Data-driven analysis approach for biomarker discovery using molecular-profiling technologies

Islet Phosphoinositide Hydrolysis and Insulin Secretory Responses from Prediabetic fA/fA ZDF Rats

Small sensory fibre dysfunction has been recently recognized as a component of impaired glucose tolerance and insulin resistance (IR) syndrome. However, few studies have investigated whether small sensory fibre dysfunction develops in normoglycaemic or pre-diabetic animal models of IR and/or hyperinsulinaemia. In addition, scant information is available on the metabolic features of IR in relation to small sensory fibre dysfunction due to the progressive failure of beta cells to compensate for IR during the development of frank diabetes. Longitudinal trends for thermal and mechanical nociceptive responses were assessed in 8-36-week-old male obese Zucker rats, 8-36-week-old male Zucker diabetic fatty (ZDF) rats, and 10-39-week-old male Wistar rats that continued to receive exogenous insulin (2-4 U/day) from subcutaneously implanted insulin pellets. Data were compared with the metabolic disorders in these rats. Both obese Zucker and ZDF rats at 8 weeks of age showed compensatory hyperinsulinaemia and developed thermal hyperalgesia prior to the onset of overt hyperglycaemia. These animals also exhibited progression from thermal hyperalgesia to hypoalgesia, which occurred more rapidly and coincided with a more rapid decline in pancreatic insulin secretion in ZDF rats than in obese Zucker rats. Non-diabetic rats treated with insulin tended to show thermal and mechanical hypoalgesia that was detectable 12-20 weeks after treatment. In addition to insulin treatment, IR with or without compensatory hyperinsulinaemia is associated with nociceptive dysfunction of different phenotypes, independent of glycaemic levels.

Elevated serum and tissue lipid stores are associated with skeletal muscle insulin resistance and diminished glucose-stimulated insulin secretion, the hallmarks of type 2 diabetes. We studied the effects of 6-wk treatment with the insulin sensitizer troglitazone on substrate storage and utilization in lean control and Zucker diabetic fatty (ZDF) rats. Troglitazone prevented development of diabetes and lowered serum triglycerides (TG) in ZDF rats. Soleus muscle glycogen and TG content were elevated twofold in untreated ZDF rats, and both were normalized by troglitazone to lean control levels (P < 0.05). Troglitazone also normalized insulin-stimulated glucose uptake as well as basal and insulin-stimulated glycogen synthesis, implying increased skeletal muscle glycogen turnover. The proportion of active pyruvate dehydrogenase (PDH) in soleus muscle was reduced in ZDF relative to lean control rat muscle (16 +/- 2 vs. 21 +/- 2%) but was restored by troglitazone treatment (30 +/- 3%). Increased PDH activation was associated with a 70% increase in glucose oxidation. Muscle lipoprotein lipase activity was decreased by 35% in ZDF compared with lean control rats and was increased twofold by troglitazone. Palmitate oxidation and incorporation into TG were higher in ZDF relative to lean control rats but were unaffected by troglitazone treatment. Troglitazone decreased the incorporation of glucose into the acyl group of TG by 60% in ZDF rats. In summary, ZDF rats demonstrate increased skeletal muscle glycogen and TG stores, both of which were reduced by troglitazone treatment. Troglitazone appears to increase both glycogen and TG turnover in skeletal muscle. Normalization of PDH activity and decreased glucose incorporation into acyl TG may underlie the improvements in intracellular substrate utilization and energy stores, which lead to decreased serum TG and glucose.

Painful neuropathy is a frequent comorbidity in diabetes. Zucker diabetic fatty (fa/fa) rats develop type 2 diabetes spontaneously with aging and show nociceptive hypersensitivity at the age of 13 weeks. In preclinical and clinical studies, the treatment of diabetic neuropathy is challenging, but complementary medicine such as transcutaneous auricular vagus nerve stimulation (taVNS) appears beneficial to the relief of neuropathic pain. However, the mechanism behind the effectiveness of taVNS remains unclear. In this study, we show that daily 30-min taVNS (2/15 Hz, 2 mA) for consecutive 27 days effectively inhibited the development of nociceptive hypersensitivity in Zucker diabetic fatty rats as detected by thermal hyperalgesia and mechanical allodynia in hindpaw. We also demonstrated that this beneficial effect in nociceptive behavior is related to an elevated serotonin (5-HT) plasma concentration and an upregulated expression of 5-HT receptor type 1A (5-HT1AR) in hypothalamus. We conclude that daily 30-min taVNS sessions lessen diabetic neuropathy development by enhancing serotonergic function in genetically diabetes prone individuals. Perspective This article presents taVNS as a new approach to inhibit the development of diabetic neuropathy in genetically prone individuals. This approach could potentially help clinicians who seek to avoid the complication of neuropathic pain in diabetic patient or to relieve the pain if there was one.

Advances in high-throughput drug screening based on pharmacotranscriptomics.

RNA-Seq, a new developing high-throughput sequencing technology in recent years, provides a new and more effective method for research in the genes’ expression. The technology has been used to further improve our understanding on the function of the gene structure information and excavate the new transcripts and new genes. In this study, RNA-seq was employed to study the changes of the proteins after castration in cattle. The results showed the differential expression proteins between castrated cattle and noncastrated cattle were mainly lied in immunity, lipid and fatty acid metabolism and protein synthesis. Through GO and KEGG pathway enrichment analysis, the differential expression proteins were enriched in PPAR pathway which involved in meat quality traits and lipid metabolism and immunity. In addition, the genes were mainly involved in metabolic pathways, such as ECM-receptor, interaction MAPK, signaling pathway PPAR, protein phosphorylation. The function of the proteins involved in castration were not clear and needed further researches.

Transplantomics and Biomarkers in Organ Transplantation: A Report From the First International Conference

Nongxiangxing-daqu (NXDQ), as a saccharification and fermentation agent, directly affects the flavor and yield of fresh Nongxiangxing Baijiu (NXBJ). The difference in fermentation temperature owing to the artificial turning operation leads to the formation of superior (S) and normal (N) grades of NXDQ. Here, aiming to explore the discriminant characteristics of two grades of NXDQ, we studied the physicochemical properties, volatile compounds and microbial communities using HS-SPME-GC/MS and high-throughput sequencing technology. The NXDQ grades presented different physicochemical properties. Staphylococcus, Weissella, Lactobacillus and Thermoascus were dominant in the S grade (S-NXDQ), while Bacillus, Thermoactinomyces and Aspergillus were predominant in the N grade (N-NXDQ). Higher alcohols, aldehydes and ketones positively correlated with the bacterial biomarkers could be used as metabolic biomarkers for N-NXDQ; the S-NXDQ had a higher abundance of key enzymes involved in lactic acid and ethanol fermentation, while N-NXDQ had a higher abundance of key enzymes involved in amino acid synthesis and long-chain fatty acid and lipid metabolism. N-NXDQ and S-NXDQ had different microbial and metabolic biomarkers. These findings provide insight into the discriminant characteristics of different grades of NXDQ, a theoretical basis for rational evaluation of NXDQ, and effective information for quality improvement of daqu.

Cotton (Gossypium hirsutum L.) is one of the most important cash crops worldwide. Cytoplasmic male sterility (CMS) is an excellent breeding system for exploitation of heterosis, which has great potential to increase crop yields. To understand the molecular mechanism of CMS in cotton, we compared transcriptome, cytomorphological, physiological and bioinformatics data between the CMS line C2P5A and its maintainer line C2P5B. By using high-throughput sequencing technology, 178,166 transcripts were assembled and 2013 differentially expression genes (DEGs) were identified at three different stages of C2P5A anther development. In this study, we identified DEGs associated with reactive oxygen species (ROS), peroxisomes, aldehyde dehydrogenases (ALDH), cytochrome oxidase subunit VI, and cytochrome P450, and DEGs associated with tapetum development, Jojoba acyl-CoA reductase-related male sterility protein, basic helix-loop-helix (bHLH) and MYB transcription factors. The abnormal expression of one of these genes may be responsible for the CMS C2P5A line. In gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, DEGs were mainly related to carbohydrate metabolism, amino acid metabolism, transport and catabolism, and signal transduction. Carbohydrate metabolism provides energy for anther development, starch and sucrose metabolism, fatty acid biosynthesis and metabolism and ascorbate and aldarate metabolism. These results showed that numerous genes and multiple complex metabolic pathways regulate cotton anther development. Weighted correlation network analysis (WGCNA) indicated that three modules, ‘turquoise,’ ‘blue,’ and ‘green,’ were specific for the CMS C2P5A line. The ‘turquoise’ and ‘blue’ modules were mainly related to carbohydrate metabolism, amino acid metabolism, energy metabolism, peroxisomes, pyruvate metabolism as well as fatty acid degradation. The ‘green’ module was mainly related to energy metabolism, carbon metabolism, translation, and lipid metabolism. RNA-sequencing and WGCNA polymerization modules were screened for key genes and pathways related to CMS in cotton. This study presents a new perspective for further research into the metabolic pathways of pollen abortion in the CMS C2P5A line and also provides a theoretical basis for its breeding and production.

Insulin resistance is associated with defects in skeletal muscle fatty acid (FA) metabolism that contribute to the development of type2 diabetes. Endurance exercise increases FA and glucose metabolism, muscle mitochondrial content and insulin sensitivity. In skeletal muscle, basal rates of FA oxidation are dependent on AMP-activated protein kinase (AMPK) phosphorylation of acetyl-CoA carboxylase2, the rate-limiting enzyme controlling the production of the metabolic intermediate malonyl-CoA. Likewise, AMPK is essential for maintaining muscle mitochondrial content in untrained mice; effects that may be mediated through regulation of the peroxisome proliferator-activated receptorγ co-activator-1α. However, the importance of AMPK in regulating glucose and FA uptake, FA oxidation and mitochondrial biogenesis during and following endurance exercise training is not fully understood. A better understanding of the mechanisms by which endurance exercise regulates substrate utilization and mitochondrial biogenesis may lead to improved therapeutic and preventative strategies for the treatment of insulin resistance and type2 diabetes.

In this chapter we discuss current trends in multivariate biomarker discovery based on high-dimensional p>>N data (such as genomic, proteomic and metabolomic data generated by high-throughput technologies). First, we take a look at common misconceptions in biomarker discovery, and provide clear guidance on when to use (and when to avoid) which methods and why. Then we talk about feature selection, which – while still neglected by some studies – is the most important aspect of biomarker discovery. Next, we present selected supervised learning algorithms (linear discriminant analysis, support vector machines and random forests), which – when coupled with appropriate feature selection techniques – may be used as the cores of efficient methods of multivariate biomarker discovery. We also stress the importance of biological interpretation of biomarkers as well as the necessity for their proper validation. Finally, a novel data mining method that allows for the identification of multivariate biomarkers that are parsimonious, robust and biologically interpretable is presented.

We report on the characterization of lipogenic tissue transcriptional networks that support physiological responses of obese rats to a lipid-lowering bioactive food compound, R-α-lipoic acid (LA). Nine-week-old male Zucker diabetic fatty (fa/fa) rats were fed a chow diet supplemented with 3 g LA per kg diet or pair fed for 2 wk. At the end of the trial, high-quality RNA was extracted from the liver and epididymal fat and subjected to transcriptome analysis by RNA-Seq technology. Results showed a substantially higher number of differentially expressed genes [DEG, false discovery rate adjusted P ≤ 0.05 and absolute log2 (fold change) ≥ 1] in the liver (110 genes) vs. epididymal fat (10 genes). Most epididymal fat DEG were also differentially expressed in liver and shared directionality of change. Gene Ontology (GO) analysis of these transcripts revealed significant enrichment of GO categories related to immune response, stress response, lipid metabolism, and carboxylic acid metabolic processes. Of interest, interferon-related genes involved in defense against microorganisms and innate immune response were induced by LA. Lipid metabolism-related transcript changes observed in LA-fed animals included downregulation of lipogenic genes (Pnpla3, Pnpla5, Elovl6, Acly, Gpam, and Aacs) and concomitant upregulation of short-, medium-, and long-chain fatty acid metabolic processes (Acot1, Acot2, Acsf2, and Crat). Transcriptional changes were accompanied by the lowering of abdominal adiposity and blood triacylglycerol levels. We conclude that LA dietary supplementation induces prominent gene expression changes in liver in support of significant improvement of whole-body lipid status.

We examined the effects of a magnesium-supplemented (Mg-S) diet in the male obese Zucker diabetic fatty rat, a model of non-insulin-dependent diabetes mellitus (NIDDM). Obese rats were maintained on either a control (0.20% Mg) or magnesium-supplemented (Mg-S; 1% Mg) diet for 6 wk beginning at 6 wk of age. The rats maintained on the Mg-S diet had markedly lower fasting and fed-state blood glucose concentrations and an improved glucose disposal. By 12 wk of age, all of the eight animals on the control diet became diabetic, whereas diabetes developed in only one of eight animals on the Mg-S diet. Insulin and C-peptide concentrations, in addition to pancreatic GLUT-2 and insulin mRNA expression, were higher in the male obese Mg-S rats than in their control-fed counterparts. A subgroup of rats on the control diet with established diabetes was switched to a Mg-S diet for an additional 4 wk. The Mg-S diet did not reverse diabetes once already established. These data indicate that an increased dietary Mg intake in male obese rats prevents deterioration of glucose tolerance, thus delaying the development of spontaneous NIDDM.

A new method is introduced for real-time detection of transient change in scenes observed by staring sensors that are subject to platform jitter, pixel defects, variable focus, and other real-world challenges. The approach uses flexible statistical models for the scene background and its variability, which are continually updated to track gradual drift in the sensor's performance and the scene under observation. Two separate models represent temporal and spatial variations in pixel intensity. For the temporal model, each new frame is projected into a low-dimensional subspace designed to capture the behavior of the frame data over a recent observation window. Per-pixel temporal standard deviation estimates are based on projection residuals. The second approach employs a simple representation of jitter to generate pixelwise moment estimates from a single frame. These estimates rely on spatial characteristics of the scene, and are used gauge each pixel's susceptibility to jitter. The temporal model handles pixels that are naturally variable due to sensor noise or moving scene elements, along with jitter displacements comparable to those observed in the recent past. The spatial model captures jitter-induced changes that may not have been seen previously. Change is declared in pixels whose current values are inconsistent with both models.

The classification of undernutrition-related diabetes as a distinct entity separate from Type 1 and Type 2 diabetes, remains under debate. Here, we show that post-natal undernutrition induces coordinated transcriptional, metabolic, and pathophysiological alterations that mediate the development of undernutrition-related diabetes in young animals. Undernourished mice exhibited hypoglycemia, reduced insulin (p<0.01) and impaired glucose tolerance (p<0.05), consistent with pancreatic insufficiency. Micro-CT analysis revealed skeletal fragility, with significant reductions in bone mineralization (p< 0.01), trabecular integrity (p < 0.05), and increased porosity (p<0.001), as commonly reported in T1D. Liver tissue histology revealed substantial triglyceride accumulation (p<0.001) and histopathological features consistent with hepatic steatosis, including hepatocyte ballooning (p< 0.001). RNA sequencing of liver tissue revealed a gene expression pattern hallmarked by upregulated fatty acid metabolism (p=0.031), and downregulation of the PI3K/AKT/mTOR signaling pathway (p=0.05). This metabolic shift was associated with PPARG activation (Z=2.3) and increased fatty acid oxidation (p<0.01). Conversely, genes involved in insulin secretion (Z=-3.6) and glucose metabolism (Z<-1.6) were downregulated. Strikingly, transitioning from early undernutrition to a standard diet for 28 days resulted in mild hyperglycemia (p<0.05), accompanied by persistent hypoinsulinemia due to impaired pancreatic catch-up growth. These findings suggest that early undernutrition fosters a distinct trajectory toward insulin deficiency and undernutrition-related diabetes, while also increasing susceptibility to metabolic comorbidities. These mechanisms could serve as foundational drivers of the double burden of malnutrition, with consequences for both metabolic and skeletal health.