DNA microarray cluster analysis reveals tissue similarity and potential neuron-specific genes expressed in cranial sensory ganglia

The differences in the anatomy of the thoracolumbar and sacral autonomic outflow are quantitative

PURPOSE

We have re-evaluated the anatomical arguments that underlie the division of the spinal visceral outflow into sympathetic and parasympathetic divisions.

METHODOLOGY

Using a systematic literature search, we mapped the location of catecholaminergic neurons throughout the mammalian peripheral nervous system. Subsequently, a narrative method was employed to characterize segment-dependent differences in the location of preganglionic cell bodies and the composition of white and gray rami communicantes.

RESULTS AND CONCLUSION

One hundred seventy studies were included in the systematic review, providing information on 389 anatomical structures. Catecholaminergic nerve fibers are present in most spinal and all cranial nerves and ganglia, including those that are known for their parasympathetic function. Along the entire spinal autonomic outflow pathways, proximal and distal catecholaminergic cell bodies are common in the head, thoracic, and abdominal and pelvic region, which invalidates the "short-versus-long preganglionic neuron" argument. Contrary to the classically confined outflow levels T1-L2 and S2-S4, preganglionic neurons have been found in the resulting lumbar gap. Preganglionic cell bodies that are located in the intermediolateral zone of the thoracolumbar spinal cord gradually nest more ventrally within the ventral motor nuclei at the lumbar and sacral levels, and their fibers bypass the white ramus communicans and sympathetic trunk to emerge directly from the spinal roots. Bypassing the sympathetic trunk, therefore, is not exclusive for the sacral outflow. We conclude that the autonomic outflow displays a conserved architecture along the entire spinal axis, and that the perceived differences in the anatomy of the autonomic thoracolumbar and sacral outflow are quantitative.

Taste transduction and channel synapses in taste buds

The variety of taste sensations, including sweet, umami, bitter, sour, and salty, arises from diverse taste cells, each of which expresses specific taste sensor molecules and associated components for downstream signal transduction cascades. Recent years have witnessed major advances in our understanding of the molecular mechanisms underlying transduction of basic tastes in taste buds, including the identification of the bona fide sour sensor H⁺ channel OTOP1, and elucidation of transduction of the amiloride-sensitive component of salty taste (the taste of sodium) and the TAS1R-independent component of sweet taste (the taste of sugar). Studies have also discovered an unconventional chemical synapse termed "channel synapse" which employs an action potential-activated CALHM1/3 ion channel instead of exocytosis of synaptic vesicles as the conduit for neurotransmitter release that links taste cells to afferent neurons. New images of the channel synapse and determinations of the structures of CALHM channels have provided structural and functional insights into this unique synapse. In this review, we discuss the current view of taste transduction and neurotransmission with emphasis on recent advances in the field.

Levels of Cocaine- and Amphetamine-Regulated Transcript in Vagal Afferents in the Mouse Are Unaltered in Response to Metabolic Challenges

Cocaine- and amphetamine-regulated transcript (CART) is one of the most abundant neuropeptides in vagal afferents, including those involved in regulating feeding. Recent observations indicate that metabolic challenges dramatically alter the neuropeptidergic profile of CART-producing vagal afferents. Here, using confocal microscopy, we reassessed the distribution and regulation of CART(55–102) immunoreactivity in vagal afferents of the male mouse in response to metabolic challenges, including fasting and high-fat-diet feeding. Importantly, the perikarya and axons of vagal C-fibers were labeled using mice expressing channelrodhopsin-2 (ChR2-YFP) in Na_v1.8-Cre–expressing neurons. In these mice, approximately 82% of the nodose ganglion neurons were labeled with ChR2-YFP. Furthermore, ChR2-YFP–labeled axons could easily be identified in the dorsovagal complex. CART(55–102) immunoreactivity was observed in 55% of the ChR2-YFP–labeled neurons in the nodose ganglion and 22% of the ChR2-YFP–labeled varicosities within the area postrema of fed, fasted, and obese mice. The distribution of positive profiles was also identical across the full range of CART staining in fed, fasted, and obese mice. In contrast to previous studies, fasting did not induce melanin-concentrating hormone (MCH) immunoreactivity in vagal afferents. Moreover, prepro-MCH mRNA was undetectable in the nodose ganglion of fasted mice. In summary, this study showed that the perikarya and central terminals of vagal afferents are invariably enriched in CART and devoid of MCH.

How do taste cells lacking synapses mediate neurotransmission? CALHM1, a voltage-gated ATP channel

CALHM1 was recently demonstrated to be a voltage-gated ATP-permeable ion channel and to serve as a bona fide conduit for ATP release from sweet-, umami-, and bitter-sensing type II taste cells. Calhm1 is expressed in taste buds exclusively in type II cells and its product has structural and functional similarities with connexins and pannexins, two families of channel protein candidates for ATP release by type II cells. Calhm1 knockout in mice leads to loss of perception of sweet, umami, and bitter compounds and to impaired gustatory nerve responses to these tastants. These new studies validate the concept of ATP as the primary neurotransmitter from type II cells to gustatory neurons. Furthermore, they identify voltage-gated ATP release through CALHM1 as an essential molecular mechanism of ATP release in taste buds. We discuss these new findings, as well as unresolved issues in peripheral taste signaling that we hope will stimulate future research.

Dorsal root ganglion neurons innervating pelvic organs in the mouse express tyrosine hydroxylase

Previous studies in rat and mouse documented that a subpopulation of dorsal root ganglion (DRG) neurons innervating non-visceral tissues express tyrosine hydroxylase (TH). Here we studied whether or not mouse DRG neurons retrogradely traced with Fast Blue (FB) from colorectum or urinary bladder also express immunohistochemically detectable TH. The lumbar sympathetic chain (LSC) and major pelvic ganglion (MPG) were included in the analysis. Previously characterized antibodies against TH, norepinephrine transporter type 1 (NET-1) and calcitonin gene-related peptide (CGRP) were used. On average, ∼14% of colorectal and ∼17% of urinary bladder DRG neurons expressed TH and spanned virtually all neuronal sizes, although more often in the medium-sized to small ranges. Also, they were more abundant in lumbosacral than thoracolumbar DRGs, and often coexpressed CGRP. We also detected several TH-immunoreactive (IR) colorectal and urinary bladder neurons in the LSC and the MPG, more frequently in the former. No NET-1-IR neurons were detected in DRGs, whereas the majority of FB-labeled, TH-IR neurons in the LSC and MPG coexpressed this marker (as did most other TH-IR neurons not labeled from the target organs). TH-IR nerve fibers were detected in all layers of the colorectum and the urinary bladder, with some also reaching the basal mucosal cells. Most TH-IR fibers in these organs lacked CGRP. Taken together, we show: (1) that a previously undescribed population of colorectal and urinary bladder DRG neurons expresses TH, often CGRP but not NET-1, suggesting the absence of a noradrenergic phenotype; and (2) that TH-IR axons/terminals in the colon or urinary bladder, naturally expected to derive from autonomic sources, could also originate from sensory neurons.

Dietary iron-deficient anemia induces a variety of metabolic changes and even apoptosis in rat liver: a DNA microarray study

Anemia can be induced by dietary iron deficiency, as well as by hemorrhagia. It may also be associated with changes in lipid metabolism. However, no global analysis detailing the consequences of iron deficiency in the liver has yet been conducted. Since the liver is a metabolically important organ and also a major iron-storing organ, we performed a comprehensive transcriptome analysis to determine the effects of iron deficiency on hepatic gene expression. Four-week-old rats were fed an iron-deficient diet, approximately 3 ppm iron, ad libitum for 16 days. These rats were compared with similar rats pair-fed a control diet with a normal iron level, 48 ppm iron. The 16-day iron-deficient diet apparently induced anemia. On day 17, the rats were killed under anesthesia, and their livers were dissected for DNA microarray analysis. We identified 600 upregulated and 500 downregulated probe sets that characterized the iron-deficient diet group. In the upregulated probe sets, genes involved in cholesterol, amino acid, and glucose metabolism were significantly enriched, while genes related to lipid metabolism were significantly enriched in the downregulated probe sets. We also found that genes for caspases 3 and 12, which mediate endoplasmic reticulum (ER)-specific apoptosis, were upregulated in the iron-deficient group. Combined, these results suggest that iron deficiency exerts various influences, not only on nutrient metabolism but also on apoptosis, as a consequence of ER stress in the liver.

Administration of tomato and paprika beverages modifies hepatic glucose and lipid metabolism in mice: a DNA microarray analysis

To examine whether the expression of hepatic genes, including biomarkers, is affected by the ingestion of tomato or paprika, mice were given tomato beverage (TB), paprika beverage (PB), or water (control) ad libitum for 6 weeks. The body weights in the TB and PB groups were significantly lower than those in the control group. Administration of PB significantly increased the plasma high-density lipoprotein-cholesterol level. Hepatic gene expression was investigated using DNA microarrays. The ingestion of TB or PB up-regulated the expression of 687 and 1045 genes and down-regulated the expression of 841 and 653 genes, respectively (false discovery rate<0.05). These changes in gene expression suggest that TB ingestion promotes glycogen accumulation and stimulates some specific steps in fatty acid oxidation. PB ingestion promoted the entire glucose and fatty acid metabolic pathways to improve lipid profiles. These results provide useful genetic information about a variety of biochemical processes by which vegetables can contribute to good health.

Biochemical and genomic analysis of neoculin compared to monocot mannose-binding lectins

Neoculin occurring in an edible tropical fruit is a heterodimeric protein which has both sweetness and a taste-modifying activity that converts sourness to sweetness. Both the primary and the overall tertiary structures of neoculin resemble those of monocot mannose-binding lectins. This study investigated differences in biochemical properties between neoculin and the lectins. Structural comparison between the mannose-binding sites of lectins and the corresponding regions of neoculin showed that there is at least one amino acid substitution at each site in neoculin, suggesting a reason for the lack of its mannose-binding ability. This was consistent with hemagglutination assay data demonstrating that neoculin had no detectable agglutinin activity. DNA microarray analysis indicated that neoculin had no significant influence on gene expression in Caco-2 cell, whereas kidney bean lectin (Phaseolus vulgaris agglutinin) greatly influenced various gene expressions. These data strongly suggest that neoculin has no lectin-like properties, encouraging its practical use in the food industry.

Tyrosine hydroxylase is expressed in a subpopulation of small dorsal root ganglion neurons in the adult mouse

The expression of tyrosine hydroxylase (TH) was studied in adult mouse dorsal root ganglia (DRGs) and spinal cord by means of immunohistochemistry and in situ hybridization. TH immunoreactivity and TH mRNA were present in 10-15% of lumbar DRG neurons, in most cases being small/medium-sized. Only very few of these neurons coexpressed calcitonin gene-related peptide (CGRP), and only around 6% bound isolectin B4 (IB4). Dopamine beta-hydroxylase-positive(+) or aromatic amino acid decarboxylase (AADC)+ DRG neurons were rare and did not colocalize TH. No evidence for dopamine transporter expression was obtained. Axotomy of the sciatic nerve only showed a tendency towards reduction in the number of TH+ neurons. In the dorsal horn of the spinal cord, moderately dense and widespread TH+ nerve terminals were observed, mainly in the gray matter and they did not show a typical primary afferent pattern. Also, dorsal rhizotomy or peripheral axotomy had no apparent effect on TH-LI in the dorsal horn. In the skin, along with an abundant TH+ innervation of blood vessels and sweat gland acini, a number of fibers was observed in close relation to the skin surface, some even penetrating into the epithelium. These results demonstrate presence, in normal adult mouse DRGs, of a subpopulation of TH+, essentially CGRP- and IB4-negative small/medium-sized neurons. No evidence for transport of TH into central afferents was obtained, but the enzyme may be present in some sensory fibers in the skin. The fact that neither AADC nor the dopamine transporter could be visualized suggests of non-dopaminergic transmitter phenotype, but the levels of these two dopaminergic markers may be too low to be detected with the present methodology. A further alternative is that L-DOPA after release is extracellularly converted to dopamine.

Sesamin ingestion regulates the transcription levels of hepatic metabolizing enzymes for alcohol and lipids in rats

BACKGROUND

Sesamin, a major lignan in sesame seeds, has multiple functions such as stimulation effect of ethanol metabolism in mice and human, and prevention of ethanol-induced fatty liver in rats. However, the mechanism has not been clarified yet.

METHODS

The changes of gene expression were investigated in rats given 250 mg/kg of sesamin (sesamin rats) or vehicle (control rats) for three days by using a DNA microarray analysis. At 4 hr after the final ingestion, the profiles of gene expression in rat livers were compared.

RESULTS

The analysis showed that 38 transcripts were up-regulated with a significant change of more than two-fold and eight transcripts were down-regulated with a significant change to less than half in the livers of sesamin rats versus control rats. The gene expression levels of the early stage enzymes of beta-oxidation including long-chain acyl-CoA synthetase, very long-chain acyl-CoA synthetase and carnitine palmitoyltransferase were not changed, however, those of the late stage enzymes of beta-oxidation including trifunctional enzyme in mitochondria, and acyl-CoA oxidase, bifunctional enzyme and 3-ketoacyl-CoA thiolase in peroxisomes, were significantly increased by sesamin ingestion. Also, in sesamin rats, the gene expression of aldehyde dehydrogenase was increased about three-fold, whereas alcohol dehydrogenase, liver catalase and CYP2E1 were not changed. Changes in the gene expression of alcohol- and aldehyde-metabolizing enzymes observed in a DNA microarray were also confirmed by a real-time PCR method.

CONCLUSIONS

These results suggested that sesamin ingestion regulated the transcription levels of hepatic metabolizing enzymes for alcohol and lipids.

Intake of soy protein isolate alters hepatic gene expression in rats

Soy protein isolate (SPI) can elicit various physiological effects such as cholesterol lowering and antiobesity effects. To examine whether hepatic gene expression is altered by SPI intake, rats were fed an SPI or casein diet for 8 weeks. After 8 weeks of feeding, liver weight and plasma triglyceride and cholesterol levels were significantly lower in the SPI group than in the casein group. Hepatic gene expression was investigated using DNA microarrays. The expression profiles and statistical analysis showed clear and significant differences between the SPI and casein groups (p < 0.05); in the SPI group, 63 genes were up-regulated and 57 genes were down-regulated, most involved in various physiological functions such as lipid metabolism, antioxidant activity, transcriptional regulation, and energy metabolism. Especially in lipid metabolism, the down-regulated genes are related to fatty acid synthesis and the up-regulated genes are related to cholesterol synthesis and steroid catabolism. These results suggest that SPI intake could maintain homeostasis primarily by modulating lipid and energy metabolism.

Ingested cocoa can prevent high-fat diet-induced obesity by regulating the expression of genes for fatty acid metabolism

OBJECTIVE

We previously found that ingested cocoa decreased visceral adipose tissue weight in rat. To elucidate the molecular mechanisms of that effect, we carried out experiments aimed at analyzing biochemical parameters and gene expression profiles.

METHODS

Rats were fed either of two high-fat diets, differing only in supplementation with real or mimetic cocoa. On day 21, body weights, mesenteric white adipose tissue weights, and concentrations of serum triacylglycerol were measured. To investigate the molecular mechanisms underlying the effects of cocoa on lipid metabolism and triacylglycerol accumulation, we examined gene expression profiles in liver and mesenteric white adipose tissues using the GeneChip microarray system.

RESULTS

Final body weights and mesenteric white adipose tissue weights were significantly lower in rats fed the real cocoa diet than in those fed the mimetic cocoa diet (P<0.05), and serum triacylglycerol concentrations tended to be lower in rats fed the real cocoa diet (P=0.072). DNA microarray analysis showed that cocoa ingestion suppressed the expression of genes for enzymes involved in fatty acid synthesis in liver and white adipose tissues. In white adipose tissue, cocoa ingestion also decreased the expression of genes for fatty acid transport-relating molecules, whereas it upregulated the expression of genes for uncoupling protein-2 as a thermogenesis factor.

CONCLUSIONS

Ingested cocoa can prevent high-fat diet-induced obesity by modulating lipid metabolism, especially by decreasing fatty acid synthesis and transport systems, and enhancement of part of the thermogenesis mechanism in liver and white adipose tissue.

Identification of candidate genes involved in somatosensory functions of cranial sensory ganglia

We have shown that the characteristics of tissue trees obtained by the hierarchical cluster analysis of DNA microarray data suggest the cellular expression patterns of genes in the gene clusters [J. Neurosci. Res. 74 (2003) 818]. We here identified three gene clusters containing 11 genes as a potential pool of candidate genes related to somatosensation in cranial structures such as the face, oral cavity and pharynx. To obtain the cellular expression profiles, eight genes other than three genes analyzed previously were subjected to in situ hybridization analysis. The results show that all of the 11 profiles are roughly similar and suggest that the positive cells are probably somatosensory neurons in two cranial sensory ganglia, the trigeminal and petrosal ganglia. The expression profiles and probable physiological functions of the 6 genes such as trkA, NaN and galanin suggest their direct involvement in specific somatosensory functions such as nociception. The function of another gene, calretinin, is putatively related to mechanosensation and proprioception. The roles of the remaining four genes, including aquaporin 1 and two EST clones, in sensory neurons are unknown, and may provide clues to understand the sensory function in TG and PG.

Discovering genes: the use of microarrays and laser capture microdissection in pain research

The DNA microarray is a powerful, high throughput technique for assessing gene expression on a system-wide genomic scale. It has great potential in pain research for determining the network of gene regulation in different pain conditions, and also for producing detailed gene expression maps in anatomical areas that process nociceptive stimuli. However, for the potential of this high throughput technology to be realised in pain research, microarrays need to be combined with other technologies. Laser capture microdissection is capable of isolating small populations of homogenous cells, allowing distinct areas involved in nociceptive processing to be examined. In combination with sophisticated PCR-based amplification protocols this technique provides sufficient amounts of messenger RNA (mRNA) for application to microarrays. Aside from the technological issues, a difficult task in any microarray study is the analysis of the resulting enormous data set to reveal the key genes, whose regulation is central to the phenotypic changes observed. For this to be achieved, the methods of data analysis, pattern searching and feature recognition, and bioinformatics have to be properly deployed all within the context of an appropriate statistical design. These issues are especially relevant to pain research where interindividual and interpopulation variation is likely to be high, and where polymorphisms can greatly affect nociceptive sensitivity and susceptibility to pain conditions. Methods for assessing the function of new candidate genes identified in microarray screening experiments are also discussed.

Gene expression profiling of cranial sensory ganglia that transmit food intake stimuli

Peripheral cranial sensory nerves projecting into the oral cavity receive food intake stimuli and transmit sensory signals to the central nervous system. They are derived from four cranial sensory ganglia, trigeminal, geniculate, petrosal, and nodose ganglia, each of which contains multiple kinds of sensory neurons with different cell morphologies and neuronal properties. We investigated the complex properties of these neurons from the viewpoint of gene expression using DNA microarrays. The 498 genes were selected from a total of 8,740 genes as showing tissue-dependent expression on the microarray by hierarchical cluster analysis, in which several genes known to be differentially expressed in cranial sensory ganglia are included. This suggests that DNA microarray cluster analysis revealed a number of characteristic genes for sensory neurons in these ganglia. Among the selected 498 genes, 44 genes are associated with neurotransmission, such as neuropeptides, their receptors, and vesicle transport, and 26 are ion channels regulating membrane potentials. The identification of a number of genes related directly to neural properties indicates that these sensory ganglia contain heterogeneous types of neurons with different neural properties.