Tandem Duplication Of Chromosome Research Articles

PMP22 duplication dysregulates lipid homeostasis and plasma membrane organization in developing human Schwann cells.

Charcot-Marie-Tooth disease type 1A (CMT1A) is the most common inherited peripheral neuropathy caused by a 1.5 Mb tandem duplication of chromosome 17 harbouring the PMP22 gene. This dose-dependent overexpression of PMP22 results in disrupted Schwann cell myelination of peripheral nerves. To obtain better insights into the underlying pathogenic mechanisms in CMT1A, we investigated the role of PMP22 duplication in cellular homeostasis in CMT1A mouse models and in patient-derived induced pluripotent stem cells differentiated into Schwann cell precursors (iPSC-SCPs). We performed lipidomic profiling and bulk RNA sequencing (RNA-seq) on sciatic nerves of two developing CMT1A mouse models and on CMT1A patient-derived iPSC-SCPs. For the sciatic nerves of the CMT1A mice, cholesterol and lipid metabolism was downregulated in a dose-dependent manner throughout development. For the CMT1A iPSC-SCPs, transcriptional analysis unveiled a strong suppression of genes related to autophagy and lipid metabolism. Gene ontology enrichment analysis identified disturbances in pathways related to plasma membrane components and cell receptor signalling. Lipidomic analysis confirmed the severe dysregulation in plasma membrane lipids, particularly sphingolipids, in CMT1A iPSC-SCPs. Furthermore, we identified reduced lipid raft dynamics, disturbed plasma membrane fluidity and impaired cholesterol incorporation and storage, all of which could result from altered lipid storage homeostasis in the patient-derived CMT1A iPSC-SCPs. Importantly, this phenotype could be rescued by stimulating autophagy and lipolysis. We conclude that PMP22 duplication disturbs intracellular lipid storage and leads to a more disordered plasma membrane owing to an alteration in the lipid composition, which might ultimately lead to impaired axo-glial interactions. Moreover, targeting lipid handling and metabolism could hold promise for the treatment of patients with CMT1A.

Tandem duplication of chromosomal segments is common in ovarian and breast cancer genomes

The application of paired-end next generation sequencing approaches has made it possible to systematically characterize rearrangements of the cancer genome to base-pair level. Utilizing this approach, we report the first detailed analysis of ovarian cancer rearrangements, comparing high-grade serous and clear cell cancers, and these histotypes with other solid cancers. Somatic rearrangements were systematically characterized in eight high-grade serous and five clear cell ovarian cancer genomes and we report here the identification of > 600 somatic rearrangements. Recurrent rearrangements of the transcriptional regulator gene, TSHZ3, were found in three of eight serous cases. Comparison to breast, pancreatic and prostate cancer genomes revealed that a subset of ovarian cancers share a marked tandem duplication phenotype with triple-negative breast cancers. The tandem duplication phenotype was not linked to BRCA1/2 mutation, suggesting that other common mechanisms or carcinogenic exposures are operative. High-grade serous cancers arising in women with germline BRCA1 or BRCA2 mutation showed a high frequency of small chromosomal deletions. These findings indicate that BRCA1/2 germline mutation may contribute to widespread structural change and that other undefined mechanism(s), which are potentially shared with triple-negative breast cancer, promote tandem chromosomal duplications that sculpt the ovarian cancer genome. Copyright © 2012 Pathological Society of Great Britain and Ireland.

A tandem duplication of chromosome 21 in a newborn showing a phenotype inconsistent with Down syndrome

Chromosome 21 is a highly studied chromosome and it is involvedfrequently in meiotic and post-zygotic non-disjunction eventscausing Down syndrome. Rare structural rearrangements due tomis-segregation of translocations have defined a Down syndromecritical region (DCR) responsible for the Down syndrome pheno-type[Barnicoatetal.,1996;Wiseman etal.,2009].Chromosome21duplications are more rare events leading to chromosomal trisomyandhavehelpedfacilitateabetterphenotype–karyotypecorrelation[Korenberg et al., 1994; Egashira et al., 2008]. We report here a caseshowingpathologicalfeaturesassociatedwithatandemduplicationof part of 21q, not involving the DCR.The patient was the first child born to unrelated healthy Cauca-sian parents. The pregnancy was uncomplicated until 34 weeks ofgestation, when ultrasound showed microcephaly and cerebellarhypoplasia. Birth was at 37 weeks of gestation without any compli-cation. The patient showed Apgar scores of 6, 8, 9 at 1, 5, 10min,respectively, and the umbilicalpH was7.4. Birth weight, length andheadcircumferencewere3,040g(50thcentile),49cm(50thcentile)and 30.5cm (<3rd centile), respectively.Clinical evaluation revealed dysmorphic features includingmicrophthalmia with severe visual loss, downslanting palpebralfissures, bulbous nasal tip, anteverted nostrils, and microstomia(Fig. 1A). ECG and echocardiography were normal.Signs of encephalopathy were present prevalently in the lefthemisphere.Brain magneticresonanceimaginghighlighted corpuscallosum complete agenesia, enlarged lateral ventricles, especiallyon the left, near trigone and the occipital lobe (Fig. 1A). Cerebellarvermis had poor development showing only the most rostralportion while cerebellar hemispheres and encephalic trunk werehypoplastic.Ophthalmologicevaluationshowedpalepapillaontheright, with only temporal zone involvement on the left. Otoacusticemission, kidneys, liver, urinary tract, spleen, and pancreas werenormal.At2yearsofage,thechildfailedtothrivewithpoorgrowth,psychomotor, and cognitive delay.Patient’s karyotype showed a tandem duplication of part of21q11.2-21.3. Parents were normal indicating that the duplicationwas de novo, and a paternal QFQ variant on the duplicatedchromosome 21 determined the origin. FISH analysis with theprobe covering DCR showed one signal on each chromosome 21indicating lack of DCR involvement. FISH with the WCP21 probeconfirmedthechromosome21originoftheduplicatedregionand2BACsmappingon21q11.2(RP11-106K13BACclone,nt15205277-15205811) and 21q21.1 (RP11-242C13 BAC clone, nt15546175-

Evidence for macrophage‐mediated myelin disruption in an animal model for Charcot‐Marie‐Tooth neuropathy type 1A

Charcot-Marie-Tooth neuropathy type 1A (CMT 1 A) is the most common inherited neuropathy in humans and is mostly caused by a 1.5-Mb tandem duplication of chromosome 17 comprising the gene for the peripheral myelin protein 22-kDa (PMP 22). Although there are numerous studies on the functional role of PMP 22, the mechanisms of myelin degeneration under PMP 22-overexpression conditions have not yet been fully understood. We have shown previously that in mouse mutants hetero- or homozygously deficient for two other myelin components, P0 and C x 32, respectively, immune cells contribute to the demyelinating neuropathy. To test this possibility for PMP 22 overexpression, we investigated a putative mouse model for CMT 1 A, i.e., the mouse strain C 6 1 mildly overexpressing human PMP 22 in peripheral nerves. Electron microscopic and electrophysiologic investigations revealed that this mouse strain develops pathologic features similar to those found in CMT 1 A patients. A novel finding, however, was the upregulation of CD8- and F4/80-positive lymphocytes and macrophages, respectively, in peripheral nerves. The observation that macrophages enter endoneurial tubes of the mutants and obviously phagocytose morphologically normal myelin strongly suggests that the myelin degeneration is mediated at least partially by these phagocytic cells. By gene array technology and quantitative RT-PCR of peripheral nerve homogenates from PMP 22 mutants, monocyte chemoattractant protein-1 (MCP-1; cc l2) could be identified as a putative factor to attract or activate macrophages that attack myelin sheaths in this model of CMT 1 A.

Mosaicism for a tandem duplication dup(1)(q12q22) in an 18 year old female.

The clinical features and cytogenetic results of an 18 year old mentally handicapped female found to be a mosaic for a tandem duplication of chromosome 1 (46,XX,dup(1)(q12q22)/46,XX) are reported. The...

Recombination between chromosomal IS200 elements supports frequent duplication formation in Salmonella typhimurium.

Spontaneous tandem chromosomal duplications are common in populations of Escherichia coli and Salmonella typhimurium. They range in frequency for a given locus from 10(-2) to 10(-4) and probably form by RecA-dependent unequal sister strand exchanges between repetitive sequences in direct order. Certain duplications have been observed previously to confer a growth advantage under specific selective conditions. Tandem chromosomal duplications are unstable and are lost at high frequencies, representing a readily reversible source of genomic variation. Six copies of a small mobile genetic element IS200 are evenly distributed around the chromosome of S. typhimurium strain LT2. A survey of 120 independent chromosomal duplications (20 for each of six loci) revealed that recombination between IS200 elements accounted for the majority of the duplications isolated for three of the loci tested. Duplications of the his operon were almost exclusively due to recombination between repeated IS200 elements. These data add further support to the idea that mobile genetic elements provide sequence repeats that play an important role in recombinational chromosome rearrangements, which may contribute to adaptation of bacteria to stressful conditions.

U‐type exchange in a paracentric inversion as a possible mechanism of origin of an inverted tandem duplication of chromosome 8

A mentally retarded male with dysmorphic features was found to have a de novo 46,XY,inv dup(8) (p.23.1-->12). Confirmation of the segments duplicated in the rearrangement was achieved by biochemical analysis of glutathione reductase, which maps to 8p21.1, and DNA studies using the chromosome specific probe y-19-1D (D85131), which maps to 8p21. Assay of cathepsin B, which has been localised to 8p22, did not differ from controls with normal chromosomal constitution. DNA studies using the Defensin 1 gene probe, which maps to 8p23, showed a previously undetected deletion of that segment. We propose that the inverted tandem duplication/deletion arose as a single U-type exchange within an inversion loop.

The Balbiani ring and the polytene chromosomes of Drosophila bicornuta

A study of the BR1 and of the most prominent puffs during larval development and after in vitro ecdysterone treatment, as well as of the banding pattern and inverted tandem chromosomal duplications of the salivary gland chromosomes of Drosophila bicornuta, is presented in this report. These data are compared and discussed with those of D. auraria and D. serrata, two other montium species.

Menadione-resistant Chinese hamster cell variants are cross-resistant to hydrogen peroxide and exhibit stable chromosomal and biochemical alterations.

We have investigated the antioxidant properties of V79 Chinese hamster cells rendered resistant to menadione by chronic exposure to increasing concentrations of this quinone. MD1, a clone of resistant cells, was compared to the parental M8 cells; the former showed increased activity of catalase (3 fold), glutathione peroxidase (1.6 fold) and DT-diaphorase (2.6 fold), as well as an increase in glutathione (3.2 fold). Although one of the products of menadione metabolism is superoxide anion, no changes in total superoxide dismutase activity was observed in MD1 cells. MD1 menadione resistant cells were also resistant to killing by hydrogen peroxide and contained tandem duplication of chromosome 6. A similar duplication of chromosome 6 was seen in several independently derived menadione resistant clones and therefore seems closed linked to the establishment of the resistance. Upon removal of menadione from the medium, some of these properties of MD1 cells, viz., resistance to menadione, elevated glutathione levels, and glutathione peroxidase activity, were lost and the cells resembled M8 cells. However, resistance to H2O2, elevated catalase activity and the duplicated chromosome remained stable for more than 40 cell passages in the absence of menadione. The increase in catalase activity was correlated with an increase in catalase mRNA content and a 50% amplification of catalase gene, as determined, respectively, by Northern and Southern blot analysis. The role of the chromosome 6 duplication in resistance to oxidative stress remains to be established. It is not responsible directly for elevated catalase levels since the catalase gene is on chromosome 3.

Cytogenetic and molecular analysis of a de novo tandem duplication of chromosome 21

We have characterised by cytogenetic and molecular analysis a de novo tandem duplication of chromosome 21. High resolution chromosome examination of lymphocytes revealed the following karyotype in 90% of the cells: 46,XY,dir dup (21)(pter----q22.300::q11.205----qter). Of these cells, 10% showed a normal karyotype. Gene dosage of chromosome 21 sequences by a slot blot method indicated that the duplication extends from D21S16 to D21S55. In situ hybridization with probes close to the borders of the duplicated segment confirmed the gene dosage data and gave results consistent with a true tandem duplication of chromosome 21. Pulsed field gel electrophoresis of the patient's DNA showed an abnormal restriction band common to D21S55 and D21S16, confirming that the junction point between the two homologous parts of the tandem chromosome brings these two sequences into proximity. Restriction fragment length polymorphism analysis indicated that the abnormal chromosome was maternal in origin and that the rearrangement of chromosome 21 could not have occurred at a post-zygotic stage of development but resulted from a recombination event during maternal gametogenesis. The possible mechanisms of formation of the abnormal chromosome are discussed, as is the presence of cells with normal chromosomes 21, in the patient.

Developmental changes in fat body and midgut chromosomes of Drosophila auraria

Changes in puffing activity of fat body (FB) and midgut (MG) chromosomes of Drosophila auraria during late larval and white prepupal development as well as after in vitro culture with or without ecdysterone were studied and compared with those of the salivary gland (SG). The Balbiani Rings characteristic of the SG chromosomes of D. auraria, are not formed in FB and MG. Most of the inverted tandem chromosomal duplications that have been found to be common to all three tissues showed differentiation of puffing activity of the bands considered to be homologous. The major early ecdysone puffs 73A and 73B (considered to be homologues of D. melanogaster puffs 74EF and 75B, respectively), together with other early ecdysone puffs were present in all three tissues. Clear intermoult and postintermoult puffs were not evident in FB and MG chromosomes. However, a small set of late ecdysone puffs could be scored in FB, while no late ecdysone puffs were abserved in MG. Other tissue-specific puffs were identified, but a very small number of them were limited to MG.

Tandem chromosomal duplications: role of REP sequences in the recombination event at the join-point.

We show that a family of prokaryotic repetitive sequences, called REP (repetitive extragenic palindromic), (Stern et al., 1984) is involved in the formation of chromosomal rearrangements such as duplications. The join-points of seven RecA+ tandem duplications previously characterized in Salmonella typhimurium, that fuse the hisD gene to distant foreign promoters, were cloned and sequenced. In all seven cases they are shown to have originated by recombination between distant REP sequences. Importantly, several join-points had also occurred at REP sequences even in a RecA-background. Thus, REPs can recombine with each other by a RecA(-)-independent mechanism involved in the generation of chromosomal rearrangements. While all RecA+ duplications analysed resulted from recombination between REP sequences, some RecA-duplications did occur also outside of REP sequences, in one case by recombination within a 7 bp homology. Possible roles for the known interaction between DNA gyrase and REP in chromosomal rearrangements are discussed.

Down's syndrome with a recombinant tandem duplication of chromosome 21 derived from a maternal ring.

An account is given of the cytogenetic investigations of a girl with Down's syndrome found to have a dicentric duplication of chromosome 21. This tandem type of rearrangement was interpreted as a recombinant derived from a single meiotic crossover between a maternal ring 21 and its normal homologue. A population of cells was also found in which breakage of the dicentric resulted in a chromosome 21 with a small terminal deletion. The mother and the proband's younger brother, who was also a ring 21 heterozygote, were both clinically normal.

Tandem duplication of chromosome 14 (q24+q32) in male newborn with congenital malformations

A tandem duplication of 14q24 leads to q32, estimated by G- and R-banding, was found in a male newborn with growth retardation and congenital malformations. His clinical picture is compared with that of three patients from the literature with partial trisomy for a similar segment of 14q due to a parental reciprocal translocation or a de novo translocation.

Tandem genetic duplications in Salmonella typhimurium: Amplification of the histidine operon

Salmonella strains harboring tandem duplications of chromosomal segments including the histidine operon may be selected from populations of hisO promoter-like mutants. The twofold increase in gene dosage of the histidine operon caused by tandem duplication provides resistance to concentrations of the histidine analogue 3-amino-1,2,4-triazole that inhibit the growth of haploid hisO mutants. Several properties of AT ‡ -resistant mutants indicate that they harbor tandem chromosomal duplications: (i) the AT-resistant phenotype of these strains is genetically unstable. Such instability is dependent upon a functional recombination system, (ii) AT-resistant mutants express approximately twice the levels of his enzymes as parental strains. (iii) Genetic tests indicate that AT-resistant mutants are merodiploid for large segments (up to 26%) of their genome. (iv) For certain isolates, the merodiploid and AT-resistant nature of these strains are properties cotransducible with a distant chromosomal marker unrelated to the his operon. We interpret these results as indicating cotransduction of the join-point of a tandem duplication with this distant marker. The spontaneous frequency of tandem his duplications is remarkably high (6·2 × 10 −5 per cell). This frequency is more than 6000-fold reduced in recA − genetic backgrounds. Two major types of tandem his duplications are repeatedly isolated, having an identical ~13% or ~22% of their genome duplicated, respectively. When duplication-containing strains are grown under conditions that select for resistance to increased AT concentrations, clones harboring additional tandem copies (amplification) of the his operon are obtained. The role which such gene amplification may play in bacterial adaptation is discussed.

Tandem chromosomal duplications in Salmonella typhimurium: Fusion of histidine genes to novel promoters

Salmonella strains harboring tandem chromosomal duplications have been identified following selection for expression of a histidine biosynthetic gene whose promoter is deleted. In such strains, tandem duplications fuse the selected his gene to “foreign” regulatory elements, thereby allowing gene expression. Selection is made for hisD + activity in deletion strain hisOG203. Among the revertants, strains harboring tandem chromosomal duplications have been identified by a number of their properties. (1) Their HisD + phenotype is genetically unstable. (2) Such instability is dependent on recombination ( recA) activity. (3) Genetic tests demonstrate that these strains are merodiploid for large regions (up to 25%) of the Salmonella genome. (4) Recipient strains that inherit the HisD + phenotype of these duplication-carrying revertants also inherit the donor's merodiploid state. (5) In certain revertants the functional hisD + gene and the sequence which promotes merodiploid transductant formation are linked to chromosomal markers located far from the normal his region. Previous reports have concluded that the instability of strains isolated by this selection is due to translocation of the hisD + gene to an extrachromosomal element (the pi-histidine factor). We believe that in all strains we have tested (33 independent isolates) instability can better be accounted for as due to tandem duplication events which permit expression of hisD. At least two mechanisms are responsible for duplication formation. One mechanism is dependent on recombination function and generates identical revertants having a duplication of 16% of the chromosome. A second mechanism operates independently of recombination activity; individual duplications produced by this process have variable endpoints.