Ali Ramezani

High‐Level Sustained Transgene Expression in Human Embryonic Stem Cells Using Lentiviral Vectors

Here we describe the sustained expression of transgenes introduced into human embryonic stem (ES) cells using self‐inactivating lentiviral vectors. At low multiplicity of infection, vesicular stomatitis virus‐pseudotyped vectors containing a green fluorescent protein (GFP) transgene under the control of a human elongation factor 1α promoter transduced human ES cells at high efficiency. The majority of the transduced ES cells, which harbored low numbers of integrated vectors, continued to express GFP after 60 days of culture. Incorporation of a scaffold attachment region (SAR) from the human interferon‐β gene into the lentiviral vector backbone increased the average level of GFP expression, and inclusion of the SAR together with a chromatin insulator from the 5′ end of the chicken β‐globin locus reduced the variability in GFP expression. When the transduced ES cells were induced to differentiate into CD34+ hematopoietic precursors in vitro, GFP expression was maintained with minimal silencing. The ability to efficiently introduce active transgenes into human ES cells will facilitate gain‐of‐function studies of early developmental processes in the human system. These results also have important implications for the possible future use of gene‐modified human ES cells in transplantation and tissue regeneration applications.

The Gut Microbiome, Kidney Disease, and Targeted Interventions

The human gut harbors >100 trillion microbial cells, which influence the nutrition, metabolism, physiology, and immune function of the host. Here, we review the quantitative and qualitative changes in gut microbiota of patients with CKD that lead to disturbance of this symbiotic relationship, how this may contribute to the progression of CKD, and targeted interventions to re-establish symbiosis. Endotoxin derived from gut bacteria incites a powerful inflammatory response in the host organism. Furthermore, protein fermentation by gut microbiota generates myriad toxic metabolites, including p-cresol and indoxyl sulfate. Disruption of gut barrier function in CKD allows translocation of endotoxin and bacterial metabolites to the systemic circulation, which contributes to uremic toxicity, inflammation, progression of CKD, and associated cardiovascular disease. Several targeted interventions that aim to re-establish intestinal symbiosis, neutralize bacterial endotoxins, or adsorb gut-derived uremic toxins have been developed. Indeed, animal and human studies suggest that prebiotics and probiotics may have therapeutic roles in maintaining a metabolically-balanced gut microbiota and reducing progression of CKD and uremia-associated complications. We propose that further research should focus on using this highly efficient metabolic machinery to alleviate uremic symptoms.

Bypass of Senescence, Immortalization, and Transformation of Human Hematopoietic Progenitor Cells

We attempted to extend the lifespan of CD34+ stem/progenitor cells in human cord blood (CB) by transduction with lentiviral vectors carrying the human telomerase catalytic subunit (hTERT) and/or the human papillomavirus type 16 (HPV16) E6 and E7 oncogenes. We found that hTERT was incapable of prolonging the replicative capacity of CB cells maintained under serum‐free conditions in the presence of stem cell factor, Flt3 ligand, thrombopoietin, and interleukin‐3 beyond 4 months (n = 3). However, transduced CB cells cultured in the same cytokine cocktail constitutively expressing HPV16 E6/E7 alone (n = 2) or in concert with hTERT (n = 9) continued to proliferate, giving rise to permanent (>2 years) cell lines with a CD45+ CD34− CD133+/− CD44+ CD235a+ CD71+ CD203+ CD33+ CD13+ myeloerythroid/mast cell progenitor phenotype. Notably, CB cell cultures expressing only HPV16 E6/E7 went through a crisis period, and the resulting oligoclonal cell lines were highly aneuploid. By comparison, the CB cell lines obtained by coexpression of HPV16 E6/E7 plus hTERT exhibited near‐diploid karyotypes with minimal chromosomal aberrations, concomitant with stabilization of telomere length, yet were clonally derived. The immortalized E6/E7 plus hTERT–expressing CB cells were not tumorigenic when injected intravenously or subcutaneously into sublethally irradiated immunodeficient nonobese diabetic/severe combined immunodeficient mice but could be converted to a malignant state by ectopic expression of a v‐H‐ras or BCR‐ABL oncogene. These findings provide new insights into the mechanisms governing the senescence checkpoint of primitive human hematopoietic precursors and establish a paradigm for studies of the multistep process of human leukemogenesis.

Combinatorial Incorporation of Enhancer Blocking Components of the Chicken β-Globin 5′HS4 and Human T-Cell Receptor α/δ BEAD-1 Insulators in Self-Inactivating Retroviral Vectors Reduces their Genotoxic Potential

Insertional mutagenesis by retroviral vectors has emerged as a serious impediment to the widespread application of hematopoietic stem cell gene transfer for the treatment of hematologic diseases. Here we report the development of a 77‐base pair element, FII/BEAD‐A (FB), which contains the minimal enhancer‐blocking components of the chicken β‐globin 5′HS4 insulator and a homologous region from the human T‐cell receptor α/δ BEAD‐1 insulator. With a new flow cytometry‐based assay, we show that the FB element is as effective in enhancer‐blocking activity as the prototypical 1.2‐kilobase 5′HS4 insulator fragment. When incorporated into the residual U3 region of the 3′ long terminal repeat (LTR) of a self‐inactivating (SIN) gammaretroviral vector, the FB element was stably transferred to the 5′ LTR during reverse transcription, flanking the integrated transgene expression cassette. Notably, using a recently established in vitro insertional mutagenesis assay involving primary murine hematopoietic cells, we found that SIN gammaretroviral vectors, as well as SIN lentiviral vectors, containing the FB element exhibited greatly reduced transforming potential—to background levels under the experimental conditions used—compared with their unshielded counterparts. These results suggest that the FB element‐mediated enhancer‐blocking modification is a promising approach to dramatically improve the safety of retroviral vectors for therapeutic gene transfer.

DNA methylation profile associated with rapid decline in kidney function: findings from the CRIC Study

BACKGROUND Epigenetic mechanisms may be important in the progression of chronic kidney disease (CKD). METHODS We studied the genome-wide DNA methylation pattern associated with rapid loss of kidney function using the Infinium HumanMethylation 450 K BeadChip in 40 Chronic Renal Insufficiency (CRIC) study participants (n = 3939) with the highest and lowest rates of decline in estimated glomerular filtration rate. RESULTS The mean eGFR slope was 2.2 (1.4) and -5.1 (1.2) mL/min/1.73 m(2) in the stable kidney function group and the rapid progression group, respectively. CpG islands in NPHP4, IQSEC1 and TCF3 were hypermethylated to a larger extent in subjects with stable kidney function (P-values of 7.8E-05 to 9.5E-05). These genes are involved in pathways known to promote the epithelial to mesenchymal transition and renal fibrosis. Other CKD-related genes that were differentially methylated are NOS3, NFKBIL2, CLU, NFKBIB, TGFB3 and TGFBI, which are involved in oxidative stress and inflammatory pathways (P-values of 4.5E-03 to 0.046). Pathway analysis using Ingenuity Pathway Analysis showed that gene networks related to cell signaling, carbohydrate metabolism and human behavior are epigenetically regulated in CKD. CONCLUSIONS Epigenetic modifications may be important in determining the rate of loss of kidney function in patients with established CKD.

Trimethylamine N-Oxide: The Good, the Bad and the Unknown

Trimethylamine N-oxide (TMAO) is a small colorless amine oxide generated from choline, betaine, and carnitine by gut microbial metabolism. It accumulates in the tissue of marine animals in high concentrations and protects against the protein-destabilizing effects of urea. Plasma level of TMAO is determined by a number of factors including diet, gut microbial flora and liver flavin monooxygenase activity. In humans, a positive correlation between elevated plasma levels of TMAO and an increased risk for major adverse cardiovascular events and death is reported. The atherogenic effect of TMAO is attributed to alterations in cholesterol and bile acid metabolism, activation of inflammatory pathways and promotion foam cell formation. TMAO levels increase with decreasing levels of kidney function and is associated with mortality in patients with chronic kidney disease. A number of therapeutic strategies are being explored to reduce TMAO levels, including use of oral broad spectrum antibiotics, promoting the growth of bacteria that utilize TMAO as substrate and the development of target-specific molecules with varying level of success. Despite the accumulating evidence, it is questioned whether TMAO is the mediator of a bystander in the disease process. Thus, it is important to undertake studies examining the cellular signaling in physiology and pathological states in order to establish the role of TMAO in health and disease in humans.

Gut microbiome in chronic kidney disease: challenges and opportunities.

&NA; More than 100 trillion microbial cells that reside in the human gut heavily influence nutrition, metabolism, and immune function of the host. Gut dysbiosis, seen commonly in patients with chronic kidney disease (CKD), results from qualitative and quantitative changes in host microbiome profile and disruption of gut barrier function. Alterations in gut microbiota and a myriad of host responses have been implicated in progression of CKD, increased cardiovascular risk, uremic toxicity, and inflammation. We present a discussion of dysbiosis, various uremic toxins produced from dysbiotic gut microbiome, and their roles in CKD progression and complications. We also review the gut microbiome in renal transplant, highlighting the role of commensal microbes in alteration of immune responses to transplantation, and conclude with therapeutic interventions that aim to restore intestinal dysbiosis.

Correction of murine hemophilia A following nonmyeloablative transplantation of hematopoietic stem cells engineered to encode an enhanced human factor VIII variant using a safety-augmented retroviral vector

Insertional mutagenesis by retroviral vectors is a major impediment to the clinical application of hematopoietic stem cell gene transfer for the treatment of hematologic disorders. We recently developed an insulated self-inactivating gammaretroviral vector, RMSinOFB, which uses a novel enhancer-blocking element that significantly decreases genotoxicity of retroviral integration. In this study, we used the RMSinOFB vector to evaluate the efficacy of a newly bioengineered factor VIII (fVIII) variant (efVIII)--containing a combination of A1 domain point mutations (L303E/F309S) and an extended partial B domain for improved secretion plus A2 domain mutations (R484A/R489A/P492A) for reduced immunogenicity--toward successful treatment of murine hemophilia A. In cell lines, efVIII was secreted at up to 6-fold higher levels than an L303E/F309S A1 domain-only fVIII variant (sfVIIIDeltaB). Most important, when compared with a conventional gammaretroviral vector expressing sfVIIIDeltaB, lower doses of RMSin-efVIII-OFB-transduced hematopoietic stem cells were needed to generate comparable curative fVIII levels in hemophilia A BALB/c mice after reduced-intensity total body irradiation or nonmyeloablative chemotherapy conditioning regimens. These data suggest that the safety-augmented RMSin-efVIII-OFB platform represents an encouraging step in the development of a clinically appropriate gene addition therapy for hemophilia A.

Overview of the HIV‐1 Lentiviral Vector System

Replication‐defective oncoretroviral vectors have been the most widely used vehicles for gene‐transfer studies because of their capacity to efficiently introduce and stably express transgenes in mammalian cells. A limitation of oncoretroviral vectors is that cell division is required for proviral integration into the host genome. By comparison, lentiviruses such as human immunodeficiency virus type 1 (HIV‐1) have evolved a nuclear‐import machinery that allows them to infect nondividing as well as dividing cells. This unique property has led to the development of lentiviral vectors for gene delivery to a variety of nondividing or slowly dividing cells including neurons and glial cells of the central nervous system and others. This unit is intended to provide an overview of HIV‐1 molecular biology and an introduction to successive generations of HIV‐1‐based lentiviral vectors.

Acetylation-dependent oncogenic activity of metastasis-associated protein 1 co-regulator

High expression of metastasis‐associated protein 1 co‐regulator (MTA1), a component of the nuclear remodelling and histone deacetylase complex, has been associated with human tumours. However, the precise role of MTA1 in tumorigenesis remains unknown. In this study, we show that induced levels of MTA1 are sufficient to transform Rat1 fibroblasts and that the transforming potential of MTA1 is dependent on its acetylation at Lys626. Underlying mechanisms of MTA1‐mediated transformation include activation of the Ras–Raf pathway by MTA1 but not by acetylation‐inactive MTA1; this was due to the repression of Gαi2 transcription, which negatively influences Ras activation. We observed that acetylated MTA1–histone deacetylase (HDAC) interaction was required for the recruitment of the MTA1–HDAC complex to the Gαi2 regulatory element and consequently for the repression of Gαi2 transcription and expression leading to activation of the Ras–Raf pathway. The findings presented in this study provide for the first time—to the best of our knowledge—evidence of acetylation‐dependent oncogenic activity of a cancer‐relevant gene product.