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Biomedical subjects

Leif E Peterson

Publications and source records attributed to Leif E Peterson.

13 recordsLinked to original sources

Characterization of BRCA1 and BRCA2 mutations in a large United States sample.

PURPOSE: An accurate evaluation of the penetrance of BRCA1 and BRCA2 mutations is essential to the identification and clinical management of families at high risk of breast and ovarian cancer. Existing studies have focused on Ashkenazi Jews (AJ) or on families from outside the United States. In this article, we consider the US population using the largest US-based cohort to date of both AJ and non-AJ families. METHODS: We collected 676 AJ families and 1,272 families of other ethnicities through the Cancer Genetics Network. Two hundred eighty-two AJ families were population based, whereas the remainder was collected through counseling clinics. We used a retrospective likelihood approach to correct for bias induced by oversampling of participants with a positive family history. Our approach takes full advantage of detailed family history information and the Mendelian transmission of mutated alleles in the family. RESULTS: In the US population, the estimated cumulative breast cancer risk at age 70 years was 0.46 (95% CI, 0.39 to 0.54) in BRCA1 carriers and 0.43 (95% CI, 0.36 to 0.51) in BRCA2 carriers, whereas ovarian cancer risk was 0.39 (95% CI, 0.30 to 0.50) in BRCA1 carriers and 0.22 (95% CI, 0.14 to 0.32) in BRCA2 carriers. We also reported the prospective risks of developing cancer for cancer-free carriers in 10-year age intervals. We noted a rapid decrease in the relative risk of breast cancer with age and derived its implication for genetic counseling. CONCLUSION: The penetrance of BRCA mutations in the United States is largely consistent with previous studies on Western populations given the large CIs on existing estimates. However, the absolute cumulative risks are on the lower end of the spectrum.

Adult↗

Spectrum of CHD7 mutations in 110 individuals with CHARGE syndrome and genotype-phenotype correlation.

CHARGE syndrome is a well-established multiple-malformation syndrome with distinctive consensus diagnostic criteria. Characteristic associated anomalies include ocular coloboma, choanal atresia, cranial nerve defects, distinctive external and inner ear abnormalities, hearing loss, cardiovascular malformations, urogenital anomalies, and growth retardation. Recently, mutations of the chromodomain helicase DNA-binding protein gene CHD7 were reported to be a major cause of CHARGE syndrome. We sequenced the CHD7 gene in 110 individuals who had received the clinical diagnosis of CHARGE syndrome, and we detected mutations in 64 (58%). Mutations were distributed throughout the coding exons and conserved splice sites of CHD7. Of the 64 mutations, 47 (73%) predicted premature truncation of the protein. These included nonsense and frameshift mutations, which most likely lead to haploinsufficiency. Phenotypically, the mutation-positive group was more likely to exhibit cardiovascular malformations (54 of 59 in the mutation-positive group vs. 30 of 42 in the mutation-negative group; P=.014), coloboma of the eye (55 of 62 in the mutation-positive group vs. 30 of 43 in the mutation-negative group; P=.022), and facial asymmetry, often caused by seventh cranial nerve abnormalities (36 of 56 in the mutation-positive group vs. 13 of 39 in the mutation-negative group; P=.004). Mouse embryo whole-mount and section in situ hybridization showed the expression of Chd7 in the outflow tract of the heart, optic vesicle, facio-acoustic preganglion complex, brain, olfactory pit, and mandibular component of the first branchial arch. Microarray gene-expression analysis showed a signature pattern of gene-expression differences that distinguished the individuals with CHARGE syndrome with CHD7 mutation from the controls. We conclude that cardiovascular malformations, coloboma, and facial asymmetry are common findings in CHARGE syndrome caused by CHD7 mutation.

Abnormalities, Multiple↗

Depressed mood and social support as predictors of quality of life in women receiving home health care.

We examined relationships among depressed mood, social support and quality of life in 58 medically ill low-income women 40 years and older receiving home health care. Analyses showed a negative relationship between depressed mood and quality of life (p's < or = 0.05). Positive relationships were found between number of people available for support and two of three quality of life domains as well as satisfaction with support and all three domains (p's < or = 0.05). Results also provided preliminary support that belonging to a church is related to emotional well-being (p = 0.039) and among those belonging to a church, recent increased activity was related to social/family well-being (p = 0.004). Mediational analyses revealed a cycle of depressed mood, dissatisfaction with social support, and loss of social support providers underlying the poor quality of life of many participants. This highlights the need to address the relationship between depression and social support when treating patients with chronic illness.

Adult↗

Low-dose irradiation alters the transcript profiles of human lymphoblastoid cells including genes associated with cytogenetic radioadaptive response.

Low-dose ionizing radiation alters the gene expression profiles of mammalian cells, yet there is little understanding of the underlying cellular mechanisms responsible for these changes or of their consequences for genomic stability. We investigated the cytogenetic adaptive response of human lymphoblastoid cell lines exposed to 5 cGy (priming dose) followed by 2 Gy (challenge dose) compared to cells that received a single 2-Gy dose to (a) determine how the priming dose influences subsequent gene transcript expression in reproducibly adapting and non-adapting cell lines, and (b) identify gene transcripts that are associated with reductions in the magnitude of chromosomal damage after the challenge dose. The transcript profiles were evaluated using oligonucleotide arrays and RNA obtained 4 h after the challenge dose. A set of 145 genes (false discovery rate = 5%) with transcripts that were affected by the 5-cGy priming dose fell into two categories: (a) a set of common genes that were similarly modulated by the 5-cGy priming dose irrespective of whether the cells subsequently adapted or not and (b) genes with differential transcription in accordance with the cell lines that showed either adaptive or non-adaptive outcomes. The common priming-dose response genes showed up-regulation for protein synthesis genes and down-regulation of metabolic and signal transduction genes (>10-fold differences). The genes associated with subsequent adaptive and non-adaptive outcomes involved DNA repair, stress response, cell cycle control and apoptosis. Our findings support the importance of TP53-related functions in the control of the low-dose cytogenetic radioadaptive response and suggest that certain low-dose-induced alterations in cellular functions are predictive for the risk of subsequent genomic damage.

Adaptation, Physiological↗

Increased noncanonical splicing of autoantigen transcripts provides the structural basis for expression of untolerized epitopes.

BACKGROUND: Alternative splicing is important for increasing the complexity of the human proteome from a limited genome. Previous studies have shown that for some autoantigens, there is differential immunogenicity among alternatively spliced isoforms. OBJECTIVES: Herein, we tested the hypothesis that alternative splicing is a common feature for transcripts of autologous proteins that are autoantigens. The corollary hypothesis tested was that nonautoantigen transcripts have a lower frequency of alternative splicing. METHODS: The extent of alternative splicing within 45 randomly selected self-proteins associated with autoimmune diseases was compared with 9554 randomly selected proteins in the human genome by using bioinformatics analyses. Isoform-specific regions that resulted from alternative splicing were studied for their potential to be epitopes for antibodies or T-cell receptors. RESULTS: Alternative splicing occurred in 100% of the autoantigen transcripts. This was significantly higher than the approximately 42% rate of alternative splicing observed in the 9554 randomly selected human gene transcripts ( P < .001). Within the isoform-specific regions of the autoantigens, 92% and 88% encoded MHC class I and class II-restricted T-cell antigen epitopes, respectively, and 70% encoded antibody binding domains. Furthermore, 80% of the autoantigen transcripts underwent noncanonical alternative splicing, which is also significantly higher than the less than 1% rate in randomly selected gene transcripts ( P < .001). CONCLUSION: These studies suggest that noncanonical alternative splicing may be an important mechanism for the generation of untolerized epitopes that may lead to autoimmunity. Furthermore, the product of a transcript that does not undergo alternative splicing is unlikely to be a target antigen in autoimmunity.

Alternative Splicing↗

Fibroblast growth factor 2 promotes tumor progression in an autochthonous mouse model of prostate cancer.

Fibroblast growth factor (FGF) 2 (or basic FGF) is expressed at increased levels in human prostate cancer. FGF2 can promote cell motility and proliferation, increase tumor angiogenesis, and inhibit apoptosis, all of which play an important role in tumor progression. To determine whether FGF2 plays a critical role in prostate cancer progression, we have used the transgenic adenocarcinoma of the mouse prostate (TRAMP) model system. A high percentage of TRAMP mice develop metastatic prostate cancer, and thus the TRAMP model is useful for evaluating cancer progression. TRAMP mice were crossed with FGF2 knockout (FGF2(-/-)) mice, and tumor progression in TRAMP mice that were either hemi- or homozygous for inactivation of the FGF2 allele was compared with progression in wild-type TRAMP mice. Inactivation of even one FGF2 allele resulted in increased survival, a decrease in metastasis, and inhibition of progression to the poorly differentiated phenotype in primary prostatic tumors. When compared with wild-type mice, poorly differentiated tumors arising in FGF(+/-) and FGF(-/-) mice expressed higher levels of vascular endothelial growth factor and, in some cases, increased levels of acidic FGF intracellular binding protein, a nuclear FGF1-binding protein. These findings suggest that both FGF2-mediated angiogenesis and intranuclear FGF2 activities may promote tumor progression and support the hypothesis that FGF2 plays a significant role in prostate cancer progression in vivo.

Alleles↗

Partitioning large-sample microarray-based gene expression profiles using principal components analysis.

Principal components analysis (PCA) is useful for reproducing the total variation among hundreds or thousands of continuously-scaled variables with a much smaller number of unobservable variables called 'latent factors'. The CLUSFAVOR computer program was used to implement PCA for identifying groups of genes with similar expression profiles from a large number of genes used on DNA microarrays. This paper describes the principal components solution to the factor model of the correlation matrix R, calculation of eigenvalues and eigenvectors of R, extraction of factors, and calculation of factor loadings and identification of genes with similar loading patterns to construct groups of genes with similar expression profiles. With regard to extraction of factors, it was found that more than 90% of the total variance in input data could be accounted for by extracting factors whose eigenvalues exceed unity. Bipolar factors containing strong positive and negative loadings can also be used for identifying two unique groups of genes, since expression profiles of genes that load positive are unlike expression profiles of genes that load negative on the same factor. While PCA does not provide the absolute answer to a multidimensional problem, it nevertheless can provide a heuristic with which natural groupings of genes with similar expression profiles can be assembled. While cluster analysis essentially generates a single dendogram (tree branch) containing every gene in the input data, PCA can be used to assemble gene expression profiles that strongly correlate with the latent factors accounting for a majority of total variance. Example results for CLUSFAVOR computer program runs are provided.

Gene Expression Profiling↗

Interleukin-6 genetic polymorphisms are not related to Helicobacter pylori-associated gastroduodenal diseases.

BACKGROUND: Polymorphisms in the promoter region of the proinflammatory cytokine, interleukin (IL)-6 have been related to several chronic inflammatory diseases. Inter-individual variation in the severity of gastric inflammation may be important in determining the clinical outcome of an Helicobacter pylori infection and relate to polymorphisms in this region. MATERIALS AND METHODS: We studied H. pylori-infected patients with duodenal ulcer or gastric cancer. In addition six gastric cancer cell lines, AGS, SNU-668, MKN-1, MKN-7, MKN28 and KATOIII, were cocultured with both cag pathogenicity island-positive and -negative H. pylori. Single nucleotide polymorphisms at positions -174, -572, and -597 in the IL-6 promoter region were identified by PCR-RFLP. The IL-6 production from the cancer cells was determined by ELISA. RESULTS: Sixty patients with gastric cancer and 60 with duodenal ulcer were studied. The alleles at positions -174 and -597 were closely linked (-174G/-597G or -174C/-597A) regardless of the ethnic group or disease presentation. There was no difference in the allele frequency at any of the sites among patient groups. H. pylori-induced IL-6 production from the gastric cancer cell lines was also independent of the IL-6 polymorphisms or the presence of the cag pathogenicity island. CONCLUSIONS: The genetic polymorphisms in IL-6 can be attributable to ethnicity and appear to be independent of the clinical outcome of an H. pylori infection.

Adult↗

CLUSFAVOR 5.0: hierarchical cluster and principal-component analysis of microarray-based transcriptional profiles.

CLUSFAVOR (CLUSter and Factor Analysis with Varimax Orthogonal Rotation) 5.0 standardizes input data; sorts data according to gene-specific coefficient of variation, standard deviation, average and total expression, and Shannon entropy; performs hierarchical cluster analysis using nearest-neighbor, unweighted pair-group method using arithmetic averages (UPGMA), or furthest-neighbor joining methods, and Euclidean, correlation, or jack-knife distances; and performs principal-component analysis.

Animals↗

Observation of intermittency in gene expression on cDNA microarrays.

We used scaled factorial moments to search for intermittency in the log expression ratios (LERs) for thousands of genes spotted on cDNA microarrays (gene chips). Results indicate varying levels of intermittency in gene expression. The observation of intermittency in the data analyzed provides a complimentary handle on moderately expressed genes, generally not tackled by conventional techniques.

Gene Expression Profiling↗

Factor analysis of cluster-specific gene expression levels from cDNA microarrays.

The ever-increasing use of cDNA microarrays in medical research will require the development of new algorithms designed specifically for desktop analysis of potentially large genetic data sets. This paper describes the CLUSFAVOR algorithm (CLUSter and Factor Analysis Using Varimax Orthogonal Rotation) for performing cluster and factor analysis of gene expression data obtained from cDNA microarrays. A unique feature of the CLUSFAVOR algorithm is that a user can perform cluster analysis, view dendograms, and run factor analysis on cluster-specific genes selected interactively within a single executable program. CLUSFAVOR also performs a varimax orthogonal rotation on the extracted factors to increase parsimony in the loadings, revealing unique expression profiles for genes and expressed sequence tags (ESTs) for which pathway and function information is unknown. Microarray data used by the program must be stored and input from a disk file. Optional output contains matrices for the input data, standardized data, distance matrices, factor loadings, eigenvalues, eigenvectors, and percentage of total variation for genes within a cluster. Color cluster image displays containing gene expression levels, dendograms for arrays and genes, and factor loadings are displayed for the entire group of genes and arrays analyzed as well as selected genes within a cluster. Cluster images are also exported to JPG and linked to HTML files for viewing.

Algorithms↗

Effect of interleukin 1 polymorphisms on gastric mucosal interleukin 1beta production in Helicobacter pylori infection.

BACKGROUND & AIMS: Although epidemiological studies suggest that interleukin (IL)-1 genetic polymorphisms are involved in Helicobacter pylori-related gastric carcinogenesis, the data are conflicting regarding the effects of these polymorphisms on IL-1beta production. METHODS: IL-1B-511 polymorphism was genotyped by polymerase chain reaction (PCR)-restriction fragment length polymorphism, and IL-1RN variable number of tandem repeats was determined by PCR. Mucosal IL-1beta levels were measured by enzyme-linked immunosorbent assay. To determine which factors influence mucosal IL-1beta levels, gastric inflammation, and atrophy, multiple regression analyses were performed. RESULTS: We studied 117 H. pylori-infected Japanese patients. Carriers of the IL-1B-511T/T genotype or IL-1RN*2 allele had higher mucosal IL-1beta levels than noncarriers (partial regression coefficient [PRC] +/- SE), TT versus CC: 37.6 +/- 6 [antrum] and 32.1 +/- 6 [corpus] pg/mg protein (P < 0.001 for each), *1/*2 versus *1/*1: 24 +/- 8 [antrum] (P <0.01) and 36.5 +/- 7 [corpus] (P <0.001). Simultaneous carriers of IL-1B-511T/T genotype and IL-1RN*2 allele had the highest IL-1beta levels (82.9 +/- 12 [antrum] and 87.2 +/- 11 [corpus]) and showed a synergistic effect between 2 loci. The *1/*2 carriers were closely related to atrophy (PRC +/- SE; 0.87 +/- 0.4 [antrum] and 0.93 +/- 0.4 [corpus], P < 0.05), whereas being a carrier of the -511T/T genotype was related to severe gastric inflammation. CONCLUSIONS: IL-1 genetic polymorphisms influenced H. pylori-related gastric mucosal IL-1beta levels and were related to gastric inflammation and atrophy, factors thought to be important in gastric carcinogenesis.

Adult↗

Histological patterns of gastritis in H. pylori-infected individuals with a family history of gastric cancer.

OBJECTIVE: Different types of chronic gastritis, including antral predominant, corpus predominant, and multifocal pangastritis, are associated with Helicobacter pylori infection. Specific patterns of H. pylori gastritis that might characterize individuals with family histories of noncardia gastric cancer (GC) were investigated. METHODS: Histopathological changes associated with H. pylori gastritis were assessed in 111 individuals with family histories of GC and in 77 without from a region with high prevalence of H. pylori infection and GC. Gastric biopsies were taken from 12 sites (antrum, five; corpus, six; and cardia, one). RESULTS: Individuals (age < 36 yr) with family histories of GC developed pangastritis and had higher H. pylori bacterial scores (p < 0.05) in the gastric corpus, whereas those without family histories of GC typically had antral predominant gastritis. The correlation between density of polymorphonuclear leukocytes and density of H. pylori at each biopsy site was statistically significant (p < 0.01). Pangastritis was associated with a higher density of lymphoid aggregates and follicles (p < 0.05) in the corpus of younger individuals (age < 36) and in the antrum of older individuals (age > or = 48) with positive family histories of GC. CONCLUSIONS: Pangastritis and high lymphoid follicle density associated with H. pylori infection were found in patients with family histories of GC. Because a family history of gastric carcinoma is associated with increased risk of gastric cancer development, characterization of histological patterns of gastritis may be applicable to gastric cancer screening and surveillance, especially in relatively young at-risk populations.

Adult↗