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C-type lectins and human epithelial membrane protein1: Are they new proteins in keratin disorders?  [PDF]
Nilüfer Karadeniz, Thomas Liehr, Kristin Mrasek, Ibrahim A??k, Zuleyha A??k, Nadezda Kosyakova, Hasmik Mkrtchyan
Open Journal of Genetics (OJGen) , 2013, DOI: 10.4236/ojgen.2013.34029
Abstract:

Here we report a family with a clinical spectrum of Pachyonychia Congenita Tarda (PCT) encompassing two generations via a balanced chromosomal translocation between 4q26 and 12p12.3. We discuss the effects of chromosomal translocations on gene expression through involved breakpoints and structural gene abnormalities detected by array CGH. We believe that the family we present gives further insight to the better understanding of molecular and structural basis of keratin disorders, and to the late onset and genetic basis of PCT through the possible role of C-type lectins and human epithelial membrane protein1 (EMP1). Better understanding of the molecular basis of keratin disorders is the foundation for improved diagnosis, genetic counseling and novel therapeutic approaches to overcome the current treatment limitations related to this disease.

Generation of multicolor banding probes for chromosomes of different species
Kosyakova Nadezda,Hamid Ahmed Basheer,Chaveerach Arunrat,Pinthong Krit
Molecular Cytogenetics , 2013, DOI: 10.1186/1755-8166-6-6
Abstract: Background The multicolor banding (MCB/mBAND) technique provides a unique opportunity to characterize intrachromosomal rearrangements and to determine chromosomal breakpoints. Until recently, MCB probes have only been available for human and some murine chromosomes. Generation of MCB probes for chromosomes of other species, useful and required in many cytogenetics research fields, was limited by technical difficulties. MCB probes are established by chromosome microdissection followed by whole genomic DNA amplification. However, unambiguous identification of the target chromosome is required for MCB-probe establishment. Previously proposed protocols suggested G-banding staining or preliminary FISH with whole chromosome paints (WCP) as methods to identify the chromosome of interest. Results Here we present a complete workflow for MCB probe generation for those cases and species where chromosome morphology is too challenging to recognize target chromosomes by conventional methods and where WCP probes are not available. The workflow was successfully applied for murine chromosomes that are difficult to identify unambiguously. Additionally, we showed that glass-needle based microdissection enables establishment of a whole set of WCP paints by microdissection of individual chromosomes of a single metaphase Conclusions The present method can be applied for generation of whole or region-specific DNA probes for species, where karyotyping of G-banded chromosomes is challenging due to similar chromosome morphology and/or chromosome banding patterns.
The hierarchically organized splitting of chromosomal bands for all human chromosomes
Nadezda Kosyakova, Anja Weise, Kristin Mrasek, Uwe Claussen, Thomas Liehr, Heike Nelle
Molecular Cytogenetics , 2009, DOI: 10.1186/1755-8166-2-4
Abstract: Here we present for the first time the hierarchically organized splitting of chromosomal bands in their sub-bands for all human chromosomes. To do this, array-proved multicolor banding (aMCB) probe-sets for all human chromosomes were applied to normal metaphase spreads of three different G-band levels. We confirmed for all chromosomes to be a general principle that only Giemsa-dark bands split into dark and light sub-bands, as we demonstrated previously by chromosome stretching. Thus, the biological band splitting is in > 50% of the sub-bands different than implemented by the ISCN nomenclature suggesting also a splitting of G-light bands. Locus-specific probes exemplary confirmed the results of MCB.Overall, the present study enables a better understanding of chromosome architecture. The observed difference of biological and ISCN band-splitting may be an explanation why mapping data from human genome project do not always fit the cytogenetic mapping.The biological nature of hierarchically organized splitting of bands of human chromosomes remained an enigma since the first banding methods were described in 1970 and 1971. The technique introduced by Lore Zech in Caspersson's laboratory involved quinacrine mustard (Q-banding) and fluorescence microscopy [1], while other used Giemsa (G-banding) [2,3]. Though several methods producing chromosome bands were developed later, G-banding became the one most widely used. A uniform system of human chromosomal nomenclature, which allowed to design not only individual chromosomes but also chromosome regions and bands, was proposed for the first time in 1971 at the Fourth International Congress of Human Genetics in Paris [4], later it developed into the document entitled "An International System for Human Cytogenetic Nomenclature", the last edition of which was published in 2005 [5]. Although recently evolved molecular cytogenetic techniques [6-8] and array-CGH [9] allow precise characterization of chromosomal abnormalities, analys
Small supernumerary marker chromosomes (sSMC) in humans; are there B chromosomes hidden among them
Thomas Liehr, Kristin Mrasek, Nadezda Kosyakova, Caroline Ogilvie, Joris Vermeesch, Vladimir Trifonov, Nikolai Rubtsov
Molecular Cytogenetics , 2008, DOI: 10.1186/1755-8166-1-12
Abstract: Here we provide first evidence and discuss, that among sSMC B-chromosomes might be hidden. We present two potential candidates which may already be, or may in future evolve into B chromosomes in human: (i) sSMC cases where the marker is stainable only by DNA derived from itself; and (ii) acrocentric-derived inverted duplication sSMC without associated clinical phenotype. Here we report on the second sSMC stainable exclusively by its own DNA and show that for acrocentric derived sSMC 3.9× more are familial cases than reported for other sSMC.The majority of sSMC are not to be considered as B-chromosomes. Nonetheless, a minority of sSMC show similarities to B-chromosomes. Further studies are necessary to come to final conclusions for that problem.Small supernumerary marker chromosomes (sSMC) are a major clinical problem, especially when detected prenatally during banding cytogenetic analysis. sSMC have been defined as structurally abnormal chromosomes that cannot be identified or characterized unambiguously by conventional banding cytogenetics alone, and are (in general) equal in size or smaller than a chromosome 20 of the same metaphase spread. As they are too small to be considered for their chromosomal origin by traditional banding techniques; molecular cytogenetic techniques (including array based comparative genomic hybridization) are needed for their characterization [1]. The risk for an abnormal phenotype in prenatally ascertained de novo cases with sSMC is given as ~13%. This has been refined to 7% (for sSMC from chromosome 13, 14, 21 or 22) and 28% (for all non-acrocentric autosomes) [2] and recently been suggested to be 30% for all sSMC carriers [3]. Lately familial sSMC turned out to be transmitted predominantly via the maternal line [4]. With a newborn rate of 0.044% for all sSMC there are presently ~2.7 × 106 carriers of sSMC worldwide [3]. However, still the statement of Paoloni-Giacobino et al. (1998) [5] is valid, i.e. that cases with a de novo sSMC are
Cross-species chromosome painting tracks the independent origin of multiple sex chromosomes in two cofamiliar Erythrinidae fishes
Marcelo B Cioffi, Antonio Sánchez, Juan A Marchal, Nadezda Kosyakova, Thomas Liehr, Vladimir Trifonov, Luiz AC Bertollo
BMC Evolutionary Biology , 2011, DOI: 10.1186/1471-2148-11-186
Abstract: Our results yield valuable information regarding the origin and evolution of these sex chromosome systems. Our data indicate that these sex chromosomes evolved independently in these two closed related Erythrinidae species. Different autosomes were first converted into a poorly differentiated XY sex pair in each species, and additional chromosomal rearrangements produced both X1X2Y sex systems that are currently present.Our data provide new insights into the origin and evolution of sex chromosomes, which increases our knowledge about fish sex chromosome evolution.Fluorescence in situ hybridization (FISH) using whole chromosome-specific probes (wcp) is an important cytogenetic tool to study the origin and evolution of sex chromosomes in several organisms [1-8]. The diversity of sex-determining mechanisms, as well as the absence of heteromorphic sex chromosomes in many fish species make this group a useful model to study the evolution of vertebrate sex chromosomes [9,10]. However, research involving chromosome painting in fish is rarely performed because it is difficult to obtain the necessary probes. The few available studies are focused on karyotypic [11,12] and sex chromosome evolution [2,5,7,13-15]. The current literature suggests that a variety of sex-determining mechanisms and sex chromosomes may have evolved independently in different fish species.Erythrinidae is a Neotropical fish family that is characterized by species that have a wide variety of chromosomal forms, as well as a wide range of distinct sex chromosomes. The red wolf fish Erythrinus erythrinus (EER) is karyotypically diverse among different populations, with four currently identified karyomorphs (A to D) [16]. Karyomorph A is characterized by 2n = 54 chromosomes that have very similar karyotypic structures and the absence of heteromorphic sex chromosomes. Karyomorphs B, C and D share an X1X1X2X2/X1X2Y sex chromosome system, but they can differ in the diploid number and chromosomal morphology. Kar
Molecular cytogenetic characterisation of a mosaic add(12)(p13.3) with an inv dup(3)(q26.31 → qter) detected in an autistic boy
Isabel M Carreira, Joana B Melo, Carlos Rodrigues, Liesbeth Backx, Joris Vermeesch, Anja Weise, Nadezda Kosyakova, Guiomar Oliveira, Eunice Matoso
Molecular Cytogenetics , 2009, DOI: 10.1186/1755-8166-2-16
Abstract: We present the results of the molecular cytogenetic characterization of an unbalanced mosaic karyotype consisting of mos 46,XY,add(12)(p13.3) [56]/46,XY [44] in a previously described 11 years old autistic boy, re-evaluated at adult age. The employment of fluorescence in situ hybridization (FISH) and multicolor banding (MCB) techniques identified the extra material on 12p to be derived from chromosome 3, defining the additional material on 12p as an inv dup(3)(qter → q26.3::q26.3 → qter). Subsequently, array-based comparative genomic hybridization (aCGH) confirmed the breakpoint at 3q26.31, defining the extra material with a length of 24.92 Mb to be between 174.37 and 199.29 Mb.This is the thirteenth reported case of inversion-duplication 3q, being the first one described as an inv dup translocated onto a non-homologous chromosome. The mosaic terminal inv dup(3q) observed could be the result of two proposed alternative mechanisms. The most striking feature of this case is the autistic behavior of the proband, a characteristic not shared by any other patient with tetrasomy for 3q26.31 → 3qter. The present work further illustrates the advantages of the use of an integrative cytogenetic strategy, composed both by conventional and molecular techniques, on providing powerful information for an accurate diagnosis. This report also highlights a chromosome region potentially involved in autistic disorders.According to the orientation of the duplicated segment, duplications may be classified either as tandem or inverted, being the last usually associated with deletion of the distal region of the duplicated chromosome [1]. The best studied cases of inverted duplications (inv dup) are the inv dup(8p) [2,3] and bisatellited inv dup(15) [4], which are usually non-mosaic. In contrast, mosaic inverted duplications are derived from different post-zygotic mechanisms for which various possible origins have been proposed [5-7]. There is also a particular subset of inv dup in which the
Early Embryonic Chromosome Instability Results in Stable Mosaic Pattern in Human Tissues
Hasmik Mkrtchyan,Madeleine Gross,Sophie Hinreiner,Anna Polytiko,Marina Manvelyan,Kristin Mrasek,Nadezda Kosyakova,Elisabeth Ewers,Heike Nelle,Thomas Liehr,Marianne Volleth,Anja Weise
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0009591
Abstract: The discovery of copy number variations (CNV) in the human genome opened new perspectives on the study of the genetic causes of inherited disorders and the aetiology of common diseases. Here, a single-cell-level investigation of CNV in different human tissues led us to uncover the phenomenon of mitotically derived genomic mosaicism, which is stable in different cell types of one individual. The CNV mosaic ratios were different between the 10 individuals studied. However, they were stable in the T lymphocytes, immortalized B lymphoblastoid cells, and skin fibroblasts analyzed in each individual. Because these cell types have a common origin in the connective tissues, we suggest that mitotic changes in CNV regions may happen early during embryonic development and occur only once, after which the stable mosaic ratio is maintained throughout the differentiated tissues. This concept is further supported by a unique study of immortalized B lymphoblastoid cell lines obtained with 20 year difference from two subjects. We provide the first evidence of somatic mosaicism for CNV, with stable variation ratios in different cell types of one individual leading to the hypothesis of early embryonic chromosome instability resulting in stable mosaic pattern in human tissues. This concept has the potential to open new perspectives in personalized genetic diagnostics and can explain genetic phenomena like diminished penetrance in autosomal dominant diseases. We propose that further genomic studies should focus on the single-cell level, to better understand the aetiology of aging and diseases mediated by somatic mutations.
Correction: Characterization of a prenatally assessed de novo supernumerary minute ring chromosome 20 in a phenotypically normal male
Sofia Kitsiou-Tzeli, Emmanouil Manolakos, Magdalini Lagou, Katerina Anagnostopoulou, Maria Kontodiou, Nadezda Kosyakova, Elisabeth Ewers, Anja Weise, Antonios Garas, Sandro Orru, Thomas Liehr, Aikaterini Metaxotou
Molecular Cytogenetics , 2009, DOI: 10.1186/1755-8166-2-8
Abstract: The authors declare that they have no competing interests.SKT conceived of the study and participated in its design and coordination. EM performed the cytogenetic studies and participated in its design and coordination. ML and MK participated in the cytogenetic analysis. NK, EE and AW participated in the molecular cytogenetic analysis. AG performed the ultrasonography of the pregnant woman. SO and KA performed the molecular analysis for uniparental disomy. TL was responsible for the molecular cytogenetic studies and participated in the drafting of the manuscript. AM participated in the design and coordination of the study and participated in the drafting of the manuscript. All authors read and approved the final manuscript.
A small supernumerary marker chromosome present in a Turner syndrome patient not derived from X- or Y-chromosome: a case report
Frenny Sheth, Elisabeth Ewers, Nadezda Kosyakova, Anja Weise, Jayesh Sheth, Manisha Desai, Joris Andrieux, Joris Vermeesch, Ahmed B Hamid, Monika Ziegler, Thomas Liehr
Molecular Cytogenetics , 2009, DOI: 10.1186/1755-8166-2-22
Abstract: Here we report the first case of an sSMC found in Turner syndrome karyotypes (sSMCT) derived from chromosome 14 in a Turner syndrome patient. According to cytogenetic and molecular cytogenetic characterization the karyotype was 46,X,+del(14)(q11.1). The present case is the third Turner syndrome case with an sSMCT not derived from the X- or the Y-chromosome.More comprehensive characterization of such sSMCT might identify them to be more frequent than only ~0.6% in Turner syndrome cases according to available data.Small supernumerary marker chromosomes (sSMC) [1] can be observed in a numerically normal 'basic karyotype', but also in numerically abnormal one like in a 'Turner-syndrome karyotype' (=sSMCT). At present 528 such cases with an sSMCT are reported [2,3]. sSMCT are very rare in the common population (1:100000 [2]) - however, they can be observed 45 and even 60 times more frequent in infertile and developmentally and/or mentally retarded patients, respectively. The majority of sSMCT(X) form ring-chromosomes, while most sSMCT(Y) are inverted duplicated/isodicentric ones. When a mos 45,X/46,X,der(Y) or 45,X/46,XY is characterized it is important to counsel the patient concerning a possibility of gonadoblastoma and a preventive removal of gonadal tissue. In this connection, the necessity to apply molecular approaches for detection of cryptic 45,X/46,XY mosaicism is discussed, as a direct relationship between percentage of cells exhibiting a 45,X karyotype and patients phenotype does not exist. Additionally, it is a well-known fact that in a karyotype of mos 45,X/46,X,der(X) it is important to test for the ability of the der(X) to be inactivated, i.e. to test for the presence of the XIST-gene [2].Even though sSMCT derive in >99% of the cases from one of the gonosomes, there are also two previous exceptional reports on sSMCT derived from one of the autosomes [4,5].Here we report the third case with an sSMCT originating not from a gonosome but the first one proven to
Two siblings with immunodeficiency, facial abnormalities and chromosomal instability without mutation in DNMT3B gene but liability towards malignancy; a new chromatin disorder delineation?
Anna Polityko, Olga Khurs, Natalia Rumyantseva, Irina Naumchik, Nadezda Kosyakova, Holger T?nnies, Karl Sperling, Heidemarie Neitzel, Anja Weise, Thomas Liehr
Molecular Cytogenetics , 2010, DOI: 10.1186/1755-8166-3-5
Abstract: We report on a family in which the unrelated spouses had two female siblings sharing similar phenotypic features resembling ICF-syndrome, i.e. congenital abnormalities, immunodeficiency, developmental delay and high level of chromosomal instability, including high frequency of centromeric/pericentromeric rearrangements and breaks, chromosomal fragments despiralization or pulverization. However, mutations in DNMT3B could not be detected.The discovery of a new so-called 'chromatin disorder' is suggested. Clinical, molecular genetic and cytogenetic characteristics are reported and compared to other 'chromatin disorders'.Several human diseases which are characterized by alterations or modification of chromatin structure caused by changes of methylation pattern are considered as so-called 'chromatin disorders' [1]. Their delineation and the encoding of mechanisms underlying these genetic syndromes is one of the ways to understanding the global principles of functioning of genomic DNA and chromatin in human. ICF syndrome (for immunodeficiency, centromere instability and facial anomalies; OMIM #242860) belongs to the aforementioned disorders and is a rare recessive disease caused by mutations of the gene DNMT3B that encodes the 'de novo DNA-methyltransferase 3B' [2-4]. Patients with ICF syndrome demonstrate immunodeficiency, facial anomalies, mental retardation and developmental delay. The main clinical feature is reduced serum immunoglobulin levels that lead to death due to severe recurrent infections, often before adulthood. The typical cytogenetic markers of ICF syndrome are distinctive 'undercondensation' of heterochromatic segments of chromosomes 1, 9, and 16 and multibranched configurations of those. The chromosomal instability observable in PHA-stimulated lymphocytes correlates with a severe hypomethylation of the classical satellites 2 and other genomic sequences such as alpha satellites, the centromeric component of constitutive heterochromatin 3, Alu sequences D4
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