins) were determined in liver samples obtained by biopsy from each cow on four occasions at 1, 2, 4, and 12 wk after calving. Results were compared with those obtained from 5 dry cows in late pregnancy and 4 dry nonpregnant cows. The hepatic concentration of apolipoprotein B was lower (approximately 25%) during wk 1, 2, and 4 after calving, a period of intense liver steatosis (44.2 to 95.7 mg of triglycerides/g of fresh tissue), than for nonsteatotic dry cows (pregnant or nonpregnant); hepatic concentrations were also lower than those during wk 12. In contrast, hepatic concentrations of mRNA coding for apolipoprotein B, total proteins, RNA, and albumin did not vary significantly during early lactation. These results suggested that synthesis of apolipoprotein B during early lactation is specifically regulated at a posttranscriptional level by a decrease in the rate of translation, or by a higher rate of intracellular degradation of apolipoprotein B, or both.