Variety Of Human Genetic Diseases Research Articles

The ATPase SRCAP is associated with the mitotic apparatus, uncovering novel molecular aspects of Floating-Harbor syndrome

BackgroundA variety of human genetic diseases is known to be caused by mutations in genes encoding chromatin factors and epigenetic regulators, such as DNA or histone modifying enzymes and members of ATP-dependent chromatin remodeling complexes. Floating-Harbor syndrome is a rare genetic disease affecting human development caused by dominant truncating mutations in the SRCAP gene, which encodes the ATPase SRCAP, the core catalytic subunit of the homonymous chromatin-remodeling complex. The main function of the SRCAP complex is to promote the exchange of histone H2A with the H2A.Z variant. According to the canonical role played by the SRCAP protein in epigenetic regulation, the Floating-Harbor syndrome is thought to be a consequence of chromatin perturbations. However, additional potential physiological functions of SRCAP have not been sufficiently explored.ResultsWe combined cell biology, reverse genetics, and biochemical approaches to study the subcellular localization of the SRCAP protein and assess its involvement in cell cycle progression in HeLa cells. Surprisingly, we found that SRCAP associates with components of the mitotic apparatus (centrosomes, spindle, midbody), interacts with a plethora of cytokinesis regulators, and positively regulates their recruitment to the midbody. Remarkably, SRCAP depletion perturbs both mitosis and cytokinesis. Similarly, DOM-A, the functional SRCAP orthologue in Drosophila melanogaster, is found at centrosomes and the midbody in Drosophila cells, and its depletion similarly affects both mitosis and cytokinesis.ConclusionsOur findings provide first evidence suggesting that SRCAP plays previously undetected and evolutionarily conserved roles in cell division, independent of its functions in chromatin regulation. SRCAP may participate in two different steps of cell division: by ensuring proper chromosome segregation during mitosis and midbody function during cytokinesis. Moreover, our findings emphasize a surprising scenario whereby alterations in cell division produced by SRCAP mutations may contribute to the onset of Floating-Harbor syndrome.

Membrane-lipid associated lncRNA: A new regulator in cancer signaling

Long noncoding RNAs (LncRNAs) are one of the emerging regulators which are involved in diverse biological processes. LncRNAs can participate in the regulation of gene expression via various ways in the cytoplasm and the nucleus. The function of the nuclear lncRNAs has been studied a lot. Recent studies have shown that the regulatory roles of cytoplasmic lncRNA, including membrane lipid associated lncRNA, which may open an unexplored mechanistic territory. LncRNA dysregulated expression represents a common event in pathogenesis of a variety of human genetic diseases including cancer. Lipid-associated lncRNA is capable of modulating critical cellular functions by directly interacting with phospholipids on the plasma membrane. Besides, it also could be a predictor for the poor prognosis of cancer. In this review, we sum up the roles of cytoplasmic lncRNA, especially lipid-associated lncRNA in cancer.

Pathophysiological consequences of receptor mistraffic: Tales from the platelet P2Y12 receptor

Genetic variations in G protein-coupled receptor (GPCR) genes can disrupt receptor function in a wide variety of human genetic diseases, including platelet bleeding disorders. Platelets are critical for haemostasis with inappropriate platelet activation leading to the development of arterial thrombosis, which can result in heart attack and stroke whilst decreased platelet activity is associated with an increased risk of bleeding. GPCRs expressed on the surface of platelets play key roles in regulating platelet activity and therefore function. Receptors include purinergic receptors (P2Y1 and P2Y12), proteinase-activated receptor (PAR1 and PAR4) and thromboxane receptors (TPα), among others. Pharmacological blockade of these receptors forms a powerful therapeutic tool in the treatment and prevention of arterial thrombosis. With the advance of genomic technologies, there has been a substantial increase in the identification of naturally occurring rare and common GPCR variants. These variants include single-nucleotide polymorphisms (SNPs) and insertion or deletions that have the potential to alter GPCR expression or function. A number of defects in platelet GPCRs that disrupt receptor function have now been characterized in patients with mild bleeding disorders. This review will focus on rare, function-disrupting variants of platelet GPCRs with particular emphasis upon mutations in the P2Y12 receptor gene that affect receptor traffic to modulate platelet function. Further this review will outline how the identification and characterization of function-disrupting GPCR mutations provides an essential link in translating our detailed understanding of receptor traffic and function in cell line studies into relevant human biological systems.

G protein-coupled receptor mutations and human genetic disease.

Genetic variations in G protein-coupled receptor genes (GPCRs) disrupt GPCR function in a wide variety of human genetic diseases. In vitro strategies and animal models have been used to identify the molecular pathologies underlying naturally occurring GPCR mutations. Inactive, overactive, or constitutively active receptors have been identified that result in pathology. These receptor variants may alter ligand binding, G protein coupling, receptor desensitization and receptor recycling. Receptor systems discussed include rhodopsin, thyrotropin, parathyroid hormone, melanocortin, follicle-stimulating hormone (FSH), luteinizing hormone, gonadotropin-releasing hormone (GNRHR), adrenocorticotropic hormone, vasopressin, endothelin-β, purinergic, and the G protein associated with asthma (GPRA or neuropeptide S receptor 1 (NPSR1)). The role of activating and inactivating calcium-sensing receptor (CaSR) mutations is discussed in detail with respect to familial hypocalciuric hypercalcemia (FHH) and autosomal dominant hypocalemia (ADH). The CASR mutations have been associated with epilepsy. Diseases caused by the genetic disruption of GPCR functions are discussed in the context of their potential to be selectively targeted by drugs that rescue altered receptors. Examples of drugs developed as a result of targeting GPCRs mutated in disease include: calcimimetics and calcilytics, therapeutics targeting melanocortin receptors in obesity, interventions that alter GNRHR loss from the cell surface in idiopathic hypogonadotropic hypogonadism and novel drugs that might rescue the P2RY12 receptor congenital bleeding phenotype. De-orphanization projects have identified novel disease-associated receptors, such as NPSR1 and GPR35. The identification of variants in these receptors provides genetic reagents useful in drug screens. Discussion of the variety of GPCRs that are disrupted in monogenic Mendelian disorders provides the basis for examining the significance of common pharmacogenetic variants.

Negative Control Region Is a Critical Element Of Insertional Oncogenesis After Gene Transfer Into Hematopoietic Progenitors With Moloney Murine Leukemia Viruses

Gene transfer into hematopoietic stem cells has been used successfully to treat a variety of human genetic diseases. Although protocols have shown positive clinical outcomes, the successes of clinical trials have been tempered by adverse events in which the use of gamma-retroviral vectors (GV) containing full-length long terminal repeats (LTRs) with strong enhancer activity increased transcription of cancer-related genes, and thereby contributed to development of leukemia. Assessing safety of integrating viral vectors for future clinical use is therefore of paramount importance. The negative control region (NCR) is a particularly well-conserved sequence among mammalian gamma-retroviruses with demonstrated regulating a transcription activity of GV in hematopoietic cells. This suggests that the NCR might play a crucial role of insertional oncogenesis after gene transfer into hematopoietic progenitors.In a series of safety studies of viral gene transfer constructs, we used an in vitro assay of murine bone marrow (BM) cell immortalization and compared the consequences of hematopoietic stem cell transduction with three different kinds of viral vectors, including Moloney murine leukemia virus- (MMLV), lentivirus- (LV), and foamy virus (FV)-based constructs. To evaluate critical elements for cell immortalization by MMLV vectors, we also tested four different MMLV LTR variants deleted of either 1) most of the two 75-bp repeats associated with the viral enhancer (delE1), 2) all of the two 75-bp repeats and the NCR (delE2), 3) only the NCR (delNCR), or 4) carrying a deleterious mutation of the NCR NFAT motif (ΔNFAT). All vectors carried an internal expression cassette including the eGFP gene under the control of a UCOE (ubiquitously acting chromatin opening element) promoter. In this assay, BM cells are harvested from C57BL6 mice, exposed to retroviral supernatants and cultured long-term. Derived lines are considered immortalized based on their ability to continue to grow in vitro for more than six weeks in the presence of interleukin-3 and stem cell factor. Real-time PCR was performed to verify comparable transduction efficiency of bone marrow cells by different vectors.In our analysis of MMLV LTR mutants, full-MMLV and delE1 transduction of 92 and 108 cultures, respectively, resulted in 37 and 37 immortalized lines (40% and 34% immortalization rate, respectively). The difference in immortalization rate between full-MMLV and delE1 was not statistically significant. Transductions using delE2-, delNCR- and ΔNFAT-carrying vectors of 60, 36 and 35 cultures resulted in 10, 3 and 10 immortalized lines (17%, 8.3% and 29% immortalization rate, respectively). The difference between the immortalization caused by delE1 and delE2 vectors was statistically significant (p<0.05). Moreover, the difference between the immortalization caused by full-MMLV and delNCR vectors was statistically significant (p<0.01), while there was no significant difference between the immortalization induced by full-MMLV and ΔNFAT vectors. Transduction of 57 and 34 cultures with LV and FV vectors, respectively, resulted in no immortalized lines. Transductions of 128 cultures with a LV construct carrying the U3 region from the murine stem cell virus LTR as an internal promoter (LV-U3) resulted in 2 immortalized lines which was not statistically different from the results obtained with LV vectors carrying the UCOE internal promoter.These results confirm that GV are prone to causing immortalization of hematopoietic cells and indicate that deletion of the whole viral enhancer sequences may not be adequate to eliminate the insertional oncogenesis risk. Importantly, our data point to the NCR as a crucial element for immortalization and justify additional studies to evaluate its specific role in MMLV-mediated insertional oncogenesis. Finally, our results suggest that vectors based on LV and FV backbones are safer alternatives for clinical gene transfer into hematopoietic stem cells. Disclosures:No relevant conflicts of interest to declare.

Analysis of Risk and Mechanism of Insertional Oncogenesis After Gene Transfer Into Hematopoietic Progenitors with Integrating Viral Vectors

AbstractAbstract 2049Gene transfer into hematopoietic stem cells has been used successfully to treat a variety of human genetic diseases. Although protocols have shown positive clinical outcomes, the successes of clinical trials have been tempered by adverse events in which the integration of the viral vectors increased transcription of cancer-related genes and thereby contributed to development of leukemias. The use of gamma-retroviral vectors containing full-length, long terminal repeats (LTRs) with strong promoter and enhancer activity has been well documented to have the potential of resulting in activation of expression of genes neighboring the vector insertion site. Assessing safety of integrating viral vectors for future clinical use is therefore of paramount importance.In preparation for gene therapy approaches for the Wiskott-Aldrich syndrome (WAS), we used an in vitro assay of murine bone marrow (BM) cell immortalization to compare the consequences of hematopoietic stem cell transduction by three different kinds of viral vectors, including Moloney murine leukemia virus (MMLV), lentivirus (LV), and foamy virus (FV) constructs. To evaluate critical elements for cell immortalization by MMLV vectors, we also tested five different MMLV LTR forms: unmodified (full-MMLV), deleted of most of the two 75-bp repeats associated with the viral enhancer (delE1), deleted of all the two 75-bp repeats and negative control region (NCR) (delE2), deleted of the viral promoter sequences (delP), and with full deletion of enhancer and promoter sequences (delEP). All vectors carried an internal expression cassette including the eGFP gene under the control of a UCOE (ubiquitously acting chromatin opening element) or the WAS endogenous promoter (WASp). In this assay, BM cells are harvested from C57BL6 mice, exposed to retroviral supernatants and cultured long-term. Derived lines are considered immortalized based on their ability to continue to grow in vitro for more than six weeks in the presence of interleukin-3 and stem cell factor. Real-time PCR was performed to verify comparable transduction efficiency of bone marrow cells by different vectors.To date, full-MMLV and delE1 transduction of 123 and 132 cultures, respectively, has given rise to 48 and 43 immortalized lines (39.0% and 32.5% immortalization rate, respectively). The difference in immortalization rate between full-MMLV and delE1 was not statistically significant. In contrast, transduction of 114 and 62 cultures with LV and FV vectors, respectively, resulted in no immortalized lines.In our analysis of MMLV LTR mutants, full-MMLV and delE1 transduction of 56 and 72 cultures, respectively, has given rise to 24 and 26 immortalized lines (43% and 36% immortalization rate). Again, the difference in immortalization rate between full-MMLV and delE1 was not statistically significant. In contrast, delE2, delP and delEP transduction of 24 cultures each has given rise to 2, 5 and 3 immortalized lines (8.3%, 21% and 13% immortalized ratio, respectively). The difference between the immortalization caused by delE1 and delE2 vectors was statistically significant (p<0.01), while there was no significant difference between the full-MMLV and delP vectors.These preliminary results confirm that gamma-retroviral vectors are prone to causing immortalization of hematopoietic cells and indicate that deletion of viral enhancer and/or promoter sequences may not be adequate to eliminate the insertional oncogenesis risk. Importantly, our data point to the NCR as a crucial element for immortalization and justify additional studies to evaluate its specific role in MMLV-mediated insertional oncogenesis. Finally, our results suggest that vectors based on LV and FV backbones are safer alternatives for clinical gene transfer into hematopoietic stem cells. Disclosures:No relevant conflicts of interest to declare.

Body axis elongation and ciliary function in zebrafish require Noni a novel ciliary protein

Cilia are highly conserved structures found from protozoa to mammals where they play major functions in motility and sensation. Ciliary dysfunction leads to a variety of human genetic diseases called ciliopathies. RFX transcription factors are key players in regulating genes involved in cilia assembly from C. elegans to mammals. Using a genomic screen to identify targets of RFX, we selected a novel gene, noni, potentially implicated in cilia biology. No known function has been described for this gene, which is highly conserved and specific of ciliated species. We show that noni expression is increased during in vitro induced ciliogenesis in primary mouse ependymal cell culture and that Noni localizes to cilia from Drosophila to mammals. We performed functional analysis in zebrafish and show that loss of function of noni mimics human symptoms associated with ciliopathies such as kidney cysts and randomized left right patterning. We demonstrate that Noni is necessary for cilia function. Indeed, we show that nodal flow is impaired in Kupffer’s vesicle of noni morphants. Moreover, noni morphants have defects in body axis elongation and present impaired basal body positioning in the floor plate suggesting that noni is implicated in planar cell polarity (PCP). To test this hypothesis, we are currently analysing genetic interaction with known PCP components associated with cilia function. In conclusion, we have identified a novel conserved ciliary gene noni, which is necessary for ciliary function and planar cell polarity in zebrafish.

Comparison of Immortalization Potential of Gamma-Retroviral, Lentiviral and Foamy Virus Gene Transfer Vectors

Abstract 3116Therapeutic gene transfer has been used successfully to treat a variety of human genetic diseases. Although protocols have shown positive clinical outcomes, the success of clinical trials were tempered by adverse events, in which integration of the viral vectors increased transcription of cancer-related genes and thereby contributed to development of leukemia. In all documented cases of insertional mutagenesis, the viral vectors used contained full-length, gamma-retrovirus long terminal repeats (LTRs) that are able to exert strong promoter and enhancer activity driving not only the expression of the transgene carried by the vector, but also that of genes neighboring the insertion site. Assessing safety of integrating viral vectors for future clinical use is therefore of paramount importance.In preparation for gene therapy approaches for the Wiskott-Aldrich syndrome (WAS), we used an in vitro assay of murine bone marrow (BM) cell immortalization to compare the consequences of transduction by four different kinds of viral vectors, including a full-length LTR Moloney leukemia virus (MLV), a self-inactivating MLV carrying a 3' LTR deleted of the viral enhancer region (SIN), a lentivirus (LV), and a foamy virus (FV) construct. All vectors carried EGFP under the control of a ubiquitously acting chromatin opening element (UCOE) or the WAS endogenous promoter (WASp). In this assay, BM cells are harvested from C57BL6 mice, exposed to retroviral supernatants and cultured long-term. Derived lines are considered immortalized based on their ability to continue to grow in vitro for more than 6 weeks in the presence of interleukin-3 and stem cell factor.To date, MLV and SIN transduction of 123 and 132 cultures, respectively, gave rise to 48 and 43 immortalized lines (39.0% and 32.6% immortalization rate). The difference in immortalization rate between MLV and SIN vectors was not statistically significant (Chi square: p=0.30). As expected, immortalized cells were negative/low for IgER, cKit and Sca1 expression, and positive to different degrees for expression of the myeloid markers CD11b/Mac1 and Ly6g/Gr1. Transduction of 114 and 62 cultures with LV and FV vectors, respectively, resulted in no immortalized lines.Real-time PCR was performed to evaluate transduction efficiency of bone marrow cells and immortalized lines. Integrated vector sequences in bone marrow cells transduced by LV and FV were detected in significantly higher quantities than in cells transduced with MLV and SIN vectors. However, expression of the EGFP transgene was markedly reduced in LV- and FV-transduced cells compared to cells exposed to MLV vectors (MFI: 14.0, 1.88, 93.2, respectively).These preliminary results confirm that gamma-retroviral gene transfer vectors are prone to causing immortalization of hematopoietic cells and suggest the vectors based on LV and FV backbones may be safer alternatives for WAS and other genetic disorders, provided that effective gene expression levels can be achieved in the biological model system under study.TableSummary of immortalization results using MLV, SIN, LV and FV vectorsVirusMOITransduction efficiencyTransduction experiments% ImmortalizationMLV/UCOE/EGFP2067%5643MLV/WASp/EGFP2065%6736SIN/UCOE/EGFP532%7236SIN/WASp/EGFP537%6028LV/UCOE/EGFP1040%570LV/WASp/EGFP1049%570FV/UCOE/EGFP1027%280FV/WASp/EGFP1022%340negativeN.A.N.A.720 Disclosures:No relevant conflicts of interest to declare.

Statistical considerations for digital approaches to non-invasive fetal genotyping

A growing body of literature has demonstrated the potential for non-invasive diagnosis of a variety of human genetic diseases using cell-free DNA extracted from maternal plasma samples in early gestation. Such methods are of great significance to the obstetrics community because of their potential use as clinical standard of care. Proof of concept for such approaches has been established for aneuploidy and paternally inherited dominant traits. Although significant progress has recently been made, the non-invasive diagnosis of monogenic diseases that segregate in a recessive mendelian fashion is more problematic. Recent developments in microfluidic digital PCR and DNA sequencing have resulted in a number of recent advances in this field. These have largely, although not exclusively, been used for the development of diagnostic methods for aneuploidy. However, given their prevalence, it is likely that such methods will be utilized towards the development of non-invasive methods for diagnosing monogenetic disorders. With this in mind, we have undertaken a statistical modeling of three contemporary (digital) analytical methods in the context of prenatal diagnosis using cell free DNA for monogenic diseases that segregate in a recessive mendelian fashion. We provide an experimental framework for the future development of diagnostic methods in this context that should be considered when designing molecular assays that seek to establish proof of concept in this field.

Expression of mTOR pathway proteins in human amniotic fluid stem cells

The discovery of human amniotic fluid stem cells initiated a new and promising stem cell research field. These cells harbor a high proliferative capacity and the potential to differentiate into cells of all three embryonic germ layers. The facts that they do not form tumors in vivo and do not raise the ethical concerns associated with human embryonic stem cells support their role as an optimal tool to study the underlying molecular mechanisms of cell differentiation processes and of their deregulation in human genetic diseases. Deregulation of the protein kinase mammalian target of rapamycin (mTOR) pathway is a hallmark of a wide variety of human genetic diseases. Here we report the establishment of an amniotic fluid stem cell line. We analysed the endogenous expression of the mTOR pathway proteins tuberin, mTOR, raptor, rictor, sin1, mLST8, Akt and p70S6K in human amniotic fluid stem cells. In addition, we studied the endogenous activity of the kinase p70S6K, one of the major targets of the mTOR complex 1 kinase, by analysing the p70S6K T389 phosphorylation status. The activity of the Akt kinase, the major mTOR complex 2 target, was studied by analysing its phosphorylation at S473. In addition, the mTOR inhibitor rapamycin was found to affect the phosphorylation status of p70S6K in amniotic fluid stem cells. Taken together, we provide evidence that the mTOR pathway is fully active in human amniotic fluid stem cells. These data demonstrate that amniotic fluid stem cell lines can be used as new tools to study the molecular and cell biological consequences of natural occurring alterations of the mTOR pathway being responsible for a wide variety of different human genetic diseases.

Copy number variation in the human genome and its implication in autoimmunity

The causes of autoimmune disease remain poorly defined. However, it is known that genetic factors contribute to disease susceptibility. Hitherto, studies have focused upon single nucleotide polymorphisms as both tools for mapping and as probable causal variants. Recent studies, using genome-wide analytical techniques, have revealed that, in the genome, segments of DNA ranging in size from kilobases to megabases can vary in copy number. These changes of DNA copy number represent an important element of genomic polymorphism in humans and in other species and may therefore make a substantial contribution to phenotypic variation and population differentiation. Furthermore, copy number variation (CNV) in genomic regions harbouring dosage-sensitive genes may cause or predispose to a variety of human genetic diseases. Several recent studies have reported an association between CNV and autoimmunity in humans such as systemic lupus, psoriasis, Crohn's disease, rheumatoid arthritis and type 1 diabetes. The use of novel analytical techniques facilitates the study of complex human genomic structures such as CNV, and allows new susceptibility loci for autoimmunity to be found that are not readily mappable by single nucleotide polymorphism-based association analyses alone.

Human FEN-1 can process the 5'-flap DNA of CTG/CAG triplet repeat derived from human genetic diseases by length and sequence dependent manner.

Trinucleotide repeat (TNR) instability can cause a variety of human genetic diseases including myotonic dystrophy and Huntington's disease. Recent genetic data show that instability of the CAG/CTG repeat DNA is dependent on its length and replication origin. In yeast, the RAD27 (human FEN-1 homologue) null mutant has a high expansion frequency at the TNR loci. We demonstrate here that FEN-1 processes the 5'-flap DNA of CTG/CAG repeats, which is dependent on the length in vitro. FEN-1 protein can cleave the 5'-flap DNA containing triplet repeating sequence up to 21 repeats, but the activity decreases with increasing size of flap above 11 repeats. In addition, FEN-1 processing of 5'-flap DNA depends on sequence, which play a role in the replication origin-dependent TNR instability. Interestingly, FEN-1 can cleave the 5'-flap DNA of CTG repeats better than CAG repeats possibly through the flap-structure. Our biochemical data of FEN-1's activity with triplet repeat DNA clearly shows length dependence, and aids our understanding on the mechanism of TNR instability.

SOX14 is a candidate gene for limb defects associated with BPES and M�bius syndrome

Members of the SOX gene family encode proteins with homology to the HMG box DNA-binding domain of SRY, the Y-linked testis-determining gene. SOX genes are expressed during embryogenesis and are involved in the development of a wide range of different tissues. Mutations in SRY, SOX9 and SOX10 have been shown to be responsible for XY sex reversal, campomelic dysplasia and Waardenburg-Hirschsprung disease, respectively. It is likely that mutations in other SOX genes are responsible for a variety of human genetic diseases. SOX14 has been identified from a human genomic library and the mouse and chicken sequences obtained by polymerase chain reaction amplification. The SOX14 amino acid sequence is highly conserved across these species, suggesting an important role for this protein in vertebrate development. SOX14 is expressed in the neural tube and apical ectodermal ridge of the developing chicken limb. This is the only SOX gene known to be expressed in the apical ectodermal ridge, a structure that directs outgrowth of the embryonic limb bud. Human SOX14 is localised to a 1.15-Mb yeast artificial chromosome on chromosome 3q23, close to loci for BPES (blepharophimosis, ptosis, epicanthus inversus syndrome) and Mobius syndrome. Although SOX14 maps outside these loci, its expression pattern and chromosomal localisation suggest that it is a candidate gene for the limb defects frequently associated with these syndromes.

Implantation of genetically engineered fibroblasts into mice: implications for gene therapy.

In a variety of human genetic diseases, replacement of the absent or defective protein provides significant therapeutic benefits. As a model for a somatic cell gene therapy system, cultured murine fibroblasts were transfected with a human growth hormone (hGH) fusion gene and cells from one of the resulting clonal lines were subsequently implanted into various locations in mice. Such implants synthesized and secreted hGH, which was detectable in the serum. The function of the implants depended on their location and size, and on the histocompatibility of the donor cells with their recipients. The expression of hGH could be modified by addition of regulatory effectors, and, with appropriate immunosuppression, the implants survived for more than 3 months. This approach to gene therapy, here termed "transkaryotic implantation," is potentially applicable to many genetic diseases in that the transfected cell line can be extensively characterized prior to implantation, several anatomical sites are suitable for implantation, and regulated expression of the gene of therapeutic interest can be obtained.