Molecular Mechanisms of Syndromic Cryptorchidism: Data Synthesis of 50 Studies and Visualization of Gene-Disease Network.

Background: Cryptorchidism is one of the most frequent congenital birth defects in male children and is present in 2-4% of full-term male births. It has several possible health effects including reduced fertility, increased risk for testicular neoplasia, testicular torsion, and psychological consequences. Cryptorchidism is often diagnosed as comorbid; copresent with other diseases. It is also present in clinical picture of several syndromes. However, this field has not been systematically studied. The aim of the present study was to catalog published cases of syndromes which include cryptorchidism in the clinical picture and associated genomic information. Methods: The literature was extracted from Public/Publisher MEDLINE and Web of Science databases, using the keywords including: syndrome, cryptorchidism, undescended testes, loci, and gene. The obtained data was organized in a table according to the previously proposed standardized data format. The results of the study were visually represented using Gephi and karyotype view. Results: Fifty publications had sufficient data for analysis. Literature analysis resulted in 60 genomic loci, associated with 44 syndromes that have cryptorchidism in clinical picture. Genomic loci included 38 protein-coding genes and 22 structural variations containing microdeletions and microduplications. Loci, associated with syndromic cryptorchidism are located on 16 chromosomes. Visualization of retrieved data is presented in a gene-disease network. Conclusions: The study is ongoing and further studies will be needed to develop a complete catalog with the data from upcoming publications. Additional studies will also be needed for revealing of molecular mechanisms associated with syndromic cryptorchidism and revealing complete diseasome network.

Expression of estrogen receptor 1 and progesterone receptor in primary goat mammary epithelial cells.

The exact role and sensitivity of cells to estrogen and progesterone mediated through the steroid receptors during lactation is not known. Expression of estrogen receptor 1 (ESR1) and progesterone receptor (PGR) was quantified in mammary tissue-derived primary goat mammary epithelial cells (pgMECs) to determine the influence of donor tissue physiology (lactating and juvenile) and cell culture growth conditions (basal and lactogenic) on ESR1 and PGR expression in the derived cells. Relative messenger RNA (mRNA) levels for both receptors were the highest in cell lines derived from mammary tissue of juvenile goats. Maintaining pgMECs in lactogenic conditions resulted in up-regulation of ESR1 (1.36- to 12.35-fold) and in down-regulation of PGR (-2.53- to -3.62-fold), compared to basal conditions. Based on Western blotting analysis we suggest that the differences in mRNA expression are translated to the protein level. We suggest that differential expression in lactating conditions is correlated with terminal differentiation of the pgMECs. Double immunostainings showed that estrogen receptor alpha (ER-α) positive cells do not exclusively belong to the luminal lineage and that ER-α and PGR can be expressed individually or co-expressed in the pgMECs. The derived primary cultures/lines in early passages are hormone-responsive and represent a useful surrogate for mammary tissue in research experiments.

Lineage-specific markers of goat mammary cells in primary culture.

The objective of this study was morphological and functional characterization of cells from the primary cell culture developed from lactating goat mammary gland, focusing on distribution of lineage-specific markers. Primary cells were grown on a thin layer of basement membrane matrix, a growth surface that resembles in vivo conditions. The cells in adherent conditions rapidly proliferated and showed cobblestone morphology, typical for epithelial cells. Under non-adherent conditions, goat mammary cells formed spherical, acini-like structures that resembled alveoli of lactating mammary gland. Immunofluorescence and RNA sequencing were employed to determine expression of lineage-specific markers. Presence of markers cytokeratin 14 and 18, integrin alpha 6, vimentin, estrogen receptor, smooth muscle actin, and cytokeratin 5 was detected using immunofluorescence. The greatest expression was observed for markers typical for myoepithelial cells, luminal cells, and mesenchymal cells. Based on our characterization, we can conclude that established primary culture was composed of mainly epithelial and stromal cells. These findings demonstrate that primary mammary cells express some of the most important functional and biochemical markers needed for their characterization. First, they grow in the characteristic cobblestone morphology of epithelial cells. Second, they express classical cytoplasmic network of cytokeratin fibers. Third, they express markers typical of mammary parenchyma and stroma. The established cell culture represents a good in vitro model for studies of mammary gland development, differentiation, and lactation. We suggest that herein revealed lineage markers are suitable for characterization of mammary cells of goat and possibly other mammalian species.

Shared epitopes of avian immunoglobulin light chains.

Like all jawed vertebrates, birds (Aves) also produce antibodies i.e. immunoglobulins (Igs) as a defence mechanism against pathogens. Their Igs are composed of two identical heavy (H) and light (L) chains which are of lambda isotype. The L chain consists of variable (VL), joining (JL) and constant (CL) region. Using enzyme immunoassays (EIA) and two monoclonal antibodies (mAbs) (3C10 and CH31) to chicken L chain, we analysed their cross-reactivity with sera from 33 avian species belonging to nine different orders. Among Galliformes tested, mAbs 3C10 and CH31 reacted with L chains of chicken, turkey, four genera of pheasants, tragopan and peafowl, but not with sera of grey partridge, quail and Japanese quail. Immunoglobulins of guinea-fowl reacted only with mAb 3C10. Both mAbs reacted also with the L chain of Eurasian griffon (order Falconiformes) and domestic sparrow (order Passeriformes). Sera from six other orders of Aves did not react with either of the two mAbs. EIA using mAbs 3C10 and CH31 enabled detection of antibodies to major avian pathogens in sera of chickens, turkeys, pheasants, peafowl, Eurasian griffon and guinea-fowl (only with mAb 3C10). The N-terminal amino acid sequence of pheasant L chain (19 residues) was identical to that of chicken. Sequences of genes encoding the L chain constant regions of pheasants, turkey and partridge were determined and deposited in the public database (GenBank accession numbers: FJ 649651, FJ 649652 and FJ 649653, respectively). Among them, amino acid sequence of pheasants is the most similar to that of chicken (97% similarity), whereas those of turkey and partridge have greater similarity to each other (89%) than to any other avian L chain sequence. The characteristic deletion of two amino acids which is present in the L chain constant region in Galliformes has been most likely introduced to their L chain after their divergence from Anseriformes.

Isolation, characterization and differentiation of cells expressing pluripotent/multipotent markers from adult human ovaries.

Pluripotent stem cells are still generally accepted not to exist in adult human ovaries, although increasing studies confirm the presence of pluripotent/multipotent stem cells in adult mammalian ovaries, including those of humans. The aim of this study is to isolate, characterize and differentiate in vitro stem cells that originate from the adult human ovarian cortex and that express markers of pluripotency/multipotency. After enzymatic degradation of small ovarian cortex biopsies retrieved from 18 women, ovarian cell cultures were successfully established from 17 and the formation of cell colonies was observed. The presence of cells/colonies expressing some markers of pluripotency (alkaline phosphatase, surface antigen SSEA-4, OCT4, SOX-2, NANOG, LIN28, STELLA), germinal lineage (DDX4/VASA) and multipotency (M-CAM/CD146, Thy-1/CD90, STRO-1) was confirmed by various methods. Stem cells from the cultures, including small round SSEA-4-positive cells with diameters of up to 4 µm, showed a relatively high degree of plasticity. We were able to differentiate them in vitro into various types of somatic cells of all three germ layers. However, these cells did not form teratoma when injected into immunodeficient mice. Our results thus show that ovarian tissue is a potential source of stem cells with a pluripotent/multipotent character for safe application in regenerative medicine.

Catalog of microRNA seed polymorphisms in vertebrates.

MicroRNAs (miRNAs) are a class of non-coding RNA that plays an important role in posttranscriptional regulation of mRNA. Evidence has shown that miRNA gene variability might interfere with its function resulting in phenotypic variation and disease susceptibility. A major role in miRNA target recognition is ascribed to complementarity with the miRNA seed region that can be affected by polymorphisms. In the present study, we developed an online tool for the detection of miRNA polymorphisms (miRNA SNiPer) in vertebrates (http://www.integratomics-time.com/miRNA-SNiPer) and generated a catalog of miRNA seed region polymorphisms (miR-seed-SNPs) consisting of 149 SNPs in six species. Although a majority of detected polymorphisms were due to point mutations, two consecutive nucleotide substitutions (double nucleotide polymorphisms, DNPs) were also identified in nine miRNAs. We determined that miR-SNPs are frequently located within the quantitative trait loci (QTL), chromosome fragile sites, and cancer susceptibility loci, indicating their potential role in the genetic control of various complex traits. To test this further, we performed an association analysis between the mmu-miR-717 seed SNP rs30372501, which is polymorphic in a large number of standard inbred strains, and all phenotypic traits in these strains deposited in the Mouse Phenome Database. Analysis showed a significant association between the mmu-miR-717 seed SNP and a diverse array of traits including behavior, blood-clinical chemistry, body weight size and growth, and immune system suggesting that seed SNPs can indeed have major pleiotropic effects. The bioinformatics analyses, data and tools developed in the present study can serve researchers as a starting point in testing more targeted hypotheses and designing experiments using optimal species or strains for further mechanistic studies.

Identification of goat mammary stem/progenitor cells.

Goat mammary gland epithelial cells have been used to establish primary and permanent cell lines, but to date, no data have been available regarding mammary stem cells (MaSCs) in this species. The detection and characterization of goat MaSCs is an important task for a better understanding of the cyclic character of mammary gland development, which will also offer the potential for manipulation of lactation yield and persistency. The objective of the present study was to demonstrate that a subpopulation of goat MaSCs resides in the goat mammary gland. Mammary tissue from lactating Saanen goats (Capra hircus) was dissociated and processed to a single-cell suspension. Using an in vitro colony-forming assay, we demonstrated that distinct colony types, which expressed specific lineage markers, arose from unipotent progenitors. Using two different growth media, we showed that the frequencies of caprine clonogenic progenitors differed according to growth conditions. Goat epithelial cells were transplanted under the kidney capsule of nonobese diabetic/severe combined immunodeficient (NOD/SCID) mice, where they formed organized, bilayered structures. Our results indicate the presence of goat MaSCs in the caprine mammary gland. To our knowledge, these data represent the first description of the tissue hierarchy of the goat mammary gland and demonstrate the regenerative potential of adult goat MaSCs.

Variation of vlhA gene in Mycoplasma synoviae clones isolated from chickens.

Mycoplasma synoviae synthesizes haemagglutinin VlhA, which cleaves into the N-terminal part, a lipoprotein MSPB, and a C-terminal part MSPA. Previous studies have shown that the 3'-end of the expressed vlhA gene can recombine with vlhA pseudogenes in a process called gene conversion, but there have been no data about diversification of the expressed vlhA gene in M. synoviae populations replicating in chickens. Following intratracheal inoculation with the M. synoviae strain ULB 02/T6, which showed only minor vlhA gene variation prior to inoculation, we investigated temporal changes in MSPB epitopes defined by monoclonal antibodies (mAbs) 3B4 and 50, as well as diversification of the vlhA gene sequence in M. synoviae populations recovered from chicken tracheas. In cultures isolated 8 and 18 days post inoculation (p.i.), most colonies showed variation of MSPB epitopes for mAbs 3B4 and 50. They also changed 3'-end vlhA gene sequences. Further diversity of the vlhA gene occurred in cultures isolated 8 weeks and 5 months p.i. The vlhA gene sequences from isolated cultures shared only 65 to 80% sequence identity with vlhA gene of the inoculated ULB 02/T6 culture. Notably, in most of those cultures their vlhA gene sequences contained stop codons potentially causing premature terminations of translation. Interestingly, in one culture isolated 8 weeks p.i. (clone T6-8W/IT2A) the 3'-vlhA gene sequence was identical in the last 1140 bases to that of the first vlhA pseudogene positioned the most far (upstream) of the expressed vlhA gene. This is the first demonstration of temporal diversity of the vlhA gene in M. synoviae populations isolated from chicken tracheas.

Epigenetic regulation of microRNAs in cancer: an integrated review of literature.

MicroRNAs (miRNAs) belong to the heterogeneous class of non-coding RNAs (ncRNAs) that regulate the translation and degradation of target mRNAs, and control approximately 30% of human genes. MiRNA genes might be silenced in human tumors (oncomiRs) by aberrant hypermethylation of CpG islands that encompass or lie adjacent to miRNA genes and/or by histone modifications. We performed literature search for research articles describing epigenetically regulated miRNAs in cancer and identified 45 studies that were published between 2006 and 7/2010. The data from those papers are fragmented and methodologically heterogeneous and our work represents first systematic review towards to integration of diverse sets of information. We reviewed the methods used for detection of miRNA epigenetic regulation, which comprise bisulfite genomic sequencing PCR (BSP), bisulfite pyrosequencing, methylation specific PCR (MSP), combined bisulfite restriction analysis (COBRA), methylation sensitive single nucleotide primer extension (Ms-SNuPE), MassARRAY technique and some modifications of those methods. This integrative study revealed 122 miRNAs that were reported to be epigenetically regulated in 23 cancer types. Compared to protein coding genes, human oncomiRs showed an order of magnitude higher methylation frequency (11.6%; 122/1048 known miRNAs). Nearly half, (45%; 55/122) epigenetically regulated miRNAs were associated with different cancer types, but other 55% (67/122) miRNAs were present in only one cancer type and therefore representing cancer-specific biomarker potential. The data integration revealed miRNA epigenomic hot spots on the chromosomes 1q, 7q, 11q, 14q and 19q. CpG island analysis of corresponding miRNA precursors (pre-miRNAs) revealed that 20% (26/133) of epigenetically regulated miRNAs had a CpG island within the range of 5kb upstream, among them 14% (19/133) of miRNAs resided within the CpG island. Our integrative survey and analyses revealed candidate cancer-specific miRNA epigenetic signatures which provide the basis for new therapeutic strategies in cancer by targeting the epigenetic regulation of miRNAs.

Mycoplasma gallisepticum and Mycoplasma synoviae express a cysteine protease CysP, which can cleave chicken IgG into Fab and Fc.

Major poultry pathogens M. gallisepticum and M. synoviae share a gene encoding a putative cysteine protease CysP similar to papain cysteine protease (C1A subfamily). Comparison of the cysP gene sequences of 18 M. synoviae and 10 M. gallisepticum strains sequenced in this study showed polymorphisms, including deletions. Seven M. synoviae strains, including the type strain WVU 1853, had a 39 bp deletion in the 3' end of the cysP gene. In the same cysP region, all M. gallisepticum strains showed a deletion of 66 bp. Immunoblot analysis with specific antibodies demonstrated that M. synoviae strains expressed CysP, which was approximately 65 kDa. Both M. synoviae and M. gallisepticum were able to digest chicken IgG (cIgG). Incubation of cIgG (∼170 kDa) with M. synoviae or M. gallisepticum cells (∼15 h at 37 °C) resulted in a papain-like cleavage pattern of cIgG and fragments corresponding to the antigen-binding fragment of IgG (Fab, ∼45 kDa) and the crystallizable region fragment (Fc) of the IgG heavy chain (dimer of ∼60 kDa). Iodoacetamide (50 mM) prevented cleavage of cIgG by both Mycoplasma species. Following site-directed mutagenesis (eight TGA codons were changed to TGG) the cysP gene of M. synoviae ULB 925 was expressed as a His-tagged protein in a cell-free system. Purified recombinant CysP (rCysP; ∼67 kDa, pI∼8) cleaved cIgG into Fab and Fc fragments. This indicates that CysP is responsible for the cIgG cleavage caused by M. synoviae and, probably, by M. gallisepticum. This is the first evidence to our knowledge that mycoplasmas have enzymes that can cleave the host IgG and indicates a novel strategy used by M. gallisepticum and M. synoviae for prolonged survival despite the antibody response of their host.

Parthenogenetic embryo-like structures in the human ovarian surface epithelium cell culture in postmenopausal women with no naturally present follicles and oocytes.

Little is known about parthenogenesis in the human ovary. What is known is related to patients with teratoma in their medical history. Ovarian surface epithelium (OSE) was often proposed as a source of ovarian stem cells with an embryonic character in the past, and was also termed "germinal epithelium." The aim of this study was to isolate putative stem cells from OSE scrapings, to set up an OSE cell culture, to follow the in vitro oogenesis and possible formation of parthenogenetic embryos in 21 postmenopausal women with no naturally present follicles and oocytes. Small round cells with a bubble-like structure and with a diameter from 2 to 4 microm were isolated from the material obtained by OSE scrapings in all women. They expressed early embryonic developmental markers such as stage-specific embryonic antigen-4 (SSEA-4) surface antigen and Oct-4, Nanog, Sox-2, and c-kit transcription factors. These cells were separated by density gradient centrifugation and grown in vitro, where they proliferated and formed embryoid body-like structures. Their markers of pluripotency such as telomerase activity were decreased during in vitro culture and they did not form teratoma after the injection into SCID mice. Some of them grew intensively and reached a diameter of approximately 20 microm after 5-7 days of culture. In the OSE cell culture, oocyte-like cells developed among them, which reached a diameter up to 95 mum, and expressed Oct-4, c-kit, VASA, and ZP2 transcription markers after 20 days of culture. Some of them expressed a zona pellucida-like structure and rarely germinal vesicle- and polar body-like structures. At the same time, parthenogenetic blastocyst-like structures developed, which expressed transcription markers Oct-4, Sox-2, and Nanog and were normal for chromosomes X, Y, 13, 16, 18, 21, and 22. In conclusion, the discovered cells expressed embryonic stem cell markers, gave rise to embryoid body-, oocyte-, and blastocyst-like structures, and might be involved in the human reproduction and formation of ovarian tumors.