Nicholas P. Anagnou

Improvements in the HbVar database of human hemoglobin variants and thalassemia mutations for population and sequence variation studies

HbVar (http://globin.cse.psu.edu/globin/hbvar/) is a relational database developed by a multi-center academic effort to provide up-to-date and high quality information on the genomic sequence changes leading to hemoglobin variants and all types of thalassemia and hemoglobinopathies. Extensive information is recorded for each variant and mutation, including sequence alterations, biochemical and hematological effects, associated pathology, ethnic occurrence and references. In addition to the regular updates to entries, we report two significant advances: (i) The frequencies for a large number of mutations causing beta-thalassemia in at-risk populations have been extracted from the published literature and made available for the user to query upon. (ii) HbVar has been linked with the GALA (Genome Alignment and Annotation database, available at http://globin.cse.psu.edu/gala/) so that users can combine information on hemoglobin variants and thalassemia mutations with a wide spectrum of genomic data. It also expands the capacity to view and analyze the data, using tools within GALA and the University of California at Santa Cruz (UCSC) Genome Browser.

Novel sources of fetal stem cells: where do they fit on the developmental continuum?

The recent isolation of fetal stem cells from several sources either at the early stages of development or during the later trimesters of gestation, sharing similar growth kinetics and expressing pluripotency markers, provides strong support to the notion that these cells may be biologically closer to embryonic stem cells, actually representing intermediates between embryonic stem cells and adult mesenchymal stem cells, regarding proliferation rates and plasticity features, and thus able to confer an advantage over postnatal mesenchymal stem cells derived from conventional adult sources such as bone marrow. This conclusion has been strengthened by the different pattern of growth potential between the two stage-specific types of sources, as assessed by transcriptomic and proteomic analysis. A series of recent studies regarding the numerous novel features of fetal stem cells has reignited our interest in the field of stem-cell biology and in the possibilities for the eventual repair of damaged organs and the generation of in vitro tissues on biomimetic scaffolds for transplantation. These studies, employing elegant approaches and novel technologies, have provided new insights regarding the nature and the potential of fetal stem cells derived from placenta, amniotic fluid, amnion or umbilical cord. In this update, we highlight the major progression that has occurred in fetal stem-cell biology and discuss the most important areas for future investigation in the field of regenerative medicine.

Genome-wide association study for ulcerative colitis identifies risk loci at 7q22 and 22q13 (IL17REL)

We performed a genome-wide association analysis of 1,897,764 SNPs in 1,043 German ulcerative colitis (UC) cases and 1,703 controls. We discovered new associations at chromosome 7q22 (rs7809799) and at chromosome 22q13 in IL17REL (rs5771069) and confirmed these associations in six replication panels (2,539 UC cases and 5,428 controls) from different regions of Europe (overall study sample Prs7809799 = 8.81 × 10−11 and Prs5771069 = 4.21 × 10−8, respectively).

Y chromosomal haplogroup J as a signature of the post-neolithic colonization of Europe

In order to attain a finer reconstruction of the peopling of southern and central-eastern Europe from the Levant, we determined the frequencies of eight lineages internal to the Y chromosomal haplogroup J, defined by biallelic markers, in 22 population samples obtained with a fine-grained sampling scheme. Our results partially resolve a major multifurcation of lineages within the haplogroup. Analyses of molecular variance show that the area covered by haplogroup J dispersal is characterized by a significant degree of molecular radiation for unique event polymorphisms within the haplogroup, with a higher incidence of the most derived sub-haplogroups on the northern Mediterranean coast, from Turkey westward; here, J diversity is not simply a subset of that present in the area in which this haplogroup first originated. Dating estimates, based on simple tandem repeat loci (STR) diversity within each lineage, confirmed the presence of a major population structuring at the time of spread of haplogroup J in Europe and a punctuation in the peopling of this continent in the post-Neolithic, compatible with the expansion of the Greek world. We also present here, for the first time, a novel method for comparative dating of lineages, free of assumptions of STR mutation rates.

Therapeutic potential of a distinct population of human amniotic fluid mesenchymal stem cells and their secreted molecules in mice with acute hepatic failure.

Background There is increasing interest in the therapeutic potential of human mesenchymal stem cells (hMSCs), especially in diseases such as acute hepatic failure (AHF) that are predominantly caused by a variety of drugs and viruses. In previous studies, a distinct population termed human spindle-shaped MSCs were isolated and expanded from second trimester amniotic fluid (AF-MSCs) and characterised based on their phenotype, pluripotency and differentiation potential. Methods AF-MSCs, hepatic progenitor-like (HPL) cells and hepatocyte-like (HL) cells derived from AF-MSCs were transplanted into CCl4-injured NOD/SCID mice with the AHF phenotype in order to evaluate their therapeutic potential. Conditioned medium (CM) derived from AF-MSCs or HPL cells was then delivered intrahepatically in order to determine whether the engraftment of the cells or their secreted molecules are the most important agents for liver repair. Results Both HPL cells and AF-MSCs were incorporated into CCl4-injured livers; HPL cell transplantation had a greater therapeutic effect. In contrast, HL cells failed to engraft and contribute to recovery. In addition, HPL-CM was found to be more efficient than CM derived from AF-MSCs in treatment of the liver. Proteome profile analysis of HPL-CM indicated the presence of anti-inflammatory factors such as interleukins IL-10, IL-1ra, IL-13 and IL-27 which may induce liver recovery. Blocking studies of IL-10 secretion from HPL cells confirmed the therapeutic significance of this cytokine in the AHF mouse model. Conclusions Human spindle-shaped AF-MSCs or HPL cells might be valuable tools to induce liver repair and support liver function by cell transplantation. More importantly, the factors they release may also play an important role in cell treatment in diseases of the liver.

Therapeutic levels of fetal hemoglobin in erythroid progeny of β-thalassemic CD34+ cells after lentiviral vector-mediated gene transfer.

β-Thalassemia major results from severely reduced or absent expression of the β-chain of adult hemoglobin (α₂β₂;HbA). Increased levels of fetal hemoglobin (α₂γ₂;HbF), such as occurs with hereditary persistence of HbF, ameliorate the severity of β-thalassemia, raising the potential for genetic therapy directed at enhancing HbF. We used an in vitro model of human erythropoiesis to assay for enhanced production of HbF after gene delivery into CD34(+) cells obtained from mobilized peripheral blood of normal adults or steady-state bone marrow from patients with β-thalassemia major. Lentiviral vectors encoding (1) a human γ-globin gene with or without an insulator, (2) a synthetic zinc-finger transcription factor designed to interact with the γ-globin gene promoters, or (3) a short-hairpin RNA targeting the γ-globin gene repressor, BCL11A, were tested. Erythroid progeny of normal CD34(+) cells demonstrated levels of HbF up to 21% per vector copy. For β-thalassemic CD34(+) cells, similar gene transfer efficiencies achieved HbF production ranging from 45% to 60%, resulting in up to a 3-fold increase in the total cellular Hb content. These observations suggest that both lentiviral-mediated γ-globin gene addition and genetic reactivation of endogenous γ-globin genes have potential to provide therapeutic HbF levels to patients with β-globin deficiency.

Clinal patterns of human Y chromosomal diversity in continental Italy and Greece are dominated by drift and founder effects.

We explored the spatial distribution of human Y chromosomal diversity on a microgeographic scale, by typing 30 population samples from closely spaced locations in Italy and Greece for 9 haplogroups and their internal microsatellite variation. We confirm a significant difference in the composition of the Y chromosomal gene pools of the two countries. However, within each country, heterogeneity is not organized along the lines of clinal variation deduced from studies on larger spatial scales. Microsatellite data indicate that local increases of haplogroup frequencies can be often explained by a limited number of founders. We conclude that local founder or drift effects are the main determinants in shaping the microgeographic Y chromosomal diversity.

Survivin -31G/C promoter polymorphism and sporadic colorectal cancer

IntroductionSurvivin is an apoptotic inhibitor, plays an important role in cell cycle regulation, and may be involved in the development and progression of cancer. A common polymorphism at the survivin gene promoter (-31 G/C) has been shown to influence survivin expression and the risk for cancer.AimThe aim of the present study was to investigate whether this polymorphism could be involved in the sporadic colorectal cancer (CRC) development, prognosis, and survival.Materials and methodsThe -31G/C polymorphism of survivin promoter was analyzed by polymerase chain reaction (PCR) restriction fragment length polymorphism method in biopsies from 312 patients with sporadic CRC and 362 healthy individuals. Survivin messenger RNA (mRNA) expression in CRC tissues was detected by quantitative reverse transcriptase PCR.Results and discussionThe genotype frequencies for -31GG, -31GC, and -31CC were 21.79%, 41.99%, and 36.22% in CRC patients and 33.98%, 45.03%, and 20.99% in healthy subjects, respectively. The frequencies of the survivin -31C allele and CC genotype were significantly higher in CRC patients than in healthy subjects (p < 0.0001). Homozygotes for the -31CC survivin genotype, expressed 1.6-fold higher mRNA levels of survivin compared to cases with the -31GG and -31GC genotypes.ConclusionThe -31CC genotype of survivin promoter is associated with CRC and may be a risk factor for CRC.

Amniotic fluid and amniotic membrane stem cells: marker discovery.

Amniotic fluid (AF) and amniotic membrane (AM) have been recently characterized as promising sources of stem or progenitor cells. Both not only contain subpopulations with stem cell characteristics resembling to adult stem cells, such as mesenchymal stem cells, but also exhibit some embryonic stem cell properties like (i) expression of pluripotency markers, (ii) high expansion in vitro, or (iii) multilineage differentiation capacity. Recent efforts have been focused on the isolation and the detailed characterization of these stem cell types. However, variations in their phenotype, their heterogeneity described by different groups, and the absence of a single marker expressed only in these cells may prevent the isolation of a pure homogeneous stem cell population from these sources and their potential use of these cells in therapeutic applications. In this paper, we aim to summarize the recent progress in marker discovery for stem cells derived from fetal sources such as AF and AM, using novel methodologies based on transcriptomics, proteomics, or secretome analyses.

In vitro and in vivo properties of distinct populations of amniotic fluid mesenchymal progenitor cells

Human mesenchymal progenitor cells (MPCs) are considered to be of great promise for use in tissue repair and regenerative medicine. MPCs represent multipotent adherent cells, able to give rise to multiple mesenchymal lineages such as osteoblasts, adipocytes or chondrocytes. Recently, we identified and characterized human second trimester amniotic fluid (AF) as a novel source of MPCs. Herein, we found that early colonies of AF‐MPCs consisted of two morphologically distinct adherent cell types, termed as spindle‐shaped (SS) and round‐shaped (RS). A detailed analysis of these two populations showed that SS‐AF‐MPCs expressed CD90 antigen in a higher level and exhibited a greater proliferation and differentiation potential. To characterize better the molecular identity of these two populations, we have generated a comparative proteomic map of SS‐AF‐MPCs and RS‐AF‐MPCs, identifying 25 differentially expressed proteins and 10 proteins uniquely expressed in RS‐AF‐MPCs. Furthermore, SS‐AF‐MPCs exhibited significantly higher migration ability on extracellular matrices, such as fibronectin and laminin in vitro, compared to RS‐AF‐MPCs and thus we further evaluated SS‐AF‐MPCs for potential use as therapeutic tools in vivo. Therefore, we tested whether GFP‐lentiviral transduced SS‐AF‐MPCs retained their stem cell identity, proliferation and differentiation potential. GFP‐SS‐AF‐MPCs were then successfully delivered into immunosuppressed mice, distributed in different tissues and survived longterm in vivo. In summary, these results demonstrated that AF‐MPCs consisted of at least two different MPC populations. In addition, SS‐AF‐MPCs, isolated based on their colony morphology and CD90 expression, represented the only MPC population that can be expanded easily in culture and used as an efficient tool for future in vivo therapeutic applications.