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At least 55 records · Page 3Linked to original sources
PubMed2006

Biallelic deletion within 16p13.13 including SOCS-1 in Karpas1106P mediastinal B-cell lymphoma line is associated with delayed degradation of JAK2 protein.

Activity of Janus kinase 2 (JAK2) in the JAK2/STAT5 signaling pathway is critically controlled by suppressor of cytokine signaling-1 (SOCS-1). We have previously shown that SOCS-1 is biallelically mutated in the primary mediastinal B-cell lymphoma (PMBL) cell line MedB-1, resulting in impaired JAK2 degradation and sustained phospho-JAK2 action. SOCS-1 is frequently mutated in PMBL tumor primaries. Here, we report that the PMBL cell line Karpas1106P has a biallelic deletion of the SOCS-1 region on chromosome 16p13.13. By fluorescence in situ hybridization and microsatellite analysis, this deletion was narrowed down to a range of 650 kb to 1.48 Mb. Like MedB-1, Karpas1106P harbors gains of the JAK2 gene on chromosomal region 9p24 and elevated levels of JAK2 mRNA. Nevertheless, JAK2 protein was not increased but constitutively phosphorylated in Karpas1106P cells. In analogy to MedB-1 cells, Karpas1106P cells exhibited a retarded degradation of de novo synthesized JAK2 protein revealed by pulse/chase experiments. Therefore, we conclude that loss of SOCS-1 function either by mutation or by the complete deletion of the gene plays an important role in the dysregulation of JAK/STAT signaling in Karpas1106P and PMBL.

Chromosomes, Human, Pair 16↗
PubMed2000

A first high-density map of 981 biallelic markers on human chromosome 14.

As the largest set of sequence variants, single-nucleotide polymorphisms (SNPs) constitute powerful assets for mapping genes and mutations related to common diseases and for pharmacogenetic studies. A major goal in human genetics is to establish a high-density map of the genome containing several hundred thousand SNPs. Here we assayed 3.7 Mb (154,397 bp in 24 alleles) of chromosome 14 expressed sequence tags (ESTs) and sequence-tagged sites, for sequence variation in DNA samples from 12 African individuals. We identified and mapped 480 biallelic markers (459 SNPs and 21 small insertions and deletions), equally distributed between EST and non-EST classes. Extensive research in public databases also yielded 604 chromosome 14 SNPs (dbSNPs), 520 of which could be mapped and 19 of which are common between CNG (i.e., identified at the Centre National de Génotypage) and dbSNP polymorphisms. We present a dense map of SNP variation of human chromosome 14 based on 981 nonredundant biallelic markers present among 1345 radiation hybrid mapped sequence objects. Next, bioinformatic tools allowed 945 significant sequence alignments to chromosome 14 contigs, giving the precise chromosome sequence position for 70% of the mapped sequences and SNPs. In addition, these tools also permitted the identification and mapping of 273 SNPs in 159 known genes. The availability of this SNP map will permit a wide range of genetic studies on a complete chromosome. The recognition of 45 genes with multiple SNPs, by allowing the construction of haplotypes, should facilitate pharmacogenetic studies in the corresponding regions.

Alleles↗
PubMed2003

The biallelic variable number of tandem repeats of the tumor necrosis factor receptor 2 promoter in systemic lupus erythematosus.

The objective of this study was to investigate whether the variable number of tandem repeats (VNTR) of the tumor necrosis factor receptor 2 (TNFR2) promoter is associated with susceptibility to systemic lupus erythematosus (SLE) and its clinical phenotypes. A biallelic VNTR within a 42-bp region in the TNFR2 gene promoter was determined by polymerase chain reaction in 88 SLE patients and 95 healthy control subjects. Clinical manifestations were analyzed in each patient and correlated with the genotypes. When the TNFR2 promoter VNTR was compared between Korean and Caucasian healthy controls with respect to allele frequencies, there was a significant difference (alleles 1 and 2: 39, 151 in Koreans vs 60, 138 in Caucasians, respectively; chi-squared test 4.38; 2 df; P=0.036). The genotype distribution of the TNFR2 promoter VNTR did not differ between SLE patients and control subjects (1.1, 1.2, and 2.2 genotypes 7, 14, 67 vs 5, 29, and 61 controls, respectively; chi-squared test 5.19; 2 df; P=0.061). According to the TNFR2 promoter genotypes in the lupus patients, clinically there was no significant difference in age at onset, anti-dsDNA titer, C4 level, systemic lupus erythematosus disease activity index (SLEDAI), Systemic Lupus International Collaborating Clinics/American College of Rheumatology (SLICC/ACR) damage index, or autoantibodies. However, the 1.1 genotype group showed the lowest C3 level and more frequent renal involvement than the 1.2 and 2.2 genotype groups. In conclusion, an ethnic difference in the TNFR2 promoter VNTR has been found and the biallelic VNTR of the TNFR2 promoter may be associated with clinical phenotypes in SLE.

Adolescent↗
PubMed2002

DDC and COBL, flanking the imprinted GRB10 gene on 7p12, are biallelically expressed.

Maternal duplication of human 7p11.2-p13 has been associated with Silver-Russell syndrome (SRS) in two familial cases. GRB10 is the only imprinted gene identified within this region to date. GRB10 demonstrates an intricate tissue- and isoform-specific imprinting profile in humans, with paternal expression in fetal brain and maternal expression of one isoform in skeletal muscle. The mouse homolog is maternally transcribed. The GRB10 protein is a potent growth inhibitor and represents a candidate for SRS, which is characterized by pre- and postnatal growth retardation and a spectrum of additional dysmorphic features. Since imprinted genes tend to be grouped in clusters, we investigated the imprinting status of the dopa-decarboxylase gene (DDC) and the Cordon-bleu gene (COBL) which flank GRB10 within the 7p11.2-p13 SRS duplicated region. Although both genes were found to replicate asynchronously, suggestive of imprinting, SNP expression analyses showed that neither gene was imprinted in multiple human fetal tissues. The mouse homologues, Ddc and Cobl, which map to the homologous imprinted region on proximal Chr 11, were also biallelically expressed in mice with uniparental maternal or paternal inheritance of this region. With the intent of using mouse Grb10 as an imprinted control, biallelic expression was consistently observed in fetal, postnatal, and adult brain of these mice, in contrast to the maternal-specific transcription previously demonstrated in brain in inter-specific F1 progeny. This may be a further example of over-expression of maternally derived transcripts in inter-specific mouse crosses. GRB10 remains the only imprinted gene identified within 7p11.2-p13.

Alleles↗
PubMed2005

The COPG2, DCN, and SDHD genes are biallelically expressed in cattle.

Imprinted genes are preferentially expressed from either the maternally inherited allele or the paternally inherited allele. Most genes known to be imprinted have been identified and studied in the human and the mouse. There is only a small number of reported imprinted genes in cattle, which is probably because of the limited sequence and polymorphism information available for bovine genes. To study the imprinting status of cattle genes and assess their conservation among mammalian species, the expression patterns of COPG2, DCN, and SDHD genes were examined in a total of 128 fetal and adult tissues. Two single nucleotide polymorphisms (SNPs) were identified in COPG2, three SNPs in DCN, and one SNP in SDHD. These polymorphisms were used to distinguish between monoallelic and biallelic expression using a primer extension method and a sequencing-based approach. In all 128 tissues, COPG2, DCN, and SDHD transcripts showed biallelic expression. Other cattle genes examined to date have been found to be imprinted like their known counterparts in human and mouse. This is the first report of genes that are not imprinted in cattle while the corresponding genes in human or mouse are imprinted. Lack of conservation of imprinting among mammals suggests important biological, developmental, and regulatory consequences.

Alleles↗
PubMed2005

Biallelic deletion and loss of expression analysis of genes at FRA2G common fragile site in tumor-derived cell lines.

Common fragile sites (CFS) are regions of chromosome instability that show gaps or breaks when cells are exposed to particular culture condition. Much evidence suggests that CFSs are causally related to cancer as breakpoints in recurrent chromosome mutations and as sites of viral integration. We investigated the FRA2G CFS (2q31) for biallelic deletions and loss of expression in a panel of 19 tumor-derived cell lines. We found that Burkitt lymphoma-derived cell line DAUDI has a biallelic deletion of eight of the nine analyzed genes. Moreover, we observed loss of expression (LOE) of the DHRS9 gene (alias RDHL), one of the deleted genes in the DAUDI cell line, in MOLT-14 and Raji cell lines derived from Burkitt lymphoma and from T-cell acute lymphoblastic leukemia, respectively. DHRS9 is involved in development and differentiation pathways.

Cell Line, Tumor↗
PubMed2026

Generation of a hiPSC from a patient with an ITSN1-associated neurodevelopmental disorder spectrum carrying biallelic c.2893_2894insA (p.Tyr965Ter) genetic variant.

De novo truncating variants in ITSN1 are implicated in neurodevelopment disorders spectrum, however, biallelic variants in ITSN1 have not been previously identified. Here we present a hiPSC line generated from a patient dermal fibroblast carrying biallelic variant, c.2893_2894insA (p.Tyr965Ter). The hiPSC line expresses core stemness markers, mycoplasma free with normal karyotype and demonstrate trilineage differentiation capacity. The hiPSC line provides a valuable in-vitro model system to investigate its role in early brain development and neurodevelopmental disorders.

Humans↗
PubMed2002

Biallelic inactivation of the von Hippel-Lindau tumor suppressor gene in sporadic renal cell carcinoma.

PURPOSE: Somatic mutations of the von Hippel-Lindau tumor suppressor gene VHL and loss of heterozygosity of 3p25 to 26 have been well analyzed in renal cell carcinoma but it is not yet clear how often complete biallelic inactivation of VHL occurs in sporadic renal cell carcinoma. We improved the estimation of loss of heterozygosity of VHL and examined 2-hit inactivation of VHL based on loss of heterozygosity, mutation and methylation of sporadic renal cell carcinoma. MATERIALS AND METHODS: DNA extracted from 59 Japanese sporadic renal cell carcinoma samples containing clear cells was examined for loss of heterozygosity of 4 intragenic markers of single nucleotide polymorphism and 2 extragenic microsatellite markers. Mutation was analyzed by sequencing amplified VHL DNA and methylation was analyzed by methylation specific polymerase chain reaction. RESULTS: Four intragenic markers showed loss of heterozygosity in 13 of 22 samples (59.1%), whereas the 2 extragenic markers D3S1560 and D3S1317 showed loss of heterozygosity in 15 of 46 (32.6%) and 11 of 49 (22.4%), respectively. Considering loss of heterozygosity in 14 renal cell carcinomas informative at all 3 loci the incidence of loss of heterozygosity of VHL in renal cell carcinoma was estimated to be 73.5% or 25 of 34 cases. Mutations in VHL were found in 25 of 59 renal cell carcinomas (42.4%) and frame shift mutations in 68% of all mutations often occurred at nucleotide repeat sequences. Of the 34 loss of heterozygosity informative renal cell carcinoma 15 (44.1%) had 2-hit inactivation of VHL and 11 (32.4%) had 1-hit inactivation. CONCLUSIONS: The frequency of biallelic inactivation of VHL in sporadic renal cell carcinomas was unexpectedly low. According to the 2-hit theory of tumor suppressor genes another hit in VHL that to our knowledge remains unknown to date is thought to be involved in the development of renal cell carcinoma.

Alleles↗
PubMed2002

Genetic distances within and across cattle breeds as indicated by biallelic AFLP markers.

We tested the use of biallelic Amplified fragment length polymorphism (AFLP) polymorphisms for the estimation of relative genetic distances of cattle individuals within or across breeds. An allele permutation procedure was developed to estimate the stochastic variation of the genetic distance that is inherent to a given dataset. In a panel of 47 Holstein-Friesian cattle analysed with 248 polymorphic markers, the average genetic distance of bulls selected for breeding was slightly lower than the distance of the cows. The observed standard deviation (SD) of the distance indicated genetic subdivision, which for the bulls was explained by variation in the additive relationship derived from herdbook data. Animals from three different breeds, the highly selected Holstein-Friesian, the Italian Brown and the historic Maremmana, were compared on the basis of 106 polymorphic markers. No breed-specific fragments were observed. The mean pair-wise genetic distance within breeds was 85% of the value across breeds, but principal coordinates analysis clustered the animals according to their breed of origin. Calculation of distances between the breeds indicated a relatively divergent position of the Maremmana, relative to the two other breeds. However, biallelic markers indicate that the process of breed formation had only a limited effect on the diversity at marker loci.

Alleles↗
PubMed2007

Patients with biallelic mutations in the chloride channel gene CLCNKB: long-term management and outcome.

BACKGROUND: Little information on the management and long-term follow-up of patients with biallelic mutations in the chloride channel gene CLCNKB is available. METHODS: Long-term follow-up was evaluated from 5.0 to 24 years (median, 14 years) after diagnosis in 13 patients with homozygous (n = 10) or compound heterozygous (n = 3) mutations. RESULTS: Medical treatment at last follow-up control included supplementation with potassium in 12 patients and sodium in 2 patients and medical treatment with indomethacin in 9 patients. At the end of follow-up, body height was 2.0 standard deviation score or less in 6 patients; 2 of these patients had growth hormone deficiency. Body weight (<or=2.0 standard deviation score in 6 patients) significantly increased (P < 0.05) at the end of follow-up in comparison to values at diagnosis. Nonpostural persistent proteinuria was present in 6 patients, and 4 patients had a glomerular filtration rate less than 75 mL/min/1.73 m(2) (<1.25 mL/s). CONCLUSION: These data show that some patients with biallelic mutations in the chloride channel gene CLCNKB tend to present with pathological proteinuria and impaired kidney function after a median follow-up of 14 years, and growth retardation is common and sometimes related to growth hormone deficiency in these patients.

Adolescent↗
PubMed1998

Bidirectional imprinting of a single gene: GNAS1 encodes maternally, paternally, and biallelically derived proteins.

The GNAS1 gene encodes the alpha subunit of the guanine nucleotide-binding protein Gs, which couples signaling through peptide hormone receptors to cAMP generation. GNAS1 mutations underlie the hormone resistance syndrome pseudohypoparathyroidism type Ia (PHP-Ia), so the maternal inheritance displayed by PHP-Ia has raised suspicions that GNAS1 is imprinted. Despite this suggestion, in most tissues Gsalpha is biallelically encoded. In contrast, the large G protein XLalphas, also encoded by GNAS1, is paternally derived. Because the inheritance of PHP-Ia predicts the existence of maternally, rather than paternally, expressed transcripts, we have investigated the allelic origin of other mRNAs derived from GNAS1. We find this gene to be remarkable in the complexity of its allele-specific regulation. Two upstream promoters, each associated with a large coding exon, lie only 11 kb apart, yet show opposite patterns of allele-specific methylation and monoallelic transcription. The more 5' of these exons encodes the neuroendocrine secretory protein NESP55, which is expressed exclusively from the maternal allele. The NESP55 exon is 11 kb 5' to the paternally expressed XLalphas exon. The transcripts from these two promoters both splice onto GNAS1 exon 2, yet share no coding sequences. Despite their structural unrelatedness, the encoded proteins, of opposite allelic origin, both have been implicated in regulated secretion in neuroendocrine tissues. Remarkably, maternally (NESP55), paternally (XLalphas), and biallelically (Gsalpha) derived proteins all are produced by different patterns of promoter use and alternative splicing of GNAS1, a gene showing simultaneous imprinting in both the paternal and maternal directions.

Alleles↗
PubMed2006

Allelic gene regulation of Pcdh-alpha and Pcdh-gamma clusters involving both monoallelic and biallelic expression in single Purkinje cells.

The molecular basis for providing the identity and diversity of single neurons is a key for realizing the brain system. Diverse protocadherin isoforms encoded by the Pcdh-alpha and Pcdh-gamma gene clusters are expressed in all of the vertebrates studied. For the Pcdh-alpha isoforms, differential expression patterns have been found in single Purkinje cells by unusual monoallelic and combinatorial types of gene regulation. Here we investigated total allelic gene regulation in the Pcdh-alpha and -gamma clusters, including the C-type variable exons (C1 to C5) and the Pcdh-gammaA and -gammaB variable exons in single Purkinje cells. Using split single-cell reverse transcription-PCR analysis, almost all of the Purkinje cells at postnatal day 21 biallelically expressed all the C-type isoforms, whereas the Pcdh-alpha isoforms showed both monoallelic and combinatorial expression. The Pcdh-gammaA and -gammaB isoforms also showed differential regulation in each cell with both monoallelic and combinatorial gene regulation. These data indicated that different types of allelic gene regulation (monoallelic versus biallelic) occurred in the Pcdh-alpha and -gamma clusters, although they were spliced into the same constant exons. It has been reported that each C-type Pcdh-alpha or -gamma transcript has a different expression pattern during brain development, suggesting that the different C-type variable exons may code temporal diversity, although the Pcdh-alpha, -gammaA, and -gammaB isoforms were differential and combinatorial gene regulation within a single cell. Thus, the multiple gene regulations in the Pcdh-alpha and -gamma clusters had a potential mechanism for increasing the diversity of individual neurons in the brain.

Alleles↗
PubMed2003

Biallelic germline transcription at the kappa immunoglobulin locus.

Rearrangement of antigen receptor genes generates a vast array of antigen receptors on lymphocytes. The establishment of allelic exclusion in immunoglobulin genes requires differential treatment of the two sequence identical alleles. In the case of the kappa immunoglobulin locus, changes in chromatin structure, methylation, and replication timing of the two alleles are all potentially involved in regulating rearrangement. Additionally, germline transcription of the kappa locus which precedes rearrangement has been proposed to reflect an opening of the chromatin structure rendering it available for rearrangement. As the initial restriction of rearrangement to one allele is critical to the establishment of allelic exclusion, a key question is whether or not germline transcription at the kappa locus is monoallelic or biallelic. We have used a sensitive reverse transcription-polymerase chain reaction (RT-PCR) assay and an RNA-fluorescence in situ hybridization (FISH) to show that germline transcription of the kappa locus is biallelic in wild-type immature B cells and in recombination activating gene (RAG)-/-, mu+ B cells. Therefore, germline transcription is unlikely to dictate which allele will be rearranged first and rather reflects a general opening on both alleles that must be accompanied by a mechanism allowing one of the two alleles to be rearranged first.

Alleles↗
PubMed2005

Cells with pathogenic biallelic mutations in the human MUTYH gene are defective in DNA damage binding and repair.

Inherited biallelic mutations in the human MUTYH gene are responsible for the recessive syndrome--adenomatous colorectal polyposis (MUTYH associated polyposis, MAP)--which significantly increases the risk of colorectal cancer (CRC). Defective MUTYH activity causes G:C to T:A transversions in tumour APC and other genes thereby altering genomic integrity. We report that of the four established cell lines, derived from patients with the MAP phenotype and containing biallelic MUTYH mutations, three contain altered expressions of MUTYH protein (MUTYH Y165C(-/-), MUTYH 1103delC/G382D and MUTYH Y165C/G382D but not MUTYH G382D(-/-)), but that all four cell lines have wild type levels of MUTYH mRNA. Mutant MUTYH proteins in these four cell lines possess significantly lowered binding and cleavage activities with heteroduplex oligonucleotides containing A.8-oxoG and 8-oxoA.G mispairs. Transfection of mitochondrial or nuclear MUTYH cDNAs partially correct altered MUTYH expression and activity in these defective cell lines. Finally, we surprisingly find that defective MUTYH may not alter cell survival after hydrogen peroxide and menadione treatments. The Y165C and 1103delC mutations significantly reduce MUTYH protein stability and thus repair activity, whereas the G382D mutation produces dysfunctional protein only suggesting different functional molecular mechanisms by which the MAP phenotype may contribute to the development of CRC.

Adenomatous Polyposis Coli↗
PubMed1993

The insulin-like growth factor 1 receptor gene is normally biallelically expressed in human juvenile tissue and tumours.

We have examined insulin-like growth factor 1 receptor (IGF1R) gene expression for evidence of imprinting in 15 informative patients with embryonal tumours. Biallelic expression was observed in all but one sample of normal juvenile kidney and liver, and in 9/10 associated Wilms' tumours, 3/3 hepatoblastomas and 2/2 adrenal tumours. A single patient with Beckwith-Wiedemann Syndrome (BWS) demonstrated monoallelic expression of the maternally derived IGF1R allele in normal kidney, associated Wilms' tumour and in peripheral blood lymphocytes. The observed biallelic expression of the IGF1R gene in all but one patient strongly suggests that the human gene is not normally imprinted.

Adrenal Gland Neoplasms↗
PubMed1996

An extended region of biallelic gene expression and rodent-human synteny downstream of the imprinted H19 gene on chromosome 11p15.5.

There is increasing evidence for chromosomal domains containing multiple imprinted genes and for domain-wide disruption of imprinting in certain diseases. In a majority of Wilms' tumors (WTs) there is an abnormal bipaternal pattern of expression at three imprinted loci, H19, IGF2 and KIP2, clustered on chromosome 11p15.5. We previously described biallelic expression of L23MRP, 40 kb downstream of H19. Here we map two additional genes, the first encoding a ubiquitously expressed RNA, 2G7, and the second encoding the fast isoform of skeletal muscle troponin-T (TNNT3), in the 55 kb of DNA downstream of L23MRP. 2G7 RNA is spliced and polyadenylated but lacks long open reading frames. 2G7 and TNNT3 are biallelically expressed in mid-fetal and adult human tissues and 2G7 shows persistent expression in WTs. The rat homologue of L23MRP is highly conserved and lies within 85 kb of H19 in a region of rat chromosome 1 which also contains IGF2 and TNNT3. Parallel expression of H19 and TNNT3 in different adult skeletal muscle types suggests that these genes may share an enhancer. These data outline multiple contiguous loci downstream of H19 which escape functional imprinting in humans. The rodent-human synteny of this region may facilitate a search for an imprinting domain boundary.

Adult↗
PubMed1996

Biallelic expression of the IGF2 gene in human breast disease.

We examined the imprinting status of the insulin-like growth factor II gene (IGF2) in a series of 20 human breast disease samples to determine if disrupted imprinting (as evidenced by biallelic expression), was a demonstrable mechanism of altered gene expression. These samples included benign (n = 7) and malignant breast lesions (n = 13). Biallelic expression of IGF2 was detectable in 67% of benign and 60% of malignant informative breast lesions. Three informative reduction mastectomies displayed normal IGF2 imprinting. The presence of this alteration in human breast tissue is a novel finding, and may contribute to tumorigenesis, possibly by favouring an enhanced proliferative milieu, during which additional mutations could occur.

Adult↗
PubMed2004

Pathogenesis of tuberous sclerosis subependymal giant cell astrocytomas: biallelic inactivation of TSC1 or TSC2 leads to mTOR activation.

In the central nervous system, tuberous sclerosis complex (TSC) is characterized by a range of lesions including cortical tubers, white matter heterotopias, subependymal nodules, and subependymal giant cell astrocytomas (SEGAs). Recent studies have implicated an important role for the TSC genes TSC1 and TSC2, in a signaling pathway involving the mammalian target of rapamycin (mTOR) kinase. We performed immunohistochemical and genetic analyses on SEGAs from 7 TSC patients, 4 with mutations in TSC1, and 3 with mutations in TSC2. SEGA cells show high levels of phospho-S6K, phospho-S6, and phospho-Stat3, all proteins downstream of and indicative of mTOR activation. Such expression is not seen in histologically normal control tissue. Five of 6 SEGAs also showed evidence of biallelic mutation of TSC1 or TSC2, suggesting that SEGAs develop due to complete loss of a functional tuberin-hamartin complex. We conclude that TSC SEGAs likely arise through a two-hit mechanism of biallelic inactivation of TSC1 or TSC2, leading to activation of the mTOR kinase.

Adolescent↗