Variants of ST8SIA1 are associated with risk of developing multiple sclerosis.

Multiple sclerosis (MS) is an inflammatory demyelinating disease of the central nervous system of unknown etiology with both genetic and environmental factors playing a role in susceptibility. To date, the HLA DR15/DQ6 haplotype within the major histocompatibility complex on chromosome 6p, is the strongest genetic risk factor associated with MS susceptibility. Additional alleles of IL7 and IL2 have been identified as risk factors for MS with small effect. Here we present two independent studies supporting an allelic association of MS with polymorphisms in the ST8SIA1 gene, located on chromosome 12p12 and encoding ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 1. The initial association was made in a single three-generation family where a single-nucleotide polymorphism (SNP) rs4762896, was segregating together with HLA DR15/DQ6 in MS patients. A study of 274 family trios (affected child and both unaffected parents) from Australia validated the association of ST8SIA1 in individuals with MS, showing transmission disequilibrium of the paternal alleles for three additional SNPs, namely rs704219, rs2041906, and rs1558793, with p = 0.001, p = 0.01 and p = 0.01 respectively. These findings implicate ST8SIA1 as a possible novel susceptibility gene for MS.

An oligonucleotide based array-CGH system for detection of genome wide copy number changes including subtelomeric regions for genetic evaluation of mental retardation.

Developmental delay (DD) and mental retardation (MR) are important child heath issues with a one percent prevalence. Karyotyping with or without subtelomeric FISH (fluorescent in situ hybridization), unless the phenotype of the patient suggests a specific aberration for a specific FISH assay, is the most common procedure in cytogenetic evaluation of MR/DD. In addition, there are several platforms utilizing microarray based comparative genomic hybridization technology (array-CGH) for genetic testing. Array-CGH can detect deletions or duplications in very small segments of chromosomes and the use of this technology is expected to increase the diagnostic yield. The major limitation of the current BAC based array technologies is the low resolution ( approximately 1 Mb) of the chip and suboptimal coverage particularly in the subtelomeric regions. Our aim was to design a novel array-CGH chip with high-density of probes in the subtelomeric regions as well as to maintain sufficient density in other regions of the genome to provide comprehensive coverage for DD/MR. For this purpose, we used Human Genome CGH Microarray 44B chip (Agilent) as the template for the novel design. Using e-array 4.0 (Agilent), one third of the probes were randomly removed from the array and replaced by 14,000 subtelomeric probes. The average density of the probe coverage is 125 kb and 250-400 probes interrogate subtelomeric regions. To evaluate the array, we tested 15 samples (including subtelomeric aberrations and other microdeletion syndromes), which were previously analyzed by karyotyping and/or FISH. The concordance rate between array results and previous results is 100%. In addition we detected two novel aberrations that were not detected by karyotyping. These results demonstrate the utility of this format of array-CGH in detecting genome wide submicroscopic copy number changes as well as providing comprehensive coverage of all subteleomeric regions.

Arvanil and anandamide up-regulate CD36 expression in human peripheral blood mononuclear cells.

In this study we analysed the regulation of gene expression by arvanil and anandamide in human peripheral blood mononuclear cells (PBMCs) to clarify their immunosuppressive properties. PBMCs were activated, leading to CD36 down regulation, that was normalized by arvanil and anandamide. We used microarray technology to identify a regulatory pattern associated with cell proliferation in the presence of both substances. CD3-CD28 stimulated PBMCs showed a pattern of up-regulated and down-regulated genes after treatment with these substances. We selected and analysed several genes chosen by their function in the regulation of cell proliferation. We showed a transcriptional control of the CD36 gene by arvanil and anandamide associated with an increased protein expression, thus suggesting a possible role of CD36 in anandamide and arvanil anti-inflammatory pattern.

Using the common sense model to understand perceived cancer risk in individuals testing for BRCA1/2 mutations.

The common sense model posits that individuals' understanding of illness is based upon somatic symptoms and life experiences and thus may differ significantly from the biomedical view of illness. The current study used the common sense model to understand cancer risk perceptions in 99 individuals testing for BRCA1/2 mutations. Specifically, we examined change from post-counseling to post-result in (1) absolute risk (risk of developing cancer in one's lifetime) and (2) comparative risk (risk relative to the general population). Results indicated that absolute risk showed a trend such that those with a personal history of cancer receiving uninformative negative results reported decreased absolute risk. Further, individuals receiving uninformative negative results reported decreased comparative risk. Those with no personal cancer history receiving informative negative results did not decrease in risk over time nor did their risk differ from those with a personal cancer history, evidencing unrealistic pessimism regarding their risk of cancer. The reasons provided for individuals' risk perceptions could be classified in terms of attributes of the common sense model and included the: (1) causes of cancer (e.g. family history, mutation status); (2) control or cure of cancer through health behaviors and/or surgery; and (3) perceived timeline for developing cancer (e.g. time left in life to develop cancer). We conclude that key to developing interventions to improve understanding of cancer risk and promoting effective cancer control mechanisms is an understanding of the specific reasons underlying individuals' perceptions of cancer risk.

The decision to test in women receiving genetic counseling for BRCA1 and BRCA2 mutations.

Functions of genetic counseling include provision of risk information and provision of support in an effort to assist with decision making. This study examines (1) the relationship among intentions to test, self-reported provision of blood sample, and receipt of test results; (2) the impact of genetic counseling on distress specific to gene status, perceived risk of developing breast and ovarian cancer in the context having BRCA1/2 mutations (mutations predisposing to increased risk of breast-ovarian cancer), and perceived risk factors for breast cancer; and (3) the clinical profile of those receiving/not receiving results. Intentions to test for BRCA1/2 mutations, self-reported provision of blood sample immediately after counseling, and receipt of test results were statistically different but highly correlated, and intentions to test increased from pre- to postcounseling. A repeated measures ANOVA found distress specific to gene status and perceived risk factors decreased from pre- to postcounseling. Further, two clinical profiles of consultands emerged: (1) those receiving results with change in intentions to test having lower levels of distress and (2) those not receiving results and those receiving results with no change in intentions to test with higher levels of distress. Our findings are consistent with the function of genetic counseling-to provide information and support to those with familial cancer, as well as to assist in decision making. The provision of support is important as distress specific to gene status may impede flexible decision making about genetic testing.

Subjective and objective risk of breast cancer in Ashkenazi Jewish individuals at risk for BRCA1/2 mutations.

The aims of the study were to (1) examine the differences between subjective and objective estimates of the risk of breast cancer in those being tested for BRCA1/2 mutations, (2) explore new ways to conceptualize risk, and (3) examine the change in subjective risk of developing breast cancer throughout the process of genetic counseling and testing. Participants were 86 Ashkenazi Jewish women with a family or personal history indicating risk for BRCA1/2 mutations. Surveys to assess subjective risk of breast cancer (percentage risk, projected age of onset, and survival time) were administered before counseling, after counseling, and after receipt of test results. Subjective percentage risk of breast cancer was compared to estimated objective risk to determine accuracy. Those with no personal history of cancer receiving positive results became more accurate from post-counseling to post-result. Those receiving positive results increased their estimate of their percentage risk, and those receiving uninformative negative results decreased their estimate of their percentage risk from post-counseling to post-result. Those without a personal history of cancer decreased in perceived risk from post-counseling to post-result. No change in projected age of onset of breast cancer or survival time with breast cancer was seen from pre- to post-counseling or from post-counseling to post-result, and no change in accuracy or in percentage risk of breast cancer was seen from pre- to post-counseling. Individuals use information from genetic counseling to form estimates of percentage risk following receipt of test results; however, projected age of onset and survival time with breast cancer, areas not targeted by genetic counseling that may be more closely linked to health behavior, do not change.

Association between gene expression profile and tumor invasion in oral squamous cell carcinoma.

There are limited studies attempting to correlate the expression changes in oral squamous cell carcinoma with clinically relevant variables. We determined the gene expression profile of 16 tumor and 4 normal tissues from 16 patients by means of Affymetrix Hu133A GeneChips. The hybridized RNA was isolated from cells obtained with laser capture microdissection, then was amplified and labeled using T7 polymerase-based in vitro transcription. The expression of 53 genes was found to differ significantly (33 upregulated, 20 downregulated) in normal versus tumor tissues under two independent statistical methods. The expression changes in four selected genes (LGALS1, MMP1, LAGY, and KRT4) were confirmed with reverse transcriptase polymerase chain reaction. Two-dimensional hierarchical clustering of the 53 genes resulted in the samples clustering according to the extent of tumor infiltration: normal epithelial tissue, tumors less than or equal to 4 cm in dimension, and tumors more than 4 cm in dimension (P = 0.0014). The same pattern of clustering was also observed for the 20 downregulated genes. We did not observe any associations with lymph node metastasis (P = 0.097).

Gene expression after crush injury of human saphenous vein: using microarrays to define the transcriptional profile.

BACKGROUND: Vein graft stenosis is believed to be the pathophysiologic response of vascular tissue to injury and is the major cause of vein graft failure. Therapeutic interventions might improve with knowledge of the physiologic pathways involved in the hyperplastic response to vascular injury. In this study, our purpose was to identify induced, early pathways that might be important in the human response to vascular injury. STUDY DESIGN: Human saphenous vein from 7 patients was organ cultured or crush injured and cultured for 48 or 72 hours after harvest. Gene expression was determined for syngeneic veins at harvest and at the experimental time points and compared to determine which genes were induced or repressed. Expressed genes (the transcriptional profile) were then assigned to functional physiologic classes. RESULTS: At 72 hours, in both organ-cultured and crush-injured vein, the gene for the Wnt ligand protein (WNT5A) was induced. At 48 hours in the organ-cultured vein only, the gene for the Frizzled protein (FZD2), a subunit of the Wnt receptor complex, was repressed. At 72 hours in injured vein only, the gene for the product of Wnt signaling (WISP1) was induced; the gene for the Wnt-binding, soluble Frizzled-related protein (FRZB) was repressed; and the gene for Dickkopf (DKK1) protein, which binds to the low density lipoprotein receptor-related protein subunit of the Wnt receptor complex, was induced. CONCLUSIONS: Early induction of WNT5A, coupled with the coordinated induction and repression of genes that modulate the Wnt signaling pathway, led to the early, selective induction of WISP1 and no other Wnt-inducible genes. This early, selective expression of a limited gene set might characterize the human vascular response to injury, and could enable development of therapies to treat the clinical sequelae of this response.

Cancer genetics knowledge and beliefs and receipt of results in Ashkenazi Jewish individuals receiving counseling for BRCA1/2 mutations.

BACKGROUND: Genetic counseling for BRCA1 and BRCA2 mutations (mutations associated with increased risk of breast-ovarian cancer) endeavors to communicate information that will help individuals make informed decisions regarding genetic testing. METHODS: This repeated-measures study examined cancer genetics knowledge and beliefs before and after counseling and their relationship to receipt of results for BRCA1/2 mutations in 120 highly educated Ashkenazi Jewish individuals. RESULTS: A repeated-measures analysis examined change in knowledge and beliefs regarding personal behavior, mechanisms of cancer inheritance, meaning of a positive result, practitioner knowledge, frequency of inherited cancer, and meaning of a negative result from pre- to post-counseling with the between subjects variables of education (with/without graduate training) and personal history of breast or ovarian cancer (yes/no), and risk of having a mutation entered as a covariate. Mechanisms of cancer inheritance, meaning of a positive result, and practitioner knowledge increased from pre- to post-counseling. Those with graduate training had higher ratings of mechanisms of cancer inheritance ratings and lower ratings of frequency of inherited cancers than those without. Mann-Whitney U tests found those testing had higher ratings in mechanisms of cancer inheritance, specifically in the association of multiple primary cancers with hereditary cancer, than those not testing. CONCLUSIONS: Genetic counseling is helpful in improving overall knowledge of cancer genetics even for highly educated individuals. Particular areas of knowledge improvement should be explored in relation to receipt of results, especially to further elucidate the relationship of knowledge of the association of multiple primary cancers with hereditary cancer to receipt of test results.

High incidence of two methylenetetrahydrofolate reductase mutations (C677T and A1298C) in Hispanics.

Mutations in the 5,10-methylenetetrahydrofolate reductase (MTHFR) and coagulation factors II and V genes have been found at high frequencies in European and American Caucasian populations and are associated with increased risk for thrombophilia, premature coronary artery disease, and a variety of adverse pregnancy outcomes. Hispanic populations in the United States exhibit high levels of some of these conditions, so we initiated a population-based study to determine the frequency of these mutations (MTHFR C677T and A1298C, Factor II G20210A and Factor V G1691A) in this group. We find comparable frequencies of the Factors II and V mutations, but a high incidence of the two MTHFR mutations in a diverse sample of American Hispanics compared to those reported in Caucasians. Prospective studies of Hispanic women with these mutations and pregnancy outcomes will establish if there is a causal relationship.

Comprehensive genome-wide comparison of DNA and RNA level scan using microarray technology for identification of candidate cancer-related genes in the HL-60 cell line.

Genome-wide scans for DNA and RNA changes in the HL-60 cell line relative to normal leukocytes were conducted. Microarray-based comparative genome hybridization (CGH) studies were performed with the Spectral Genomics Human Bacterial Artificial Chromosome (BAC) 3MB system. Transcriptional measurements of approximately 12,500 human genes were monitored using Affymetrix U95A GeneChips. In HL-60, genomic DNA amplification of the 8q24 locus, trisomy 18, and deletions at loci 5q11.2 approximately q31, 6q12, 9p21.3 approximately p22, 10p12 approximately p15, 14q22 approximately q31, 17p12 approximately p13.3, and monosomy X were detected. After obtaining locus information about the RNA transcripts from the Affymetrix database, 4368 genes were stratified both according to status of RNA expression and the DNA copy number of their designated loci. The expression level of 2326 (53.25%) of 4368 transcripts is concordant with DNA copy number. Examples of specific, highly expressed, cancer-associated genes in amplified loci include SERPINB10, MYC, TYMS, HEC, and EPB41L3, while CD14, GZMK, TCF7, FOS, MLH3, CTNNA1, IRF1, VIM, CRK, MAP3K1, STAM, MAX, SFRG5, ENC1, PURA, MNT, RASA1, GLRX, UBE2B, NR3C1, PTENP1, BS69, COPEB, SKIP, PIM2, and MIC2 represent cancer-associated genes in deleted loci with decreased expression. The complementary usage of genome-wide DNA and RNA scans should enhance the identification of candidate genes in the neoplastic process.

Subjective and Objective Risks of Carrying a BRCA1/2 Mutation in Individuals of Ashkenazi Jewish Descent.

This repeated measures study examines (1) the change in subjective risk of mutations pre- to postcounseling, (2) the accuracy of BRCAPRO estimates of mutations, and (3) the discrepancy between subjective risk and BRCAPRO estimates of mutations before and after genetic counseling. Ninety-nine Ashkenazi Jewish individuals pursued testing for BRCA1/2 mutations. Most had a personal cancer history (N = 51; family only: N = 48); and received uninformative negative results (N = 66; positives: N = 23; informative negative: N = 10). The coping strategy of defensive pessimism predicts that individuals will believe the worst case scenario to better cope with a potential negative outcome. Consistent with this, most felt they would have a mutation, if not mutations in both genes. The BRCAPRO model appeared to overestimate risk of having a mutation in this sample (p < .001). BRCAPRO overestimates notwithstanding, genetic counseling increased accuracy of subjective risk (p < .01). Individuals with a family-only cancer history had the least accurate estimates of risk (p < .05) and may need further intervention to either manage anxiety or improve knowledge.

Linkage analysis conditional on HLA status in a large North American pedigree supports the presence of a multiple sclerosis susceptibility locus on chromosome 12p12.

Multiple sclerosis (MS) is a chronic inflammatory demyelinating disease of the central nervous system with a probable immune-mediated pathogenesis. Strong evidence supports the hypothesis that MS is determined by genetic and environmental factors, but these factors remain largely undefined. The genetic component is suggested by a higher concordance rate in monozygotic (28%) versus dizygotic (5%) twins as well as familial recurrence risk. Several studies have shown association of MS with the histocompatibility leukocyte antigen (HLA) class II region, specifically DR15, DQ6. However, there is no convincing evidence of a common susceptibility locus. We have identified a pedigree of Pennsylvania Dutch extraction, in which MS segregates with an autosomal dominant inheritance pattern. We have collected blood samples from 18 family members, seven of whom show typical signs of MS lesions by magnetic resonance imaging. The 18 individuals were serotyped for HLA class I and II and analyzed by a genome-wide screen for linkage analysis. We have found evidence for suggestive linkage to markers on 12p12 with a maximum multipoint LOD score of 2.71, conditional on the presence of DR15, DQ6. Contingency table analysis showed that all MS affected individuals have both the DR15, DQ6 allele and the 12p12 haplotype whereas the unaffected individuals have either one or neither of these markers (P = 0.00011). Our data suggests that both HLA DR15, DQ6 and a novel locus on chromosome 12p12 may be necessary for development of MS in this family.