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PubMedDate not supplied

Somatic change in the estrogen receptor gene associated with altered expression of the progesterone receptor.

Using a fragment of the estrogen receptor (ER) cDNA as a probe, Southern blots of HindIII-digested genomic DNA, from breast tumours and non-cancerous tissue, revealed a 1.6 kb hybridizing fragment (1.6KbHF) in 3 out of 30 tumours, and in 31 out of 80 mastectomy samples (16 sectors from each of 5 patients), which was significantly correlated with the absence of progesterone receptor. In 4 of the patients, sectors which showed the 1.6KbHF co-existed in the same breast with sectors which did not. Neither the use of higher concentrations of the restriction enzyme, not high salt extraction of DNA changed the abundance of the 1.6KbHF relative to other bands. Similar studies on EcoRI digests of the same DNA samples failed to show any variants. As a further control, hybridization of the same Southern blots of HindIII-digested DNA, with a cytochrome P450IIA3 cDNA, also failed to show variants in these samples. It is concluded that the presence of the 1.6KbHF represents a somatic change in the nucleus of these samples which may have functional importance.

Blotting, Southern↗
PubMed1984

Albumin extinction without methylation of its gene.

In earlier work we identified at the 5' end of the rat albumin gene an Msp I site whose undermethylation appears to be necessary but not sufficient for stable expression of the gene in rat hepatoma cells. Here, we ask whether the block to expression of albumin production, which occurs when rat hepatoma cells are hybridized with cells that do not produce the protein, could be the result of de novo methylation of this site. In two types of somatic hybrids, rat hepatoma-mouse L cell fibroblasts, and rat hepatoma-dedifferentiated variant rat hepatoma cells, extinction occurs and is maintained during the first 5-15 generations after fusion. During this time the Msp I site of the now inactive rat albumin gene remained unmethylated.

Albumins↗
PubMed1985

A drug-resistant mutation in the ribosomal DNA of Tetrahymena.

A mutation that confers resistance to the drug paromomycin is shown to be in the structural gene that codes for the ribosomal RNA in Tetrahymena. This observation was made by exploiting a variant of the ribosomal DNA that distorts amplification of this locus when a new somatic nucleus develops during conjugation. Because the allelic forms of this locus have a restriction endonuclease site polymorphism, it was possible to correlate drug resistance with presence of a specific allele. The genetic results have been confirmed by sequence analysis (presented elsewhere). Thus, the crosses presented here provide a unique opportunity to identify mutations in the ribosomal DNA.

Alleles↗
PubMed1989

Polyadenylated H3 histone transcripts and H3 histone variants in alfalfa.

Histone H3 mRNAs were found in polyA(+) fractions of total RNA prepared from alfalfa plants, calli and somatic embryos. The sequence analysis of cDNAs revealed the presence of a polyA tail on independent alfalfa H3 mRNAs. A highly conserved sequence motif AAUGAAA identified about 20bp upstream from the 3' ends of the alfalfa H3 cDNAs was suggested to be one of the possible regulatory elements in the 3' end formation and polyadenylation. Three out of the four analysed H3 cDNAs have more than 97% homology with a genomic clone and encode the same protein. While the fourth represents a minor species with only 78.8% homology to the coding region of the genomic clone and encodes a H3 histone with four amino acid replacements. On the basis of compilation analysis we suggest a consensus sequence for plant H3 histones which differs from that of animal's by four amino acid changes.

Amino Acid Sequence↗
PubMed1972

Seminal vesicle formation and specific male protein secretion by female cells in allophenic mice.

The relation of cellular sex genotype to phenotype was examined in seminal vesicles of adult allophenic mice with cellular sex chromosome mosaicism. Each animal originated from conjoined blastomeres of an embryo of female (XX) and one of male (XY) constitution, from different inbred strains. Cells of both sexes were detected in bone marrow and certain other somatic tissues; cellular sex of seminal vesicles was deduced from strain-associated electrophoretic variants of proteins coded for at autosomal loci. Seminal vesicles composed partly or entirely of female cells were found in male and pseudohermaphrodite individuals. In a pseudohermaphrodite, both allelic variants of the tissue-specific normal male seminal vesicle protein (Svp-locus) were present, signifying that female as well as male cells were synthesizing the protein. Male-determining factors on the Y chromosome are thus not required in cells that differentiate into functional seminal vesicles.

Animals↗
PubMed1987

[Clinical and pathogenetic aspects of symmetrical diabetic neuropathy].

A total of 2000 patients of different age, suffering from diabetes were studied, giving consideration to clinical, neurophysiological and diabetological parameters. The authors have identified syndromes of damage to somatic and visceral peripheral nerves in such patients. It is suggested that three main variants of damage to the peripheral nerves be differentiated: (1) subclinical disorders; (2) somatovisceral polyneuropathies in type I diabetes; (3) polyneuropathies in type II diabetes. Neural dysfunction in the first variant of the disease may be reversed following normalization of metabolic disturbances. Polyneuropathies in type I diabetes are largely related to axonal involvement whereas in type II diabetes they are characterized by a more complex pathogenesis and are largely due to damage to the myelin membranes of axons.

Adult↗
PubMed1996

The generation of antibody diversity in the turtle.

The Ab response in reptiles has been studied at the protein level, and in turtles some aspects resemble those of cold-blooded vertebrates from other classes. The genetic bases for these features are not clear. The present study is the first on the IgH organization and complexity of a reptilian Ig gene system. The approach to cloning turtle (Pseudemys scripta) sequences is entirely PCR based, and its efficacy is demonstrated by obtaining extensive information on a heretofore unexplored Ig gene system. A number of genomic VH sequences, representing possibly four families, were isolated, as was a genomic C mu 4 clone. These sequences, used as probes, provided proof that in the turtle there is a single IgH locus with multiple VH genes and one C mu gene. In Northern hybridizations, the C mu 4 probe detected two transcripts; of the four VH groups, only one was expressed, and multiple bands indicated the presence of at least two non-mu transcripts. Using reverse transcription-PCR on spleen or liver RNA, an IgM heavy chain sequence was obtained, as were a number of VDJ rearrangements. Among 32 unique VDJ rearrangements from one animal, there were 22 sequence variants at framework 4, suggesting either a very large number of J segments or somatic modification in the variable region. The latter interpretation is supported by point mutations found in framework 3 and CDR3. The number of changes is considerably greater than the deduced Taq misincorporation rate (0.05%).

Amino Acid Sequence↗
PubMed1997

Glycophorin A as a biological dosimeter for radiation dose to the bone marrow from iodine-131.

The frequency of peripheral blood erythrocyte variants exhibiting allelic loss of glycophorin A (N/M antigen) has been used previously as a biological dosimeter to assess somatic mutations in bone marrow cells from external whole-body irradiation. The aim of the present study was to determine whether this marker could be used as a measure of bone marrow genotoxicity induced by 131I in the treatment of thyroid cancer. Flow cytometry of immunolabeled erythrocytes was performed to enumerate glycophorin A variants before and after eight therapy doses of 131I administered to five patients with differentiated thyroid carcinoma. Bone marrow radiation exposure from each dose was calculated from the integrated retention of 131I in the whole body and in the blood. In addition, the accumulated dose to the bone marrow received from earlier 131I therapy was calculated for each patient. Regression analysis was performed on the frequency of two glycophorin A variant cell types (N/O and N/N) as a function of accumulated dose to the bone marrow. Frequency of N/O variant cells showed a significant dose-related increase with a slope of 10.9 x 10(-6) per sievert. This dose effect is about one-half that previously observed after whole-body external irradiation at high dose rate. This decreased response could be explained by the low dose rate of the radiation to the bone marrow from 131I.

Bone Marrow↗
PubMed2005

Phenotypic and genotypic characterisation of Pasteurella multocida isolated from pigs at slaughter in New Zealand.

AIMS: To examine pigs at slaughter in New Zealand for the presence of Pasteurella multocida, and to determine for isolates, their biochemical profiles, somatic and capsular types, and the presence or absence of the HSB and toxA genes, associated with haemorrhagic septicaemia (HS) and progressive atrophic rhinitis (PAR), respectively. METHODS: Swabs from 173 lungs, 158 palatine tonsils and 82 nasal passages of pigs at two abattoirs in New Zealand were cultured for P. multocida using conventional techniques, and isolated colonies were subjected to biochemical tests for identification of biovars. Somatic serotyping was conducted using an agar gel immunodiffusion (AGID) test. Polymerase chain reaction (PCR) assays were used to confirm phenotypic identification of colonies using species-specific primers, capsule type using serogroup-specific primers and multiplex PCR, and to test for the presence of HSB and toxA genes. RESULTS: Pasteurella multocida was isolated from 11/173 (6.4%) lung, 32/158 (20.2%) palatine tonsil and 5/82 (6.1 %) nasal swab samples, a total of 48 isolates from 413 samples (11.6%). Isolation rates per farm ranged from 1-53% of tissue samples collected from pigs 5-6 months of age. On phenotypic characterisation, isolates were allocated to seven main biovars, viz 1, 2, 3, 5, 9, 12, and a dulcitol-negative variant of Biovar 8, the majority (30/48) being Biovar 3. Of the 42 isolates for which somatic serotyping was conducted, 10% were Serovar 1, 79% were Serovar 3, 2% were Serovar 6,1, 2% were Serovar 12, and 7% could not be typed. All 48 isolates were confirmed as P. multocida using a species-specific PCR. In the capsular multiplex PCR, 92% of isolates were Capsular (Cap) type A, 2% were Cap D, and 6% could not be typed. None of the samples were positive for the HSB or toxA genes. CONCLUSION: Serovars or capsular types of P. multocida associated with HS or PAR in pigs were not detected. Establishment of species-specific, capsular and toxin PCR assays allowed the rapid screening of isolates of P. multocida, while serotyping provided an additional tool for epidemiological and tracing purposes.

Abattoirs↗
PubMed2025

Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing.

For the detection of somatic structural variation (SV) in cancer genomes, long-read sequencing is advantageous over short-read sequencing with respect to mappability and variant phasing. However, most current long-read SV detection methods are not developed for the analysis of tumor genomes characterized by complex rearrangements and heterogeneity. Here, we present Severus, a breakpoint graph-based algorithm for somatic SV calling from long-read cancer sequencing. Severus works with matching normal samples, supports unbalanced cancer karyotypes, can characterize complex multibreak SV patterns and produces haplotype-specific calls. On a comprehensive multitechnology cell line panel, Severus consistently outperforms other long-read and short-read methods in terms of SV detection F1 score (harmonic mean of the precision and recall). We also illustrate that compared to long-read methods, short-read sequencing systematically misses certain classes of somatic SVs, such as insertions or clustered rearrangements. We apply Severus to several clinical cases of pediatric leukemia/lymphoma, revealing clinically relevant cryptic rearrangements missed by standard genomic panels.

Humans↗
PubMedDate not supplied

Alterations of the hprt gene in human in vivo-derived 6-thioguanine-resistant T lymphocytes.

Investigations into the extent and significance of somatic gene mutations occurring in vivo in humans have been hampered by the lack of a means of unambiguously defining the mutational origin of in vivo-derived variant cells. Several years ago we proposed that 6-thioguanine-resistant T lymphocytes, present at low frequencies in human peripheral blood, might be useful markers of in vivo somatic mutation. We and others have since described methods for the isolation and study of these unusual cells. The thioguanine-resistant T cell stably lack hypoxanthine-guanine phosphoribosyltransferase (HPRT) activity, suggesting that they are somatic equivalents in normal individuals to cells from individuals with the X-chromosomal hprt Lesch-Nyhan germinal mutation. We now report that in vivo-derived thioguanine-resistant T-cell colonies from a single normal individual show a variety of hprt structural alterations, as determined by Southern blot analysis. This finding demonstrates unequivocally that these cells are genetic mutants and validates their use for fundamental and applied mutational studies in humans.

Clone Cells↗
PubMed2003

Differential expression of two estrogen receptor beta isoforms in the human fetal testis during the second trimester of pregnancy.

Testicular cancer is more common in individuals with disorders of the male reproductive tract. It has been suggested that inappropriate exposure to estrogens during fetal life may have an impact on maturation of testicular germ cells that are the cells of origin of the majority of testis cancers. The aim of the present study was to establish whether human fetal germ cells (gonocytes) are a potential target of estrogen action. To address this issue, we used RT-PCR and immunohistochemistry to examine the pattern of expression of estrogen receptors (ER alpha, ER beta, and ER beta 2 variant) in human fetal testes at 12-19 wk gestation. ER alpha, mRNA, and protein were not detected in any of the fetal testes. In contrast, using an antibody directed against the hinge domain of ER beta expression was detected in multiple testicular nuclei. RT-PCR with primers specific for full-length wild-type ER beta (ER beta 1) or the ER beta 2 variant formed by splicing of an alternative eighth exon, was performed on whole-tissue extracts and materials recovered by laser capture and revealed that mRNAs for both isoforms were expressed. Immunohistochemistry with isotype-specific monoclonal antibodies showed that ER beta 1 was low/undetectable in gonocytes, whereas these cells expressed the highest levels of ER beta 2, compared with other testicular cell types. Both ER beta 1 and ER beta 2 were detected in some but not all Sertoli cells, peritubular cells, and other interstitial cells including those tentatively identified as Leydig cells. Our immunohistochemical results demonstrate that during the second trimester, some but not all somatic cells within the human fetal testis express wild-type ER beta (ER beta 1) protein and/or the variant isoform of ER beta (ER beta 2) that lacks amino acids essential for binding of estradiol. ER beta 2 protein was readily detectable in fetal gonocytes, whereas ER beta 1 was not. We did not detect expression of ER alpha. The expression of ER beta 2, a variant proposed act as a dominant negative receptor, might prevent estrogen action in gonocytes. We suggest that during this period of fetal life, estrogenic ligands are most likely to act on somatic cells that contain ER beta 1 protein.

Estrogen Receptor alpha↗
PubMed2003

Mutation analysis of CDP, TP53, and KRAS in uterine leiomyomas.

Leiomyomas are the most common gynecologic tumors in women, but very little is known about their molecular pathology. We used single-stranded conformational polymorphism/heteroduplex analysis to analyze 42 unselected uterine leiomyomas for somatic mutations in all coding exons of the gene encoding CCAAT displacement protein (CDP), as well as exons 5-8 of TP53 and codons 1-36 and 38-80 of KRAS. No somatic mutations were identified in either TP53 or KRAS, indicating that disregulation of these genes is not required for leiomyomas development. Aberrant band shifts were identified in CDP, but these were all germline nonpathogenic variants that have been reported previously. There is good functional and genetic evidence indicating that CDP is a leiomyoma suppressor, but our data suggested that somatic mutations in this gene were rare in unselected uterine leiomyomas. It is possible that CDP belongs to a class of tumor suppressor in which loss of only one copy of the gene, either by genetic or epigenetic mechanisms, is sufficient to allow tumor growth.

DNA Mutational Analysis↗
PubMed1984

The amino acid sequence of boar H1t, a testis-specific H1 histone variant.

H1t is a testis-specific H1 variant found in spermatocytes and spermatids of mammals. The complete amino acid sequence has been determined for H1t isolated from boar testes. The protein is composed of 211 amino acids with the composition 3 aspartic acids, 6 asparagines, 13 threonines, 21 serines, 7 glutamic acids, 7 glutamines, 15 prolines, 14 glycines, 37 alanines, 11 valines, 1 methionine, 3 isoleucines, 14 leucines, 1 tyrosine, 1 phenylalanine, 42 lysines, 15 arginines and a calculated molecular weight of 22,059 disregarding the post-translational acetylation of the amino-terminal alanine. The protein shows typical H1 domains with basic amino- and carboxyl-terminal regions separated by a conserved, presumably globular, core sequence. The core region is very homologous to the highly conserved core sequence found in somatic mammalian H1 histones but does differ from this sequence in 15 places. Accordingly, it may be appropriate to consider H1t as new variant category. The carboxyl-terminal half of H1t is distinguished from the standard somatic family by being somewhat shorter and by the presence of 10 arginine residues. In contrast to many H1 proteins, the carboxyl-terminal region of H1t does not show an obvious pattern of peptide repeats.

Amino Acid Sequence↗
PubMed1987

N segment insertion and region-directed somatic hypermutation in a kappa gene of a t(2;8) chromosomal translocation.

A detailed molecular analysis of both reciprocal recombination products of the variant t(2;8) chromosomal translocation of the Burkitt lymphoma derived cell line JI and their germline counterparts was carried out. The breakpoint on chromosome 8 is localized 28 kb to the 3' side of the c-myc protooncogene, the breakpoint on chromosome 2 was found to be within an aberrantly rearranged VK gene (abbreviations ref. 1). Novel features of the immunoglobulin moiety involved in this process include insertion of extra nucleotides in the V-J junction which have the characteristics of a N segment as it has been found up to now only in heavy chain and T cell receptor genes; the occurrence of somatic mutations in 8q+ and not in 2p-. These data allow a reconstruction of the course of events in the cell line JI; remarkable sequence regularities at the chromosomal breakpoints consisting of symmetrically placed dinucleotides and elements related to the hepta- and nonanucleotide recombinase recognition sequences are discussed in the context of the translocation mechanism.

Base Sequence↗
PubMed1989

Frequency of variant erythrocytes at the glycophorin-A locus in two Bloom's syndrome patients.

Blood type MN is determined by a glycoprotein termed glycophorin A (GPA) which exists on the surface of erythrocytes, and the difference between the M and N types is derived from the presence of 2 different amino acids in the amino-terminal portion (Furthmayer, 1978). Using a pair of fluorescence-labeled monoclonal antibodies specific to each GPA, somatic mutations in erythrocytes of MN heterozygotes at the GPA-M and -N alleles can be quantitatively determined using a flow sorter (Langlois et al., 1986). Our results for 2 Bloom's syndrome (BS) patients showed that variants either lost expression of one allele (simple gene inactivation or loss) or expressed only one allele at twice the normal level (most probably somatic recombination) occurring at a frequency of about 1-3 per 10(3) erythrocytes. The flow cytometric patterns of erythrocytes from the BS patients showed a typical smear of variants bearing intermediate levels of expression of one GPA allele, indicating that the real variant frequency is even greater than that measured. On the other hand, the parents heterozygous for the BS gene showed variant frequencies (1-8 x 10(-5)) within the normal range. These data strongly support the hypothesis that the cancer proneness of BS patients is due to their increased frequency of spontaneous mutations and somatic recombination.

Alleles↗
PubMed2026

Prevalence of BRCA1/2 variants in an Ovarian Cancer Cohort: outcomes from a Nationwide Testing Program.

Poly(ADP-ribose) polymerase inhibitors (PARPi) have revolutionized the management of BRCA1- and BRCA2-associated ovarian cancer (OC). In 2020, Ireland implemented a nationwide, oncology-led pathway for mainstreamed BRCA1/2 testing in patients with OC. This study evaluated the pathway and characterised the BRCA1/2 landscape in an Irish cohort of patients with OC. Samples collected between January 2020 and December 2023 were tested in two national molecular diagnostic laboratories. Single-molecule molecular inversion probe sequencing was used to detect single nucleotide variants, while multiplex ligation-dependent probe amplification assessed large genomic rearrangements. Variants were classified according to the American College of Medical Genetics and Genomics and Association for Clinical Genomic Science 2020 guidelines and CanVIG-UK specifications. In total, 535 patients were included, with a median age of 65.5 years (range, 27-89 years). Of these, 455/535 (85.0%) underwent germline BRCA1/2 (gBRCA) testing using peripheral blood, and 360/535 (67.2%) underwent tumour BRCA1/2 (tBRCA) testing, resulting in 292/535 (54.6%) patients having paired testing. Among gBRCA-tested patients, 10.3% (47/455) had a clinically actionable variant (CAV), while 2.1% (10/455) had a variant of uncertain significance. Of the 262 patients who underwent paired testing and had negative gBRCA results, 9.5% (25/262) had a somatic BRCA CAV. Recurrent germline BRCA CAVs were identified in regional clusters, including BRCA1 c.5266dup, BRCA1 c.1175_1214del, and BRCA2 c.4398_4402del. This nationwide real-world study demonstrates that mainstreamed germline and somatic BRCA1/2 testing is feasible in Ireland and reports the prevalence of BRCA CAVs in a cohort of patients with OC. Although the observed prevalence of germline BRCA CAVs was lower than anticipated, it is consistent with UK real-world data. The identification of recurrent, regionally clustered germline variants further enhances the characterisation of the Irish genomic landscape.

Journal Article↗
PubMed1998

Determination of somatic mutant frequencies at glycophorin A and T-cell receptor loci for biodosimetry of prolonged irradiation.

PURPOSE: To determine the variant frequencies (VF) at glycophorin A (GPA) and T-cell receptor (TCR) loci in persons exposed to prolonged ionizing radiation at different doses and to assess the significance of the GPA and TCR assays for biodosimetry of prolonged irradiation. MATERIALS AND METHODS: The VF values were determined by means of flow cytometry in 120 persons exposed between 1968-1996. Most exposures were in Chernobyl clean-up workers in 1986-1987. RESULTS: A significant correlation was shown between the NO GPA variant cell frequency and dose (r = 0.61, p < 0.0001). The slope of the linear regression was 6.3 x 10(-6) NO mutant cells/Gy. Dose-dependent increase in the TCR VF was found in the group with recent exposures (slope 2.1 x 10(-4) variant cells/Gy, r = 0.75, p = 0.0002). In the Chernobyl clean up workers who received doses less than 0.25 Gy the TCR VF unlike the GPA VF was significantly higher than in the control non-irradiated individuals (p < 0.01 and p > 0.05 respectively). CONCLUSIONS: The GPA assay has limited potential to be used as a biodosimeter of prolonged irradiation, at least in dose interval up to 2.0 Gy. The TCR assay is likely to have greater potential in estimation of recent radiation exposure than the GPA assay.

Adult↗