Skew in the human caveolin 1 gene upstream purine complex homozygote haplotype compartment in multiple sclerosis

Physiological and pathological roles of caveolins in the central nervous system

Caveolins are a family of transmembrane proteins located in caveolae, small lipid raft invaginations of the plasma membrane. The roles of caveolin-enriched lipid rafts are diverse, and include mechano-protection, lipid homeostasis, metabolism, transport, and cell signaling. Caveolin-1 (Cav-1) and other caveolins were described in endothelial cells and later in other cell types of the central nervous system (CNS), including neurons, astrocytes, oligodendrocytes, microglia, and pericytes. This pancellular presence of caveolins demands a better understanding of their functional roles in each cell type. In this review we describe the various functions of Cav-1 in the cells of normal and pathological brains. Several emerging preclinical findings suggest that Cav-1 could represent a potential therapeutic target in brain disorders.

Support for "Disease-Only" Genotypes and Excess of Homozygosity at the CYTH4 Primate-Specific GTTT-Repeat in Schizophrenia

OBJECTIVE

The role of short tandem repeats (STRs) in the control of gene expression among species is being increasingly understood following the identification of several instances in which certain STRs occur identically, or expand differentially, in primates versus nonprimates. These STRs may regulate genes that participate in characteristics that are associated with the divergence of primates from sibling orders (e.g., brain higher order functions). The CYTH4 gene contains the longest tetranucleotide STR in its core promoter, at 7-repeats, and links to the evolution of human and nonhuman primates. Allele and genotype distribution of this STR were studied in patients affected by schizophrenia (SCZ) and controls.

METHODS

High-resolution data were obtained on the allele and genotype distribution of the CYTH4 STR and a novel C > T single-nucleotide polymorphism (SNP) at its immediate upstream sequence in 255 patients with SCZ and 249 controls. Each sample was sequenced twice using the fluorescent dye termination method.

RESULTS

Novel alleles were detected at the long extreme of the GTTT-repeat, at 10- and 11-repeats, in the SCZ cases and controls. Excess of homozygosity was observed for the entire range of alleles across the GTTT-repeat and the C > T SNP in the SCZ patients in comparison with the controls (Yates corrected p < 0.011). Three genotypes consisting of the 11-repeat allele (i.e., 11/11, 10/11, and 7/11) were detected only in the SCZ patients (i.e., disease-only genotypes), and contributed to 2.3% of the SCZ genotypes (Mid p exact <0.007). The frequency of the 11-repeat allele was estimated at 0.02 and 0.006 in the SCZ patients and controls, respectively (Mid p exact <0.006).

CONCLUSION

This indicates that STR genotypes that are absent in the control group may be risk factors for SCZ. Future studies are warranted to test the significance of our findings.

Caveolin-1 in the anterior cingulate cortex modulates chronic neuropathic pain via regulation of NMDA receptor 2B subunit

Chronic pain is still a basic science and clinical challenge. Unraveling of the neurobiological mechanisms involved in chronic pain will offer novel targets for the development of therapeutic strategies. It is well known that central sensitization in the anterior cingulate cortex (ACC) plays a critical role in initiation, development, and maintenance of chronic pain. However, the underlying mechanisms still remain elusive. Here, we reported that caveolin-1 (Cav-1), a scaffolding protein in membrane rafts, was persistently upregulated and activated in the ACC neurons after chronic constriction injury (CCI) in mice. Knockdown or blocking of Cav-1 in the contralateral ACC to the injury side reversed CCI-induced pain behavioral and neuronal sensitization and overexpression of Cav-1 in the ipsilateral ACC-induced pain behavior in the unaffected hindpaw. Furthermore, we found that Cav-1 directly binding with NMDA receptor 2B subunit (NR2B) and promotion of NR2B surface levels in the ACC contributed to modulation of chronic neuropathic pain. Disrupting the interaction of Cav-1 and NR2B through microinjection of a short peptide derived from the C-terminal of NR2B into the ACC exhibited a significant anti-nociception effect associated with decrease of surface NR2B expression. Moreover, Cav-1 increased intracellular Ca(2+) concentration and activated the ERK/CREB signaling pathway in an NR2B-dependent manner in the ACC. Our findings implicate that Cav-1 in the ACC neurons modulates chronic neuropathic pain via regulation of NR2B and subsequent activation of ERK/CREB signaling, suggesting a possible caveolin-mediated process would participate in neuronal transmission pathways implicated in pain modulation.

Association between upstream purine complexes of human caveolin-1 gene and schizophrenia in qazvin province of iran

Background:

Caveolin is a multifunctional and scaffolding membrane protein, which involves cholesterol trafficking to plasma lipid microdomain. It organizes and targets synaptic parts of the neurotransmitter and neurotrophic receptor signaling pathways. Caveolins are encoded by CAV-1, 2 and 3 genes. Disruption of the CAV1 would likely ruin the neuronal signaling, which leads to symptoms of schizophrenia in predisposed individuals.

Objectives:

The upper area of CAV-1 gene is highly conserved and can have a regulatory role in neurodegenerative diseases. This study was designed to find out the possible association of polymorphisms of this area and schizophrenia.

Patients and Methods:

In a case-control study, 254 blood samples were obtained from 127 patients with schizophrenia and 127 well matched controls referred to 22 Bahman Hospital of Qazvin University of Medical Sciences (QUMS) in Qazvin province, Iran, using simple random sampling method. After extracting DNA, the upper region of the human CAV1- gene was amplified by PCR in all collected samples. The products were visualized by silver staining in 10% polyacrylamide gel and then sequenced.

Results:

We detected nine homozygotes in patients and 15 in control subjects. Homozygosity was 7.08% and 11.8% in cases and control, respectively. Nine types homozygote haplotype were detected in upper region of the CAV1 gene in cases and controls. Three haplotypes were common in cases and controls; four haplotypes were seen in controls only and two in cases.

Conclusions:

Our findings implied a significant correlation between some haplotypes of upper region of CAV1 gene and schizophrenia. Existence of some haplotypes and lack of another in CAV1 upstream can suggest a significant correlation between schizophrenia and some haplotypes.

Core promoter short tandem repeats as evolutionary switch codes for primate speciation

Alteration in gene expression levels underlies many of the phenotypic differences across species. Because of their highly mutable nature, proximity to the +1 transcription start site (TSS), and the emerging evidence of functional impact on gene expression, core promoter short tandem repeats (STRs) may be considered an ideal source of variation across species. In a genome-scale analysis of the entire Homo sapiens protein-coding genes, we have previously identified core promoters with at least one STR of ≥ 6-repeats, with possible selective advantage in this species. In the current study, we performed reverse analysis of the entire Homo sapiens orthologous genes in mouse in the Ensembl database, in order to identify conserved STRs that have shrunk as an evolutionary advantage to humans. Two protocols were used to minimize ascertainment bias. Firstly, two species sharing a more recent ancestor with Homo sapiens (i.e. Pan troglodytes and Gorilla gorilla gorilla) were also included in the study. Secondly, four non-primate species encompassing the major orders across Mammals, including Scandentia, Laurasiatheria, Afrotheria, and Xenarthra were analyzed as out-groups. We introduce STR evolutionary events specifically identical in primates (i.e. Homo sapiens, Pan troglodytes, and Gorilla gorilla gorilla) vs. non-primate out-groups. The average frequency of the identically shared STR motifs across those primates ranged between 0.00005 and 0.06. The identified genes are involved in important evolutionary and developmental processes, such as normal craniofacial development (TFAP2B), regulation of cell shape (PALMD), learning and long-term memory (RGS14), nervous system development (GFRA2), embryonic limb morphogenesis (PBX2), and forebrain development (APAF1). We provide evidence of core promoter STRs as evolutionary switch codes for primate speciation, and the first instance of identity-by-descent for those motifs at the interspecies level.

Biased homozygous haplotypes across the human caveolin 1 upstream purine complex in Parkinson's disease

The alpha-synuclein-caveolin 1 axis is suggested to be of role in the pathogenesis of Parkinson's disease in cell line models. The objective of this study was to analyze the homozygous haplotype compartment of the human caveolin 1 gene upstream purine complex in patients afflicted with Parkinson's disease. This complex was screened in patients with Parkinson's disease (n = 141) and compared with a group of controls (n = 760) using polymerase chain reaction and sequencing. The expression activity of the homozygous haplotypes was then examined using luciferase Dual-Glo system in human neuronal cell line, LAN-5. Six haplotypes were found to be homozygous in the patients, and not in the control pool (Fisher exact p < 1 × 10(-6)). Three of those haplotypes were specific to Parkinson's disease (Fisher exact p < 0.002), and the remaining three overlapped with homozygous haplotypes in Alzheimer's disease and multiple sclerosis (Fisher exact p < 0.002). The disease haplotypes contained motif lengths that were nonexistent in the control homozygous haplotype pool and significantly increased gene expression (p < 9 × 10(-6)). We conclude that skew in the caveolin 1 purine complex homozygous haplotype compartment and an additive effect of those haplotypes may be linked with Parkinson's disease.

Haplotypes across the human caveolin 1 gene upstream purine complex significantly alter gene expression: implication in neurodegenerative disorders

We have previously reported a polymorphic purine complex at the 1.5 kb upstream region of the human caveolin 1 (CAV1) gene that is conserved across several species in respect with sequence motifs and the location of the complex. The IRF and Ets transcription factors have common binding sites for this region across those species. We have also shown skew in the homozygote haplotype compartment of this complex in two neurodegenerative disorders, sporadic late-onset Alzheimer's disease (AD), and multiple sclerosis (MS), versus disease-free controls (p<0.0000001). In the current study, we analyze the functional implication of the disease homozygote haplotypes (i.e. 102-bp and 142-bp) vs. control homozygote haplotype (110-bp) in three neuronal cell lines, LAN-5, U-87 MG, and N2A, using dual luciferase reporter system. A significant increase in gene expression was observed in the cell lines with the disease haplotype constructs vs. control haplotype in the three cell lines (t-test p<4 × 10(-4), 1 × 10(-6), and 3 × 10(-4)), respectively. We conclude that the human CAV1 upstream purine complex modifies gene expression. An additive effect of the haplotypes in the homozygous status is speculated based on the skew in the homozygote haplotypes in neurodegenerative disorders.

Core promoter STRs: novel mechanism for inter-individual variation in gene expression in humans

In a genome-scale analysis of the composition of core promoter sequences, we have recently shown that approximately 25% of the human protein-coding genes have at least one short tandem repeat (STR) of 3-repeats in their core promoters (i.e. the interval between -120 to +1). Through their nucleosome processing effect, GA-repeats play a crucial role in the regulation of gene transcription. In this study, we chose the human SRY (sex determining region Y)-box 5 (SOX5) gene as a prototype of the GA-rich core promoters to investigate the role of core promoter GA-STRs in gene expression. The human SOX5 gene is indispensable for diverse embryonic developmental processes, ranging from oligodendrocyte development and corticogenesis to chondrogenesis, and regulation of the cell cycle. Whereas the absolute ratio of 99% of the genes range between 0.2 and 2, the composition of the core promoter of the two most ubiquitously expressed mRNAs of the human SOX5 gene (transcripts ID: ENST00000451604 and ENST00000309359) is exceptionally rich in purine nucleotides (purine/pyrimidine ratio: 61.5). Indeed, this core promoter is an island of four tandem GA-STRs, and lacks the known TATA and TATA-less elements for gene transcription. Evolutionary conservation of this region between human and mouse (75% homology) supports important functional role for this promoter. In this study, we show that this nucleotide composition is indeed a potent promoter (p<1×10(-10)), and different haplotypes across the region result in significant difference in gene expression (p<1×10(-6)). To our knowledge, this is the first report of functional STRs in a human gene core promoter. Based on our search on the core promoters of the entire human protein-coding genes annotated in the GeneCards database (19,927genes) for the presence of pure GA-STRs, 429 genes contain at least one GA(3)-repeat in their core promoter. Core promoters with pure GA-STRs of GA(4) and above were observed in 61 genes. Our data unravel a novel mechanism for inter-individual variation in gene expression and complex traits/phenotypes through core promoter GA-STRs.

Exceptional human core promoter nucleotide compositions

The proximal promoter sequences contain basic motifs for the expression of the downstream genes. We present genome-scale computational analyses of the 120-bp immediate upstream sequences to the +1 transcription start sites (TSSs) of 10,117 human protein-coding genes, and unravel exceptional genes in respect with the core promoter nucleotide composition. Our data reveal that while in 99% of the genes the absolute purine/pyrimidine ratio ranges between 0.2 and 2.5, certain genes show exceptional skew in this balance (e.g. ratios of 82.3 in VWA3A, 61.5 in Sox5, and 24.0 in BRWD3), and consist of islands of purines or pyrimidines. Furthermore, while over 95% of the genes lack more than one short tandem repeat (STR) in their core promoters, certain gene promoters are exceptionally rich in multiple STRs (e.g. eight consecutive STRs in UBE2QL1, and six STRs in GRIA2). We found sequence bias for the majority of those promoters across species, supporting functional roles for them in gene expression. Genes downstream to those promoters were also found to be of ontologic importance (i.e. we were able to track the majority of those genes to the lower species such as Saccharomyces cerevisiae and Caenorhabditis elegans). The exceptional promoters presented in this study lack the conventional motifs for the TATA, and TATA-less promoters, hence offering novel mechanisms for gene expression. They may also provide potential mechanisms for inter-individual variations in gene expression, and complex traits/disorders.