High-Resolution Integrated Map Encompassing the Breast Cancer Loss of Heterozygosity Region on Human Chromosome 16q22.1

Frengen, Eirik; Rocca-Serra, Philippe; Shaposhnikov, Sergey; Taine, Laurence; Thorsen, Jim; Bepoldin, Christophe; Krekling, Martin; Lafon, D; Klykken, Kaja Marianne; Moneim, Azza Abd El; Johansen, Henning; Longy, Michel; Prydz, Hans; Dorion-Bonnet, Françoise

doi:10.1006/geno.2000.6389

Cited by 14 publications

(11 citation statements)

References 42 publications

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“…Fragments containing a previously localized CpG island were subcloned into pZero-2 to give, among others, pEco29 (2.9 kb, 2 GenBank TM Accession Number AF329821) and pKURT (a 1.1-kb insert in pEco29, from base 179 -1346) (10,11). Three clones were obtained from a human testis cDNA library (kindly provided by Dr. K. Taskèn, University of Oslo) and hybridized to pEco29.…”

Section: Methodsmentioning

confidence: 99%

Cloning and Characterization of MDDX28, a Putative DEAD-box Helicase with Mitochondrial and Nuclear Localization

Valgardsdóttir¹,

Brede²,

Eide³

et al. 2001

Journal of Biological Chemistry

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A cDNA encoding a novel member of the helicase family, MDDX28, has been cloned from a human testis library. This apparently intronless gene was transcribed in all tissues studied. MDDX28 encodes a protein of 540 amino acids, with ϳ30% homology to other helicases over the core region, containing all the conserved DEAD-box helicase motifs. No homologue is known. MDDX28 has RNA and Mg 2؉ -dependent ATPase activity. Subcellular localization studies of MDDX28 using oligoclonal antibodies raised against the protein as well as its enhanced green fluorescence protein (EGFP) demonstrated that the protein is localized in the mitochondria and the nucleus. To our knowledge, MDDX28 is the first member of the RNA helicase described with this dual location. The nuclear localization of MDDX28 depended on active RNA polymerase II transcription, suggesting that the protein could be transported to and from the nucleus. This was confirmed further in an interspecies heterokaryon assay, in which MDDX28 was seen to translocate to the nucleus and mitochondria. The mitochondrial uptake of the MDDX28-EGFP-N1 fusion protein was inhibited by carbonyl cyanide p-(trichloromethoxy)phenylhydrazone. Our results indicate that MDDX28 can be transported between the mitochondria and the nucleus.RNA helicases constitute a family of proteins that unwind double-stranded RNA by using nucleoside triphosphates as a source of energy. They are characterized by a conserved core region of ϳ300 amino acids that contains eight highly conserved domains. Some of these motifs are involved in hydrolyzing NTP, mainly ATP, and in coupling the hydrolysis to the unwinding process. RNA helicases have also been nicknamed DEAD-box helicases after the conserved motif II, the so-called DEAD box (Asp-Glu-Ala-Asp). Amino acid variation in the DEAD-box motif further divides the RNA helicases into three subfamilies, subsequently called the DEAD, DEAH, and DExH families (reviewed in Ref.

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Section: Methodsmentioning

confidence: 99%

Cloning and Characterization of MDDX28, a Putative DEAD-box Helicase with Mitochondrial and Nuclear Localization

Valgardsdóttir¹,

Brede²,

Eide³

et al. 2001

Journal of Biological Chemistry

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“…They were prepared from genomic clones from a particularly well defined domain, the lecithin-cholesterol acyltransferase (LCAT) gene cluster on human chromosome 16 ( Fig. 2) [7]. These probes were applied to metaphase spreads, halos and neutral and alkaline comets, to address questions such as whether the comet tail is really comprised of loops, whether these loops have fixed anchorage points in the head, and whether these correspond to the structural organization of the DNA in the living cell.…”

Section: Introductionmentioning

confidence: 99%

Single‐cell gel electrophoresis (the comet assay): Loops or fragments?

et al. 2008

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Single-cell gel electrophoresis, or the comet assay, is widely used to measure DNA damage and repair. Upon electrophoresis, the DNA of lysed, agarose-embedded cells known as nucleoids, extends towards the anode in a structure resembling a comet, the relative intensity of the tail reflecting the frequency of DNA breaks. The structural organization of the DNA within comet preparations is not fully understood. We have used fluorescent in situ hybridization with large-insert genomic probes and human Cot-I DNA to investigate whether the production of the comet tail is simply explained by the relaxation of supercoiled DNA loops. We find that, under neutral electrophoresis conditions, when the tail and head DNA are double-stranded, the probed sequence of DNA is seen as a linear array, consistent with extension from a fixed point on the nuclear core or matrix. After alkaline electrophoresis, the appearance of the fluorescent probes suggests that linear DNA has coalesced into a granular form.

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“…10 Previous allelotype of breast cancer did not further minimise the region of LOH to a size that makes functional studies of all genes located in its vicinity feasible. In addition, previous assessment of genomic copy number in cancer is performed either at a relatively low resolution by comparative genomic hybridisation (CGH) (5-10 Mb) 11,12 or at higher resolution by laborious individual locus specific techniques that can analyse only a few loci simultaneously.…”

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“…16 MAPH has previously been used to detect DNA copy number alterations in some forms of genetic disorders 18 -21 and recently in patients with chronic myeloid leukaemia. 22 A physical map covering the 16q22.1 region has been constructed 10 and the publication of the draft sequence of the human genome has facilitated the study of multiple genes located in its vicinity. The most obvious candidate TSGs in breast cancer at this region are, firstly, genes that are involved in cell-cell adhesion (members of the cadherin family) [E-cadherin (CDH1), 8,23,24 ], P-cadherin (CDH3), 25,26 VE-cadherin (CDH5) 27 and Ks-cadherin (CDH16) 28 ]; second, genes involved in cell cycle control and cell growth [E2F-transcription factor-4 (E2F-4) 29 and CTCF gene 30 ;] and, third, genes related to telomere function and hence cell senescence and cell immortality [Telomeric repeat binding factor-2 (TRF2) 31,32 ].…”

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confidence: 99%

High‐resolution analysis of 16q22.1 in breast carcinoma using DNA amplifiable probes (multiplex amplifiable probe hybridization technique) and immunohistochemistry

Rakha

Armour

Pinder

et al. 2005

Intl Journal of Cancer

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Loss of the chromosomal material at 16q22.1 is one of the most frequent genetic aberrations found in both lobular and low-grade nonlobular invasive carcinoma of the breast, indicating the presence of a tumour suppressor gene (TSG) at this region in these tumours. However, the TSG (s) at the 16q22.1 in the more frequent nonlobular carcinomas is still unknown. Multiplex Amplifiable Probe Hybridisation (MAPH) is a simple, accurate and a high-resolution technique that provides an alternative approach to DNA copy-number measurement. The aim of our study was to examine the most likely candidate genes at 16q22.1 using MAPH assay combined with protein expression analysis by immunohistochemistry. We identified deletion at 16q22.1 that involves some or all of these genes. We also noticed that the smallest region of deletion at 16q22.1 could be delineated to a 3 Mb region centromeric to the P-cadherin gene. Apart from the correlation between E-cadherin protein expression and its gene copy number, no correlation was detected between the expression of E2F-4, CTCF, TRF2 or P-cadherin with their gene's copy number. In the malignant tissues, no significant loss or decrease of protein expression of any gene other than E-cadherin was seen in association with any specific tumour type. No expression of VE-cadherin or Ksp-cadherin was detected in the normal and/or malignant tissues of the breast in these cases. However, there was a correlation between increased nuclear expression of E2F-4 and tumours with higher histological grade (p ‫؍‬ 0.04) and positive lymph node disease (p ‫؍‬ 0.02), suggesting that it may have an oncogenic rather than a tumour suppressor role. The malignant breast tissues also showed abnormal cytoplasmic cellular localisation of CTCF, compared to its expression in the normal parenchymal cells. In conclusion, we have demonstrated that MAPH is a potential technique for assessment of genomic imbalances in malignant tissues. Although our results support E-cadherin as the TSG in invasive lobular carcinoma, they argue against the candidacy of E2F-4, CTCF, TRF2, P-cadherin, Ksp-cadherin and VE-cadherin as TSGs in breast cancer.

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High-Resolution Integrated Map Encompassing the Breast Cancer Loss of Heterozygosity Region on Human Chromosome 16q22.1

Cited by 14 publications

References 42 publications

Cloning and Characterization of MDDX28, a Putative DEAD-box Helicase with Mitochondrial and Nuclear Localization

Cloning and Characterization of MDDX28, a Putative DEAD-box Helicase with Mitochondrial and Nuclear Localization

Single‐cell gel electrophoresis (the comet assay): Loops or fragments?

High‐resolution analysis of 16q22.1 in breast carcinoma using DNA amplifiable probes (multiplex amplifiable probe hybridization technique) and immunohistochemistry

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