Differentially expressed olfactomedin-related glycoproteins (Pancortins) in the brain

Correlation of peripheral olfactomedin 1 with Alzheimer's disease and cognitive functions

Olfactomedin 1 (OLFM1) is thought to be involved in neuronal development, synaptic structure and function. However, the expression level of peripheral OLFM1 in Alzheimer's disease (AD) and its role in AD are unclear. The present study was conducted to assess the relationship of serum OLFM1 with AD and cognitive function. This study comprised 120 patients with AD and 118 healthy controls (HC). Serum OLFM1 levels, cognitive functions, and brain region volumes were evaluated in all participants. The results demonstrated a significant reduction in serum OLFM1 levels in AD patients (749.8 ± 42.3 pg/mL) compared to HC (804.4 ± 45.7 pg/mL). Among participants carrying the APOE ε4 allele, a significant positive correlation was observed between OLFM1 levels and cognitive assessments, including Mini-Mental State Examination (MMSE), Montreal Cognitive Assessment (MoCA), and Memory and Executive Screening (MES). Furthermore, reduced OLFM1 levels were significantly associated with hippocampus (β = 0.005, 95% CI = 0.001-0.011, p = 0.042) and angular gyrus (β = 0.012, 95% CI = 0.001-0.022, p = 0.025) atrophy. The integration of serum OLFM1 with basic clinical characteristics exhibited robust discriminatory power in differentiating AD patients from HC, evidenced by an area under the curve of 0.881 (95% CI = 0.834-0.926). In summary, serum OLFM1 is a potential peripheral biomarker for AD, that correlates with cognitive function and specific brain volumes. In addition, APOE ε4 may modulate the influence of OLFM1 on cognitive function.

Olfactomedin-like protein OLFML1 inhibits Hippo signaling and mineralization in osteoblasts

Congenital scoliosis is a lateral curvature of the spine that is due to the presence of vertebral anomalies. Although genetic and environmental factors are involved in the pathogenesis of congenital scoliosis, the specific cause of only a small number of individuals has been identified to date. We identified a de novo missense mutation in the olfactomedin-like 1 (OLFML1) gene by whole-exome sequencing of a patient with congenital scoliosis. Then, we carried out further functional investigation in mice. An assessment of the tissue distribution of Olfml1 revealed it to be prominently expressed in developing skeletal tissues, specifically osteoblasts. Short hairpin RNA-mediated knockdown of Olfml1 in osteoblasts induced the translocation of Yes-associated protein (YAP) transcriptional coactivator from the cytoplasm to the nucleus, which accelerated the Hippo signaling pathway to promote osteoblast mineralization. In contrast, experimentally induced gain of function of Olfml1 retained YAP in the cytoplasm. There appears to exist a novel cell-autonomous mechanism by which osteoblasts avoid excess mineralization through Olfml1. Our results also indicate that mutation of OLFML1 leads to impaired osteoblast differentiation and abnormal development of bone tissue.

Proteomic Analysis of the Human Olfactory Bulb

The importance of olfaction to human health and disease is often underappreciated. Olfactory dysfunction has been reported in association with a host of common complex diseases, including neurological diseases such as Alzheimer's disease and Parkinson's disease. For health, olfaction or the sense of smell is also important for most mammals, for optimal engagement with their environment. Indeed, animals have developed sophisticated olfactory systems to detect and interpret the rich information presented to them to assist in day-to-day activities such as locating food sources, differentiating food from poisons, identifying mates, promoting reproduction, avoiding predators, and averting death. In this context, the olfactory bulb is a vital component of the olfactory system receiving sensory information from the axons of the olfactory receptor neurons located in the nasal cavity and the first place that processes the olfactory information. We report in this study original observations on the human olfactory bulb proteome in healthy subjects, using a high-resolution mass spectrometry-based proteomic approach. We identified 7750 nonredundant proteins from human olfactory bulbs. Bioinformatics analysis of these proteins showed their involvement in biological processes associated with signal transduction, metabolism, transport, and olfaction. These new observations provide a crucial baseline molecular profile of the human olfactory bulb proteome, and should assist the future discovery of biomarker proteins and novel diagnostics associated with diseases characterized by olfactory dysfunction.

Mutated olfactomedin 1 in the interphotoreceptor matrix of the mouse retina causes functional deficits and vulnerability to light damage

Olfactomedin 1 (OLFM1) is a secreted glycoprotein and member of the olfactomedin protein family, which is preferentially expressed in various areas throughout the central nervous system. To learn about the functional properties of OLFM1 in the eye, we investigated its localization in the mouse and pig eye. In addition, we analyzed the ocular phenotype of Olfm1 mutant mice in which 52 amino acids were deleted in the central part (M2 region) of OLFM1. OLFM1 was detected in cornea, sclera, retina, and optic nerve of both wild-type and Olfm1 mutant littermates. By immunohistochemistry and double labeling with the lectin peanut agglutinin, OLFM1 was found in the interphotoreceptor matrix (IPM) of mouse and pig retina where it was directly localized to the inner segments of photoreceptors. Western blotting confirmed the presence of the OLFM1 isoforms pancortin 1 (BMY) and pancortin 2 (BMZ) in the IPM. The retinal phenotype of Olfm1 mutant mice did not obviously differ from that of wild-type littermates. In addition, outer nuclear layer (ONL) and total retinal thickness were not different, and the same was true for the area of the optic nerve in cross sections. Functional changes were observed though by electroretinography, which showed significantly lower a- and b-wave amplitudes in Olfm1 mutant mice when compared to age-matched wild-type mice. When light damage experiments were performed as an experimental paradigm of photoreceptor apoptosis, significantly more TUNEL-positive cells were observed in Olfm1 mutant mice 30 h after light exposure. One week after light exposure, the ONL was significantly thinner in Olfm1 mutant mice than in wild-type littermates indicating increased photoreceptor loss. No differences were observed when rhodopsin turnover or ERK1/2 signaling was investigated. We conclude that OLFM1 is a newly identified IPM molecule that serves an important role for photoreceptor homeostasis, which is significantly compromised in the eyes of Olfm1 mutant mice.

Olfactomedin 1 Deficiency Leads to Defective Olfaction and Impaired Female Fertility

Olfactomedin 1 (OLFM1) is a glycoprotein highly expressed in the brain. Olfm1(-/-) female mice were previously reported to have reduced fertility. Previous microarray analysis revealed Olfm1 among the most highly upregulated genes in the uterine luminal epithelium upon embryo implantation, which was confirmed by in situ hybridization. We hypothesized that Olfm1 deficiency led to defective embryo implantation and thus impaired fertility. Indeed, Olfm1(-/-) females had defective embryo implantation. However, Olfm1(-/-) females rarely mated and those that mated rarely became pregnant. Ovarian histology indicated the absence of corpora lutea in Olfm1(-/-) females, indicating defective ovulation. Superovulation using equine chorionic gonadotropin-human chorionic gonadotropin rescued mating, ovulation, and pregnancy, and equine chorionic gonadotropin alone rescued ovulation in Olfm1(-/-) females. Olfm1(-/-) females had a 13% reduction of hypothalamic GnRH neurons but comparable basal serum LH levels and GnRH-induced LH levels compared with wild-type controls. These results indicated no obvious local defects in the female reproductive system and a functional hypothalamic-pituitary-gonadal axis. Olfm1(-/-) females were unresponsive to the effects of male bedding stimulation on pubertal development and estrous cycle. There were 41% fewer cFos-positive cells in the mitral cell layer of accessory olfactory bulb upon male urine stimulation for 90 minutes. OLFM1 was expressed in the main and accessory olfactory systems including main olfactory epithelium, vomeronasal organ, main olfactory bulb, and accessory olfactory bulb, with the highest expression detected in the axon bundles of olfactory sensory neurons. These data demonstrate that defective fertility in Olfm1(-/-) females is most likely a secondary effect of defective olfaction.

A t(3;9)(q25.1;q34.3) translocation leading to OLFM1 fusion transcripts in Gilles de la Tourette syndrome, OCD and ADHD

Gilles de la Tourette syndrome (GTS) is a neuropsychiatric disorder with a strong genetic etiology; however, finding of candidate genes is hampered by its genetic heterogeneity and the influence of non-genetic factors on disease pathogenesis. We report a case of a male patient with GTS, obsessive compulsive disorder, attention-deficit/hyperactivity-disorder, as well as other comorbidities, and a translocation t(3;9)(q25.1;q34.3) inherited from a mother with tics. Mate-pair sequencing revealed that the translocation breakpoints truncated the olfactomedin 1 (OLFM1) gene and two uncharacterized transcripts. Reverse-transcription PCR identified several fusion transcripts in the carriers, and OLFM1 expression was found to be high in GTS-related human brain regions. As OLFM1 plays a role in neuronal development it is a likely candidate gene for neuropsychiatric disorders and haploinsufficiency of OLFM1 could be a contributing risk factor to the phenotype of the carriers. In addition, one of the fusion transcripts may exert a dominant-negative or gain-of-function effect. OLFM1 is unlikely to be a major GTS susceptibility gene as no point mutations or copy number variants affecting OLFM1 were identified in 175 additional patients. The translocation described is thus a unique event, but further studies in larger cohorts are required to elucidate involvement of OLFM1 in GTS pathogenesis.

Amygdala nuclei critical for emotional learning exhibit unique gene expression patterns

The amygdala is a heterogeneous, medial temporal lobe structure that has been implicated in the formation, expression and extinction of emotional memories. This structure is composed of numerous nuclei that vary in cytoarchitectonics and neural connections. In particular the lateral nucleus of the amygdala (LA), central nucleus of the amygdala (CeA), and the basal (B) nucleus contribute an essential role to emotional learning. However, to date it is still unclear to what extent these nuclei differ at the molecular level. Therefore we have performed whole genome gene expression analysis on these nuclei to gain a better understanding of the molecular differences and similarities among these nuclei. Specifically the LA, CeA and B nuclei were laser microdissected from the rat brain, and total RNA was isolated from these nuclei and subjected to RNA amplification. Amplified RNA was analyzed by whole genome microarray analysis which revealed that 129 genes are differentially expressed among these nuclei. Notably gene expression patterns differed between the CeA nucleus and the LA and B nuclei. However gene expression differences were not considerably different between the LA and B nuclei. Secondary confirmation of numerous genes was performed by in situ hybridization to validate the microarray findings, which also revealed that for many genes, expression differences among these nuclei were consistent with the embryological origins of these nuclei. Knowing the stable gene expression differences among these nuclei will provide novel avenues of investigation into how these nuclei contribute to emotional arousal and emotional learning, and potentially offer new genetic targets to manipulate emotional learning and memory.

Pancortins interact with amyloid precursor protein and modulate cortical cell migration

Neuronal precursor cell migration in the developing mammalian brain is a complex process requiring the coordinated interaction of numerous proteins. We have recently shown that amyloid precursor protein (APP) plays a role in migration into the cortical plate through its interaction with two cytosolic signaling proteins, disabled 1 (DAB1) and disrupted in schizophrenia 1 (DISC1). In order to identify extracellular factors that may signal through APP to regulate migration, we performed an unbiased mass spectrometry-based screen for factors that bind to the extracellular domain of APP in the rodent brain. Through this screen, we identified an interaction between APP and pancortins, proteins expressed throughout the developing and mature cerebral cortex. Via co-immunoprecipitation, we show that APP interacts with all four of the mammalian pancortin isoforms (AMY, AMZ, BMY, BMZ). We demonstrate that the BMZ and BMY isoforms of pancortin can specifically reduce β-secretase- but not α-secretase-mediated cleavage of endogenous APP in cell culture, suggesting a biochemical consequence of the association between pancortins and APP. Using in utero electroporation to overexpress and knock down specific pancortin isoforms, we reveal a novel role for pancortins in migration into the cortical plate. Interestingly, we observe opposing roles for alternate pancortin isoforms, with AMY overexpression and BMZ knock down both preventing proper migration of neuronal precursor cells. Finally, we show that BMZ can partially rescue a loss of APP expression and that APP can rescue effects of AMY overexpression, suggesting that pancortins act in conjunction with APP to regulate entry into the cortical plate. Taken together, these results suggest a biochemical and functional interaction between APP and pancortins, and reveal a previously unidentified role for pancortins in mammalian cortical development.

Olfactomedin 1 interacts with the Nogo A receptor complex to regulate axon growth

Olfm1, a secreted highly conserved glycoprotein, is detected in peripheral and central nervous tissues and participates in neural progenitor maintenance, cell death in brain, and optic nerve arborization. In this study, we identified Olfm1 as a molecule promoting axon growth through interaction with the Nogo A receptor (NgR1) complex. Olfm1 is coexpressed with NgR1 in dorsal root ganglia and retinal ganglion cells in embryonic and postnatal mice. Olfm1 specifically binds to NgR1, as judged by alkaline phosphatase assay and coimmunoprecipitation. The addition of Olfm1 inhibited the growth cone collapse of dorsal root ganglia neurons induced by myelin-associated inhibitors, indicating that Olfm1 attenuates the NgR1 receptor functions. Olfm1 caused the inhibition of NgR1 signaling by interfering with interaction between NgR1 and its coreceptors p75NTR or LINGO-1. In zebrafish, inhibition of optic nerve extension by olfm1 morpholino oligonucleotides was partially rescued by dominant negative ngr1 or lingo-1. These data introduce Olfm1 as a novel NgR1 ligand that may modulate the functions of the NgR1 complex in axonal growth.

Olfactomedin 2: expression in the eye and interaction with other olfactomedin domain-containing proteins

PURPOSE

Olfactomedin 2 (OLFM2) belongs to the family of olfactomedin domain-containing proteins. Genetic data suggest its association with glaucoma in Japanese patients. However, its functions are still elusive. In this study, the properties of mammalian OLFM2 were investigated.

METHODS

Expression of the rat and mouse Olfm2 gene was studied by using real-time PCR and in situ hybridization. Substitutions were introduced into OLFM2 by mutagenesis in vitro. Intracellular localization of OLFM2 was studied by confocal microscopy after transient transfection in HEK293 cells. Interaction of OLFM2 with olfactomedin 1 (Olfm1), olfactomedin 3 (Olfm3), myocilin, and gliomedin was studied by using co-immunoprecipitation.

RESULTS

Two major human OLFM2 mRNAs encode secreted proteins with a length of 454 and 478 amino acids. OLFM2 is more closely related to OLFM1 and -3 than to any other family members. Olfm2 showed the most dynamic expression pattern compared with Olfm1 and -3 during mouse eye development and was expressed preferentially in the developing retinal ganglion cell layer. Among three OLFM2 substitutions tested (T86M, R144Q, and L420S), only L420S completely blocked secretion of the protein. OLFM2 interacted with Olfm1 and -3, but not with myocilin and gliomedin. Co-transfection of the L420S mutant with wild-type Olfm1 and -3 significantly inhibited secretion of Olfm1 and -3.

CONCLUSIONS

Highly conserved OLFM2 protein may play an important role in the course of retinal and eye development. Severe mutations in one of the closely related olfactomedin domain-containing proteins (Olfm1-3) may block the secretion and probably the activity of all three family members, leading to more pronounced diseases of the retina than the knockout of individual genes.

Increased expression of olfactomedin-1 and myocilin in podocytes during puromycin aminonucleoside nephrosis

BACKGROUND

The olfactomedin domain proteins Olfm-1 and myocilin are expressed in podocytes. Myocilin stimulates the formation of focal contacts and actin stress fibres in podocytes and other cell types, effects that are mediated through the Wnt signalling pathway. Here, we tested if the expression of both proteins is modified during puromycin aminonucleoside (PAN) nephrosis, which leads to structural changes in the actin cytoskeleton of podocytes.

METHODS

Rats were treated with PAN, and the effectiveness of treatment was analysed by electron microscopy of podocytes and protein detection in the urine. The expression of Olfm-1 and myocilin was studied by immunohistochemistry, western blot analysis of glomerular proteins and real-time RT-PCR of glomerular proteins. In parallel experiments, the expression of Olfm-1 was studied in cultured podocytes treated with dexamethasone, TGF-β, TNF-α and PAN.

RESULTS

Between Days 5 and 22 after treatment, the amounts of the BMZ and BMY splice variants of Olfm-1 and their mRNA were markedly elevated in proteins and mRNA from isolated glomeruli. Immunohistochemistry showed that the expression of Olfm-1 was confined to podocytes. Essentially, comparable results were obtained for myocilin. The BMZ variant of Olfm-1 appeared to be secreted from podocytes and was found in high amounts in urine of treated animals. Treatment of cultured podocytes with dexamethasone and PAN caused an increase in Olfm-1 expression, while treatment with recombinant Olfm-1 increased the formation of actin stress fibres.

CONCLUSIONS

Olfm-1 and myocilin are markedly induced in podocytes during PAN nephrosis and appear to be involved in the processes that govern the reorganization of the actin cytoskeleton during podocyte repair.

Odor-evoked gene regulation and visualization in olfactory receptor neurons

Odorant-evoked activity contributes to olfactory epithelium organization and axon targeting. We examined the consequences on gene expression of a genetic disruption of the channel responsible for olfactory transduction. Genes encoding calcium-binding EF-hand motifs, were among the most highly regulated transcripts consistent with the central role of Ca(2+) influx in neuronal depolarization. Several genes encoding integral membrane proteins are also highly regulated. One gene, Lrrc3b, was regulated more than 10-fold by odorant activity. Changes in expression occur within thirty minutes and are maintained for several hours. In genetic disruptions of Lrrc3b, a Lrrc3b-promoter-driven reporter adopts the activity-regulated expression of the endogenous gene. Individual olfactory glomeruli have a wide spectrum of activity levels that can be modulated by altering odor exposure. The Lrrc3b reporter mouse permits direct assessment of activity in identified glomeruli. In stable odorant environments, activity-regulated proteins provide a characteristic signature that is correlated with the olfactory receptor they express.

Gene expression profiling of rat cerebral cortex development using cDNA microarrays

A large amount of genetic information is devoted to brain development. In this study, the cortical development in rats at eight developmental time points (four embryonic [E15, E16, E18, E20] and four postnatal [P0, P7, P14, P21]) was studied using a rat brain 10K cDNA microarray. Significant differential expression was observed in 467 of the 9,805 genes represented on the microarray. Two major Gene Ontology classes-cell differentiation and cell-cell signaling-were found to be important for cortical development. Genes for ribosomal proteins, heterogeneous nuclear ribonucleoproteins, and tubulin proteins were up-regulated in the embryonic stage, coincidently with extensive proliferation of neural precursor cells as the major component of the cerebral cortex. Genes related to neurogenesis, including neurite regeneration, neuron development, and synaptic transmission, were more active in adulthood, when the cerebral cortex reached maturity. The many developmentally modulated genes identified by this approach will facilitate further studies of cortical functions.

Regulation of myocilin-associated exosome release from human trabecular meshwork cells

PURPOSE

The goal of the present study was to determine whether the release of exosomes containing MYOC from trabecular meshwork (TM) cells is constitutive or regulated.

METHODS

Conditioned media from TM cells were analyzed for MYOC-associated exosomes after treatment with IFN-gamma, porcine aqueous humor, dexamethasone, or a calcium ionophore in cells pretreated with dexamethasone. Aqueous humor was tested whole or fractionated by size exclusion filters. Exosomes from conditioned media were purified by differential centrifugation. Proteins in whole, exosome, and soluble fractions were separated by SDS-PAGE and analyzed for MYOC content by Western blot and densitometry.

RESULTS

Although treatment of TM cells with IFN-gamma increased the appearance of extracellular MYOC-associated exosomes, results were not significantly different from those of control (P = 0.13). In contrast, treatment with dexamethasone increased the appearance of MYOC in the exosome fraction by 376% (P < 0.01). The increase in MYOC-associated exosomes caused by dexamethasone was enhanced by an additional 379% after short-term exposure to ionomycin (P < 0.05). When cultured in media containing aqueous humor, MYOC-associated exosomes increased 514% over control (P < 0.01). Such an increase was diminished in cells treated with aqueous humor that was first passed through a 3-kDa or a 30-kDa, but not a 100-kDa, size exclusion filter.

CONCLUSIONS

The appearance of MYOC-associated exosomes in conditioned media from human TM cells is regulated by a corticosteroid, a calcium ionophore, and a component of aqueous humor, suggesting that TM cells respond to environmental cues by releasing MYOC-associated exosomes.

Zebrafish olfactomedin 1 regulates retinal axon elongation in vivo and is a modulator of Wnt signaling pathway

Olfactomedin 1 (Olfm1) is a secreted glycoprotein belonging to a family of olfactomedin domain-containing proteins. It is involved in the regulation of neural crest production in chicken and promotes neuronal differentiation in Xenopus. Here, we investigate the functions of Olfm1 in zebrafish eye development. Overexpression of full-length Olfm1, and especially its BMY form lacking the olfactomedin domain, increased the thickness of the optic nerve and produced a more extended projection field in the optic tectum compared with control embryos. In contrast, injection of olfm1-morpholino oligonucleotide (Olfm1-MO) reduced the eye size, inhibited optic nerve extension, and increased the number of apoptotic cells in the retinal ganglion cell and inner nuclear layers. Overexpression of full-length Olfm1 increased the lateral separation of the expression domains of eye-field markers, rx3 and six3. The Olfm1-MO had the opposite effect. These data suggest that zebrafish Olfm1 may play roles in the early eye determination, differentiation, optic nerve extension, and branching of the retinal ganglion cell axon terminals, with the N-terminal region of Olfm1 being critical for these effects. Injection of RNA encoding WIF-1, a secreted inhibitor of Wnt signaling, caused changes in the expression pattern of rx3 similar to those observed after Olfm1-MO injection. Simultaneous overexpression of WIF-1 and Olfm1 abolished the WIF-1 effect. Physical interaction of WIF-1 and Olfm1 was demonstrated by coimmunoprecipitation experiments. We concluded that Olfm1 serves as a modulator of Wnt signaling.

Reduced hGC-1 protein expression is associated with malignant progression of colon carcinoma

PURPOSE

hGC-1 (human granulocyte colony-stimulating factor-stimulated clone 1) is a gastrointestinal protein that is a member of the olfactomedin glycoprotein family. Its biological function remains poorly understood. Aberrant expression of hGC-1 in some human carcinomas has been recently reported. The purpose of this study was to examine hGC-1 expression in colon carcinoma and explore the relationship between hGC-1 expression and the clinicopathologic features of patients with colon cancer.

EXPERIMENTAL DESIGN

The expression of hGC-1 in colon adenocarcinoma tissues was examined by dot-blot analysis, in situ hybridization, and immunohistochemistry. The association of hGC-1 expression pattern with patient differentiation grade, tumor stage, metastasis, and survival were examined. To further investigate the involvement of hGC-1 in colon cancer progression, human colon carcinoma (HT-29) cells overexpressing hGC-1 were established and cell proliferation, adhesion, and migration were studied.

RESULTS

Compared with normal colon mucosa, the up-regulation of hGC-1 was more frequently detected in more differentiated colon cancers, whereas down-regulation or no expression was associated with poorly differentiated colon cancers. Interestingly, hGC-1 down-regulation was also found in late tumor-node-metastasis stage, metastasis, and in patients with shorter survival. The morphology and cortical actin distribution of HT-29 cells were altered by hGC-1 overexpression. However, this did not change cell proliferation, but decreased cell adhesion and migration.

CONCLUSION

Our findings indicate that hGC-1 is involved in colon cancer adhesion and metastasis, and that hGC-1 may be a useful marker for tumor differentiation and progression of human colon carcinoma.

Expression patterns of alternative transcripts of the zebrafish olfactomedin 1 genes

Olfactomedin 1 (Olfm1) is a founding member of the family of olfactomedin domain-containing proteins. It is a secreted protein that performs different roles in different species. Although the molecular mechanisms of Olfm1 action are not known, its possible roles include the regulation of neural crest cell production, neuronal differentiation, and ischemic neuronal death in adult. Two zebrafish olfm1 genes (olfm1a and olfm1b) located on chromosomes 5 and 21 were identified in zebrafish genome. Four different transcripts are produced from each olfm1 gene. The distribution of these transcripts in the course of zebrafish early development was studied by in situ hybridization and quantitative RT-PCR. Different variants of olfm1 mRNA were present mainly in neurogenic tissues and demonstrated overlapping expression patterns.

Pancortin-2 interacts with WAVE1 and Bcl-xL in a mitochondria-associated protein complex that mediates ischemic neuronal death

The actin-modulating protein Wiskott-Aldrich syndrome protein verprolin homologous-1 (WAVE1) and a novel CNS-specific protein, pancortin, are highly enriched in adult cerebral cortex, but their functions are unknown. Here we show that WAVE1 and pancortin-2 interact in a novel cell death cascade in adult, but not embryonic, cerebral cortical neurons. Focal ischemic stroke induces the formation of a protein complex that includes pancortin-2, WAVE1, and the anti-apoptotic protein Bcl-xL. The three-protein complex is associated with mitochondria resulting in increased association of Bax with mitochondria, cytochrome c release, and neuronal apoptosis. In pancortin null mice generated using a Cre-loxP system, ischemia-induced WAVE1-Bcl-xL interaction is diminished, and cortical neurons in these mice are protected against ischemic injury. Thus, pancortin-2 is a mediator of ischemia-induced apoptosis of neurons in the adult cerebral cortex and functions in a novel mitochondrial/actin-associated protein complex that sequesters Bcl-xL.

Pathways and genes differentially expressed in the motor cortex of patients with sporadic amyotrophic lateral sclerosis

BACKGROUND

Amyotrophic lateral sclerosis (ALS) is a fatal disorder caused by the progressive degeneration of motoneurons in brain and spinal cord. Despite identification of disease-linked mutations, the diversity of processes involved and the ambiguity of their relative importance in ALS pathogenesis still represent a major impediment to disease models as a basis for effective therapies. Moreover, the human motor cortex, although critical to ALS pathology and physiologically altered in most forms of the disease, has not been screened systematically for therapeutic targets.

RESULTS

By whole-genome expression profiling and stringent significance tests we identify genes and gene groups de-regulated in the motor cortex of patients with sporadic ALS, and interpret the role of individual candidate genes in a framework of differentially expressed pathways. Our findings emphasize the importance of defense responses and cytoskeletal, mitochondrial and proteasomal dysfunction, reflect reduced neuronal maintenance and vesicle trafficking, and implicate impaired ion homeostasis and glycolysis in ALS pathogenesis. Additionally, we compared our dataset with publicly available data for the SALS spinal cord, and show a high correlation of changes linked to the diseased state in the SALS motor cortex. In an analogous comparison with data for the Alzheimer's disease hippocampus we demonstrate a low correlation of global changes and a moderate correlation for changes specifically linked to the SALS diseased state.

CONCLUSION

Gene and sample numbers investigated allow pathway- and gene-based analyses by established error-correction methods, drawing a molecular portrait of the ALS motor cortex that faithfully represents many known disease features and uncovers several novel aspects of ALS pathology. Contrary to expectations for a tissue under oxidative stress, nuclear-encoded mitochondrial genes are uniformly down-regulated. Moreover, the down-regulation of mitochondrial and glycolytic genes implies a combined reduction of mitochondrial and cytoplasmic energy supply, with a possible role in the death of ALS motoneurons. Identifying candidate genes exclusively expressed in non-neuronal cells, we also highlight the importance of these cells in disease development in the motor cortex. Notably, some pathways and candidate genes identified by this study are direct or indirect targets of medication already applied to unrelated illnesses and point the way towards the rapid development of effective symptomatic ALS therapies.

β-dystrobrevin, a kinesin-binding receptor, interacts with the extracellular matrix components pancortins

The dystrobrevins (alpha and beta) are components of the dystrophin-associated protein complex (DPC), which links the cytoskeleton to the extracellular matrix and serves as a scaffold for signaling proteins. The precise functions of the beta-dystrobrevin isoform, which is expressed in nonmuscle tissues, have not yet been determined. To gain further insights into the role of beta-dystrobrevin in brain, we performed a yeast two-hybrid screen and identified pancortin-2 as a novel beta-dystrobrevin-binding partner. Pancortins-1-4 are neuron-specific olfactomedin-related glycoproteins, highly expressed during brain development and widely distributed in the mature cerebral cortex of the mouse. Pancortins are important constituents of the extracellular matrix and are thought to play an essential role in neuronal differentiation. We characterized the interaction between pancortin-2 and beta-dystrobrevin by in vitro and in vivo association assays and mapped the binding site of pancortin-2 on beta-dystrobrevin to amino acids 202-236 of the beta-dystrobrevin molecule. We also found that the domain of interaction for beta-dystrobrevin is contained in the B part of pancortin-2, a central region that is common to all four pancortins. Our results indicate that beta-dystrobrevin could interact with all members of the pancortin family, implying that beta-dystrobrevin may be involved in brain development. We suggest that dystrobrevin, a motor protein receptor that binds kinesin heavy chain, might play a role in intracellular transport of pancortin to specific sites in the cell.

Feature selection using Haar wavelet power spectrum

Background

Feature selection is an approach to overcome the 'curse of dimensionality' in complex researches like disease classification using microarrays. Statistical methods are utilized more in this domain. Most of them do not fit for a wide range of datasets. The transform oriented signal processing domains are not probed much when other fields like image and video processing utilize them well. Wavelets, one of such techniques, have the potential to be utilized in feature selection method. The aim of this paper is to assess the capability of Haar wavelet power spectrum in the problem of clustering and gene selection based on expression data in the context of disease classification and to propose a method based on Haar wavelet power spectrum.

Results

Haar wavelet power spectra of genes were analysed and it was observed to be different in different diagnostic categories. This difference in trend and magnitude of the spectrum may be utilized in gene selection. Most of the genes selected by earlier complex methods were selected by the very simple present method. Each earlier works proved only few genes are quite enough to approach the classification problem [1]. Hence the present method may be tried in conjunction with other classification methods. The technique was applied without removing the noise in data to validate the robustness of the method against the noise or outliers in the data. No special softwares or complex implementation is needed. The qualities of the genes selected by the present method were analysed through their gene expression data. Most of them were observed to be related to solve the classification issue since they were dominant in the diagnostic category of the dataset for which they were selected as features.

Conclusion

In the present paper, the problem of feature selection of microarray gene expression data was considered. We analyzed the wavelet power spectrum of genes and proposed a clustering and feature selection method useful for classification based on Haar wavelet power spectrum. Application of this technique in this area is novel, simple, and faster than other methods, fit for a wide range of data types. The results are encouraging and throw light into the possibility of using this technique for problem domains like disease classification, gene network identification and personalized drug design.

The glycoprotein hGC-1 binds to cadherin and lectins

Human granulocyte colony stimulating factor stimulated clone-1 (hGC-1, also known as GW112, OLM4, and hOlfD) is an olfactomedin-related glycoprotein of unknown function. We performed a series of biochemical studies to characterize its function. Using hGC-1 purified from baculovirus Sf9 cells we demonstrated that hGC-1 is a secreted glycoprotein containing N-linked carbohydrate chains and forms disulfide-bonded multimers. It binds to cell surfaces and to the locutions ricinus communis agglutinin I, concanavalin A and wheat germ agglutinin. Purified hGC-1 enhanced NIH3T3 and 293T/17 cell spreading and attachment, as did hGC-1-enriched culture supernatants of 293T/17 cells transfected with an hGC-1 expression vector. Coimmunoprecipitation studies demonstrated that hGC-1 interacts with cadherin in 293T/17 cells. This interaction depends on the C-terminal olfactomedin domain, but does not require the five well-conserved cysteine residues. However, cysteine residues at 83, 85, 246 and 437 are essential for secretion, and cysteine 226 is critical for hGC-1 multimer formation. Our studies demonstrated that hGC-1, an extracellular matrix glycoprotein, facilitates cell adhesion. Its potential interaction with endogenous cell surface lectins and cadherin may mediate this function.

Noelins modulate the timing of neuronal differentiation during development

Noelins comprise a family of extracellular proteins with proposed roles in neural and neural crest development. Here, we show that a previously uncharacterized family member, Noelin-4, functions to maintain neural precursors in an undifferentiated state and biases ectoderm toward a neural fate. We show that Noelin-4 is induced by the neurogenic genes X-ngnr-1 and XNeuroD. Over-expression of Noelin-4 causes expansion of the neural plate at the expense of neural crest and epidermis. Although there is an apparent increase in the neural precursor pool, no increase was noted in differentiated neurons. Later, derivatives such as the neural tube and retina appear enlarged. We show biochemically that Noelin-4 protein is glycosylated and secreted and that it interacts with Noelin-1, an isoform previously found to promote differentiation in neuralized animal caps. Accordingly, the neural precursor expansion activity of Noelin-4 is reversed by co-expression of Noelin-1. Our finding that Noelin isoforms can bind to and antagonize one another suggests that interacting Noelin isoforms may play a role in regulating timing of differentiation.

Elucidation of subfamily segregation and intramolecular coevolution of the olfactomedin-like proteins by comprehensive phylogenetic analysis and gene expression pattern assessment

The categorization of genes by structural distinctions relevant to biological characteristics is very important for understanding of gene functions and predicting functional implications of uncharacterized genes. It was absolutely necessary to deploy an effective and efficient strategy to deal with the complexity of the large olfactomedin-like (OLF) gene family sharing sequence similarity but playing diversified roles in many important biological processes, as the simple highest-hit homology analysis gave incomprehensive results and led to inappropriate annotation for some uncharacterized OLF members. In light of evolutionary information that may facilitate the classification of the OLF family and proper association of novel OLF genes with characterized homologs, we performed phylogenetic analysis on all 116 OLF proteins currently available, including two novel members cloned by our group. The OLF family segregated into seven subfamilies and members with similar domain compositions or functional properties all fell into relevant subfamilies. Furthermore, our Northern blot analysis and previous studies revealed that the typical human OLF members in each subfamily exhibited tissue-specific expression patterns, which in turn supported the segregation of the OLF subfamilies with functional divergence. Interestingly, the phylogenetic tree topology for the OLF domains alone was almost identical with that of the full-length tree representing the unique phylogenetic feature of full-length OLF proteins and their particular domain compositions. Moreover, each of the major functional domains of OLF proteins kept the same phylogenetic feature in defining similar topology of the tree. It indicates that the OLF domain and the various domains in flanking non-OLF regions have coevolved and are likely to be functionally interdependent. Expanded by a plausible gene duplication and domain couplings scenario, the OLF family comprises seven evolutionarily and functionally distinct subfamilies, in which each member shares similar structural and functional characteristics including the composition of coevolved and interdependent domains. The phylogenetically classified and preliminarily assessed subfamily framework may greatly facilitate the studying on the OLF proteins. Furthermore, it also demonstrated a feasible and reliable strategy to categorize novel genes and predict the functional implications of uncharacterized proteins based on the comprehensive phylogenetic classification of the subfamilies and their relevance to preliminary functional characteristics.

Extracellular Trafficking of Myocilin in Human Trabecular Meshwork Cells

Myocilin (MYOC) is a protein with a broad expression pattern, but unknown function. MYOC associates with intracellular structures that are consistent with secretory vesicles, however, in most cell types studied, MYOC is limited to the intracellular compartment. In the trabecular meshwork, MYOC associates with intracellular vesicles, but is also found in the extracellular space. The purpose of the present study was to better understand the mechanism of extracellular transport of MYOC in trabecular meshwork cells. Using a biochemical approach, we found that MYOC localizes intracellularly to both the cytosolic and particulate fractions. When intracellular membranes were separated over a linear sucrose gradient, MYOC equilibrated in a fraction less dense than traditional secretory vesicles and lysosomes. In pulse-labeling experiments that followed nascent MYOC over time, the characteristic doublet observed for MYOC by SDS-PAGE did not change, even in the presence of brefeldin A; indicating that MYOC is not glycosylated and is not released via a traditional secretory mechanism. When conditioned media from human trabecular meshwork cells were examined, both native and recombinant MYOC associated with an extracellular membrane population having biochemical characteristics of exosomes, and containing the major histocompatibility complex class II antigen, HLA-DR. The association of MYOC with exosome-like membranes appeared to be specific, on the extracellular face, and reversible. Taken together, data suggest that MYOC appears in the extracellular space of trabecular meshwork cells by an unconventional mechanism, likely associated with exosome-like vesicles.

Myocilin is expressed in the glomerulus of the kidney and induced in mesangioproliferative glomerulonephritis

BACKGROUND

Myocilin is a 55 to 57 kD secreted glycoprotein and member of the olfactomedin protein family. It is expressed in high amounts in the outflow tissues of the aqueous humor in the eye where it is supposed to contribute to outflow resistance. Myocilin is mutated in some forms of primary open angle glaucoma and affected patients show very high intraocular pressures because of an increase in resistance to aqueous humor outflow. To obtain information, if myocilin may play a comparable role in other tissues with transendothelial fluid flow, we investigated its expression in the rat kidney.

METHODS

The expression of myocilin in the normal rat kidney and its changes during mesangioproliferative glomerulonephritis were investigated by immunohistochemistry, one- and two-dimensional gel electrophoresis with Western blotting, and reverse transcription-polymerase chain reaction (RT-PCR).

RESULTS

Myocilin and its mRNA were detected in isolated glomeruli. Immunohistochemistry showed specific labeling of glomerular cells, while tubular and interstitial regions were essentially negative. Double staining with the podocyte-specific markers synaptopodin and ezrin indicated that myocilin-positive cells were predominately podocytes. During mesangioproliferative glomerulonephritis, an induction of myocilin immunoreactivity was observed. Labeling for myocilin was now observed in activated mesangial cells and areas of glomerular sclerosis. In parallel cell culture experiments, mRNA for myocilin was detected in cultured murine podocytes and rat mesangial cells.

CONCLUSION

Myocilin is expressed in podocytes of the kidney and induced in mesangial cells during experimental mesangioproliferative glomerulonephritis. The specific function of myocilin in the kidney is not clear, but in a parallel to functions of other olfactomedin proteins, it might have a role in cell-cell adhesion and/or signaling processes.

Expression and characterization of disulfide bond use of oligomerized A2-Pancortins: Extracellular matrix constituents in the developing brain

The region-specific characteristics of the extracellular matrix are crucial for diverse functions in the brain. Pancortins/neuron-specific olfactomedin-related glycoproteins are components of the extracellular matrix. They comprise four alternatively spliced variants, Pancortin-1 to -4, which share a common portion, the B part, in the middle of their structure, have two pairs of alternatively spliced 5' regions, A1 and A2, and 3' regions, C1 and C2. Here we demonstrate that in mice, Pancortin-3 (A2-B-C1) and Pancortin-4 (A2-B-C2), which we have grouped together the A2-Pancortins, were transcribed early during the development of the brain in a region specific manner and were expressed very stably in vivo. They are N-glycosylated and secreted. Furthermore, we examined their ontogenetical expression profiles in the developing thalamus using antiserum against the common B region, since transient expressions of their mRNAs were notable there. In the developing thalami, they lasted long in oligomerized form even after the transcription of their mRNAs decreased to an undetectable level. Further analyses revealed that cysteine residues that are located in the common B part are important for homo- and hetero-oligomer formation of A2-Pancortins. When we substituted cysteine residues 45 and 47 with serine residues in that common B part, oligomerization of the A2-Pancortins was highly disturbed.

The expression of myocilin during murine eye development

PURPOSE

To study the expression and localization of myocilin in the developing mouse eye. Myocilin is a 55- to 57-kDa secreted glycoprotein that is mutated in some forms of primary open-angle glaucoma.

METHODS

The eyes of NMRI mice were studied from embryonic day (E) 14.5 to postnatal day (P) 21, and at 2-3 months of age. Immunohistochemistry was performed with antibodies against myocilin. The specificity of the antibodies was checked by two-dimensional gel electrophoresis. RNA was isolated from eyes at various ages, and the presence of myocilin mRNA was analyzed by northern blot hybridization.

RESULTS

No immunostaining for myocilin was seen before E16.5. At around E17.5, a distinct positive immunoreactivity of optic nerve axons in the developing nerve fiber layer of the retina was observed. At P5-6, immunostaining appeared in perikarya of optic nerve ganglion cells. In the anterior eye, no immunoreactivity was observed until P10. At P12-14, the cells of the epithelial layers of ciliary body and iris, as well as the cells of the trabecular meshwork and iris stroma, became immunoreactive for myocilin. At that time, positive staining for myocilin was also seen in the corneal endothelium and in keratocytes of the corneal stroma. An essentially similar staining pattern was seen in adult eyes. Northern blot analysis for myocilin mRNA in RNA from developing mouse eyes was negative until P9. At P12, a distinct band was observed. A band with similar mobility, but somewhat more intense, was detected in mRNA from adult mouse eyes 2-3 months of age.

CONCLUSIONS

The onset of immunoreactivity for myocilin in the retina occurs in parallel with the maturation of optic nerve ganglion cells. In the anterior eye, the expression of myocilin is associated with the final development of those tissues that are directly involved in aqueous humor dynamics. The presence of myocilin might be important for proper function and structure of mature optic nerve ganglion cells and aqueous humor outflow.

Secreted glycoprotein myocilin is a component of the myelin sheath in peripheral nerves

The structure of the myelin sheath in peripheral nerves requires the expression of a specific set of proteins. In the present study, we report that myocilin, a member of the olfactomedin protein family, is a component of the myelin sheath in peripheral nerves. Myocilin is a secreted glycoprotein that forms multimers and contains a leucine zipper and an olfactomedin domain. Mutations in myocilin are responsible for some forms of glaucoma, a neurodegenerative disease that is characterized by a continuous loss of optic nerve axons. Myocilin mRNA was detected by Northern blotting in RNA from the rat sciatic and ophthalmic nerves. By one- and two-dimensional gel electrophoresis of proteins from the rat and human sciatic nerves, myocilin was found to migrate at an isoelectric point (pI) of 5.2-5.3 and a molecular weight of 55-57 kDa. Immunohistochemistry showed immunoreactivity for myocilin in paranodal terminal loops of the nodes of Ranvier and outer mesaxons and basal/abaxonal regions of the myelin sheath. Double-labeling experiments with antibodies against myelin basic protein showed no overlapping, while overlapping immunoreactivity was observed with antibodies against myelin-associated glycoprotein. The expression of myocilin in the sciatic nerve became detectable at postnatal day (P) 15 and reached adult levels at P20. No or minor expression of myocilin mRNA was found in brain, spinal cord, and optic nerve. mRNA of myocilin was detected in schwannoma cells in situ, but at considerably lower levels than in myelinated nerves. Myocilin might significantly contribute to the structure of the myelin sheath in peripheral nerves.

Quantitative assessment of transcriptome differences between brain territories

Transcriptome analysis of mammalian brain structures is a potentially powerful approach in addressing the diversity of cerebral functions. Here, we used a microassay for serial analysis of gene expression (SAGE) to generate quantitative mRNA expression profiles of normal adult mouse striatum, nucleus accumbens, and somatosensory cortex. Comparison of these profiles revealed 135 transcripts heterogeneously distributed in the brain. Among them, a majority (78), although matching a registered sequence, are novel regional markers. To improve the anatomical resolution of our analysis, we performed in situ hybridization and observed unique expression patterns in discrete brain regions for a number of candidates. We assessed the distribution of the new markers in peripheral tissues using quantitative RT-PCR, Northern hybridization, and published SAGE data. In most cases, expression was higher in the brain than in peripheral tissues. Because the markers were selected according to their expression level, without reference to prior knowledge, our studies provide an unbiased, comprehensive molecular signature for various mammalian brain structures that can be used to investigate their plasticity under a variety of circumstances.

Expression and characterization of the olfactomedin domain of human myocilin

The olfactomedin-domain has been first identified in olfactomedin, an extracellular matrix protein of the olfactory neuroepithelium. Members of this extracellular domain-family have since been shown to be present in several metazoan proteins, such as latrophilins, myocilins, and noelins, but their biological function is unknown. The olfactomedin-domain of myocilin is of considerable interest, since mutations affecting this domain are associated with primary open angle glaucoma. In order to define structural features of this domain-type we have expressed the olfactomedin-domain of human myocilin in Pichia pastoris. The olfactomedin-domain contains a single disulphide-bond connecting Cys-245 and Cys-433 residues; secondary structure predictions and circular dichroism studies indicate that it consists primarily of beta-strands. It is noteworthy that the majority of mutations associated with severe forms of glaucoma affect residues that reside in conserved secondary structural elements of the olfactomedin-domain or are otherwise critical for the integrity of this protein-fold.

Neural expression of mouse Noelin-1/2 and comparison with other vertebrates

Noelins are secreted glycoproteins with important developmental functions in frogs and birds. Here, we present the expression pattern of the mouse homolog of Noelin-1/2 at E8-10 of development and compare this pattern to other vertebrates. Expression was observed in the neural plate and neural crest, as well as in the cranial ganglia. Later, expression is prominent in brain tissue and in the zone of polarizing activity in the limb.

Myocilin and glaucoma: facts and ideas

Mutations in the MYOC gene that encodes for myocilin are causative for some forms of juvenile and adult-onset primary open-angle glaucoma (POAG). Myocilin is a secreted 55-57kDa glycoprotein that forms dimers and multimers. Characteristic structural motifs include a myosin-like domain, a leucine zipper region and an olfactomedin domain. Most of the mutations that have been identified in patients with POAG are localized in the olfactomedin domain, which is highly conserved among species. In the eye, myocilin is expressed in high amounts in the trabecular meshwork (TM), sclera, ciliary body and iris, and at considerable lower amounts in retina and optic nerve head. Secreted myocilin is present in the aqueous humor. In the TM, myocilin is found within the cytoplasm of TM cells and in the juxtacanalicular region in association with fibrillar extracellular matrix components. Since patients with mutations in myocilin may have high intraocular pressures, the role of myocilin for aqueous humor outflow has been investigated and conflicting results have been obtained. Recombinant myocilin increases outflow resistance in perfused anterior segment organ cultures, while overexpression of myocilin after viral gene transfer appears to reduce outflow resistance. In TM cells, the expression of myocilin is induced upon treatment with dexamethasone at a time course similar to that observed in steroid-induced glaucoma. Other factors that induce myocilin expression are transforming growth factor-beta and mechanical stretch. Promoter elements that are important for the glucocorticoid induction have not been identified, but it has been shown that upstream stimulatory factor is critical for the basal promoter activity of MYOC. Mice with a targeted disruption of the myocilin gene do not express a phenotype, indicating that the glaucomatous phenotype in humans is not because of a loss-of-function effect. Experimental studies show that mutated myocilin is not secreted, but appears to accumulate in the cells. Such an accumulation might interfere with TM function and lead to impaired outflow resistance, but, so far, experimental evidence for such a scenario is lacking. In addition, the normal function(s) of myocilin is (are) still elusive.

Dorsalization of the neural tube by Xenopus tiarin, a novel patterning factor secreted by the flanking nonneural head ectoderm

We have isolated a novel secreted dorsalizing factor of the neural tube, Xenopus Tiarin, which belongs to the olfactomedin-related family. Tiarin expression starts at the late gastrula stage in the nonneural ectoderm adjacent to the anterior neural plate. Overexpression of Tiarin in the embryo causes expansion of dorsal neural markers and suppression of ventral markers. In the eye-forming field, Tiarin overexpression induces the retinal markers and represses optic stalk markers. Tiarin directly dorsalizes neural tissues in the absence of mesodermal tissues and antagonizes the ventralizing activity of Sonic hedghog (Shh). Unlike BMP4, another dorsalizing factor, Tiarin does not display antineuralizing activity on the ectoderm or mesoderm-ventralizing activity. These findings show that Tiarin is a novel patterning signal candidate acting in the specification of the dorsal neural tube.

The secreted glycoprotein Noelin-1 promotes neurogenesis in Xenopus

Neurogenesis in Xenopus neural ectoderm involves multiple gene families, including basic helix-loop-helix transcription factors, which initiate and control primary neurogenesis. Equally important, though less well understood, are the downstream effectors of the activity of these transcription factors. We have investigated the role of a candidate downstream effector, Noelin-1, during Xenopus development. Noelin-1 is a secreted glycoprotein that likely forms large multiunit complexes. In avians, overexpression of Noelin-1 causes prolonged and excessive neural crest migration. Our studies in Xenopus reveal that this gene, while highly conserved in sequence, has a divergent function in primary neurogenesis. Xenopus Noelin-1 is expressed mainly by postmitotic neurogenic tissues in the developing central and peripheral nervous systems, first appearing after neural tube closure. Its expression is upregulated in ectopic locations upon overexpression of the neurogenic genes X-ngnr-1 and XNeuroD. Noelin-1 expression in animal caps induces expression of neural markers XBrn-3d and XNeuroD, and co-expression of secreted Noelin-1 with noggin amplifies noggin-induced expression of XBrn-3d and XNeuroD. Furthermore, in animal caps neuralized by expression of noggin, co-expression of Noelin-1 causes expression of neuronal differentiation markers several stages before neurogenesis normally occurs in this tissue. Finally, only secreted forms of the protein can activate sensory marker expression, while all forms of the protein can induce early neurogenesis. This suggests that the cellular localization of Noelin-1 may be important to its function. Thus, Noelin-1 represents a novel secreted factor involved in neurogenesis.

Association of a single nucleotide polymorphism in the TIGR/MYOCILIN gene promoter with the severity of primary open-angle glaucoma

Primary open-angle glaucoma (POAG) is a highly prevalent optic neuropathy and a major cause of irreversible blindness, with elevation of intraocular pressure (IOP) being a primary risk factor. The trabecular meshwork-inducible glucocorticoid response (TIGR)/MYOCILIN (MYOC) gene coding region is mutated in 3-4% of POAG patients. Here, in a retrospective study of 142 POAG patients, we evaluated the influence on glaucoma phenotype of a novel biallelic polymorphism (-1000C/G) located in the upstream region of the MYOC gene. Allele frequencies were similar among patients and controls. However, the G allele (frequency 17.6%), also designated as MYOC.mt1, was associated with an increased IOP (+4.9 mmHg, p=0.0004) and a more damaged visual field (p=0.02). Both effects were predominant in females. Moreover, whereas IOP in MYOC.mt1 noncarriers decreased very markedly to the normal range between diagnosis and inclusion in the study (p=3 x 10(-5) in both males and females), reflecting successful therapy, it decreased less noticeably in MYOC.mt1+ male patients (p=0.005) and not at all in MYOC.mt1+ female patients. MYOC.mt1 appears therefore to be an indicator of poor IOP control and greater visual field damage in diagnosed POAG patients, potentially due to a lack of response to therapeutic intervention. Its typing might help in the selection of treatment paradigms for the management of POAG patients.

The role of myocilin/TIGR in glaucoma: results of the Glaucoma Research Foundation catalyst meeting in Berkeley, California, March 2000

Approximately 3 years ago, the first major (biochemical, molecular biologic, and biologic) insight into primary open-angle glaucoma was the finding that mutations in the myocilin (MYOC/TIGR) gene were related to certain forms of juvenile onset of this disease. Since then, a great deal of work has been done to determine the possible mechanisms by which MYOC/TIGR might cause not only juvenile but also adult-onset primary open-angle glaucoma. To assess the current knowledge and those areas in which more research is necessary, a meeting of scientists was held by the Glaucoma Research Foundation of San Francisco, California in the spring of 2000. This meeting attempted to concentrate on the MYOC/TIGR protein rather than the genetics of this gene. Possible functions and roles of this protein intracellularly and extracellularly were critically examined and discussed. Normal transcriptional and translational events and the effect of mutations on these events were explored. The discussions yielded insight not only in those areas in which important information is known but also in vital areas in which little is currently understood. This review attempts to summarize the current knowledge regarding MYOC/TIGR and to elucidate the points that the people attending the meeting thought needed further study.

JDD1, a novel member of the DnaJ family, is expressed in the germinal zone of the rat brain

We identified a novel gene encoding a new member of the DnaJ family, JDD1 (J domain of DnaJ-like-protein 1), from the rat. The cloned JDD1 cDNA is 1689 bp in size and its deduced amino acid sequence consists of 259 amino acid residues. Immunoblot analysis revealed that JDD1 protein is approximately 30 kDa in size. JDD1 has a J domain that is unique to the DnaJ family but lacks the G/F region (a region that is rich in the amino acids glycine and phenylalanine) and the zinc finger region (also known as the cysteine-rich region)-both characteristic to the DnaJ. JDD1 mRNA is expressed heterogeneously in vivo. In the central nervous system, JDD1 mRNA expression is confined to the germinal (ventricular and subventricular) zone where, except for cells situated deepest in the ventricular zone, neurons and glias are generated and then differentiate during the embryonic period. Expression of JDD1 mRNA in the subventricular zone persists after birth. In addition to the brain, its robust expression is notable in the liver, lung, cortex of the kidney, and several other tissues in the embryo.

Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks

The purpose of this study was to develop a method of classifying cancers to specific diagnostic categories based on their gene expression signatures using artificial neural networks (ANNs). We trained the ANNs using the small, round blue-cell tumors (SRBCTs) as a model. These cancers belong to four distinct diagnostic categories and often present diagnostic dilemmas in clinical practice. The ANNs correctly classified all samples and identified the genes most relevant to the classification. Expression of several of these genes has been reported in SRBCTs, but most have not been associated with these cancers. To test the ability of the trained ANN models to recognize SRBCTs, we analyzed additional blinded samples that were not previously used for the training procedure, and correctly classified them in all cases. This study demonstrates the potential applications of these methods for tumor diagnosis and the identification of candidate targets for therapy.

Rhombex-29, a novel gene of the PLP/DM20-M6 family cloned from rat medulla oblongata by differential display

The ventral medullary surface (VMS) is known as the site of the central chemosensitive neurons. These neurons sense excess CO(2)/H(+) dissolved in the cerebrospinal fluid that superfuses the VMS and induce hyperventilation. We hypothesized that genes specific for hyperventilation are expressed much more highly in VMS neurons than in extra-VMS neurons in other parts of the central nervous system (CNS). Applying the differential display technique to the brain of adult rats, we differentiated the mRNAs of the VMS neurons from those of cerebral cortex neurons. Seventeen candidate clones were selected, and their sequences were analyzed. Among these 17 clones, one encodes a novel four-transmembrane protein, which we named rat Rhombex-29. Structural analysis and the phylogenic tree showed that rat Rhombex-29 is homologous to the major CNS myelin protein PLP/DM20-M6 family and belongs to the intermediate type between mouse M6b and shark DMgamma. As the embryos grew into adult rats, constant expression of rat Rhombex-29 mRNA was found in the brain. Hypercapnic stimulation increased expression of rat Rhombex-29 mRNA in the VMS neurons but not in the cerebral cortex neurons. These results indicate that the VMS neurons are endowed with a novel gene, rat Rhombex-29, that is sensitive to H(+).

A2-Pancortins (Pancortin-3 and -4) are the dominant pancortins during neocortical development

We have identified a novel mouse gene named pancortin that is expressed dominantly in the mature cerebral cortex. This gene produces four different species of proteins, Pancortin-1-4, sharing a common region in the middle of their structure with two variations at the N-terminal (A1 or A2 part) and C-terminal (C1 or C2 part) sides, respectively. In the present study, we showed that expression of mRNAs for A2-Pancortins (Pancortin species that contain the A2 part, i.e., Pancortin-3 and -4) is more dominant than that of mRNAs for A1-Pancortins (Pancortin species that contain the A1 part, i.e., Pancortin-1 and -2) in the prenatal mouse cerebral neocortex. Using western blot analysis, we found that substantial amounts of both A2-Pancortins were present in the prenatal cerebral neocortex and P19 cells after inducing neuronal differentiation. A2-Pancortins were still present in the cerebral neocortex of the adult, although their mRNAs were hardly detected. In contrast, the amount of A1-Pancortins did not increase after the third postnatal week in spite of their intense gene expression. Furthermore, we showed that recombinant Pancortin-3, one of the A2-Pancortins, was a secreted protein, in contrast to Pancortin-1 (one of the A1-Pancortins). These results suggest that A2-Pancortins are extracellular proteins essential for neuronal differentiation and that their molecular behavior is distinct from that of A1-Pancortins.

Localization of olfactomedin-related glycoprotein isoform (BMZ) in the golgi apparatus of glomerular podocytes in rat kidneys

Agene encoding olfactomedin-related glycoprotein was isolated from rat glomerulus despite its prior identification as a neuron-specific gene. The mRNA expression was remarkably intense in renal glomerulus and brain and faint in the lung and eye among rat systemic organs. Although the brain contained four mRNA variants (AMY, AMZ, BMY, and BMZ) transcribed from a single gene, the glomerulus, lung, and eye expressed only two variants (BMZ and BMY). The glycoprotein was intensely immunolocalized in glomerular podocytes and neurons by using an antibody against synthetic peptide of the M region, but weak in endothelial cells of the kidney and lung. Bronchiolar epithelial cells in the lung, and ciliary, corneal, and iris epithelial cells in the eye were also stained. Immunogold electron microscopy revealed selective localization of olfactomedin-related glycoprotein at the Golgi apparatus in podocytes. In glomerular culture, the staining was also intense at a juxtanuclear region in synaptopodin-positive epithelial cells of irregular shape (phenotypic feature of podocytes), whereas it was weak in synaptopodin-negative ones of cobblestone-like appearance (phenotypic feature of parietal epithelial cells of Bowman's capsule). Interestingly, Western blot analysis identified an intense band corresponding to BMZ isoform and another faint band corresponding to BMY isoform in the glomerulus, whereas the intensity of these two bands were nearly equal in the lung and eye. In the brain, four bands corresponding to four isoforms were observed apparently. Computer sequence analysis predicted coiled-coil structures in the secondary structure of the glycoprotein similar to those in Golgi autoantigens, suggesting significant roles in the unique functions of the Golgi apparatus in rat podocytes and neurons.

Molecular cloning of Rhombex-40 a transmembrane protein from the ventral medullary surface of the rat brain by differential display

Respiration-related neurons, which detect various chemicals in cerebrospinal fluid, are localized to the ventral medullary surface (VMS). We hypothesized that expression of genes involved in respiratory function is upregulated in the VMS. By differential display, we looked for genes differentially expressed in VMS neurons and cerebral cortical neurons. Seventeen clones of interest were isolated, and sequence analysis revealed that one of these clones encoded a putative transmembrane protein, rhombencephalic expression protein-40 kDa (Rhombex-40). The rat Rhombex-40 was composed of 374 amino acid residues, and the predicted secondary structure displays a signal peptide in the N-terminus and single-pass transmembrane domain in the center of the sequence. An analysis of consensus sequences identified several phosphorylation sites in the intracellular domain. Expression of rat Rhombex-40 mRNA is high in the brain, and low in lung, liver and kidney. No homologous protein sequence was found in database searches. Whereas the biological function of this protein is presently unknown, its structural features and high expression in the brain suggest that Rhombex-40 may function as a novel transmembrane molecule in neural cells of the brain.

Noelin-1 is a secreted glycoprotein involved in generation of the neural crest

The vertebrate neural crest arises at the border of the neural plate during early stages of nervous system development; however, little is known about the molecular mechanisms underlying neural crest formation. Here we identify a secreted protein, Noelin-1, which has the ability to prolong neural crest production. Noelin-1 messenger RNA is expressed in a graded pattern in the closing neural tube. It subsequently becomes restricted to the dorsal neural folds and migrating neural crest. Over expression of Noelin-1 using recombinant retroviruses causes an excess of neural crest emigration and extends the time that the neural tube is competent to generate as well as regenerate neural crest cells. These results support an important role for Noelin-1 in regulating the production of neural crest cells by the neural tube.

Expression pattern and in situ localization of the mouse homologue of the human MYOC (GLC1A) gene in adult brain

The MYOC (GLC1A) gene has recently been associated with both juvenile-onset primary open angle glaucoma (JOAG) and typical late-onset primary open angle glaucoma (POAG). As a result, much scrutiny has been focused on the pathology of these diseases. In order to better understand the pathophysiology of POAG, we have been developing a mouse model of the disease. As a step in this development, we have investigated the expression pattern of Myoc transcripts in embryonic and adult mouse tissue using Northern blot and in situ hybridization analyses. Myoc transcripts were found in high levels in adult eye, heart, brain, skeletal muscle and testis and to a lesser extent in lung and kidney. They were also present, albeit in very low amounts, during mouse embryogenesis. We present new evidence using in situ hybridization analysis that Myoc transcripts were present in widespread regions of the adult brain including the ependymal lining of the third and fourth ventricles, in the choroid plexus, the zonal layer of the junction of the inferior and superior colliculi, the neurons of the habenula, the piriform cortex, the median pre-optic nucleus of the hypothalamus, the olfactory tubercle, and in the inferior olive. In a functional sense, Myoc expression in the ependyma and choroid plexus, two regions of the brain involved in cerebrospinal fluid synthesis and resorption, parallels Myoc expression in the ciliary body and trabecular meshwork of the anterior segment of the eye where aqueous humor synthesis and outflow occur.

The Genexpress IMAGE Knowledge Base of the Human Brain Transcriptome: A Prototype Integrated Resource for Functional and Computational Genomics

Expression profiles of 5058 human gene transcripts represented by an array of 7451 clones from the first IMAGE Consortium cDNA library from infant brain have been collected by semiquantitative hybridization of the array with complex probes derived by reverse transcription of mRNA from brain and five other human tissues. Twenty-one percent of the clones corresponded to transcripts that could be classified in general categories of low, moderate, or high abundance. These expression profiles were integrated with cDNA clone and sequence clustering and gene mapping information from an upgraded version of the Genexpress Index. For seven gene transcripts found to be transcribed preferentially or specifically in brain, the expression profiles were confirmed by Northern blot analyses of mRNA from eight adult and four fetal tissues, and 15 distinct regions of brain. In four instances, further documentation of the sites of expression was obtained by in situ hybridization of rat-brain tissue sections. A systematic effort was undertaken to further integrate available cytogenetic, genetic, physical, and genic map informations through radiation-hybrid mapping to provide a unique validated map location for each of these genes in relation to the disease map. The resulting Genexpress IMAGE Knowledge Base is illustrated by five examples presented in the printed article with additional data available on a dedicated Web site at the addresshttp://idefix.upr420.vjf.cnrs.fr/EXPR/welcome.html.

alpha-Latrotoxin receptor CIRL/latrophilin 1 (CL1) defines an unusual family of ubiquitous G-protein-linked receptors. G-protein coupling not required for triggering exocytosis

alpha-Latrotoxin, a potent excitatory neurotoxin, binds to two receptors: a G-protein-coupled receptor called CIRL/latrophilin 1 (CL1) and a cell-surface protein called neurexin Ialpha. We now show that CL1 belongs to a family of closely related receptors called CL1, CL2, and CL3. CLs exhibit an unusual multidomain structure with similar alternative splicing and large extra- and intracellular sequences. CLs share domains with other G-protein-coupled receptors, lectins, and olfactomedins/myocilin. In addition, CLs contain a novel, widespread cysteine-rich domain that may direct endoproteolytic processing of CLs during transport to the cell surface. Although the mRNAs for CLs are enriched in brain, CLs are ubiquitously expressed in all tissues. To examine how binding of alpha-latrotoxin to CL1 triggers exocytosis, we used PC12 cells transfected with human growth hormone. Ca2+-dependent secretion of human growth hormone from transfected PC12 cells was triggered by KCl depolarization or alpha-latrotoxin and was inhibited by tetanus toxin and by phenylarsine oxide, a phosphoinositide kinase inhibitor. When CL1 was transfected into PC12 cells, their response to alpha-latrotoxin was sensitized dramatically. A similar sensitization to alpha-latrotoxin was observed with different splice variants of CL1, whereas CL2 and CL3 were inactive in this assay. A truncated form of CL1 that contains only a single transmembrane region and presumably is unable to mediate G-protein-signaling was as active as wild type CL1 in alpha-latrotoxin-triggered exocytosis. Our data show that CL1, CL2, and CL3 perform a general and ubiquitous function as G-protein-coupled receptors in cellular signaling. In addition, CL1 serves a specialized role as an alpha-latrotoxin receptor that does not require G-protein-signaling for triggering exocytosis. This suggests that as an alpha-latrotoxin receptor, CL1 recruits alpha-latrotoxin to target membranes without participating in exocytosis directly.

In-vitro study of the activity of ciprofloxacin alone and in combination against strains of Pseudomonas aeruginosa with multiple antibiotic resistance

Ciprofloxacin appears to have useful activity against Pseudomonas aeruginosa. We have studied its in-vitro activity against ten strains of Ps. aeruginosa with multiple antibiotic resistance. We have confirmed that ciprofloxacin is very active against Ps. aeruginosa with minimal inhibitory concentrations ranging from 0.07 to 0.7 mg/l. Killing curves show ciprofloxacin to be rapidly bactericidal with no regrowth after 24 h. Checkerboard studies with ciprofloxacin in combination with gentamicin, azlocillin and ceftazidime show no consistent interaction. These studies suggest that ciprofloxacin should prove a useful antibiotic in treating infections caused by multiresistant Ps. aeruginosa.