Somatic genomic variations in extra-embryonic tissues

In the mature chorion, one of the membranes that exist during pregnancy between the developing fetus and mother, human placental cells form highly specialized tissues composed of mesenchyme and floating or anchoring villi. Using fluorescence in situ hybridization, we found that human invasive cytotrophoblasts isolated from anchoring villi or the uterine wall had gained individual chromosomes; however, chromosome losses were detected infrequently. With chromosomes gained in what appeared to be a chromosome-specific manner, more than half of the invasive cytotrophoblasts in normal pregnancies were found to be hyperdiploid. Interestingly, the rates of hyperdiploid cells depended not only on gestational age, but were strongly associated with the extraembryonic compartment at the fetal-maternal interface from which they were isolated. Since hyperdiploid cells showed drastically reduced DNA replication as measured by bromodeoxyuridine incorporation, we conclude that aneuploidy is a part of the normal process of placentation potentially limiting the proliferative capabilities of invasive cytotrophoblasts. Thus, under the special circumstances of human reproduction, somatic genomic variations may exert a beneficial, anti-neoplastic effect on the organism.     

Localization of glutamate in the human retina during early prenatal development

In this study we have localized glutamate (GLU) in fetal (14–25 weeks gestation, Wg) human retinas by immunohistochemistry. At 14 Wg, GLU-immunoreactivity (IR) was localized only in the central part of retina, showing a prominently labelled nerve fiber layero A few ganglion cells and displaced amacrine cells were very weakly labelled. At 17 Wg, GLU was localized conspicuously in many ganglion cells, displaced amacrine cells, some amacrine cells and the prospective photoreceptor cell bodies in the neuroepithelial layero With progressive development at 20 and 25 Wg, the IR for GLU was found additionally in the Müller cell endfeet, some bipolar cells as well as in the horizontal cells that were aligned in a row along the outer border of the inner nuclear layer of the central retinao The photoreceptor cell bodies in the outer nuclear layer were also prominently immunopositive for GLU. The developmental distribution of GLU in the human retina tends to indicate that it plays an important role in the differentiation and maturation of retinal neurons.     

Pathology of amniogenesis in the early prenatal period of human development

Morphological and, in a number of cases, cytogenetical investigation has been performed in 420 intact embryonal sacs and in embryos 7-8-week-old, obtained at spontaneous abortions (272) and at tubal pregnancy (148). Among these cases 202 (48.1%) intact empty embryonal sacs, 75 (17.9%) embryos with panorganodysplasia, 25 (6%) embryos with isolated developmental defects and 118 (28%) phenotypically normal embryos have been revealed. Pathology of amniogenesis such as aplasia or hypoplasia of the amniotic cavity is noted in 136 (32.4%) cases. Among 75 embryos with panorganodysplasia anomalies such as hypoplasia of the amniotic cavity in combination with a partial extra-amniotic++ position of the embryos in exocelom (10.7%), aplasia (5.3%) or hypoplasia (17.3%) amniotic peduncle is present in 43 (57.3%) observations. Out of 40 such cases at spontaneous abortions, cytogenetically investigated, in 27 (67.5%) chromosomal disorders (tetraploidy, triploidy, autosomal trisomy and monosomy) are revealed. Aplasia and hypoplasia of the amniotic cavity are considered as pathology of histogenesis at the tissue stage of the early human ontogenesis, that most evidently occurs as a result of asplasia, destruction or anomaly of embryoblast during the first phase of gastrulation on the 7th-11th day of the intrauterine development.     

Expression of different liver cell markers during the early prenatal human development

The expression of the liver cell markers, vimentin, desmin, cytokeratins 7, 18, 19, and stem cell markers CD34 and Bcl-2 in the early stages of the human prenatal development was studied. Desmin was revealed in sinusoidal liver cells between 3.5 and 12 weeks of gestation; in mesenchymal cells of ventral mesentery and hepatoblasts it was detected at the 4–7th weeks of gestation. During the hepatic period of hemopoiesis, desmin-positive sinusoidal cells were located close to blood cells. So-called “cholangio-” cytokeratins 7 and 19 displayed different expression patterns. Cytokeratin 7 was found only in cholangiocytes, and cytokeratin 19 in hepatoblasts until 15–16 weeks of prenatal development. Mesenchymal cells of the ventral mesentery expressed cytokeratins 18 and 19 more than hepatoblasts at the 4–7th weeks of gestation. Bcl-2 was seen in the same period in most sinusoidal and mesenchymal cells of the ventral mesentery. CD34 positive cells were detected in liver sinusoids between the 4th and 9th weeks of gestation but probably they are not progenitors of hepatocytes during embryonic development. Ventral mesentery mesenchyma was negative for CD34. These results let us hypothesize that hepatocytes and cholangiocytes may arise from different embryonic sources: cholangyocytes derive only from duodenal epithelial cells, while hepatoblasts develop most likely with the participation of mesenchymal cells.     

Changes in bilirubins in human prenatal development.

1. A densitometric method has been developed for the quantification of azodipyrroles derived from dog bile pigments treated with diazotized ethyl anthranilate. 2. This method was used to estimate the bilirubins in bile and meconium from foetuses of 14-36 weeks gestation. 3. The proportion of the bilirubins in foetal bile changed during gestation. (a) No bile pigments were found until 14 weeks. (b) Between 14 and 15 weeks bilirubin-IX beta was the only bile pigment detected. (c) At 16-17 weeks some unconjugated bilirubin-IX alpha was found in the bile, but up to 20 weeks bilirubin-IX beta was the predominant bilirubin in the bile. (d) At about 20 weeks glucose, xylose, and an unidentified bilirubin-IX alpha monoconjugate were found in the bile. (e) Between 20 and 23 weeks bilirubin-IX alpha glucuronide appeared in the bile. (f) At 30 weeks monoconjugates of bilirubin-IX alpha were the predominant bilirubins in the bile. (g) Only in full-term foetuses was bilirubin-IX alpha monoglucuronide the major bilirubin derivative.     

Synapses of the human brain in early prenatal ontogeny

Synaptogenesis in presumptive cerebral cortex was studied in 7-8 week human embryos by electron microscopy. The first synapses in the regions studied appeared in 7-week embryos. These synapses were detected only in the marginal zone of the developing human cerebral cortex, where they were localized on the somas and processes of the young Cajal-Retzius' neurons. A functional role of early embryonic synaptogenesis in the developing human cerebral cortex is suggested.     

Somatic genome variations in health and disease

It is hard to imagine that all the cells of the human organism (about 10(14)) share identical genome. Moreover, the number of mitoses (about 10(16)) required for the organism's development and maturation during ontogeny suggests that at least a proportion of them could be abnormal leading, thereby, to large-scale genomic alterations in somatic cells. Experimental data do demonstrate such genomic variations to exist and to be involved in human development and interindividual genetic variability in health and disease. However, since current genomic technologies are mainly based on methods, which analyze genomes from a large pool of cells, intercellular or somatic genome variations are significantly less appreciated in modern bioscience. Here, a review of somatic genome variations occurring at all levels of genome organization (i.e. DNA sequence, subchromosomal and chromosomal) in health and disease is presented. Looking through the available literature, it was possible to show that the somatic cell genome is extremely variable. Additionally, being mainly associated with chromosome or genome instability (most commonly manifesting as aneuploidy), somatic genome variations are involved in pathogenesis of numerous human diseases. The latter mainly concerns diseases of the brain (i.e. autism, schizophrenia, Alzheimer's disease) and immune system (autoimmune diseases), chromosomal and some monogenic syndromes, cancers, infertility and prenatal mortality. Taking into account data on somatic genome variations and chromosome instability, it becomes possible to show that related processes can underlie non-malignant pathology such as (neuro)degeneration or other local tissue dysfunctions. Together, we suggest that detection and characterization of somatic genome behavior and variations can provide new opportunities for human genome research and genetics.     

Major genomic mitochondrial lineages delineate early human expansions

Background  

The phylogeographic distribution of human mitochondrial DNA variations allows a genetic approach to the study of modern Homo sapiens dispersals throughout the world from a female perspective. As a new contribution to this study we have phylogenetically analysed complete mitochondrial DNA(mtDNA) sequences from 42 human lineages, representing major clades with known geographic assignation.     

Responses to lightness variations in early human visual cortex

Lightness is the apparent reflectance of a surface, and it depends not only on the actual luminance of the surface but also on the context in which the surface is viewed [1-10]. The cortical mechanisms of lightness processing are largely unknown, and the role of early cortical areas is still a matter of debate [11-17]. We studied the cortical responses to lightness variations in early stages of the human visual system with functional magnetic resonance imaging (fMRI) while observers were performing a demanding fixation task. The set of dynamically presented visual stimuli included the rectangular version of the classic Craik-O'Brien stimulus [3, 18, 19] and a variant that led to a weaker lightness effect, as well as a pattern with actual luminance variations. We found that the cortical activity in retinotopic areas, including the primary visual cortex (V1), is correlated with context-dependent lightness variations.     

PTEN-mediated Akt activation in human neocortex during prenatal development

Akt is a crucial factor for cell survival and migration. Phosphatase and tensin (PTEN) negatively regulates cell growth and survival by inhibiting PI3K-dependent signaling. PTEN also blocks Akt phosphorylation, a main downstream molecule of PI3K cascade. So far, no studies have shown PTEN expression and Akt phosphorylation levels in the developing human neocortex. Our hypothesis is that spatial and temporal expression of PTEN is likely to modulate developing human brain cortical modeling by regulating Akt activation. Therefore, our aim is to analyze the expression pattern of PTEN and phospho-Akt levels using immunohistochemistry, Western blot, and semiquantitative analysis in the developing human neocortex (n=13 fetuses from first, second, and third trimesters). PTEN expression was decreased parallel to development, but some cells revealed strong nuclear immunoreactivity in the developing neocortex while the active Akt level was increased. Double immunohistochemistry was performed for proliferating cell nuclear antigen (PCNA)-Tuj1 (as neuronal marker) and PCNA-GFAP (Glial marker) to the subsequent sections of PTEN and Akt-stained slides. PCNA (+) cells were mostly positive for glial fibrillary acidic protein (GFAP) and correlated with active-Akt immunoreactivity. Our results suggest that Akt-mediated signaling plays an active role in cell migration, survival, and cerebral cortical modeling throughout prenatal life and that PTEN is the most likely protein to regulate this signaling.     

Distribution of N-cadherin in human cerebral cortex during prenatal development

An important subgroup of adhesion molecules is the superfamily of cadherins, which takes part in cell recognition and differentiation during development. To our knowledge only one study describing N-cadherin expression in developing human brain has been performed so far. Our aim is to identify N-cadherin expression to establish a relationship between its expression and function in human cerebral cortex during prenatal development. In the present study, localization and intensity of N-cadherin was investigated in developing cerebral cortex. Fetuses from spontaneous abortions (n=13) were obtained from first, second, and third trimesters. Western blot analysis revealed three bands and the third trimester samples showed the strongest bands for N-cadherin. Cell processes, axon bundles, and some of the developing neurons revealed immunoreactivity for N-cadherin throughout pregnancy. The immunoreactivity increased in the developing neocortex and expanded from the ventricular layer toward the marginal zone as development progressed. Moreover, the immunoreactivity was strong in vascular endothelium during all three trimesters. We conclude that N-cadherin is dynamically related to the organization of cerebral cortex layers during prenatal development. The dynamic expression pattern implicates N-cadherin as a potential regulator of cell migration, axon extension and fasciculation, the establishment of synaptic contacts, and neurovascular angiogenesis in the developing human cerebral cortex.     

Matrix metalloproteinases in early human liver development

Matrix metalloproteinases (MMPs) regulate matrix deposition in tissues. Collagens I, III, and IV are involved in early human liver development. To establish whether MMPs specific for these collagens participate in early human liver development, we localized immunohistochemically MMP-1 and MMP-13 (for collagens I and III) and MMP-2 and MMP-7 (for collagen IV) in the early human liver anlage [6th–10th gestational week (GW)]. MMP-1 was found from the 6th GW onward in hepatocytes and later also in outer limiting plate hepatocytes, early bile ducts, and periportal mesenchymal cells. In the 6th GW, MMP-2 was found only in microvascular endothelium. In the 7th GW, MMP-2 was also detected in hepatocytes. From the 9th GW onward, MMP-2 was detectable in all hepatocytes and erythropoietic, endothelial, and periportal mesenchymal cells. MMP-7 was present in the 6th GW in some hepatocytes and endothelial cells, but from the 7th GW onward, only in hematopoietic cells. MMP-13 was found exclusively in hematopoietic cells. This study has shown that production of MMP -1, MMP-2, MMP-7, and MMP-13 during human liver development already occurs from the 6th GW. At this time-point their substrates are only traces or are not yet present in the tissue. A possible role of MMPs in early liver development is discussed. Accepted: 1 July 1999     

Epigenetic silencing of genomic structural variations

A great amount of copy number variations (CNVs) are identified in the human genome. Most of them are neutral; nevertheless, the role of CNVs in the pathogenesis of hereditary diseases is still significant. Especially, this is important for neuropsychiatric disorders, such as intellectual disability and autism. When analyzing the CNV-associated diseases, the controversial question is to distinguish the pathogenic CNVs among common polymorphic variants and to predict the disease risk in other children of the family. Unfortunately, the mechanisms of phenotypic expression and incomplete penetrance of CNVs remain largely unknown. Currently, incomplete penetrance and variable expressivity of CNVs are attributed mainly to allelic interaction of different genetic variations. However, epigenetic mechanisms of gene expression regulation in the context of structural variation of the genome are poorly explored. It is possible that epigenetic modifications of the genome regions with CNVs may underlie the understanding of ways of phenotypic manifestations of structural variations in the human genome.     

Formation of primary microvessels in the early stages of prenatal human morphogenesis

By means of light and electron microscopy, the most general mechanisms of formation and development of primary blood microvessels in functionally different organs (adenohypophysis, thyroid, thymus, liver, spleen, small and large intestine) have been studied in human embryos 4-8 weeks of age. Ultrastructure of cells in the extra- and intraorganic mesenchyme is described; to the latter belongs the leading role in organization the pathways of the prevascular microcirculation. The primary microvessels are formed as a result of canalization of the intercellular clefts, lining with mesenchymal cells, that gradually transfer into primordial endotheliocytes. Basing on ultrastructural analysis, certain stages of differentiation of protocapillary endotheliocytes have been defined and described in different organs. The change of the prevascular microcirculation into the intraorganic protocapillary bed (the primary blood bed) is an essential and necessary stage of the organogenesis.     

Somatic mosaicism for copy-neutral loss of heterozygosity and DNA copy number variations in the human genome

Background

Somatic mosaicism denotes the presence of genetically distinct populations of somatic cells in one individual who has developed from a single fertilised oocyte. Mosaicism may result from a mutation that occurs during postzygotic development and is propagated to only a subset of the adult cells. Our aim was to investigate both somatic mosaicism for copy-neutral loss of heterozygosity (cn-LOH) events and DNA copy number variations (CNVs) in fully differentiated tissues.

Results

We studied panels of tissue samples (11–12 tissues per individual) from four autopsy subjects using high-resolution Illumina HumanOmniExpress-12 BeadChips to reveal the presence of possible intra-individual tissue-specific cn-LOH and CNV patterns.We detected five mosaic cn-LOH regions >5 Mb in some tissue samples in three out of four individuals. We also detected three CNVs that affected only a portion of the tissues studied in one out of four individuals. These three somatic CNVs range from 123 to 796 kb and are also found in the general population. An attempt was made to explain the succession of genomic events that led to the observed somatic genetic mosaicism under the assumption that the specific mosaic patterns of CNV and cn-LOH changes reflect their formation during the postzygotic embryonic development of germinal layers and organ systems.

Conclusions

Our results give further support to the idea that somatic mosaicism for CNVs, and also cn-LOHs, is a common phenomenon in phenotypically normal humans. Thus, the examination of only a single tissue might not provide enough information to diagnose potentially deleterious CNVs within an individual. During routine CNV and cn-LOH analysis, DNA derived from a buccal swab can be used in addition to blood DNA to get information about the CNV/cn-LOH content in tissues of both mesodermal and ectodermal origin. Currently, the real frequency and possible phenotypic consequences of both CNVs and cn-LOHs that display somatic mosaicism remain largely unknown. To answer these questions, future studies should involve larger cohorts of individuals and a range of tissues.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1916-3) contains supplementary material, which is available to authorized users.